chore(rpscore): handle errors differently

brsynth · Oct 16, 2023 · d924a48 · d924a48
1 parent 49859fb
commit d924a48
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Showing 3 changed files with 34 additions and 21 deletions.
diff --git a/rptools/rpscore/__init__.py b/rptools/rpscore/__init__.py
@@ -4,6 +4,8 @@
 @author: Joan Hérisson, Jean_Loup Faulon
 """
 
-from rptools.rpscore.rpScore import (
-    predict_score
+from rptools.rpscore.rpscore import (
+    predict_score,
+    ThermoError,
+    FBAError
 )
diff --git a/rptools/rpscore/__main__.py b/rptools/rpscore/__main__.py
@@ -6,13 +6,13 @@
     Logger,
     getLogger
 )
-from os import (
-    path as os_path,
-    makedirs
+from os import path as os_path
+from .rpscore import (
+    predict_score,
+    ThermoError,
+    FBAError
 )
-from tempfile import NamedTemporaryFile
-from rptools.rpscore import predict_score
-from rptools.rpscore.Args import add_arguments
+from .Args import add_arguments
 from rptools.rplibs import rpPathway
 from rptools import build_args_parser
 
@@ -47,13 +47,20 @@ def entry_point():
         logger=logger
     )
 
-    score = predict_score(
-        pathway=pathway,
-        # data_train_file=args.data_train_file,
-        # models_path=models_path,
-        no_of_rxns_thres=args.no_of_rxns_thres,
-        logger=logger
-    )
+    try:
+        score = predict_score(
+            pathway=pathway,
+            # data_train_file=args.data_train_file,
+            # models_path=models_path,
+            no_of_rxns_thres=args.no_of_rxns_thres,
+            logger=logger
+        )
+    except ThermoError as e:
+        logger.error(e)
+        exit(1)
+    except FBAError as e:
+        logger.error(e)
+        exit(2)
 
     # if len(pathways) > 1:
     #     if not os_path.exists(args.outdir):

diff --git a/rptools/rpscore/rpScore.py b/rptools/rpscore/rpScore.py
@@ -44,6 +44,14 @@
 )
 
 
+class ThermoError(Exception):
+    pass
+
+
+class FBAError(Exception):
+    pass
+
+
 ##############################################################################################
 
 def feature_template_df(no_of_rxns_thres):
@@ -481,16 +489,12 @@ def format_files(
     if pathway.get_thermo_dGm_prime():
         data['dfG_prime_m'] = pathway.get_thermo_dGm_prime()['value']
     else:
-        logger.error('No thermodynamics data available')
-        logger.error('Exiting...')
-        sys_exit(1)
+        raise ThermoError('No thermodynamics data available')
     if pathway.get_fba():
         data['FBA'] = ';'.join(pathway.get_fba().keys())
         data['FBA Flux'] = ';'.join([str(v['value']) for v in pathway.get_fba().values()])
     else:
-        logger.error('No FBA data available')
-        logger.error('Exiting...')
-        sys_exit(2)
+        raise FBAError('No FBA data available')
     pathways_fp.write(
         ','.join(
         [str(data.get(c, '')) for c in columns]