bug fix

Author: mshahneh

modifinder/classes/ModiFinder.py

@@ -140,15 +140,14 @@ def __init__(
         self.network = None
         self.unknowns = None
         self.ppm_tolerance = ppm_tolerance
-        self.args = kwargs
 
         if alignmentEngine is None:
-            self.alignmentEngine = CosineAlignmentEngine(**kwargs)
+            self.alignmentEngine = CosineAlignmentEngine(ppm_tolerance = self.ppm_tolerance, **kwargs)
         else:
             self.alignmentEngine = alignmentEngine
 
         if annotationEngine is None:
-            self.annotationEngine = MAGMaAnnotationEngine(**kwargs)
+            self.annotationEngine = MAGMaAnnotationEngine(ppm_tolerance = self.ppm_tolerance, **kwargs)
         else:
             self.annotationEngine = annotationEngine
 
@@ -252,6 +251,8 @@ def re_align(self, alignmentEngine: AlignmentEngine, **kwargs):
 
         if alignmentEngine is None:
             raise ValueError("Alignment engine is required to re-align the network")
+        ppm_tolerance = kwargs.get("ppm_tolerance", self.ppm_tolerance)
+        kwargs["ppm_tolerance"] = ppm_tolerance
         alignmentEngine.align(self.network, **kwargs)
 
 

modifinder/runner.py

@@ -64,7 +64,7 @@ def run_single(match_index, network = None, networkUnknowns = None, unknown_comp
         knowns = mf.get_neighbors(node_id=unknown_id)
 
     except Exception as err:
-        final_result = [{"match_index": match_index, "error": str(err)} for _ in range(len(known_compounds))]
+        final_result = [{"match_index": match_index, "error": "error in creating the network. "  + str(err)} for _ in range(len(known_compounds))]
         for known_index, node in enumerate(known_compounds):
             try:
                 try:
@@ -116,7 +116,7 @@ def run_single(match_index, network = None, networkUnknowns = None, unknown_comp
             final_result[known_index] = result
 
         except Exception as err:
-            final_result[known_index] = {"error": str(err), "match_index": match_index, "unknown_id": unknown_id, "known_id": node}
+            final_result[known_index] = {"error": "error when making prediction. " + str(err), "match_index": match_index, "unknown_id": unknown_id, "known_id": node}
             # raise err
 
     try: