Adds documents_status StudyInfo script. Adds Documents & Approvals workflow spec.

crc/scripts/documents.py

@@ -48,7 +48,7 @@ For example:
 
     def get_documents(self, study_id, pb_docs):
         """Takes data from the protocol builder, and merges it with data from the IRB Pro Categories spreadsheet to return
-        pertinant details about the required documents."""
+        pertinent details about the required documents."""
 
         doc_dictionary = FileService.get_file_reference_dictionary()
         required_docs = {}

crc/scripts/study_info.py

@@ -3,6 +3,7 @@ from ldap3.core.exceptions import LDAPSocketOpenError
 from crc import session, app
 from crc.api.common import ApiError
 from crc.models.study import StudyModel, StudySchema
+from crc.models.workflow import WorkflowStatus
 from crc.scripts.script import Script
 from crc.services.ldap_service import LdapService
 from crc.services.protocol_builder import ProtocolBuilderService
@@ -14,7 +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']
+    type_options = ['info', 'investigators', 'details', 'approvals', 'documents_status']
 
     def get_description(self):
         return """StudyInfo [TYPE], where TYPE is one of 'info', 'investigators', or 'details'
@@ -47,7 +48,27 @@ class StudyInfo(Script):
                         "NETBADGEID": "dhf8r"
                     },
                 "details":
-                    {}
+                    {},
+                "approvals": {
+                    "id": 321,
+                    "display_name": "IRB API Details",
+                    "name": "irb_api_details",
+                    "status": WorkflowStatus.not_started.value,
+                    "workflow_spec_id": "irb_api_details",
+                },
+                "documents_status": [
+                    {
+                        'category1': 'Ancillary Document',
+                        'category2': 'CoC Application',
+                        'category3': '',
+                        'Who Uploads?': 'CRC',
+                        'Id': '12',
+                        'Name': 'Certificate of Confidentiality Application',
+                        'count': 0,
+                        'required': False,
+                        'code': 'AD_CoCApp'
+                    }
+                ]
             }
         }
         self.add_data_to_task(task=task, data=data["study"])
@@ -71,6 +92,9 @@ class StudyInfo(Script):
             self.add_data_to_task(task, {cmd: self.pb.get_study_details(study_id)})
         if cmd == 'approvals':
             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)})
+
         task.data["study"] = study_info
 
 

crc/services/study_service.py

@@ -4,11 +4,14 @@ from SpiffWorkflow import WorkflowException
 
 from crc import db, session
 from crc.api.common import ApiError
+from crc.models.file import FileModel
 from crc.models.protocol_builder import ProtocolBuilderStudy, ProtocolBuilderStatus
 from crc.models.stats import WorkflowStatsModel, TaskEventModel
 from crc.models.study import StudyModel, Study, Category, WorkflowMetadata
 from crc.models.workflow import WorkflowSpecCategoryModel, WorkflowModel, WorkflowSpecModel, WorkflowState, \
     WorkflowStatus
+from crc.scripts.documents import Documents
+from crc.services.file_service import FileService
 from crc.services.protocol_builder import ProtocolBuilderService
 from crc.services.workflow_processor import WorkflowProcessor
 
@@ -64,13 +67,13 @@ class StudyService(object):
 
     @staticmethod
     def get_approvals(study_id):
-        """Returns a list of category objects, in the correct order."""
+        """Returns a list of approval workflows."""
         cat = session.query(WorkflowSpecCategoryModel).filter_by(name="approvals").first()
         specs = session.query(WorkflowSpecModel).filter_by(category_id=cat.id).all()
         spec_ids = [spec.id for spec in specs]
-        workflows = session.query(WorkflowModel)\
+        workflows = session.query(WorkflowModel) \
-            .filter(WorkflowModel.study_id == study_id)\
+            .filter(WorkflowModel.study_id == study_id) \
-            .filter(WorkflowModel.workflow_spec_id.in_(spec_ids))\
+            .filter(WorkflowModel.workflow_spec_id.in_(spec_ids)) \
             .all()
 
         approvals = []
@@ -80,11 +83,44 @@ class StudyService(object):
                 'id': workflow.id,
                 'display_name': workflow.workflow_spec.display_name,
                 'name': workflow.workflow_spec.display_name,
-                'status': workflow.status,
+                'status': workflow.status.value,
                 'workflow_spec_id': workflow.workflow_spec_id,
             })
         return approvals
 
+    @staticmethod
+    def get_documents_status(study_id):
+        """Returns a list of required documents and related workflow status."""
+        doc_service = Documents()
+
+        # Get PB required docs
+        pb_docs = ProtocolBuilderService.get_required_docs(study_id)
+
+        # Get required docs for study
+        study_docs = doc_service.get_documents(study_id=study_id, pb_docs=pb_docs)
+
+        # Container for results
+        documents = []
+
+        # For each required doc, get file(s)
+        for code, doc in study_docs.items():
+            doc['study_id'] = study_id
+            doc['code'] = code
+            doc_files = FileService.get_files(study_id=study_id, irb_doc_code=code)
+
+            # For each file, get associated workflow status
+            for file in doc_files:
+                doc['file_id'] = file.id
+                doc['workflow_id'] = file.workflow_id
+
+                if doc['status'] is None:
+                    workflow: WorkflowModel = session.query(WorkflowModel).filter_by(id=file.workflow_id).first()
+                    doc['status'] = workflow.status.value
+
+            documents.append(doc)
+
+        return documents
+
     @staticmethod
     def synch_all_studies_with_protocol_builder(user):
         """Assures that the studies we have locally for the given user are
@@ -135,10 +171,10 @@ class StudyService(object):
     @staticmethod
     def __get_workflow_metas(study_id):
         # Add in the Workflows for each category
-        workflow_models = db.session.query(WorkflowModel).\
+        workflow_models = db.session.query(WorkflowModel). \
-            join(WorkflowSpecModel).\
+            join(WorkflowSpecModel). \
-            filter(WorkflowSpecModel.is_master_spec == False).\
+            filter(WorkflowSpecModel.is_master_spec == False). \
-            filter(WorkflowModel.study_id == study_id).\
+            filter(WorkflowModel.study_id == study_id). \
             all()
         workflow_metas = []
         for workflow in workflow_models:

crc/static/bpmn/documents_approvals/documents_approvals.bpmn

@@ -0,0 +1,85 @@
+<?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" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" id="Definitions_00j2iu5" targetNamespace="http://bpmn.io/schema/bpmn" exporter="Camunda Modeler" exporterVersion="3.7.0">
+  <bpmn:process id="Process_1gmf4la" isExecutable="true">
+    <bpmn:documentation />
+    <bpmn:startEvent id="StartEvent_1">
+      <bpmn:outgoing>Flow_1k3su2q</bpmn:outgoing>
+    </bpmn:startEvent>
+    <bpmn:endEvent id="EndEvent_1qvyxg7">
+      <bpmn:incoming>Flow_0m7unlb</bpmn:incoming>
+    </bpmn:endEvent>
+    <bpmn:sequenceFlow id="Flow_0m7unlb" sourceRef="Activity_DisplayDocsAndApprovals" targetRef="EndEvent_1qvyxg7" />
+    <bpmn:manualTask id="Activity_DisplayDocsAndApprovals" name="Display Documents and Approvals">
+      <bpmn:documentation>## Approvals
+| Name | Status | Help |
+|:-------------- |:-------- |:------ |
+{% for approval in StudyInfo.approvals -%}
+| [{{approval.display_name}}](/workflow/{{approval.id}}) | {{approval.status}} | [Context here](/help/{{approval.workflow_spec_id}}) |
+{% endfor -%}
+
+
+## Documents
+| Code | Status | Help |
+|:-------------- |:-------- |:------ |
+{% for doc in study.documents_status -%}
+| [{{doc.code}}](/study/{{doc.study_id}}/workflow/{{doc.workflow_id}}) | {{doc.status}} | [Context here](/help/{{doc.workflow_spec_id}}) |
+{% endfor -%}
+</bpmn:documentation>
+      <bpmn:extensionElements>
+        <camunda:properties>
+          <camunda:property name="display_name" value="Documents and Approvals" />
+        </camunda:properties>
+      </bpmn:extensionElements>
+      <bpmn:incoming>Flow_142jtxs</bpmn:incoming>
+      <bpmn:outgoing>Flow_0m7unlb</bpmn:outgoing>
+    </bpmn:manualTask>
+    <bpmn:scriptTask id="Activity_0a14x7j" name="Load Approvals">
+      <bpmn:incoming>Flow_0c7ryff</bpmn:incoming>
+      <bpmn:outgoing>Flow_142jtxs</bpmn:outgoing>
+      <bpmn:script>StudyInfo approvals</bpmn:script>
+    </bpmn:scriptTask>
+    <bpmn:scriptTask id="Activity_1aju60t" name="Load Documents">
+      <bpmn:incoming>Flow_1k3su2q</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:process>
+  <bpmndi:BPMNDiagram id="BPMNDiagram_1">
+    <bpmndi:BPMNPlane id="BPMNPlane_1" bpmnElement="Process_1gmf4la">
+      <bpmndi:BPMNEdge id="Flow_0m7unlb_di" bpmnElement="Flow_0m7unlb">
+        <di:waypoint x="710" y="117" />
+        <di:waypoint x="782" y="117" />
+      </bpmndi:BPMNEdge>
+      <bpmndi:BPMNShape id="_BPMNShape_StartEvent_2" bpmnElement="StartEvent_1">
+        <dc:Bounds x="192" 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" />
+      </bpmndi:BPMNShape>
+      <bpmndi:BPMNShape id="Activity_19nawos_di" bpmnElement="Activity_DisplayDocsAndApprovals">
+        <dc:Bounds x="610" 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" />
+      </bpmndi:BPMNShape>
+      <bpmndi:BPMNShape id="Activity_07ytvmv_di" bpmnElement="Activity_1aju60t">
+        <dc:Bounds x="290" y="77" width="100" height="80" />
+      </bpmndi:BPMNShape>
+      <bpmndi:BPMNEdge id="Flow_142jtxs_di" bpmnElement="Flow_142jtxs">
+        <di:waypoint x="540" y="117" />
+        <di:waypoint x="610" 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" />
+      </bpmndi:BPMNEdge>
+      <bpmndi:BPMNEdge id="Flow_1k3su2q_di" bpmnElement="Flow_1k3su2q">
+        <di:waypoint x="228" y="117" />
+        <di:waypoint x="290" y="117" />
+      </bpmndi:BPMNEdge>
+    </bpmndi:BPMNPlane>
+  </bpmndi:BPMNDiagram>
+</bpmn:definitions>

example_data.py

@@ -79,6 +79,12 @@ class ExampleDataLoader:
                          description="TBD",
                          category_id=0,
                          display_order=1)
+        self.create_spec(id="documents_approvals",
+                         name="documents_approvals",
+                         display_name="Documents & Approvals",
+                         description="TBD",
+                         category_id=0,
+                         display_order=2)
 
         # Core Info
         self.create_spec(id="core_info",