Merge pull request #333 from sartography/check-study-script-273

Check study script #273

config/default.py

@@ -63,6 +63,7 @@ PB_REQUIRED_DOCS_URL = environ.get('PB_REQUIRED_DOCS_URL', default=PB_BASE_URL +
 PB_STUDY_DETAILS_URL = environ.get('PB_STUDY_DETAILS_URL', default=PB_BASE_URL + "study?studyid=%i")
 PB_SPONSORS_URL = environ.get('PB_SPONSORS_URL', default=PB_BASE_URL + "sponsors?studyid=%i")
 PB_IRB_INFO_URL = environ.get('PB_IRB_INFO_URL', default=PB_BASE_URL + "current_irb_info/%i")
+PB_CHECK_STUDY_URL = environ.get('PB_CHECK_STUDY_URL', default=PB_BASE_URL + "check_study/%i")
 
 # Ldap Configuration
 LDAP_URL = environ.get('LDAP_URL', default="ldap.virginia.edu").strip('/')  # No trailing slash or http://

crc/scripts/check_study.py

@@ -0,0 +1,30 @@
+from crc.scripts.script import Script
+from crc.api.common import ApiError
+from crc.services.protocol_builder import ProtocolBuilderService
+from crc.services.study_service import StudyService
+
+
+class CheckStudy(Script):
+
+    pb = ProtocolBuilderService()
+
+    def get_description(self):
+        return """Returns the Check Study data for a Study"""
+
+    def do_task_validate_only(self, task, study_id, workflow_id, *args, **kwargs):
+        study = StudyService.get_study(study_id)
+        if study:
+            return {"DETAIL": "Passed validation.", "STATUS": "No Error"}
+        else:
+            raise ApiError.from_task(code='bad_study',
+                                     message=f'No study for study_id {study_id}',
+                                     task=task)
+
+    def do_task(self, task, study_id, workflow_id, *args, **kwargs):
+        check_study = self.pb.check_study(study_id)
+        if check_study:
+            return check_study
+        else:
+            raise ApiError.from_task(code='missing_check_study',
+                                     message='There was a problem checking information for this study.',
+                                     task=task)

crc/services/protocol_builder.py

@@ -15,6 +15,7 @@ class ProtocolBuilderService(object):
     STUDY_DETAILS_URL = app.config['PB_STUDY_DETAILS_URL']
     SPONSORS_URL = app.config['PB_SPONSORS_URL']
     IRB_INFO_URL = app.config['PB_IRB_INFO_URL']
+    CHECK_STUDY_URL = app.config['PB_CHECK_STUDY_URL']
 
     @staticmethod
     def is_enabled():
@@ -64,6 +65,10 @@ class ProtocolBuilderService(object):
     def get_sponsors(study_id) -> {}:
         return ProtocolBuilderService.__make_request(study_id, ProtocolBuilderService.SPONSORS_URL)
 
+    @staticmethod
+    def check_study(study_id) -> {}:
+        return ProtocolBuilderService.__make_request(study_id, ProtocolBuilderService.CHECK_STUDY_URL)
+
     @staticmethod
     def __enabled_or_raise():
         if not ProtocolBuilderService.is_enabled():

tests/data/check_study_script/check_study_script.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_3fd9241" targetNamespace="http://bpmn.io/schema/bpmn" exporter="Camunda Modeler" exporterVersion="3.0.0-dev">
+  <bpmn:process id="Process_9d7b2c2" isExecutable="true">
+    <bpmn:startEvent id="StartEvent_1">
+      <bpmn:outgoing>Flow_17nzcku</bpmn:outgoing>
+    </bpmn:startEvent>
+    <bpmn:sequenceFlow id="Flow_17nzcku" sourceRef="StartEvent_1" targetRef="Activity_GetCheckStudy" />
+    <bpmn:scriptTask id="Activity_GetCheckStudy" name="Get Check Study">
+      <bpmn:incoming>Flow_17nzcku</bpmn:incoming>
+      <bpmn:outgoing>Flow_0oozrfg</bpmn:outgoing>
+      <bpmn:script>check_study = check_study()</bpmn:script>
+    </bpmn:scriptTask>
+    <bpmn:sequenceFlow id="Flow_0oozrfg" sourceRef="Activity_GetCheckStudy" targetRef="Activity_DisplayCheckStudy" />
+    <bpmn:manualTask id="Activity_DisplayCheckStudy" name="Display Check Study">
+      <bpmn:documentation># Check Study
+&lt;div&gt;&lt;span&gt;{{check_study}}&lt;/span&gt;&lt;/div&gt;</bpmn:documentation>
+      <bpmn:incoming>Flow_0oozrfg</bpmn:incoming>
+      <bpmn:outgoing>Flow_10sc31i</bpmn:outgoing>
+    </bpmn:manualTask>
+    <bpmn:endEvent id="Event_0embsc7">
+      <bpmn:incoming>Flow_10sc31i</bpmn:incoming>
+    </bpmn:endEvent>
+    <bpmn:sequenceFlow id="Flow_10sc31i" sourceRef="Activity_DisplayCheckStudy" targetRef="Event_0embsc7" />
+  </bpmn:process>
+  <bpmndi:BPMNDiagram id="BPMNDiagram_1">
+    <bpmndi:BPMNPlane id="BPMNPlane_1" bpmnElement="Process_9d7b2c2">
+      <bpmndi:BPMNEdge id="Flow_10sc31i_di" bpmnElement="Flow_10sc31i">
+        <di:waypoint x="530" y="177" />
+        <di:waypoint x="592" y="177" />
+      </bpmndi:BPMNEdge>
+      <bpmndi:BPMNEdge id="Flow_0oozrfg_di" bpmnElement="Flow_0oozrfg">
+        <di:waypoint x="370" y="177" />
+        <di:waypoint x="430" y="177" />
+      </bpmndi:BPMNEdge>
+      <bpmndi:BPMNEdge id="Flow_17nzcku_di" bpmnElement="Flow_17nzcku">
+        <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="Activity_1f9d5ew_di" bpmnElement="Activity_GetCheckStudy">
+        <dc:Bounds x="270" y="137" width="100" height="80" />
+      </bpmndi:BPMNShape>
+      <bpmndi:BPMNShape id="Activity_01vscea_di" bpmnElement="Activity_DisplayCheckStudy">
+        <dc:Bounds x="430" y="137" width="100" height="80" />
+      </bpmndi:BPMNShape>
+      <bpmndi:BPMNShape id="Event_0embsc7_di" bpmnElement="Event_0embsc7">
+        <dc:Bounds x="592" y="159" width="36" height="36" />
+      </bpmndi:BPMNShape>
+    </bpmndi:BPMNPlane>
+  </bpmndi:BPMNDiagram>
+</bpmn:definitions>

tests/data/pb_responses/check_study.json

@@ -0,0 +1,3 @@
+[
+  {"DETAIL": "Passed validation.", "STATUS": "No Error"}
+]

tests/scripts/test_check_study.py

@@ -0,0 +1,25 @@
+from tests.base_test import BaseTest
+from crc import app
+from unittest.mock import patch
+
+
+class TestCheckStudy(BaseTest):
+
+    def test_check_study_script_validation(self):
+        self.load_example_data()
+        spec_model = self.load_test_spec('check_study_script')
+        rv = self.app.get('/v1.0/workflow-specification/%s/validate' % spec_model.id, headers=self.logged_in_headers())
+        self.assertEqual([], rv.json)
+
+    @patch('crc.services.protocol_builder.requests.get')
+    def test_check_study(self, mock_get):
+        app.config['PB_ENABLED'] = True
+        app.config['PB_ENABLED'] = True
+        mock_get.return_value.ok = True
+        mock_get.return_value.text = self.protocol_builder_response('check_study.json')
+        workflow = self.create_workflow('check_study_script')
+        workflow_api = self.get_workflow_api(workflow)
+        task = workflow_api.next_task
+
+        self.assertIn('DETAIL', task.documentation)
+        self.assertIn('STATUS', task.documentation)

tests/test_protocol_builder.py

@@ -72,3 +72,13 @@ class TestProtocolBuilder(BaseTest):
         self.assertEqual('IRB Event 1', response[0]["IRBEVENT"])
         self.assertEqual('IRB Event 2', response[1]["IRBEVENT"])
         self.assertEqual('IRB Event 3', response[2]["IRBEVENT"])
+
+    @patch('crc.services.protocol_builder.requests.get')
+    def test_check_study(self, mock_get):
+        app.config['PB_ENABLED'] = True
+        mock_get.return_value.ok = True
+        mock_get.return_value.text = self.protocol_builder_response('check_study.json')
+        response = ProtocolBuilderService.check_study(self.test_study_id)
+        self.assertIsNotNone(response)
+        self.assertIn('DETAIL', response[0].keys())
+        self.assertIn('STATUS', response[0].keys())