update

app.py

@@ -26,10 +26,9 @@ site_mapper = {
 def run_inference(
     smiles: Optional[str],
     smiles_path: Optional[str],
-    omic_path: Optional[str],
+    omic: Optional[str],
     confidence: bool,
 ):
-
     # Read SMILES
     if smiles is None and smiles_path is None:
         raise TypeError("Pass either single SMILES or a file")
@@ -43,8 +42,10 @@ def run_inference(
                 raise ValueError(f"Found invalid SMILES {smi}")
 
     # Read omics and otherwise load baseline
-    if not isinstance(omic_path, (str, type(None))):
-        raise TypeError(f"Omics file pass has to be None or str, not {type(omic_path)}")
+    if omic is not None:
+        omic_path = omic.name
+    else:
+        omic_path = None
 
     # ToDo: Add progress bar for multiple smiles
     results = {}
@@ -106,7 +107,6 @@ def run_inference(
 
 
 if __name__ == "__main__":
-
     # Load metadata
     metadata_root = pathlib.Path(__file__).parent.joinpath("model_cards")
 

requirements.txt

@@ -10,11 +10,12 @@ numpy>=1.14.3
 scikit-learn==0.21.3
 pandas==0.24.1
 torch>=1.3.0
-matplotlib>=2.2.2
-seaborn>=0.9.0
+matplotlib==3.3.4
+seaborn==0.11.2
 boto3==1.11.16
 boto3_type_annotations==0.3.1
 gunicorn==20.0.4
 regex==2020.1.8
 bokeh==1.4.0
-importlib_resources
+importlib_resources
+urllib3==1.25.11

submission.py

@@ -37,7 +37,7 @@ def submission(
         task_id (str): task identifier.
         estimate_confidence (bool, optional): estimate confidence of the
             prediction. Defaults to False.
-        omics_file (Optional[str], optional): binary string containing
+        omics_file (Optional[str], optional): path to file containing
             expression data. Defaults to None.
     """
     prefix = os.path.join(RESULTS_PREFIX, workspace_id, task_id)