Refactoring shared code
This commit is contained in:
Carlos Lopez
parent
e5541e4950
commit
dc5ffd29d0
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@ -90,8 +90,8 @@ def get_approvals_for_study(study_id=None):
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return results
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def get_health_attesting_csv(all_approvals=True):
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records = ApprovalService.get_health_attesting_records(all_approvals)
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def get_health_attesting_csv():
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records = ApprovalService.get_health_attesting_records()
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si = io.StringIO()
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cw = csv.writer(si)
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cw.writerows(records)
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@ -105,67 +105,10 @@ def get_health_attesting_csv(all_approvals=True):
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def get_csv():
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"""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
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man to do just about anything"""
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approvals = ApprovalService.get_all_approvals(include_cancelled=False)
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output = []
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errors = []
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for approval in approvals:
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try:
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if approval.status != ApprovalStatus.APPROVED.value:
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continue
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for related_approval in approval.related_approvals:
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if related_approval.status != ApprovalStatus.APPROVED.value:
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continue
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workflow = db.session.query(WorkflowModel).filter(WorkflowModel.id == approval.workflow_id).first()
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data = json.loads(workflow.bpmn_workflow_json)
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last_task = find_task(data['last_task']['__uuid__'], data['task_tree'])
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personnel = extract_value(last_task, 'personnel')
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training_val = extract_value(last_task, 'RequiredTraining')
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pi_supervisor = extract_value(last_task, 'PISupervisor')['value']
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review_complete = 'AllRequiredTraining' in training_val
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pi_uid = workflow.study.primary_investigator_id
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pi_details = LdapService.user_info(pi_uid)
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details = []
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details.append(pi_details)
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for person in personnel:
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uid = person['PersonnelComputingID']['value']
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details.append(LdapService.user_info(uid))
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content = ApprovalService.get_not_really_csv_content()
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for person in details:
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record = {
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"study_id": approval.study_id,
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"pi_uid": pi_details.uid,
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"pi": pi_details.display_name,
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"name": person.display_name,
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"uid": person.uid,
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"email": person.email_address,
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"supervisor": "",
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"review_complete": review_complete,
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}
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# We only know the PI's supervisor.
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if person.uid == pi_details.uid:
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record["supervisor"] = pi_supervisor
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return content
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output.append(record)
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except Exception as e:
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errors.append("Error pulling data for workflow #%i: %s" % (approval.workflow_id, str(e)))
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return {"results": output, "errors": errors }
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def extract_value(task, key):
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if key in task['data']:
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return pickle.loads(b64decode(task['data'][key]['__bytes__']))
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else:
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return ""
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def find_task(uuid, task):
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if task['id']['__uuid__'] == uuid:
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return task
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for child in task['children']:
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task = find_task(uuid, child)
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if task:
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return task
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# ----- come back to the world of the living ---- #
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@ -1,3 +1,6 @@
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import json
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import pickle
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from base64 import b64decode
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from datetime import datetime, timedelta
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from sqlalchemy import desc, func
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@ -110,19 +113,51 @@ class ApprovalService(object):
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return [Approval.from_model(approval_model) for approval_model in db_approvals]
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@staticmethod
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def get_health_attesting_records(all_approvals=True):
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"""Return a list with prepared information related to all approvals
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approved or filtered by today """
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if all_approvals:
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approvals = session.query(ApprovalModel).filter(
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ApprovalModel.status==ApprovalStatus.APPROVED.value
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)
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else:
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today = datetime.now().date()
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approvals = session.query(ApprovalModel).filter(
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func.date(ApprovalModel.date_created)==today,
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ApprovalModel.status==ApprovalStatus.APPROVED.value
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)
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def get_approval_details(approval):
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"""Returns a list of packed approval details, obtained from
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the task data sent during the workflow """
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def extract_value(task, key):
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if key in task['data']:
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return pickle.loads(b64decode(task['data'][key]['__bytes__']))
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else:
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return ""
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def find_task(uuid, task):
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if task['id']['__uuid__'] == uuid:
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return task
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for child in task['children']:
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task = find_task(uuid, child)
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if task:
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return task
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if approval.status != ApprovalStatus.APPROVED.value:
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return {}
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for related_approval in approval.related_approvals:
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if related_approval.status != ApprovalStatus.APPROVED.value:
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continue
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workflow = db.session.query(WorkflowModel).filter(WorkflowModel.id == approval.workflow_id).first()
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data = json.loads(workflow.bpmn_workflow_json)
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last_task = find_task(data['last_task']['__uuid__'], data['task_tree'])
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personnel = extract_value(last_task, 'personnel')
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training_val = extract_value(last_task, 'RequiredTraining')
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pi_supervisor = extract_value(last_task, 'PISupervisor')['value']
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review_complete = 'AllRequiredTraining' in training_val
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pi_uid = workflow.study.primary_investigator_id
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pi_details = LdapService.user_info(pi_uid)
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details = {'Supervisor': pi_supervisor}
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details['person_details'] = []
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details['person_details'].append(pi_details)
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for person in personnel:
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uid = person['PersonnelComputingID']['value']
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details['person_details'].append(LdapService.user_info(uid))
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return details
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@staticmethod
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def get_health_attesting_records():
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"""Return a list with prepared information related to all approvals """
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approvals = ApprovalService.get_all_approvals(include_cancelled=False)
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health_attesting_rows = [
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['university_computing_id',
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@ -132,22 +167,60 @@ class ApprovalService(object):
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'job_title',
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'supervisor_university_computing_id']
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]
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for approval in approvals:
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pi_info = LdapService.user_info(approval.study.primary_investigator_id)
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approver_info = LdapService.user_info(approval.approver_uid)
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first_name = pi_info.given_name
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last_name = pi_info.display_name.replace(first_name, '').strip()
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health_attesting_rows.append([
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pi_info.uid,
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last_name,
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first_name,
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'',
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'Academic Researcher',
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approver_info.uid
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])
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try:
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details = ApprovalService.get_approval_details(approval)
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if not details:
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continue
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for person in details['person_details']:
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first_name = person.given_name
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last_name = person.display_name.replace(first_name, '').strip()
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record = [
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person.uid,
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last_name,
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first_name,
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'',
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'Academic Researcher',
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details['Supervisor'] if person.uid == details['person_details'][0].uid else 'askresearch'
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]
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if record not in health_attesting_rows:
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health_attesting_rows.append(record)
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except Exception as e:
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app.logger.error("Error pulling data for workflow #%i: %s" % (approval.workflow_id, str(e)))
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return health_attesting_rows
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@staticmethod
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def get_not_really_csv_content():
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approvals = ApprovalService.get_all_approvals(include_cancelled=False)
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output = []
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errors = []
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for approval in approvals:
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try:
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details = ApprovalService.get_approval_details(approval)
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for person in details['person_details']:
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record = {
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"study_id": approval.study_id,
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"pi_uid": pi_details.uid,
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"pi": pi_details.display_name,
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"name": person.display_name,
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"uid": person.uid,
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"email": person.email_address,
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"supervisor": details['Supervisor'] if person.uid == details['person_details'][0].uid else "",
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"review_complete": review_complete,
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}
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output.append(record)
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except Exception as e:
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errors.append("Error pulling data for workflow #%i: %s" % (approval.workflow_id, str(e)))
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return {"results": output, "errors": errors }
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@staticmethod
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def update_approval(approval_id, approver_uid):
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"""Update a specific approval
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@ -57,6 +57,32 @@ class TestApprovalsService(BaseTest):
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self.assertEqual(1, models[0].version)
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self.assertEqual(2, models[1].version)
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def test_get_health_attesting_records(self):
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self.load_example_data()
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self.create_reference_document()
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workflow = self.create_workflow('empty_workflow')
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FileService.add_workflow_file(workflow_id=workflow.id,
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name="anything.png", content_type="text",
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binary_data=b'5678', irb_doc_code="AD_CoCAppr")
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ApprovalService.add_approval(study_id=workflow.study_id, workflow_id=workflow.id, approver_uid="dhf8r")
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records = ApprovalService.get_health_attesting_records()
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self.assertEqual(len(records), 1)
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def test_get_not_really_csv_content(self):
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self.load_example_data()
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self.create_reference_document()
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workflow = self.create_workflow('empty_workflow')
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FileService.add_workflow_file(workflow_id=workflow.id,
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name="anything.png", content_type="text",
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binary_data=b'5678', irb_doc_code="AD_CoCAppr")
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ApprovalService.add_approval(study_id=workflow.study_id, workflow_id=workflow.id, approver_uid="dhf8r")
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records = ApprovalService.get_not_really_csv_content()
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self.assertEqual(len(records), 1)
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def test_new_approval_sends_proper_emails(self):
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self.assertEqual(1, 1)
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@ -47,7 +47,7 @@ class TestTasksApi(BaseTest):
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# The total number of tasks may change over time, as users move through gateways
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# branches may be pruned. As we hit parallel Multi-Instance new tasks may be created...
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self.assertIsNotNone(workflow.total_tasks)
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self.assertEquals(prev_completed_task_count + 1, workflow.completed_tasks)
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self.assertEqual(prev_completed_task_count + 1, workflow.completed_tasks)
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# Assure a record exists in the Task Events
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task_events = session.query(TaskEventModel) \
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.filter_by(workflow_id=workflow.id) \
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@ -56,25 +56,25 @@ class TestTasksApi(BaseTest):
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self.assertGreater(len(task_events), 0)
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event = task_events[0]
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self.assertIsNotNone(event.study_id)
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self.assertEquals("dhf8r", event.user_uid)
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self.assertEquals(workflow.id, event.workflow_id)
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self.assertEquals(workflow.workflow_spec_id, event.workflow_spec_id)
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self.assertEquals(workflow.spec_version, event.spec_version)
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self.assertEquals(WorkflowService.TASK_ACTION_COMPLETE, event.action)
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self.assertEquals(task_in.id, task_id)
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self.assertEquals(task_in.name, event.task_name)
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self.assertEquals(task_in.title, event.task_title)
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self.assertEquals(task_in.type, event.task_type)
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self.assertEquals("COMPLETED", event.task_state)
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self.assertEqual("dhf8r", event.user_uid)
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self.assertEqual(workflow.id, event.workflow_id)
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self.assertEqual(workflow.workflow_spec_id, event.workflow_spec_id)
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self.assertEqual(workflow.spec_version, event.spec_version)
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self.assertEqual(WorkflowService.TASK_ACTION_COMPLETE, event.action)
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self.assertEqual(task_in.id, task_id)
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self.assertEqual(task_in.name, event.task_name)
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self.assertEqual(task_in.title, event.task_title)
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self.assertEqual(task_in.type, event.task_type)
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self.assertEqual("COMPLETED", event.task_state)
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# Not sure what vodoo is happening inside of marshmallow to get me in this state.
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if isinstance(task_in.multi_instance_type, MultiInstanceType):
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self.assertEquals(task_in.multi_instance_type.value, event.mi_type)
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self.assertEqual(task_in.multi_instance_type.value, event.mi_type)
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else:
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self.assertEquals(task_in.multi_instance_type, event.mi_type)
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self.assertEqual(task_in.multi_instance_type, event.mi_type)
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self.assertEquals(task_in.multi_instance_count, event.mi_count)
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self.assertEquals(task_in.multi_instance_index, event.mi_index)
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self.assertEquals(task_in.process_name, event.process_name)
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self.assertEqual(task_in.multi_instance_count, event.mi_count)
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self.assertEqual(task_in.multi_instance_index, event.mi_index)
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self.assertEqual(task_in.process_name, event.process_name)
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self.assertIsNotNone(event.date)
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# Assure that there is data in the form_data
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