diff --git a/cwltool/process.py b/cwltool/process.py index 243d89b22..a2b63115c 100644 --- a/cwltool/process.py +++ b/cwltool/process.py @@ -89,7 +89,9 @@ def get_schema(version): return SCHEMA_CACHE[version] cache = {} - version = version.split("#")[-1].split(".")[0] + version = version.split("#")[-1] + if 'dev' in version: + version = ".".join(version.split(".")[:-1]) for f in cwl_files: try: res = resource_stream(__name__, 'schemas/%s/%s' % (version, f)) @@ -314,13 +316,13 @@ def __init__(self, toolpath_object, **kwargs): global SCHEMA_FILE, SCHEMA_DIR, SCHEMA_ANY # pylint: disable=global-statement if SCHEMA_FILE is None: - get_schema("draft-4") + get_schema("v1.0") SCHEMA_ANY = cast(Dict[unicode, Any], - SCHEMA_CACHE["draft-4"][3].idx["https://w3id.org/cwl/salad#Any"]) + SCHEMA_CACHE["v1.0"][3].idx["https://w3id.org/cwl/salad#Any"]) SCHEMA_FILE = cast(Dict[unicode, Any], - SCHEMA_CACHE["draft-4"][3].idx["https://w3id.org/cwl/cwl#File"]) + SCHEMA_CACHE["v1.0"][3].idx["https://w3id.org/cwl/cwl#File"]) SCHEMA_DIR = cast(Dict[unicode, Any], - SCHEMA_CACHE["draft-4"][3].idx["https://w3id.org/cwl/cwl#Directory"]) + SCHEMA_CACHE["v1.0"][3].idx["https://w3id.org/cwl/cwl#Directory"]) names = schema_salad.schema.make_avro_schema([SCHEMA_FILE, SCHEMA_DIR, SCHEMA_ANY], schema_salad.ref_resolver.Loader({}))[0] diff --git a/cwltool/schemas/site/cwlsite-draft4-job.json b/cwltool/schemas/site/cwlsite-draft4-job.json index 1f3078d09..bc4548c76 100644 --- a/cwltool/schemas/site/cwlsite-draft4-job.json +++ b/cwltool/schemas/site/cwlsite-draft4-job.json @@ -43,7 +43,7 @@ "https://w3id.org/cwl/cwl#CreateFileRequirement=CommandLineTool.html#CreateFileRequirement", "https://w3id.org/cwl/cwl#EnvVarRequirement=CommandLineTool.html#EnvVarRequirement", "https://w3id.org/cwl/cwl#ShellCommandRequirement=CommandLineTool.html#ShellCommandRequirement", - "https://w3id.org/cwl/cwl#ResourceRequirement=CommandLineTool.html#ResourceRequirement", + "https://w3id.org/cwl/cwl#ResourceRequirement=CommandLineTool.html#ResourceRequirement" ], "brandlink": "index.html", "brandimg": "", @@ -62,5 +62,15 @@ "brandlink": "index.html", "brandimg": "", "primtype": null - } + }, + #{ + # "source": {"$import": "userguide-draft4-input.json"}, + # "target": "draft-4/UserGuide.html", + # "renderlist": [], + # "redirect": [], + # "brandlink": "index.html", + # "brandimg": "", + # "primtype": null + #} + ] diff --git a/cwltool/schemas/site/draft3-deps.json b/cwltool/schemas/site/draft3-deps.json index 98b90f6e8..00a4a3530 100644 --- a/cwltool/schemas/site/draft3-deps.json +++ b/cwltool/schemas/site/draft3-deps.json @@ -2,75 +2,187 @@ { "secondaryFiles": [ { + "basename": "concepts.md", "class": "File", "location": "../draft-3/concepts.md" }, { - "entry": { - "class": "Directory", - "listing": [ - { - "entry": { + "basename": "salad", + "location": "_:0600cfcc-4e4b-4213-a821-1009e8a44f5a", + "class": "Directory", + "listing": [ + { + "basename": "schema_salad", + "location": "_:1b18d943-4f8f-4c39-80ba-b30d2656d64e", + "class": "Directory", + "listing": [ + { + "basename": "metaschema", + "location": "_:ae5f64e3-e9d7-41db-b59e-97c1611182ee", "class": "Directory", "listing": [ { - "entry": { - "class": "Directory", - "listing": [ - {$import: draft3-metaschema.json} - ] - }, - "entryname": "metaschema" + "secondaryFiles": [ + { + "secondaryFiles": [ + { + "basename": "link_res_schema.yml", + "class": "File", + "location": "../draft-3/salad/schema_salad/metaschema/link_res_schema.yml" + }, + { + "basename": "link_res_src.yml", + "class": "File", + "location": "../draft-3/salad/schema_salad/metaschema/link_res_src.yml" + }, + { + "basename": "link_res_proc.yml", + "class": "File", + "location": "../draft-3/salad/schema_salad/metaschema/link_res_proc.yml" + } + ], + "basename": "link_res.yml", + "class": "File", + "location": "../draft-3/salad/schema_salad/metaschema/link_res.yml" + }, + { + "basename": "salad.md", + "class": "File", + "location": "../draft-3/salad/schema_salad/metaschema/salad.md" + }, + { + "basename": "import_include.md", + "class": "File", + "location": "../draft-3/salad/schema_salad/metaschema/import_include.md" + }, + { + "secondaryFiles": [ + { + "basename": "field_name_src.yml", + "class": "File", + "location": "../draft-3/salad/schema_salad/metaschema/field_name_src.yml" + }, + { + "basename": "field_name_schema.yml", + "class": "File", + "location": "../draft-3/salad/schema_salad/metaschema/field_name_schema.yml" + }, + { + "basename": "field_name_proc.yml", + "class": "File", + "location": "../draft-3/salad/schema_salad/metaschema/field_name_proc.yml" + } + ], + "basename": "field_name.yml", + "class": "File", + "location": "../draft-3/salad/schema_salad/metaschema/field_name.yml" + }, + { + "secondaryFiles": [ + { + "basename": "ident_res_proc.yml", + "class": "File", + "location": "../draft-3/salad/schema_salad/metaschema/ident_res_proc.yml" + }, + { + "basename": "ident_res_schema.yml", + "class": "File", + "location": "../draft-3/salad/schema_salad/metaschema/ident_res_schema.yml" + }, + { + "basename": "ident_res_src.yml", + "class": "File", + "location": "../draft-3/salad/schema_salad/metaschema/ident_res_src.yml" + } + ], + "basename": "ident_res.yml", + "class": "File", + "location": "../draft-3/salad/schema_salad/metaschema/ident_res.yml" + }, + { + "secondaryFiles": [ + { + "basename": "vocab_res_schema.yml", + "class": "File", + "location": "../draft-3/salad/schema_salad/metaschema/vocab_res_schema.yml" + }, + { + "basename": "vocab_res_proc.yml", + "class": "File", + "location": "../draft-3/salad/schema_salad/metaschema/vocab_res_proc.yml" + }, + { + "basename": "vocab_res_src.yml", + "class": "File", + "location": "../draft-3/salad/schema_salad/metaschema/vocab_res_src.yml" + } + ], + "basename": "vocab_res.yml", + "class": "File", + "location": "../draft-3/salad/schema_salad/metaschema/vocab_res.yml" + } + ], + "basename": "metaschema.yml", + "class": "File", + "location": "../draft-3/salad/schema_salad/metaschema/metaschema.yml" } ] - }, - "entryname": "schema_salad" - } - ] - }, - "entryname": "salad" + } + ] + } + ] } ], + "basename": "Process.yml", "class": "File", "location": "../draft-3/Process.yml" }, { "secondaryFiles": [ { + "basename": "contrib.md", "class": "File", "location": "../draft-3/contrib.md" }, { + "basename": "concepts.md", "class": "File", - "location": "../draft-3/intro.md" + "location": "../draft-3/concepts.md" }, { + "basename": "invocation.md", "class": "File", - "location": "../draft-3/concepts.md" + "location": "../draft-3/invocation.md" }, { + "basename": "intro.md", "class": "File", - "location": "../draft-3/invocation.md" + "location": "../draft-3/intro.md" } ], + "basename": "CommandLineTool.yml", "class": "File", "location": "../draft-3/CommandLineTool.yml" }, { "secondaryFiles": [ { + "basename": "contrib.md", "class": "File", "location": "../draft-3/contrib.md" }, { + "basename": "concepts.md", "class": "File", - "location": "../draft-3/intro.md" + "location": "../draft-3/concepts.md" }, { + "basename": "intro.md", "class": "File", - "location": "../draft-3/concepts.md" + "location": "../draft-3/intro.md" } ], + "basename": "Workflow.yml", "class": "File", "location": "../draft-3/Workflow.yml" } diff --git a/cwltool/schemas/site/draft3-metaschema.json b/cwltool/schemas/site/draft3-metaschema.json new file mode 100644 index 000000000..e66dca738 --- /dev/null +++ b/cwltool/schemas/site/draft3-metaschema.json @@ -0,0 +1,104 @@ +{ + "secondaryFiles": [ + { + "secondaryFiles": [ + { + "basename": "link_res_schema.yml", + "class": "File", + "location": "../draft-3/salad/schema_salad/metaschema/link_res_schema.yml" + }, + { + "basename": "link_res_src.yml", + "class": "File", + "location": "../draft-3/salad/schema_salad/metaschema/link_res_src.yml" + }, + { + "basename": "link_res_proc.yml", + "class": "File", + "location": "../draft-3/salad/schema_salad/metaschema/link_res_proc.yml" + } + ], + "basename": "link_res.yml", + "class": "File", + "location": "../draft-3/salad/schema_salad/metaschema/link_res.yml" + }, + { + "basename": "salad.md", + "class": "File", + "location": "../draft-3/salad/schema_salad/metaschema/salad.md" + }, + { + "basename": "import_include.md", + "class": "File", + "location": "../draft-3/salad/schema_salad/metaschema/import_include.md" + }, + { + "secondaryFiles": [ + { + "basename": "field_name_src.yml", + "class": "File", + "location": "../draft-3/salad/schema_salad/metaschema/field_name_src.yml" + }, + { + "basename": "field_name_schema.yml", + "class": "File", + "location": "../draft-3/salad/schema_salad/metaschema/field_name_schema.yml" + }, + { + "basename": "field_name_proc.yml", + "class": "File", + "location": "../draft-3/salad/schema_salad/metaschema/field_name_proc.yml" + } + ], + "basename": "field_name.yml", + "class": "File", + "location": "../draft-3/salad/schema_salad/metaschema/field_name.yml" + }, + { + "secondaryFiles": [ + { + "basename": "ident_res_proc.yml", + "class": "File", + "location": "../draft-3/salad/schema_salad/metaschema/ident_res_proc.yml" + }, + { + "basename": "ident_res_schema.yml", + "class": "File", + "location": "../draft-3/salad/schema_salad/metaschema/ident_res_schema.yml" + }, + { + "basename": "ident_res_src.yml", + "class": "File", + "location": "../draft-3/salad/schema_salad/metaschema/ident_res_src.yml" + } + ], + "basename": "ident_res.yml", + "class": "File", + "location": "../draft-3/salad/schema_salad/metaschema/ident_res.yml" + }, + { + "secondaryFiles": [ + { + "basename": "vocab_res_schema.yml", + "class": "File", + "location": "../draft-3/salad/schema_salad/metaschema/vocab_res_schema.yml" + }, + { + "basename": "vocab_res_proc.yml", + "class": "File", + "location": "../draft-3/salad/schema_salad/metaschema/vocab_res_proc.yml" + }, + { + "basename": "vocab_res_src.yml", + "class": "File", + "location": "../draft-3/salad/schema_salad/metaschema/vocab_res_src.yml" + } + ], + "basename": "vocab_res.yml", + "class": "File", + "location": "../draft-3/salad/schema_salad/metaschema/vocab_res.yml" + } + ], + "class": "File", + "location": "../draft-3/salad/schema_salad/metaschema/metaschema.yml" +} \ No newline at end of file diff --git a/cwltool/schemas/site/draft4-deps.json b/cwltool/schemas/site/draft4-deps.json index 3cddeb186..f7e949354 100644 --- a/cwltool/schemas/site/draft4-deps.json +++ b/cwltool/schemas/site/draft4-deps.json @@ -1,79 +1,89 @@ + [ { "secondaryFiles": [ { + "basename": "concepts.md", "class": "File", "location": "../draft-4/concepts.md" }, { - "entry": { - "class": "Directory", - "listing": [ - { - "entry": { + "basename": "salad", + "location": "_:4a097285-861e-42ac-9322-20244d69dc96", + "class": "Directory", + "listing": [ + { + "basename": "schema_salad", + "location": "_:31c5c0f1-dfcb-4a68-a5e1-063d03e85d3a", + "class": "Directory", + "listing": [ + { + "basename": "metaschema", + "location": "_:8d932277-54ee-49f7-b7b3-007108151ed4", "class": "Directory", "listing": [ { - "entry": { - "class": "Directory", - "listing": [ - { - "class": "File", - "location": "../draft-4/salad/schema_salad/metaschema/metaschema_base.yml" - } - ] - }, - "entryname": "metaschema" + "basename": "metaschema_base.yml", + "class": "File", + "location": "../draft-4/salad/schema_salad/metaschema/metaschema_base.yml" } ] - }, - "entryname": "schema_salad" - } - ] - }, - "entryname": "salad" + } + ] + } + ] } ], + "basename": "Process.yml", "class": "File", "location": "../draft-4/Process.yml" }, { "secondaryFiles": [ { + "basename": "contrib.md", "class": "File", "location": "../draft-4/contrib.md" }, { + "basename": "concepts.md", "class": "File", - "location": "../draft-4/intro.md" + "location": "../draft-4/concepts.md" }, { + "basename": "invocation.md", "class": "File", - "location": "../draft-4/concepts.md" + "location": "../draft-4/invocation.md" }, { + "basename": "intro.md", "class": "File", - "location": "../draft-4/invocation.md" + "location": "../draft-4/intro.md" } ], + "basename": "CommandLineTool.yml", "class": "File", "location": "../draft-4/CommandLineTool.yml" }, { "secondaryFiles": [ { + "basename": "contrib.md", "class": "File", "location": "../draft-4/contrib.md" }, { + "basename": "concepts.md", "class": "File", - "location": "../draft-4/intro.md" + "location": "../draft-4/concepts.md" }, { + "basename": "intro.md", "class": "File", - "location": "../draft-4/concepts.md" + "location": "../draft-4/intro.md" } ], + "basename": "Workflow.yml", "class": "File", "location": "../draft-4/Workflow.yml" } diff --git a/cwltool/schemas/site/draft4-metaschema.json b/cwltool/schemas/site/draft4-metaschema.json new file mode 100644 index 000000000..855081443 --- /dev/null +++ b/cwltool/schemas/site/draft4-metaschema.json @@ -0,0 +1,109 @@ +{ + "secondaryFiles": [ + { + "secondaryFiles": [ + { + "basename": "link_res_schema.yml", + "class": "File", + "location": "../draft-4/salad/schema_salad/metaschema/link_res_schema.yml" + }, + { + "basename": "link_res_src.yml", + "class": "File", + "location": "../draft-4/salad/schema_salad/metaschema/link_res_src.yml" + }, + { + "basename": "link_res_proc.yml", + "class": "File", + "location": "../draft-4/salad/schema_salad/metaschema/link_res_proc.yml" + } + ], + "basename": "link_res.yml", + "class": "File", + "location": "../draft-4/salad/schema_salad/metaschema/link_res.yml" + }, + { + "basename": "salad.md", + "class": "File", + "location": "../draft-4/salad/schema_salad/metaschema/salad.md" + }, + { + "basename": "metaschema_base.yml", + "class": "File", + "location": "../draft-4/salad/schema_salad/metaschema/metaschema_base.yml" + }, + { + "basename": "import_include.md", + "class": "File", + "location": "../draft-4/salad/schema_salad/metaschema/import_include.md" + }, + { + "secondaryFiles": [ + { + "basename": "field_name_src.yml", + "class": "File", + "location": "../draft-4/salad/schema_salad/metaschema/field_name_src.yml" + }, + { + "basename": "field_name_schema.yml", + "class": "File", + "location": "../draft-4/salad/schema_salad/metaschema/field_name_schema.yml" + }, + { + "basename": "field_name_proc.yml", + "class": "File", + "location": "../draft-4/salad/schema_salad/metaschema/field_name_proc.yml" + } + ], + "basename": "field_name.yml", + "class": "File", + "location": "../draft-4/salad/schema_salad/metaschema/field_name.yml" + }, + { + "secondaryFiles": [ + { + "basename": "ident_res_proc.yml", + "class": "File", + "location": "../draft-4/salad/schema_salad/metaschema/ident_res_proc.yml" + }, + { + "basename": "ident_res_schema.yml", + "class": "File", + "location": "../draft-4/salad/schema_salad/metaschema/ident_res_schema.yml" + }, + { + "basename": "ident_res_src.yml", + "class": "File", + "location": "../draft-4/salad/schema_salad/metaschema/ident_res_src.yml" + } + ], + "basename": "ident_res.yml", + "class": "File", + "location": "../draft-4/salad/schema_salad/metaschema/ident_res.yml" + }, + { + "secondaryFiles": [ + { + "basename": "vocab_res_schema.yml", + "class": "File", + "location": "../draft-4/salad/schema_salad/metaschema/vocab_res_schema.yml" + }, + { + "basename": "vocab_res_proc.yml", + "class": "File", + "location": "../draft-4/salad/schema_salad/metaschema/vocab_res_proc.yml" + }, + { + "basename": "vocab_res_src.yml", + "class": "File", + "location": "../draft-4/salad/schema_salad/metaschema/vocab_res_src.yml" + } + ], + "basename": "vocab_res.yml", + "class": "File", + "location": "../draft-4/salad/schema_salad/metaschema/vocab_res.yml" + } + ], + "class": "File", + "location": "../draft-4/salad/schema_salad/metaschema/metaschema.yml" +} \ No newline at end of file diff --git a/cwltool/schemas/site/mergesecondary.cwl b/cwltool/schemas/site/mergesecondary.cwl new file mode 100644 index 000000000..be1d4ad40 --- /dev/null +++ b/cwltool/schemas/site/mergesecondary.cwl @@ -0,0 +1,25 @@ +class: ExpressionTool +cwlVersion: draft-4.dev3 +inputs: + primary: File + secondary: File[] + dirs: string[] +outputs: + dir: File +expression: | + ${ + inputs.primary.secondaryFiles = []; + for (var i = 0; i < inputs.secondary.length; i++) { + var k = inputs.secondary[i]; + if (inputs.dirs[i] != "") { + inputs.primary.secondaryFiles.push({ + class: "Directory", + basename: inputs.dirs[i], + listing: [k] + }); + } else { + inputs.primary.secondaryFiles.push(k); + } + } + return {dir: inputs.primary}; + } \ No newline at end of file diff --git a/cwltool/schemas/site/userguide-input.json b/cwltool/schemas/site/userguide-input.json index 86e500051..ed8547f0a 100644 --- a/cwltool/schemas/site/userguide-input.json +++ b/cwltool/schemas/site/userguide-input.json @@ -1,140 +1,146 @@ { "secondaryFiles": [ { + "basename": "userguide-intro.md", "class": "File", "location": "../draft-3/userguide-intro.md" }, { - "entry": { - "class": "Directory", - "listing": [ - { - "class": "File", - "location": "../draft-3/examples/1st-tool.cwl" - }, - { - "class": "File", - "location": "../draft-3/examples/echo-job.yml" - }, - { - "class": "File", - "location": "../draft-3/examples/inp.cwl" - }, - { - "class": "File", - "location": "../draft-3/examples/inp-job.yml" - }, - { - "class": "File", - "location": "../draft-3/examples/tar.cwl" - }, - { - "class": "File", - "location": "../draft-3/examples/tar-job.yml" - }, - { - "class": "File", - "location": "../draft-3/examples/stdout.cwl" - }, - { - "class": "File", - "location": "../draft-3/examples/echo-job.yml" - }, - { - "class": "File", - "location": "../draft-3/examples/tar-param.cwl" - }, - { - "class": "File", - "location": "../draft-3/examples/tar-param-job.yml" - }, - { - "class": "File", - "location": "../draft-3/examples/docker.cwl" - }, - { - "class": "File", - "location": "../draft-3/examples/docker-job.yml" - }, - { - "class": "File", - "location": "../draft-3/examples/arguments.cwl" - }, - { - "class": "File", - "location": "../draft-3/examples/arguments-job.yml" - }, - { - "class": "File", - "location": "../draft-3/examples/array-inputs.cwl" - }, - { - "class": "File", - "location": "../draft-3/examples/array-inputs-job.yml" - }, - { - "class": "File", - "location": "../draft-3/examples/array-outputs.cwl" - }, - { - "class": "File", - "location": "../draft-3/examples/array-outputs-job.yml" - }, - { - "class": "File", - "location": "../draft-3/examples/record.cwl" - }, - { - "class": "File", - "location": "../draft-3/examples/record-job1.yml" - }, - { - "class": "File", - "location": "../draft-3/examples/record-job2.yml" - }, - { - "class": "File", - "location": "../draft-3/examples/record-job2.yml" - }, - { - "class": "File", - "location": "../draft-3/examples/env.cwl" - }, - { - "class": "File", - "location": "../draft-3/examples/echo-job.yml" - }, - { - "class": "File", - "location": "../draft-3/examples/expression.cwl" - }, - { - "class": "File", - "location": "../draft-3/examples/createfile.cwl" - }, - { - "class": "File", - "location": "../draft-3/examples/echo-job.yml" - }, - { - "class": "File", - "location": "../draft-3/examples/linkfile.cwl" - }, - { - "class": "File", - "location": "../draft-3/examples/arguments-job.yml" - }, - { - "class": "File", - "location": "../draft-3/examples/1st-workflow.cwl" - }, - { - "class": "File", - "location": "../draft-3/examples/1st-workflow-job.yml" - } - ] - }, - "entryname": "examples" + "basename": "examples", + "location": "_:acab810d-f57a-41f6-a875-0b0ad729fd1a", + "class": "Directory", + "listing": [ + { + "basename": "record-job1.yml", + "class": "File", + "location": "../draft-3/examples/record-job1.yml" + }, + { + "basename": "expression.cwl", + "class": "File", + "location": "../draft-3/examples/expression.cwl" + }, + { + "basename": "array-outputs-job.yml", + "class": "File", + "location": "../draft-3/examples/array-outputs-job.yml" + }, + { + "basename": "tar-param.cwl", + "class": "File", + "location": "../draft-3/examples/tar-param.cwl" + }, + { + "basename": "inp-job.yml", + "class": "File", + "location": "../draft-3/examples/inp-job.yml" + }, + { + "basename": "1st-workflow-job.yml", + "class": "File", + "location": "../draft-3/examples/1st-workflow-job.yml" + }, + { + "basename": "record-job2.yml", + "class": "File", + "location": "../draft-3/examples/record-job2.yml" + }, + { + "basename": "echo-job.yml", + "class": "File", + "location": "../draft-3/examples/echo-job.yml" + }, + { + "basename": "array-outputs.cwl", + "class": "File", + "location": "../draft-3/examples/array-outputs.cwl" + }, + { + "basename": "array-inputs-job.yml", + "class": "File", + "location": "../draft-3/examples/array-inputs-job.yml" + }, + { + "basename": "1st-workflow.cwl", + "class": "File", + "location": "../draft-3/examples/1st-workflow.cwl" + }, + { + "basename": "docker.cwl", + "class": "File", + "location": "../draft-3/examples/docker.cwl" + }, + { + "basename": "stdout.cwl", + "class": "File", + "location": "../draft-3/examples/stdout.cwl" + }, + { + "basename": "docker-job.yml", + "class": "File", + "location": "../draft-3/examples/docker-job.yml" + }, + { + "basename": "tar.cwl", + "class": "File", + "location": "../draft-3/examples/tar.cwl" + }, + { + "basename": "createfile.cwl", + "class": "File", + "location": "../draft-3/examples/createfile.cwl" + }, + { + "basename": "1st-tool.cwl", + "class": "File", + "location": "../draft-3/examples/1st-tool.cwl" + }, + { + "basename": "env.cwl", + "class": "File", + "location": "../draft-3/examples/env.cwl" + }, + { + "basename": "arguments-job.yml", + "class": "File", + "location": "../draft-3/examples/arguments-job.yml" + }, + { + "basename": "tar-param-job.yml", + "class": "File", + "location": "../draft-3/examples/tar-param-job.yml" + }, + { + "basename": "array-inputs.cwl", + "class": "File", + "location": "../draft-3/examples/array-inputs.cwl" + }, + { + "basename": "inp.cwl", + "class": "File", + "location": "../draft-3/examples/inp.cwl" + }, + { + "basename": "arguments.cwl", + "class": "File", + "location": "../draft-3/examples/arguments.cwl" + }, + { + "basename": "linkfile.cwl", + "class": "File", + "location": "../draft-3/examples/linkfile.cwl" + }, + { + "basename": "record.cwl", + "class": "File", + "location": "../draft-3/examples/record.cwl" + }, + { + "basename": "tar-job.yml", + "class": "File", + "location": "../draft-3/examples/tar-job.yml" + } + ] } ], "class": "File", diff --git a/cwltool/schemas/draft-4/CommandLineTool-standalone.yml b/cwltool/schemas/v1.0/CommandLineTool-standalone.yml similarity index 100% rename from cwltool/schemas/draft-4/CommandLineTool-standalone.yml rename to cwltool/schemas/v1.0/CommandLineTool-standalone.yml diff --git a/cwltool/schemas/draft-4/CommandLineTool.yml b/cwltool/schemas/v1.0/CommandLineTool.yml similarity index 92% rename from cwltool/schemas/draft-4/CommandLineTool.yml rename to cwltool/schemas/v1.0/CommandLineTool.yml index 9d4fa1bec..7b32e2d6b 100644 --- a/cwltool/schemas/draft-4/CommandLineTool.yml +++ b/cwltool/schemas/v1.0/CommandLineTool.yml @@ -41,9 +41,16 @@ $graph: This specification represents the fourth milestone of the CWL group. Since draft-3, this draft introduces the following changes and additions: - * Preliminary support for initialWorkDir & the Directory type + * The [Directory](#Directory) type. * "id: name" is now just "name"; "class: Classname" is now just - "Classtname". + "Classname". + * [InitialWorkDirRequirement](#InitialWorkDirRequirement): list of + files and subdirectories to be present in the output directory prior + to execution. + * Shortcuts for specifying the standard [output](#stdout) and/or + [error](#stderr) streams as a (streamable) File output. + * SoftwareRequirement: a lightweight method of describing software + dependencies ## Purpose @@ -385,15 +392,33 @@ $graph: is equivalent to ``` outputs: - an_output_name: - type: File - outputBinding: - glob: a_stdout_file + an_output_name: + type: File + streamable: true + outputBinding: + glob: a_stdout_file stdout: a_stdout_file ``` If there is no `stdout` name provided, a random filename will be created. + For example, the following + ``` + outputs: + an_output_name: + type: stdout + ``` + is equivalent to + ``` + outputs: + an_output_name: + type: File + streamable: true + outputBinding: + glob: random_stdout_filenameABCDEFG + + stdout: random_stdout_filenameABCDEFG + ``` - name: stderr @@ -407,21 +432,42 @@ $graph: The following ``` outputs: - an_output_name: - type: stderr + an_output_name: + type: stderr stderr: a_stderr_file ``` is equivalent to ``` outputs: - an_output_name: - type: File - outputBinding: - glob: a_stderr_file + an_output_name: + type: File + streamable: true + outputBinding: + glob: a_stderr_file + + stderr: a_stderr_file ``` If there is no `stderr` name provided, a random filename will be created. + For example, the following + ``` + outputs: + an_output_name: + type: stderr + ``` + is equivalent to + ``` + outputs: + an_output_name: + type: File + streamable: true + outputBinding: + glob: random_stderr_filenameABCDEFG + + stderr: random_stderr_filenameABCDEFG + ``` + - type: record name: CommandLineTool @@ -565,6 +611,12 @@ $graph: environment as defined by Docker. fields: + - name: "class" + type: "string" + doc: "Always 'DockerRequirement'" + jsonldPredicate: + "_id": "@type" + "_type": "@vocab" - name: dockerPull type: ["null", "string"] doc: "Specify a Docker image to retrieve using `docker pull`." @@ -607,6 +659,12 @@ $graph: namespaced. The optional `identifier` field is recommended so that users and platforms can distinguish between software that has the same name. fields: + - name: "class" + type: "string" + doc: "Always 'SoftwareRequirement'" + jsonldPredicate: + "_id": "@type" + "_type": "@vocab" - name: spec type: type: array @@ -682,6 +740,12 @@ $graph: workflow platform in the designated output directory prior to executing the command line tool. fields: + - name: "class" + type: "string" + doc: "InitialWorkDirRequirement" + jsonldPredicate: + "_id": "@type" + "_type": "@vocab" - name: listing type: - type: array @@ -705,6 +769,12 @@ $graph: Define a list of environment variables which will be set in the execution environment of the tool. See `EnvironmentDef` for details. fields: + - name: "class" + type: "string" + doc: "Always 'EnvVarRequirement'" + jsonldPredicate: + "_id": "@type" + "_type": "@vocab" - name: envDef type: type: "array" @@ -726,6 +796,13 @@ $graph: contains `shellQuote: false`. If `shellQuote: false` is specified, the argument is joined into the command string without quoting, which allows the use of shell metacharacters such as `|` for pipes. + fields: + - name: "class" + type: "string" + doc: "Always 'ShellCommandRequirement'" + jsonldPredicate: + "_id": "@type" + "_type": "@vocab" - type: record @@ -754,6 +831,12 @@ $graph: If neither "min" nor "max" is specified for a resource, an implementation may provide a default. fields: + - name: "class" + type: "string" + doc: "Always 'ResourceRequirement'" + jsonldPredicate: + "_id": "@type" + "_type": "@vocab" - name: coresMin type: ["null", long, string, "#Expression"] doc: Minimum reserved number of CPU cores diff --git a/cwltool/schemas/draft-4/CommonWorkflowLanguage.yml b/cwltool/schemas/v1.0/CommonWorkflowLanguage.yml similarity index 100% rename from cwltool/schemas/draft-4/CommonWorkflowLanguage.yml rename to cwltool/schemas/v1.0/CommonWorkflowLanguage.yml diff --git a/cwltool/schemas/draft-4/Process.yml b/cwltool/schemas/v1.0/Process.yml similarity index 90% rename from cwltool/schemas/draft-4/Process.yml rename to cwltool/schemas/v1.0/Process.yml index 6c74cacd5..2b312778c 100644 --- a/cwltool/schemas/draft-4/Process.yml +++ b/cwltool/schemas/v1.0/Process.yml @@ -34,6 +34,7 @@ $graph: - cwl:draft-4.dev1 - cwl:draft-4.dev2 - cwl:draft-4.dev3 + - cwl:v1.0.dev4 - name: CWLType type: enum @@ -67,10 +68,10 @@ $graph: - name: location type: string? doc: | - A URI that identifies the file resource. This may be a relative - reference, in which case it must be resolved using the base URI of the + An IRI that identifies the file resource. This may be a relative + reference, in which case it must be resolved using the base IRI of the document. The location may refer to a local or remote resource; the - implementation must use the URI to retrieve file content. If an + implementation must use the IRI to retrieve file content. If an implementation is unable to retrieve the file content stored at a remote resource (due to unsupported protocol, access denied, or other issue) it must signal an error. @@ -98,11 +99,19 @@ $graph: As a special case, if the `path` field is provided but the `location` field is not, an implementation may assign the value of the `path` field to `location`, and remove the `path` field. + + If the `path` contains [POSIX shell metacharacters](http://pubs.opengroup.org/onlinepubs/9699919799/utilities/V3_chap02.html#tag_18_02) + (`|`,`&`, `;`, `<`, `>`, `(`,`)`, `$`,`` ` ``, `\`, `"`, `'`, + ``, ``, and ``) or characters + [not allowed](http://www.iana.org/assignments/idna-tables-6.3.0/idna-tables-6.3.0.xhtml) + for [Internationalized Domain Names for Applications](https://tools.ietf.org/html/rfc6452) + then implementations may terminate the process with a + `permanentFailure`. jsonldPredicate: "_id": "cwl:path" "_type": "@id" - name: basename - type: string + type: string? doc: | The base name of the file, that is, the name of the file without any leading directory path. The base name must not contain a slash `/`. @@ -175,7 +184,7 @@ $graph: _type: "@id" identity: true doc: | - The format of the file. This must be a URI of a concept node that + The format of the file. This must be a IRI of a concept node that represents the file format, preferrably defined within an ontology. If no ontology is available, file formats may be tested by exact match. @@ -199,9 +208,9 @@ $graph: `location` field. When the file is staged as input to CommandLineTool, the value of `contents` must be written to a file. - If `loadContents` of `Binding` is true and `location` is valid, the - implementation must read up to the first 64 KiB of text from the file - and place it in the "contents" field. + If `loadContents` of `inputBinding` or `outputBinding` is true and + `location` is valid, the implementation must read up to the first 64 + KiB of text from the file and place it in the "contents" field. - name: Directory @@ -223,11 +232,11 @@ $graph: - name: location type: string? doc: | - A URI that identifies the directory resource. This may be a relative - reference, in which case it must be resolved using the base URI of the + An IRI that identifies the directory resource. This may be a relative + reference, in which case it must be resolved using the base IRI of the document. The location may refer to a local or remote resource. If the `listing` field is not set, the implementation must use the - location URI to retrieve directory listing. If an implementation is + location IRI to retrieve directory listing. If an implementation is unable to retrieve the directory listing stored at a remote resource (due to unsupported protocol, access denied, or other issue) it must signal an error. @@ -250,11 +259,19 @@ $graph: must not be used in any other context. The command line tool being executed must be able to to access the directory at `path` using the POSIX `opendir(2)` syscall. + + If the `path` contains [POSIX shell metacharacters](http://pubs.opengroup.org/onlinepubs/9699919799/utilities/V3_chap02.html#tag_18_02) + (`|`,`&`, `;`, `<`, `>`, `(`,`)`, `$`,`` ` ``, `\`, `"`, `'`, + ``, ``, and ``) or characters + [not allowed](http://www.iana.org/assignments/idna-tables-6.3.0/idna-tables-6.3.0.xhtml) + for [Internationalized Domain Names for Applications](https://tools.ietf.org/html/rfc6452) + then implementations may terminate the process with a + `permanentFailure`. jsonldPredicate: _id: "cwl:path" _type: "@id" - name: basename - type: string + type: string? doc: | The base name of the directory, that is, the name of the file without any leading directory path. The base name must not contain a slash `/`. @@ -349,7 +366,7 @@ $graph: doc: | Only valid when `type: File` or is an array of `items: File`. - For input parameters, this must be one or more URIs of a concept nodes + For input parameters, this must be one or more IRIs of a concept nodes that represents file formats which are allowed as input to this parameter, preferrably defined within an ontology. If no ontology is available, file formats may be tested by exact match. @@ -592,14 +609,6 @@ $graph: Process requirements are the primary mechanism for specifying extensions to the CWL core specification. - fields: - - name: "class" - type: "string" - doc: "The specific requirement type." - jsonldPredicate: - "_id": "@type" - "_type": "@vocab" - - type: record name: Process @@ -682,10 +691,10 @@ $graph: jsonldPredicate: "rdfs:comment" doc: "A long, human-readable description of this process object." - name: cwlVersion - type: - - "null" - - "#CWLVersions" - doc: "CWL document version" + type: CWLVersions? + doc: | + CWL document version. Always required at the document root. Not + required for a Process embedded inside another Process. jsonldPredicate: "_id": "cwl:cwlVersion" "_type": "@vocab" @@ -698,6 +707,12 @@ $graph: If this requirement is not present, the workflow platform must not perform expression interpolatation. fields: + - name: "class" + type: "string" + doc: "Always 'InlineJavascriptRequirement'" + jsonldPredicate: + "_id": "@type" + "_type": "@vocab" - name: expressionLib type: - "null" @@ -715,12 +730,18 @@ $graph: doc: | This field consists of an array of type definitions which must be used when interpreting the `inputs` and `outputs` fields. When a `type` field - contain a URI, the implementation must check if the type is defined in + contain a IRI, the implementation must check if the type is defined in `schemaDefs` and use that definition. If the type is not found in `schemaDefs`, it is an error. The entries in `schemaDefs` must be processed in the order listed such that later schema definitions may refer to earlier schema definitions. fields: + - name: "class" + type: "string" + doc: "Always 'SchemaDefRequirement'" + jsonldPredicate: + "_id": "@type" + "_type": "@vocab" - name: types type: type: array diff --git a/cwltool/schemas/draft-4/README.md b/cwltool/schemas/v1.0/README.md similarity index 100% rename from cwltool/schemas/draft-4/README.md rename to cwltool/schemas/v1.0/README.md diff --git a/cwltool/schemas/draft-4/UserGuide.yml b/cwltool/schemas/v1.0/UserGuide.yml similarity index 100% rename from cwltool/schemas/draft-4/UserGuide.yml rename to cwltool/schemas/v1.0/UserGuide.yml diff --git a/cwltool/schemas/draft-4/Workflow.yml b/cwltool/schemas/v1.0/Workflow.yml similarity index 89% rename from cwltool/schemas/draft-4/Workflow.yml rename to cwltool/schemas/v1.0/Workflow.yml index d1f00fc32..76d064c12 100644 --- a/cwltool/schemas/draft-4/Workflow.yml +++ b/cwltool/schemas/v1.0/Workflow.yml @@ -22,11 +22,12 @@ $graph: - | # Abstract - A Workflow is an analysis task represented by a directed graph describing - a sequence of operations that transform an input data set to output. - This specification defines the Common Workflow Language (CWL) Workflow - description, a vendor-neutral standard for representing workflows - intended to be portable across a variety of computing platforms. + One way to define a workflow is: an analysis task represented by a + directed graph describing a sequence of operations that transform an + input data set to output. This specification defines the Common Workflow + Language (CWL) Workflow description, a vendor-neutral standard for + representing workflows intended to be portable across a variety of + computing platforms. - {$include: intro.md} @@ -85,7 +86,7 @@ $graph: specializeTo: "#ExpressionToolOutputParameter" documentRoot: true doc: | - Execute an expression as a process step. + Execute an expression as a Workflow step. fields: - name: "class" jsonldPredicate: @@ -164,7 +165,7 @@ $graph: - name: source doc: | Specifies one or more workflow parameters that will provide input to - the underlying process parameter. + the underlying step parameter. jsonldPredicate: "_id": "cwl:source" "_type": "@id" @@ -187,7 +188,7 @@ $graph: doc: | The input of a workflow step connects an upstream parameter (from the workflow inputs, or the outputs of other workflows steps) with the input - parameters of the underlying process. + parameters of the underlying step. ## Input object @@ -296,9 +297,9 @@ $graph: docParent: "#Workflow" doc: | A workflow step is an executable element of a workflow. It specifies the - underlying process implementation (such as `CommandLineTool`) in the `run` - field and connects the input and output parameters of the underlying - process to workflow parameters. + underlying process implementation (such as `CommandLineTool` or another + `Workflow`) in the `run` field and connects the input and output parameters + of the underlying process to workflow parameters. # Scatter/gather @@ -436,15 +437,15 @@ $graph: specializeTo: "#WorkflowOutputParameter" doc: | A workflow describes a set of **steps** and the **dependencies** between - those processes. When a process produces output that will be consumed by a - second process, the first process is a dependency of the second process. + those steps. When a step produces output that will be consumed by a + second step, the first step is a dependency of the second step. When there is a dependency, the workflow engine must execute the preceeding - process and wait for it to successfully produce output before executing the - dependent process. If two processes are defined in the workflow graph that - are not directly or indirectly dependent, these processes are - **independent**, and may execute in any order or execute concurrently. A - workflow is complete when all steps have been executed. + step and wait for it to successfully produce output before executing the + dependent step. If two steps are defined in the workflow graph that + are not directly or indirectly dependent, these steps are **independent**, + and may execute in any order or execute concurrently. A workflow is + complete when all steps have been executed. Dependencies between parameters are expressed using the `source` field on [workflow step input parameters](#WorkflowStepInput) and [workflow output @@ -458,21 +459,21 @@ $graph: ## Workflow success and failure - A completed process must result in one of `success`, `temporaryFailure` or - `permanentFailure` states. An implementation may choose to retry a process + A completed step must result in one of `success`, `temporaryFailure` or + `permanentFailure` states. An implementation may choose to retry a step execution which resulted in `temporaryFailure`. An implementation may choose to either continue running other steps of a workflow, or terminate immediately upon `permanentFailure`. - * If any step of a workflow execution results in `permanentFailure`, then the - workflow status is `permanentFailure`. + * If any step of a workflow execution results in `permanentFailure`, then + the workflow status is `permanentFailure`. * If one or more steps result in `temporaryFailure` and all other steps complete `success` or are not executed, then the workflow status is `temporaryFailure`. - * If all workflow steps are executed and complete with `success`, then the workflow - status is `success`. + * If all workflow steps are executed and complete with `success`, then the + workflow status is `success`. # Extensions @@ -505,6 +506,13 @@ $graph: doc: | Indicates that the workflow platform must support nested workflows in the `run` field of [WorkflowStep](#WorkflowStep). + fields: + - name: "class" + type: "string" + doc: "Always 'SubworkflowFeatureRequirement'" + jsonldPredicate: + "_id": "@type" + "_type": "@vocab" - name: ScatterFeatureRequirement type: record @@ -512,6 +520,13 @@ $graph: doc: | Indicates that the workflow platform must support the `scatter` and `scatterMethod` fields of [WorkflowStep](#WorkflowStep). + fields: + - name: "class" + type: "string" + doc: "Always 'ScatterFeatureRequirement'" + jsonldPredicate: + "_id": "@type" + "_type": "@vocab" - name: MultipleInputFeatureRequirement type: record @@ -519,6 +534,13 @@ $graph: doc: | Indicates that the workflow platform must support multiple inbound data links listed in the `source` field of [WorkflowStepInput](#WorkflowStepInput). + fields: + - name: "class" + type: "string" + doc: "Always 'MultipleInputFeatureRequirement'" + jsonldPredicate: + "_id": "@type" + "_type": "@vocab" - type: record name: StepInputExpressionRequirement @@ -526,3 +548,10 @@ $graph: doc: | Indicate that the workflow platform must support the `valueFrom` field of [WorkflowStepInput](#WorkflowStepInput). + fields: + - name: "class" + type: "string" + doc: "Always 'StepInputExpressionRequirement'" + jsonldPredicate: + "_id": "@type" + "_type": "@vocab" diff --git a/cwltool/schemas/draft-4/concepts.md b/cwltool/schemas/v1.0/concepts.md similarity index 90% rename from cwltool/schemas/draft-4/concepts.md rename to cwltool/schemas/v1.0/concepts.md index d4a9f9aa3..81780ba41 100644 --- a/cwltool/schemas/draft-4/concepts.md +++ b/cwltool/schemas/v1.0/concepts.md @@ -10,6 +10,9 @@ **Uniform Resource Identifier (URI) Generic Syntax**: https://tools.ietf.org/html/rfc3986) +**Internationalized Resource Identifiers (IRIs)**: +https://tools.ietf.org/html/rfc3987 + **Portable Operating System Interface (POSIX.1-2008)**: http://pubs.opengroup.org/onlinepubs/9699919799/ **Resource Description Framework (RDF)**: http://www.w3.org/RDF/ @@ -62,19 +65,21 @@ boolean, array, or object. A **document** is a file containing a serialized object, or an array of objects. A **process** is a basic unit of computation which accepts input data, -performs some computation, and produces output data. +performs some computation, and produces output data. Examples include +CommandLineTools, Workflows, and ExpressionTools. -An **input object** is an object describing the inputs to a invocation of process. +An **input object** is an object describing the inputs to a invocation of +process. -An **output object** is an object describing the output of an invocation of a process. +An **output object** is an object describing the output of an invocation of a +process. An **input schema** describes the valid format (required fields, data types) for an input object. An **output schema** describes the valid format for a output object. -**Metadata** is information about workflows, tools, or input items that is -not used directly in the computation. +**Metadata** is information about workflows, tools, or input items. ## Syntax @@ -103,6 +108,10 @@ An implementation must resolve [$import](SchemaSalad.html#Import) and [$include](SchemaSalad.html#Import) directives as described in the [Schema Salad specification](SchemaSalad.html). +Another transformation defined in Schema salad is simplification of data type definitions. +Type `` ending with `?` should be transformed to `[, "null"]`. +Type `` ending with `[]` should be transformed to `{"type": "array", "items": }` + ## Extensions and Metadata Input metadata (for example, a lab sample identifier) may be represented within @@ -140,8 +149,9 @@ form a directed graph, and independent steps may run concurrently. A **runtime environment** is the actual hardware and software environment when executing a command line tool. It includes, but is not limited to, the hardware architecture, hardware resources, operating system, software runtime -(if applicable, such as the Python interpreter or the JVM), libraries, modules, -packages, utilities, and data files required to run the tool. +(if applicable, such as the specific Python interpreter or the specific Java +virtual machine), libraries, modules, packages, utilities, and data files +required to run the tool. A **workflow platform** is a specific hardware and software implementation capable of interpreting CWL documents and executing the processes specified by @@ -201,7 +211,7 @@ warning if a hint cannot be satisfied. Requirements are inherited. A requirement specified in a Workflow applies to all workflow steps; a requirement specified on a workflow step will -apply to the process implementation. +apply to the process implementation of that step and any of its substeps. If the same process requirement appears at different levels of the workflow, the most specific instance of the requirement is used, that is, @@ -223,7 +233,7 @@ field permitting the pseudo-type `Expression`, as specified by this document. Conforming implementations must support parameter references. Parameter references use the following subset of [Javascript/ECMAScript 5.1](http://www.ecma-international.org/ecma-262/5.1/) -syntax. +syntax but they are designed to not require a Javascript engine for evaluation. In the following BNF grammar, character classes and grammar rules are denoted in '{}', '-' denotes exclusion from a character class, '(())' denotes grouping, @@ -232,12 +242,12 @@ one or more repeats, all other characters are literal values.

- - - - - - + + + + + +
symbol:: {Unicode alphanumeric}+
singleq:: [' (( {character - '} | \' ))* ']
doubleq:: [" (( {character - "} | \" ))* "]
index:: [ {decimal digit}+ ]
segment:: . {symbol} | {singleq} | {doubleq} | {index}
parameter::$( {symbol} {segment}*)
symbol:: {Unicode alphanumeric}+
singleq:: [' (( {character - '} | \' ))* ']
doubleq:: [" (( {character - "} | \" ))* "]
index:: [ {decimal digit}+ ]
segment:: . {symbol} | {singleq} | {doubleq} | {index}
parameter reference::$( {symbol} {segment}*)

@@ -345,6 +355,9 @@ Implementations may apply other limits, such as process isolation, timeouts, and operating system containers/jails to minimize the security risks associated with running untrusted code embedded in a CWL document. +Exceptions thrown from an exception must result in a `permanentFailure` of the +process. + ## Success and failure A completed process must result in one of `success`, `temporaryFailure` or @@ -373,6 +386,19 @@ platform's CWL implementation. A CWL input object document may similarly begin with `#!/usr/bin/env cwl-runner` and be marked as executable. In this case, the input object -must include the field `cwl:tool` supplying a URI to the default CWL +must include the field `cwl:tool` supplying a IRI to the default CWL document that should be executed using the fields of the input object as input parameters. + +## Discovering CWL documents on a local filesystem + +To discover CWL documents look in the following locations: + +`/usr/share/commonwl/` + +`/usr/local/share/commonwl/` + +`$XDG_DATA_HOME/commonwl/` (usually `$HOME/.local/share/commonwl`) + +`$XDF_DATA_HOME` is from the [XDG Base Directory +Specification](http://standards.freedesktop.org/basedir-spec/basedir-spec-0.6.html) diff --git a/cwltool/schemas/draft-4/conformance_test_draft-4.yaml b/cwltool/schemas/v1.0/conformance_test_v1.0.yaml similarity index 98% rename from cwltool/schemas/draft-4/conformance_test_draft-4.yaml rename to cwltool/schemas/v1.0/conformance_test_v1.0.yaml index 7d4b31a6d..6d6ada806 100644 --- a/cwltool/schemas/draft-4/conformance_test_draft-4.yaml +++ b/cwltool/schemas/v1.0/conformance_test_v1.0.yaml @@ -732,18 +732,12 @@ "class": "Directory", "listing": [ { - "entryname": "hello.txt", - "entry": { - "class": "File", - "location": "hello.txt" - } + "class": "File", + "location": "hello.txt" }, { - "entryname": "goodbye.txt", - "entry": { - "class": "File", - "location": "goodbye.txt" - } + "class": "File", + "location": "goodbye.txt" } ], } @@ -785,3 +779,13 @@ } tool: draft-4/stagefile.cwl doc: Test writable staged files. + +- job: draft-4/file-literal.yml + output: + output_file: + class: File + checksum: sha1$d0e04ff6c413c7d57f9a0ca0a33cd3ab52e2dd9c + location: output.txt + size: 18 + tool: draft-4/cat3-tool.cwl + doc: Test file literal as input diff --git a/cwltool/schemas/draft-4/contrib.md b/cwltool/schemas/v1.0/contrib.md similarity index 100% rename from cwltool/schemas/draft-4/contrib.md rename to cwltool/schemas/v1.0/contrib.md diff --git a/cwltool/schemas/draft-4/draft-4/EDAM.owl b/cwltool/schemas/v1.0/draft-4/EDAM.owl similarity index 100% rename from cwltool/schemas/draft-4/draft-4/EDAM.owl rename to cwltool/schemas/v1.0/draft-4/EDAM.owl diff --git a/cwltool/schemas/draft-4/draft-4/abc.json b/cwltool/schemas/v1.0/draft-4/abc.json similarity index 100% rename from cwltool/schemas/draft-4/draft-4/abc.json rename to cwltool/schemas/v1.0/draft-4/abc.json diff --git a/cwltool/schemas/draft-4/draft-4/args.py b/cwltool/schemas/v1.0/draft-4/args.py similarity index 100% rename from cwltool/schemas/draft-4/draft-4/args.py rename to cwltool/schemas/v1.0/draft-4/args.py diff --git a/cwltool/schemas/draft-4/draft-4/binding-test.cwl b/cwltool/schemas/v1.0/draft-4/binding-test.cwl similarity index 94% rename from cwltool/schemas/draft-4/draft-4/binding-test.cwl rename to cwltool/schemas/v1.0/draft-4/binding-test.cwl index 395c50a92..e93b347d8 100755 --- a/cwltool/schemas/draft-4/draft-4/binding-test.cwl +++ b/cwltool/schemas/v1.0/draft-4/binding-test.cwl @@ -1,7 +1,7 @@ #!/usr/bin/env cwl-runner class: CommandLineTool -cwlVersion: cwl:draft-4.dev3 +cwlVersion: v1.0.dev4 inputs: - id: reference diff --git a/cwltool/schemas/draft-4/draft-4/bwa-mem-job.json b/cwltool/schemas/v1.0/draft-4/bwa-mem-job.json similarity index 100% rename from cwltool/schemas/draft-4/draft-4/bwa-mem-job.json rename to cwltool/schemas/v1.0/draft-4/bwa-mem-job.json diff --git a/cwltool/schemas/draft-4/draft-4/bwa-mem-tool.cwl b/cwltool/schemas/v1.0/draft-4/bwa-mem-tool.cwl similarity index 97% rename from cwltool/schemas/draft-4/draft-4/bwa-mem-tool.cwl rename to cwltool/schemas/v1.0/draft-4/bwa-mem-tool.cwl index 63ecb885e..d77376871 100755 --- a/cwltool/schemas/draft-4/draft-4/bwa-mem-tool.cwl +++ b/cwltool/schemas/v1.0/draft-4/bwa-mem-tool.cwl @@ -1,6 +1,6 @@ #!/usr/bin/env cwl-runner -cwlVersion: draft-4.dev3 +cwlVersion: v1.0.dev4 class: CommandLineTool diff --git a/cwltool/schemas/draft-4/draft-4/cat-job.json b/cwltool/schemas/v1.0/draft-4/cat-job.json similarity index 100% rename from cwltool/schemas/draft-4/draft-4/cat-job.json rename to cwltool/schemas/v1.0/draft-4/cat-job.json diff --git a/cwltool/schemas/draft-4/draft-4/cat-n-job.json b/cwltool/schemas/v1.0/draft-4/cat-n-job.json similarity index 100% rename from cwltool/schemas/draft-4/draft-4/cat-n-job.json rename to cwltool/schemas/v1.0/draft-4/cat-n-job.json diff --git a/cwltool/schemas/draft-4/draft-4/cat1-testcli.cwl b/cwltool/schemas/v1.0/draft-4/cat1-testcli.cwl similarity index 95% rename from cwltool/schemas/draft-4/draft-4/cat1-testcli.cwl rename to cwltool/schemas/v1.0/draft-4/cat1-testcli.cwl index 04c3857f6..d767c0a9b 100755 --- a/cwltool/schemas/draft-4/draft-4/cat1-testcli.cwl +++ b/cwltool/schemas/v1.0/draft-4/cat1-testcli.cwl @@ -1,7 +1,7 @@ #!/usr/bin/env cwl-runner { "class": "CommandLineTool", - "cwlVersion": "cwl:draft-4.dev3", + "cwlVersion": "v1.0.dev4", "description": "Print the contents of a file to stdout using 'cat' running in a docker container.", "inputs": [ { diff --git a/cwltool/schemas/draft-4/draft-4/cat1-tool.cwl b/cwltool/schemas/v1.0/draft-4/cat1-tool.cwl similarity index 93% rename from cwltool/schemas/draft-4/draft-4/cat1-tool.cwl rename to cwltool/schemas/v1.0/draft-4/cat1-tool.cwl index 4b14f7bda..ed8b110e1 100755 --- a/cwltool/schemas/draft-4/draft-4/cat1-tool.cwl +++ b/cwltool/schemas/v1.0/draft-4/cat1-tool.cwl @@ -1,5 +1,5 @@ #!/usr/bin/env cwl-runner -cwlVersion: cwl:draft-4.dev3 +cwlVersion: v1.0.dev4 class: CommandLineTool description: "Print the contents of a file to stdout using 'cat' running in a docker container." hints: diff --git a/cwltool/schemas/draft-4/draft-4/cat2-tool.cwl b/cwltool/schemas/v1.0/draft-4/cat2-tool.cwl similarity index 90% rename from cwltool/schemas/draft-4/draft-4/cat2-tool.cwl rename to cwltool/schemas/v1.0/draft-4/cat2-tool.cwl index 8348a82f5..224c7a431 100755 --- a/cwltool/schemas/draft-4/draft-4/cat2-tool.cwl +++ b/cwltool/schemas/v1.0/draft-4/cat2-tool.cwl @@ -1,6 +1,6 @@ #!/usr/bin/env cwl-runner class: CommandLineTool -cwlVersion: cwl:draft-4.dev3 +cwlVersion: v1.0.dev4 description: "Print the contents of a file to stdout using 'cat' running in a docker container." hints: DockerRequirement: diff --git a/cwltool/schemas/draft-4/draft-4/cat3-tool-mediumcut.cwl b/cwltool/schemas/v1.0/draft-4/cat3-tool-mediumcut.cwl similarity index 93% rename from cwltool/schemas/draft-4/draft-4/cat3-tool-mediumcut.cwl rename to cwltool/schemas/v1.0/draft-4/cat3-tool-mediumcut.cwl index 2e3f7282a..800cf022e 100755 --- a/cwltool/schemas/draft-4/draft-4/cat3-tool-mediumcut.cwl +++ b/cwltool/schemas/v1.0/draft-4/cat3-tool-mediumcut.cwl @@ -1,6 +1,6 @@ #!/usr/bin/env cwl-runner class: CommandLineTool -cwlVersion: cwl:draft-4.dev3 +cwlVersion: v1.0.dev4 description: "Print the contents of a file to stdout using 'cat' running in a docker container." hints: DockerRequirement: diff --git a/cwltool/schemas/draft-4/draft-4/cat3-tool-shortcut.cwl b/cwltool/schemas/v1.0/draft-4/cat3-tool-shortcut.cwl similarity index 93% rename from cwltool/schemas/draft-4/draft-4/cat3-tool-shortcut.cwl rename to cwltool/schemas/v1.0/draft-4/cat3-tool-shortcut.cwl index 04eb14d5e..edf432d72 100755 --- a/cwltool/schemas/draft-4/draft-4/cat3-tool-shortcut.cwl +++ b/cwltool/schemas/v1.0/draft-4/cat3-tool-shortcut.cwl @@ -1,6 +1,6 @@ #!/usr/bin/env cwl-runner class: CommandLineTool -cwlVersion: cwl:draft-4.dev3 +cwlVersion: v1.0.dev4 description: "Print the contents of a file to stdout using 'cat' running in a docker container." hints: DockerRequirement: diff --git a/cwltool/schemas/draft-4/draft-4/cat3-tool.cwl b/cwltool/schemas/v1.0/draft-4/cat3-tool.cwl similarity index 94% rename from cwltool/schemas/draft-4/draft-4/cat3-tool.cwl rename to cwltool/schemas/v1.0/draft-4/cat3-tool.cwl index f67588a9b..5a629c5cb 100755 --- a/cwltool/schemas/draft-4/draft-4/cat3-tool.cwl +++ b/cwltool/schemas/v1.0/draft-4/cat3-tool.cwl @@ -1,6 +1,6 @@ #!/usr/bin/env cwl-runner class: CommandLineTool -cwlVersion: cwl:draft-4.dev3 +cwlVersion: v1.0.dev4 description: "Print the contents of a file to stdout using 'cat' running in a docker container." hints: DockerRequirement: diff --git a/cwltool/schemas/draft-4/draft-4/cat4-tool.cwl b/cwltool/schemas/v1.0/draft-4/cat4-tool.cwl similarity index 92% rename from cwltool/schemas/draft-4/draft-4/cat4-tool.cwl rename to cwltool/schemas/v1.0/draft-4/cat4-tool.cwl index 733bc9167..09addfead 100755 --- a/cwltool/schemas/draft-4/draft-4/cat4-tool.cwl +++ b/cwltool/schemas/v1.0/draft-4/cat4-tool.cwl @@ -1,6 +1,6 @@ #!/usr/bin/env cwl-runner class: CommandLineTool -cwlVersion: cwl:draft-4.dev3 +cwlVersion: v1.0.dev4 description: "Print the contents of a file to stdout using 'cat' running in a docker container." hints: DockerRequirement: diff --git a/cwltool/schemas/draft-4/draft-4/cat5-tool.cwl b/cwltool/schemas/v1.0/draft-4/cat5-tool.cwl similarity index 94% rename from cwltool/schemas/draft-4/draft-4/cat5-tool.cwl rename to cwltool/schemas/v1.0/draft-4/cat5-tool.cwl index 24e89d91d..5dbc8c0d4 100755 --- a/cwltool/schemas/draft-4/draft-4/cat5-tool.cwl +++ b/cwltool/schemas/v1.0/draft-4/cat5-tool.cwl @@ -1,5 +1,5 @@ #!/usr/bin/env cwl-runner -cwlVersion: cwl:draft-4.dev3 +cwlVersion: v1.0.dev4 class: CommandLineTool description: "Print the contents of a file to stdout using 'cat' running in a docker container." hints: diff --git a/cwltool/schemas/draft-4/draft-4/chr20.fa b/cwltool/schemas/v1.0/draft-4/chr20.fa similarity index 100% rename from cwltool/schemas/draft-4/draft-4/chr20.fa rename to cwltool/schemas/v1.0/draft-4/chr20.fa diff --git a/cwltool/schemas/draft-4/draft-4/conflict-job.json b/cwltool/schemas/v1.0/draft-4/conflict-job.json similarity index 100% rename from cwltool/schemas/draft-4/draft-4/conflict-job.json rename to cwltool/schemas/v1.0/draft-4/conflict-job.json diff --git a/cwltool/schemas/draft-4/draft-4/conflict-wf.cwl b/cwltool/schemas/v1.0/draft-4/conflict-wf.cwl similarity index 97% rename from cwltool/schemas/draft-4/draft-4/conflict-wf.cwl rename to cwltool/schemas/v1.0/draft-4/conflict-wf.cwl index c72b27bf2..f8cb8604d 100644 --- a/cwltool/schemas/draft-4/draft-4/conflict-wf.cwl +++ b/cwltool/schemas/v1.0/draft-4/conflict-wf.cwl @@ -1,4 +1,4 @@ -cwlVersion: cwl:draft-4.dev3 +cwlVersion: v1.0.dev4 $graph: - id: echo class: CommandLineTool diff --git a/cwltool/schemas/draft-4/draft-4/count-lines1-wf.cwl b/cwltool/schemas/v1.0/draft-4/count-lines1-wf.cwl similarity index 91% rename from cwltool/schemas/draft-4/draft-4/count-lines1-wf.cwl rename to cwltool/schemas/v1.0/draft-4/count-lines1-wf.cwl index 7c58ec84f..dd5b9adb6 100755 --- a/cwltool/schemas/draft-4/draft-4/count-lines1-wf.cwl +++ b/cwltool/schemas/v1.0/draft-4/count-lines1-wf.cwl @@ -1,6 +1,6 @@ #!/usr/bin/env cwl-runner class: Workflow -cwlVersion: cwl:draft-4.dev3 +cwlVersion: v1.0.dev4 inputs: file1: diff --git a/cwltool/schemas/draft-4/draft-4/count-lines2-wf.cwl b/cwltool/schemas/v1.0/draft-4/count-lines2-wf.cwl similarity index 97% rename from cwltool/schemas/draft-4/draft-4/count-lines2-wf.cwl rename to cwltool/schemas/v1.0/draft-4/count-lines2-wf.cwl index 267f949ba..ce66ba3dd 100755 --- a/cwltool/schemas/draft-4/draft-4/count-lines2-wf.cwl +++ b/cwltool/schemas/v1.0/draft-4/count-lines2-wf.cwl @@ -1,6 +1,6 @@ #!/usr/bin/env cwl-runner class: Workflow -cwlVersion: cwl:draft-4.dev3 +cwlVersion: v1.0.dev4 requirements: InlineJavascriptRequirement: {} diff --git a/cwltool/schemas/draft-4/draft-4/count-lines3-job.json b/cwltool/schemas/v1.0/draft-4/count-lines3-job.json similarity index 100% rename from cwltool/schemas/draft-4/draft-4/count-lines3-job.json rename to cwltool/schemas/v1.0/draft-4/count-lines3-job.json diff --git a/cwltool/schemas/draft-4/draft-4/count-lines3-wf.cwl b/cwltool/schemas/v1.0/draft-4/count-lines3-wf.cwl similarity index 91% rename from cwltool/schemas/draft-4/draft-4/count-lines3-wf.cwl rename to cwltool/schemas/v1.0/draft-4/count-lines3-wf.cwl index d48cd9258..b33d0fef8 100755 --- a/cwltool/schemas/draft-4/draft-4/count-lines3-wf.cwl +++ b/cwltool/schemas/v1.0/draft-4/count-lines3-wf.cwl @@ -1,6 +1,6 @@ #!/usr/bin/env cwl-runner class: Workflow -cwlVersion: cwl:draft-4.dev3 +cwlVersion: v1.0.dev4 inputs: file1: diff --git a/cwltool/schemas/draft-4/draft-4/count-lines4-job.json b/cwltool/schemas/v1.0/draft-4/count-lines4-job.json similarity index 100% rename from cwltool/schemas/draft-4/draft-4/count-lines4-job.json rename to cwltool/schemas/v1.0/draft-4/count-lines4-job.json diff --git a/cwltool/schemas/draft-4/draft-4/count-lines4-wf.cwl b/cwltool/schemas/v1.0/draft-4/count-lines4-wf.cwl similarity index 93% rename from cwltool/schemas/draft-4/draft-4/count-lines4-wf.cwl rename to cwltool/schemas/v1.0/draft-4/count-lines4-wf.cwl index 8aada50e3..cf458bcc7 100755 --- a/cwltool/schemas/draft-4/draft-4/count-lines4-wf.cwl +++ b/cwltool/schemas/v1.0/draft-4/count-lines4-wf.cwl @@ -1,6 +1,6 @@ #!/usr/bin/env cwl-runner class: Workflow -cwlVersion: cwl:draft-4.dev3 +cwlVersion: v1.0.dev4 inputs: file1: diff --git a/cwltool/schemas/draft-4/draft-4/count-lines5-wf.cwl b/cwltool/schemas/v1.0/draft-4/count-lines5-wf.cwl similarity index 90% rename from cwltool/schemas/draft-4/draft-4/count-lines5-wf.cwl rename to cwltool/schemas/v1.0/draft-4/count-lines5-wf.cwl index eb38e2231..67e23d16c 100755 --- a/cwltool/schemas/draft-4/draft-4/count-lines5-wf.cwl +++ b/cwltool/schemas/v1.0/draft-4/count-lines5-wf.cwl @@ -1,6 +1,6 @@ #!/usr/bin/env cwl-runner class: Workflow -cwlVersion: cwl:draft-4.dev3 +cwlVersion: v1.0.dev4 inputs: file1: diff --git a/cwltool/schemas/draft-4/draft-4/count-lines6-job.json b/cwltool/schemas/v1.0/draft-4/count-lines6-job.json similarity index 100% rename from cwltool/schemas/draft-4/draft-4/count-lines6-job.json rename to cwltool/schemas/v1.0/draft-4/count-lines6-job.json diff --git a/cwltool/schemas/draft-4/draft-4/count-lines6-wf.cwl b/cwltool/schemas/v1.0/draft-4/count-lines6-wf.cwl similarity index 93% rename from cwltool/schemas/draft-4/draft-4/count-lines6-wf.cwl rename to cwltool/schemas/v1.0/draft-4/count-lines6-wf.cwl index 36296bffa..b22214e3b 100755 --- a/cwltool/schemas/draft-4/draft-4/count-lines6-wf.cwl +++ b/cwltool/schemas/v1.0/draft-4/count-lines6-wf.cwl @@ -1,6 +1,6 @@ #!/usr/bin/env cwl-runner class: Workflow -cwlVersion: cwl:draft-4.dev3 +cwlVersion: v1.0.dev4 inputs: file1: File[] diff --git a/cwltool/schemas/draft-4/draft-4/count-lines7-wf.cwl b/cwltool/schemas/v1.0/draft-4/count-lines7-wf.cwl similarity index 93% rename from cwltool/schemas/draft-4/draft-4/count-lines7-wf.cwl rename to cwltool/schemas/v1.0/draft-4/count-lines7-wf.cwl index cf0e3d8dd..11e016a30 100755 --- a/cwltool/schemas/draft-4/draft-4/count-lines7-wf.cwl +++ b/cwltool/schemas/v1.0/draft-4/count-lines7-wf.cwl @@ -1,6 +1,6 @@ #!/usr/bin/env cwl-runner class: Workflow -cwlVersion: cwl:draft-4.dev3 +cwlVersion: v1.0.dev4 requirements: - class: MultipleInputFeatureRequirement diff --git a/cwltool/schemas/draft-4/draft-4/count-lines8-wf.cwl b/cwltool/schemas/v1.0/draft-4/count-lines8-wf.cwl similarity index 91% rename from cwltool/schemas/draft-4/draft-4/count-lines8-wf.cwl rename to cwltool/schemas/v1.0/draft-4/count-lines8-wf.cwl index 02895b549..2d80666b6 100755 --- a/cwltool/schemas/draft-4/draft-4/count-lines8-wf.cwl +++ b/cwltool/schemas/v1.0/draft-4/count-lines8-wf.cwl @@ -1,6 +1,6 @@ #!/usr/bin/env cwl-runner class: Workflow -cwlVersion: cwl:draft-4.dev3 +cwlVersion: v1.0.dev4 inputs: file1: File diff --git a/cwltool/schemas/draft-4/draft-4/count-lines9-wf.cwl b/cwltool/schemas/v1.0/draft-4/count-lines9-wf.cwl similarity index 92% rename from cwltool/schemas/draft-4/draft-4/count-lines9-wf.cwl rename to cwltool/schemas/v1.0/draft-4/count-lines9-wf.cwl index 9a340adc6..0e6075ccf 100755 --- a/cwltool/schemas/draft-4/draft-4/count-lines9-wf.cwl +++ b/cwltool/schemas/v1.0/draft-4/count-lines9-wf.cwl @@ -1,6 +1,6 @@ #!/usr/bin/env cwl-runner class: Workflow -cwlVersion: cwl:draft-4.dev3 +cwlVersion: v1.0.dev4 inputs: [] diff --git a/cwltool/schemas/draft-4/draft-4/dcterms.rdf b/cwltool/schemas/v1.0/draft-4/dcterms.rdf similarity index 100% rename from cwltool/schemas/draft-4/draft-4/dcterms.rdf rename to cwltool/schemas/v1.0/draft-4/dcterms.rdf diff --git a/cwltool/schemas/draft-4/draft-4/dir-job.yml b/cwltool/schemas/v1.0/draft-4/dir-job.yml similarity index 100% rename from cwltool/schemas/draft-4/draft-4/dir-job.yml rename to cwltool/schemas/v1.0/draft-4/dir-job.yml diff --git a/cwltool/schemas/draft-4/draft-4/dir.cwl b/cwltool/schemas/v1.0/draft-4/dir.cwl similarity index 93% rename from cwltool/schemas/draft-4/draft-4/dir.cwl rename to cwltool/schemas/v1.0/draft-4/dir.cwl index 0cfe978e8..14ac1ef32 100644 --- a/cwltool/schemas/draft-4/draft-4/dir.cwl +++ b/cwltool/schemas/v1.0/draft-4/dir.cwl @@ -1,5 +1,5 @@ class: CommandLineTool -cwlVersion: draft-4.dev3 +cwlVersion: v1.0.dev4 requirements: - class: ShellCommandRequirement inputs: diff --git a/cwltool/schemas/draft-4/draft-4/dir2.cwl b/cwltool/schemas/v1.0/draft-4/dir2.cwl similarity index 93% rename from cwltool/schemas/draft-4/draft-4/dir2.cwl rename to cwltool/schemas/v1.0/draft-4/dir2.cwl index e64af2c7b..e3309d76b 100644 --- a/cwltool/schemas/draft-4/draft-4/dir2.cwl +++ b/cwltool/schemas/v1.0/draft-4/dir2.cwl @@ -1,5 +1,5 @@ class: CommandLineTool -cwlVersion: draft-4.dev3 +cwlVersion: v1.0.dev4 hints: DockerRequirement: dockerPull: debian:8 diff --git a/cwltool/schemas/draft-4/draft-4/dir3-job.yml b/cwltool/schemas/v1.0/draft-4/dir3-job.yml similarity index 100% rename from cwltool/schemas/draft-4/draft-4/dir3-job.yml rename to cwltool/schemas/v1.0/draft-4/dir3-job.yml diff --git a/cwltool/schemas/draft-4/draft-4/dir3.cwl b/cwltool/schemas/v1.0/draft-4/dir3.cwl similarity index 88% rename from cwltool/schemas/draft-4/draft-4/dir3.cwl rename to cwltool/schemas/v1.0/draft-4/dir3.cwl index 61fb96eba..ac306a219 100644 --- a/cwltool/schemas/draft-4/draft-4/dir3.cwl +++ b/cwltool/schemas/v1.0/draft-4/dir3.cwl @@ -1,5 +1,5 @@ class: CommandLineTool -cwlVersion: draft-4.dev3 +cwlVersion: v1.0.dev4 baseCommand: [tar, xvf] inputs: inf: diff --git a/cwltool/schemas/draft-4/draft-4/dir4-job.yml b/cwltool/schemas/v1.0/draft-4/dir4-job.yml similarity index 100% rename from cwltool/schemas/draft-4/draft-4/dir4-job.yml rename to cwltool/schemas/v1.0/draft-4/dir4-job.yml diff --git a/cwltool/schemas/draft-4/draft-4/dir4.cwl b/cwltool/schemas/v1.0/draft-4/dir4.cwl similarity index 93% rename from cwltool/schemas/draft-4/draft-4/dir4.cwl rename to cwltool/schemas/v1.0/draft-4/dir4.cwl index 07341cf7d..6fd7583b2 100644 --- a/cwltool/schemas/draft-4/draft-4/dir4.cwl +++ b/cwltool/schemas/v1.0/draft-4/dir4.cwl @@ -1,5 +1,5 @@ class: CommandLineTool -cwlVersion: draft-4.dev3 +cwlVersion: v1.0.dev4 requirements: - class: ShellCommandRequirement inputs: diff --git a/cwltool/schemas/draft-4/draft-4/dir5.cwl b/cwltool/schemas/v1.0/draft-4/dir5.cwl similarity index 93% rename from cwltool/schemas/draft-4/draft-4/dir5.cwl rename to cwltool/schemas/v1.0/draft-4/dir5.cwl index 27d9ac9e9..5b26f4d40 100644 --- a/cwltool/schemas/draft-4/draft-4/dir5.cwl +++ b/cwltool/schemas/v1.0/draft-4/dir5.cwl @@ -1,5 +1,5 @@ class: CommandLineTool -cwlVersion: draft-4.dev3 +cwlVersion: v1.0.dev4 requirements: - class: ShellCommandRequirement - class: InitialWorkDirRequirement diff --git a/cwltool/schemas/draft-4/draft-4/echo-tool.cwl b/cwltool/schemas/v1.0/draft-4/echo-tool.cwl similarity index 90% rename from cwltool/schemas/draft-4/draft-4/echo-tool.cwl rename to cwltool/schemas/v1.0/draft-4/echo-tool.cwl index f207942ea..f46abb30f 100644 --- a/cwltool/schemas/draft-4/draft-4/echo-tool.cwl +++ b/cwltool/schemas/v1.0/draft-4/echo-tool.cwl @@ -1,7 +1,7 @@ #!/usr/bin/env cwl-runner class: CommandLineTool -cwlVersion: cwl:draft-4.dev3 +cwlVersion: v1.0.dev4 inputs: in: type: Any diff --git a/cwltool/schemas/draft-4/draft-4/egrep-stderr-mediumcut.cwl b/cwltool/schemas/v1.0/draft-4/egrep-stderr-mediumcut.cwl similarity index 90% rename from cwltool/schemas/draft-4/draft-4/egrep-stderr-mediumcut.cwl rename to cwltool/schemas/v1.0/draft-4/egrep-stderr-mediumcut.cwl index a224a5c50..18ea0ce44 100644 --- a/cwltool/schemas/draft-4/draft-4/egrep-stderr-mediumcut.cwl +++ b/cwltool/schemas/v1.0/draft-4/egrep-stderr-mediumcut.cwl @@ -1,6 +1,6 @@ #!/usr/bin/env cwl-runner class: CommandLineTool -cwlVersion: cwl:draft-4.dev3 +cwlVersion: v1.0.dev4 description: "Test of capturing stderr output in a docker container." hints: DockerRequirement: diff --git a/cwltool/schemas/draft-4/draft-4/egrep-stderr-shortcut.cwl b/cwltool/schemas/v1.0/draft-4/egrep-stderr-shortcut.cwl similarity index 90% rename from cwltool/schemas/draft-4/draft-4/egrep-stderr-shortcut.cwl rename to cwltool/schemas/v1.0/draft-4/egrep-stderr-shortcut.cwl index 9a8c26aa1..c4c4525a2 100644 --- a/cwltool/schemas/draft-4/draft-4/egrep-stderr-shortcut.cwl +++ b/cwltool/schemas/v1.0/draft-4/egrep-stderr-shortcut.cwl @@ -1,6 +1,6 @@ #!/usr/bin/env cwl-runner class: CommandLineTool -cwlVersion: cwl:draft-4.dev3 +cwlVersion: v1.0.dev4 description: "Test of capturing stderr output in a docker container." hints: DockerRequirement: diff --git a/cwltool/schemas/draft-4/draft-4/egrep-stderr.cwl b/cwltool/schemas/v1.0/draft-4/egrep-stderr.cwl similarity index 91% rename from cwltool/schemas/draft-4/draft-4/egrep-stderr.cwl rename to cwltool/schemas/v1.0/draft-4/egrep-stderr.cwl index 86ec03d05..68821b873 100644 --- a/cwltool/schemas/draft-4/draft-4/egrep-stderr.cwl +++ b/cwltool/schemas/v1.0/draft-4/egrep-stderr.cwl @@ -1,6 +1,6 @@ #!/usr/bin/env cwl-runner class: CommandLineTool -cwlVersion: cwl:draft-4.dev3 +cwlVersion: v1.0.dev4 description: "Test of capturing stderr output in a docker container." hints: DockerRequirement: diff --git a/cwltool/schemas/draft-4/draft-4/empty.json b/cwltool/schemas/v1.0/draft-4/empty.json similarity index 100% rename from cwltool/schemas/draft-4/draft-4/empty.json rename to cwltool/schemas/v1.0/draft-4/empty.json diff --git a/cwltool/schemas/draft-4/draft-4/env-job.json b/cwltool/schemas/v1.0/draft-4/env-job.json similarity index 100% rename from cwltool/schemas/draft-4/draft-4/env-job.json rename to cwltool/schemas/v1.0/draft-4/env-job.json diff --git a/cwltool/schemas/draft-4/draft-4/env-tool1.cwl b/cwltool/schemas/v1.0/draft-4/env-tool1.cwl similarity index 89% rename from cwltool/schemas/draft-4/draft-4/env-tool1.cwl rename to cwltool/schemas/v1.0/draft-4/env-tool1.cwl index af33b3b54..145dffc54 100644 --- a/cwltool/schemas/draft-4/draft-4/env-tool1.cwl +++ b/cwltool/schemas/v1.0/draft-4/env-tool1.cwl @@ -1,5 +1,5 @@ class: CommandLineTool -cwlVersion: cwl:draft-4.dev3 +cwlVersion: v1.0.dev4 inputs: in: string outputs: diff --git a/cwltool/schemas/draft-4/draft-4/env-tool2.cwl b/cwltool/schemas/v1.0/draft-4/env-tool2.cwl similarity index 89% rename from cwltool/schemas/draft-4/draft-4/env-tool2.cwl rename to cwltool/schemas/v1.0/draft-4/env-tool2.cwl index 8df0b64da..e8726d0e2 100644 --- a/cwltool/schemas/draft-4/draft-4/env-tool2.cwl +++ b/cwltool/schemas/v1.0/draft-4/env-tool2.cwl @@ -1,5 +1,5 @@ class: CommandLineTool -cwlVersion: cwl:draft-4.dev3 +cwlVersion: v1.0.dev4 inputs: in: string outputs: diff --git a/cwltool/schemas/draft-4/draft-4/env-wf1.cwl b/cwltool/schemas/v1.0/draft-4/env-wf1.cwl similarity index 91% rename from cwltool/schemas/draft-4/draft-4/env-wf1.cwl rename to cwltool/schemas/v1.0/draft-4/env-wf1.cwl index 09268c5a1..eb99ac230 100644 --- a/cwltool/schemas/draft-4/draft-4/env-wf1.cwl +++ b/cwltool/schemas/v1.0/draft-4/env-wf1.cwl @@ -1,6 +1,6 @@ #!/usr/bin/env cwl-runner class: Workflow -cwlVersion: cwl:draft-4.dev3 +cwlVersion: v1.0.dev4 inputs: in: string diff --git a/cwltool/schemas/draft-4/draft-4/env-wf2.cwl b/cwltool/schemas/v1.0/draft-4/env-wf2.cwl similarity index 91% rename from cwltool/schemas/draft-4/draft-4/env-wf2.cwl rename to cwltool/schemas/v1.0/draft-4/env-wf2.cwl index 9de645356..10d986a94 100644 --- a/cwltool/schemas/draft-4/draft-4/env-wf2.cwl +++ b/cwltool/schemas/v1.0/draft-4/env-wf2.cwl @@ -1,6 +1,6 @@ #!/usr/bin/env cwl-runner class: Workflow -cwlVersion: cwl:draft-4.dev3 +cwlVersion: v1.0.dev4 inputs: in: string diff --git a/cwltool/schemas/draft-4/draft-4/example_human_Illumina.pe_1.fastq b/cwltool/schemas/v1.0/draft-4/example_human_Illumina.pe_1.fastq similarity index 100% rename from cwltool/schemas/draft-4/draft-4/example_human_Illumina.pe_1.fastq rename to cwltool/schemas/v1.0/draft-4/example_human_Illumina.pe_1.fastq diff --git a/cwltool/schemas/draft-4/draft-4/example_human_Illumina.pe_2.fastq b/cwltool/schemas/v1.0/draft-4/example_human_Illumina.pe_2.fastq similarity index 100% rename from cwltool/schemas/draft-4/draft-4/example_human_Illumina.pe_2.fastq rename to cwltool/schemas/v1.0/draft-4/example_human_Illumina.pe_2.fastq diff --git a/cwltool/schemas/v1.0/draft-4/file-literal.yml b/cwltool/schemas/v1.0/draft-4/file-literal.yml new file mode 100644 index 000000000..604f9ece9 --- /dev/null +++ b/cwltool/schemas/v1.0/draft-4/file-literal.yml @@ -0,0 +1,3 @@ +file1: + class: File + contents: "Hello file literal" diff --git a/cwltool/schemas/draft-4/draft-4/foaf.rdf b/cwltool/schemas/v1.0/draft-4/foaf.rdf similarity index 100% rename from cwltool/schemas/draft-4/draft-4/foaf.rdf rename to cwltool/schemas/v1.0/draft-4/foaf.rdf diff --git a/cwltool/schemas/draft-4/draft-4/formattest-job.json b/cwltool/schemas/v1.0/draft-4/formattest-job.json similarity index 100% rename from cwltool/schemas/draft-4/draft-4/formattest-job.json rename to cwltool/schemas/v1.0/draft-4/formattest-job.json diff --git a/cwltool/schemas/draft-4/draft-4/formattest.cwl b/cwltool/schemas/v1.0/draft-4/formattest.cwl similarity index 92% rename from cwltool/schemas/draft-4/draft-4/formattest.cwl rename to cwltool/schemas/v1.0/draft-4/formattest.cwl index d97e9be4d..275d970e7 100644 --- a/cwltool/schemas/draft-4/draft-4/formattest.cwl +++ b/cwltool/schemas/v1.0/draft-4/formattest.cwl @@ -1,6 +1,6 @@ $namespaces: edam: "http://edamontology.org/" -cwlVersion: cwl:draft-4.dev3 +cwlVersion: v1.0.dev4 class: CommandLineTool description: "Reverse each line using the `rev` command" inputs: diff --git a/cwltool/schemas/draft-4/draft-4/formattest2-job.json b/cwltool/schemas/v1.0/draft-4/formattest2-job.json similarity index 100% rename from cwltool/schemas/draft-4/draft-4/formattest2-job.json rename to cwltool/schemas/v1.0/draft-4/formattest2-job.json diff --git a/cwltool/schemas/draft-4/draft-4/formattest2.cwl b/cwltool/schemas/v1.0/draft-4/formattest2.cwl similarity index 92% rename from cwltool/schemas/draft-4/draft-4/formattest2.cwl rename to cwltool/schemas/v1.0/draft-4/formattest2.cwl index 7ed3f9daa..dd5872b19 100644 --- a/cwltool/schemas/draft-4/draft-4/formattest2.cwl +++ b/cwltool/schemas/v1.0/draft-4/formattest2.cwl @@ -3,7 +3,7 @@ $namespaces: $schemas: - EDAM.owl class: CommandLineTool -cwlVersion: cwl:draft-4.dev3 +cwlVersion: v1.0.dev4 description: "Reverse each line using the `rev` command" inputs: diff --git a/cwltool/schemas/draft-4/draft-4/formattest3.cwl b/cwltool/schemas/v1.0/draft-4/formattest3.cwl similarity index 93% rename from cwltool/schemas/draft-4/draft-4/formattest3.cwl rename to cwltool/schemas/v1.0/draft-4/formattest3.cwl index e6342dfb4..9312417cf 100644 --- a/cwltool/schemas/draft-4/draft-4/formattest3.cwl +++ b/cwltool/schemas/v1.0/draft-4/formattest3.cwl @@ -5,7 +5,7 @@ $schemas: - EDAM.owl - gx_edam.ttl class: CommandLineTool -cwlVersion: cwl:draft-4.dev3 +cwlVersion: v1.0.dev4 description: "Reverse each line using the `rev` command" inputs: diff --git a/cwltool/schemas/draft-4/draft-4/glob-expr-list.cwl b/cwltool/schemas/v1.0/draft-4/glob-expr-list.cwl similarity index 87% rename from cwltool/schemas/draft-4/draft-4/glob-expr-list.cwl rename to cwltool/schemas/v1.0/draft-4/glob-expr-list.cwl index 6144a785c..b2784b614 100644 --- a/cwltool/schemas/draft-4/draft-4/glob-expr-list.cwl +++ b/cwltool/schemas/v1.0/draft-4/glob-expr-list.cwl @@ -1,5 +1,5 @@ class: CommandLineTool -cwlVersion: cwl:draft-4.dev3 +cwlVersion: v1.0.dev4 inputs: ids: diff --git a/cwltool/schemas/draft-4/draft-4/gx_edam.ttl b/cwltool/schemas/v1.0/draft-4/gx_edam.ttl similarity index 100% rename from cwltool/schemas/draft-4/draft-4/gx_edam.ttl rename to cwltool/schemas/v1.0/draft-4/gx_edam.ttl diff --git a/cwltool/schemas/draft-4/draft-4/hello.tar b/cwltool/schemas/v1.0/draft-4/hello.tar similarity index 100% rename from cwltool/schemas/draft-4/draft-4/hello.tar rename to cwltool/schemas/v1.0/draft-4/hello.tar diff --git a/cwltool/schemas/draft-4/draft-4/hello.txt b/cwltool/schemas/v1.0/draft-4/hello.txt similarity index 100% rename from cwltool/schemas/draft-4/draft-4/hello.txt rename to cwltool/schemas/v1.0/draft-4/hello.txt diff --git a/cwltool/schemas/draft-4/draft-4/index.py b/cwltool/schemas/v1.0/draft-4/index.py similarity index 100% rename from cwltool/schemas/draft-4/draft-4/index.py rename to cwltool/schemas/v1.0/draft-4/index.py diff --git a/cwltool/schemas/draft-4/draft-4/metadata.cwl b/cwltool/schemas/v1.0/draft-4/metadata.cwl similarity index 95% rename from cwltool/schemas/draft-4/draft-4/metadata.cwl rename to cwltool/schemas/v1.0/draft-4/metadata.cwl index 71c55e61a..bc524f0df 100644 --- a/cwltool/schemas/draft-4/draft-4/metadata.cwl +++ b/cwltool/schemas/v1.0/draft-4/metadata.cwl @@ -6,7 +6,7 @@ $schemas: - foaf.rdf - dcterms.rdf -cwlVersion: cwl:draft-4.dev3 +cwlVersion: v1.0.dev4 class: CommandLineTool description: "Print the contents of a file to stdout using 'cat' running in a docker container." diff --git a/cwltool/schemas/draft-4/draft-4/null-expression1-job.json b/cwltool/schemas/v1.0/draft-4/null-expression1-job.json similarity index 100% rename from cwltool/schemas/draft-4/draft-4/null-expression1-job.json rename to cwltool/schemas/v1.0/draft-4/null-expression1-job.json diff --git a/cwltool/schemas/draft-4/draft-4/null-expression1-tool.cwl b/cwltool/schemas/v1.0/draft-4/null-expression1-tool.cwl similarity index 89% rename from cwltool/schemas/draft-4/draft-4/null-expression1-tool.cwl rename to cwltool/schemas/v1.0/draft-4/null-expression1-tool.cwl index d953be546..7f34f3412 100644 --- a/cwltool/schemas/draft-4/draft-4/null-expression1-tool.cwl +++ b/cwltool/schemas/v1.0/draft-4/null-expression1-tool.cwl @@ -3,7 +3,7 @@ class: ExpressionTool requirements: - class: InlineJavascriptRequirement -cwlVersion: cwl:draft-4.dev3 +cwlVersion: v1.0.dev4 inputs: i1: diff --git a/cwltool/schemas/draft-4/draft-4/null-expression2-job.json b/cwltool/schemas/v1.0/draft-4/null-expression2-job.json similarity index 100% rename from cwltool/schemas/draft-4/draft-4/null-expression2-job.json rename to cwltool/schemas/v1.0/draft-4/null-expression2-job.json diff --git a/cwltool/schemas/draft-4/draft-4/null-expression2-tool.cwl b/cwltool/schemas/v1.0/draft-4/null-expression2-tool.cwl similarity index 87% rename from cwltool/schemas/draft-4/draft-4/null-expression2-tool.cwl rename to cwltool/schemas/v1.0/draft-4/null-expression2-tool.cwl index 8cfb02dc8..50259b4b8 100644 --- a/cwltool/schemas/draft-4/draft-4/null-expression2-tool.cwl +++ b/cwltool/schemas/v1.0/draft-4/null-expression2-tool.cwl @@ -3,7 +3,7 @@ class: ExpressionTool requirements: - class: InlineJavascriptRequirement -cwlVersion: cwl:draft-4.dev3 +cwlVersion: v1.0.dev4 inputs: i1: Any diff --git a/cwltool/schemas/draft-4/draft-4/number.txt b/cwltool/schemas/v1.0/draft-4/number.txt similarity index 100% rename from cwltool/schemas/draft-4/draft-4/number.txt rename to cwltool/schemas/v1.0/draft-4/number.txt diff --git a/cwltool/schemas/draft-4/draft-4/optional-output.cwl b/cwltool/schemas/v1.0/draft-4/optional-output.cwl similarity index 94% rename from cwltool/schemas/draft-4/draft-4/optional-output.cwl rename to cwltool/schemas/v1.0/draft-4/optional-output.cwl index ea058d3e9..de2ef7673 100644 --- a/cwltool/schemas/draft-4/draft-4/optional-output.cwl +++ b/cwltool/schemas/v1.0/draft-4/optional-output.cwl @@ -1,6 +1,6 @@ #!/usr/bin/env cwl-runner class: CommandLineTool -cwlVersion: "cwl:draft-4.dev3" +cwlVersion: "v1.0.dev4" description: "Print the contents of a file to stdout using 'cat' running in a docker container." hints: DockerRequirement: diff --git a/cwltool/schemas/draft-4/draft-4/params.cwl b/cwltool/schemas/v1.0/draft-4/params.cwl similarity index 90% rename from cwltool/schemas/draft-4/draft-4/params.cwl rename to cwltool/schemas/v1.0/draft-4/params.cwl index 6fd43a50f..0c113ac38 100644 --- a/cwltool/schemas/draft-4/draft-4/params.cwl +++ b/cwltool/schemas/v1.0/draft-4/params.cwl @@ -1,5 +1,5 @@ class: CommandLineTool -cwlVersion: cwl:draft-4.dev3 +cwlVersion: v1.0.dev4 inputs: bar: type: Any diff --git a/cwltool/schemas/draft-4/draft-4/params2.cwl b/cwltool/schemas/v1.0/draft-4/params2.cwl similarity index 91% rename from cwltool/schemas/draft-4/draft-4/params2.cwl rename to cwltool/schemas/v1.0/draft-4/params2.cwl index 01967fcb3..78cbf88af 100644 --- a/cwltool/schemas/draft-4/draft-4/params2.cwl +++ b/cwltool/schemas/v1.0/draft-4/params2.cwl @@ -1,5 +1,5 @@ class: CommandLineTool -cwlVersion: cwl:draft-4.dev3 +cwlVersion: v1.0.dev4 requirements: - class: InlineJavascriptRequirement diff --git a/cwltool/schemas/draft-4/draft-4/params_inc.yml b/cwltool/schemas/v1.0/draft-4/params_inc.yml similarity index 100% rename from cwltool/schemas/draft-4/draft-4/params_inc.yml rename to cwltool/schemas/v1.0/draft-4/params_inc.yml diff --git a/cwltool/schemas/draft-4/draft-4/parseInt-job.json b/cwltool/schemas/v1.0/draft-4/parseInt-job.json similarity index 100% rename from cwltool/schemas/draft-4/draft-4/parseInt-job.json rename to cwltool/schemas/v1.0/draft-4/parseInt-job.json diff --git a/cwltool/schemas/draft-4/draft-4/parseInt-tool.cwl b/cwltool/schemas/v1.0/draft-4/parseInt-tool.cwl similarity index 90% rename from cwltool/schemas/draft-4/draft-4/parseInt-tool.cwl rename to cwltool/schemas/v1.0/draft-4/parseInt-tool.cwl index 5c3a77557..09a160f4d 100755 --- a/cwltool/schemas/draft-4/draft-4/parseInt-tool.cwl +++ b/cwltool/schemas/v1.0/draft-4/parseInt-tool.cwl @@ -3,7 +3,7 @@ class: ExpressionTool requirements: - class: InlineJavascriptRequirement -cwlVersion: cwl:draft-4.dev3 +cwlVersion: v1.0.dev4 inputs: file1: diff --git a/cwltool/schemas/draft-4/draft-4/reads.fastq b/cwltool/schemas/v1.0/draft-4/reads.fastq similarity index 100% rename from cwltool/schemas/draft-4/draft-4/reads.fastq rename to cwltool/schemas/v1.0/draft-4/reads.fastq diff --git a/cwltool/schemas/draft-4/draft-4/record-output-job.json b/cwltool/schemas/v1.0/draft-4/record-output-job.json similarity index 100% rename from cwltool/schemas/draft-4/draft-4/record-output-job.json rename to cwltool/schemas/v1.0/draft-4/record-output-job.json diff --git a/cwltool/schemas/draft-4/draft-4/record-output.cwl b/cwltool/schemas/v1.0/draft-4/record-output.cwl similarity index 96% rename from cwltool/schemas/draft-4/draft-4/record-output.cwl rename to cwltool/schemas/v1.0/draft-4/record-output.cwl index 2e718da98..c397912e3 100644 --- a/cwltool/schemas/draft-4/draft-4/record-output.cwl +++ b/cwltool/schemas/v1.0/draft-4/record-output.cwl @@ -1,5 +1,5 @@ class: CommandLineTool -cwlVersion: cwl:draft-4.dev3 +cwlVersion: v1.0.dev4 requirements: - class: ShellCommandRequirement inputs: diff --git a/cwltool/schemas/draft-4/draft-4/ref.fasta b/cwltool/schemas/v1.0/draft-4/ref.fasta similarity index 100% rename from cwltool/schemas/draft-4/draft-4/ref.fasta rename to cwltool/schemas/v1.0/draft-4/ref.fasta diff --git a/cwltool/schemas/draft-4/draft-4/rename-job.json b/cwltool/schemas/v1.0/draft-4/rename-job.json similarity index 100% rename from cwltool/schemas/draft-4/draft-4/rename-job.json rename to cwltool/schemas/v1.0/draft-4/rename-job.json diff --git a/cwltool/schemas/draft-4/draft-4/rename.cwl b/cwltool/schemas/v1.0/draft-4/rename.cwl similarity index 70% rename from cwltool/schemas/draft-4/draft-4/rename.cwl rename to cwltool/schemas/v1.0/draft-4/rename.cwl index ca3ae58f4..37d29a297 100644 --- a/cwltool/schemas/draft-4/draft-4/rename.cwl +++ b/cwltool/schemas/v1.0/draft-4/rename.cwl @@ -1,10 +1,11 @@ class: CommandLineTool -cwlVersion: cwl:draft-4.dev3 +cwlVersion: v1.0.dev4 baseCommand: "true" requirements: InitialWorkDirRequirement: listing: - $(inputs.newname): $(inputs.srcfile.location) + - entryname: $(inputs.newname) + entry: $(inputs.srcfile) inputs: srcfile: File newname: string diff --git a/cwltool/schemas/draft-4/draft-4/revsort-job.json b/cwltool/schemas/v1.0/draft-4/revsort-job.json similarity index 100% rename from cwltool/schemas/draft-4/draft-4/revsort-job.json rename to cwltool/schemas/v1.0/draft-4/revsort-job.json diff --git a/cwltool/schemas/draft-4/draft-4/revsort.cwl b/cwltool/schemas/v1.0/draft-4/revsort.cwl similarity index 98% rename from cwltool/schemas/draft-4/draft-4/revsort.cwl rename to cwltool/schemas/v1.0/draft-4/revsort.cwl index e94b30ada..e9792dfef 100644 --- a/cwltool/schemas/draft-4/draft-4/revsort.cwl +++ b/cwltool/schemas/v1.0/draft-4/revsort.cwl @@ -3,7 +3,7 @@ # class: Workflow description: "Reverse the lines in a document, then sort those lines." -cwlVersion: cwl:draft-4.dev3 +cwlVersion: v1.0.dev4 # Requirements & hints specify prerequisites and extensions to the workflow. # In this example, DockerRequirement specifies a default Docker container diff --git a/cwltool/schemas/draft-4/draft-4/revtool.cwl b/cwltool/schemas/v1.0/draft-4/revtool.cwl similarity index 97% rename from cwltool/schemas/draft-4/draft-4/revtool.cwl rename to cwltool/schemas/v1.0/draft-4/revtool.cwl index ba3033c09..f6aada9f8 100644 --- a/cwltool/schemas/draft-4/draft-4/revtool.cwl +++ b/cwltool/schemas/v1.0/draft-4/revtool.cwl @@ -2,7 +2,7 @@ # Simplest example command line program wrapper for the Unix tool "rev". # class: CommandLineTool -cwlVersion: cwl:draft-4.dev3 +cwlVersion: v1.0.dev4 description: "Reverse each line using the `rev` command" # The "inputs" array defines the structure of the input object that describes diff --git a/cwltool/schemas/draft-4/draft-4/scatter-job1.json b/cwltool/schemas/v1.0/draft-4/scatter-job1.json similarity index 100% rename from cwltool/schemas/draft-4/draft-4/scatter-job1.json rename to cwltool/schemas/v1.0/draft-4/scatter-job1.json diff --git a/cwltool/schemas/draft-4/draft-4/scatter-job2.json b/cwltool/schemas/v1.0/draft-4/scatter-job2.json similarity index 100% rename from cwltool/schemas/draft-4/draft-4/scatter-job2.json rename to cwltool/schemas/v1.0/draft-4/scatter-job2.json diff --git a/cwltool/schemas/draft-4/draft-4/scatter-valuefrom-job1.json b/cwltool/schemas/v1.0/draft-4/scatter-valuefrom-job1.json similarity index 100% rename from cwltool/schemas/draft-4/draft-4/scatter-valuefrom-job1.json rename to cwltool/schemas/v1.0/draft-4/scatter-valuefrom-job1.json diff --git a/cwltool/schemas/draft-4/draft-4/scatter-valuefrom-job2.json b/cwltool/schemas/v1.0/draft-4/scatter-valuefrom-job2.json similarity index 100% rename from cwltool/schemas/draft-4/draft-4/scatter-valuefrom-job2.json rename to cwltool/schemas/v1.0/draft-4/scatter-valuefrom-job2.json diff --git a/cwltool/schemas/draft-4/draft-4/scatter-valuefrom-wf1.cwl b/cwltool/schemas/v1.0/draft-4/scatter-valuefrom-wf1.cwl similarity index 97% rename from cwltool/schemas/draft-4/draft-4/scatter-valuefrom-wf1.cwl rename to cwltool/schemas/v1.0/draft-4/scatter-valuefrom-wf1.cwl index 0256066b3..d74449718 100644 --- a/cwltool/schemas/draft-4/draft-4/scatter-valuefrom-wf1.cwl +++ b/cwltool/schemas/v1.0/draft-4/scatter-valuefrom-wf1.cwl @@ -1,5 +1,5 @@ #!/usr/bin/env cwl-runner -cwlVersion: cwl:draft-4.dev3 +cwlVersion: v1.0.dev4 class: Workflow inputs: inp: diff --git a/cwltool/schemas/draft-4/draft-4/scatter-valuefrom-wf2.cwl b/cwltool/schemas/v1.0/draft-4/scatter-valuefrom-wf2.cwl similarity index 97% rename from cwltool/schemas/draft-4/draft-4/scatter-valuefrom-wf2.cwl rename to cwltool/schemas/v1.0/draft-4/scatter-valuefrom-wf2.cwl index 1894abee6..6b632e8c5 100644 --- a/cwltool/schemas/draft-4/draft-4/scatter-valuefrom-wf2.cwl +++ b/cwltool/schemas/v1.0/draft-4/scatter-valuefrom-wf2.cwl @@ -1,5 +1,5 @@ #!/usr/bin/env cwl-runner -cwlVersion: cwl:draft-4.dev3 +cwlVersion: v1.0.dev4 class: Workflow inputs: diff --git a/cwltool/schemas/draft-4/draft-4/scatter-valuefrom-wf3.cwl b/cwltool/schemas/v1.0/draft-4/scatter-valuefrom-wf3.cwl similarity index 97% rename from cwltool/schemas/draft-4/draft-4/scatter-valuefrom-wf3.cwl rename to cwltool/schemas/v1.0/draft-4/scatter-valuefrom-wf3.cwl index a691acf5d..c1ef5245e 100644 --- a/cwltool/schemas/draft-4/draft-4/scatter-valuefrom-wf3.cwl +++ b/cwltool/schemas/v1.0/draft-4/scatter-valuefrom-wf3.cwl @@ -1,6 +1,6 @@ #!/usr/bin/env cwl-runner -cwlVersion: cwl:draft-4.dev3 +cwlVersion: v1.0.dev4 $graph: - id: echo diff --git a/cwltool/schemas/draft-4/draft-4/scatter-valuefrom-wf4.cwl b/cwltool/schemas/v1.0/draft-4/scatter-valuefrom-wf4.cwl similarity index 97% rename from cwltool/schemas/draft-4/draft-4/scatter-valuefrom-wf4.cwl rename to cwltool/schemas/v1.0/draft-4/scatter-valuefrom-wf4.cwl index 9cae1a2b2..4a5aecc1b 100644 --- a/cwltool/schemas/draft-4/draft-4/scatter-valuefrom-wf4.cwl +++ b/cwltool/schemas/v1.0/draft-4/scatter-valuefrom-wf4.cwl @@ -1,5 +1,5 @@ #!/usr/bin/env cwl-runner -cwlVersion: cwl:draft-4.dev3 +cwlVersion: v1.0.dev4 $graph: - id: echo class: CommandLineTool diff --git a/cwltool/schemas/draft-4/draft-4/scatter-valuefrom-wf5.cwl b/cwltool/schemas/v1.0/draft-4/scatter-valuefrom-wf5.cwl similarity index 97% rename from cwltool/schemas/draft-4/draft-4/scatter-valuefrom-wf5.cwl rename to cwltool/schemas/v1.0/draft-4/scatter-valuefrom-wf5.cwl index 417ea4997..db9719839 100644 --- a/cwltool/schemas/draft-4/draft-4/scatter-valuefrom-wf5.cwl +++ b/cwltool/schemas/v1.0/draft-4/scatter-valuefrom-wf5.cwl @@ -1,5 +1,5 @@ #!/usr/bin/env cwl-runner -cwlVersion: cwl:draft-4.dev3 +cwlVersion: v1.0.dev4 class: Workflow inputs: inp: diff --git a/cwltool/schemas/draft-4/draft-4/scatter-wf1.cwl b/cwltool/schemas/v1.0/draft-4/scatter-wf1.cwl similarity index 95% rename from cwltool/schemas/draft-4/draft-4/scatter-wf1.cwl rename to cwltool/schemas/v1.0/draft-4/scatter-wf1.cwl index a8ffc6531..647e4f2dc 100644 --- a/cwltool/schemas/draft-4/draft-4/scatter-wf1.cwl +++ b/cwltool/schemas/v1.0/draft-4/scatter-wf1.cwl @@ -1,5 +1,5 @@ #!/usr/bin/env cwl-runner -cwlVersion: cwl:draft-4.dev3 +cwlVersion: v1.0.dev4 class: Workflow inputs: inp: string[] diff --git a/cwltool/schemas/draft-4/draft-4/scatter-wf2.cwl b/cwltool/schemas/v1.0/draft-4/scatter-wf2.cwl similarity index 96% rename from cwltool/schemas/draft-4/draft-4/scatter-wf2.cwl rename to cwltool/schemas/v1.0/draft-4/scatter-wf2.cwl index abc20be26..9a761cd58 100644 --- a/cwltool/schemas/draft-4/draft-4/scatter-wf2.cwl +++ b/cwltool/schemas/v1.0/draft-4/scatter-wf2.cwl @@ -1,5 +1,5 @@ #!/usr/bin/env cwl-runner -cwlVersion: cwl:draft-4.dev3 +cwlVersion: v1.0.dev4 class: Workflow inputs: diff --git a/cwltool/schemas/draft-4/draft-4/scatter-wf3.cwl b/cwltool/schemas/v1.0/draft-4/scatter-wf3.cwl similarity index 96% rename from cwltool/schemas/draft-4/draft-4/scatter-wf3.cwl rename to cwltool/schemas/v1.0/draft-4/scatter-wf3.cwl index ce32fbd69..0bc79a267 100644 --- a/cwltool/schemas/draft-4/draft-4/scatter-wf3.cwl +++ b/cwltool/schemas/v1.0/draft-4/scatter-wf3.cwl @@ -1,6 +1,6 @@ #!/usr/bin/env cwl-runner -cwlVersion: cwl:draft-4.dev3 +cwlVersion: v1.0.dev4 $graph: - id: echo diff --git a/cwltool/schemas/draft-4/draft-4/scatter-wf4.cwl b/cwltool/schemas/v1.0/draft-4/scatter-wf4.cwl similarity index 96% rename from cwltool/schemas/draft-4/draft-4/scatter-wf4.cwl rename to cwltool/schemas/v1.0/draft-4/scatter-wf4.cwl index c01d5650d..9138ddd11 100644 --- a/cwltool/schemas/draft-4/draft-4/scatter-wf4.cwl +++ b/cwltool/schemas/v1.0/draft-4/scatter-wf4.cwl @@ -1,5 +1,5 @@ #!/usr/bin/env cwl-runner -cwlVersion: cwl:draft-4.dev3 +cwlVersion: v1.0.dev4 $graph: - id: echo class: CommandLineTool diff --git a/cwltool/schemas/draft-4/draft-4/schemadef-job.json b/cwltool/schemas/v1.0/draft-4/schemadef-job.json similarity index 100% rename from cwltool/schemas/draft-4/draft-4/schemadef-job.json rename to cwltool/schemas/v1.0/draft-4/schemadef-job.json diff --git a/cwltool/schemas/draft-4/draft-4/schemadef-tool.cwl b/cwltool/schemas/v1.0/draft-4/schemadef-tool.cwl similarity index 93% rename from cwltool/schemas/draft-4/draft-4/schemadef-tool.cwl rename to cwltool/schemas/v1.0/draft-4/schemadef-tool.cwl index 0d8447442..b93549cdb 100644 --- a/cwltool/schemas/draft-4/draft-4/schemadef-tool.cwl +++ b/cwltool/schemas/v1.0/draft-4/schemadef-tool.cwl @@ -1,6 +1,6 @@ #!/usr/bin/env cwl-runner class: CommandLineTool -cwlVersion: cwl:draft-4.dev3 +cwlVersion: v1.0.dev4 requirements: - $import: schemadef-type.yml - class: InlineJavascriptRequirement diff --git a/cwltool/schemas/draft-4/draft-4/schemadef-type.yml b/cwltool/schemas/v1.0/draft-4/schemadef-type.yml similarity index 100% rename from cwltool/schemas/draft-4/draft-4/schemadef-type.yml rename to cwltool/schemas/v1.0/draft-4/schemadef-type.yml diff --git a/cwltool/schemas/draft-4/draft-4/schemadef-wf.cwl b/cwltool/schemas/v1.0/draft-4/schemadef-wf.cwl similarity index 91% rename from cwltool/schemas/draft-4/draft-4/schemadef-wf.cwl rename to cwltool/schemas/v1.0/draft-4/schemadef-wf.cwl index 4667f7894..6a016679c 100644 --- a/cwltool/schemas/draft-4/draft-4/schemadef-wf.cwl +++ b/cwltool/schemas/v1.0/draft-4/schemadef-wf.cwl @@ -1,6 +1,6 @@ #!/usr/bin/env cwl-runner -cwlVersion: cwl:draft-4.dev3 +cwlVersion: v1.0.dev4 class: Workflow requirements: diff --git a/cwltool/schemas/draft-4/draft-4/search-job.json b/cwltool/schemas/v1.0/draft-4/search-job.json similarity index 100% rename from cwltool/schemas/draft-4/draft-4/search-job.json rename to cwltool/schemas/v1.0/draft-4/search-job.json diff --git a/cwltool/schemas/draft-4/draft-4/search.cwl b/cwltool/schemas/v1.0/draft-4/search.cwl similarity index 95% rename from cwltool/schemas/draft-4/draft-4/search.cwl rename to cwltool/schemas/v1.0/draft-4/search.cwl index dc32c0955..952b04b93 100644 --- a/cwltool/schemas/draft-4/draft-4/search.cwl +++ b/cwltool/schemas/v1.0/draft-4/search.cwl @@ -1,4 +1,4 @@ -cwlVersion: cwl:draft-4.dev3 +cwlVersion: v1.0.dev4 $graph: - id: index class: CommandLineTool @@ -9,7 +9,8 @@ $graph: requirements: - class: InitialWorkDirRequirement listing: - input.txt: $(inputs.file) + - entryname: input.txt + entry: $(inputs.file) - class: InlineJavascriptRequirement inputs: diff --git a/cwltool/schemas/draft-4/draft-4/search.py b/cwltool/schemas/v1.0/draft-4/search.py similarity index 100% rename from cwltool/schemas/draft-4/draft-4/search.py rename to cwltool/schemas/v1.0/draft-4/search.py diff --git a/cwltool/schemas/draft-4/draft-4/shelltest.cwl b/cwltool/schemas/v1.0/draft-4/shelltest.cwl similarity index 93% rename from cwltool/schemas/draft-4/draft-4/shelltest.cwl rename to cwltool/schemas/v1.0/draft-4/shelltest.cwl index 9ccb34d52..c127fa5b0 100644 --- a/cwltool/schemas/draft-4/draft-4/shelltest.cwl +++ b/cwltool/schemas/v1.0/draft-4/shelltest.cwl @@ -1,5 +1,5 @@ class: CommandLineTool -cwlVersion: cwl:draft-4.dev3 +cwlVersion: v1.0.dev4 description: "Reverse each line using the `rev` command then sort." requirements: - class: ShellCommandRequirement diff --git a/cwltool/schemas/draft-4/draft-4/sorttool.cwl b/cwltool/schemas/v1.0/draft-4/sorttool.cwl similarity index 97% rename from cwltool/schemas/draft-4/draft-4/sorttool.cwl rename to cwltool/schemas/v1.0/draft-4/sorttool.cwl index 7aeeadc03..f4c6f1506 100644 --- a/cwltool/schemas/draft-4/draft-4/sorttool.cwl +++ b/cwltool/schemas/v1.0/draft-4/sorttool.cwl @@ -2,7 +2,7 @@ # demonstrating command line flags. class: CommandLineTool description: "Sort lines using the `sort` command" -cwlVersion: cwl:draft-4.dev3 +cwlVersion: v1.0.dev4 # This example is similar to the previous one, with an additional input # parameter called "reverse". It is a boolean parameter, which is diff --git a/cwltool/schemas/draft-4/draft-4/stagefile-job.yml b/cwltool/schemas/v1.0/draft-4/stagefile-job.yml similarity index 100% rename from cwltool/schemas/draft-4/draft-4/stagefile-job.yml rename to cwltool/schemas/v1.0/draft-4/stagefile-job.yml diff --git a/cwltool/schemas/draft-4/draft-4/stagefile.cwl b/cwltool/schemas/v1.0/draft-4/stagefile.cwl similarity index 92% rename from cwltool/schemas/draft-4/draft-4/stagefile.cwl rename to cwltool/schemas/v1.0/draft-4/stagefile.cwl index bf73c73db..e09f59b63 100644 --- a/cwltool/schemas/draft-4/draft-4/stagefile.cwl +++ b/cwltool/schemas/v1.0/draft-4/stagefile.cwl @@ -1,5 +1,5 @@ class: CommandLineTool -cwlVersion: draft-4.dev3 +cwlVersion: v1.0.dev4 requirements: InitialWorkDirRequirement: listing: diff --git a/cwltool/schemas/draft-4/draft-4/step-valuefrom-job.json b/cwltool/schemas/v1.0/draft-4/step-valuefrom-job.json similarity index 100% rename from cwltool/schemas/draft-4/draft-4/step-valuefrom-job.json rename to cwltool/schemas/v1.0/draft-4/step-valuefrom-job.json diff --git a/cwltool/schemas/draft-4/draft-4/step-valuefrom-wf.cwl b/cwltool/schemas/v1.0/draft-4/step-valuefrom-wf.cwl similarity index 94% rename from cwltool/schemas/draft-4/draft-4/step-valuefrom-wf.cwl rename to cwltool/schemas/v1.0/draft-4/step-valuefrom-wf.cwl index 75b251d02..a73b37ac4 100644 --- a/cwltool/schemas/draft-4/draft-4/step-valuefrom-wf.cwl +++ b/cwltool/schemas/v1.0/draft-4/step-valuefrom-wf.cwl @@ -1,6 +1,6 @@ #!/usr/bin/env cwl-runner class: Workflow -cwlVersion: cwl:draft-4.dev3 +cwlVersion: v1.0.dev4 requirements: - class: StepInputExpressionRequirement diff --git a/cwltool/schemas/draft-4/draft-4/step-valuefrom-wf.json b/cwltool/schemas/v1.0/draft-4/step-valuefrom-wf.json similarity index 100% rename from cwltool/schemas/draft-4/draft-4/step-valuefrom-wf.json rename to cwltool/schemas/v1.0/draft-4/step-valuefrom-wf.json diff --git a/cwltool/schemas/draft-4/draft-4/step-valuefrom2-wf.cwl b/cwltool/schemas/v1.0/draft-4/step-valuefrom2-wf.cwl similarity index 96% rename from cwltool/schemas/draft-4/draft-4/step-valuefrom2-wf.cwl rename to cwltool/schemas/v1.0/draft-4/step-valuefrom2-wf.cwl index 8d085aa37..c13a9f662 100644 --- a/cwltool/schemas/draft-4/draft-4/step-valuefrom2-wf.cwl +++ b/cwltool/schemas/v1.0/draft-4/step-valuefrom2-wf.cwl @@ -1,6 +1,6 @@ #!/usr/bin/env cwl-runner class: Workflow -cwlVersion: cwl:draft-4.dev3 +cwlVersion: v1.0.dev4 requirements: - class: StepInputExpressionRequirement - class: InlineJavascriptRequirement diff --git a/cwltool/schemas/draft-4/draft-4/step-valuefrom3-wf.cwl b/cwltool/schemas/v1.0/draft-4/step-valuefrom3-wf.cwl similarity index 96% rename from cwltool/schemas/draft-4/draft-4/step-valuefrom3-wf.cwl rename to cwltool/schemas/v1.0/draft-4/step-valuefrom3-wf.cwl index 54f70ba85..ecdfdf9a3 100644 --- a/cwltool/schemas/draft-4/draft-4/step-valuefrom3-wf.cwl +++ b/cwltool/schemas/v1.0/draft-4/step-valuefrom3-wf.cwl @@ -1,6 +1,6 @@ #!/usr/bin/env cwl-runner class: Workflow -cwlVersion: cwl:draft-4.dev3 +cwlVersion: v1.0.dev4 requirements: - class: StepInputExpressionRequirement - class: InlineJavascriptRequirement diff --git a/cwltool/schemas/draft-4/draft-4/template-tool.cwl b/cwltool/schemas/v1.0/draft-4/template-tool.cwl similarity index 81% rename from cwltool/schemas/draft-4/draft-4/template-tool.cwl rename to cwltool/schemas/v1.0/draft-4/template-tool.cwl index b3ec7b85d..53393cb11 100755 --- a/cwltool/schemas/draft-4/draft-4/template-tool.cwl +++ b/cwltool/schemas/v1.0/draft-4/template-tool.cwl @@ -1,5 +1,5 @@ #!/usr/bin/env cwl-runner -cwlVersion: cwl:draft-4.dev3 +cwlVersion: v1.0.dev4 class: CommandLineTool requirements: - class: DockerRequirement @@ -10,7 +10,8 @@ requirements: - "var t = function(s) { return _.template(s)({'inputs': inputs}); };" - class: InitialWorkDirRequirement listing: - foo.txt: $(t("The file is <%= inputs.file1.path.split('/').slice(-1)[0] %>\n")) + - entryname: foo.txt + entry: $(t("The file is <%= inputs.file1.path.split('/').slice(-1)[0] %>\n")) inputs: - id: file1 type: File diff --git a/cwltool/schemas/draft-4/draft-4/test-cwl-out.cwl b/cwltool/schemas/v1.0/draft-4/test-cwl-out.cwl similarity index 92% rename from cwltool/schemas/draft-4/draft-4/test-cwl-out.cwl rename to cwltool/schemas/v1.0/draft-4/test-cwl-out.cwl index 884054d74..e18462b30 100644 --- a/cwltool/schemas/draft-4/draft-4/test-cwl-out.cwl +++ b/cwltool/schemas/v1.0/draft-4/test-cwl-out.cwl @@ -1,5 +1,5 @@ class: CommandLineTool -cwlVersion: cwl:draft-4.dev3 +cwlVersion: v1.0.dev4 requirements: - class: ShellCommandRequirement - class: DockerRequirement diff --git a/cwltool/schemas/draft-4/draft-4/testdir/a b/cwltool/schemas/v1.0/draft-4/testdir/a similarity index 100% rename from cwltool/schemas/draft-4/draft-4/testdir/a rename to cwltool/schemas/v1.0/draft-4/testdir/a diff --git a/cwltool/schemas/draft-4/draft-4/testdir/b b/cwltool/schemas/v1.0/draft-4/testdir/b similarity index 100% rename from cwltool/schemas/draft-4/draft-4/testdir/b rename to cwltool/schemas/v1.0/draft-4/testdir/b diff --git a/cwltool/schemas/draft-4/draft-4/testdir/c/d b/cwltool/schemas/v1.0/draft-4/testdir/c/d similarity index 100% rename from cwltool/schemas/draft-4/draft-4/testdir/c/d rename to cwltool/schemas/v1.0/draft-4/testdir/c/d diff --git a/cwltool/schemas/draft-4/draft-4/tmap-job.json b/cwltool/schemas/v1.0/draft-4/tmap-job.json similarity index 100% rename from cwltool/schemas/draft-4/draft-4/tmap-job.json rename to cwltool/schemas/v1.0/draft-4/tmap-job.json diff --git a/cwltool/schemas/draft-4/draft-4/tmap-tool.cwl b/cwltool/schemas/v1.0/draft-4/tmap-tool.cwl similarity index 99% rename from cwltool/schemas/draft-4/draft-4/tmap-tool.cwl rename to cwltool/schemas/v1.0/draft-4/tmap-tool.cwl index 1b6273e26..ef9748424 100755 --- a/cwltool/schemas/draft-4/draft-4/tmap-tool.cwl +++ b/cwltool/schemas/v1.0/draft-4/tmap-tool.cwl @@ -1,6 +1,6 @@ #!/usr/bin/env cwl-runner { - "cwlVersion": "cwl:draft-4.dev3", + "cwlVersion": "v1.0.dev4", "class": "CommandLineTool", diff --git a/cwltool/schemas/draft-4/draft-4/underscore.js b/cwltool/schemas/v1.0/draft-4/underscore.js similarity index 100% rename from cwltool/schemas/draft-4/draft-4/underscore.js rename to cwltool/schemas/v1.0/draft-4/underscore.js diff --git a/cwltool/schemas/draft-4/draft-4/wc-job.json b/cwltool/schemas/v1.0/draft-4/wc-job.json similarity index 100% rename from cwltool/schemas/draft-4/draft-4/wc-job.json rename to cwltool/schemas/v1.0/draft-4/wc-job.json diff --git a/cwltool/schemas/draft-4/draft-4/wc-tool.cwl b/cwltool/schemas/v1.0/draft-4/wc-tool.cwl similarity index 87% rename from cwltool/schemas/draft-4/draft-4/wc-tool.cwl rename to cwltool/schemas/v1.0/draft-4/wc-tool.cwl index 08ef2e77b..592b3cc50 100755 --- a/cwltool/schemas/draft-4/draft-4/wc-tool.cwl +++ b/cwltool/schemas/v1.0/draft-4/wc-tool.cwl @@ -1,7 +1,7 @@ #!/usr/bin/env cwl-runner class: CommandLineTool -cwlVersion: cwl:draft-4.dev3 +cwlVersion: v1.0.dev4 inputs: file1: File diff --git a/cwltool/schemas/draft-4/draft-4/wc2-tool.cwl b/cwltool/schemas/v1.0/draft-4/wc2-tool.cwl similarity index 92% rename from cwltool/schemas/draft-4/draft-4/wc2-tool.cwl rename to cwltool/schemas/v1.0/draft-4/wc2-tool.cwl index 510a6dc5c..d0ff6419d 100755 --- a/cwltool/schemas/draft-4/draft-4/wc2-tool.cwl +++ b/cwltool/schemas/v1.0/draft-4/wc2-tool.cwl @@ -1,6 +1,6 @@ #!/usr/bin/env cwl-runner class: CommandLineTool -cwlVersion: cwl:draft-4.dev3 +cwlVersion: v1.0.dev4 requirements: - class: InlineJavascriptRequirement diff --git a/cwltool/schemas/draft-4/draft-4/wc3-tool.cwl b/cwltool/schemas/v1.0/draft-4/wc3-tool.cwl similarity index 94% rename from cwltool/schemas/draft-4/draft-4/wc3-tool.cwl rename to cwltool/schemas/v1.0/draft-4/wc3-tool.cwl index 6aa6986f4..f9c7d03d2 100644 --- a/cwltool/schemas/draft-4/draft-4/wc3-tool.cwl +++ b/cwltool/schemas/v1.0/draft-4/wc3-tool.cwl @@ -1,6 +1,6 @@ #!/usr/bin/env cwl-runner class: CommandLineTool -cwlVersion: cwl:draft-4.dev3 +cwlVersion: v1.0.dev4 requirements: - class: InlineJavascriptRequirement diff --git a/cwltool/schemas/draft-4/draft-4/wc4-tool.cwl b/cwltool/schemas/v1.0/draft-4/wc4-tool.cwl similarity index 94% rename from cwltool/schemas/draft-4/draft-4/wc4-tool.cwl rename to cwltool/schemas/v1.0/draft-4/wc4-tool.cwl index 21e08a530..380fab372 100644 --- a/cwltool/schemas/draft-4/draft-4/wc4-tool.cwl +++ b/cwltool/schemas/v1.0/draft-4/wc4-tool.cwl @@ -1,6 +1,6 @@ #!/usr/bin/env cwl-runner class: CommandLineTool -cwlVersion: cwl:draft-4.dev3 +cwlVersion: v1.0.dev4 requirements: - class: InlineJavascriptRequirement diff --git a/cwltool/schemas/draft-4/draft-4/whale.txt b/cwltool/schemas/v1.0/draft-4/whale.txt similarity index 100% rename from cwltool/schemas/draft-4/draft-4/whale.txt rename to cwltool/schemas/v1.0/draft-4/whale.txt diff --git a/cwltool/schemas/draft-4/examples/1st.cwl b/cwltool/schemas/v1.0/examples/1st.cwl similarity index 100% rename from cwltool/schemas/draft-4/examples/1st.cwl rename to cwltool/schemas/v1.0/examples/1st.cwl diff --git a/cwltool/schemas/draft-4/examples/Hello.java b/cwltool/schemas/v1.0/examples/Hello.java similarity index 100% rename from cwltool/schemas/draft-4/examples/Hello.java rename to cwltool/schemas/v1.0/examples/Hello.java diff --git a/cwltool/schemas/draft-4/examples/arguments-job.yml b/cwltool/schemas/v1.0/examples/arguments-job.yml similarity index 100% rename from cwltool/schemas/draft-4/examples/arguments-job.yml rename to cwltool/schemas/v1.0/examples/arguments-job.yml diff --git a/cwltool/schemas/draft-4/examples/arguments.cwl b/cwltool/schemas/v1.0/examples/arguments.cwl similarity index 100% rename from cwltool/schemas/draft-4/examples/arguments.cwl rename to cwltool/schemas/v1.0/examples/arguments.cwl diff --git a/cwltool/schemas/draft-4/examples/array-inputs-job.yml b/cwltool/schemas/v1.0/examples/array-inputs-job.yml similarity index 100% rename from cwltool/schemas/draft-4/examples/array-inputs-job.yml rename to cwltool/schemas/v1.0/examples/array-inputs-job.yml diff --git a/cwltool/schemas/draft-4/examples/array-inputs.cwl b/cwltool/schemas/v1.0/examples/array-inputs.cwl similarity index 100% rename from cwltool/schemas/draft-4/examples/array-inputs.cwl rename to cwltool/schemas/v1.0/examples/array-inputs.cwl diff --git a/cwltool/schemas/draft-4/examples/createfile-job.yml b/cwltool/schemas/v1.0/examples/createfile-job.yml similarity index 100% rename from cwltool/schemas/draft-4/examples/createfile-job.yml rename to cwltool/schemas/v1.0/examples/createfile-job.yml diff --git a/cwltool/schemas/draft-4/examples/createfile.cwl b/cwltool/schemas/v1.0/examples/createfile.cwl similarity index 100% rename from cwltool/schemas/draft-4/examples/createfile.cwl rename to cwltool/schemas/v1.0/examples/createfile.cwl diff --git a/cwltool/schemas/draft-4/examples/docker-job.yml b/cwltool/schemas/v1.0/examples/docker-job.yml similarity index 100% rename from cwltool/schemas/draft-4/examples/docker-job.yml rename to cwltool/schemas/v1.0/examples/docker-job.yml diff --git a/cwltool/schemas/draft-4/examples/docker.cwl b/cwltool/schemas/v1.0/examples/docker.cwl similarity index 100% rename from cwltool/schemas/draft-4/examples/docker.cwl rename to cwltool/schemas/v1.0/examples/docker.cwl diff --git a/cwltool/schemas/draft-4/examples/echo-job.yml b/cwltool/schemas/v1.0/examples/echo-job.yml similarity index 100% rename from cwltool/schemas/draft-4/examples/echo-job.yml rename to cwltool/schemas/v1.0/examples/echo-job.yml diff --git a/cwltool/schemas/draft-4/examples/empty.yml b/cwltool/schemas/v1.0/examples/empty.yml similarity index 100% rename from cwltool/schemas/draft-4/examples/empty.yml rename to cwltool/schemas/v1.0/examples/empty.yml diff --git a/cwltool/schemas/draft-4/examples/env.cwl b/cwltool/schemas/v1.0/examples/env.cwl similarity index 100% rename from cwltool/schemas/draft-4/examples/env.cwl rename to cwltool/schemas/v1.0/examples/env.cwl diff --git a/cwltool/schemas/draft-4/examples/expression.cwl b/cwltool/schemas/v1.0/examples/expression.cwl similarity index 100% rename from cwltool/schemas/draft-4/examples/expression.cwl rename to cwltool/schemas/v1.0/examples/expression.cwl diff --git a/cwltool/schemas/draft-4/examples/hello.js b/cwltool/schemas/v1.0/examples/hello.js similarity index 100% rename from cwltool/schemas/draft-4/examples/hello.js rename to cwltool/schemas/v1.0/examples/hello.js diff --git a/cwltool/schemas/draft-4/examples/inp-job.yml b/cwltool/schemas/v1.0/examples/inp-job.yml similarity index 100% rename from cwltool/schemas/draft-4/examples/inp-job.yml rename to cwltool/schemas/v1.0/examples/inp-job.yml diff --git a/cwltool/schemas/draft-4/examples/inp.cwl b/cwltool/schemas/v1.0/examples/inp.cwl similarity index 100% rename from cwltool/schemas/draft-4/examples/inp.cwl rename to cwltool/schemas/v1.0/examples/inp.cwl diff --git a/cwltool/schemas/draft-4/examples/linkfile.cwl b/cwltool/schemas/v1.0/examples/linkfile.cwl similarity index 100% rename from cwltool/schemas/draft-4/examples/linkfile.cwl rename to cwltool/schemas/v1.0/examples/linkfile.cwl diff --git a/cwltool/schemas/draft-4/examples/record-job1.yml b/cwltool/schemas/v1.0/examples/record-job1.yml similarity index 100% rename from cwltool/schemas/draft-4/examples/record-job1.yml rename to cwltool/schemas/v1.0/examples/record-job1.yml diff --git a/cwltool/schemas/draft-4/examples/record-job2.yml b/cwltool/schemas/v1.0/examples/record-job2.yml similarity index 100% rename from cwltool/schemas/draft-4/examples/record-job2.yml rename to cwltool/schemas/v1.0/examples/record-job2.yml diff --git a/cwltool/schemas/draft-4/examples/record-job3.yml b/cwltool/schemas/v1.0/examples/record-job3.yml similarity index 100% rename from cwltool/schemas/draft-4/examples/record-job3.yml rename to cwltool/schemas/v1.0/examples/record-job3.yml diff --git a/cwltool/schemas/draft-4/examples/record.cwl b/cwltool/schemas/v1.0/examples/record.cwl similarity index 100% rename from cwltool/schemas/draft-4/examples/record.cwl rename to cwltool/schemas/v1.0/examples/record.cwl diff --git a/cwltool/schemas/draft-4/examples/stdout.cwl b/cwltool/schemas/v1.0/examples/stdout.cwl similarity index 100% rename from cwltool/schemas/draft-4/examples/stdout.cwl rename to cwltool/schemas/v1.0/examples/stdout.cwl diff --git a/cwltool/schemas/draft-4/examples/tar-job.yml b/cwltool/schemas/v1.0/examples/tar-job.yml similarity index 100% rename from cwltool/schemas/draft-4/examples/tar-job.yml rename to cwltool/schemas/v1.0/examples/tar-job.yml diff --git a/cwltool/schemas/draft-4/examples/tar-param-job.yml b/cwltool/schemas/v1.0/examples/tar-param-job.yml similarity index 100% rename from cwltool/schemas/draft-4/examples/tar-param-job.yml rename to cwltool/schemas/v1.0/examples/tar-param-job.yml diff --git a/cwltool/schemas/draft-4/examples/tar-param.cwl b/cwltool/schemas/v1.0/examples/tar-param.cwl similarity index 100% rename from cwltool/schemas/draft-4/examples/tar-param.cwl rename to cwltool/schemas/v1.0/examples/tar-param.cwl diff --git a/cwltool/schemas/draft-4/examples/tar.cwl b/cwltool/schemas/v1.0/examples/tar.cwl similarity index 100% rename from cwltool/schemas/draft-4/examples/tar.cwl rename to cwltool/schemas/v1.0/examples/tar.cwl diff --git a/cwltool/schemas/draft-4/intro.md b/cwltool/schemas/v1.0/intro.md similarity index 100% rename from cwltool/schemas/draft-4/intro.md rename to cwltool/schemas/v1.0/intro.md diff --git a/cwltool/schemas/draft-4/invocation.md b/cwltool/schemas/v1.0/invocation.md similarity index 97% rename from cwltool/schemas/draft-4/invocation.md rename to cwltool/schemas/v1.0/invocation.md index 1d1791a38..c92e0201d 100644 --- a/cwltool/schemas/draft-4/invocation.md +++ b/cwltool/schemas/v1.0/invocation.md @@ -109,7 +109,7 @@ not perform computation on the contents. * `runtime.outdir`: an absolute path to the designated output directory * `runtime.tmpdir`: an absolute path to the designated temporary directory * `runtime.cores`: number of CPU cores reserved for the tool process - * `runtime.ram`: amount of RAM in mebibytes (2**20) reserved for the tool process + * `runtime.ram`: amount of RAM in mebibytes (2\*\*20) reserved for the tool process * `runtime.outdirSize`: reserved storage space available in the designated output directory * `runtime.tmpdirSize`: reserved storage space available in the designated temporary directory @@ -125,8 +125,8 @@ Once the command line is built and the runtime environment is created, the actual tool is executed. The standard error stream and standard output stream (unless redirected by -setting `stdout`) may be captured by platform logging facilities for -storage and reporting. +setting `stdout` or `stderr`) may be captured by platform logging facilities +for storage and reporting. Tools may be multithreaded or spawn child processes; however, when the parent process exits, the tool is considered finished regardless of whether diff --git a/cwltool/schemas/draft-4/salad/.gitignore b/cwltool/schemas/v1.0/salad/.gitignore similarity index 100% rename from cwltool/schemas/draft-4/salad/.gitignore rename to cwltool/schemas/v1.0/salad/.gitignore diff --git a/cwltool/schemas/draft-4/salad/.travis.yml b/cwltool/schemas/v1.0/salad/.travis.yml similarity index 100% rename from cwltool/schemas/draft-4/salad/.travis.yml rename to cwltool/schemas/v1.0/salad/.travis.yml diff --git a/cwltool/schemas/draft-4/salad/LICENSE.txt b/cwltool/schemas/v1.0/salad/LICENSE.txt similarity index 100% rename from cwltool/schemas/draft-4/salad/LICENSE.txt rename to cwltool/schemas/v1.0/salad/LICENSE.txt diff --git a/cwltool/schemas/draft-4/salad/MANIFEST.in b/cwltool/schemas/v1.0/salad/MANIFEST.in similarity index 100% rename from cwltool/schemas/draft-4/salad/MANIFEST.in rename to cwltool/schemas/v1.0/salad/MANIFEST.in diff --git a/cwltool/schemas/draft-4/salad/Makefile b/cwltool/schemas/v1.0/salad/Makefile similarity index 100% rename from cwltool/schemas/draft-4/salad/Makefile rename to cwltool/schemas/v1.0/salad/Makefile diff --git a/cwltool/schemas/draft-4/salad/README.rst b/cwltool/schemas/v1.0/salad/README.rst similarity index 100% rename from cwltool/schemas/draft-4/salad/README.rst rename to cwltool/schemas/v1.0/salad/README.rst diff --git a/cwltool/schemas/draft-4/salad/ez_setup.py b/cwltool/schemas/v1.0/salad/ez_setup.py similarity index 100% rename from cwltool/schemas/draft-4/salad/ez_setup.py rename to cwltool/schemas/v1.0/salad/ez_setup.py diff --git a/cwltool/schemas/draft-4/salad/gittaggers.py b/cwltool/schemas/v1.0/salad/gittaggers.py similarity index 100% rename from cwltool/schemas/draft-4/salad/gittaggers.py rename to cwltool/schemas/v1.0/salad/gittaggers.py diff --git a/cwltool/schemas/draft-4/salad/requirements.txt b/cwltool/schemas/v1.0/salad/requirements.txt similarity index 100% rename from cwltool/schemas/draft-4/salad/requirements.txt rename to cwltool/schemas/v1.0/salad/requirements.txt diff --git a/cwltool/schemas/draft-4/salad/schema_salad/__init__.py b/cwltool/schemas/v1.0/salad/schema_salad/__init__.py similarity index 100% rename from cwltool/schemas/draft-4/salad/schema_salad/__init__.py rename to cwltool/schemas/v1.0/salad/schema_salad/__init__.py diff --git a/cwltool/schemas/draft-4/salad/schema_salad/__main__.py b/cwltool/schemas/v1.0/salad/schema_salad/__main__.py similarity index 100% rename from cwltool/schemas/draft-4/salad/schema_salad/__main__.py rename to cwltool/schemas/v1.0/salad/schema_salad/__main__.py diff --git a/cwltool/schemas/draft-4/salad/schema_salad/add_dictlist.py b/cwltool/schemas/v1.0/salad/schema_salad/add_dictlist.py similarity index 100% rename from cwltool/schemas/draft-4/salad/schema_salad/add_dictlist.py rename to cwltool/schemas/v1.0/salad/schema_salad/add_dictlist.py diff --git a/cwltool/schemas/draft-4/salad/schema_salad/aslist.py b/cwltool/schemas/v1.0/salad/schema_salad/aslist.py similarity index 100% rename from cwltool/schemas/draft-4/salad/schema_salad/aslist.py rename to cwltool/schemas/v1.0/salad/schema_salad/aslist.py diff --git a/cwltool/schemas/draft-4/salad/schema_salad/flatten.py b/cwltool/schemas/v1.0/salad/schema_salad/flatten.py similarity index 100% rename from cwltool/schemas/draft-4/salad/schema_salad/flatten.py rename to cwltool/schemas/v1.0/salad/schema_salad/flatten.py diff --git a/cwltool/schemas/draft-4/salad/schema_salad/jsonld_context.py b/cwltool/schemas/v1.0/salad/schema_salad/jsonld_context.py similarity index 100% rename from cwltool/schemas/draft-4/salad/schema_salad/jsonld_context.py rename to cwltool/schemas/v1.0/salad/schema_salad/jsonld_context.py diff --git a/cwltool/schemas/draft-4/salad/schema_salad/main.py b/cwltool/schemas/v1.0/salad/schema_salad/main.py similarity index 100% rename from cwltool/schemas/draft-4/salad/schema_salad/main.py rename to cwltool/schemas/v1.0/salad/schema_salad/main.py diff --git a/cwltool/schemas/draft-4/salad/schema_salad/makedoc.py b/cwltool/schemas/v1.0/salad/schema_salad/makedoc.py similarity index 100% rename from cwltool/schemas/draft-4/salad/schema_salad/makedoc.py rename to cwltool/schemas/v1.0/salad/schema_salad/makedoc.py diff --git a/cwltool/schemas/draft-4/salad/schema_salad/metaschema/field_name.yml b/cwltool/schemas/v1.0/salad/schema_salad/metaschema/field_name.yml similarity index 100% rename from cwltool/schemas/draft-4/salad/schema_salad/metaschema/field_name.yml rename to cwltool/schemas/v1.0/salad/schema_salad/metaschema/field_name.yml diff --git a/cwltool/schemas/draft-4/salad/schema_salad/metaschema/field_name_proc.yml b/cwltool/schemas/v1.0/salad/schema_salad/metaschema/field_name_proc.yml similarity index 100% rename from cwltool/schemas/draft-4/salad/schema_salad/metaschema/field_name_proc.yml rename to cwltool/schemas/v1.0/salad/schema_salad/metaschema/field_name_proc.yml diff --git a/cwltool/schemas/draft-4/salad/schema_salad/metaschema/field_name_schema.yml b/cwltool/schemas/v1.0/salad/schema_salad/metaschema/field_name_schema.yml similarity index 100% rename from cwltool/schemas/draft-4/salad/schema_salad/metaschema/field_name_schema.yml rename to cwltool/schemas/v1.0/salad/schema_salad/metaschema/field_name_schema.yml diff --git a/cwltool/schemas/draft-4/salad/schema_salad/metaschema/field_name_src.yml b/cwltool/schemas/v1.0/salad/schema_salad/metaschema/field_name_src.yml similarity index 100% rename from cwltool/schemas/draft-4/salad/schema_salad/metaschema/field_name_src.yml rename to cwltool/schemas/v1.0/salad/schema_salad/metaschema/field_name_src.yml diff --git a/cwltool/schemas/draft-4/salad/schema_salad/metaschema/ident_res.yml b/cwltool/schemas/v1.0/salad/schema_salad/metaschema/ident_res.yml similarity index 100% rename from cwltool/schemas/draft-4/salad/schema_salad/metaschema/ident_res.yml rename to cwltool/schemas/v1.0/salad/schema_salad/metaschema/ident_res.yml diff --git a/cwltool/schemas/draft-4/salad/schema_salad/metaschema/ident_res_proc.yml b/cwltool/schemas/v1.0/salad/schema_salad/metaschema/ident_res_proc.yml similarity index 100% rename from cwltool/schemas/draft-4/salad/schema_salad/metaschema/ident_res_proc.yml rename to cwltool/schemas/v1.0/salad/schema_salad/metaschema/ident_res_proc.yml diff --git a/cwltool/schemas/draft-4/salad/schema_salad/metaschema/ident_res_schema.yml b/cwltool/schemas/v1.0/salad/schema_salad/metaschema/ident_res_schema.yml similarity index 100% rename from cwltool/schemas/draft-4/salad/schema_salad/metaschema/ident_res_schema.yml rename to cwltool/schemas/v1.0/salad/schema_salad/metaschema/ident_res_schema.yml diff --git a/cwltool/schemas/draft-4/salad/schema_salad/metaschema/ident_res_src.yml b/cwltool/schemas/v1.0/salad/schema_salad/metaschema/ident_res_src.yml similarity index 100% rename from cwltool/schemas/draft-4/salad/schema_salad/metaschema/ident_res_src.yml rename to cwltool/schemas/v1.0/salad/schema_salad/metaschema/ident_res_src.yml diff --git a/cwltool/schemas/draft-4/salad/schema_salad/metaschema/import_include.md b/cwltool/schemas/v1.0/salad/schema_salad/metaschema/import_include.md similarity index 100% rename from cwltool/schemas/draft-4/salad/schema_salad/metaschema/import_include.md rename to cwltool/schemas/v1.0/salad/schema_salad/metaschema/import_include.md diff --git a/cwltool/schemas/draft-4/salad/schema_salad/metaschema/link_res.yml b/cwltool/schemas/v1.0/salad/schema_salad/metaschema/link_res.yml similarity index 100% rename from cwltool/schemas/draft-4/salad/schema_salad/metaschema/link_res.yml rename to cwltool/schemas/v1.0/salad/schema_salad/metaschema/link_res.yml diff 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a/cwltool/schemas/draft-4/salad/typeshed/2.7/requests/packages/urllib3/packages/ssl_match_hostname/_implementation.pyi b/cwltool/schemas/v1.0/salad/typeshed/2.7/requests/packages/urllib3/packages/ssl_match_hostname/_implementation.pyi similarity index 100% rename from cwltool/schemas/draft-4/salad/typeshed/2.7/requests/packages/urllib3/packages/ssl_match_hostname/_implementation.pyi rename to cwltool/schemas/v1.0/salad/typeshed/2.7/requests/packages/urllib3/packages/ssl_match_hostname/_implementation.pyi diff --git a/cwltool/schemas/draft-4/salad/typeshed/2.7/requests/packages/urllib3/poolmanager.pyi b/cwltool/schemas/v1.0/salad/typeshed/2.7/requests/packages/urllib3/poolmanager.pyi similarity index 100% rename from cwltool/schemas/draft-4/salad/typeshed/2.7/requests/packages/urllib3/poolmanager.pyi rename to cwltool/schemas/v1.0/salad/typeshed/2.7/requests/packages/urllib3/poolmanager.pyi diff --git a/cwltool/schemas/draft-4/salad/typeshed/2.7/requests/packages/urllib3/request.pyi 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to cwltool/schemas/v1.0/salad/typeshed/2.7/requests/packages/urllib3/util/timeout.pyi diff --git a/cwltool/schemas/draft-4/salad/typeshed/2.7/requests/packages/urllib3/util/url.pyi b/cwltool/schemas/v1.0/salad/typeshed/2.7/requests/packages/urllib3/util/url.pyi similarity index 100% rename from cwltool/schemas/draft-4/salad/typeshed/2.7/requests/packages/urllib3/util/url.pyi rename to cwltool/schemas/v1.0/salad/typeshed/2.7/requests/packages/urllib3/util/url.pyi diff --git a/cwltool/schemas/draft-4/salad/typeshed/2.7/requests/sessions.pyi b/cwltool/schemas/v1.0/salad/typeshed/2.7/requests/sessions.pyi similarity index 100% rename from cwltool/schemas/draft-4/salad/typeshed/2.7/requests/sessions.pyi rename to cwltool/schemas/v1.0/salad/typeshed/2.7/requests/sessions.pyi diff --git a/cwltool/schemas/draft-4/salad/typeshed/2.7/requests/status_codes.pyi b/cwltool/schemas/v1.0/salad/typeshed/2.7/requests/status_codes.pyi similarity index 100% rename from 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rename to cwltool/schemas/v1.0/salad/typeshed/2.7/ruamel/__init__.py diff --git a/cwltool/schemas/draft-4/salad/typeshed/2.7/ruamel/yaml/__init__.pyi b/cwltool/schemas/v1.0/salad/typeshed/2.7/ruamel/yaml/__init__.pyi similarity index 100% rename from cwltool/schemas/draft-4/salad/typeshed/2.7/ruamel/yaml/__init__.pyi rename to cwltool/schemas/v1.0/salad/typeshed/2.7/ruamel/yaml/__init__.pyi diff --git a/cwltool/schemas/draft-4/salad/typeshed/2.7/ruamel/yaml/cyaml.pyi b/cwltool/schemas/v1.0/salad/typeshed/2.7/ruamel/yaml/cyaml.pyi similarity index 100% rename from cwltool/schemas/draft-4/salad/typeshed/2.7/ruamel/yaml/cyaml.pyi rename to cwltool/schemas/v1.0/salad/typeshed/2.7/ruamel/yaml/cyaml.pyi diff --git a/cwltool/schemas/draft-4/salad/typeshed/2.7/ruamel/yaml/error.pyi b/cwltool/schemas/v1.0/salad/typeshed/2.7/ruamel/yaml/error.pyi similarity index 100% rename from cwltool/schemas/draft-4/salad/typeshed/2.7/ruamel/yaml/error.pyi rename to 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cwltool/schemas/v1.0/salad/typeshed/2.7/ruamel/yaml/parser.pyi diff --git a/cwltool/schemas/draft-4/salad/typeshed/2.7/urlparse.pyi b/cwltool/schemas/v1.0/salad/typeshed/2.7/urlparse.pyi similarity index 100% rename from cwltool/schemas/draft-4/salad/typeshed/2.7/urlparse.pyi rename to cwltool/schemas/v1.0/salad/typeshed/2.7/urlparse.pyi diff --git a/cwltool/schemas/draft-4/userguide-intro.md b/cwltool/schemas/v1.0/userguide-intro.md similarity index 100% rename from cwltool/schemas/draft-4/userguide-intro.md rename to cwltool/schemas/v1.0/userguide-intro.md diff --git a/cwltool/update.py b/cwltool/update.py index dd0dc4090..2943ef68b 100644 --- a/cwltool/update.py +++ b/cwltool/update.py @@ -428,7 +428,7 @@ def draft4Dev2toDev3(doc, loader, baseuri): ALLUPDATES = UPDATES.copy() ALLUPDATES.update(DEVUPDATES) -LATEST = "draft-4.dev3" +LATEST = "v1.0.dev4" def identity(doc, loader, baseuri): # pylint: disable=unused-argument # type: (Any, Loader, str) -> Tuple[Any, Union[str, unicode]] diff --git a/setup.py b/setup.py index dfc73756e..035afac30 100755 --- a/setup.py +++ b/setup.py @@ -31,17 +31,17 @@ 'schemas/draft-3/*.md', 'schemas/draft-3/salad/schema_salad/metaschema/*.yml', 'schemas/draft-3/salad/schema_salad/metaschema/*.md', - 'schemas/draft-4/*.yml', - 'schemas/draft-4/*.md', - 'schemas/draft-4/salad/schema_salad/metaschema/*.yml', - 'schemas/draft-4/salad/schema_salad/metaschema/*.md']}, + 'schemas/v1.0/*.yml', + 'schemas/v1.0/*.md', + 'schemas/v1.0/salad/schema_salad/metaschema/*.yml', + 'schemas/v1.0/salad/schema_salad/metaschema/*.md']}, install_requires=[ 'requests', 'ruamel.yaml', 'rdflib >= 4.1.0', 'rdflib-jsonld >= 0.3.0', 'shellescape', - 'schema-salad==1.13.20160630144631', + 'schema-salad==1.13.20160702001514', 'typing' ], test_suite='tests',