Merge pull request #135 from sartography/feature/multi_instance_titles

* Modifying the StudyInfo script to return both "investigators" and "…

crc/scripts/study_info.py

@@ -14,7 +14,7 @@ class StudyInfo(Script):
     """Please see the detailed description that is provided below. """
 
     pb = ProtocolBuilderService()
-    type_options = ['info', 'investigators', 'details', 'approvals', 'documents', 'protocol']
+    type_options = ['info', 'investigators', 'roles', 'details', 'approvals', 'documents', 'protocol']
 
     # This is used for test/workflow validation, as well as documentation.
     example_data = {
@@ -106,11 +106,20 @@ Returns the basic information such as the id and title
 ### Investigators ###
 Returns detailed information about related personnel.
 The order returned is guaranteed to match the order provided in the investigators.xslx reference file.
-If possible, detailed information is added in from LDAP about each personnel based on their user_id.
+Detailed information is added in from LDAP about each personnel based on their user_id. 
 ```
 {investigators_example}
 ```
 
+### Investigator Roles ###
+Returns a list of all investigator roles, populating any roles with additional information available from
+the Protocol Builder and LDAP.  Its basically just like Investigators, but it includes all the roles, rather
+that just those that were set in Protocol Builder.
+```
+{investigators_example}
+```
+
+
 ### Details ###
 Returns detailed information about variable keys read in from the Protocol Builder.
 
@@ -161,6 +170,12 @@ Returns information specific to the protocol.
                         "INVESTIGATORTYPEFULL": "Primary Investigator",
                         "NETBADGEID": "dhf8r"
                     },
+                "roles":
+                    {
+                        "INVESTIGATORTYPE": "PI",
+                        "INVESTIGATORTYPEFULL": "Primary Investigator",
+                        "NETBADGEID": "dhf8r"
+                    },
                 "details":
                     {
                         "IS_IND": 0,
@@ -198,6 +213,8 @@ Returns information specific to the protocol.
             self.add_data_to_task(task, {cmd: schema.dump(study)})
         if cmd == 'investigators':
             self.add_data_to_task(task, {cmd: StudyService().get_investigators(study_id)})
+        if cmd == 'roles':
+            self.add_data_to_task(task, {cmd: StudyService().get_investigators(study_id, all=True)})
         if cmd == 'details':
             self.add_data_to_task(task, {cmd: self.pb.get_study_details(study_id)})
         if cmd == 'approvals':

crc/services/study_service.py

@@ -182,7 +182,7 @@ class StudyService(object):
         return documents
 
     @staticmethod
-    def get_investigators(study_id):
+    def get_investigators(study_id, all=False):
 
         # Loop through all known investigator types as set in the reference file
         inv_dictionary = FileService.get_reference_data(FileService.INVESTIGATOR_LIST, 'code')
@@ -199,6 +199,8 @@ class StudyService(object):
             else:
                 inv_dictionary[i_type]['user_id'] = None
 
+        if not all:
+            inv_dictionary = dict(filter(lambda elem: elem[1]['user_id'] is not None, inv_dictionary.items()))
         return inv_dictionary
 
     @staticmethod

crc/services/workflow_service.py

@@ -207,8 +207,10 @@ class WorkflowService(object):
             if spiff_task:
                 nav_item['task'] = WorkflowService.spiff_task_to_api_task(spiff_task, add_docs_and_forms=False)
                 nav_item['title'] = nav_item['task'].title  # Prefer the task title.
+
             else:
                 nav_item['task'] = None
+
             if not 'is_decision' in nav_item:
                 nav_item['is_decision'] = False
 
@@ -333,10 +335,12 @@ class WorkflowService(object):
         # otherwise strip off the first word of the task, as that should be following
         # a BPMN standard, and should not be included in the display.
         if task.properties and "display_name" in task.properties:
-            task.title = task.properties['display_name']
+            try:
+                task.title = spiff_task.workflow.script_engine.evaluate_expression(spiff_task, task.properties['display_name'])
+            except Exception as e:
+                app.logger.info("Failed to set title on task due to type error." + str(e))
         elif task.title and ' ' in task.title:
             task.title = task.title.partition(' ')[2]
-
         return task
 
     @staticmethod

tests/data/multi_instance_parallel/multi_instance_parallel.bpmn

@@ -17,6 +17,9 @@
         <camunda:formData>
           <camunda:formField id="email" label="Email Address:" type="string" />
         </camunda:formData>
+        <camunda:properties>
+          <camunda:property name="display_name" value="investigator.label" />
+        </camunda:properties>
       </bpmn:extensionElements>
       <bpmn:incoming>SequenceFlow_1p568pp</bpmn:incoming>
       <bpmn:outgoing>Flow_0ugjw69</bpmn:outgoing>

tests/study/test_study_api.py

@@ -182,8 +182,8 @@ class TestStudyApi(BaseTest):
         self.assertGreater(num_db_studies_after, num_db_studies_before)
         self.assertEqual(num_abandoned, 1)
         self.assertEqual(num_open, 1)
-        self.assertEqual(num_active, 1)
+        self.assertEqual(num_active, 2)
-        self.assertEqual(num_incomplete, 1)
+        self.assertEqual(num_incomplete, 0)
         self.assertEqual(len(json_data), num_db_studies_after)
         self.assertEqual(num_open + num_active + num_incomplete + num_abandoned, num_db_studies_after)
 

tests/study/test_study_service.py

@@ -183,7 +183,7 @@ class TestStudyService(BaseTest):
 
 
     @patch('crc.services.protocol_builder.ProtocolBuilderService.get_investigators')  # mock_docs
-    def test_get_personnel(self, mock_docs):
+    def test_get_personnel_roles(self, mock_docs):
         self.load_example_data()
 
         # mock out the protocol builder
@@ -191,7 +191,7 @@ class TestStudyService(BaseTest):
         mock_docs.return_value = json.loads(docs_response)
 
         workflow = self.create_workflow('docx') # The workflow really doesnt matter in this case.
-        investigators = StudyService().get_investigators(workflow.study_id)
+        investigators = StudyService().get_investigators(workflow.study_id, all=True)
 
         self.assertEqual(9, len(investigators))
 
@@ -207,3 +207,22 @@ class TestStudyService(BaseTest):
 
         # No value is provided for Department Chair
         self.assertIsNone(investigators['DEPT_CH']['user_id'])
+
+    @patch('crc.services.protocol_builder.ProtocolBuilderService.get_investigators')  # mock_docs
+    def test_get_study_personnel(self, mock_docs):
+        self.load_example_data()
+
+        # mock out the protocol builder
+        docs_response = self.protocol_builder_response('investigators.json')
+        mock_docs.return_value = json.loads(docs_response)
+
+        workflow = self.create_workflow('docx') # The workflow really doesnt matter in this case.
+        investigators = StudyService().get_investigators(workflow.study_id, all=False)
+
+        self.assertEqual(3, len(investigators))
+
+        # dhf8r is in the ldap mock data.
+        self.assertEqual("dhf8r", investigators['PI']['user_id'])
+        self.assertEqual("Dan Funk", investigators['PI']['display_name']) # Data from ldap
+        self.assertEqual("Primary Investigator", investigators['PI']['label']) # Data from xls file.
+        self.assertEqual("Always", investigators['PI']['display']) # Data from xls file.

tests/test_tasks_api.py

@@ -322,7 +322,7 @@ class TestTasksApi(BaseTest):
         self.assertEqual(4, len(navigation)) # Start task, form_task, multi_task, end task
         self.assertEqual("UserTask", workflow.next_task.type)
         self.assertEqual(MultiInstanceType.sequential.value, workflow.next_task.multi_instance_type)
-        self.assertEqual(9, workflow.next_task.multi_instance_count)
+        self.assertEqual(3, workflow.next_task.multi_instance_count)
 
         # Assure that the names for each task are properly updated, so they aren't all the same.
         self.assertEqual("Primary Investigator", workflow.next_task.properties['display_name'])
@@ -480,17 +480,23 @@ class TestTasksApi(BaseTest):
         workflow = self.create_workflow('multi_instance_parallel')
 
         workflow_api = self.get_workflow_api(workflow)
-        self.assertEqual(12, len(workflow_api.navigation))
+        self.assertEqual(6, len(workflow_api.navigation))
         ready_items = [nav for nav in workflow_api.navigation if nav['state'] == "READY"]
-        self.assertEqual(9, len(ready_items))
+        self.assertEqual(3, len(ready_items))
 
         self.assertEqual("UserTask", workflow_api.next_task.type)
         self.assertEqual("MultiInstanceTask",workflow_api.next_task.name)
-        self.assertEqual("more information", workflow_api.next_task.title)
+        self.assertEqual("Primary Investigator", workflow_api.next_task.title)
 
-        for i in random.sample(range(9), 9):
+        for i in random.sample(range(3), 3):
             task = TaskSchema().load(ready_items[i]['task'])
-            data = workflow_api.next_task.data
+            rv = self.app.put('/v1.0/workflow/%i/task/%s/set_token' % (workflow.id, task.id),
+                              headers=self.logged_in_headers(),
+                              content_type="application/json")
+            self.assert_success(rv)
+            json_data = json.loads(rv.get_data(as_text=True))
+            workflow = WorkflowApiSchema().load(json_data)
+            data = workflow.next_task.data
             data['investigator']['email'] = "dhf8r@virginia.edu"
             self.complete_form(workflow, task, data)
             #tasks = self.get_workflow_api(workflow).user_tasks

tests/workflow/test_workflow_processor_multi_instance.py

@@ -146,6 +146,11 @@ class TestWorkflowProcessorMultiInstance(BaseTest):
 
         api_task = WorkflowService.spiff_task_to_api_task(task)
         self.assertEqual(MultiInstanceType.parallel, api_task.multi_instance_type)
+
+        # Assure navigation picks up the label of the current element variable.
+        nav = WorkflowService.processor_to_workflow_api(processor, task).navigation
+        self.assertEquals("Primary Investigator", nav[2].title)
+
         task.update_data({"investigator": {"email": "dhf8r@virginia.edu"}})
         processor.complete_task(task)
         processor.do_engine_steps()