Merge pull request #311 from sartography/deprecate-study-info-protocol-261

Deprecate study info protocol #261
2021-05-14 14:14:18 -04:00 · 2021-05-14 14:14:18 -04:00 · 4d7ce5eda9
parent 7e6645db89 1a8c374ac0
commit 4d7ce5eda9
6 changed files with 168 additions and 26 deletions
--- a/crc/scripts/study_info.py
+++ b/crc/scripts/study_info.py
@ -18,7 +18,7 @@ class StudyInfo(Script):
    """Please see the detailed description that is provided below. """

    pb = ProtocolBuilderService()
-    type_options = ['info', 'investigators', 'roles', 'details', 'documents', 'protocol', 'sponsors']
+    type_options = ['info', 'investigators', 'roles', 'details', 'documents', 'sponsors']

    # This is used for test/workflow validation, as well as documentation.
    example_data = {
@ -110,9 +110,6 @@ class StudyInfo(Script):
            },
            "details":
                {},
-            'protocol': {
-                id: 0,
-            }
        }
    }

@ -392,8 +389,6 @@ Returns information specific to the protocol.
            retval = self.pb.get_sponsors(study_id)
        if cmd == 'documents':
            retval = StudyService().get_documents_status(study_id)
-        if cmd == 'protocol':
-            retval = StudyService().get_protocol(study_id)

        return self.box_it(retval, prefix)

--- a/crc/services/study_service.py
+++ b/crc/services/study_service.py
@ -355,16 +355,6 @@ class StudyService(object):
            app.logger.info("Failed to connect to LDAP Server.")
            return {}

-    @staticmethod
-    def get_protocol(study_id):
-        """Returns the study protocol, if it has been uploaded."""
-        file = db.session.query(FileModel) \
-            .filter_by(study_id=study_id) \
-            .filter_by(form_field_key='Study_Protocol_Document') \
-            .first()
-
-        return FileModelSchema().dump(file)
-
    @staticmethod
    def synch_with_protocol_builder_if_enabled(user):
        """Assures that the studies we have locally for the given user are
--- a/tests/data/pb_responses/study_details.json
+++ b/tests/data/pb_responses/study_details.json
@ -1,12 +1,12 @@
 {
-  "DSMB": null,
-  "DSMB_FREQUENCY": null,
-  "GCRC_NUMBER": null,
-  "IBC_NUMBER": null,
-  "IDE": null,
-  "IND_1": 1234,
-  "IND_2": null,
-  "IND_3": null,
+  "DSMB": 1,
+  "DSMB_FREQUENCY": 2,
+  "GCRC_NUMBER": "9",
+  "IBC_NUMBER": "7",
+  "IDE": "12345",
+  "IND_1": "1234",
+  "IND_2": "2345",
+  "IND_3": "3456",
  "IRBREVIEWERADMIN": null,
  "IS_ADULT_PARTICIPANT": null,
  "IS_APPROVED_DEVICE": null,
@ -61,6 +61,6 @@
  "NON_UVA_LOCATION": null,
  "OTHER_VULNERABLE_DESC": null,
  "PRC_NUMBER": null,
-  "SPONSORS_PROTOCOL_REVISION_DATE": null,
+  "SPONSORS_PROTOCOL_REVISION_DATE": "2021-04-20",
  "UPLOAD_COMPLETE": null
 }
--- a/tests/data/study_info_script/study_info_script.bpmn
+++ b/tests/data/study_info_script/study_info_script.bpmn
@ -0,0 +1,78 @@
+<?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_07672t3" targetNamespace="http://bpmn.io/schema/bpmn" exporter="Camunda Modeler" exporterVersion="3.5.0">
+  <bpmn:process id="Process_StudyInfo" name="Study Info" isExecutable="true">
+    <bpmn:startEvent id="StartEvent_1">
+      <bpmn:outgoing>SequenceFlow_0wpuk5u</bpmn:outgoing>
+    </bpmn:startEvent>
+    <bpmn:sequenceFlow id="SequenceFlow_0wpuk5u" sourceRef="StartEvent_1" targetRef="Task_WhichInfo" />
+    <bpmn:userTask id="Task_WhichInfo" name="Which Info" camunda:formKey="WhichForm">
+      <bpmn:extensionElements>
+        <camunda:formData>
+          <camunda:formField id="which" label="Which" type="enum">
+            <camunda:value id="info" name="Info" />
+            <camunda:value id="investigators" name="Investigators" />
+            <camunda:value id="roles" name="Roles" />
+            <camunda:value id="details" name="Details" />
+            <camunda:value id="documents" name="Documents" />
+            <camunda:value id="sponsors" name="Sponsors" />
+          </camunda:formField>
+        </camunda:formData>
+      </bpmn:extensionElements>
+      <bpmn:incoming>SequenceFlow_0wpuk5u</bpmn:incoming>
+      <bpmn:outgoing>SequenceFlow_0vpsh2s</bpmn:outgoing>
+    </bpmn:userTask>
+    <bpmn:sequenceFlow id="SequenceFlow_0vpsh2s" sourceRef="Task_WhichInfo" targetRef="Task_GetInfo" />
+    <bpmn:scriptTask id="Task_GetInfo" name="Get Info">
+      <bpmn:incoming>SequenceFlow_0vpsh2s</bpmn:incoming>
+      <bpmn:outgoing>SequenceFlow_0y0c2i4</bpmn:outgoing>
+      <bpmn:script>info = study_info(which)</bpmn:script>
+    </bpmn:scriptTask>
+    <bpmn:sequenceFlow id="SequenceFlow_0y0c2i4" sourceRef="Task_GetInfo" targetRef="Task_PrintInfo" />
+    <bpmn:manualTask id="Task_PrintInfo" name="Print Info">
+      <bpmn:documentation># Info
+&lt;div&gt;&lt;span&gt;info is {{info}}&lt;/span&gt;&lt;/div&gt;
+</bpmn:documentation>
+      <bpmn:incoming>SequenceFlow_0y0c2i4</bpmn:incoming>
+      <bpmn:outgoing>SequenceFlow_1s1u06z</bpmn:outgoing>
+    </bpmn:manualTask>
+    <bpmn:endEvent id="EndEvent_0681rbo">
+      <bpmn:incoming>SequenceFlow_1s1u06z</bpmn:incoming>
+    </bpmn:endEvent>
+    <bpmn:sequenceFlow id="SequenceFlow_1s1u06z" sourceRef="Task_PrintInfo" targetRef="EndEvent_0681rbo" />
+  </bpmn:process>
+  <bpmndi:BPMNDiagram id="BPMNDiagram_1">
+    <bpmndi:BPMNPlane id="BPMNPlane_1" bpmnElement="Process_StudyInfo">
+      <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_0wpuk5u_di" bpmnElement="SequenceFlow_0wpuk5u">
+        <di:waypoint x="215" y="117" />
+        <di:waypoint x="270" y="117" />
+      </bpmndi:BPMNEdge>
+      <bpmndi:BPMNShape id="UserTask_1id33on_di" bpmnElement="Task_WhichInfo">
+        <dc:Bounds x="270" y="77" width="100" height="80" />
+      </bpmndi:BPMNShape>
+      <bpmndi:BPMNEdge id="SequenceFlow_0vpsh2s_di" bpmnElement="SequenceFlow_0vpsh2s">
+        <di:waypoint x="370" y="117" />
+        <di:waypoint x="430" y="117" />
+      </bpmndi:BPMNEdge>
+      <bpmndi:BPMNShape id="ScriptTask_0vpqnbr_di" bpmnElement="Task_GetInfo">
+        <dc:Bounds x="430" y="77" width="100" height="80" />
+      </bpmndi:BPMNShape>
+      <bpmndi:BPMNEdge id="SequenceFlow_0y0c2i4_di" bpmnElement="SequenceFlow_0y0c2i4">
+        <di:waypoint x="530" y="117" />
+        <di:waypoint x="590" y="117" />
+      </bpmndi:BPMNEdge>
+      <bpmndi:BPMNShape id="ManualTask_09vvuig_di" bpmnElement="Task_PrintInfo">
+        <dc:Bounds x="590" y="77" width="100" height="80" />
+      </bpmndi:BPMNShape>
+      <bpmndi:BPMNShape id="EndEvent_0681rbo_di" bpmnElement="EndEvent_0681rbo">
+        <dc:Bounds x="752" y="99" width="36" height="36" />
+      </bpmndi:BPMNShape>
+      <bpmndi:BPMNEdge id="SequenceFlow_1s1u06z_di" bpmnElement="SequenceFlow_1s1u06z">
+        <di:waypoint x="690" y="117" />
+        <di:waypoint x="752" y="117" />
+      </bpmndi:BPMNEdge>
+    </bpmndi:BPMNPlane>
+  </bpmndi:BPMNDiagram>
+</bpmn:definitions>
--- a/tests/test_protocol_builder.py
+++ b/tests/test_protocol_builder.py
@ -47,7 +47,7 @@ class TestProtocolBuilder(BaseTest):
        response = ProtocolBuilderService.get_study_details(self.test_study_id)
        self.assertIsNotNone(response)
        self.assertEqual(64, len(response))
-        self.assertEqual(1234, response['IND_1'])
+        self.assertEqual('1234', response['IND_1'])

    @patch('crc.services.protocol_builder.requests.get')
    def test_get_study_sponsors(self, mock_get):
--- a/tests/test_study_info_script.py
+++ b/tests/test_study_info_script.py
@ -0,0 +1,79 @@
+from tests.base_test import BaseTest
+from crc.scripts.study_info import StudyInfo
+from crc import app
+from unittest.mock import patch
+from crc.services.protocol_builder import ProtocolBuilderService
+
+
+class TestStudyInfoScript(BaseTest):
+
+    test_uid = "dhf8r"
+    test_study_id = 1
+
+    def do_work(self, info_type):
+        app.config['PB_ENABLED'] = True
+        self.load_example_data()
+        workflow = self.create_workflow('study_info_script')
+        workflow_api = self.get_workflow_api(workflow)
+        # grab study_info directly from script
+        study_info = StudyInfo().do_task(workflow_api.study_id, workflow.study.id, workflow.id, info_type)
+
+        # grab study info through a workflow
+        first_task = workflow_api.next_task
+        self.complete_form(workflow, first_task, {'which': info_type})
+        workflow_api = self.get_workflow_api(workflow)
+        second_task = workflow_api.next_task
+
+        return study_info, second_task
+
+    def test_info_script_info(self):
+        study_info, second_task = self.do_work(info_type='info')
+
+        self.assertEqual(study_info['title'], second_task.data['info']['title'])
+        self.assertEqual(study_info['primary_investigator_id'], second_task.data['info']['primary_investigator_id'])
+        self.assertIn(study_info['title'], second_task.documentation)
+
+    @patch('crc.services.protocol_builder.requests.get')
+    def test_info_script_investigators(self, mock_get):
+        app.config['PB_ENABLED'] = True
+        mock_get.return_value.ok = True
+        mock_get.return_value.text = self.protocol_builder_response('investigators.json')
+        response = ProtocolBuilderService.get_investigators(self.test_study_id)
+        study_info, second_task = self.do_work(info_type='investigators')
+        for i in range(len(response)):
+            r = response[i]
+            s = second_task.data['info'][response[i]['INVESTIGATORTYPE']]
+            self.assertEqual(r['INVESTIGATORTYPEFULL'], s['label'])
+
+    # def test_info_script_roles(self):
+    #     study_info, second_task = self.do_work(info_type='roles')
+    #     self.assertEqual(study_info, second_task.data['info'])
+
+    @patch('crc.services.protocol_builder.requests.get')
+    def test_info_script_details(self, mock_get):
+        app.config['PB_ENABLED'] = True
+        mock_get.return_value.ok = True
+        mock_get.return_value.text = self.protocol_builder_response('study_details.json')
+        response = ProtocolBuilderService.get_study_details(self.test_study_id)
+        study_info, second_task = self.do_work(info_type='details')
+        self.assertEqual(response['IBC_NUMBER'], second_task.data['info']['IBC_NUMBER'])
+        self.assertEqual(response['IDE'], second_task.data['info']['IDE'])
+        self.assertEqual(response['IND_1'], second_task.data['info']['IND_1'])
+        self.assertEqual(response['IND_2'], second_task.data['info']['IND_2'])
+        self.assertEqual(response['IND_3'], second_task.data['info']['IND_3'])
+
+    # def test_info_script_documents(self):
+    #     study_info, second_task = self.do_work(info_type='documents')
+    #     self.assertEqual(study_info, second_task.data['info'])
+
+    @patch('crc.services.protocol_builder.requests.get')
+    def test_info_script_sponsors(self, mock_get):
+        app.config['PB_ENABLED'] = True
+        mock_get.return_value.ok = True
+        mock_get.return_value.text = self.protocol_builder_response('sponsors.json')
+        response = ProtocolBuilderService.get_sponsors(self.test_study_id)
+        study_info, second_task = self.do_work(info_type='sponsors')
+        for i in range(len(response)):
+            self.assertEqual(response[i]['SPONSOR_ID'], second_task.data['info'][i]['SPONSOR_ID'])
+            self.assertEqual(response[i]['SP_NAME'], second_task.data['info'][i]['SP_NAME'])
+            self.assertEqual(response[i]['SS_STUDY'], second_task.data['info'][i]['SS_STUDY'])