throw a sensible error when study is not found on get_study (don't 500)

some ugly fixes in the file_service for improving panda output from spreadsheet processing that I need to revist.
now that the spiff-workflow handles multi-instance, we can't have random multi-instance tasks around.
Improved tests around study deletion.

crc/api/study.py

@@ -47,6 +47,8 @@ def update_study(study_id, body):
 def get_study(study_id):
     study_service = StudyService()
     study = study_service.get_study(study_id)
+`    if(study is None):
+        raise ApiError("Study not found", status_code=404)
     schema = StudySchema()
     return schema.dump(study)
 

crc/services/file_service.py

@@ -1,3 +1,4 @@
+import json
 import os
 from datetime import datetime
 from uuid import UUID
@@ -67,7 +68,14 @@ class FileService(object):
         data_model = FileService.get_reference_file_data(FileService.IRB_PRO_CATEGORIES_FILE)
         xls = ExcelFile(data_model.data)
         df = xls.parse(xls.sheet_names[0])
-        return df.set_index('Code').to_dict('index')
+        df['Id'] = df['Id'].fillna(0)
+        df = df.astype({'Id': 'Int64'})
+        df = df.fillna('')
+        df = df.applymap(str)
+        df = df.set_index('Code')
+        #        IF we need to convert the column names to something more sensible.
+        #        df.columns = [snakeCase(x) for x in df.columns]
+        return json.loads(df.to_json(orient='index'))
 #        # Pandas is lovely, but weird. Here we drop records without an Id, and convert it to an integer.
 #        df = df.drop_duplicates(subset='Id').astype({'Id': 'Int64'})
         # Now we index on the ID column and convert to a dictionary, where the key is the id, and the value

crc/services/study_service.py

@@ -50,6 +50,7 @@ class StudyService(object):
         session.query(TaskEventModel).filter_by(study_id=study_id).delete()
         session.query(WorkflowModel).filter_by(study_id=study_id).delete()
         session.query(StudyModel).filter_by(id=study_id).delete()
+        session.commit()
 
     @staticmethod
     def get_categories():

tests/data/two_forms/mods/two_forms_struc_mod.bpmn

@@ -27,7 +27,6 @@
       </bpmn:extensionElements>
       <bpmn:incoming>SequenceFlow_00p5po6</bpmn:incoming>
       <bpmn:outgoing>SequenceFlow_17ggqu2</bpmn:outgoing>
-      <bpmn:multiInstanceLoopCharacteristics />
     </bpmn:userTask>
     <bpmn:textAnnotation id="TextAnnotation_1haj11l">
       <bpmn:text>We have a test that replaces tow_forms with this file, which adds a new step to the process.  A breaking change.</bpmn:text>

tests/test_study_api.py

@@ -195,6 +195,9 @@ class TestStudyApi(BaseTest):
         session.commit()
         rv = self.app.delete('/v1.0/study/%i' % study.id, headers=self.logged_in_headers())
         self.assert_success(rv)
+        del_study = session.query(StudyModel).filter(StudyModel.id == study.id).first()
+        self.assertIsNone(del_study)
+
 
 
     # """