Skeleton of mint command

docs/mint.md

@@ -0,0 +1,30 @@
+# Mint
+
+ROBOT can mint sequential numeric identifiers for temporary IRIS. For example, in a decentralized development workflow,
+curators may submit pull requests creating new terms using UUID-based identifiers, such as:
+
+- `http://purl.obolibrary.org/temp#65969F4B-4050-4AB9-9EE4-6E136A7A335F`
+- `http://purl.obolibrary.org/temp#829D9A75-572B-4F79-9A52-F74F53FDD687`
+
+To replace occurrences of these IRIs with IRIs following a given ontology identifier scheme, you can run a command like this:
+
+    robot mint \
+      --input needs-minting.owl \
+      --output results/minted.owl
+      --minted-id-prefix "http://purl.obolibrary.org/obo/EXAMPLE_"
+      --temp-id-prefix "http://purl.obolibrary.org/temp#"
+      --minted-from-property "http://purl.obolibrary.org/obo/OMO_mintedfrom"
+
+If, for example, the ontology already contains a term with IRI `http://purl.obolibrary.org/obo/EXAMPLE_0000004`,
+this will result in all occurrences of the above IRIs being replaced with these corresponding IRIs:
+
+- `http://purl.obolibrary.org/obo/EXAMPLE_0000005`
+- `http://purl.obolibrary.org/obo/EXAMPLE_0000006`
+
+`mint` provides some additional options to modify identifier generation:
+
+- `--pad-width`: apply leading zeroes to minted identifiers up to this width (default `7`)
+- `--min-id`: start minted identifiers from the max of either this number or the highest identifier found which is less than or equal to `max-id` (default `0`)
+- `--max-id`: fail the operation if no identifier can be minted less than or equal to this number (default `Integer.MAX_VALUE`)
+- `--keep-deprecated `: whether to keep temporary terms in the ontology as deprecated entities (default `false`).
+  Deprecated temporary entities are linked to the minted replacement term with a [term_replaced_by](http://purl.obolibrary.org/obo/IAO_0100001) annotation.

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

@@ -30,6 +30,7 @@ private static CommandManager initManager() {
     m.addCommand("filter", new FilterCommand());
     m.addCommand("materialize", new MaterializeCommand());
     m.addCommand("merge", new MergeCommand());
+    m.addCommand("mint", new MintCommand());
     m.addCommand("mirror", new MirrorCommand());
     m.addCommand("python", new PythonCommand());
     m.addCommand("query", new QueryCommand());

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

@@ -0,0 +1,128 @@
+package org.obolibrary.robot;
+
+import java.io.IOException;
+import org.apache.commons.cli.CommandLine;
+import org.apache.commons.cli.Options;
+import org.semanticweb.owlapi.apibinding.OWLManager;
+import org.semanticweb.owlapi.model.IRI;
+import org.semanticweb.owlapi.model.OWLOntology;
+
+public class MintCommand implements Command {
+
+  /** Store the command-line options for the command. */
+  private Options options;
+
+  public MintCommand() {
+    Options o = CommandLineHelper.getCommonOptions();
+    o.addOption("i", "input", true, "load ontology from a file");
+    o.addOption("I", "input-iri", true, "load ontology from an IRI");
+    o.addOption("o", "output", true, "save processed ontology to a file");
+    o.addOption(null, "minted-id-prefix", true, "IRI prefix to prepend to minted identifiers");
+    o.addOption(
+        null,
+        "minted-from-property",
+        true,
+        "property IRI used to link minted identifiers to temporary identifiers");
+    o.addOption(null, "temp-id-prefix", true, "IRI prefix indicating temporary identifiers");
+    o.addOption(
+        null,
+        "min-id",
+        true,
+        "start minted identifiers from the max of either this number or the highest identifier found which is less than or equal to max-id");
+    o.addOption(
+        null,
+        "max-id",
+        true,
+        "fail if no identifier can be minted less than or equal to this number");
+    o.addOption(
+        null, "pad-width", true, "apply leading zeroes to minted identifiers up to this width");
+    o.addOption(
+        null,
+        "keep-deprecated",
+        true,
+        "keep temporary terms in the ontology as deprecated entities");
+    options = o;
+  }
+
+  @Override
+  public String getName() {
+    return "mint";
+  }
+
+  @Override
+  public String getDescription() {
+    return "replace temporary identifiers with newly minted official identifiers";
+  }
+
+  @Override
+  public String getUsage() {
+    return "robot mint --input <file> --minted-id-prefix <iri-prefix> --temp-id-prefix <iri-prefix> --minted-from-property <iri> --min-id <integer> --max-id <integer> --pad-width <integer> --keep-deprecated <bool> --output <file>";
+  }
+
+  @Override
+  public Options getOptions() {
+    return options;
+  }
+
+  @Override
+  public void main(String[] args) {
+    try {
+      execute(null, args);
+    } catch (Exception e) {
+      CommandLineHelper.handleException(e);
+    }
+  }
+
+  @Override
+  public CommandState execute(CommandState state, String[] args) throws Exception {
+    CommandLine line = CommandLineHelper.getCommandLine(getUsage(), getOptions(), args);
+    if (line == null) {
+      return null;
+    }
+    IOHelper ioHelper = CommandLineHelper.getIOHelper(line);
+    if (state == null) {
+      state = new CommandState();
+    }
+    state = CommandLineHelper.updateInputOntology(ioHelper, state, line);
+    OWLOntology ontology = state.getOntology();
+
+    MintOperation.MintConfig config = parseConfig(line);
+    MintOperation.mintIdentifiers(ontology, config);
+
+    CommandLineHelper.maybeSaveOutput(line, ontology);
+    state.setOntology(ontology);
+    return state;
+  }
+
+  private MintOperation.MintConfig parseConfig(CommandLine line)
+      throws IOException, NumberFormatException {
+    IOHelper ioHelper = CommandLineHelper.getIOHelper(line);
+    MintOperation.MintConfig config = new MintOperation.MintConfig();
+    config.setMintedIDPrefix(
+        CommandLineHelper.getDefaultValue(line, "minted-id-prefix", config.getMintedIDPrefix()));
+    config.setTempIDPrefix(
+        CommandLineHelper.getDefaultValue(line, "temp-id-prefix", config.getTempIDPrefix()));
+    String propertyID = CommandLineHelper.getDefaultValue(line, "minted-from-property", "");
+    if (!propertyID.isEmpty()) {
+      IRI propertyIRI =
+          CommandLineHelper.maybeCreateIRI(ioHelper, propertyID, "minted-from-property");
+      config.setMintedFromProperty(
+          OWLManager.getOWLDataFactory().getOWLAnnotationProperty(propertyIRI));
+    }
+    String minID = CommandLineHelper.getDefaultValue(line, "min-id", "");
+    if (!minID.isEmpty()) {
+      config.setMinIdentifier(Integer.parseInt(minID));
+    }
+    String maxID = CommandLineHelper.getDefaultValue(line, "max-id", "");
+    if (!maxID.isEmpty()) {
+      config.setMaxIdentifier(Integer.parseInt(maxID));
+    }
+    String padding = CommandLineHelper.getDefaultValue(line, "pad-width", "");
+    if (!padding.isEmpty()) {
+      config.setPadWidth(Integer.parseInt(padding));
+    }
+    config.setKeepDeprecated(
+        CommandLineHelper.getBooleanValue(line, "keep-deprecated", config.isKeepDeprecated()));
+    return config;
+  }
+}

robot-core/src/main/java/org/obolibrary/robot/MintOperation.java

@@ -0,0 +1,82 @@
+package org.obolibrary.robot;
+
+import org.semanticweb.owlapi.apibinding.OWLManager;
+import org.semanticweb.owlapi.model.IRI;
+import org.semanticweb.owlapi.model.OWLAnnotationProperty;
+import org.semanticweb.owlapi.model.OWLOntology;
+
+public class MintOperation {
+
+  public static class MintConfig {
+
+    private String mintedIDPrefix = "http://purl.obolibrary.org/obo/EXAMPLE_";
+    private String tempIDPrefix = "http://purl.obolibrary.org/temp#";
+    private OWLAnnotationProperty mintedFromProperty =
+        OWLManager.getOWLDataFactory()
+            .getOWLAnnotationProperty(IRI.create("http://purl.obolibrary.org/obo/OMO_mintedfrom"));
+    private int minIdentifier = 0;
+    private int maxIdentifier = Integer.MAX_VALUE;
+    private int padWidth = 7;
+    private boolean keepDeprecated = false;
+
+    public String getMintedIDPrefix() {
+      return mintedIDPrefix;
+    }
+
+    public void setMintedIDPrefix(String mintedIDPrefix) {
+      this.mintedIDPrefix = mintedIDPrefix;
+    }
+
+    public String getTempIDPrefix() {
+      return tempIDPrefix;
+    }
+
+    public void setTempIDPrefix(String tempIDPrefix) {
+      this.tempIDPrefix = tempIDPrefix;
+    }
+
+    public OWLAnnotationProperty getMintedFromProperty() {
+      return mintedFromProperty;
+    }
+
+    public void setMintedFromProperty(OWLAnnotationProperty mintedFromProperty) {
+      this.mintedFromProperty = mintedFromProperty;
+    }
+
+    public int getMinIdentifier() {
+      return minIdentifier;
+    }
+
+    public void setMinIdentifier(int minIdentifier) {
+      this.minIdentifier = minIdentifier;
+    }
+
+    public int getMaxIdentifier() {
+      return maxIdentifier;
+    }
+
+    public void setMaxIdentifier(int maxIdentifier) {
+      this.maxIdentifier = maxIdentifier;
+    }
+
+    public int getPadWidth() {
+      return padWidth;
+    }
+
+    public void setPadWidth(int padWidth) {
+      this.padWidth = padWidth;
+    }
+
+    public boolean isKeepDeprecated() {
+      return keepDeprecated;
+    }
+
+    public void setKeepDeprecated(boolean keepDeprecated) {
+      this.keepDeprecated = keepDeprecated;
+    }
+  }
+
+  public static void mintIdentifiers(OWLOntology ontology, MintConfig config) {
+    // TODO
+  }
+}