Merge pull request #579 from ontodev/562-feature

Add tautologies & structural-tautologies axiom selectors
ontodev · Nov 20, 2019 · 13531f6 · 13531f6
2 parents ab0d9e8 + cbd55b7
commit 13531f6
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diff --git a/docs/examples/mitochondrion-full.owl b/docs/examples/mitochondrion-full.owl
diff --git a/docs/examples/no-tautologies.owl b/docs/examples/no-tautologies.owl
@@ -0,0 +1,51 @@
+<?xml version="1.0"?>
+<rdf:RDF xmlns="http://www.semanticweb.org/tauber/ontologies/2019/9/untitled-ontology-995#"
+     xml:base="http://www.semanticweb.org/tauber/ontologies/2019/9/untitled-ontology-995"
+     xmlns:owl="http://www.w3.org/2002/07/owl#"
+     xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+     xmlns:xml="http://www.w3.org/XML/1998/namespace"
+     xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
+     xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#">
+    <owl:Ontology rdf:about="http://www.semanticweb.org/tauber/ontologies/2019/9/untitled-ontology-995"/>
+
+
+
+    <!-- 
+    ///////////////////////////////////////////////////////////////////////////////////////
+    //
+    // Classes
+    //
+    ///////////////////////////////////////////////////////////////////////////////////////
+     -->
+
+
+
+
+    <!-- http://robot.obolibrary.org/example/A -->
+
+    <owl:Class rdf:about="http://robot.obolibrary.org/example/A">
+        <rdfs:label>A</rdfs:label>
+    </owl:Class>
+
+
+
+    <!-- http://robot.obolibrary.org/example/B -->
+
+    <owl:Class rdf:about="http://robot.obolibrary.org/example/B">
+        <rdfs:subClassOf rdf:resource="http://robot.obolibrary.org/example/A"/>
+        <rdfs:label>B</rdfs:label>
+    </owl:Class>
+
+
+
+    <!-- http://robot.obolibrary.org/example/C -->
+
+    <owl:Class rdf:about="http://robot.obolibrary.org/example/C">
+        <rdfs:label>C</rdfs:label>
+    </owl:Class>
+</rdf:RDF>
+
+
+
+<!-- Generated by the OWL API (version 4.5.6) https://github.com/owlcs/owlapi -->
+
diff --git a/docs/examples/tautologies.owl b/docs/examples/tautologies.owl
@@ -0,0 +1,67 @@
+<?xml version="1.0"?>
+<rdf:RDF xmlns="http://www.semanticweb.org/tauber/ontologies/2019/9/untitled-ontology-995#"
+     xml:base="http://www.semanticweb.org/tauber/ontologies/2019/9/untitled-ontology-995"
+     xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+     xmlns:owl="http://www.w3.org/2002/07/owl#"
+     xmlns:xml="http://www.w3.org/XML/1998/namespace"
+     xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
+     xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#">
+    <owl:Ontology rdf:about="http://www.semanticweb.org/tauber/ontologies/2019/9/untitled-ontology-995"/>
+
+
+
+    <!-- 
+    ///////////////////////////////////////////////////////////////////////////////////////
+    //
+    // Classes
+    //
+    ///////////////////////////////////////////////////////////////////////////////////////
+     -->
+
+
+
+
+    <!-- http://robot.obolibrary.org/example/A -->
+
+    <owl:Class rdf:about="http://robot.obolibrary.org/example/A">
+        <rdfs:subClassOf rdf:resource="http://robot.obolibrary.org/example/A"/>
+        <rdfs:label>A</rdfs:label>
+    </owl:Class>
+
+
+
+    <!-- http://robot.obolibrary.org/example/B -->
+
+    <owl:Class rdf:about="http://robot.obolibrary.org/example/B">
+        <rdfs:subClassOf rdf:resource="http://robot.obolibrary.org/example/A"/>
+        <rdfs:label>B</rdfs:label>
+    </owl:Class>
+
+
+
+    <!-- http://robot.obolibrary.org/example/C -->
+
+    <owl:Class rdf:about="http://robot.obolibrary.org/example/C">
+        <rdfs:subClassOf rdf:resource="http://www.w3.org/2002/07/owl#Thing"/>
+        <rdfs:label>C</rdfs:label>
+    </owl:Class>
+
+
+
+    <!-- http://www.w3.org/2002/07/owl#Nothing -->
+
+    <owl:Class rdf:about="http://www.w3.org/2002/07/owl#Nothing">
+        <rdfs:subClassOf rdf:resource="http://robot.obolibrary.org/example/B"/>
+    </owl:Class>
+
+
+
+    <!-- http://www.w3.org/2002/07/owl#Thing -->
+
+    <owl:Class rdf:about="http://www.w3.org/2002/07/owl#Thing"/>
+</rdf:RDF>
+
+
+
+<!-- Generated by the OWL API (version 4.2.8.20170104-2310) https://github.com/owlcs/owlapi -->
+
diff --git a/docs/extract.md b/docs/extract.md
@@ -136,7 +136,7 @@ By default, `extract` will include imported ontologies. To exclude imported onto
       --input imports-nucleus.owl \
       --term GO:0005739 \
       --imports exclude \
-      --output mitochondrion.owl
+      --output results/mitochondrion.owl
 
 This only includes what is asserted in `imports-nucleus.owl`, which imports `nucleus.owl`. `imports-nucleus.owl` only includes the term 'mitochondrion' (`GO:0005739`) and links it to its parent class, 'intracellular membrane-bounded organelle' (`GO:0043231`). `nucleus.owl` contains the full hierarchy down to 'intracellular membrane-bounded organelle'. The output module, `mitochondrion.owl`, only includes the term 'mitochondrion' and this subClassOf statement.
 
@@ -146,7 +146,7 @@ By contrast, including imports returns the full hierarchy down to 'mitochondrion
       --input imports-nucleus.owl \
       --term GO:0005739 \
       --imports include \
-      --output mitochondrion-full.owl
+      --output results/mitochondrion-full.owl
 
 ## Extracting Ontology Annotations
 

diff --git a/docs/filter.md b/docs/filter.md
@@ -75,11 +75,11 @@ Copy a subset of classes based on an annotation property (maintains hierarchy):
       --signature true \
       --output results/uberon_slim.owl
 
-Copy a class, all axioms that a class appears in, annotations on all the classes (only `UBERON:0000062` here) in the filter set, and the ontology annotations:
+Copy a class, all axioms that a class appears in and annotations on all the classes (only `UBERON:0000062` here) in the filter set:
 
     robot filter --input uberon_module.owl \
       --term UBERON:0000062 \
-      --select "ontology annotations" \
+      --select annotations \
       --trim false \
       --signature true \
       --output results/uberon_annotated.owl

diff --git a/docs/remove.md b/docs/remove.md
@@ -125,22 +125,27 @@ For CURIEs, the pattern must always come after the prefix and colon.
 
 ## Axioms
 
-The `--axioms` option allows you to specify the type of OWLAxiom to remove. More than one type can be provided and the order is not significant. For each axiom in the ontology (not including its imports closure), if the axiom implements one of the specified axiom types AND *any* of the selected terms are in the axiom's signature, then the axiom is removed from the ontology.
+The `--axioms` option allows you to specify the type of OWLAxiom to remove. More than one type can be provided and these will be processed **in order**. For each axiom in the ontology (not including its imports closure), if the axiom implements one of the specified axiom types AND *any* of the selected terms are in the axiom's signature, then the axiom is removed from the ontology.
 
+Basic axiom selectors select the axiom(s) based on the OWLAPI AxiomType. We have included some special shortcuts to group related axiom types together.
 - `all` (default)
 - `logical`
 - `annotation`
 - `subclass`
 - `subproperty`
-- `equivalent` (classes and properties)
-- `disjoint` (classes and properties)
-- `type` (class assertions)
-- `tbox` (classes and class axioms)
-- `abox` (instances and instance-level axioms)
-- `rbox` (object properties, aka relations)
+- `equivalent`: classes and properties
+- `disjoint`: classes and properties
+- `type`: class assertions
+- `tbox`: classes and class axioms
+- `abox`: instances and instance-level axioms
+- `rbox`: object properties, i.e., relations
 - [OWLAPI AxiomType](http://owlcs.github.io/owlapi/apidocs_4/org/semanticweb/owlapi/model/AxiomType.html) name (e.g., `ObjectPropertyRange`)
-- `internal` (all entities that are in one of the `--base-iri` namespaces)
-- `external` (all entities that are not in one of the `--base-iri` namespaces)
+
+There are also some special axiom selectors that use additional processing to find certain axioms:
+- `internal`: all entities that are in one of the `--base-iri` namespaces
+- `external`: all entities that are not in one of the `--base-iri` namespaces
+- `tautologies`: all axioms that are *always* true; these would be entailed in an empty ontology. WARNING: this may remove more axioms than desired.
+- `structural-tautologies`: all axioms that match a set of tautological patterns (e.g., `X SubClassOf owl:Thing`, `owl:Nothing SubClassOf X`, `X SubClassOf X`)
 
 The `--base-iri <namespace>` is a special option for use with `internal` and `external` axioms. It allows you to specify one or more "base namespaces" (e.g., `--base-iri http://purl.obolibrary.org/obo/OBI_`). You can also use any defined prefix (e.g., `--base-iri OBI`) An axiom is considered internal if the subject is in one of the base namespaces.
 
@@ -181,6 +186,12 @@ robot remove --input obi.owl \
   --select "owl:deprecated='true'^^xsd:boolean"
 ```
 
+Remove structural tautologies (e.g., `owl:Nothing`):
+
+    robot remove --input tautologies.owl \
+      --axioms structural-tautologies \
+      --output results/no-tautologies.owl
+
 Create a "base" subset by removing external axioms (alternatively, use `filter --axioms internal`):
 
     robot remove --input template.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
@@ -10,7 +10,6 @@
 import java.util.jar.JarFile;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
-import java.util.stream.Collectors;
 import java.util.zip.ZipEntry;
 import org.apache.commons.cli.CommandLine;
 import org.apache.commons.cli.CommandLineParser;
@@ -38,9 +37,6 @@ public class CommandLineHelper {
   /** Namespace for general input error messages. */
   private static final String NS = "errors#";
 
-  /** Error message when --axioms is not a valid AxiomType. Expects: input string. */
-  private static final String axiomTypeError = NS + "AXIOM TYPE ERROR %s is not a valid axiom type";
-
   /** Error message when a boolean value is not "true" or "false". Expects option name. */
   private static final String booleanValueError =
       NS + "BOOLEAN VALUE ERROR arg for %s must be true or false";
@@ -224,6 +220,33 @@ public static boolean hasFlagOrCommand(CommandLine line, String name) {
     return command != null && command.equals(name);
   }
 
+  /**
+   * Given a command line, get the 'axioms' option(s) and make sure all are properly split and
+   * return one axiom selector per list entry.
+   *
+   * @param line the command line to use
+   * @return cleaned list of input axiom type strings
+   */
+  public static List<String> cleanAxiomStrings(CommandLine line) {
+    List<String> axiomTypeStrings = getOptionalValues(line, "axioms");
+
+    if (axiomTypeStrings.isEmpty()) {
+      axiomTypeStrings.add("all");
+    }
+
+    // Split if it's one arg with spaces
+    List<String> axiomTypeFixedStrings = new ArrayList<>();
+    for (String axiom : axiomTypeStrings) {
+      if (axiom.contains(" ")) {
+        axiomTypeFixedStrings.addAll(Arrays.asList(axiom.split(" ")));
+      } else {
+        axiomTypeFixedStrings.add(axiom);
+      }
+    }
+
+    return axiomTypeFixedStrings;
+  }
+
   /**
    * Given a command line and an IOHelper, return a list of base namespaces from the '--base-iri'
    * option.
@@ -281,78 +304,20 @@ public static boolean getBooleanValue(
   /**
    * Given a command line, return the value of --axioms as a set of classes that extend OWLAxiom.
    *
+   * @deprecated split into methods {@link #cleanAxiomStrings(CommandLine)} and others in {@link
+   *     org.obolibrary.robot.RelatedObjectsHelper}
    * @param line the command line to use
    * @return set of OWLAxiom types
    */
+  @Deprecated
   public static Set<Class<? extends OWLAxiom>> getAxiomValues(CommandLine line) {
     Set<Class<? extends OWLAxiom>> axiomTypes = new HashSet<>();
-    List<String> axiomTypeStrings = getOptionValues(line, "axioms");
-    if (axiomTypeStrings.isEmpty()) {
-      axiomTypeStrings.add("all");
-    }
-    // Split if it's one arg with spaces
-    List<String> axiomTypeFixedStrings = new ArrayList<>();
-    for (String axiom : axiomTypeStrings) {
-      if (axiom.contains(" ")) {
-        axiomTypeFixedStrings.addAll(Arrays.asList(axiom.split(" ")));
-      } else {
-        axiomTypeFixedStrings.add(axiom);
-      }
-    }
+    List<String> axiomTypeStrings = cleanAxiomStrings(line);
     // Then get the actual types
-    for (String axiom : axiomTypeFixedStrings) {
-      if (axiom.equalsIgnoreCase("internal") || axiom.equalsIgnoreCase("external")) {
-        // Ignore internal/external axiom options
-        continue;
-      }
-      if (axiom.equalsIgnoreCase("all")) {
-        axiomTypes.add(OWLAxiom.class);
-      } else if (axiom.equalsIgnoreCase("logical")) {
-        axiomTypes.add(OWLLogicalAxiom.class);
-      } else if (axiom.equalsIgnoreCase("annotation")) {
-        axiomTypes.add(OWLAnnotationAxiom.class);
-      } else if (axiom.equalsIgnoreCase("subclass")) {
-        axiomTypes.add(OWLSubClassOfAxiom.class);
-      } else if (axiom.equalsIgnoreCase("subproperty")) {
-        axiomTypes.add(OWLSubObjectPropertyOfAxiom.class);
-        axiomTypes.add(OWLSubDataPropertyOfAxiom.class);
-        axiomTypes.add(OWLSubAnnotationPropertyOfAxiom.class);
-      } else if (axiom.equalsIgnoreCase("equivalent")) {
-        axiomTypes.add(OWLEquivalentClassesAxiom.class);
-        axiomTypes.add(OWLEquivalentObjectPropertiesAxiom.class);
-        axiomTypes.add(OWLEquivalentDataPropertiesAxiom.class);
-      } else if (axiom.equalsIgnoreCase("disjoint")) {
-        axiomTypes.add(OWLDisjointClassesAxiom.class);
-        axiomTypes.add(OWLDisjointObjectPropertiesAxiom.class);
-        axiomTypes.add(OWLDisjointDataPropertiesAxiom.class);
-        axiomTypes.add(OWLDisjointUnionAxiom.class);
-      } else if (axiom.equalsIgnoreCase("type")) {
-        axiomTypes.add(OWLClassAssertionAxiom.class);
-      } else if (axiom.equalsIgnoreCase("abox")) {
-        axiomTypes.addAll(
-            AxiomType.ABoxAxiomTypes.stream()
-                .map(AxiomType::getActualClass)
-                .collect(Collectors.toSet()));
-      } else if (axiom.equalsIgnoreCase("tbox")) {
-        axiomTypes.addAll(
-            AxiomType.TBoxAxiomTypes.stream()
-                .map(AxiomType::getActualClass)
-                .collect(Collectors.toSet()));
-      } else if (axiom.equalsIgnoreCase("rbox")) {
-        axiomTypes.addAll(
-            AxiomType.RBoxAxiomTypes.stream()
-                .map(AxiomType::getActualClass)
-                .collect(Collectors.toSet()));
-      } else if (axiom.equalsIgnoreCase("declaration")) {
-        axiomTypes.add(OWLDeclarationAxiom.class);
-      } else {
-        AxiomType<?> at = AxiomType.getAxiomType(axiom);
-        if (at != null) {
-          // Attempt to get the axiom type based on AxiomType names
-          axiomTypes.add(at.getActualClass());
-        } else {
-          throw new IllegalArgumentException(String.format(axiomTypeError, axiom));
-        }
+    for (String axiom : axiomTypeStrings) {
+      Set<Class<? extends OWLAxiom>> addTypes = RelatedObjectsHelper.getAxiomValues(axiom);
+      if (addTypes != null) {
+        axiomTypes.addAll(addTypes);
       }
     }
     return axiomTypes;