Merge pull request #474 from sartography/dev

dev to master
2025-02-23 05:08:32 +00:00 · 2022-02-25 16:21:09 -05:00 · 2022-02-25 16:21:09 -05:00 · 9c098717da
commit 9c098717da
parent 99a1e1c31a 9b004d0dc6
10 changed files with 250 additions and 31 deletions
--- a/2
+++ b/2
@ -13,7 +13,7 @@ alembic = "*"
 coverage = "*"
 docxtpl = "*"
 flask = "*"
-celery = "<5"
+celery = "<6"
 flask-admin = "*"
 flask-bcrypt = "*"
 flask-cors = "*"
--- a/Pipfile.lock
+++ b/Pipfile.lock
@ -1,7 +1,7 @@
 {
    "_meta": {
        "hash": {
-            "sha256": "eb924ba10433552dcde585064a905bb8b78e96b28fc23391eee486ca34e22aad"
+            "sha256": "89204202883b76908f866ebe652cb214c079575f87cb05f677d602e3f9040c4b"
        },
        "pipfile-spec": 6,
        "requires": {
@ -33,11 +33,11 @@
        },
        "amqp": {
            "hashes": [
-                "sha256:70cdb10628468ff14e57ec2f751c7aa9e48e7e3651cfd62d431213c0c4e58f21",
-                "sha256:aa7f313fb887c91f15474c1229907a04dac0b8135822d6603437803424c0aa59"
+                "sha256:1e5f707424e544078ca196e72ae6a14887ce74e02bd126be54b7c03c971bef18",
+                "sha256:9cd81f7b023fc04bbb108718fbac674f06901b77bfcdce85b10e2a5d0ee91be5"
            ],
-            "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'",
-            "version": "==2.6.1"
+            "markers": "python_version >= '3.6'",
+            "version": "==5.0.9"
        },
        "aniso8601": {
            "hashes": [
@ -89,7 +89,7 @@
                "sha256:f04e857b59d9d1ccc39ce2da1021d196e47234873820cbeaad210724b1ee28ac",
                "sha256:fadbfe37f74051d024037f223b8e001611eac868b5c5b06144ef4d8b799862f2"
            ],
-            "markers": "python_version >= '3.6' and python_version < '3.9'",
+            "markers": "python_version < '3.9'",
            "version": "==0.2.1"
        },
        "bcrypt": {
@ -131,11 +131,11 @@
        },
        "celery": {
            "hashes": [
-                "sha256:a92e1d56e650781fb747032a3997d16236d037c8199eacd5217d1a72893bca45",
-                "sha256:d220b13a8ed57c78149acf82c006785356071844afe0b27012a4991d44026f9f"
+                "sha256:2844eb040e915398623a43253a8e1016723442ece6b0751a3c416d8a2b34216f",
+                "sha256:5a68a351076cfac4f678fa5ffd898105c28825a2224902da006970005196d061"
            ],
            "index": "pypi",
-            "version": "==4.4.7"
+            "version": "==5.2.2"
        },
        "certifi": {
            "hashes": [
@ -215,6 +215,28 @@
            "markers": "python_version >= '3.6'",
            "version": "==8.0.4"
        },
+        "click-didyoumean": {
+            "hashes": [
+                "sha256:a0713dc7a1de3f06bc0df5a9567ad19ead2d3d5689b434768a6145bff77c0667",
+                "sha256:f184f0d851d96b6d29297354ed981b7dd71df7ff500d82fa6d11f0856bee8035"
+            ],
+            "markers": "python_version < '4' and python_full_version >= '3.6.2'",
+            "version": "==0.3.0"
+        },
+        "click-plugins": {
+            "hashes": [
+                "sha256:46ab999744a9d831159c3411bb0c79346d94a444df9a3a3742e9ed63645f264b",
+                "sha256:5d262006d3222f5057fd81e1623d4443e41dcda5dc815c06b442aa3c02889fc8"
+            ],
+            "version": "==1.1.1"
+        },
+        "click-repl": {
+            "hashes": [
+                "sha256:94b3fbbc9406a236f176e0506524b2937e4b23b6f4c0c0b2a0a83f8a64e9194b",
+                "sha256:cd12f68d745bf6151210790540b4cb064c7b13e571bc64b6957d98d120dacfd8"
+            ],
+            "version": "==0.2.0"
+        },
        "clickclick": {
            "hashes": [
                "sha256:4efb13e62353e34c5eef7ed6582c4920b418d7dedc86d819e22ee089ba01802c",
@ -530,7 +552,7 @@
                "sha256:175f4ee440a0317f6e8d81b7f8d4869f93316170a65ad2b007d2929186c8052c",
                "sha256:e0bc84ff355328a4adfc5240c4f211e0ab386f80aa640d1b11f0618a1d282094"
            ],
-            "markers": "python_version < '3.10'",
+            "markers": "python_version < '3.9'",
            "version": "==4.11.1"
        },
        "importlib-resources": {
@ -575,11 +597,11 @@
        },
        "kombu": {
            "hashes": [
-                "sha256:be48cdffb54a2194d93ad6533d73f69408486483d189fe9f5990ee24255b0e0a",
-                "sha256:ca1b45faac8c0b18493d02a8571792f3c40291cf2bcf1f55afed3d8f3aa7ba74"
+                "sha256:81a90c1de97e08d3db37dbf163eaaf667445e1068c98bfd89f051a40e9f6dbbd",
+                "sha256:eeaeb8024f3a5cfc71c9250e45cddb8493f269d74ada2f74909a93c59c4b4179"
            ],
-            "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'",
-            "version": "==4.6.11"
+            "markers": "python_version >= '3.7'",
+            "version": "==5.2.3"
        },
        "ldap3": {
            "hashes": [
@ -813,6 +835,14 @@
            "index": "pypi",
            "version": "==1.4.1"
        },
+        "prompt-toolkit": {
+            "hashes": [
+                "sha256:30129d870dcb0b3b6a53efdc9d0a83ea96162ffd28ffe077e94215b233dc670c",
+                "sha256:9f1cd16b1e86c2968f2519d7fb31dd9d669916f515612c269d14e9ed52b51650"
+            ],
+            "markers": "python_full_version >= '3.6.2'",
+            "version": "==3.0.28"
+        },
        "psycopg2-binary": {
            "hashes": [
                "sha256:01310cf4cf26db9aea5158c217caa92d291f0500051a6469ac52166e1a16f5b7",
@ -1146,6 +1176,14 @@
            "index": "pypi",
            "version": "==0.14.4"
        },
+        "setuptools": {
+            "hashes": [
+                "sha256:2347b2b432c891a863acadca2da9ac101eae6169b1d3dfee2ec605ecd50dbfe5",
+                "sha256:e4f30b9f84e5ab3decf945113119649fec09c1fc3507c6ebffec75646c56e62b"
+            ],
+            "markers": "python_version >= '3.7'",
+            "version": "==60.9.3"
+        },
        "six": {
            "hashes": [
                "sha256:1e61c37477a1626458e36f7b1d82aa5c9b094fa4802892072e49de9c60c4c926",
@ -1313,11 +1351,11 @@
        },
        "vine": {
            "hashes": [
-                "sha256:133ee6d7a9016f177ddeaf191c1f58421a1dcc6ee9a42c58b34bed40e1d2cd87",
-                "sha256:ea4947cc56d1fd6f2095c8d543ee25dad966f78692528e68b4fada11ba3f98af"
+                "sha256:4c9dceab6f76ed92105027c49c823800dd33cacce13bdedc5b914e3514b7fb30",
+                "sha256:7d3b1624a953da82ef63462013bbd271d3eb75751489f9807598e8f340bd637e"
            ],
-            "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'",
-            "version": "==1.3.0"
+            "markers": "python_version >= '3.6'",
+            "version": "==5.0.0"
        },
        "waitress": {
            "hashes": [
@ -1327,6 +1365,13 @@
            "markers": "python_version >= '3.6'",
            "version": "==2.0.0"
        },
+        "wcwidth": {
+            "hashes": [
+                "sha256:beb4802a9cebb9144e99086eff703a642a13d6a0052920003a230f3294bbe784",
+                "sha256:c4d647b99872929fdb7bdcaa4fbe7f01413ed3d98077df798530e5b04f116c83"
+            ],
+            "version": "==0.2.5"
+        },
        "webob": {
            "hashes": [
                "sha256:73aae30359291c14fa3b956f8b5ca31960e420c28c1bec002547fb04928cf89b",
@ -1437,7 +1482,7 @@
                "sha256:9f50f446828eb9d45b267433fd3e9da8d801f614129124863f9c51ebceafb87d",
                "sha256:b47250dd24f92b7dd6a0a8fc5244da14608f3ca90a5efcd37a3b1642fac9a375"
            ],
-            "markers": "python_version < '3.10'",
+            "markers": "python_version >= '3.7'",
            "version": "==3.7.0"
        }
    },
--- a/crc/api/workflow.py
+++ b/crc/api/workflow.py
@ -244,9 +244,10 @@ def get_task_events(action = None, workflow = None, study = None):
        study = session.query(StudyModel).filter(StudyModel.id == event.study_id).first()
        workflow = session.query(WorkflowModel).filter(WorkflowModel.id == event.workflow_id).first()
        spec = WorkflowSpecService().get_spec(workflow.workflow_spec_id)
-        workflow_meta = WorkflowMetadata.from_workflow(workflow, spec)
-        if study and study.status in [StudyStatus.open_for_enrollment, StudyStatus.in_progress]:
-            task_events.append(TaskEvent(event, study, workflow_meta))
+        if spec is not None:
+            workflow_meta = WorkflowMetadata.from_workflow(workflow, spec)
+            if study and study.status in [StudyStatus.open_for_enrollment, StudyStatus.in_progress]:
+                task_events.append(TaskEvent(event, study, workflow_meta))
    return TaskEventSchema(many=True).dump(task_events)


--- a/crc/scripts/delete_variables.py
+++ b/crc/scripts/delete_variables.py
@ -0,0 +1,17 @@
+from crc.api.common import ApiError
+from crc.scripts.script import Script
+
+
+class DeleteVariables(Script):
+
+    def get_description(self):
+        return """Script to delete variables from task_data, if they exist.
+        Accepts a list of variables to delete."""
+
+    def do_task_validate_only(self, task, study_id, workflow_id, *args, **kwargs):
+        return self.do_task(task, study_id, workflow_id, *args, **kwargs)
+
+    def do_task(self, task, study_id, workflow_id, *args, **kwargs):
+        for arg in args:
+            if arg in task.data:
+                del(task.data[arg])
--- a/crc/scripts/get_spec_from_id.py
+++ b/crc/scripts/get_spec_from_id.py
@ -4,7 +4,7 @@ from crc.scripts.script import Script
 from crc.services.workflow_spec_service import WorkflowSpecService


-class ScriptTemplate(Script):
+class GetSpecFromID(Script):

    def get_description(self):
        return """Get workflow spec information from a workflow spec id"""
--- a/crc/scripts/get_spec_from_workflow_id.py
+++ b/crc/scripts/get_spec_from_workflow_id.py
@ -5,7 +5,7 @@ from crc.scripts.script import Script
 from crc.services.workflow_spec_service import WorkflowSpecService


-class ScriptTemplate(Script):
+class GetSpecFromWorkflowID(Script):

    def get_description(self):
        return """Get a workflow spec, from a workflow id. You must pass in a workflow id."""
--- a/crc/services/workflow_service.py
+++ b/crc/services/workflow_service.py
@ -172,10 +172,9 @@ class WorkflowService(object):
        """Raise an exception of the workflow is not enabled and can not be executed."""
        if study_id is not None:
            study_model = session.query(StudyModel).filter(StudyModel.id == study_id).first()
-            spec_model = session.query(WorkflowSpecModel).filter(WorkflowSpecModel.id == spec_id).first()
            status = StudyService._get_study_status(study_model)
-            if spec_model.id in status and status[spec_model.id]['status'] == 'disabled':
-                raise ApiError(code='disabled_workflow', message=f"This workflow is disabled. {status[spec_model.id]['message']}")
+            if spec_id in status and status[spec_id]['status'] == 'disabled':
+                raise ApiError(code='disabled_workflow', message=f"This workflow is disabled. {status[spec_id]['message']}")

    @staticmethod
    def test_spec(spec_id, validate_study_id=None, test_until=None, required_only=False):
@ -190,6 +189,7 @@ class WorkflowService(object):
          """

        workflow_model = WorkflowService.make_test_workflow(spec_id, validate_study_id)
+        WorkflowService.raise_if_disabled(spec_id, validate_study_id)
        try:
            processor = WorkflowProcessor(workflow_model, validate_only=True)
            count = 0
--- a/tests/data/delete_variables/delete_variables.bpmn
+++ b/tests/data/delete_variables/delete_variables.bpmn
@ -0,0 +1,84 @@
+<?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_0vysnuw" targetNamespace="http://bpmn.io/schema/bpmn" exporter="Camunda Modeler" exporterVersion="4.2.0">
+  <bpmn:process id="Process_1so2rqu" name="Delete Variables from Task Data" isExecutable="true">
+    <bpmn:startEvent id="StartEvent_1">
+      <bpmn:outgoing>Flow_0zdl9n2</bpmn:outgoing>
+    </bpmn:startEvent>
+    <bpmn:sequenceFlow id="Flow_0zdl9n2" sourceRef="StartEvent_1" targetRef="Activity_1ufzsi0" />
+    <bpmn:sequenceFlow id="Flow_14niiph" sourceRef="Activity_1ufzsi0" targetRef="Activity_16c0ane" />
+    <bpmn:sequenceFlow id="Flow_1wjlzq0" sourceRef="Activity_0nuz6z0" targetRef="Activity_0gtt0h2" />
+    <bpmn:endEvent id="Event_1dxgxez">
+      <bpmn:incoming>Flow_0aftk6v</bpmn:incoming>
+    </bpmn:endEvent>
+    <bpmn:sequenceFlow id="Flow_0aftk6v" sourceRef="Activity_0gtt0h2" targetRef="Event_1dxgxez" />
+    <bpmn:scriptTask id="Activity_1ufzsi0" name="Create Variables">
+      <bpmn:incoming>Flow_0zdl9n2</bpmn:incoming>
+      <bpmn:outgoing>Flow_14niiph</bpmn:outgoing>
+      <bpmn:script>a_item = 1
+b_item = 2
+c_item = 'a string'
+d_item = a_item + b_item
+e_item = datetime.datetime.now()</bpmn:script>
+    </bpmn:scriptTask>
+    <bpmn:scriptTask id="Activity_0nuz6z0" name="Delete Variables">
+      <bpmn:incoming>Flow_0ke44z0</bpmn:incoming>
+      <bpmn:outgoing>Flow_1wjlzq0</bpmn:outgoing>
+      <bpmn:script>delete_variables('a_item', 'b_item', 'c_item', 'd_item', 'e_item')</bpmn:script>
+    </bpmn:scriptTask>
+    <bpmn:manualTask id="Activity_0gtt0h2" name="Print Task Data">
+      <bpmn:documentation>## Task Data
+{{ task_data }}</bpmn:documentation>
+      <bpmn:incoming>Flow_1wjlzq0</bpmn:incoming>
+      <bpmn:outgoing>Flow_0aftk6v</bpmn:outgoing>
+    </bpmn:manualTask>
+    <bpmn:sequenceFlow id="Flow_0ke44z0" sourceRef="Activity_16c0ane" targetRef="Activity_0nuz6z0" />
+    <bpmn:manualTask id="Activity_16c0ane" name="Print Task Data">
+      <bpmn:documentation>## Task Data
+{{ task_data }}</bpmn:documentation>
+      <bpmn:incoming>Flow_14niiph</bpmn:incoming>
+      <bpmn:outgoing>Flow_0ke44z0</bpmn:outgoing>
+    </bpmn:manualTask>
+  </bpmn:process>
+  <bpmndi:BPMNDiagram id="BPMNDiagram_1">
+    <bpmndi:BPMNPlane id="BPMNPlane_1" bpmnElement="Process_1so2rqu">
+      <bpmndi:BPMNEdge id="Flow_0ke44z0_di" bpmnElement="Flow_0ke44z0">
+        <di:waypoint x="530" y="117" />
+        <di:waypoint x="588" y="117" />
+      </bpmndi:BPMNEdge>
+      <bpmndi:BPMNEdge id="Flow_0aftk6v_di" bpmnElement="Flow_0aftk6v">
+        <di:waypoint x="848" y="117" />
+        <di:waypoint x="910" y="117" />
+      </bpmndi:BPMNEdge>
+      <bpmndi:BPMNEdge id="Flow_1wjlzq0_di" bpmnElement="Flow_1wjlzq0">
+        <di:waypoint x="688" y="117" />
+        <di:waypoint x="748" y="117" />
+      </bpmndi:BPMNEdge>
+      <bpmndi:BPMNEdge id="Flow_14niiph_di" bpmnElement="Flow_14niiph">
+        <di:waypoint x="370" y="117" />
+        <di:waypoint x="430" y="117" />
+      </bpmndi:BPMNEdge>
+      <bpmndi:BPMNEdge id="Flow_0zdl9n2_di" bpmnElement="Flow_0zdl9n2">
+        <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_1dxgxez_di" bpmnElement="Event_1dxgxez">
+        <dc:Bounds x="910" y="99" width="36" height="36" />
+      </bpmndi:BPMNShape>
+      <bpmndi:BPMNShape id="Activity_0ukmng8_di" bpmnElement="Activity_1ufzsi0">
+        <dc:Bounds x="270" y="77" width="100" height="80" />
+      </bpmndi:BPMNShape>
+      <bpmndi:BPMNShape id="Activity_0ykd81y_di" bpmnElement="Activity_0nuz6z0">
+        <dc:Bounds x="588" y="77" width="100" height="80" />
+      </bpmndi:BPMNShape>
+      <bpmndi:BPMNShape id="Activity_1x2rbnn_di" bpmnElement="Activity_0gtt0h2">
+        <dc:Bounds x="748" y="77" width="100" height="80" />
+      </bpmndi:BPMNShape>
+      <bpmndi:BPMNShape id="Activity_0baxotx_di" bpmnElement="Activity_16c0ane">
+        <dc:Bounds x="430" y="77" width="100" height="80" />
+      </bpmndi:BPMNShape>
+    </bpmndi:BPMNPlane>
+  </bpmndi:BPMNDiagram>
+</bpmn:definitions>
--- a/tests/test_workflow_api.py
+++ b/tests/test_workflow_api.py
@ -1,11 +1,10 @@
 from tests.base_test import BaseTest

 from crc import session
+from crc.models.task_event import TaskEventModel
 from crc.models.user import UserModel
-from crc.services.user_service import UserService
 from crc.services.workflow_service import WorkflowService
-
-from example_data import ExampleDataLoader
+from crc.services.workflow_spec_service import WorkflowSpecService

 import json

@ -26,6 +25,60 @@ class TestWorkflowApi(BaseTest):
                          headers=self.logged_in_headers())
        self.assert_success(rv)

+    def test_get_task_events_bad_spec(self):
+        self.add_studies()
+        workflow = self.create_workflow('hello_world')
+
+        # add a task_event
+        task_event = TaskEventModel(
+            study_id=workflow.study_id,
+            user_uid='dhf8r',
+            workflow_id=workflow.id,
+            workflow_spec_id=workflow.workflow_spec_id,
+            spec_version='',
+            action='',
+            task_id='',
+            task_name='my task name',
+            task_title='my task title',
+            task_state='',
+            task_lane='',
+            form_data='',
+            mi_type='',
+            mi_count=None,
+            mi_index=None,
+            process_name='',
+            date=None
+        )
+        session.add(task_event)
+        session.commit()
+
+        # make sure we have a task_event
+        tasks = session.query(TaskEventModel).filter(TaskEventModel.user_uid=='dhf8r').all()
+        self.assertEqual(1, len(tasks))
+
+        rv = self.app.get(f'/v1.0/task_events',
+                          follow_redirects=True,
+                          content_type="application/json",
+                          headers=self.logged_in_headers())
+        self.assert_success(rv)
+        data = json.loads(rv.get_data(as_text=True))
+        # make sure we get the task_event
+        self.assertEqual('my task title', data[0]['task_title'])
+
+        # delete the workflow spec
+        WorkflowSpecService().delete_spec('hello_world')
+
+        # try to get the task_event again
+        rv = self.app.get(f'/v1.0/task_events',
+                          follow_redirects=True,
+                          content_type="application/json",
+                          headers=self.logged_in_headers())
+        # make sure we don't get an error, even though the spec no longer exists
+        self.assert_success(rv)
+
+        # make sure we don't get any events back.
+        self.assertEqual([], rv.json)
+
    def test_library_code(self):

        spec1 = self.load_test_spec('hello_world')
--- a/tests/workflow/test_workflow_delete_variables.py
+++ b/tests/workflow/test_workflow_delete_variables.py
@ -0,0 +1,19 @@
+from tests.base_test import BaseTest
+
+
+class TestDeleteVariables(BaseTest):
+
+    def test_delete_variables(self):
+        """This workflow creates variables 'a', 'b', 'c', 'd', and 'e',
+        then deletes them with the delete_variables script.
+        We assert that they are no longer in task.data"""
+        workflow = self.create_workflow('delete_variables')
+        workflow_api = self.get_workflow_api(workflow)
+        task = workflow_api.next_task
+        items = ('a_item', 'b_item', 'c_item', 'd_item', 'e_item')
+        for item in items:
+            self.assertIn(item, task.data)
+        workflow_api = self.complete_form(workflow, task, {})
+        task = workflow_api.next_task
+        for item in items:
+            self.assertNotIn(item, task.data)