mirror of
https://github.com/sartography/cr-connect-workflow.git
synced 2025-02-23 05:08:32 +00:00
cd7f67ab48
From an API point of view you can do the following (and only the following) /files?workflow_spec_id=x * You can find all files associated with a workflow_spec_id, and add a file with a workflow_spec_id /files?workflow_id=x * You can find all files associated with a workflow_id, and add a file that is directly associated with the workflow /files?workflow_id=x&form_field_key=y * You can find all files associated with a form element on a running workflow, and add a new file. Note: you can add multiple files to the same form_field_key, IF they have different file names. If the same name, the original file is archived, and the new file takes its place. The study endpoints always return a list of the file metadata associated with the study. Removed /studies-files, but there is an endpoint called /studies/all - that returns all the studies in the system, and does include their files. On a deeper level: The File model no longer contains: - study_id, - task_id, - form_field_key Instead, if the file is associated with workflow - then that is the one way it is connected to the study, and we use this relationship to find files for a study. A file is never associated with a task_id, as these change when the workflow is reloaded. The form_field_key must match the irb_doc_code, so when requesting files for a form field, we just look up the irb_doc_code.
81 lines
2.8 KiB
Python
81 lines
2.8 KiB
Python
from datetime import datetime
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from flask import g
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from sqlalchemy.exc import IntegrityError
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from crc import session
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from crc.api.common import ApiError, ApiErrorSchema
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from crc.models.protocol_builder import ProtocolBuilderStatus
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from crc.models.study import StudySchema, StudyModel, Study
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from crc.services.study_service import StudyService
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def add_study(body):
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"""Or any study like object. Body should include a title, and primary_investigator_id """
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if 'primary_investigator_id' not in body:
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raise ApiError("missing_pi", "Can't create a new study without a Primary Investigator.")
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if 'title' not in body:
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raise ApiError("missing_title", "Can't create a new study without a title.")
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study_model = StudyModel(user_uid=g.user.uid,
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title=body['title'],
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primary_investigator_id=body['primary_investigator_id'],
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last_updated=datetime.now(),
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protocol_builder_status=ProtocolBuilderStatus.ACTIVE)
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session.add(study_model)
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errors = StudyService._add_all_workflow_specs_to_study(study_model)
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session.commit()
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study = StudyService().get_study(study_model.id)
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study_data = StudySchema().dump(study)
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study_data["errors"] = ApiErrorSchema(many=True).dump(errors)
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return study_data
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def update_study(study_id, body):
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if study_id is None:
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raise ApiError('unknown_study', 'Please provide a valid Study ID.')
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study_model = session.query(StudyModel).filter_by(id=study_id).first()
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if study_model is None:
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raise ApiError('unknown_study', 'The study "' + study_id + '" is not recognized.')
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study: Study = StudySchema().load(body)
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study.update_model(study_model)
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session.add(study_model)
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session.commit()
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return StudySchema().dump(study)
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def get_study(study_id):
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study_service = StudyService()
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study = study_service.get_study(study_id)
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if (study is None):
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raise ApiError("Study not found", status_code=404)
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schema = StudySchema()
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return schema.dump(study)
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def delete_study(study_id):
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try:
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StudyService.delete_study(study_id)
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except IntegrityError as ie:
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session.rollback()
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message = "Failed to delete Study #%i due to an Integrity Error: %s" % (study_id, str(ie))
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raise ApiError(code="study_integrity_error", message=message)
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def user_studies():
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"""Returns all the studies associated with the current user. """
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StudyService.synch_with_protocol_builder_if_enabled(g.user)
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studies = StudyService.get_studies_for_user(g.user)
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results = StudySchema(many=True).dump(studies)
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return results
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def all_studies():
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"""Returns all studies (regardless of user) with submitted files"""
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studies = StudyService.get_all_studies_with_files()
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results = StudySchema(many=True).dump(studies)
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return results
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