Merge remote-tracking branch 'origin/master'

crc/__init__.py

@@ -2,6 +2,7 @@ import logging
 import os
 
 import connexion
+from flask_cors import CORS
 from flask_marshmallow import Marshmallow
 from flask_sqlalchemy import SQLAlchemy
 from flask_migrate import Migrate
@@ -26,6 +27,7 @@ ma = Marshmallow(app)
 from crc import models
 
 connexion_app.add_api('api.yml')
+cors = CORS(connexion_app.app)
 
 @app.cli.command()
 def load_example_data():

crc/api.py

@@ -3,7 +3,7 @@ from flask_marshmallow import Schema
 
 from crc import db, ma
 from crc.models import WorkflowModel, WorkflowSchema, StudySchema, StudyModel, WorkflowSpecSchema, WorkflowSpecModel, \
-    WorkflowStatus
+    WorkflowStatus, Task, TaskSchema
 from crc.workflow_processor import WorkflowProcessor
 
 
@@ -61,11 +61,24 @@ def add_workflow_to_study(study_id, body):
                              workflow_spec_id=workflow_spec_model.id)
     db.session.add(workflow)
     db.session.commit()
+    return get_study_workflows(study_id)
+
 
 def get_workflow(workflow_id):
-    return db.session.query(WorkflowModel).filter_by(id=workflow_id).first()
+    schema = WorkflowSchema()
+    workflow = db.session.query(WorkflowModel).filter_by(id=workflow_id).first()
+    return schema.dump(workflow)
 
 
+def get_tasks(workflow_id):
+    workflow = db.session.query(WorkflowModel).filter_by(id=workflow_id).first()
+    processor = WorkflowProcessor(workflow.workflow_spec_id, workflow.bpmn_workflow_json)
+    spiff_tasks = processor.get_ready_user_tasks()
+    tasks = []
+    for st in spiff_tasks:
+        tasks.append(Task.from_spiff(st))
+    return TaskSchema(many=True).dump(tasks)
+
 def get_task(workflow_id, task_id):
     workflow = db.session.query(WorkflowModel).filter_by(id=workflow_id).first()
     return workflow.bpmn_workflow().get_task(task_id)

crc/api.yml

@@ -192,7 +192,35 @@ paths:
             application/json:
               schema:
                 $ref: "#/components/schemas/Error"
-
+  /workflow/{workflow_id}/tasks:
+    get:
+      operationId: crc.api.get_tasks
+      summary: Return a list of all tasks for this workflow
+      tags:
+        - Workflows and Tasks
+      parameters:
+        - name: workflow_id
+          in: path
+          required: true
+          description: The id of the workflow
+          schema:
+            type: integer
+            format: int32
+      responses:
+        '200':
+          description: Expected response to a valid request
+          content:
+            application/json:
+              schema:
+                type: array
+                items:
+                  $ref: "#/components/schemas/Task"
+        default:
+          description: unexpected error
+          content:
+            application/json:
+              schema:
+                $ref: "#/components/schemas/Error"
   # /v1.0/workflow/0/task/0
   /workflow/{workflow_id}/task/{task_id}:
     get:
@@ -265,19 +293,10 @@ paths:
 components:
   schemas:
     Study:
-      required:
-      - id
-      - title
-      - last_updated
-      - pb_status
-      - pi
-      - sponsor
-      - ind_number
       properties:
         id:
-          type: string
-          format: string
-          example: AB1234
+          type: integer
+          example: 1234
         title:
           type: string
           example: The impact of fried pickles on beer consumption in bipedal software developers.
@@ -285,11 +304,11 @@ components:
           type: string
           format: date_time
           example: "2019-12-25T09:12:33.001Z"
-        pb_status:
+        protocol_builder_status:
           type: string
-          enum: [started, done]
+          enum: [out_of_date, in_process, complete, updating]
           example: done
-        pi:
+        primary_investigator_id:
           type: string
           example: dhf8r
         sponsor:
@@ -356,16 +375,20 @@ components:
           type: string
         type:
           type: string
+        status:
+          type: string
         form:
           $ref: "#/components/schemas/Form"
       example:
         {
           id: study_identification,
           name: "Study Identification",
-          type: form,
+          state: "ready",
+          type: "form",
           form: {
+            key: "oncology_form",
             field: {
-              id: adult_oncology,
+              id: "is_adult_patient",
               type: enum,
               label: "Is this study treating adult oncology patients?",
               options: ["yes", "no"],

crc/models.py

@@ -1,10 +1,12 @@
 import enum
 
+from SpiffWorkflow import Task
 from flask_marshmallow.sqla import ModelSchema
+from marshmallow import post_load, fields, Schema
 from marshmallow_enum import EnumField
 from sqlalchemy import func
 
-from crc import db
+from crc import db, ma
 
 
 class ProtocolBuilderStatus(enum.Enum):
@@ -56,10 +58,58 @@ class WorkflowModel(db.Model):
     study_id = db.Column(db.Integer, db.ForeignKey('study.id'))
     workflow_spec_id = db.Column(db.Integer, db.ForeignKey('workflow_spec.id'))
 
+
 class WorkflowSchema(ModelSchema):
     class Meta:
         model = WorkflowModel
     status = EnumField(WorkflowStatus)
 
 
+class Task:
+    def __init__(self, id, name, type, state, form):
+        self.id = id
+        self.name = name
+        self.type = type
+        self.state = state
+        self.form = form
+
+    @classmethod
+    def from_spiff(cls, spiff_task):
+        instance = cls(spiff_task.id,
+                       spiff_task.task_spec.name,
+                       spiff_task.get_state_name(),
+                       "task",
+                       {})
+        if hasattr(spiff_task.task_spec, "form"):
+            instance.type = "form"
+            instance.form = spiff_task.task_spec.form
+        return instance
+
+
+class OptionSchema(ma.Schema):
+    class Meta:
+        fields = ["id", "name"]
+
+
+class FieldSchema(ma.Schema):
+    class Meta:
+        fields = ["id", "type", "label", "defaultValue", "options"]
+    options = fields.List(fields.Nested(OptionSchema))
+
+
+class FormSchema(ma.Schema):
+    class Meta:
+        fields = ["key", "fields"]
+    fields = fields.List(fields.Nested(FieldSchema))
+
+
+class TaskSchema(ma.Schema):
+    class Meta:
+        fields = ["id", "name", "type", "state", "form"]
+
+    form = fields.Nested(FormSchema)
+    @post_load
+    def make_task(self, data, **kwargs):
+        return Task(**data)
+
 

crc/workflow_processor.py

@@ -67,7 +67,7 @@ class WorkflowProcessor:
         self.bpmn_workflow.do_engine_steps()
 
     def serialize(self):
-        return self.bpmn_workflow.serialize(JSONSerializer())
+        return self._serializer.serialize_workflow(self.bpmn_workflow)
 
     def next_user_tasks(self):
         return self.bpmn_workflow.get_ready_user_tasks()
@@ -77,3 +77,6 @@ class WorkflowProcessor:
 
     def get_data(self):
         return self.bpmn_workflow.data
+
+    def get_ready_user_tasks(self):
+        return self.bpmn_workflow.get_ready_user_tasks()

tests/test_api.py

@@ -4,7 +4,9 @@ import unittest
 from sqlalchemy import func
 
 from crc import db
-from crc.models import StudyModel, StudySchema, WorkflowSpecModel, WorkflowSpecSchema, WorkflowModel, WorkflowStatus
+from crc.models import StudyModel, StudySchema, WorkflowSpecModel, WorkflowSpecSchema, WorkflowModel, WorkflowStatus, \
+    WorkflowSchema, TaskSchema
+from crc.workflow_processor import WorkflowProcessor
 from tests.base_test import BaseTest
 
 
@@ -62,3 +64,19 @@ class TestStudy(BaseTest, unittest.TestCase):
         self.assertIsNotNone(workflow.bpmn_workflow_json)
         self.assertEqual(spec.id, workflow.workflow_spec_id)
 
+        json_data = json.loads(rv.get_data(as_text=True))
+        workflows = WorkflowSchema(many=True).load(json_data, session=db.session)
+        self.assertEqual(workflows[0].id, workflow.id)
+
+    def test_get_current_user_tasks(self):
+        self.load_example_data()
+        study = db.session.query(StudyModel).first()
+        spec = db.session.query(WorkflowSpecModel).filter_by(id='random_fact').first()
+        self.app.post('/v1.0/study/%i/workflows' % study.id, content_type="application/json",
+                      data=json.dumps(WorkflowSpecSchema().dump(spec)))
+        rv = self.app.get('/v1.0/workflow/%i/tasks' % study.id, content_type="application/json")
+        self.assert_success(rv)
+        json_data = json.loads(rv.get_data(as_text=True))
+        tasks = TaskSchema(many=True).load(json_data)
+        self.assertEqual("Task_User_Select_Type", tasks[0].name)
+        self.assertEqual(3, len(tasks[0].form["fields"][0]["options"]))