Merge remote-tracking branch 'origin/dev' into master-workflow-status-messages-222

Dockerfile

@@ -1,4 +1,4 @@
-FROM python:3.8
+FROM quay.io/sartography/python:3.8
 
 RUN pip install pipenv
 RUN useradd _gunicorn --no-create-home --user-group

crc/scripts/email.py

@@ -1,8 +1,7 @@
 from crc import app
 from crc.api.common import ApiError
-from crc.models.user import UserModel
 from crc.scripts.script import Script
-# from crc.services.ldap_service import LdapService
+from crc.services.ldap_service import LdapService
 from crc.services.email_service import EmailService
 from crc.services.study_service import StudyService
 
@@ -101,13 +100,10 @@ email (subject="My Subject", recipients=["dhf8r@virginia.edu", pi.email], cc='as
 
     @staticmethod
     def get_associated_emails(study_id):
-        associated_uids = []
         associated_emails = []
         associates = StudyService.get_study_associates(study_id)
         for associate in associates:
             if associate['send_email'] is True:
-                associated_uids.append(associate['uid'])
-        returned = UserModel.query.filter(UserModel.uid.in_(associated_uids)).all()
-        for item in returned:
-            associated_emails.append(item.email_address)
+                user_info = LdapService.user_info(associate['uid'])
+                associated_emails.append(user_info.email_address)
         return associated_emails

crc/scripts/get_study_associates.py

@@ -19,8 +19,11 @@ example : get_study_associates() => [{'uid':'sbp3ey','role':'Unicorn Herder', 's
 """
 
     def do_task_validate_only(self, task, study_id, workflow_id, *args, **kwargs):
-        return True
-
+        study_associates = [
+            {'uid': 'dhf8r', 'role': 'Chief Bee Keeper', 'send_email': True, 'access': True},
+            {'uid': 'lb3dp', 'role': 'Chief Cat Herder', 'send_email': True, 'access': True}
+        ]
+        return study_associates
 
     def do_task(self, task, study_id, workflow_id, *args, **kwargs):
 

deploy/requirements.txt

@@ -34,7 +34,7 @@ imagesize==1.2.0
 inflection==0.5.1
 itsdangerous==1.1.0
 jdcal==1.4.1
-jinja2==2.11.2
+jinja2==2.11.3
 jsonschema==3.2.0
 ldap3==2.8.1
 lxml==4.6.2
@@ -63,7 +63,7 @@ python-docx==0.8.10
 python-editor==1.0.4
 python-levenshtein==0.12.0
 pytz==2020.4
-pyyaml==5.3.1
+pyyaml==5.4
 recommonmark==0.6.0
 requests==2.25.0
 sentry-sdk==0.14.4

tests/data/study_sponsors_associate/study_sponsors_associate.bpmn

@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<bpmn:definitions xmlns:bpmn="http://www.omg.org/spec/BPMN/20100524/MODEL" xmlns:bpmndi="http://www.omg.org/spec/BPMN/20100524/DI" xmlns:dc="http://www.omg.org/spec/DD/20100524/DC" xmlns:di="http://www.omg.org/spec/DD/20100524/DI" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" id="Definitions_0kmksnn" targetNamespace="http://bpmn.io/schema/bpmn" exporter="Camunda Modeler" exporterVersion="3.7.0">
+<bpmn:definitions xmlns:bpmn="http://www.omg.org/spec/BPMN/20100524/MODEL" xmlns:bpmndi="http://www.omg.org/spec/BPMN/20100524/DI" xmlns:dc="http://www.omg.org/spec/DD/20100524/DC" xmlns:di="http://www.omg.org/spec/DD/20100524/DI" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" id="Definitions_0kmksnn" targetNamespace="http://bpmn.io/schema/bpmn" exporter="Camunda Modeler" exporterVersion="3.5.0">
   <bpmn:process id="Process_0exnnpv" isExecutable="true">
     <bpmn:startEvent id="StartEvent_1">
       <bpmn:outgoing>SequenceFlow_1nfe5m9</bpmn:outgoing>
@@ -30,7 +30,10 @@ out4 = get_study_associate('lb3dp')</bpmn:script>
     <bpmn:scriptTask id="Activity_0run091" name="setval - 2">
       <bpmn:incoming>Flow_14n3ixy</bpmn:incoming>
       <bpmn:outgoing>Flow_1vlh6s0</bpmn:outgoing>
-      <bpmn:script>update_study_associates([{'uid':'lb3dp','role':'SuperGal','send_email':False,'access':True}])</bpmn:script>
+      <bpmn:script>uids = []
+for assoc in out:
+   uids.append(assoc['uid'])
+update_study_associates([{'uid':'lb3dp','role':'SuperGal','send_email':False,'access':True}])</bpmn:script>
     </bpmn:scriptTask>
     <bpmn:sequenceFlow id="Flow_1vlh6s0" sourceRef="Activity_0run091" targetRef="Activity_0d8iftx" />
     <bpmn:scriptTask id="Activity_14td33q" name="getval">

tests/study/test_study_associate_script.py

@@ -1,10 +1,10 @@
+from tests.base_test import BaseTest
 import json
 from unittest.mock import patch
 import flask
 
 from crc.api.common import ApiError
 from crc.services.user_service import UserService
-from tests.base_test import BaseTest
 
 from crc import session, app
 from crc.models.study import StudyModel