Add the '--only-(subject|object)-in' options.

Add an option to filter mappings according to their subject ID:
'--only-subject-in PFX' will filter out any mapping whose subject ID
does not start with the specified prefix.

Likewise, the '--only-object-in PFX' option will filter out any mapping
whose object ID does not start the specified prefix.

core/src/site/apt/robot-sssom-inject.apt

@@ -49,8 +49,24 @@ ROBOT sssom-inject command
   ontology with the generated axioms. The newly created ontology becomes
   ROBOT’s current ontology, and will passed down the command pipeline.
 
-  Use the option <<<--invert>>> to invert the entire mapping set before
-  generating any axioms out of it.
+* Mapping preprocessing
+
+  A few options allow for basic preprocessing of a mapping set. They are
+  intended to avoid having to use SSSOM/Transform rules for simple use
+  cases.
+
+  The <<<--invert>>> option allows to invert the entire mapping set.
+
+  The <<<--only-subject-in>>> allows to filter the mapping set to only
+  keep mappings whose subject ID starts with the specified prefix. For
+  example, use <<<---only-subject-in CL>>> to only keep (and process)
+  mappings with a subject in CL.
+
+  The <<<--only-object-in>>> is similar, but for the object side of
+  mappings.
+
+  These options are applied before any other processing. Inversion, if
+  specified, is always performed first. 
 
 * Checking for the existence of the subject and/or object
 

robot/src/main/java/org/incenp/obofoundry/sssom/robot/SSSOMInjectionCommand.java

@@ -91,6 +91,8 @@ public SSSOMInjectionCommand() {
                 "write generated axioms to several output ontologies according to dispatch table");
         options.addOption("r", "reasoner", true, "reasoner to use");
         options.addOption(null, "invert", false, "invert the mapping set prior to any processing");
+        options.addOption(null, "only-subject-in", true, "Only process mappings whose subject has the given prefix");
+        options.addOption(null, "only-object-in", true, "Only process mappings whose object has the given prefix");
     }
 
     @Override
@@ -172,6 +174,20 @@ public CommandState execute(CommandState state, String[] args) throws Exception
             axiomGenerator.addRule(null, (mapping) -> CommonPredicate.invert(mapping), null);
         }
 
+        if ( line.hasOption("only-subject-in") ) {
+            String pr = ioHelper.getPrefixes().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"));
+            if ( pr != null ) {
+                axiomGenerator.addStopingRule((mapping) -> !mapping.getObjectId().startsWith(pr));
+            }
+        }
+
         if ( line.hasOption("check-subject") ) {
             axiomGenerator.setCheckSubjectExistence(ontology);
         }