Merge f4f792f into 8a4d713

SciGraph · Sep 20, 2018 · 635cd26 · 635cd26
2 parents 8a4d713 + f4f792f
commit 635cd26
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Showing 10 changed files with 20 additions and 11 deletions.
diff --git a/.gitignore b/.gitignore
@@ -58,6 +58,10 @@ local.properties
 .project
 .classpath
 
+### IntelliJ ###
+.idea/
+*.iml
+
 # External tool builders
 .externalToolBuilders/
 

diff --git a/SciGraph-core/src/main/java/io/scigraph/neo4j/Neo4jModule.java b/SciGraph-core/src/main/java/io/scigraph/neo4j/Neo4jModule.java
@@ -99,7 +99,7 @@ private static void setupIndex(AutoIndexer<?> index, Collection<String> properti
   public static void setupAutoIndexing(GraphDatabaseService graphDb, Neo4jConfiguration config) {
     try (Transaction tx = graphDb.beginTx()) {
       graphDb.index().forNodes("node_auto_index", INDEX_CONFIG);
-      Set<String> indexProperties = newHashSet(CommonProperties.IRI);
+      Set<String> indexProperties = newHashSet();
       indexProperties.addAll(config.getIndexedNodeProperties());
       indexProperties
           .addAll(transform(config.getExactNodeProperties(), new Function<String, String>() {
@@ -163,7 +163,7 @@ public void run() {
         }
       });
 
-      if (!readOnly) { // No need of auto-indexing in read-only mode
+      if (!readOnly && configuration.getIndexedNodeProperties().size() > 0) { // No need of auto-indexing in read-only mode
         setupAutoIndexing(graphDb, configuration);
       }
 

diff --git a/SciGraph-core/src/test/java/io/scigraph/internal/GraphApiTest.java b/SciGraph-core/src/test/java/io/scigraph/internal/GraphApiTest.java
@@ -85,9 +85,9 @@ public void allPropertyKeys_areReturned() {
   public void allRelationshipTypes_areReturned() {
     // TODO: RelationshipTypeTokens don't equal RelationshipTypes
     assertThat(getFirst(graphApi.getAllRelationshipTypes(), null).name(),
-        is(OwlRelationships.RDFS_SUBCLASS_OF.name()));
-    assertThat(getLast(graphApi.getAllRelationshipTypes()).name(),
         is(OwlRelationships.OWL_EQUIVALENT_CLASS.name()));
+    assertThat(getLast(graphApi.getAllRelationshipTypes()).name(),
+        is(OwlRelationships.RDFS_SUBCLASS_OF.name()));
   }
 
   @Test

diff --git a/SciGraph-core/src/test/java/io/scigraph/owlapi/GraphOwlVisitorTransactionalGraphTest.java b/SciGraph-core/src/test/java/io/scigraph/owlapi/GraphOwlVisitorTransactionalGraphTest.java
@@ -18,6 +18,7 @@
 import static com.google.common.collect.Sets.newHashSet;
 import io.scigraph.frames.Concept;
 import io.scigraph.frames.NodeProperties;
+import io.scigraph.frames.CommonProperties;
 import io.scigraph.neo4j.GraphTransactionalImpl;
 import io.scigraph.neo4j.IdMap;
 import io.scigraph.neo4j.Neo4jConfiguration;
@@ -41,6 +42,7 @@ protected GraphTransactionalImpl createInstance() throws Exception {
       Concept.ABREVIATION,
       Concept.ACRONYM));
     config.getIndexedNodeProperties().addAll(newHashSet(
+        CommonProperties.IRI,
         NodeProperties.LABEL,
         Concept.CATEGORY, Concept.SYNONYM,
         Concept.ABREVIATION,

diff --git a/SciGraph-core/src/test/java/io/scigraph/util/GraphTestBase.java b/SciGraph-core/src/test/java/io/scigraph/util/GraphTestBase.java
@@ -48,6 +48,7 @@ public class GraphTestBase {
   protected static Graph graph;
   protected static CurieUtil curieUtil;
   static ConcurrentHashMap<String, Long> idMap = new ConcurrentHashMap<>();
+  static RelationshipMap relMap = new RelationshipMap();
 
   Transaction tx;
 
@@ -75,10 +76,10 @@ public static void setupDb() {
     config.getExactNodeProperties().addAll(
         newHashSet(NodeProperties.LABEL, Concept.SYNONYM, Concept.ABREVIATION, Concept.ACRONYM));
     config.getIndexedNodeProperties().addAll(
-        newHashSet(NodeProperties.LABEL, Concept.CATEGORY, Concept.SYNONYM, Concept.ABREVIATION,
-            Concept.ACRONYM));
+        newHashSet(CommonProperties.IRI, NodeProperties.LABEL, Concept.CATEGORY, Concept.SYNONYM,
+                Concept.ABREVIATION, Concept.ACRONYM));
     Neo4jModule.setupAutoIndexing(graphDb, config);
-    graph = new GraphTransactionalImpl(graphDb, idMap, new RelationshipMap());
+    graph = new GraphTransactionalImpl(graphDb, idMap, relMap);
     curieUtil = new CurieUtil(Collections.<String, String>emptyMap());
     cypherUtil = new CypherUtil(graphDb, curieUtil);
   }
@@ -96,6 +97,7 @@ public void startTransaction() {
   @After
   public void failTransaction() {
     idMap.clear();
+    relMap.clear();
     tx.failure();
     // tx.success(); // convenient for debugging
     tx.close();

diff --git a/SciGraph-core/src/test/resources/cliqueConfiguration.yaml b/SciGraph-core/src/test/resources/cliqueConfiguration.yaml
@@ -6,7 +6,7 @@ graphConfiguration:
     indexedNodeProperties:
       - category
       - label
-      - fragment
+      - iri
     exactNodeProperties:
       - label
       - synonym

diff --git a/SciGraph-core/src/test/resources/pizzaExample.yaml b/SciGraph-core/src/test/resources/pizzaExample.yaml
@@ -7,6 +7,7 @@ graphConfiguration:
       - category
       - label
       - fragment
+      - iri
     exactNodeProperties:
       - label
       - synonym

diff --git a/SciGraph-services/src/test/resources/pizzaConfiguration.swagger1.yaml b/SciGraph-services/src/test/resources/pizzaConfiguration.swagger1.yaml
@@ -16,7 +16,7 @@ graphConfiguration:
   indexedNodeProperties:
     - category
     - label
-    - fragment
+    - iri
   exactNodeProperties:
     - label
     - synonym

diff --git a/SciGraph-services/src/test/resources/pizzaConfiguration.yaml b/SciGraph-services/src/test/resources/pizzaConfiguration.yaml
@@ -18,7 +18,7 @@ graphConfiguration:
   indexedNodeProperties:
     - category
     - label
-    - fragment
+    - iri
   exactNodeProperties:
     - label
     - synonym

diff --git a/pom.xml b/pom.xml
@@ -76,7 +76,7 @@
     <dropwizard.version>1.1.0</dropwizard.version>
     <guice.version>4.0</guice.version>
     <blueprints.version>2.6.0</blueprints.version>
-    <neo4j.version>3.3.1</neo4j.version>
+    <neo4j.version>3.4.7</neo4j.version>
     <neo4j-graphviz.version>3.1.1</neo4j-graphviz.version>
   </properties>