513 lines
24 KiB
Python
513 lines
24 KiB
Python
import urllib
|
|
from copy import copy
|
|
from datetime import datetime
|
|
from typing import List
|
|
|
|
import flask
|
|
import requests
|
|
from SpiffWorkflow import WorkflowException
|
|
from SpiffWorkflow.bpmn.PythonScriptEngine import Box
|
|
from SpiffWorkflow.exceptions import WorkflowTaskExecException
|
|
from ldap3.core.exceptions import LDAPSocketOpenError
|
|
|
|
from crc import db, session, app
|
|
from crc.api.common import ApiError
|
|
from crc.models.data_store import DataStoreModel
|
|
from crc.models.email import EmailModel
|
|
from crc.models.file import FileDataModel, FileModel, FileModelSchema, File, LookupFileModel, LookupDataModel
|
|
from crc.models.ldap import LdapSchema
|
|
from crc.models.protocol_builder import ProtocolBuilderStudy, ProtocolBuilderStatus
|
|
from crc.models.study import StudyModel, Study, StudyStatus, Category, WorkflowMetadata, StudyEventType, StudyEvent, \
|
|
IrbStatus, StudyAssociated
|
|
from crc.models.task_event import TaskEventModel, TaskEvent
|
|
from crc.models.workflow import WorkflowSpecCategoryModel, WorkflowModel, WorkflowSpecModel, WorkflowState, \
|
|
WorkflowStatus, WorkflowSpecDependencyFile
|
|
from crc.services.file_service import FileService
|
|
from crc.services.ldap_service import LdapService
|
|
from crc.services.protocol_builder import ProtocolBuilderService
|
|
from crc.services.workflow_processor import WorkflowProcessor
|
|
|
|
class StudyService(object):
|
|
"""Provides common tools for working with a Study"""
|
|
|
|
@staticmethod
|
|
def get_studies_for_user(user):
|
|
"""Returns a list of all studies for the given user."""
|
|
associated = session.query(StudyAssociated).filter_by(uid=user.uid,access=True).all()
|
|
associated_studies = [x.study_id for x in associated]
|
|
db_studies = session.query(StudyModel).filter((StudyModel.user_uid==user.uid)|
|
|
(StudyModel.id.in_(associated_studies))).all()
|
|
|
|
studies = []
|
|
for study_model in db_studies:
|
|
studies.append(StudyService.get_study(study_model.id, study_model,do_status=False))
|
|
return studies
|
|
|
|
@staticmethod
|
|
def get_all_studies_with_files():
|
|
"""Returns a list of all studies"""
|
|
db_studies = session.query(StudyModel).all()
|
|
studies = []
|
|
for s in db_studies:
|
|
study = Study.from_model(s)
|
|
study.files = FileService.get_files_for_study(study.id)
|
|
studies.append(study)
|
|
return studies
|
|
|
|
@staticmethod
|
|
def get_study(study_id, study_model: StudyModel = None, do_status=False):
|
|
"""Returns a study model that contains all the workflows organized by category.
|
|
IMPORTANT: This is intended to be a lightweight call, it should never involve
|
|
loading up and executing all the workflows in a study to calculate information."""
|
|
if not study_model:
|
|
study_model = session.query(StudyModel).filter_by(id=study_id).first()
|
|
|
|
study = Study.from_model(study_model)
|
|
study.create_user_display = LdapService.user_info(study.user_uid).display_name
|
|
last_event: TaskEventModel = session.query(TaskEventModel)\
|
|
.filter_by(study_id=study_id,action='COMPLETE')\
|
|
.order_by(TaskEventModel.date.desc()).first()
|
|
if last_event is None:
|
|
study.last_activity_user = 'Not Started'
|
|
study.last_activity_date = ""
|
|
else:
|
|
study.last_activity_user = LdapService.user_info(last_event.user_uid).display_name
|
|
study.last_activity_date = last_event.date
|
|
study.categories = StudyService.get_categories()
|
|
workflow_metas = StudyService._get_workflow_metas(study_id)
|
|
files = FileService.get_files_for_study(study.id)
|
|
files = (File.from_models(model, FileService.get_file_data(model.id),
|
|
FileService.get_doc_dictionary()) for model in files)
|
|
study.files = list(files)
|
|
# Calling this line repeatedly is very very slow. It creates the
|
|
# master spec and runs it. Don't execute this for Abandoned studies, as
|
|
# we don't have the information to process them.
|
|
if study.status != StudyStatus.abandoned:
|
|
# this line is taking 99% of the time that is used in get_study.
|
|
# see ticket #196
|
|
if do_status:
|
|
# __get_study_status() runs the master workflow to generate the status dictionary
|
|
status = StudyService._get_study_status(study_model)
|
|
study.warnings = StudyService._update_status_of_workflow_meta(workflow_metas, status)
|
|
|
|
# Group the workflows into their categories.
|
|
for category in study.categories:
|
|
category.workflows = {w for w in workflow_metas if w.category_id == category.id}
|
|
|
|
return study
|
|
|
|
@staticmethod
|
|
def get_study_associate(study_id = None, uid=None):
|
|
"""
|
|
gets all associated people for a study from the database
|
|
"""
|
|
study = db.session.query(StudyModel).filter(StudyModel.id == study_id).first()
|
|
|
|
if study is None:
|
|
raise ApiError('study_not_found', 'No study found with id = %d' % study_id)
|
|
|
|
if uid is None:
|
|
raise ApiError('uid not specified','A valid uva uid is required for this function')
|
|
|
|
if uid == study.user_uid:
|
|
return {'uid': ownerid, 'role': 'owner', 'send_email': True, 'access': True}
|
|
|
|
|
|
|
|
person = db.session.query(StudyAssociated).filter((StudyAssociated.study_id == study_id)&(
|
|
StudyAssociated.uid == uid)).first()
|
|
if person:
|
|
newAssociate = {'uid':person.uid}
|
|
newAssociate['role'] = person.role
|
|
newAssociate['send_email'] = person.send_email
|
|
newAssociate['access'] = person.access
|
|
return newAssociate
|
|
raise ApiError('uid_not_associated_with_study',"user id %s was not associated with study number %d"%(uid,
|
|
study_id))
|
|
|
|
@staticmethod
|
|
def get_study_associates(study_id):
|
|
"""
|
|
gets all associated people for a study from the database
|
|
"""
|
|
study = db.session.query(StudyModel).filter(StudyModel.id == study_id).first()
|
|
|
|
if study is None:
|
|
raise ApiError('study_not_found','No study found with id = %d'%study_id)
|
|
|
|
ownerid = study.user_uid
|
|
people_list = [{'uid':ownerid,'role':'owner','send_email':True,'access':True}]
|
|
people = db.session.query(StudyAssociated).filter(StudyAssociated.study_id == study_id)
|
|
for person in people:
|
|
newAssociate = {'uid':person.uid}
|
|
newAssociate['role'] = person.role
|
|
newAssociate['send_email'] = person.send_email
|
|
newAssociate['access'] = person.access
|
|
people_list.append(newAssociate)
|
|
return people_list
|
|
|
|
|
|
@staticmethod
|
|
def update_study_associates(study_id,associates):
|
|
"""
|
|
updates the list of associates in the database for a study_id and a list
|
|
of dicts that contains associates
|
|
"""
|
|
if study_id is None:
|
|
raise ApiError('study_id not specified', "This function requires the study_id parameter")
|
|
|
|
for person in associates:
|
|
if not LdapService.user_exists(person.get('uid','impossible_uid')):
|
|
if person.get('uid','impossible_uid') == 'impossible_uid':
|
|
raise ApiError('associate with no uid','One of the associates passed as a parameter doesnt have '
|
|
'a uid specified')
|
|
raise ApiError('trying_to_grant_access_to_user_not_found_in_ldap',"You are trying to grant access to "
|
|
"%s, but that user was not found in "
|
|
"ldap "
|
|
"- please check to ensure it is a "
|
|
"valid uva uid"%person.get('uid'))
|
|
|
|
study = db.session.query(StudyModel).filter(StudyModel.id == study_id).first()
|
|
if study is None:
|
|
raise ApiError('study_id not found', "A study with id# %d was not found"%study_id)
|
|
|
|
|
|
db.session.query(StudyAssociated).filter(StudyAssociated.study_id == study_id).delete()
|
|
for person in associates:
|
|
newAssociate = StudyAssociated()
|
|
newAssociate.study_id = study_id
|
|
newAssociate.uid = person['uid']
|
|
newAssociate.role = person.get('role', None)
|
|
newAssociate.send_email = person.get('send_email', False)
|
|
newAssociate.access = person.get('access',False)
|
|
session.add(newAssociate)
|
|
session.commit()
|
|
|
|
@staticmethod
|
|
def update_study_associate(study_id=None,uid=None,role="",send_email=False,access=False):
|
|
if study_id is None:
|
|
raise ApiError('study_id not specified', "This function requires the study_id parameter")
|
|
if uid is None:
|
|
raise ApiError('uid not specified', "This function requires a uva uid parameter")
|
|
|
|
if not LdapService.user_exists(uid):
|
|
raise ApiError('trying_to_grant_access_to_user_not_found_in_ldap',"You are trying to grant access to "
|
|
"%s but they were not found in ldap "
|
|
"- please check to ensure it is a "
|
|
"valid uva uid"%uid)
|
|
study = db.session.query(StudyModel).filter(StudyModel.id == study_id).first()
|
|
if study is None:
|
|
raise ApiError('study_id not found', "A study with id# %d was not found"%study_id)
|
|
db.session.query(StudyAssociated).filter((StudyAssociated.study_id == study_id)&(StudyAssociated.uid ==
|
|
uid) ).delete()
|
|
|
|
newAssociate = StudyAssociated()
|
|
newAssociate.study_id = study_id
|
|
newAssociate.uid = uid
|
|
newAssociate.role = role
|
|
newAssociate.send_email = send_email
|
|
newAssociate.access = access
|
|
session.add(newAssociate)
|
|
session.commit()
|
|
return True
|
|
|
|
|
|
@staticmethod
|
|
def delete_study(study_id):
|
|
session.query(TaskEventModel).filter_by(study_id=study_id).delete()
|
|
session.query(StudyAssociated).filter_by(study_id=study_id).delete()
|
|
session.query(EmailModel).filter_by(study_id=study_id).delete()
|
|
session.query(StudyEvent).filter_by(study_id=study_id).delete()
|
|
|
|
for workflow in session.query(WorkflowModel).filter_by(study_id=study_id):
|
|
StudyService.delete_workflow(workflow.id)
|
|
study = session.query(StudyModel).filter_by(id=study_id).first()
|
|
session.delete(study)
|
|
session.commit()
|
|
|
|
@staticmethod
|
|
def delete_workflow(workflow_id):
|
|
workflow = session.query(WorkflowModel).get(workflow_id)
|
|
if not workflow:
|
|
return
|
|
|
|
session.query(TaskEventModel).filter_by(workflow_id=workflow.id).delete()
|
|
session.query(WorkflowSpecDependencyFile).filter_by(workflow_id=workflow_id).delete(synchronize_session='fetch')
|
|
session.query(FileModel).filter_by(workflow_id=workflow_id).update({'archived': True, 'workflow_id': None})
|
|
|
|
session.delete(workflow)
|
|
session.commit()
|
|
|
|
@staticmethod
|
|
def get_categories():
|
|
"""Returns a list of category objects, in the correct order."""
|
|
cat_models = db.session.query(WorkflowSpecCategoryModel) \
|
|
.order_by(WorkflowSpecCategoryModel.display_order).all()
|
|
categories = []
|
|
for cat_model in cat_models:
|
|
categories.append(Category(cat_model))
|
|
return categories
|
|
|
|
@staticmethod
|
|
def get_documents_status(study_id):
|
|
"""Returns a list of documents related to the study, and any file information
|
|
that is available.."""
|
|
|
|
# Get PB required docs, if Protocol Builder Service is enabled.
|
|
if ProtocolBuilderService.is_enabled() and study_id is not None:
|
|
try:
|
|
pb_docs = ProtocolBuilderService.get_required_docs(study_id=study_id)
|
|
except requests.exceptions.ConnectionError as ce:
|
|
app.logger.error(f'Failed to connect to the Protocol Builder - {str(ce)}', exc_info=True)
|
|
pb_docs = []
|
|
else:
|
|
pb_docs = []
|
|
|
|
# Loop through all known document types, get the counts for those files,
|
|
# and use pb_docs to mark those as required.
|
|
doc_dictionary = FileService.get_reference_data(FileService.DOCUMENT_LIST, 'code', ['id'])
|
|
|
|
documents = {}
|
|
for code, doc in doc_dictionary.items():
|
|
|
|
if ProtocolBuilderService.is_enabled():
|
|
pb_data = next((item for item in pb_docs if int(item['AUXDOCID']) == int(doc['id'])), None)
|
|
doc['required'] = False
|
|
if pb_data:
|
|
doc['required'] = True
|
|
|
|
doc['study_id'] = study_id
|
|
doc['code'] = code
|
|
|
|
# Make a display name out of categories
|
|
name_list = []
|
|
for cat_key in ['category1', 'category2', 'category3']:
|
|
if doc[cat_key] not in ['', 'NULL']:
|
|
name_list.append(doc[cat_key])
|
|
doc['display_name'] = ' / '.join(name_list)
|
|
|
|
# For each file, get associated workflow status
|
|
doc_files = FileService.get_files_for_study(study_id=study_id, irb_doc_code=code)
|
|
doc['count'] = len(doc_files)
|
|
doc['files'] = []
|
|
|
|
# when we run tests - it doesn't look like the user is available
|
|
# so we return a bogus token
|
|
token = 'not_available'
|
|
if hasattr(flask.g,'user'):
|
|
token = flask.g.user.encode_auth_token()
|
|
for file in doc_files:
|
|
file_data = {'file_id': file.id,
|
|
'name': file.name,
|
|
'url': app.config['APPLICATION_ROOT']+
|
|
'file/' + str(file.id) +
|
|
'/download?auth_token='+
|
|
urllib.parse.quote_plus(token),
|
|
'workflow_id': file.workflow_id
|
|
}
|
|
data = db.session.query(DataStoreModel).filter(DataStoreModel.file_id==file.id).all()
|
|
data_store_data = {}
|
|
for d in data:
|
|
data_store_data[d.key] = d.value
|
|
file_data["data_store"] = data_store_data
|
|
doc['files'].append(Box(file_data))
|
|
# update the document status to match the status of the workflow it is in.
|
|
if 'status' not in doc or doc['status'] is None:
|
|
workflow: WorkflowModel = session.query(WorkflowModel).filter_by(id=file.workflow_id).first()
|
|
doc['status'] = workflow.status.value
|
|
|
|
documents[code] = doc
|
|
return Box(documents)
|
|
|
|
@staticmethod
|
|
def get_investigators(study_id, all=False):
|
|
"""Convert array of investigators from protocol builder into a dictionary keyed on the type. """
|
|
|
|
# Loop through all known investigator types as set in the reference file
|
|
inv_dictionary = FileService.get_reference_data(FileService.INVESTIGATOR_LIST, 'code')
|
|
|
|
# Get PB required docs
|
|
pb_investigators = ProtocolBuilderService.get_investigators(study_id=study_id)
|
|
|
|
# It is possible for the same type to show up more than once in some circumstances, in those events
|
|
# append a counter to the name.
|
|
investigators = {}
|
|
for i_type in inv_dictionary:
|
|
pb_data_entries = list(item for item in pb_investigators if item['INVESTIGATORTYPE'] == i_type)
|
|
entry_count = 0
|
|
investigators[i_type] = copy(inv_dictionary[i_type])
|
|
investigators[i_type]['user_id'] = None
|
|
for pb_data in pb_data_entries:
|
|
entry_count += 1
|
|
if entry_count == 1:
|
|
t = i_type
|
|
else:
|
|
t = i_type + "_" + str(entry_count)
|
|
investigators[t] = copy(inv_dictionary[i_type])
|
|
investigators[t]['user_id'] = pb_data["NETBADGEID"]
|
|
investigators[t].update(StudyService.get_ldap_dict_if_available(pb_data["NETBADGEID"]))
|
|
if not all:
|
|
investigators = dict(filter(lambda elem: elem[1]['user_id'] is not None, investigators.items()))
|
|
return investigators
|
|
|
|
@staticmethod
|
|
def get_ldap_dict_if_available(user_id):
|
|
try:
|
|
return LdapSchema().dump(LdapService().user_info(user_id))
|
|
except ApiError as ae:
|
|
app.logger.info(str(ae))
|
|
return {"error": str(ae)}
|
|
except LDAPSocketOpenError:
|
|
app.logger.info("Failed to connect to LDAP Server.")
|
|
return {}
|
|
|
|
@staticmethod
|
|
def synch_with_protocol_builder_if_enabled(user):
|
|
"""Assures that the studies we have locally for the given user are
|
|
in sync with the studies available in protocol builder. """
|
|
|
|
if ProtocolBuilderService.is_enabled():
|
|
|
|
app.logger.info("The Protocol Builder is enabled. app.config['PB_ENABLED'] = " +
|
|
str(app.config['PB_ENABLED']))
|
|
|
|
# Get studies matching this user from Protocol Builder
|
|
pb_studies: List[ProtocolBuilderStudy] = ProtocolBuilderService.get_studies(user.uid)
|
|
|
|
# Get studies from the database
|
|
db_studies = session.query(StudyModel).filter_by(user_uid=user.uid).all()
|
|
|
|
# Update all studies from the protocol builder, create new studies as needed.
|
|
# Further assures that every active study (that does exist in the protocol builder)
|
|
# has a reference to every available workflow (though some may not have started yet)
|
|
for pb_study in pb_studies:
|
|
new_status = None
|
|
db_study = next((s for s in db_studies if s.id == pb_study.STUDYID), None)
|
|
if not db_study:
|
|
db_study = StudyModel(id=pb_study.STUDYID)
|
|
db_study.status = None # Force a new sa
|
|
new_status = StudyStatus.in_progress
|
|
session.add(db_study)
|
|
db_studies.append(db_study)
|
|
|
|
if pb_study.HSRNUMBER:
|
|
db_study.irb_status = IrbStatus.hsr_assigned
|
|
if db_study.status != StudyStatus.open_for_enrollment:
|
|
new_status = StudyStatus.open_for_enrollment
|
|
|
|
db_study.update_from_protocol_builder(pb_study)
|
|
StudyService._add_all_workflow_specs_to_study(db_study)
|
|
|
|
# If there is a new automatic status change and there isn't a manual change in place, record it.
|
|
if new_status and db_study.status != StudyStatus.hold:
|
|
db_study.status = new_status
|
|
StudyService.add_study_update_event(db_study,
|
|
status=new_status,
|
|
event_type=StudyEventType.automatic)
|
|
|
|
# Mark studies as inactive that are no longer in Protocol Builder
|
|
for study in db_studies:
|
|
pb_study = next((pbs for pbs in pb_studies if pbs.STUDYID == study.id), None)
|
|
if not pb_study and study.status != StudyStatus.abandoned:
|
|
study.status = StudyStatus.abandoned
|
|
StudyService.add_study_update_event(study,
|
|
status=StudyStatus.abandoned,
|
|
event_type=StudyEventType.automatic)
|
|
|
|
db.session.commit()
|
|
|
|
@staticmethod
|
|
def add_study_update_event(study, status, event_type, user_uid=None, comment=''):
|
|
study_event = StudyEvent(study=study,
|
|
status=status,
|
|
event_type=event_type,
|
|
user_uid=user_uid,
|
|
comment=comment)
|
|
db.session.add(study_event)
|
|
db.session.commit()
|
|
|
|
@staticmethod
|
|
def _update_status_of_workflow_meta(workflow_metas, status):
|
|
# Update the status on each workflow
|
|
warnings = []
|
|
for wfm in workflow_metas:
|
|
wfm.state_message = ''
|
|
# do we have a status for you
|
|
if wfm.name not in status.keys():
|
|
warnings.append(ApiError("missing_status", "No status specified for workflow %s" % wfm.name))
|
|
continue
|
|
if not isinstance(status[wfm.name], dict):
|
|
warnings.append(ApiError(code='invalid_status',
|
|
message=f'Status must be a dictionary with "status" and "message" keys. Name is {wfm.name}. Status is {status[wfm.name]}'))
|
|
continue
|
|
if 'status' not in status[wfm.name].keys():
|
|
warnings.append(ApiError("missing_status",
|
|
"Workflow '%s' does not have a status setting" % wfm.name))
|
|
continue
|
|
if not WorkflowState.has_value(status[wfm.name]['status']):
|
|
warnings.append(ApiError("invalid_state",
|
|
"Workflow '%s' can not be set to '%s', should be one of %s" % (
|
|
wfm.name, status[wfm.name]['status'], ",".join(WorkflowState.list())
|
|
)))
|
|
continue
|
|
wfm.state = WorkflowState[status[wfm.name]['status']]
|
|
if 'message' in status[wfm.name].keys():
|
|
wfm.state_message = status[wfm.name]['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(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
|