Get the prefixes from ROBOT only once.

Obtain the prefixes known to ROBOT only once and then use the same prefix map everywhere we need it. The 'getPrefixes()' method of the IOHelper object creates a new map everytime it is used, so it's better to call it only once.
gouttegd · Sep 3, 2023 · b73167c · b73167c
1 parent 5a7bb89
commit b73167c
Showing 1 changed file with 7 additions and 7 deletions.
diff --git a/robot/src/main/java/org/incenp/obofoundry/sssom/robot/SSSOMInjectionCommand.java b/robot/src/main/java/org/incenp/obofoundry/sssom/robot/SSSOMInjectionCommand.java
@@ -144,6 +144,7 @@ public CommandState execute(CommandState state, String[] args) throws Exception
 
         OWLOntology ontology = state.getOntology();
         OWLGenerator axiomGenerator = new OWLGenerator();
+        Map<String, String> prefixes = ioHelper.getPrefixes();
 
         MappingSet mappingSet = null;
         if ( line.hasOption("sssom") ) {
@@ -158,7 +159,7 @@ public CommandState execute(CommandState state, String[] args) throws Exception
         }
         if ( line.hasOption("extract") ) {
             XrefExtractor extractor = new XrefExtractor();
-            extractor.setPrefixMap(ioHelper.getPrefixes());
+            extractor.setPrefixMap(prefixes);
             extractor.fillPrefixToPredicateMap(ontology);
             if ( mappingSet == null ) {
                 mappingSet = extractor.extract(ontology);
@@ -175,14 +176,14 @@ public CommandState execute(CommandState state, String[] args) throws Exception
         }
 
         if ( line.hasOption("only-subject-in") ) {
-            String pr = ioHelper.getPrefixes().get(line.getOptionValue("only-subject-in"));
+            String pr = prefixes.get(line.getOptionValue("only-subject-in"));
             if ( pr != null ) {
                 axiomGenerator.addStopingRule((mapping) -> !mapping.getSubjectId().startsWith(pr));
             }
         }
 
         if ( line.hasOption("only-object-in") ) {
-            String pr = ioHelper.getPrefixes().get(line.getOptionValue("only-object-in"));
+            String pr = prefixes.get(line.getOptionValue("only-object-in"));
             if ( pr != null ) {
                 axiomGenerator.addStopingRule((mapping) -> !mapping.getObjectId().startsWith(pr));
             }
@@ -209,9 +210,8 @@ public CommandState execute(CommandState state, String[] args) throws Exception
 
         if (line.hasOption("hasdbxref")) {
             PrefixManager pm = new PrefixManager();
-            Map<String, String> clMap = ioHelper.getPrefixes();
-            for ( String prefixName : clMap.keySet() ) {
-                pm.add(prefixName, clMap.get(prefixName));
+            for ( String prefixName : prefixes.keySet() ) {
+                pm.add(prefixName, prefixes.get(prefixName));
             }
             IMappingTransformer<String> texter = (mapping) -> pm.shortenIdentifier(mapping.getObjectId());
             axiomGenerator.addRule(null, null, new AnnotationAxiomGenerator(ontology,
@@ -223,7 +223,7 @@ public CommandState execute(CommandState state, String[] args) throws Exception
             SSSOMTransformReader<OWLAxiom> sssomtReader = new SSSOMTransformReader<OWLAxiom>(sssomApplication,
                     line.getOptionValue("ruleset"));
             if ( !line.hasOption("no-default-prefixes") ) {
-                sssomtReader.addPrefixMap(ioHelper.getPrefixes());
+                sssomtReader.addPrefixMap(prefixes);
             }
             sssomtReader.read();