Mercurial > repos > bimib > marea_2_0

changeset 245:59830a48b19d draft

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Uploaded
author luca_milaz
date Mon, 08 Jul 2024 13:37:38 +0000
parents e9757480e74a
children c2981cdb2dd7
files marea_2_0/model_generator.py
diffstat 1 files changed, 1 insertions(+), 32 deletions(-) [+]
line wrap: on
line diff
--- a/marea_2_0/model_generator.py	Mon Jul 08 13:33:51 2024 +0000
+++ b/marea_2_0/model_generator.py	Mon Jul 08 13:37:38 2024 +0000
@@ -84,35 +84,6 @@
     pass
 
 
-
-################################- INPUT DATA LOADING -################################
-def load_custom_model(file_path :utils.FilePath, ext :Optional[utils.FileFormat] = None) -> cobra.Model:
-    """
-    Loads a custom model from a file, either in JSON or XML format.
-
-    Args:
-        file_path : The path to the file containing the custom model.
-        ext : explicit file extension. Necessary for standard use in galaxy because of its weird behaviour.
-
-    Raises:
-        DataErr : if the file is in an invalid format or cannot be opened for whatever reason.    
-    
-    Returns:
-        cobra.Model : the model, if successfully opened.
-    """
-    ext = ext if ext else file_path.ext
-    try:
-        if ext is utils.FileFormat.XML:
-            return cobra.io.read_sbml_model(file_path.show())
-        
-        if ext is utils.FileFormat.JSON:
-            return cobra.io.load_json_model(file_path.show())
-
-    except Exception as e: raise utils.DataErr(file_path, e.__str__())
-    raise utils.DataErr(file_path,
-        f"Fomat \"{file_path.ext}\" is not recognized, only JSON and XML files are supported.")
-
-
 ############################# main ###########################################
 def main() -> None:
     """
@@ -141,9 +112,7 @@
 
     model_type :utils.Model = ARGS.model_selector
     if model_type is utils.Model.Custom:
-        #model = model_type.getCOBRAmodel(customPath = utils.FilePath.fromStrPath(ARGS.model_name), customExtension = utils.FilePath.fromStrPath(ARGS.model_name).ext)
-        model = load_custom_model(
-        utils.FilePath.fromStrPath(ARGS.model_name), utils.FilePath.fromStrPath(ARGS.model_name).ext)
+        model = model_type.getCOBRAmodel(customPath = utils.FilePath.fromStrPath(ARGS.model), customExtension = utils.FilePath.fromStrPath(ARGS.model_name).ext)
     else:
         model = model_type.getCOBRAmodel()
     '''for index, row in ras.iterrows(): #iterate over cells RAS