Merge remote-tracking branch 'origin/chore/update_specs' into feature/previous_task

# Conflicts:
#	Pipfile.lock

Assuring that all documents from the xls spreadsheet are loaded when doing validations.

crc/scripts/study_info.py

@@ -61,32 +61,13 @@ class StudyInfo(Script):
                     "status": WorkflowStatus.not_started.value,
                     "workflow_spec_id": "irb_api_details",
                 },
-                "documents": {
-                    "AD_CoCApp":
-                    {
-                        'category1': 'Ancillary Document',
-                        'category2': 'CoC Application',
-                        'category3': '',
-                        'Who Uploads?': 'CRC',
-                        'Id': '12',
-                        'Name': 'Certificate of Confidentiality Application',
-                        'count': 0,
-                        'required': True,
-                        'code': 'AD_CoCApp',
-                        'display_name': 'Certificate of Confidentiality Application',
-                        'file_id': 123,
-                        'task_id': 'abcdef14236890',
-                        'workflow_id': 456,
-                        'workflow_spec_id': 'irb_api_details',
-                        'status': 'complete',
-                    }
-                },
                 'protocol': {
                     id: 0,
                 }
             }
         }
         self.add_data_to_task(task=task, data=data["study"])
+        self.add_data_to_task(task, {"documents": StudyService().get_documents_status(study_id)})
 
     def do_task(self, task, study_id, *args, **kwargs):
         self.check_args(args)

crc/services/study_service.py

@@ -104,7 +104,7 @@ class StudyService(object):
 
     @staticmethod
     def get_documents_status(study_id):
-        """Returns a list of documents related to the study, if they are required, and any file information
+        """Returns a list of documents related to the study, and any file information
         that is available.."""
 
         # Get PB required docs

crc/static/bpmn/core_info/core_info.bpmn

@@ -70,6 +70,9 @@
               <camunda:property id="placeholder" value="Limit Length: 11" />
               <camunda:property id="hide_expression" value="model.CTG_NA &#38;&#38; model.CTG_NA.enumNoRegister" />
             </camunda:properties>
+            <camunda:validation>
+              <camunda:constraint name="max_length" config="11" />
+            </camunda:validation>
           </camunda:formField>
           <camunda:formField id="CTG_StudyType" label="ClinicalTrials.gov Study Type" type="enum">
             <camunda:properties>
@@ -307,6 +310,18 @@
       <bpmndi:BPMNShape id="StartEvent_1mhzkcr_di" bpmnElement="StartEvent_1mhzkcr">
         <dc:Bounds x="-218" y="307" width="36" height="36" />
       </bpmndi:BPMNShape>
+      <bpmndi:BPMNShape id="UserTask_1y1qon7_di" bpmnElement="UserTask_1y1qon7">
+        <dc:Bounds x="620" y="340" width="100" height="80" />
+      </bpmndi:BPMNShape>
+      <bpmndi:BPMNShape id="UserTask_01zzzg9_di" bpmnElement="UserTask_01zzzg9">
+        <dc:Bounds x="620" y="460" width="100" height="80" />
+      </bpmndi:BPMNShape>
+      <bpmndi:BPMNShape id="UserTask_0gtuk1e_di" bpmnElement="UserTask_EnterMultiSiteInfo">
+        <dc:Bounds x="620" y="210" width="100" height="80" />
+      </bpmndi:BPMNShape>
+      <bpmndi:BPMNShape id="UserTask_0ebxkp7_di" bpmnElement="UserTask_0ebxkp7">
+        <dc:Bounds x="620" y="90" width="100" height="80" />
+      </bpmndi:BPMNShape>
       <bpmndi:BPMNShape id="Activity_0vthni9_di" bpmnElement="Activity_10nxpt2">
         <dc:Bounds x="-120" y="285" width="100" height="80" />
       </bpmndi:BPMNShape>
@@ -319,18 +334,6 @@
       <bpmndi:BPMNShape id="Activity_0x7b58m_di" bpmnElement="Activity_PBMultiSiteCheckQ28">
         <dc:Bounds x="350" y="285" width="100" height="80" />
       </bpmndi:BPMNShape>
-      <bpmndi:BPMNShape id="UserTask_01zzzg9_di" bpmnElement="UserTask_01zzzg9">
-        <dc:Bounds x="620" y="460" width="100" height="80" />
-      </bpmndi:BPMNShape>
-      <bpmndi:BPMNShape id="UserTask_1y1qon7_di" bpmnElement="UserTask_1y1qon7">
-        <dc:Bounds x="620" y="340" width="100" height="80" />
-      </bpmndi:BPMNShape>
-      <bpmndi:BPMNShape id="UserTask_0gtuk1e_di" bpmnElement="UserTask_EnterMultiSiteInfo">
-        <dc:Bounds x="620" y="210" width="100" height="80" />
-      </bpmndi:BPMNShape>
-      <bpmndi:BPMNShape id="UserTask_0ebxkp7_di" bpmnElement="UserTask_0ebxkp7">
-        <dc:Bounds x="620" y="90" width="100" height="80" />
-      </bpmndi:BPMNShape>
     </bpmndi:BPMNPlane>
   </bpmndi:BPMNDiagram>
 </bpmn:definitions>

crc/static/bpmn/finance/finance.bpmn

@@ -119,14 +119,14 @@ If you have any questions about the process, contact contract negotiator or Offi
         <di:waypoint x="682" y="337" />
       </bpmndi:BPMNEdge>
       <bpmndi:BPMNEdge id="SequenceFlow_0afrh4e_di" bpmnElement="SequenceFlow_0afrh4e">
-        <di:waypoint x="460" y="160" />
+        <di:waypoint x="460" y="190" />
-        <di:waypoint x="570" y="160" />
+        <di:waypoint x="570" y="190" />
         <di:waypoint x="570" y="312" />
       </bpmndi:BPMNEdge>
       <bpmndi:BPMNEdge id="SequenceFlow_0bvhrqu_di" bpmnElement="SequenceFlow_0bvhrqu">
         <di:waypoint x="250" y="312" />
-        <di:waypoint x="250" y="160" />
+        <di:waypoint x="250" y="190" />
-        <di:waypoint x="360" y="160" />
+        <di:waypoint x="360" y="190" />
       </bpmndi:BPMNEdge>
       <bpmndi:BPMNEdge id="SequenceFlow_1uxqr6o_di" bpmnElement="SequenceFlow_1uxqr6o">
         <di:waypoint x="158" y="337" />
@@ -144,14 +144,14 @@ If you have any questions about the process, contact contract negotiator or Offi
       <bpmndi:BPMNShape id="ParallelGateway_0f68xmc_di" bpmnElement="ExclusiveGateway_0tqopul">
         <dc:Bounds x="545" y="312" width="50" height="50" />
       </bpmndi:BPMNShape>
-      <bpmndi:BPMNShape id="UserTask_1fv8l08_di" bpmnElement="Task_0xn3d6z">
-        <dc:Bounds x="360" y="430" width="100" height="80" />
-      </bpmndi:BPMNShape>
       <bpmndi:BPMNShape id="UserTask_0tz5ojx_di" bpmnElement="Task_0dj66yz">
         <dc:Bounds x="360" y="297" width="100" height="80" />
       </bpmndi:BPMNShape>
+      <bpmndi:BPMNShape id="UserTask_1fv8l08_di" bpmnElement="Task_0xn3d6z">
+        <dc:Bounds x="360" y="430" width="100" height="80" />
+      </bpmndi:BPMNShape>
       <bpmndi:BPMNShape id="UserTask_03iirsg_di" bpmnElement="UserTask_03iirsg">
-        <dc:Bounds x="360" y="120" width="100" height="80" />
+        <dc:Bounds x="360" y="150" width="100" height="80" />
       </bpmndi:BPMNShape>
     </bpmndi:BPMNPlane>
   </bpmndi:BPMNDiagram>

crc/static/bpmn/hold/hold.bpmn

@@ -17,6 +17,8 @@
           <camunda:formField id="HoldNotes" label="Why was this study moved to Hold Status?" type="textarea">
             <camunda:properties>
               <camunda:property id="rows" value="5" />
+              <camunda:property id="group" value="Reason for Hold Notes" />
+              <camunda:property id="repeat" value="Reason for Hold Notes" />
             </camunda:properties>
           </camunda:formField>
         </camunda:formData>

crc/static/bpmn/ids_full_submission/investigators_brochure.dmn

@@ -11,7 +11,7 @@
         </inputExpression>
       </input>
       <output id="output_1" label="Investigator&#39;s Brochure(s) Uploaded?" name="isInvestigatorsBrochure" typeRef="boolean" />
-      <output id="OutputClause_1f3mlfn" label="Investigator&#39;s Broshure Form Banner" name="ElementDoc_InvestigatorsBrochure" typeRef="string" />
+      <output id="OutputClause_1f3mlfn" label="Investigator&#39;s Brochure Form Banner" name="ElementDoc_InvestigatorsBrochure" typeRef="string" />
       <rule id="DecisionRule_0zvgaym">
         <inputEntry id="UnaryTests_0mwq0my">
           <text>0</text>

crc/static/bpmn/ids_full_submission/pharmacy_manual.dmn

@@ -7,7 +7,7 @@
     <decisionTable id="decisionTable_1">
       <input id="input_1" label="Pharmacy Manual Upload Count">
         <inputExpression id="inputExpression_1" typeRef="integer">
-          <text>StudyInfo.documents.DrugDevDoc_PharmManual.count</text>
+          <text>StudyInfo.documents["DrugDevDoc_PharmManual"]["count"]</text>
         </inputExpression>
       </input>
       <output id="output_1" label="Pharmacy Manual(s) Uploaded?" name="isPharmacyManual" typeRef="boolean" />

crc/static/bpmn/top_level_workflow/data_security_plan.dmn

@@ -6,8 +6,8 @@
     </extensionElements>
     <decisionTable id="DecisionTable_1mjqwlv">
       <input id="InputClause_18pwfqu" label="Required Doc Keys">
-        <inputExpression id="LiteralExpression_1y84stb" typeRef="boolean" expressionLanguage="feel">
+        <inputExpression id="LiteralExpression_1y84stb" typeRef="boolean" expressionLanguage="python">
-          <text>StudyInfo.documents.Study_DataSecurityPlan.required</text>
+          <text>StudyInfo.documents['Study_DataSecurityPlan']['required']</text>
         </inputExpression>
       </input>
       <output id="OutputClause_05y0j7c" label="data_security_plan" name="data_security_plan" typeRef="string" />

crc/static/bpmn/top_level_workflow/enter_core_info.dmn

@@ -7,7 +7,7 @@
     <decisionTable id="decisionTable_1">
       <input id="InputClause_1ki80j6" label="required doc ids">
         <inputExpression id="LiteralExpression_10mfcy7" typeRef="boolean" expressionLanguage="Python">
-          <text>StudyInfo.documents.UVACompl_PRCAppr.required</text>
+          <text>StudyInfo.documents['UVACompl_PRCAppr']['required']</text>
         </inputExpression>
       </input>
       <output id="output_1" label="enter_core_info" name="enter_core_info" typeRef="string" />

crc/static/bpmn/top_level_workflow/top_level_workflow.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:camunda="http://camunda.org/schema/1.0/bpmn" xmlns:di="http://www.omg.org/spec/DD/20100524/DI" id="Definitions_1kudwnk" targetNamespace="http://bpmn.io/schema/bpmn" exporter="Camunda Modeler" exporterVersion="3.4.1">
+<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:camunda="http://camunda.org/schema/1.0/bpmn" xmlns:di="http://www.omg.org/spec/DD/20100524/DI" id="Definitions_1kudwnk" targetNamespace="http://bpmn.io/schema/bpmn" exporter="Camunda Modeler" exporterVersion="3.7.0">
   <bpmn:process id="Process_0jhpidf" isExecutable="true">
     <bpmn:startEvent id="StartEvent_1">
       <bpmn:outgoing>SequenceFlow_1ees8ka</bpmn:outgoing>
@@ -26,7 +26,12 @@
       <bpmn:outgoing>Flow_0pwtiqm</bpmn:outgoing>
     </bpmn:parallelGateway>
     <bpmn:sequenceFlow id="Flow_0pwtiqm" sourceRef="Gateway_12tpgcy" targetRef="Activity_0f295la" />
-    <bpmn:parallelGateway id="Gateway_1nta7st">
+    <bpmn:parallelGateway id="Gateway_1nta7st" name="Some Name">
+      <bpmn:extensionElements>
+        <camunda:properties>
+          <camunda:property name="display_name" value="Some Name" />
+        </camunda:properties>
+      </bpmn:extensionElements>
       <bpmn:incoming>SequenceFlow_17ct47v</bpmn:incoming>
       <bpmn:outgoing>Flow_1m8285h</bpmn:outgoing>
       <bpmn:outgoing>Flow_18pl92p</bpmn:outgoing>
@@ -211,6 +216,9 @@
       </bpmndi:BPMNShape>
       <bpmndi:BPMNShape id="Gateway_1m22g4p_di" bpmnElement="Gateway_1nta7st">
         <dc:Bounds x="468" y="414" width="50" height="50" />
+        <bpmndi:BPMNLabel>
+          <dc:Bounds x="462" y="471" width="62" height="14" />
+        </bpmndi:BPMNLabel>
       </bpmndi:BPMNShape>
       <bpmndi:BPMNShape id="Activity_16cm213_di" bpmnElement="Activity_16cm213">
         <dc:Bounds x="550" y="650" width="100" height="80" />

example_data.py

@@ -221,6 +221,7 @@ class ExampleDataLoader:
 
             is_status = filename.lower() == 'status.bpmn'
             is_primary = filename.lower() == id + '.bpmn'
+            file = None
             try:
                 file = open(file_path, 'rb')
                 data = file.read()

migrations/versions/89073ca446a3_.py

@@ -0,0 +1,60 @@
+"""empty message
+
+Revision ID: 89073ca446a3
+Revises: 1685be1cc232
+Create Date: 2020-05-05 11:09:00.307363
+
+"""
+from alembic import op
+import sqlalchemy as sa
+from sqlalchemy.dialects import postgresql
+
+# revision identifiers, used by Alembic.
+revision = '89073ca446a3'
+down_revision = '1685be1cc232'
+branch_labels = None
+depends_on = None
+
+
+def upgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.drop_table('workflow_stats')
+    op.add_column('task_event', sa.Column('action', sa.String(), nullable=True))
+    op.add_column('task_event', sa.Column('mi_count', sa.Integer(), nullable=True))
+    op.add_column('task_event', sa.Column('mi_index', sa.Integer(), nullable=True))
+    op.add_column('task_event', sa.Column('mi_type', sa.String(), nullable=True))
+    op.add_column('task_event', sa.Column('process_name', sa.String(), nullable=True))
+    op.add_column('task_event', sa.Column('task_name', sa.String(), nullable=True))
+    op.add_column('task_event', sa.Column('task_title', sa.String(), nullable=True))
+    op.add_column('task_event', sa.Column('task_type', sa.String(), nullable=True))
+    op.add_column('workflow', sa.Column('last_updated', sa.DateTime(), nullable=True))
+    # ### end Alembic commands ###
+
+
+def downgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.drop_column('workflow', 'last_updated')
+    op.drop_column('task_event', 'task_type')
+    op.drop_column('task_event', 'task_title')
+    op.drop_column('task_event', 'task_name')
+    op.drop_column('task_event', 'process_name')
+    op.drop_column('task_event', 'mi_type')
+    op.drop_column('task_event', 'mi_index')
+    op.drop_column('task_event', 'mi_count')
+    op.drop_column('task_event', 'action')
+    op.create_table('workflow_stats',
+    sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False),
+    sa.Column('study_id', sa.INTEGER(), autoincrement=False, nullable=False),
+    sa.Column('workflow_id', sa.INTEGER(), autoincrement=False, nullable=False),
+    sa.Column('workflow_spec_id', sa.VARCHAR(), autoincrement=False, nullable=True),
+    sa.Column('spec_version', sa.VARCHAR(), autoincrement=False, nullable=True),
+    sa.Column('num_tasks_total', sa.INTEGER(), autoincrement=False, nullable=True),
+    sa.Column('num_tasks_complete', sa.INTEGER(), autoincrement=False, nullable=True),
+    sa.Column('num_tasks_incomplete', sa.INTEGER(), autoincrement=False, nullable=True),
+    sa.Column('last_updated', postgresql.TIMESTAMP(), autoincrement=False, nullable=True),
+    sa.ForeignKeyConstraint(['study_id'], ['study.id'], name='workflow_stats_study_id_fkey'),
+    sa.ForeignKeyConstraint(['workflow_id'], ['workflow.id'], name='workflow_stats_workflow_id_fkey'),
+    sa.ForeignKeyConstraint(['workflow_spec_id'], ['workflow_spec.id'], name='workflow_stats_workflow_spec_id_fkey'),
+    sa.PrimaryKeyConstraint('id', name='workflow_stats_pkey')
+    )
+    # ### end Alembic commands ###

tests/test_workflow_processor.py

@@ -392,9 +392,9 @@ class TestWorkflowProcessor(BaseTest):
         self.assertTrue("enter_core_info" in data)
         self.assertEqual("required", data["enter_core_info"])
 
-        # It should mark the Data Security Plan as required, because InfoSec Approval (24) is included in required docs.
+        # It should mark Personnel as required, because StudyInfo.investigators is not empty.
-        # self.assertTrue("data_security_plan" in data)
+        self.assertTrue("personnel" in data)
-        # self.assertEqual("required", data["data_security_plan"])
+        self.assertEqual("required", data["personnel"])
 
         # It should mark the sponsor funding source as disabled since the funding required (12) is not included in the required docs.
         self.assertTrue("sponsor_funding_source" in data)