Darwin Core Archive Controlled Field Assessor

This workflow:

• creates a given directory as a workspace
• downloads a Darwin Core Archive from a given URL
• downloads vocabulary lookup files from https://github.com/kurator-org/kurator-validation/tree/master/packages/kurator_dwca/data/vocabularies.
• extracts the core file of a Darwin Core Archive to a tab-separated text file
• for each field in a the list of Darwin Core Controlled Value fields (see below), creates a report of counts of distinct values
• for each field in a the list of Darwin Core Controlled Value fields (see below), creates a report of recommended values for values that are not standard.

The files produced by this workflow are:

• count_[field].csv - for each Darwin Core Controlled Value field found in the extracted file, a file containing the distinct values and the number of times they appeared in the extracted core file. See https://github.com/kurator-org/kurator-validation/wiki/Field-Value-Count-Report
• dwca.zip - the Darwin Core archive file (see https://en.wikipedia.org/wiki/Darwin_Core_Archive) downloaded from the given URL
• dwca_extracted_occurrences.txt - the core file of the downloaded Darwin Core Archive as a TXT file
• recommended_[field].csv - for each Darwin Core Controlled Value field found in the extracted file for which recommendations could be found, a file containing the recommendations to standardize values in that field. See https://github.com/kurator-org/kurator-validation/wiki/Field-Value-Recommendation-Report
• vocab_[field].txt - for each Darwin Core Controlled Value field found in the extracted file, a file containing the lookup file to use for standardizing that field. See https://github.com/kurator-org/kurator-validation/wiki/Vocabulary-File-Structure

References

Workflow configuration file: https://github.com/kurator-org/kurator-validation/blob/master/packages/kurator_dwca/workflows/dwca_controlled_term_assessor.yaml

Darwin Core Controlled Value lookup files: https://github.com/kurator-org/kurator-validation/tree/master/packages/kurator_dwca/data/vocabularies

Darwin Core Controlled Value fields (from http://rs.tdwg.org/dwc/terms/index.htm):

• basisOfRecord (http://rs.tdwg.org/dwc/terms/index.htm#basisOfRecord)
• day (http://rs.tdwg.org/dwc/terms/index.htm#day)
• disposition (http://rs.tdwg.org/dwc/terms/index.htm#disposition)
• establishmentMeans (http://rs.tdwg.org/dwc/terms/index.htm#establishmentMeans)
• geodeticDatum (http://rs.tdwg.org/dwc/terms/index.htm#geodeticDatum)
• georeferenceVerificationStatus (http://rs.tdwg.org/dwc/terms/index.htm#georeferenceVerificationStatus)
• identificationQualifier (http://rs.tdwg.org/dwc/terms/index.htm#identificationQualifier)
• identificationVerificationStatus (http://rs.tdwg.org/dwc/terms/index.htm#identificationVerificationStatus)
• language (http://rs.tdwg.org/dwc/terms/index.htm#language)
• license (http://rs.tdwg.org/dwc/terms/index.htm#license)
• lifeStage (http://rs.tdwg.org/dwc/terms/index.htm#lifeStage)
• month (http://rs.tdwg.org/dwc/terms/index.htm#month)
• nomenclaturalCode (http://rs.tdwg.org/dwc/terms/index.htm#nomenclaturalCode)
• nomenclaturalStatus (http://rs.tdwg.org/dwc/terms/index.htm#nomenclaturalStatus)
• occurrenceStatus (http://rs.tdwg.org/dwc/terms/index.htm#occurrenceStatus)
• organismScope (http://rs.tdwg.org/dwc/terms/index.htm#organismScope)
• preparations (http://rs.tdwg.org/dwc/terms/index.htm#preparations)
• reproductiveCondition (http://rs.tdwg.org/dwc/terms/index.htm#reproductiveCondition)
• sex (http://rs.tdwg.org/dwc/terms/index.htm#sex)
• typeStatus (http://rs.tdwg.org/dwc/terms/index.htm#typeStatus)
• taxonRank (http://rs.tdwg.org/dwc/terms/index.htm#taxonRank)
• taxonomicStatus (http://rs.tdwg.org/dwc/terms/index.htm#taxonomicStatus)
• type (http://rs.tdwg.org/dwc/terms/index.htm#type)