Merge pull request #30 from sartography/feature_personnel_multi_instance

Feature multi instance

Pipfile.lock

@@ -717,11 +717,11 @@
         },
         "sphinx": {
             "hashes": [
-                "sha256:50972d83b78990fd61d0d3fe8620814cae53db29443e92c13661bc43dff46ec8",
+                "sha256:3145d87d0962366d4c5264c39094eae3f5788d01d4b1a12294051bfe4271d91b",
-                "sha256:8411878f4768ec2a8896b844d68070204f9354a831b37937989c2e559d29dffc"
+                "sha256:d7c6e72c6aa229caf96af82f60a0d286a1521d42496c226fe37f5a75dcfe2941"
             ],
             "index": "pypi",
-            "version": "==3.0.1"
+            "version": "==3.0.2"
         },
         "sphinxcontrib-applehelp": {
             "hashes": [
@@ -768,7 +768,7 @@
         "spiffworkflow": {
             "editable": true,
             "git": "https://github.com/sartography/SpiffWorkflow.git",
-            "ref": "d5f385f74ca2f755589aab2588333aa007d20852"
+            "ref": "69cbb9d67d87895f8bcad7e6017802ba38f76895"
         },
         "sqlalchemy": {
             "hashes": [
@@ -805,10 +805,10 @@
         },
         "urllib3": {
             "hashes": [
-                "sha256:2f3db8b19923a873b3e5256dc9c2dedfa883e33d87c690d9c7913e1f40673cdc",
+                "sha256:3018294ebefce6572a474f0604c2021e33b3fd8006ecd11d62107a5d2a963527",
-                "sha256:87716c2d2a7121198ebcb7ce7cccf6ce5e9ba539041cfbaeecfb641dc0bf6acc"
+                "sha256:88206b0eb87e6d677d424843ac5209e3fb9d0190d0ee169599165ec25e9d9115"
             ],
-            "version": "==1.25.8"
+            "version": "==1.25.9"
         },
         "vine": {
             "hashes": [

crc/api.yml

@@ -584,7 +584,7 @@ paths:
             format: int32
     get:
       operationId: crc.api.workflow.get_workflow
-      summary: Detailed information for a specific workflow instance
+      summary: Returns a workflow, can also be used to do a soft or hard reset on the workflow.
       parameters:
         - name: soft_reset
           in: query

crc/models/api_models.py

@@ -12,7 +12,7 @@ class Task(object):
     EMUM_OPTIONS_VALUE_COL_PROP = "enum.options.value.column"
     EMUM_OPTIONS_LABEL_COL_PROP = "enum.options.label.column"
 
-    def __init__(self, id, name, title, type, state, form, documentation, data):
+    def __init__(self, id, name, title, type, state, form, documentation, data, is_multi_instance, mi_count, mi_index):
         self.id = id
         self.name = name
         self.title = title
@@ -21,7 +21,9 @@ class Task(object):
         self.form = form
         self.documentation = documentation
         self.data = data
-
+        self.is_multi_instance = is_multi_instance
+        self.mi_count = mi_count
+        self.mi_index = mi_index
 
 class OptionSchema(ma.Schema):
     class Meta:
@@ -57,7 +59,8 @@ class FormSchema(ma.Schema):
 
 class TaskSchema(ma.Schema):
     class Meta:
-        fields = ["id", "name", "title", "type", "state", "form", "documentation", "data"]
+        fields = ["id", "name", "title", "type", "state", "form", "documentation", "data", "is_multi_instance",
+                  "mi_count", "mi_index"]
 
     documentation = marshmallow.fields.String(required=False, allow_none=True)
     form = marshmallow.fields.Nested(FormSchema, required=False, allow_none=True)

crc/scripts/complete_template.py

@@ -36,7 +36,9 @@ Takes two arguments:
 
         file_name = args[0]
         irb_doc_code = args[1]
-        FileService.add_task_file(study_id=study_id, workflow_id=workflow_id, task_id=task.id,
+        FileService.add_task_file(study_id=study_id,
+                                  workflow_id=workflow_id,
+                                  task_id=task.id,
                                   name=file_name,
                                   content_type=CONTENT_TYPES['docx'],
                                   binary_data=final_document_stream.read(),

crc/scripts/study_info.py

@@ -58,11 +58,12 @@ class StudyInfo(Script):
         if cmd == 'info':
             study = session.query(StudyModel).filter_by(id=study_id).first()
             schema = StudySchema()
-            study_info["info"] = schema.dump(study)
+            self.add_data_to_task(task, {cmd: schema.dump(study)})
         if cmd == 'investigators':
-            study_info["investigators"] = self.pb.get_investigators(study_id)
+            pb_response = self.pb.get_investigators(study_id)
+            self.add_data_to_task(task, {cmd: self.organize_investigators_by_type(pb_response)})
         if cmd == 'details':
-            study_info["details"] = self.pb.get_study_details(study_id)
+            self.add_data_to_task(task, {cmd: self.pb.get_study_details(study_id)})
         task.data["study"] = study_info
 
 
@@ -71,3 +72,11 @@ class StudyInfo(Script):
             raise ApiError(code="missing_argument",
                            message="The StudyInfo script requires a single argument which must be "
                                    "one of %s" % ",".join(StudyInfo.type_options))
+
+
+    def organize_investigators_by_type(self, pb_investigators):
+        """Convert array of investigators from protocol builder into a dictionary keyed on the type"""
+        output = {}
+        for i in pb_investigators:
+            output[i["INVESTIGATORTYPE"]] = {"user_id": i["NETBADGEID"], "type_full": i["INVESTIGATORTYPEFULL"]}
+        return output

crc/services/file_service.py

@@ -199,7 +199,7 @@ class FileService(object):
     @staticmethod
     def get_workflow_file_data(workflow, file_name):
         """Given a SPIFF Workflow Model, tracks down a file with the given name in the datbase and returns it's data"""
-        workflow_spec_model = FileService.__find_spec_model_in_db(workflow)
+        workflow_spec_model = FileService.find_spec_model_in_db(workflow)
         study_id = workflow.data[WorkflowProcessor.STUDY_ID_KEY]
 
         if workflow_spec_model is None:
@@ -219,7 +219,7 @@ class FileService(object):
         return file_data_model
 
     @staticmethod
-    def __find_spec_model_in_db(workflow):
+    def find_spec_model_in_db(workflow):
         """ Search for the workflow """
         # When the workflow spec model is created, we record the primary process id,
         # then we can look it up.  As there is the potential for sub-workflows, we
@@ -228,7 +228,7 @@ class FileService(object):
         workflow_model = session.query(WorkflowSpecModel).join(FileModel). \
             filter(FileModel.primary_process_id == spec.name).first()
         if workflow_model is None and workflow != workflow.outer_workflow:
-            return FileService.__find_spec_model_in_db(workflow.outer_workflow)
+            return FileService.find_spec_model_in_db(workflow.outer_workflow)
 
         return workflow_model
 

crc/services/workflow_service.py

@@ -1,4 +1,11 @@
+from SpiffWorkflow.bpmn.specs.ManualTask import ManualTask
+from SpiffWorkflow.bpmn.specs.MultiInstanceTask import MultiInstanceTask
+from SpiffWorkflow.bpmn.specs.NoneTask import NoneTask
+from SpiffWorkflow.bpmn.specs.ScriptTask import ScriptTask
+from SpiffWorkflow.bpmn.specs.UserTask import UserTask
 from SpiffWorkflow.bpmn.workflow import BpmnWorkflow
+from SpiffWorkflow.dmn.specs.BuisnessRuleTask import BusinessRuleTask
+from SpiffWorkflow.specs import CancelTask, StartTask
 from pandas import ExcelFile
 
 from crc.api.common import ApiError
@@ -45,14 +52,44 @@ class WorkflowService(object):
 
     @staticmethod
     def spiff_task_to_api_task(spiff_task):
+        task_type = spiff_task.task_spec.__class__.__name__
+
+        if isinstance(spiff_task.task_spec, UserTask):
+            task_type = "UserTask"
+        elif isinstance(spiff_task.task_spec, ManualTask):
+            task_type = "ManualTask"
+        elif isinstance(spiff_task.task_spec, BusinessRuleTask):
+            task_type = "BusinessRuleTask"
+        elif isinstance(spiff_task.task_spec, CancelTask):
+            task_type = "CancelTask"
+        elif isinstance(spiff_task.task_spec, ScriptTask):
+            task_type = "ScriptTask"
+        elif isinstance(spiff_task.task_spec, StartTask):
+            task_type = "StartTask"
+        else:
+            task_type = "NoneTask"
+
+        multi_instance = isinstance(spiff_task.task_spec, MultiInstanceTask)
+        mi_count = 0
+        mi_index = 0
+        if multi_instance:
+            mi_count = spiff_task.task_spec._get_count(spiff_task)
+            mi_index = int(spiff_task._get_internal_data('runtimes', 1))
+
+
         task = Task(spiff_task.id,
                     spiff_task.task_spec.name,
                     spiff_task.task_spec.description,
-                    spiff_task.task_spec.__class__.__name__,
+                    task_type,
                     spiff_task.get_state_name(),
                     None,
                     "",
-                    spiff_task.data)
+                    spiff_task.data,
+                    multi_instance,
+                    mi_count,
+                    mi_index)
+
+
 
         # Only process the form and documentation if this is something that is ready or completed.
         if not (spiff_task._is_predicted()):
@@ -100,8 +137,8 @@ class WorkflowService(object):
                 raise ApiError.from_task("invalid_emum",
                                          "For emumerations based on an xls file, you must include 3 properties: %s, "
                                          "%s, and %s, you supplied %s" % (Task.ENUM_OPTIONS_FILE_PROP,
-                                                         Task.EMUM_OPTIONS_VALUE_COL_PROP,
+                                                                          Task.EMUM_OPTIONS_VALUE_COL_PROP,
-                                                         Task.EMUM_OPTIONS_LABEL_COL_PROP),
+                                                                          Task.EMUM_OPTIONS_LABEL_COL_PROP),
                                          task=spiff_task)
 
             # Get the file data from the File Service

tests/data/multi_instance/multi_instance.bpmn

@@ -0,0 +1,66 @@
+<?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:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:di="http://www.omg.org/spec/DD/20100524/DI" xmlns:camunda="http://camunda.org/schema/1.0/bpmn" id="Definitions_17fwemw" targetNamespace="http://bpmn.io/schema/bpmn" exporter="Camunda Modeler" exporterVersion="3.4.1">
+  <bpmn:process id="MultiInstance" isExecutable="true">
+    <bpmn:startEvent id="StartEvent_1" name="StartEvent_1">
+      <bpmn:outgoing>Flow_0t6p1sb</bpmn:outgoing>
+    </bpmn:startEvent>
+    <bpmn:sequenceFlow id="Flow_0t6p1sb" sourceRef="StartEvent_1" targetRef="Task_1v0e2zu" />
+    <bpmn:endEvent id="Event_End" name="Event_End">
+      <bpmn:incoming>Flow_0ugjw69</bpmn:incoming>
+    </bpmn:endEvent>
+    <bpmn:sequenceFlow id="Flow_0ugjw69" sourceRef="MutiInstanceTask" targetRef="Event_End" />
+    <bpmn:userTask id="MutiInstanceTask" name="Gather more information" camunda:formKey="GetEmail">
+      <bpmn:documentation># Please provide addtional information about:
+## Investigator ID: {{investigator.NETBADGEID}} 
+## Role: {{investigator.INVESTIGATORTYPEFULL}}</bpmn:documentation>
+      <bpmn:extensionElements>
+        <camunda:formData>
+          <camunda:formField id="email" label="Email Address:" type="string" />
+        </camunda:formData>
+      </bpmn:extensionElements>
+      <bpmn:incoming>SequenceFlow_1p568pp</bpmn:incoming>
+      <bpmn:outgoing>Flow_0ugjw69</bpmn:outgoing>
+      <bpmn:multiInstanceLoopCharacteristics isSequential="true" camunda:collection="StudyInfo.investigators" camunda:elementVariable="investigator" />
+    </bpmn:userTask>
+    <bpmn:sequenceFlow id="SequenceFlow_1p568pp" sourceRef="Task_1v0e2zu" targetRef="MutiInstanceTask" />
+    <bpmn:scriptTask id="Task_1v0e2zu" name="Load Personnel">
+      <bpmn:incoming>Flow_0t6p1sb</bpmn:incoming>
+      <bpmn:outgoing>SequenceFlow_1p568pp</bpmn:outgoing>
+      <bpmn:script>StudyInfo investigators</bpmn:script>
+    </bpmn:scriptTask>
+  </bpmn:process>
+  <bpmndi:BPMNDiagram id="BPMNDiagram_1">
+    <bpmndi:BPMNPlane id="BPMNPlane_1" bpmnElement="MultiInstance">
+      <bpmndi:BPMNShape id="_BPMNShape_StartEvent_2" bpmnElement="StartEvent_1">
+        <dc:Bounds x="142" y="99" width="36" height="36" />
+        <bpmndi:BPMNLabel>
+          <dc:Bounds x="129" y="142" width="64" height="14" />
+        </bpmndi:BPMNLabel>
+      </bpmndi:BPMNShape>
+      <bpmndi:BPMNEdge id="Flow_0t6p1sb_di" bpmnElement="Flow_0t6p1sb">
+        <di:waypoint x="178" y="117" />
+        <di:waypoint x="250" y="117" />
+      </bpmndi:BPMNEdge>
+      <bpmndi:BPMNShape id="Event_1g0pmib_di" bpmnElement="Event_End">
+        <dc:Bounds x="592" y="99" width="36" height="36" />
+        <bpmndi:BPMNLabel>
+          <dc:Bounds x="585" y="142" width="54" height="14" />
+        </bpmndi:BPMNLabel>
+      </bpmndi:BPMNShape>
+      <bpmndi:BPMNEdge id="Flow_0ugjw69_di" bpmnElement="Flow_0ugjw69">
+        <di:waypoint x="530" y="117" />
+        <di:waypoint x="592" y="117" />
+      </bpmndi:BPMNEdge>
+      <bpmndi:BPMNShape id="Activity_1iyilui_di" bpmnElement="MutiInstanceTask">
+        <dc:Bounds x="430" y="77" width="100" height="80" />
+      </bpmndi:BPMNShape>
+      <bpmndi:BPMNEdge id="SequenceFlow_1p568pp_di" bpmnElement="SequenceFlow_1p568pp">
+        <di:waypoint x="350" y="117" />
+        <di:waypoint x="430" y="117" />
+      </bpmndi:BPMNEdge>
+      <bpmndi:BPMNShape id="ScriptTask_0cbbirp_di" bpmnElement="Task_1v0e2zu">
+        <dc:Bounds x="250" y="77" width="100" height="80" />
+      </bpmndi:BPMNShape>
+    </bpmndi:BPMNPlane>
+  </bpmndi:BPMNDiagram>
+</bpmn:definitions>

tests/test_tasks_api.py

@@ -1,5 +1,6 @@
 import json
 import os
+from unittest.mock import patch
 
 from crc import session, app
 from crc.models.api_models import WorkflowApiSchema
@@ -257,3 +258,21 @@ class TestTasksApi(BaseTest):
         self.assertEquals('ManualTask', workflow_api.next_task['type'])
         self.assertTrue('Markdown' in workflow_api.next_task['documentation'])
         self.assertTrue('Dan' in workflow_api.next_task['documentation'])
+
+    @patch('crc.services.protocol_builder.requests.get')
+    def test_multi_instance_task(self, mock_get):
+        # This depends on getting a list of investigators back from the protocol builder.
+        mock_get.return_value.ok = True
+        mock_get.return_value.text = self.protocol_builder_response('investigators.json')
+
+        self.load_example_data()
+        workflow = self.create_workflow('multi_instance')
+
+        # get the first form in the two form workflow.
+        tasks = self.get_workflow_api(workflow).user_tasks
+        self.assertEquals(1, len(tasks))
+        self.assertEquals("UserTask", tasks[0].type)
+        self.assertTrue(tasks[0].is_multi_instance)
+        self.assertEquals(3, tasks[0].mi_count)
+
+        workflow_api = self.complete_form(workflow, tasks[0], {"name": "Dan"})

tests/test_workflow_processor.py

@@ -238,11 +238,11 @@ class TestWorkflowProcessor(BaseTest):
         processor.do_engine_steps()
         task = processor.bpmn_workflow.last_task
         self.assertIsNotNone(task.data)
-        self.assertIn("study", task.data)
+        self.assertIn("StudyInfo", task.data)
-        self.assertIn("info", task.data["study"])
+        self.assertIn("info", task.data["StudyInfo"])
-        self.assertIn("title", task.data["study"]["info"])
+        self.assertIn("title", task.data["StudyInfo"]["info"])
-        self.assertIn("last_updated", task.data["study"]["info"])
+        self.assertIn("last_updated", task.data["StudyInfo"]["info"])
-        self.assertIn("sponsor", task.data["study"]["info"])
+        self.assertIn("sponsor", task.data["StudyInfo"]["info"])
 
     def test_spec_versioning(self):
         self.load_example_data()

tests/test_workflow_processor_multi_instance.py

@@ -0,0 +1,97 @@
+import logging
+import os
+import string
+import random
+from unittest.mock import patch
+
+from SpiffWorkflow.bpmn.specs.EndEvent import EndEvent
+
+from crc import session, db, app
+from crc.api.common import ApiError
+from crc.models.file import FileModel, FileDataModel, CONTENT_TYPES
+from crc.models.study import StudyModel
+from crc.models.workflow import WorkflowSpecModel, WorkflowStatus, WorkflowModel
+from crc.services.file_service import FileService
+from crc.services.study_service import StudyService
+from crc.services.workflow_service import WorkflowService
+from tests.base_test import BaseTest
+from crc.services.workflow_processor import WorkflowProcessor
+
+
+class TestWorkflowProcessorMultiInstance(BaseTest):
+    """Tests the Workflow Processor as it deals with a Multi-Instance task"""
+
+
+    def _populate_form_with_random_data(self, task):
+        WorkflowProcessor.populate_form_with_random_data(task)
+
+    def get_processor(self, study_model, spec_model):
+        workflow_model = StudyService._create_workflow_model(study_model, spec_model)
+        return WorkflowProcessor(workflow_model)
+
+    @patch('crc.services.protocol_builder.requests.get')
+    def test_create_and_complete_workflow(self, mock_get):
+        # This depends on getting a list of investigators back from the protocol builder.
+        mock_get.return_value.ok = True
+        mock_get.return_value.text = self.protocol_builder_response('investigators.json')
+
+
+        self.load_example_data()
+        workflow_spec_model = self.load_test_spec("multi_instance")
+        study = session.query(StudyModel).first()
+        processor = self.get_processor(study, workflow_spec_model)
+        self.assertEqual(study.id, processor.bpmn_workflow.data[WorkflowProcessor.STUDY_ID_KEY])
+        self.assertIsNotNone(processor)
+        self.assertEqual(WorkflowStatus.user_input_required, processor.get_status())
+        processor.bpmn_workflow.do_engine_steps()
+        next_user_tasks = processor.next_user_tasks()
+        self.assertEqual(1, len(next_user_tasks))
+
+        task = next_user_tasks[0]
+
+        self.assertEquals(
+            {
+                'DC': {'user_id': 'asd3v', 'type_full': 'Department Contact'},
+                'IRBC': {'user_id': 'asdf32', 'type_full': 'IRB Coordinator'},
+                'PI': {'user_id': 'dhf8r', 'type_full': 'Primary Investigator'}
+            },
+            task.data['StudyInfo']['investigators'])
+
+        self.assertEqual(WorkflowStatus.user_input_required, processor.get_status())
+        self.assertEquals("asd3v", task.data["investigator"]["user_id"])
+
+        self.assertEqual("MutiInstanceTask", task.get_name())
+        api_task = WorkflowService.spiff_task_to_api_task(task)
+        self.assertEquals(3, api_task.mi_count)
+        self.assertEquals(1, api_task.mi_index)
+        task.update_data({"email":"asd3v@virginia.edu"})
+        processor.complete_task(task)
+        processor.do_engine_steps()
+
+        task = next_user_tasks[0]
+        api_task = WorkflowService.spiff_task_to_api_task(task)
+        self.assertEqual("MutiInstanceTask", api_task.name)
+        task.update_data({"email":"asdf32@virginia.edu"})
+        self.assertEquals(3, api_task.mi_count)
+        self.assertEquals(2, api_task.mi_index)
+        processor.complete_task(task)
+        processor.do_engine_steps()
+
+        task = next_user_tasks[0]
+        api_task = WorkflowService.spiff_task_to_api_task(task)
+        self.assertEqual("MutiInstanceTask", task.get_name())
+        task.update_data({"email":"dhf8r@virginia.edu"})
+        self.assertEquals(3, api_task.mi_count)
+        self.assertEquals(3, api_task.mi_index)
+        processor.complete_task(task)
+        processor.do_engine_steps()
+
+        self.assertEquals(
+            {
+                'DC': {'user_id': 'asd3v', 'type_full': 'Department Contact', 'email': 'asd3v@virginia.edu'},
+                'IRBC': {'user_id': 'asdf32', 'type_full': 'IRB Coordinator', "email": "asdf32@virginia.edu"},
+                'PI': {'user_id': 'dhf8r', 'type_full': 'Primary Investigator', "email": "dhf8r@virginia.edu"}
+            },
+            task.data['StudyInfo']['investigators'])
+
+        self.assertEqual(WorkflowStatus.complete, processor.get_status())