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Merge pull request #638 from sartography/dev
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Adding code to troubleshoot Personnel workflow problem
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@cullerton
cullerton authored Jan 23, 2025
2 parents 9a2f409 + abc4c9e commit 35165d3
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Showing 2 changed files with 41 additions and 71 deletions.
1 change: 1 addition & 0 deletions crc/scripts/load_irb_personnel.py
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Original file line number Diff line number Diff line change
Expand Up @@ -161,6 +161,7 @@ def do_task(self, task, study_id, workflow_id, *args, **kwargs):
'dc_invalid_uid': dc_invalid_uid,
'pcs_invalid_uid': pcs_invalid_uid,
'subs_invalid_uid': subs_invalid_uid,
'pb_create_uid': pb_create_uid,
}

return data
111 changes: 40 additions & 71 deletions tests/scripts/test_set_pb_associates.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2,31 +2,38 @@
from crc import app
from crc.models.ldap import LdapModel
from unittest.mock import patch
import os
import random
from unittest import skip
import random
import json


class TestSetPBAssociates(BaseTest):

user_data = {'PI': ('Alice Thompson', 'ghg3qe'), 'SC_I': ('Brian Edwards', 'zxriuk'), 'DEPT_CH': ('Catherine Wilson', '80vn'),
'AS_C': ('Daniel Martinez', '676pe'), 'AS_C_2': ('Emily Johnson', 'tl5h'), 'SI': ('Franklin Harris', 'y4suzz'),
'SI_2': ('Georgia Clarke', 'jci60'), 'SI_3': ('Henry Robinson', 'ouvhr'), 'IRBC': ('Isabel Carter', 'dxigow')}

def get_associated_users(self, study_id):
rv = self.app.get(f'/v1.0/study/{study_id}/associates',
headers=self.logged_in_headers(),
content_type="application/json")
self.assert_success(rv)
return json.loads(rv.get_data(as_text=True))

def get_mock_investigators(self):
investigators = {}
for (role, (name, uid)) in self.user_data.items():
investigators[role] = {'code': role, 'label': role, 'display': 'Always', 'unique': 'Yes', 'user_id': uid,
'uid': uid, 'display_name': name, 'given_name': name.split()[0],
'email_address': f'{uid}@virginia.edu',
'telephone_number': ''.join([random.choice('0123456789') for _ in range(10)]),
'title': 'E0:Staff', 'department': 'EN:Engineering', 'affiliation': 'staff',
'sponsor_type': '', 'date_cached': '2024-04-11T19:24:35.980782-04:00'}
return investigators

def create_additional_users(self):
data = [('Alice Thompson', 'ghg3qe'), ('Brian Edwards', 'zxriuk'), ('Catherine Wilson', '80vn'),
('Daniel Martinez', '676pe'), ('Emily Johnson', 'tl5h'), ('Franklin Harris', 'y4suzz'),
('Georgia Clarke', 'jci60'), ('Henry Robinson', 'ouvhr'), ('Isabel Carter', 'dxigow'),
('Jack Peterson', 'w11ei'), ('Karen Bennett', 'jlzglh'), ('Louis Fisher', 'kump0'),
('Megan Richardson', 'xiai4c'), ('Nathan Cooper', '999hdr'), ('Olivia Scott', 'k8f6'),
('Patrick Howard', '51wqn0'), ('Quincy Parker', '934no'), ('Rachel Turner', 'd3cj0'),
('Samuel Baker', 'qmn3w8'), ('Teresa Mitchell', 'zcj7r'),]
for (name, uid) in data:
"""LdapModel(uid=entry.uid.value,
display_name=entry.displayName.value,
given_name=", ".join(entry.givenName),
email_address=entry.mail.value,
telephone_number=entry.telephoneNumber.value,
title=", ".join(entry.title),
department=", ".join(entry.uvaDisplayDepartment),
affiliation=", ".join(entry.uvaPersonIAMAffiliation),
sponsor_type=", ".join(entry.uvaPersonSponsoredType))"""
user_data = self.user_data
for key, (name, uid) in user_data.items():
ldap_model = LdapModel(uid=uid,
display_name=name,
given_name=name.split()[0],
Expand All @@ -46,55 +53,7 @@ def test_set_pb_associates(self, mock_investigators):
self.create_additional_users()

mock_investigators.return_value.ok = True
mock_investigators.return_value = \
{'PI': {'code': 'PI', 'label': 'Primary Investigator', 'display': 'Always', 'unique': 'Yes',
'user_id': 'cm4r', 'uid': 'cm4r', 'display_name': 'Carol A Manning', 'given_name': 'Carol',
'email_address': '[email protected]', 'telephone_number': '4349821012',
'title': 'E1:Clinician Physician, E0:Professor',
'department': 'E1:UPG-MD-NEUR Neurology, E0:MD-NEUR Neurology', 'affiliation': 'faculty, staff',
'sponsor_type': '', 'date_cached': '2024-04-11T19:24:35.980782-04:00'},
'SC_I': {'code': 'SC_I', 'label': 'Study Coordinator I', 'display': 'Always', 'unique': 'Yes',
'user_id': 'cdn4q', 'uid': 'cdn4q', 'display_name': 'Courtney Nightengale',
'given_name': 'Courtney', 'email_address': '[email protected]', 'telephone_number': '4342431927',
'title': 'E1:Temp D, E0:Compliance Analyst',
'department': 'E1:MD-OBGY Gyn Oncology, E0:MD-DMED Clinical Research Unit',
'affiliation': 'staff', 'sponsor_type': '', 'date_cached': '2024-04-23T14:50:11.759861-04:00'},
'DEPT_CH': {'code': 'DEPT_CH', 'label': 'Department Chair', 'display': 'Always', 'unique': 'Yes',
'user_id': 'jpn2r', 'uid': 'jpn2r', 'display_name': 'James P Nataro', 'given_name': 'James',
'email_address': '[email protected]', 'telephone_number': '4349245093',
'title': 'E1:Clinician Physician, E0:Professor',
'department': 'E1:UPG-MD-PEDT Infectious Diseases, E0:MD-PEDT Pediatrics-Admin',
'affiliation': 'faculty, staff', 'sponsor_type': '',
'date_cached': '2024-04-11T19:26:17.849182-04:00'},
'AS_C': {'code': 'AS_C', 'label': 'Additional Study Coordinators', 'display': 'Optional', 'unique': 'No',
'user_id': 'kcu5hm', 'uid': 'kcu5hm', 'display_name': 'Pat Junhasavasdikul', 'given_name': 'Pat',
'email_address': '[email protected]', 'telephone_number': None, 'title': '',
'department': 'U1:Arts & Sciences Undergraduate', 'affiliation': 'student', 'sponsor_type': '',
'date_cached': '2025-01-08T08:50:23.340718-05:00'},
'AS_C_2': {'code': 'AS_C', 'label': 'Additional Study Coordinators', 'display': 'Optional', 'unique': 'No',
'user_id': 'lmw2d', 'uid': 'lmw2d', 'display_name': 'Lindsey Sites', 'given_name': 'Lindsey',
'email_address': '[email protected]', 'telephone_number': '4349823500',
'title': 'E1:APP - CRNA Saturday Elective, E0:Lead RN Anesthetist',
'department': "E1:Anesthesia CRNA's, E0:Anesthesia CRNA's",
'affiliation': 'alumni, staff, former_student', 'sponsor_type': '',
'date_cached': '2025-01-08T09:06:07.004507-05:00'},
'SI': {'code': 'SI', 'label': 'Sub Investigator', 'display': 'Optional', 'unique': 'No',
'user_id': 'ghg3qe', 'uid': 'ghg3qe', 'display_name': 'Jessica L Morris', 'given_name': 'Jessica',
'email_address': '[email protected]', 'telephone_number': '4349821058',
'title': 'E0:Compliance Manager-CMPL74', 'department': 'E0:MD-DMED Clinical Research Unit',
'affiliation': 'staff', 'sponsor_type': '', 'date_cached': '2024-04-23T12:47:09.643532-04:00'},
'SI_2': {'code': 'SI', 'label': 'Sub Investigator', 'display': 'Optional', 'unique': 'No',
'user_id': 'pdb7u', 'uid': 'pdb7u', 'display_name': 'Penny D Baker', 'given_name': 'Penny',
'email_address': '[email protected]', 'telephone_number': '4349245078',
'title': 'E0:Patient Care Technician', 'department': 'E0:Perianesthesia Main',
'affiliation': 'staff', 'sponsor_type': '', 'date_cached': '2025-01-08T09:25:37.002183-05:00'},
'SI_3': {'code': 'SI', 'label': 'Sub Investigator', 'display': 'Optional', 'unique': 'No',
'user_id': 'zzzz', 'error': 'ApiError: Unable to locate a user with id zzzz in LDAP. '},
'IRBC': {'code': 'IRBC', 'label': 'IRB Coordinator', 'display': 'Optional', 'unique': 'Yes',
'user_id': 'jp2pz', 'uid': 'jp2pz', 'display_name': 'Jeff Pitts', 'given_name': 'Jeff',
'email_address': '[email protected]', 'telephone_number': '4349248590',
'title': 'E0:Software Engineer 4', 'department': 'E0:MD-DMED Research & Clinical Trial Analytics',
'affiliation': 'staff', 'sponsor_type': '', 'date_cached': '2024-04-17T12:31:02.593919-04:00'}}
mock_investigators.return_value = self.get_mock_investigators()

workflow = self.create_workflow('set_pb_associates')

Expand All @@ -104,6 +63,9 @@ def test_set_pb_associates(self, mock_investigators):
assert task.name == 'Activity_Review_Before_Load_IRB'
assert task.data == {}

associated_users = self.get_associated_users(workflow_api.study_id)
assert len(associated_users) == 1

self.complete_form(workflow, task, {})

workflow_api = self.get_workflow_api(workflow)
Expand All @@ -118,8 +80,8 @@ def test_set_pb_associates(self, mock_investigators):
assert len(task.data['pi']) == 14
assert len(task.data['dc']) == 14
assert len(task.data['pcs']) == 4
assert len(task.data['subs']) == 2
assert len(task.data['subx']) == 1
assert len(task.data['subs']) == 3
assert len(task.data['subx']) == 0

self.complete_form(workflow, task, {})

Expand Down Expand Up @@ -155,9 +117,16 @@ def test_set_pb_associates(self, mock_investigators):
assert len(task.data) == 24
assert task.data['AP'] == form_data['AP']

associated_users = self.get_associated_users(workflow_api.study_id)
assert len(associated_users) == 1

self.complete_form(workflow, task, {})

workflow_api = self.get_workflow_api(workflow)
task = workflow_api.next_task

print('here')
assert task.name == 'Activity_Review_Before_End'
assert len(task.data) == 24

associated_users = self.get_associated_users(workflow_api.study_id)
assert len(associated_users) == 10

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