Add mostly-working elements of the data-store, compare with dev to see why db is not working after running tests

crc/models/data_store.py

@@ -0,0 +1,15 @@
+from flask_marshmallow.sqla import SQLAlchemyAutoSchema
+from marshmallow import EXCLUDE
+from sqlalchemy import func
+
+from crc import db
+
+class DataStoreModel(db.Model):
+    __tablename__ = 'data_store'
+    key = db.Column(db.String, primary_key=True)
+    workflow_id = db.Column(db.Integer)
+    study_id = db.Column(db.Integer)
+    task_id = db.Column(db.String)
+    spec_id = db.Column(db.String)
+    user_id = db.Column(db.String)
+    value = db.Column(db.String)

crc/scripts/script.py

@@ -109,3 +109,14 @@ class ScriptValidationError:
     @classmethod
     def from_api_error(cls, api_error: ApiError):
         return cls(api_error.code, api_error.message)
+
+class DataStoreBase():
+    def overwritten(self,value,prev_value):
+        if prev_value == None:
+            overwritten = False
+        else:
+            if prev_value == value:
+                overwritten = False
+            else:
+                overwritten = True
+        return overwritten

crc/scripts/study_data_get.py

@@ -0,0 +1,27 @@
+import requests
+
+from crc.scripts.script import Script, DataStoreBase
+from crc import session
+from crc.models.data_store import DataStoreModel
+
+class StudyDataGet(Script,DataStoreBase):
+    def get_description(self):
+        return """Gets study data from the data store."""
+
+
+    def do_task_validate_only(self, task, study_id, workflow_id, *args, **kwargs):
+        self.do_task(task, study_id, workflow_id, *args, **kwargs)
+
+    def do_task(self, task, study_id, workflow_id, *args, **kwargs):
+        self.check_args(args,2)
+        study = session.query(DataStoreModel).filter_by(study_id=study_id,user_id=None,key=args[0]).first()
+        if study:
+            return study.value
+        else:
+            return args[1]
+
+    def check_args(self, args, maxlen=1):
+        if len(args) < 1 or len(args) > maxlen :
+            raise ApiError(code="missing_argument",
+            message="The study_data_get script takes either one or two arguments, starting with the key and an " + \
+                    "optional default")

crc/scripts/study_data_set.py

@@ -0,0 +1,48 @@
+import requests
+
+from crc.scripts.script import Script, DataStoreBase
+from crc import session
+from crc.models.workflow import WorkflowModel
+from crc.models.data_store import DataStoreModel
+
+class StudyDataSet(Script,DataStoreBase):
+    def get_description(self):
+        return """Sets study data from the data store."""
+
+
+    def do_task_validate_only(self, task, study_id, workflow_id, *args, **kwargs):
+        self.check_args(args)
+        workflow = session.query(WorkflowModel).filter(WorkflowModel.id == workflow_id).first()
+        self.get_prev_value(study_id,args[0])
+
+
+    def do_task(self, task, study_id, workflow_id, *args, **kwargs):
+        self.check_args(args)
+        study = self.get_prev_value(study_id,args[0])
+        workflow = session.query(WorkflowModel).filter(WorkflowModel.id == workflow_id).first()
+        if study is not None:
+            prev_value = study.key
+        else:
+            prev_value = None
+            study = DataStoreModel(key=args[0],value=args[1],
+                                   study_id=study_id,
+                                   task_id=task.id,
+                                   user_id=None,             # Make this available to any User
+                                   workflow_id= workflow_id,
+                                   spec_id=workflow.workflow_spec_id)
+
+        overwritten = self.overwritten(study.value,prev_value)
+        session.add(study)
+        return (study.value, prev_value, overwritten)
+
+
+    def get_prev_value(self,study_id,key):
+        study = session.query(DataStoreModel).filter_by(study_id=study_id,user_id=None,key=key).first()
+        return study
+
+
+    def check_args(self, args):
+        if len(args) != 2:
+            raise ApiError(code="missing_argument",
+            message="The study_data_set script takes two arguments, starting with the key and a " +\
+                    "value for the key")

tests/study/test_study_data_store_script.py

@@ -0,0 +1,45 @@
+from unittest.mock import patch
+
+from tests.base_test import BaseTest
+
+from crc import session, app
+from crc.models.study import StudyModel
+from crc.services.study_service import StudyService
+from crc.services.workflow_processor import WorkflowProcessor
+from crc.services.workflow_service import WorkflowService
+
+class TestSudySponsorsScript(BaseTest):
+    test_uid = "dhf8r"
+    test_study_id = 1
+
+
+    def test_study_sponsors_script_validation(self):
+        self.load_example_data() # study_info script complains if irb_documents.xls is not loaded
+                                 # during the validate phase I'm going to assume that we will never
+                                 # have a case where irb_documents.xls is not loaded ??
+
+        self.load_test_spec("study_sponsors_data_store")
+        WorkflowService.test_spec("study_sponsors_data_store")  # This would raise errors if it didn't validate
+
+
+    @patch('crc.services.protocol_builder.requests.get')
+    def test_study_sponsors_script(self, mock_get):
+
+        mock_get.return_value.ok = True
+        mock_get.return_value.text = self.protocol_builder_response('sponsors.json')
+        app.config['PB_ENABLED'] = True
+
+        self.load_example_data()
+        self.create_reference_document()
+        study = session.query(StudyModel).first()
+        workflow_spec_model = self.load_test_spec("study_sponsors_data_store")
+        workflow_model = StudyService._create_workflow_model(study, workflow_spec_model)
+        WorkflowService.test_spec("study_sponsors_data_store")
+        processor = WorkflowProcessor(workflow_model)
+        processor.do_engine_steps()
+        self.assertTrue(processor.bpmn_workflow.is_completed())
+        data = processor.next_task().data
+        self.assertIn('sponsors', data)
+        self.assertIn('out', data)
+        self.assertEquals('newval', data['out'])
+        self.assertEquals(3, len(data['sponsors']))