pom.xml: several cleanups and improvements

opencb · Jul 18, 2016 · 81c571b · 81c571b
1 parent 919b013
commit 81c571b
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Showing 5 changed files with 13 additions and 55 deletions.
diff --git a/bionetdb-app/pom.xml b/bionetdb-app/pom.xml
@@ -47,18 +47,6 @@
             <artifactId>jcommander</artifactId>
             <version>1.47</version>
         </dependency>
-        <dependency>
-            <groupId>commons-lang</groupId>
-            <artifactId>commons-lang</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>org.slf4j</groupId>
-            <artifactId>slf4j-api</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>org.slf4j</groupId>
-            <artifactId>slf4j-simple</artifactId>
-        </dependency>
         <dependency>
             <groupId>com.fasterxml.jackson.core</groupId>
             <artifactId>jackson-databind</artifactId>

diff --git a/bionetdb-core/pom.xml b/bionetdb-core/pom.xml
@@ -29,20 +29,21 @@
             <artifactId>commons-datastore-core</artifactId>
         </dependency>
 
+        <dependency>
+            <groupId>org.neo4j</groupId>
+            <artifactId>neo4j</artifactId>
+            <version>3.0.3</version>
+            <scope>provided</scope>
+        </dependency>
         <dependency>
             <groupId>org.neo4j.driver</groupId>
             <artifactId>neo4j-java-driver</artifactId>
-            <version>1.0.2</version>
+            <version>1.0.4</version>
         </dependency>
         <dependency>
             <groupId>com.fasterxml.jackson.dataformat</groupId>
             <artifactId>jackson-dataformat-yaml</artifactId>
         </dependency>
-        <dependency>
-            <groupId>org.neo4j</groupId>
-            <artifactId>neo4j</artifactId>
-            <version>3.0.2</version>
-        </dependency>
         <dependency>
             <groupId>org.biopax.paxtools</groupId>
             <artifactId>paxtools-core</artifactId>
@@ -56,14 +57,6 @@
             <groupId>psidev.psi.mi</groupId>
             <artifactId>psimitab</artifactId>
         </dependency>
-        <dependency>
-            <groupId>org.slf4j</groupId>
-            <artifactId>slf4j-api</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>org.slf4j</groupId>
-            <artifactId>slf4j-simple</artifactId>
-        </dependency>
         <dependency>
             <groupId>com.fasterxml.jackson.core</groupId>
             <artifactId>jackson-databind</artifactId>

diff --git a/bionetdb-core/src/main/java/org/opencb/bionetdb/core/neo4j/Neo4JNetworkDBAdaptor.java b/bionetdb-core/src/main/java/org/opencb/bionetdb/core/neo4j/Neo4JNetworkDBAdaptor.java
@@ -1,10 +1,9 @@
 package org.opencb.bionetdb.core.neo4j;
 
-import org.apache.commons.collections.IteratorUtils;
 import org.apache.commons.math3.util.CombinatoricsUtils;
 import org.neo4j.driver.v1.*;
-import org.neo4j.graphdb.*;
 import org.neo4j.driver.v1.Transaction;
+import org.neo4j.graphdb.*;
 import org.neo4j.graphdb.factory.GraphDatabaseFactory;
 import org.opencb.bionetdb.core.api.NetworkDBAdaptor;
 import org.opencb.bionetdb.core.config.BioNetDBConfiguration;
@@ -430,7 +429,8 @@ private void insertInteractions(List<Interaction> interactionList, QueryOptions
                         Reaction myreaction = (Reaction) i;
                         for (String myId : myreaction.getReactants()) {
                             StatementResult reactant = getNode(tx, "", new ObjectMap("id", myId));
-                            addRelationship(tx, oriLabel, interactionLabel, reactant.peek().get("ID").toString(), interactionID, RelTypes.REACTANT);
+                            addRelationship(tx, oriLabel, interactionLabel, reactant.peek().get("ID").toString(), interactionID,
+                            RelTypes.REACTANT);
                         }
 
                         for (String myId : myreaction.getProducts()) {

diff --git a/bionetdb-server/pom.xml b/bionetdb-server/pom.xml
@@ -30,14 +30,6 @@
             <systemPath>${basedir}/../bionetdb-app/app/ext-libs/libsbmlj.jar</systemPath>
         </dependency>
 
-        <dependency>
-            <groupId>org.slf4j</groupId>
-            <artifactId>slf4j-api</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>org.slf4j</groupId>
-            <artifactId>slf4j-simple</artifactId>
-        </dependency>
         <dependency>
             <groupId>com.fasterxml.jackson.core</groupId>
             <artifactId>jackson-databind</artifactId>

diff --git a/pom.xml b/pom.xml
@@ -20,12 +20,12 @@
     </modules>
 
     <properties>
-        <java.version>1.8</java.version>
         <bionetdb.version>0.1.0</bionetdb.version>
+        <java.version>1.8</java.version>
         <java-common-libs.version>3.3.0-SNAPSHOT</java-common-libs.version>
         <biodata.version>0.8.0-SNAPSHOT</biodata.version>
         <jackson.version>2.6.4</jackson.version>
-        <jersey.version>2.22.1</jersey.version>
+        <jersey.version>2.23</jersey.version>
         <build.dir>build</build.dir>
     </properties>
 
@@ -101,7 +101,7 @@
             <dependency>
                 <groupId>org.biopax.paxtools</groupId>
                 <artifactId>paxtools-core</artifactId>
-                <version>4.3.0</version>
+                <version>4.3.1</version>
             </dependency>
             <dependency>
                 <groupId>org.sbml.libsbml</groupId>
@@ -115,21 +115,6 @@
                 <artifactId>psimitab</artifactId>
                 <version>1.8.5</version>
             </dependency>
-            <dependency>
-                <groupId>commons-lang</groupId>
-                <artifactId>commons-lang</artifactId>
-                <version>2.6</version>
-            </dependency>
-            <dependency>
-                <groupId>org.slf4j</groupId>
-                <artifactId>slf4j-api</artifactId>
-                <version>1.7.12</version>
-            </dependency>
-            <dependency>
-                <groupId>org.slf4j</groupId>
-                <artifactId>slf4j-simple</artifactId>
-                <version>1.7.12</version>
-            </dependency>
             <dependency>
                 <groupId>com.fasterxml.jackson.core</groupId>
                 <artifactId>jackson-databind</artifactId>