Merge branch 'dev' of github.com:sartography/cr-connect-workflow into dev

config/default.py

@@ -17,7 +17,10 @@ API_TOKEN = environ.get('API_TOKEN', default = 'af95596f327c9ecc007b60414fc84b61
 NAME = "CR Connect Workflow"
 DEFAULT_PORT = "5000"
 FLASK_PORT = environ.get('PORT0') or environ.get('FLASK_PORT', default=DEFAULT_PORT)
-CORS_ALLOW_ORIGINS = re.split(r',\s*', environ.get('CORS_ALLOW_ORIGINS', default="localhost:4200, localhost:5002"))
+FRONTEND = "localhost:4200"
+BPMN = "localhost:5002"
+CORS_DEFAULT = f'{FRONTEND}, {BPMN}'
+CORS_ALLOW_ORIGINS = re.split(r',\s*', environ.get('CORS_ALLOW_ORIGINS', default=CORS_DEFAULT))
 TESTING = environ.get('TESTING', default="false") == "true"
 PRODUCTION = (environ.get('PRODUCTION', default="false") == "true")
 TEST_UID = environ.get('TEST_UID', default="dhf8r")
@@ -50,7 +53,6 @@ SQLALCHEMY_DATABASE_URI = environ.get(
 
 TOKEN_AUTH_TTL_HOURS = float(environ.get('TOKEN_AUTH_TTL_HOURS', default=24))
 SECRET_KEY = environ.get('SECRET_KEY', default="Shhhh!!! This is secret!  And better darn well not show up in prod.")
-FRONTEND_AUTH_CALLBACK = environ.get('FRONTEND_AUTH_CALLBACK', default="http://localhost:4200/session")
 SWAGGER_AUTH_KEY = environ.get('SWAGGER_AUTH_KEY', default="SWAGGER")
 # %s/%i placeholders expected for uva_id and study_id in various calls.
 PB_ENABLED = environ.get('PB_ENABLED', default="false") == "true"

crc/api.yml

@@ -740,6 +740,41 @@ paths:
                 type: string
                 format: binary
                 example: '<?xml version="1.0" encoding="UTF-8"?><bpmn:definitions></bpmn:definitions>'
+  /file/{file_id}/download :
+    parameters :
+      - name : file_id
+        in : path
+        required : true
+        description : The id of the File requested
+        schema :
+          type : integer
+      - name : auth_token
+        in : query
+        required : true
+        description : User Auth Toeken
+        schema :
+          type : string
+      - name : version
+        in : query
+        required : false
+        description : The version of the file, or none for latest version
+        schema :
+          type : integer
+    get :
+      operationId : crc.api.file.get_file_data_link
+      summary : Returns only the file contents
+      security: []
+      tags :
+        - Files
+      responses :
+        '200' :
+          description : Returns the actual file
+          content :
+            application/octet-stream :
+              schema :
+                type : string
+                format : binary
+                example : '<?xml version="1.0" encoding="UTF-8"?><bpmn:definitions></bpmn:definitions>'
   /file/{file_id}/data:
     parameters:
       - name: file_id
@@ -1574,6 +1609,7 @@ components:
         standalone:
           type: boolean
           example: false
+          default: false
         workflow_spec_category:
           $ref: "#/components/schemas/WorkflowSpecCategory"
         is_status:

crc/api/file.py

@@ -6,6 +6,7 @@ from flask import send_file
 
 from crc import session
 from crc.api.common import ApiError
+from crc.api.user import verify_token
 from crc.models.api_models import DocumentDirectory, DocumentDirectorySchema
 from crc.models.file import FileSchema, FileModel, File, FileModelSchema, FileDataModel, FileType
 from crc.models.workflow import WorkflowSpecModel
@@ -182,6 +183,22 @@ def get_file_data(file_id, version=None):
     )
 
 
+def get_file_data_link(file_id, auth_token, version=None):
+    if not verify_token(auth_token):
+        raise ApiError('not_authenticated', 'You need to include an authorization token in the URL with this')
+    file_data = FileService.get_file_data(file_id, version)
+    if file_data is None:
+        raise ApiError('no_such_file', 'The file id you provided does not exist')
+    return send_file(
+        io.BytesIO(file_data.data),
+        attachment_filename=file_data.file_model.name,
+        mimetype=file_data.file_model.content_type,
+        cache_timeout=-1,  # Don't cache these files on the browser.
+        last_modified=file_data.date_created,
+        as_attachment = True
+    )
+
+
 def get_file_info(file_id):
     file_model = session.query(FileModel).filter_by(id=file_id).with_for_update().first()
     if file_model is None:

crc/scripts/get_dashboard_url.py

@@ -0,0 +1,16 @@
+from crc.scripts.script import Script
+from crc import app
+
+
+class GetDashboardURL(Script):
+
+    def get_description(self):
+        """Get the URL for the main dashboard. This should be system instance aware.
+        I.e., dev, testing, production, etc."""
+
+    def do_task_validate_only(self, task, study_id, workflow_id, *args, **kwargs):
+        self.do_task(task, study_id, workflow_id, *args, **kwargs)
+
+    def do_task(self, task, study_id, workflow_id, *args, **kwargs):
+        frontend = app.config['FRONTEND']
+        return f'https://{frontend}'

crc/services/study_service.py

@@ -1,7 +1,9 @@
+import urllib
 from copy import copy
 from datetime import datetime
 from typing import List
 
+import flask
 import requests
 from SpiffWorkflow import WorkflowException
 from SpiffWorkflow.exceptions import WorkflowTaskExecException
@@ -288,9 +290,19 @@ class StudyService(object):
             doc_files = FileService.get_files_for_study(study_id=study_id, irb_doc_code=code)
             doc['count'] = len(doc_files)
             doc['files'] = []
+
+            # when we run tests - it doesn't look like the user is available
+            # so we return a bogus token
+            token = 'not_available'
+            if hasattr(flask.g,'user'):
+                token = flask.g.user.encode_auth_token()
             for file in doc_files:
                 doc['files'].append({'file_id': file.id,
                                      'name': file.name,
+                                     'url': app.config['APPLICATION_ROOT']+
+                                            'file/' + str(file.id) +
+                                            '/download?auth_token='+
+                                            urllib.parse.quote_plus(token),
                                      'workflow_id': file.workflow_id})
 
                 # update the document status to match the status of the workflow it is in.

crc/services/workflow_service.py

@@ -22,7 +22,7 @@ from jinja2 import Template
 from crc import db, app
 from crc.api.common import ApiError
 from crc.models.api_models import Task, MultiInstanceType, WorkflowApi
-from crc.models.file import LookupDataModel
+from crc.models.file import LookupDataModel, FileModel
 from crc.models.study import StudyModel
 from crc.models.task_event import TaskEventModel
 from crc.models.user import UserModel, UserModelSchema
@@ -739,10 +739,7 @@ class WorkflowService(object):
 
         if hasattr(task.task_spec, 'form'):
             for field in task.task_spec.form.fields:
-                if field.has_property(Task.FIELD_PROP_READ_ONLY) and \
+                if field.has_property(Task.FIELD_PROP_REPEAT):
-                        field.get_property(Task.FIELD_PROP_READ_ONLY).lower().strip() == "true":
-                    continue  # Don't add read-only data
-                elif field.has_property(Task.FIELD_PROP_REPEAT):
                     group = field.get_property(Task.FIELD_PROP_REPEAT)
                     if group in latest_data:
                         data[group] = latest_data[group]
@@ -811,3 +808,12 @@ class WorkflowService(object):
     def get_standalone_workflow_specs():
         specs = db.session.query(WorkflowSpecModel).filter_by(standalone=True).all()
         return specs
+
+    @staticmethod
+    def get_primary_workflow(workflow_spec_id):
+        # Returns the FileModel of the primary workflow for a workflow_spec
+        primary = None
+        file = db.session.query(FileModel).filter(FileModel.workflow_spec_id==workflow_spec_id, FileModel.primary==True).first()
+        if file:
+            primary = file
+        return primary

crc/static/jinja_extensions.py

@@ -0,0 +1,6 @@
+from crc.api.file import get_document_directory
+
+
+def render_files(study_id,irb_codes):
+    files = get_document_directory(study_id)
+    print(files)

tests/data/email_dashboard_url/email_dashboard_url.bpmn

@@ -0,0 +1,53 @@
+<?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" id="Definitions_024561a" targetNamespace="http://bpmn.io/schema/bpmn" exporter="Camunda Modeler" exporterVersion="3.5.0">
+  <bpmn:process id="Process_1796d29" isExecutable="true">
+    <bpmn:startEvent id="StartEvent_1">
+      <bpmn:outgoing>Flow_0c51a4b</bpmn:outgoing>
+    </bpmn:startEvent>
+    <bpmn:sequenceFlow id="Flow_0c51a4b" sourceRef="StartEvent_1" targetRef="Activity_GetURL" />
+    <bpmn:sequenceFlow id="Flow_1ker6ik" sourceRef="Activity_GetURL" targetRef="Activity_EmailURL" />
+    <bpmn:endEvent id="Event_17hmyob">
+      <bpmn:incoming>Flow_1rfvzi5</bpmn:incoming>
+    </bpmn:endEvent>
+    <bpmn:sequenceFlow id="Flow_1rfvzi5" sourceRef="Activity_EmailURL" targetRef="Event_17hmyob" />
+    <bpmn:scriptTask id="Activity_GetURL" name="Get Dashboard URL&#10;">
+      <bpmn:incoming>Flow_0c51a4b</bpmn:incoming>
+      <bpmn:outgoing>Flow_1ker6ik</bpmn:outgoing>
+      <bpmn:script>dashboard_url = get_dashboard_url()</bpmn:script>
+    </bpmn:scriptTask>
+    <bpmn:scriptTask id="Activity_EmailURL" name="Email Dashboard URL">
+      <bpmn:documentation>&lt;a href="{{dashboard_url}}"&gt;{{dashboard_url}}&lt;/a&gt;</bpmn:documentation>
+      <bpmn:incoming>Flow_1ker6ik</bpmn:incoming>
+      <bpmn:outgoing>Flow_1rfvzi5</bpmn:outgoing>
+      <bpmn:script>email(subject='My Email Subject', recipients="test@example.com")</bpmn:script>
+    </bpmn:scriptTask>
+  </bpmn:process>
+  <bpmndi:BPMNDiagram id="BPMNDiagram_1">
+    <bpmndi:BPMNPlane id="BPMNPlane_1" bpmnElement="Process_1796d29">
+      <bpmndi:BPMNEdge id="Flow_1rfvzi5_di" bpmnElement="Flow_1rfvzi5">
+        <di:waypoint x="530" y="117" />
+        <di:waypoint x="592" y="117" />
+      </bpmndi:BPMNEdge>
+      <bpmndi:BPMNEdge id="Flow_1ker6ik_di" bpmnElement="Flow_1ker6ik">
+        <di:waypoint x="370" y="117" />
+        <di:waypoint x="430" y="117" />
+      </bpmndi:BPMNEdge>
+      <bpmndi:BPMNEdge id="Flow_0c51a4b_di" bpmnElement="Flow_0c51a4b">
+        <di:waypoint x="215" y="117" />
+        <di:waypoint x="270" y="117" />
+      </bpmndi:BPMNEdge>
+      <bpmndi:BPMNShape id="_BPMNShape_StartEvent_2" bpmnElement="StartEvent_1">
+        <dc:Bounds x="179" y="99" width="36" height="36" />
+      </bpmndi:BPMNShape>
+      <bpmndi:BPMNShape id="Event_17hmyob_di" bpmnElement="Event_17hmyob">
+        <dc:Bounds x="592" y="99" width="36" height="36" />
+      </bpmndi:BPMNShape>
+      <bpmndi:BPMNShape id="Activity_1n7b49v_di" bpmnElement="Activity_GetURL">
+        <dc:Bounds x="270" y="77" width="100" height="80" />
+      </bpmndi:BPMNShape>
+      <bpmndi:BPMNShape id="Activity_1dn6kw2_di" bpmnElement="Activity_EmailURL">
+        <dc:Bounds x="430" y="77" width="100" height="80" />
+      </bpmndi:BPMNShape>
+    </bpmndi:BPMNPlane>
+  </bpmndi:BPMNDiagram>
+</bpmn:definitions>

tests/data/file_data_store/file_data_store.bpmn

@@ -18,6 +18,10 @@
 
 fileid = documents['UVACompl_PRCAppr'].files[0]['file_id']
 
+fileurl = documents['UVACompl_PRCAppr'].files[0]['url']
+
+filename = documents['UVACompl_PRCAppr'].files[0]['name']
+
 file_data_set(file_id=fileid,key='test',value='me')</bpmn:script>
     </bpmn:scriptTask>
     <bpmn:endEvent id="Event_1pdyoyv">

tests/data/read_only_field/read_only_field.bpmn

@@ -0,0 +1,77 @@
+<?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_5e40639" targetNamespace="http://bpmn.io/schema/bpmn" exporter="Camunda Modeler" exporterVersion="3.0.0-dev">
+  <bpmn:process id="Process_ReadOnlyField" name="Test Read Only Field" isExecutable="true">
+    <bpmn:startEvent id="StartEvent_1">
+      <bpmn:outgoing>Flow_0to8etb</bpmn:outgoing>
+    </bpmn:startEvent>
+    <bpmn:sequenceFlow id="Flow_0to8etb" sourceRef="StartEvent_1" targetRef="Activity_SetData" />
+    <bpmn:sequenceFlow id="Flow_04r75ca" sourceRef="Activity_SetData" targetRef="Activity_DisplayOnlyField" />
+    <bpmn:sequenceFlow id="Flow_0g25v76" sourceRef="Activity_DisplayOnlyField" targetRef="Activity_CheckData" />
+    <bpmn:endEvent id="Event_0cfckhy">
+      <bpmn:incoming>Flow_0a95kns</bpmn:incoming>
+    </bpmn:endEvent>
+    <bpmn:sequenceFlow id="Flow_0a95kns" sourceRef="Activity_CheckData" targetRef="Event_0cfckhy" />
+    <bpmn:scriptTask id="Activity_SetData" name="Set Data">
+      <bpmn:incoming>Flow_0to8etb</bpmn:incoming>
+      <bpmn:outgoing>Flow_04r75ca</bpmn:outgoing>
+      <bpmn:script>string_value = 'asdf'</bpmn:script>
+    </bpmn:scriptTask>
+    <bpmn:userTask id="Activity_DisplayOnlyField" name="Display Only Field&#10;" camunda:formKey="ReadOnlyFormField">
+      <bpmn:extensionElements>
+        <camunda:formData>
+          <camunda:formField id="read_only_field" label="Read Only" type="string">
+            <camunda:properties>
+              <camunda:property id="read_only" value="True" />
+              <camunda:property id="value_expression" value="string_value" />
+            </camunda:properties>
+          </camunda:formField>
+        </camunda:formData>
+      </bpmn:extensionElements>
+      <bpmn:incoming>Flow_04r75ca</bpmn:incoming>
+      <bpmn:outgoing>Flow_0g25v76</bpmn:outgoing>
+    </bpmn:userTask>
+    <bpmn:manualTask id="Activity_CheckData" name="Check Data Persistence">
+      <bpmn:documentation>Read only is {{ read_only_field }}</bpmn:documentation>
+      <bpmn:incoming>Flow_0g25v76</bpmn:incoming>
+      <bpmn:outgoing>Flow_0a95kns</bpmn:outgoing>
+    </bpmn:manualTask>
+  </bpmn:process>
+  <bpmndi:BPMNDiagram id="BPMNDiagram_1">
+    <bpmndi:BPMNPlane id="BPMNPlane_1" bpmnElement="Process_ReadOnlyField">
+      <bpmndi:BPMNEdge id="Flow_0a95kns_di" bpmnElement="Flow_0a95kns">
+        <di:waypoint x="690" y="177" />
+        <di:waypoint x="752" y="177" />
+      </bpmndi:BPMNEdge>
+      <bpmndi:BPMNEdge id="Flow_0g25v76_di" bpmnElement="Flow_0g25v76">
+        <di:waypoint x="530" y="177" />
+        <di:waypoint x="590" y="177" />
+      </bpmndi:BPMNEdge>
+      <bpmndi:BPMNEdge id="Flow_04r75ca_di" bpmnElement="Flow_04r75ca">
+        <di:waypoint x="370" y="177" />
+        <di:waypoint x="430" y="177" />
+      </bpmndi:BPMNEdge>
+      <bpmndi:BPMNEdge id="Flow_0to8etb_di" bpmnElement="Flow_0to8etb">
+        <di:waypoint x="215" y="177" />
+        <di:waypoint x="270" y="177" />
+      </bpmndi:BPMNEdge>
+      <bpmndi:BPMNShape id="_BPMNShape_StartEvent_2" bpmnElement="StartEvent_1">
+        <dc:Bounds x="179" y="159" width="36" height="36" />
+      </bpmndi:BPMNShape>
+      <bpmndi:BPMNShape id="Event_0cfckhy_di" bpmnElement="Event_0cfckhy">
+        <dc:Bounds x="752" y="159" width="36" height="36" />
+        <bpmndi:BPMNLabel>
+          <dc:Bounds x="733" y="202" width="76" height="27" />
+        </bpmndi:BPMNLabel>
+      </bpmndi:BPMNShape>
+      <bpmndi:BPMNShape id="Activity_10544ek_di" bpmnElement="Activity_SetData">
+        <dc:Bounds x="270" y="137" width="100" height="80" />
+      </bpmndi:BPMNShape>
+      <bpmndi:BPMNShape id="Activity_0ho1wsm_di" bpmnElement="Activity_DisplayOnlyField">
+        <dc:Bounds x="430" y="137" width="100" height="80" />
+      </bpmndi:BPMNShape>
+      <bpmndi:BPMNShape id="Activity_10ds6m4_di" bpmnElement="Activity_CheckData">
+        <dc:Bounds x="590" y="137" width="100" height="80" />
+      </bpmndi:BPMNShape>
+    </bpmndi:BPMNPlane>
+  </bpmndi:BPMNDiagram>
+</bpmn:definitions>

tests/test_file_datastore.py

@@ -27,6 +27,8 @@ class TestFileDatastore(BaseTest):
         processor = WorkflowProcessor(workflow)
         processor.do_engine_steps()
         task_data = processor.bpmn_workflow.last_task.data
+        self.assertTrue(str(task_data['fileid']) in task_data['fileurl'])
+        self.assertEqual(task_data['filename'],'anything.png')
         self.assertEqual(task_data['output'], 'me')
         self.assertEqual(task_data['output2'], 'nope')
 

tests/test_get_dashboard_url_script.py

@@ -0,0 +1,17 @@
+from tests.base_test import BaseTest
+from crc import app, mail
+
+
+class TestGetDashboardURL(BaseTest):
+
+    def test_get_dashboard_url(self):
+        with mail.record_messages() as outbox:
+
+            dashboard_url = f'https://{app.config["FRONTEND"]}'
+            workflow = self.create_workflow('email_dashboard_url')
+            self.get_workflow_api(workflow)
+
+            self.assertEqual(1, len(outbox))
+            self.assertEqual('My Email Subject', outbox[0].subject)
+            self.assertEqual(['test@example.com'], outbox[0].recipients)
+            self.assertIn(dashboard_url, outbox[0].body)

tests/workflow/test_workflow_read_only_field.py

@@ -0,0 +1,16 @@
+from tests.base_test import BaseTest
+
+
+class TestReadOnlyField(BaseTest):
+
+    def test_read_only(self):
+
+        workflow = self.create_workflow('read_only_field')
+        workflow_api = self.get_workflow_api(workflow)
+        first_task = workflow_api.next_task
+        read_only_field = first_task.data['read_only_field']
+        self.complete_form(workflow, first_task, {'read_only_field': read_only_field})
+        workflow_api = self.get_workflow_api(workflow)
+        task = workflow_api.next_task
+
+        self.assertEqual('Read only is asdf', task.documentation)

tests/workflow/test_workflow_service.py

@@ -10,6 +10,7 @@ from example_data import ExampleDataLoader
 from crc import db
 from crc.models.task_event import TaskEventModel
 from crc.models.api_models import Task
+from crc.models.file import FileModel
 from crc.api.common import ApiError
 
 
@@ -114,3 +115,12 @@ class TestWorkflowService(BaseTest):
 
         result2 = WorkflowService.get_dot_value(path, {"a.b.c":"garbage"})
         self.assertEqual("garbage", result2)
+
+    def test_get_primary_workflow(self):
+
+        workflow = self.create_workflow('hello_world')
+        workflow_spec_id = workflow.workflow_spec.id
+        primary_workflow = WorkflowService.get_primary_workflow(workflow_spec_id)
+        self.assertIsInstance(primary_workflow, FileModel)
+        self.assertEqual(workflow_spec_id, primary_workflow.workflow_spec_id)
+        self.assertEqual('hello_world.bpmn', primary_workflow.name)