Add the CommandLineHelper whenever possible.

Refactor to use the helper methods from the CommandLineHelper class. In
particular, use the `getTerms` method instead of having our own code to
read a list of IRIs from a file.

Author: gouttegd

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

@@ -18,12 +18,6 @@
 
 package org.incenp.obofoundry.odk;
 
-import java.io.BufferedReader;
-import java.io.FileReader;
-import java.io.IOException;
-import java.util.HashSet;
-import java.util.Set;
-
 import org.apache.commons.cli.CommandLine;
 import org.apache.commons.cli.Options;
 import org.obolibrary.robot.Command;
@@ -138,54 +132,4 @@ public CommandState execute(CommandState state, String[] args) throws Exception
     protected IRI getIRI(String term, String field) {
         return CommandLineHelper.maybeCreateIRI(ioHelper, term, field);
     }
-
-    /**
-     * Reads a file and gets its contents as a set, one entry per line, excluding
-     * any blank line and lines starting with a '#' character.
-     * 
-     * @param filename The name of the file to read.
-     * @return The file's lines as a set of unique strings.
-     * @throws IOException If any I/O error occurs when reading the file.
-     */
-    protected Set<String> readFile(String filename) throws IOException {
-        BufferedReader reader = new BufferedReader(new FileReader(filename));
-        Set<String> lines = new HashSet<>();
-        String line = null;
-        while ( (line = reader.readLine()) != null ) {
-            line = line.trim();
-            if ( !line.isEmpty() && line.charAt(0) != '#' ) {
-                lines.add(line);
-            }
-        }
-        reader.close();
-
-        return lines;
-    }
-
-    /**
-     * Reads a file and gets its contents as a set of IRIs, assuming one IRI per
-     * line, excluding any blank line and lines starting with a '#' character.
-     * CURIEs that cannot be converted to a full-length IRI are silently ignored.
-     * 
-     * @param filename The name of the file to read.
-     * @return The set of IRIs contained in the file.
-     * @throws IOException If any I/O error occurs when reading the file.
-     */
-    protected Set<IRI> readFileAsIRIs(String filename) throws IOException {
-        BufferedReader reader = new BufferedReader(new FileReader(filename));
-        Set<IRI> terms = new HashSet<>();
-        String line = null;
-        while ( (line = reader.readLine()) != null ) {
-            line = line.trim();
-            if ( !line.isEmpty() && line.charAt(0) != '#' ) {
-                IRI termIRI = ioHelper.createIRI(line);
-                if ( termIRI != null ) {
-                    terms.add(termIRI);
-                }
-            }
-        }
-        reader.close();
-
-        return terms;
-    }
 }

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

@@ -93,20 +93,14 @@ public void performOperation(CommandState state, CommandLine line) throws Except
         extractor.setFillGaps(CommandLineHelper.getBooleanValue(line, "fill-gaps", false));
         extractor.setExcludeDangling(CommandLineHelper.getBooleanValue(line, "no-dangling", true));
         extractor.includeImports(useImports);
-        if ( line.hasOption("follow-property") ) {
-            for ( String property : line.getOptionValues("follow-property") ) {
-                extractor.followProperty(getIRI(property, "follow-property"));
-            }
+        for ( String property : CommandLineHelper.getOptionalValues(line, "follow-property") ) {
+            extractor.followProperty(getIRI(property, "follow-property"));
         }
-        if ( line.hasOption("follow-in") ) {
-            for ( String prefix : line.getOptionValues("follow-in") ) {
-                extractor.includePrefix(getIRI(prefix, "follow-in").toString());
-            }
+        for ( String prefix : CommandLineHelper.getOptionalValues(line, "follow-in") ) {
+            extractor.includePrefix(getIRI(prefix, "follow-in").toString());
         }
-        if ( line.hasOption("not-follow-in") ) {
-            for ( String prefix : line.getOptionValues("not-follow-in") ) {
-                extractor.excludePrefix(getIRI(prefix, "not-follow-in").toString());
-            }
+        for ( String prefix : CommandLineHelper.getOptionalValues(line, "not-follow-in") ) {
+            extractor.excludePrefix(getIRI(prefix, "not-follow-in").toString());
         }
 
         // Setting up the initial subset
@@ -136,30 +130,17 @@ public void performOperation(CommandState state, CommandLine line) throws Except
         }
 
         // 2. From the name or IRI of a subset defined in the ontology
-        if ( line.hasOption("subset") ) {
-            for ( String subsetName : line.getOptionValues("subset") ) {
-                IRI subsetIRI = ioHelper.createIRI(subsetName);
-                if ( subsetIRI != null ) {
-                    addToSubset(subset, extractor.getSubset(subsetIRI), "Adding tagged class {}");
-                } else {
-                    addToSubset(subset, extractor.getSubset(subsetName), "Adding tagged class {}");
-                }
+        for ( String subsetName : CommandLineHelper.getOptionalValues(line, "subset") ) {
+            IRI subsetIRI = ioHelper.createIRI(subsetName);
+            if ( subsetIRI != null ) {
+                addToSubset(subset, extractor.getSubset(subsetIRI), "Adding tagged class {}");
+            } else {
+                addToSubset(subset, extractor.getSubset(subsetName), "Adding tagged class {}");
             }
         }
 
         // 3. From an explicit list of terms
-        Set<IRI> terms = new HashSet<>();
-        if ( line.hasOption("term") ) {
-            for ( String term : line.getOptionValues("term") ) {
-                terms.add(getIRI(term, "term"));
-            }
-        }
-        if ( line.hasOption("term-file") ) {
-            for ( String termFile : line.getOptionValues("term-file") ) {
-                terms.addAll(readFileAsIRIs(termFile));
-            }
-        }
-        for ( IRI term : terms ) {
+        for ( IRI term : CommandLineHelper.getTerms(ioHelper, line, true) ) {
             if ( ontology.containsClassInSignature(term, useImports ? Imports.INCLUDED : Imports.EXCLUDED) ) {
                 subset.add(factory.getOWLClass(term));
                 logger.debug("Adding selected class {}", term);