275 lines
12 KiB
Python
275 lines
12 KiB
Python
import uuid
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from flask import g
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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.api_models import WorkflowApiSchema
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from crc.models.file import FileModel, LookupDataSchema
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from crc.models.study import StudyModel, WorkflowMetadata
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from crc.models.task_event import TaskEventModel, TaskEvent, TaskEventSchema
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from crc.models.user import UserModelSchema
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from crc.models.workflow import WorkflowModel, WorkflowSpecModelSchema, WorkflowSpecModel, WorkflowSpecCategoryModel, \
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WorkflowSpecCategoryModelSchema
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from crc.services.file_service import FileService
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from crc.services.lookup_service import LookupService
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from crc.services.study_service import StudyService
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from crc.services.user_service import UserService
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from crc.services.workflow_processor import WorkflowProcessor
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from crc.services.workflow_service import WorkflowService
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def all_specifications():
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schema = WorkflowSpecModelSchema(many=True)
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return schema.dump(session.query(WorkflowSpecModel).all())
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def add_workflow_specification(body):
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count = session.query(WorkflowSpecModel).filter_by(category_id=body['category_id']).count()
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body['display_order'] = count
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new_spec: WorkflowSpecModel = WorkflowSpecModelSchema().load(body, session=session)
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session.add(new_spec)
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session.commit()
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return WorkflowSpecModelSchema().dump(new_spec)
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def get_workflow_specification(spec_id):
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if spec_id is None:
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raise ApiError('unknown_spec', 'Please provide a valid Workflow Specification ID.')
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spec: WorkflowSpecModel = session.query(WorkflowSpecModel).filter_by(id=spec_id).first()
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if spec is None:
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raise ApiError('unknown_spec', 'The Workflow Specification "' + spec_id + '" is not recognized.')
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return WorkflowSpecModelSchema().dump(spec)
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def validate_workflow_specification(spec_id):
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errors = []
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try:
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WorkflowService.test_spec(spec_id)
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except ApiError as ae:
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ae.message = "When populating all fields ... " + ae.message
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errors.append(ae)
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try:
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# Run the validation twice, the second time, just populate the required fields.
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WorkflowService.test_spec(spec_id, required_only=True)
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except ApiError as ae:
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ae.message = "When populating only required fields ... " + ae.message
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errors.append(ae)
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return ApiErrorSchema(many=True).dump(errors)
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def update_workflow_specification(spec_id, body):
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if spec_id is None:
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raise ApiError('unknown_spec', 'Please provide a valid Workflow Spec ID.')
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spec = session.query(WorkflowSpecModel).filter_by(id=spec_id).first()
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if spec is None:
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raise ApiError('unknown_study', 'The spec "' + spec_id + '" is not recognized.')
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schema = WorkflowSpecModelSchema()
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spec = schema.load(body, session=session, instance=spec, partial=True)
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session.add(spec)
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session.commit()
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return schema.dump(spec)
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def delete_workflow_specification(spec_id):
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if spec_id is None:
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raise ApiError('unknown_spec', 'Please provide a valid Workflow Specification ID.')
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spec: WorkflowSpecModel = session.query(WorkflowSpecModel).filter_by(id=spec_id).first()
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if spec is None:
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raise ApiError('unknown_spec', 'The Workflow Specification "' + spec_id + '" is not recognized.')
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# Delete all items in the database related to the deleted workflow spec.
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files = session.query(FileModel).filter_by(workflow_spec_id=spec_id).all()
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for file in files:
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FileService.delete_file(file.id)
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session.query(TaskEventModel).filter(TaskEventModel.workflow_spec_id == spec_id).delete()
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# Delete all events and workflow models related to this specification
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for workflow in session.query(WorkflowModel).filter_by(workflow_spec_id=spec_id):
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StudyService.delete_workflow(workflow.id)
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session.query(WorkflowSpecModel).filter_by(id=spec_id).delete()
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session.commit()
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def get_workflow(workflow_id, do_engine_steps=True):
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"""Retrieve workflow based on workflow_id, and return it in the last saved State.
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If do_engine_steps is False, return the workflow without running any engine tasks or logging any events. """
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workflow_model: WorkflowModel = session.query(WorkflowModel).filter_by(id=workflow_id).first()
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processor = WorkflowProcessor(workflow_model)
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if do_engine_steps:
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processor.do_engine_steps()
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processor.save()
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WorkflowService.update_task_assignments(processor)
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workflow_api_model = WorkflowService.processor_to_workflow_api(processor)
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return WorkflowApiSchema().dump(workflow_api_model)
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def restart_workflow(workflow_id, clear_data=False):
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"""Restart a workflow with the latest spec.
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Clear data allows user to restart the workflow without previous data."""
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workflow_model: WorkflowModel = session.query(WorkflowModel).filter_by(id=workflow_id).first()
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WorkflowProcessor(workflow_model).reset(workflow_model, clear_data=clear_data)
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return get_workflow(workflow_model.id)
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def get_task_events(action = None, workflow = None, study = None):
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"""Provides a way to see a history of what has happened, or get a list of tasks that need your attention."""
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user = UserService.current_user(allow_admin_impersonate=True)
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studies = session.query(StudyModel).filter(StudyModel.user_uid==user.uid)
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studyids = [s.id for s in studies]
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query = session.query(TaskEventModel).filter((TaskEventModel.study_id.in_(studyids)) | \
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(TaskEventModel.user_uid==user.uid))
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if action:
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query = query.filter(TaskEventModel.action == action)
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if workflow:
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query = query.filter(TaskEventModel.workflow_id == workflow)
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if study:
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query = query.filter(TaskEventModel.study_id == study)
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events = query.all()
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# Turn the database records into something a little richer for the UI to use.
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task_events = []
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for event in events:
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study = session.query(StudyModel).filter(StudyModel.id == event.study_id).first()
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workflow = session.query(WorkflowModel).filter(WorkflowModel.id == event.workflow_id).first()
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workflow_meta = WorkflowMetadata.from_workflow(workflow)
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task_events.append(TaskEvent(event, study, workflow_meta))
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return TaskEventSchema(many=True).dump(task_events)
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def delete_workflow(workflow_id):
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StudyService.delete_workflow(workflow_id)
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def set_current_task(workflow_id, task_id):
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workflow_model = session.query(WorkflowModel).filter_by(id=workflow_id).first()
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processor = WorkflowProcessor(workflow_model)
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task_id = uuid.UUID(task_id)
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spiff_task = processor.bpmn_workflow.get_task(task_id)
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_verify_user_and_role(processor, spiff_task)
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user_uid = UserService.current_user(allow_admin_impersonate=True).uid
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if spiff_task.state != spiff_task.COMPLETED and spiff_task.state != spiff_task.READY:
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raise ApiError("invalid_state", "You may not move the token to a task who's state is not "
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"currently set to COMPLETE or READY.")
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# If we have an interrupt task, run it.
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processor.cancel_notify()
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# Only reset the token if the task doesn't already have it.
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if spiff_task.state == spiff_task.COMPLETED:
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spiff_task.reset_token(reset_data=True) # Don't try to copy the existing data back into this task.
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processor.save()
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WorkflowService.log_task_action(user_uid, processor, spiff_task, WorkflowService.TASK_ACTION_TOKEN_RESET)
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WorkflowService.update_task_assignments(processor)
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workflow_api_model = WorkflowService.processor_to_workflow_api(processor, spiff_task)
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return WorkflowApiSchema().dump(workflow_api_model)
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def update_task(workflow_id, task_id, body, terminate_loop=None):
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workflow_model = session.query(WorkflowModel).filter_by(id=workflow_id).first()
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if workflow_model is None:
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raise ApiError("invalid_workflow_id", "The given workflow id is not valid.", status_code=404)
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elif workflow_model.study is None:
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raise ApiError("invalid_study", "There is no study associated with the given workflow.", status_code=404)
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processor = WorkflowProcessor(workflow_model)
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task_id = uuid.UUID(task_id)
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spiff_task = processor.bpmn_workflow.get_task(task_id)
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_verify_user_and_role(processor, spiff_task)
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if not spiff_task:
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raise ApiError("empty_task", "Processor failed to obtain task.", status_code=404)
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if spiff_task.state != spiff_task.READY:
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raise ApiError("invalid_state", "You may not update a task unless it is in the READY state. "
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"Consider calling a token reset to make this task Ready.")
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if terminate_loop:
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spiff_task.terminate_loop()
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spiff_task.update_data(body)
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processor.complete_task(spiff_task)
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processor.do_engine_steps()
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processor.save()
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# Log the action, and any pending task assignments in the event of lanes in the workflow.
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user = UserService.current_user(allow_admin_impersonate=False) # Always log as the real user.
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WorkflowService.log_task_action(user.uid, processor, spiff_task, WorkflowService.TASK_ACTION_COMPLETE)
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WorkflowService.update_task_assignments(processor)
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workflow_api_model = WorkflowService.processor_to_workflow_api(processor)
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return WorkflowApiSchema().dump(workflow_api_model)
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def list_workflow_spec_categories():
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schema = WorkflowSpecCategoryModelSchema(many=True)
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return schema.dump(session.query(WorkflowSpecCategoryModel).all())
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def get_workflow_spec_category(cat_id):
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schema = WorkflowSpecCategoryModelSchema()
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return schema.dump(session.query(WorkflowSpecCategoryModel).filter_by(id=cat_id).first())
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def add_workflow_spec_category(body):
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schema = WorkflowSpecCategoryModelSchema()
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new_cat: WorkflowSpecCategoryModel = schema.load(body, session=session)
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session.add(new_cat)
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session.commit()
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return schema.dump(new_cat)
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def update_workflow_spec_category(cat_id, body):
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if cat_id is None:
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raise ApiError('unknown_category', 'Please provide a valid Workflow Spec Category ID.')
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category = session.query(WorkflowSpecCategoryModel).filter_by(id=cat_id).first()
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if category is None:
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raise ApiError('unknown_category', 'The category "' + cat_id + '" is not recognized.')
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schema = WorkflowSpecCategoryModelSchema()
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category = schema.load(body, session=session, instance=category, partial=True)
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session.add(category)
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session.commit()
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return schema.dump(category)
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def delete_workflow_spec_category(cat_id):
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session.query(WorkflowSpecCategoryModel).filter_by(id=cat_id).delete()
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session.commit()
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def lookup(workflow_id, field_id, query=None, value=None, limit=10):
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"""
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given a field in a task, attempts to find the lookup table or function associated
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with that field and runs a full-text query against it to locate the values and
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labels that would be returned to a type-ahead box.
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Tries to be fast, but first runs will be very slow.
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"""
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workflow = session.query(WorkflowModel).filter(WorkflowModel.id == workflow_id).first()
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lookup_data = LookupService.lookup(workflow, field_id, query, value, limit)
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return LookupDataSchema(many=True).dump(lookup_data)
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def _verify_user_and_role(processor, spiff_task):
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"""Assures the currently logged in user can access the given workflow and task, or
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raises an error. """
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user = UserService.current_user(allow_admin_impersonate=True)
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allowed_users = WorkflowService.get_users_assigned_to_task(processor, spiff_task)
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if user.uid not in allowed_users:
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raise ApiError.from_task("permission_denied",
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f"This task must be completed by '{allowed_users}', "
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f"but you are {user.uid}", spiff_task)
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