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Fix a bug from recent performance improvments - be sure that our study info script returns dicts that can be referenced immediately with dot notation, as this is a common pattern in our bpmn script tasks.

This commit is contained in:
Dan 2021-04-05 11:31:06 -04:00
parent 9f66a938f2
commit 727aa72e18
2 changed files with 98 additions and 82 deletions
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164
crc/scripts/study_info.py
View File

@ -1,5 +1,7 @@
import json
from SpiffWorkflow.bpmn.PythonScriptEngine import Box
from crc import session
from crc.api.common import ApiError
from crc.models.protocol_builder import ProtocolBuilderInvestigatorType
@ -11,11 +13,12 @@ from crc.services.file_service import FileService
from crc.services.protocol_builder import ProtocolBuilderService
from crc.services.study_service import StudyService
class StudyInfo(Script):
"""Please see the detailed description that is provided below. """
pb = ProtocolBuilderService()
type_options = ['info', 'investigators', 'roles', 'details', 'approvals', 'documents', 'protocol','sponsors']
type_options = ['info', 'investigators', 'roles', 'details', 'approvals', 'documents', 'protocol', 'sponsors']
# This is used for test/workflow validation, as well as documentation.
example_data = {
@ -30,31 +33,31 @@ class StudyInfo(Script):
"inactive": False
},
"sponsors": [
{
"COMMONRULEAGENCY": None,
"SPONSOR_ID": 2453,
"SP_NAME": "Abbott Ltd",
"SP_TYPE": "Private",
"SP_TYPE_GROUP_NAME": None,
"SS_STUDY": 2
},
{
"COMMONRULEAGENCY": None,
"SPONSOR_ID": 2387,
"SP_NAME": "Abbott-Price",
"SP_TYPE": "Incoming Sub Award",
"SP_TYPE_GROUP_NAME": "Government",
"SS_STUDY": 2
},
{
"COMMONRULEAGENCY": None,
"SPONSOR_ID": 1996,
"SP_NAME": "Abernathy-Heidenreich",
"SP_TYPE": "Foundation/Not for Profit",
"SP_TYPE_GROUP_NAME": "Other External Funding",
"SS_STUDY": 2
}
],
{
"COMMONRULEAGENCY": None,
"SPONSOR_ID": 2453,
"SP_NAME": "Abbott Ltd",
"SP_TYPE": "Private",
"SP_TYPE_GROUP_NAME": None,
"SS_STUDY": 2
},
{
"COMMONRULEAGENCY": None,
"SPONSOR_ID": 2387,
"SP_NAME": "Abbott-Price",
"SP_TYPE": "Incoming Sub Award",
"SP_TYPE_GROUP_NAME": "Government",
"SS_STUDY": 2
},
{
"COMMONRULEAGENCY": None,
"SPONSOR_ID": 1996,
"SP_NAME": "Abernathy-Heidenreich",
"SP_TYPE": "Foundation/Not for Profit",
"SP_TYPE_GROUP_NAME": "Other External Funding",
"SS_STUDY": 2
}
],
"investigators": {
'PI': {
@ -89,19 +92,21 @@ class StudyInfo(Script):
},
"documents": {
'AD_CoCApp': {'category1': 'Ancillary Document', 'category2': 'CoC Application', 'category3': '',
'Who Uploads?': 'CRC', 'id': '12',
'description': 'Certificate of Confidentiality Application', 'required': False,
'study_id': 1, 'code': 'AD_CoCApp', 'display_name': 'Ancillary Document / CoC Application',
'count': 0, 'files': []},
'Who Uploads?': 'CRC', 'id': '12',
'description': 'Certificate of Confidentiality Application', 'required': False,
'study_id': 1, 'code': 'AD_CoCApp',
'display_name': 'Ancillary Document / CoC Application',
'count': 0, 'files': []},
'UVACompl_PRCAppr': {'category1': 'UVA Compliance', 'category2': 'PRC Approval', 'category3': '',
'Who Uploads?': 'CRC', 'id': '6', 'description': "Cancer Center's PRC Approval Form",
'required': True, 'study_id': 1, 'code': 'UVACompl_PRCAppr',
'display_name': 'UVA Compliance / PRC Approval', 'count': 1, 'files': [
{'file_id': 10,
'task_id': 'fakingthisout',
'workflow_id': 2,
'workflow_spec_id': 'docx'}],
'status': 'complete'}
'Who Uploads?': 'CRC', 'id': '6',
'description': "Cancer Center's PRC Approval Form",
'required': True, 'study_id': 1, 'code': 'UVACompl_PRCAppr',
'display_name': 'UVA Compliance / PRC Approval', 'count': 1, 'files': [
{'file_id': 10,
'task_id': 'fakingthisout',
'workflow_id': 2,
'workflow_spec_id': 'docx'}],
'status': 'complete'}
},
"details":
{},
@ -182,48 +187,48 @@ Returns information specific to the protocol.
def do_task_validate_only(self, task, study_id, workflow_id, *args, **kwargs):
"""For validation only, pretend no results come back from pb"""
self.check_args(args,2)
self.check_args(args, 2)
# Assure the reference file exists (a bit hacky, but we want to raise this error early, and cleanly.)
FileService.get_reference_file_data(FileService.DOCUMENT_LIST)
FileService.get_reference_file_data(FileService.INVESTIGATOR_LIST)
data = {
"study":{
"study": {
"info": {
"id": 12,
"title": "test",
"short_title": "tst",
"primary_investigator_id":21,
"primary_investigator_id": 21,
"user_uid": "dif84",
"sponsor": "sponsor",
"ind_number": "1234",
"inactive": False
},
"sponsors": [
{
"COMMONRULEAGENCY": None,
"SPONSOR_ID": 2453,
"SP_NAME": "Abbott Ltd",
"SP_TYPE": "Private",
"SP_TYPE_GROUP_NAME": None,
"SS_STUDY": 2
},
{
"COMMONRULEAGENCY": None,
"SPONSOR_ID": 2387,
"SP_NAME": "Abbott-Price",
"SP_TYPE": "Incoming Sub Award",
"SP_TYPE_GROUP_NAME": "Government",
"SS_STUDY": 2
},
{
"COMMONRULEAGENCY": None,
"SPONSOR_ID": 1996,
"SP_NAME": "Abernathy-Heidenreich",
"SP_TYPE": "Foundation/Not for Profit",
"SP_TYPE_GROUP_NAME": "Other External Funding",
"SS_STUDY": 2
}
],
"sponsors": [
{
"COMMONRULEAGENCY": None,
"SPONSOR_ID": 2453,
"SP_NAME": "Abbott Ltd",
"SP_TYPE": "Private",
"SP_TYPE_GROUP_NAME": None,
"SS_STUDY": 2
},
{
"COMMONRULEAGENCY": None,
"SPONSOR_ID": 2387,
"SP_NAME": "Abbott-Price",
"SP_TYPE": "Incoming Sub Award",
"SP_TYPE_GROUP_NAME": "Government",
"SS_STUDY": 2
},
{
"COMMONRULEAGENCY": None,
"SPONSOR_ID": 1996,
"SP_NAME": "Abernathy-Heidenreich",
"SP_TYPE": "Foundation/Not for Profit",
"SP_TYPE_GROUP_NAME": "Other External Funding",
"SS_STUDY": 2
}
],
"investigators": {
"PI": {
@ -379,15 +384,15 @@ Returns information specific to the protocol.
}
}
}
if args[0]=='documents':
if args[0] == 'documents':
return StudyService().get_documents_status(study_id)
return data['study'][args[0]]
#self.add_data_to_task(task=task, data=data["study"])
#self.add_data_to_task(task, {"documents": StudyService().get_documents_status(study_id)})
# self.add_data_to_task(task=task, data=data["study"])
# self.add_data_to_task(task, {"documents": StudyService().get_documents_status(study_id)})
@timeit
def do_task(self, task, study_id, workflow_id, *args, **kwargs):
self.check_args(args,2)
self.check_args(args, 2)
prefix = None
if len(args) > 1:
prefix = args[1]
@ -414,21 +419,16 @@ Returns information specific to the protocol.
retval = StudyService().get_documents_status(study_id)
if cmd == 'protocol':
retval = StudyService().get_protocol(study_id)
# if isinstance(retval, list):
# retval = [Box(item) for item in retval]
# if isinstance(retval,dict) and prefix is not None:
# return Box({x:retval[x] for x in retval.keys() if x[:len(prefix)] == prefix})
# elif isinstance(retval,dict) :
# return Box(retval)
else:
return retval
if isinstance(retval, list):
return [Box(item) for item in retval]
if isinstance(retval, dict) and prefix is not None:
return Box({x: retval[x] for x in retval.keys() if x[:len(prefix)] == prefix})
elif isinstance(retval, dict):
return Box(retval)
def check_args(self, args, maxlen=1):
if len(args) < 1 or len(args) > maxlen or (args[0] not in StudyInfo.type_options):
raise ApiError(code="missing_argument",
message="The StudyInfo script requires a single argument which must be "
"one of %s" % ",".join(StudyInfo.type_options))

16
tests/study/test_study_details_documents.py
View File

@ -1,4 +1,7 @@
import json
from SpiffWorkflow.bpmn.PythonScriptEngine import Box
from tests.base_test import BaseTest
from unittest.mock import patch
@ -74,3 +77,16 @@ class TestStudyDetailsDocumentsScript(BaseTest):
string_data = self.protocol_builder_response('required_docs.json')
return ProtocolBuilderRequiredDocumentSchema(many=True).loads(string_data)
@patch('crc.services.protocol_builder.requests.get')
def test_study_info_returns_a_box_object(self, mock_get):
mock_get.return_value.ok = True
mock_get.return_value.text = self.protocol_builder_response('required_docs.json')
self.load_example_data()
self.create_reference_document()
study = session.query(StudyModel).first()
workflow_spec_model = self.load_test_spec("two_forms")
workflow_model = StudyService._create_workflow_model(study, workflow_spec_model)
processor = WorkflowProcessor(workflow_model)
task = processor.next_task()
docs = StudyInfo().do_task(task, study.id, workflow_model.id, "documents")
self.assertTrue(isinstance(docs, Box))