fixing filter saving in attributes

cshenry · Aug 4, 2023 · f02a4a7 · f02a4a7
1 parent 8c70448
commit f02a4a7
Show file tree

Hide file tree

Showing 3 changed files with 9 additions and 12 deletions.
diff --git a/modelseedpy/core/msatpcorrection.py b/modelseedpy/core/msatpcorrection.py
@@ -444,7 +444,7 @@ def expand_model_to_genome_scale(self):
         self.restore_noncore_reactions(noncore=True, othercompartment=False)
         # Extending model with non core reactions while retaining ATP accuracy
         self.filtered_noncore = self.modelutl.reaction_expansion_test(
-            self.noncore_reactions, tests,atp_expansion=True
+            self.noncore_reactions, tests,attribute_label="atp_expansion_filter"
         )
         # Removing filtered reactions
         for item in self.filtered_noncore:

diff --git a/modelseedpy/core/msgapfill.py b/modelseedpy/core/msgapfill.py
@@ -148,11 +148,16 @@ def prefilter(self, media, target):
             self.gfpkgmgr.getpkg("GapfillingPkg").filter_database_based_on_tests(
                 self.test_conditions
             )
+            with open("OriginalAttributes.json", 'w') as f:
+                json.dump(self.mdlutl.get_attributes(), f,indent=4,skipkeys=True)
+            with open("GapfillingAttributes.json", 'w') as f:
+                json.dump(self.gfpkgmgr.getpkg("GapfillingPkg").modelutl.get_attributes(), f,indent=4,skipkeys=True)
             gf_filter = self.gfpkgmgr.getpkg("GapfillingPkg").modelutl.get_attributes("gf_filter", {})
             base_filter = self.mdlutl.get_attributes("gf_filter", {})
             for media_id in gf_filter:
                 base_filter[media_id] = gf_filter[media_id]
-            base_filter = self.mdlutl.save_attributes(base_filter, "gf_filter")
+            with open("FinalAttributes.json", 'w') as f:
+                json.dump(self.mdlutl.get_attributes(), f,indent=4,skipkeys=True)
 
         # Testing if gapfilling can work after filtering
         if not self.test_gapfill_database(media, target, before_filtering=False):

diff --git a/modelseedpy/core/msmodelutl.py b/modelseedpy/core/msmodelutl.py
@@ -902,7 +902,7 @@ def binary_expansion_test(self, reaction_list, condition, currmodel, depth=0):
         return filtered_list
 
     def reaction_expansion_test(
-        self, reaction_list, condition_list, binary_search=True,atp_expansion=False
+        self, reaction_list, condition_list, binary_search=True,attribute_label="gf_filter"
     ):
         """Adds reactions in reaction list one by one and appplies tests, filtering reactions that fail
 
@@ -961,11 +961,7 @@ def reaction_expansion_test(
                 + str(len(reaction_list))
             )
             # Adding filter results to attributes
-            gf_filter_att = self.get_attributes("gf_filter", {})
-            if atp_expansion:
-                atp_analysis = self.get_attributes("ATP_analysis", {})
-                atp_analysis["atp_expansion_filter"] = {}
-                gf_filter_att = atp_analysis["atp_expansion_filter"]
+            gf_filter_att = self.get_attributes(attribute_label, {})
             if condition["media"].id not in gf_filter_att:
                 gf_filter_att[condition["media"].id] = {}
             if condition["objective"] not in gf_filter_att[condition["media"].id]:
@@ -1001,10 +997,6 @@ def reaction_expansion_test(
                         gf_filter_att[condition["media"].id][condition["objective"]][
                             condition["threshold"]
                         ][item[0].id][item[1]] = item[2]
-            if atp_expansion:
-                atp_analysis = self.save_attributes(atp_analysis, "ATP_analysis")
-            else:
-                gf_filter_att = self.save_attributes(gf_filter_att, "gf_filter")
         return filtered_list
 
     #################################################################################