changeset 331:7557495e090c draft

Uploaded

--- a/marea_2/ras_generator.py	Mon Aug 05 19:37:33 2024 +0000
+++ b/marea_2/ras_generator.py	Mon Aug 05 19:50:41 2024 +0000
@@ -626,6 +626,26 @@
     if geneName in supportedGenesInEncoding: return supportedGenesInEncoding[geneName]
     raise ValueError(f"Gene \"{geneName}\" non trovato, verifica di star utilizzando il modello corretto!")
 
+def load_custom_rules2() -> Dict[str, ruleUtils.OpList]:
+    """
+    Opens custom rules file and extracts the rules. If the file is in .csv format an additional parsing step will be
+    performed, significantly impacting the runtime.
+
+    Returns:
+        Dict[str, ruleUtils.OpList] : dict mapping reaction IDs to rules.
+    """
+    datFilePath = utils.FilePath.fromStrPath(ARGS.rule_list) # actual file, stored in galaxy as a .dat
+    
+    try: filenamePath = utils.FilePath.fromStrPath(ARGS.rules_name) # file's name in input, to determine its original ext
+    except utils.PathErr as err:
+        raise utils.PathErr(filenamePath, f"Please make sure your file's name is a valid file path, {err.msg}")
+    
+     
+    if filenamePath.ext is utils.FileFormat.PICKLE: return utils.readPickle(datFilePath)
+
+    # csv rules need to be parsed, those in a pickle format are taken to be pre-parsed.
+    return { line[0] : ruleUtils.parseRuleToNestedList(line[1]) for line in utils.readCsv(datFilePath) }
+
 def load_custom_rules() -> Dict[str, ruleUtils.OpList]:
     """
     Opens custom rules file and extracts the rules. If the file is in .csv format an additional parsing step will be
@@ -639,11 +659,12 @@
     try: filenamePath = utils.FilePath.fromStrPath(ARGS.rules_name) # file's name in input, to determine its original ext
     except utils.PathErr as err:
         raise utils.PathErr(filenamePath, f"Please make sure your file's name is a valid file path, {err.msg}")
+    
      
-    if filenamePath.ext is utils.FileFormat.PICKLE: return utils.readPickle(datFilePath)
+    if filenamePath.ext is utils.FileFormat.PICKLE: return utils.readPickle(ARGS.rule_list)
 
     # csv rules need to be parsed, those in a pickle format are taken to be pre-parsed.
-    return { line[0] : ruleUtils.parseRuleToNestedList(line[1]) for line in utils.readCsv(datFilePath) }
+    return { line[0] : ruleUtils.parseRuleToNestedList(line[1]) for line in utils.readCsv(ARGS.rule_list) }
 
 def main() -> None:
     """