From e42507a41ca0329ac2966e46ceb556ecaf8d48ca Mon Sep 17 00:00:00 2001 From: Jinghui Geng Date: Mon, 16 Mar 2026 16:13:56 -0700 Subject: [PATCH 1/6] add global caption to db --- apiv2/README.md | 2 +- .../versions/20260316_142504_autogenerated.py | 23 + apiv2/db_import/tests/conftest.py | 2 +- .../tests/test_db_annotation_import.py | 9 + apiv2/graphql_api/schema.graphql | 7189 ----------------- apiv2/graphql_api/types/annotation_shape.py | 6 +- apiv2/schema/schema.yaml | 7 +- apiv2/support/enums.py | 1 + .../test_infra/factories/annotation_shape.py | 10 +- .../Annotations/100/foo-1.0.json | 6 + 10 files changed, 58 insertions(+), 7197 deletions(-) create mode 100644 apiv2/database/migrations/versions/20260316_142504_autogenerated.py diff --git a/apiv2/README.md b/apiv2/README.md index 4d90d75ee..d047c6c65 100644 --- a/apiv2/README.md +++ b/apiv2/README.md @@ -1,4 +1,4 @@ -# Getting started +Did# Getting started ``` make apiv2-init # from the root of the repo diff --git a/apiv2/database/migrations/versions/20260316_142504_autogenerated.py b/apiv2/database/migrations/versions/20260316_142504_autogenerated.py new file mode 100644 index 000000000..d03386fe9 --- /dev/null +++ b/apiv2/database/migrations/versions/20260316_142504_autogenerated.py @@ -0,0 +1,23 @@ +"""autogenerated + +Create Date: 2026-03-16 21:25:06.002149 + +""" + +# revision identifiers, used by Alembic. +revision = '20260316_142504' +down_revision = '20260306_160839' +branch_labels = None +depends_on = None + + +def upgrade() -> None: + # ### commands auto generated by Alembic - please adjust! ### + pass + # ### end Alembic commands ### + + +def downgrade() -> None: + # ### commands auto generated by Alembic - please adjust! ### + pass + # ### end Alembic commands ### diff --git a/apiv2/db_import/tests/conftest.py b/apiv2/db_import/tests/conftest.py index 11b8dfb06..008332eb6 100644 --- a/apiv2/db_import/tests/conftest.py +++ b/apiv2/db_import/tests/conftest.py @@ -133,5 +133,5 @@ def expected_dataset(http_prefix: str) -> dict[str, Any]: "key_photo_url": f"{http_prefix}/{DATASET_ID}/KeyPhoto/snapshot.png", "key_photo_thumbnail_url": f"{http_prefix}/{DATASET_ID}/KeyPhoto/thumbnail.png", "deposition_id": 300, - "file_size": 1374849.0, + "file_size": 1375064.0, } diff --git a/apiv2/db_import/tests/test_db_annotation_import.py b/apiv2/db_import/tests/test_db_annotation_import.py index 9d1750c0e..4b0e79ec6 100644 --- a/apiv2/db_import/tests/test_db_annotation_import.py +++ b/apiv2/db_import/tests/test_db_annotation_import.py @@ -54,6 +54,15 @@ def expected_annotations(http_prefix: str) -> list[dict[str, Any]]: def expected_annotation_files(http_prefix: str) -> list[dict[str, Any]]: path = f"{DATASET_ID}/RUN1/Reconstructions/VoxelSpacing12.300/Annotations/" return [ + { + "tomogram_voxel_spacing_id": TOMOGRAM_VOXEL_ID1, + "s3_path": f"s3://test-public-bucket/{path}100-foo-1.0_globalcaption.json", + "https_path": f"{http_prefix}/{path}100-foo-1.0_globalcaption.json", + "source": "community", + "format": "json", + "is_visualization_default": False, + "file_size": 0, + }, { "tomogram_voxel_spacing_id": TOMOGRAM_VOXEL_ID1, "s3_path": f"s3://test-public-bucket/{path}100-foo-1.0_instancesegmask.mrc", diff --git a/apiv2/graphql_api/schema.graphql b/apiv2/graphql_api/schema.graphql index 9ac2c95fa..e69de29bb 100644 --- a/apiv2/graphql_api/schema.graphql +++ b/apiv2/graphql_api/schema.graphql @@ -1,7189 +0,0 @@ -"""Tiltseries Alignment""" -type Alignment implements EntityInterface & Node { - """The Globally Unique ID of this object""" - _id: GlobalID! - - """Numeric identifier (May change!)""" - id: Int! - annotationFiles( - where: AnnotationFileWhereClause = null - orderBy: [AnnotationFileOrderByClause!] = [] - - """Returns the items in the list that come before the specified cursor.""" - before: String = null - - """Returns the items in the list that come after the specified cursor.""" - after: String = null - - """Returns the first n items from the list.""" - first: Int = null - - """Returns the items in the list that come after the specified cursor.""" - last: Int = null - ): AnnotationFileConnection! - annotationFilesAggregate(where: AnnotationFileWhereClause = null): AnnotationFileAggregate - perSectionAlignments( - where: PerSectionAlignmentParametersWhereClause = null - orderBy: [PerSectionAlignmentParametersOrderByClause!] = [] - - """Returns the items in the list that come before the specified cursor.""" - before: String = null - - """Returns the items in the list that come after the specified cursor.""" - after: String = null - - """Returns the first n items from the list.""" - first: Int = null - - """Returns the items in the list that come after the specified cursor.""" - last: Int = null - ): PerSectionAlignmentParametersConnection! - perSectionAlignmentsAggregate(where: PerSectionAlignmentParametersWhereClause = null): PerSectionAlignmentParametersAggregate - deposition(where: DepositionWhereClause = null, orderBy: [DepositionOrderByClause!] = []): Deposition - depositionId: Int - tiltseries(where: TiltseriesWhereClause = null, orderBy: [TiltseriesOrderByClause!] = []): Tiltseries - tiltseriesId: Int - tomograms( - where: TomogramWhereClause = null - orderBy: [TomogramOrderByClause!] = [] - - """Returns the items in the list that come before the specified cursor.""" - before: String = null - - """Returns the items in the list that come after the specified cursor.""" - after: String = null - - """Returns the first n items from the list.""" - first: Int = null - - """Returns the items in the list that come after the specified cursor.""" - last: Int = null - ): TomogramConnection! - tomogramsAggregate(where: TomogramWhereClause = null): TomogramAggregate - run(where: RunWhereClause = null, orderBy: [RunOrderByClause!] = []): Run - runId: Int - - """Whether this a LOCAL or GLOBAL alignment""" - alignmentType: alignment_type_enum - - """The method used to create this alignment""" - alignmentMethod: alignment_method_type_enum - - """X dimension of the reconstruction volume in angstrom""" - volumeXDimension: Float - - """Y dimension of the reconstruction volume in angstrom""" - volumeYDimension: Float - - """Z dimension of the reconstruction volume in angstrom""" - volumeZDimension: Float - - """X shift of the reconstruction volume in angstrom""" - volumeXOffset: Float - - """Y shift of the reconstruction volume in angstrom""" - volumeYOffset: Float - - """Z shift of the reconstruction volume in angstrom""" - volumeZOffset: Float - - """Additional X rotation of the reconstruction volume in degrees""" - xRotationOffset: Float - - """Additional tilt offset in degrees""" - tiltOffset: Float - - """A placeholder for the affine transformation matrix.""" - affineTransformationMatrix: String - - """S3 path to the metadata file for this alignment""" - s3AlignmentMetadata: String - - """HTTPS url to the metadata file for this alignment""" - httpsAlignmentMetadata: String - - """Whether this is the portal standard alignment""" - isPortalStandard: Boolean -} - -type AlignmentAggregate { - aggregate: [AlignmentAggregateFunctions!] -} - -type AlignmentAggregateFunctions { - sum: AlignmentNumericalColumns - avg: AlignmentNumericalColumns - stddev: AlignmentNumericalColumns - variance: AlignmentNumericalColumns - min: AlignmentMinMaxColumns - max: AlignmentMinMaxColumns - groupBy: AlignmentGroupByOptions - count(distinct: Boolean = false, columns: AlignmentCountColumns = null): Int -} - -input AlignmentAggregateWhereClause { - count: AlignmentAggregateWhereClauseCount! -} - -input AlignmentAggregateWhereClauseCount { - arguments: AlignmentCountColumns - distinct: Boolean - filter: AlignmentWhereClause - predicate: IntComparators -} - -"""A connection to a list of items.""" -type AlignmentConnection { - """Pagination data for this connection""" - pageInfo: PageInfo! - - """Contains the nodes in this connection""" - edges: [AlignmentEdge!]! -} - -enum AlignmentCountColumns { - alignmentType - alignmentMethod - volumeXDimension - volumeYDimension - volumeZDimension - volumeXOffset - volumeYOffset - volumeZOffset - xRotationOffset - tiltOffset - affineTransformationMatrix - s3AlignmentMetadata - httpsAlignmentMetadata - isPortalStandard - id -} - -input AlignmentCreateInput { - depositionId: ID = null - tiltseriesId: ID = null - runId: ID = null - - """Whether this a LOCAL or GLOBAL alignment""" - alignmentType: alignment_type_enum = null - - """The method used to create this alignment""" - alignmentMethod: alignment_method_type_enum = null - - """X dimension of the reconstruction volume in angstrom""" - volumeXDimension: Float = null - - """Y dimension of the reconstruction volume in angstrom""" - volumeYDimension: Float = null - - """Z dimension of the reconstruction volume in angstrom""" - volumeZDimension: Float = null - - """X shift of the reconstruction volume in angstrom""" - volumeXOffset: Float = null - - """Y shift of the reconstruction volume in angstrom""" - volumeYOffset: Float = null - - """Z shift of the reconstruction volume in angstrom""" - volumeZOffset: Float = null - - """Additional X rotation of the reconstruction volume in degrees""" - xRotationOffset: Float = null - - """Additional tilt offset in degrees""" - tiltOffset: Float = null - - """A placeholder for the affine transformation matrix.""" - affineTransformationMatrix: String = null - - """S3 path to the metadata file for this alignment""" - s3AlignmentMetadata: String = null - - """HTTPS url to the metadata file for this alignment""" - httpsAlignmentMetadata: String = null - - """Whether this is the portal standard alignment""" - isPortalStandard: Boolean = null - - """Numeric identifier (May change!)""" - id: Int! -} - -"""An edge in a connection.""" -type AlignmentEdge { - """A cursor for use in pagination""" - cursor: String! - - """The item at the end of the edge""" - node: Alignment! -} - -type AlignmentGroupByOptions { - annotationFiles: AnnotationFileGroupByOptions - perSectionAlignments: PerSectionAlignmentParametersGroupByOptions - deposition: DepositionGroupByOptions - tiltseries: TiltseriesGroupByOptions - tomograms: TomogramGroupByOptions - run: RunGroupByOptions - alignmentType: alignment_type_enum - alignmentMethod: alignment_method_type_enum - volumeXDimension: Float - volumeYDimension: Float - volumeZDimension: Float - volumeXOffset: Float - volumeYOffset: Float - volumeZOffset: Float - xRotationOffset: Float - tiltOffset: Float - affineTransformationMatrix: String - s3AlignmentMetadata: String - httpsAlignmentMetadata: String - isPortalStandard: Boolean - id: Int -} - -type AlignmentMinMaxColumns { - volumeXDimension: Float - volumeYDimension: Float - volumeZDimension: Float - volumeXOffset: Float - volumeYOffset: Float - volumeZOffset: Float - xRotationOffset: Float - tiltOffset: Float - affineTransformationMatrix: String - s3AlignmentMetadata: String - httpsAlignmentMetadata: String - id: Int -} - -type AlignmentNumericalColumns { - volumeXDimension: Float - volumeYDimension: Float - volumeZDimension: Float - volumeXOffset: Float - volumeYOffset: Float - volumeZOffset: Float - xRotationOffset: Float - tiltOffset: Float - id: Int -} - -input AlignmentOrderByClause { - deposition: DepositionOrderByClause - tiltseries: TiltseriesOrderByClause - run: RunOrderByClause - alignmentType: orderBy - alignmentMethod: orderBy - volumeXDimension: orderBy - volumeYDimension: orderBy - volumeZDimension: orderBy - volumeXOffset: orderBy - volumeYOffset: orderBy - volumeZOffset: orderBy - xRotationOffset: orderBy - tiltOffset: orderBy - affineTransformationMatrix: orderBy - s3AlignmentMetadata: orderBy - httpsAlignmentMetadata: orderBy - isPortalStandard: orderBy - id: orderBy -} - -input AlignmentUpdateInput { - depositionId: ID = null - tiltseriesId: ID = null - runId: ID = null - - """Whether this a LOCAL or GLOBAL alignment""" - alignmentType: alignment_type_enum = null - - """The method used to create this alignment""" - alignmentMethod: alignment_method_type_enum = null - - """X dimension of the reconstruction volume in angstrom""" - volumeXDimension: Float = null - - """Y dimension of the reconstruction volume in angstrom""" - volumeYDimension: Float = null - - """Z dimension of the reconstruction volume in angstrom""" - volumeZDimension: Float = null - - """X shift of the reconstruction volume in angstrom""" - volumeXOffset: Float = null - - """Y shift of the reconstruction volume in angstrom""" - volumeYOffset: Float = null - - """Z shift of the reconstruction volume in angstrom""" - volumeZOffset: Float = null - - """Additional X rotation of the reconstruction volume in degrees""" - xRotationOffset: Float = null - - """Additional tilt offset in degrees""" - tiltOffset: Float = null - - """A placeholder for the affine transformation matrix.""" - affineTransformationMatrix: String = null - - """S3 path to the metadata file for this alignment""" - s3AlignmentMetadata: String = null - - """HTTPS url to the metadata file for this alignment""" - httpsAlignmentMetadata: String = null - - """Whether this is the portal standard alignment""" - isPortalStandard: Boolean = null - - """Numeric identifier (May change!)""" - id: Int -} - -input AlignmentWhereClause { - annotationFiles: AnnotationFileWhereClause - annotationFilesAggregate: AnnotationFileAggregateWhereClause - perSectionAlignments: PerSectionAlignmentParametersWhereClause - perSectionAlignmentsAggregate: PerSectionAlignmentParametersAggregateWhereClause - deposition: DepositionWhereClause - depositionId: IntComparators - tiltseries: TiltseriesWhereClause - tiltseriesId: IntComparators - tomograms: TomogramWhereClause - tomogramsAggregate: TomogramAggregateWhereClause - run: RunWhereClause - runId: IntComparators - alignmentType: Alignment_type_enumEnumComparators - alignmentMethod: Alignment_method_type_enumEnumComparators - volumeXDimension: FloatComparators - volumeYDimension: FloatComparators - volumeZDimension: FloatComparators - volumeXOffset: FloatComparators - volumeYOffset: FloatComparators - volumeZOffset: FloatComparators - xRotationOffset: FloatComparators - tiltOffset: FloatComparators - affineTransformationMatrix: StrComparators - s3AlignmentMetadata: StrComparators - httpsAlignmentMetadata: StrComparators - isPortalStandard: BoolComparators - id: IntComparators -} - -input AlignmentWhereClauseMutations { - id: IntComparators -} - -input Alignment_method_type_enumEnumComparators { - _eq: alignment_method_type_enum - _neq: alignment_method_type_enum - _in: [alignment_method_type_enum!] - _nin: [alignment_method_type_enum!] - _gt: alignment_method_type_enum - _gte: alignment_method_type_enum - _lt: alignment_method_type_enum - _lte: alignment_method_type_enum - _is_null: Boolean -} - -input Alignment_type_enumEnumComparators { - _eq: alignment_type_enum - _neq: alignment_type_enum - _in: [alignment_type_enum!] - _nin: [alignment_type_enum!] - _gt: alignment_type_enum - _gte: alignment_type_enum - _lt: alignment_type_enum - _lte: alignment_type_enum - _is_null: Boolean -} - -"""Metadata for an annotation""" -type Annotation implements EntityInterface & Node { - """The Globally Unique ID of this object""" - _id: GlobalID! - - """Numeric identifier (May change!)""" - id: Int! - run(where: RunWhereClause = null, orderBy: [RunOrderByClause!] = []): Run - runId: Int - annotationShapes( - where: AnnotationShapeWhereClause = null - orderBy: [AnnotationShapeOrderByClause!] = [] - - """Returns the items in the list that come before the specified cursor.""" - before: String = null - - """Returns the items in the list that come after the specified cursor.""" - after: String = null - - """Returns the first n items from the list.""" - first: Int = null - - """Returns the items in the list that come after the specified cursor.""" - last: Int = null - ): AnnotationShapeConnection! - annotationShapesAggregate(where: AnnotationShapeWhereClause = null): AnnotationShapeAggregate - methodLinks( - where: AnnotationMethodLinkWhereClause = null - orderBy: [AnnotationMethodLinkOrderByClause!] = [] - - """Returns the items in the list that come before the specified cursor.""" - before: String = null - - """Returns the items in the list that come after the specified cursor.""" - after: String = null - - """Returns the first n items from the list.""" - first: Int = null - - """Returns the items in the list that come after the specified cursor.""" - last: Int = null - ): AnnotationMethodLinkConnection! - methodLinksAggregate(where: AnnotationMethodLinkWhereClause = null): AnnotationMethodLinkAggregate - authors( - where: AnnotationAuthorWhereClause = null - orderBy: [AnnotationAuthorOrderByClause!] = [] - - """Returns the items in the list that come before the specified cursor.""" - before: String = null - - """Returns the items in the list that come after the specified cursor.""" - after: String = null - - """Returns the first n items from the list.""" - first: Int = null - - """Returns the items in the list that come after the specified cursor.""" - last: Int = null - ): AnnotationAuthorConnection! - authorsAggregate(where: AnnotationAuthorWhereClause = null): AnnotationAuthorAggregate - deposition(where: DepositionWhereClause = null, orderBy: [DepositionOrderByClause!] = []): Deposition - depositionId: Int - - """S3 path for the metadata json file for this annotation""" - s3MetadataPath: String! - - """HTTPS path for the metadata json file for this annotation""" - httpsMetadataPath: String! - - """ - DOIs for publications that describe the dataset. Use a comma to separate multiple DOIs. - """ - annotationPublication: String - - """ - Describe how the annotation is made (e.g. Manual, crYoLO, Positive Unlabeled Learning, template matching) - """ - annotationMethod: String! - - """An identifier for the annotation to be used during ingestion.""" - annotationIngestId: String - - """ - Whether an annotation is considered ground truth, as determined by the annotator. - """ - groundTruthStatus: Boolean - - """Ontology identifier for the annotation object.""" - objectId: String! - - """ - Name of the object being annotated (e.g. ribosome, nuclear pore complex, actin filament, membrane) - """ - objectName: String! - - """ - A textual description of the annotation object, can be a longer description to include additional information not covered by the Annotation object name and state. - """ - objectDescription: String - - """Molecule state annotated (e.g. open, closed)""" - objectState: String - - """Number of objects identified""" - objectCount: Int - - """ - Describe the confidence level of the annotation. Precision is defined as the % of annotation objects being true positive - """ - confidencePrecision: Float - - """ - Describe the confidence level of the annotation. Recall is defined as the % of true positives being annotated correctly - """ - confidenceRecall: Float - - """Annotation filename used as ground truth for precision and recall""" - groundTruthUsed: String - - """Software used for generating this annotation""" - annotationSoftware: String - - """ - Data curator’s subjective choice as the best annotation of the same annotation object ID - """ - isCuratorRecommended: Boolean - - """ - The method type for generating the annotation (e.g. manual, hybrid, automated) - """ - methodType: annotation_method_type_enum! - - """Date when an annotation set is initially received by the Data Portal.""" - depositionDate: DateTime! - - """Date when annotation data is made public by the Data Portal.""" - releaseDate: DateTime! - - """Date when an annotation was last modified in the Data Portal""" - lastModifiedDate: DateTime! -} - -type AnnotationAggregate { - aggregate: [AnnotationAggregateFunctions!] -} - -type AnnotationAggregateFunctions { - sum: AnnotationNumericalColumns - avg: AnnotationNumericalColumns - stddev: AnnotationNumericalColumns - variance: AnnotationNumericalColumns - min: AnnotationMinMaxColumns - max: AnnotationMinMaxColumns - groupBy: AnnotationGroupByOptions - count(distinct: Boolean = false, columns: AnnotationCountColumns = null): Int -} - -input AnnotationAggregateWhereClause { - count: AnnotationAggregateWhereClauseCount! -} - -input AnnotationAggregateWhereClauseCount { - arguments: AnnotationCountColumns - distinct: Boolean - filter: AnnotationWhereClause - predicate: IntComparators -} - -"""Metadata for an annotation's authors""" -type AnnotationAuthor implements EntityInterface & Node { - """The Globally Unique ID of this object""" - _id: GlobalID! - - """Numeric identifier (May change!)""" - id: Int! - annotation(where: AnnotationWhereClause = null, orderBy: [AnnotationOrderByClause!] = []): Annotation - annotationId: Int - - """The order in which the author appears in the publication""" - authorListOrder: Int! - - """A unique, persistent identifier for researchers, provided by ORCID.""" - orcid: String - - """A unique, persistent identifier for kaggle users at kaggle.com.""" - kaggleId: String - - """Full name of an annotation author (e.g. Jane Doe).""" - name: String! - - """Email address for this author""" - email: String - - """ - Name of the institution an annotator is affiliated with. Sometimes, one annotator may have multiple affiliations. - """ - affiliationName: String - - """Address of the institution an annotator is affiliated with.""" - affiliationAddress: String - - """ - A unique identifier assigned to the affiliated institution by The Research Organization Registry (ROR). - """ - affiliationIdentifier: String - - """Indicates whether an annotator is the corresponding author""" - correspondingAuthorStatus: Boolean - - """ - Indicates whether an author is the main person executing the annotation, especially on manual annotation - """ - primaryAuthorStatus: Boolean -} - -type AnnotationAuthorAggregate { - aggregate: [AnnotationAuthorAggregateFunctions!] -} - -type AnnotationAuthorAggregateFunctions { - sum: AnnotationAuthorNumericalColumns - avg: AnnotationAuthorNumericalColumns - stddev: AnnotationAuthorNumericalColumns - variance: AnnotationAuthorNumericalColumns - min: AnnotationAuthorMinMaxColumns - max: AnnotationAuthorMinMaxColumns - groupBy: AnnotationAuthorGroupByOptions - count(distinct: Boolean = false, columns: AnnotationAuthorCountColumns = null): Int -} - -input AnnotationAuthorAggregateWhereClause { - count: AnnotationAuthorAggregateWhereClauseCount! -} - -input AnnotationAuthorAggregateWhereClauseCount { - arguments: AnnotationAuthorCountColumns - distinct: Boolean - filter: AnnotationAuthorWhereClause - predicate: IntComparators -} - -"""A connection to a list of items.""" -type AnnotationAuthorConnection { - """Pagination data for this connection""" - pageInfo: PageInfo! - - """Contains the nodes in this connection""" - edges: [AnnotationAuthorEdge!]! -} - -enum AnnotationAuthorCountColumns { - id - authorListOrder - orcid - kaggleId - name - email - affiliationName - affiliationAddress - affiliationIdentifier - correspondingAuthorStatus - primaryAuthorStatus -} - -input AnnotationAuthorCreateInput { - """Reference to the annotation this author contributed to""" - annotationId: ID = null - - """Numeric identifier (May change!)""" - id: Int! - - """The order in which the author appears in the publication""" - authorListOrder: Int! - - """A unique, persistent identifier for researchers, provided by ORCID.""" - orcid: String = null - - """A unique, persistent identifier for kaggle users at kaggle.com.""" - kaggleId: String = null - - """Full name of an annotation author (e.g. Jane Doe).""" - name: String! - - """Email address for this author""" - email: String = null - - """ - Name of the institution an annotator is affiliated with. Sometimes, one annotator may have multiple affiliations. - """ - affiliationName: String = null - - """Address of the institution an annotator is affiliated with.""" - affiliationAddress: String = null - - """ - A unique identifier assigned to the affiliated institution by The Research Organization Registry (ROR). - """ - affiliationIdentifier: String = null - - """Indicates whether an annotator is the corresponding author""" - correspondingAuthorStatus: Boolean = null - - """ - Indicates whether an author is the main person executing the annotation, especially on manual annotation - """ - primaryAuthorStatus: Boolean = null -} - -"""An edge in a connection.""" -type AnnotationAuthorEdge { - """A cursor for use in pagination""" - cursor: String! - - """The item at the end of the edge""" - node: AnnotationAuthor! -} - -type AnnotationAuthorGroupByOptions { - annotation: AnnotationGroupByOptions - id: Int - authorListOrder: Int - orcid: String - kaggleId: String - name: String - email: String - affiliationName: String - affiliationAddress: String - affiliationIdentifier: String - correspondingAuthorStatus: Boolean - primaryAuthorStatus: Boolean -} - -type AnnotationAuthorMinMaxColumns { - id: Int - authorListOrder: Int - orcid: String - kaggleId: String - name: String - email: String - affiliationName: String - affiliationAddress: String - affiliationIdentifier: String -} - -type AnnotationAuthorNumericalColumns { - id: Int - authorListOrder: Int -} - -input AnnotationAuthorOrderByClause { - annotation: AnnotationOrderByClause - id: orderBy - authorListOrder: orderBy - orcid: orderBy - kaggleId: orderBy - name: orderBy - email: orderBy - affiliationName: orderBy - affiliationAddress: orderBy - affiliationIdentifier: orderBy - correspondingAuthorStatus: orderBy - primaryAuthorStatus: orderBy -} - -input AnnotationAuthorUpdateInput { - """Reference to the annotation this author contributed to""" - annotationId: ID = null - - """Numeric identifier (May change!)""" - id: Int - - """The order in which the author appears in the publication""" - authorListOrder: Int - - """A unique, persistent identifier for researchers, provided by ORCID.""" - orcid: String = null - - """A unique, persistent identifier for kaggle users at kaggle.com.""" - kaggleId: String = null - - """Full name of an annotation author (e.g. Jane Doe).""" - name: String - - """Email address for this author""" - email: String = null - - """ - Name of the institution an annotator is affiliated with. Sometimes, one annotator may have multiple affiliations. - """ - affiliationName: String = null - - """Address of the institution an annotator is affiliated with.""" - affiliationAddress: String = null - - """ - A unique identifier assigned to the affiliated institution by The Research Organization Registry (ROR). - """ - affiliationIdentifier: String = null - - """Indicates whether an annotator is the corresponding author""" - correspondingAuthorStatus: Boolean = null - - """ - Indicates whether an author is the main person executing the annotation, especially on manual annotation - """ - primaryAuthorStatus: Boolean = null -} - -input AnnotationAuthorWhereClause { - annotation: AnnotationWhereClause - annotationId: IntComparators - id: IntComparators - authorListOrder: IntComparators - orcid: StrComparators - kaggleId: StrComparators - name: StrComparators - email: StrComparators - affiliationName: StrComparators - affiliationAddress: StrComparators - affiliationIdentifier: StrComparators - correspondingAuthorStatus: BoolComparators - primaryAuthorStatus: BoolComparators -} - -input AnnotationAuthorWhereClauseMutations { - id: IntComparators -} - -"""A connection to a list of items.""" -type AnnotationConnection { - """Pagination data for this connection""" - pageInfo: PageInfo! - - """Contains the nodes in this connection""" - edges: [AnnotationEdge!]! -} - -enum AnnotationCountColumns { - s3MetadataPath - httpsMetadataPath - annotationPublication - annotationMethod - annotationIngestId - groundTruthStatus - objectId - objectName - objectDescription - objectState - objectCount - confidencePrecision - confidenceRecall - groundTruthUsed - annotationSoftware - isCuratorRecommended - methodType - depositionDate - releaseDate - lastModifiedDate - id -} - -input AnnotationCreateInput { - runId: ID = null - depositionId: ID = null - - """S3 path for the metadata json file for this annotation""" - s3MetadataPath: String! - - """HTTPS path for the metadata json file for this annotation""" - httpsMetadataPath: String! - - """ - DOIs for publications that describe the dataset. Use a comma to separate multiple DOIs. - """ - annotationPublication: String = null - - """ - Describe how the annotation is made (e.g. Manual, crYoLO, Positive Unlabeled Learning, template matching) - """ - annotationMethod: String! - - """An identifier for the annotation to be used during ingestion.""" - annotationIngestId: String = null - - """ - Whether an annotation is considered ground truth, as determined by the annotator. - """ - groundTruthStatus: Boolean = null - - """Ontology identifier for the annotation object.""" - objectId: String! - - """ - Name of the object being annotated (e.g. ribosome, nuclear pore complex, actin filament, membrane) - """ - objectName: String! - - """ - A textual description of the annotation object, can be a longer description to include additional information not covered by the Annotation object name and state. - """ - objectDescription: String = null - - """Molecule state annotated (e.g. open, closed)""" - objectState: String = null - - """Number of objects identified""" - objectCount: Int = null - - """ - Describe the confidence level of the annotation. Precision is defined as the % of annotation objects being true positive - """ - confidencePrecision: Float = null - - """ - Describe the confidence level of the annotation. Recall is defined as the % of true positives being annotated correctly - """ - confidenceRecall: Float = null - - """Annotation filename used as ground truth for precision and recall""" - groundTruthUsed: String = null - - """Software used for generating this annotation""" - annotationSoftware: String = null - - """ - Data curator’s subjective choice as the best annotation of the same annotation object ID - """ - isCuratorRecommended: Boolean = null - - """ - The method type for generating the annotation (e.g. manual, hybrid, automated) - """ - methodType: annotation_method_type_enum! - - """Date when an annotation set is initially received by the Data Portal.""" - depositionDate: DateTime! - - """Date when annotation data is made public by the Data Portal.""" - releaseDate: DateTime! - - """Date when an annotation was last modified in the Data Portal""" - lastModifiedDate: DateTime! - - """Numeric identifier (May change!)""" - id: Int! -} - -"""An edge in a connection.""" -type AnnotationEdge { - """A cursor for use in pagination""" - cursor: String! - - """The item at the end of the edge""" - node: Annotation! -} - -"""Metadata for files associated with an annotation""" -type AnnotationFile implements EntityInterface & Node { - """The Globally Unique ID of this object""" - _id: GlobalID! - - """Numeric identifier (May change!)""" - id: Int! - alignment(where: AlignmentWhereClause = null, orderBy: [AlignmentOrderByClause!] = []): Alignment - alignmentId: Int - annotationShape(where: AnnotationShapeWhereClause = null, orderBy: [AnnotationShapeOrderByClause!] = []): AnnotationShape - annotationShapeId: Int - tomogramVoxelSpacing(where: TomogramVoxelSpacingWhereClause = null, orderBy: [TomogramVoxelSpacingOrderByClause!] = []): TomogramVoxelSpacing - tomogramVoxelSpacingId: Int - - """File format for this file""" - format: String! - - """s3 path of the annotation file""" - s3Path: String! - - """Size of annota file in bytes""" - fileSize: Float - - """HTTPS path for this annotation file""" - httpsPath: String! - - """ - Data curator’s subjective choice of default annotation to display in visualization for an object - """ - isVisualizationDefault: Boolean - - """ - The source type for the annotation file (dataset_author, community, or portal_standard) - """ - source: annotation_file_source_enum -} - -type AnnotationFileAggregate { - aggregate: [AnnotationFileAggregateFunctions!] -} - -type AnnotationFileAggregateFunctions { - sum: AnnotationFileNumericalColumns - avg: AnnotationFileNumericalColumns - stddev: AnnotationFileNumericalColumns - variance: AnnotationFileNumericalColumns - min: AnnotationFileMinMaxColumns - max: AnnotationFileMinMaxColumns - groupBy: AnnotationFileGroupByOptions - count(distinct: Boolean = false, columns: AnnotationFileCountColumns = null): Int -} - -input AnnotationFileAggregateWhereClause { - count: AnnotationFileAggregateWhereClauseCount! -} - -input AnnotationFileAggregateWhereClauseCount { - arguments: AnnotationFileCountColumns - distinct: Boolean - filter: AnnotationFileWhereClause - predicate: IntComparators -} - -"""A connection to a list of items.""" -type AnnotationFileConnection { - """Pagination data for this connection""" - pageInfo: PageInfo! - - """Contains the nodes in this connection""" - edges: [AnnotationFileEdge!]! -} - -enum AnnotationFileCountColumns { - format - s3Path - fileSize - httpsPath - isVisualizationDefault - source - id -} - -input AnnotationFileCreateInput { - """Tiltseries Alignment""" - alignmentId: ID = null - - """Shapes associated with an annotation""" - annotationShapeId: ID = null - - """Voxel spacing that this annotation file is associated with""" - tomogramVoxelSpacingId: ID = null - - """File format for this file""" - format: String! - - """s3 path of the annotation file""" - s3Path: String! - - """Size of annota file in bytes""" - fileSize: Float = null - - """HTTPS path for this annotation file""" - httpsPath: String! - - """ - Data curator’s subjective choice of default annotation to display in visualization for an object - """ - isVisualizationDefault: Boolean = null - - """ - The source type for the annotation file (dataset_author, community, or portal_standard) - """ - source: annotation_file_source_enum = null - - """Numeric identifier (May change!)""" - id: Int! -} - -"""An edge in a connection.""" -type AnnotationFileEdge { - """A cursor for use in pagination""" - cursor: String! - - """The item at the end of the edge""" - node: AnnotationFile! -} - -type AnnotationFileGroupByOptions { - alignment: AlignmentGroupByOptions - annotationShape: AnnotationShapeGroupByOptions - tomogramVoxelSpacing: TomogramVoxelSpacingGroupByOptions - format: String - s3Path: String - fileSize: Float - httpsPath: String - isVisualizationDefault: Boolean - source: annotation_file_source_enum - id: Int -} - -type AnnotationFileMinMaxColumns { - format: String - s3Path: String - fileSize: Float - httpsPath: String - id: Int -} - -type AnnotationFileNumericalColumns { - fileSize: Float - id: Int -} - -input AnnotationFileOrderByClause { - alignment: AlignmentOrderByClause - annotationShape: AnnotationShapeOrderByClause - tomogramVoxelSpacing: TomogramVoxelSpacingOrderByClause - format: orderBy - s3Path: orderBy - fileSize: orderBy - httpsPath: orderBy - isVisualizationDefault: orderBy - source: orderBy - id: orderBy -} - -input AnnotationFileUpdateInput { - """Tiltseries Alignment""" - alignmentId: ID = null - - """Shapes associated with an annotation""" - annotationShapeId: ID = null - - """Voxel spacing that this annotation file is associated with""" - tomogramVoxelSpacingId: ID = null - - """File format for this file""" - format: String - - """s3 path of the annotation file""" - s3Path: String - - """Size of annota file in bytes""" - fileSize: Float = null - - """HTTPS path for this annotation file""" - httpsPath: String - - """ - Data curator’s subjective choice of default annotation to display in visualization for an object - """ - isVisualizationDefault: Boolean = null - - """ - The source type for the annotation file (dataset_author, community, or portal_standard) - """ - source: annotation_file_source_enum = null - - """Numeric identifier (May change!)""" - id: Int -} - -input AnnotationFileWhereClause { - alignment: AlignmentWhereClause - alignmentId: IntComparators - annotationShape: AnnotationShapeWhereClause - annotationShapeId: IntComparators - tomogramVoxelSpacing: TomogramVoxelSpacingWhereClause - tomogramVoxelSpacingId: IntComparators - format: StrComparators - s3Path: StrComparators - fileSize: FloatComparators - httpsPath: StrComparators - isVisualizationDefault: BoolComparators - source: Annotation_file_source_enumEnumComparators - id: IntComparators -} - -input AnnotationFileWhereClauseMutations { - id: IntComparators -} - -type AnnotationGroupByOptions { - run: RunGroupByOptions - annotationShapes: AnnotationShapeGroupByOptions - methodLinks: AnnotationMethodLinkGroupByOptions - authors: AnnotationAuthorGroupByOptions - deposition: DepositionGroupByOptions - s3MetadataPath: String - httpsMetadataPath: String - annotationPublication: String - annotationMethod: String - annotationIngestId: String - groundTruthStatus: Boolean - objectId: String - objectName: String - objectDescription: String - objectState: String - objectCount: Int - confidencePrecision: Float - confidenceRecall: Float - groundTruthUsed: String - annotationSoftware: String - isCuratorRecommended: Boolean - methodType: annotation_method_type_enum - depositionDate: DateTime - releaseDate: DateTime - lastModifiedDate: DateTime - id: Int -} - -""" -A set of links to models, source code, documentation, etc referenced by annotation method -""" -type AnnotationMethodLink implements EntityInterface & Node { - """The Globally Unique ID of this object""" - _id: GlobalID! - - """Numeric identifier (May change!)""" - id: Int! - annotation(where: AnnotationWhereClause = null, orderBy: [AnnotationOrderByClause!] = []): Annotation - annotationId: Int - - """Type of link (e.g. model, source code, documentation)""" - linkType: annotation_method_link_type_enum! - - """user readable name of the resource""" - name: String - - """URL to the resource""" - link: String! -} - -type AnnotationMethodLinkAggregate { - aggregate: [AnnotationMethodLinkAggregateFunctions!] -} - -type AnnotationMethodLinkAggregateFunctions { - sum: AnnotationMethodLinkNumericalColumns - avg: AnnotationMethodLinkNumericalColumns - stddev: AnnotationMethodLinkNumericalColumns - variance: AnnotationMethodLinkNumericalColumns - min: AnnotationMethodLinkMinMaxColumns - max: AnnotationMethodLinkMinMaxColumns - groupBy: AnnotationMethodLinkGroupByOptions - count(distinct: Boolean = false, columns: AnnotationMethodLinkCountColumns = null): Int -} - -input AnnotationMethodLinkAggregateWhereClause { - count: AnnotationMethodLinkAggregateWhereClauseCount! -} - -input AnnotationMethodLinkAggregateWhereClauseCount { - arguments: AnnotationMethodLinkCountColumns - distinct: Boolean - filter: AnnotationMethodLinkWhereClause - predicate: IntComparators -} - -"""A connection to a list of items.""" -type AnnotationMethodLinkConnection { - """Pagination data for this connection""" - pageInfo: PageInfo! - - """Contains the nodes in this connection""" - edges: [AnnotationMethodLinkEdge!]! -} - -enum AnnotationMethodLinkCountColumns { - linkType - name - link - id -} - -input AnnotationMethodLinkCreateInput { - """Reference to annotation this link applies to""" - annotationId: ID = null - - """Type of link (e.g. model, source code, documentation)""" - linkType: annotation_method_link_type_enum! - - """user readable name of the resource""" - name: String = null - - """URL to the resource""" - link: String! - - """Numeric identifier (May change!)""" - id: Int! -} - -"""An edge in a connection.""" -type AnnotationMethodLinkEdge { - """A cursor for use in pagination""" - cursor: String! - - """The item at the end of the edge""" - node: AnnotationMethodLink! -} - -type AnnotationMethodLinkGroupByOptions { - annotation: AnnotationGroupByOptions - linkType: annotation_method_link_type_enum - name: String - link: String - id: Int -} - -type AnnotationMethodLinkMinMaxColumns { - name: String - link: String - id: Int -} - -type AnnotationMethodLinkNumericalColumns { - id: Int -} - -input AnnotationMethodLinkOrderByClause { - annotation: AnnotationOrderByClause - linkType: orderBy - name: orderBy - link: orderBy - id: orderBy -} - -input AnnotationMethodLinkUpdateInput { - """Reference to annotation this link applies to""" - annotationId: ID = null - - """Type of link (e.g. model, source code, documentation)""" - linkType: annotation_method_link_type_enum - - """user readable name of the resource""" - name: String = null - - """URL to the resource""" - link: String - - """Numeric identifier (May change!)""" - id: Int -} - -input AnnotationMethodLinkWhereClause { - annotation: AnnotationWhereClause - annotationId: IntComparators - linkType: Annotation_method_link_type_enumEnumComparators - name: StrComparators - link: StrComparators - id: IntComparators -} - -input AnnotationMethodLinkWhereClauseMutations { - id: IntComparators -} - -type AnnotationMinMaxColumns { - s3MetadataPath: String - httpsMetadataPath: String - annotationPublication: String - annotationMethod: String - annotationIngestId: String - objectId: String - objectName: String - objectDescription: String - objectState: String - objectCount: Int - confidencePrecision: Float - confidenceRecall: Float - groundTruthUsed: String - annotationSoftware: String - depositionDate: DateTime - releaseDate: DateTime - lastModifiedDate: DateTime - id: Int -} - -type AnnotationNumericalColumns { - objectCount: Int - confidencePrecision: Float - confidenceRecall: Float - id: Int -} - -input AnnotationOrderByClause { - run: RunOrderByClause - deposition: DepositionOrderByClause - s3MetadataPath: orderBy - httpsMetadataPath: orderBy - annotationPublication: orderBy - annotationMethod: orderBy - annotationIngestId: orderBy - groundTruthStatus: orderBy - objectId: orderBy - objectName: orderBy - objectDescription: orderBy - objectState: orderBy - objectCount: orderBy - confidencePrecision: orderBy - confidenceRecall: orderBy - groundTruthUsed: orderBy - annotationSoftware: orderBy - isCuratorRecommended: orderBy - methodType: orderBy - depositionDate: orderBy - releaseDate: orderBy - lastModifiedDate: orderBy - id: orderBy -} - -"""Shapes associated with an annotation""" -type AnnotationShape implements EntityInterface & Node { - """The Globally Unique ID of this object""" - _id: GlobalID! - - """Numeric identifier (May change!)""" - id: Int! - annotation(where: AnnotationWhereClause = null, orderBy: [AnnotationOrderByClause!] = []): Annotation - annotationId: Int - annotationFiles( - where: AnnotationFileWhereClause = null - orderBy: [AnnotationFileOrderByClause!] = [] - - """Returns the items in the list that come before the specified cursor.""" - before: String = null - - """Returns the items in the list that come after the specified cursor.""" - after: String = null - - """Returns the first n items from the list.""" - first: Int = null - - """Returns the items in the list that come after the specified cursor.""" - last: Int = null - ): AnnotationFileConnection! - annotationFilesAggregate(where: AnnotationFileWhereClause = null): AnnotationFileAggregate - - """ - The shape of the annotation (SegmentationMask, OrientedPoint, Point, InstanceSegmentation, Mesh, InstanceSegmentationMask) - """ - shapeType: annotation_file_shape_type_enum -} - -type AnnotationShapeAggregate { - aggregate: [AnnotationShapeAggregateFunctions!] -} - -type AnnotationShapeAggregateFunctions { - sum: AnnotationShapeNumericalColumns - avg: AnnotationShapeNumericalColumns - stddev: AnnotationShapeNumericalColumns - variance: AnnotationShapeNumericalColumns - min: AnnotationShapeMinMaxColumns - max: AnnotationShapeMinMaxColumns - groupBy: AnnotationShapeGroupByOptions - count(distinct: Boolean = false, columns: AnnotationShapeCountColumns = null): Int -} - -input AnnotationShapeAggregateWhereClause { - count: AnnotationShapeAggregateWhereClauseCount! -} - -input AnnotationShapeAggregateWhereClauseCount { - arguments: AnnotationShapeCountColumns - distinct: Boolean - filter: AnnotationShapeWhereClause - predicate: IntComparators -} - -"""A connection to a list of items.""" -type AnnotationShapeConnection { - """Pagination data for this connection""" - pageInfo: PageInfo! - - """Contains the nodes in this connection""" - edges: [AnnotationShapeEdge!]! -} - -enum AnnotationShapeCountColumns { - shapeType - id -} - -input AnnotationShapeCreateInput { - """Metadata about an shapes for an annotation""" - annotationId: ID = null - - """ - The shape of the annotation (SegmentationMask, OrientedPoint, Point, InstanceSegmentation, Mesh, InstanceSegmentationMask) - """ - shapeType: annotation_file_shape_type_enum = null - - """Numeric identifier (May change!)""" - id: Int! -} - -"""An edge in a connection.""" -type AnnotationShapeEdge { - """A cursor for use in pagination""" - cursor: String! - - """The item at the end of the edge""" - node: AnnotationShape! -} - -type AnnotationShapeGroupByOptions { - annotation: AnnotationGroupByOptions - annotationFiles: AnnotationFileGroupByOptions - shapeType: annotation_file_shape_type_enum - id: Int -} - -type AnnotationShapeMinMaxColumns { - id: Int -} - -type AnnotationShapeNumericalColumns { - id: Int -} - -input AnnotationShapeOrderByClause { - annotation: AnnotationOrderByClause - shapeType: orderBy - id: orderBy -} - -input AnnotationShapeUpdateInput { - """Metadata about an shapes for an annotation""" - annotationId: ID = null - - """ - The shape of the annotation (SegmentationMask, OrientedPoint, Point, InstanceSegmentation, Mesh, InstanceSegmentationMask) - """ - shapeType: annotation_file_shape_type_enum = null - - """Numeric identifier (May change!)""" - id: Int -} - -input AnnotationShapeWhereClause { - annotation: AnnotationWhereClause - annotationId: IntComparators - annotationFiles: AnnotationFileWhereClause - annotationFilesAggregate: AnnotationFileAggregateWhereClause - shapeType: Annotation_file_shape_type_enumEnumComparators - id: IntComparators -} - -input AnnotationShapeWhereClauseMutations { - id: IntComparators -} - -input AnnotationUpdateInput { - runId: ID = null - depositionId: ID = null - - """S3 path for the metadata json file for this annotation""" - s3MetadataPath: String - - """HTTPS path for the metadata json file for this annotation""" - httpsMetadataPath: String - - """ - DOIs for publications that describe the dataset. Use a comma to separate multiple DOIs. - """ - annotationPublication: String = null - - """ - Describe how the annotation is made (e.g. Manual, crYoLO, Positive Unlabeled Learning, template matching) - """ - annotationMethod: String - - """An identifier for the annotation to be used during ingestion.""" - annotationIngestId: String = null - - """ - Whether an annotation is considered ground truth, as determined by the annotator. - """ - groundTruthStatus: Boolean = null - - """Ontology identifier for the annotation object.""" - objectId: String - - """ - Name of the object being annotated (e.g. ribosome, nuclear pore complex, actin filament, membrane) - """ - objectName: String - - """ - A textual description of the annotation object, can be a longer description to include additional information not covered by the Annotation object name and state. - """ - objectDescription: String = null - - """Molecule state annotated (e.g. open, closed)""" - objectState: String = null - - """Number of objects identified""" - objectCount: Int = null - - """ - Describe the confidence level of the annotation. Precision is defined as the % of annotation objects being true positive - """ - confidencePrecision: Float = null - - """ - Describe the confidence level of the annotation. Recall is defined as the % of true positives being annotated correctly - """ - confidenceRecall: Float = null - - """Annotation filename used as ground truth for precision and recall""" - groundTruthUsed: String = null - - """Software used for generating this annotation""" - annotationSoftware: String = null - - """ - Data curator’s subjective choice as the best annotation of the same annotation object ID - """ - isCuratorRecommended: Boolean = null - - """ - The method type for generating the annotation (e.g. manual, hybrid, automated) - """ - methodType: annotation_method_type_enum - - """Date when an annotation set is initially received by the Data Portal.""" - depositionDate: DateTime - - """Date when annotation data is made public by the Data Portal.""" - releaseDate: DateTime - - """Date when an annotation was last modified in the Data Portal""" - lastModifiedDate: DateTime - - """Numeric identifier (May change!)""" - id: Int -} - -input AnnotationWhereClause { - run: RunWhereClause - runId: IntComparators - annotationShapes: AnnotationShapeWhereClause - annotationShapesAggregate: AnnotationShapeAggregateWhereClause - methodLinks: AnnotationMethodLinkWhereClause - methodLinksAggregate: AnnotationMethodLinkAggregateWhereClause - authors: AnnotationAuthorWhereClause - authorsAggregate: AnnotationAuthorAggregateWhereClause - deposition: DepositionWhereClause - depositionId: IntComparators - s3MetadataPath: StrComparators - httpsMetadataPath: StrComparators - annotationPublication: StrComparators - annotationMethod: StrComparators - annotationIngestId: StrComparators - groundTruthStatus: BoolComparators - objectId: StrComparators - objectName: StrComparators - objectDescription: StrComparators - objectState: StrComparators - objectCount: IntComparators - confidencePrecision: FloatComparators - confidenceRecall: FloatComparators - groundTruthUsed: StrComparators - annotationSoftware: StrComparators - isCuratorRecommended: BoolComparators - methodType: Annotation_method_type_enumEnumComparators - depositionDate: DatetimeComparators - releaseDate: DatetimeComparators - lastModifiedDate: DatetimeComparators - id: IntComparators -} - -input AnnotationWhereClauseMutations { - id: IntComparators -} - -input Annotation_file_shape_type_enumEnumComparators { - _eq: annotation_file_shape_type_enum - _neq: annotation_file_shape_type_enum - _in: [annotation_file_shape_type_enum!] - _nin: [annotation_file_shape_type_enum!] - _gt: annotation_file_shape_type_enum - _gte: annotation_file_shape_type_enum - _lt: annotation_file_shape_type_enum - _lte: annotation_file_shape_type_enum - _is_null: Boolean -} - -input Annotation_file_source_enumEnumComparators { - _eq: annotation_file_source_enum - _neq: annotation_file_source_enum - _in: [annotation_file_source_enum!] - _nin: [annotation_file_source_enum!] - _gt: annotation_file_source_enum - _gte: annotation_file_source_enum - _lt: annotation_file_source_enum - _lte: annotation_file_source_enum - _is_null: Boolean -} - -input Annotation_method_link_type_enumEnumComparators { - _eq: annotation_method_link_type_enum - _neq: annotation_method_link_type_enum - _in: [annotation_method_link_type_enum!] - _nin: [annotation_method_link_type_enum!] - _gt: annotation_method_link_type_enum - _gte: annotation_method_link_type_enum - _lt: annotation_method_link_type_enum - _lte: annotation_method_link_type_enum - _is_null: Boolean -} - -input Annotation_method_type_enumEnumComparators { - _eq: annotation_method_type_enum - _neq: annotation_method_type_enum - _in: [annotation_method_type_enum!] - _nin: [annotation_method_type_enum!] - _gt: annotation_method_type_enum - _gte: annotation_method_type_enum - _lt: annotation_method_type_enum - _lte: annotation_method_type_enum - _is_null: Boolean -} - -input BoolComparators { - _eq: Boolean - _neq: Boolean - _in: [Boolean!] - _nin: [Boolean!] - _is_null: Boolean -} - -"""A collection of imaging experiments on the same organism""" -type Dataset implements EntityInterface & Node { - """The Globally Unique ID of this object""" - _id: GlobalID! - - """ - An identifier for a CryoET dataset, assigned by the Data Portal. Used to identify the dataset as the directory name in data tree - """ - id: Int! - deposition(where: DepositionWhereClause = null, orderBy: [DepositionOrderByClause!] = []): Deposition - depositionId: Int! - fundingSources( - where: DatasetFundingWhereClause = null - orderBy: [DatasetFundingOrderByClause!] = [] - - """Returns the items in the list that come before the specified cursor.""" - before: String = null - - """Returns the items in the list that come after the specified cursor.""" - after: String = null - - """Returns the first n items from the list.""" - first: Int = null - - """Returns the items in the list that come after the specified cursor.""" - last: Int = null - ): DatasetFundingConnection! - fundingSourcesAggregate(where: DatasetFundingWhereClause = null): DatasetFundingAggregate - authors( - where: DatasetAuthorWhereClause = null - orderBy: [DatasetAuthorOrderByClause!] = [] - - """Returns the items in the list that come before the specified cursor.""" - before: String = null - - """Returns the items in the list that come after the specified cursor.""" - after: String = null - - """Returns the first n items from the list.""" - first: Int = null - - """Returns the items in the list that come after the specified cursor.""" - last: Int = null - ): DatasetAuthorConnection! - authorsAggregate(where: DatasetAuthorWhereClause = null): DatasetAuthorAggregate - runs( - where: RunWhereClause = null - orderBy: [RunOrderByClause!] = [] - - """Returns the items in the list that come before the specified cursor.""" - before: String = null - - """Returns the items in the list that come after the specified cursor.""" - after: String = null - - """Returns the first n items from the list.""" - first: Int = null - - """Returns the items in the list that come after the specified cursor.""" - last: Int = null - ): RunConnection! - runsAggregate(where: RunWhereClause = null): RunAggregate - - """Title of a CryoET dataset""" - title: String! - - """ - A short description of a CryoET dataset, similar to an abstract for a journal article or dataset. - """ - description: String! - - """ - Label for the type of assay performed in a CryoET dataset, e.g. cryo-electron tomography - """ - assayLabel: String - - """ - EFO ontology identifier for the type of assay performed in a CryoET dataset - """ - assayOntologyId: String - - """ - Development stage of the organism from which a biological sample used the study is derived. - """ - developmentStageName: String - - """Ontology identifier for the development stage""" - developmentStageOntologyId: String - - """ - Name of the disease associated with the biological sample used in a CryoET study, e.g. Alzheimer’s disease - """ - diseaseName: String - - """ - Ontology identifier for the disease associated with the biological sample used in a CryoET study - """ - diseaseOntologyId: String - - """ - Name of the organism from which a biological sample used in a CryoET study is derived from, e.g. homo sapiens - """ - organismName: String - - """NCBI taxonomy identifier for the organism, e.g. 9606""" - organismTaxid: Int - - """ - Name of the tissue from which a biological sample used in a CryoET study is derived from. - """ - tissueName: String - - """The ontology identifier for the tissue.""" - tissueId: String - - """ - Name of the cell from which a biological sample used in a CryoET study is derived from. - """ - cellName: String - - """The ontology identifier for the cell type.""" - cellTypeId: String - - """Cell line or strain for the sample.""" - cellStrainName: String - - """Link to more information about the cell strain""" - cellStrainId: String - - """ - Type of samples used in a CryoET study. (cell, tissue, organism, intact organelle, in-vitro mixture, in-silico synthetic data, other) - """ - sampleType: sample_type_enum - - """Describe how the sample was prepared.""" - samplePreparation: String - - """Describe Cryo-ET grid preparation.""" - gridPreparation: String - - """ - Describe other setup not covered by sample preparation or grid preparation that may make this dataset unique in the same publication - """ - otherSetup: String - - """URL for the dataset preview image.""" - keyPhotoUrl: String - - """URL for the thumbnail of preview image.""" - keyPhotoThumbnailUrl: String - - """Name of the cellular component""" - cellComponentName: String - - """ - If the dataset focuses on a specific part of a cell, the subset is included here - """ - cellComponentId: String - - """Date when a dataset is initially received by the Data Portal.""" - depositionDate: DateTime! - - """Date when a dataset is made available on the Data Portal.""" - releaseDate: DateTime! - - """Date when a released dataset is last modified.""" - lastModifiedDate: DateTime! - - """ - Comma-separated list of DOIs for publications associated with the dataset. - """ - datasetPublications: String - - """ - If a CryoET dataset is also deposited into another database, enter the database identifier here (e.g. EMPIAR-11445). Use a comma to separate multiple identifiers. - """ - relatedDatabaseEntries: String - - """The S3 public bucket path where this dataset is contained""" - s3Prefix: String! - - """The https directory path where this dataset is contained""" - httpsPrefix: String! - - """Size of the dataset in bytes""" - fileSize: Float -} - -type DatasetAggregate { - aggregate: [DatasetAggregateFunctions!] -} - -type DatasetAggregateFunctions { - sum: DatasetNumericalColumns - avg: DatasetNumericalColumns - stddev: DatasetNumericalColumns - variance: DatasetNumericalColumns - min: DatasetMinMaxColumns - max: DatasetMinMaxColumns - groupBy: DatasetGroupByOptions - count(distinct: Boolean = false, columns: DatasetCountColumns = null): Int -} - -input DatasetAggregateWhereClause { - count: DatasetAggregateWhereClauseCount! -} - -input DatasetAggregateWhereClauseCount { - arguments: DatasetCountColumns - distinct: Boolean - filter: DatasetWhereClause - predicate: IntComparators -} - -"""An author of a dataset""" -type DatasetAuthor implements EntityInterface & Node { - """The Globally Unique ID of this object""" - _id: GlobalID! - - """Numeric identifier (May change!)""" - id: Int! - dataset(where: DatasetWhereClause = null, orderBy: [DatasetOrderByClause!] = []): Dataset - datasetId: Int - - """The order in which the author appears in the publication""" - authorListOrder: Int! - - """A unique, persistent identifier for researchers, provided by ORCID.""" - orcid: String - - """A unique, persistent identifier for kaggle users at kaggle.com.""" - kaggleId: String - - """Full name of a dataset author (e.g. Jane Doe).""" - name: String! - - """Email address for this author""" - email: String - - """Name of the institutions an author is affiliated with. Comma separated""" - affiliationName: String - - """Address of the institution an author is affiliated with.""" - affiliationAddress: String - - """ - A unique identifier assigned to the affiliated institution by The Research Organization Registry (ROR). - """ - affiliationIdentifier: String - - """Indicates whether an author is the corresponding author""" - correspondingAuthorStatus: Boolean - - """ - Indicates whether an author is the main person associated with the corresponding dataset - """ - primaryAuthorStatus: Boolean -} - -type DatasetAuthorAggregate { - aggregate: [DatasetAuthorAggregateFunctions!] -} - -type DatasetAuthorAggregateFunctions { - sum: DatasetAuthorNumericalColumns - avg: DatasetAuthorNumericalColumns - stddev: DatasetAuthorNumericalColumns - variance: DatasetAuthorNumericalColumns - min: DatasetAuthorMinMaxColumns - max: DatasetAuthorMinMaxColumns - groupBy: DatasetAuthorGroupByOptions - count(distinct: Boolean = false, columns: DatasetAuthorCountColumns = null): Int -} - -input DatasetAuthorAggregateWhereClause { - count: DatasetAuthorAggregateWhereClauseCount! -} - -input DatasetAuthorAggregateWhereClauseCount { - arguments: DatasetAuthorCountColumns - distinct: Boolean - filter: DatasetAuthorWhereClause - predicate: IntComparators -} - -"""A connection to a list of items.""" -type DatasetAuthorConnection { - """Pagination data for this connection""" - pageInfo: PageInfo! - - """Contains the nodes in this connection""" - edges: [DatasetAuthorEdge!]! -} - -enum DatasetAuthorCountColumns { - id - authorListOrder - orcid - kaggleId - name - email - affiliationName - affiliationAddress - affiliationIdentifier - correspondingAuthorStatus - primaryAuthorStatus -} - -input DatasetAuthorCreateInput { - """Dataset authored by this person""" - datasetId: ID = null - - """Numeric identifier (May change!)""" - id: Int! - - """The order in which the author appears in the publication""" - authorListOrder: Int! - - """A unique, persistent identifier for researchers, provided by ORCID.""" - orcid: String = null - - """A unique, persistent identifier for kaggle users at kaggle.com.""" - kaggleId: String = null - - """Full name of a dataset author (e.g. Jane Doe).""" - name: String! - - """Email address for this author""" - email: String = null - - """Name of the institutions an author is affiliated with. Comma separated""" - affiliationName: String = null - - """Address of the institution an author is affiliated with.""" - affiliationAddress: String = null - - """ - A unique identifier assigned to the affiliated institution by The Research Organization Registry (ROR). - """ - affiliationIdentifier: String = null - - """Indicates whether an author is the corresponding author""" - correspondingAuthorStatus: Boolean = null - - """ - Indicates whether an author is the main person associated with the corresponding dataset - """ - primaryAuthorStatus: Boolean = null -} - -"""An edge in a connection.""" -type DatasetAuthorEdge { - """A cursor for use in pagination""" - cursor: String! - - """The item at the end of the edge""" - node: DatasetAuthor! -} - -type DatasetAuthorGroupByOptions { - dataset: DatasetGroupByOptions - id: Int - authorListOrder: Int - orcid: String - kaggleId: String - name: String - email: String - affiliationName: String - affiliationAddress: String - affiliationIdentifier: String - correspondingAuthorStatus: Boolean - primaryAuthorStatus: Boolean -} - -type DatasetAuthorMinMaxColumns { - id: Int - authorListOrder: Int - orcid: String - kaggleId: String - name: String - email: String - affiliationName: String - affiliationAddress: String - affiliationIdentifier: String -} - -type DatasetAuthorNumericalColumns { - id: Int - authorListOrder: Int -} - -input DatasetAuthorOrderByClause { - dataset: DatasetOrderByClause - id: orderBy - authorListOrder: orderBy - orcid: orderBy - kaggleId: orderBy - name: orderBy - email: orderBy - affiliationName: orderBy - affiliationAddress: orderBy - affiliationIdentifier: orderBy - correspondingAuthorStatus: orderBy - primaryAuthorStatus: orderBy -} - -input DatasetAuthorUpdateInput { - """Dataset authored by this person""" - datasetId: ID = null - - """Numeric identifier (May change!)""" - id: Int - - """The order in which the author appears in the publication""" - authorListOrder: Int - - """A unique, persistent identifier for researchers, provided by ORCID.""" - orcid: String = null - - """A unique, persistent identifier for kaggle users at kaggle.com.""" - kaggleId: String = null - - """Full name of a dataset author (e.g. Jane Doe).""" - name: String - - """Email address for this author""" - email: String = null - - """Name of the institutions an author is affiliated with. Comma separated""" - affiliationName: String = null - - """Address of the institution an author is affiliated with.""" - affiliationAddress: String = null - - """ - A unique identifier assigned to the affiliated institution by The Research Organization Registry (ROR). - """ - affiliationIdentifier: String = null - - """Indicates whether an author is the corresponding author""" - correspondingAuthorStatus: Boolean = null - - """ - Indicates whether an author is the main person associated with the corresponding dataset - """ - primaryAuthorStatus: Boolean = null -} - -input DatasetAuthorWhereClause { - dataset: DatasetWhereClause - datasetId: IntComparators - id: IntComparators - authorListOrder: IntComparators - orcid: StrComparators - kaggleId: StrComparators - name: StrComparators - email: StrComparators - affiliationName: StrComparators - affiliationAddress: StrComparators - affiliationIdentifier: StrComparators - correspondingAuthorStatus: BoolComparators - primaryAuthorStatus: BoolComparators -} - -input DatasetAuthorWhereClauseMutations { - id: IntComparators -} - -"""A connection to a list of items.""" -type DatasetConnection { - """Pagination data for this connection""" - pageInfo: PageInfo! - - """Contains the nodes in this connection""" - edges: [DatasetEdge!]! -} - -enum DatasetCountColumns { - title - description - assayLabel - assayOntologyId - developmentStageName - developmentStageOntologyId - diseaseName - diseaseOntologyId - organismName - organismTaxid - tissueName - tissueId - cellName - cellTypeId - cellStrainName - cellStrainId - sampleType - samplePreparation - gridPreparation - otherSetup - keyPhotoUrl - keyPhotoThumbnailUrl - cellComponentName - cellComponentId - depositionDate - releaseDate - lastModifiedDate - datasetPublications - relatedDatabaseEntries - s3Prefix - httpsPrefix - fileSize - id -} - -input DatasetCreateInput { - """Reference to the deposition this dataset is associated with""" - depositionId: ID! - - """Title of a CryoET dataset""" - title: String! - - """ - A short description of a CryoET dataset, similar to an abstract for a journal article or dataset. - """ - description: String! - - """ - Label for the type of assay performed in a CryoET dataset, e.g. cryo-electron tomography - """ - assayLabel: String = null - - """ - EFO ontology identifier for the type of assay performed in a CryoET dataset - """ - assayOntologyId: String = null - - """ - Development stage of the organism from which a biological sample used the study is derived. - """ - developmentStageName: String = null - - """Ontology identifier for the development stage""" - developmentStageOntologyId: String = null - - """ - Name of the disease associated with the biological sample used in a CryoET study, e.g. Alzheimer’s disease - """ - diseaseName: String = null - - """ - Ontology identifier for the disease associated with the biological sample used in a CryoET study - """ - diseaseOntologyId: String = null - - """ - Name of the organism from which a biological sample used in a CryoET study is derived from, e.g. homo sapiens - """ - organismName: String = null - - """NCBI taxonomy identifier for the organism, e.g. 9606""" - organismTaxid: Int = null - - """ - Name of the tissue from which a biological sample used in a CryoET study is derived from. - """ - tissueName: String = null - - """The ontology identifier for the tissue.""" - tissueId: String = null - - """ - Name of the cell from which a biological sample used in a CryoET study is derived from. - """ - cellName: String = null - - """The ontology identifier for the cell type.""" - cellTypeId: String = null - - """Cell line or strain for the sample.""" - cellStrainName: String = null - - """Link to more information about the cell strain""" - cellStrainId: String = null - - """ - Type of samples used in a CryoET study. (cell, tissue, organism, intact organelle, in-vitro mixture, in-silico synthetic data, other) - """ - sampleType: sample_type_enum = null - - """Describe how the sample was prepared.""" - samplePreparation: String = null - - """Describe Cryo-ET grid preparation.""" - gridPreparation: String = null - - """ - Describe other setup not covered by sample preparation or grid preparation that may make this dataset unique in the same publication - """ - otherSetup: String = null - - """URL for the dataset preview image.""" - keyPhotoUrl: String = null - - """URL for the thumbnail of preview image.""" - keyPhotoThumbnailUrl: String = null - - """Name of the cellular component""" - cellComponentName: String = null - - """ - If the dataset focuses on a specific part of a cell, the subset is included here - """ - cellComponentId: String = null - - """Date when a dataset is initially received by the Data Portal.""" - depositionDate: DateTime! - - """Date when a dataset is made available on the Data Portal.""" - releaseDate: DateTime! - - """Date when a released dataset is last modified.""" - lastModifiedDate: DateTime! - - """ - Comma-separated list of DOIs for publications associated with the dataset. - """ - datasetPublications: String = null - - """ - If a CryoET dataset is also deposited into another database, enter the database identifier here (e.g. EMPIAR-11445). Use a comma to separate multiple identifiers. - """ - relatedDatabaseEntries: String = null - - """The S3 public bucket path where this dataset is contained""" - s3Prefix: String! - - """The https directory path where this dataset is contained""" - httpsPrefix: String! - - """Size of the dataset in bytes""" - fileSize: Float = null - - """ - An identifier for a CryoET dataset, assigned by the Data Portal. Used to identify the dataset as the directory name in data tree - """ - id: Int! -} - -"""An edge in a connection.""" -type DatasetEdge { - """A cursor for use in pagination""" - cursor: String! - - """The item at the end of the edge""" - node: Dataset! -} - -"""Metadata for a dataset's funding sources""" -type DatasetFunding implements EntityInterface & Node { - """The Globally Unique ID of this object""" - _id: GlobalID! - - """Numeric identifier (May change!)""" - id: Int! - dataset(where: DatasetWhereClause = null, orderBy: [DatasetOrderByClause!] = []): Dataset - datasetId: Int - - """Name of the funding agency.""" - fundingAgencyName: String - - """Grant identifier provided by the funding agency.""" - grantId: String -} - -type DatasetFundingAggregate { - aggregate: [DatasetFundingAggregateFunctions!] -} - -type DatasetFundingAggregateFunctions { - sum: DatasetFundingNumericalColumns - avg: DatasetFundingNumericalColumns - stddev: DatasetFundingNumericalColumns - variance: DatasetFundingNumericalColumns - min: DatasetFundingMinMaxColumns - max: DatasetFundingMinMaxColumns - groupBy: DatasetFundingGroupByOptions - count(distinct: Boolean = false, columns: DatasetFundingCountColumns = null): Int -} - -input DatasetFundingAggregateWhereClause { - count: DatasetFundingAggregateWhereClauseCount! -} - -input DatasetFundingAggregateWhereClauseCount { - arguments: DatasetFundingCountColumns - distinct: Boolean - filter: DatasetFundingWhereClause - predicate: IntComparators -} - -"""A connection to a list of items.""" -type DatasetFundingConnection { - """Pagination data for this connection""" - pageInfo: PageInfo! - - """Contains the nodes in this connection""" - edges: [DatasetFundingEdge!]! -} - -enum DatasetFundingCountColumns { - fundingAgencyName - grantId - id -} - -input DatasetFundingCreateInput { - """The dataset this dataset funding is a part of""" - datasetId: ID = null - - """Name of the funding agency.""" - fundingAgencyName: String = null - - """Grant identifier provided by the funding agency.""" - grantId: String = null - - """Numeric identifier (May change!)""" - id: Int! -} - -"""An edge in a connection.""" -type DatasetFundingEdge { - """A cursor for use in pagination""" - cursor: String! - - """The item at the end of the edge""" - node: DatasetFunding! -} - -type DatasetFundingGroupByOptions { - dataset: DatasetGroupByOptions - fundingAgencyName: String - grantId: String - id: Int -} - -type DatasetFundingMinMaxColumns { - fundingAgencyName: String - grantId: String - id: Int -} - -type DatasetFundingNumericalColumns { - id: Int -} - -input DatasetFundingOrderByClause { - dataset: DatasetOrderByClause - fundingAgencyName: orderBy - grantId: orderBy - id: orderBy -} - -input DatasetFundingUpdateInput { - """The dataset this dataset funding is a part of""" - datasetId: ID = null - - """Name of the funding agency.""" - fundingAgencyName: String = null - - """Grant identifier provided by the funding agency.""" - grantId: String = null - - """Numeric identifier (May change!)""" - id: Int -} - -input DatasetFundingWhereClause { - dataset: DatasetWhereClause - datasetId: IntComparators - fundingAgencyName: StrComparators - grantId: StrComparators - id: IntComparators -} - -input DatasetFundingWhereClauseMutations { - id: IntComparators -} - -type DatasetGroupByOptions { - deposition: DepositionGroupByOptions - fundingSources: DatasetFundingGroupByOptions - authors: DatasetAuthorGroupByOptions - runs: RunGroupByOptions - title: String - description: String - assayLabel: String - assayOntologyId: String - developmentStageName: String - developmentStageOntologyId: String - diseaseName: String - diseaseOntologyId: String - organismName: String - organismTaxid: Int - tissueName: String - tissueId: String - cellName: String - cellTypeId: String - cellStrainName: String - cellStrainId: String - sampleType: sample_type_enum - samplePreparation: String - gridPreparation: String - otherSetup: String - keyPhotoUrl: String - keyPhotoThumbnailUrl: String - cellComponentName: String - cellComponentId: String - depositionDate: DateTime - releaseDate: DateTime - lastModifiedDate: DateTime - datasetPublications: String - relatedDatabaseEntries: String - s3Prefix: String - httpsPrefix: String - fileSize: Float - id: Int -} - -type DatasetMinMaxColumns { - title: String - description: String - assayLabel: String - assayOntologyId: String - developmentStageName: String - developmentStageOntologyId: String - diseaseName: String - diseaseOntologyId: String - organismName: String - organismTaxid: Int - tissueName: String - tissueId: String - cellName: String - cellTypeId: String - cellStrainName: String - cellStrainId: String - samplePreparation: String - gridPreparation: String - otherSetup: String - keyPhotoUrl: String - keyPhotoThumbnailUrl: String - cellComponentName: String - cellComponentId: String - depositionDate: DateTime - releaseDate: DateTime - lastModifiedDate: DateTime - datasetPublications: String - relatedDatabaseEntries: String - s3Prefix: String - httpsPrefix: String - fileSize: Float - id: Int -} - -type DatasetNumericalColumns { - organismTaxid: Int - fileSize: Float - id: Int -} - -input DatasetOrderByClause { - deposition: DepositionOrderByClause - title: orderBy - description: orderBy - assayLabel: orderBy - assayOntologyId: orderBy - developmentStageName: orderBy - developmentStageOntologyId: orderBy - diseaseName: orderBy - diseaseOntologyId: orderBy - organismName: orderBy - organismTaxid: orderBy - tissueName: orderBy - tissueId: orderBy - cellName: orderBy - cellTypeId: orderBy - cellStrainName: orderBy - cellStrainId: orderBy - sampleType: orderBy - samplePreparation: orderBy - gridPreparation: orderBy - otherSetup: orderBy - keyPhotoUrl: orderBy - keyPhotoThumbnailUrl: orderBy - cellComponentName: orderBy - cellComponentId: orderBy - depositionDate: orderBy - releaseDate: orderBy - lastModifiedDate: orderBy - datasetPublications: orderBy - relatedDatabaseEntries: orderBy - s3Prefix: orderBy - httpsPrefix: orderBy - fileSize: orderBy - id: orderBy -} - -input DatasetUpdateInput { - """Reference to the deposition this dataset is associated with""" - depositionId: ID - - """Title of a CryoET dataset""" - title: String - - """ - A short description of a CryoET dataset, similar to an abstract for a journal article or dataset. - """ - description: String - - """ - Label for the type of assay performed in a CryoET dataset, e.g. cryo-electron tomography - """ - assayLabel: String = null - - """ - EFO ontology identifier for the type of assay performed in a CryoET dataset - """ - assayOntologyId: String = null - - """ - Development stage of the organism from which a biological sample used the study is derived. - """ - developmentStageName: String = null - - """Ontology identifier for the development stage""" - developmentStageOntologyId: String = null - - """ - Name of the disease associated with the biological sample used in a CryoET study, e.g. Alzheimer’s disease - """ - diseaseName: String = null - - """ - Ontology identifier for the disease associated with the biological sample used in a CryoET study - """ - diseaseOntologyId: String = null - - """ - Name of the organism from which a biological sample used in a CryoET study is derived from, e.g. homo sapiens - """ - organismName: String = null - - """NCBI taxonomy identifier for the organism, e.g. 9606""" - organismTaxid: Int = null - - """ - Name of the tissue from which a biological sample used in a CryoET study is derived from. - """ - tissueName: String = null - - """The ontology identifier for the tissue.""" - tissueId: String = null - - """ - Name of the cell from which a biological sample used in a CryoET study is derived from. - """ - cellName: String = null - - """The ontology identifier for the cell type.""" - cellTypeId: String = null - - """Cell line or strain for the sample.""" - cellStrainName: String = null - - """Link to more information about the cell strain""" - cellStrainId: String = null - - """ - Type of samples used in a CryoET study. (cell, tissue, organism, intact organelle, in-vitro mixture, in-silico synthetic data, other) - """ - sampleType: sample_type_enum = null - - """Describe how the sample was prepared.""" - samplePreparation: String = null - - """Describe Cryo-ET grid preparation.""" - gridPreparation: String = null - - """ - Describe other setup not covered by sample preparation or grid preparation that may make this dataset unique in the same publication - """ - otherSetup: String = null - - """URL for the dataset preview image.""" - keyPhotoUrl: String = null - - """URL for the thumbnail of preview image.""" - keyPhotoThumbnailUrl: String = null - - """Name of the cellular component""" - cellComponentName: String = null - - """ - If the dataset focuses on a specific part of a cell, the subset is included here - """ - cellComponentId: String = null - - """Date when a dataset is initially received by the Data Portal.""" - depositionDate: DateTime - - """Date when a dataset is made available on the Data Portal.""" - releaseDate: DateTime - - """Date when a released dataset is last modified.""" - lastModifiedDate: DateTime - - """ - Comma-separated list of DOIs for publications associated with the dataset. - """ - datasetPublications: String = null - - """ - If a CryoET dataset is also deposited into another database, enter the database identifier here (e.g. EMPIAR-11445). Use a comma to separate multiple identifiers. - """ - relatedDatabaseEntries: String = null - - """The S3 public bucket path where this dataset is contained""" - s3Prefix: String - - """The https directory path where this dataset is contained""" - httpsPrefix: String - - """Size of the dataset in bytes""" - fileSize: Float = null - - """ - An identifier for a CryoET dataset, assigned by the Data Portal. Used to identify the dataset as the directory name in data tree - """ - id: Int -} - -input DatasetWhereClause { - deposition: DepositionWhereClause - depositionId: IntComparators - fundingSources: DatasetFundingWhereClause - fundingSourcesAggregate: DatasetFundingAggregateWhereClause - authors: DatasetAuthorWhereClause - authorsAggregate: DatasetAuthorAggregateWhereClause - runs: RunWhereClause - runsAggregate: RunAggregateWhereClause - title: StrComparators - description: StrComparators - assayLabel: StrComparators - assayOntologyId: StrComparators - developmentStageName: StrComparators - developmentStageOntologyId: StrComparators - diseaseName: StrComparators - diseaseOntologyId: StrComparators - organismName: StrComparators - organismTaxid: IntComparators - tissueName: StrComparators - tissueId: StrComparators - cellName: StrComparators - cellTypeId: StrComparators - cellStrainName: StrComparators - cellStrainId: StrComparators - sampleType: Sample_type_enumEnumComparators - samplePreparation: StrComparators - gridPreparation: StrComparators - otherSetup: StrComparators - keyPhotoUrl: StrComparators - keyPhotoThumbnailUrl: StrComparators - cellComponentName: StrComparators - cellComponentId: StrComparators - depositionDate: DatetimeComparators - releaseDate: DatetimeComparators - lastModifiedDate: DatetimeComparators - datasetPublications: StrComparators - relatedDatabaseEntries: StrComparators - s3Prefix: StrComparators - httpsPrefix: StrComparators - fileSize: FloatComparators - id: IntComparators -} - -input DatasetWhereClauseMutations { - id: IntComparators -} - -"""Date with time (isoformat)""" -scalar DateTime - -input DatetimeComparators { - _eq: DateTime - _neq: DateTime - _in: [DateTime!] - _nin: [DateTime!] - _gt: DateTime - _gte: DateTime - _lt: DateTime - _lte: DateTime - _is_null: Boolean -} - -"""Deposition metadata""" -type Deposition implements EntityInterface & Node { - """The Globally Unique ID of this object""" - _id: GlobalID! - - """Numeric identifier (May change!)""" - id: Int! - authors( - where: DepositionAuthorWhereClause = null - orderBy: [DepositionAuthorOrderByClause!] = [] - - """Returns the items in the list that come before the specified cursor.""" - before: String = null - - """Returns the items in the list that come after the specified cursor.""" - after: String = null - - """Returns the first n items from the list.""" - first: Int = null - - """Returns the items in the list that come after the specified cursor.""" - last: Int = null - ): DepositionAuthorConnection! - authorsAggregate(where: DepositionAuthorWhereClause = null): DepositionAuthorAggregate - alignments( - where: AlignmentWhereClause = null - orderBy: [AlignmentOrderByClause!] = [] - - """Returns the items in the list that come before the specified cursor.""" - before: String = null - - """Returns the items in the list that come after the specified cursor.""" - after: String = null - - """Returns the first n items from the list.""" - first: Int = null - - """Returns the items in the list that come after the specified cursor.""" - last: Int = null - ): AlignmentConnection! - alignmentsAggregate(where: AlignmentWhereClause = null): AlignmentAggregate - annotations( - where: AnnotationWhereClause = null - orderBy: [AnnotationOrderByClause!] = [] - - """Returns the items in the list that come before the specified cursor.""" - before: String = null - - """Returns the items in the list that come after the specified cursor.""" - after: String = null - - """Returns the first n items from the list.""" - first: Int = null - - """Returns the items in the list that come after the specified cursor.""" - last: Int = null - ): AnnotationConnection! - annotationsAggregate(where: AnnotationWhereClause = null): AnnotationAggregate - datasets( - where: DatasetWhereClause = null - orderBy: [DatasetOrderByClause!] = [] - - """Returns the items in the list that come before the specified cursor.""" - before: String = null - - """Returns the items in the list that come after the specified cursor.""" - after: String = null - - """Returns the first n items from the list.""" - first: Int = null - - """Returns the items in the list that come after the specified cursor.""" - last: Int = null - ): DatasetConnection! - datasetsAggregate(where: DatasetWhereClause = null): DatasetAggregate - frames( - where: FrameWhereClause = null - orderBy: [FrameOrderByClause!] = [] - - """Returns the items in the list that come before the specified cursor.""" - before: String = null - - """Returns the items in the list that come after the specified cursor.""" - after: String = null - - """Returns the first n items from the list.""" - first: Int = null - - """Returns the items in the list that come after the specified cursor.""" - last: Int = null - ): FrameConnection! - framesAggregate(where: FrameWhereClause = null): FrameAggregate - tiltseries( - where: TiltseriesWhereClause = null - orderBy: [TiltseriesOrderByClause!] = [] - - """Returns the items in the list that come before the specified cursor.""" - before: String = null - - """Returns the items in the list that come after the specified cursor.""" - after: String = null - - """Returns the first n items from the list.""" - first: Int = null - - """Returns the items in the list that come after the specified cursor.""" - last: Int = null - ): TiltseriesConnection! - tiltseriesAggregate(where: TiltseriesWhereClause = null): TiltseriesAggregate - tomograms( - where: TomogramWhereClause = null - orderBy: [TomogramOrderByClause!] = [] - - """Returns the items in the list that come before the specified cursor.""" - before: String = null - - """Returns the items in the list that come after the specified cursor.""" - after: String = null - - """Returns the first n items from the list.""" - first: Int = null - - """Returns the items in the list that come after the specified cursor.""" - last: Int = null - ): TomogramConnection! - tomogramsAggregate(where: TomogramWhereClause = null): TomogramAggregate - - """Title for the deposition""" - title: String! - - """Description for the deposition""" - description: String! - - """Tag for the deposition - like ml competition""" - tag: String - depositionTypes( - where: DepositionTypeWhereClause = null - orderBy: [DepositionTypeOrderByClause!] = [] - - """Returns the items in the list that come before the specified cursor.""" - before: String = null - - """Returns the items in the list that come after the specified cursor.""" - after: String = null - - """Returns the first n items from the list.""" - first: Int = null - - """Returns the items in the list that come after the specified cursor.""" - last: Int = null - ): DepositionTypeConnection! - depositionTypesAggregate(where: DepositionTypeWhereClause = null): DepositionTypeAggregate - - """The publications related to this deposition""" - depositionPublications: String - - """The related database entries to this deposition""" - relatedDatabaseEntries: String - - """The date the deposition was deposited""" - depositionDate: DateTime! - - """The date the deposition was released""" - releaseDate: DateTime! - - """The date the deposition was last modified""" - lastModifiedDate: DateTime! - - """URL for the deposition preview image.""" - keyPhotoUrl: String - - """URL for the deposition thumbnail image.""" - keyPhotoThumbnailUrl: String -} - -type DepositionAggregate { - aggregate: [DepositionAggregateFunctions!] -} - -type DepositionAggregateFunctions { - sum: DepositionNumericalColumns - avg: DepositionNumericalColumns - stddev: DepositionNumericalColumns - variance: DepositionNumericalColumns - min: DepositionMinMaxColumns - max: DepositionMinMaxColumns - groupBy: DepositionGroupByOptions - count(distinct: Boolean = false, columns: DepositionCountColumns = null): Int -} - -"""Authors for a deposition""" -type DepositionAuthor implements EntityInterface & Node { - """The Globally Unique ID of this object""" - _id: GlobalID! - - """Numeric identifier (May change!)""" - id: Int! - deposition(where: DepositionWhereClause = null, orderBy: [DepositionOrderByClause!] = []): Deposition - depositionId: Int! - - """The order in which the author appears in the publication""" - authorListOrder: Int! - - """A unique, persistent identifier for researchers, provided by ORCID.""" - orcid: String - - """A unique, persistent identifier for kaggle users at kaggle.com.""" - kaggleId: String - - """Full name of a deposition author (e.g. Jane Doe).""" - name: String! - - """Email address for this author""" - email: String - - """Name of the institutions an author is affiliated with. Comma separated""" - affiliationName: String - - """Address of the institution an author is affiliated with.""" - affiliationAddress: String - - """ - A unique identifier assigned to the affiliated institution by The Research Organization Registry (ROR). - """ - affiliationIdentifier: String - - """Indicates whether an author is the corresponding author""" - correspondingAuthorStatus: Boolean - - """Indicates whether an author is the main person creating the deposition""" - primaryAuthorStatus: Boolean -} - -type DepositionAuthorAggregate { - aggregate: [DepositionAuthorAggregateFunctions!] -} - -type DepositionAuthorAggregateFunctions { - sum: DepositionAuthorNumericalColumns - avg: DepositionAuthorNumericalColumns - stddev: DepositionAuthorNumericalColumns - variance: DepositionAuthorNumericalColumns - min: DepositionAuthorMinMaxColumns - max: DepositionAuthorMinMaxColumns - groupBy: DepositionAuthorGroupByOptions - count(distinct: Boolean = false, columns: DepositionAuthorCountColumns = null): Int -} - -input DepositionAuthorAggregateWhereClause { - count: DepositionAuthorAggregateWhereClauseCount! -} - -input DepositionAuthorAggregateWhereClauseCount { - arguments: DepositionAuthorCountColumns - distinct: Boolean - filter: DepositionAuthorWhereClause - predicate: IntComparators -} - -"""A connection to a list of items.""" -type DepositionAuthorConnection { - """Pagination data for this connection""" - pageInfo: PageInfo! - - """Contains the nodes in this connection""" - edges: [DepositionAuthorEdge!]! -} - -enum DepositionAuthorCountColumns { - id - authorListOrder - orcid - kaggleId - name - email - affiliationName - affiliationAddress - affiliationIdentifier - correspondingAuthorStatus - primaryAuthorStatus -} - -input DepositionAuthorCreateInput { - depositionId: ID! - - """Numeric identifier (May change!)""" - id: Int! - - """The order in which the author appears in the publication""" - authorListOrder: Int! - - """A unique, persistent identifier for researchers, provided by ORCID.""" - orcid: String = null - - """A unique, persistent identifier for kaggle users at kaggle.com.""" - kaggleId: String = null - - """Full name of a deposition author (e.g. Jane Doe).""" - name: String! - - """Email address for this author""" - email: String = null - - """Name of the institutions an author is affiliated with. Comma separated""" - affiliationName: String = null - - """Address of the institution an author is affiliated with.""" - affiliationAddress: String = null - - """ - A unique identifier assigned to the affiliated institution by The Research Organization Registry (ROR). - """ - affiliationIdentifier: String = null - - """Indicates whether an author is the corresponding author""" - correspondingAuthorStatus: Boolean = null - - """Indicates whether an author is the main person creating the deposition""" - primaryAuthorStatus: Boolean = null -} - -"""An edge in a connection.""" -type DepositionAuthorEdge { - """A cursor for use in pagination""" - cursor: String! - - """The item at the end of the edge""" - node: DepositionAuthor! -} - -type DepositionAuthorGroupByOptions { - deposition: DepositionGroupByOptions - id: Int - authorListOrder: Int - orcid: String - kaggleId: String - name: String - email: String - affiliationName: String - affiliationAddress: String - affiliationIdentifier: String - correspondingAuthorStatus: Boolean - primaryAuthorStatus: Boolean -} - -type DepositionAuthorMinMaxColumns { - id: Int - authorListOrder: Int - orcid: String - kaggleId: String - name: String - email: String - affiliationName: String - affiliationAddress: String - affiliationIdentifier: String -} - -type DepositionAuthorNumericalColumns { - id: Int - authorListOrder: Int -} - -input DepositionAuthorOrderByClause { - deposition: DepositionOrderByClause - id: orderBy - authorListOrder: orderBy - orcid: orderBy - kaggleId: orderBy - name: orderBy - email: orderBy - affiliationName: orderBy - affiliationAddress: orderBy - affiliationIdentifier: orderBy - correspondingAuthorStatus: orderBy - primaryAuthorStatus: orderBy -} - -input DepositionAuthorUpdateInput { - depositionId: ID - - """Numeric identifier (May change!)""" - id: Int - - """The order in which the author appears in the publication""" - authorListOrder: Int - - """A unique, persistent identifier for researchers, provided by ORCID.""" - orcid: String = null - - """A unique, persistent identifier for kaggle users at kaggle.com.""" - kaggleId: String = null - - """Full name of a deposition author (e.g. Jane Doe).""" - name: String - - """Email address for this author""" - email: String = null - - """Name of the institutions an author is affiliated with. Comma separated""" - affiliationName: String = null - - """Address of the institution an author is affiliated with.""" - affiliationAddress: String = null - - """ - A unique identifier assigned to the affiliated institution by The Research Organization Registry (ROR). - """ - affiliationIdentifier: String = null - - """Indicates whether an author is the corresponding author""" - correspondingAuthorStatus: Boolean = null - - """Indicates whether an author is the main person creating the deposition""" - primaryAuthorStatus: Boolean = null -} - -input DepositionAuthorWhereClause { - deposition: DepositionWhereClause - depositionId: IntComparators - id: IntComparators - authorListOrder: IntComparators - orcid: StrComparators - kaggleId: StrComparators - name: StrComparators - email: StrComparators - affiliationName: StrComparators - affiliationAddress: StrComparators - affiliationIdentifier: StrComparators - correspondingAuthorStatus: BoolComparators - primaryAuthorStatus: BoolComparators -} - -input DepositionAuthorWhereClauseMutations { - id: IntComparators -} - -enum DepositionCountColumns { - title - description - tag - depositionPublications - relatedDatabaseEntries - depositionDate - releaseDate - lastModifiedDate - keyPhotoUrl - keyPhotoThumbnailUrl - id -} - -input DepositionCreateInput { - """Title for the deposition""" - title: String! - - """Description for the deposition""" - description: String! - - """Tag for the deposition - like ml competition""" - tag: String = null - - """The publications related to this deposition""" - depositionPublications: String = null - - """The related database entries to this deposition""" - relatedDatabaseEntries: String = null - - """The date the deposition was deposited""" - depositionDate: DateTime! - - """The date the deposition was released""" - releaseDate: DateTime! - - """The date the deposition was last modified""" - lastModifiedDate: DateTime! - - """URL for the deposition preview image.""" - keyPhotoUrl: String = null - - """URL for the deposition thumbnail image.""" - keyPhotoThumbnailUrl: String = null - - """Numeric identifier (May change!)""" - id: Int! -} - -type DepositionGroupByOptions { - authors: DepositionAuthorGroupByOptions - alignments: AlignmentGroupByOptions - annotations: AnnotationGroupByOptions - datasets: DatasetGroupByOptions - frames: FrameGroupByOptions - tiltseries: TiltseriesGroupByOptions - tomograms: TomogramGroupByOptions - title: String - description: String - tag: String - depositionTypes: DepositionTypeGroupByOptions - depositionPublications: String - relatedDatabaseEntries: String - depositionDate: DateTime - releaseDate: DateTime - lastModifiedDate: DateTime - keyPhotoUrl: String - keyPhotoThumbnailUrl: String - id: Int -} - -type DepositionMinMaxColumns { - title: String - description: String - tag: String - depositionPublications: String - relatedDatabaseEntries: String - depositionDate: DateTime - releaseDate: DateTime - lastModifiedDate: DateTime - keyPhotoUrl: String - keyPhotoThumbnailUrl: String - id: Int -} - -type DepositionNumericalColumns { - id: Int -} - -input DepositionOrderByClause { - title: orderBy - description: orderBy - tag: orderBy - depositionPublications: orderBy - relatedDatabaseEntries: orderBy - depositionDate: orderBy - releaseDate: orderBy - lastModifiedDate: orderBy - keyPhotoUrl: orderBy - keyPhotoThumbnailUrl: orderBy - id: orderBy -} - -type DepositionType implements EntityInterface & Node { - """The Globally Unique ID of this object""" - _id: GlobalID! - - """Numeric identifier (May change!)""" - id: Int! - deposition(where: DepositionWhereClause = null, orderBy: [DepositionOrderByClause!] = []): Deposition - depositionId: Int! - - """ - The type of data submitted as a part of this deposition (annotation, dataset, tomogram) - """ - type: deposition_types_enum -} - -type DepositionTypeAggregate { - aggregate: [DepositionTypeAggregateFunctions!] -} - -type DepositionTypeAggregateFunctions { - sum: DepositionTypeNumericalColumns - avg: DepositionTypeNumericalColumns - stddev: DepositionTypeNumericalColumns - variance: DepositionTypeNumericalColumns - min: DepositionTypeMinMaxColumns - max: DepositionTypeMinMaxColumns - groupBy: DepositionTypeGroupByOptions - count(distinct: Boolean = false, columns: DepositionTypeCountColumns = null): Int -} - -input DepositionTypeAggregateWhereClause { - count: DepositionTypeAggregateWhereClauseCount! -} - -input DepositionTypeAggregateWhereClauseCount { - arguments: DepositionTypeCountColumns - distinct: Boolean - filter: DepositionTypeWhereClause - predicate: IntComparators -} - -"""A connection to a list of items.""" -type DepositionTypeConnection { - """Pagination data for this connection""" - pageInfo: PageInfo! - - """Contains the nodes in this connection""" - edges: [DepositionTypeEdge!]! -} - -enum DepositionTypeCountColumns { - type - id -} - -input DepositionTypeCreateInput { - depositionId: ID! - - """ - The type of data submitted as a part of this deposition (annotation, dataset, tomogram) - """ - type: deposition_types_enum = null - - """Numeric identifier (May change!)""" - id: Int! -} - -"""An edge in a connection.""" -type DepositionTypeEdge { - """A cursor for use in pagination""" - cursor: String! - - """The item at the end of the edge""" - node: DepositionType! -} - -type DepositionTypeGroupByOptions { - deposition: DepositionGroupByOptions - type: deposition_types_enum - id: Int -} - -type DepositionTypeMinMaxColumns { - id: Int -} - -type DepositionTypeNumericalColumns { - id: Int -} - -input DepositionTypeOrderByClause { - deposition: DepositionOrderByClause - type: orderBy - id: orderBy -} - -input DepositionTypeUpdateInput { - depositionId: ID - - """ - The type of data submitted as a part of this deposition (annotation, dataset, tomogram) - """ - type: deposition_types_enum = null - - """Numeric identifier (May change!)""" - id: Int -} - -input DepositionTypeWhereClause { - deposition: DepositionWhereClause - depositionId: IntComparators - type: Deposition_types_enumEnumComparators - id: IntComparators -} - -input DepositionTypeWhereClauseMutations { - id: IntComparators -} - -input DepositionUpdateInput { - """Title for the deposition""" - title: String - - """Description for the deposition""" - description: String - - """Tag for the deposition - like ml competition""" - tag: String = null - - """The publications related to this deposition""" - depositionPublications: String = null - - """The related database entries to this deposition""" - relatedDatabaseEntries: String = null - - """The date the deposition was deposited""" - depositionDate: DateTime - - """The date the deposition was released""" - releaseDate: DateTime - - """The date the deposition was last modified""" - lastModifiedDate: DateTime - - """URL for the deposition preview image.""" - keyPhotoUrl: String = null - - """URL for the deposition thumbnail image.""" - keyPhotoThumbnailUrl: String = null - - """Numeric identifier (May change!)""" - id: Int -} - -input DepositionWhereClause { - authors: DepositionAuthorWhereClause - authorsAggregate: DepositionAuthorAggregateWhereClause - alignments: AlignmentWhereClause - alignmentsAggregate: AlignmentAggregateWhereClause - annotations: AnnotationWhereClause - annotationsAggregate: AnnotationAggregateWhereClause - datasets: DatasetWhereClause - datasetsAggregate: DatasetAggregateWhereClause - frames: FrameWhereClause - framesAggregate: FrameAggregateWhereClause - tiltseries: TiltseriesWhereClause - tiltseriesAggregate: TiltseriesAggregateWhereClause - tomograms: TomogramWhereClause - tomogramsAggregate: TomogramAggregateWhereClause - title: StrComparators - description: StrComparators - tag: StrComparators - depositionTypes: DepositionTypeWhereClause - depositionTypesAggregate: DepositionTypeAggregateWhereClause - depositionPublications: StrComparators - relatedDatabaseEntries: StrComparators - depositionDate: DatetimeComparators - releaseDate: DatetimeComparators - lastModifiedDate: DatetimeComparators - keyPhotoUrl: StrComparators - keyPhotoThumbnailUrl: StrComparators - id: IntComparators -} - -input DepositionWhereClauseMutations { - id: IntComparators -} - -input Deposition_types_enumEnumComparators { - _eq: deposition_types_enum - _neq: deposition_types_enum - _in: [deposition_types_enum!] - _nin: [deposition_types_enum!] - _gt: deposition_types_enum - _gte: deposition_types_enum - _lt: deposition_types_enum - _lte: deposition_types_enum - _is_null: Boolean -} - -interface EntityInterface implements Node { - """The Globally Unique ID of this object""" - _id: GlobalID! -} - -input Fiducial_alignment_status_enumEnumComparators { - _eq: fiducial_alignment_status_enum - _neq: fiducial_alignment_status_enum - _in: [fiducial_alignment_status_enum!] - _nin: [fiducial_alignment_status_enum!] - _gt: fiducial_alignment_status_enum - _gte: fiducial_alignment_status_enum - _lt: fiducial_alignment_status_enum - _lte: fiducial_alignment_status_enum - _is_null: Boolean -} - -input FloatComparators { - _eq: Float - _neq: Float - _in: [Float!] - _nin: [Float!] - _gt: Float - _gte: Float - _lt: Float - _lte: Float - _is_null: Boolean -} - -type Frame implements EntityInterface & Node { - """The Globally Unique ID of this object""" - _id: GlobalID! - - """Numeric identifier (May change!)""" - id: Int! - deposition(where: DepositionWhereClause = null, orderBy: [DepositionOrderByClause!] = []): Deposition - depositionId: Int! - run(where: RunWhereClause = null, orderBy: [RunOrderByClause!] = []): Run - runId: Int! - - """Frame's acquistion order within a tilt experiment""" - acquisitionOrder: Int - - """The total accumulated dose exposure frame""" - accumulatedDose: Float - - """The dose exposure of this frame""" - exposureDose: Float - - """Whether this frame has been gain corrected""" - isGainCorrected: Boolean - perSectionParameters( - where: PerSectionParametersWhereClause = null - orderBy: [PerSectionParametersOrderByClause!] = [] - - """Returns the items in the list that come before the specified cursor.""" - before: String = null - - """Returns the items in the list that come after the specified cursor.""" - after: String = null - - """Returns the first n items from the list.""" - first: Int = null - - """Returns the items in the list that come after the specified cursor.""" - last: Int = null - ): PerSectionParametersConnection! - perSectionParametersAggregate(where: PerSectionParametersWhereClause = null): PerSectionParametersAggregate - - """S3 path to the frame file""" - s3FramePath: String - - """HTTPS path to the frame file""" - httpsFramePath: String - - """Size of the frame file in bytes""" - fileSize: Float -} - -""" -References to files containing more information about frame acquisition -""" -type FrameAcquisitionFile implements EntityInterface & Node { - """The Globally Unique ID of this object""" - _id: GlobalID! - - """Numeric identifier (May change!)""" - id: Int! - run(where: RunWhereClause = null, orderBy: [RunOrderByClause!] = []): Run - runId: Int - - """Path to the frame acquisition mdoc file in s3""" - s3MdocPath: String! - - """Path to the frame acquisition mdoc file as an https url""" - httpsMdocPath: String! -} - -type FrameAcquisitionFileAggregate { - aggregate: [FrameAcquisitionFileAggregateFunctions!] -} - -type FrameAcquisitionFileAggregateFunctions { - sum: FrameAcquisitionFileNumericalColumns - avg: FrameAcquisitionFileNumericalColumns - stddev: FrameAcquisitionFileNumericalColumns - variance: FrameAcquisitionFileNumericalColumns - min: FrameAcquisitionFileMinMaxColumns - max: FrameAcquisitionFileMinMaxColumns - groupBy: FrameAcquisitionFileGroupByOptions - count(distinct: Boolean = false, columns: FrameAcquisitionFileCountColumns = null): Int -} - -input FrameAcquisitionFileAggregateWhereClause { - count: FrameAcquisitionFileAggregateWhereClauseCount! -} - -input FrameAcquisitionFileAggregateWhereClauseCount { - arguments: FrameAcquisitionFileCountColumns - distinct: Boolean - filter: FrameAcquisitionFileWhereClause - predicate: IntComparators -} - -"""A connection to a list of items.""" -type FrameAcquisitionFileConnection { - """Pagination data for this connection""" - pageInfo: PageInfo! - - """Contains the nodes in this connection""" - edges: [FrameAcquisitionFileEdge!]! -} - -enum FrameAcquisitionFileCountColumns { - s3MdocPath - httpsMdocPath - id -} - -input FrameAcquisitionFileCreateInput { - runId: ID = null - - """Path to the frame acquisition mdoc file in s3""" - s3MdocPath: String! - - """Path to the frame acquisition mdoc file as an https url""" - httpsMdocPath: String! - - """Numeric identifier (May change!)""" - id: Int! -} - -"""An edge in a connection.""" -type FrameAcquisitionFileEdge { - """A cursor for use in pagination""" - cursor: String! - - """The item at the end of the edge""" - node: FrameAcquisitionFile! -} - -type FrameAcquisitionFileGroupByOptions { - run: RunGroupByOptions - s3MdocPath: String - httpsMdocPath: String - id: Int -} - -type FrameAcquisitionFileMinMaxColumns { - s3MdocPath: String - httpsMdocPath: String - id: Int -} - -type FrameAcquisitionFileNumericalColumns { - id: Int -} - -input FrameAcquisitionFileOrderByClause { - run: RunOrderByClause - s3MdocPath: orderBy - httpsMdocPath: orderBy - id: orderBy -} - -input FrameAcquisitionFileUpdateInput { - runId: ID = null - - """Path to the frame acquisition mdoc file in s3""" - s3MdocPath: String - - """Path to the frame acquisition mdoc file as an https url""" - httpsMdocPath: String - - """Numeric identifier (May change!)""" - id: Int -} - -input FrameAcquisitionFileWhereClause { - run: RunWhereClause - runId: IntComparators - s3MdocPath: StrComparators - httpsMdocPath: StrComparators - id: IntComparators -} - -input FrameAcquisitionFileWhereClauseMutations { - id: IntComparators -} - -type FrameAggregate { - aggregate: [FrameAggregateFunctions!] -} - -type FrameAggregateFunctions { - sum: FrameNumericalColumns - avg: FrameNumericalColumns - stddev: FrameNumericalColumns - variance: FrameNumericalColumns - min: FrameMinMaxColumns - max: FrameMinMaxColumns - groupBy: FrameGroupByOptions - count(distinct: Boolean = false, columns: FrameCountColumns = null): Int -} - -input FrameAggregateWhereClause { - count: FrameAggregateWhereClauseCount! -} - -input FrameAggregateWhereClauseCount { - arguments: FrameCountColumns - distinct: Boolean - filter: FrameWhereClause - predicate: IntComparators -} - -"""A connection to a list of items.""" -type FrameConnection { - """Pagination data for this connection""" - pageInfo: PageInfo! - - """Contains the nodes in this connection""" - edges: [FrameEdge!]! -} - -enum FrameCountColumns { - acquisitionOrder - accumulatedDose - exposureDose - isGainCorrected - s3FramePath - httpsFramePath - fileSize - id -} - -input FrameCreateInput { - depositionId: ID! - runId: ID! - - """Frame's acquistion order within a tilt experiment""" - acquisitionOrder: Int = null - - """The total accumulated dose exposure frame""" - accumulatedDose: Float = null - - """The dose exposure of this frame""" - exposureDose: Float = null - - """Whether this frame has been gain corrected""" - isGainCorrected: Boolean = null - - """S3 path to the frame file""" - s3FramePath: String = null - - """HTTPS path to the frame file""" - httpsFramePath: String = null - - """Size of the frame file in bytes""" - fileSize: Float = null - - """Numeric identifier (May change!)""" - id: Int! -} - -"""An edge in a connection.""" -type FrameEdge { - """A cursor for use in pagination""" - cursor: String! - - """The item at the end of the edge""" - node: Frame! -} - -type FrameGroupByOptions { - deposition: DepositionGroupByOptions - run: RunGroupByOptions - acquisitionOrder: Int - accumulatedDose: Float - exposureDose: Float - isGainCorrected: Boolean - perSectionParameters: PerSectionParametersGroupByOptions - s3FramePath: String - httpsFramePath: String - fileSize: Float - id: Int -} - -type FrameMinMaxColumns { - acquisitionOrder: Int - accumulatedDose: Float - exposureDose: Float - s3FramePath: String - httpsFramePath: String - fileSize: Float - id: Int -} - -type FrameNumericalColumns { - acquisitionOrder: Int - accumulatedDose: Float - exposureDose: Float - fileSize: Float - id: Int -} - -input FrameOrderByClause { - deposition: DepositionOrderByClause - run: RunOrderByClause - acquisitionOrder: orderBy - accumulatedDose: orderBy - exposureDose: orderBy - isGainCorrected: orderBy - s3FramePath: orderBy - httpsFramePath: orderBy - fileSize: orderBy - id: orderBy -} - -input FrameUpdateInput { - depositionId: ID - runId: ID - - """Frame's acquistion order within a tilt experiment""" - acquisitionOrder: Int = null - - """The total accumulated dose exposure frame""" - accumulatedDose: Float = null - - """The dose exposure of this frame""" - exposureDose: Float = null - - """Whether this frame has been gain corrected""" - isGainCorrected: Boolean = null - - """S3 path to the frame file""" - s3FramePath: String = null - - """HTTPS path to the frame file""" - httpsFramePath: String = null - - """Size of the frame file in bytes""" - fileSize: Float = null - - """Numeric identifier (May change!)""" - id: Int -} - -input FrameWhereClause { - deposition: DepositionWhereClause - depositionId: IntComparators - run: RunWhereClause - runId: IntComparators - acquisitionOrder: IntComparators - accumulatedDose: FloatComparators - exposureDose: FloatComparators - isGainCorrected: BoolComparators - perSectionParameters: PerSectionParametersWhereClause - perSectionParametersAggregate: PerSectionParametersAggregateWhereClause - s3FramePath: StrComparators - httpsFramePath: StrComparators - fileSize: FloatComparators - id: IntComparators -} - -input FrameWhereClauseMutations { - id: IntComparators -} - -"""Gain values for frames in this run""" -type GainFile implements EntityInterface & Node { - """The Globally Unique ID of this object""" - _id: GlobalID! - - """Numeric identifier (May change!)""" - id: Int! - run(where: RunWhereClause = null, orderBy: [RunOrderByClause!] = []): Run - runId: Int! - - """Path to the file in s3""" - s3FilePath: String! - - """Path to the file as an https url""" - httpsFilePath: String! -} - -type GainFileAggregate { - aggregate: [GainFileAggregateFunctions!] -} - -type GainFileAggregateFunctions { - sum: GainFileNumericalColumns - avg: GainFileNumericalColumns - stddev: GainFileNumericalColumns - variance: GainFileNumericalColumns - min: GainFileMinMaxColumns - max: GainFileMinMaxColumns - groupBy: GainFileGroupByOptions - count(distinct: Boolean = false, columns: GainFileCountColumns = null): Int -} - -input GainFileAggregateWhereClause { - count: GainFileAggregateWhereClauseCount! -} - -input GainFileAggregateWhereClauseCount { - arguments: GainFileCountColumns - distinct: Boolean - filter: GainFileWhereClause - predicate: IntComparators -} - -"""A connection to a list of items.""" -type GainFileConnection { - """Pagination data for this connection""" - pageInfo: PageInfo! - - """Contains the nodes in this connection""" - edges: [GainFileEdge!]! -} - -enum GainFileCountColumns { - s3FilePath - httpsFilePath - id -} - -input GainFileCreateInput { - runId: ID! - - """Path to the file in s3""" - s3FilePath: String! - - """Path to the file as an https url""" - httpsFilePath: String! - - """Numeric identifier (May change!)""" - id: Int! -} - -"""An edge in a connection.""" -type GainFileEdge { - """A cursor for use in pagination""" - cursor: String! - - """The item at the end of the edge""" - node: GainFile! -} - -type GainFileGroupByOptions { - run: RunGroupByOptions - s3FilePath: String - httpsFilePath: String - id: Int -} - -type GainFileMinMaxColumns { - s3FilePath: String - httpsFilePath: String - id: Int -} - -type GainFileNumericalColumns { - id: Int -} - -input GainFileOrderByClause { - run: RunOrderByClause - s3FilePath: orderBy - httpsFilePath: orderBy - id: orderBy -} - -input GainFileUpdateInput { - runId: ID - - """Path to the file in s3""" - s3FilePath: String - - """Path to the file as an https url""" - httpsFilePath: String - - """Numeric identifier (May change!)""" - id: Int -} - -input GainFileWhereClause { - run: RunWhereClause - runId: IntComparators - s3FilePath: StrComparators - httpsFilePath: StrComparators - id: IntComparators -} - -input GainFileWhereClauseMutations { - id: IntComparators -} - -""" -The `ID` scalar type represents a unique identifier, often used to refetch an object or as key for a cache. The ID type appears in a JSON response as a String; however, it is not intended to be human-readable. When expected as an input type, any string (such as `"4"`) or integer (such as `4`) input value will be accepted as an ID. -""" -scalar GlobalID @specifiedBy(url: "https://relay.dev/graphql/objectidentification.htm") - -""" -An ontology term/ID or accession code, state and description associated with a Run, describing cellular components that were visually identified, but not labeled, in a tomogram associated with the Run -""" -type IdentifiedObject implements EntityInterface & Node { - """The Globally Unique ID of this object""" - _id: GlobalID! - - """Numeric identifier (May change!)""" - id: Int! - run(where: RunWhereClause = null, orderBy: [RunOrderByClause!] = []): Run - runId: Int - - """ - Gene Ontology Cellular Component identifier or UniProtKB accession for the identified object. - """ - objectId: String! - - """ - Name of the identified object (e.g. ribosome, nuclear pore complex, actin filament, membrane) - """ - objectName: String! - - """ - A textual description of the identified object, can be a longer description to include additional information not covered by the IdentifiedObject object name and state. - """ - objectDescription: String - - """Molecule state of the identified object (e.g. open, closed)""" - objectState: String -} - -type IdentifiedObjectAggregate { - aggregate: [IdentifiedObjectAggregateFunctions!] -} - -type IdentifiedObjectAggregateFunctions { - sum: IdentifiedObjectNumericalColumns - avg: IdentifiedObjectNumericalColumns - stddev: IdentifiedObjectNumericalColumns - variance: IdentifiedObjectNumericalColumns - min: IdentifiedObjectMinMaxColumns - max: IdentifiedObjectMinMaxColumns - groupBy: IdentifiedObjectGroupByOptions - count(distinct: Boolean = false, columns: IdentifiedObjectCountColumns = null): Int -} - -input IdentifiedObjectAggregateWhereClause { - count: IdentifiedObjectAggregateWhereClauseCount! -} - -input IdentifiedObjectAggregateWhereClauseCount { - arguments: IdentifiedObjectCountColumns - distinct: Boolean - filter: IdentifiedObjectWhereClause - predicate: IntComparators -} - -"""A connection to a list of items.""" -type IdentifiedObjectConnection { - """Pagination data for this connection""" - pageInfo: PageInfo! - - """Contains the nodes in this connection""" - edges: [IdentifiedObjectEdge!]! -} - -enum IdentifiedObjectCountColumns { - objectId - objectName - objectDescription - objectState - id -} - -input IdentifiedObjectCreateInput { - """Run that this identified object is a part of""" - runId: ID = null - - """ - Gene Ontology Cellular Component identifier or UniProtKB accession for the identified object. - """ - objectId: String! - - """ - Name of the identified object (e.g. ribosome, nuclear pore complex, actin filament, membrane) - """ - objectName: String! - - """ - A textual description of the identified object, can be a longer description to include additional information not covered by the IdentifiedObject object name and state. - """ - objectDescription: String = null - - """Molecule state of the identified object (e.g. open, closed)""" - objectState: String = null - - """Numeric identifier (May change!)""" - id: Int! -} - -"""An edge in a connection.""" -type IdentifiedObjectEdge { - """A cursor for use in pagination""" - cursor: String! - - """The item at the end of the edge""" - node: IdentifiedObject! -} - -type IdentifiedObjectGroupByOptions { - run: RunGroupByOptions - objectId: String - objectName: String - objectDescription: String - objectState: String - id: Int -} - -type IdentifiedObjectMinMaxColumns { - objectId: String - objectName: String - objectDescription: String - objectState: String - id: Int -} - -type IdentifiedObjectNumericalColumns { - id: Int -} - -input IdentifiedObjectOrderByClause { - run: RunOrderByClause - objectId: orderBy - objectName: orderBy - objectDescription: orderBy - objectState: orderBy - id: orderBy -} - -input IdentifiedObjectUpdateInput { - """Run that this identified object is a part of""" - runId: ID = null - - """ - Gene Ontology Cellular Component identifier or UniProtKB accession for the identified object. - """ - objectId: String - - """ - Name of the identified object (e.g. ribosome, nuclear pore complex, actin filament, membrane) - """ - objectName: String - - """ - A textual description of the identified object, can be a longer description to include additional information not covered by the IdentifiedObject object name and state. - """ - objectDescription: String = null - - """Molecule state of the identified object (e.g. open, closed)""" - objectState: String = null - - """Numeric identifier (May change!)""" - id: Int -} - -input IdentifiedObjectWhereClause { - run: RunWhereClause - runId: IntComparators - objectId: StrComparators - objectName: StrComparators - objectDescription: StrComparators - objectState: StrComparators - id: IntComparators -} - -input IdentifiedObjectWhereClauseMutations { - id: IntComparators -} - -input IntComparators { - _eq: Int - _neq: Int - _in: [Int!] - _nin: [Int!] - _gt: Int - _gte: Int - _lt: Int - _lte: Int - _is_null: Boolean -} - -input LimitOffsetClause { - limit: Int - offset: Int -} - -type Mutation { - createGainFile(input: GainFileCreateInput!): GainFile! - updateGainFile(input: GainFileUpdateInput!, where: GainFileWhereClauseMutations!): [GainFile!]! - deleteGainFile(where: GainFileWhereClauseMutations!): [GainFile!]! - createFrameAcquisitionFile(input: FrameAcquisitionFileCreateInput!): FrameAcquisitionFile! - updateFrameAcquisitionFile(input: FrameAcquisitionFileUpdateInput!, where: FrameAcquisitionFileWhereClauseMutations!): [FrameAcquisitionFile!]! - deleteFrameAcquisitionFile(where: FrameAcquisitionFileWhereClauseMutations!): [FrameAcquisitionFile!]! - createAlignment(input: AlignmentCreateInput!): Alignment! - updateAlignment(input: AlignmentUpdateInput!, where: AlignmentWhereClauseMutations!): [Alignment!]! - deleteAlignment(where: AlignmentWhereClauseMutations!): [Alignment!]! - createAnnotationAuthor(input: AnnotationAuthorCreateInput!): AnnotationAuthor! - updateAnnotationAuthor(input: AnnotationAuthorUpdateInput!, where: AnnotationAuthorWhereClauseMutations!): [AnnotationAuthor!]! - deleteAnnotationAuthor(where: AnnotationAuthorWhereClauseMutations!): [AnnotationAuthor!]! - createAnnotationFile(input: AnnotationFileCreateInput!): AnnotationFile! - updateAnnotationFile(input: AnnotationFileUpdateInput!, where: AnnotationFileWhereClauseMutations!): [AnnotationFile!]! - deleteAnnotationFile(where: AnnotationFileWhereClauseMutations!): [AnnotationFile!]! - createAnnotationShape(input: AnnotationShapeCreateInput!): AnnotationShape! - updateAnnotationShape(input: AnnotationShapeUpdateInput!, where: AnnotationShapeWhereClauseMutations!): [AnnotationShape!]! - deleteAnnotationShape(where: AnnotationShapeWhereClauseMutations!): [AnnotationShape!]! - createAnnotation(input: AnnotationCreateInput!): Annotation! - updateAnnotation(input: AnnotationUpdateInput!, where: AnnotationWhereClauseMutations!): [Annotation!]! - deleteAnnotation(where: AnnotationWhereClauseMutations!): [Annotation!]! - createDatasetAuthor(input: DatasetAuthorCreateInput!): DatasetAuthor! - updateDatasetAuthor(input: DatasetAuthorUpdateInput!, where: DatasetAuthorWhereClauseMutations!): [DatasetAuthor!]! - deleteDatasetAuthor(where: DatasetAuthorWhereClauseMutations!): [DatasetAuthor!]! - createDatasetFunding(input: DatasetFundingCreateInput!): DatasetFunding! - updateDatasetFunding(input: DatasetFundingUpdateInput!, where: DatasetFundingWhereClauseMutations!): [DatasetFunding!]! - deleteDatasetFunding(where: DatasetFundingWhereClauseMutations!): [DatasetFunding!]! - createDataset(input: DatasetCreateInput!): Dataset! - updateDataset(input: DatasetUpdateInput!, where: DatasetWhereClauseMutations!): [Dataset!]! - deleteDataset(where: DatasetWhereClauseMutations!): [Dataset!]! - createDepositionAuthor(input: DepositionAuthorCreateInput!): DepositionAuthor! - updateDepositionAuthor(input: DepositionAuthorUpdateInput!, where: DepositionAuthorWhereClauseMutations!): [DepositionAuthor!]! - deleteDepositionAuthor(where: DepositionAuthorWhereClauseMutations!): [DepositionAuthor!]! - createDeposition(input: DepositionCreateInput!): Deposition! - updateDeposition(input: DepositionUpdateInput!, where: DepositionWhereClauseMutations!): [Deposition!]! - deleteDeposition(where: DepositionWhereClauseMutations!): [Deposition!]! - createDepositionType(input: DepositionTypeCreateInput!): DepositionType! - updateDepositionType(input: DepositionTypeUpdateInput!, where: DepositionTypeWhereClauseMutations!): [DepositionType!]! - deleteDepositionType(where: DepositionTypeWhereClauseMutations!): [DepositionType!]! - createFrame(input: FrameCreateInput!): Frame! - updateFrame(input: FrameUpdateInput!, where: FrameWhereClauseMutations!): [Frame!]! - deleteFrame(where: FrameWhereClauseMutations!): [Frame!]! - createIdentifiedObject(input: IdentifiedObjectCreateInput!): IdentifiedObject! - updateIdentifiedObject(input: IdentifiedObjectUpdateInput!, where: IdentifiedObjectWhereClauseMutations!): [IdentifiedObject!]! - deleteIdentifiedObject(where: IdentifiedObjectWhereClauseMutations!): [IdentifiedObject!]! - createPerSectionAlignmentParameters(input: PerSectionAlignmentParametersCreateInput!): PerSectionAlignmentParameters! - updatePerSectionAlignmentParameters(input: PerSectionAlignmentParametersUpdateInput!, where: PerSectionAlignmentParametersWhereClauseMutations!): [PerSectionAlignmentParameters!]! - deletePerSectionAlignmentParameters(where: PerSectionAlignmentParametersWhereClauseMutations!): [PerSectionAlignmentParameters!]! - createPerSectionParameters(input: PerSectionParametersCreateInput!): PerSectionParameters! - updatePerSectionParameters(input: PerSectionParametersUpdateInput!, where: PerSectionParametersWhereClauseMutations!): [PerSectionParameters!]! - deletePerSectionParameters(where: PerSectionParametersWhereClauseMutations!): [PerSectionParameters!]! - createRun(input: RunCreateInput!): Run! - updateRun(input: RunUpdateInput!, where: RunWhereClauseMutations!): [Run!]! - deleteRun(where: RunWhereClauseMutations!): [Run!]! - createTiltseries(input: TiltseriesCreateInput!): Tiltseries! - updateTiltseries(input: TiltseriesUpdateInput!, where: TiltseriesWhereClauseMutations!): [Tiltseries!]! - deleteTiltseries(where: TiltseriesWhereClauseMutations!): [Tiltseries!]! - createTomogramAuthor(input: TomogramAuthorCreateInput!): TomogramAuthor! - updateTomogramAuthor(input: TomogramAuthorUpdateInput!, where: TomogramAuthorWhereClauseMutations!): [TomogramAuthor!]! - deleteTomogramAuthor(where: TomogramAuthorWhereClauseMutations!): [TomogramAuthor!]! - createTomogramVoxelSpacing(input: TomogramVoxelSpacingCreateInput!): TomogramVoxelSpacing! - updateTomogramVoxelSpacing(input: TomogramVoxelSpacingUpdateInput!, where: TomogramVoxelSpacingWhereClauseMutations!): [TomogramVoxelSpacing!]! - deleteTomogramVoxelSpacing(where: TomogramVoxelSpacingWhereClauseMutations!): [TomogramVoxelSpacing!]! - createTomogram(input: TomogramCreateInput!): Tomogram! - updateTomogram(input: TomogramUpdateInput!, where: TomogramWhereClauseMutations!): [Tomogram!]! - deleteTomogram(where: TomogramWhereClauseMutations!): [Tomogram!]! - createAnnotationMethodLink(input: AnnotationMethodLinkCreateInput!): AnnotationMethodLink! - updateAnnotationMethodLink(input: AnnotationMethodLinkUpdateInput!, where: AnnotationMethodLinkWhereClauseMutations!): [AnnotationMethodLink!]! - deleteAnnotationMethodLink(where: AnnotationMethodLinkWhereClauseMutations!): [AnnotationMethodLink!]! -} - -"""An object with a Globally Unique ID""" -interface Node { - """The Globally Unique ID of this object""" - _id: GlobalID! -} - -"""Information to aid in pagination.""" -type PageInfo { - """When paginating forwards, are there more items?""" - hasNextPage: Boolean! - - """When paginating backwards, are there more items?""" - hasPreviousPage: Boolean! - - """When paginating backwards, the cursor to continue.""" - startCursor: String - - """When paginating forwards, the cursor to continue.""" - endCursor: String -} - -"""Map alignment parameters to tilt series frames""" -type PerSectionAlignmentParameters implements EntityInterface & Node { - """The Globally Unique ID of this object""" - _id: GlobalID! - - """Numeric identifier (May change!)""" - id: Int! - alignment(where: AlignmentWhereClause = null, orderBy: [AlignmentOrderByClause!] = []): Alignment - alignmentId: Int! - - """z-index of the frame in the tiltseries""" - zIndex: Int! - - """In-plane X-shift of the projection in angstrom""" - xOffset: Float - - """In-plane Y-shift of the projection in angstrom""" - yOffset: Float - - """X-axis rotation in degrees""" - volumeXRotation: Float - - """In-plane rotation of the projection in degrees""" - inPlaneRotation: [[Float!]!] - - """Tilt angle of the projection in degrees""" - tiltAngle: Float -} - -type PerSectionAlignmentParametersAggregate { - aggregate: [PerSectionAlignmentParametersAggregateFunctions!] -} - -type PerSectionAlignmentParametersAggregateFunctions { - sum: PerSectionAlignmentParametersNumericalColumns - avg: PerSectionAlignmentParametersNumericalColumns - stddev: PerSectionAlignmentParametersNumericalColumns - variance: PerSectionAlignmentParametersNumericalColumns - min: PerSectionAlignmentParametersMinMaxColumns - max: PerSectionAlignmentParametersMinMaxColumns - groupBy: PerSectionAlignmentParametersGroupByOptions - count(distinct: Boolean = false, columns: PerSectionAlignmentParametersCountColumns = null): Int -} - -input PerSectionAlignmentParametersAggregateWhereClause { - count: PerSectionAlignmentParametersAggregateWhereClauseCount! -} - -input PerSectionAlignmentParametersAggregateWhereClauseCount { - arguments: PerSectionAlignmentParametersCountColumns - distinct: Boolean - filter: PerSectionAlignmentParametersWhereClause - predicate: IntComparators -} - -"""A connection to a list of items.""" -type PerSectionAlignmentParametersConnection { - """Pagination data for this connection""" - pageInfo: PageInfo! - - """Contains the nodes in this connection""" - edges: [PerSectionAlignmentParametersEdge!]! -} - -enum PerSectionAlignmentParametersCountColumns { - zIndex - xOffset - yOffset - volumeXRotation - inPlaneRotation - tiltAngle - id -} - -input PerSectionAlignmentParametersCreateInput { - """Tiltseries Alignment""" - alignmentId: ID! - - """z-index of the frame in the tiltseries""" - zIndex: Int! - - """In-plane X-shift of the projection in angstrom""" - xOffset: Float = null - - """In-plane Y-shift of the projection in angstrom""" - yOffset: Float = null - - """X-axis rotation in degrees""" - volumeXRotation: Float = null - - """In-plane rotation of the projection in degrees""" - inPlaneRotation: [[Float!]!] = null - - """Tilt angle of the projection in degrees""" - tiltAngle: Float = null - - """Numeric identifier (May change!)""" - id: Int! -} - -"""An edge in a connection.""" -type PerSectionAlignmentParametersEdge { - """A cursor for use in pagination""" - cursor: String! - - """The item at the end of the edge""" - node: PerSectionAlignmentParameters! -} - -type PerSectionAlignmentParametersGroupByOptions { - alignment: AlignmentGroupByOptions - zIndex: Int - xOffset: Float - yOffset: Float - volumeXRotation: Float - inPlaneRotation: [[Float!]!] - tiltAngle: Float - id: Int -} - -type PerSectionAlignmentParametersMinMaxColumns { - zIndex: Int - xOffset: Float - yOffset: Float - volumeXRotation: Float - tiltAngle: Float - id: Int -} - -type PerSectionAlignmentParametersNumericalColumns { - zIndex: Int - xOffset: Float - yOffset: Float - volumeXRotation: Float - tiltAngle: Float - id: Int -} - -input PerSectionAlignmentParametersOrderByClause { - alignment: AlignmentOrderByClause - zIndex: orderBy - xOffset: orderBy - yOffset: orderBy - volumeXRotation: orderBy - inPlaneRotation: orderBy - tiltAngle: orderBy - id: orderBy -} - -input PerSectionAlignmentParametersUpdateInput { - """Tiltseries Alignment""" - alignmentId: ID - - """z-index of the frame in the tiltseries""" - zIndex: Int - - """In-plane X-shift of the projection in angstrom""" - xOffset: Float = null - - """In-plane Y-shift of the projection in angstrom""" - yOffset: Float = null - - """X-axis rotation in degrees""" - volumeXRotation: Float = null - - """In-plane rotation of the projection in degrees""" - inPlaneRotation: [[Float!]!] = null - - """Tilt angle of the projection in degrees""" - tiltAngle: Float = null - - """Numeric identifier (May change!)""" - id: Int -} - -input PerSectionAlignmentParametersWhereClause { - alignment: AlignmentWhereClause - alignmentId: IntComparators - zIndex: IntComparators - xOffset: FloatComparators - yOffset: FloatComparators - volumeXRotation: FloatComparators - tiltAngle: FloatComparators - id: IntComparators -} - -input PerSectionAlignmentParametersWhereClauseMutations { - id: IntComparators -} - -"""Map individual Frames to a Tiltseries""" -type PerSectionParameters implements EntityInterface & Node { - """The Globally Unique ID of this object""" - _id: GlobalID! - - """Numeric identifier (May change!)""" - id: Int! - - """ - Angle (in degrees) from reciprocal space X axis to the major axis of defocus. - """ - astigmaticAngle: Float - frame(where: FrameWhereClause = null, orderBy: [FrameOrderByClause!] = []): Frame - frameId: Int! - - """ - Defocus (major axis) estimated for this tilt image in Angstrom (underfocus has positive sign). - """ - majorDefocus: Float - - """Maximum resolution of the frame""" - maxResolution: Float - - """ - Defocus (minor axis) estimated for this tilt image in Angstrom (underfocus has positive sign). - """ - minorDefocus: Float - - """Phase shift estimated for this tilt image in radians.""" - phaseShift: Float - - """Nominal tilt angle for this tilt image reported by the microscope.""" - rawAngle: Float! - run(where: RunWhereClause = null, orderBy: [RunOrderByClause!] = []): Run - runId: Int! - tiltseries(where: TiltseriesWhereClause = null, orderBy: [TiltseriesOrderByClause!] = []): Tiltseries - tiltseriesId: Int! - - """Index (0-based) of this tilt image in the tilt series stack.""" - zIndex: Int! -} - -type PerSectionParametersAggregate { - aggregate: [PerSectionParametersAggregateFunctions!] -} - -type PerSectionParametersAggregateFunctions { - sum: PerSectionParametersNumericalColumns - avg: PerSectionParametersNumericalColumns - stddev: PerSectionParametersNumericalColumns - variance: PerSectionParametersNumericalColumns - min: PerSectionParametersMinMaxColumns - max: PerSectionParametersMinMaxColumns - groupBy: PerSectionParametersGroupByOptions - count(distinct: Boolean = false, columns: PerSectionParametersCountColumns = null): Int -} - -input PerSectionParametersAggregateWhereClause { - count: PerSectionParametersAggregateWhereClauseCount! -} - -input PerSectionParametersAggregateWhereClauseCount { - arguments: PerSectionParametersCountColumns - distinct: Boolean - filter: PerSectionParametersWhereClause - predicate: IntComparators -} - -"""A connection to a list of items.""" -type PerSectionParametersConnection { - """Pagination data for this connection""" - pageInfo: PageInfo! - - """Contains the nodes in this connection""" - edges: [PerSectionParametersEdge!]! -} - -enum PerSectionParametersCountColumns { - astigmaticAngle - majorDefocus - maxResolution - minorDefocus - phaseShift - rawAngle - zIndex - id -} - -input PerSectionParametersCreateInput { - """ - Angle (in degrees) from reciprocal space X axis to the major axis of defocus. - """ - astigmaticAngle: Float = null - - """Frame that this section is a part of""" - frameId: ID! - - """ - Defocus (major axis) estimated for this tilt image in Angstrom (underfocus has positive sign). - """ - majorDefocus: Float = null - - """Maximum resolution of the frame""" - maxResolution: Float = null - - """ - Defocus (minor axis) estimated for this tilt image in Angstrom (underfocus has positive sign). - """ - minorDefocus: Float = null - - """Phase shift estimated for this tilt image in radians.""" - phaseShift: Float = null - - """Nominal tilt angle for this tilt image reported by the microscope.""" - rawAngle: Float! - - """Run that this section is a part of""" - runId: ID! - - """Tiltseries that this section is a part of""" - tiltseriesId: ID! - - """Index (0-based) of this tilt image in the tilt series stack.""" - zIndex: Int! - - """Numeric identifier (May change!)""" - id: Int! -} - -"""An edge in a connection.""" -type PerSectionParametersEdge { - """A cursor for use in pagination""" - cursor: String! - - """The item at the end of the edge""" - node: PerSectionParameters! -} - -type PerSectionParametersGroupByOptions { - astigmaticAngle: Float - frame: FrameGroupByOptions - majorDefocus: Float - maxResolution: Float - minorDefocus: Float - phaseShift: Float - rawAngle: Float - run: RunGroupByOptions - tiltseries: TiltseriesGroupByOptions - zIndex: Int - id: Int -} - -type PerSectionParametersMinMaxColumns { - astigmaticAngle: Float - majorDefocus: Float - maxResolution: Float - minorDefocus: Float - phaseShift: Float - rawAngle: Float - zIndex: Int - id: Int -} - -type PerSectionParametersNumericalColumns { - astigmaticAngle: Float - majorDefocus: Float - maxResolution: Float - minorDefocus: Float - phaseShift: Float - rawAngle: Float - zIndex: Int - id: Int -} - -input PerSectionParametersOrderByClause { - astigmaticAngle: orderBy - frame: FrameOrderByClause - majorDefocus: orderBy - maxResolution: orderBy - minorDefocus: orderBy - phaseShift: orderBy - rawAngle: orderBy - run: RunOrderByClause - tiltseries: TiltseriesOrderByClause - zIndex: orderBy - id: orderBy -} - -input PerSectionParametersUpdateInput { - """ - Angle (in degrees) from reciprocal space X axis to the major axis of defocus. - """ - astigmaticAngle: Float = null - - """Frame that this section is a part of""" - frameId: ID - - """ - Defocus (major axis) estimated for this tilt image in Angstrom (underfocus has positive sign). - """ - majorDefocus: Float = null - - """Maximum resolution of the frame""" - maxResolution: Float = null - - """ - Defocus (minor axis) estimated for this tilt image in Angstrom (underfocus has positive sign). - """ - minorDefocus: Float = null - - """Phase shift estimated for this tilt image in radians.""" - phaseShift: Float = null - - """Nominal tilt angle for this tilt image reported by the microscope.""" - rawAngle: Float - - """Run that this section is a part of""" - runId: ID - - """Tiltseries that this section is a part of""" - tiltseriesId: ID - - """Index (0-based) of this tilt image in the tilt series stack.""" - zIndex: Int - - """Numeric identifier (May change!)""" - id: Int -} - -input PerSectionParametersWhereClause { - astigmaticAngle: FloatComparators - frame: FrameWhereClause - frameId: IntComparators - majorDefocus: FloatComparators - maxResolution: FloatComparators - minorDefocus: FloatComparators - phaseShift: FloatComparators - rawAngle: FloatComparators - run: RunWhereClause - runId: IntComparators - tiltseries: TiltseriesWhereClause - tiltseriesId: IntComparators - zIndex: IntComparators - id: IntComparators -} - -input PerSectionParametersWhereClauseMutations { - id: IntComparators -} - -type Query { - gainFiles(where: GainFileWhereClause = null, orderBy: [GainFileOrderByClause!] = [], limitOffset: LimitOffsetClause = null): [GainFile!]! - frameAcquisitionFiles(where: FrameAcquisitionFileWhereClause = null, orderBy: [FrameAcquisitionFileOrderByClause!] = [], limitOffset: LimitOffsetClause = null): [FrameAcquisitionFile!]! - alignments(where: AlignmentWhereClause = null, orderBy: [AlignmentOrderByClause!] = [], limitOffset: LimitOffsetClause = null): [Alignment!]! - annotationAuthors(where: AnnotationAuthorWhereClause = null, orderBy: [AnnotationAuthorOrderByClause!] = [], limitOffset: LimitOffsetClause = null): [AnnotationAuthor!]! - annotationFiles(where: AnnotationFileWhereClause = null, orderBy: [AnnotationFileOrderByClause!] = [], limitOffset: LimitOffsetClause = null): [AnnotationFile!]! - annotationShapes(where: AnnotationShapeWhereClause = null, orderBy: [AnnotationShapeOrderByClause!] = [], limitOffset: LimitOffsetClause = null): [AnnotationShape!]! - annotations(where: AnnotationWhereClause = null, orderBy: [AnnotationOrderByClause!] = [], limitOffset: LimitOffsetClause = null): [Annotation!]! - datasetAuthors(where: DatasetAuthorWhereClause = null, orderBy: [DatasetAuthorOrderByClause!] = [], limitOffset: LimitOffsetClause = null): [DatasetAuthor!]! - datasetFunding(where: DatasetFundingWhereClause = null, orderBy: [DatasetFundingOrderByClause!] = [], limitOffset: LimitOffsetClause = null): [DatasetFunding!]! - datasets(where: DatasetWhereClause = null, orderBy: [DatasetOrderByClause!] = [], limitOffset: LimitOffsetClause = null): [Dataset!]! - depositionAuthors(where: DepositionAuthorWhereClause = null, orderBy: [DepositionAuthorOrderByClause!] = [], limitOffset: LimitOffsetClause = null): [DepositionAuthor!]! - depositions(where: DepositionWhereClause = null, orderBy: [DepositionOrderByClause!] = [], limitOffset: LimitOffsetClause = null): [Deposition!]! - depositionTypes(where: DepositionTypeWhereClause = null, orderBy: [DepositionTypeOrderByClause!] = [], limitOffset: LimitOffsetClause = null): [DepositionType!]! - frames(where: FrameWhereClause = null, orderBy: [FrameOrderByClause!] = [], limitOffset: LimitOffsetClause = null): [Frame!]! - identifiedObjects(where: IdentifiedObjectWhereClause = null, orderBy: [IdentifiedObjectOrderByClause!] = [], limitOffset: LimitOffsetClause = null): [IdentifiedObject!]! - perSectionAlignmentParameters(where: PerSectionAlignmentParametersWhereClause = null, orderBy: [PerSectionAlignmentParametersOrderByClause!] = [], limitOffset: LimitOffsetClause = null): [PerSectionAlignmentParameters!]! - perSectionParameters(where: PerSectionParametersWhereClause = null, orderBy: [PerSectionParametersOrderByClause!] = [], limitOffset: LimitOffsetClause = null): [PerSectionParameters!]! - runs(where: RunWhereClause = null, orderBy: [RunOrderByClause!] = [], limitOffset: LimitOffsetClause = null): [Run!]! - tiltseries(where: TiltseriesWhereClause = null, orderBy: [TiltseriesOrderByClause!] = [], limitOffset: LimitOffsetClause = null): [Tiltseries!]! - tomogramAuthors(where: TomogramAuthorWhereClause = null, orderBy: [TomogramAuthorOrderByClause!] = [], limitOffset: LimitOffsetClause = null): [TomogramAuthor!]! - tomogramVoxelSpacings(where: TomogramVoxelSpacingWhereClause = null, orderBy: [TomogramVoxelSpacingOrderByClause!] = [], limitOffset: LimitOffsetClause = null): [TomogramVoxelSpacing!]! - tomograms(where: TomogramWhereClause = null, orderBy: [TomogramOrderByClause!] = [], limitOffset: LimitOffsetClause = null): [Tomogram!]! - annotationMethodLinks(where: AnnotationMethodLinkWhereClause = null, orderBy: [AnnotationMethodLinkOrderByClause!] = [], limitOffset: LimitOffsetClause = null): [AnnotationMethodLink!]! - gainFilesAggregate(where: GainFileWhereClause = null): GainFileAggregate! - frameAcquisitionFilesAggregate(where: FrameAcquisitionFileWhereClause = null): FrameAcquisitionFileAggregate! - alignmentsAggregate(where: AlignmentWhereClause = null): AlignmentAggregate! - annotationAuthorsAggregate(where: AnnotationAuthorWhereClause = null): AnnotationAuthorAggregate! - annotationFilesAggregate(where: AnnotationFileWhereClause = null): AnnotationFileAggregate! - annotationShapesAggregate(where: AnnotationShapeWhereClause = null): AnnotationShapeAggregate! - annotationsAggregate(where: AnnotationWhereClause = null): AnnotationAggregate! - datasetAuthorsAggregate(where: DatasetAuthorWhereClause = null): DatasetAuthorAggregate! - datasetFundingAggregate(where: DatasetFundingWhereClause = null): DatasetFundingAggregate! - datasetsAggregate(where: DatasetWhereClause = null): DatasetAggregate! - depositionAuthorsAggregate(where: DepositionAuthorWhereClause = null): DepositionAuthorAggregate! - depositionsAggregate(where: DepositionWhereClause = null): DepositionAggregate! - depositionTypesAggregate(where: DepositionTypeWhereClause = null): DepositionTypeAggregate! - framesAggregate(where: FrameWhereClause = null): FrameAggregate! - identifiedObjectsAggregate(where: IdentifiedObjectWhereClause = null): IdentifiedObjectAggregate! - perSectionAlignmentParametersAggregate(where: PerSectionAlignmentParametersWhereClause = null): PerSectionAlignmentParametersAggregate! - perSectionParametersAggregate(where: PerSectionParametersWhereClause = null): PerSectionParametersAggregate! - runsAggregate(where: RunWhereClause = null): RunAggregate! - tiltseriesAggregate(where: TiltseriesWhereClause = null): TiltseriesAggregate! - tomogramAuthorsAggregate(where: TomogramAuthorWhereClause = null): TomogramAuthorAggregate! - tomogramVoxelSpacingsAggregate(where: TomogramVoxelSpacingWhereClause = null): TomogramVoxelSpacingAggregate! - tomogramsAggregate(where: TomogramWhereClause = null): TomogramAggregate! - annotationMethodLinksAggregate(where: AnnotationMethodLinkWhereClause = null): AnnotationMethodLinkAggregate! -} - -type Run implements EntityInterface & Node { - """The Globally Unique ID of this object""" - _id: GlobalID! - - """Numeric identifier (May change!)""" - id: Int! - alignments( - where: AlignmentWhereClause = null - orderBy: [AlignmentOrderByClause!] = [] - - """Returns the items in the list that come before the specified cursor.""" - before: String = null - - """Returns the items in the list that come after the specified cursor.""" - after: String = null - - """Returns the first n items from the list.""" - first: Int = null - - """Returns the items in the list that come after the specified cursor.""" - last: Int = null - ): AlignmentConnection! - alignmentsAggregate(where: AlignmentWhereClause = null): AlignmentAggregate - annotations( - where: AnnotationWhereClause = null - orderBy: [AnnotationOrderByClause!] = [] - - """Returns the items in the list that come before the specified cursor.""" - before: String = null - - """Returns the items in the list that come after the specified cursor.""" - after: String = null - - """Returns the first n items from the list.""" - first: Int = null - - """Returns the items in the list that come after the specified cursor.""" - last: Int = null - ): AnnotationConnection! - annotationsAggregate(where: AnnotationWhereClause = null): AnnotationAggregate - dataset(where: DatasetWhereClause = null, orderBy: [DatasetOrderByClause!] = []): Dataset - datasetId: Int! - frames( - where: FrameWhereClause = null - orderBy: [FrameOrderByClause!] = [] - - """Returns the items in the list that come before the specified cursor.""" - before: String = null - - """Returns the items in the list that come after the specified cursor.""" - after: String = null - - """Returns the first n items from the list.""" - first: Int = null - - """Returns the items in the list that come after the specified cursor.""" - last: Int = null - ): FrameConnection! - framesAggregate(where: FrameWhereClause = null): FrameAggregate - gainFiles( - where: GainFileWhereClause = null - orderBy: [GainFileOrderByClause!] = [] - - """Returns the items in the list that come before the specified cursor.""" - before: String = null - - """Returns the items in the list that come after the specified cursor.""" - after: String = null - - """Returns the first n items from the list.""" - first: Int = null - - """Returns the items in the list that come after the specified cursor.""" - last: Int = null - ): GainFileConnection! - gainFilesAggregate(where: GainFileWhereClause = null): GainFileAggregate - identifiedObjects( - where: IdentifiedObjectWhereClause = null - orderBy: [IdentifiedObjectOrderByClause!] = [] - - """Returns the items in the list that come before the specified cursor.""" - before: String = null - - """Returns the items in the list that come after the specified cursor.""" - after: String = null - - """Returns the first n items from the list.""" - first: Int = null - - """Returns the items in the list that come after the specified cursor.""" - last: Int = null - ): IdentifiedObjectConnection! - identifiedObjectsAggregate(where: IdentifiedObjectWhereClause = null): IdentifiedObjectAggregate - frameAcquisitionFiles( - where: FrameAcquisitionFileWhereClause = null - orderBy: [FrameAcquisitionFileOrderByClause!] = [] - - """Returns the items in the list that come before the specified cursor.""" - before: String = null - - """Returns the items in the list that come after the specified cursor.""" - after: String = null - - """Returns the first n items from the list.""" - first: Int = null - - """Returns the items in the list that come after the specified cursor.""" - last: Int = null - ): FrameAcquisitionFileConnection! - frameAcquisitionFilesAggregate(where: FrameAcquisitionFileWhereClause = null): FrameAcquisitionFileAggregate - perSectionParameters( - where: PerSectionParametersWhereClause = null - orderBy: [PerSectionParametersOrderByClause!] = [] - - """Returns the items in the list that come before the specified cursor.""" - before: String = null - - """Returns the items in the list that come after the specified cursor.""" - after: String = null - - """Returns the first n items from the list.""" - first: Int = null - - """Returns the items in the list that come after the specified cursor.""" - last: Int = null - ): PerSectionParametersConnection! - perSectionParametersAggregate(where: PerSectionParametersWhereClause = null): PerSectionParametersAggregate - tiltseries( - where: TiltseriesWhereClause = null - orderBy: [TiltseriesOrderByClause!] = [] - - """Returns the items in the list that come before the specified cursor.""" - before: String = null - - """Returns the items in the list that come after the specified cursor.""" - after: String = null - - """Returns the first n items from the list.""" - first: Int = null - - """Returns the items in the list that come after the specified cursor.""" - last: Int = null - ): TiltseriesConnection! - tiltseriesAggregate(where: TiltseriesWhereClause = null): TiltseriesAggregate - tomogramVoxelSpacings( - where: TomogramVoxelSpacingWhereClause = null - orderBy: [TomogramVoxelSpacingOrderByClause!] = [] - - """Returns the items in the list that come before the specified cursor.""" - before: String = null - - """Returns the items in the list that come after the specified cursor.""" - after: String = null - - """Returns the first n items from the list.""" - first: Int = null - - """Returns the items in the list that come after the specified cursor.""" - last: Int = null - ): TomogramVoxelSpacingConnection! - tomogramVoxelSpacingsAggregate(where: TomogramVoxelSpacingWhereClause = null): TomogramVoxelSpacingAggregate - tomograms( - where: TomogramWhereClause = null - orderBy: [TomogramOrderByClause!] = [] - - """Returns the items in the list that come before the specified cursor.""" - before: String = null - - """Returns the items in the list that come after the specified cursor.""" - after: String = null - - """Returns the first n items from the list.""" - first: Int = null - - """Returns the items in the list that come after the specified cursor.""" - last: Int = null - ): TomogramConnection! - tomogramsAggregate(where: TomogramWhereClause = null): TomogramAggregate - - """Short name for this experiment run""" - name: String! - - """The S3 public bucket path where this run is contained""" - s3Prefix: String! - - """The HTTPS directory path where this run is contained url""" - httpsPrefix: String! -} - -type RunAggregate { - aggregate: [RunAggregateFunctions!] -} - -type RunAggregateFunctions { - sum: RunNumericalColumns - avg: RunNumericalColumns - stddev: RunNumericalColumns - variance: RunNumericalColumns - min: RunMinMaxColumns - max: RunMinMaxColumns - groupBy: RunGroupByOptions - count(distinct: Boolean = false, columns: RunCountColumns = null): Int -} - -input RunAggregateWhereClause { - count: RunAggregateWhereClauseCount! -} - -input RunAggregateWhereClauseCount { - arguments: RunCountColumns - distinct: Boolean - filter: RunWhereClause - predicate: IntComparators -} - -"""A connection to a list of items.""" -type RunConnection { - """Pagination data for this connection""" - pageInfo: PageInfo! - - """Contains the nodes in this connection""" - edges: [RunEdge!]! -} - -enum RunCountColumns { - name - s3Prefix - httpsPrefix - id -} - -input RunCreateInput { - """Dataset that this run is a part of""" - datasetId: ID! - - """Short name for this experiment run""" - name: String! - - """The S3 public bucket path where this run is contained""" - s3Prefix: String! - - """The HTTPS directory path where this run is contained url""" - httpsPrefix: String! - - """Numeric identifier (May change!)""" - id: Int! -} - -"""An edge in a connection.""" -type RunEdge { - """A cursor for use in pagination""" - cursor: String! - - """The item at the end of the edge""" - node: Run! -} - -type RunGroupByOptions { - alignments: AlignmentGroupByOptions - annotations: AnnotationGroupByOptions - dataset: DatasetGroupByOptions - frames: FrameGroupByOptions - gainFiles: GainFileGroupByOptions - identifiedObjects: IdentifiedObjectGroupByOptions - frameAcquisitionFiles: FrameAcquisitionFileGroupByOptions - perSectionParameters: PerSectionParametersGroupByOptions - tiltseries: TiltseriesGroupByOptions - tomogramVoxelSpacings: TomogramVoxelSpacingGroupByOptions - tomograms: TomogramGroupByOptions - name: String - s3Prefix: String - httpsPrefix: String - id: Int -} - -type RunMinMaxColumns { - name: String - s3Prefix: String - httpsPrefix: String - id: Int -} - -type RunNumericalColumns { - id: Int -} - -input RunOrderByClause { - dataset: DatasetOrderByClause - name: orderBy - s3Prefix: orderBy - httpsPrefix: orderBy - id: orderBy -} - -input RunUpdateInput { - """Dataset that this run is a part of""" - datasetId: ID - - """Short name for this experiment run""" - name: String - - """The S3 public bucket path where this run is contained""" - s3Prefix: String - - """The HTTPS directory path where this run is contained url""" - httpsPrefix: String - - """Numeric identifier (May change!)""" - id: Int -} - -input RunWhereClause { - alignments: AlignmentWhereClause - alignmentsAggregate: AlignmentAggregateWhereClause - annotations: AnnotationWhereClause - annotationsAggregate: AnnotationAggregateWhereClause - dataset: DatasetWhereClause - datasetId: IntComparators - frames: FrameWhereClause - framesAggregate: FrameAggregateWhereClause - gainFiles: GainFileWhereClause - gainFilesAggregate: GainFileAggregateWhereClause - identifiedObjects: IdentifiedObjectWhereClause - identifiedObjectsAggregate: IdentifiedObjectAggregateWhereClause - frameAcquisitionFiles: FrameAcquisitionFileWhereClause - frameAcquisitionFilesAggregate: FrameAcquisitionFileAggregateWhereClause - perSectionParameters: PerSectionParametersWhereClause - perSectionParametersAggregate: PerSectionParametersAggregateWhereClause - tiltseries: TiltseriesWhereClause - tiltseriesAggregate: TiltseriesAggregateWhereClause - tomogramVoxelSpacings: TomogramVoxelSpacingWhereClause - tomogramVoxelSpacingsAggregate: TomogramVoxelSpacingAggregateWhereClause - tomograms: TomogramWhereClause - tomogramsAggregate: TomogramAggregateWhereClause - name: StrComparators - s3Prefix: StrComparators - httpsPrefix: StrComparators - id: IntComparators -} - -input RunWhereClauseMutations { - id: IntComparators -} - -input Sample_type_enumEnumComparators { - _eq: sample_type_enum - _neq: sample_type_enum - _in: [sample_type_enum!] - _nin: [sample_type_enum!] - _gt: sample_type_enum - _gte: sample_type_enum - _lt: sample_type_enum - _lte: sample_type_enum - _is_null: Boolean -} - -input StrComparators { - _eq: String - _neq: String - _in: [String!] - _nin: [String!] - _is_null: Boolean - _gt: String - _gte: String - _lt: String - _lte: String - _like: String - _nlike: String - _ilike: String - _nilike: String - _regex: String - _nregex: String - _iregex: String - _niregex: String -} - -type Tiltseries implements EntityInterface & Node { - """The Globally Unique ID of this object""" - _id: GlobalID! - - """Numeric identifier (May change!)""" - id: Int! - alignments( - where: AlignmentWhereClause = null - orderBy: [AlignmentOrderByClause!] = [] - - """Returns the items in the list that come before the specified cursor.""" - before: String = null - - """Returns the items in the list that come after the specified cursor.""" - after: String = null - - """Returns the first n items from the list.""" - first: Int = null - - """Returns the items in the list that come after the specified cursor.""" - last: Int = null - ): AlignmentConnection! - alignmentsAggregate(where: AlignmentWhereClause = null): AlignmentAggregate - run(where: RunWhereClause = null, orderBy: [RunOrderByClause!] = []): Run - runId: Int! - deposition(where: DepositionWhereClause = null, orderBy: [DepositionOrderByClause!] = []): Deposition - depositionId: Int - - """S3 path to this tiltseries in multiscale OME-Zarr format""" - s3OmezarrDir: String - - """Size of the tiltseries in OME-Zarr format in bytes""" - fileSizeOmezarr: Float - - """S3 path to this tiltseries in MRC format (no scaling)""" - s3MrcFile: String - - """Size of the tiltseries in MRC format in bytes""" - fileSizeMrc: Float - - """HTTPS path to this tiltseries in multiscale OME-Zarr format""" - httpsOmezarrDir: String - - """HTTPS path to this tiltseries in MRC format (no scaling)""" - httpsMrcFile: String - - """S3 path to the angle list file for this tiltseries""" - s3AngleList: String - - """HTTPS path to the angle list file for this tiltseries""" - httpsAngleList: String - - """Electron Microscope Accelerator voltage in volts""" - accelerationVoltage: Int! - - """Spherical Aberration Constant of the objective lens in millimeters""" - sphericalAberrationConstant: Float! - - """Name of the microscope manufacturer (FEI, TFS, JEOL)""" - microscopeManufacturer: tiltseries_microscope_manufacturer_enum! - - """Microscope model name""" - microscopeModel: String! - - """Energy filter setup used""" - microscopeEnergyFilter: String! - - """Phase plate configuration""" - microscopePhasePlate: String - - """Image corrector setup""" - microscopeImageCorrector: String - - """ - Other microscope optical setup information, in addition to energy filter, phase plate and image corrector - """ - microscopeAdditionalInfo: String - perSectionParameters( - where: PerSectionParametersWhereClause = null - orderBy: [PerSectionParametersOrderByClause!] = [] - - """Returns the items in the list that come before the specified cursor.""" - before: String = null - - """Returns the items in the list that come after the specified cursor.""" - after: String = null - - """Returns the first n items from the list.""" - first: Int = null - - """Returns the items in the list that come after the specified cursor.""" - last: Int = null - ): PerSectionParametersConnection! - perSectionParametersAggregate(where: PerSectionParametersWhereClause = null): PerSectionParametersAggregate - - """Name of the camera manufacturer""" - cameraManufacturer: String! - - """Camera model name""" - cameraModel: String! - - """Minimal tilt angle in degrees""" - tiltMin: Float! - - """Maximal tilt angle in degrees""" - tiltMax: Float! - - """Total tilt range in degrees""" - tiltRange: Float! - - """Tilt step in degrees""" - tiltStep: Float! - - """The order of stage tilting during acquisition of the data""" - tiltingScheme: String! - - """Rotation angle in degrees""" - tiltAxis: Float! - - """ - Number of Electrons reaching the specimen in a square Angstrom area for the entire tilt series - """ - totalFlux: Float! - - """Software used to collect data""" - dataAcquisitionSoftware: String! - - """ - If a tilt series is deposited into EMPIAR, enter the EMPIAR dataset identifier - """ - relatedEmpiarEntry: String - - """Describes the binning factor from frames to tilt series file""" - binningFromFrames: Float - - """ - Author assessment of tilt series quality within the dataset (1-5, 5 is best) - """ - tiltSeriesQuality: Int! - - """Whether this tilt series is aligned""" - isAligned: Boolean! - - """Pixel spacing equal in both axes in angstroms""" - pixelSpacing: Float! - - """Binning factor of the aligned tilt series""" - alignedTiltseriesBinning: Int - - """Number of pixels in the 3D data fast axis""" - sizeX: Int - - """Number of pixels in the 3D data medium axis""" - sizeY: Int - - """Number of pixels in the 3D data slow axis""" - sizeZ: Int -} - -type TiltseriesAggregate { - aggregate: [TiltseriesAggregateFunctions!] -} - -type TiltseriesAggregateFunctions { - sum: TiltseriesNumericalColumns - avg: TiltseriesNumericalColumns - stddev: TiltseriesNumericalColumns - variance: TiltseriesNumericalColumns - min: TiltseriesMinMaxColumns - max: TiltseriesMinMaxColumns - groupBy: TiltseriesGroupByOptions - count(distinct: Boolean = false, columns: TiltseriesCountColumns = null): Int -} - -input TiltseriesAggregateWhereClause { - count: TiltseriesAggregateWhereClauseCount! -} - -input TiltseriesAggregateWhereClauseCount { - arguments: TiltseriesCountColumns - distinct: Boolean - filter: TiltseriesWhereClause - predicate: IntComparators -} - -"""A connection to a list of items.""" -type TiltseriesConnection { - """Pagination data for this connection""" - pageInfo: PageInfo! - - """Contains the nodes in this connection""" - edges: [TiltseriesEdge!]! -} - -enum TiltseriesCountColumns { - s3OmezarrDir - fileSizeOmezarr - s3MrcFile - fileSizeMrc - httpsOmezarrDir - httpsMrcFile - s3AngleList - httpsAngleList - accelerationVoltage - sphericalAberrationConstant - microscopeManufacturer - microscopeModel - microscopeEnergyFilter - microscopePhasePlate - microscopeImageCorrector - microscopeAdditionalInfo - cameraManufacturer - cameraModel - tiltMin - tiltMax - tiltRange - tiltStep - tiltingScheme - tiltAxis - totalFlux - dataAcquisitionSoftware - relatedEmpiarEntry - binningFromFrames - tiltSeriesQuality - isAligned - pixelSpacing - alignedTiltseriesBinning - sizeX - sizeY - sizeZ - id -} - -input TiltseriesCreateInput { - runId: ID! - depositionId: ID = null - - """S3 path to this tiltseries in multiscale OME-Zarr format""" - s3OmezarrDir: String = null - - """Size of the tiltseries in OME-Zarr format in bytes""" - fileSizeOmezarr: Float = null - - """S3 path to this tiltseries in MRC format (no scaling)""" - s3MrcFile: String = null - - """Size of the tiltseries in MRC format in bytes""" - fileSizeMrc: Float = null - - """HTTPS path to this tiltseries in multiscale OME-Zarr format""" - httpsOmezarrDir: String = null - - """HTTPS path to this tiltseries in MRC format (no scaling)""" - httpsMrcFile: String = null - - """S3 path to the angle list file for this tiltseries""" - s3AngleList: String = null - - """HTTPS path to the angle list file for this tiltseries""" - httpsAngleList: String = null - - """Electron Microscope Accelerator voltage in volts""" - accelerationVoltage: Int! - - """Spherical Aberration Constant of the objective lens in millimeters""" - sphericalAberrationConstant: Float! - - """Name of the microscope manufacturer (FEI, TFS, JEOL)""" - microscopeManufacturer: tiltseries_microscope_manufacturer_enum! - - """Microscope model name""" - microscopeModel: String! - - """Energy filter setup used""" - microscopeEnergyFilter: String! - - """Phase plate configuration""" - microscopePhasePlate: String = null - - """Image corrector setup""" - microscopeImageCorrector: String = null - - """ - Other microscope optical setup information, in addition to energy filter, phase plate and image corrector - """ - microscopeAdditionalInfo: String = null - - """Name of the camera manufacturer""" - cameraManufacturer: String! - - """Camera model name""" - cameraModel: String! - - """Minimal tilt angle in degrees""" - tiltMin: Float! - - """Maximal tilt angle in degrees""" - tiltMax: Float! - - """Total tilt range in degrees""" - tiltRange: Float! - - """Tilt step in degrees""" - tiltStep: Float! - - """The order of stage tilting during acquisition of the data""" - tiltingScheme: String! - - """Rotation angle in degrees""" - tiltAxis: Float! - - """ - Number of Electrons reaching the specimen in a square Angstrom area for the entire tilt series - """ - totalFlux: Float! - - """Software used to collect data""" - dataAcquisitionSoftware: String! - - """ - If a tilt series is deposited into EMPIAR, enter the EMPIAR dataset identifier - """ - relatedEmpiarEntry: String = null - - """Describes the binning factor from frames to tilt series file""" - binningFromFrames: Float = null - - """ - Author assessment of tilt series quality within the dataset (1-5, 5 is best) - """ - tiltSeriesQuality: Int! - - """Whether this tilt series is aligned""" - isAligned: Boolean! - - """Pixel spacing equal in both axes in angstroms""" - pixelSpacing: Float! - - """Binning factor of the aligned tilt series""" - alignedTiltseriesBinning: Int = null - - """Number of pixels in the 3D data fast axis""" - sizeX: Int = null - - """Number of pixels in the 3D data medium axis""" - sizeY: Int = null - - """Number of pixels in the 3D data slow axis""" - sizeZ: Int = null - - """Numeric identifier (May change!)""" - id: Int! -} - -"""An edge in a connection.""" -type TiltseriesEdge { - """A cursor for use in pagination""" - cursor: String! - - """The item at the end of the edge""" - node: Tiltseries! -} - -type TiltseriesGroupByOptions { - alignments: AlignmentGroupByOptions - run: RunGroupByOptions - deposition: DepositionGroupByOptions - s3OmezarrDir: String - fileSizeOmezarr: Float - s3MrcFile: String - fileSizeMrc: Float - httpsOmezarrDir: String - httpsMrcFile: String - s3AngleList: String - httpsAngleList: String - accelerationVoltage: Int - sphericalAberrationConstant: Float - microscopeManufacturer: tiltseries_microscope_manufacturer_enum - microscopeModel: String - microscopeEnergyFilter: String - microscopePhasePlate: String - microscopeImageCorrector: String - microscopeAdditionalInfo: String - perSectionParameters: PerSectionParametersGroupByOptions - cameraManufacturer: String - cameraModel: String - tiltMin: Float - tiltMax: Float - tiltRange: Float - tiltStep: Float - tiltingScheme: String - tiltAxis: Float - totalFlux: Float - dataAcquisitionSoftware: String - relatedEmpiarEntry: String - binningFromFrames: Float - tiltSeriesQuality: Int - isAligned: Boolean - pixelSpacing: Float - alignedTiltseriesBinning: Int - sizeX: Int - sizeY: Int - sizeZ: Int - id: Int -} - -type TiltseriesMinMaxColumns { - s3OmezarrDir: String - fileSizeOmezarr: Float - s3MrcFile: String - fileSizeMrc: Float - httpsOmezarrDir: String - httpsMrcFile: String - s3AngleList: String - httpsAngleList: String - accelerationVoltage: Int - sphericalAberrationConstant: Float - microscopeModel: String - microscopeEnergyFilter: String - microscopePhasePlate: String - microscopeImageCorrector: String - microscopeAdditionalInfo: String - cameraManufacturer: String - cameraModel: String - tiltMin: Float - tiltMax: Float - tiltRange: Float - tiltStep: Float - tiltingScheme: String - tiltAxis: Float - totalFlux: Float - dataAcquisitionSoftware: String - relatedEmpiarEntry: String - binningFromFrames: Float - tiltSeriesQuality: Int - pixelSpacing: Float - alignedTiltseriesBinning: Int - sizeX: Int - sizeY: Int - sizeZ: Int - id: Int -} - -type TiltseriesNumericalColumns { - fileSizeOmezarr: Float - fileSizeMrc: Float - accelerationVoltage: Int - sphericalAberrationConstant: Float - tiltMin: Float - tiltMax: Float - tiltRange: Float - tiltStep: Float - tiltAxis: Float - totalFlux: Float - binningFromFrames: Float - tiltSeriesQuality: Int - pixelSpacing: Float - alignedTiltseriesBinning: Int - sizeX: Int - sizeY: Int - sizeZ: Int - id: Int -} - -input TiltseriesOrderByClause { - run: RunOrderByClause - deposition: DepositionOrderByClause - s3OmezarrDir: orderBy - fileSizeOmezarr: orderBy - s3MrcFile: orderBy - fileSizeMrc: orderBy - httpsOmezarrDir: orderBy - httpsMrcFile: orderBy - s3AngleList: orderBy - httpsAngleList: orderBy - accelerationVoltage: orderBy - sphericalAberrationConstant: orderBy - microscopeManufacturer: orderBy - microscopeModel: orderBy - microscopeEnergyFilter: orderBy - microscopePhasePlate: orderBy - microscopeImageCorrector: orderBy - microscopeAdditionalInfo: orderBy - cameraManufacturer: orderBy - cameraModel: orderBy - tiltMin: orderBy - tiltMax: orderBy - tiltRange: orderBy - tiltStep: orderBy - tiltingScheme: orderBy - tiltAxis: orderBy - totalFlux: orderBy - dataAcquisitionSoftware: orderBy - relatedEmpiarEntry: orderBy - binningFromFrames: orderBy - tiltSeriesQuality: orderBy - isAligned: orderBy - pixelSpacing: orderBy - alignedTiltseriesBinning: orderBy - sizeX: orderBy - sizeY: orderBy - sizeZ: orderBy - id: orderBy -} - -input TiltseriesUpdateInput { - runId: ID - depositionId: ID = null - - """S3 path to this tiltseries in multiscale OME-Zarr format""" - s3OmezarrDir: String = null - - """Size of the tiltseries in OME-Zarr format in bytes""" - fileSizeOmezarr: Float = null - - """S3 path to this tiltseries in MRC format (no scaling)""" - s3MrcFile: String = null - - """Size of the tiltseries in MRC format in bytes""" - fileSizeMrc: Float = null - - """HTTPS path to this tiltseries in multiscale OME-Zarr format""" - httpsOmezarrDir: String = null - - """HTTPS path to this tiltseries in MRC format (no scaling)""" - httpsMrcFile: String = null - - """S3 path to the angle list file for this tiltseries""" - s3AngleList: String = null - - """HTTPS path to the angle list file for this tiltseries""" - httpsAngleList: String = null - - """Electron Microscope Accelerator voltage in volts""" - accelerationVoltage: Int - - """Spherical Aberration Constant of the objective lens in millimeters""" - sphericalAberrationConstant: Float - - """Name of the microscope manufacturer (FEI, TFS, JEOL)""" - microscopeManufacturer: tiltseries_microscope_manufacturer_enum - - """Microscope model name""" - microscopeModel: String - - """Energy filter setup used""" - microscopeEnergyFilter: String - - """Phase plate configuration""" - microscopePhasePlate: String = null - - """Image corrector setup""" - microscopeImageCorrector: String = null - - """ - Other microscope optical setup information, in addition to energy filter, phase plate and image corrector - """ - microscopeAdditionalInfo: String = null - - """Name of the camera manufacturer""" - cameraManufacturer: String - - """Camera model name""" - cameraModel: String - - """Minimal tilt angle in degrees""" - tiltMin: Float - - """Maximal tilt angle in degrees""" - tiltMax: Float - - """Total tilt range in degrees""" - tiltRange: Float - - """Tilt step in degrees""" - tiltStep: Float - - """The order of stage tilting during acquisition of the data""" - tiltingScheme: String - - """Rotation angle in degrees""" - tiltAxis: Float - - """ - Number of Electrons reaching the specimen in a square Angstrom area for the entire tilt series - """ - totalFlux: Float - - """Software used to collect data""" - dataAcquisitionSoftware: String - - """ - If a tilt series is deposited into EMPIAR, enter the EMPIAR dataset identifier - """ - relatedEmpiarEntry: String = null - - """Describes the binning factor from frames to tilt series file""" - binningFromFrames: Float = null - - """ - Author assessment of tilt series quality within the dataset (1-5, 5 is best) - """ - tiltSeriesQuality: Int - - """Whether this tilt series is aligned""" - isAligned: Boolean - - """Pixel spacing equal in both axes in angstroms""" - pixelSpacing: Float - - """Binning factor of the aligned tilt series""" - alignedTiltseriesBinning: Int = null - - """Number of pixels in the 3D data fast axis""" - sizeX: Int = null - - """Number of pixels in the 3D data medium axis""" - sizeY: Int = null - - """Number of pixels in the 3D data slow axis""" - sizeZ: Int = null - - """Numeric identifier (May change!)""" - id: Int -} - -input TiltseriesWhereClause { - alignments: AlignmentWhereClause - alignmentsAggregate: AlignmentAggregateWhereClause - run: RunWhereClause - runId: IntComparators - deposition: DepositionWhereClause - depositionId: IntComparators - s3OmezarrDir: StrComparators - fileSizeOmezarr: FloatComparators - s3MrcFile: StrComparators - fileSizeMrc: FloatComparators - httpsOmezarrDir: StrComparators - httpsMrcFile: StrComparators - s3AngleList: StrComparators - httpsAngleList: StrComparators - accelerationVoltage: IntComparators - sphericalAberrationConstant: FloatComparators - microscopeManufacturer: Tiltseries_microscope_manufacturer_enumEnumComparators - microscopeModel: StrComparators - microscopeEnergyFilter: StrComparators - microscopePhasePlate: StrComparators - microscopeImageCorrector: StrComparators - microscopeAdditionalInfo: StrComparators - perSectionParameters: PerSectionParametersWhereClause - perSectionParametersAggregate: PerSectionParametersAggregateWhereClause - cameraManufacturer: StrComparators - cameraModel: StrComparators - tiltMin: FloatComparators - tiltMax: FloatComparators - tiltRange: FloatComparators - tiltStep: FloatComparators - tiltingScheme: StrComparators - tiltAxis: FloatComparators - totalFlux: FloatComparators - dataAcquisitionSoftware: StrComparators - relatedEmpiarEntry: StrComparators - binningFromFrames: FloatComparators - tiltSeriesQuality: IntComparators - isAligned: BoolComparators - pixelSpacing: FloatComparators - alignedTiltseriesBinning: IntComparators - sizeX: IntComparators - sizeY: IntComparators - sizeZ: IntComparators - id: IntComparators -} - -input TiltseriesWhereClauseMutations { - id: IntComparators -} - -input Tiltseries_microscope_manufacturer_enumEnumComparators { - _eq: tiltseries_microscope_manufacturer_enum - _neq: tiltseries_microscope_manufacturer_enum - _in: [tiltseries_microscope_manufacturer_enum!] - _nin: [tiltseries_microscope_manufacturer_enum!] - _gt: tiltseries_microscope_manufacturer_enum - _gte: tiltseries_microscope_manufacturer_enum - _lt: tiltseries_microscope_manufacturer_enum - _lte: tiltseries_microscope_manufacturer_enum - _is_null: Boolean -} - -"""Metadata describing a tomogram.""" -type Tomogram implements EntityInterface & Node { - """The Globally Unique ID of this object""" - _id: GlobalID! - - """Numeric identifier (May change!)""" - id: Int! - alignment(where: AlignmentWhereClause = null, orderBy: [AlignmentOrderByClause!] = []): Alignment - alignmentId: Int - authors( - where: TomogramAuthorWhereClause = null - orderBy: [TomogramAuthorOrderByClause!] = [] - - """Returns the items in the list that come before the specified cursor.""" - before: String = null - - """Returns the items in the list that come after the specified cursor.""" - after: String = null - - """Returns the first n items from the list.""" - first: Int = null - - """Returns the items in the list that come after the specified cursor.""" - last: Int = null - ): TomogramAuthorConnection! - authorsAggregate(where: TomogramAuthorWhereClause = null): TomogramAuthorAggregate - deposition(where: DepositionWhereClause = null, orderBy: [DepositionOrderByClause!] = []): Deposition - depositionId: Int! - run(where: RunWhereClause = null, orderBy: [RunOrderByClause!] = []): Run - runId: Int - tomogramVoxelSpacing(where: TomogramVoxelSpacingWhereClause = null, orderBy: [TomogramVoxelSpacingOrderByClause!] = []): TomogramVoxelSpacing - tomogramVoxelSpacingId: Int - - """Short name for this tomogram""" - name: String - - """Number of pixels in the 3D data fast axis""" - sizeX: Int! - - """Number of pixels in the 3D data medium axis""" - sizeY: Int! - - """ - Number of pixels in the 3D data slow axis. This is the image projection direction at zero stage tilt - """ - sizeZ: Int! - - """Voxel spacing equal in all three axes in angstroms""" - voxelSpacing: Float! - - """ - Fiducial Alignment status: True = aligned with fiducial False = aligned without fiducial - """ - fiducialAlignmentStatus: fiducial_alignment_status_enum! - - """Describe reconstruction method (WBP, SART, SIRT)""" - reconstructionMethod: tomogram_reconstruction_method_enum! - - """Describe additional processing used to derive the tomogram""" - processing: tomogram_processing_enum! - - """Version of tomogram""" - tomogramVersion: Float - - """Processing software used to derive the tomogram""" - processingSoftware: String - - """Name of software used for reconstruction""" - reconstructionSoftware: String! - - """whether this tomogram adheres to portal standards""" - isPortalStandard: Boolean - - """ - Whether this tomogram was submitted by the author of the dataset it belongs to. - """ - isAuthorSubmitted: Boolean - - """ - Data curator’s subjective choice of default tomogram to display in visualization for a run - """ - isVisualizationDefault: Boolean - - """S3 path to this tomogram in multiscale OME-Zarr format""" - s3OmezarrDir: String - - """HTTPS path to this tomogram in multiscale OME-Zarr format""" - httpsOmezarrDir: String - - """Size of the tomogram in OME-Zarr format in bytes""" - fileSizeOmezarr: Float - - """S3 path to this tomogram in MRC format (no scaling)""" - s3MrcFile: String - - """HTTPS path to this tomogram in MRC format (no scaling)""" - httpsMrcFile: String - - """Size of the tomogram in MRC format in bytes""" - fileSizeMrc: Float - - """comma separated x,y,z dimensions of the unscaled tomogram""" - scale0Dimensions: String - - """comma separated x,y,z dimensions of the scale1 tomogram""" - scale1Dimensions: String - - """comma separated x,y,z dimensions of the scale2 tomogram""" - scale2Dimensions: String - - """Whether this tomogram is CTF corrected""" - ctfCorrected: Boolean - - """x offset data relative to the canonical tomogram in pixels""" - offsetX: Int! - - """y offset data relative to the canonical tomogram in pixels""" - offsetY: Int! - - """z offset data relative to the canonical tomogram in pixels""" - offsetZ: Int! - - """URL for the key photo""" - keyPhotoUrl: String - - """URL for the thumbnail of key photo""" - keyPhotoThumbnailUrl: String - - """the compact json of neuroglancer config""" - neuroglancerConfig: String - - """ - Comma-separated list of DOIs for publications associated with the tomogram. - """ - publications: String - - """ - If a CryoET tomogram is also deposited into another database, enter the database identifier here (e.g. EMPIAR-11445). Use a comma to separate multiple identifiers. - """ - relatedDatabaseEntries: String - - """The date a data item was received by the cryoET data portal.""" - depositionDate: DateTime - - """The date a data item was received by the cryoET data portal.""" - releaseDate: DateTime - - """The date a piece of data was last modified on the cryoET data portal.""" - lastModifiedDate: DateTime -} - -type TomogramAggregate { - aggregate: [TomogramAggregateFunctions!] -} - -type TomogramAggregateFunctions { - sum: TomogramNumericalColumns - avg: TomogramNumericalColumns - stddev: TomogramNumericalColumns - variance: TomogramNumericalColumns - min: TomogramMinMaxColumns - max: TomogramMinMaxColumns - groupBy: TomogramGroupByOptions - count(distinct: Boolean = false, columns: TomogramCountColumns = null): Int -} - -input TomogramAggregateWhereClause { - count: TomogramAggregateWhereClauseCount! -} - -input TomogramAggregateWhereClauseCount { - arguments: TomogramCountColumns - distinct: Boolean - filter: TomogramWhereClause - predicate: IntComparators -} - -"""Author of a tomogram""" -type TomogramAuthor implements EntityInterface & Node { - """The Globally Unique ID of this object""" - _id: GlobalID! - - """Numeric identifier (May change!)""" - id: Int! - tomogram(where: TomogramWhereClause = null, orderBy: [TomogramOrderByClause!] = []): Tomogram - tomogramId: Int - - """The order in which the author appears in the publication""" - authorListOrder: Int! - - """A unique, persistent identifier for researchers, provided by ORCID.""" - orcid: String - - """A unique, persistent identifier for kaggle users at kaggle.com.""" - kaggleId: String - - """Full name of an author (e.g. Jane Doe).""" - name: String! - - """Email address for this author""" - email: String - - """Name of the institutions an author is affiliated with. Comma separated""" - affiliationName: String - - """Address of the institution an author is affiliated with.""" - affiliationAddress: String - - """ - A unique identifier assigned to the affiliated institution by The Research Organization Registry (ROR). - """ - affiliationIdentifier: String - - """Indicates whether an author is the corresponding author""" - correspondingAuthorStatus: Boolean - - """Indicates whether an author is the main person creating the tomogram""" - primaryAuthorStatus: Boolean -} - -type TomogramAuthorAggregate { - aggregate: [TomogramAuthorAggregateFunctions!] -} - -type TomogramAuthorAggregateFunctions { - sum: TomogramAuthorNumericalColumns - avg: TomogramAuthorNumericalColumns - stddev: TomogramAuthorNumericalColumns - variance: TomogramAuthorNumericalColumns - min: TomogramAuthorMinMaxColumns - max: TomogramAuthorMinMaxColumns - groupBy: TomogramAuthorGroupByOptions - count(distinct: Boolean = false, columns: TomogramAuthorCountColumns = null): Int -} - -input TomogramAuthorAggregateWhereClause { - count: TomogramAuthorAggregateWhereClauseCount! -} - -input TomogramAuthorAggregateWhereClauseCount { - arguments: TomogramAuthorCountColumns - distinct: Boolean - filter: TomogramAuthorWhereClause - predicate: IntComparators -} - -"""A connection to a list of items.""" -type TomogramAuthorConnection { - """Pagination data for this connection""" - pageInfo: PageInfo! - - """Contains the nodes in this connection""" - edges: [TomogramAuthorEdge!]! -} - -enum TomogramAuthorCountColumns { - id - authorListOrder - orcid - kaggleId - name - email - affiliationName - affiliationAddress - affiliationIdentifier - correspondingAuthorStatus - primaryAuthorStatus -} - -input TomogramAuthorCreateInput { - """The tomogram this tomogram author is a part of""" - tomogramId: ID = null - - """Numeric identifier (May change!)""" - id: Int! - - """The order in which the author appears in the publication""" - authorListOrder: Int! - - """A unique, persistent identifier for researchers, provided by ORCID.""" - orcid: String = null - - """A unique, persistent identifier for kaggle users at kaggle.com.""" - kaggleId: String = null - - """Full name of an author (e.g. Jane Doe).""" - name: String! - - """Email address for this author""" - email: String = null - - """Name of the institutions an author is affiliated with. Comma separated""" - affiliationName: String = null - - """Address of the institution an author is affiliated with.""" - affiliationAddress: String = null - - """ - A unique identifier assigned to the affiliated institution by The Research Organization Registry (ROR). - """ - affiliationIdentifier: String = null - - """Indicates whether an author is the corresponding author""" - correspondingAuthorStatus: Boolean = null - - """Indicates whether an author is the main person creating the tomogram""" - primaryAuthorStatus: Boolean = null -} - -"""An edge in a connection.""" -type TomogramAuthorEdge { - """A cursor for use in pagination""" - cursor: String! - - """The item at the end of the edge""" - node: TomogramAuthor! -} - -type TomogramAuthorGroupByOptions { - tomogram: TomogramGroupByOptions - id: Int - authorListOrder: Int - orcid: String - kaggleId: String - name: String - email: String - affiliationName: String - affiliationAddress: String - affiliationIdentifier: String - correspondingAuthorStatus: Boolean - primaryAuthorStatus: Boolean -} - -type TomogramAuthorMinMaxColumns { - id: Int - authorListOrder: Int - orcid: String - kaggleId: String - name: String - email: String - affiliationName: String - affiliationAddress: String - affiliationIdentifier: String -} - -type TomogramAuthorNumericalColumns { - id: Int - authorListOrder: Int -} - -input TomogramAuthorOrderByClause { - tomogram: TomogramOrderByClause - id: orderBy - authorListOrder: orderBy - orcid: orderBy - kaggleId: orderBy - name: orderBy - email: orderBy - affiliationName: orderBy - affiliationAddress: orderBy - affiliationIdentifier: orderBy - correspondingAuthorStatus: orderBy - primaryAuthorStatus: orderBy -} - -input TomogramAuthorUpdateInput { - """The tomogram this tomogram author is a part of""" - tomogramId: ID = null - - """Numeric identifier (May change!)""" - id: Int - - """The order in which the author appears in the publication""" - authorListOrder: Int - - """A unique, persistent identifier for researchers, provided by ORCID.""" - orcid: String = null - - """A unique, persistent identifier for kaggle users at kaggle.com.""" - kaggleId: String = null - - """Full name of an author (e.g. Jane Doe).""" - name: String - - """Email address for this author""" - email: String = null - - """Name of the institutions an author is affiliated with. Comma separated""" - affiliationName: String = null - - """Address of the institution an author is affiliated with.""" - affiliationAddress: String = null - - """ - A unique identifier assigned to the affiliated institution by The Research Organization Registry (ROR). - """ - affiliationIdentifier: String = null - - """Indicates whether an author is the corresponding author""" - correspondingAuthorStatus: Boolean = null - - """Indicates whether an author is the main person creating the tomogram""" - primaryAuthorStatus: Boolean = null -} - -input TomogramAuthorWhereClause { - tomogram: TomogramWhereClause - tomogramId: IntComparators - id: IntComparators - authorListOrder: IntComparators - orcid: StrComparators - kaggleId: StrComparators - name: StrComparators - email: StrComparators - affiliationName: StrComparators - affiliationAddress: StrComparators - affiliationIdentifier: StrComparators - correspondingAuthorStatus: BoolComparators - primaryAuthorStatus: BoolComparators -} - -input TomogramAuthorWhereClauseMutations { - id: IntComparators -} - -"""A connection to a list of items.""" -type TomogramConnection { - """Pagination data for this connection""" - pageInfo: PageInfo! - - """Contains the nodes in this connection""" - edges: [TomogramEdge!]! -} - -enum TomogramCountColumns { - name - sizeX - sizeY - sizeZ - voxelSpacing - fiducialAlignmentStatus - reconstructionMethod - processing - tomogramVersion - processingSoftware - reconstructionSoftware - isPortalStandard - isAuthorSubmitted - isVisualizationDefault - s3OmezarrDir - httpsOmezarrDir - fileSizeOmezarr - s3MrcFile - httpsMrcFile - fileSizeMrc - scale0Dimensions - scale1Dimensions - scale2Dimensions - ctfCorrected - offsetX - offsetY - offsetZ - keyPhotoUrl - keyPhotoThumbnailUrl - neuroglancerConfig - publications - relatedDatabaseEntries - id - depositionDate - releaseDate - lastModifiedDate -} - -input TomogramCreateInput { - """Tiltseries Alignment""" - alignmentId: ID = null - - """If the tomogram is part of a deposition, the related deposition""" - depositionId: ID! - runId: ID = null - - """Voxel spacings for a run""" - tomogramVoxelSpacingId: ID = null - - """Short name for this tomogram""" - name: String = null - - """Number of pixels in the 3D data fast axis""" - sizeX: Int! - - """Number of pixels in the 3D data medium axis""" - sizeY: Int! - - """ - Number of pixels in the 3D data slow axis. This is the image projection direction at zero stage tilt - """ - sizeZ: Int! - - """Voxel spacing equal in all three axes in angstroms""" - voxelSpacing: Float! - - """ - Fiducial Alignment status: True = aligned with fiducial False = aligned without fiducial - """ - fiducialAlignmentStatus: fiducial_alignment_status_enum! - - """Describe reconstruction method (WBP, SART, SIRT)""" - reconstructionMethod: tomogram_reconstruction_method_enum! - - """Describe additional processing used to derive the tomogram""" - processing: tomogram_processing_enum! - - """Version of tomogram""" - tomogramVersion: Float = null - - """Processing software used to derive the tomogram""" - processingSoftware: String = null - - """Name of software used for reconstruction""" - reconstructionSoftware: String! - - """whether this tomogram adheres to portal standards""" - isPortalStandard: Boolean = null - - """ - Whether this tomogram was submitted by the author of the dataset it belongs to. - """ - isAuthorSubmitted: Boolean = null - - """ - Data curator’s subjective choice of default tomogram to display in visualization for a run - """ - isVisualizationDefault: Boolean = null - - """S3 path to this tomogram in multiscale OME-Zarr format""" - s3OmezarrDir: String = null - - """HTTPS path to this tomogram in multiscale OME-Zarr format""" - httpsOmezarrDir: String = null - - """Size of the tomogram in OME-Zarr format in bytes""" - fileSizeOmezarr: Float = null - - """S3 path to this tomogram in MRC format (no scaling)""" - s3MrcFile: String = null - - """HTTPS path to this tomogram in MRC format (no scaling)""" - httpsMrcFile: String = null - - """Size of the tomogram in MRC format in bytes""" - fileSizeMrc: Float = null - - """comma separated x,y,z dimensions of the unscaled tomogram""" - scale0Dimensions: String = null - - """comma separated x,y,z dimensions of the scale1 tomogram""" - scale1Dimensions: String = null - - """comma separated x,y,z dimensions of the scale2 tomogram""" - scale2Dimensions: String = null - - """Whether this tomogram is CTF corrected""" - ctfCorrected: Boolean = null - - """x offset data relative to the canonical tomogram in pixels""" - offsetX: Int! - - """y offset data relative to the canonical tomogram in pixels""" - offsetY: Int! - - """z offset data relative to the canonical tomogram in pixels""" - offsetZ: Int! - - """URL for the key photo""" - keyPhotoUrl: String = null - - """URL for the thumbnail of key photo""" - keyPhotoThumbnailUrl: String = null - - """the compact json of neuroglancer config""" - neuroglancerConfig: String = null - - """ - Comma-separated list of DOIs for publications associated with the tomogram. - """ - publications: String = null - - """ - If a CryoET tomogram is also deposited into another database, enter the database identifier here (e.g. EMPIAR-11445). Use a comma to separate multiple identifiers. - """ - relatedDatabaseEntries: String = null - - """Numeric identifier (May change!)""" - id: Int! - - """The date a data item was received by the cryoET data portal.""" - depositionDate: DateTime = null - - """The date a data item was received by the cryoET data portal.""" - releaseDate: DateTime = null - - """The date a piece of data was last modified on the cryoET data portal.""" - lastModifiedDate: DateTime = null -} - -"""An edge in a connection.""" -type TomogramEdge { - """A cursor for use in pagination""" - cursor: String! - - """The item at the end of the edge""" - node: Tomogram! -} - -type TomogramGroupByOptions { - alignment: AlignmentGroupByOptions - authors: TomogramAuthorGroupByOptions - deposition: DepositionGroupByOptions - run: RunGroupByOptions - tomogramVoxelSpacing: TomogramVoxelSpacingGroupByOptions - name: String - sizeX: Int - sizeY: Int - sizeZ: Int - voxelSpacing: Float - fiducialAlignmentStatus: fiducial_alignment_status_enum - reconstructionMethod: tomogram_reconstruction_method_enum - processing: tomogram_processing_enum - tomogramVersion: Float - processingSoftware: String - reconstructionSoftware: String - isPortalStandard: Boolean - isAuthorSubmitted: Boolean - isVisualizationDefault: Boolean - s3OmezarrDir: String - httpsOmezarrDir: String - fileSizeOmezarr: Float - s3MrcFile: String - httpsMrcFile: String - fileSizeMrc: Float - scale0Dimensions: String - scale1Dimensions: String - scale2Dimensions: String - ctfCorrected: Boolean - offsetX: Int - offsetY: Int - offsetZ: Int - keyPhotoUrl: String - keyPhotoThumbnailUrl: String - neuroglancerConfig: String - publications: String - relatedDatabaseEntries: String - id: Int - depositionDate: DateTime - releaseDate: DateTime - lastModifiedDate: DateTime -} - -type TomogramMinMaxColumns { - name: String - sizeX: Int - sizeY: Int - sizeZ: Int - voxelSpacing: Float - tomogramVersion: Float - processingSoftware: String - reconstructionSoftware: String - s3OmezarrDir: String - httpsOmezarrDir: String - fileSizeOmezarr: Float - s3MrcFile: String - httpsMrcFile: String - fileSizeMrc: Float - scale0Dimensions: String - scale1Dimensions: String - scale2Dimensions: String - offsetX: Int - offsetY: Int - offsetZ: Int - keyPhotoUrl: String - keyPhotoThumbnailUrl: String - neuroglancerConfig: String - publications: String - relatedDatabaseEntries: String - id: Int - depositionDate: DateTime - releaseDate: DateTime - lastModifiedDate: DateTime -} - -type TomogramNumericalColumns { - sizeX: Int - sizeY: Int - sizeZ: Int - voxelSpacing: Float - tomogramVersion: Float - fileSizeOmezarr: Float - fileSizeMrc: Float - offsetX: Int - offsetY: Int - offsetZ: Int - id: Int -} - -input TomogramOrderByClause { - alignment: AlignmentOrderByClause - deposition: DepositionOrderByClause - run: RunOrderByClause - tomogramVoxelSpacing: TomogramVoxelSpacingOrderByClause - name: orderBy - sizeX: orderBy - sizeY: orderBy - sizeZ: orderBy - voxelSpacing: orderBy - fiducialAlignmentStatus: orderBy - reconstructionMethod: orderBy - processing: orderBy - tomogramVersion: orderBy - processingSoftware: orderBy - reconstructionSoftware: orderBy - isPortalStandard: orderBy - isAuthorSubmitted: orderBy - isVisualizationDefault: orderBy - s3OmezarrDir: orderBy - httpsOmezarrDir: orderBy - fileSizeOmezarr: orderBy - s3MrcFile: orderBy - httpsMrcFile: orderBy - fileSizeMrc: orderBy - scale0Dimensions: orderBy - scale1Dimensions: orderBy - scale2Dimensions: orderBy - ctfCorrected: orderBy - offsetX: orderBy - offsetY: orderBy - offsetZ: orderBy - keyPhotoUrl: orderBy - keyPhotoThumbnailUrl: orderBy - neuroglancerConfig: orderBy - publications: orderBy - relatedDatabaseEntries: orderBy - id: orderBy - depositionDate: orderBy - releaseDate: orderBy - lastModifiedDate: orderBy -} - -input TomogramUpdateInput { - """Tiltseries Alignment""" - alignmentId: ID = null - - """If the tomogram is part of a deposition, the related deposition""" - depositionId: ID - runId: ID = null - - """Voxel spacings for a run""" - tomogramVoxelSpacingId: ID = null - - """Short name for this tomogram""" - name: String = null - - """Number of pixels in the 3D data fast axis""" - sizeX: Int - - """Number of pixels in the 3D data medium axis""" - sizeY: Int - - """ - Number of pixels in the 3D data slow axis. This is the image projection direction at zero stage tilt - """ - sizeZ: Int - - """Voxel spacing equal in all three axes in angstroms""" - voxelSpacing: Float - - """ - Fiducial Alignment status: True = aligned with fiducial False = aligned without fiducial - """ - fiducialAlignmentStatus: fiducial_alignment_status_enum - - """Describe reconstruction method (WBP, SART, SIRT)""" - reconstructionMethod: tomogram_reconstruction_method_enum - - """Describe additional processing used to derive the tomogram""" - processing: tomogram_processing_enum - - """Version of tomogram""" - tomogramVersion: Float = null - - """Processing software used to derive the tomogram""" - processingSoftware: String = null - - """Name of software used for reconstruction""" - reconstructionSoftware: String - - """whether this tomogram adheres to portal standards""" - isPortalStandard: Boolean = null - - """ - Whether this tomogram was submitted by the author of the dataset it belongs to. - """ - isAuthorSubmitted: Boolean = null - - """ - Data curator’s subjective choice of default tomogram to display in visualization for a run - """ - isVisualizationDefault: Boolean = null - - """S3 path to this tomogram in multiscale OME-Zarr format""" - s3OmezarrDir: String = null - - """HTTPS path to this tomogram in multiscale OME-Zarr format""" - httpsOmezarrDir: String = null - - """Size of the tomogram in OME-Zarr format in bytes""" - fileSizeOmezarr: Float = null - - """S3 path to this tomogram in MRC format (no scaling)""" - s3MrcFile: String = null - - """HTTPS path to this tomogram in MRC format (no scaling)""" - httpsMrcFile: String = null - - """Size of the tomogram in MRC format in bytes""" - fileSizeMrc: Float = null - - """comma separated x,y,z dimensions of the unscaled tomogram""" - scale0Dimensions: String = null - - """comma separated x,y,z dimensions of the scale1 tomogram""" - scale1Dimensions: String = null - - """comma separated x,y,z dimensions of the scale2 tomogram""" - scale2Dimensions: String = null - - """Whether this tomogram is CTF corrected""" - ctfCorrected: Boolean = null - - """x offset data relative to the canonical tomogram in pixels""" - offsetX: Int - - """y offset data relative to the canonical tomogram in pixels""" - offsetY: Int - - """z offset data relative to the canonical tomogram in pixels""" - offsetZ: Int - - """URL for the key photo""" - keyPhotoUrl: String = null - - """URL for the thumbnail of key photo""" - keyPhotoThumbnailUrl: String = null - - """the compact json of neuroglancer config""" - neuroglancerConfig: String = null - - """ - Comma-separated list of DOIs for publications associated with the tomogram. - """ - publications: String = null - - """ - If a CryoET tomogram is also deposited into another database, enter the database identifier here (e.g. EMPIAR-11445). Use a comma to separate multiple identifiers. - """ - relatedDatabaseEntries: String = null - - """Numeric identifier (May change!)""" - id: Int - - """The date a data item was received by the cryoET data portal.""" - depositionDate: DateTime = null - - """The date a data item was received by the cryoET data portal.""" - releaseDate: DateTime = null - - """The date a piece of data was last modified on the cryoET data portal.""" - lastModifiedDate: DateTime = null -} - -"""Voxel spacings for a run""" -type TomogramVoxelSpacing implements EntityInterface & Node { - """The Globally Unique ID of this object""" - _id: GlobalID! - - """Numeric identifier (May change!)""" - id: Int! - annotationFiles( - where: AnnotationFileWhereClause = null - orderBy: [AnnotationFileOrderByClause!] = [] - - """Returns the items in the list that come before the specified cursor.""" - before: String = null - - """Returns the items in the list that come after the specified cursor.""" - after: String = null - - """Returns the first n items from the list.""" - first: Int = null - - """Returns the items in the list that come after the specified cursor.""" - last: Int = null - ): AnnotationFileConnection! - annotationFilesAggregate(where: AnnotationFileWhereClause = null): AnnotationFileAggregate - run(where: RunWhereClause = null, orderBy: [RunOrderByClause!] = []): Run - runId: Int - tomograms( - where: TomogramWhereClause = null - orderBy: [TomogramOrderByClause!] = [] - - """Returns the items in the list that come before the specified cursor.""" - before: String = null - - """Returns the items in the list that come after the specified cursor.""" - after: String = null - - """Returns the first n items from the list.""" - first: Int = null - - """Returns the items in the list that come after the specified cursor.""" - last: Int = null - ): TomogramConnection! - tomogramsAggregate(where: TomogramWhereClause = null): TomogramAggregate - - """The voxel spacing for the tomograms in this set in angstroms""" - voxelSpacing: Float! - - """ - The S3 public bucket path where this tomogram voxel spacing is contained - """ - s3Prefix: String! - - """ - The HTTPS directory path where this tomogram voxel spacing is contained - """ - httpsPrefix: String! -} - -type TomogramVoxelSpacingAggregate { - aggregate: [TomogramVoxelSpacingAggregateFunctions!] -} - -type TomogramVoxelSpacingAggregateFunctions { - sum: TomogramVoxelSpacingNumericalColumns - avg: TomogramVoxelSpacingNumericalColumns - stddev: TomogramVoxelSpacingNumericalColumns - variance: TomogramVoxelSpacingNumericalColumns - min: TomogramVoxelSpacingMinMaxColumns - max: TomogramVoxelSpacingMinMaxColumns - groupBy: TomogramVoxelSpacingGroupByOptions - count(distinct: Boolean = false, columns: TomogramVoxelSpacingCountColumns = null): Int -} - -input TomogramVoxelSpacingAggregateWhereClause { - count: TomogramVoxelSpacingAggregateWhereClauseCount! -} - -input TomogramVoxelSpacingAggregateWhereClauseCount { - arguments: TomogramVoxelSpacingCountColumns - distinct: Boolean - filter: TomogramVoxelSpacingWhereClause - predicate: IntComparators -} - -"""A connection to a list of items.""" -type TomogramVoxelSpacingConnection { - """Pagination data for this connection""" - pageInfo: PageInfo! - - """Contains the nodes in this connection""" - edges: [TomogramVoxelSpacingEdge!]! -} - -enum TomogramVoxelSpacingCountColumns { - voxelSpacing - s3Prefix - httpsPrefix - id -} - -input TomogramVoxelSpacingCreateInput { - """The the run this tomogram voxel spacing is a part of""" - runId: ID = null - - """The voxel spacing for the tomograms in this set in angstroms""" - voxelSpacing: Float! - - """ - The S3 public bucket path where this tomogram voxel spacing is contained - """ - s3Prefix: String! - - """ - The HTTPS directory path where this tomogram voxel spacing is contained - """ - httpsPrefix: String! - - """Numeric identifier (May change!)""" - id: Int! -} - -"""An edge in a connection.""" -type TomogramVoxelSpacingEdge { - """A cursor for use in pagination""" - cursor: String! - - """The item at the end of the edge""" - node: TomogramVoxelSpacing! -} - -type TomogramVoxelSpacingGroupByOptions { - annotationFiles: AnnotationFileGroupByOptions - run: RunGroupByOptions - tomograms: TomogramGroupByOptions - voxelSpacing: Float - s3Prefix: String - httpsPrefix: String - id: Int -} - -type TomogramVoxelSpacingMinMaxColumns { - voxelSpacing: Float - s3Prefix: String - httpsPrefix: String - id: Int -} - -type TomogramVoxelSpacingNumericalColumns { - voxelSpacing: Float - id: Int -} - -input TomogramVoxelSpacingOrderByClause { - run: RunOrderByClause - voxelSpacing: orderBy - s3Prefix: orderBy - httpsPrefix: orderBy - id: orderBy -} - -input TomogramVoxelSpacingUpdateInput { - """The the run this tomogram voxel spacing is a part of""" - runId: ID = null - - """The voxel spacing for the tomograms in this set in angstroms""" - voxelSpacing: Float - - """ - The S3 public bucket path where this tomogram voxel spacing is contained - """ - s3Prefix: String - - """ - The HTTPS directory path where this tomogram voxel spacing is contained - """ - httpsPrefix: String - - """Numeric identifier (May change!)""" - id: Int -} - -input TomogramVoxelSpacingWhereClause { - annotationFiles: AnnotationFileWhereClause - annotationFilesAggregate: AnnotationFileAggregateWhereClause - run: RunWhereClause - runId: IntComparators - tomograms: TomogramWhereClause - tomogramsAggregate: TomogramAggregateWhereClause - voxelSpacing: FloatComparators - s3Prefix: StrComparators - httpsPrefix: StrComparators - id: IntComparators -} - -input TomogramVoxelSpacingWhereClauseMutations { - id: IntComparators -} - -input TomogramWhereClause { - alignment: AlignmentWhereClause - alignmentId: IntComparators - authors: TomogramAuthorWhereClause - authorsAggregate: TomogramAuthorAggregateWhereClause - deposition: DepositionWhereClause - depositionId: IntComparators - run: RunWhereClause - runId: IntComparators - tomogramVoxelSpacing: TomogramVoxelSpacingWhereClause - tomogramVoxelSpacingId: IntComparators - name: StrComparators - sizeX: IntComparators - sizeY: IntComparators - sizeZ: IntComparators - voxelSpacing: FloatComparators - fiducialAlignmentStatus: Fiducial_alignment_status_enumEnumComparators - reconstructionMethod: Tomogram_reconstruction_method_enumEnumComparators - processing: Tomogram_processing_enumEnumComparators - tomogramVersion: FloatComparators - processingSoftware: StrComparators - reconstructionSoftware: StrComparators - isPortalStandard: BoolComparators - isAuthorSubmitted: BoolComparators - isVisualizationDefault: BoolComparators - s3OmezarrDir: StrComparators - httpsOmezarrDir: StrComparators - fileSizeOmezarr: FloatComparators - s3MrcFile: StrComparators - httpsMrcFile: StrComparators - fileSizeMrc: FloatComparators - scale0Dimensions: StrComparators - scale1Dimensions: StrComparators - scale2Dimensions: StrComparators - ctfCorrected: BoolComparators - offsetX: IntComparators - offsetY: IntComparators - offsetZ: IntComparators - keyPhotoUrl: StrComparators - keyPhotoThumbnailUrl: StrComparators - neuroglancerConfig: StrComparators - publications: StrComparators - relatedDatabaseEntries: StrComparators - id: IntComparators - depositionDate: DatetimeComparators - releaseDate: DatetimeComparators - lastModifiedDate: DatetimeComparators -} - -input TomogramWhereClauseMutations { - id: IntComparators -} - -input Tomogram_processing_enumEnumComparators { - _eq: tomogram_processing_enum - _neq: tomogram_processing_enum - _in: [tomogram_processing_enum!] - _nin: [tomogram_processing_enum!] - _gt: tomogram_processing_enum - _gte: tomogram_processing_enum - _lt: tomogram_processing_enum - _lte: tomogram_processing_enum - _is_null: Boolean -} - -input Tomogram_reconstruction_method_enumEnumComparators { - _eq: tomogram_reconstruction_method_enum - _neq: tomogram_reconstruction_method_enum - _in: [tomogram_reconstruction_method_enum!] - _nin: [tomogram_reconstruction_method_enum!] - _gt: tomogram_reconstruction_method_enum - _gte: tomogram_reconstruction_method_enum - _lt: tomogram_reconstruction_method_enum - _lte: tomogram_reconstruction_method_enum - _is_null: Boolean -} - -enum alignment_method_type_enum { - projection_matching - patch_tracking - fiducial_based -} - -enum alignment_type_enum { - LOCAL - GLOBAL -} - -enum annotation_file_shape_type_enum { - SegmentationMask - OrientedPoint - Point - InstanceSegmentation - InstanceSegmentationMask - Mesh -} - -enum annotation_file_source_enum { - dataset_author - community - portal_standard -} - -enum annotation_method_link_type_enum { - documentation - models_weights - other - source_code - website -} - -enum annotation_method_type_enum { - manual - automated - hybrid - simulated -} - -enum deposition_types_enum { - annotation - dataset - tomogram -} - -enum fiducial_alignment_status_enum { - FIDUCIAL - NON_FIDUCIAL -} - -enum orderBy { - asc - asc_nulls_first - asc_nulls_last - desc - desc_nulls_first - desc_nulls_last -} - -enum sample_type_enum { - cell - cell_line - in_silico - in_vitro - organelle - organism - organoid - other - primary_cell_culture - tissue - virus -} - -enum tiltseries_microscope_manufacturer_enum { - FEI - TFS - JEOL - SIMULATED -} - -enum tomogram_processing_enum { - denoised - filtered - raw - filtered_even - filtered_odd -} - -enum tomogram_reconstruction_method_enum { - SART - Fourier_Space - SIRT - WBP - Unknown -} diff --git a/apiv2/graphql_api/types/annotation_shape.py b/apiv2/graphql_api/types/annotation_shape.py index 326fc065a..4a615fbb0 100644 --- a/apiv2/graphql_api/types/annotation_shape.py +++ b/apiv2/graphql_api/types/annotation_shape.py @@ -197,7 +197,7 @@ class AnnotationShape(EntityInterface): Annotated["AnnotationFileAggregate", strawberry.lazy("graphql_api.types.annotation_file")] ] = load_annotation_file_aggregate_rows # type:ignore shape_type: Optional[annotation_file_shape_type_enum] = strawberry.field( - description="The shape of the annotation (SegmentationMask, OrientedPoint, Point, InstanceSegmentation, Mesh, InstanceSegmentationMask)", + description="The shape of the annotation (SegmentationMask, OrientedPoint, Point, InstanceSegmentation, Mesh, InstanceSegmentationMask, GlobalCaption)", default=None, ) id: int = strawberry.field(description="Numeric identifier (May change!)") @@ -312,7 +312,7 @@ class AnnotationShapeCreateInput: description="Metadata about an shapes for an annotation", default=None, ) shape_type: Optional[annotation_file_shape_type_enum] = strawberry.field( - description="The shape of the annotation (SegmentationMask, OrientedPoint, Point, InstanceSegmentation, Mesh, InstanceSegmentationMask)", + description="The shape of the annotation (SegmentationMask, OrientedPoint, Point, InstanceSegmentation, Mesh, InstanceSegmentationMask, GlobalCaption)", default=None, ) id: int = strawberry.field(description="Numeric identifier (May change!)") @@ -324,7 +324,7 @@ class AnnotationShapeUpdateInput: description="Metadata about an shapes for an annotation", default=None, ) shape_type: Optional[annotation_file_shape_type_enum] = strawberry.field( - description="The shape of the annotation (SegmentationMask, OrientedPoint, Point, InstanceSegmentation, Mesh, InstanceSegmentationMask)", + description="The shape of the annotation (SegmentationMask, OrientedPoint, Point, InstanceSegmentation, Mesh, InstanceSegmentationMask, GlobalCaption)", default=None, ) id: Optional[int] = strawberry.field(description="Numeric identifier (May change!)") diff --git a/apiv2/schema/schema.yaml b/apiv2/schema/schema.yaml index 92068187d..2a44f550a 100644 --- a/apiv2/schema/schema.yaml +++ b/apiv2/schema/schema.yaml @@ -285,6 +285,9 @@ enums: Mesh: text: Mesh description: A surface mesh volumes + GlobalCaption: + text: GlobalCaption + description: A text caption for the tomogram annotation_method_link_type_enum: name: annotation_method_link_type_enum description: Describes the type of link associated to the annotation method. @@ -925,11 +928,11 @@ classes: annotations: cascade_delete: true shape_type: - description: The shape of the annotation (SegmentationMask, OrientedPoint, Point, InstanceSegmentation, Mesh, InstanceSegmentationMask) + description: The shape of the annotation (SegmentationMask, OrientedPoint, Point, InstanceSegmentation, Mesh, InstanceSegmentationMask, GlobalCaption) name: shape_type from_schema: cdp-dataset-config range: annotation_file_shape_type_enum - pattern: (^SegmentationMask$)|(^OrientedPoint$)|(^Point$)|(^InstanceSegmentation$)|(^Mesh$)|(^InstanceSegmentationMask$) + pattern: (^SegmentationMask$)|(^OrientedPoint$)|(^Point$)|(^InstanceSegmentation$)|(^Mesh$)|(^InstanceSegmentationMask$)|(^GlobalCaption$) Annotation: name: Annotation annotations: diff --git a/apiv2/support/enums.py b/apiv2/support/enums.py index f281dcaf4..94937ad70 100644 --- a/apiv2/support/enums.py +++ b/apiv2/support/enums.py @@ -40,6 +40,7 @@ class annotation_file_shape_type_enum(enum.StrEnum): InstanceSegmentation = "InstanceSegmentation" InstanceSegmentationMask = "InstanceSegmentationMask" Mesh = "Mesh" + GlobalCaption = "GlobalCaption" @strawberry.enum diff --git a/apiv2/test_infra/factories/annotation_shape.py b/apiv2/test_infra/factories/annotation_shape.py index 6de536ad4..0209fedb0 100644 --- a/apiv2/test_infra/factories/annotation_shape.py +++ b/apiv2/test_infra/factories/annotation_shape.py @@ -33,7 +33,15 @@ class Meta: AnnotationFactory, ) shape_type = fuzzy.FuzzyChoice( - ["SegmentationMask", "OrientedPoint", "Point", "InstanceSegmentation", "InstanceSegmentationMask", "Mesh"], + [ + "SegmentationMask", + "OrientedPoint", + "Point", + "InstanceSegmentation", + "InstanceSegmentationMask", + "Mesh", + "GlobalCaption", + ], ) # Auto increment integer identifiers starting with 1 diff --git a/test_infra/test_files/30001/RUN1/Reconstructions/VoxelSpacing12.300/Annotations/100/foo-1.0.json b/test_infra/test_files/30001/RUN1/Reconstructions/VoxelSpacing12.300/Annotations/100/foo-1.0.json index 46ea06db4..847ad3459 100644 --- a/test_infra/test_files/30001/RUN1/Reconstructions/VoxelSpacing12.300/Annotations/100/foo-1.0.json +++ b/test_infra/test_files/30001/RUN1/Reconstructions/VoxelSpacing12.300/Annotations/100/foo-1.0.json @@ -66,6 +66,12 @@ "path": "30001/RUN1/Reconstructions/VoxelSpacing12.300/Annotations/100-foo-1.0_instancesegmask.zarr", "shape": "InstanceSegmentationMask", "is_visualization_default": false + }, + { + "format": "json", + "path": "30001/RUN1/Reconstructions/VoxelSpacing12.300/Annotations/100-foo-1.0_globalcaption.json", + "shape": "GlobalCaption", + "is_visualization_default": false } ], "method_links": [ From 03941a67a422dbc0041377047cb5a82a70b16d9a Mon Sep 17 00:00:00 2001 From: Jinghui Geng Date: Mon, 16 Mar 2026 16:26:00 -0700 Subject: [PATCH 2/6] remove typo --- apiv2/README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/apiv2/README.md b/apiv2/README.md index d047c6c65..4d90d75ee 100644 --- a/apiv2/README.md +++ b/apiv2/README.md @@ -1,4 +1,4 @@ -Did# Getting started +# Getting started ``` make apiv2-init # from the root of the repo From 7a2b02a9f7d603b52602aaf6e091faaa730f219c Mon Sep 17 00:00:00 2001 From: Jinghui Geng Date: Mon, 16 Mar 2026 16:28:57 -0700 Subject: [PATCH 3/6] update --- apiv2/graphql_api/schema.graphql | 7189 ++++++++++++++++++++++++++++++ 1 file changed, 7189 insertions(+) diff --git a/apiv2/graphql_api/schema.graphql b/apiv2/graphql_api/schema.graphql index e69de29bb..9ac2c95fa 100644 --- a/apiv2/graphql_api/schema.graphql +++ b/apiv2/graphql_api/schema.graphql @@ -0,0 +1,7189 @@ +"""Tiltseries Alignment""" +type Alignment implements EntityInterface & Node { + """The Globally Unique ID of this object""" + _id: GlobalID! + + """Numeric identifier (May change!)""" + id: Int! + annotationFiles( + where: AnnotationFileWhereClause = null + orderBy: [AnnotationFileOrderByClause!] = [] + + """Returns the items in the list that come before the specified cursor.""" + before: String = null + + """Returns the items in the list that come after the specified cursor.""" + after: String = null + + """Returns the first n items from the list.""" + first: Int = null + + """Returns the items in the list that come after the specified cursor.""" + last: Int = null + ): AnnotationFileConnection! + annotationFilesAggregate(where: AnnotationFileWhereClause = null): AnnotationFileAggregate + perSectionAlignments( + where: PerSectionAlignmentParametersWhereClause = null + orderBy: [PerSectionAlignmentParametersOrderByClause!] = [] + + """Returns the items in the list that come before the specified cursor.""" + before: String = null + + """Returns the items in the list that come after the specified cursor.""" + after: String = null + + """Returns the first n items from the list.""" + first: Int = null + + """Returns the items in the list that come after the specified cursor.""" + last: Int = null + ): PerSectionAlignmentParametersConnection! + perSectionAlignmentsAggregate(where: PerSectionAlignmentParametersWhereClause = null): PerSectionAlignmentParametersAggregate + deposition(where: DepositionWhereClause = null, orderBy: [DepositionOrderByClause!] = []): Deposition + depositionId: Int + tiltseries(where: TiltseriesWhereClause = null, orderBy: [TiltseriesOrderByClause!] = []): Tiltseries + tiltseriesId: Int + tomograms( + where: TomogramWhereClause = null + orderBy: [TomogramOrderByClause!] = [] + + """Returns the items in the list that come before the specified cursor.""" + before: String = null + + """Returns the items in the list that come after the specified cursor.""" + after: String = null + + """Returns the first n items from the list.""" + first: Int = null + + """Returns the items in the list that come after the specified cursor.""" + last: Int = null + ): TomogramConnection! + tomogramsAggregate(where: TomogramWhereClause = null): TomogramAggregate + run(where: RunWhereClause = null, orderBy: [RunOrderByClause!] = []): Run + runId: Int + + """Whether this a LOCAL or GLOBAL alignment""" + alignmentType: alignment_type_enum + + """The method used to create this alignment""" + alignmentMethod: alignment_method_type_enum + + """X dimension of the reconstruction volume in angstrom""" + volumeXDimension: Float + + """Y dimension of the reconstruction volume in angstrom""" + volumeYDimension: Float + + """Z dimension of the reconstruction volume in angstrom""" + volumeZDimension: Float + + """X shift of the reconstruction volume in angstrom""" + volumeXOffset: Float + + """Y shift of the reconstruction volume in angstrom""" + volumeYOffset: Float + + """Z shift of the reconstruction volume in angstrom""" + volumeZOffset: Float + + """Additional X rotation of the reconstruction volume in degrees""" + xRotationOffset: Float + + """Additional tilt offset in degrees""" + tiltOffset: Float + + """A placeholder for the affine transformation matrix.""" + affineTransformationMatrix: String + + """S3 path to the metadata file for this alignment""" + s3AlignmentMetadata: String + + """HTTPS url to the metadata file for this alignment""" + httpsAlignmentMetadata: String + + """Whether this is the portal standard alignment""" + isPortalStandard: Boolean +} + +type AlignmentAggregate { + aggregate: [AlignmentAggregateFunctions!] +} + +type AlignmentAggregateFunctions { + sum: AlignmentNumericalColumns + avg: AlignmentNumericalColumns + stddev: AlignmentNumericalColumns + variance: AlignmentNumericalColumns + min: AlignmentMinMaxColumns + max: AlignmentMinMaxColumns + groupBy: AlignmentGroupByOptions + count(distinct: Boolean = false, columns: AlignmentCountColumns = null): Int +} + +input AlignmentAggregateWhereClause { + count: AlignmentAggregateWhereClauseCount! +} + +input AlignmentAggregateWhereClauseCount { + arguments: AlignmentCountColumns + distinct: Boolean + filter: AlignmentWhereClause + predicate: IntComparators +} + +"""A connection to a list of items.""" +type AlignmentConnection { + """Pagination data for this connection""" + pageInfo: PageInfo! + + """Contains the nodes in this connection""" + edges: [AlignmentEdge!]! +} + +enum AlignmentCountColumns { + alignmentType + alignmentMethod + volumeXDimension + volumeYDimension + volumeZDimension + volumeXOffset + volumeYOffset + volumeZOffset + xRotationOffset + tiltOffset + affineTransformationMatrix + s3AlignmentMetadata + httpsAlignmentMetadata + isPortalStandard + id +} + +input AlignmentCreateInput { + depositionId: ID = null + tiltseriesId: ID = null + runId: ID = null + + """Whether this a LOCAL or GLOBAL alignment""" + alignmentType: alignment_type_enum = null + + """The method used to create this alignment""" + alignmentMethod: alignment_method_type_enum = null + + """X dimension of the reconstruction volume in angstrom""" + volumeXDimension: Float = null + + """Y dimension of the reconstruction volume in angstrom""" + volumeYDimension: Float = null + + """Z dimension of the reconstruction volume in angstrom""" + volumeZDimension: Float = null + + """X shift of the reconstruction volume in angstrom""" + volumeXOffset: Float = null + + """Y shift of the reconstruction volume in angstrom""" + volumeYOffset: Float = null + + """Z shift of the reconstruction volume in angstrom""" + volumeZOffset: Float = null + + """Additional X rotation of the reconstruction volume in degrees""" + xRotationOffset: Float = null + + """Additional tilt offset in degrees""" + tiltOffset: Float = null + + """A placeholder for the affine transformation matrix.""" + affineTransformationMatrix: String = null + + """S3 path to the metadata file for this alignment""" + s3AlignmentMetadata: String = null + + """HTTPS url to the metadata file for this alignment""" + httpsAlignmentMetadata: String = null + + """Whether this is the portal standard alignment""" + isPortalStandard: Boolean = null + + """Numeric identifier (May change!)""" + id: Int! +} + +"""An edge in a connection.""" +type AlignmentEdge { + """A cursor for use in pagination""" + cursor: String! + + """The item at the end of the edge""" + node: Alignment! +} + +type AlignmentGroupByOptions { + annotationFiles: AnnotationFileGroupByOptions + perSectionAlignments: PerSectionAlignmentParametersGroupByOptions + deposition: DepositionGroupByOptions + tiltseries: TiltseriesGroupByOptions + tomograms: TomogramGroupByOptions + run: RunGroupByOptions + alignmentType: alignment_type_enum + alignmentMethod: alignment_method_type_enum + volumeXDimension: Float + volumeYDimension: Float + volumeZDimension: Float + volumeXOffset: Float + volumeYOffset: Float + volumeZOffset: Float + xRotationOffset: Float + tiltOffset: Float + affineTransformationMatrix: String + s3AlignmentMetadata: String + httpsAlignmentMetadata: String + isPortalStandard: Boolean + id: Int +} + +type AlignmentMinMaxColumns { + volumeXDimension: Float + volumeYDimension: Float + volumeZDimension: Float + volumeXOffset: Float + volumeYOffset: Float + volumeZOffset: Float + xRotationOffset: Float + tiltOffset: Float + affineTransformationMatrix: String + s3AlignmentMetadata: String + httpsAlignmentMetadata: String + id: Int +} + +type AlignmentNumericalColumns { + volumeXDimension: Float + volumeYDimension: Float + volumeZDimension: Float + volumeXOffset: Float + volumeYOffset: Float + volumeZOffset: Float + xRotationOffset: Float + tiltOffset: Float + id: Int +} + +input AlignmentOrderByClause { + deposition: DepositionOrderByClause + tiltseries: TiltseriesOrderByClause + run: RunOrderByClause + alignmentType: orderBy + alignmentMethod: orderBy + volumeXDimension: orderBy + volumeYDimension: orderBy + volumeZDimension: orderBy + volumeXOffset: orderBy + volumeYOffset: orderBy + volumeZOffset: orderBy + xRotationOffset: orderBy + tiltOffset: orderBy + affineTransformationMatrix: orderBy + s3AlignmentMetadata: orderBy + httpsAlignmentMetadata: orderBy + isPortalStandard: orderBy + id: orderBy +} + +input AlignmentUpdateInput { + depositionId: ID = null + tiltseriesId: ID = null + runId: ID = null + + """Whether this a LOCAL or GLOBAL alignment""" + alignmentType: alignment_type_enum = null + + """The method used to create this alignment""" + alignmentMethod: alignment_method_type_enum = null + + """X dimension of the reconstruction volume in angstrom""" + volumeXDimension: Float = null + + """Y dimension of the reconstruction volume in angstrom""" + volumeYDimension: Float = null + + """Z dimension of the reconstruction volume in angstrom""" + volumeZDimension: Float = null + + """X shift of the reconstruction volume in angstrom""" + volumeXOffset: Float = null + + """Y shift of the reconstruction volume in angstrom""" + volumeYOffset: Float = null + + """Z shift of the reconstruction volume in angstrom""" + volumeZOffset: Float = null + + """Additional X rotation of the reconstruction volume in degrees""" + xRotationOffset: Float = null + + """Additional tilt offset in degrees""" + tiltOffset: Float = null + + """A placeholder for the affine transformation matrix.""" + affineTransformationMatrix: String = null + + """S3 path to the metadata file for this alignment""" + s3AlignmentMetadata: String = null + + """HTTPS url to the metadata file for this alignment""" + httpsAlignmentMetadata: String = null + + """Whether this is the portal standard alignment""" + isPortalStandard: Boolean = null + + """Numeric identifier (May change!)""" + id: Int +} + +input AlignmentWhereClause { + annotationFiles: AnnotationFileWhereClause + annotationFilesAggregate: AnnotationFileAggregateWhereClause + perSectionAlignments: PerSectionAlignmentParametersWhereClause + perSectionAlignmentsAggregate: PerSectionAlignmentParametersAggregateWhereClause + deposition: DepositionWhereClause + depositionId: IntComparators + tiltseries: TiltseriesWhereClause + tiltseriesId: IntComparators + tomograms: TomogramWhereClause + tomogramsAggregate: TomogramAggregateWhereClause + run: RunWhereClause + runId: IntComparators + alignmentType: Alignment_type_enumEnumComparators + alignmentMethod: Alignment_method_type_enumEnumComparators + volumeXDimension: FloatComparators + volumeYDimension: FloatComparators + volumeZDimension: FloatComparators + volumeXOffset: FloatComparators + volumeYOffset: FloatComparators + volumeZOffset: FloatComparators + xRotationOffset: FloatComparators + tiltOffset: FloatComparators + affineTransformationMatrix: StrComparators + s3AlignmentMetadata: StrComparators + httpsAlignmentMetadata: StrComparators + isPortalStandard: BoolComparators + id: IntComparators +} + +input AlignmentWhereClauseMutations { + id: IntComparators +} + +input Alignment_method_type_enumEnumComparators { + _eq: alignment_method_type_enum + _neq: alignment_method_type_enum + _in: [alignment_method_type_enum!] + _nin: [alignment_method_type_enum!] + _gt: alignment_method_type_enum + _gte: alignment_method_type_enum + _lt: alignment_method_type_enum + _lte: alignment_method_type_enum + _is_null: Boolean +} + +input Alignment_type_enumEnumComparators { + _eq: alignment_type_enum + _neq: alignment_type_enum + _in: [alignment_type_enum!] + _nin: [alignment_type_enum!] + _gt: alignment_type_enum + _gte: alignment_type_enum + _lt: alignment_type_enum + _lte: alignment_type_enum + _is_null: Boolean +} + +"""Metadata for an annotation""" +type Annotation implements EntityInterface & Node { + """The Globally Unique ID of this object""" + _id: GlobalID! + + """Numeric identifier (May change!)""" + id: Int! + run(where: RunWhereClause = null, orderBy: [RunOrderByClause!] = []): Run + runId: Int + annotationShapes( + where: AnnotationShapeWhereClause = null + orderBy: [AnnotationShapeOrderByClause!] = [] + + """Returns the items in the list that come before the specified cursor.""" + before: String = null + + """Returns the items in the list that come after the specified cursor.""" + after: String = null + + """Returns the first n items from the list.""" + first: Int = null + + """Returns the items in the list that come after the specified cursor.""" + last: Int = null + ): AnnotationShapeConnection! + annotationShapesAggregate(where: AnnotationShapeWhereClause = null): AnnotationShapeAggregate + methodLinks( + where: AnnotationMethodLinkWhereClause = null + orderBy: [AnnotationMethodLinkOrderByClause!] = [] + + """Returns the items in the list that come before the specified cursor.""" + before: String = null + + """Returns the items in the list that come after the specified cursor.""" + after: String = null + + """Returns the first n items from the list.""" + first: Int = null + + """Returns the items in the list that come after the specified cursor.""" + last: Int = null + ): AnnotationMethodLinkConnection! + methodLinksAggregate(where: AnnotationMethodLinkWhereClause = null): AnnotationMethodLinkAggregate + authors( + where: AnnotationAuthorWhereClause = null + orderBy: [AnnotationAuthorOrderByClause!] = [] + + """Returns the items in the list that come before the specified cursor.""" + before: String = null + + """Returns the items in the list that come after the specified cursor.""" + after: String = null + + """Returns the first n items from the list.""" + first: Int = null + + """Returns the items in the list that come after the specified cursor.""" + last: Int = null + ): AnnotationAuthorConnection! + authorsAggregate(where: AnnotationAuthorWhereClause = null): AnnotationAuthorAggregate + deposition(where: DepositionWhereClause = null, orderBy: [DepositionOrderByClause!] = []): Deposition + depositionId: Int + + """S3 path for the metadata json file for this annotation""" + s3MetadataPath: String! + + """HTTPS path for the metadata json file for this annotation""" + httpsMetadataPath: String! + + """ + DOIs for publications that describe the dataset. Use a comma to separate multiple DOIs. + """ + annotationPublication: String + + """ + Describe how the annotation is made (e.g. Manual, crYoLO, Positive Unlabeled Learning, template matching) + """ + annotationMethod: String! + + """An identifier for the annotation to be used during ingestion.""" + annotationIngestId: String + + """ + Whether an annotation is considered ground truth, as determined by the annotator. + """ + groundTruthStatus: Boolean + + """Ontology identifier for the annotation object.""" + objectId: String! + + """ + Name of the object being annotated (e.g. ribosome, nuclear pore complex, actin filament, membrane) + """ + objectName: String! + + """ + A textual description of the annotation object, can be a longer description to include additional information not covered by the Annotation object name and state. + """ + objectDescription: String + + """Molecule state annotated (e.g. open, closed)""" + objectState: String + + """Number of objects identified""" + objectCount: Int + + """ + Describe the confidence level of the annotation. Precision is defined as the % of annotation objects being true positive + """ + confidencePrecision: Float + + """ + Describe the confidence level of the annotation. Recall is defined as the % of true positives being annotated correctly + """ + confidenceRecall: Float + + """Annotation filename used as ground truth for precision and recall""" + groundTruthUsed: String + + """Software used for generating this annotation""" + annotationSoftware: String + + """ + Data curator’s subjective choice as the best annotation of the same annotation object ID + """ + isCuratorRecommended: Boolean + + """ + The method type for generating the annotation (e.g. manual, hybrid, automated) + """ + methodType: annotation_method_type_enum! + + """Date when an annotation set is initially received by the Data Portal.""" + depositionDate: DateTime! + + """Date when annotation data is made public by the Data Portal.""" + releaseDate: DateTime! + + """Date when an annotation was last modified in the Data Portal""" + lastModifiedDate: DateTime! +} + +type AnnotationAggregate { + aggregate: [AnnotationAggregateFunctions!] +} + +type AnnotationAggregateFunctions { + sum: AnnotationNumericalColumns + avg: AnnotationNumericalColumns + stddev: AnnotationNumericalColumns + variance: AnnotationNumericalColumns + min: AnnotationMinMaxColumns + max: AnnotationMinMaxColumns + groupBy: AnnotationGroupByOptions + count(distinct: Boolean = false, columns: AnnotationCountColumns = null): Int +} + +input AnnotationAggregateWhereClause { + count: AnnotationAggregateWhereClauseCount! +} + +input AnnotationAggregateWhereClauseCount { + arguments: AnnotationCountColumns + distinct: Boolean + filter: AnnotationWhereClause + predicate: IntComparators +} + +"""Metadata for an annotation's authors""" +type AnnotationAuthor implements EntityInterface & Node { + """The Globally Unique ID of this object""" + _id: GlobalID! + + """Numeric identifier (May change!)""" + id: Int! + annotation(where: AnnotationWhereClause = null, orderBy: [AnnotationOrderByClause!] = []): Annotation + annotationId: Int + + """The order in which the author appears in the publication""" + authorListOrder: Int! + + """A unique, persistent identifier for researchers, provided by ORCID.""" + orcid: String + + """A unique, persistent identifier for kaggle users at kaggle.com.""" + kaggleId: String + + """Full name of an annotation author (e.g. Jane Doe).""" + name: String! + + """Email address for this author""" + email: String + + """ + Name of the institution an annotator is affiliated with. Sometimes, one annotator may have multiple affiliations. + """ + affiliationName: String + + """Address of the institution an annotator is affiliated with.""" + affiliationAddress: String + + """ + A unique identifier assigned to the affiliated institution by The Research Organization Registry (ROR). + """ + affiliationIdentifier: String + + """Indicates whether an annotator is the corresponding author""" + correspondingAuthorStatus: Boolean + + """ + Indicates whether an author is the main person executing the annotation, especially on manual annotation + """ + primaryAuthorStatus: Boolean +} + +type AnnotationAuthorAggregate { + aggregate: [AnnotationAuthorAggregateFunctions!] +} + +type AnnotationAuthorAggregateFunctions { + sum: AnnotationAuthorNumericalColumns + avg: AnnotationAuthorNumericalColumns + stddev: AnnotationAuthorNumericalColumns + variance: AnnotationAuthorNumericalColumns + min: AnnotationAuthorMinMaxColumns + max: AnnotationAuthorMinMaxColumns + groupBy: AnnotationAuthorGroupByOptions + count(distinct: Boolean = false, columns: AnnotationAuthorCountColumns = null): Int +} + +input AnnotationAuthorAggregateWhereClause { + count: AnnotationAuthorAggregateWhereClauseCount! +} + +input AnnotationAuthorAggregateWhereClauseCount { + arguments: AnnotationAuthorCountColumns + distinct: Boolean + filter: AnnotationAuthorWhereClause + predicate: IntComparators +} + +"""A connection to a list of items.""" +type AnnotationAuthorConnection { + """Pagination data for this connection""" + pageInfo: PageInfo! + + """Contains the nodes in this connection""" + edges: [AnnotationAuthorEdge!]! +} + +enum AnnotationAuthorCountColumns { + id + authorListOrder + orcid + kaggleId + name + email + affiliationName + affiliationAddress + affiliationIdentifier + correspondingAuthorStatus + primaryAuthorStatus +} + +input AnnotationAuthorCreateInput { + """Reference to the annotation this author contributed to""" + annotationId: ID = null + + """Numeric identifier (May change!)""" + id: Int! + + """The order in which the author appears in the publication""" + authorListOrder: Int! + + """A unique, persistent identifier for researchers, provided by ORCID.""" + orcid: String = null + + """A unique, persistent identifier for kaggle users at kaggle.com.""" + kaggleId: String = null + + """Full name of an annotation author (e.g. Jane Doe).""" + name: String! + + """Email address for this author""" + email: String = null + + """ + Name of the institution an annotator is affiliated with. Sometimes, one annotator may have multiple affiliations. + """ + affiliationName: String = null + + """Address of the institution an annotator is affiliated with.""" + affiliationAddress: String = null + + """ + A unique identifier assigned to the affiliated institution by The Research Organization Registry (ROR). + """ + affiliationIdentifier: String = null + + """Indicates whether an annotator is the corresponding author""" + correspondingAuthorStatus: Boolean = null + + """ + Indicates whether an author is the main person executing the annotation, especially on manual annotation + """ + primaryAuthorStatus: Boolean = null +} + +"""An edge in a connection.""" +type AnnotationAuthorEdge { + """A cursor for use in pagination""" + cursor: String! + + """The item at the end of the edge""" + node: AnnotationAuthor! +} + +type AnnotationAuthorGroupByOptions { + annotation: AnnotationGroupByOptions + id: Int + authorListOrder: Int + orcid: String + kaggleId: String + name: String + email: String + affiliationName: String + affiliationAddress: String + affiliationIdentifier: String + correspondingAuthorStatus: Boolean + primaryAuthorStatus: Boolean +} + +type AnnotationAuthorMinMaxColumns { + id: Int + authorListOrder: Int + orcid: String + kaggleId: String + name: String + email: String + affiliationName: String + affiliationAddress: String + affiliationIdentifier: String +} + +type AnnotationAuthorNumericalColumns { + id: Int + authorListOrder: Int +} + +input AnnotationAuthorOrderByClause { + annotation: AnnotationOrderByClause + id: orderBy + authorListOrder: orderBy + orcid: orderBy + kaggleId: orderBy + name: orderBy + email: orderBy + affiliationName: orderBy + affiliationAddress: orderBy + affiliationIdentifier: orderBy + correspondingAuthorStatus: orderBy + primaryAuthorStatus: orderBy +} + +input AnnotationAuthorUpdateInput { + """Reference to the annotation this author contributed to""" + annotationId: ID = null + + """Numeric identifier (May change!)""" + id: Int + + """The order in which the author appears in the publication""" + authorListOrder: Int + + """A unique, persistent identifier for researchers, provided by ORCID.""" + orcid: String = null + + """A unique, persistent identifier for kaggle users at kaggle.com.""" + kaggleId: String = null + + """Full name of an annotation author (e.g. Jane Doe).""" + name: String + + """Email address for this author""" + email: String = null + + """ + Name of the institution an annotator is affiliated with. Sometimes, one annotator may have multiple affiliations. + """ + affiliationName: String = null + + """Address of the institution an annotator is affiliated with.""" + affiliationAddress: String = null + + """ + A unique identifier assigned to the affiliated institution by The Research Organization Registry (ROR). + """ + affiliationIdentifier: String = null + + """Indicates whether an annotator is the corresponding author""" + correspondingAuthorStatus: Boolean = null + + """ + Indicates whether an author is the main person executing the annotation, especially on manual annotation + """ + primaryAuthorStatus: Boolean = null +} + +input AnnotationAuthorWhereClause { + annotation: AnnotationWhereClause + annotationId: IntComparators + id: IntComparators + authorListOrder: IntComparators + orcid: StrComparators + kaggleId: StrComparators + name: StrComparators + email: StrComparators + affiliationName: StrComparators + affiliationAddress: StrComparators + affiliationIdentifier: StrComparators + correspondingAuthorStatus: BoolComparators + primaryAuthorStatus: BoolComparators +} + +input AnnotationAuthorWhereClauseMutations { + id: IntComparators +} + +"""A connection to a list of items.""" +type AnnotationConnection { + """Pagination data for this connection""" + pageInfo: PageInfo! + + """Contains the nodes in this connection""" + edges: [AnnotationEdge!]! +} + +enum AnnotationCountColumns { + s3MetadataPath + httpsMetadataPath + annotationPublication + annotationMethod + annotationIngestId + groundTruthStatus + objectId + objectName + objectDescription + objectState + objectCount + confidencePrecision + confidenceRecall + groundTruthUsed + annotationSoftware + isCuratorRecommended + methodType + depositionDate + releaseDate + lastModifiedDate + id +} + +input AnnotationCreateInput { + runId: ID = null + depositionId: ID = null + + """S3 path for the metadata json file for this annotation""" + s3MetadataPath: String! + + """HTTPS path for the metadata json file for this annotation""" + httpsMetadataPath: String! + + """ + DOIs for publications that describe the dataset. Use a comma to separate multiple DOIs. + """ + annotationPublication: String = null + + """ + Describe how the annotation is made (e.g. Manual, crYoLO, Positive Unlabeled Learning, template matching) + """ + annotationMethod: String! + + """An identifier for the annotation to be used during ingestion.""" + annotationIngestId: String = null + + """ + Whether an annotation is considered ground truth, as determined by the annotator. + """ + groundTruthStatus: Boolean = null + + """Ontology identifier for the annotation object.""" + objectId: String! + + """ + Name of the object being annotated (e.g. ribosome, nuclear pore complex, actin filament, membrane) + """ + objectName: String! + + """ + A textual description of the annotation object, can be a longer description to include additional information not covered by the Annotation object name and state. + """ + objectDescription: String = null + + """Molecule state annotated (e.g. open, closed)""" + objectState: String = null + + """Number of objects identified""" + objectCount: Int = null + + """ + Describe the confidence level of the annotation. Precision is defined as the % of annotation objects being true positive + """ + confidencePrecision: Float = null + + """ + Describe the confidence level of the annotation. Recall is defined as the % of true positives being annotated correctly + """ + confidenceRecall: Float = null + + """Annotation filename used as ground truth for precision and recall""" + groundTruthUsed: String = null + + """Software used for generating this annotation""" + annotationSoftware: String = null + + """ + Data curator’s subjective choice as the best annotation of the same annotation object ID + """ + isCuratorRecommended: Boolean = null + + """ + The method type for generating the annotation (e.g. manual, hybrid, automated) + """ + methodType: annotation_method_type_enum! + + """Date when an annotation set is initially received by the Data Portal.""" + depositionDate: DateTime! + + """Date when annotation data is made public by the Data Portal.""" + releaseDate: DateTime! + + """Date when an annotation was last modified in the Data Portal""" + lastModifiedDate: DateTime! + + """Numeric identifier (May change!)""" + id: Int! +} + +"""An edge in a connection.""" +type AnnotationEdge { + """A cursor for use in pagination""" + cursor: String! + + """The item at the end of the edge""" + node: Annotation! +} + +"""Metadata for files associated with an annotation""" +type AnnotationFile implements EntityInterface & Node { + """The Globally Unique ID of this object""" + _id: GlobalID! + + """Numeric identifier (May change!)""" + id: Int! + alignment(where: AlignmentWhereClause = null, orderBy: [AlignmentOrderByClause!] = []): Alignment + alignmentId: Int + annotationShape(where: AnnotationShapeWhereClause = null, orderBy: [AnnotationShapeOrderByClause!] = []): AnnotationShape + annotationShapeId: Int + tomogramVoxelSpacing(where: TomogramVoxelSpacingWhereClause = null, orderBy: [TomogramVoxelSpacingOrderByClause!] = []): TomogramVoxelSpacing + tomogramVoxelSpacingId: Int + + """File format for this file""" + format: String! + + """s3 path of the annotation file""" + s3Path: String! + + """Size of annota file in bytes""" + fileSize: Float + + """HTTPS path for this annotation file""" + httpsPath: String! + + """ + Data curator’s subjective choice of default annotation to display in visualization for an object + """ + isVisualizationDefault: Boolean + + """ + The source type for the annotation file (dataset_author, community, or portal_standard) + """ + source: annotation_file_source_enum +} + +type AnnotationFileAggregate { + aggregate: [AnnotationFileAggregateFunctions!] +} + +type AnnotationFileAggregateFunctions { + sum: AnnotationFileNumericalColumns + avg: AnnotationFileNumericalColumns + stddev: AnnotationFileNumericalColumns + variance: AnnotationFileNumericalColumns + min: AnnotationFileMinMaxColumns + max: AnnotationFileMinMaxColumns + groupBy: AnnotationFileGroupByOptions + count(distinct: Boolean = false, columns: AnnotationFileCountColumns = null): Int +} + +input AnnotationFileAggregateWhereClause { + count: AnnotationFileAggregateWhereClauseCount! +} + +input AnnotationFileAggregateWhereClauseCount { + arguments: AnnotationFileCountColumns + distinct: Boolean + filter: AnnotationFileWhereClause + predicate: IntComparators +} + +"""A connection to a list of items.""" +type AnnotationFileConnection { + """Pagination data for this connection""" + pageInfo: PageInfo! + + """Contains the nodes in this connection""" + edges: [AnnotationFileEdge!]! +} + +enum AnnotationFileCountColumns { + format + s3Path + fileSize + httpsPath + isVisualizationDefault + source + id +} + +input AnnotationFileCreateInput { + """Tiltseries Alignment""" + alignmentId: ID = null + + """Shapes associated with an annotation""" + annotationShapeId: ID = null + + """Voxel spacing that this annotation file is associated with""" + tomogramVoxelSpacingId: ID = null + + """File format for this file""" + format: String! + + """s3 path of the annotation file""" + s3Path: String! + + """Size of annota file in bytes""" + fileSize: Float = null + + """HTTPS path for this annotation file""" + httpsPath: String! + + """ + Data curator’s subjective choice of default annotation to display in visualization for an object + """ + isVisualizationDefault: Boolean = null + + """ + The source type for the annotation file (dataset_author, community, or portal_standard) + """ + source: annotation_file_source_enum = null + + """Numeric identifier (May change!)""" + id: Int! +} + +"""An edge in a connection.""" +type AnnotationFileEdge { + """A cursor for use in pagination""" + cursor: String! + + """The item at the end of the edge""" + node: AnnotationFile! +} + +type AnnotationFileGroupByOptions { + alignment: AlignmentGroupByOptions + annotationShape: AnnotationShapeGroupByOptions + tomogramVoxelSpacing: TomogramVoxelSpacingGroupByOptions + format: String + s3Path: String + fileSize: Float + httpsPath: String + isVisualizationDefault: Boolean + source: annotation_file_source_enum + id: Int +} + +type AnnotationFileMinMaxColumns { + format: String + s3Path: String + fileSize: Float + httpsPath: String + id: Int +} + +type AnnotationFileNumericalColumns { + fileSize: Float + id: Int +} + +input AnnotationFileOrderByClause { + alignment: AlignmentOrderByClause + annotationShape: AnnotationShapeOrderByClause + tomogramVoxelSpacing: TomogramVoxelSpacingOrderByClause + format: orderBy + s3Path: orderBy + fileSize: orderBy + httpsPath: orderBy + isVisualizationDefault: orderBy + source: orderBy + id: orderBy +} + +input AnnotationFileUpdateInput { + """Tiltseries Alignment""" + alignmentId: ID = null + + """Shapes associated with an annotation""" + annotationShapeId: ID = null + + """Voxel spacing that this annotation file is associated with""" + tomogramVoxelSpacingId: ID = null + + """File format for this file""" + format: String + + """s3 path of the annotation file""" + s3Path: String + + """Size of annota file in bytes""" + fileSize: Float = null + + """HTTPS path for this annotation file""" + httpsPath: String + + """ + Data curator’s subjective choice of default annotation to display in visualization for an object + """ + isVisualizationDefault: Boolean = null + + """ + The source type for the annotation file (dataset_author, community, or portal_standard) + """ + source: annotation_file_source_enum = null + + """Numeric identifier (May change!)""" + id: Int +} + +input AnnotationFileWhereClause { + alignment: AlignmentWhereClause + alignmentId: IntComparators + annotationShape: AnnotationShapeWhereClause + annotationShapeId: IntComparators + tomogramVoxelSpacing: TomogramVoxelSpacingWhereClause + tomogramVoxelSpacingId: IntComparators + format: StrComparators + s3Path: StrComparators + fileSize: FloatComparators + httpsPath: StrComparators + isVisualizationDefault: BoolComparators + source: Annotation_file_source_enumEnumComparators + id: IntComparators +} + +input AnnotationFileWhereClauseMutations { + id: IntComparators +} + +type AnnotationGroupByOptions { + run: RunGroupByOptions + annotationShapes: AnnotationShapeGroupByOptions + methodLinks: AnnotationMethodLinkGroupByOptions + authors: AnnotationAuthorGroupByOptions + deposition: DepositionGroupByOptions + s3MetadataPath: String + httpsMetadataPath: String + annotationPublication: String + annotationMethod: String + annotationIngestId: String + groundTruthStatus: Boolean + objectId: String + objectName: String + objectDescription: String + objectState: String + objectCount: Int + confidencePrecision: Float + confidenceRecall: Float + groundTruthUsed: String + annotationSoftware: String + isCuratorRecommended: Boolean + methodType: annotation_method_type_enum + depositionDate: DateTime + releaseDate: DateTime + lastModifiedDate: DateTime + id: Int +} + +""" +A set of links to models, source code, documentation, etc referenced by annotation method +""" +type AnnotationMethodLink implements EntityInterface & Node { + """The Globally Unique ID of this object""" + _id: GlobalID! + + """Numeric identifier (May change!)""" + id: Int! + annotation(where: AnnotationWhereClause = null, orderBy: [AnnotationOrderByClause!] = []): Annotation + annotationId: Int + + """Type of link (e.g. model, source code, documentation)""" + linkType: annotation_method_link_type_enum! + + """user readable name of the resource""" + name: String + + """URL to the resource""" + link: String! +} + +type AnnotationMethodLinkAggregate { + aggregate: [AnnotationMethodLinkAggregateFunctions!] +} + +type AnnotationMethodLinkAggregateFunctions { + sum: AnnotationMethodLinkNumericalColumns + avg: AnnotationMethodLinkNumericalColumns + stddev: AnnotationMethodLinkNumericalColumns + variance: AnnotationMethodLinkNumericalColumns + min: AnnotationMethodLinkMinMaxColumns + max: AnnotationMethodLinkMinMaxColumns + groupBy: AnnotationMethodLinkGroupByOptions + count(distinct: Boolean = false, columns: AnnotationMethodLinkCountColumns = null): Int +} + +input AnnotationMethodLinkAggregateWhereClause { + count: AnnotationMethodLinkAggregateWhereClauseCount! +} + +input AnnotationMethodLinkAggregateWhereClauseCount { + arguments: AnnotationMethodLinkCountColumns + distinct: Boolean + filter: AnnotationMethodLinkWhereClause + predicate: IntComparators +} + +"""A connection to a list of items.""" +type AnnotationMethodLinkConnection { + """Pagination data for this connection""" + pageInfo: PageInfo! + + """Contains the nodes in this connection""" + edges: [AnnotationMethodLinkEdge!]! +} + +enum AnnotationMethodLinkCountColumns { + linkType + name + link + id +} + +input AnnotationMethodLinkCreateInput { + """Reference to annotation this link applies to""" + annotationId: ID = null + + """Type of link (e.g. model, source code, documentation)""" + linkType: annotation_method_link_type_enum! + + """user readable name of the resource""" + name: String = null + + """URL to the resource""" + link: String! + + """Numeric identifier (May change!)""" + id: Int! +} + +"""An edge in a connection.""" +type AnnotationMethodLinkEdge { + """A cursor for use in pagination""" + cursor: String! + + """The item at the end of the edge""" + node: AnnotationMethodLink! +} + +type AnnotationMethodLinkGroupByOptions { + annotation: AnnotationGroupByOptions + linkType: annotation_method_link_type_enum + name: String + link: String + id: Int +} + +type AnnotationMethodLinkMinMaxColumns { + name: String + link: String + id: Int +} + +type AnnotationMethodLinkNumericalColumns { + id: Int +} + +input AnnotationMethodLinkOrderByClause { + annotation: AnnotationOrderByClause + linkType: orderBy + name: orderBy + link: orderBy + id: orderBy +} + +input AnnotationMethodLinkUpdateInput { + """Reference to annotation this link applies to""" + annotationId: ID = null + + """Type of link (e.g. model, source code, documentation)""" + linkType: annotation_method_link_type_enum + + """user readable name of the resource""" + name: String = null + + """URL to the resource""" + link: String + + """Numeric identifier (May change!)""" + id: Int +} + +input AnnotationMethodLinkWhereClause { + annotation: AnnotationWhereClause + annotationId: IntComparators + linkType: Annotation_method_link_type_enumEnumComparators + name: StrComparators + link: StrComparators + id: IntComparators +} + +input AnnotationMethodLinkWhereClauseMutations { + id: IntComparators +} + +type AnnotationMinMaxColumns { + s3MetadataPath: String + httpsMetadataPath: String + annotationPublication: String + annotationMethod: String + annotationIngestId: String + objectId: String + objectName: String + objectDescription: String + objectState: String + objectCount: Int + confidencePrecision: Float + confidenceRecall: Float + groundTruthUsed: String + annotationSoftware: String + depositionDate: DateTime + releaseDate: DateTime + lastModifiedDate: DateTime + id: Int +} + +type AnnotationNumericalColumns { + objectCount: Int + confidencePrecision: Float + confidenceRecall: Float + id: Int +} + +input AnnotationOrderByClause { + run: RunOrderByClause + deposition: DepositionOrderByClause + s3MetadataPath: orderBy + httpsMetadataPath: orderBy + annotationPublication: orderBy + annotationMethod: orderBy + annotationIngestId: orderBy + groundTruthStatus: orderBy + objectId: orderBy + objectName: orderBy + objectDescription: orderBy + objectState: orderBy + objectCount: orderBy + confidencePrecision: orderBy + confidenceRecall: orderBy + groundTruthUsed: orderBy + annotationSoftware: orderBy + isCuratorRecommended: orderBy + methodType: orderBy + depositionDate: orderBy + releaseDate: orderBy + lastModifiedDate: orderBy + id: orderBy +} + +"""Shapes associated with an annotation""" +type AnnotationShape implements EntityInterface & Node { + """The Globally Unique ID of this object""" + _id: GlobalID! + + """Numeric identifier (May change!)""" + id: Int! + annotation(where: AnnotationWhereClause = null, orderBy: [AnnotationOrderByClause!] = []): Annotation + annotationId: Int + annotationFiles( + where: AnnotationFileWhereClause = null + orderBy: [AnnotationFileOrderByClause!] = [] + + """Returns the items in the list that come before the specified cursor.""" + before: String = null + + """Returns the items in the list that come after the specified cursor.""" + after: String = null + + """Returns the first n items from the list.""" + first: Int = null + + """Returns the items in the list that come after the specified cursor.""" + last: Int = null + ): AnnotationFileConnection! + annotationFilesAggregate(where: AnnotationFileWhereClause = null): AnnotationFileAggregate + + """ + The shape of the annotation (SegmentationMask, OrientedPoint, Point, InstanceSegmentation, Mesh, InstanceSegmentationMask) + """ + shapeType: annotation_file_shape_type_enum +} + +type AnnotationShapeAggregate { + aggregate: [AnnotationShapeAggregateFunctions!] +} + +type AnnotationShapeAggregateFunctions { + sum: AnnotationShapeNumericalColumns + avg: AnnotationShapeNumericalColumns + stddev: AnnotationShapeNumericalColumns + variance: AnnotationShapeNumericalColumns + min: AnnotationShapeMinMaxColumns + max: AnnotationShapeMinMaxColumns + groupBy: AnnotationShapeGroupByOptions + count(distinct: Boolean = false, columns: AnnotationShapeCountColumns = null): Int +} + +input AnnotationShapeAggregateWhereClause { + count: AnnotationShapeAggregateWhereClauseCount! +} + +input AnnotationShapeAggregateWhereClauseCount { + arguments: AnnotationShapeCountColumns + distinct: Boolean + filter: AnnotationShapeWhereClause + predicate: IntComparators +} + +"""A connection to a list of items.""" +type AnnotationShapeConnection { + """Pagination data for this connection""" + pageInfo: PageInfo! + + """Contains the nodes in this connection""" + edges: [AnnotationShapeEdge!]! +} + +enum AnnotationShapeCountColumns { + shapeType + id +} + +input AnnotationShapeCreateInput { + """Metadata about an shapes for an annotation""" + annotationId: ID = null + + """ + The shape of the annotation (SegmentationMask, OrientedPoint, Point, InstanceSegmentation, Mesh, InstanceSegmentationMask) + """ + shapeType: annotation_file_shape_type_enum = null + + """Numeric identifier (May change!)""" + id: Int! +} + +"""An edge in a connection.""" +type AnnotationShapeEdge { + """A cursor for use in pagination""" + cursor: String! + + """The item at the end of the edge""" + node: AnnotationShape! +} + +type AnnotationShapeGroupByOptions { + annotation: AnnotationGroupByOptions + annotationFiles: AnnotationFileGroupByOptions + shapeType: annotation_file_shape_type_enum + id: Int +} + +type AnnotationShapeMinMaxColumns { + id: Int +} + +type AnnotationShapeNumericalColumns { + id: Int +} + +input AnnotationShapeOrderByClause { + annotation: AnnotationOrderByClause + shapeType: orderBy + id: orderBy +} + +input AnnotationShapeUpdateInput { + """Metadata about an shapes for an annotation""" + annotationId: ID = null + + """ + The shape of the annotation (SegmentationMask, OrientedPoint, Point, InstanceSegmentation, Mesh, InstanceSegmentationMask) + """ + shapeType: annotation_file_shape_type_enum = null + + """Numeric identifier (May change!)""" + id: Int +} + +input AnnotationShapeWhereClause { + annotation: AnnotationWhereClause + annotationId: IntComparators + annotationFiles: AnnotationFileWhereClause + annotationFilesAggregate: AnnotationFileAggregateWhereClause + shapeType: Annotation_file_shape_type_enumEnumComparators + id: IntComparators +} + +input AnnotationShapeWhereClauseMutations { + id: IntComparators +} + +input AnnotationUpdateInput { + runId: ID = null + depositionId: ID = null + + """S3 path for the metadata json file for this annotation""" + s3MetadataPath: String + + """HTTPS path for the metadata json file for this annotation""" + httpsMetadataPath: String + + """ + DOIs for publications that describe the dataset. Use a comma to separate multiple DOIs. + """ + annotationPublication: String = null + + """ + Describe how the annotation is made (e.g. Manual, crYoLO, Positive Unlabeled Learning, template matching) + """ + annotationMethod: String + + """An identifier for the annotation to be used during ingestion.""" + annotationIngestId: String = null + + """ + Whether an annotation is considered ground truth, as determined by the annotator. + """ + groundTruthStatus: Boolean = null + + """Ontology identifier for the annotation object.""" + objectId: String + + """ + Name of the object being annotated (e.g. ribosome, nuclear pore complex, actin filament, membrane) + """ + objectName: String + + """ + A textual description of the annotation object, can be a longer description to include additional information not covered by the Annotation object name and state. + """ + objectDescription: String = null + + """Molecule state annotated (e.g. open, closed)""" + objectState: String = null + + """Number of objects identified""" + objectCount: Int = null + + """ + Describe the confidence level of the annotation. Precision is defined as the % of annotation objects being true positive + """ + confidencePrecision: Float = null + + """ + Describe the confidence level of the annotation. Recall is defined as the % of true positives being annotated correctly + """ + confidenceRecall: Float = null + + """Annotation filename used as ground truth for precision and recall""" + groundTruthUsed: String = null + + """Software used for generating this annotation""" + annotationSoftware: String = null + + """ + Data curator’s subjective choice as the best annotation of the same annotation object ID + """ + isCuratorRecommended: Boolean = null + + """ + The method type for generating the annotation (e.g. manual, hybrid, automated) + """ + methodType: annotation_method_type_enum + + """Date when an annotation set is initially received by the Data Portal.""" + depositionDate: DateTime + + """Date when annotation data is made public by the Data Portal.""" + releaseDate: DateTime + + """Date when an annotation was last modified in the Data Portal""" + lastModifiedDate: DateTime + + """Numeric identifier (May change!)""" + id: Int +} + +input AnnotationWhereClause { + run: RunWhereClause + runId: IntComparators + annotationShapes: AnnotationShapeWhereClause + annotationShapesAggregate: AnnotationShapeAggregateWhereClause + methodLinks: AnnotationMethodLinkWhereClause + methodLinksAggregate: AnnotationMethodLinkAggregateWhereClause + authors: AnnotationAuthorWhereClause + authorsAggregate: AnnotationAuthorAggregateWhereClause + deposition: DepositionWhereClause + depositionId: IntComparators + s3MetadataPath: StrComparators + httpsMetadataPath: StrComparators + annotationPublication: StrComparators + annotationMethod: StrComparators + annotationIngestId: StrComparators + groundTruthStatus: BoolComparators + objectId: StrComparators + objectName: StrComparators + objectDescription: StrComparators + objectState: StrComparators + objectCount: IntComparators + confidencePrecision: FloatComparators + confidenceRecall: FloatComparators + groundTruthUsed: StrComparators + annotationSoftware: StrComparators + isCuratorRecommended: BoolComparators + methodType: Annotation_method_type_enumEnumComparators + depositionDate: DatetimeComparators + releaseDate: DatetimeComparators + lastModifiedDate: DatetimeComparators + id: IntComparators +} + +input AnnotationWhereClauseMutations { + id: IntComparators +} + +input Annotation_file_shape_type_enumEnumComparators { + _eq: annotation_file_shape_type_enum + _neq: annotation_file_shape_type_enum + _in: [annotation_file_shape_type_enum!] + _nin: [annotation_file_shape_type_enum!] + _gt: annotation_file_shape_type_enum + _gte: annotation_file_shape_type_enum + _lt: annotation_file_shape_type_enum + _lte: annotation_file_shape_type_enum + _is_null: Boolean +} + +input Annotation_file_source_enumEnumComparators { + _eq: annotation_file_source_enum + _neq: annotation_file_source_enum + _in: [annotation_file_source_enum!] + _nin: [annotation_file_source_enum!] + _gt: annotation_file_source_enum + _gte: annotation_file_source_enum + _lt: annotation_file_source_enum + _lte: annotation_file_source_enum + _is_null: Boolean +} + +input Annotation_method_link_type_enumEnumComparators { + _eq: annotation_method_link_type_enum + _neq: annotation_method_link_type_enum + _in: [annotation_method_link_type_enum!] + _nin: [annotation_method_link_type_enum!] + _gt: annotation_method_link_type_enum + _gte: annotation_method_link_type_enum + _lt: annotation_method_link_type_enum + _lte: annotation_method_link_type_enum + _is_null: Boolean +} + +input Annotation_method_type_enumEnumComparators { + _eq: annotation_method_type_enum + _neq: annotation_method_type_enum + _in: [annotation_method_type_enum!] + _nin: [annotation_method_type_enum!] + _gt: annotation_method_type_enum + _gte: annotation_method_type_enum + _lt: annotation_method_type_enum + _lte: annotation_method_type_enum + _is_null: Boolean +} + +input BoolComparators { + _eq: Boolean + _neq: Boolean + _in: [Boolean!] + _nin: [Boolean!] + _is_null: Boolean +} + +"""A collection of imaging experiments on the same organism""" +type Dataset implements EntityInterface & Node { + """The Globally Unique ID of this object""" + _id: GlobalID! + + """ + An identifier for a CryoET dataset, assigned by the Data Portal. Used to identify the dataset as the directory name in data tree + """ + id: Int! + deposition(where: DepositionWhereClause = null, orderBy: [DepositionOrderByClause!] = []): Deposition + depositionId: Int! + fundingSources( + where: DatasetFundingWhereClause = null + orderBy: [DatasetFundingOrderByClause!] = [] + + """Returns the items in the list that come before the specified cursor.""" + before: String = null + + """Returns the items in the list that come after the specified cursor.""" + after: String = null + + """Returns the first n items from the list.""" + first: Int = null + + """Returns the items in the list that come after the specified cursor.""" + last: Int = null + ): DatasetFundingConnection! + fundingSourcesAggregate(where: DatasetFundingWhereClause = null): DatasetFundingAggregate + authors( + where: DatasetAuthorWhereClause = null + orderBy: [DatasetAuthorOrderByClause!] = [] + + """Returns the items in the list that come before the specified cursor.""" + before: String = null + + """Returns the items in the list that come after the specified cursor.""" + after: String = null + + """Returns the first n items from the list.""" + first: Int = null + + """Returns the items in the list that come after the specified cursor.""" + last: Int = null + ): DatasetAuthorConnection! + authorsAggregate(where: DatasetAuthorWhereClause = null): DatasetAuthorAggregate + runs( + where: RunWhereClause = null + orderBy: [RunOrderByClause!] = [] + + """Returns the items in the list that come before the specified cursor.""" + before: String = null + + """Returns the items in the list that come after the specified cursor.""" + after: String = null + + """Returns the first n items from the list.""" + first: Int = null + + """Returns the items in the list that come after the specified cursor.""" + last: Int = null + ): RunConnection! + runsAggregate(where: RunWhereClause = null): RunAggregate + + """Title of a CryoET dataset""" + title: String! + + """ + A short description of a CryoET dataset, similar to an abstract for a journal article or dataset. + """ + description: String! + + """ + Label for the type of assay performed in a CryoET dataset, e.g. cryo-electron tomography + """ + assayLabel: String + + """ + EFO ontology identifier for the type of assay performed in a CryoET dataset + """ + assayOntologyId: String + + """ + Development stage of the organism from which a biological sample used the study is derived. + """ + developmentStageName: String + + """Ontology identifier for the development stage""" + developmentStageOntologyId: String + + """ + Name of the disease associated with the biological sample used in a CryoET study, e.g. Alzheimer’s disease + """ + diseaseName: String + + """ + Ontology identifier for the disease associated with the biological sample used in a CryoET study + """ + diseaseOntologyId: String + + """ + Name of the organism from which a biological sample used in a CryoET study is derived from, e.g. homo sapiens + """ + organismName: String + + """NCBI taxonomy identifier for the organism, e.g. 9606""" + organismTaxid: Int + + """ + Name of the tissue from which a biological sample used in a CryoET study is derived from. + """ + tissueName: String + + """The ontology identifier for the tissue.""" + tissueId: String + + """ + Name of the cell from which a biological sample used in a CryoET study is derived from. + """ + cellName: String + + """The ontology identifier for the cell type.""" + cellTypeId: String + + """Cell line or strain for the sample.""" + cellStrainName: String + + """Link to more information about the cell strain""" + cellStrainId: String + + """ + Type of samples used in a CryoET study. (cell, tissue, organism, intact organelle, in-vitro mixture, in-silico synthetic data, other) + """ + sampleType: sample_type_enum + + """Describe how the sample was prepared.""" + samplePreparation: String + + """Describe Cryo-ET grid preparation.""" + gridPreparation: String + + """ + Describe other setup not covered by sample preparation or grid preparation that may make this dataset unique in the same publication + """ + otherSetup: String + + """URL for the dataset preview image.""" + keyPhotoUrl: String + + """URL for the thumbnail of preview image.""" + keyPhotoThumbnailUrl: String + + """Name of the cellular component""" + cellComponentName: String + + """ + If the dataset focuses on a specific part of a cell, the subset is included here + """ + cellComponentId: String + + """Date when a dataset is initially received by the Data Portal.""" + depositionDate: DateTime! + + """Date when a dataset is made available on the Data Portal.""" + releaseDate: DateTime! + + """Date when a released dataset is last modified.""" + lastModifiedDate: DateTime! + + """ + Comma-separated list of DOIs for publications associated with the dataset. + """ + datasetPublications: String + + """ + If a CryoET dataset is also deposited into another database, enter the database identifier here (e.g. EMPIAR-11445). Use a comma to separate multiple identifiers. + """ + relatedDatabaseEntries: String + + """The S3 public bucket path where this dataset is contained""" + s3Prefix: String! + + """The https directory path where this dataset is contained""" + httpsPrefix: String! + + """Size of the dataset in bytes""" + fileSize: Float +} + +type DatasetAggregate { + aggregate: [DatasetAggregateFunctions!] +} + +type DatasetAggregateFunctions { + sum: DatasetNumericalColumns + avg: DatasetNumericalColumns + stddev: DatasetNumericalColumns + variance: DatasetNumericalColumns + min: DatasetMinMaxColumns + max: DatasetMinMaxColumns + groupBy: DatasetGroupByOptions + count(distinct: Boolean = false, columns: DatasetCountColumns = null): Int +} + +input DatasetAggregateWhereClause { + count: DatasetAggregateWhereClauseCount! +} + +input DatasetAggregateWhereClauseCount { + arguments: DatasetCountColumns + distinct: Boolean + filter: DatasetWhereClause + predicate: IntComparators +} + +"""An author of a dataset""" +type DatasetAuthor implements EntityInterface & Node { + """The Globally Unique ID of this object""" + _id: GlobalID! + + """Numeric identifier (May change!)""" + id: Int! + dataset(where: DatasetWhereClause = null, orderBy: [DatasetOrderByClause!] = []): Dataset + datasetId: Int + + """The order in which the author appears in the publication""" + authorListOrder: Int! + + """A unique, persistent identifier for researchers, provided by ORCID.""" + orcid: String + + """A unique, persistent identifier for kaggle users at kaggle.com.""" + kaggleId: String + + """Full name of a dataset author (e.g. Jane Doe).""" + name: String! + + """Email address for this author""" + email: String + + """Name of the institutions an author is affiliated with. Comma separated""" + affiliationName: String + + """Address of the institution an author is affiliated with.""" + affiliationAddress: String + + """ + A unique identifier assigned to the affiliated institution by The Research Organization Registry (ROR). + """ + affiliationIdentifier: String + + """Indicates whether an author is the corresponding author""" + correspondingAuthorStatus: Boolean + + """ + Indicates whether an author is the main person associated with the corresponding dataset + """ + primaryAuthorStatus: Boolean +} + +type DatasetAuthorAggregate { + aggregate: [DatasetAuthorAggregateFunctions!] +} + +type DatasetAuthorAggregateFunctions { + sum: DatasetAuthorNumericalColumns + avg: DatasetAuthorNumericalColumns + stddev: DatasetAuthorNumericalColumns + variance: DatasetAuthorNumericalColumns + min: DatasetAuthorMinMaxColumns + max: DatasetAuthorMinMaxColumns + groupBy: DatasetAuthorGroupByOptions + count(distinct: Boolean = false, columns: DatasetAuthorCountColumns = null): Int +} + +input DatasetAuthorAggregateWhereClause { + count: DatasetAuthorAggregateWhereClauseCount! +} + +input DatasetAuthorAggregateWhereClauseCount { + arguments: DatasetAuthorCountColumns + distinct: Boolean + filter: DatasetAuthorWhereClause + predicate: IntComparators +} + +"""A connection to a list of items.""" +type DatasetAuthorConnection { + """Pagination data for this connection""" + pageInfo: PageInfo! + + """Contains the nodes in this connection""" + edges: [DatasetAuthorEdge!]! +} + +enum DatasetAuthorCountColumns { + id + authorListOrder + orcid + kaggleId + name + email + affiliationName + affiliationAddress + affiliationIdentifier + correspondingAuthorStatus + primaryAuthorStatus +} + +input DatasetAuthorCreateInput { + """Dataset authored by this person""" + datasetId: ID = null + + """Numeric identifier (May change!)""" + id: Int! + + """The order in which the author appears in the publication""" + authorListOrder: Int! + + """A unique, persistent identifier for researchers, provided by ORCID.""" + orcid: String = null + + """A unique, persistent identifier for kaggle users at kaggle.com.""" + kaggleId: String = null + + """Full name of a dataset author (e.g. Jane Doe).""" + name: String! + + """Email address for this author""" + email: String = null + + """Name of the institutions an author is affiliated with. Comma separated""" + affiliationName: String = null + + """Address of the institution an author is affiliated with.""" + affiliationAddress: String = null + + """ + A unique identifier assigned to the affiliated institution by The Research Organization Registry (ROR). + """ + affiliationIdentifier: String = null + + """Indicates whether an author is the corresponding author""" + correspondingAuthorStatus: Boolean = null + + """ + Indicates whether an author is the main person associated with the corresponding dataset + """ + primaryAuthorStatus: Boolean = null +} + +"""An edge in a connection.""" +type DatasetAuthorEdge { + """A cursor for use in pagination""" + cursor: String! + + """The item at the end of the edge""" + node: DatasetAuthor! +} + +type DatasetAuthorGroupByOptions { + dataset: DatasetGroupByOptions + id: Int + authorListOrder: Int + orcid: String + kaggleId: String + name: String + email: String + affiliationName: String + affiliationAddress: String + affiliationIdentifier: String + correspondingAuthorStatus: Boolean + primaryAuthorStatus: Boolean +} + +type DatasetAuthorMinMaxColumns { + id: Int + authorListOrder: Int + orcid: String + kaggleId: String + name: String + email: String + affiliationName: String + affiliationAddress: String + affiliationIdentifier: String +} + +type DatasetAuthorNumericalColumns { + id: Int + authorListOrder: Int +} + +input DatasetAuthorOrderByClause { + dataset: DatasetOrderByClause + id: orderBy + authorListOrder: orderBy + orcid: orderBy + kaggleId: orderBy + name: orderBy + email: orderBy + affiliationName: orderBy + affiliationAddress: orderBy + affiliationIdentifier: orderBy + correspondingAuthorStatus: orderBy + primaryAuthorStatus: orderBy +} + +input DatasetAuthorUpdateInput { + """Dataset authored by this person""" + datasetId: ID = null + + """Numeric identifier (May change!)""" + id: Int + + """The order in which the author appears in the publication""" + authorListOrder: Int + + """A unique, persistent identifier for researchers, provided by ORCID.""" + orcid: String = null + + """A unique, persistent identifier for kaggle users at kaggle.com.""" + kaggleId: String = null + + """Full name of a dataset author (e.g. Jane Doe).""" + name: String + + """Email address for this author""" + email: String = null + + """Name of the institutions an author is affiliated with. Comma separated""" + affiliationName: String = null + + """Address of the institution an author is affiliated with.""" + affiliationAddress: String = null + + """ + A unique identifier assigned to the affiliated institution by The Research Organization Registry (ROR). + """ + affiliationIdentifier: String = null + + """Indicates whether an author is the corresponding author""" + correspondingAuthorStatus: Boolean = null + + """ + Indicates whether an author is the main person associated with the corresponding dataset + """ + primaryAuthorStatus: Boolean = null +} + +input DatasetAuthorWhereClause { + dataset: DatasetWhereClause + datasetId: IntComparators + id: IntComparators + authorListOrder: IntComparators + orcid: StrComparators + kaggleId: StrComparators + name: StrComparators + email: StrComparators + affiliationName: StrComparators + affiliationAddress: StrComparators + affiliationIdentifier: StrComparators + correspondingAuthorStatus: BoolComparators + primaryAuthorStatus: BoolComparators +} + +input DatasetAuthorWhereClauseMutations { + id: IntComparators +} + +"""A connection to a list of items.""" +type DatasetConnection { + """Pagination data for this connection""" + pageInfo: PageInfo! + + """Contains the nodes in this connection""" + edges: [DatasetEdge!]! +} + +enum DatasetCountColumns { + title + description + assayLabel + assayOntologyId + developmentStageName + developmentStageOntologyId + diseaseName + diseaseOntologyId + organismName + organismTaxid + tissueName + tissueId + cellName + cellTypeId + cellStrainName + cellStrainId + sampleType + samplePreparation + gridPreparation + otherSetup + keyPhotoUrl + keyPhotoThumbnailUrl + cellComponentName + cellComponentId + depositionDate + releaseDate + lastModifiedDate + datasetPublications + relatedDatabaseEntries + s3Prefix + httpsPrefix + fileSize + id +} + +input DatasetCreateInput { + """Reference to the deposition this dataset is associated with""" + depositionId: ID! + + """Title of a CryoET dataset""" + title: String! + + """ + A short description of a CryoET dataset, similar to an abstract for a journal article or dataset. + """ + description: String! + + """ + Label for the type of assay performed in a CryoET dataset, e.g. cryo-electron tomography + """ + assayLabel: String = null + + """ + EFO ontology identifier for the type of assay performed in a CryoET dataset + """ + assayOntologyId: String = null + + """ + Development stage of the organism from which a biological sample used the study is derived. + """ + developmentStageName: String = null + + """Ontology identifier for the development stage""" + developmentStageOntologyId: String = null + + """ + Name of the disease associated with the biological sample used in a CryoET study, e.g. Alzheimer’s disease + """ + diseaseName: String = null + + """ + Ontology identifier for the disease associated with the biological sample used in a CryoET study + """ + diseaseOntologyId: String = null + + """ + Name of the organism from which a biological sample used in a CryoET study is derived from, e.g. homo sapiens + """ + organismName: String = null + + """NCBI taxonomy identifier for the organism, e.g. 9606""" + organismTaxid: Int = null + + """ + Name of the tissue from which a biological sample used in a CryoET study is derived from. + """ + tissueName: String = null + + """The ontology identifier for the tissue.""" + tissueId: String = null + + """ + Name of the cell from which a biological sample used in a CryoET study is derived from. + """ + cellName: String = null + + """The ontology identifier for the cell type.""" + cellTypeId: String = null + + """Cell line or strain for the sample.""" + cellStrainName: String = null + + """Link to more information about the cell strain""" + cellStrainId: String = null + + """ + Type of samples used in a CryoET study. (cell, tissue, organism, intact organelle, in-vitro mixture, in-silico synthetic data, other) + """ + sampleType: sample_type_enum = null + + """Describe how the sample was prepared.""" + samplePreparation: String = null + + """Describe Cryo-ET grid preparation.""" + gridPreparation: String = null + + """ + Describe other setup not covered by sample preparation or grid preparation that may make this dataset unique in the same publication + """ + otherSetup: String = null + + """URL for the dataset preview image.""" + keyPhotoUrl: String = null + + """URL for the thumbnail of preview image.""" + keyPhotoThumbnailUrl: String = null + + """Name of the cellular component""" + cellComponentName: String = null + + """ + If the dataset focuses on a specific part of a cell, the subset is included here + """ + cellComponentId: String = null + + """Date when a dataset is initially received by the Data Portal.""" + depositionDate: DateTime! + + """Date when a dataset is made available on the Data Portal.""" + releaseDate: DateTime! + + """Date when a released dataset is last modified.""" + lastModifiedDate: DateTime! + + """ + Comma-separated list of DOIs for publications associated with the dataset. + """ + datasetPublications: String = null + + """ + If a CryoET dataset is also deposited into another database, enter the database identifier here (e.g. EMPIAR-11445). Use a comma to separate multiple identifiers. + """ + relatedDatabaseEntries: String = null + + """The S3 public bucket path where this dataset is contained""" + s3Prefix: String! + + """The https directory path where this dataset is contained""" + httpsPrefix: String! + + """Size of the dataset in bytes""" + fileSize: Float = null + + """ + An identifier for a CryoET dataset, assigned by the Data Portal. Used to identify the dataset as the directory name in data tree + """ + id: Int! +} + +"""An edge in a connection.""" +type DatasetEdge { + """A cursor for use in pagination""" + cursor: String! + + """The item at the end of the edge""" + node: Dataset! +} + +"""Metadata for a dataset's funding sources""" +type DatasetFunding implements EntityInterface & Node { + """The Globally Unique ID of this object""" + _id: GlobalID! + + """Numeric identifier (May change!)""" + id: Int! + dataset(where: DatasetWhereClause = null, orderBy: [DatasetOrderByClause!] = []): Dataset + datasetId: Int + + """Name of the funding agency.""" + fundingAgencyName: String + + """Grant identifier provided by the funding agency.""" + grantId: String +} + +type DatasetFundingAggregate { + aggregate: [DatasetFundingAggregateFunctions!] +} + +type DatasetFundingAggregateFunctions { + sum: DatasetFundingNumericalColumns + avg: DatasetFundingNumericalColumns + stddev: DatasetFundingNumericalColumns + variance: DatasetFundingNumericalColumns + min: DatasetFundingMinMaxColumns + max: DatasetFundingMinMaxColumns + groupBy: DatasetFundingGroupByOptions + count(distinct: Boolean = false, columns: DatasetFundingCountColumns = null): Int +} + +input DatasetFundingAggregateWhereClause { + count: DatasetFundingAggregateWhereClauseCount! +} + +input DatasetFundingAggregateWhereClauseCount { + arguments: DatasetFundingCountColumns + distinct: Boolean + filter: DatasetFundingWhereClause + predicate: IntComparators +} + +"""A connection to a list of items.""" +type DatasetFundingConnection { + """Pagination data for this connection""" + pageInfo: PageInfo! + + """Contains the nodes in this connection""" + edges: [DatasetFundingEdge!]! +} + +enum DatasetFundingCountColumns { + fundingAgencyName + grantId + id +} + +input DatasetFundingCreateInput { + """The dataset this dataset funding is a part of""" + datasetId: ID = null + + """Name of the funding agency.""" + fundingAgencyName: String = null + + """Grant identifier provided by the funding agency.""" + grantId: String = null + + """Numeric identifier (May change!)""" + id: Int! +} + +"""An edge in a connection.""" +type DatasetFundingEdge { + """A cursor for use in pagination""" + cursor: String! + + """The item at the end of the edge""" + node: DatasetFunding! +} + +type DatasetFundingGroupByOptions { + dataset: DatasetGroupByOptions + fundingAgencyName: String + grantId: String + id: Int +} + +type DatasetFundingMinMaxColumns { + fundingAgencyName: String + grantId: String + id: Int +} + +type DatasetFundingNumericalColumns { + id: Int +} + +input DatasetFundingOrderByClause { + dataset: DatasetOrderByClause + fundingAgencyName: orderBy + grantId: orderBy + id: orderBy +} + +input DatasetFundingUpdateInput { + """The dataset this dataset funding is a part of""" + datasetId: ID = null + + """Name of the funding agency.""" + fundingAgencyName: String = null + + """Grant identifier provided by the funding agency.""" + grantId: String = null + + """Numeric identifier (May change!)""" + id: Int +} + +input DatasetFundingWhereClause { + dataset: DatasetWhereClause + datasetId: IntComparators + fundingAgencyName: StrComparators + grantId: StrComparators + id: IntComparators +} + +input DatasetFundingWhereClauseMutations { + id: IntComparators +} + +type DatasetGroupByOptions { + deposition: DepositionGroupByOptions + fundingSources: DatasetFundingGroupByOptions + authors: DatasetAuthorGroupByOptions + runs: RunGroupByOptions + title: String + description: String + assayLabel: String + assayOntologyId: String + developmentStageName: String + developmentStageOntologyId: String + diseaseName: String + diseaseOntologyId: String + organismName: String + organismTaxid: Int + tissueName: String + tissueId: String + cellName: String + cellTypeId: String + cellStrainName: String + cellStrainId: String + sampleType: sample_type_enum + samplePreparation: String + gridPreparation: String + otherSetup: String + keyPhotoUrl: String + keyPhotoThumbnailUrl: String + cellComponentName: String + cellComponentId: String + depositionDate: DateTime + releaseDate: DateTime + lastModifiedDate: DateTime + datasetPublications: String + relatedDatabaseEntries: String + s3Prefix: String + httpsPrefix: String + fileSize: Float + id: Int +} + +type DatasetMinMaxColumns { + title: String + description: String + assayLabel: String + assayOntologyId: String + developmentStageName: String + developmentStageOntologyId: String + diseaseName: String + diseaseOntologyId: String + organismName: String + organismTaxid: Int + tissueName: String + tissueId: String + cellName: String + cellTypeId: String + cellStrainName: String + cellStrainId: String + samplePreparation: String + gridPreparation: String + otherSetup: String + keyPhotoUrl: String + keyPhotoThumbnailUrl: String + cellComponentName: String + cellComponentId: String + depositionDate: DateTime + releaseDate: DateTime + lastModifiedDate: DateTime + datasetPublications: String + relatedDatabaseEntries: String + s3Prefix: String + httpsPrefix: String + fileSize: Float + id: Int +} + +type DatasetNumericalColumns { + organismTaxid: Int + fileSize: Float + id: Int +} + +input DatasetOrderByClause { + deposition: DepositionOrderByClause + title: orderBy + description: orderBy + assayLabel: orderBy + assayOntologyId: orderBy + developmentStageName: orderBy + developmentStageOntologyId: orderBy + diseaseName: orderBy + diseaseOntologyId: orderBy + organismName: orderBy + organismTaxid: orderBy + tissueName: orderBy + tissueId: orderBy + cellName: orderBy + cellTypeId: orderBy + cellStrainName: orderBy + cellStrainId: orderBy + sampleType: orderBy + samplePreparation: orderBy + gridPreparation: orderBy + otherSetup: orderBy + keyPhotoUrl: orderBy + keyPhotoThumbnailUrl: orderBy + cellComponentName: orderBy + cellComponentId: orderBy + depositionDate: orderBy + releaseDate: orderBy + lastModifiedDate: orderBy + datasetPublications: orderBy + relatedDatabaseEntries: orderBy + s3Prefix: orderBy + httpsPrefix: orderBy + fileSize: orderBy + id: orderBy +} + +input DatasetUpdateInput { + """Reference to the deposition this dataset is associated with""" + depositionId: ID + + """Title of a CryoET dataset""" + title: String + + """ + A short description of a CryoET dataset, similar to an abstract for a journal article or dataset. + """ + description: String + + """ + Label for the type of assay performed in a CryoET dataset, e.g. cryo-electron tomography + """ + assayLabel: String = null + + """ + EFO ontology identifier for the type of assay performed in a CryoET dataset + """ + assayOntologyId: String = null + + """ + Development stage of the organism from which a biological sample used the study is derived. + """ + developmentStageName: String = null + + """Ontology identifier for the development stage""" + developmentStageOntologyId: String = null + + """ + Name of the disease associated with the biological sample used in a CryoET study, e.g. Alzheimer’s disease + """ + diseaseName: String = null + + """ + Ontology identifier for the disease associated with the biological sample used in a CryoET study + """ + diseaseOntologyId: String = null + + """ + Name of the organism from which a biological sample used in a CryoET study is derived from, e.g. homo sapiens + """ + organismName: String = null + + """NCBI taxonomy identifier for the organism, e.g. 9606""" + organismTaxid: Int = null + + """ + Name of the tissue from which a biological sample used in a CryoET study is derived from. + """ + tissueName: String = null + + """The ontology identifier for the tissue.""" + tissueId: String = null + + """ + Name of the cell from which a biological sample used in a CryoET study is derived from. + """ + cellName: String = null + + """The ontology identifier for the cell type.""" + cellTypeId: String = null + + """Cell line or strain for the sample.""" + cellStrainName: String = null + + """Link to more information about the cell strain""" + cellStrainId: String = null + + """ + Type of samples used in a CryoET study. (cell, tissue, organism, intact organelle, in-vitro mixture, in-silico synthetic data, other) + """ + sampleType: sample_type_enum = null + + """Describe how the sample was prepared.""" + samplePreparation: String = null + + """Describe Cryo-ET grid preparation.""" + gridPreparation: String = null + + """ + Describe other setup not covered by sample preparation or grid preparation that may make this dataset unique in the same publication + """ + otherSetup: String = null + + """URL for the dataset preview image.""" + keyPhotoUrl: String = null + + """URL for the thumbnail of preview image.""" + keyPhotoThumbnailUrl: String = null + + """Name of the cellular component""" + cellComponentName: String = null + + """ + If the dataset focuses on a specific part of a cell, the subset is included here + """ + cellComponentId: String = null + + """Date when a dataset is initially received by the Data Portal.""" + depositionDate: DateTime + + """Date when a dataset is made available on the Data Portal.""" + releaseDate: DateTime + + """Date when a released dataset is last modified.""" + lastModifiedDate: DateTime + + """ + Comma-separated list of DOIs for publications associated with the dataset. + """ + datasetPublications: String = null + + """ + If a CryoET dataset is also deposited into another database, enter the database identifier here (e.g. EMPIAR-11445). Use a comma to separate multiple identifiers. + """ + relatedDatabaseEntries: String = null + + """The S3 public bucket path where this dataset is contained""" + s3Prefix: String + + """The https directory path where this dataset is contained""" + httpsPrefix: String + + """Size of the dataset in bytes""" + fileSize: Float = null + + """ + An identifier for a CryoET dataset, assigned by the Data Portal. Used to identify the dataset as the directory name in data tree + """ + id: Int +} + +input DatasetWhereClause { + deposition: DepositionWhereClause + depositionId: IntComparators + fundingSources: DatasetFundingWhereClause + fundingSourcesAggregate: DatasetFundingAggregateWhereClause + authors: DatasetAuthorWhereClause + authorsAggregate: DatasetAuthorAggregateWhereClause + runs: RunWhereClause + runsAggregate: RunAggregateWhereClause + title: StrComparators + description: StrComparators + assayLabel: StrComparators + assayOntologyId: StrComparators + developmentStageName: StrComparators + developmentStageOntologyId: StrComparators + diseaseName: StrComparators + diseaseOntologyId: StrComparators + organismName: StrComparators + organismTaxid: IntComparators + tissueName: StrComparators + tissueId: StrComparators + cellName: StrComparators + cellTypeId: StrComparators + cellStrainName: StrComparators + cellStrainId: StrComparators + sampleType: Sample_type_enumEnumComparators + samplePreparation: StrComparators + gridPreparation: StrComparators + otherSetup: StrComparators + keyPhotoUrl: StrComparators + keyPhotoThumbnailUrl: StrComparators + cellComponentName: StrComparators + cellComponentId: StrComparators + depositionDate: DatetimeComparators + releaseDate: DatetimeComparators + lastModifiedDate: DatetimeComparators + datasetPublications: StrComparators + relatedDatabaseEntries: StrComparators + s3Prefix: StrComparators + httpsPrefix: StrComparators + fileSize: FloatComparators + id: IntComparators +} + +input DatasetWhereClauseMutations { + id: IntComparators +} + +"""Date with time (isoformat)""" +scalar DateTime + +input DatetimeComparators { + _eq: DateTime + _neq: DateTime + _in: [DateTime!] + _nin: [DateTime!] + _gt: DateTime + _gte: DateTime + _lt: DateTime + _lte: DateTime + _is_null: Boolean +} + +"""Deposition metadata""" +type Deposition implements EntityInterface & Node { + """The Globally Unique ID of this object""" + _id: GlobalID! + + """Numeric identifier (May change!)""" + id: Int! + authors( + where: DepositionAuthorWhereClause = null + orderBy: [DepositionAuthorOrderByClause!] = [] + + """Returns the items in the list that come before the specified cursor.""" + before: String = null + + """Returns the items in the list that come after the specified cursor.""" + after: String = null + + """Returns the first n items from the list.""" + first: Int = null + + """Returns the items in the list that come after the specified cursor.""" + last: Int = null + ): DepositionAuthorConnection! + authorsAggregate(where: DepositionAuthorWhereClause = null): DepositionAuthorAggregate + alignments( + where: AlignmentWhereClause = null + orderBy: [AlignmentOrderByClause!] = [] + + """Returns the items in the list that come before the specified cursor.""" + before: String = null + + """Returns the items in the list that come after the specified cursor.""" + after: String = null + + """Returns the first n items from the list.""" + first: Int = null + + """Returns the items in the list that come after the specified cursor.""" + last: Int = null + ): AlignmentConnection! + alignmentsAggregate(where: AlignmentWhereClause = null): AlignmentAggregate + annotations( + where: AnnotationWhereClause = null + orderBy: [AnnotationOrderByClause!] = [] + + """Returns the items in the list that come before the specified cursor.""" + before: String = null + + """Returns the items in the list that come after the specified cursor.""" + after: String = null + + """Returns the first n items from the list.""" + first: Int = null + + """Returns the items in the list that come after the specified cursor.""" + last: Int = null + ): AnnotationConnection! + annotationsAggregate(where: AnnotationWhereClause = null): AnnotationAggregate + datasets( + where: DatasetWhereClause = null + orderBy: [DatasetOrderByClause!] = [] + + """Returns the items in the list that come before the specified cursor.""" + before: String = null + + """Returns the items in the list that come after the specified cursor.""" + after: String = null + + """Returns the first n items from the list.""" + first: Int = null + + """Returns the items in the list that come after the specified cursor.""" + last: Int = null + ): DatasetConnection! + datasetsAggregate(where: DatasetWhereClause = null): DatasetAggregate + frames( + where: FrameWhereClause = null + orderBy: [FrameOrderByClause!] = [] + + """Returns the items in the list that come before the specified cursor.""" + before: String = null + + """Returns the items in the list that come after the specified cursor.""" + after: String = null + + """Returns the first n items from the list.""" + first: Int = null + + """Returns the items in the list that come after the specified cursor.""" + last: Int = null + ): FrameConnection! + framesAggregate(where: FrameWhereClause = null): FrameAggregate + tiltseries( + where: TiltseriesWhereClause = null + orderBy: [TiltseriesOrderByClause!] = [] + + """Returns the items in the list that come before the specified cursor.""" + before: String = null + + """Returns the items in the list that come after the specified cursor.""" + after: String = null + + """Returns the first n items from the list.""" + first: Int = null + + """Returns the items in the list that come after the specified cursor.""" + last: Int = null + ): TiltseriesConnection! + tiltseriesAggregate(where: TiltseriesWhereClause = null): TiltseriesAggregate + tomograms( + where: TomogramWhereClause = null + orderBy: [TomogramOrderByClause!] = [] + + """Returns the items in the list that come before the specified cursor.""" + before: String = null + + """Returns the items in the list that come after the specified cursor.""" + after: String = null + + """Returns the first n items from the list.""" + first: Int = null + + """Returns the items in the list that come after the specified cursor.""" + last: Int = null + ): TomogramConnection! + tomogramsAggregate(where: TomogramWhereClause = null): TomogramAggregate + + """Title for the deposition""" + title: String! + + """Description for the deposition""" + description: String! + + """Tag for the deposition - like ml competition""" + tag: String + depositionTypes( + where: DepositionTypeWhereClause = null + orderBy: [DepositionTypeOrderByClause!] = [] + + """Returns the items in the list that come before the specified cursor.""" + before: String = null + + """Returns the items in the list that come after the specified cursor.""" + after: String = null + + """Returns the first n items from the list.""" + first: Int = null + + """Returns the items in the list that come after the specified cursor.""" + last: Int = null + ): DepositionTypeConnection! + depositionTypesAggregate(where: DepositionTypeWhereClause = null): DepositionTypeAggregate + + """The publications related to this deposition""" + depositionPublications: String + + """The related database entries to this deposition""" + relatedDatabaseEntries: String + + """The date the deposition was deposited""" + depositionDate: DateTime! + + """The date the deposition was released""" + releaseDate: DateTime! + + """The date the deposition was last modified""" + lastModifiedDate: DateTime! + + """URL for the deposition preview image.""" + keyPhotoUrl: String + + """URL for the deposition thumbnail image.""" + keyPhotoThumbnailUrl: String +} + +type DepositionAggregate { + aggregate: [DepositionAggregateFunctions!] +} + +type DepositionAggregateFunctions { + sum: DepositionNumericalColumns + avg: DepositionNumericalColumns + stddev: DepositionNumericalColumns + variance: DepositionNumericalColumns + min: DepositionMinMaxColumns + max: DepositionMinMaxColumns + groupBy: DepositionGroupByOptions + count(distinct: Boolean = false, columns: DepositionCountColumns = null): Int +} + +"""Authors for a deposition""" +type DepositionAuthor implements EntityInterface & Node { + """The Globally Unique ID of this object""" + _id: GlobalID! + + """Numeric identifier (May change!)""" + id: Int! + deposition(where: DepositionWhereClause = null, orderBy: [DepositionOrderByClause!] = []): Deposition + depositionId: Int! + + """The order in which the author appears in the publication""" + authorListOrder: Int! + + """A unique, persistent identifier for researchers, provided by ORCID.""" + orcid: String + + """A unique, persistent identifier for kaggle users at kaggle.com.""" + kaggleId: String + + """Full name of a deposition author (e.g. Jane Doe).""" + name: String! + + """Email address for this author""" + email: String + + """Name of the institutions an author is affiliated with. Comma separated""" + affiliationName: String + + """Address of the institution an author is affiliated with.""" + affiliationAddress: String + + """ + A unique identifier assigned to the affiliated institution by The Research Organization Registry (ROR). + """ + affiliationIdentifier: String + + """Indicates whether an author is the corresponding author""" + correspondingAuthorStatus: Boolean + + """Indicates whether an author is the main person creating the deposition""" + primaryAuthorStatus: Boolean +} + +type DepositionAuthorAggregate { + aggregate: [DepositionAuthorAggregateFunctions!] +} + +type DepositionAuthorAggregateFunctions { + sum: DepositionAuthorNumericalColumns + avg: DepositionAuthorNumericalColumns + stddev: DepositionAuthorNumericalColumns + variance: DepositionAuthorNumericalColumns + min: DepositionAuthorMinMaxColumns + max: DepositionAuthorMinMaxColumns + groupBy: DepositionAuthorGroupByOptions + count(distinct: Boolean = false, columns: DepositionAuthorCountColumns = null): Int +} + +input DepositionAuthorAggregateWhereClause { + count: DepositionAuthorAggregateWhereClauseCount! +} + +input DepositionAuthorAggregateWhereClauseCount { + arguments: DepositionAuthorCountColumns + distinct: Boolean + filter: DepositionAuthorWhereClause + predicate: IntComparators +} + +"""A connection to a list of items.""" +type DepositionAuthorConnection { + """Pagination data for this connection""" + pageInfo: PageInfo! + + """Contains the nodes in this connection""" + edges: [DepositionAuthorEdge!]! +} + +enum DepositionAuthorCountColumns { + id + authorListOrder + orcid + kaggleId + name + email + affiliationName + affiliationAddress + affiliationIdentifier + correspondingAuthorStatus + primaryAuthorStatus +} + +input DepositionAuthorCreateInput { + depositionId: ID! + + """Numeric identifier (May change!)""" + id: Int! + + """The order in which the author appears in the publication""" + authorListOrder: Int! + + """A unique, persistent identifier for researchers, provided by ORCID.""" + orcid: String = null + + """A unique, persistent identifier for kaggle users at kaggle.com.""" + kaggleId: String = null + + """Full name of a deposition author (e.g. Jane Doe).""" + name: String! + + """Email address for this author""" + email: String = null + + """Name of the institutions an author is affiliated with. Comma separated""" + affiliationName: String = null + + """Address of the institution an author is affiliated with.""" + affiliationAddress: String = null + + """ + A unique identifier assigned to the affiliated institution by The Research Organization Registry (ROR). + """ + affiliationIdentifier: String = null + + """Indicates whether an author is the corresponding author""" + correspondingAuthorStatus: Boolean = null + + """Indicates whether an author is the main person creating the deposition""" + primaryAuthorStatus: Boolean = null +} + +"""An edge in a connection.""" +type DepositionAuthorEdge { + """A cursor for use in pagination""" + cursor: String! + + """The item at the end of the edge""" + node: DepositionAuthor! +} + +type DepositionAuthorGroupByOptions { + deposition: DepositionGroupByOptions + id: Int + authorListOrder: Int + orcid: String + kaggleId: String + name: String + email: String + affiliationName: String + affiliationAddress: String + affiliationIdentifier: String + correspondingAuthorStatus: Boolean + primaryAuthorStatus: Boolean +} + +type DepositionAuthorMinMaxColumns { + id: Int + authorListOrder: Int + orcid: String + kaggleId: String + name: String + email: String + affiliationName: String + affiliationAddress: String + affiliationIdentifier: String +} + +type DepositionAuthorNumericalColumns { + id: Int + authorListOrder: Int +} + +input DepositionAuthorOrderByClause { + deposition: DepositionOrderByClause + id: orderBy + authorListOrder: orderBy + orcid: orderBy + kaggleId: orderBy + name: orderBy + email: orderBy + affiliationName: orderBy + affiliationAddress: orderBy + affiliationIdentifier: orderBy + correspondingAuthorStatus: orderBy + primaryAuthorStatus: orderBy +} + +input DepositionAuthorUpdateInput { + depositionId: ID + + """Numeric identifier (May change!)""" + id: Int + + """The order in which the author appears in the publication""" + authorListOrder: Int + + """A unique, persistent identifier for researchers, provided by ORCID.""" + orcid: String = null + + """A unique, persistent identifier for kaggle users at kaggle.com.""" + kaggleId: String = null + + """Full name of a deposition author (e.g. Jane Doe).""" + name: String + + """Email address for this author""" + email: String = null + + """Name of the institutions an author is affiliated with. Comma separated""" + affiliationName: String = null + + """Address of the institution an author is affiliated with.""" + affiliationAddress: String = null + + """ + A unique identifier assigned to the affiliated institution by The Research Organization Registry (ROR). + """ + affiliationIdentifier: String = null + + """Indicates whether an author is the corresponding author""" + correspondingAuthorStatus: Boolean = null + + """Indicates whether an author is the main person creating the deposition""" + primaryAuthorStatus: Boolean = null +} + +input DepositionAuthorWhereClause { + deposition: DepositionWhereClause + depositionId: IntComparators + id: IntComparators + authorListOrder: IntComparators + orcid: StrComparators + kaggleId: StrComparators + name: StrComparators + email: StrComparators + affiliationName: StrComparators + affiliationAddress: StrComparators + affiliationIdentifier: StrComparators + correspondingAuthorStatus: BoolComparators + primaryAuthorStatus: BoolComparators +} + +input DepositionAuthorWhereClauseMutations { + id: IntComparators +} + +enum DepositionCountColumns { + title + description + tag + depositionPublications + relatedDatabaseEntries + depositionDate + releaseDate + lastModifiedDate + keyPhotoUrl + keyPhotoThumbnailUrl + id +} + +input DepositionCreateInput { + """Title for the deposition""" + title: String! + + """Description for the deposition""" + description: String! + + """Tag for the deposition - like ml competition""" + tag: String = null + + """The publications related to this deposition""" + depositionPublications: String = null + + """The related database entries to this deposition""" + relatedDatabaseEntries: String = null + + """The date the deposition was deposited""" + depositionDate: DateTime! + + """The date the deposition was released""" + releaseDate: DateTime! + + """The date the deposition was last modified""" + lastModifiedDate: DateTime! + + """URL for the deposition preview image.""" + keyPhotoUrl: String = null + + """URL for the deposition thumbnail image.""" + keyPhotoThumbnailUrl: String = null + + """Numeric identifier (May change!)""" + id: Int! +} + +type DepositionGroupByOptions { + authors: DepositionAuthorGroupByOptions + alignments: AlignmentGroupByOptions + annotations: AnnotationGroupByOptions + datasets: DatasetGroupByOptions + frames: FrameGroupByOptions + tiltseries: TiltseriesGroupByOptions + tomograms: TomogramGroupByOptions + title: String + description: String + tag: String + depositionTypes: DepositionTypeGroupByOptions + depositionPublications: String + relatedDatabaseEntries: String + depositionDate: DateTime + releaseDate: DateTime + lastModifiedDate: DateTime + keyPhotoUrl: String + keyPhotoThumbnailUrl: String + id: Int +} + +type DepositionMinMaxColumns { + title: String + description: String + tag: String + depositionPublications: String + relatedDatabaseEntries: String + depositionDate: DateTime + releaseDate: DateTime + lastModifiedDate: DateTime + keyPhotoUrl: String + keyPhotoThumbnailUrl: String + id: Int +} + +type DepositionNumericalColumns { + id: Int +} + +input DepositionOrderByClause { + title: orderBy + description: orderBy + tag: orderBy + depositionPublications: orderBy + relatedDatabaseEntries: orderBy + depositionDate: orderBy + releaseDate: orderBy + lastModifiedDate: orderBy + keyPhotoUrl: orderBy + keyPhotoThumbnailUrl: orderBy + id: orderBy +} + +type DepositionType implements EntityInterface & Node { + """The Globally Unique ID of this object""" + _id: GlobalID! + + """Numeric identifier (May change!)""" + id: Int! + deposition(where: DepositionWhereClause = null, orderBy: [DepositionOrderByClause!] = []): Deposition + depositionId: Int! + + """ + The type of data submitted as a part of this deposition (annotation, dataset, tomogram) + """ + type: deposition_types_enum +} + +type DepositionTypeAggregate { + aggregate: [DepositionTypeAggregateFunctions!] +} + +type DepositionTypeAggregateFunctions { + sum: DepositionTypeNumericalColumns + avg: DepositionTypeNumericalColumns + stddev: DepositionTypeNumericalColumns + variance: DepositionTypeNumericalColumns + min: DepositionTypeMinMaxColumns + max: DepositionTypeMinMaxColumns + groupBy: DepositionTypeGroupByOptions + count(distinct: Boolean = false, columns: DepositionTypeCountColumns = null): Int +} + +input DepositionTypeAggregateWhereClause { + count: DepositionTypeAggregateWhereClauseCount! +} + +input DepositionTypeAggregateWhereClauseCount { + arguments: DepositionTypeCountColumns + distinct: Boolean + filter: DepositionTypeWhereClause + predicate: IntComparators +} + +"""A connection to a list of items.""" +type DepositionTypeConnection { + """Pagination data for this connection""" + pageInfo: PageInfo! + + """Contains the nodes in this connection""" + edges: [DepositionTypeEdge!]! +} + +enum DepositionTypeCountColumns { + type + id +} + +input DepositionTypeCreateInput { + depositionId: ID! + + """ + The type of data submitted as a part of this deposition (annotation, dataset, tomogram) + """ + type: deposition_types_enum = null + + """Numeric identifier (May change!)""" + id: Int! +} + +"""An edge in a connection.""" +type DepositionTypeEdge { + """A cursor for use in pagination""" + cursor: String! + + """The item at the end of the edge""" + node: DepositionType! +} + +type DepositionTypeGroupByOptions { + deposition: DepositionGroupByOptions + type: deposition_types_enum + id: Int +} + +type DepositionTypeMinMaxColumns { + id: Int +} + +type DepositionTypeNumericalColumns { + id: Int +} + +input DepositionTypeOrderByClause { + deposition: DepositionOrderByClause + type: orderBy + id: orderBy +} + +input DepositionTypeUpdateInput { + depositionId: ID + + """ + The type of data submitted as a part of this deposition (annotation, dataset, tomogram) + """ + type: deposition_types_enum = null + + """Numeric identifier (May change!)""" + id: Int +} + +input DepositionTypeWhereClause { + deposition: DepositionWhereClause + depositionId: IntComparators + type: Deposition_types_enumEnumComparators + id: IntComparators +} + +input DepositionTypeWhereClauseMutations { + id: IntComparators +} + +input DepositionUpdateInput { + """Title for the deposition""" + title: String + + """Description for the deposition""" + description: String + + """Tag for the deposition - like ml competition""" + tag: String = null + + """The publications related to this deposition""" + depositionPublications: String = null + + """The related database entries to this deposition""" + relatedDatabaseEntries: String = null + + """The date the deposition was deposited""" + depositionDate: DateTime + + """The date the deposition was released""" + releaseDate: DateTime + + """The date the deposition was last modified""" + lastModifiedDate: DateTime + + """URL for the deposition preview image.""" + keyPhotoUrl: String = null + + """URL for the deposition thumbnail image.""" + keyPhotoThumbnailUrl: String = null + + """Numeric identifier (May change!)""" + id: Int +} + +input DepositionWhereClause { + authors: DepositionAuthorWhereClause + authorsAggregate: DepositionAuthorAggregateWhereClause + alignments: AlignmentWhereClause + alignmentsAggregate: AlignmentAggregateWhereClause + annotations: AnnotationWhereClause + annotationsAggregate: AnnotationAggregateWhereClause + datasets: DatasetWhereClause + datasetsAggregate: DatasetAggregateWhereClause + frames: FrameWhereClause + framesAggregate: FrameAggregateWhereClause + tiltseries: TiltseriesWhereClause + tiltseriesAggregate: TiltseriesAggregateWhereClause + tomograms: TomogramWhereClause + tomogramsAggregate: TomogramAggregateWhereClause + title: StrComparators + description: StrComparators + tag: StrComparators + depositionTypes: DepositionTypeWhereClause + depositionTypesAggregate: DepositionTypeAggregateWhereClause + depositionPublications: StrComparators + relatedDatabaseEntries: StrComparators + depositionDate: DatetimeComparators + releaseDate: DatetimeComparators + lastModifiedDate: DatetimeComparators + keyPhotoUrl: StrComparators + keyPhotoThumbnailUrl: StrComparators + id: IntComparators +} + +input DepositionWhereClauseMutations { + id: IntComparators +} + +input Deposition_types_enumEnumComparators { + _eq: deposition_types_enum + _neq: deposition_types_enum + _in: [deposition_types_enum!] + _nin: [deposition_types_enum!] + _gt: deposition_types_enum + _gte: deposition_types_enum + _lt: deposition_types_enum + _lte: deposition_types_enum + _is_null: Boolean +} + +interface EntityInterface implements Node { + """The Globally Unique ID of this object""" + _id: GlobalID! +} + +input Fiducial_alignment_status_enumEnumComparators { + _eq: fiducial_alignment_status_enum + _neq: fiducial_alignment_status_enum + _in: [fiducial_alignment_status_enum!] + _nin: [fiducial_alignment_status_enum!] + _gt: fiducial_alignment_status_enum + _gte: fiducial_alignment_status_enum + _lt: fiducial_alignment_status_enum + _lte: fiducial_alignment_status_enum + _is_null: Boolean +} + +input FloatComparators { + _eq: Float + _neq: Float + _in: [Float!] + _nin: [Float!] + _gt: Float + _gte: Float + _lt: Float + _lte: Float + _is_null: Boolean +} + +type Frame implements EntityInterface & Node { + """The Globally Unique ID of this object""" + _id: GlobalID! + + """Numeric identifier (May change!)""" + id: Int! + deposition(where: DepositionWhereClause = null, orderBy: [DepositionOrderByClause!] = []): Deposition + depositionId: Int! + run(where: RunWhereClause = null, orderBy: [RunOrderByClause!] = []): Run + runId: Int! + + """Frame's acquistion order within a tilt experiment""" + acquisitionOrder: Int + + """The total accumulated dose exposure frame""" + accumulatedDose: Float + + """The dose exposure of this frame""" + exposureDose: Float + + """Whether this frame has been gain corrected""" + isGainCorrected: Boolean + perSectionParameters( + where: PerSectionParametersWhereClause = null + orderBy: [PerSectionParametersOrderByClause!] = [] + + """Returns the items in the list that come before the specified cursor.""" + before: String = null + + """Returns the items in the list that come after the specified cursor.""" + after: String = null + + """Returns the first n items from the list.""" + first: Int = null + + """Returns the items in the list that come after the specified cursor.""" + last: Int = null + ): PerSectionParametersConnection! + perSectionParametersAggregate(where: PerSectionParametersWhereClause = null): PerSectionParametersAggregate + + """S3 path to the frame file""" + s3FramePath: String + + """HTTPS path to the frame file""" + httpsFramePath: String + + """Size of the frame file in bytes""" + fileSize: Float +} + +""" +References to files containing more information about frame acquisition +""" +type FrameAcquisitionFile implements EntityInterface & Node { + """The Globally Unique ID of this object""" + _id: GlobalID! + + """Numeric identifier (May change!)""" + id: Int! + run(where: RunWhereClause = null, orderBy: [RunOrderByClause!] = []): Run + runId: Int + + """Path to the frame acquisition mdoc file in s3""" + s3MdocPath: String! + + """Path to the frame acquisition mdoc file as an https url""" + httpsMdocPath: String! +} + +type FrameAcquisitionFileAggregate { + aggregate: [FrameAcquisitionFileAggregateFunctions!] +} + +type FrameAcquisitionFileAggregateFunctions { + sum: FrameAcquisitionFileNumericalColumns + avg: FrameAcquisitionFileNumericalColumns + stddev: FrameAcquisitionFileNumericalColumns + variance: FrameAcquisitionFileNumericalColumns + min: FrameAcquisitionFileMinMaxColumns + max: FrameAcquisitionFileMinMaxColumns + groupBy: FrameAcquisitionFileGroupByOptions + count(distinct: Boolean = false, columns: FrameAcquisitionFileCountColumns = null): Int +} + +input FrameAcquisitionFileAggregateWhereClause { + count: FrameAcquisitionFileAggregateWhereClauseCount! +} + +input FrameAcquisitionFileAggregateWhereClauseCount { + arguments: FrameAcquisitionFileCountColumns + distinct: Boolean + filter: FrameAcquisitionFileWhereClause + predicate: IntComparators +} + +"""A connection to a list of items.""" +type FrameAcquisitionFileConnection { + """Pagination data for this connection""" + pageInfo: PageInfo! + + """Contains the nodes in this connection""" + edges: [FrameAcquisitionFileEdge!]! +} + +enum FrameAcquisitionFileCountColumns { + s3MdocPath + httpsMdocPath + id +} + +input FrameAcquisitionFileCreateInput { + runId: ID = null + + """Path to the frame acquisition mdoc file in s3""" + s3MdocPath: String! + + """Path to the frame acquisition mdoc file as an https url""" + httpsMdocPath: String! + + """Numeric identifier (May change!)""" + id: Int! +} + +"""An edge in a connection.""" +type FrameAcquisitionFileEdge { + """A cursor for use in pagination""" + cursor: String! + + """The item at the end of the edge""" + node: FrameAcquisitionFile! +} + +type FrameAcquisitionFileGroupByOptions { + run: RunGroupByOptions + s3MdocPath: String + httpsMdocPath: String + id: Int +} + +type FrameAcquisitionFileMinMaxColumns { + s3MdocPath: String + httpsMdocPath: String + id: Int +} + +type FrameAcquisitionFileNumericalColumns { + id: Int +} + +input FrameAcquisitionFileOrderByClause { + run: RunOrderByClause + s3MdocPath: orderBy + httpsMdocPath: orderBy + id: orderBy +} + +input FrameAcquisitionFileUpdateInput { + runId: ID = null + + """Path to the frame acquisition mdoc file in s3""" + s3MdocPath: String + + """Path to the frame acquisition mdoc file as an https url""" + httpsMdocPath: String + + """Numeric identifier (May change!)""" + id: Int +} + +input FrameAcquisitionFileWhereClause { + run: RunWhereClause + runId: IntComparators + s3MdocPath: StrComparators + httpsMdocPath: StrComparators + id: IntComparators +} + +input FrameAcquisitionFileWhereClauseMutations { + id: IntComparators +} + +type FrameAggregate { + aggregate: [FrameAggregateFunctions!] +} + +type FrameAggregateFunctions { + sum: FrameNumericalColumns + avg: FrameNumericalColumns + stddev: FrameNumericalColumns + variance: FrameNumericalColumns + min: FrameMinMaxColumns + max: FrameMinMaxColumns + groupBy: FrameGroupByOptions + count(distinct: Boolean = false, columns: FrameCountColumns = null): Int +} + +input FrameAggregateWhereClause { + count: FrameAggregateWhereClauseCount! +} + +input FrameAggregateWhereClauseCount { + arguments: FrameCountColumns + distinct: Boolean + filter: FrameWhereClause + predicate: IntComparators +} + +"""A connection to a list of items.""" +type FrameConnection { + """Pagination data for this connection""" + pageInfo: PageInfo! + + """Contains the nodes in this connection""" + edges: [FrameEdge!]! +} + +enum FrameCountColumns { + acquisitionOrder + accumulatedDose + exposureDose + isGainCorrected + s3FramePath + httpsFramePath + fileSize + id +} + +input FrameCreateInput { + depositionId: ID! + runId: ID! + + """Frame's acquistion order within a tilt experiment""" + acquisitionOrder: Int = null + + """The total accumulated dose exposure frame""" + accumulatedDose: Float = null + + """The dose exposure of this frame""" + exposureDose: Float = null + + """Whether this frame has been gain corrected""" + isGainCorrected: Boolean = null + + """S3 path to the frame file""" + s3FramePath: String = null + + """HTTPS path to the frame file""" + httpsFramePath: String = null + + """Size of the frame file in bytes""" + fileSize: Float = null + + """Numeric identifier (May change!)""" + id: Int! +} + +"""An edge in a connection.""" +type FrameEdge { + """A cursor for use in pagination""" + cursor: String! + + """The item at the end of the edge""" + node: Frame! +} + +type FrameGroupByOptions { + deposition: DepositionGroupByOptions + run: RunGroupByOptions + acquisitionOrder: Int + accumulatedDose: Float + exposureDose: Float + isGainCorrected: Boolean + perSectionParameters: PerSectionParametersGroupByOptions + s3FramePath: String + httpsFramePath: String + fileSize: Float + id: Int +} + +type FrameMinMaxColumns { + acquisitionOrder: Int + accumulatedDose: Float + exposureDose: Float + s3FramePath: String + httpsFramePath: String + fileSize: Float + id: Int +} + +type FrameNumericalColumns { + acquisitionOrder: Int + accumulatedDose: Float + exposureDose: Float + fileSize: Float + id: Int +} + +input FrameOrderByClause { + deposition: DepositionOrderByClause + run: RunOrderByClause + acquisitionOrder: orderBy + accumulatedDose: orderBy + exposureDose: orderBy + isGainCorrected: orderBy + s3FramePath: orderBy + httpsFramePath: orderBy + fileSize: orderBy + id: orderBy +} + +input FrameUpdateInput { + depositionId: ID + runId: ID + + """Frame's acquistion order within a tilt experiment""" + acquisitionOrder: Int = null + + """The total accumulated dose exposure frame""" + accumulatedDose: Float = null + + """The dose exposure of this frame""" + exposureDose: Float = null + + """Whether this frame has been gain corrected""" + isGainCorrected: Boolean = null + + """S3 path to the frame file""" + s3FramePath: String = null + + """HTTPS path to the frame file""" + httpsFramePath: String = null + + """Size of the frame file in bytes""" + fileSize: Float = null + + """Numeric identifier (May change!)""" + id: Int +} + +input FrameWhereClause { + deposition: DepositionWhereClause + depositionId: IntComparators + run: RunWhereClause + runId: IntComparators + acquisitionOrder: IntComparators + accumulatedDose: FloatComparators + exposureDose: FloatComparators + isGainCorrected: BoolComparators + perSectionParameters: PerSectionParametersWhereClause + perSectionParametersAggregate: PerSectionParametersAggregateWhereClause + s3FramePath: StrComparators + httpsFramePath: StrComparators + fileSize: FloatComparators + id: IntComparators +} + +input FrameWhereClauseMutations { + id: IntComparators +} + +"""Gain values for frames in this run""" +type GainFile implements EntityInterface & Node { + """The Globally Unique ID of this object""" + _id: GlobalID! + + """Numeric identifier (May change!)""" + id: Int! + run(where: RunWhereClause = null, orderBy: [RunOrderByClause!] = []): Run + runId: Int! + + """Path to the file in s3""" + s3FilePath: String! + + """Path to the file as an https url""" + httpsFilePath: String! +} + +type GainFileAggregate { + aggregate: [GainFileAggregateFunctions!] +} + +type GainFileAggregateFunctions { + sum: GainFileNumericalColumns + avg: GainFileNumericalColumns + stddev: GainFileNumericalColumns + variance: GainFileNumericalColumns + min: GainFileMinMaxColumns + max: GainFileMinMaxColumns + groupBy: GainFileGroupByOptions + count(distinct: Boolean = false, columns: GainFileCountColumns = null): Int +} + +input GainFileAggregateWhereClause { + count: GainFileAggregateWhereClauseCount! +} + +input GainFileAggregateWhereClauseCount { + arguments: GainFileCountColumns + distinct: Boolean + filter: GainFileWhereClause + predicate: IntComparators +} + +"""A connection to a list of items.""" +type GainFileConnection { + """Pagination data for this connection""" + pageInfo: PageInfo! + + """Contains the nodes in this connection""" + edges: [GainFileEdge!]! +} + +enum GainFileCountColumns { + s3FilePath + httpsFilePath + id +} + +input GainFileCreateInput { + runId: ID! + + """Path to the file in s3""" + s3FilePath: String! + + """Path to the file as an https url""" + httpsFilePath: String! + + """Numeric identifier (May change!)""" + id: Int! +} + +"""An edge in a connection.""" +type GainFileEdge { + """A cursor for use in pagination""" + cursor: String! + + """The item at the end of the edge""" + node: GainFile! +} + +type GainFileGroupByOptions { + run: RunGroupByOptions + s3FilePath: String + httpsFilePath: String + id: Int +} + +type GainFileMinMaxColumns { + s3FilePath: String + httpsFilePath: String + id: Int +} + +type GainFileNumericalColumns { + id: Int +} + +input GainFileOrderByClause { + run: RunOrderByClause + s3FilePath: orderBy + httpsFilePath: orderBy + id: orderBy +} + +input GainFileUpdateInput { + runId: ID + + """Path to the file in s3""" + s3FilePath: String + + """Path to the file as an https url""" + httpsFilePath: String + + """Numeric identifier (May change!)""" + id: Int +} + +input GainFileWhereClause { + run: RunWhereClause + runId: IntComparators + s3FilePath: StrComparators + httpsFilePath: StrComparators + id: IntComparators +} + +input GainFileWhereClauseMutations { + id: IntComparators +} + +""" +The `ID` scalar type represents a unique identifier, often used to refetch an object or as key for a cache. The ID type appears in a JSON response as a String; however, it is not intended to be human-readable. When expected as an input type, any string (such as `"4"`) or integer (such as `4`) input value will be accepted as an ID. +""" +scalar GlobalID @specifiedBy(url: "https://relay.dev/graphql/objectidentification.htm") + +""" +An ontology term/ID or accession code, state and description associated with a Run, describing cellular components that were visually identified, but not labeled, in a tomogram associated with the Run +""" +type IdentifiedObject implements EntityInterface & Node { + """The Globally Unique ID of this object""" + _id: GlobalID! + + """Numeric identifier (May change!)""" + id: Int! + run(where: RunWhereClause = null, orderBy: [RunOrderByClause!] = []): Run + runId: Int + + """ + Gene Ontology Cellular Component identifier or UniProtKB accession for the identified object. + """ + objectId: String! + + """ + Name of the identified object (e.g. ribosome, nuclear pore complex, actin filament, membrane) + """ + objectName: String! + + """ + A textual description of the identified object, can be a longer description to include additional information not covered by the IdentifiedObject object name and state. + """ + objectDescription: String + + """Molecule state of the identified object (e.g. open, closed)""" + objectState: String +} + +type IdentifiedObjectAggregate { + aggregate: [IdentifiedObjectAggregateFunctions!] +} + +type IdentifiedObjectAggregateFunctions { + sum: IdentifiedObjectNumericalColumns + avg: IdentifiedObjectNumericalColumns + stddev: IdentifiedObjectNumericalColumns + variance: IdentifiedObjectNumericalColumns + min: IdentifiedObjectMinMaxColumns + max: IdentifiedObjectMinMaxColumns + groupBy: IdentifiedObjectGroupByOptions + count(distinct: Boolean = false, columns: IdentifiedObjectCountColumns = null): Int +} + +input IdentifiedObjectAggregateWhereClause { + count: IdentifiedObjectAggregateWhereClauseCount! +} + +input IdentifiedObjectAggregateWhereClauseCount { + arguments: IdentifiedObjectCountColumns + distinct: Boolean + filter: IdentifiedObjectWhereClause + predicate: IntComparators +} + +"""A connection to a list of items.""" +type IdentifiedObjectConnection { + """Pagination data for this connection""" + pageInfo: PageInfo! + + """Contains the nodes in this connection""" + edges: [IdentifiedObjectEdge!]! +} + +enum IdentifiedObjectCountColumns { + objectId + objectName + objectDescription + objectState + id +} + +input IdentifiedObjectCreateInput { + """Run that this identified object is a part of""" + runId: ID = null + + """ + Gene Ontology Cellular Component identifier or UniProtKB accession for the identified object. + """ + objectId: String! + + """ + Name of the identified object (e.g. ribosome, nuclear pore complex, actin filament, membrane) + """ + objectName: String! + + """ + A textual description of the identified object, can be a longer description to include additional information not covered by the IdentifiedObject object name and state. + """ + objectDescription: String = null + + """Molecule state of the identified object (e.g. open, closed)""" + objectState: String = null + + """Numeric identifier (May change!)""" + id: Int! +} + +"""An edge in a connection.""" +type IdentifiedObjectEdge { + """A cursor for use in pagination""" + cursor: String! + + """The item at the end of the edge""" + node: IdentifiedObject! +} + +type IdentifiedObjectGroupByOptions { + run: RunGroupByOptions + objectId: String + objectName: String + objectDescription: String + objectState: String + id: Int +} + +type IdentifiedObjectMinMaxColumns { + objectId: String + objectName: String + objectDescription: String + objectState: String + id: Int +} + +type IdentifiedObjectNumericalColumns { + id: Int +} + +input IdentifiedObjectOrderByClause { + run: RunOrderByClause + objectId: orderBy + objectName: orderBy + objectDescription: orderBy + objectState: orderBy + id: orderBy +} + +input IdentifiedObjectUpdateInput { + """Run that this identified object is a part of""" + runId: ID = null + + """ + Gene Ontology Cellular Component identifier or UniProtKB accession for the identified object. + """ + objectId: String + + """ + Name of the identified object (e.g. ribosome, nuclear pore complex, actin filament, membrane) + """ + objectName: String + + """ + A textual description of the identified object, can be a longer description to include additional information not covered by the IdentifiedObject object name and state. + """ + objectDescription: String = null + + """Molecule state of the identified object (e.g. open, closed)""" + objectState: String = null + + """Numeric identifier (May change!)""" + id: Int +} + +input IdentifiedObjectWhereClause { + run: RunWhereClause + runId: IntComparators + objectId: StrComparators + objectName: StrComparators + objectDescription: StrComparators + objectState: StrComparators + id: IntComparators +} + +input IdentifiedObjectWhereClauseMutations { + id: IntComparators +} + +input IntComparators { + _eq: Int + _neq: Int + _in: [Int!] + _nin: [Int!] + _gt: Int + _gte: Int + _lt: Int + _lte: Int + _is_null: Boolean +} + +input LimitOffsetClause { + limit: Int + offset: Int +} + +type Mutation { + createGainFile(input: GainFileCreateInput!): GainFile! + updateGainFile(input: GainFileUpdateInput!, where: GainFileWhereClauseMutations!): [GainFile!]! + deleteGainFile(where: GainFileWhereClauseMutations!): [GainFile!]! + createFrameAcquisitionFile(input: FrameAcquisitionFileCreateInput!): FrameAcquisitionFile! + updateFrameAcquisitionFile(input: FrameAcquisitionFileUpdateInput!, where: FrameAcquisitionFileWhereClauseMutations!): [FrameAcquisitionFile!]! + deleteFrameAcquisitionFile(where: FrameAcquisitionFileWhereClauseMutations!): [FrameAcquisitionFile!]! + createAlignment(input: AlignmentCreateInput!): Alignment! + updateAlignment(input: AlignmentUpdateInput!, where: AlignmentWhereClauseMutations!): [Alignment!]! + deleteAlignment(where: AlignmentWhereClauseMutations!): [Alignment!]! + createAnnotationAuthor(input: AnnotationAuthorCreateInput!): AnnotationAuthor! + updateAnnotationAuthor(input: AnnotationAuthorUpdateInput!, where: AnnotationAuthorWhereClauseMutations!): [AnnotationAuthor!]! + deleteAnnotationAuthor(where: AnnotationAuthorWhereClauseMutations!): [AnnotationAuthor!]! + createAnnotationFile(input: AnnotationFileCreateInput!): AnnotationFile! + updateAnnotationFile(input: AnnotationFileUpdateInput!, where: AnnotationFileWhereClauseMutations!): [AnnotationFile!]! + deleteAnnotationFile(where: AnnotationFileWhereClauseMutations!): [AnnotationFile!]! + createAnnotationShape(input: AnnotationShapeCreateInput!): AnnotationShape! + updateAnnotationShape(input: AnnotationShapeUpdateInput!, where: AnnotationShapeWhereClauseMutations!): [AnnotationShape!]! + deleteAnnotationShape(where: AnnotationShapeWhereClauseMutations!): [AnnotationShape!]! + createAnnotation(input: AnnotationCreateInput!): Annotation! + updateAnnotation(input: AnnotationUpdateInput!, where: AnnotationWhereClauseMutations!): [Annotation!]! + deleteAnnotation(where: AnnotationWhereClauseMutations!): [Annotation!]! + createDatasetAuthor(input: DatasetAuthorCreateInput!): DatasetAuthor! + updateDatasetAuthor(input: DatasetAuthorUpdateInput!, where: DatasetAuthorWhereClauseMutations!): [DatasetAuthor!]! + deleteDatasetAuthor(where: DatasetAuthorWhereClauseMutations!): [DatasetAuthor!]! + createDatasetFunding(input: DatasetFundingCreateInput!): DatasetFunding! + updateDatasetFunding(input: DatasetFundingUpdateInput!, where: DatasetFundingWhereClauseMutations!): [DatasetFunding!]! + deleteDatasetFunding(where: DatasetFundingWhereClauseMutations!): [DatasetFunding!]! + createDataset(input: DatasetCreateInput!): Dataset! + updateDataset(input: DatasetUpdateInput!, where: DatasetWhereClauseMutations!): [Dataset!]! + deleteDataset(where: DatasetWhereClauseMutations!): [Dataset!]! + createDepositionAuthor(input: DepositionAuthorCreateInput!): DepositionAuthor! + updateDepositionAuthor(input: DepositionAuthorUpdateInput!, where: DepositionAuthorWhereClauseMutations!): [DepositionAuthor!]! + deleteDepositionAuthor(where: DepositionAuthorWhereClauseMutations!): [DepositionAuthor!]! + createDeposition(input: DepositionCreateInput!): Deposition! + updateDeposition(input: DepositionUpdateInput!, where: DepositionWhereClauseMutations!): [Deposition!]! + deleteDeposition(where: DepositionWhereClauseMutations!): [Deposition!]! + createDepositionType(input: DepositionTypeCreateInput!): DepositionType! + updateDepositionType(input: DepositionTypeUpdateInput!, where: DepositionTypeWhereClauseMutations!): [DepositionType!]! + deleteDepositionType(where: DepositionTypeWhereClauseMutations!): [DepositionType!]! + createFrame(input: FrameCreateInput!): Frame! + updateFrame(input: FrameUpdateInput!, where: FrameWhereClauseMutations!): [Frame!]! + deleteFrame(where: FrameWhereClauseMutations!): [Frame!]! + createIdentifiedObject(input: IdentifiedObjectCreateInput!): IdentifiedObject! + updateIdentifiedObject(input: IdentifiedObjectUpdateInput!, where: IdentifiedObjectWhereClauseMutations!): [IdentifiedObject!]! + deleteIdentifiedObject(where: IdentifiedObjectWhereClauseMutations!): [IdentifiedObject!]! + createPerSectionAlignmentParameters(input: PerSectionAlignmentParametersCreateInput!): PerSectionAlignmentParameters! + updatePerSectionAlignmentParameters(input: PerSectionAlignmentParametersUpdateInput!, where: PerSectionAlignmentParametersWhereClauseMutations!): [PerSectionAlignmentParameters!]! + deletePerSectionAlignmentParameters(where: PerSectionAlignmentParametersWhereClauseMutations!): [PerSectionAlignmentParameters!]! + createPerSectionParameters(input: PerSectionParametersCreateInput!): PerSectionParameters! + updatePerSectionParameters(input: PerSectionParametersUpdateInput!, where: PerSectionParametersWhereClauseMutations!): [PerSectionParameters!]! + deletePerSectionParameters(where: PerSectionParametersWhereClauseMutations!): [PerSectionParameters!]! + createRun(input: RunCreateInput!): Run! + updateRun(input: RunUpdateInput!, where: RunWhereClauseMutations!): [Run!]! + deleteRun(where: RunWhereClauseMutations!): [Run!]! + createTiltseries(input: TiltseriesCreateInput!): Tiltseries! + updateTiltseries(input: TiltseriesUpdateInput!, where: TiltseriesWhereClauseMutations!): [Tiltseries!]! + deleteTiltseries(where: TiltseriesWhereClauseMutations!): [Tiltseries!]! + createTomogramAuthor(input: TomogramAuthorCreateInput!): TomogramAuthor! + updateTomogramAuthor(input: TomogramAuthorUpdateInput!, where: TomogramAuthorWhereClauseMutations!): [TomogramAuthor!]! + deleteTomogramAuthor(where: TomogramAuthorWhereClauseMutations!): [TomogramAuthor!]! + createTomogramVoxelSpacing(input: TomogramVoxelSpacingCreateInput!): TomogramVoxelSpacing! + updateTomogramVoxelSpacing(input: TomogramVoxelSpacingUpdateInput!, where: TomogramVoxelSpacingWhereClauseMutations!): [TomogramVoxelSpacing!]! + deleteTomogramVoxelSpacing(where: TomogramVoxelSpacingWhereClauseMutations!): [TomogramVoxelSpacing!]! + createTomogram(input: TomogramCreateInput!): Tomogram! + updateTomogram(input: TomogramUpdateInput!, where: TomogramWhereClauseMutations!): [Tomogram!]! + deleteTomogram(where: TomogramWhereClauseMutations!): [Tomogram!]! + createAnnotationMethodLink(input: AnnotationMethodLinkCreateInput!): AnnotationMethodLink! + updateAnnotationMethodLink(input: AnnotationMethodLinkUpdateInput!, where: AnnotationMethodLinkWhereClauseMutations!): [AnnotationMethodLink!]! + deleteAnnotationMethodLink(where: AnnotationMethodLinkWhereClauseMutations!): [AnnotationMethodLink!]! +} + +"""An object with a Globally Unique ID""" +interface Node { + """The Globally Unique ID of this object""" + _id: GlobalID! +} + +"""Information to aid in pagination.""" +type PageInfo { + """When paginating forwards, are there more items?""" + hasNextPage: Boolean! + + """When paginating backwards, are there more items?""" + hasPreviousPage: Boolean! + + """When paginating backwards, the cursor to continue.""" + startCursor: String + + """When paginating forwards, the cursor to continue.""" + endCursor: String +} + +"""Map alignment parameters to tilt series frames""" +type PerSectionAlignmentParameters implements EntityInterface & Node { + """The Globally Unique ID of this object""" + _id: GlobalID! + + """Numeric identifier (May change!)""" + id: Int! + alignment(where: AlignmentWhereClause = null, orderBy: [AlignmentOrderByClause!] = []): Alignment + alignmentId: Int! + + """z-index of the frame in the tiltseries""" + zIndex: Int! + + """In-plane X-shift of the projection in angstrom""" + xOffset: Float + + """In-plane Y-shift of the projection in angstrom""" + yOffset: Float + + """X-axis rotation in degrees""" + volumeXRotation: Float + + """In-plane rotation of the projection in degrees""" + inPlaneRotation: [[Float!]!] + + """Tilt angle of the projection in degrees""" + tiltAngle: Float +} + +type PerSectionAlignmentParametersAggregate { + aggregate: [PerSectionAlignmentParametersAggregateFunctions!] +} + +type PerSectionAlignmentParametersAggregateFunctions { + sum: PerSectionAlignmentParametersNumericalColumns + avg: PerSectionAlignmentParametersNumericalColumns + stddev: PerSectionAlignmentParametersNumericalColumns + variance: PerSectionAlignmentParametersNumericalColumns + min: PerSectionAlignmentParametersMinMaxColumns + max: PerSectionAlignmentParametersMinMaxColumns + groupBy: PerSectionAlignmentParametersGroupByOptions + count(distinct: Boolean = false, columns: PerSectionAlignmentParametersCountColumns = null): Int +} + +input PerSectionAlignmentParametersAggregateWhereClause { + count: PerSectionAlignmentParametersAggregateWhereClauseCount! +} + +input PerSectionAlignmentParametersAggregateWhereClauseCount { + arguments: PerSectionAlignmentParametersCountColumns + distinct: Boolean + filter: PerSectionAlignmentParametersWhereClause + predicate: IntComparators +} + +"""A connection to a list of items.""" +type PerSectionAlignmentParametersConnection { + """Pagination data for this connection""" + pageInfo: PageInfo! + + """Contains the nodes in this connection""" + edges: [PerSectionAlignmentParametersEdge!]! +} + +enum PerSectionAlignmentParametersCountColumns { + zIndex + xOffset + yOffset + volumeXRotation + inPlaneRotation + tiltAngle + id +} + +input PerSectionAlignmentParametersCreateInput { + """Tiltseries Alignment""" + alignmentId: ID! + + """z-index of the frame in the tiltseries""" + zIndex: Int! + + """In-plane X-shift of the projection in angstrom""" + xOffset: Float = null + + """In-plane Y-shift of the projection in angstrom""" + yOffset: Float = null + + """X-axis rotation in degrees""" + volumeXRotation: Float = null + + """In-plane rotation of the projection in degrees""" + inPlaneRotation: [[Float!]!] = null + + """Tilt angle of the projection in degrees""" + tiltAngle: Float = null + + """Numeric identifier (May change!)""" + id: Int! +} + +"""An edge in a connection.""" +type PerSectionAlignmentParametersEdge { + """A cursor for use in pagination""" + cursor: String! + + """The item at the end of the edge""" + node: PerSectionAlignmentParameters! +} + +type PerSectionAlignmentParametersGroupByOptions { + alignment: AlignmentGroupByOptions + zIndex: Int + xOffset: Float + yOffset: Float + volumeXRotation: Float + inPlaneRotation: [[Float!]!] + tiltAngle: Float + id: Int +} + +type PerSectionAlignmentParametersMinMaxColumns { + zIndex: Int + xOffset: Float + yOffset: Float + volumeXRotation: Float + tiltAngle: Float + id: Int +} + +type PerSectionAlignmentParametersNumericalColumns { + zIndex: Int + xOffset: Float + yOffset: Float + volumeXRotation: Float + tiltAngle: Float + id: Int +} + +input PerSectionAlignmentParametersOrderByClause { + alignment: AlignmentOrderByClause + zIndex: orderBy + xOffset: orderBy + yOffset: orderBy + volumeXRotation: orderBy + inPlaneRotation: orderBy + tiltAngle: orderBy + id: orderBy +} + +input PerSectionAlignmentParametersUpdateInput { + """Tiltseries Alignment""" + alignmentId: ID + + """z-index of the frame in the tiltseries""" + zIndex: Int + + """In-plane X-shift of the projection in angstrom""" + xOffset: Float = null + + """In-plane Y-shift of the projection in angstrom""" + yOffset: Float = null + + """X-axis rotation in degrees""" + volumeXRotation: Float = null + + """In-plane rotation of the projection in degrees""" + inPlaneRotation: [[Float!]!] = null + + """Tilt angle of the projection in degrees""" + tiltAngle: Float = null + + """Numeric identifier (May change!)""" + id: Int +} + +input PerSectionAlignmentParametersWhereClause { + alignment: AlignmentWhereClause + alignmentId: IntComparators + zIndex: IntComparators + xOffset: FloatComparators + yOffset: FloatComparators + volumeXRotation: FloatComparators + tiltAngle: FloatComparators + id: IntComparators +} + +input PerSectionAlignmentParametersWhereClauseMutations { + id: IntComparators +} + +"""Map individual Frames to a Tiltseries""" +type PerSectionParameters implements EntityInterface & Node { + """The Globally Unique ID of this object""" + _id: GlobalID! + + """Numeric identifier (May change!)""" + id: Int! + + """ + Angle (in degrees) from reciprocal space X axis to the major axis of defocus. + """ + astigmaticAngle: Float + frame(where: FrameWhereClause = null, orderBy: [FrameOrderByClause!] = []): Frame + frameId: Int! + + """ + Defocus (major axis) estimated for this tilt image in Angstrom (underfocus has positive sign). + """ + majorDefocus: Float + + """Maximum resolution of the frame""" + maxResolution: Float + + """ + Defocus (minor axis) estimated for this tilt image in Angstrom (underfocus has positive sign). + """ + minorDefocus: Float + + """Phase shift estimated for this tilt image in radians.""" + phaseShift: Float + + """Nominal tilt angle for this tilt image reported by the microscope.""" + rawAngle: Float! + run(where: RunWhereClause = null, orderBy: [RunOrderByClause!] = []): Run + runId: Int! + tiltseries(where: TiltseriesWhereClause = null, orderBy: [TiltseriesOrderByClause!] = []): Tiltseries + tiltseriesId: Int! + + """Index (0-based) of this tilt image in the tilt series stack.""" + zIndex: Int! +} + +type PerSectionParametersAggregate { + aggregate: [PerSectionParametersAggregateFunctions!] +} + +type PerSectionParametersAggregateFunctions { + sum: PerSectionParametersNumericalColumns + avg: PerSectionParametersNumericalColumns + stddev: PerSectionParametersNumericalColumns + variance: PerSectionParametersNumericalColumns + min: PerSectionParametersMinMaxColumns + max: PerSectionParametersMinMaxColumns + groupBy: PerSectionParametersGroupByOptions + count(distinct: Boolean = false, columns: PerSectionParametersCountColumns = null): Int +} + +input PerSectionParametersAggregateWhereClause { + count: PerSectionParametersAggregateWhereClauseCount! +} + +input PerSectionParametersAggregateWhereClauseCount { + arguments: PerSectionParametersCountColumns + distinct: Boolean + filter: PerSectionParametersWhereClause + predicate: IntComparators +} + +"""A connection to a list of items.""" +type PerSectionParametersConnection { + """Pagination data for this connection""" + pageInfo: PageInfo! + + """Contains the nodes in this connection""" + edges: [PerSectionParametersEdge!]! +} + +enum PerSectionParametersCountColumns { + astigmaticAngle + majorDefocus + maxResolution + minorDefocus + phaseShift + rawAngle + zIndex + id +} + +input PerSectionParametersCreateInput { + """ + Angle (in degrees) from reciprocal space X axis to the major axis of defocus. + """ + astigmaticAngle: Float = null + + """Frame that this section is a part of""" + frameId: ID! + + """ + Defocus (major axis) estimated for this tilt image in Angstrom (underfocus has positive sign). + """ + majorDefocus: Float = null + + """Maximum resolution of the frame""" + maxResolution: Float = null + + """ + Defocus (minor axis) estimated for this tilt image in Angstrom (underfocus has positive sign). + """ + minorDefocus: Float = null + + """Phase shift estimated for this tilt image in radians.""" + phaseShift: Float = null + + """Nominal tilt angle for this tilt image reported by the microscope.""" + rawAngle: Float! + + """Run that this section is a part of""" + runId: ID! + + """Tiltseries that this section is a part of""" + tiltseriesId: ID! + + """Index (0-based) of this tilt image in the tilt series stack.""" + zIndex: Int! + + """Numeric identifier (May change!)""" + id: Int! +} + +"""An edge in a connection.""" +type PerSectionParametersEdge { + """A cursor for use in pagination""" + cursor: String! + + """The item at the end of the edge""" + node: PerSectionParameters! +} + +type PerSectionParametersGroupByOptions { + astigmaticAngle: Float + frame: FrameGroupByOptions + majorDefocus: Float + maxResolution: Float + minorDefocus: Float + phaseShift: Float + rawAngle: Float + run: RunGroupByOptions + tiltseries: TiltseriesGroupByOptions + zIndex: Int + id: Int +} + +type PerSectionParametersMinMaxColumns { + astigmaticAngle: Float + majorDefocus: Float + maxResolution: Float + minorDefocus: Float + phaseShift: Float + rawAngle: Float + zIndex: Int + id: Int +} + +type PerSectionParametersNumericalColumns { + astigmaticAngle: Float + majorDefocus: Float + maxResolution: Float + minorDefocus: Float + phaseShift: Float + rawAngle: Float + zIndex: Int + id: Int +} + +input PerSectionParametersOrderByClause { + astigmaticAngle: orderBy + frame: FrameOrderByClause + majorDefocus: orderBy + maxResolution: orderBy + minorDefocus: orderBy + phaseShift: orderBy + rawAngle: orderBy + run: RunOrderByClause + tiltseries: TiltseriesOrderByClause + zIndex: orderBy + id: orderBy +} + +input PerSectionParametersUpdateInput { + """ + Angle (in degrees) from reciprocal space X axis to the major axis of defocus. + """ + astigmaticAngle: Float = null + + """Frame that this section is a part of""" + frameId: ID + + """ + Defocus (major axis) estimated for this tilt image in Angstrom (underfocus has positive sign). + """ + majorDefocus: Float = null + + """Maximum resolution of the frame""" + maxResolution: Float = null + + """ + Defocus (minor axis) estimated for this tilt image in Angstrom (underfocus has positive sign). + """ + minorDefocus: Float = null + + """Phase shift estimated for this tilt image in radians.""" + phaseShift: Float = null + + """Nominal tilt angle for this tilt image reported by the microscope.""" + rawAngle: Float + + """Run that this section is a part of""" + runId: ID + + """Tiltseries that this section is a part of""" + tiltseriesId: ID + + """Index (0-based) of this tilt image in the tilt series stack.""" + zIndex: Int + + """Numeric identifier (May change!)""" + id: Int +} + +input PerSectionParametersWhereClause { + astigmaticAngle: FloatComparators + frame: FrameWhereClause + frameId: IntComparators + majorDefocus: FloatComparators + maxResolution: FloatComparators + minorDefocus: FloatComparators + phaseShift: FloatComparators + rawAngle: FloatComparators + run: RunWhereClause + runId: IntComparators + tiltseries: TiltseriesWhereClause + tiltseriesId: IntComparators + zIndex: IntComparators + id: IntComparators +} + +input PerSectionParametersWhereClauseMutations { + id: IntComparators +} + +type Query { + gainFiles(where: GainFileWhereClause = null, orderBy: [GainFileOrderByClause!] = [], limitOffset: LimitOffsetClause = null): [GainFile!]! + frameAcquisitionFiles(where: FrameAcquisitionFileWhereClause = null, orderBy: [FrameAcquisitionFileOrderByClause!] = [], limitOffset: LimitOffsetClause = null): [FrameAcquisitionFile!]! + alignments(where: AlignmentWhereClause = null, orderBy: [AlignmentOrderByClause!] = [], limitOffset: LimitOffsetClause = null): [Alignment!]! + annotationAuthors(where: AnnotationAuthorWhereClause = null, orderBy: [AnnotationAuthorOrderByClause!] = [], limitOffset: LimitOffsetClause = null): [AnnotationAuthor!]! + annotationFiles(where: AnnotationFileWhereClause = null, orderBy: [AnnotationFileOrderByClause!] = [], limitOffset: LimitOffsetClause = null): [AnnotationFile!]! + annotationShapes(where: AnnotationShapeWhereClause = null, orderBy: [AnnotationShapeOrderByClause!] = [], limitOffset: LimitOffsetClause = null): [AnnotationShape!]! + annotations(where: AnnotationWhereClause = null, orderBy: [AnnotationOrderByClause!] = [], limitOffset: LimitOffsetClause = null): [Annotation!]! + datasetAuthors(where: DatasetAuthorWhereClause = null, orderBy: [DatasetAuthorOrderByClause!] = [], limitOffset: LimitOffsetClause = null): [DatasetAuthor!]! + datasetFunding(where: DatasetFundingWhereClause = null, orderBy: [DatasetFundingOrderByClause!] = [], limitOffset: LimitOffsetClause = null): [DatasetFunding!]! + datasets(where: DatasetWhereClause = null, orderBy: [DatasetOrderByClause!] = [], limitOffset: LimitOffsetClause = null): [Dataset!]! + depositionAuthors(where: DepositionAuthorWhereClause = null, orderBy: [DepositionAuthorOrderByClause!] = [], limitOffset: LimitOffsetClause = null): [DepositionAuthor!]! + depositions(where: DepositionWhereClause = null, orderBy: [DepositionOrderByClause!] = [], limitOffset: LimitOffsetClause = null): [Deposition!]! + depositionTypes(where: DepositionTypeWhereClause = null, orderBy: [DepositionTypeOrderByClause!] = [], limitOffset: LimitOffsetClause = null): [DepositionType!]! + frames(where: FrameWhereClause = null, orderBy: [FrameOrderByClause!] = [], limitOffset: LimitOffsetClause = null): [Frame!]! + identifiedObjects(where: IdentifiedObjectWhereClause = null, orderBy: [IdentifiedObjectOrderByClause!] = [], limitOffset: LimitOffsetClause = null): [IdentifiedObject!]! + perSectionAlignmentParameters(where: PerSectionAlignmentParametersWhereClause = null, orderBy: [PerSectionAlignmentParametersOrderByClause!] = [], limitOffset: LimitOffsetClause = null): [PerSectionAlignmentParameters!]! + perSectionParameters(where: PerSectionParametersWhereClause = null, orderBy: [PerSectionParametersOrderByClause!] = [], limitOffset: LimitOffsetClause = null): [PerSectionParameters!]! + runs(where: RunWhereClause = null, orderBy: [RunOrderByClause!] = [], limitOffset: LimitOffsetClause = null): [Run!]! + tiltseries(where: TiltseriesWhereClause = null, orderBy: [TiltseriesOrderByClause!] = [], limitOffset: LimitOffsetClause = null): [Tiltseries!]! + tomogramAuthors(where: TomogramAuthorWhereClause = null, orderBy: [TomogramAuthorOrderByClause!] = [], limitOffset: LimitOffsetClause = null): [TomogramAuthor!]! + tomogramVoxelSpacings(where: TomogramVoxelSpacingWhereClause = null, orderBy: [TomogramVoxelSpacingOrderByClause!] = [], limitOffset: LimitOffsetClause = null): [TomogramVoxelSpacing!]! + tomograms(where: TomogramWhereClause = null, orderBy: [TomogramOrderByClause!] = [], limitOffset: LimitOffsetClause = null): [Tomogram!]! + annotationMethodLinks(where: AnnotationMethodLinkWhereClause = null, orderBy: [AnnotationMethodLinkOrderByClause!] = [], limitOffset: LimitOffsetClause = null): [AnnotationMethodLink!]! + gainFilesAggregate(where: GainFileWhereClause = null): GainFileAggregate! + frameAcquisitionFilesAggregate(where: FrameAcquisitionFileWhereClause = null): FrameAcquisitionFileAggregate! + alignmentsAggregate(where: AlignmentWhereClause = null): AlignmentAggregate! + annotationAuthorsAggregate(where: AnnotationAuthorWhereClause = null): AnnotationAuthorAggregate! + annotationFilesAggregate(where: AnnotationFileWhereClause = null): AnnotationFileAggregate! + annotationShapesAggregate(where: AnnotationShapeWhereClause = null): AnnotationShapeAggregate! + annotationsAggregate(where: AnnotationWhereClause = null): AnnotationAggregate! + datasetAuthorsAggregate(where: DatasetAuthorWhereClause = null): DatasetAuthorAggregate! + datasetFundingAggregate(where: DatasetFundingWhereClause = null): DatasetFundingAggregate! + datasetsAggregate(where: DatasetWhereClause = null): DatasetAggregate! + depositionAuthorsAggregate(where: DepositionAuthorWhereClause = null): DepositionAuthorAggregate! + depositionsAggregate(where: DepositionWhereClause = null): DepositionAggregate! + depositionTypesAggregate(where: DepositionTypeWhereClause = null): DepositionTypeAggregate! + framesAggregate(where: FrameWhereClause = null): FrameAggregate! + identifiedObjectsAggregate(where: IdentifiedObjectWhereClause = null): IdentifiedObjectAggregate! + perSectionAlignmentParametersAggregate(where: PerSectionAlignmentParametersWhereClause = null): PerSectionAlignmentParametersAggregate! + perSectionParametersAggregate(where: PerSectionParametersWhereClause = null): PerSectionParametersAggregate! + runsAggregate(where: RunWhereClause = null): RunAggregate! + tiltseriesAggregate(where: TiltseriesWhereClause = null): TiltseriesAggregate! + tomogramAuthorsAggregate(where: TomogramAuthorWhereClause = null): TomogramAuthorAggregate! + tomogramVoxelSpacingsAggregate(where: TomogramVoxelSpacingWhereClause = null): TomogramVoxelSpacingAggregate! + tomogramsAggregate(where: TomogramWhereClause = null): TomogramAggregate! + annotationMethodLinksAggregate(where: AnnotationMethodLinkWhereClause = null): AnnotationMethodLinkAggregate! +} + +type Run implements EntityInterface & Node { + """The Globally Unique ID of this object""" + _id: GlobalID! + + """Numeric identifier (May change!)""" + id: Int! + alignments( + where: AlignmentWhereClause = null + orderBy: [AlignmentOrderByClause!] = [] + + """Returns the items in the list that come before the specified cursor.""" + before: String = null + + """Returns the items in the list that come after the specified cursor.""" + after: String = null + + """Returns the first n items from the list.""" + first: Int = null + + """Returns the items in the list that come after the specified cursor.""" + last: Int = null + ): AlignmentConnection! + alignmentsAggregate(where: AlignmentWhereClause = null): AlignmentAggregate + annotations( + where: AnnotationWhereClause = null + orderBy: [AnnotationOrderByClause!] = [] + + """Returns the items in the list that come before the specified cursor.""" + before: String = null + + """Returns the items in the list that come after the specified cursor.""" + after: String = null + + """Returns the first n items from the list.""" + first: Int = null + + """Returns the items in the list that come after the specified cursor.""" + last: Int = null + ): AnnotationConnection! + annotationsAggregate(where: AnnotationWhereClause = null): AnnotationAggregate + dataset(where: DatasetWhereClause = null, orderBy: [DatasetOrderByClause!] = []): Dataset + datasetId: Int! + frames( + where: FrameWhereClause = null + orderBy: [FrameOrderByClause!] = [] + + """Returns the items in the list that come before the specified cursor.""" + before: String = null + + """Returns the items in the list that come after the specified cursor.""" + after: String = null + + """Returns the first n items from the list.""" + first: Int = null + + """Returns the items in the list that come after the specified cursor.""" + last: Int = null + ): FrameConnection! + framesAggregate(where: FrameWhereClause = null): FrameAggregate + gainFiles( + where: GainFileWhereClause = null + orderBy: [GainFileOrderByClause!] = [] + + """Returns the items in the list that come before the specified cursor.""" + before: String = null + + """Returns the items in the list that come after the specified cursor.""" + after: String = null + + """Returns the first n items from the list.""" + first: Int = null + + """Returns the items in the list that come after the specified cursor.""" + last: Int = null + ): GainFileConnection! + gainFilesAggregate(where: GainFileWhereClause = null): GainFileAggregate + identifiedObjects( + where: IdentifiedObjectWhereClause = null + orderBy: [IdentifiedObjectOrderByClause!] = [] + + """Returns the items in the list that come before the specified cursor.""" + before: String = null + + """Returns the items in the list that come after the specified cursor.""" + after: String = null + + """Returns the first n items from the list.""" + first: Int = null + + """Returns the items in the list that come after the specified cursor.""" + last: Int = null + ): IdentifiedObjectConnection! + identifiedObjectsAggregate(where: IdentifiedObjectWhereClause = null): IdentifiedObjectAggregate + frameAcquisitionFiles( + where: FrameAcquisitionFileWhereClause = null + orderBy: [FrameAcquisitionFileOrderByClause!] = [] + + """Returns the items in the list that come before the specified cursor.""" + before: String = null + + """Returns the items in the list that come after the specified cursor.""" + after: String = null + + """Returns the first n items from the list.""" + first: Int = null + + """Returns the items in the list that come after the specified cursor.""" + last: Int = null + ): FrameAcquisitionFileConnection! + frameAcquisitionFilesAggregate(where: FrameAcquisitionFileWhereClause = null): FrameAcquisitionFileAggregate + perSectionParameters( + where: PerSectionParametersWhereClause = null + orderBy: [PerSectionParametersOrderByClause!] = [] + + """Returns the items in the list that come before the specified cursor.""" + before: String = null + + """Returns the items in the list that come after the specified cursor.""" + after: String = null + + """Returns the first n items from the list.""" + first: Int = null + + """Returns the items in the list that come after the specified cursor.""" + last: Int = null + ): PerSectionParametersConnection! + perSectionParametersAggregate(where: PerSectionParametersWhereClause = null): PerSectionParametersAggregate + tiltseries( + where: TiltseriesWhereClause = null + orderBy: [TiltseriesOrderByClause!] = [] + + """Returns the items in the list that come before the specified cursor.""" + before: String = null + + """Returns the items in the list that come after the specified cursor.""" + after: String = null + + """Returns the first n items from the list.""" + first: Int = null + + """Returns the items in the list that come after the specified cursor.""" + last: Int = null + ): TiltseriesConnection! + tiltseriesAggregate(where: TiltseriesWhereClause = null): TiltseriesAggregate + tomogramVoxelSpacings( + where: TomogramVoxelSpacingWhereClause = null + orderBy: [TomogramVoxelSpacingOrderByClause!] = [] + + """Returns the items in the list that come before the specified cursor.""" + before: String = null + + """Returns the items in the list that come after the specified cursor.""" + after: String = null + + """Returns the first n items from the list.""" + first: Int = null + + """Returns the items in the list that come after the specified cursor.""" + last: Int = null + ): TomogramVoxelSpacingConnection! + tomogramVoxelSpacingsAggregate(where: TomogramVoxelSpacingWhereClause = null): TomogramVoxelSpacingAggregate + tomograms( + where: TomogramWhereClause = null + orderBy: [TomogramOrderByClause!] = [] + + """Returns the items in the list that come before the specified cursor.""" + before: String = null + + """Returns the items in the list that come after the specified cursor.""" + after: String = null + + """Returns the first n items from the list.""" + first: Int = null + + """Returns the items in the list that come after the specified cursor.""" + last: Int = null + ): TomogramConnection! + tomogramsAggregate(where: TomogramWhereClause = null): TomogramAggregate + + """Short name for this experiment run""" + name: String! + + """The S3 public bucket path where this run is contained""" + s3Prefix: String! + + """The HTTPS directory path where this run is contained url""" + httpsPrefix: String! +} + +type RunAggregate { + aggregate: [RunAggregateFunctions!] +} + +type RunAggregateFunctions { + sum: RunNumericalColumns + avg: RunNumericalColumns + stddev: RunNumericalColumns + variance: RunNumericalColumns + min: RunMinMaxColumns + max: RunMinMaxColumns + groupBy: RunGroupByOptions + count(distinct: Boolean = false, columns: RunCountColumns = null): Int +} + +input RunAggregateWhereClause { + count: RunAggregateWhereClauseCount! +} + +input RunAggregateWhereClauseCount { + arguments: RunCountColumns + distinct: Boolean + filter: RunWhereClause + predicate: IntComparators +} + +"""A connection to a list of items.""" +type RunConnection { + """Pagination data for this connection""" + pageInfo: PageInfo! + + """Contains the nodes in this connection""" + edges: [RunEdge!]! +} + +enum RunCountColumns { + name + s3Prefix + httpsPrefix + id +} + +input RunCreateInput { + """Dataset that this run is a part of""" + datasetId: ID! + + """Short name for this experiment run""" + name: String! + + """The S3 public bucket path where this run is contained""" + s3Prefix: String! + + """The HTTPS directory path where this run is contained url""" + httpsPrefix: String! + + """Numeric identifier (May change!)""" + id: Int! +} + +"""An edge in a connection.""" +type RunEdge { + """A cursor for use in pagination""" + cursor: String! + + """The item at the end of the edge""" + node: Run! +} + +type RunGroupByOptions { + alignments: AlignmentGroupByOptions + annotations: AnnotationGroupByOptions + dataset: DatasetGroupByOptions + frames: FrameGroupByOptions + gainFiles: GainFileGroupByOptions + identifiedObjects: IdentifiedObjectGroupByOptions + frameAcquisitionFiles: FrameAcquisitionFileGroupByOptions + perSectionParameters: PerSectionParametersGroupByOptions + tiltseries: TiltseriesGroupByOptions + tomogramVoxelSpacings: TomogramVoxelSpacingGroupByOptions + tomograms: TomogramGroupByOptions + name: String + s3Prefix: String + httpsPrefix: String + id: Int +} + +type RunMinMaxColumns { + name: String + s3Prefix: String + httpsPrefix: String + id: Int +} + +type RunNumericalColumns { + id: Int +} + +input RunOrderByClause { + dataset: DatasetOrderByClause + name: orderBy + s3Prefix: orderBy + httpsPrefix: orderBy + id: orderBy +} + +input RunUpdateInput { + """Dataset that this run is a part of""" + datasetId: ID + + """Short name for this experiment run""" + name: String + + """The S3 public bucket path where this run is contained""" + s3Prefix: String + + """The HTTPS directory path where this run is contained url""" + httpsPrefix: String + + """Numeric identifier (May change!)""" + id: Int +} + +input RunWhereClause { + alignments: AlignmentWhereClause + alignmentsAggregate: AlignmentAggregateWhereClause + annotations: AnnotationWhereClause + annotationsAggregate: AnnotationAggregateWhereClause + dataset: DatasetWhereClause + datasetId: IntComparators + frames: FrameWhereClause + framesAggregate: FrameAggregateWhereClause + gainFiles: GainFileWhereClause + gainFilesAggregate: GainFileAggregateWhereClause + identifiedObjects: IdentifiedObjectWhereClause + identifiedObjectsAggregate: IdentifiedObjectAggregateWhereClause + frameAcquisitionFiles: FrameAcquisitionFileWhereClause + frameAcquisitionFilesAggregate: FrameAcquisitionFileAggregateWhereClause + perSectionParameters: PerSectionParametersWhereClause + perSectionParametersAggregate: PerSectionParametersAggregateWhereClause + tiltseries: TiltseriesWhereClause + tiltseriesAggregate: TiltseriesAggregateWhereClause + tomogramVoxelSpacings: TomogramVoxelSpacingWhereClause + tomogramVoxelSpacingsAggregate: TomogramVoxelSpacingAggregateWhereClause + tomograms: TomogramWhereClause + tomogramsAggregate: TomogramAggregateWhereClause + name: StrComparators + s3Prefix: StrComparators + httpsPrefix: StrComparators + id: IntComparators +} + +input RunWhereClauseMutations { + id: IntComparators +} + +input Sample_type_enumEnumComparators { + _eq: sample_type_enum + _neq: sample_type_enum + _in: [sample_type_enum!] + _nin: [sample_type_enum!] + _gt: sample_type_enum + _gte: sample_type_enum + _lt: sample_type_enum + _lte: sample_type_enum + _is_null: Boolean +} + +input StrComparators { + _eq: String + _neq: String + _in: [String!] + _nin: [String!] + _is_null: Boolean + _gt: String + _gte: String + _lt: String + _lte: String + _like: String + _nlike: String + _ilike: String + _nilike: String + _regex: String + _nregex: String + _iregex: String + _niregex: String +} + +type Tiltseries implements EntityInterface & Node { + """The Globally Unique ID of this object""" + _id: GlobalID! + + """Numeric identifier (May change!)""" + id: Int! + alignments( + where: AlignmentWhereClause = null + orderBy: [AlignmentOrderByClause!] = [] + + """Returns the items in the list that come before the specified cursor.""" + before: String = null + + """Returns the items in the list that come after the specified cursor.""" + after: String = null + + """Returns the first n items from the list.""" + first: Int = null + + """Returns the items in the list that come after the specified cursor.""" + last: Int = null + ): AlignmentConnection! + alignmentsAggregate(where: AlignmentWhereClause = null): AlignmentAggregate + run(where: RunWhereClause = null, orderBy: [RunOrderByClause!] = []): Run + runId: Int! + deposition(where: DepositionWhereClause = null, orderBy: [DepositionOrderByClause!] = []): Deposition + depositionId: Int + + """S3 path to this tiltseries in multiscale OME-Zarr format""" + s3OmezarrDir: String + + """Size of the tiltseries in OME-Zarr format in bytes""" + fileSizeOmezarr: Float + + """S3 path to this tiltseries in MRC format (no scaling)""" + s3MrcFile: String + + """Size of the tiltseries in MRC format in bytes""" + fileSizeMrc: Float + + """HTTPS path to this tiltseries in multiscale OME-Zarr format""" + httpsOmezarrDir: String + + """HTTPS path to this tiltseries in MRC format (no scaling)""" + httpsMrcFile: String + + """S3 path to the angle list file for this tiltseries""" + s3AngleList: String + + """HTTPS path to the angle list file for this tiltseries""" + httpsAngleList: String + + """Electron Microscope Accelerator voltage in volts""" + accelerationVoltage: Int! + + """Spherical Aberration Constant of the objective lens in millimeters""" + sphericalAberrationConstant: Float! + + """Name of the microscope manufacturer (FEI, TFS, JEOL)""" + microscopeManufacturer: tiltseries_microscope_manufacturer_enum! + + """Microscope model name""" + microscopeModel: String! + + """Energy filter setup used""" + microscopeEnergyFilter: String! + + """Phase plate configuration""" + microscopePhasePlate: String + + """Image corrector setup""" + microscopeImageCorrector: String + + """ + Other microscope optical setup information, in addition to energy filter, phase plate and image corrector + """ + microscopeAdditionalInfo: String + perSectionParameters( + where: PerSectionParametersWhereClause = null + orderBy: [PerSectionParametersOrderByClause!] = [] + + """Returns the items in the list that come before the specified cursor.""" + before: String = null + + """Returns the items in the list that come after the specified cursor.""" + after: String = null + + """Returns the first n items from the list.""" + first: Int = null + + """Returns the items in the list that come after the specified cursor.""" + last: Int = null + ): PerSectionParametersConnection! + perSectionParametersAggregate(where: PerSectionParametersWhereClause = null): PerSectionParametersAggregate + + """Name of the camera manufacturer""" + cameraManufacturer: String! + + """Camera model name""" + cameraModel: String! + + """Minimal tilt angle in degrees""" + tiltMin: Float! + + """Maximal tilt angle in degrees""" + tiltMax: Float! + + """Total tilt range in degrees""" + tiltRange: Float! + + """Tilt step in degrees""" + tiltStep: Float! + + """The order of stage tilting during acquisition of the data""" + tiltingScheme: String! + + """Rotation angle in degrees""" + tiltAxis: Float! + + """ + Number of Electrons reaching the specimen in a square Angstrom area for the entire tilt series + """ + totalFlux: Float! + + """Software used to collect data""" + dataAcquisitionSoftware: String! + + """ + If a tilt series is deposited into EMPIAR, enter the EMPIAR dataset identifier + """ + relatedEmpiarEntry: String + + """Describes the binning factor from frames to tilt series file""" + binningFromFrames: Float + + """ + Author assessment of tilt series quality within the dataset (1-5, 5 is best) + """ + tiltSeriesQuality: Int! + + """Whether this tilt series is aligned""" + isAligned: Boolean! + + """Pixel spacing equal in both axes in angstroms""" + pixelSpacing: Float! + + """Binning factor of the aligned tilt series""" + alignedTiltseriesBinning: Int + + """Number of pixels in the 3D data fast axis""" + sizeX: Int + + """Number of pixels in the 3D data medium axis""" + sizeY: Int + + """Number of pixels in the 3D data slow axis""" + sizeZ: Int +} + +type TiltseriesAggregate { + aggregate: [TiltseriesAggregateFunctions!] +} + +type TiltseriesAggregateFunctions { + sum: TiltseriesNumericalColumns + avg: TiltseriesNumericalColumns + stddev: TiltseriesNumericalColumns + variance: TiltseriesNumericalColumns + min: TiltseriesMinMaxColumns + max: TiltseriesMinMaxColumns + groupBy: TiltseriesGroupByOptions + count(distinct: Boolean = false, columns: TiltseriesCountColumns = null): Int +} + +input TiltseriesAggregateWhereClause { + count: TiltseriesAggregateWhereClauseCount! +} + +input TiltseriesAggregateWhereClauseCount { + arguments: TiltseriesCountColumns + distinct: Boolean + filter: TiltseriesWhereClause + predicate: IntComparators +} + +"""A connection to a list of items.""" +type TiltseriesConnection { + """Pagination data for this connection""" + pageInfo: PageInfo! + + """Contains the nodes in this connection""" + edges: [TiltseriesEdge!]! +} + +enum TiltseriesCountColumns { + s3OmezarrDir + fileSizeOmezarr + s3MrcFile + fileSizeMrc + httpsOmezarrDir + httpsMrcFile + s3AngleList + httpsAngleList + accelerationVoltage + sphericalAberrationConstant + microscopeManufacturer + microscopeModel + microscopeEnergyFilter + microscopePhasePlate + microscopeImageCorrector + microscopeAdditionalInfo + cameraManufacturer + cameraModel + tiltMin + tiltMax + tiltRange + tiltStep + tiltingScheme + tiltAxis + totalFlux + dataAcquisitionSoftware + relatedEmpiarEntry + binningFromFrames + tiltSeriesQuality + isAligned + pixelSpacing + alignedTiltseriesBinning + sizeX + sizeY + sizeZ + id +} + +input TiltseriesCreateInput { + runId: ID! + depositionId: ID = null + + """S3 path to this tiltseries in multiscale OME-Zarr format""" + s3OmezarrDir: String = null + + """Size of the tiltseries in OME-Zarr format in bytes""" + fileSizeOmezarr: Float = null + + """S3 path to this tiltseries in MRC format (no scaling)""" + s3MrcFile: String = null + + """Size of the tiltseries in MRC format in bytes""" + fileSizeMrc: Float = null + + """HTTPS path to this tiltseries in multiscale OME-Zarr format""" + httpsOmezarrDir: String = null + + """HTTPS path to this tiltseries in MRC format (no scaling)""" + httpsMrcFile: String = null + + """S3 path to the angle list file for this tiltseries""" + s3AngleList: String = null + + """HTTPS path to the angle list file for this tiltseries""" + httpsAngleList: String = null + + """Electron Microscope Accelerator voltage in volts""" + accelerationVoltage: Int! + + """Spherical Aberration Constant of the objective lens in millimeters""" + sphericalAberrationConstant: Float! + + """Name of the microscope manufacturer (FEI, TFS, JEOL)""" + microscopeManufacturer: tiltseries_microscope_manufacturer_enum! + + """Microscope model name""" + microscopeModel: String! + + """Energy filter setup used""" + microscopeEnergyFilter: String! + + """Phase plate configuration""" + microscopePhasePlate: String = null + + """Image corrector setup""" + microscopeImageCorrector: String = null + + """ + Other microscope optical setup information, in addition to energy filter, phase plate and image corrector + """ + microscopeAdditionalInfo: String = null + + """Name of the camera manufacturer""" + cameraManufacturer: String! + + """Camera model name""" + cameraModel: String! + + """Minimal tilt angle in degrees""" + tiltMin: Float! + + """Maximal tilt angle in degrees""" + tiltMax: Float! + + """Total tilt range in degrees""" + tiltRange: Float! + + """Tilt step in degrees""" + tiltStep: Float! + + """The order of stage tilting during acquisition of the data""" + tiltingScheme: String! + + """Rotation angle in degrees""" + tiltAxis: Float! + + """ + Number of Electrons reaching the specimen in a square Angstrom area for the entire tilt series + """ + totalFlux: Float! + + """Software used to collect data""" + dataAcquisitionSoftware: String! + + """ + If a tilt series is deposited into EMPIAR, enter the EMPIAR dataset identifier + """ + relatedEmpiarEntry: String = null + + """Describes the binning factor from frames to tilt series file""" + binningFromFrames: Float = null + + """ + Author assessment of tilt series quality within the dataset (1-5, 5 is best) + """ + tiltSeriesQuality: Int! + + """Whether this tilt series is aligned""" + isAligned: Boolean! + + """Pixel spacing equal in both axes in angstroms""" + pixelSpacing: Float! + + """Binning factor of the aligned tilt series""" + alignedTiltseriesBinning: Int = null + + """Number of pixels in the 3D data fast axis""" + sizeX: Int = null + + """Number of pixels in the 3D data medium axis""" + sizeY: Int = null + + """Number of pixels in the 3D data slow axis""" + sizeZ: Int = null + + """Numeric identifier (May change!)""" + id: Int! +} + +"""An edge in a connection.""" +type TiltseriesEdge { + """A cursor for use in pagination""" + cursor: String! + + """The item at the end of the edge""" + node: Tiltseries! +} + +type TiltseriesGroupByOptions { + alignments: AlignmentGroupByOptions + run: RunGroupByOptions + deposition: DepositionGroupByOptions + s3OmezarrDir: String + fileSizeOmezarr: Float + s3MrcFile: String + fileSizeMrc: Float + httpsOmezarrDir: String + httpsMrcFile: String + s3AngleList: String + httpsAngleList: String + accelerationVoltage: Int + sphericalAberrationConstant: Float + microscopeManufacturer: tiltseries_microscope_manufacturer_enum + microscopeModel: String + microscopeEnergyFilter: String + microscopePhasePlate: String + microscopeImageCorrector: String + microscopeAdditionalInfo: String + perSectionParameters: PerSectionParametersGroupByOptions + cameraManufacturer: String + cameraModel: String + tiltMin: Float + tiltMax: Float + tiltRange: Float + tiltStep: Float + tiltingScheme: String + tiltAxis: Float + totalFlux: Float + dataAcquisitionSoftware: String + relatedEmpiarEntry: String + binningFromFrames: Float + tiltSeriesQuality: Int + isAligned: Boolean + pixelSpacing: Float + alignedTiltseriesBinning: Int + sizeX: Int + sizeY: Int + sizeZ: Int + id: Int +} + +type TiltseriesMinMaxColumns { + s3OmezarrDir: String + fileSizeOmezarr: Float + s3MrcFile: String + fileSizeMrc: Float + httpsOmezarrDir: String + httpsMrcFile: String + s3AngleList: String + httpsAngleList: String + accelerationVoltage: Int + sphericalAberrationConstant: Float + microscopeModel: String + microscopeEnergyFilter: String + microscopePhasePlate: String + microscopeImageCorrector: String + microscopeAdditionalInfo: String + cameraManufacturer: String + cameraModel: String + tiltMin: Float + tiltMax: Float + tiltRange: Float + tiltStep: Float + tiltingScheme: String + tiltAxis: Float + totalFlux: Float + dataAcquisitionSoftware: String + relatedEmpiarEntry: String + binningFromFrames: Float + tiltSeriesQuality: Int + pixelSpacing: Float + alignedTiltseriesBinning: Int + sizeX: Int + sizeY: Int + sizeZ: Int + id: Int +} + +type TiltseriesNumericalColumns { + fileSizeOmezarr: Float + fileSizeMrc: Float + accelerationVoltage: Int + sphericalAberrationConstant: Float + tiltMin: Float + tiltMax: Float + tiltRange: Float + tiltStep: Float + tiltAxis: Float + totalFlux: Float + binningFromFrames: Float + tiltSeriesQuality: Int + pixelSpacing: Float + alignedTiltseriesBinning: Int + sizeX: Int + sizeY: Int + sizeZ: Int + id: Int +} + +input TiltseriesOrderByClause { + run: RunOrderByClause + deposition: DepositionOrderByClause + s3OmezarrDir: orderBy + fileSizeOmezarr: orderBy + s3MrcFile: orderBy + fileSizeMrc: orderBy + httpsOmezarrDir: orderBy + httpsMrcFile: orderBy + s3AngleList: orderBy + httpsAngleList: orderBy + accelerationVoltage: orderBy + sphericalAberrationConstant: orderBy + microscopeManufacturer: orderBy + microscopeModel: orderBy + microscopeEnergyFilter: orderBy + microscopePhasePlate: orderBy + microscopeImageCorrector: orderBy + microscopeAdditionalInfo: orderBy + cameraManufacturer: orderBy + cameraModel: orderBy + tiltMin: orderBy + tiltMax: orderBy + tiltRange: orderBy + tiltStep: orderBy + tiltingScheme: orderBy + tiltAxis: orderBy + totalFlux: orderBy + dataAcquisitionSoftware: orderBy + relatedEmpiarEntry: orderBy + binningFromFrames: orderBy + tiltSeriesQuality: orderBy + isAligned: orderBy + pixelSpacing: orderBy + alignedTiltseriesBinning: orderBy + sizeX: orderBy + sizeY: orderBy + sizeZ: orderBy + id: orderBy +} + +input TiltseriesUpdateInput { + runId: ID + depositionId: ID = null + + """S3 path to this tiltseries in multiscale OME-Zarr format""" + s3OmezarrDir: String = null + + """Size of the tiltseries in OME-Zarr format in bytes""" + fileSizeOmezarr: Float = null + + """S3 path to this tiltseries in MRC format (no scaling)""" + s3MrcFile: String = null + + """Size of the tiltseries in MRC format in bytes""" + fileSizeMrc: Float = null + + """HTTPS path to this tiltseries in multiscale OME-Zarr format""" + httpsOmezarrDir: String = null + + """HTTPS path to this tiltseries in MRC format (no scaling)""" + httpsMrcFile: String = null + + """S3 path to the angle list file for this tiltseries""" + s3AngleList: String = null + + """HTTPS path to the angle list file for this tiltseries""" + httpsAngleList: String = null + + """Electron Microscope Accelerator voltage in volts""" + accelerationVoltage: Int + + """Spherical Aberration Constant of the objective lens in millimeters""" + sphericalAberrationConstant: Float + + """Name of the microscope manufacturer (FEI, TFS, JEOL)""" + microscopeManufacturer: tiltseries_microscope_manufacturer_enum + + """Microscope model name""" + microscopeModel: String + + """Energy filter setup used""" + microscopeEnergyFilter: String + + """Phase plate configuration""" + microscopePhasePlate: String = null + + """Image corrector setup""" + microscopeImageCorrector: String = null + + """ + Other microscope optical setup information, in addition to energy filter, phase plate and image corrector + """ + microscopeAdditionalInfo: String = null + + """Name of the camera manufacturer""" + cameraManufacturer: String + + """Camera model name""" + cameraModel: String + + """Minimal tilt angle in degrees""" + tiltMin: Float + + """Maximal tilt angle in degrees""" + tiltMax: Float + + """Total tilt range in degrees""" + tiltRange: Float + + """Tilt step in degrees""" + tiltStep: Float + + """The order of stage tilting during acquisition of the data""" + tiltingScheme: String + + """Rotation angle in degrees""" + tiltAxis: Float + + """ + Number of Electrons reaching the specimen in a square Angstrom area for the entire tilt series + """ + totalFlux: Float + + """Software used to collect data""" + dataAcquisitionSoftware: String + + """ + If a tilt series is deposited into EMPIAR, enter the EMPIAR dataset identifier + """ + relatedEmpiarEntry: String = null + + """Describes the binning factor from frames to tilt series file""" + binningFromFrames: Float = null + + """ + Author assessment of tilt series quality within the dataset (1-5, 5 is best) + """ + tiltSeriesQuality: Int + + """Whether this tilt series is aligned""" + isAligned: Boolean + + """Pixel spacing equal in both axes in angstroms""" + pixelSpacing: Float + + """Binning factor of the aligned tilt series""" + alignedTiltseriesBinning: Int = null + + """Number of pixels in the 3D data fast axis""" + sizeX: Int = null + + """Number of pixels in the 3D data medium axis""" + sizeY: Int = null + + """Number of pixels in the 3D data slow axis""" + sizeZ: Int = null + + """Numeric identifier (May change!)""" + id: Int +} + +input TiltseriesWhereClause { + alignments: AlignmentWhereClause + alignmentsAggregate: AlignmentAggregateWhereClause + run: RunWhereClause + runId: IntComparators + deposition: DepositionWhereClause + depositionId: IntComparators + s3OmezarrDir: StrComparators + fileSizeOmezarr: FloatComparators + s3MrcFile: StrComparators + fileSizeMrc: FloatComparators + httpsOmezarrDir: StrComparators + httpsMrcFile: StrComparators + s3AngleList: StrComparators + httpsAngleList: StrComparators + accelerationVoltage: IntComparators + sphericalAberrationConstant: FloatComparators + microscopeManufacturer: Tiltseries_microscope_manufacturer_enumEnumComparators + microscopeModel: StrComparators + microscopeEnergyFilter: StrComparators + microscopePhasePlate: StrComparators + microscopeImageCorrector: StrComparators + microscopeAdditionalInfo: StrComparators + perSectionParameters: PerSectionParametersWhereClause + perSectionParametersAggregate: PerSectionParametersAggregateWhereClause + cameraManufacturer: StrComparators + cameraModel: StrComparators + tiltMin: FloatComparators + tiltMax: FloatComparators + tiltRange: FloatComparators + tiltStep: FloatComparators + tiltingScheme: StrComparators + tiltAxis: FloatComparators + totalFlux: FloatComparators + dataAcquisitionSoftware: StrComparators + relatedEmpiarEntry: StrComparators + binningFromFrames: FloatComparators + tiltSeriesQuality: IntComparators + isAligned: BoolComparators + pixelSpacing: FloatComparators + alignedTiltseriesBinning: IntComparators + sizeX: IntComparators + sizeY: IntComparators + sizeZ: IntComparators + id: IntComparators +} + +input TiltseriesWhereClauseMutations { + id: IntComparators +} + +input Tiltseries_microscope_manufacturer_enumEnumComparators { + _eq: tiltseries_microscope_manufacturer_enum + _neq: tiltseries_microscope_manufacturer_enum + _in: [tiltseries_microscope_manufacturer_enum!] + _nin: [tiltseries_microscope_manufacturer_enum!] + _gt: tiltseries_microscope_manufacturer_enum + _gte: tiltseries_microscope_manufacturer_enum + _lt: tiltseries_microscope_manufacturer_enum + _lte: tiltseries_microscope_manufacturer_enum + _is_null: Boolean +} + +"""Metadata describing a tomogram.""" +type Tomogram implements EntityInterface & Node { + """The Globally Unique ID of this object""" + _id: GlobalID! + + """Numeric identifier (May change!)""" + id: Int! + alignment(where: AlignmentWhereClause = null, orderBy: [AlignmentOrderByClause!] = []): Alignment + alignmentId: Int + authors( + where: TomogramAuthorWhereClause = null + orderBy: [TomogramAuthorOrderByClause!] = [] + + """Returns the items in the list that come before the specified cursor.""" + before: String = null + + """Returns the items in the list that come after the specified cursor.""" + after: String = null + + """Returns the first n items from the list.""" + first: Int = null + + """Returns the items in the list that come after the specified cursor.""" + last: Int = null + ): TomogramAuthorConnection! + authorsAggregate(where: TomogramAuthorWhereClause = null): TomogramAuthorAggregate + deposition(where: DepositionWhereClause = null, orderBy: [DepositionOrderByClause!] = []): Deposition + depositionId: Int! + run(where: RunWhereClause = null, orderBy: [RunOrderByClause!] = []): Run + runId: Int + tomogramVoxelSpacing(where: TomogramVoxelSpacingWhereClause = null, orderBy: [TomogramVoxelSpacingOrderByClause!] = []): TomogramVoxelSpacing + tomogramVoxelSpacingId: Int + + """Short name for this tomogram""" + name: String + + """Number of pixels in the 3D data fast axis""" + sizeX: Int! + + """Number of pixels in the 3D data medium axis""" + sizeY: Int! + + """ + Number of pixels in the 3D data slow axis. This is the image projection direction at zero stage tilt + """ + sizeZ: Int! + + """Voxel spacing equal in all three axes in angstroms""" + voxelSpacing: Float! + + """ + Fiducial Alignment status: True = aligned with fiducial False = aligned without fiducial + """ + fiducialAlignmentStatus: fiducial_alignment_status_enum! + + """Describe reconstruction method (WBP, SART, SIRT)""" + reconstructionMethod: tomogram_reconstruction_method_enum! + + """Describe additional processing used to derive the tomogram""" + processing: tomogram_processing_enum! + + """Version of tomogram""" + tomogramVersion: Float + + """Processing software used to derive the tomogram""" + processingSoftware: String + + """Name of software used for reconstruction""" + reconstructionSoftware: String! + + """whether this tomogram adheres to portal standards""" + isPortalStandard: Boolean + + """ + Whether this tomogram was submitted by the author of the dataset it belongs to. + """ + isAuthorSubmitted: Boolean + + """ + Data curator’s subjective choice of default tomogram to display in visualization for a run + """ + isVisualizationDefault: Boolean + + """S3 path to this tomogram in multiscale OME-Zarr format""" + s3OmezarrDir: String + + """HTTPS path to this tomogram in multiscale OME-Zarr format""" + httpsOmezarrDir: String + + """Size of the tomogram in OME-Zarr format in bytes""" + fileSizeOmezarr: Float + + """S3 path to this tomogram in MRC format (no scaling)""" + s3MrcFile: String + + """HTTPS path to this tomogram in MRC format (no scaling)""" + httpsMrcFile: String + + """Size of the tomogram in MRC format in bytes""" + fileSizeMrc: Float + + """comma separated x,y,z dimensions of the unscaled tomogram""" + scale0Dimensions: String + + """comma separated x,y,z dimensions of the scale1 tomogram""" + scale1Dimensions: String + + """comma separated x,y,z dimensions of the scale2 tomogram""" + scale2Dimensions: String + + """Whether this tomogram is CTF corrected""" + ctfCorrected: Boolean + + """x offset data relative to the canonical tomogram in pixels""" + offsetX: Int! + + """y offset data relative to the canonical tomogram in pixels""" + offsetY: Int! + + """z offset data relative to the canonical tomogram in pixels""" + offsetZ: Int! + + """URL for the key photo""" + keyPhotoUrl: String + + """URL for the thumbnail of key photo""" + keyPhotoThumbnailUrl: String + + """the compact json of neuroglancer config""" + neuroglancerConfig: String + + """ + Comma-separated list of DOIs for publications associated with the tomogram. + """ + publications: String + + """ + If a CryoET tomogram is also deposited into another database, enter the database identifier here (e.g. EMPIAR-11445). Use a comma to separate multiple identifiers. + """ + relatedDatabaseEntries: String + + """The date a data item was received by the cryoET data portal.""" + depositionDate: DateTime + + """The date a data item was received by the cryoET data portal.""" + releaseDate: DateTime + + """The date a piece of data was last modified on the cryoET data portal.""" + lastModifiedDate: DateTime +} + +type TomogramAggregate { + aggregate: [TomogramAggregateFunctions!] +} + +type TomogramAggregateFunctions { + sum: TomogramNumericalColumns + avg: TomogramNumericalColumns + stddev: TomogramNumericalColumns + variance: TomogramNumericalColumns + min: TomogramMinMaxColumns + max: TomogramMinMaxColumns + groupBy: TomogramGroupByOptions + count(distinct: Boolean = false, columns: TomogramCountColumns = null): Int +} + +input TomogramAggregateWhereClause { + count: TomogramAggregateWhereClauseCount! +} + +input TomogramAggregateWhereClauseCount { + arguments: TomogramCountColumns + distinct: Boolean + filter: TomogramWhereClause + predicate: IntComparators +} + +"""Author of a tomogram""" +type TomogramAuthor implements EntityInterface & Node { + """The Globally Unique ID of this object""" + _id: GlobalID! + + """Numeric identifier (May change!)""" + id: Int! + tomogram(where: TomogramWhereClause = null, orderBy: [TomogramOrderByClause!] = []): Tomogram + tomogramId: Int + + """The order in which the author appears in the publication""" + authorListOrder: Int! + + """A unique, persistent identifier for researchers, provided by ORCID.""" + orcid: String + + """A unique, persistent identifier for kaggle users at kaggle.com.""" + kaggleId: String + + """Full name of an author (e.g. Jane Doe).""" + name: String! + + """Email address for this author""" + email: String + + """Name of the institutions an author is affiliated with. Comma separated""" + affiliationName: String + + """Address of the institution an author is affiliated with.""" + affiliationAddress: String + + """ + A unique identifier assigned to the affiliated institution by The Research Organization Registry (ROR). + """ + affiliationIdentifier: String + + """Indicates whether an author is the corresponding author""" + correspondingAuthorStatus: Boolean + + """Indicates whether an author is the main person creating the tomogram""" + primaryAuthorStatus: Boolean +} + +type TomogramAuthorAggregate { + aggregate: [TomogramAuthorAggregateFunctions!] +} + +type TomogramAuthorAggregateFunctions { + sum: TomogramAuthorNumericalColumns + avg: TomogramAuthorNumericalColumns + stddev: TomogramAuthorNumericalColumns + variance: TomogramAuthorNumericalColumns + min: TomogramAuthorMinMaxColumns + max: TomogramAuthorMinMaxColumns + groupBy: TomogramAuthorGroupByOptions + count(distinct: Boolean = false, columns: TomogramAuthorCountColumns = null): Int +} + +input TomogramAuthorAggregateWhereClause { + count: TomogramAuthorAggregateWhereClauseCount! +} + +input TomogramAuthorAggregateWhereClauseCount { + arguments: TomogramAuthorCountColumns + distinct: Boolean + filter: TomogramAuthorWhereClause + predicate: IntComparators +} + +"""A connection to a list of items.""" +type TomogramAuthorConnection { + """Pagination data for this connection""" + pageInfo: PageInfo! + + """Contains the nodes in this connection""" + edges: [TomogramAuthorEdge!]! +} + +enum TomogramAuthorCountColumns { + id + authorListOrder + orcid + kaggleId + name + email + affiliationName + affiliationAddress + affiliationIdentifier + correspondingAuthorStatus + primaryAuthorStatus +} + +input TomogramAuthorCreateInput { + """The tomogram this tomogram author is a part of""" + tomogramId: ID = null + + """Numeric identifier (May change!)""" + id: Int! + + """The order in which the author appears in the publication""" + authorListOrder: Int! + + """A unique, persistent identifier for researchers, provided by ORCID.""" + orcid: String = null + + """A unique, persistent identifier for kaggle users at kaggle.com.""" + kaggleId: String = null + + """Full name of an author (e.g. Jane Doe).""" + name: String! + + """Email address for this author""" + email: String = null + + """Name of the institutions an author is affiliated with. Comma separated""" + affiliationName: String = null + + """Address of the institution an author is affiliated with.""" + affiliationAddress: String = null + + """ + A unique identifier assigned to the affiliated institution by The Research Organization Registry (ROR). + """ + affiliationIdentifier: String = null + + """Indicates whether an author is the corresponding author""" + correspondingAuthorStatus: Boolean = null + + """Indicates whether an author is the main person creating the tomogram""" + primaryAuthorStatus: Boolean = null +} + +"""An edge in a connection.""" +type TomogramAuthorEdge { + """A cursor for use in pagination""" + cursor: String! + + """The item at the end of the edge""" + node: TomogramAuthor! +} + +type TomogramAuthorGroupByOptions { + tomogram: TomogramGroupByOptions + id: Int + authorListOrder: Int + orcid: String + kaggleId: String + name: String + email: String + affiliationName: String + affiliationAddress: String + affiliationIdentifier: String + correspondingAuthorStatus: Boolean + primaryAuthorStatus: Boolean +} + +type TomogramAuthorMinMaxColumns { + id: Int + authorListOrder: Int + orcid: String + kaggleId: String + name: String + email: String + affiliationName: String + affiliationAddress: String + affiliationIdentifier: String +} + +type TomogramAuthorNumericalColumns { + id: Int + authorListOrder: Int +} + +input TomogramAuthorOrderByClause { + tomogram: TomogramOrderByClause + id: orderBy + authorListOrder: orderBy + orcid: orderBy + kaggleId: orderBy + name: orderBy + email: orderBy + affiliationName: orderBy + affiliationAddress: orderBy + affiliationIdentifier: orderBy + correspondingAuthorStatus: orderBy + primaryAuthorStatus: orderBy +} + +input TomogramAuthorUpdateInput { + """The tomogram this tomogram author is a part of""" + tomogramId: ID = null + + """Numeric identifier (May change!)""" + id: Int + + """The order in which the author appears in the publication""" + authorListOrder: Int + + """A unique, persistent identifier for researchers, provided by ORCID.""" + orcid: String = null + + """A unique, persistent identifier for kaggle users at kaggle.com.""" + kaggleId: String = null + + """Full name of an author (e.g. Jane Doe).""" + name: String + + """Email address for this author""" + email: String = null + + """Name of the institutions an author is affiliated with. Comma separated""" + affiliationName: String = null + + """Address of the institution an author is affiliated with.""" + affiliationAddress: String = null + + """ + A unique identifier assigned to the affiliated institution by The Research Organization Registry (ROR). + """ + affiliationIdentifier: String = null + + """Indicates whether an author is the corresponding author""" + correspondingAuthorStatus: Boolean = null + + """Indicates whether an author is the main person creating the tomogram""" + primaryAuthorStatus: Boolean = null +} + +input TomogramAuthorWhereClause { + tomogram: TomogramWhereClause + tomogramId: IntComparators + id: IntComparators + authorListOrder: IntComparators + orcid: StrComparators + kaggleId: StrComparators + name: StrComparators + email: StrComparators + affiliationName: StrComparators + affiliationAddress: StrComparators + affiliationIdentifier: StrComparators + correspondingAuthorStatus: BoolComparators + primaryAuthorStatus: BoolComparators +} + +input TomogramAuthorWhereClauseMutations { + id: IntComparators +} + +"""A connection to a list of items.""" +type TomogramConnection { + """Pagination data for this connection""" + pageInfo: PageInfo! + + """Contains the nodes in this connection""" + edges: [TomogramEdge!]! +} + +enum TomogramCountColumns { + name + sizeX + sizeY + sizeZ + voxelSpacing + fiducialAlignmentStatus + reconstructionMethod + processing + tomogramVersion + processingSoftware + reconstructionSoftware + isPortalStandard + isAuthorSubmitted + isVisualizationDefault + s3OmezarrDir + httpsOmezarrDir + fileSizeOmezarr + s3MrcFile + httpsMrcFile + fileSizeMrc + scale0Dimensions + scale1Dimensions + scale2Dimensions + ctfCorrected + offsetX + offsetY + offsetZ + keyPhotoUrl + keyPhotoThumbnailUrl + neuroglancerConfig + publications + relatedDatabaseEntries + id + depositionDate + releaseDate + lastModifiedDate +} + +input TomogramCreateInput { + """Tiltseries Alignment""" + alignmentId: ID = null + + """If the tomogram is part of a deposition, the related deposition""" + depositionId: ID! + runId: ID = null + + """Voxel spacings for a run""" + tomogramVoxelSpacingId: ID = null + + """Short name for this tomogram""" + name: String = null + + """Number of pixels in the 3D data fast axis""" + sizeX: Int! + + """Number of pixels in the 3D data medium axis""" + sizeY: Int! + + """ + Number of pixels in the 3D data slow axis. This is the image projection direction at zero stage tilt + """ + sizeZ: Int! + + """Voxel spacing equal in all three axes in angstroms""" + voxelSpacing: Float! + + """ + Fiducial Alignment status: True = aligned with fiducial False = aligned without fiducial + """ + fiducialAlignmentStatus: fiducial_alignment_status_enum! + + """Describe reconstruction method (WBP, SART, SIRT)""" + reconstructionMethod: tomogram_reconstruction_method_enum! + + """Describe additional processing used to derive the tomogram""" + processing: tomogram_processing_enum! + + """Version of tomogram""" + tomogramVersion: Float = null + + """Processing software used to derive the tomogram""" + processingSoftware: String = null + + """Name of software used for reconstruction""" + reconstructionSoftware: String! + + """whether this tomogram adheres to portal standards""" + isPortalStandard: Boolean = null + + """ + Whether this tomogram was submitted by the author of the dataset it belongs to. + """ + isAuthorSubmitted: Boolean = null + + """ + Data curator’s subjective choice of default tomogram to display in visualization for a run + """ + isVisualizationDefault: Boolean = null + + """S3 path to this tomogram in multiscale OME-Zarr format""" + s3OmezarrDir: String = null + + """HTTPS path to this tomogram in multiscale OME-Zarr format""" + httpsOmezarrDir: String = null + + """Size of the tomogram in OME-Zarr format in bytes""" + fileSizeOmezarr: Float = null + + """S3 path to this tomogram in MRC format (no scaling)""" + s3MrcFile: String = null + + """HTTPS path to this tomogram in MRC format (no scaling)""" + httpsMrcFile: String = null + + """Size of the tomogram in MRC format in bytes""" + fileSizeMrc: Float = null + + """comma separated x,y,z dimensions of the unscaled tomogram""" + scale0Dimensions: String = null + + """comma separated x,y,z dimensions of the scale1 tomogram""" + scale1Dimensions: String = null + + """comma separated x,y,z dimensions of the scale2 tomogram""" + scale2Dimensions: String = null + + """Whether this tomogram is CTF corrected""" + ctfCorrected: Boolean = null + + """x offset data relative to the canonical tomogram in pixels""" + offsetX: Int! + + """y offset data relative to the canonical tomogram in pixels""" + offsetY: Int! + + """z offset data relative to the canonical tomogram in pixels""" + offsetZ: Int! + + """URL for the key photo""" + keyPhotoUrl: String = null + + """URL for the thumbnail of key photo""" + keyPhotoThumbnailUrl: String = null + + """the compact json of neuroglancer config""" + neuroglancerConfig: String = null + + """ + Comma-separated list of DOIs for publications associated with the tomogram. + """ + publications: String = null + + """ + If a CryoET tomogram is also deposited into another database, enter the database identifier here (e.g. EMPIAR-11445). Use a comma to separate multiple identifiers. + """ + relatedDatabaseEntries: String = null + + """Numeric identifier (May change!)""" + id: Int! + + """The date a data item was received by the cryoET data portal.""" + depositionDate: DateTime = null + + """The date a data item was received by the cryoET data portal.""" + releaseDate: DateTime = null + + """The date a piece of data was last modified on the cryoET data portal.""" + lastModifiedDate: DateTime = null +} + +"""An edge in a connection.""" +type TomogramEdge { + """A cursor for use in pagination""" + cursor: String! + + """The item at the end of the edge""" + node: Tomogram! +} + +type TomogramGroupByOptions { + alignment: AlignmentGroupByOptions + authors: TomogramAuthorGroupByOptions + deposition: DepositionGroupByOptions + run: RunGroupByOptions + tomogramVoxelSpacing: TomogramVoxelSpacingGroupByOptions + name: String + sizeX: Int + sizeY: Int + sizeZ: Int + voxelSpacing: Float + fiducialAlignmentStatus: fiducial_alignment_status_enum + reconstructionMethod: tomogram_reconstruction_method_enum + processing: tomogram_processing_enum + tomogramVersion: Float + processingSoftware: String + reconstructionSoftware: String + isPortalStandard: Boolean + isAuthorSubmitted: Boolean + isVisualizationDefault: Boolean + s3OmezarrDir: String + httpsOmezarrDir: String + fileSizeOmezarr: Float + s3MrcFile: String + httpsMrcFile: String + fileSizeMrc: Float + scale0Dimensions: String + scale1Dimensions: String + scale2Dimensions: String + ctfCorrected: Boolean + offsetX: Int + offsetY: Int + offsetZ: Int + keyPhotoUrl: String + keyPhotoThumbnailUrl: String + neuroglancerConfig: String + publications: String + relatedDatabaseEntries: String + id: Int + depositionDate: DateTime + releaseDate: DateTime + lastModifiedDate: DateTime +} + +type TomogramMinMaxColumns { + name: String + sizeX: Int + sizeY: Int + sizeZ: Int + voxelSpacing: Float + tomogramVersion: Float + processingSoftware: String + reconstructionSoftware: String + s3OmezarrDir: String + httpsOmezarrDir: String + fileSizeOmezarr: Float + s3MrcFile: String + httpsMrcFile: String + fileSizeMrc: Float + scale0Dimensions: String + scale1Dimensions: String + scale2Dimensions: String + offsetX: Int + offsetY: Int + offsetZ: Int + keyPhotoUrl: String + keyPhotoThumbnailUrl: String + neuroglancerConfig: String + publications: String + relatedDatabaseEntries: String + id: Int + depositionDate: DateTime + releaseDate: DateTime + lastModifiedDate: DateTime +} + +type TomogramNumericalColumns { + sizeX: Int + sizeY: Int + sizeZ: Int + voxelSpacing: Float + tomogramVersion: Float + fileSizeOmezarr: Float + fileSizeMrc: Float + offsetX: Int + offsetY: Int + offsetZ: Int + id: Int +} + +input TomogramOrderByClause { + alignment: AlignmentOrderByClause + deposition: DepositionOrderByClause + run: RunOrderByClause + tomogramVoxelSpacing: TomogramVoxelSpacingOrderByClause + name: orderBy + sizeX: orderBy + sizeY: orderBy + sizeZ: orderBy + voxelSpacing: orderBy + fiducialAlignmentStatus: orderBy + reconstructionMethod: orderBy + processing: orderBy + tomogramVersion: orderBy + processingSoftware: orderBy + reconstructionSoftware: orderBy + isPortalStandard: orderBy + isAuthorSubmitted: orderBy + isVisualizationDefault: orderBy + s3OmezarrDir: orderBy + httpsOmezarrDir: orderBy + fileSizeOmezarr: orderBy + s3MrcFile: orderBy + httpsMrcFile: orderBy + fileSizeMrc: orderBy + scale0Dimensions: orderBy + scale1Dimensions: orderBy + scale2Dimensions: orderBy + ctfCorrected: orderBy + offsetX: orderBy + offsetY: orderBy + offsetZ: orderBy + keyPhotoUrl: orderBy + keyPhotoThumbnailUrl: orderBy + neuroglancerConfig: orderBy + publications: orderBy + relatedDatabaseEntries: orderBy + id: orderBy + depositionDate: orderBy + releaseDate: orderBy + lastModifiedDate: orderBy +} + +input TomogramUpdateInput { + """Tiltseries Alignment""" + alignmentId: ID = null + + """If the tomogram is part of a deposition, the related deposition""" + depositionId: ID + runId: ID = null + + """Voxel spacings for a run""" + tomogramVoxelSpacingId: ID = null + + """Short name for this tomogram""" + name: String = null + + """Number of pixels in the 3D data fast axis""" + sizeX: Int + + """Number of pixels in the 3D data medium axis""" + sizeY: Int + + """ + Number of pixels in the 3D data slow axis. This is the image projection direction at zero stage tilt + """ + sizeZ: Int + + """Voxel spacing equal in all three axes in angstroms""" + voxelSpacing: Float + + """ + Fiducial Alignment status: True = aligned with fiducial False = aligned without fiducial + """ + fiducialAlignmentStatus: fiducial_alignment_status_enum + + """Describe reconstruction method (WBP, SART, SIRT)""" + reconstructionMethod: tomogram_reconstruction_method_enum + + """Describe additional processing used to derive the tomogram""" + processing: tomogram_processing_enum + + """Version of tomogram""" + tomogramVersion: Float = null + + """Processing software used to derive the tomogram""" + processingSoftware: String = null + + """Name of software used for reconstruction""" + reconstructionSoftware: String + + """whether this tomogram adheres to portal standards""" + isPortalStandard: Boolean = null + + """ + Whether this tomogram was submitted by the author of the dataset it belongs to. + """ + isAuthorSubmitted: Boolean = null + + """ + Data curator’s subjective choice of default tomogram to display in visualization for a run + """ + isVisualizationDefault: Boolean = null + + """S3 path to this tomogram in multiscale OME-Zarr format""" + s3OmezarrDir: String = null + + """HTTPS path to this tomogram in multiscale OME-Zarr format""" + httpsOmezarrDir: String = null + + """Size of the tomogram in OME-Zarr format in bytes""" + fileSizeOmezarr: Float = null + + """S3 path to this tomogram in MRC format (no scaling)""" + s3MrcFile: String = null + + """HTTPS path to this tomogram in MRC format (no scaling)""" + httpsMrcFile: String = null + + """Size of the tomogram in MRC format in bytes""" + fileSizeMrc: Float = null + + """comma separated x,y,z dimensions of the unscaled tomogram""" + scale0Dimensions: String = null + + """comma separated x,y,z dimensions of the scale1 tomogram""" + scale1Dimensions: String = null + + """comma separated x,y,z dimensions of the scale2 tomogram""" + scale2Dimensions: String = null + + """Whether this tomogram is CTF corrected""" + ctfCorrected: Boolean = null + + """x offset data relative to the canonical tomogram in pixels""" + offsetX: Int + + """y offset data relative to the canonical tomogram in pixels""" + offsetY: Int + + """z offset data relative to the canonical tomogram in pixels""" + offsetZ: Int + + """URL for the key photo""" + keyPhotoUrl: String = null + + """URL for the thumbnail of key photo""" + keyPhotoThumbnailUrl: String = null + + """the compact json of neuroglancer config""" + neuroglancerConfig: String = null + + """ + Comma-separated list of DOIs for publications associated with the tomogram. + """ + publications: String = null + + """ + If a CryoET tomogram is also deposited into another database, enter the database identifier here (e.g. EMPIAR-11445). Use a comma to separate multiple identifiers. + """ + relatedDatabaseEntries: String = null + + """Numeric identifier (May change!)""" + id: Int + + """The date a data item was received by the cryoET data portal.""" + depositionDate: DateTime = null + + """The date a data item was received by the cryoET data portal.""" + releaseDate: DateTime = null + + """The date a piece of data was last modified on the cryoET data portal.""" + lastModifiedDate: DateTime = null +} + +"""Voxel spacings for a run""" +type TomogramVoxelSpacing implements EntityInterface & Node { + """The Globally Unique ID of this object""" + _id: GlobalID! + + """Numeric identifier (May change!)""" + id: Int! + annotationFiles( + where: AnnotationFileWhereClause = null + orderBy: [AnnotationFileOrderByClause!] = [] + + """Returns the items in the list that come before the specified cursor.""" + before: String = null + + """Returns the items in the list that come after the specified cursor.""" + after: String = null + + """Returns the first n items from the list.""" + first: Int = null + + """Returns the items in the list that come after the specified cursor.""" + last: Int = null + ): AnnotationFileConnection! + annotationFilesAggregate(where: AnnotationFileWhereClause = null): AnnotationFileAggregate + run(where: RunWhereClause = null, orderBy: [RunOrderByClause!] = []): Run + runId: Int + tomograms( + where: TomogramWhereClause = null + orderBy: [TomogramOrderByClause!] = [] + + """Returns the items in the list that come before the specified cursor.""" + before: String = null + + """Returns the items in the list that come after the specified cursor.""" + after: String = null + + """Returns the first n items from the list.""" + first: Int = null + + """Returns the items in the list that come after the specified cursor.""" + last: Int = null + ): TomogramConnection! + tomogramsAggregate(where: TomogramWhereClause = null): TomogramAggregate + + """The voxel spacing for the tomograms in this set in angstroms""" + voxelSpacing: Float! + + """ + The S3 public bucket path where this tomogram voxel spacing is contained + """ + s3Prefix: String! + + """ + The HTTPS directory path where this tomogram voxel spacing is contained + """ + httpsPrefix: String! +} + +type TomogramVoxelSpacingAggregate { + aggregate: [TomogramVoxelSpacingAggregateFunctions!] +} + +type TomogramVoxelSpacingAggregateFunctions { + sum: TomogramVoxelSpacingNumericalColumns + avg: TomogramVoxelSpacingNumericalColumns + stddev: TomogramVoxelSpacingNumericalColumns + variance: TomogramVoxelSpacingNumericalColumns + min: TomogramVoxelSpacingMinMaxColumns + max: TomogramVoxelSpacingMinMaxColumns + groupBy: TomogramVoxelSpacingGroupByOptions + count(distinct: Boolean = false, columns: TomogramVoxelSpacingCountColumns = null): Int +} + +input TomogramVoxelSpacingAggregateWhereClause { + count: TomogramVoxelSpacingAggregateWhereClauseCount! +} + +input TomogramVoxelSpacingAggregateWhereClauseCount { + arguments: TomogramVoxelSpacingCountColumns + distinct: Boolean + filter: TomogramVoxelSpacingWhereClause + predicate: IntComparators +} + +"""A connection to a list of items.""" +type TomogramVoxelSpacingConnection { + """Pagination data for this connection""" + pageInfo: PageInfo! + + """Contains the nodes in this connection""" + edges: [TomogramVoxelSpacingEdge!]! +} + +enum TomogramVoxelSpacingCountColumns { + voxelSpacing + s3Prefix + httpsPrefix + id +} + +input TomogramVoxelSpacingCreateInput { + """The the run this tomogram voxel spacing is a part of""" + runId: ID = null + + """The voxel spacing for the tomograms in this set in angstroms""" + voxelSpacing: Float! + + """ + The S3 public bucket path where this tomogram voxel spacing is contained + """ + s3Prefix: String! + + """ + The HTTPS directory path where this tomogram voxel spacing is contained + """ + httpsPrefix: String! + + """Numeric identifier (May change!)""" + id: Int! +} + +"""An edge in a connection.""" +type TomogramVoxelSpacingEdge { + """A cursor for use in pagination""" + cursor: String! + + """The item at the end of the edge""" + node: TomogramVoxelSpacing! +} + +type TomogramVoxelSpacingGroupByOptions { + annotationFiles: AnnotationFileGroupByOptions + run: RunGroupByOptions + tomograms: TomogramGroupByOptions + voxelSpacing: Float + s3Prefix: String + httpsPrefix: String + id: Int +} + +type TomogramVoxelSpacingMinMaxColumns { + voxelSpacing: Float + s3Prefix: String + httpsPrefix: String + id: Int +} + +type TomogramVoxelSpacingNumericalColumns { + voxelSpacing: Float + id: Int +} + +input TomogramVoxelSpacingOrderByClause { + run: RunOrderByClause + voxelSpacing: orderBy + s3Prefix: orderBy + httpsPrefix: orderBy + id: orderBy +} + +input TomogramVoxelSpacingUpdateInput { + """The the run this tomogram voxel spacing is a part of""" + runId: ID = null + + """The voxel spacing for the tomograms in this set in angstroms""" + voxelSpacing: Float + + """ + The S3 public bucket path where this tomogram voxel spacing is contained + """ + s3Prefix: String + + """ + The HTTPS directory path where this tomogram voxel spacing is contained + """ + httpsPrefix: String + + """Numeric identifier (May change!)""" + id: Int +} + +input TomogramVoxelSpacingWhereClause { + annotationFiles: AnnotationFileWhereClause + annotationFilesAggregate: AnnotationFileAggregateWhereClause + run: RunWhereClause + runId: IntComparators + tomograms: TomogramWhereClause + tomogramsAggregate: TomogramAggregateWhereClause + voxelSpacing: FloatComparators + s3Prefix: StrComparators + httpsPrefix: StrComparators + id: IntComparators +} + +input TomogramVoxelSpacingWhereClauseMutations { + id: IntComparators +} + +input TomogramWhereClause { + alignment: AlignmentWhereClause + alignmentId: IntComparators + authors: TomogramAuthorWhereClause + authorsAggregate: TomogramAuthorAggregateWhereClause + deposition: DepositionWhereClause + depositionId: IntComparators + run: RunWhereClause + runId: IntComparators + tomogramVoxelSpacing: TomogramVoxelSpacingWhereClause + tomogramVoxelSpacingId: IntComparators + name: StrComparators + sizeX: IntComparators + sizeY: IntComparators + sizeZ: IntComparators + voxelSpacing: FloatComparators + fiducialAlignmentStatus: Fiducial_alignment_status_enumEnumComparators + reconstructionMethod: Tomogram_reconstruction_method_enumEnumComparators + processing: Tomogram_processing_enumEnumComparators + tomogramVersion: FloatComparators + processingSoftware: StrComparators + reconstructionSoftware: StrComparators + isPortalStandard: BoolComparators + isAuthorSubmitted: BoolComparators + isVisualizationDefault: BoolComparators + s3OmezarrDir: StrComparators + httpsOmezarrDir: StrComparators + fileSizeOmezarr: FloatComparators + s3MrcFile: StrComparators + httpsMrcFile: StrComparators + fileSizeMrc: FloatComparators + scale0Dimensions: StrComparators + scale1Dimensions: StrComparators + scale2Dimensions: StrComparators + ctfCorrected: BoolComparators + offsetX: IntComparators + offsetY: IntComparators + offsetZ: IntComparators + keyPhotoUrl: StrComparators + keyPhotoThumbnailUrl: StrComparators + neuroglancerConfig: StrComparators + publications: StrComparators + relatedDatabaseEntries: StrComparators + id: IntComparators + depositionDate: DatetimeComparators + releaseDate: DatetimeComparators + lastModifiedDate: DatetimeComparators +} + +input TomogramWhereClauseMutations { + id: IntComparators +} + +input Tomogram_processing_enumEnumComparators { + _eq: tomogram_processing_enum + _neq: tomogram_processing_enum + _in: [tomogram_processing_enum!] + _nin: [tomogram_processing_enum!] + _gt: tomogram_processing_enum + _gte: tomogram_processing_enum + _lt: tomogram_processing_enum + _lte: tomogram_processing_enum + _is_null: Boolean +} + +input Tomogram_reconstruction_method_enumEnumComparators { + _eq: tomogram_reconstruction_method_enum + _neq: tomogram_reconstruction_method_enum + _in: [tomogram_reconstruction_method_enum!] + _nin: [tomogram_reconstruction_method_enum!] + _gt: tomogram_reconstruction_method_enum + _gte: tomogram_reconstruction_method_enum + _lt: tomogram_reconstruction_method_enum + _lte: tomogram_reconstruction_method_enum + _is_null: Boolean +} + +enum alignment_method_type_enum { + projection_matching + patch_tracking + fiducial_based +} + +enum alignment_type_enum { + LOCAL + GLOBAL +} + +enum annotation_file_shape_type_enum { + SegmentationMask + OrientedPoint + Point + InstanceSegmentation + InstanceSegmentationMask + Mesh +} + +enum annotation_file_source_enum { + dataset_author + community + portal_standard +} + +enum annotation_method_link_type_enum { + documentation + models_weights + other + source_code + website +} + +enum annotation_method_type_enum { + manual + automated + hybrid + simulated +} + +enum deposition_types_enum { + annotation + dataset + tomogram +} + +enum fiducial_alignment_status_enum { + FIDUCIAL + NON_FIDUCIAL +} + +enum orderBy { + asc + asc_nulls_first + asc_nulls_last + desc + desc_nulls_first + desc_nulls_last +} + +enum sample_type_enum { + cell + cell_line + in_silico + in_vitro + organelle + organism + organoid + other + primary_cell_culture + tissue + virus +} + +enum tiltseries_microscope_manufacturer_enum { + FEI + TFS + JEOL + SIMULATED +} + +enum tomogram_processing_enum { + denoised + filtered + raw + filtered_even + filtered_odd +} + +enum tomogram_reconstruction_method_enum { + SART + Fourier_Space + SIRT + WBP + Unknown +} From d344f5fb2e3a507827e868b3d087e6321b49ff44 Mon Sep 17 00:00:00 2001 From: Jinghui Geng Date: Tue, 17 Mar 2026 14:36:53 -0700 Subject: [PATCH 4/6] use saber not json --- apiv2/db_import/tests/conftest.py | 2 +- apiv2/db_import/tests/test_db_annotation_import.py | 2 +- .../VoxelSpacing12.300/Annotations/100/foo-1.0.json | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/apiv2/db_import/tests/conftest.py b/apiv2/db_import/tests/conftest.py index 008332eb6..6cb018b07 100644 --- a/apiv2/db_import/tests/conftest.py +++ b/apiv2/db_import/tests/conftest.py @@ -133,5 +133,5 @@ def expected_dataset(http_prefix: str) -> dict[str, Any]: "key_photo_url": f"{http_prefix}/{DATASET_ID}/KeyPhoto/snapshot.png", "key_photo_thumbnail_url": f"{http_prefix}/{DATASET_ID}/KeyPhoto/thumbnail.png", "deposition_id": 300, - "file_size": 1375064.0, + "file_size": 1375065.0, } diff --git a/apiv2/db_import/tests/test_db_annotation_import.py b/apiv2/db_import/tests/test_db_annotation_import.py index 4b0e79ec6..62afeacf6 100644 --- a/apiv2/db_import/tests/test_db_annotation_import.py +++ b/apiv2/db_import/tests/test_db_annotation_import.py @@ -59,7 +59,7 @@ def expected_annotation_files(http_prefix: str) -> list[dict[str, Any]]: "s3_path": f"s3://test-public-bucket/{path}100-foo-1.0_globalcaption.json", "https_path": f"{http_prefix}/{path}100-foo-1.0_globalcaption.json", "source": "community", - "format": "json", + "format": "saber", "is_visualization_default": False, "file_size": 0, }, diff --git a/test_infra/test_files/30001/RUN1/Reconstructions/VoxelSpacing12.300/Annotations/100/foo-1.0.json b/test_infra/test_files/30001/RUN1/Reconstructions/VoxelSpacing12.300/Annotations/100/foo-1.0.json index 847ad3459..013f3358a 100644 --- a/test_infra/test_files/30001/RUN1/Reconstructions/VoxelSpacing12.300/Annotations/100/foo-1.0.json +++ b/test_infra/test_files/30001/RUN1/Reconstructions/VoxelSpacing12.300/Annotations/100/foo-1.0.json @@ -68,7 +68,7 @@ "is_visualization_default": false }, { - "format": "json", + "format": "saber", "path": "30001/RUN1/Reconstructions/VoxelSpacing12.300/Annotations/100-foo-1.0_globalcaption.json", "shape": "GlobalCaption", "is_visualization_default": false From 78e1de5336d51780ed786c45c4c96e351f69fbc2 Mon Sep 17 00:00:00 2001 From: Jinghui Geng Date: Tue, 17 Mar 2026 15:52:58 -0700 Subject: [PATCH 5/6] Fix annotation metadata glob to exclude globalcaption files --- apiv2/db_import/importers/annotation.py | 4 +++- apiv2/db_import/tests/conftest.py | 2 +- .../100/100-foo-1.0_globalcaption.json | 16 ++++++++++++++++ 3 files changed, 20 insertions(+), 2 deletions(-) create mode 100644 test_infra/test_files/30001/RUN1/Reconstructions/VoxelSpacing12.300/Annotations/100/100-foo-1.0_globalcaption.json diff --git a/apiv2/db_import/importers/annotation.py b/apiv2/db_import/importers/annotation.py index 187c1c4f5..6502097c0 100644 --- a/apiv2/db_import/importers/annotation.py +++ b/apiv2/db_import/importers/annotation.py @@ -106,7 +106,9 @@ def get_filters(self) -> dict[str, Any]: def get_finder_args(self) -> dict[str, Any]: return { "path": os.path.join(self.tomogram_voxel_spacing.s3_prefix, "Annotations/"), - "file_glob": "*/*.json", + # Use *[0-9].json to match only annotation metadata files (e.g., foo-1.0.json) + # and exclude annotation data files which have a _{shape} suffix (e.g., foo-1.0_globalcaption.json) + "file_glob": "*/*[0-9].json", } diff --git a/apiv2/db_import/tests/conftest.py b/apiv2/db_import/tests/conftest.py index 6cb018b07..ae4eebec6 100644 --- a/apiv2/db_import/tests/conftest.py +++ b/apiv2/db_import/tests/conftest.py @@ -133,5 +133,5 @@ def expected_dataset(http_prefix: str) -> dict[str, Any]: "key_photo_url": f"{http_prefix}/{DATASET_ID}/KeyPhoto/snapshot.png", "key_photo_thumbnail_url": f"{http_prefix}/{DATASET_ID}/KeyPhoto/thumbnail.png", "deposition_id": 300, - "file_size": 1375065.0, + "file_size": 1375370.0, } diff --git a/test_infra/test_files/30001/RUN1/Reconstructions/VoxelSpacing12.300/Annotations/100/100-foo-1.0_globalcaption.json b/test_infra/test_files/30001/RUN1/Reconstructions/VoxelSpacing12.300/Annotations/100/100-foo-1.0_globalcaption.json new file mode 100644 index 000000000..711f79416 --- /dev/null +++ b/test_infra/test_files/30001/RUN1/Reconstructions/VoxelSpacing12.300/Annotations/100/100-foo-1.0_globalcaption.json @@ -0,0 +1,16 @@ +{ + "captions": [ + { + "id": 0, + "text": "A caption for tomogram X." + }, + { + "id": 1, + "text": "A 2nd caption for tomogram X." + }, + { + "id": 2, + "text": "A 3rd caption for tomogram X." + } + ] +} From 53df1365a3a0f3d7185d9c7395e8e831263fbf05 Mon Sep 17 00:00:00 2001 From: Jinghui Geng Date: Tue, 17 Mar 2026 15:59:02 -0700 Subject: [PATCH 6/6] remove empty autogenerated migration --- .../versions/20260316_142504_autogenerated.py | 23 ------------------- 1 file changed, 23 deletions(-) delete mode 100644 apiv2/database/migrations/versions/20260316_142504_autogenerated.py diff --git a/apiv2/database/migrations/versions/20260316_142504_autogenerated.py b/apiv2/database/migrations/versions/20260316_142504_autogenerated.py deleted file mode 100644 index d03386fe9..000000000 --- a/apiv2/database/migrations/versions/20260316_142504_autogenerated.py +++ /dev/null @@ -1,23 +0,0 @@ -"""autogenerated - -Create Date: 2026-03-16 21:25:06.002149 - -""" - -# revision identifiers, used by Alembic. -revision = '20260316_142504' -down_revision = '20260306_160839' -branch_labels = None -depends_on = None - - -def upgrade() -> None: - # ### commands auto generated by Alembic - please adjust! ### - pass - # ### end Alembic commands ### - - -def downgrade() -> None: - # ### commands auto generated by Alembic - please adjust! ### - pass - # ### end Alembic commands ###