Merge pull request #296 from sartography/launch-workflow-outside-study-204

Launch workflow outside study 204

crc/api.yml

@@ -425,7 +425,7 @@ paths:
       - name: spec_id
         in: path
         required: true
-        description: The unique id of an existing workflow specification to modify.
+        description: The unique id of an existing workflow specification.
         schema:
           type: string
     get:
@@ -440,6 +440,18 @@ paths:
             application/json:
               schema:
                 $ref: "#/components/schemas/WorkflowSpec"
+    post:
+      operationId: crc.api.workflow.get_workflow_from_spec
+      summary: Creates a workflow from a workflow spec and returns the workflow
+      tags:
+        - Workflow Specifications
+      responses:
+        '200':
+          description: Workflow generated successfully
+          content:
+            application/json:
+              schema:
+                $ref: "#/components/schemas/Workflow"
     put:
       operationId: crc.api.workflow.update_workflow_specification
       security:
@@ -469,6 +481,21 @@ paths:
       responses:
         '204':
           description: The workflow specification has been removed.
+  /workflow-specification/standalone:
+    get:
+      operationId: crc.api.workflow.standalone_workflow_specs
+      summary: Provides a list of workflow specifications that can be run outside a study.
+      tags:
+        - Workflow Specifications
+      responses:
+        '200':
+          description: A list of workflow specifications
+          content:
+            application/json:
+              schema:
+                type: array
+                items:
+                  $ref: "#/components/schemas/WorkflowSpec"
   /workflow-specification/{spec_id}/validate:
     parameters:
       - name: spec_id
@@ -1536,6 +1563,9 @@ components:
         category_id:
           type: integer
           nullable: true
+        standalone:
+          type: boolean
+          example: false
         workflow_spec_category:
           $ref: "#/components/schemas/WorkflowSpecCategory"
         is_status:
@@ -1608,6 +1638,8 @@ components:
           type: integer
         num_tasks_incomplete:
           type: integer
+        study_id:
+          type: integer
 
       example:
         id: 291234

crc/api/workflow.py

@@ -101,6 +101,24 @@ def delete_workflow_specification(spec_id):
     session.commit()
 
 
+def get_workflow_from_spec(spec_id):
+    workflow_model = WorkflowService.get_workflow_from_spec(spec_id, g.user)
+    processor = WorkflowProcessor(workflow_model)
+
+    processor.do_engine_steps()
+    processor.save()
+    WorkflowService.update_task_assignments(processor)
+
+    workflow_api_model = WorkflowService.processor_to_workflow_api(processor)
+    return WorkflowApiSchema().dump(workflow_api_model)
+
+
+def standalone_workflow_specs():
+    schema = WorkflowSpecModelSchema(many=True)
+    specs = WorkflowService.get_standalone_workflow_specs()
+    return schema.dump(specs)
+
+
 def get_workflow(workflow_id, do_engine_steps=True):
     """Retrieve workflow based on workflow_id, and return it in the last saved State.
        If do_engine_steps is False, return the workflow without running any engine tasks or logging any events. """
@@ -185,9 +203,6 @@ def update_task(workflow_id, task_id, body, terminate_loop=None, update_all=Fals
     if workflow_model is None:
         raise ApiError("invalid_workflow_id", "The given workflow id is not valid.", status_code=404)
 
-    elif workflow_model.study is None:
-        raise ApiError("invalid_study", "There is no study associated with the given workflow.", status_code=404)
-
     processor = WorkflowProcessor(workflow_model)
     task_id = uuid.UUID(task_id)
     spiff_task = processor.bpmn_workflow.get_task(task_id)

crc/models/api_models.py

@@ -191,7 +191,7 @@ class DocumentDirectory(object):
 class WorkflowApi(object):
     def __init__(self, id, status, next_task, navigation,
                  spec_version, is_latest_spec, workflow_spec_id, total_tasks, completed_tasks,
-                 last_updated, is_review, title):
+                 last_updated, is_review, title, study_id):
         self.id = id
         self.status = status
         self.next_task = next_task  # The next task that requires user input.
@@ -204,13 +204,14 @@ class WorkflowApi(object):
         self.last_updated = last_updated
         self.title = title
         self.is_review = is_review
+        self.study_id = study_id or ''
 
 class WorkflowApiSchema(ma.Schema):
     class Meta:
         model = WorkflowApi
         fields = ["id", "status", "next_task", "navigation",
                   "workflow_spec_id", "spec_version", "is_latest_spec", "total_tasks", "completed_tasks",
-                  "last_updated", "is_review", "title"]
+                  "last_updated", "is_review", "title", "study_id"]
         unknown = INCLUDE
 
     status = EnumField(WorkflowStatus)
@@ -221,7 +222,7 @@ class WorkflowApiSchema(ma.Schema):
     def make_workflow(self, data, **kwargs):
         keys = ['id', 'status', 'next_task', 'navigation',
                 'workflow_spec_id', 'spec_version', 'is_latest_spec', "total_tasks", "completed_tasks",
-                "last_updated", "is_review", "title"]
+                "last_updated", "is_review", "title", "study_id"]
         filtered_fields = {key: data[key] for key in keys}
         filtered_fields['next_task'] = TaskSchema().make_task(data['next_task'])
         return WorkflowApi(**filtered_fields)

crc/models/task_event.py

@@ -10,7 +10,7 @@ from crc.services.ldap_service import LdapService
 class TaskEventModel(db.Model):
     __tablename__ = 'task_event'
     id = db.Column(db.Integer, primary_key=True)
-    study_id = db.Column(db.Integer, db.ForeignKey('study.id'), nullable=False)
+    study_id = db.Column(db.Integer, db.ForeignKey('study.id'))
     user_uid = db.Column(db.String, nullable=False) # In some cases the unique user id may not exist in the db yet.
     workflow_id = db.Column(db.Integer, db.ForeignKey('workflow.id'), nullable=False)
     workflow_spec_id = db.Column(db.String, db.ForeignKey('workflow_spec.id'))

crc/models/workflow.py

@@ -33,6 +33,7 @@ class WorkflowSpecModel(db.Model):
     category_id = db.Column(db.Integer, db.ForeignKey('workflow_spec_category.id'), nullable=True)
     category = db.relationship("WorkflowSpecCategoryModel")
     is_master_spec = db.Column(db.Boolean, default=False)
+    standalone = db.Column(db.Boolean, default=False)
 
 
 class WorkflowSpecModelSchema(SQLAlchemyAutoSchema):
@@ -88,6 +89,7 @@ class WorkflowModel(db.Model):
     total_tasks = db.Column(db.Integer, default=0)
     completed_tasks = db.Column(db.Integer, default=0)
     last_updated = db.Column(db.DateTime)
+    user_id = db.Column(db.String, default=None)
     # Order By is important or generating hashes on reviews.
     dependencies = db.relationship(WorkflowSpecDependencyFile, cascade="all, delete, delete-orphan",
                                    order_by="WorkflowSpecDependencyFile.file_data_id")

crc/services/study_service.py

@@ -495,6 +495,7 @@ class StudyService(object):
     def _create_workflow_model(study: StudyModel, spec):
         workflow_model = WorkflowModel(status=WorkflowStatus.not_started,
                                        study=study,
+                                       user_id=None,
                                        workflow_spec_id=spec.id,
                                        last_updated=datetime.now())
         session.add(workflow_model)

crc/services/workflow_service.py

@@ -408,7 +408,8 @@ class WorkflowService(object):
             completed_tasks=processor.workflow_model.completed_tasks,
             last_updated=processor.workflow_model.last_updated,
             is_review=is_review,
-            title=spec.display_name
+            title=spec.display_name,
+            study_id=processor.workflow_model.study_id or None
         )
         if not next_task:  # The Next Task can be requested to be a certain task, useful for parallel tasks.
             # This may or may not work, sometimes there is no next task to complete.
@@ -667,30 +668,39 @@ class WorkflowService(object):
 
     @staticmethod
     def get_users_assigned_to_task(processor, spiff_task) -> List[str]:
-        if not hasattr(spiff_task.task_spec, 'lane') or spiff_task.task_spec.lane is None:
+        if processor.workflow_model.study_id is None and processor.workflow_model.user_id is None:
-            associated = StudyService.get_study_associates(processor.workflow_model.study.id)
+            raise ApiError.from_task(code='invalid_workflow',
-            return [user['uid'] for user in associated if user['access']]
+                                     message='A workflow must have either a study_id or a user_id.',
-        if spiff_task.task_spec.lane not in spiff_task.data:
+                                     task=spiff_task)
-            return []  # No users are assignable to the task at this moment
+        # Standalone workflow - we only care about the current user
-        lane_users = spiff_task.data[spiff_task.task_spec.lane]
+        elif processor.workflow_model.study_id is None and processor.workflow_model.user_id is not None:
-        if not isinstance(lane_users, list):
+            return [processor.workflow_model.user_id]
-            lane_users = [lane_users]
+        # Workflow associated with a study - get all the users
+        else:
+            if not hasattr(spiff_task.task_spec, 'lane') or spiff_task.task_spec.lane is None:
+                associated = StudyService.get_study_associates(processor.workflow_model.study.id)
+                return [user['uid'] for user in associated if user['access']]
+            if spiff_task.task_spec.lane not in spiff_task.data:
+                return []  # No users are assignable to the task at this moment
+            lane_users = spiff_task.data[spiff_task.task_spec.lane]
+            if not isinstance(lane_users, list):
+                lane_users = [lane_users]
 
-        lane_uids = []
+            lane_uids = []
-        for user in lane_users:
+            for user in lane_users:
-            if isinstance(user, dict):
+                if isinstance(user, dict):
-                if 'value' in user and user['value'] is not None:
+                    if 'value' in user and user['value'] is not None:
-                    lane_uids.append(user['value'])
+                        lane_uids.append(user['value'])
+                    else:
+                        raise ApiError.from_task(code="task_lane_user_error", message="Spiff Task %s lane user dict must have a key called 'value' with the user's uid in it." %
+                                                                  spiff_task.task_spec.name, task=spiff_task)
+                elif isinstance(user, str):
+                    lane_uids.append(user)
                 else:
-                    raise ApiError.from_task(code="task_lane_user_error", message="Spiff Task %s lane user dict must have a key called 'value' with the user's uid in it." %
+                    raise ApiError.from_task(code="task_lane_user_error", message="Spiff Task %s lane user is not a string or dict" %
-                                                              spiff_task.task_spec.name, task=spiff_task)
+                                                                  spiff_task.task_spec.name, task=spiff_task)
-            elif isinstance(user, str):
-                lane_uids.append(user)
-            else:
-                raise ApiError.from_task(code="task_lane_user_error", message="Spiff Task %s lane user is not a string or dict" %
-                                                              spiff_task.task_spec.name, task=spiff_task)
 
-        return lane_uids
+            return lane_uids
 
     @staticmethod
     def log_task_action(user_uid, processor, spiff_task, action):
@@ -783,3 +793,19 @@ class WorkflowService(object):
         for workflow in workflows:
             if workflow.status == WorkflowStatus.user_input_required or workflow.status == WorkflowStatus.waiting:
                 WorkflowProcessor.reset(workflow, clear_data=False)
+
+    @staticmethod
+    def get_workflow_from_spec(workflow_spec_id, user):
+        workflow_model = WorkflowModel(status=WorkflowStatus.not_started,
+                                       study=None,
+                                       user_id=user.uid,
+                                       workflow_spec_id=workflow_spec_id,
+                                       last_updated=datetime.now())
+        db.session.add(workflow_model)
+        db.session.commit()
+        return workflow_model
+
+    @staticmethod
+    def get_standalone_workflow_specs():
+        specs = db.session.query(WorkflowSpecModel).filter_by(standalone=True).all()
+        return specs

example_data.py

@@ -266,7 +266,7 @@ class ExampleDataLoader:
                          from_tests=True)
 
     def create_spec(self, id, name, display_name="", description="", filepath=None, master_spec=False,
-                    category_id=None, display_order=None, from_tests=False):
+                    category_id=None, display_order=None, from_tests=False, standalone=False):
         """Assumes that a directory exists in static/bpmn with the same name as the given id.
            further assumes that the [id].bpmn is the primary file for the workflow.
            returns an array of data models to be added to the database."""
@@ -278,7 +278,8 @@ class ExampleDataLoader:
                                  description=description,
                                  is_master_spec=master_spec,
                                  category_id=category_id,
-                                 display_order=display_order)
+                                 display_order=display_order,
+                                 standalone=standalone)
         db.session.add(spec)
         db.session.commit()
         if not filepath and not from_tests:

migrations/versions/8b976945a54e_.py

@@ -0,0 +1,30 @@
+"""empty message
+
+Revision ID: 8b976945a54e
+Revises: c872232ebdcb
+Create Date: 2021-04-18 11:42:41.894378
+
+"""
+from alembic import op
+import sqlalchemy as sa
+
+
+# revision identifiers, used by Alembic.
+revision = '8b976945a54e'
+down_revision = 'c872232ebdcb'
+branch_labels = None
+depends_on = None
+
+
+def upgrade():
+    op.add_column('workflow', sa.Column('user_id', sa.String(), nullable=True))
+    op.add_column('workflow_spec', sa.Column('standalone', sa.Boolean(), default=False))
+    op.execute("UPDATE workflow_spec SET standalone=False WHERE standalone is null;")
+    op.execute("ALTER TABLE task_event ALTER COLUMN study_id DROP NOT NULL")
+
+
+def downgrade():
+    op.execute("UPDATE workflow SET user_id=NULL WHERE user_id is not NULL")
+    op.drop_column('workflow', 'user_id')
+    op.drop_column('workflow_spec', 'standalone')
+    op.execute("ALTER TABLE task_event ALTER COLUMN study_id SET NOT NULL ")

tests/base_test.py

@@ -175,11 +175,6 @@ class BaseTest(unittest.TestCase):
         specs = session.query(WorkflowSpecModel).all()
         self.assertIsNotNone(specs)
 
-        for spec in specs:
-            files = session.query(FileModel).filter_by(workflow_spec_id=spec.id).all()
-            self.assertIsNotNone(files)
-            self.assertGreater(len(files), 0)
-
         for spec in specs:
             files = session.query(FileModel).filter_by(workflow_spec_id=spec.id).all()
             self.assertIsNotNone(files)
@@ -379,6 +374,10 @@ class BaseTest(unittest.TestCase):
 
     def complete_form(self, workflow_in, task_in, dict_data, update_all=False, error_code=None, terminate_loop=None,
                       user_uid="dhf8r"):
+        # workflow_in should be a workflow, not a workflow_api
+        # we were passing in workflow_api in many of our tests, and
+        # this caused problems testing standalone workflows
+        standalone = getattr(workflow_in.workflow_spec, 'standalone', False)
         prev_completed_task_count = workflow_in.completed_tasks
         if isinstance(task_in, dict):
             task_id = task_in["id"]
@@ -421,7 +420,8 @@ class BaseTest(unittest.TestCase):
             .order_by(TaskEventModel.date.desc()).all()
         self.assertGreater(len(task_events), 0)
         event = task_events[0]
-        self.assertIsNotNone(event.study_id)
+        if not standalone:
+            self.assertIsNotNone(event.study_id)
         self.assertEqual(user_uid, event.user_uid)
         self.assertEqual(workflow.id, event.workflow_id)
         self.assertEqual(workflow.workflow_spec_id, event.workflow_spec_id)

tests/data/hello_world/hello_world.bpmn

@@ -0,0 +1,58 @@
+<?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:camunda="http://camunda.org/schema/1.0/bpmn" id="Definitions_0ixyfs0" targetNamespace="http://bpmn.io/schema/bpmn" exporter="Camunda Modeler" exporterVersion="3.5.0">
+  <bpmn:process id="Process_HelloWorld" name="Hello World Process" isExecutable="true">
+    <bpmn:documentation>This workflow asks for a name and says hello</bpmn:documentation>
+    <bpmn:startEvent id="StartEvent_1">
+      <bpmn:outgoing>SequenceFlow_0qyd2b7</bpmn:outgoing>
+    </bpmn:startEvent>
+    <bpmn:sequenceFlow id="SequenceFlow_0qyd2b7" sourceRef="StartEvent_1" targetRef="Task_GetName" />
+    <bpmn:userTask id="Task_GetName" name="Get Name" camunda:formKey="Name">
+      <bpmn:documentation>Hello</bpmn:documentation>
+      <bpmn:extensionElements>
+        <camunda:formData>
+          <camunda:formField id="name" label="Name" type="string" defaultValue="World" />
+        </camunda:formData>
+      </bpmn:extensionElements>
+      <bpmn:incoming>SequenceFlow_0qyd2b7</bpmn:incoming>
+      <bpmn:outgoing>SequenceFlow_1h46b40</bpmn:outgoing>
+    </bpmn:userTask>
+    <bpmn:sequenceFlow id="SequenceFlow_1h46b40" sourceRef="Task_GetName" targetRef="Task_SayHello" />
+    <bpmn:manualTask id="Task_SayHello" name="Say Hello">
+      <bpmn:documentation>Hello {{name}}</bpmn:documentation>
+      <bpmn:incoming>SequenceFlow_1h46b40</bpmn:incoming>
+      <bpmn:outgoing>SequenceFlow_0lqrc6e</bpmn:outgoing>
+    </bpmn:manualTask>
+    <bpmn:endEvent id="EndEvent_1l03lqw">
+      <bpmn:incoming>SequenceFlow_0lqrc6e</bpmn:incoming>
+    </bpmn:endEvent>
+    <bpmn:sequenceFlow id="SequenceFlow_0lqrc6e" sourceRef="Task_SayHello" targetRef="EndEvent_1l03lqw" />
+  </bpmn:process>
+  <bpmndi:BPMNDiagram id="BPMNDiagram_1">
+    <bpmndi:BPMNPlane id="BPMNPlane_1" bpmnElement="Process_HelloWorld">
+      <bpmndi:BPMNShape id="_BPMNShape_StartEvent_2" bpmnElement="StartEvent_1">
+        <dc:Bounds x="179" y="99" width="36" height="36" />
+      </bpmndi:BPMNShape>
+      <bpmndi:BPMNEdge id="SequenceFlow_0qyd2b7_di" bpmnElement="SequenceFlow_0qyd2b7">
+        <di:waypoint x="215" y="117" />
+        <di:waypoint x="270" y="117" />
+      </bpmndi:BPMNEdge>
+      <bpmndi:BPMNShape id="UserTask_0fbucz7_di" bpmnElement="Task_GetName">
+        <dc:Bounds x="270" y="77" width="100" height="80" />
+      </bpmndi:BPMNShape>
+      <bpmndi:BPMNEdge id="SequenceFlow_1h46b40_di" bpmnElement="SequenceFlow_1h46b40">
+        <di:waypoint x="370" y="117" />
+        <di:waypoint x="430" y="117" />
+      </bpmndi:BPMNEdge>
+      <bpmndi:BPMNShape id="ManualTask_1tia2zr_di" bpmnElement="Task_SayHello">
+        <dc:Bounds x="430" y="77" width="100" height="80" />
+      </bpmndi:BPMNShape>
+      <bpmndi:BPMNShape id="EndEvent_1l03lqw_di" bpmnElement="EndEvent_1l03lqw">
+        <dc:Bounds x="592" y="99" width="36" height="36" />
+      </bpmndi:BPMNShape>
+      <bpmndi:BPMNEdge id="SequenceFlow_0lqrc6e_di" bpmnElement="SequenceFlow_0lqrc6e">
+        <di:waypoint x="530" y="117" />
+        <di:waypoint x="592" y="117" />
+      </bpmndi:BPMNEdge>
+    </bpmndi:BPMNPlane>
+  </bpmndi:BPMNDiagram>
+</bpmn:definitions>

tests/study/test_study_cancellations.py

@@ -72,7 +72,7 @@ class TestStudyCancellations(BaseTest):
         workflow, study_id = self.load_workflow()
         workflow_api, first_task = self.get_first_task(workflow)
 
-        self.complete_form(workflow_api, first_task, {})
+        self.complete_form(workflow, first_task, {})
 
         study_result = self.put_study_on_hold(study_id)
         self.assertEqual('New Title', study_result.title)
@@ -82,10 +82,10 @@ class TestStudyCancellations(BaseTest):
         workflow, study_id = self.load_workflow()
         workflow_api, first_task = self.get_first_task(workflow)
 
-        self.complete_form(workflow_api, first_task, {})
+        self.complete_form(workflow, first_task, {})
 
         workflow_api, next_task = self.get_second_task(workflow)
-        self.complete_form(workflow_api, next_task, {'how_many': 3})
+        self.complete_form(workflow, next_task, {'how_many': 3})
 
         study_result = self.put_study_on_hold(study_id)
         self.assertEqual('Second Title', study_result.title)
@@ -95,13 +95,13 @@ class TestStudyCancellations(BaseTest):
         workflow, study_id = self.load_workflow()
         workflow_api, first_task = self.get_first_task(workflow)
 
-        self.complete_form(workflow_api, first_task, {})
+        self.complete_form(workflow, first_task, {})
 
         workflow_api, second_task = self.get_second_task(workflow)
-        self.complete_form(workflow_api, second_task, {'how_many': 3})
+        self.complete_form(workflow, second_task, {'how_many': 3})
 
         workflow_api, third_task = self.get_third_task(workflow)
-        self.complete_form(workflow_api, third_task, {})
+        self.complete_form(workflow, third_task, {})
 
         study_result = self.put_study_on_hold(study_id)
         self.assertEqual('Beer consumption in the bipedal software engineer', study_result.title)

tests/test_auto_set_primary_bpmn.py

@@ -13,7 +13,8 @@ class TestAutoSetPrimaryBPMN(BaseTest):
         category_id = session.query(WorkflowSpecCategoryModel).first().id
         # Add a workflow spec
         spec = WorkflowSpecModel(id='make_cookies', name='make_cookies', display_name='Cooooookies',
-                                 description='Om nom nom delicious cookies', category_id=category_id)
+                                 description='Om nom nom delicious cookies', category_id=category_id,
+                                 standalone=False)
         rv = self.app.post('/v1.0/workflow-specification',
                            headers=self.logged_in_headers(),
                            content_type="application/json",

tests/test_email_script.py

@@ -23,7 +23,6 @@ class TestEmailScript(BaseTest):
 
             first_task = self.get_workflow_api(workflow).next_task
 
-            workflow = self.get_workflow_api(workflow)
             self.complete_form(workflow, first_task, {'subject': 'My Email Subject', 'recipients': 'test@example.com'})
 
             self.assertEqual(1, len(outbox))
@@ -49,7 +48,6 @@ class TestEmailScript(BaseTest):
     def test_bad_email_address_1(self):
         workflow = self.create_workflow('email_script')
         first_task = self.get_workflow_api(workflow).next_task
-        workflow = self.get_workflow_api(workflow)
 
         with self.assertRaises(AssertionError):
             self.complete_form(workflow, first_task, {'recipients': 'test@example'})
@@ -57,7 +55,6 @@ class TestEmailScript(BaseTest):
     def test_bad_email_address_2(self):
         workflow = self.create_workflow('email_script')
         first_task = self.get_workflow_api(workflow).next_task
-        workflow = self.get_workflow_api(workflow)
 
         with self.assertRaises(AssertionError):
             self.complete_form(workflow, first_task, {'recipients': 'test'})

tests/test_launch_workflow_outside_study.py

@@ -0,0 +1,23 @@
+from tests.base_test import BaseTest
+
+from crc import session
+from crc.models.user import UserModel
+from crc.services.workflow_service import WorkflowService
+
+from example_data import ExampleDataLoader
+
+
+class TestNoStudyWorkflow(BaseTest):
+
+    def test_no_study_workflow(self):
+        self.load_example_data()
+        spec = ExampleDataLoader().create_spec('hello_world', 'Hello World', standalone=True, from_tests=True)
+        user = session.query(UserModel).first()
+        self.assertIsNotNone(user)
+        workflow_model = WorkflowService.get_workflow_from_spec(spec.id, user)
+        workflow_api = self.get_workflow_api(workflow_model)
+        first_task = workflow_api.next_task
+        self.complete_form(workflow_model, first_task, {'name': 'Big Guy'})
+        workflow_api = self.get_workflow_api(workflow_model)
+        second_task = workflow_api.next_task
+        self.assertEqual(second_task.documentation, 'Hello Big Guy')

tests/test_message_event.py

@@ -13,10 +13,10 @@ class TestMessageEvent(BaseTest):
         # Start the workflow.
         first_task = self.get_workflow_api(workflow).next_task
         self.assertEqual('Activity_GetData', first_task.name)
-        workflow = self.get_workflow_api(workflow)
+
         self.complete_form(workflow, first_task, {'formdata': 'asdf'})
-        workflow = self.get_workflow_api(workflow)
+        workflow_api = self.get_workflow_api(workflow)
-        self.assertEqual('Activity_HowMany', workflow.next_task.name)
+        self.assertEqual('Activity_HowMany', workflow_api.next_task.name)
 
         # reset the workflow
         # this ultimately calls crc.api.workflow.set_current_task

tests/test_multi_instance_tasks_api.py

@@ -67,14 +67,14 @@ class TestMultiinstanceTasksApi(BaseTest):
                               content_type="application/json")
             self.assert_success(rv)
             json_data = json.loads(rv.get_data(as_text=True))
-            workflow = WorkflowApiSchema().load(json_data)
+            workflow_api = WorkflowApiSchema().load(json_data)
-            data = workflow.next_task.data
+            data = workflow_api.next_task.data
             data['investigator']['email'] = "dhf8r@virginia.edu"
-            self.complete_form(workflow, workflow.next_task, data)
+            self.complete_form(workflow, workflow_api.next_task, data)
             #tasks = self.get_workflow_api(workflow).user_tasks
 
-        workflow = self.get_workflow_api(workflow)
+        workflow_api = self.get_workflow_api(workflow)
-        self.assertEqual(WorkflowStatus.complete, workflow.status)
+        self.assertEqual(WorkflowStatus.complete, workflow_api.status)
 
 
     @patch('crc.services.protocol_builder.requests.get')

tests/test_tasks_api.py

@@ -386,15 +386,15 @@ class TestTasksApi(BaseTest):
         # Start the workflow.
         first_task = self.get_workflow_api(workflow).next_task
         self.complete_form(workflow, first_task, {"has_bananas": True})
-        workflow = self.get_workflow_api(workflow)
+        workflow_api = self.get_workflow_api(workflow)
-        self.assertEqual('Task_Num_Bananas', workflow.next_task.name)
+        self.assertEqual('Task_Num_Bananas', workflow_api.next_task.name)
 
         # Trying to re-submit the initial task, and answer differently, should result in an error.
         self.complete_form(workflow, first_task, {"has_bananas": False}, error_code="invalid_state")
 
         # Go ahead and set the number of bananas.
-        workflow = self.get_workflow_api(workflow)
+        workflow_api = self.get_workflow_api(workflow)
-        task = workflow.next_task
+        task = workflow_api.next_task
 
         self.complete_form(workflow, task, {"num_bananas": 4})
         # We are now at the end of the workflow.
@@ -405,19 +405,19 @@ class TestTasksApi(BaseTest):
                           content_type="application/json")
         self.assert_success(rv)
         json_data = json.loads(rv.get_data(as_text=True))
-        workflow = WorkflowApiSchema().load(json_data)
+        workflow_api = WorkflowApiSchema().load(json_data)
 
         # Assure the Next Task is the one we just reset the token to be on.
-        self.assertEqual("Task_Has_Bananas", workflow.next_task.name)
+        self.assertEqual("Task_Has_Bananas", workflow_api.next_task.name)
 
         # Go ahead and get that workflow one more time, it should still be right.
-        workflow = self.get_workflow_api(workflow)
+        workflow_api = self.get_workflow_api(workflow)
 
         # Assure the Next Task is the one we just reset the token to be on.
-        self.assertEqual("Task_Has_Bananas", workflow.next_task.name)
+        self.assertEqual("Task_Has_Bananas", workflow_api.next_task.name)
 
         # The next task should be a different value.
-        self.complete_form(workflow, workflow.next_task, {"has_bananas": False})
+        self.complete_form(workflow, workflow_api.next_task, {"has_bananas": False})
-        workflow = self.get_workflow_api(workflow)
+        workflow_api = self.get_workflow_api(workflow)
-        self.assertEqual('Task_Why_No_Bananas', workflow.next_task.name)
+        self.assertEqual('Task_Why_No_Bananas', workflow_api.next_task.name)
 

tests/workflow/test_workflow_boolean_default.py

@@ -7,7 +7,7 @@ class TestBooleanDefault(BaseTest):
         workflow = self.create_workflow('boolean_default_value')
         workflow_api = self.get_workflow_api(workflow)
         set_default_task = workflow_api.next_task
-        result = self.complete_form(workflow_api, set_default_task, {'yes_no': yes_no})
+        result = self.complete_form(workflow, set_default_task, {'yes_no': yes_no})
         return result
 
     def test_boolean_true_string(self):

tests/workflow/test_workflow_enum_default_value_expression.py

@@ -7,35 +7,35 @@ class TestWorkflowEnumDefault(BaseTest):
     def test_enum_default_from_value_expression(self):
         workflow = self.create_workflow('enum_value_expression')
 
-        first_task = self.get_workflow_api(workflow).next_task
-        self.assertEqual('Activity_UserInput', first_task.name)
         workflow_api = self.get_workflow_api(workflow)
+        first_task = workflow_api.next_task
+        self.assertEqual('Activity_UserInput', first_task.name)
 
-        result = self.complete_form(workflow_api, first_task, {'user_input': True})
+        result = self.complete_form(workflow, first_task, {'user_input': True})
         self.assertIn('user_input', result.next_task.data)
         self.assertEqual(True, result.next_task.data['user_input'])
         self.assertIn('lookup_output', result.next_task.data)
         self.assertEqual('black', result.next_task.data['lookup_output'])
 
         workflow_api = self.get_workflow_api(workflow)
-        self.assertEqual('Activity_PickColor', self.get_workflow_api(workflow_api).next_task.name)
+        self.assertEqual('Activity_PickColor', workflow_api.next_task.name)
         self.assertEqual({'value': 'black', 'label': 'Black'}, workflow_api.next_task.data['color_select'])
 
         #
         workflow = self.create_workflow('enum_value_expression')
 
-        first_task = self.get_workflow_api(workflow).next_task
-        self.assertEqual('Activity_UserInput', first_task.name)
         workflow_api = self.get_workflow_api(workflow)
+        first_task = workflow_api.next_task
+        self.assertEqual('Activity_UserInput', first_task.name)
 
-        result = self.complete_form(workflow_api, first_task, {'user_input': False})
+        result = self.complete_form(workflow, first_task, {'user_input': False})
         self.assertIn('user_input', result.next_task.data)
         self.assertEqual(False, result.next_task.data['user_input'])
         self.assertIn('lookup_output', result.next_task.data)
         self.assertEqual('white', result.next_task.data['lookup_output'])
 
         workflow_api = self.get_workflow_api(workflow)
-        self.assertEqual('Activity_PickColor', self.get_workflow_api(workflow_api).next_task.name)
+        self.assertEqual('Activity_PickColor', workflow_api.next_task.name)
         self.assertEqual({'value': 'white', 'label': 'White'}, workflow_api.next_task.data['color_select'])
 
     def test_enum_value_expression_and_default(self):

tests/workflow/test_workflow_form_field_name.py

@@ -18,7 +18,7 @@ class TestFormFieldName(BaseTest):
 
         workflow_api = self.get_workflow_api(workflow)
         first_task = workflow_api.next_task
-        self.complete_form(workflow_api, first_task, {})
+        self.complete_form(workflow, first_task, {})
 
         workflow_api = self.get_workflow_api(workflow)
         second_task = workflow_api.next_task

tests/workflow/test_workflow_hidden_required_field.py

@@ -34,14 +34,13 @@ class TestWorkflowHiddenRequiredField(BaseTest):
 
         first_task = workflow_api.next_task
         self.assertEqual('Activity_Hello', first_task.name)
-        workflow_api = self.get_workflow_api(workflow)
 
-        self.complete_form(workflow_api, first_task, {})
+        self.complete_form(workflow, first_task, {})
         workflow_api = self.get_workflow_api(workflow)
 
         second_task = workflow_api.next_task
         self.assertEqual('Activity_HiddenField', second_task.name)
-        self.complete_form(workflow_api, second_task, {})
+        self.complete_form(workflow, second_task, {})
         workflow_api = self.get_workflow_api(workflow)
 
         # The color field is hidden and required. Make sure we use the default value

tests/workflow/test_workflow_restart.py

@@ -12,20 +12,20 @@ class TestWorkflowRestart(BaseTest):
 
         workflow = self.create_workflow('message_event')
 
-        first_task = self.get_workflow_api(workflow).next_task
-        self.assertEqual('Activity_GetData', first_task.name)
         workflow_api = self.get_workflow_api(workflow)
+        first_task = workflow_api.next_task
+        self.assertEqual('Activity_GetData', first_task.name)
 
-        result = self.complete_form(workflow_api, first_task, {'formdata': 'asdf'})
+        result = self.complete_form(workflow, first_task, {'formdata': 'asdf'})
         self.assertIn('formdata', result.next_task.data)
         self.assertEqual('asdf', result.next_task.data['formdata'])
 
         workflow_api = self.get_workflow_api(workflow)
-        self.assertEqual('Activity_HowMany', self.get_workflow_api(workflow_api).next_task.name)
+        self.assertEqual('Activity_HowMany', workflow_api.next_task.name)
 
         # restart with data. should land at beginning with data
         workflow_api = self.restart_workflow_api(result)
-        first_task = self.get_workflow_api(workflow_api).next_task
+        first_task = workflow_api.next_task
         self.assertEqual('Activity_GetData', first_task.name)
         self.assertIn('formdata', workflow_api.next_task.data)
         self.assertEqual('asdf', workflow_api.next_task.data['formdata'])
@@ -36,7 +36,6 @@ class TestWorkflowRestart(BaseTest):
         self.assertEqual('Activity_GetData', first_task.name)
         self.assertNotIn('formdata', workflow_api.next_task.data)
 
-
     def test_workflow_restart_delete_files(self):
         self.load_example_data()
         irb_code = 'Study_Protocol_Document'
@@ -80,14 +79,14 @@ class TestWorkflowRestart(BaseTest):
         study_id = workflow.study_id
 
         # Start the workflow.
-        first_task = self.get_workflow_api(workflow).next_task
-        self.assertEqual('Activity_GetData', first_task.name)
         workflow_api = self.get_workflow_api(workflow)
-        self.complete_form(workflow_api, first_task, {'formdata': 'asdf'})
+        first_task = workflow_api.next_task
+        self.assertEqual('Activity_GetData', first_task.name)
+        self.complete_form(workflow, first_task, {'formdata': 'asdf'})
         workflow_api = self.get_workflow_api(workflow)
         self.assertEqual('Activity_HowMany', workflow_api.next_task.name)
 
-        workflow_api = self.restart_workflow_api(workflow)
+        self.restart_workflow_api(workflow)
         study_result = session.query(StudyModel).filter(StudyModel.id == study_id).first()
         self.assertEqual('New Title', study_result.title)
 
@@ -106,17 +105,16 @@ class TestWorkflowRestart(BaseTest):
         study_id = workflow.study_id
 
         # Start the workflow.
-        first_task = self.get_workflow_api(workflow).next_task
-        self.assertEqual('Activity_GetData', first_task.name)
         workflow_api = self.get_workflow_api(workflow)
-        self.complete_form(workflow_api, first_task, {'formdata': 'asdf'})
+        first_task = workflow_api.next_task
+        self.assertEqual('Activity_GetData', first_task.name)
+        self.complete_form(workflow, first_task, {'formdata': 'asdf'})
 
         workflow_api = self.get_workflow_api(workflow)
         next_task = workflow_api.next_task
         self.assertEqual('Activity_HowMany', next_task.name)
-        self.complete_form(workflow_api, next_task, {'how_many': 3})
+        self.complete_form(workflow, next_task, {'how_many': 3})
 
-        workflow_api = self.restart_workflow_api(workflow)
         study_result = session.query(StudyModel).filter(StudyModel.id == study_id).first()
         self.assertEqual('Beer consumption in the bipedal software engineer', study_result.title)
 

tests/workflow/test_workflow_spec_api.py

@@ -3,7 +3,9 @@ import json
 from tests.base_test import BaseTest
 from crc import session
 from crc.models.file import FileModel
-from crc.models.workflow import WorkflowSpecModel, WorkflowSpecModelSchema, WorkflowModel, WorkflowSpecCategoryModel
+from crc.models.workflow import WorkflowSpecModel, WorkflowSpecModelSchema, WorkflowModel, WorkflowSpecCategoryModel, WorkflowSpecCategoryModelSchema
+
+from example_data import ExampleDataLoader
 
 
 class TestWorkflowSpec(BaseTest):
@@ -28,7 +30,8 @@ class TestWorkflowSpec(BaseTest):
         category_id = session.query(WorkflowSpecCategoryModel).first().id
         category_count = session.query(WorkflowSpecModel).filter_by(category_id=category_id).count()
         spec = WorkflowSpecModel(id='make_cookies', name='make_cookies', display_name='Cooooookies',
-                                 description='Om nom nom delicious cookies', category_id=category_id)
+                                 description='Om nom nom delicious cookies', category_id=category_id,
+                                 standalone=False)
         rv = self.app.post('/v1.0/workflow-specification',
                            headers=self.logged_in_headers(),
                            content_type="application/json",
@@ -101,3 +104,60 @@ class TestWorkflowSpec(BaseTest):
         num_workflows_after = session.query(WorkflowModel).filter_by(workflow_spec_id=spec_id).count()
         self.assertEqual(num_files_after + num_workflows_after, 0)
 
+    def test_get_standalone_workflow_specs(self):
+        self.load_example_data()
+        category = session.query(WorkflowSpecCategoryModel).first()
+        ExampleDataLoader().create_spec('hello_world', 'Hello World', category_id=category.id,
+                                        standalone=True, from_tests=True)
+        rv = self.app.get('/v1.0/workflow-specification/standalone', headers=self.logged_in_headers())
+        self.assertEqual(1, len(rv.json))
+
+        ExampleDataLoader().create_spec('email_script', 'Email Script', category_id=category.id,
+                                        standalone=True, from_tests=True)
+
+        rv = self.app.get('/v1.0/workflow-specification/standalone', headers=self.logged_in_headers())
+        self.assertEqual(2, len(rv.json))
+
+    def test_get_workflow_from_workflow_spec(self):
+        self.load_example_data()
+        spec = ExampleDataLoader().create_spec('hello_world', 'Hello World', standalone=True, from_tests=True)
+        rv = self.app.post(f'/v1.0/workflow-specification/{spec.id}', headers=self.logged_in_headers())
+        self.assert_success(rv)
+        self.assertEqual('hello_world', rv.json['workflow_spec_id'])
+        self.assertEqual('Task_GetName', rv.json['next_task']['name'])
+
+    def test_add_workflow_spec_category(self):
+        self.load_example_data()
+        count = session.query(WorkflowSpecCategoryModel).count()
+        category = WorkflowSpecCategoryModel(
+            id=count,
+            name='another_test_category',
+            display_name='Another Test Category',
+            display_order=0
+        )
+        rv = self.app.post(f'/v1.0/workflow-specification-category',
+                           headers=self.logged_in_headers(),
+                           content_type="application/json",
+                           data=json.dumps(WorkflowSpecCategoryModelSchema().dump(category))
+                           )
+        self.assert_success(rv)
+        result = session.query(WorkflowSpecCategoryModel).filter(WorkflowSpecCategoryModel.name=='another_test_category').first()
+        self.assertEqual('Another Test Category', result.display_name)
+        self.assertEqual(count, result.id)
+
+    def test_update_workflow_spec_category(self):
+        self.load_example_data()
+        category = session.query(WorkflowSpecCategoryModel).first()
+        category_name_before = category.name
+        new_category_name = category_name_before + '_asdf'
+        self.assertNotEqual(category_name_before, new_category_name)
+
+        category.name = new_category_name
+
+        rv = self.app.put(f'/v1.0/workflow-specification-category/{category.id}',
+                          content_type="application/json",
+                          headers=self.logged_in_headers(),
+                          data=json.dumps(WorkflowSpecCategoryModelSchema().dump(category)))
+        self.assert_success(rv)
+        json_data = json.loads(rv.get_data(as_text=True))
+        self.assertEqual(new_category_name, json_data['name'])

tests/workflow/test_workflow_value_expression.py

@@ -9,7 +9,7 @@ class TestValueExpression(BaseTest):
 
         workflow_api = self.get_workflow_api(workflow)
         first_task = workflow_api.next_task
-        self.complete_form(workflow_api, first_task, {'value_expression_value': ''})
+        self.complete_form(workflow, first_task, {'value_expression_value': ''})
 
         workflow_api = self.get_workflow_api(workflow)
         second_task = workflow_api.next_task
@@ -26,7 +26,7 @@ class TestValueExpression(BaseTest):
 
         workflow_api = self.get_workflow_api(workflow)
         first_task = workflow_api.next_task
-        self.complete_form(workflow_api, first_task, {'value_expression_value': 'black'})
+        self.complete_form(workflow, first_task, {'value_expression_value': 'black'})
 
         workflow_api = self.get_workflow_api(workflow)
         second_task = workflow_api.next_task