Merge pull request #253 from sartography/220-short-study-name

Add short_title to study, change update_study task to use kw argument…

crc/models/study.py

@@ -40,6 +40,7 @@ class StudyModel(db.Model):
     __tablename__ = 'study'
     id = db.Column(db.Integer, primary_key=True)
     title = db.Column(db.String)
+    short_title = db.Column(db.String, nullable=True)
     last_updated = db.Column(db.DateTime(timezone=True), default=func.now())
     status = db.Column(db.Enum(StudyStatus))
     irb_status = db.Column(db.Enum(IrbStatus))
@@ -161,7 +162,7 @@ class CategorySchema(ma.Schema):
 
 class Study(object):
 
-    def __init__(self, title, last_updated, primary_investigator_id, user_uid,
+    def __init__(self, title, short_title, last_updated, primary_investigator_id, user_uid,
                  id=None, status=None, irb_status=None, comment="",
                  sponsor="", hsr_number="", ind_number="", categories=[],
                  files=[], approvals=[], enrollment_date=None, events_history=[],
@@ -172,6 +173,7 @@ class Study(object):
         self.last_activity_date = last_activity_date
         self.last_activity_user = last_activity_user
         self.title = title
+        self.short_title = short_title
         self.last_updated = last_updated
         self.status = status
         self.irb_status = irb_status
@@ -243,6 +245,7 @@ class StudySchema(ma.Schema):
     protocol_builder_status = EnumField(StudyStatus, by_value=True)
     status = EnumField(StudyStatus, by_value=True)
     hsr_number = fields.String(allow_none=True)
+    short_title = fields.String(allow_none=True)
     sponsor = fields.String(allow_none=True)
     ind_number = fields.String(allow_none=True)
     files = fields.List(fields.Nested(FileSchema), dump_only=True)
@@ -251,7 +254,7 @@ class StudySchema(ma.Schema):
 
     class Meta:
         model = Study
-        additional = ["id", "title", "last_updated", "primary_investigator_id", "user_uid",
+        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",
                       "events_history"]

crc/scripts/study_info.py

@@ -186,6 +186,7 @@ Returns information specific to the protocol.
                 "info": {
                     "id": 12,
                     "title": "test",
+                    "short_title": "tst",
                     "primary_investigator_id":21,
                     "user_uid": "dif84",
                     "sponsor": "sponsor",

crc/scripts/update_study.py

@@ -15,44 +15,37 @@ class mock_study:
 class UpdateStudy(Script):
 
     argument_error_message = "You must supply at least one argument to the " \
-                             "update_study task, in the form [study_field]:[value]",
+                             "update_study task, in the form [study_field]=[value]",
 
     def get_description(self):
         return """
 Allows you to set specific attributes on the Study model by mapping them to 
-values in the task data.  Should be called with the value to set (either title, or pi)
+values in the task data.  Should be called with the value to set (either title, short_title, or pi)
-followed by a ":" and then the value to use in dot notation.
 
 Example:
-UpdateStudy title:PIComputingID.label pi:PIComputingID.value
+update_study(title=PIComputingID.label, short_title="Really Short Name")
 """
     def do_task_validate_only(self, task, study_id, workflow_id, *args, **kwargs):
         study = mock_study
-        self.__update_study(task, study, *args)
+        self.__update_study(task, study, *args, **kwargs)
 
     def do_task(self, task, study_id, workflow_id, *args, **kwargs):
         study = db.session.query(StudyModel).filter(StudyModel.id == study_id).first()
-        self.__update_study(task, study, *args)
+        self.__update_study(task, study, *args, **kwargs)
         db.session.add(study)
 
-    def __update_study(self, task, study, *args):
+    def __update_study(self, task, study, *args, **kwargs):
-        if len(args) < 1:
+        if len(kwargs.keys()) < 1:
             raise ApiError.from_task("missing_argument", self.argument_error_message,
                                      task=task)
 
-        for arg in args:
+        for arg in kwargs.keys():
-            try:
+            if arg.lower() == "title":
-                field, value_lookup = arg.split(':')
+                study.title = kwargs[arg]
-            except:
+            elif arg.lower() == "short_title":
-                raise ApiError.from_task("invalid_argument", self.argument_error_message,
+                study.short_title = kwargs[arg]
-                                         task=task)
+            elif arg.lower() == "pi":
-
+                study.primary_investigator_id = kwargs[arg]
-            value = task.workflow.script_engine.evaluate_expression(task, value_lookup)
-
-            if field.lower() == "title":
-                study.title = value
-            elif field.lower() == "pi":
-                study.primary_investigator_id = value
             else:
                 raise ApiError.from_task("invalid_argument", self.argument_error_message,
                                          task=task)

crc/services/study_service.py

@@ -36,7 +36,7 @@ class StudyService(object):
 
         studies = []
         for study_model in db_studies:
-            studies.append(StudyService.get_study(study_model.id, study_model))
+            studies.append(StudyService.get_study(study_model.id, study_model,do_status=False))
         return studies
 
     @staticmethod
@@ -51,7 +51,7 @@ class StudyService(object):
         return studies
 
     @staticmethod
-    def get_study(study_id, study_model: StudyModel = None):
+    def get_study(study_id, study_model: StudyModel = None, do_status=True):
         """Returns a study model that contains all the workflows organized by category.
         IMPORTANT:  This is intended to be a lightweight call, it should never involve
         loading up and executing all the workflows in a study to calculate information."""
@@ -81,8 +81,9 @@ class StudyService(object):
         if study.status != StudyStatus.abandoned:
             # this line is taking 99% of the time that is used in get_study.
             # see ticket #196
-            status = StudyService.__get_study_status(study_model)
+            if do_status:
-            study.warnings = StudyService.__update_status_of_workflow_meta(workflow_metas, status)
+                status = StudyService.__get_study_status(study_model)
+                study.warnings = StudyService.__update_status_of_workflow_meta(workflow_metas, status)
 
             # Group the workflows into their categories.
             for category in study.categories:

migrations/versions/f28ee3722c49_.py

@@ -0,0 +1,28 @@
+"""empty message
+
+Revision ID: f28ee3722c49
+Revises: cb892916166a
+Create Date: 2021-03-02 08:30:22.879266
+
+"""
+from alembic import op
+import sqlalchemy as sa
+
+
+# revision identifiers, used by Alembic.
+revision = 'f28ee3722c49'
+down_revision = 'cb892916166a'
+branch_labels = None
+depends_on = None
+
+
+def upgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.add_column('study', sa.Column('short_title', sa.String(), nullable=True))
+    # ### end Alembic commands ###
+
+
+def downgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.drop_column('study', 'short_title')
+    # ### end Alembic commands ###

tests/data/message_event/message_event.bpmn

@@ -1,5 +1,5 @@
 <?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_0a9entn" targetNamespace="http://bpmn.io/schema/bpmn" exporter="Camunda Modeler" exporterVersion="3.7.3">
+<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_0a9entn" targetNamespace="http://bpmn.io/schema/bpmn" exporter="Camunda Modeler" exporterVersion="3.7.0">
   <bpmn:process id="Process_1dagb7t" name="TestMessage" isExecutable="true">
     <bpmn:startEvent id="StartEvent_1" name="Start">
       <bpmn:outgoing>Flow_0xym55y</bpmn:outgoing>
@@ -7,7 +7,7 @@
     <bpmn:sequenceFlow id="Flow_16q1uec" name="TestMessageFlow" sourceRef="Event_TokenReset" targetRef="Activity_TestMessage" />
     <bpmn:scriptTask id="Activity_TestMessage" name="Test Message" camunda:resultVariable="test_message">
       <bpmn:incoming>Flow_16q1uec</bpmn:incoming>
-      <bpmn:script>update_study("title:'New Title'")
+      <bpmn:script>update_study(title='New Title')
 print('New Title')</bpmn:script>
     </bpmn:scriptTask>
     <bpmn:userTask id="Activity_GetData" name="GetData" camunda:formKey="FirstTaskForm">

tests/data/study_cancellations/study_cancellations.bpmn

@@ -1,5 +1,5 @@
 <?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_0a9entn" targetNamespace="http://bpmn.io/schema/bpmn" exporter="Camunda Modeler" exporterVersion="4.2.0">
+<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_0a9entn" targetNamespace="http://bpmn.io/schema/bpmn" exporter="Camunda Modeler" exporterVersion="3.7.0">
   <bpmn:process id="Process_1dagb7t" name="TestMessage" isExecutable="true">
     <bpmn:startEvent id="StartEvent_1" name="Start">
       <bpmn:outgoing>Flow_0xym55y</bpmn:outgoing>
@@ -7,7 +7,7 @@
     <bpmn:sequenceFlow id="Flow_16q1uec" name="TestMessageFlow" sourceRef="Event_TokenReset" targetRef="Activity_TestMessage" />
     <bpmn:scriptTask id="Activity_TestMessage" name="Test Message" camunda:resultVariable="test_message">
       <bpmn:incoming>Flow_16q1uec</bpmn:incoming>
-      <bpmn:script>update_study("title:'New Title'")
+      <bpmn:script>update_study(title='New Title')
 print('New Title')</bpmn:script>
     </bpmn:scriptTask>
     <bpmn:sequenceFlow id="Flow_0xym55y" sourceRef="StartEvent_1" targetRef="Activity_Hello" />
@@ -58,7 +58,7 @@ print('New Title')</bpmn:script>
     <bpmn:scriptTask id="Activity_CancelMessage" name="Cancel Message" camunda:resultVariable="cancel_message">
       <bpmn:documentation>&lt;H1&gt;Cancel Message&lt;/H1&gt;</bpmn:documentation>
       <bpmn:incoming>Flow_13xidv2</bpmn:incoming>
-      <bpmn:script>update_study("title:'Second Title'")
+      <bpmn:script>update_study(title='Second Title')
 print('Second Title')</bpmn:script>
     </bpmn:scriptTask>
   </bpmn:process>

tests/study/test_update_study_script.py

@@ -2,7 +2,7 @@ from tests.base_test import BaseTest
 
 from crc.scripts.update_study import UpdateStudy
 from crc.services.workflow_processor import WorkflowProcessor
-
+from box import Box
 
 class TestUpdateStudyScript(BaseTest):
 
@@ -12,12 +12,22 @@ class TestUpdateStudyScript(BaseTest):
         workflow = self.create_workflow('empty_workflow')
         processor = WorkflowProcessor(workflow)
         task = processor.next_task()
-        task.data = {"details": {
+        details = Box({
             "label": "My New Title",
-            "value": "dhf8r"}
+            "short": "My New Short Title",
-        }
+            "value": "dhf8r"})
+
 
         script = UpdateStudy()
-        script.do_task(task, workflow.study_id, workflow.id, "title:details.label", "pi:details.value")
+        # note that we changed where the argument gets evaluated
+        # previsously, it took the arguments and then evaluated them within the script
+        # now, it evaluates the arugments in the context of the main script so they get
+        # 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,
+                                                             short_title = details.short,
+                                                             pi = details.value)
         self.assertEqual("My New Title", workflow.study.title)
+        self.assertEqual("My New Short Title", workflow.study.short_title)
         self.assertEqual("dhf8r", workflow.study.primary_investigator_id)

tests/test_message_event.py

@@ -26,7 +26,7 @@ class TestMessageEvent(BaseTest):
                      headers=self.logged_in_headers(),
                      content_type="application/json")
 
-        # set_current_task should call the interupt (signal) task
+        # set_current_task should call the interrupt (signal) task
         # which should run the script in our task
         #
         # test to see if our changes made it to the DB