[#191] added all nodes labeler configuration

SciGraph · Feb 13, 2017 · 02822fc · 02822fc
1 parent 96e098b
commit 02822fc
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Showing 5 changed files with 98 additions and 38 deletions.
diff --git a/SciGraph-core/src/main/java/io/scigraph/owlapi/loader/BatchOwlLoader.java b/SciGraph-core/src/main/java/io/scigraph/owlapi/loader/BatchOwlLoader.java
@@ -17,20 +17,6 @@
 
 import static com.google.common.collect.Iterables.size;
 import static java.lang.String.format;
-import io.scigraph.neo4j.Graph;
-import io.scigraph.neo4j.Neo4jModule;
-import io.scigraph.owlapi.OwlApiUtils;
-import io.scigraph.owlapi.OwlPostprocessor;
-import io.scigraph.owlapi.loader.OwlLoadConfiguration.MappedProperty;
-import io.scigraph.owlapi.loader.OwlLoadConfiguration.OntologySetup;
-import io.scigraph.owlapi.loader.bindings.IndicatesAddEdgeLabel;
-import io.scigraph.owlapi.loader.bindings.IndicatesCliqueConfiguration;
-import io.scigraph.owlapi.loader.bindings.IndicatesMappedProperties;
-import io.scigraph.owlapi.loader.bindings.IndicatesNumberOfConsumerThreads;
-import io.scigraph.owlapi.loader.bindings.IndicatesNumberOfProducerThreads;
-import io.scigraph.owlapi.postprocessors.Clique;
-import io.scigraph.owlapi.postprocessors.CliqueConfiguration;
-import io.scigraph.owlapi.postprocessors.EdgeLabeler;
 
 import java.io.File;
 import java.util.HashSet;
@@ -65,6 +51,23 @@
 import com.google.inject.Guice;
 import com.google.inject.Injector;
 
+import io.scigraph.neo4j.Graph;
+import io.scigraph.neo4j.Neo4jModule;
+import io.scigraph.owlapi.OwlApiUtils;
+import io.scigraph.owlapi.OwlPostprocessor;
+import io.scigraph.owlapi.loader.OwlLoadConfiguration.MappedProperty;
+import io.scigraph.owlapi.loader.OwlLoadConfiguration.OntologySetup;
+import io.scigraph.owlapi.loader.bindings.IndicatesAddEdgeLabel;
+import io.scigraph.owlapi.loader.bindings.IndicatesAllNodesLabel;
+import io.scigraph.owlapi.loader.bindings.IndicatesCliqueConfiguration;
+import io.scigraph.owlapi.loader.bindings.IndicatesMappedProperties;
+import io.scigraph.owlapi.loader.bindings.IndicatesNumberOfConsumerThreads;
+import io.scigraph.owlapi.loader.bindings.IndicatesNumberOfProducerThreads;
+import io.scigraph.owlapi.postprocessors.AllNodesLabeler;
+import io.scigraph.owlapi.postprocessors.Clique;
+import io.scigraph.owlapi.postprocessors.CliqueConfiguration;
+import io.scigraph.owlapi.postprocessors.EdgeLabeler;
+
 public class BatchOwlLoader {
 
   private static final Logger logger = Logger.getLogger(BatchOwlLoader.class.getName());
@@ -114,6 +117,10 @@ public class BatchOwlLoader {
   @Inject
   @IndicatesAddEdgeLabel
   Optional<Boolean> addEdgeLabel;
+
+  @Inject
+  @IndicatesAllNodesLabel
+  Optional<String> allNodesLabel;
 
   static {
     System.setProperty("entityExpansionLimit", Integer.toString(1_000_000));
@@ -164,7 +171,11 @@ public void loadOntology() throws InterruptedException, ExecutionException {
     if (addEdgeLabel.or(false)) {
       postprocessorProvider.runEdgeLabelerPostprocessor();
     }
-
+
+    if(allNodesLabel.isPresent()) {
+      postprocessorProvider.runAllNodesLabeler(allNodesLabel.get());
+    }
+
     postprocessorProvider.shutdown();
 
   }
@@ -195,6 +206,11 @@ public void runEdgeLabelerPostprocessor() {
       edgeLabeler.run();
     }
 
+    public void runAllNodesLabeler(String label) {
+      AllNodesLabeler allNodesLabeler = new AllNodesLabeler(label, graphDb);
+      allNodesLabeler.run();
+    }
+
     public void shutdown() {
       try (Transaction tx = graphDb.beginTx()) {
         logger.info(size(graphDb.getAllNodes()) + " nodes");
@@ -206,11 +222,10 @@ public void shutdown() {
 
   }
 
-  public static void load(OwlLoadConfiguration config) throws InterruptedException,
-      ExecutionException {
-    Injector i =
-        Guice.createInjector(new OwlLoaderModule(config),
-            new Neo4jModule(config.getGraphConfiguration()));
+  public static void load(OwlLoadConfiguration config)
+      throws InterruptedException, ExecutionException {
+    Injector i = Guice.createInjector(new OwlLoaderModule(config),
+        new Neo4jModule(config.getGraphConfiguration()));
     BatchOwlLoader loader = i.getInstance(BatchOwlLoader.class);
     logger.info("Loading ontologies...");
     Stopwatch timer = Stopwatch.createStarted();

diff --git a/SciGraph-core/src/main/java/io/scigraph/owlapi/loader/OwlLoadConfiguration.java b/SciGraph-core/src/main/java/io/scigraph/owlapi/loader/OwlLoadConfiguration.java
@@ -34,6 +34,15 @@ public class OwlLoadConfiguration {
   private List<MappedProperty> mappedProperties = new ArrayList<>();
   private Optional<CliqueConfiguration> cliqueConfiguration = Optional.absent();
   private Optional<Boolean> addEdgeLabel = Optional.absent();
+  private Optional<String> allNodesLabel = Optional.absent();
+
+  public Optional<String> getAllNodesLabel() {
+    return allNodesLabel;
+  }
+
+  public void setAllNodesLabel(String allNodesLabel) {
+    this.allNodesLabel = Optional.of(allNodesLabel);
+  }
 
   public Optional<Boolean> getAddEdgeLabel() {
     return addEdgeLabel;

diff --git a/SciGraph-core/src/main/java/io/scigraph/owlapi/loader/OwlLoaderModule.java b/SciGraph-core/src/main/java/io/scigraph/owlapi/loader/OwlLoaderModule.java
@@ -15,23 +15,6 @@
  */
 package io.scigraph.owlapi.loader;
 
-import io.scigraph.frames.CommonProperties;
-import io.scigraph.neo4j.Graph;
-import io.scigraph.neo4j.GraphBatchImpl;
-import io.scigraph.owlapi.loader.OwlLoadConfiguration.MappedProperty;
-import io.scigraph.owlapi.loader.OwlLoadConfiguration.OntologySetup;
-import io.scigraph.owlapi.loader.bindings.IndicatesAddEdgeLabel;
-import io.scigraph.owlapi.loader.bindings.IndicatesCliqueConfiguration;
-import io.scigraph.owlapi.loader.bindings.IndicatesExactIndexedProperties;
-import io.scigraph.owlapi.loader.bindings.IndicatesIndexedProperties;
-import io.scigraph.owlapi.loader.bindings.IndicatesMappedCategories;
-import io.scigraph.owlapi.loader.bindings.IndicatesMappedProperties;
-import io.scigraph.owlapi.loader.bindings.IndicatesNumberOfConsumerThreads;
-import io.scigraph.owlapi.loader.bindings.IndicatesNumberOfProducerThreads;
-import io.scigraph.owlapi.loader.bindings.IndicatesNumberOfShutdownProducers;
-import io.scigraph.owlapi.loader.bindings.IndicatesUniqueProperty;
-import io.scigraph.owlapi.postprocessors.CliqueConfiguration;
-
 import java.io.File;
 import java.io.IOException;
 import java.util.List;
@@ -55,6 +38,24 @@
 import com.google.inject.Scopes;
 import com.google.inject.TypeLiteral;
 
+import io.scigraph.frames.CommonProperties;
+import io.scigraph.neo4j.Graph;
+import io.scigraph.neo4j.GraphBatchImpl;
+import io.scigraph.owlapi.loader.OwlLoadConfiguration.MappedProperty;
+import io.scigraph.owlapi.loader.OwlLoadConfiguration.OntologySetup;
+import io.scigraph.owlapi.loader.bindings.IndicatesAddEdgeLabel;
+import io.scigraph.owlapi.loader.bindings.IndicatesAllNodesLabel;
+import io.scigraph.owlapi.loader.bindings.IndicatesCliqueConfiguration;
+import io.scigraph.owlapi.loader.bindings.IndicatesExactIndexedProperties;
+import io.scigraph.owlapi.loader.bindings.IndicatesIndexedProperties;
+import io.scigraph.owlapi.loader.bindings.IndicatesMappedCategories;
+import io.scigraph.owlapi.loader.bindings.IndicatesMappedProperties;
+import io.scigraph.owlapi.loader.bindings.IndicatesNumberOfConsumerThreads;
+import io.scigraph.owlapi.loader.bindings.IndicatesNumberOfProducerThreads;
+import io.scigraph.owlapi.loader.bindings.IndicatesNumberOfShutdownProducers;
+import io.scigraph.owlapi.loader.bindings.IndicatesUniqueProperty;
+import io.scigraph.owlapi.postprocessors.CliqueConfiguration;
+
 public class OwlLoaderModule extends AbstractModule {
 
   private static final Logger logger = Logger.getLogger(OwlLoaderModule.class.getName());
@@ -97,6 +98,8 @@ protected void configure() {
         IndicatesCliqueConfiguration.class).toInstance(config.getCliqueConfiguration());
     bind(new TypeLiteral<Optional<Boolean>>() {}).annotatedWith(IndicatesAddEdgeLabel.class)
         .toInstance(config.getAddEdgeLabel());
+    bind(new TypeLiteral<Optional<String>>() {}).annotatedWith(IndicatesAllNodesLabel.class)
+    .toInstance(config.getAllNodesLabel());
   }
 
   /*

diff --git a/SciGraph-core/src/main/java/io/scigraph/owlapi/loader/bindings/IndicatesAllNodesLabel.java b/SciGraph-core/src/main/java/io/scigraph/owlapi/loader/bindings/IndicatesAllNodesLabel.java
@@ -0,0 +1,29 @@
+/**
+ * Copyright (C) 2014 The SciGraph authors
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *         http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package io.scigraph.owlapi.loader.bindings;
+
+import static java.lang.annotation.ElementType.FIELD;
+import static java.lang.annotation.ElementType.METHOD;
+import static java.lang.annotation.ElementType.PARAMETER;
+import static java.lang.annotation.RetentionPolicy.RUNTIME;
+
+import java.lang.annotation.Retention;
+import java.lang.annotation.Target;
+
+import com.google.inject.BindingAnnotation;
+
+@BindingAnnotation @Target({ FIELD, PARAMETER, METHOD }) @Retention(RUNTIME)
+public @interface IndicatesAllNodesLabel {}
diff --git a/SciGraph-core/src/test/resources/pizzaExample.yaml b/SciGraph-core/src/test/resources/pizzaExample.yaml
@@ -11,7 +11,7 @@ graphConfiguration:
       - label
       - synonym
     schemaIndexes:
-      pizza :
+      food :
         - label
     curies:
       'pizza' : 'http://www.co-ode.org/ontologies/pizza/pizza.owl#'
@@ -56,3 +56,7 @@ mappedProperties:
   - name: comment
     properties:
     - rdfs:comment
+
+# To label all the nodes with a specific label.
+# Useful for schema indexes.
+allNodesLabel: food