convert_annotations.cwl

#!/usr/bin/env cwl-runner
#
# Convert annotated notes to annotation store annotations
#
cwlVersion: v1.0
class: CommandLineTool
baseCommand: python

hints:
  DockerRequirement:
    dockerPull: python:3.7

inputs:

  - id: annotation_json
    type: File
  - id: annotator_type
    type: string

arguments:
  - valueFrom: convert_annotations.py
  - valueFrom: $(inputs.annotation_json)
    prefix: -j
  - valueFrom: results.json
    prefix: -r
  - valueFrom: $(inputs.annotator_type)
    prefix: -a

requirements:
  - class: InlineJavascriptRequirement
  - class: InitialWorkDirRequirement
    listing:
      - entryname: convert_annotations.py
        entry: |
          #!/usr/bin/env python
          import argparse
          import json
          import os

          parser = argparse.ArgumentParser()
          parser.add_argument("-j", "--annotation_json", required=True, help="Annotation json file")
          parser.add_argument("-r", "--results", required=True, help="Results file")
          parser.add_argument("-a", "--annotator_type", required=True, help="Annotator type")
          args = parser.parse_args()

          with open(args.annotation_json, "r") as annote_f:
              annotations = json.load(annote_f)

          if args.annotator_type == "nlpsandbox:date-annotator":
            annotation_key = "date_annotations"
            post_path = "textDateAnnotations"
          elif args.annotator_type == "nlpsandbox:person-name-annotator":
            annotation_key = "person_name_annotations"
            post_path = "textPersonNameAnnotations"
          elif args.annotator_type == "nlpsandbox:location-annotator":
            annotation_key = "physical_location_annotations"
            post_path = "textLocationAnnotations"
          elif args.annotator_type == "nlpsandbox:id-annotator":
            annotation_key = "id_annotations"
            post_path = "textIdAnnotations"
          elif args.annotator_type == "nlpsandbox:contact-annotator":
            annotation_key = "contact_annotations"
            post_path = "textContactAnnotations"
          elif args.annotator_type == "nlpsandbox:covid-symptom-annotator":
            annotation_key = "covid_symptom_annotations"
            post_path = "textCovidSymptomAnnotations"

          all_annotations = []
          for annotation in annotations:
              # print(annotation)
              noteid = annotation['annotationSource']['resourceSource']['name']
              for annots in annotation[post_path]:
                  annots['noteId'] = os.path.basename(noteid)
                  all_annotations.append(annots)

          new_annotations = {annotation_key: all_annotations}
          # print(new_annotations)
          with open(args.results, "w") as results_f:
              json.dump(new_annotations, results_f)

     
outputs:

  - id: results
    type: File
    outputBinding:
      glob: results.json