164 lines
7.4 KiB
Python
164 lines
7.4 KiB
Python
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from typing import List
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from SpiffWorkflow import WorkflowException
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from crc import db, session
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from crc.api.common import ApiError
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from crc.models.protocol_builder import ProtocolBuilderStudy, ProtocolBuilderStatus
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from crc.models.study import StudyModel, Study, Category, WorkflowMetadata
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from crc.models.workflow import WorkflowSpecCategoryModel, WorkflowModel, WorkflowSpecModel, WorkflowState, \
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WorkflowStatus
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from crc.services.protocol_builder import ProtocolBuilderService
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from crc.services.workflow_processor import WorkflowProcessor
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class StudyService(object):
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"""Provides common tools for working with a Study"""
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@staticmethod
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def get_studies_for_user(user):
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"""Returns a list of all studies for the given user."""
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db_studies = session.query(StudyModel).filter_by(user_uid=user.uid).all()
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studies = []
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for study_model in db_studies:
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studies.append(StudyService.get_study(study_model.id, study_model))
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return studies
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@staticmethod
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def get_study(study_id, study_model: StudyModel = None):
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"""Returns a study model that contains all the workflows organized by category.
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IMPORTANT: This is intended to be a lightweight call, it should never involve
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loading up and executing all the workflows in a study to calculate information."""
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if not study_model:
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study_model = session.query(StudyModel).filter_by(id=study_id).first()
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study = Study.from_model(study_model)
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study.categories = StudyService.get_categories()
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workflow_metas = StudyService.__get_workflow_metas(study_id)
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status = StudyService.__get_study_status(study_model)
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study.warnings = StudyService.__update_status_of_workflow_meta(workflow_metas, status)
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# Group the workflows into their categories.
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for category in study.categories:
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category.workflows = {w for w in workflow_metas if w.category_id == category.id}
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return study
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@staticmethod
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def delete_study(study_id):
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session.query(WorkflowModel).filter_by(study_id=study_id).delete()
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session.query(StudyModel).filter_by(id=study_id).delete()
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@staticmethod
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def get_categories():
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"""Returns a list of category objects, in the correct order."""
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cat_models = db.session.query(WorkflowSpecCategoryModel) \
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.order_by(WorkflowSpecCategoryModel.display_order).all()
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categories = []
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for cat_model in cat_models:
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categories.append(Category(cat_model))
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return categories
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@staticmethod
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def synch_all_studies_with_protocol_builder(user):
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"""Assures that the studies we have locally for the given user are
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in sync with the studies available in protocol builder. """
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# Get studies matching this user from Protocol Builder
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pb_studies: List[ProtocolBuilderStudy] = ProtocolBuilderService.get_studies(user.uid)
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# Get studies from the database
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db_studies = session.query(StudyModel).filter_by(user_uid=user.uid).all()
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# Update all studies from the protocol builder, create new studies as needed.
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# Futher assures that every active study (that does exist in the protocol builder)
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# has a reference to every available workflow (though some may not have started yet)
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for pb_study in pb_studies:
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db_study = next((s for s in db_studies if s.id == pb_study.STUDYID), None)
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if not db_study:
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db_study = StudyModel(id=pb_study.STUDYID)
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session.add(db_study)
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db_studies.append(db_study)
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db_study.update_from_protocol_builder(pb_study)
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StudyService._add_all_workflow_specs_to_study(db_study)
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# Mark studies as inactive that are no longer in Protocol Builder
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for study in db_studies:
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pb_study = next((pbs for pbs in pb_studies if pbs.STUDYID == study.id), None)
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if not pb_study:
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study.inactive = True
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study.protocol_builder_status = ProtocolBuilderStatus.INACTIVE
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db.session.commit()
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@staticmethod
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def __update_status_of_workflow_meta(workflow_metas, status):
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# Update the status on each workflow
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warnings = []
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for wfm in workflow_metas:
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if wfm.name in status.keys():
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if not WorkflowState.has_value(status[wfm.name]):
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warnings.append(ApiError("invalid_status",
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"Workflow '%s' can not be set to '%s', should be one of %s" % (
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wfm.name, status[wfm.name], ",".join(WorkflowState.list())
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)))
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else:
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wfm.state = WorkflowState[status[wfm.name]]
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else:
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warnings.append(ApiError("missing_status", "No status specified for workflow %s" % wfm.name))
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return warnings
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@staticmethod
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def __get_workflow_metas(study_id):
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# Add in the Workflows for each category
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workflow_models = db.session.query(WorkflowModel).filter_by(study_id=study_id).all()
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workflow_metas = []
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for workflow in workflow_models:
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workflow_metas.append(WorkflowMetadata.from_workflow(workflow))
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return workflow_metas
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@staticmethod
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def __get_study_status(study_model):
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"""Uses the Top Level Workflow to calculate the status of the study, and it's
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workflow models."""
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master_specs = db.session.query(WorkflowSpecModel). \
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filter_by(is_master_spec=True).all()
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if len(master_specs) < 1:
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raise ApiError("missing_master_spec", "No specifications are currently marked as the master spec.")
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if len(master_specs) > 1:
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raise ApiError("multiple_master_specs",
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"There is more than one master specification, and I don't know what to do.")
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master_spec = master_specs[0]
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master_workflow = StudyService._create_workflow_model(study_model, master_spec)
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processor = WorkflowProcessor(master_workflow)
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processor.do_engine_steps()
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if not processor.bpmn_workflow.is_completed():
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raise ApiError("master_spec_not_automatic",
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"The master spec should only contain fully automated tasks, it failed to complete.")
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return processor.bpmn_workflow.last_task.data
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@staticmethod
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def _add_all_workflow_specs_to_study(study):
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existing_models = session.query(WorkflowModel).filter(WorkflowModel.study_id == study.id).all()
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existing_specs = list(m.workflow_spec_id for m in existing_models)
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new_specs = session.query(WorkflowSpecModel). \
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filter(WorkflowSpecModel.is_master_spec == False). \
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filter(WorkflowSpecModel.id.notin_(existing_specs)). \
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all()
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errors = []
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for workflow_spec in new_specs:
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try:
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StudyService._create_workflow_model(study, workflow_spec)
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except WorkflowException as we:
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errors.append(ApiError.from_task_spec("workflow_execution_exception", str(we), we.sender))
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return errors
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@staticmethod
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def _create_workflow_model(study, spec):
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workflow_model = WorkflowModel(status=WorkflowStatus.not_started,
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study_id=study.id,
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workflow_spec_id=spec.id)
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session.add(workflow_model)
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session.commit()
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return workflow_model
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