Added reduce command, fixes #16

Added relax command, fixes #7

robot-command/src/main/java/org/obolibrary/robot/ReduceCommand.java

@@ -0,0 +1,151 @@
+package org.obolibrary.robot;
+
+import java.util.Map;
+
+import org.apache.commons.cli.CommandLine;
+import org.apache.commons.cli.Options;
+import org.semanticweb.owlapi.model.OWLOntology;
+import org.semanticweb.owlapi.reasoner.OWLReasonerFactory;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+/**
+ * Handles inputs and outputs for the {@link ReduceOperation}.
+ *
+ * @author <a href="mailto:cjmungall@lbl.gov">Chris Mungall</a>
+ */
+public class ReduceCommand implements Command {
+    /**
+     * Logger.
+     */
+    private static final Logger logger =
+        LoggerFactory.getLogger(ReduceCommand.class);
+
+    /**
+     * Store the command-line options for the command.
+     */
+    private Options options;
+
+    /**
+     * Initialize the command.
+     */
+    public ReduceCommand() {
+        Options o = CommandLineHelper.getCommonOptions();
+        o.addOption("r", "reasoner",  true, "reasoner to use: (ELK, HermiT)");
+        o.addOption("s", "remove-redundant-subclass-axioms",
+                true, "remove redundant subclass axioms");
+        o.addOption("i", "input",     true, "reduce ontology from a file");
+        o.addOption("I", "input-iri", true, "reduce ontology from an IRI");
+        o.addOption("o", "output",    true, "save reduceed ontology to a file");
+        options = o;
+    }
+
+    /**
+     * Name of the command.
+     *
+     * @return name
+     */
+    public String getName() {
+        return "reduce";
+    }
+
+    /**
+     * Brief description of the command.
+     *
+     * @return description
+     */
+    public String getDescription() {
+        return "reduce ontology";
+    }
+
+    /**
+     * Command-line usage for the command.
+     *
+     * @return usage
+     */
+    public String getUsage() {
+        return "robot reduce --input <file> "
+             + "--reasoner <name> "
+             + "[options] "
+             + "--output <file>";
+    }
+
+    /**
+     * Command-line options for the command.
+     *
+     * @return options
+     */
+    public Options getOptions() {
+        return options;
+    }
+
+    /**
+     * Handle the command-line and file operations for the reduceOperation.
+     *
+     * @param args strings to use as arguments
+     */
+    public void main(String[] args) {
+        try {
+            execute(null, args);
+        } catch (Exception e) {
+            CommandLineHelper.handleException(getUsage(), getOptions(), e);
+        }
+    }
+
+    /**
+     * Given an input state and command line arguments,
+     * run a reasoner, and add axioms to the input ontology,
+     * returning a state with the updated ontology.
+     *
+     * @param state the state from the previous command, or null
+     * @param args the command-line arguments
+     * @return the state with inferred axioms added to the ontology
+     * @throws Exception on any problem
+     */
+    public CommandState execute(CommandState state, String[] args)
+            throws Exception {
+        CommandLine line = CommandLineHelper
+            .getCommandLine(getUsage(), getOptions(), args);
+        if (line == null) {
+            return null;
+        }
+
+        if (state == null) {
+            state = new CommandState();
+        }
+
+        IOHelper ioHelper = CommandLineHelper.getIOHelper(line);
+        state = CommandLineHelper.updateInputOntology(ioHelper, state, line);
+        OWLOntology ontology = state.getOntology();
+
+        // ELK is the default reasoner
+        String reasonerName = CommandLineHelper.getDefaultValue(
+                line, "reasoner", "ELK").trim().toLowerCase();
+        OWLReasonerFactory reasonerFactory;
+        if (reasonerName.equals("structural")) {
+            reasonerFactory = new org.semanticweb.owlapi.reasoner
+                .structural.StructuralReasonerFactory();
+        } else if (reasonerName.equals("hermit")) {
+            reasonerFactory = new org.semanticweb
+                .HermiT.Reasoner.ReasonerFactory();
+        } else {
+            reasonerFactory = new org.semanticweb
+                .elk.owlapi.ElkReasonerFactory();
+        }
+
+        // Override default reasoner options with command-line options
+        Map<String, String> reasonerOptions =
+            ReduceOperation.getDefaultOptions();
+        for (String option: reasonerOptions.keySet()) {
+            if (line.hasOption(option)) {
+                reasonerOptions.put(option, line.getOptionValue(option));
+            }
+        }
+
+        ReduceOperation.reduce(ontology, reasonerFactory, reasonerOptions);
+
+        CommandLineHelper.maybeSaveOutput(line, ontology);
+
+        return state;
+    }
+}

robot-command/src/main/java/org/obolibrary/robot/RelaxCommand.java

@@ -0,0 +1,134 @@
+package org.obolibrary.robot;
+
+import java.util.Map;
+
+import org.apache.commons.cli.CommandLine;
+import org.apache.commons.cli.Options;
+import org.semanticweb.owlapi.model.OWLOntology;
+import org.semanticweb.owlapi.reasoner.OWLReasonerFactory;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+/**
+ * Handles inputs and outputs for the {@link relaxOperation}.
+ *
+ * @author <a href="mailto:cjmungall@lbl.gov">Chris Mungall</a>
+ */
+public class RelaxCommand implements Command {
+    /**
+     * Logger.
+     */
+    private static final Logger logger =
+        LoggerFactory.getLogger(RelaxCommand.class);
+
+    /**
+     * Store the command-line options for the command.
+     */
+    private Options options;
+
+    /**
+     * Initialize the command.
+     */
+    public RelaxCommand() {
+        Options o = CommandLineHelper.getCommonOptions();
+        o.addOption("i", "input",     true, "relax ontology from a file");
+        o.addOption("I", "input-iri", true, "relax ontology from an IRI");
+        o.addOption("o", "output",    true, "save relaxed ontology to a file");
+        options = o;
+    }
+
+    /**
+     * Name of the command.
+     *
+     * @return name
+     */
+    public String getName() {
+        return "relax";
+    }
+
+    /**
+     * Brief description of the command.
+     *
+     * @return description
+     */
+    public String getDescription() {
+        return "relax ontology";
+    }
+
+    /**
+     * Command-line usage for the command.
+     *
+     * @return usage
+     */
+    public String getUsage() {
+        return "robot relax --input <file> "
+             + "--reasoner <name> "
+             + "[options] "
+             + "--output <file>";
+    }
+
+    /**
+     * Command-line options for the command.
+     *
+     * @return options
+     */
+    public Options getOptions() {
+        return options;
+    }
+
+    /**
+     * Handle the command-line and file operations for the relaxOperation.
+     *
+     * @param args strings to use as arguments
+     */
+    public void main(String[] args) {
+        try {
+            execute(null, args);
+        } catch (Exception e) {
+            CommandLineHelper.handleException(getUsage(), getOptions(), e);
+        }
+    }
+
+    /**
+     * Given an input state and command line arguments,
+     * run a reasoner, and add axioms to the input ontology,
+     * returning a state with the updated ontology.
+     *
+     * @param state the state from the previous command, or null
+     * @param args the command-line arguments
+     * @return the state with inferred axioms added to the ontology
+     * @throws Exception on any problem
+     */
+    public CommandState execute(CommandState state, String[] args)
+            throws Exception {
+        CommandLine line = CommandLineHelper
+            .getCommandLine(getUsage(), getOptions(), args);
+        if (line == null) {
+            return null;
+        }
+
+        if (state == null) {
+            state = new CommandState();
+        }
+
+        IOHelper ioHelper = CommandLineHelper.getIOHelper(line);
+        state = CommandLineHelper.updateInputOntology(ioHelper, state, line);
+        OWLOntology ontology = state.getOntology();
+
+
+        // Override default reasoner options with command-line options
+        Map<String, String> relaxOptions =
+            RelaxOperation.getDefaultOptions();
+        for (String option: relaxOptions.keySet()) {
+            if (line.hasOption(option)) {
+                relaxOptions.put(option, line.getOptionValue(option));
+            }
+        }
+
+        RelaxOperation.relax(ontology, relaxOptions);
+
+        CommandLineHelper.maybeSaveOutput(line, ontology);
+
+        return state;
+    }
+}