def get_study(study_id, study_model: StudyModel = None):
"""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.categories = StudyService.get_categories()
workflow_metas = StudyService.__get_workflow_metas(study_id)
study.approvals = ApprovalService.get_approvals_for_study(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.protocol_builder_status != ProtocolBuilderStatus.ABANDONED:
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
def from_model(cls, model: ApprovalModel):
args = dict(
(k, v) for k, v in model.__dict__.items() if not k.startswith('_'))
instance = cls(**args)
instance.related_approvals = []
instance.title = model.study.title if model.study else ''
try:
instance.approver = LdapService.user_info(model.approver_uid)
instance.primary_investigator = LdapService.user_info(
model.study.primary_investigator_id)
except ApiError as ae:
app.logger.error(
f'Ldap lookup failed for approval record {model.id}',
exc_info=True)
doc_dictionary = FileService.get_doc_dictionary()
instance.associated_files = []
for approval_file in model.approval_files:
try:
# fixme: This is slow because we are doing a ton of queries to find the irb code.
extra_info = doc_dictionary[
approval_file.file_data.file_model.irb_doc_code]
except:
extra_info = None
associated_file = {}
associated_file['id'] = approval_file.file_data.file_model.id
if extra_info:
associated_file['name'] = '_'.join(
(extra_info['category1'],
approval_file.file_data.file_model.name))
associated_file['description'] = extra_info['description']
else:
associated_file[
'name'] = approval_file.file_data.file_model.name
associated_file['description'] = 'No description available'
associated_file[
'name'] = '(' + model.study.primary_investigator_id + ')' + associated_file[
'name']
associated_file[
'content_type'] = approval_file.file_data.file_model.content_type
instance.associated_files.append(associated_file)
return instance
def to_file_api(file_model):
"""Converts a FileModel object to something we can return via the api"""
return File.from_models(file_model, FileService.get_file_data(file_model.id),
FileService.get_doc_dictionary())