service and scripts with working test - still needs a few more tests to try out, but should work to get Mike going

crc/scripts/script.py

@@ -68,7 +68,7 @@ class Script(object):
 
         def make_closure_validate(subclass,task,study_id,workflow_id):
             instance = subclass()
-            return lambda *a : subclass.do_task_validate_only(instance,task,study_id,workflow_id,*a)
+            return lambda *a, **b: subclass.do_task_validate_only(instance,task,study_id,workflow_id,*a,**b)
         execlist = {}
         subclasses = Script.get_all_subclasses()
         for x in range(len(subclasses)):

crc/services/study_service.py

@@ -107,7 +107,7 @@ class StudyService(object):
         person = db.session.query(StudyAssociated).filter((StudyAssociated.study_id == study_id)&(
                 StudyAssociated.uid == uid))
         if person:
-            newAssociate = {'uid',person.uid}
+            newAssociate = {'uid':person.uid}
             newAssociate['role'] = person.role
             newAssociate['send_email'] = person.send_email
             newAssociate['access'] = person.access
@@ -129,7 +129,7 @@ class StudyService(object):
         people_list = [{'uid':ownerid,'role':'owner','send_email':True,'access':True}]
         people = db.session.query(StudyAssociated).filter(StudyAssociated.study_id == study_id)
         for person in people:
-            newAssociate = {'uid',person.uid}
+            newAssociate = {'uid':person.uid}
             newAssociate['role'] = person.role
             newAssociate['send_email'] = person.send_email
             newAssociate['access'] = person.access
@@ -165,12 +165,13 @@ class StudyService(object):
         db.session.query(StudyAssociated).filter(StudyAssociated.study_id == study_id).delete()
         for person in associates:
             newAssociate = StudyAssociated()
+            newAssociate.study_id = study_id
             newAssociate.uid = person['uid']
             newAssociate.role = person.get('role', None)
             newAssociate.send_email = person.get('send_email', False)
             newAssociate.access = person.get('access',False)
-            db.session.add(newAssociate)
+            session.add(newAssociate)
-        db.commit()
+        session.commit()
 
     @staticmethod
     def update_study_associate(study_id=None,uid=None,role="",send_email=False,access=False):
@@ -191,13 +192,14 @@ class StudyService(object):
                                                                                          uid) ).delete()
 
         newAssociate = StudyAssociated()
+        newAssociate.study_id = study_id
         newAssociate.uid = uid
         newAssociate.role = role
         newAssociate.send_email = send_email
         newAssociate.access = access
-        db.session.add(newAssociate)
+        session.add(newAssociate)
-        db.commit()
+        session.commit()
-        return true
+        return True
 
 
     @staticmethod

migrations/versions/cb892916166a_.py

@@ -0,0 +1,38 @@
+"""empty message
+
+Revision ID: cb892916166a
+Revises: ff29528a9909
+Create Date: 2021-02-24 12:16:45.779821
+
+"""
+from alembic import op
+import sqlalchemy as sa
+
+
+# revision identifiers, used by Alembic.
+revision = 'cb892916166a'
+down_revision = 'ff29528a9909'
+branch_labels = None
+depends_on = None
+
+
+def upgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.create_table('study_associated_user',
+    sa.Column('id', sa.Integer(), nullable=False),
+    sa.Column('study_id', sa.Integer(), nullable=False),
+    sa.Column('uid', sa.String(), nullable=False),
+    sa.Column('role', sa.String(), nullable=True),
+    sa.Column('send_email', sa.Boolean(), nullable=True),
+    sa.Column('access', sa.Boolean(), nullable=True),
+    sa.ForeignKeyConstraint(['study_id'], ['study.id'], ),
+    sa.ForeignKeyConstraint(['uid'], ['ldap_model.uid'], ),
+    sa.PrimaryKeyConstraint('id')
+    )
+    # ### end Alembic commands ###
+
+
+def downgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.drop_table('study_associated_user')
+    # ### end Alembic commands ###

tests/data/study_sponsors_associate/study_sponsors_associate.bpmn

@@ -0,0 +1,65 @@
+<?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:process id="Process_0exnnpv" isExecutable="true">
+    <bpmn:startEvent id="StartEvent_1">
+      <bpmn:outgoing>SequenceFlow_1nfe5m9</bpmn:outgoing>
+    </bpmn:startEvent>
+    <bpmn:sequenceFlow id="SequenceFlow_1nfe5m9" sourceRef="StartEvent_1" targetRef="Task_Script_Load_Study_Sponsors" />
+    <bpmn:scriptTask id="Task_Script_Load_Study_Sponsors" name="Load Study Sponsors">
+      <bpmn:incoming>SequenceFlow_1nfe5m9</bpmn:incoming>
+      <bpmn:outgoing>SequenceFlow_1bqiin0</bpmn:outgoing>
+      <bpmn:script>sponsors = study_info('sponsors')</bpmn:script>
+    </bpmn:scriptTask>
+    <bpmn:sequenceFlow id="SequenceFlow_1bqiin0" sourceRef="Task_Script_Load_Study_Sponsors" targetRef="Activity_0cm6tn2" />
+    <bpmn:sequenceFlow id="Flow_09cika8" sourceRef="Activity_0cm6tn2" targetRef="Activity_0d8iftx" />
+    <bpmn:scriptTask id="Activity_0cm6tn2" name="setval">
+      <bpmn:incoming>SequenceFlow_1bqiin0</bpmn:incoming>
+      <bpmn:outgoing>Flow_09cika8</bpmn:outgoing>
+      <bpmn:script>update_study_associate(uid='lb3dp',role='SuperDude',send_email=False,access=True)</bpmn:script>
+    </bpmn:scriptTask>
+    <bpmn:scriptTask id="Activity_0d8iftx" name="getval">
+      <bpmn:incoming>Flow_09cika8</bpmn:incoming>
+      <bpmn:outgoing>Flow_0cttkwp</bpmn:outgoing>
+      <bpmn:script>out = get_study_associates()</bpmn:script>
+    </bpmn:scriptTask>
+    <bpmn:endEvent id="Event_0c8gcuh">
+      <bpmn:incoming>Flow_0cttkwp</bpmn:incoming>
+    </bpmn:endEvent>
+    <bpmn:sequenceFlow id="Flow_0cttkwp" sourceRef="Activity_0d8iftx" targetRef="Event_0c8gcuh" />
+  </bpmn:process>
+  <bpmndi:BPMNDiagram id="BPMNDiagram_1">
+    <bpmndi:BPMNPlane id="BPMNPlane_1" bpmnElement="Process_0exnnpv">
+      <bpmndi:BPMNEdge id="SequenceFlow_1bqiin0_di" bpmnElement="SequenceFlow_1bqiin0">
+        <di:waypoint x="370" y="117" />
+        <di:waypoint x="440" y="117" />
+      </bpmndi:BPMNEdge>
+      <bpmndi:BPMNEdge id="SequenceFlow_1nfe5m9_di" bpmnElement="SequenceFlow_1nfe5m9">
+        <di:waypoint x="215" y="117" />
+        <di:waypoint x="270" y="117" />
+      </bpmndi:BPMNEdge>
+      <bpmndi:BPMNShape id="_BPMNShape_StartEvent_2" bpmnElement="StartEvent_1">
+        <dc:Bounds x="179" y="99" width="36" height="36" />
+      </bpmndi:BPMNShape>
+      <bpmndi:BPMNShape id="ScriptTask_1mp6xid_di" bpmnElement="Task_Script_Load_Study_Sponsors">
+        <dc:Bounds x="270" y="77" width="100" height="80" />
+      </bpmndi:BPMNShape>
+      <bpmndi:BPMNEdge id="Flow_09cika8_di" bpmnElement="Flow_09cika8">
+        <di:waypoint x="540" y="117" />
+        <di:waypoint x="600" y="117" />
+      </bpmndi:BPMNEdge>
+      <bpmndi:BPMNShape id="Activity_0wnwluq_di" bpmnElement="Activity_0cm6tn2">
+        <dc:Bounds x="440" y="77" width="100" height="80" />
+      </bpmndi:BPMNShape>
+      <bpmndi:BPMNShape id="Activity_0cq37mm_di" bpmnElement="Activity_0d8iftx">
+        <dc:Bounds x="600" y="77" width="100" height="80" />
+      </bpmndi:BPMNShape>
+      <bpmndi:BPMNShape id="Event_0c8gcuh_di" bpmnElement="Event_0c8gcuh">
+        <dc:Bounds x="762" y="99" width="36" height="36" />
+      </bpmndi:BPMNShape>
+      <bpmndi:BPMNEdge id="Flow_0cttkwp_di" bpmnElement="Flow_0cttkwp">
+        <di:waypoint x="700" y="117" />
+        <di:waypoint x="762" y="117" />
+      </bpmndi:BPMNEdge>
+    </bpmndi:BPMNPlane>
+  </bpmndi:BPMNDiagram>
+</bpmn:definitions>

tests/study/test_study_associate_script.py

@@ -0,0 +1,52 @@
+from unittest.mock import patch
+import flask
+
+
+from tests.base_test import BaseTest
+
+from crc import session, app
+from crc.models.study import StudyModel
+from crc.models.user import UserModel
+from crc.services.study_service import StudyService
+from crc.services.workflow_processor import WorkflowProcessor
+from crc.services.workflow_service import WorkflowService
+
+class TestSudySponsorsScript(BaseTest):
+    test_uid = "dhf8r"
+    test_study_id = 1
+
+
+    def test_study_sponsors_script_validation(self):
+        flask.g.user = UserModel(uid='dhf8r')
+        self.load_example_data() # study_info script complains if irb_documents.xls is not loaded
+                                 # during the validate phase I'm going to assume that we will never
+                                 # have a case where irb_documents.xls is not loaded ??
+
+        self.load_test_spec("study_sponsors_associate")
+        WorkflowService.test_spec("study_sponsors_associate")  # This would raise errors if it didn't validate
+
+
+    @patch('crc.services.protocol_builder.requests.get')
+    def test_study_sponsors_script(self, mock_get):
+        mock_get.return_value.ok = True
+        mock_get.return_value.text = self.protocol_builder_response('sponsors.json')
+        flask.g.user = UserModel(uid='dhf8r')
+        app.config['PB_ENABLED'] = True
+
+        self.load_example_data()
+        self.create_reference_document()
+        study = session.query(StudyModel).first()
+        workflow_spec_model = self.load_test_spec("study_sponsors_associate")
+        workflow_model = StudyService._create_workflow_model(study, workflow_spec_model)
+        WorkflowService.test_spec("study_sponsors_associate")
+        processor = WorkflowProcessor(workflow_model)
+        processor.do_engine_steps()
+        self.assertTrue(processor.bpmn_workflow.is_completed())
+        data = processor.next_task().data
+        self.assertIn('sponsors', data)
+        self.assertIn('out', data)
+        print(data['out'])
+        self.assertEquals([{'uid': 'dhf8r', 'role': 'owner', 'send_email': True, 'access': True},
+                           {'uid': 'lb3dp', 'role': 'SuperDude', 'send_email': False, 'access': True}]
+                           , data['out'])
+        self.assertEquals(3, len(data['sponsors']))