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
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'] = []
for file in doc_files:
doc['files'].append({'file_id': file.id,
'workflow_id': file.workflow_id})
# 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 documents
def test_load_lookup_data(self):
self.create_reference_document()
dict = FileService.get_reference_data(FileService.DOCUMENT_LIST,
'code', ['id'])
self.assertIsNotNone(dict)