Merge pull request #1193 from ontodev/extend-drop-annotation-assertio…

…n-selector Add --drop-axiom-annotations feature with value constraints
ontodev · May 2, 2024 · fcc06fc · fcc06fc
2 parents 62e0d3d + d332928
commit fcc06fc
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -12,6 +12,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Changed
 - Updated `duplicate_exact_syonym` [`report`] query to be case-insensitive and ignore synoyms annotated as abbreviation or acronym synonym types [#1179]
+- Extend `--drop-axiom-annotations` option to support value-specific removal of axiom annotations [#1193]
 - Add `--enforce-obo-format`, `--exclude-named-classes` and `--include-subclass-of` features to relax command [#1060, #1183]
 
 ### Fixed

diff --git a/docs/examples/filter_annotations_drop_axioms.owl b/docs/examples/filter_annotations_drop_axioms.owl
diff --git a/docs/remove.md b/docs/remove.md
@@ -230,13 +230,11 @@ Create a "base" subset by removing external axioms (alternatively, use `filter -
       --signature true \
       --output results/filter_annotations.owl
 
-Create a "base" subset in which axiom annotations involving IAO:0000117 and IAO:0000119 are removed:
+Extracts a base module, then removing _all_ `oboInOwl:hasDbXref` annotations on the remaining axioms, and all `oboInOwl:hasDbXref` axiom annotations whose value matches the regular expression `GO.*`:
 
-    robot remove --input template.owl \
-      --base-iri http://example.com/ \
+    robot remove --input uberon_module.owl \
+      --base-iri http://purl.obolibrary.org/obo/UBERON_ \
       --axioms external \
-      --drop-axiom-annotations IAO:0000117 \
-      --drop-axiom-annotations IAO:0000119 \
-      --output results/template-drop-axiom-remove.owl
-
-      
+      --drop-axiom-annotations oboInOwl:source=~'GO.*' \
+      --drop-axiom-annotations oboInOwl:hasDbXref \
+      --output results/filter_annotations_drop_axioms.owl
diff --git a/robot-command/src/main/java/org/obolibrary/robot/CommandLineHelper.java b/robot-command/src/main/java/org/obolibrary/robot/CommandLineHelper.java
@@ -1121,4 +1121,36 @@ public static List<OWLOntology> getInputOntologies(
     }
     return inputOntologies;
   }
+
+  /**
+   * Given an IOHelper and a list of unparsed patterns to select annotation assertions to be dropped
+   * build a Map of property IRIs, and value patterns for further processing.
+   *
+   * @param ioHelper the IOHelper to load the ontology with
+   * @param dropParameters The list of unparsed command line parameters describing the annotations
+   *     to select
+   * @return A map of IRI to annotation value to drop
+   */
+  public static Map<IRI, String> createAnnotationToDropMap(
+      IOHelper ioHelper, List<String> dropParameters) throws IOException {
+    Map<IRI, String> annotationsToDrop = new HashMap<>();
+
+    for (String dropParameter : dropParameters) {
+      if (dropParameter.equalsIgnoreCase("all")) {
+        // ignore, we communicate this through the dropParameters list
+      } else if (dropParameter.contains("=")) {
+        String[] parts = dropParameter.split("=");
+        String annotationIRI = parts[0];
+        String annotationValue = parts[1];
+        IRI iri =
+            CommandLineHelper.maybeCreateIRI(ioHelper, annotationIRI, "drop-axiom-annotations");
+        annotationsToDrop.put(iri, annotationValue);
+      } else {
+        IRI iri =
+            CommandLineHelper.maybeCreateIRI(ioHelper, dropParameter, "drop-axiom-annotations");
+        annotationsToDrop.put(iri, null);
+      }
+    }
+    return annotationsToDrop;
+  }
 }
diff --git a/robot-command/src/main/java/org/obolibrary/robot/FilterCommand.java b/robot-command/src/main/java/org/obolibrary/robot/FilterCommand.java
@@ -2,8 +2,8 @@
 
 import java.util.ArrayList;
 import java.util.List;
+import java.util.Map;
 import java.util.Set;
-import java.util.stream.Collectors;
 import org.apache.commons.cli.CommandLine;
 import org.apache.commons.cli.Options;
 import org.semanticweb.owlapi.apibinding.OWLManager;
@@ -167,13 +167,9 @@ public CommandState execute(CommandState state, String[] args) throws Exception
 
     List<String> dropParameters =
         CommandLineHelper.getOptionalValues(line, "drop-axiom-annotations");
-    List<IRI> annotationsToDrop =
-        dropParameters.stream()
-            .filter(s -> !s.equalsIgnoreCase("all"))
-            .map(
-                curie ->
-                    CommandLineHelper.maybeCreateIRI(ioHelper, curie, "drop-axiom-annotations"))
-            .collect(Collectors.toList());
+
+    Map<IRI, String> annotationsToDrop =
+        CommandLineHelper.createAnnotationToDropMap(ioHelper, dropParameters);
 
     // Use the select statements to get a set of objects to filter
     Set<OWLObject> relatedObjects =

diff --git a/robot-command/src/main/java/org/obolibrary/robot/RemoveCommand.java b/robot-command/src/main/java/org/obolibrary/robot/RemoveCommand.java
@@ -1,7 +1,6 @@
 package org.obolibrary.robot;
 
 import java.util.*;
-import java.util.stream.Collectors;
 import org.apache.commons.cli.CommandLine;
 import org.apache.commons.cli.Options;
 import org.semanticweb.owlapi.apibinding.OWLManager;
@@ -157,13 +156,9 @@ public CommandState execute(CommandState state, String[] args) throws Exception
 
     List<String> dropParameters =
         CommandLineHelper.getOptionalValues(line, "drop-axiom-annotations");
-    List<IRI> annotationsToDrop =
-        dropParameters.stream()
-            .filter(s -> !s.equalsIgnoreCase("all"))
-            .map(
-                curie ->
-                    CommandLineHelper.maybeCreateIRI(ioHelper, curie, "drop-axiom-annotations"))
-            .collect(Collectors.toList());
+
+    Map<IRI, String> annotationsToDrop =
+        CommandLineHelper.createAnnotationToDropMap(ioHelper, dropParameters);
 
     // Get the objects to remove
     Set<OWLObject> relatedObjects = getObjects(line, ioHelper, ontology, selectGroups);

diff --git a/robot-core/src/main/java/org/obolibrary/robot/OntologyHelper.java b/robot-core/src/main/java/org/obolibrary/robot/OntologyHelper.java
@@ -4,6 +4,8 @@
 import java.io.StringWriter;
 import java.util.*;
 import java.util.function.Function;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
 import org.obolibrary.robot.checks.InvalidReferenceChecker;
 import org.obolibrary.robot.export.RendererType;
 import org.obolibrary.robot.providers.QuotedAnnotationValueShortFormProvider;
@@ -1658,13 +1660,29 @@ public static void trimOntology(OWLOntology ontology) {
    * Removes all of the axiom annotations for the given annotation properties.
    *
    * @param ontology OWLOntology to remove axiom annotations
-   * @param properties Annotation property IRIs to remove related axiom annotations.
+   * @param properties List of annotation property IRIs to remove related axiom annotations.
    */
   public static void removeAxiomAnnotations(OWLOntology ontology, List<IRI> properties) {
+    Map<IRI, String> annotationsToDrop = new HashMap<>();
+    properties.forEach(iri -> annotationsToDrop.put(iri, null));
+    removeAxiomAnnotations(ontology, annotationsToDrop);
+  }
+
+  /**
+   * Removes all of the axiom annotations for the given annotation properties.
+   *
+   * @param ontology OWLOntology to remove axiom annotations
+   * @param properties Annotation property IRIs to remove related axiom annotations.
+   */
+  public static void removeAxiomAnnotations(
+      OWLOntology ontology, Map<IRI, String> annotationsToDrop) {
     OWLDataFactory owlDataFactory = ontology.getOWLOntologyManager().getOWLDataFactory();
-    properties.stream()
-        .map(iri -> owlDataFactory.getOWLAnnotationProperty(iri))
-        .forEach(p -> OntologyHelper.removeAxiomAnnotations(ontology, p));
+
+    for (IRI iri : annotationsToDrop.keySet()) {
+      OWLAnnotationProperty property = owlDataFactory.getOWLAnnotationProperty(iri);
+      String value = annotationsToDrop.get(iri);
+      OntologyHelper.removeAxiomAnnotations(ontology, property, value);
+    }
   }
 
   /**
@@ -1674,11 +1692,57 @@ public static void removeAxiomAnnotations(OWLOntology ontology, List<IRI> proper
    * @param property Annotation property to remove related axiom annotations.
    */
   public static void removeAxiomAnnotations(OWLOntology ontology, OWLAnnotationProperty property) {
+    removeAxiomAnnotations(ontology, property, null);
+  }
+
+  /**
+   * Removes all of the axiom annotations for the given annotation property and an optional value
+   * pattern The value pattern should follow
+   * https://robot.obolibrary.org/remove#pattern-subset-selectors
+   *
+   * @param ontology OWLOntology to remove axiom annotations
+   * @param property Annotation property to remove related axiom annotations.
+   * @param value a value or value pattern the restrict what is deleted. Can be null.
+   */
+  public static void removeAxiomAnnotations(
+      OWLOntology ontology, OWLAnnotationProperty property, String value) {
     OWLOntologyManager manager = ontology.getOWLOntologyManager();
     for (OWLAxiom axiom : ontology.getAxioms(Imports.EXCLUDED)) {
-      Set<OWLAnnotation> annotationsToRemove = axiom.getAnnotations(property);
+      Set<OWLAnnotation> annotationsToRemove = new HashSet<>();
+      Set<OWLAnnotation> allAxiomAnnotations = axiom.getAnnotations();
+      for (OWLAnnotation annotation : allAxiomAnnotations) {
+        if (annotation.getProperty().equals(property)) {
+          String annotationValue = getAnnotationValueAsStringOrNull(annotation);
+          if (value == null) {
+            // If there is no value set, we assume all annotations for the property should be
+            // removed
+            annotationsToRemove.add(annotation);
+          } else if (value.startsWith("~")) {
+            // If a value is set, and it starts with ~, we assume it is a regex pattern
+            String patternString = value.substring(1).replace("'", "");
+            Pattern pattern = Pattern.compile(patternString);
+            Matcher matcher = pattern.matcher(annotationValue);
+            if (matcher.find()) {
+              annotationsToRemove.add(annotation);
+            }
+          } else {
+            // If a value is set, and it does not start with ~, we assume its an exact value
+            String processed_value = value.replace("'", "");
+            if (annotationValue.equals(processed_value)) {
+              annotationsToRemove.add(annotation);
+            } else {
+              logger.warn(
+                  "Annotation assertion value pattern must start with ~' to indicate a regex pattern"
+                      + "or else correspond to the exact value. "
+                      + "The value is: "
+                      + value
+                      + ". Other patterns are not supported.");
+            }
+          }
+        }
+      }
       if (!annotationsToRemove.isEmpty()) {
-        Set<OWLAnnotation> axiomAnnotations = axiom.getAnnotations();
+        Set<OWLAnnotation> axiomAnnotations = new HashSet<>(allAxiomAnnotations);
         axiomAnnotations.removeAll(annotationsToRemove);
         OWLAxiom cleanedAxiom =
             axiom.getAxiomWithoutAnnotations().getAnnotatedAxiom(axiomAnnotations);
@@ -1689,6 +1753,19 @@ public static void removeAxiomAnnotations(OWLOntology ontology, OWLAnnotationPro
     }
   }
 
+  private static String getAnnotationValueAsStringOrNull(OWLAnnotation annotation) {
+    OWLAnnotationValue v = annotation.getValue();
+    if (v.isIRI()) {
+      return v.asIRI().get().toString();
+    } else if (v.isLiteral()) {
+      return v.asLiteral().get().getLiteral().toString();
+    } else if (v.isIndividual()) {
+      return v.asAnonymousIndividual().get().toString();
+    } else {
+      return null;
+    }
+  }
+
   /**
    * Removes all axiom annotations from the given ontology.
    *

diff --git a/robot-core/src/main/java/org/obolibrary/robot/RelatedObjectsHelper.java b/robot-core/src/main/java/org/obolibrary/robot/RelatedObjectsHelper.java
@@ -2409,7 +2409,7 @@ private static void spanGapsHelper(
    * @param dropParameters list of drop-axiom-annotations parameters
    */
   public static void dropAxiomAnnotations(
-      OWLOntology ontology, List<IRI> annotationsToDrop, List<String> dropParameters) {
+      OWLOntology ontology, Map<IRI, String> annotationsToDrop, List<String> dropParameters) {
     if (dropParameters.stream().anyMatch(x -> x.equalsIgnoreCase("all"))) {
       OntologyHelper.removeAllAxiomAnnotations(ontology);
     } else {