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cr-connect-workflow
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Merge pull request #127 from sartography/feature/health-attesting-spreadsheet 

Health attesting spreadsheet
This commit is contained in:
Dan Funk 2020-06-25 13:23:40 -04:00 committed by GitHub
parent 0424ed04cb dd10e56d1a
commit 83621df53a
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5 changed files with 195 additions and 82 deletions
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15
crc/api.yml
View File

@ -917,6 +917,21 @@ paths:
application/json:
schema:
type: object
/health_attesting:
get:
operationId: crc.api.approval.get_health_attesting_csv
summary: Returns a CSV file with health attesting records
tags:
- Approvals
responses:
'200':
description: A CSV file
content:
application/json:
schema:
type: array
items:
$ref: "#/components/schemas/Approval"
components:
securitySchemes:
jwt:

76
crc/api/approval.py
View File

@ -1,9 +1,11 @@
import csv
import io
import json
import pickle
from base64 import b64decode
from datetime import datetime
from flask import g
from flask import g, make_response
from crc import db, session
from crc.api.common import ApiError
@ -88,71 +90,25 @@ def get_approvals_for_study(study_id=None):
return results
def get_health_attesting_csv():
records = ApprovalService.get_health_attesting_records()
si = io.StringIO()
cw = csv.writer(si)
cw.writerows(records)
output = make_response(si.getvalue())
output.headers["Content-Disposition"] = "attachment; filename=health_attesting.csv"
output.headers["Content-type"] = "text/csv"
return output
# ----- Begin descent into madness ---- #
def get_csv():
"""A damn lie, it's a json file. A huge bit of a one-off for RRT, but 3 weeks of midnight work can convince a
man to do just about anything"""
approvals = ApprovalService.get_all_approvals(include_cancelled=False)
output = []
errors = []
for approval in approvals:
try:
if approval.status != ApprovalStatus.APPROVED.value:
continue
for related_approval in approval.related_approvals:
if related_approval.status != ApprovalStatus.APPROVED.value:
continue
workflow = db.session.query(WorkflowModel).filter(WorkflowModel.id == approval.workflow_id).first()
data = json.loads(workflow.bpmn_workflow_json)
last_task = find_task(data['last_task']['__uuid__'], data['task_tree'])
personnel = extract_value(last_task, 'personnel')
training_val = extract_value(last_task, 'RequiredTraining')
pi_supervisor = extract_value(last_task, 'PISupervisor')['value']
review_complete = 'AllRequiredTraining' in training_val
pi_uid = workflow.study.primary_investigator_id
pi_details = LdapService.user_info(pi_uid)
details = []
details.append(pi_details)
for person in personnel:
uid = person['PersonnelComputingID']['value']
details.append(LdapService.user_info(uid))
content = ApprovalService.get_not_really_csv_content()
for person in details:
record = {
"study_id": approval.study_id,
"pi_uid": pi_details.uid,
"pi": pi_details.display_name,
"name": person.display_name,
"uid": person.uid,
"email": person.email_address,
"supervisor": "",
"review_complete": review_complete,
}
# We only know the PI's supervisor.
if person.uid == pi_details.uid:
record["supervisor"] = pi_supervisor
return content
output.append(record)
except Exception as e:
errors.append("Error pulling data for workflow #%i: %s" % (approval.workflow_id, str(e)))
return {"results": output, "errors": errors }
def extract_value(task, key):
if key in task['data']:
return pickle.loads(b64decode(task['data'][key]['__bytes__']))
else:
return ""
def find_task(uuid, task):
if task['id']['__uuid__'] == uuid:
return task
for child in task['children']:
task = find_task(uuid, child)
if task:
return task
# ----- come back to the world of the living ---- #

128
crc/services/approval_service.py
View File

@ -1,6 +1,9 @@
from datetime import datetime
import json
import pickle
from base64 import b64decode
from datetime import datetime, timedelta
from sqlalchemy import desc
from sqlalchemy import desc, func
from crc import app, db, session
from crc.api.common import ApiError
@ -109,16 +112,129 @@ class ApprovalService(object):
db_approvals = query.all()
return [Approval.from_model(approval_model) for approval_model in db_approvals]
@staticmethod
def get_approval_details(approval):
"""Returns a list of packed approval details, obtained from
the task data sent during the workflow """
def extract_value(task, key):
if key in task['data']:
return pickle.loads(b64decode(task['data'][key]['__bytes__']))
else:
return ""
def find_task(uuid, task):
if task['id']['__uuid__'] == uuid:
return task
for child in task['children']:
task = find_task(uuid, child)
if task:
return task
if approval.status != ApprovalStatus.APPROVED.value:
return {}
for related_approval in approval.related_approvals:
if related_approval.status != ApprovalStatus.APPROVED.value:
continue
workflow = db.session.query(WorkflowModel).filter(WorkflowModel.id == approval.workflow_id).first()
data = json.loads(workflow.bpmn_workflow_json)
last_task = find_task(data['last_task']['__uuid__'], data['task_tree'])
personnel = extract_value(last_task, 'personnel')
training_val = extract_value(last_task, 'RequiredTraining')
pi_supervisor = extract_value(last_task, 'PISupervisor')['value']
review_complete = 'AllRequiredTraining' in training_val
pi_uid = workflow.study.primary_investigator_id
pi_details = LdapService.user_info(pi_uid)
details = {
'Supervisor': pi_supervisor,
'PI_Details': pi_details,
'Review': review_complete
}
details['person_details'] = []
details['person_details'].append(pi_details)
for person in personnel:
uid = person['PersonnelComputingID']['value']
details['person_details'].append(LdapService.user_info(uid))
return details
@staticmethod
def get_health_attesting_records():
"""Return a list with prepared information related to all approvals """
approvals = ApprovalService.get_all_approvals(include_cancelled=False)
health_attesting_rows = [
['university_computing_id',
'last_name',
'first_name',
'department',
'job_title',
'supervisor_university_computing_id']
]
for approval in approvals:
try:
details = ApprovalService.get_approval_details(approval)
if not details:
continue
for person in details['person_details']:
first_name = person.given_name
last_name = person.display_name.replace(first_name, '').strip()
record = [
person.uid,
last_name,
first_name,
'',
'Academic Researcher',
details['Supervisor'] if person.uid == details['person_details'][0].uid else 'askresearch'
]
if record not in health_attesting_rows:
health_attesting_rows.append(record)
except Exception as e:
app.logger.error("Error pulling data for workflow #%i: %s" % (approval.workflow_id, str(e)))
return health_attesting_rows
@staticmethod
def get_not_really_csv_content():
approvals = ApprovalService.get_all_approvals(include_cancelled=False)
output = []
errors = []
for approval in approvals:
try:
details = ApprovalService.get_approval_details(approval)
for person in details['person_details']:
record = {
"study_id": approval.study_id,
"pi_uid": details['PI_Details'].uid,
"pi": details['PI_Details'].display_name,
"name": person.display_name,
"uid": person.uid,
"email": person.email_address,
"supervisor": details['Supervisor'] if person.uid == details['person_details'][0].uid else "",
"review_complete": details['Review'],
}
output.append(record)
except Exception as e:
errors.append("Error pulling data for workflow #%i: %s" % (approval.workflow_id, str(e)))
return {"results": output, "errors": errors }
@staticmethod
def update_approval(approval_id, approver_uid):
"""Update a specific approval"""
"""Update a specific approval
NOTE: Actual update happens in the API layer, this
funtion is currently in charge of only sending
corresponding emails
"""
db_approval = session.query(ApprovalModel).get(approval_id)
status = db_approval.status
if db_approval:
# db_approval.status = status
# session.add(db_approval)
# session.commit()
if status == ApprovalStatus.APPROVED.value:
# second_approval = ApprovalModel().query.filter_by(
# study_id=db_approval.study_id, workflow_id=db_approval.workflow_id,

26
tests/test_approvals_service.py
View File

@ -57,6 +57,32 @@ class TestApprovalsService(BaseTest):
self.assertEqual(1, models[0].version)
self.assertEqual(2, models[1].version)
def test_get_health_attesting_records(self):
self.load_example_data()
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="AD_CoCAppr")
ApprovalService.add_approval(study_id=workflow.study_id, workflow_id=workflow.id, approver_uid="dhf8r")
records = ApprovalService.get_health_attesting_records()
self.assertEqual(len(records), 1)
def test_get_not_really_csv_content(self):
self.load_example_data()
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="AD_CoCAppr")
ApprovalService.add_approval(study_id=workflow.study_id, workflow_id=workflow.id, approver_uid="dhf8r")
records = ApprovalService.get_not_really_csv_content()
self.assertEqual(len(records), 2)
def test_new_approval_sends_proper_emails(self):
self.assertEqual(1, 1)

32
tests/test_tasks_api.py
View File

@ -47,7 +47,7 @@ class TestTasksApi(BaseTest):
# The total number of tasks may change over time, as users move through gateways
# branches may be pruned. As we hit parallel Multi-Instance new tasks may be created...
self.assertIsNotNone(workflow.total_tasks)
self.assertEquals(prev_completed_task_count + 1, workflow.completed_tasks)
self.assertEqual(prev_completed_task_count + 1, workflow.completed_tasks)
# Assure a record exists in the Task Events
task_events = session.query(TaskEventModel) \
.filter_by(workflow_id=workflow.id) \
@ -56,25 +56,25 @@ class TestTasksApi(BaseTest):
self.assertGreater(len(task_events), 0)
event = task_events[0]
self.assertIsNotNone(event.study_id)
self.assertEquals("dhf8r", event.user_uid)
self.assertEquals(workflow.id, event.workflow_id)
self.assertEquals(workflow.workflow_spec_id, event.workflow_spec_id)
self.assertEquals(workflow.spec_version, event.spec_version)
self.assertEquals(WorkflowService.TASK_ACTION_COMPLETE, event.action)
self.assertEquals(task_in.id, task_id)
self.assertEquals(task_in.name, event.task_name)
self.assertEquals(task_in.title, event.task_title)
self.assertEquals(task_in.type, event.task_type)
self.assertEquals("COMPLETED", event.task_state)
self.assertEqual("dhf8r", event.user_uid)
self.assertEqual(workflow.id, event.workflow_id)
self.assertEqual(workflow.workflow_spec_id, event.workflow_spec_id)
self.assertEqual(workflow.spec_version, event.spec_version)
self.assertEqual(WorkflowService.TASK_ACTION_COMPLETE, event.action)
self.assertEqual(task_in.id, task_id)
self.assertEqual(task_in.name, event.task_name)
self.assertEqual(task_in.title, event.task_title)
self.assertEqual(task_in.type, event.task_type)
self.assertEqual("COMPLETED", event.task_state)
# Not sure what vodoo is happening inside of marshmallow to get me in this state.
if isinstance(task_in.multi_instance_type, MultiInstanceType):
self.assertEquals(task_in.multi_instance_type.value, event.mi_type)
self.assertEqual(task_in.multi_instance_type.value, event.mi_type)
else:
self.assertEquals(task_in.multi_instance_type, event.mi_type)
self.assertEqual(task_in.multi_instance_type, event.mi_type)
self.assertEquals(task_in.multi_instance_count, event.mi_count)
self.assertEquals(task_in.multi_instance_index, event.mi_index)
self.assertEquals(task_in.process_name, event.process_name)
self.assertEqual(task_in.multi_instance_count, event.mi_count)
self.assertEqual(task_in.multi_instance_index, event.mi_index)
self.assertEqual(task_in.process_name, event.process_name)
self.assertIsNotNone(event.date)
# Assure that there is data in the form_data