Merge branch 'master' of https://github.com/SciGraph/SciGraph into up…

…stream
SciCrunch · Jun 15, 2017 · 4633a79 · 4633a79
2 parents 3e1c0e1 + 46049b9
commit 4633a79
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diff --git a/.travis.yml b/.travis.yml
@@ -1,8 +1,6 @@
 language: java
 jdk:
   - oraclejdk8
-  - oraclejdk7
-  - openjdk7
 
 before_install:
   - "export DISPLAY=:99.0"

diff --git a/README.md b/README.md
@@ -100,7 +100,7 @@ Also browse the [generated REST documentation](http://localhost:9000/scigraph/do
 to see some of the other resources.
 
 -------
-<img src="http://github.nfsdb.org/images/yklogo.png" />
+<img src="https://www.yourkit.com/images/yklogo.png" />
 -------
 Thanks to YourKit for providing an Open Source license.
 

diff --git a/SciGraph-analysis/pom.xml b/SciGraph-analysis/pom.xml
@@ -20,7 +20,7 @@
   <parent>
     <groupId>io.scigraph</groupId>
     <artifactId>scigraph</artifactId>
-    <version>1.5-SNAPSHOT</version>
+    <version>2.1-SNAPSHOT</version>
   </parent>
   <artifactId>scigraph-analysis</artifactId>
   <name>SciGraph - analysis</name>
@@ -41,7 +41,7 @@
     <dependency>
       <groupId>org.apache.commons</groupId>
       <artifactId>commons-math3</artifactId>
-      <version>3.5</version>
+      <version>3.6.1</version>
     </dependency>
   </dependencies>
 

diff --git a/SciGraph-analysis/src/main/java/io/scigraph/analyzer/HyperGeometricAnalyzer.java b/SciGraph-analysis/src/main/java/io/scigraph/analyzer/HyperGeometricAnalyzer.java
@@ -15,19 +15,14 @@
  */
 package io.scigraph.analyzer;
 
-import io.scigraph.frames.CommonProperties;
-import io.scigraph.frames.NodeProperties;
-import io.scigraph.internal.CypherUtil;
-import io.scigraph.neo4j.Graph;
-import io.scigraph.owlapi.curies.CurieUtil;
-
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.Collections;
 import java.util.HashMap;
 import java.util.HashSet;
 import java.util.List;
 import java.util.Map;
+import java.util.Optional;
 import java.util.Set;
 
 import javax.inject.Inject;
@@ -38,8 +33,12 @@
 import org.neo4j.graphdb.Node;
 import org.neo4j.graphdb.Result;
 import org.neo4j.graphdb.Transaction;
+import org.prefixcommons.CurieUtil;
 
-import com.google.common.base.Optional;
+import io.scigraph.frames.CommonProperties;
+import io.scigraph.frames.NodeProperties;
+import io.scigraph.internal.CypherUtil;
+import io.scigraph.neo4j.Graph;
 
 public class HyperGeometricAnalyzer {
 
@@ -206,7 +205,7 @@ public List<AnalyzerResult> analyze(AnalyzeRequest request) {
             hypergeometricDistribution.upperCumulativeProbability((int) n.getCount())
                 * bonferroniCoeff;
         String iri = graph.getNodeProperty(n.getNodeId(), CommonProperties.IRI, String.class).get();
-        String curie = curieUtil.getCurie(iri).or(iri);
+        String curie = curieUtil.getCurie(iri).orElse(iri);
         String labels =
             StringUtils.join(
                 graph.getNodeProperties(n.getNodeId(), NodeProperties.LABEL, String.class), ", ");

diff --git a/SciGraph-analysis/src/test/java/io/scigraph/analyzer/HyperGeometricAnalyzerTest.java b/SciGraph-analysis/src/test/java/io/scigraph/analyzer/HyperGeometricAnalyzerTest.java
@@ -26,7 +26,6 @@
 import io.scigraph.internal.CypherUtil;
 import io.scigraph.owlapi.GraphOwlVisitor;
 import io.scigraph.owlapi.OwlPostprocessor;
-import io.scigraph.owlapi.curies.CurieUtil;
 import io.scigraph.owlapi.loader.OwlLoadConfiguration.MappedProperty;
 import io.scigraph.util.GraphTestBase;
 
@@ -38,6 +37,7 @@
 import org.junit.BeforeClass;
 import org.junit.Test;
 import org.neo4j.graphdb.Transaction;
+import org.prefixcommons.CurieUtil;
 import org.semanticweb.owlapi.apibinding.OWLManager;
 import org.semanticweb.owlapi.model.IRI;
 import org.semanticweb.owlapi.model.OWLOntologyManager;

diff --git a/SciGraph-core/pom.xml b/SciGraph-core/pom.xml
@@ -20,13 +20,13 @@
   <parent>
     <artifactId>scigraph</artifactId>
     <groupId>io.scigraph</groupId>
-    <version>1.5-SNAPSHOT</version>
+    <version>2.1-SNAPSHOT</version>
   </parent>
   <artifactId>scigraph-core</artifactId>
   <name>SciGraph - core</name>
 
   <properties>
-    <lucene.version>3.6.2</lucene.version>
+    <lucene.version>5.5.0</lucene.version>
     <openrdf.version>2.7.6</openrdf.version>
   </properties>
 
@@ -68,34 +68,39 @@
 
     <dependency>
       <groupId>org.apache.lucene</groupId>
-      <artifactId>lucene-analyzers</artifactId>
+      <artifactId>lucene-suggest</artifactId>
       <version>${lucene.version}</version>
     </dependency>
     <dependency>
       <groupId>org.apache.lucene</groupId>
-      <artifactId>lucene-spellchecker</artifactId>
+      <artifactId>lucene-analyzers-common</artifactId>
+      <version>${lucene.version}</version>
+    </dependency>
+    <dependency>
+      <groupId>org.apache.lucene</groupId>
+      <artifactId>lucene-misc</artifactId>
       <version>${lucene.version}</version>
     </dependency>
     <dependency>
       <groupId>org.apache.lucene</groupId>
       <artifactId>lucene-queryparser</artifactId>
       <version>${lucene.version}</version>
     </dependency>
-
+    
     <dependency>
       <groupId>commons-cli</groupId>
       <artifactId>commons-cli</artifactId>
-      <version>1.3.1</version>
+      <version>1.4</version>
     </dependency>
     <dependency>
       <groupId>commons-io</groupId>
       <artifactId>commons-io</artifactId>
-      <version>2.4</version>
+      <version>2.5</version>
     </dependency>
     <dependency>
       <groupId>org.apache.commons</groupId>
       <artifactId>commons-lang3</artifactId>
-      <version>3.4</version>
+      <version>3.5</version>
     </dependency>
 
     <dependency>
@@ -114,7 +119,7 @@
     <dependency>
       <groupId>commons-validator</groupId>
       <artifactId>commons-validator</artifactId>
-      <version>1.4.1</version>
+      <version>1.6</version>
     </dependency>
     <dependency>
       <groupId>org.semanticweb.elk</groupId>
@@ -126,6 +131,11 @@
       <artifactId>mapdb</artifactId>
       <version>1.0.9</version>
     </dependency>
+    <dependency>
+      <groupId>org.prefixcommons</groupId>
+      <artifactId>curie-util</artifactId>
+      <version>0.0.2</version>
+    </dependency>
   </dependencies>
 
   <build>

diff --git a/SciGraph-core/src/main/java/io/scigraph/bbop/BbopGraphUtil.java b/SciGraph-core/src/main/java/io/scigraph/bbop/BbopGraphUtil.java
@@ -16,10 +16,6 @@
 package io.scigraph.bbop;
 
 import static com.google.common.collect.Iterables.getFirst;
-import io.scigraph.frames.CommonProperties;
-import io.scigraph.frames.NodeProperties;
-import io.scigraph.internal.TinkerGraphUtil;
-import io.scigraph.owlapi.curies.CurieUtil;
 
 import java.util.Collection;
 
@@ -31,35 +27,43 @@
 import com.tinkerpop.blueprints.Graph;
 import com.tinkerpop.blueprints.Vertex;
 
+import io.scigraph.frames.CommonProperties;
+import io.scigraph.frames.NodeProperties;
+import io.scigraph.internal.TinkerGraphUtil;
+import org.prefixcommons.CurieUtil;
+
 public class BbopGraphUtil {
 
   private final CurieUtil curieUtil;
 
   private static final ImmutableSet<String> IGNORED_PROPERTY_KEYS =
       ImmutableSet.of(CommonProperties.IRI, NodeProperties.LABEL, CommonProperties.CURIE);
+  private static final ImmutableSet<String> IGNORED_PROPERTY_KEYS_FOR_EDGES =
+      ImmutableSet.of(CommonProperties.IRI);
 
   @Inject
   public BbopGraphUtil(CurieUtil curieUtil) {
     this.curieUtil = curieUtil;
   }
 
   String getCurieOrIri(Vertex vertex) {
-    String iri = (String)vertex.getProperty(CommonProperties.IRI);
-    return curieUtil.getCurie(iri).or(iri);
+    String iri = (String) vertex.getProperty(CommonProperties.IRI);
+    return curieUtil.getCurie(iri).orElse(iri);
   }
-  
+
   /***
    * @param graph The graph to convert
    * @return a bbop representation of a {@link Graph}
    */
   public BbopGraph convertGraph(Graph graph) {
     BbopGraph bbopGraph = new BbopGraph();
-    for (Vertex vertex: graph.getVertices()) {
+    for (Vertex vertex : graph.getVertices()) {
       BbopNode bbopNode = new BbopNode();
       bbopNode.setId(getCurieOrIri(vertex));
-      String label = getFirst(TinkerGraphUtil.getProperties(vertex, NodeProperties.LABEL, String.class), null);
+      String label =
+          getFirst(TinkerGraphUtil.getProperties(vertex, NodeProperties.LABEL, String.class), null);
       bbopNode.setLbl(label);
-      for (String key: vertex.getPropertyKeys()) {
+      for (String key : vertex.getPropertyKeys()) {
         if (IGNORED_PROPERTY_KEYS.contains(key)) {
           continue;
         }
@@ -68,13 +72,20 @@ public BbopGraph convertGraph(Graph graph) {
       }
       bbopGraph.getNodes().add(bbopNode);
     }
-    for (Edge edge: graph.getEdges()) {
+    for (Edge edge : graph.getEdges()) {
       BbopEdge bbopEdge = new BbopEdge();
-      Vertex subject= edge.getVertex(Direction.OUT);
-      Vertex object= edge.getVertex(Direction.IN);
+      Vertex subject = edge.getVertex(Direction.OUT);
+      Vertex object = edge.getVertex(Direction.IN);
       bbopEdge.setSub(getCurieOrIri(subject));
       bbopEdge.setObj(getCurieOrIri(object));
       bbopEdge.setPred(edge.getLabel());
+      for (String key : edge.getPropertyKeys()) {
+        if (IGNORED_PROPERTY_KEYS_FOR_EDGES.contains(key)) {
+          continue;
+        }
+        Collection<Object> values = TinkerGraphUtil.getProperties(edge, key, Object.class);
+        bbopEdge.getMeta().put(key, values);
+      }
       bbopGraph.getEdges().add(bbopEdge);
     }
     return bbopGraph;

diff --git a/SciGraph-core/src/main/java/io/scigraph/internal/CypherUtil.java b/SciGraph-core/src/main/java/io/scigraph/internal/CypherUtil.java
@@ -19,7 +19,6 @@
 import static com.google.common.collect.Collections2.transform;
 import static com.google.common.collect.Iterables.getFirst;
 import static com.google.common.collect.Sets.newHashSet;
-import io.scigraph.owlapi.curies.CurieUtil;
 
 import java.util.Collection;
 import java.util.Collections;
@@ -35,7 +34,6 @@
 
 import org.apache.commons.lang3.text.StrLookup;
 import org.apache.commons.lang3.text.StrSubstitutor;
-import org.neo4j.graphdb.DynamicRelationshipType;
 import org.neo4j.graphdb.GraphDatabaseService;
 import org.neo4j.graphdb.RelationshipType;
 import org.neo4j.graphdb.Result;
@@ -45,6 +43,7 @@
 import com.google.common.base.Splitter;
 import com.google.common.collect.HashMultimap;
 import com.google.common.collect.Multimap;
+import org.prefixcommons.CurieUtil;
 
 /***
  * A utility for more expressive Cypher queries.
@@ -101,7 +100,7 @@ public Set<RelationshipType> getEntailedRelationshipTypes(Collection<String> par
       relationshipTypes = transform(relationshipNames, new Function<String, RelationshipType>() {
         @Override
         public RelationshipType apply(String name) {
-          return DynamicRelationshipType.withName(name);
+          return RelationshipType.withName(name);
         }
       });
       tx.success();
@@ -136,7 +135,7 @@ Collection<String> resolveTypes(String types, boolean entail) {
             new Function<String, String>() {
               @Override
               public String apply(String type) {
-                return curieUtil.getIri(type).or(type);
+                return curieUtil.getIri(type).orElse(type);
               }
             });
     if (entail) {
@@ -161,7 +160,7 @@ public String resolveStartQuery(String cypher) {
     Matcher m = p.matcher(cypher);
     while (m.find()) {
       String curie = m.group(1);
-      String iri = curieUtil.getIri(curie).or(curie);
+      String iri = curieUtil.getIri(curie).orElse(curie);
       resolvedCypher = resolvedCypher.replace(curie, iri);
     }
 
@@ -196,7 +195,7 @@ public String apply(Object input) {
                   throw new IllegalArgumentException(
                       "Cypher relationship templates must not contain spaces");
                 }
-                return curieUtil.getIri(input.toString()).or(input.toString());
+                return curieUtil.getIri(input.toString()).orElse(input.toString());
               }
 
             });