Merge branch 'master' into robot-header

ontodev · Nov 29, 2023 · e29282c · e29282c
2 parents a5f7581 + 4630074
commit e29282c
Show file tree

Hide file tree

Showing 10 changed files with 219 additions and 108 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -10,6 +10,10 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Added
 -- Added option to input template strings from external file [##1152]
 
+### Fixed
+- '--annotate-with-source true' does not work with extract --method subset [#1160]
+- Fix how Template adds entities to the QuotedEntityChecker [#1104]
+
 ## [1.9.5] - 2023-09-20
 
 ### Added
@@ -379,9 +383,11 @@ First official release of ROBOT!
 [`template`]: http://robot.obolibrary.org/template
 [`validate`]: http://robot.obolibrary.org/validate
 
+[#1160]: https://github.com/ontodev/robot/pull/1160
 [#1148]: https://github.com/ontodev/robot/pull/1148
 [#1135]: https://github.com/ontodev/robot/pull/1135
 [#1119]: https://github.com/ontodev/robot/pull/1119
+[#1104]: https://github.com/ontodev/robot/pull/1104
 [#1100]: https://github.com/ontodev/robot/pull/1100
 [#1091]: https://github.com/ontodev/robot/issues/1091
 [#1089]: https://github.com/ontodev/robot/issues/1089

diff --git a/docs/extract.md b/docs/extract.md
@@ -79,12 +79,14 @@ For more details see the [MIREOT paper](http://dx.doi.org/10.3233/AO-2011-0087).
 
 The subset method extracts a sub-ontology that contains only the seed terms (that you specify with `--term` and `--term-file` options) and the relations between them. This method uses the [relation-graph](https://github.com/balhoff/relation-graph) to materialize the existential relations among the seed terms. Procedurally, the subset method materializes the input ontology and adds the inferred axioms to the input ontology. Then filters the ontology with the given seed terms. Finally, it reduces the filtered ontology to remove redundant subClassOf axioms.
 
-    robot extract --method subset \
-        --input subset.obo \
-        --term "obo:ONT_1" \
-        --term "obo:ONT_5" \
-        --term "BFO:0000050" \
-        --output results/subset_result.owl
+```
+robot extract --method subset \
+    --input subset.obo \
+    --term "obo:ONT_1" \
+    --term "obo:ONT_5" \
+    --term "BFO:0000050" \
+    --output results/subset_result.owl
+```
         
 ROBOT expects any `--term` or IRI in the `--term-file` to exist in the input ontology. If none of the input terms exist, the command will fail with an [empty terms error](errors#empty-terms-error). This can be overridden by including `--force true`. 
 

diff --git a/docs/rename.md b/docs/rename.md
@@ -54,8 +54,8 @@ The mappings for renaming should be specified with the `--mappings` (for full re
 For a full rename (you can use prefixes as long as they are defined by the defaults, `--prefix`, or `--add-prefix`):
 
 ```tsv
-Old IRI New IRI
-obo:BFO_0000051 fb:BFO_1234567
+Old IRI	New IRI
+obo:BFO_0000051	fb:BFO_1234567
 ```
 
 If you also want to update the `rdfs:label` of the term you replaced, you can add a third column with the new label value (note that this removes *all* old label annotations):
@@ -68,8 +68,8 @@ obo:BFO_0000051	fb:BFO_1234567	foo bar
 For a prefix rename:
 
 ```tsv
-Old Base  New Base
-http://purl.obolibrary.org/obo/ http://foo.bar/
+Old Base	New Base
+http://purl.obolibrary.org/obo/	http://foo.bar/
 ```
 
 The `rename` command expects the first line to contain headers.

diff --git a/robot-core/src/main/java/org/obolibrary/robot/ExtractOperation.java b/robot-core/src/main/java/org/obolibrary/robot/ExtractOperation.java
@@ -189,20 +189,7 @@ public static OWLOntology extract(
     }
     // Maybe annotate entities with rdfs:isDefinedBy
     if (OptionsHelper.optionIsTrue(options, "annotate-with-source")) {
-      Set<OWLAnnotationAxiom> sourceAxioms = new HashSet<>();
-      for (OWLEntity entity : OntologyHelper.getEntities(outputOntology)) {
-        // Check if rdfs:isDefinedBy already exists
-        Set<OWLAnnotationValue> existingValues =
-            OntologyHelper.getAnnotationValues(outputOntology, isDefinedBy, entity.getIRI());
-        if (existingValues == null || existingValues.size() == 0) {
-          // If not, add it
-          OWLAnnotationAxiom def = getIsDefinedBy(entity, sourceMap);
-          if (def != null) {
-            sourceAxioms.add(def);
-          }
-        }
-      }
-      manager.addAxioms(outputOntology, sourceAxioms);
+      annotateWithSource(sourceMap, outputOntology, manager);
     }
 
     // Determine what to do based on intermediates
@@ -219,6 +206,31 @@ public static OWLOntology extract(
     }
   }
 
+  /**
+   * Annotates entities of the outputOntology with rdfs:isDefinedBy.
+   *
+   * @param sourceMap map of term IRI to source IRI, or null.
+   * @param outputOntology output ontology.
+   * @param manager OWL ontology manager.
+   */
+  private static void annotateWithSource(
+      Map<IRI, IRI> sourceMap, OWLOntology outputOntology, OWLOntologyManager manager) {
+    Set<OWLAnnotationAxiom> sourceAxioms = new HashSet<>();
+    for (OWLEntity entity : OntologyHelper.getEntities(outputOntology)) {
+      // Check if rdfs:isDefinedBy already exists
+      Set<OWLAnnotationValue> existingValues =
+          OntologyHelper.getAnnotationValues(outputOntology, isDefinedBy, entity.getIRI());
+      if (existingValues == null || existingValues.size() == 0) {
+        // If not, add it
+        OWLAnnotationAxiom def = getIsDefinedBy(entity, sourceMap);
+        if (def != null) {
+          sourceAxioms.add(def);
+        }
+      }
+    }
+    manager.addAxioms(outputOntology, sourceAxioms);
+  }
+
   /**
    * Extracts a materialized sub-ontology from the given ontology that only contains the given terms
    * and the relations between them. The input ontology is not changed.
@@ -249,6 +261,11 @@ public static OWLOntology extractSubset(
     copyPropertyAnnotations(inputOntology, filteredOnt);
     ReduceOperation.reduce(filteredOnt, new org.semanticweb.elk.owlapi.ElkReasonerFactory());
 
+    // Maybe annotate entities with rdfs:isDefinedBy
+    if (OptionsHelper.optionIsTrue(options, "annotate-with-source")) {
+      annotateWithSource(sourceMap, filteredOnt, OWLManager.createOWLOntologyManager());
+    }
+
     return filteredOnt;
   }
 

diff --git a/robot-core/src/main/java/org/obolibrary/robot/QuotedEntityChecker.java b/robot-core/src/main/java/org/obolibrary/robot/QuotedEntityChecker.java
@@ -249,6 +249,9 @@ public void add(OWLEntity entity, String name) {
     if (entity == null) {
       return;
     }
+    if (name == null) {
+      return;
+    }
 
     Map<String, IRI> map = pickMap(entity);
     if (map == null) {

diff --git a/robot-core/src/main/java/org/obolibrary/robot/Template.java b/robot-core/src/main/java/org/obolibrary/robot/Template.java
@@ -173,7 +173,7 @@ public Template(@Nonnull String name, @Nonnull List<List<String>> rows) throws E
 
     // Add the contents of the tableRows
     addTable(rows);
-    addLabels();
+    addEntities();
     createParser();
   }
 
@@ -203,7 +203,7 @@ public Template(@Nonnull String name, @Nonnull List<List<String>> rows, IOHelper
 
     // Add the contents of the tableRows
     addTable(rows);
-    addLabels();
+    addEntities();
     createParser();
   }
 
@@ -237,7 +237,7 @@ public Template(@Nonnull String name, @Nonnull List<List<String>> rows, OWLOntol
 
     // Add the contents of the tableRows
     addTable(rows);
-    addLabels();
+    addEntities();
     createParser();
   }
 
@@ -276,7 +276,7 @@ public Template(
 
     // Add the contents of the tableRows
     addTable(rows);
-    addLabels();
+    addEntities();
     createParser();
   }
 
@@ -320,7 +320,7 @@ public Template(
 
     // Add the contents of the tableRows
     addTable(rows);
-    addLabels();
+    addEntities();
     createParser();
     parser.setOWLEntityChecker(this.checker);
   }
@@ -564,102 +564,103 @@ private void addTable(List<List<String>> rows) throws Exception {
     }
   }
 
-  /** Add the labels from the rows of the template to the QuotedEntityChecker. */
-  private void addLabels() {
-    // If there's no label column, we can't add labels
-    if (labelColumn == -1) {
+  /** Add the entities from the rows of the template to the QuotedEntityChecker. */
+  private void addEntities() {
+    for (List<String> row : tableRows) {
+      addEntity(row);
+    }
+  }
+
+  /** Add the entity from this row of the template to the QuotedEntityChecker. */
+  private void addEntity(List<String> row) {
+    String id = null;
+    try {
+      id = row.get(idColumn);
+    } catch (IndexOutOfBoundsException e) {
+      // ignore
+    }
+
+    if (id == null) {
       return;
     }
-    for (List<String> row : tableRows) {
-      String id = null;
-      if (idColumn != -1) {
-        try {
-          id = row.get(idColumn);
-        } catch (IndexOutOfBoundsException e) {
-          // ignore
-        }
-      }
 
-      String label = null;
+    String label = null;
+    try {
+      label = row.get(labelColumn);
+    } catch (IndexOutOfBoundsException e) {
+      // ignore
+    }
+
+    String type = null;
+    if (typeColumn != -1) {
       try {
-        label = row.get(labelColumn);
+        type = row.get(typeColumn);
       } catch (IndexOutOfBoundsException e) {
         // ignore
       }
+    }
+    if (type == null || type.trim().isEmpty()) {
+      type = "class";
+    }
 
-      if (idColumn != -1 && id == null) {
-        continue;
-      }
-
-      if (id == null || label == null) {
-        continue;
-      }
-
-      String type = null;
-      if (typeColumn != -1) {
-        try {
-          type = row.get(typeColumn);
-        } catch (IndexOutOfBoundsException e) {
-          // ignore
-        }
-      }
-      if (type == null || type.trim().isEmpty()) {
-        type = "class";
-      }
+    IRI iri = ioHelper.createIRI(id);
+    if (iri == null) {
+      iri = IRI.create(id);
+    }
 
-      IRI iri = ioHelper.createIRI(id);
-      if (iri == null) {
-        iri = IRI.create(id);
-      }
+    // Try to resolve a CURIE
+    IRI typeIRI = ioHelper.createIRI(type);
 
-      // Try to resolve a CURIE
-      IRI typeIRI = ioHelper.createIRI(type);
+    // Set to IRI string or to type string
+    String typeOrIRI = type;
+    if (typeIRI != null) {
+      typeOrIRI = typeIRI.toString();
+    }
 
-      // Set to IRI string or to type string
-      String typeOrIRI = type;
-      if (typeIRI != null) {
-        typeOrIRI = typeIRI.toString();
-      }
+    // Check against builtin types (ignore case), otherwise treat as individual
+    OWLEntity entity;
+    String lowerCaseType = typeOrIRI.toLowerCase();
+    switch (lowerCaseType) {
+      case "":
+      case "http://www.w3.org/2002/07/owl#class":
+      case "class":
+        entity = dataFactory.getOWLEntity(EntityType.CLASS, iri);
+        break;
 
-      // Check against builtin types (ignore case), otherwise treat as individual
-      OWLEntity entity;
-      String lowerCaseType = typeOrIRI.toLowerCase();
-      switch (lowerCaseType) {
-        case "":
-        case "http://www.w3.org/2002/07/owl#class":
-        case "class":
-          entity = dataFactory.getOWLEntity(EntityType.CLASS, iri);
-          break;
+      case "http://www.w3.org/2002/07/owl#objectproperty":
+      case "object property":
+        entity = dataFactory.getOWLEntity(EntityType.OBJECT_PROPERTY, iri);
+        break;
 
-        case "http://www.w3.org/2002/07/owl#objectproperty":
-        case "object property":
-          entity = dataFactory.getOWLEntity(EntityType.OBJECT_PROPERTY, iri);
-          break;
+      case "http://www.w3.org/2002/07/owl#dataproperty":
+      case "data property":
+        entity = dataFactory.getOWLEntity(EntityType.DATA_PROPERTY, iri);
+        break;
 
-        case "http://www.w3.org/2002/07/owl#dataproperty":
-        case "data property":
-          entity = dataFactory.getOWLEntity(EntityType.DATA_PROPERTY, iri);
-          break;
+      case "http://www.w3.org/2002/07/owl#annotationproperty":
+      case "annotation property":
+        entity = dataFactory.getOWLEntity(EntityType.ANNOTATION_PROPERTY, iri);
+        break;
 
-        case "http://www.w3.org/2002/07/owl#annotationproperty":
-        case "annotation property":
-          entity = dataFactory.getOWLEntity(EntityType.ANNOTATION_PROPERTY, iri);
-          break;
+      case "http://www.w3.org/2002/07/owl#datatype":
+      case "datatype":
+        entity = dataFactory.getOWLEntity(EntityType.DATATYPE, iri);
+        break;
 
-        case "http://www.w3.org/2002/07/owl#datatype":
-        case "datatype":
-          entity = dataFactory.getOWLEntity(EntityType.DATATYPE, iri);
-          break;
+      case "http://www.w3.org/2002/07/owl#individual":
+      case "individual":
+      case "http://www.w3.org/2002/07/owl#namedindividual":
+      case "named individual":
+      default:
+        // Assume type is an individual (checked later)
+        entity = dataFactory.getOWLEntity(EntityType.NAMED_INDIVIDUAL, iri);
+        break;
+    }
 
-        case "http://www.w3.org/2002/07/owl#individual":
-        case "individual":
-        case "http://www.w3.org/2002/07/owl#namedindividual":
-        case "named individual":
-        default:
-          // Assume type is an individual (checked later)
-          entity = dataFactory.getOWLEntity(EntityType.NAMED_INDIVIDUAL, iri);
-          break;
-      }
+    if (id != null) {
+      checker.add(entity, id);
+    }
+    if (label != null) {
       checker.add(entity, label);
     }
   }
@@ -802,6 +803,8 @@ private void processRow(List<String> row) throws Exception {
       case "http://www.w3.org/2002/07/owl#namedindividual":
       case "named individual":
       default:
+        // This is a bit unsafe imo, for example in the case of where the datatype turns out to be
+        // http://www.w3.org/2002/07/owl#DatatypeProperty""
         addIndividualAxioms(iri, row);
         break;
     }