Adds protocol script to study service

2020-04-29 10:21:24 -04:00 · 2020-04-29 10:21:24 -04:00 · beb86f0453
parent 13333fb306
commit beb86f0453
5 changed files with 72 additions and 23 deletions
--- a/crc/scripts/study_info.py
+++ b/crc/scripts/study_info.py
@ -15,7 +15,7 @@ class StudyInfo(Script):

    """Just your basic class that can pull in data from a few api endpoints and do a basic task."""
    pb = ProtocolBuilderService()
-    type_options = ['info', 'investigators', 'details', 'approvals', 'documents_status']
+    type_options = ['info', 'investigators', 'details', 'approvals', 'documents_status', 'protocol']

    def get_description(self):
        return """StudyInfo [TYPE], where TYPE is one of 'info', 'investigators', or 'details'
@ -75,7 +75,10 @@ class StudyInfo(Script):
                        'workflow_spec_id': 'irb_api_details',
                        'status': 'complete',
                    }
-                ]
+                ],
+                'protocol': {
+                    id: 0,
+                }
            }
        }
        self.add_data_to_task(task=task, data=data["study"])
@ -101,6 +104,8 @@ class StudyInfo(Script):
            self.add_data_to_task(task, {cmd: StudyService().get_approvals(study_id)})
        if cmd == 'documents_status':
            self.add_data_to_task(task, {cmd: StudyService().get_documents_status(study_id)})
+        if cmd == 'protocol':
+            self.add_data_to_task(task, {cmd: StudyService().get_protocol(study_id)})


    def check_args(self, args):
--- a/crc/services/file_service.py
+++ b/crc/services/file_service.py
@ -168,7 +168,7 @@ class FileService(object):
        if form_field_key:
            query = query.filter_by(form_field_key=form_field_key)
        if name:
-            query = query.filter_by(name=form_field_key)
+            query = query.filter_by(name=name)
        if irb_doc_code:
            query = query.filter_by(irb_doc_code=irb_doc_code)

--- a/crc/services/study_service.py
+++ b/crc/services/study_service.py
@ -1,10 +1,11 @@
+import json
 from typing import List

 from SpiffWorkflow import WorkflowException

 from crc import db, session
 from crc.api.common import ApiError
-from crc.models.file import FileModel
+from crc.models.file import FileModel, FileModelSchema
 from crc.models.protocol_builder import ProtocolBuilderStudy, ProtocolBuilderStatus
 from crc.models.stats import WorkflowStatsModel, TaskEventModel
 from crc.models.study import StudyModel, Study, Category, WorkflowMetadata
@ -105,6 +106,9 @@ class StudyService(object):
        # Container for results
        documents = []

+        # Study > Categories > Workflows
+        study = StudyService.get_study(study_id)
+
        # For each required doc, get file(s)
        for code, doc in study_docs.items():
            if not doc['required']:
@ -123,6 +127,15 @@ class StudyService(object):
                        name_list.append(doc[cat_key])
                doc['display_name'] = ' '.join(name_list)

+            # print('code', code)
+            #
+            # # Find which workflows have the associated irb_doc_code???
+            # wf = db.session.query(WorkflowModel)\
+            #     .filter_by(study_id=study_id)\
+            #     .filter(WorkflowModel.bpmn_workflow_json.contains(code))\
+            #     .first()
+            # print('wf', wf)
+
            # For each file, get associated workflow status
            doc_files = FileService.get_files(study_id=study_id, irb_doc_code=code)
            for file in doc_files:
@ -139,6 +152,18 @@ class StudyService(object):

        return documents

+
+    @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_all_studies_with_protocol_builder(user):
        """Assures that the studies we have locally for the given user are
--- a/crc/static/bpmn/documents_approvals/documents_approvals.bpmn
+++ b/crc/static/bpmn/documents_approvals/documents_approvals.bpmn
@ -13,13 +13,19 @@
      <bpmn:documentation># Documents &amp; Approvals

 &gt; ## Protocol Document Management
-&gt; [Upload Protocol Here](/)
+{% if StudyInfo.protocol is defined -%}
+{%- set p = StudyInfo.protocol -%}
+
+&gt; [{{p.name}}](/study/{{p.study_id}}/workflow/{{p.workflow_id}}/task/{{p.task_id}})
+{%- else -%}
+&gt; No protocol uploaded yet.
+{% endif %}

 &gt; ## Approvals
 &gt; | Name | Status | Help |
 |:---- |:------ |:---- |
 {% for approval in StudyInfo.approvals -%}
-| [{{approval.display_name}}](/study/{{approval.study_id}}/workflow/{{approval.workflow_id}}) | {{approval.status}} | [Context here](/help/{{approval.workflow_spec_id}}) |
+| [{{approval.display_name}}](/study/{{approval.study_id}}/workflow/{{approval.workflow_id}}) | {{approval.status}} | [?](/help/{{approval.workflow_spec_id}}) |
 {% endfor %}

 &gt; ## Documents
@ -27,9 +33,9 @@
 |:---- |:------ |:---- |:-------- |
 {% for doc in StudyInfo.documents_status -%}
    {% if doc.file_id is defined -%}
-        | [{{doc.display_name}}](/study/{{doc.study_id}}/workflow/{{doc.workflow_id}}/task/{{doc.task_id}}) | {{doc.status}} | [Context here](/help/documents/{{doc.code}}) | [Download](/file/{{doc.file_id}}) |
+        | [{{doc.display_name}}](/study/{{doc.study_id}}/workflow/{{doc.workflow_id}}/task/{{doc.task_id}}) | {{doc.status}} | [Context here](/help/documents/{{doc.code}}) | [Download](/file/{{doc.file_id}}/data) |
    {%- else -%}
-        | {{doc.display_name}} | Not started | [Context here](/help/documents/{{doc.code}}) | No file yet |
+        | {{doc.display_name}} | Not started | [?](/help/documents/{{doc.code}}) | No file yet |
    {%- endif %}
 {% endfor %}</bpmn:documentation>
      <bpmn:extensionElements>
@ -46,47 +52,60 @@
      <bpmn:script>StudyInfo approvals</bpmn:script>
    </bpmn:scriptTask>
    <bpmn:scriptTask id="Activity_1aju60t" name="Load Documents">
-      <bpmn:incoming>Flow_1k3su2q</bpmn:incoming>
+      <bpmn:incoming>Flow_0w20w9j</bpmn:incoming>
      <bpmn:outgoing>Flow_0c7ryff</bpmn:outgoing>
      <bpmn:script>StudyInfo documents_status</bpmn:script>
    </bpmn:scriptTask>
    <bpmn:sequenceFlow id="Flow_142jtxs" sourceRef="Activity_0a14x7j" targetRef="Activity_DisplayDocsAndApprovals" />
    <bpmn:sequenceFlow id="Flow_0c7ryff" sourceRef="Activity_1aju60t" targetRef="Activity_0a14x7j" />
-    <bpmn:sequenceFlow id="Flow_1k3su2q" sourceRef="StartEvent_1" targetRef="Activity_1aju60t" />
+    <bpmn:sequenceFlow id="Flow_1k3su2q" sourceRef="StartEvent_1" targetRef="Activity_0b4ojeq" />
+    <bpmn:scriptTask id="Activity_0b4ojeq" name="Load Protocol">
+      <bpmn:incoming>Flow_1k3su2q</bpmn:incoming>
+      <bpmn:outgoing>Flow_0w20w9j</bpmn:outgoing>
+      <bpmn:script>StudyInfo protocol</bpmn:script>
+    </bpmn:scriptTask>
+    <bpmn:sequenceFlow id="Flow_0w20w9j" sourceRef="Activity_0b4ojeq" targetRef="Activity_1aju60t" />
  </bpmn:process>
  <bpmndi:BPMNDiagram id="BPMNDiagram_1">
    <bpmndi:BPMNPlane id="BPMNPlane_1" bpmnElement="Process_1gmf4la">
      <bpmndi:BPMNEdge id="Flow_1k3su2q_di" bpmnElement="Flow_1k3su2q">
-        <di:waypoint x="228" y="117" />
-        <di:waypoint x="290" y="117" />
+        <di:waypoint x="188" y="117" />
+        <di:waypoint x="240" y="117" />
      </bpmndi:BPMNEdge>
      <bpmndi:BPMNEdge id="Flow_0c7ryff_di" bpmnElement="Flow_0c7ryff">
-        <di:waypoint x="390" y="117" />
-        <di:waypoint x="440" y="117" />
+        <di:waypoint x="490" y="117" />
+        <di:waypoint x="540" y="117" />
      </bpmndi:BPMNEdge>
      <bpmndi:BPMNEdge id="Flow_142jtxs_di" bpmnElement="Flow_142jtxs">
-        <di:waypoint x="540" y="117" />
-        <di:waypoint x="610" y="117" />
+        <di:waypoint x="640" y="117" />
+        <di:waypoint x="710" y="117" />
      </bpmndi:BPMNEdge>
      <bpmndi:BPMNEdge id="Flow_0m7unlb_di" bpmnElement="Flow_0m7unlb">
-        <di:waypoint x="710" y="117" />
-        <di:waypoint x="782" y="117" />
+        <di:waypoint x="810" y="117" />
+        <di:waypoint x="882" y="117" />
      </bpmndi:BPMNEdge>
      <bpmndi:BPMNShape id="_BPMNShape_StartEvent_2" bpmnElement="StartEvent_1">
-        <dc:Bounds x="192" y="99" width="36" height="36" />
+        <dc:Bounds x="152" y="99" width="36" height="36" />
      </bpmndi:BPMNShape>
      <bpmndi:BPMNShape id="EndEvent_1qvyxg7_di" bpmnElement="EndEvent_1qvyxg7">
-        <dc:Bounds x="782" y="99" width="36" height="36" />
+        <dc:Bounds x="882" y="99" width="36" height="36" />
      </bpmndi:BPMNShape>
      <bpmndi:BPMNShape id="Activity_19nawos_di" bpmnElement="Activity_DisplayDocsAndApprovals">
-        <dc:Bounds x="610" y="77" width="100" height="80" />
+        <dc:Bounds x="710" y="77" width="100" height="80" />
      </bpmndi:BPMNShape>
      <bpmndi:BPMNShape id="Activity_1bxk8h3_di" bpmnElement="Activity_0a14x7j">
-        <dc:Bounds x="440" y="77" width="100" height="80" />
+        <dc:Bounds x="540" y="77" width="100" height="80" />
      </bpmndi:BPMNShape>
      <bpmndi:BPMNShape id="Activity_07ytvmv_di" bpmnElement="Activity_1aju60t">
-        <dc:Bounds x="290" y="77" width="100" height="80" />
+        <dc:Bounds x="390" y="77" width="100" height="80" />
      </bpmndi:BPMNShape>
+      <bpmndi:BPMNShape id="Activity_0wf6u3m_di" bpmnElement="Activity_0b4ojeq">
+        <dc:Bounds x="240" y="77" width="100" height="80" />
+      </bpmndi:BPMNShape>
+      <bpmndi:BPMNEdge id="Flow_0w20w9j_di" bpmnElement="Flow_0w20w9j">
+        <di:waypoint x="340" y="117" />
+        <di:waypoint x="390" y="117" />
+      </bpmndi:BPMNEdge>
    </bpmndi:BPMNPlane>
  </bpmndi:BPMNDiagram>
 </bpmn:definitions>
--- a/crc/static/reference/irb_documents.xlsx
+++ b/crc/static/reference/irb_documents.xlsx