remove inconsitencies in how files are added;

Adding files is now the callers task and not handled by persistence;

koi_api/persistence/core.py

@@ -13,7 +13,6 @@
 # GNU Lesser General Public License is distributed along with this
 # software and can be found at http://www.gnu.org/licenses/lgpl.html
 
-from koi_api.orm import db
 from koi_api.orm.file import ORMFile
 import gzip
 from uuid import uuid4
@@ -54,9 +53,6 @@ def store_file(self, data):
         f.write(data)
         f.close()
 
-        db.session.add(newFile)
-        db.session.commit()
-
         return newFile
 
     def remove_file(self, file: ORMFile):

koi_api/resources/instance.py

@@ -637,6 +637,8 @@ def post(self, model_uuid, model, instance_uuid, instance, me):
             data = request.data
             file_pers = persistence.store_file(data)
 
+            db.session.add(file_pers)
+
             # TODO: prevent existing inferencedata to become orphaned
             newRequest = ORMInstanceInferenceData()
             newRequest.file = file_pers
@@ -707,6 +709,9 @@ def post(self, model_uuid, model, instance_uuid, instance, me):
 
             data = request.data
             file_pers = persistence.store_file(data)
+
+            db.session.add(file_pers)
+
             new_uuid = uuid4()
 
             # TODO: prevent existing inferencedata to become orphaned
@@ -865,6 +870,8 @@ def post(self, model_uuid, model, instance_uuid, instance, me, json_object):
 
                 file_pers = persistence.store_file(value)
 
+                db.session.add(file_pers)
+
                 new_desc.descriptor_file = file_pers
                 db.session.add(new_desc)
 

koi_api/resources/label_request.py

@@ -153,6 +153,8 @@ def post(self, model_uuid, model, instance_uuid, instance, me, request_uuid):
         label = request.data
         file_pers = persistence.store_file(label)
 
+        db.session.add(file_pers)
+
         new_uuid = uuid4()
 
         new_data = ORMSampleLabel()

koi_api/resources/model.py

@@ -332,6 +332,7 @@ def post(self, model_uuid, model, me):
                     db.session.add(new_param)
 
             # TODO: prevent existing code to become orphaned
+            db.session.add(file_pers)
             newCode = ORMModelCode()
             newCode.file = file_pers
             db.session.add(newCode)
@@ -379,6 +380,8 @@ def post(self, model_uuid, model, me):
         data = request.data
         file_pers = persistence.store_file(data)
 
+        db.session.add(file_pers)
+
         # TODO: prevent existing plugin to become orphaned
         newVisual = ORMModelVisualPlugin()
         newVisual.file = file_pers
@@ -425,6 +428,8 @@ def post(self, model_uuid, model, me):
         data = request.data
         file_pers = persistence.store_file(data)
 
+        db.session.add(file_pers)
+
         # TODO: prevent existing plugin to become orphaned
         newRequest = ORMModelLabelRequestPlugin()
         newRequest.file = file_pers

koi_api/resources/sample.py

@@ -925,6 +925,8 @@ def post(
         data_raw = request.data
         file_pers = persistence.store_file(data_raw)
 
+        db.session.add(file_pers)
+
         sample.sample_last_modified = datetime.utcnow()
         sample.sample_etag = token_hex(16)
         data.data_last_modified = datetime.utcnow()
@@ -933,7 +935,6 @@ def post(
         instance.instance_samples_etag = token_hex(16)
 
         data.file = file_pers
-        db.session.add(file_pers)
         db.session.commit()
 
         return SUCCESS()
@@ -1056,6 +1057,8 @@ def post(
         data_raw = request.data
         file_pers = persistence.store_file(data_raw)
 
+        db.session.add(file_pers)
+
         label.file = file_pers
 
         sample.sample_last_modified = datetime.utcnow()
@@ -1065,7 +1068,6 @@ def post(
         instance.instance_samples_last_modified = datetime.utcnow()
         instance.instance_samples_etag = token_hex(16)
 
-        db.session.add(file_pers)
         db.session.commit()
 
         return SUCCESS()