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cr-connect-workflow
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Merge branch 'dev' into feature/enum_lookup_data

This commit is contained in:
Aaron Louie 2020-07-10 10:27:51 -04:00
parent 4cfaa62a8e ff7c30b879
commit 7f0b35ff27
14 changed files with 144 additions and 71 deletions
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18
crc/models/approval.py
View File

@ -57,23 +57,11 @@ class Approval(object):
@classmethod
def from_model(cls, model: ApprovalModel):
# TODO: Reduce the code by iterating over model's dict keys
instance = cls()
instance.id = model.id
instance.study_id = model.study_id
instance.workflow_id = model.workflow_id
instance.version = model.version
instance.approver_uid = model.approver_uid
instance.status = model.status
instance.message = model.message
instance.date_created = model.date_created
instance.date_approved = model.date_approved
instance.version = model.version
instance.title = ''
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 ''
if model.study:
instance.title = model.study.title
try:
instance.approver = LdapService.user_info(model.approver_uid)
instance.primary_investigator = LdapService.user_info(model.study.primary_investigator_id)

27
crc/services/approval_service.py
View File

@ -287,7 +287,7 @@ class ApprovalService(object):
)
if mail_result:
app.logger.error(mail_result, exc_info=True)
# TODO: Log update action by approver_uid - maybe ?
return db_approval
@staticmethod
@ -299,11 +299,12 @@ class ApprovalService(object):
pending approvals and create a new approval for the latest version
of the workflow."""
# Find any existing approvals for this workflow and approver.
latest_approval_request = db.session.query(ApprovalModel). \
# Find any existing approvals for this workflow.
latest_approval_requests = db.session.query(ApprovalModel). \
filter(ApprovalModel.workflow_id == workflow_id). \
filter(ApprovalModel.approver_uid == approver_uid). \
order_by(desc(ApprovalModel.version)).first()
order_by(desc(ApprovalModel.version))
latest_approver_request = latest_approval_requests.filter(ApprovalModel.approver_uid == approver_uid).first()
# Construct as hash of the latest files to see if things have changed since
# the last approval.
@ -318,16 +319,20 @@ class ApprovalService(object):
# If an existing approval request exists and no changes were made, do nothing.
# If there is an existing approval request for a previous version of the workflow
# then add a new request, and cancel any waiting/pending requests.
if latest_approval_request:
request_file_ids = list(file.file_data_id for file in latest_approval_request.approval_files)
if latest_approver_request:
request_file_ids = list(file.file_data_id for file in latest_approver_request.approval_files)
current_data_file_ids.sort()
request_file_ids.sort()
other_approver = latest_approval_requests.filter(ApprovalModel.approver_uid != approver_uid).first()
if current_data_file_ids == request_file_ids:
return # This approval already exists.
return # This approval already exists or we're updating other approver.
else:
latest_approval_request.status = ApprovalStatus.CANCELED.value
db.session.add(latest_approval_request)
version = latest_approval_request.version + 1
for approval_request in latest_approval_requests:
if (approval_request.version == latest_approver_request.version and
approval_request.status != ApprovalStatus.CANCELED.value):
approval_request.status = ApprovalStatus.CANCELED.value
db.session.add(approval_request)
version = latest_approver_request.version + 1
else:
version = 1

2
crc/services/email_service.py
View File

@ -13,7 +13,7 @@ class EmailService(object):
"""Provides common tools for working with an Email"""
@staticmethod
def add_email(subject, sender, recipients, content, content_html, study_id):
def add_email(subject, sender, recipients, content, content_html, study_id=None):
"""We will receive all data related to an email and store it"""
# Find corresponding study - if any

28
crc/services/study_service.py
View File

@ -1,3 +1,4 @@
from copy import copy
from datetime import datetime
import json
from typing import List
@ -185,6 +186,7 @@ class StudyService(object):
@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')
@ -192,18 +194,26 @@ class StudyService(object):
# Get PB required docs
pb_investigators = ProtocolBuilderService.get_investigators(study_id=study_id)
"""Convert array of investigators from protocol builder into a dictionary keyed on the type"""
# 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 = next((item for item in pb_investigators if item['INVESTIGATORTYPE'] == i_type), None)
if pb_data:
inv_dictionary[i_type]['user_id'] = pb_data["NETBADGEID"]
inv_dictionary[i_type].update(StudyService.get_ldap_dict_if_available(pb_data["NETBADGEID"]))
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:
inv_dictionary[i_type]['user_id'] = None
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:
inv_dictionary = dict(filter(lambda elem: elem[1]['user_id'] is not None, inv_dictionary.items()))
return inv_dictionary
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):

3
crc/services/workflow_service.py
View File

@ -385,7 +385,8 @@ class WorkflowService(object):
except TypeError as te:
raise ApiError.from_task(code="template_error", message="Error processing template for task %s: %s" %
(spiff_task.task_spec.name, str(te)), task=spiff_task)
# TODO: Catch additional errors and report back.
except Exception as e:
app.logger.error(str(e), exc_info=True)
@staticmethod
def process_options(spiff_task, field):

21
tests/approval/test_approvals_api.py
View File

@ -217,27 +217,6 @@ class TestApprovals(BaseTest):
total_counts = sum(counts[status] for status in statuses)
self.assertEqual(total_counts, len(approvals), 'Total approval counts for user should match number of approvals for user')
def _create_study_workflow_approvals(self, user_uid, title, primary_investigator_id, approver_uids, statuses,
workflow_spec_name="random_fact"):
study = self.create_study(uid=user_uid, title=title, primary_investigator_id=primary_investigator_id)
workflow = self.create_workflow(workflow_name=workflow_spec_name, study=study)
approvals = []
for i in range(len(approver_uids)):
approvals.append(self.create_approval(
study=study,
workflow=workflow,
approver_uid=approver_uids[i],
status=statuses[i],
version=1
))
return {
'study': study,
'workflow': workflow,
'approvals': approvals,
}
def _add_lots_of_random_approvals(self, n=100, workflow_spec_name="random_fact"):
num_studies_before = db.session.query(StudyModel).count()
statuses = [name for name, value in ApprovalStatus.__members__.items()]

30
tests/approval/test_approvals_service.py
View File

@ -1,7 +1,7 @@
from tests.base_test import BaseTest
from crc import db
from crc.models.approval import ApprovalModel
from crc.services.approval_service import ApprovalService
from crc.services.approval_service import ApprovalService, ApprovalStatus
from crc.services.file_service import FileService
from crc.services.workflow_processor import WorkflowProcessor
@ -83,6 +83,34 @@ class TestApprovalsService(BaseTest):
self.assertEqual(len(records), 2)
def test_new_approval_cancels_all_previous_approvals(self):
self.create_reference_document()
workflow = self.create_workflow("empty_workflow")
FileService.add_workflow_file(workflow_id=workflow.id,
name="anything.png", content_type="text",
binary_data=b'5678', irb_doc_code="UVACompl_PRCAppr" )
ApprovalService.add_approval(study_id=workflow.study_id, workflow_id=workflow.id, approver_uid="dhf8r")
ApprovalService.add_approval(study_id=workflow.study_id, workflow_id=workflow.id, approver_uid="lb3dp")
current_count = ApprovalModel.query.count()
self.assertTrue(current_count, 2)
FileService.add_workflow_file(workflow_id=workflow.id,
name="borderline.png", content_type="text",
binary_data=b'906090', irb_doc_code="AD_CoCAppr" )
ApprovalService.add_approval(study_id=workflow.study_id, workflow_id=workflow.id, approver_uid="dhf8r")
current_count = ApprovalModel.query.count()
canceled_count = ApprovalModel.query.filter(ApprovalModel.status == ApprovalStatus.CANCELED.value)
self.assertTrue(current_count, 2)
self.assertTrue(current_count, 3)
ApprovalService.add_approval(study_id=workflow.study_id, workflow_id=workflow.id, approver_uid="lb3dp")
current_count = ApprovalModel.query.count()
self.assertTrue(current_count, 4)
def test_new_approval_sends_proper_emails(self):
self.assertEqual(1, 1)

23
tests/base_test.py
View File

@ -240,6 +240,29 @@ class BaseTest(unittest.TestCase):
db.session.commit()
return study
def _create_study_workflow_approvals(self, user_uid, title, primary_investigator_id, approver_uids, statuses,
workflow_spec_name="random_fact"):
study = self.create_study(uid=user_uid, title=title, primary_investigator_id=primary_investigator_id)
workflow = self.create_workflow(workflow_name=workflow_spec_name, study=study)
approvals = []
for i in range(len(approver_uids)):
approvals.append(self.create_approval(
study=study,
workflow=workflow,
approver_uid=approver_uids[i],
status=statuses[i],
version=1
))
full_study = {
'study': study,
'workflow': workflow,
'approvals': approvals,
}
return full_study
def create_workflow(self, workflow_name, study=None, category_id=None):
db.session.flush()
spec = db.session.query(WorkflowSpecModel).filter(WorkflowSpecModel.name == workflow_name).first()

10
tests/data/pb_responses/investigators.json
View File

@ -13,5 +13,15 @@
"INVESTIGATORTYPE": "PI",
"INVESTIGATORTYPEFULL": "Primary Investigator",
"NETBADGEID": "dhf8r"
},
{
"INVESTIGATORTYPE": "SI",
"INVESTIGATORTYPEFULL": "Sub Investigator",
"NETBADGEID": "ajl2j"
},
{
"INVESTIGATORTYPE": "SI",
"INVESTIGATORTYPEFULL": "Sub Investigator",
"NETBADGEID": "cah3us"
}
]

13
tests/emails/test_email_service.py
View File

@ -31,4 +31,15 @@ class TestEmailService(BaseTest):
self.assertEqual(email_model.content_html, content_html)
self.assertEqual(email_model.study, study)
# TODO: Create email model without study
subject = 'Email Subject - Empty study'
EmailService.add_email(subject=subject, sender=sender, recipients=recipients,
content=content, content_html=content_html)
email_model = EmailModel.query.order_by(EmailModel.id.desc()).first()
self.assertEqual(email_model.subject, subject)
self.assertEqual(email_model.sender, sender)
self.assertEqual(email_model.recipients, str(recipients))
self.assertEqual(email_model.content, content)
self.assertEqual(email_model.content_html, content_html)
self.assertEqual(email_model.study, None)

18
tests/study/test_study_api.py
View File

@ -7,6 +7,7 @@ from unittest.mock import patch
from crc import session, app
from crc.models.protocol_builder import ProtocolBuilderStatus, \
ProtocolBuilderStudySchema
from crc.models.approval import ApprovalStatus
from crc.models.stats import TaskEventModel
from crc.models.study import StudyModel, StudySchema
from crc.models.workflow import WorkflowSpecModel, WorkflowModel
@ -95,8 +96,21 @@ class TestStudyApi(BaseTest):
# TODO: WRITE A TEST FOR STUDY FILES
def test_get_study_has_details_about_approvals(self):
# TODO: WRITE A TEST FOR STUDY APPROVALS
pass
self.load_example_data()
full_study = self._create_study_workflow_approvals(
user_uid="dhf8r", title="first study", primary_investigator_id="lb3dp",
approver_uids=["lb3dp", "dhf8r"], statuses=[ApprovalStatus.PENDING.value, ApprovalStatus.PENDING.value]
)
api_response = self.app.get('/v1.0/study/%i' % full_study['study'].id,
headers=self.logged_in_headers(), content_type="application/json")
self.assert_success(api_response)
study = StudySchema().loads(api_response.get_data(as_text=True))
self.assertEqual(len(study.approvals), 2)
for approval in study.approvals:
self.assertEqual(full_study['study'].title, approval['title'])
def test_add_study(self):
self.load_example_data()

8
tests/study/test_study_service.py
View File

@ -193,7 +193,7 @@ class TestStudyService(BaseTest):
workflow = self.create_workflow('docx') # The workflow really doesnt matter in this case.
investigators = StudyService().get_investigators(workflow.study_id, all=True)
self.assertEqual(9, len(investigators))
self.assertEqual(10, len(investigators))
# dhf8r is in the ldap mock data.
self.assertEqual("dhf8r", investigators['PI']['user_id'])
@ -219,10 +219,14 @@ class TestStudyService(BaseTest):
workflow = self.create_workflow('docx') # The workflow really doesnt matter in this case.
investigators = StudyService().get_investigators(workflow.study_id, all=False)
self.assertEqual(3, len(investigators))
self.assertEqual(5, len(investigators))
# dhf8r is in the ldap mock data.
self.assertEqual("dhf8r", investigators['PI']['user_id'])
self.assertEqual("Dan Funk", investigators['PI']['display_name']) # Data from ldap
self.assertEqual("Primary Investigator", investigators['PI']['label']) # Data from xls file.
self.assertEqual("Always", investigators['PI']['display']) # Data from xls file.
# Both Alex and Aaron are SI, and both should be returned.
self.assertEqual("ajl2j", investigators['SI']['user_id'])
self.assertEqual("cah3us", investigators['SI_2']['user_id'])

2
tests/test_protocol_builder.py
View File

@ -24,7 +24,7 @@ class TestProtocolBuilder(BaseTest):
mock_get.return_value.text = self.protocol_builder_response('investigators.json')
response = ProtocolBuilderService.get_investigators(self.test_study_id)
self.assertIsNotNone(response)
self.assertEqual(3, len(response))
self.assertEqual(5, len(response))
self.assertEqual("DC", response[0]["INVESTIGATORTYPE"])
self.assertEqual("Department Contact", response[0]["INVESTIGATORTYPEFULL"])
self.assertEqual("asd3v", response[0]["NETBADGEID"])

8
tests/test_tasks_api.py
View File

@ -322,7 +322,7 @@ class TestTasksApi(BaseTest):
self.assertEqual(4, len(navigation)) # Start task, form_task, multi_task, end task
self.assertEqual("UserTask", workflow.next_task.type)
self.assertEqual(MultiInstanceType.sequential.value, workflow.next_task.multi_instance_type)
self.assertEqual(3, workflow.next_task.multi_instance_count)
self.assertEqual(5, workflow.next_task.multi_instance_count)
# Assure that the names for each task are properly updated, so they aren't all the same.
self.assertEqual("Primary Investigator", workflow.next_task.properties['display_name'])
@ -480,15 +480,15 @@ class TestTasksApi(BaseTest):
workflow = self.create_workflow('multi_instance_parallel')
workflow_api = self.get_workflow_api(workflow)
self.assertEqual(6, len(workflow_api.navigation))
self.assertEqual(8, len(workflow_api.navigation))
ready_items = [nav for nav in workflow_api.navigation if nav['state'] == "READY"]
self.assertEqual(3, len(ready_items))
self.assertEqual(5, len(ready_items))
self.assertEqual("UserTask", workflow_api.next_task.type)
self.assertEqual("MultiInstanceTask",workflow_api.next_task.name)
self.assertEqual("Primary Investigator", workflow_api.next_task.title)
for i in random.sample(range(3), 3):
for i in random.sample(range(5), 5):
task = TaskSchema().load(ready_items[i]['task'])
rv = self.app.put('/v1.0/workflow/%i/task/%s/set_token' % (workflow.id, task.id),
headers=self.logged_in_headers(),