ontodev · jamesaoverton · Feb 19, 2020 · Feb 18, 2020
diff --git a/docs/extract.md b/docs/extract.md
@@ -206,6 +206,10 @@ MIREOT requires either `--lower-term` or `--branch-from-term` to proceed. `--upp
 
 If an `--upper-term` is specified for MIREOT, `--lower-term` (or terms) must also be specified.
 
+### Invalid Imports Error
+
+The input for `--imports` must be either `exclude` or `include`.
+
 ### Invalid Method Error
 
 The `--method` option only accepts: MIREOT, STAR, TOP, and BOT.

diff --git a/robot-command/src/main/java/org/obolibrary/robot/ExtractCommand.java b/robot-command/src/main/java/org/obolibrary/robot/ExtractCommand.java
@@ -8,6 +8,7 @@
 import org.apache.commons.cli.CommandLine;
 import org.apache.commons.cli.Options;
 import org.semanticweb.owlapi.model.*;
+import org.semanticweb.owlapi.model.parameters.Imports;
 import org.semanticweb.owlapi.util.DefaultPrefixManager;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -37,6 +38,10 @@ public class ExtractCommand implements Command {
           + "MISSING LOWER TERMS ERROR "
           + "lower term(s) must be specified with upper term(s) for MIREOT";
 
+  /** Error message when user provides invalid imports option. */
+  private static final String invalidImportsError =
+      NS + "INVALID IMPORTS ERROR --imports must be 'include' or 'exclude'";
+
   /** Error message when user provides invalid extraction method. */
   private static final String invalidMethodError =
       NS + "INVALID METHOD ERROR method must be: MIREOT, STAR, TOP, BOT";
@@ -221,6 +226,7 @@ private static OWLOntology mireotExtract(
       CommandLine line,
       Map<String, String> extractOptions)
       throws Exception {
+    Imports imports = getImportsOption(extractOptions);
     List<OWLOntology> outputOntologies = new ArrayList<>();
     // Get terms from input (ensuring that they are in the input ontology)
     // It's okay for any of these to return empty (allowEmpty = true)
@@ -229,23 +235,26 @@ private static OWLOntology mireotExtract(
         OntologyHelper.filterExistingTerms(
             inputOntology,
             CommandLineHelper.getTerms(ioHelper, line, "upper-term", "upper-terms"),
-            true);
+            true,
+            imports);
     if (upperIRIs.size() == 0) {
       upperIRIs = null;
     }
     Set<IRI> lowerIRIs =
         OntologyHelper.filterExistingTerms(
             inputOntology,
             CommandLineHelper.getTerms(ioHelper, line, "lower-term", "lower-terms"),
-            true);
+            true,
+            imports);
     if (lowerIRIs.size() == 0) {
       lowerIRIs = null;
     }
     Set<IRI> branchIRIs =
         OntologyHelper.filterExistingTerms(
             inputOntology,
             CommandLineHelper.getTerms(ioHelper, line, "branch-from-term", "branch-from-terms"),
-            true);
+            true,
+            imports);
     if (branchIRIs.size() == 0) {
       branchIRIs = null;
     }
@@ -303,6 +312,7 @@ private static OWLOntology slmeExtract(
       CommandLine line,
       Map<String, String> extractOptions)
       throws Exception {
+    Imports imports = getImportsOption(extractOptions);
     // upper-term, lower-term, and branch-from term should not be used
     List<String> mireotTerms =
         Arrays.asList(
@@ -322,7 +332,8 @@ private static OWLOntology slmeExtract(
         OntologyHelper.filterExistingTerms(
             inputOntology,
             CommandLineHelper.getTerms(ioHelper, line),
-            OptionsHelper.optionIsTrue(extractOptions, "force"));
+            OptionsHelper.optionIsTrue(extractOptions, "force"),
+            imports);
 
     // Determine what to do with sources
     Map<IRI, IRI> sourceMap =
@@ -337,6 +348,24 @@ private static OWLOntology slmeExtract(
         inputOntology, terms, outputIRI, moduleType, extractOptions, sourceMap);
   }
 
+  /**
+   * Given a map of options, return the imports option as Imports.
+   *
+   * @param extractOptions map of options
+   * @return Imports INCLUDED or EXCLUDED
+   * @throws Exception if option is not 'include' or 'exclude'
+   */
+  private static Imports getImportsOption(Map<String, String> extractOptions) throws Exception {
+    String importsOption = OptionsHelper.getOption(extractOptions, "imports", "include");
+    if (importsOption.equalsIgnoreCase("include")) {
+      return Imports.INCLUDED;
+    } else if (importsOption.equalsIgnoreCase("exclude")) {
+      return Imports.EXCLUDED;
+    } else {
+      throw new Exception(invalidImportsError);
+    }
+  }
+
   /**
    * Given an IOHelper and the path to a term-to-source map, return a map of term IRI to source IRI.
    *

diff --git a/robot-core/src/main/java/org/obolibrary/robot/OntologyHelper.java b/robot-core/src/main/java/org/obolibrary/robot/OntologyHelper.java
@@ -290,7 +290,7 @@ public static void copyAnnotations(
 
   /**
    * Given an ontology and a set of IRIs, filter the set of IRIs to only include those that exist in
-   * the ontology.
+   * the ontology. Always include terms in imports.
    *
    * @param ontology the ontology to check for IRIs
    * @param IRIs Set of IRIs to filter
@@ -299,9 +299,24 @@ public static void copyAnnotations(
    */
   public static Set<IRI> filterExistingTerms(
       OWLOntology ontology, Set<IRI> IRIs, boolean allowEmpty) {
+    return filterExistingTerms(ontology, IRIs, allowEmpty, Imports.INCLUDED);
+  }
+
+  /**
+   * Given an ontology and a set of IRIs, filter the set of IRIs to only include those that exist in
+   * the ontology. Maybe include terms in imports.
+   *
+   * @param ontology the ontology to check for IRIs
+   * @param IRIs Set of IRIs to filter
+   * @param allowEmpty boolean specifying if an empty set can be returned
+   * @param imports Imports INCLUDED or EXCLUDED
+   * @return Set of filtered IRIs
+   */
+  public static Set<IRI> filterExistingTerms(
+      OWLOntology ontology, Set<IRI> IRIs, boolean allowEmpty, Imports imports) {
     Set<IRI> missingIRIs = new HashSet<>();
     for (IRI iri : IRIs) {
-      if (!ontology.containsEntityInSignature(iri)) {
+      if (!ontology.containsEntityInSignature(iri, imports)) {
         logger.warn("Ontology does not contain {}", iri.toQuotedString());
         missingIRIs.add(iri);
       }