515 lines
25 KiB
Python
Executable File
515 lines
25 KiB
Python
Executable File
import urllib
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from copy import copy
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from datetime import datetime
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from typing import List
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import flask
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import requests
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from SpiffWorkflow import WorkflowException
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from SpiffWorkflow.bpmn.PythonScriptEngine import Box
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from SpiffWorkflow.exceptions import WorkflowTaskExecException
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from ldap3.core.exceptions import LDAPSocketOpenError
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from crc import db, session, app
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from crc.api.common import ApiError
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from crc.models.data_store import DataStoreModel
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from crc.models.email import EmailModel
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from crc.models.file import FileModel, File, FileSchema
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from crc.models.ldap import LdapSchema
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from crc.models.protocol_builder import ProtocolBuilderStudy, ProtocolBuilderStatus
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from crc.models.study import StudyModel, Study, StudyStatus, Category, WorkflowMetadata, StudyEventType, StudyEvent, \
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IrbStatus, StudyAssociated, StudyAssociatedSchema
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from crc.models.task_event import TaskEventModel, TaskEvent
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from crc.models.workflow import WorkflowSpecCategoryModel, WorkflowModel, WorkflowSpecModel, WorkflowState, \
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WorkflowStatus, WorkflowSpecDependencyFile
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from crc.services.document_service import DocumentService
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from crc.services.file_service import FileService
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from crc.services.ldap_service import LdapService
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from crc.services.lookup_service import LookupService
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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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INVESTIGATOR_LIST = "investigators.xlsx" # A reference document containing details about what investigators to show, and when.
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@staticmethod
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def _is_valid_study(study_id):
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study_info = ProtocolBuilderService().get_study_details(study_id)
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if 'REVIEW_TYPE' in study_info.keys() and study_info['REVIEW_TYPE'] in [2, 3, 23, 24]:
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return True
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return False
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def get_studies_for_user(self, user, include_invalid=False):
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"""Returns a list of all studies for the given user."""
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associated = session.query(StudyAssociated).filter_by(uid=user.uid, access=True).all()
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associated_studies = [x.study_id for x in associated]
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db_studies = session.query(StudyModel).filter((StudyModel.user_uid == user.uid) |
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(StudyModel.id.in_(associated_studies))).all()
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studies = []
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for study_model in db_studies:
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if include_invalid or self._is_valid_study(study_model.id):
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studies.append(StudyService.get_study(study_model.id, study_model, do_status=False))
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return studies
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@staticmethod
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def get_all_studies_with_files():
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"""Returns a list of all studies"""
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db_studies = session.query(StudyModel).all()
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studies = []
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for s in db_studies:
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study = Study.from_model(s)
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study.files = FileService.get_files_for_study(study.id)
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studies.append(study)
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return studies
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@staticmethod
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def get_study(study_id, study_model: StudyModel = None, do_status=False):
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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.create_user_display = LdapService.user_info(study.user_uid).display_name
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last_event: TaskEventModel = session.query(TaskEventModel) \
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.filter_by(study_id=study_id, action='COMPLETE') \
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.order_by(TaskEventModel.date.desc()).first()
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if last_event is None:
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study.last_activity_user = 'Not Started'
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study.last_activity_date = ""
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else:
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study.last_activity_user = LdapService.user_info(last_event.user_uid).display_name
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study.last_activity_date = last_event.date
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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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files = FileService.get_files_for_study(study.id)
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files = (File.from_models(model, FileService.get_file_data(model.id),
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DocumentService.get_dictionary()) for model in files)
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study.files = list(files)
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# Calling this line repeatedly is very very slow. It creates the
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# master spec and runs it. Don't execute this for Abandoned studies, as
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# we don't have the information to process them.
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if study.status != StudyStatus.abandoned:
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# this line is taking 99% of the time that is used in get_study.
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# see ticket #196
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if do_status:
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# __get_study_status() runs the master workflow to generate the status dictionary
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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 get_study_associate(study_id=None, uid=None):
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"""
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gets details on how one uid is related to a study, returns a StudyAssociated model
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"""
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study = db.session.query(StudyModel).filter(StudyModel.id == study_id).first()
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if study is None:
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raise ApiError('study_not_found', 'No study found with id = %d' % study_id)
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if uid is None:
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raise ApiError('uid not specified', 'A valid uva uid is required for this function')
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if uid == study.user_uid:
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return StudyAssociated(uid=uid, role='owner', send_email=True, access=True)
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people = db.session.query(StudyAssociated).filter((StudyAssociated.study_id == study_id) &
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(StudyAssociated.uid == uid)).first()
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if people:
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return people
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else:
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raise ApiError('uid_not_associated_with_study', "user id %s was not associated with study number %d" % (uid,
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study_id))
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@staticmethod
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def get_study_associates(study_id):
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"""
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gets all associated people for a study from the database
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"""
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study = db.session.query(StudyModel).filter(StudyModel.id == study_id).first()
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if study is None:
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raise ApiError('study_not_found', 'No study found with id = %d' % study_id)
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people = db.session.query(StudyAssociated).filter(StudyAssociated.study_id == study_id).all()
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ldap_info = LdapService.user_info(study.user_uid)
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owner = StudyAssociated(uid=study.user_uid, role='owner', send_email=True, access=True,
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ldap_info=ldap_info)
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people.append(owner)
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return people
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@staticmethod
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def update_study_associates(study_id, associates):
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"""
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updates the list of associates in the database for a study_id and a list
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of dicts that contains associates
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"""
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if study_id is None:
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raise ApiError('study_id not specified', "This function requires the study_id parameter")
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for person in associates:
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if not LdapService.user_exists(person.get('uid', 'impossible_uid')):
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if person.get('uid', 'impossible_uid') == 'impossible_uid':
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raise ApiError('associate with no uid', 'One of the associates passed as a parameter doesnt have '
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'a uid specified')
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raise ApiError('trying_to_grant_access_to_user_not_found_in_ldap', "You are trying to grant access to "
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"%s, but that user was not found in "
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"ldap "
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"- please check to ensure it is a "
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"valid uva uid" % person.get('uid'))
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study = db.session.query(StudyModel).filter(StudyModel.id == study_id).first()
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if study is None:
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raise ApiError('study_id not found', "A study with id# %d was not found" % study_id)
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db.session.query(StudyAssociated).filter(StudyAssociated.study_id == study_id).delete()
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for person in associates:
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newAssociate = StudyAssociated()
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newAssociate.study_id = study_id
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newAssociate.uid = person['uid']
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newAssociate.role = person.get('role', None)
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newAssociate.send_email = person.get('send_email', False)
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newAssociate.access = person.get('access', False)
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session.add(newAssociate)
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session.commit()
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@staticmethod
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def update_study_associate(study_id=None, uid=None, role="", send_email=False, access=False):
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if study_id is None:
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raise ApiError('study_id not specified', "This function requires the study_id parameter")
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if uid is None:
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raise ApiError('uid not specified', "This function requires a uva uid parameter")
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if not LdapService.user_exists(uid):
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raise ApiError('trying_to_grant_access_to_user_not_found_in_ldap', "You are trying to grant access to "
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"%s but they were not found in ldap "
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"- please check to ensure it is a "
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"valid uva uid" % uid)
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study = db.session.query(StudyModel).filter(StudyModel.id == study_id).first()
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if study is None:
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raise ApiError('study_id not found', "A study with id# %d was not found" % study_id)
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db.session.query(StudyAssociated).filter((StudyAssociated.study_id == study_id) & (StudyAssociated.uid ==
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uid)).delete()
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newAssociate = StudyAssociated()
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newAssociate.study_id = study_id
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newAssociate.uid = uid
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newAssociate.role = role
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newAssociate.send_email = send_email
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newAssociate.access = access
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session.add(newAssociate)
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session.commit()
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return True
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@staticmethod
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def delete_study(study_id):
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session.query(TaskEventModel).filter_by(study_id=study_id).delete()
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session.query(StudyAssociated).filter_by(study_id=study_id).delete()
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session.query(EmailModel).filter_by(study_id=study_id).delete()
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session.query(StudyEvent).filter_by(study_id=study_id).delete()
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for workflow in session.query(WorkflowModel).filter_by(study_id=study_id):
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StudyService.delete_workflow(workflow.id)
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study = session.query(StudyModel).filter_by(id=study_id).first()
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session.delete(study)
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session.commit()
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@staticmethod
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def delete_workflow(workflow_id):
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workflow = session.query(WorkflowModel).get(workflow_id)
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if not workflow:
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return
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session.query(TaskEventModel).filter_by(workflow_id=workflow.id).delete()
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session.query(WorkflowSpecDependencyFile).filter_by(workflow_id=workflow_id).delete(synchronize_session='fetch')
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session.query(FileModel).filter_by(workflow_id=workflow_id).update({'archived': True, 'workflow_id': None})
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session.delete(workflow)
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session.commit()
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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 get_documents_status(study_id):
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"""Returns a list of documents related to the study, and any file information
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that is available.."""
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# Get PB required docs, if Protocol Builder Service is enabled.
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if ProtocolBuilderService.is_enabled() and study_id is not None:
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try:
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pb_docs = ProtocolBuilderService.get_required_docs(study_id=study_id)
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except requests.exceptions.ConnectionError as ce:
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app.logger.error(f'Failed to connect to the Protocol Builder - {str(ce)}', exc_info=True)
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pb_docs = []
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else:
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pb_docs = []
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# Loop through all known document types, get the counts for those files,
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# and use pb_docs to mark those as required.
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doc_dictionary = DocumentService.get_dictionary()
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documents = {}
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for code, doc in doc_dictionary.items():
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doc['required'] = False
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if ProtocolBuilderService.is_enabled() and doc['id']:
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pb_data = next((item for item in pb_docs if int(item['AUXDOCID']) == int(doc['id'])), None)
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if pb_data:
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doc['required'] = True
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doc['study_id'] = study_id
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doc['code'] = code
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# Make a display name out of categories
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name_list = []
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for cat_key in ['category1', 'category2', 'category3']:
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if doc[cat_key] not in ['', 'NULL', None]:
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name_list.append(doc[cat_key])
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doc['display_name'] = ' / '.join(name_list)
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# For each file, get associated workflow status
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doc_files = FileService.get_files_for_study(study_id=study_id, irb_doc_code=code)
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doc['count'] = len(doc_files)
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doc['files'] = []
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# when we run tests - it doesn't look like the user is available
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# so we return a bogus token
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token = 'not_available'
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if hasattr(flask.g, 'user'):
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token = flask.g.user.encode_auth_token()
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for file_model in doc_files:
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file = File.from_models(file_model, FileService.get_file_data(file_model.id), [])
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file_data = FileSchema().dump(file)
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del file_data['document']
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data = db.session.query(DataStoreModel).filter(DataStoreModel.file_id == file.id).all()
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data_store_data = {}
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for d in data:
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data_store_data[d.key] = d.value
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file_data["data_store"] = data_store_data
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doc['files'].append(Box(file_data))
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# update the document status to match the status of the workflow it is in.
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if 'status' not in doc or doc['status'] is None:
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workflow: WorkflowModel = session.query(WorkflowModel).filter_by(id=file.workflow_id).first()
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doc['status'] = workflow.status.value
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documents[code] = doc
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return Box(documents)
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@staticmethod
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def get_investigator_dictionary():
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"""Returns a dictionary of document details keyed on the doc_code."""
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file_data = FileService.get_reference_file_data(StudyService.INVESTIGATOR_LIST)
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lookup_model = LookupService.get_lookup_model_for_file_data(file_data, 'code', 'label')
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doc_dict = {}
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for lookup_data in lookup_model.dependencies:
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doc_dict[lookup_data.value] = lookup_data.data
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return doc_dict
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@staticmethod
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def get_investigators(study_id, all=False):
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"""Convert array of investigators from protocol builder into a dictionary keyed on the type. """
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# Loop through all known investigator types as set in the reference file
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inv_dictionary = StudyService.get_investigator_dictionary()
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# Get PB required docs
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pb_investigators = ProtocolBuilderService.get_investigators(study_id=study_id)
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# It is possible for the same type to show up more than once in some circumstances, in those events
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# append a counter to the name.
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investigators = {}
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for i_type in inv_dictionary:
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pb_data_entries = list(item for item in pb_investigators if item['INVESTIGATORTYPE'] == i_type)
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entry_count = 0
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investigators[i_type] = copy(inv_dictionary[i_type])
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investigators[i_type]['user_id'] = None
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for pb_data in pb_data_entries:
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entry_count += 1
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if entry_count == 1:
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t = i_type
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else:
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t = i_type + "_" + str(entry_count)
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investigators[t] = copy(inv_dictionary[i_type])
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investigators[t]['user_id'] = pb_data["NETBADGEID"]
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investigators[t].update(StudyService.get_ldap_dict_if_available(pb_data["NETBADGEID"]))
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if not all:
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investigators = dict(filter(lambda elem: elem[1]['user_id'] is not None, investigators.items()))
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return investigators
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@staticmethod
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def get_ldap_dict_if_available(user_id):
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try:
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return LdapSchema().dump(LdapService().user_info(user_id))
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except ApiError as ae:
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app.logger.info(str(ae))
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return {"error": str(ae)}
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except LDAPSocketOpenError:
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app.logger.info("Failed to connect to LDAP Server.")
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return {}
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@staticmethod
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def synch_with_protocol_builder_if_enabled(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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if ProtocolBuilderService.is_enabled():
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app.logger.info("The Protocol Builder is enabled. app.config['PB_ENABLED'] = " +
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str(app.config['PB_ENABLED']))
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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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# Further 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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new_status = None
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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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db_study.status = None # Force a new sa
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new_status = StudyStatus.in_progress
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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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# If there is a new automatic status change and there isn't a manual change in place, record it.
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if new_status and db_study.status != StudyStatus.hold:
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db_study.status = new_status
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StudyService.add_study_update_event(db_study,
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status=new_status,
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event_type=StudyEventType.automatic)
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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 and study.status != StudyStatus.abandoned:
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study.status = StudyStatus.abandoned
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StudyService.add_study_update_event(study,
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status=StudyStatus.abandoned,
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event_type=StudyEventType.automatic)
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db.session.commit()
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@staticmethod
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def add_study_update_event(study, status, event_type, user_uid=None, comment=''):
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study_event = StudyEvent(study=study,
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status=status,
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event_type=event_type,
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user_uid=user_uid,
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comment=comment)
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db.session.add(study_event)
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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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wfm.state_message = ''
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# do we have a status for you
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if wfm.workflow_spec_id not in status.keys():
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warnings.append(ApiError("missing_status", "No status specified for workflow %s" % wfm.workflow_spec_id))
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continue
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if not isinstance(status[wfm.workflow_spec_id], dict):
|
|
warnings.append(ApiError(code='invalid_status',
|
|
message=f'Status must be a dictionary with "status" and "message" keys. Name is {wfm.workflow_spec_id}. Status is {status[wfm.workflow_spec_id]}'))
|
|
continue
|
|
if 'status' not in status[wfm.workflow_spec_id].keys():
|
|
warnings.append(ApiError("missing_status",
|
|
"Workflow '%s' does not have a status setting" % wfm.workflow_spec_id))
|
|
continue
|
|
if not WorkflowState.has_value(status[wfm.workflow_spec_id]['status']):
|
|
warnings.append(ApiError("invalid_state",
|
|
"Workflow '%s' can not be set to '%s', should be one of %s" % (
|
|
wfm.workflow_spec_id, status[wfm.workflow_spec_id]['status'], ",".join(WorkflowState.list())
|
|
)))
|
|
continue
|
|
wfm.state = WorkflowState[status[wfm.workflow_spec_id]['status']]
|
|
if 'message' in status[wfm.workflow_spec_id].keys():
|
|
wfm.state_message = status[wfm.workflow_spec_id]['message']
|
|
return warnings
|
|
|
|
@staticmethod
|
|
def _get_workflow_metas(study_id):
|
|
# Add in the Workflows for each category
|
|
workflow_models = db.session.query(WorkflowModel). \
|
|
join(WorkflowSpecModel). \
|
|
filter(WorkflowSpecModel.is_master_spec == False). \
|
|
filter((WorkflowSpecModel.library == False) | \
|
|
(WorkflowSpecModel.library == None)). \
|
|
filter(WorkflowModel.study_id == study_id). \
|
|
all()
|
|
workflow_metas = []
|
|
for workflow in workflow_models:
|
|
workflow_metas.append(WorkflowMetadata.from_workflow(workflow))
|
|
return workflow_metas
|
|
|
|
@staticmethod
|
|
def _get_study_status(study_model):
|
|
"""Uses the Top Level Workflow to calculate the status of the study, and it's
|
|
workflow models."""
|
|
master_specs = db.session.query(WorkflowSpecModel). \
|
|
filter_by(is_master_spec=True).all()
|
|
if len(master_specs) < 1:
|
|
raise ApiError("missing_master_spec", "No specifications are currently marked as the master spec.")
|
|
if len(master_specs) > 1:
|
|
raise ApiError("multiple_master_specs",
|
|
"There is more than one master specification, and I don't know what to do.")
|
|
|
|
return WorkflowProcessor.run_master_spec(master_specs[0], study_model)
|
|
|
|
@staticmethod
|
|
def _add_all_workflow_specs_to_study(study_model: StudyModel):
|
|
existing_models = session.query(WorkflowModel).filter(WorkflowModel.study == study_model).all()
|
|
existing_specs = list(m.workflow_spec_id for m in existing_models)
|
|
new_specs = session.query(WorkflowSpecModel). \
|
|
filter(WorkflowSpecModel.is_master_spec == False). \
|
|
filter(WorkflowSpecModel.id.notin_(existing_specs)). \
|
|
all()
|
|
errors = []
|
|
for workflow_spec in new_specs:
|
|
try:
|
|
StudyService._create_workflow_model(study_model, workflow_spec)
|
|
except WorkflowTaskExecException as wtee:
|
|
errors.append(ApiError.from_task("workflow_startup_exception", str(wtee), wtee.task))
|
|
except WorkflowException as we:
|
|
errors.append(ApiError.from_task_spec("workflow_startup_exception", str(we), we.sender))
|
|
return errors
|
|
|
|
@staticmethod
|
|
def _create_workflow_model(study: StudyModel, spec):
|
|
workflow_model = WorkflowModel(status=WorkflowStatus.not_started,
|
|
study=study,
|
|
user_id=None,
|
|
workflow_spec_id=spec.id,
|
|
last_updated=datetime.utcnow())
|
|
session.add(workflow_model)
|
|
session.commit()
|
|
return workflow_model
|