Merge pull request #375 from sartography/study-info-adds-463

Study info adds #463

crc/models/study.py

@@ -53,6 +53,8 @@ class StudyModel(db.Model):
     enrollment_date = db.Column(db.DateTime(timezone=True), nullable=True)
     #events = db.relationship("TaskEventModel")
     events_history = db.relationship("StudyEvent", cascade="all, delete, delete-orphan")
+    short_name = db.Column(db.String, nullable=True)
+    proposal_name = db.Column(db.String, nullable=True)
 
     def update_from_protocol_builder(self, pbs: ProtocolBuilderStudy):
         self.title = pbs.TITLE
@@ -168,7 +170,7 @@ class CategorySchema(ma.Schema):
 class Study(object):
 
     def __init__(self, title, short_title, last_updated, primary_investigator_id, user_uid,
-                 id=None, status=None, irb_status=None, comment="",
+                 id=None, status=None, irb_status=None, short_name=None, proposal_name=None, comment="",
                  sponsor="", ind_number="", categories=[],
                  files=[], approvals=[], enrollment_date=None, events_history=[],
                  last_activity_user="",last_activity_date =None,create_user_display="", **argsv):
@@ -192,6 +194,8 @@ class Study(object):
         self.files = files
         self.enrollment_date = enrollment_date
         self.events_history = events_history
+        self.short_name = short_name
+        self.proposal_name = proposal_name
 
     @classmethod
     def from_model(cls, study_model: StudyModel):
@@ -253,13 +257,15 @@ class StudySchema(ma.Schema):
     files = fields.List(fields.Nested(FileSchema), dump_only=True)
     enrollment_date = fields.Date(allow_none=True)
     events_history = fields.List(fields.Nested('StudyEventSchema'), dump_only=True)
+    short_name = fields.String(allow_none=True)
+    proposal_name = fields.String(allow_none=True)
 
     class Meta:
         model = Study
         additional = ["id", "title", "short_title", "last_updated", "primary_investigator_id", "user_uid",
                       "sponsor", "ind_number", "files", "enrollment_date",
-                      "create_user_display", "last_activity_date","last_activity_user",
+                      "create_user_display", "last_activity_date", "last_activity_user",
-                      "events_history"]
+                      "events_history", "short_name", "proposal_name"]
         unknown = INCLUDE
 
     @marshmallow.post_load

crc/scripts/update_study.py

@@ -44,6 +44,10 @@ update_study(title=PIComputingID.label, short_title="Really Short Name")
                 study.title = kwargs[arg]
             elif arg.lower() == "short_title":
                 study.short_title = kwargs[arg]
+            elif arg.lower() == "short_name":
+                study.short_name = kwargs[arg]
+            elif arg.lower() == "proposal_name":
+                study.proposal_name = kwargs[arg]
             elif arg.lower() == "pi":
                 study.primary_investigator_id = kwargs[arg]
             else:

migrations/versions/9afbd55082a0_new_study_info_data_points.py

@@ -0,0 +1,26 @@
+"""new study info data points
+
+Revision ID: 9afbd55082a0
+Revises: 981156283cb9
+Create Date: 2021-09-17 10:31:05.094062
+
+"""
+from alembic import op
+import sqlalchemy as sa
+
+
+# revision identifiers, used by Alembic.
+revision = '9afbd55082a0'
+down_revision = '981156283cb9'
+branch_labels = None
+depends_on = None
+
+
+def upgrade():
+    op.add_column('study', sa.Column('short_name', sa.String(), nullable=True))
+    op.add_column('study', sa.Column('proposal_name', sa.String(), nullable=True))
+
+
+def downgrade():
+    op.drop_column('study', 'short_name')
+    op.drop_column('study', 'proposal_name')

tests/data/update_study_info/update_study_info.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" id="Definitions_3435c8d" targetNamespace="http://bpmn.io/schema/bpmn" exporter="Camunda Modeler" exporterVersion="3.0.0-dev">
+  <bpmn:process id="Process_3435c8d" isExecutable="true">
+    <bpmn:startEvent id="StartEvent_1">
+      <bpmn:outgoing>Flow_0g8e1jy</bpmn:outgoing>
+    </bpmn:startEvent>
+    <bpmn:sequenceFlow id="Flow_0g8e1jy" sourceRef="StartEvent_1" targetRef="Activity_GetData" />
+    <bpmn:userTask id="Activity_GetData" name="Get Data" camunda:formKey="GetDataForm">
+      <bpmn:extensionElements>
+        <camunda:formData>
+          <camunda:formField id="short_name" label="Short Name" type="string" />
+          <camunda:formField id="proposal_name" label="Proposal Name" type="string" />
+        </camunda:formData>
+      </bpmn:extensionElements>
+      <bpmn:incoming>Flow_0g8e1jy</bpmn:incoming>
+      <bpmn:outgoing>Flow_09flr91</bpmn:outgoing>
+    </bpmn:userTask>
+    <bpmn:sequenceFlow id="Flow_09flr91" sourceRef="Activity_GetData" targetRef="Activity_UpdateStudy" />
+    <bpmn:scriptTask id="Activity_UpdateStudy" name="Update Study">
+      <bpmn:incoming>Flow_09flr91</bpmn:incoming>
+      <bpmn:outgoing>Flow_0xf0u0k</bpmn:outgoing>
+      <bpmn:script>update_study(short_name=short_name, proposal_name=proposal_name)</bpmn:script>
+    </bpmn:scriptTask>
+    <bpmn:sequenceFlow id="Flow_0xf0u0k" sourceRef="Activity_UpdateStudy" targetRef="Activity_GetStudyInfo" />
+    <bpmn:scriptTask id="Activity_GetStudyInfo" name="Get Study Info">
+      <bpmn:incoming>Flow_0xf0u0k</bpmn:incoming>
+      <bpmn:outgoing>Flow_0tzamxo</bpmn:outgoing>
+      <bpmn:script>study_info = study_info("info")</bpmn:script>
+    </bpmn:scriptTask>
+    <bpmn:sequenceFlow id="Flow_0tzamxo" sourceRef="Activity_GetStudyInfo" targetRef="Activity_DisplayInfo" />
+    <bpmn:manualTask id="Activity_DisplayInfo" name="Display Study Info">
+      <bpmn:documentation># Info
+{{ study_info }}
+</bpmn:documentation>
+      <bpmn:incoming>Flow_0tzamxo</bpmn:incoming>
+      <bpmn:outgoing>Flow_0x5ex3d</bpmn:outgoing>
+    </bpmn:manualTask>
+    <bpmn:endEvent id="Event_05xjsir">
+      <bpmn:incoming>Flow_0x5ex3d</bpmn:incoming>
+    </bpmn:endEvent>
+    <bpmn:sequenceFlow id="Flow_0x5ex3d" sourceRef="Activity_DisplayInfo" targetRef="Event_05xjsir" />
+  </bpmn:process>
+  <bpmndi:BPMNDiagram id="BPMNDiagram_1">
+    <bpmndi:BPMNPlane id="BPMNPlane_1" bpmnElement="Process_3435c8d">
+      <bpmndi:BPMNEdge id="Flow_0x5ex3d_di" bpmnElement="Flow_0x5ex3d">
+        <di:waypoint x="850" y="177" />
+        <di:waypoint x="912" y="177" />
+      </bpmndi:BPMNEdge>
+      <bpmndi:BPMNEdge id="Flow_0tzamxo_di" bpmnElement="Flow_0tzamxo">
+        <di:waypoint x="690" y="177" />
+        <di:waypoint x="750" y="177" />
+      </bpmndi:BPMNEdge>
+      <bpmndi:BPMNEdge id="Flow_0xf0u0k_di" bpmnElement="Flow_0xf0u0k">
+        <di:waypoint x="530" y="177" />
+        <di:waypoint x="590" y="177" />
+      </bpmndi:BPMNEdge>
+      <bpmndi:BPMNEdge id="Flow_09flr91_di" bpmnElement="Flow_09flr91">
+        <di:waypoint x="370" y="177" />
+        <di:waypoint x="430" y="177" />
+      </bpmndi:BPMNEdge>
+      <bpmndi:BPMNEdge id="Flow_0g8e1jy_di" bpmnElement="Flow_0g8e1jy">
+        <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_06lg3xc_di" bpmnElement="Activity_GetData">
+        <dc:Bounds x="270" y="137" width="100" height="80" />
+      </bpmndi:BPMNShape>
+      <bpmndi:BPMNShape id="Activity_0ulzpsr_di" bpmnElement="Activity_UpdateStudy">
+        <dc:Bounds x="430" y="137" width="100" height="80" />
+      </bpmndi:BPMNShape>
+      <bpmndi:BPMNShape id="Activity_15xfbrf_di" bpmnElement="Activity_GetStudyInfo">
+        <dc:Bounds x="590" y="137" width="100" height="80" />
+      </bpmndi:BPMNShape>
+      <bpmndi:BPMNShape id="Activity_1yteq9j_di" bpmnElement="Activity_DisplayInfo">
+        <dc:Bounds x="750" y="137" width="100" height="80" />
+      </bpmndi:BPMNShape>
+      <bpmndi:BPMNShape id="Event_05xjsir_di" bpmnElement="Event_05xjsir">
+        <dc:Bounds x="912" y="159" width="36" height="36" />
+      </bpmndi:BPMNShape>
+    </bpmndi:BPMNPlane>
+  </bpmndi:BPMNDiagram>
+</bpmn:definitions>

tests/study/test_update_study_script.py

@@ -14,9 +14,12 @@ class TestUpdateStudyScript(BaseTest):
         processor = WorkflowProcessor(workflow)
         task = processor.next_task()
         details = Box({
-            "label": "My New Title",
+            "title": "My New Title",
-            "short": "My New Short Title",
+            "short_title": "My New Short Title",
-            "value": "dhf8r"})
+            "pi": "dhf8r",
+            "short_name": "My Short Name",
+            "proposal_name": "My Proposal Name"
+        })
 
 
         script = UpdateStudy()
@@ -26,9 +29,14 @@ class TestUpdateStudyScript(BaseTest):
         # evaluated before they are passed to the script -
         # this allows us to do a lot more things like strings, functions, etc.
         # and it makes the arguments less confusing to use.
-        script.do_task(task, workflow.study_id, workflow.id, title = details.label,
+        script.do_task(task, workflow.study_id, workflow.id,
-                                                             short_title = details.short,
+                       title=details.title,
-                                                             pi = details.value)
+                       short_title=details.short_title,
-        self.assertEqual("My New Title", workflow.study.title)
+                       pi=details.pi,
-        self.assertEqual("My New Short Title", workflow.study.short_title)
+                       short_name=details.short_name,
-        self.assertEqual("dhf8r", workflow.study.primary_investigator_id)
+                       proposal_name=details.proposal_name)
+        self.assertEqual(details.title, workflow.study.title)
+        self.assertEqual(details.short_title, workflow.study.short_title)
+        self.assertEqual(details.pi, workflow.study.primary_investigator_id)
+        self.assertEqual(details.short_name, workflow.study.short_name)
+        self.assertEqual(details.proposal_name, workflow.study.proposal_name)

tests/test_study_info_script.py

@@ -33,6 +33,25 @@ class TestStudyInfoScript(BaseTest):
         self.assertEqual(study_info['primary_investigator_id'], second_task.data['info']['primary_investigator_id'])
         self.assertIn(study_info['title'], second_task.documentation)
 
+    def test_info_script_updated_study_info(self):
+        self.load_example_data()
+        short_name = "My Short Name"
+        proposal_name = "My Proposal Name"
+        workflow = self.create_workflow('update_study_info')
+        workflow_api = self.get_workflow_api(workflow)
+        task = workflow_api.next_task
+
+        workflow_api = self.complete_form(workflow, task, {'short_name': short_name, 'proposal_name': proposal_name})
+        task = workflow_api.next_task
+        # The workflow calls study_info('info') and puts the result in Element Documentation
+        # I create a dictionary of that info with `eval` to make the asserts easier to read
+        study_info = eval(task.documentation)
+
+        self.assertIn('short_name', study_info.keys())
+        self.assertEqual(short_name, study_info['short_name'])
+        self.assertIn('proposal_name', study_info.keys())
+        self.assertIn(proposal_name, study_info['proposal_name'])
+
     @patch('crc.services.protocol_builder.requests.get')
     def test_info_script_investigators(self, mock_get):
         app.config['PB_ENABLED'] = True