Allow using CURIEs in some command line options.

Make it possible to use a CURIE-like syntax with the `--follow-in` and
`--not-follow-in` options of the `odk:subset` command (as advertised in
the documentation). That is,

  --follow-in UBERON:

is treated as equivalent to:

  --follow-in http://purl.obolibrary.org/obo/UBERON_

Likewise for the `--base-iri` option in the `odk:check-align` command.

Author: gouttegd

src/main/java/org/incenp/obofoundry/odk/CheckAlignmentCommand.java

@@ -90,7 +90,7 @@ public void performOperation(CommandState state, CommandLine line) throws Except
         boolean failOnError = CommandLineHelper.getBooleanValue(line, "fail", true);
         if ( line.hasOption("base-iri") ) {
             for ( String iri : line.getOptionValues("base-iri") ) {
-                basePrefixes.add(iri);
+                basePrefixes.add(getIRI(iri, "base-iri").toString());
             }
         }
         factory = state.getOntology().getOWLOntologyManager().getOWLDataFactory();

src/main/java/org/incenp/obofoundry/odk/SubsetCommand.java

@@ -100,12 +100,12 @@ public void performOperation(CommandState state, CommandLine line) throws Except
         }
         if ( line.hasOption("follow-in") ) {
             for ( String prefix : line.getOptionValues("follow-in") ) {
-                extractor.includePrefix(prefix);
+                extractor.includePrefix(getIRI(prefix, "follow-in").toString());
             }
         }
         if ( line.hasOption("not-follow-in") ) {
             for ( String prefix : line.getOptionValues("not-follow-in") ) {
-                extractor.excludePrefix(prefix);
+                extractor.excludePrefix(getIRI(prefix, "not-follow-in").toString());
             }
         }