Merge branch 'dev' into dependabot/pip/lxml-4.6.3

crc/api.yml

@@ -160,7 +160,6 @@ paths:
     parameters:
       - name: workflow_spec_id
         in: path
-        required: false
         description: The unique id of an existing workflow specification to modify.
         schema:
           type: string

crc/models/study.py

@@ -96,7 +96,7 @@ class WorkflowMetadata(object):
     def __init__(self, id, name = None, display_name = None, description = None, spec_version = None,
                  category_id  = None, category_display_name  = None, state: WorkflowState  = None,
                  status: WorkflowStatus  = None, total_tasks  = None, completed_tasks  = None,
-                 is_review=None,display_order = None):
+                 is_review=None,display_order = None, state_message = None):
         self.id = id
         self.name = name
         self.display_name = display_name
@@ -105,6 +105,7 @@ class WorkflowMetadata(object):
         self.category_id = category_id
         self.category_display_name = category_display_name
         self.state = state
+        self.state_message = state_message
         self.status = status
         self.total_tasks = total_tasks
         self.completed_tasks = completed_tasks
@@ -140,7 +141,7 @@ class WorkflowMetadataSchema(ma.Schema):
         model = WorkflowMetadata
         additional = ["id", "name", "display_name", "description",
                  "total_tasks", "completed_tasks", "display_order",
-                      "category_id", "is_review", "category_display_name"]
+                      "category_id", "is_review", "category_display_name", "state_message"]
         unknown = INCLUDE
 
 

crc/services/study_service.py

@@ -71,7 +71,7 @@ class StudyService(object):
             study.last_activity_user = LdapService.user_info(last_event.user_uid).display_name
             study.last_activity_date = last_event.date
         study.categories = StudyService.get_categories()
-        workflow_metas = StudyService.__get_workflow_metas(study_id)
+        workflow_metas = StudyService._get_workflow_metas(study_id)
         files = FileService.get_files_for_study(study.id)
         files = (File.from_models(model, FileService.get_file_data(model.id),
                                   FileService.get_doc_dictionary()) for model in files)
@@ -83,8 +83,9 @@ class StudyService(object):
             # this line is taking 99% of the time that is used in get_study.
             # see ticket #196
             if do_status:
-                status = StudyService.__get_study_status(study_model)
+                # __get_study_status() runs the master workflow to generate the status dictionary
-                study.warnings = StudyService.__update_status_of_workflow_meta(workflow_metas, status)
+                status = StudyService._get_study_status(study_model)
+                study.warnings = StudyService._update_status_of_workflow_meta(workflow_metas, status)
 
             # Group the workflows into their categories.
             for category in study.categories:
@@ -416,24 +417,36 @@ class StudyService(object):
         db.session.commit()
 
     @staticmethod
-    def __update_status_of_workflow_meta(workflow_metas, status):
+    def _update_status_of_workflow_meta(workflow_metas, status):
         # Update the status on each workflow
         warnings = []
         for wfm in workflow_metas:
-            if wfm.name in status.keys():
+            wfm.state_message = ''
-                if not WorkflowState.has_value(status[wfm.name]):
+            # do we have a status for you
-                    warnings.append(ApiError("invalid_status",
+            if wfm.name not in status.keys():
-                                             "Workflow '%s' can not be set to '%s', should be one of %s" % (
-                                                 wfm.name, status[wfm.name], ",".join(WorkflowState.list())
-                                             )))
-                else:
-                    wfm.state = WorkflowState[status[wfm.name]]
-            else:
                 warnings.append(ApiError("missing_status", "No status specified for workflow %s" % wfm.name))
+                continue
+            if not isinstance(status[wfm.name], dict):
+                warnings.append(ApiError(code='invalid_status',
+                                         message=f'Status must be a dictionary with "status" and "message" keys. Name is {wfm.name}. Status is {status[wfm.name]}'))
+                continue
+            if 'status' not in status[wfm.name].keys():
+                warnings.append(ApiError("missing_status",
+                                         "Workflow '%s' does not have a status setting" % wfm.name))
+                continue
+            if not WorkflowState.has_value(status[wfm.name]['status']):
+                warnings.append(ApiError("invalid_state",
+                                         "Workflow '%s' can not be set to '%s', should be one of %s" % (
+                                             wfm.name, status[wfm.name]['status'], ",".join(WorkflowState.list())
+                                         )))
+                continue
+            wfm.state = WorkflowState[status[wfm.name]['status']]
+            if 'message' in status[wfm.name].keys():
+                wfm.state_message = status[wfm.name]['message']
         return warnings
 
     @staticmethod
-    def __get_workflow_metas(study_id):
+    def _get_workflow_metas(study_id):
         # Add in the Workflows for each category
         workflow_models = db.session.query(WorkflowModel). \
             join(WorkflowSpecModel). \
@@ -446,7 +459,7 @@ class StudyService(object):
         return workflow_metas
 
     @staticmethod
-    def __get_study_status(study_model):
+    def _get_study_status(study_model):
         """Uses the Top Level Workflow to calculate the status of the study, and it's
         workflow models."""
         master_specs = db.session.query(WorkflowSpecModel). \

tests/data/decision_table_dictionary_output/decision_table_dictionary_output.bpmn

@@ -0,0 +1,71 @@
+<?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_09rv9vf" targetNamespace="http://bpmn.io/schema/bpmn" exporter="Camunda Modeler" exporterVersion="3.5.0">
+  <bpmn:process id="Process_StatusMessage" name="Status Message" isExecutable="true">
+    <bpmn:documentation>Testing Workflow Status Messages</bpmn:documentation>
+    <bpmn:startEvent id="StartEvent_1">
+      <bpmn:outgoing>SequenceFlow_0x4n744</bpmn:outgoing>
+    </bpmn:startEvent>
+    <bpmn:sequenceFlow id="SequenceFlow_0x4n744" sourceRef="StartEvent_1" targetRef="Task_SetName" />
+    <bpmn:sequenceFlow id="SequenceFlow_1o630oy" sourceRef="Task_SetName" targetRef="Task_Decision" />
+    <bpmn:businessRuleTask id="Task_Decision" name="Make Decision" camunda:decisionRef="Decision_Dog">
+      <bpmn:incoming>SequenceFlow_1o630oy</bpmn:incoming>
+      <bpmn:outgoing>SequenceFlow_1foyag7</bpmn:outgoing>
+    </bpmn:businessRuleTask>
+    <bpmn:sequenceFlow id="SequenceFlow_1foyag7" sourceRef="Task_Decision" targetRef="Task_GoodBye" />
+    <bpmn:manualTask id="Task_GoodBye" name="Say Good Bye">
+      <bpmn:documentation>&lt;div&gt;&lt;span&gt;Good Bye {{ dog.name }}&lt;/span&gt;&lt;/div&gt;
+&lt;div&gt;&lt;span&gt;You are such a good {{ dog.breed }}&lt;/span&gt;&lt;/div&gt;
+</bpmn:documentation>
+      <bpmn:incoming>SequenceFlow_1foyag7</bpmn:incoming>
+      <bpmn:outgoing>SequenceFlow_1bc1ugw</bpmn:outgoing>
+    </bpmn:manualTask>
+    <bpmn:endEvent id="EndEvent_19dasnt">
+      <bpmn:incoming>SequenceFlow_1bc1ugw</bpmn:incoming>
+    </bpmn:endEvent>
+    <bpmn:sequenceFlow id="SequenceFlow_1bc1ugw" sourceRef="Task_GoodBye" targetRef="EndEvent_19dasnt" />
+    <bpmn:userTask id="Task_SetName" name="Set Name" camunda:formKey="NameForm">
+      <bpmn:extensionElements>
+        <camunda:formData>
+          <camunda:formField id="name" label="Name" type="string" defaultValue="Layla" />
+        </camunda:formData>
+      </bpmn:extensionElements>
+      <bpmn:incoming>SequenceFlow_0x4n744</bpmn:incoming>
+      <bpmn:outgoing>SequenceFlow_1o630oy</bpmn:outgoing>
+    </bpmn:userTask>
+  </bpmn:process>
+  <bpmndi:BPMNDiagram id="BPMNDiagram_1">
+    <bpmndi:BPMNPlane id="BPMNPlane_1" bpmnElement="Process_StatusMessage">
+      <bpmndi:BPMNShape id="_BPMNShape_StartEvent_2" bpmnElement="StartEvent_1">
+        <dc:Bounds x="165" y="99" width="36" height="36" />
+      </bpmndi:BPMNShape>
+      <bpmndi:BPMNEdge id="SequenceFlow_0x4n744_di" bpmnElement="SequenceFlow_0x4n744">
+        <di:waypoint x="201" y="117" />
+        <di:waypoint x="260" y="117" />
+      </bpmndi:BPMNEdge>
+      <bpmndi:BPMNEdge id="SequenceFlow_1o630oy_di" bpmnElement="SequenceFlow_1o630oy">
+        <di:waypoint x="360" y="117" />
+        <di:waypoint x="420" y="117" />
+      </bpmndi:BPMNEdge>
+      <bpmndi:BPMNShape id="BusinessRuleTask_0dwwkqn_di" bpmnElement="Task_Decision">
+        <dc:Bounds x="420" y="77" width="100" height="80" />
+      </bpmndi:BPMNShape>
+      <bpmndi:BPMNEdge id="SequenceFlow_1foyag7_di" bpmnElement="SequenceFlow_1foyag7">
+        <di:waypoint x="520" y="117" />
+        <di:waypoint x="580" y="117" />
+      </bpmndi:BPMNEdge>
+      <bpmndi:BPMNShape id="ManualTask_0nb6k7f_di" bpmnElement="Task_GoodBye">
+        <dc:Bounds x="580" y="77" width="100" height="80" />
+      </bpmndi:BPMNShape>
+      <bpmndi:BPMNShape id="EndEvent_19dasnt_di" bpmnElement="EndEvent_19dasnt">
+        <dc:Bounds x="742" y="99" width="36" height="36" />
+      </bpmndi:BPMNShape>
+      <bpmndi:BPMNEdge id="SequenceFlow_1bc1ugw_di" bpmnElement="SequenceFlow_1bc1ugw">
+        <di:waypoint x="680" y="117" />
+        <di:waypoint x="742" y="117" />
+      </bpmndi:BPMNEdge>
+      <bpmndi:BPMNShape id="UserTask_1h3sio1_di" bpmnElement="Task_SetName">
+        <dc:Bounds x="260" y="77" width="100" height="80" />
+      </bpmndi:BPMNShape>
+    </bpmndi:BPMNPlane>
+  </bpmndi:BPMNDiagram>
+</bpmn:definitions>

tests/data/decision_table_dictionary_output/decision_table_dictionary_output.dmn

@@ -0,0 +1,69 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<definitions xmlns="http://www.omg.org/spec/DMN/20151101/dmn.xsd" id="Definitions_1eg3sxk" name="DRD" namespace="http://camunda.org/schema/1.0/dmn" exporter="Camunda Modeler" exporterVersion="3.5.0">
+  <decision id="Decision_Dog" name="Dogs">
+    <decisionTable id="decisionTable_1">
+      <input id="input_1" label="Name">
+        <inputExpression id="inputExpression_1" typeRef="string">
+          <text>name</text>
+        </inputExpression>
+      </input>
+      <output id="output_1" label="Name" name="dog.name" typeRef="string" />
+      <output id="OutputClause_1wqk5xi" label="Breed" name="dog.breed" typeRef="string" />
+      <rule id="DecisionRule_1h6w5qu">
+        <inputEntry id="UnaryTests_0m8eblt">
+          <text>'Layla'</text>
+        </inputEntry>
+        <outputEntry id="LiteralExpression_186aovp">
+          <text>'Layla'</text>
+        </outputEntry>
+        <outputEntry id="LiteralExpression_10jbx5v">
+          <text>'Aussie'</text>
+        </outputEntry>
+      </rule>
+      <rule id="DecisionRule_0ziemrx">
+        <inputEntry id="UnaryTests_0okkroj">
+          <text>'Mona'</text>
+        </inputEntry>
+        <outputEntry id="LiteralExpression_0r1apkh">
+          <text>'Mona'</text>
+        </outputEntry>
+        <outputEntry id="LiteralExpression_08vl869">
+          <text>'Aussie Mix'</text>
+        </outputEntry>
+      </rule>
+      <rule id="DecisionRule_0fykwob">
+        <inputEntry id="UnaryTests_044ophk">
+          <text>'Jerry'</text>
+        </inputEntry>
+        <outputEntry id="LiteralExpression_0508umo">
+          <text>'Jerry'</text>
+        </outputEntry>
+        <outputEntry id="LiteralExpression_0ysgqib">
+          <text>'Aussie Mix'</text>
+        </outputEntry>
+      </rule>
+      <rule id="DecisionRule_05jugdn">
+        <inputEntry id="UnaryTests_1jri40s">
+          <text>'Zoey'</text>
+        </inputEntry>
+        <outputEntry id="LiteralExpression_1r5jrzq">
+          <text>'Zoey'</text>
+        </outputEntry>
+        <outputEntry id="LiteralExpression_0aqjmjy">
+          <text>'Healer'</text>
+        </outputEntry>
+      </rule>
+      <rule id="DecisionRule_0gehtk4">
+        <inputEntry id="UnaryTests_09f1t9t">
+          <text>'Etta'</text>
+        </inputEntry>
+        <outputEntry id="LiteralExpression_0kp8mvr">
+          <text>'Etta'</text>
+        </outputEntry>
+        <outputEntry id="LiteralExpression_0wwry9c">
+          <text>'Healer Mix'</text>
+        </outputEntry>
+      </rule>
+    </decisionTable>
+  </decision>
+</definitions>

tests/study/test_study_status_message.py

@@ -0,0 +1,66 @@
+from tests.base_test import BaseTest
+from crc import db, session
+from crc.models.study import StudyModel
+from crc.models.workflow import WorkflowState
+from crc.services.study_service import StudyService
+
+
+class TestStudyStatusMessage(BaseTest):
+
+    """The workflow runs with a workflow_meta.name of `random_fact`
+       Add an entry to `status` dictionary with a key of `random_fact`"""
+
+    def run_update_status(self, status):
+        # shared code
+        self.load_example_data()
+        study_model = session.query(StudyModel).first()
+        workflow_metas = StudyService._get_workflow_metas(study_model.id)
+        warnings = StudyService._update_status_of_workflow_meta(workflow_metas, status)
+        return workflow_metas, warnings
+
+    def test_study_status_message(self):
+        # these are the passing tests
+        # we loop through each Workflow state
+        # (hidden,disabled,required,optional)
+        for state in WorkflowState:
+            # use state.value to set status['status'],
+            status = {'random_fact':
+                      {'status': state.value,
+                       'message': 'This is my status message!'}}
+
+            # call run_update_status(),
+            workflow_metas, warnings = self.run_update_status(status)
+
+            # and assert the values of workflow_metas[0].state and workflow_metas[0].state_message
+            self.assertEqual(0, len(warnings))
+            self.assertEqual(state, workflow_metas[0].state)
+            self.assertEqual('This is my status message!', workflow_metas[0].state_message)
+
+    def test_study_status_message_bad_name(self):
+        # we don't have an entry for you in the status dictionary
+        status = {'bad_name': {'status': 'hidden', 'message': 'This is my status message!'}}
+        workflow_metas, warnings = self.run_update_status(status)
+
+        self.assertEqual(1, len(warnings))
+        self.assertEqual('missing_status', warnings[0].code)
+        self.assertEqual('No status specified for workflow random_fact', warnings[0].message)
+
+    def test_study_status_message_not_dict(self):
+        # your entry in the status dictionary is not a dictionary
+        status = {'random_fact':  'This is my status message!'}
+        workflow_metas, warnings = self.run_update_status(status)
+
+        self.assertEqual(1, len(warnings))
+        self.assertEqual('invalid_status', warnings[0].code)
+        self.assertEqual('Status must be a dictionary with "status" and "message" keys. Name is random_fact. Status is This is my status message!',
+                         warnings[0].message)
+
+    def test_study_status_message_bad_state(self):
+        # you have an invalid state
+        # I.e., not in (hidden,disabled,required,optional)
+        status = {'random_fact': {'status': 'hide', 'message': 'This is my status message!'}}
+        workflow_metas, warnings = self.run_update_status(status)
+        self.assertEqual(1, len(warnings))
+        self.assertEqual('invalid_state', warnings[0].code)
+        self.assertEqual('Workflow \'random_fact\' can not be set to \'hide\', should be one of hidden,disabled,required,optional',
+                         warnings[0].message)

tests/test_decision_table_dictionary_output.py

@@ -0,0 +1,15 @@
+from tests.base_test import BaseTest
+
+
+class TestDecisionTableDictionaryOutput(BaseTest):
+
+    def test_decision_table_dictionary_output(self):
+
+        workflow = self.create_workflow('decision_table_dictionary_output')
+        workflow_api = self.get_workflow_api(workflow)
+        first_task = workflow_api.next_task
+
+        result = self.complete_form(workflow, first_task, {'name': 'Mona'})
+        self.assertIn('dog', result.next_task.data)
+        self.assertEqual('Mona', result.next_task.data['dog']['name'])
+        self.assertEqual('Aussie Mix', result.next_task.data['dog']['breed'])