fix(JAQPOT-407): remove extra config (#49)

* fix(JAQPOT-407): remove extra config

* fix: remove dict access to featurizers and preprocessors

* chore: do not reformat openapi files

ruff.toml

@@ -1,3 +1,5 @@
 [lint]
 ignore = ["D100", "E722", "F401", "F403"]
 exclude = ["src/api/openapi/**"]
+[format]
+exclude = ["src/api/openapi/**"]

src/handlers/predict_pyg.py

@@ -11,7 +11,7 @@
 
 
 def graph_post_handler(request: PredictionRequest) -> PredictionResponse:
-    feat_config = request.extra_config["torchConfig"]["featurizerConfig"]
+    feat_config = request.model.torch_config
     featurizer = _load_featurizer(feat_config)
     target_name = request.model.dependent_features[0].name
     model_task = request.model.task

src/helpers/json_to_predreq.py

@@ -20,10 +20,10 @@ def decode(request):
         if feature.feature_type != "SMILES"
     ]
     featurizers = []
-    if request.model.extra_config["featurizers"]:
-        for i in range(len(request.model.extra_config["featurizers"])):
-            featurizer_name = request.model.extra_config["featurizers"][i]["name"]
-            featurizer_config = request.model.extra_config["featurizers"][i]["config"]
+    if request.model.featurizers:
+        for featurizer in request.model.featurizers:
+            featurizer_name = featurizer.name
+            featurizer_config = featurizer.config
             featurizer = recreate_featurizer(featurizer_name, featurizer_config)
             featurizers.append(featurizer)
     else:

src/helpers/predict_methods.py

@@ -112,12 +112,10 @@ def predict_onnx(model, preprocessor, dataset: JaqpotpyDataset, request):
     }
     onnx_prediction = model_session.run(None, input_feed)
 
-    if request.model.extra_config["preprocessors"]:
-        for i in reversed(range(len(request.model.extra_config["preprocessors"]))):
-            preprocessor_name = request.model.extra_config["preprocessors"][i]["name"]
-            preprocessor_config = request.model.extra_config["preprocessors"][i][
-                "config"
-            ]
+    if request.model.preprocessors:
+        for preprocessor in reversed(request.model.preprocessors):
+            preprocessor_name = preprocessor.name
+            preprocessor_config = preprocessor.config
             preprocessor_recreated = recreate_preprocessor(
                 preprocessor_name, preprocessor_config
             )
@@ -144,13 +142,10 @@ def predict_onnx(model, preprocessor, dataset: JaqpotpyDataset, request):
         for instance in onnx_prediction[1]:
             rounded_instance = {k: round(v, 3) for k, v in instance.items()}
             if (
-                request.model.extra_config["preprocessors"]
-                and request.model.extra_config["preprocessors"][0]["name"]
-                == "LabelEncoder"
+                request.model.preprocessors
+                and request.model.preprocessors[0].name == "LabelEncoder"
             ):
-                labels = request.model.extra_config["preprocessors"][0]["config"][
-                    "classes_"
-                ]
+                labels = request.model.preprocessors[0].config["classes_"]
                 rounded_instance = {labels[k]: v for k, v in rounded_instance.items()}
 
             probs_list.append(rounded_instance)

src/loggers/logger.py

@@ -1,6 +1,6 @@
 import json
 import logging
-from logging import Formatter
+from logging import Formatter, RootLogger
 
 
 class JsonFormatter(Formatter):
@@ -18,9 +18,9 @@ def format(self, record):
         return json.dumps(json_record)
 
 
-logger = logging.root
+logger: RootLogger = logging.root
 handler = logging.StreamHandler()
-handler.setFormatter(JsonFormatter())
+# handler.setFormatter(JsonFormatter())
 logger.handlers = [handler]
 logger.setLevel(logging.INFO)