Migrate datastore dependency to commons-datastore

opencb · Jun 8, 2016 · 9662861 · 9662861
1 parent af35a73
commit 9662861
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Showing 12 changed files with 44 additions and 45 deletions.
diff --git a/bionetdb-app/src/main/java/org/opencb/bionetdb/app/cli/ExpressionCommandExecutor.java b/bionetdb-app/src/main/java/org/opencb/bionetdb/app/cli/ExpressionCommandExecutor.java
@@ -6,7 +6,7 @@
 import org.opencb.bionetdb.core.models.Expression;
 import org.opencb.bionetdb.core.neo4j.Neo4JNetworkDBAdaptor;
 import org.opencb.commons.utils.FileUtils;
-import org.opencb.datastore.core.QueryOptions;
+import org.opencb.commons.datastore.core.QueryOptions;
 
 import java.io.IOException;
 import java.nio.file.Path;

diff --git a/bionetdb-app/src/main/java/org/opencb/bionetdb/app/cli/QueryCommandExecutor.java b/bionetdb-app/src/main/java/org/opencb/bionetdb/app/cli/QueryCommandExecutor.java
@@ -2,8 +2,8 @@
 
 import org.opencb.bionetdb.core.api.NetworkDBAdaptor;
 import org.opencb.bionetdb.core.neo4j.Neo4JNetworkDBAdaptor;
-import org.opencb.datastore.core.Query;
-import org.opencb.datastore.core.QueryResult;
+import org.opencb.commons.datastore.core.Query;
+import org.opencb.commons.datastore.core.QueryResult;
 
 /**
  * Created by imedina on 28/09/15.

diff --git a/bionetdb-core/pom.xml b/bionetdb-core/pom.xml
@@ -21,12 +21,12 @@
             <artifactId>biodata-formats</artifactId>
         </dependency>
         <dependency>
-            <groupId>org.opencb.datastore</groupId>
-            <artifactId>datastore-core</artifactId>
+            <groupId>org.opencb.commons</groupId>
+            <artifactId>commons-lib</artifactId>
         </dependency>
         <dependency>
             <groupId>org.opencb.commons</groupId>
-            <artifactId>commons-lib</artifactId>
+            <artifactId>commons-datastore-core</artifactId>
         </dependency>
 
         <dependency>

diff --git a/bionetdb-core/src/main/java/org/opencb/bionetdb/core/api/NetworkDBAdaptor.java b/bionetdb-core/src/main/java/org/opencb/bionetdb/core/api/NetworkDBAdaptor.java
@@ -4,15 +4,15 @@
 import org.opencb.bionetdb.core.models.Expression;
 import org.opencb.bionetdb.core.models.Network;
 import org.opencb.bionetdb.core.models.Xref;
-import org.opencb.datastore.core.Query;
-import org.opencb.datastore.core.QueryOptions;
-import org.opencb.datastore.core.QueryParam;
-import org.opencb.datastore.core.QueryResult;
+import org.opencb.commons.datastore.core.Query;
+import org.opencb.commons.datastore.core.QueryOptions;
+import org.opencb.commons.datastore.core.QueryParam;
+import org.opencb.commons.datastore.core.QueryResult;
 
 import java.util.List;
 
-import static org.opencb.datastore.core.QueryParam.Type.INTEGER;
-import static org.opencb.datastore.core.QueryParam.Type.TEXT_ARRAY;
+import static org.opencb.commons.datastore.core.QueryParam.Type.INTEGER;
+import static org.opencb.commons.datastore.core.QueryParam.Type.TEXT_ARRAY;
 
 /**
  * Created by imedina on 05/08/15.

diff --git a/bionetdb-core/src/main/java/org/opencb/bionetdb/core/config/DatabaseConfiguration.java b/bionetdb-core/src/main/java/org/opencb/bionetdb/core/config/DatabaseConfiguration.java
@@ -1,6 +1,6 @@
 package org.opencb.bionetdb.core.config;
 
-import org.opencb.datastore.core.ObjectMap;
+import org.opencb.commons.datastore.core.ObjectMap;
 
 /**
  * Created by imedina on 05/10/15.

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
@@ -10,10 +10,10 @@
 import org.opencb.bionetdb.core.config.DatabaseConfiguration;
 import org.opencb.bionetdb.core.exceptions.BioNetDBException;
 import org.opencb.bionetdb.core.models.*;
-import org.opencb.datastore.core.ObjectMap;
-import org.opencb.datastore.core.Query;
-import org.opencb.datastore.core.QueryOptions;
-import org.opencb.datastore.core.QueryResult;
+import org.opencb.commons.datastore.core.ObjectMap;
+import org.opencb.commons.datastore.core.Query;
+import org.opencb.commons.datastore.core.QueryOptions;
+import org.opencb.commons.datastore.core.QueryResult;
 
 import java.io.File;
 import java.text.DecimalFormat;

diff --git a/bionetdb-core/src/main/java/org/opencb/bionetdb/core/neo4j/Neo4JQueryParser.java b/bionetdb-core/src/main/java/org/opencb/bionetdb/core/neo4j/Neo4JQueryParser.java
@@ -2,8 +2,8 @@
 
 import org.opencb.bionetdb.core.api.NetworkDBAdaptor;
 import org.opencb.bionetdb.core.exceptions.BioNetDBException;
-import org.opencb.datastore.core.Query;
-import org.opencb.datastore.core.QueryOptions;
+import org.opencb.commons.datastore.core.Query;
+import org.opencb.commons.datastore.core.QueryOptions;
 
 import java.util.ArrayList;
 import java.util.List;

diff --git a/bionetdb-core/src/test/java/org/opencb/bionetdb/core/neo4j/Neo4JNetworkDBAdaptorTest.java b/bionetdb-core/src/test/java/org/opencb/bionetdb/core/neo4j/Neo4JNetworkDBAdaptorTest.java
@@ -11,10 +11,10 @@
 import org.opencb.bionetdb.core.models.Expression;
 import org.opencb.bionetdb.core.models.Network;
 import org.opencb.bionetdb.core.models.Xref;
-import org.opencb.datastore.core.ObjectMap;
-import org.opencb.datastore.core.Query;
-import org.opencb.datastore.core.QueryOptions;
-import org.opencb.datastore.core.QueryResult;
+import org.opencb.commons.datastore.core.ObjectMap;
+import org.opencb.commons.datastore.core.Query;
+import org.opencb.commons.datastore.core.QueryOptions;
+import org.opencb.commons.datastore.core.QueryResult;
 
 import java.io.File;
 import java.io.IOException;

diff --git a/bionetdb-server/pom.xml b/bionetdb-server/pom.xml
@@ -21,8 +21,8 @@
             <artifactId>bionetdb-core</artifactId>
         </dependency>
         <dependency>
-            <groupId>org.opencb.datastore</groupId>
-            <artifactId>datastore-core</artifactId>
+            <groupId>org.opencb.commons</groupId>
+            <artifactId>commons-datastore-core</artifactId>
         </dependency>
         <dependency>
             <groupId>org.sbml.libsbml</groupId>

diff --git a/bionetdb-server/src/main/java/org/opencb/bionetdb/server/ws/GenericRestWSServer.java b/bionetdb-server/src/main/java/org/opencb/bionetdb/server/ws/GenericRestWSServer.java
@@ -12,10 +12,10 @@
 import org.opencb.bionetdb.core.config.BioNetDBConfiguration;
 import org.opencb.bionetdb.server.exception.DatabaseException;
 import org.opencb.bionetdb.server.exception.VersionException;
-import org.opencb.datastore.core.ObjectMap;
-import org.opencb.datastore.core.QueryOptions;
-import org.opencb.datastore.core.QueryResponse;
-import org.opencb.datastore.core.QueryResult;
+import org.opencb.commons.datastore.core.ObjectMap;
+import org.opencb.commons.datastore.core.QueryOptions;
+import org.opencb.commons.datastore.core.QueryResponse;
+import org.opencb.commons.datastore.core.QueryResult;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 

diff --git a/bionetdb-server/src/main/java/org/opencb/bionetdb/server/ws/PhysicalEntityWSServer.java b/bionetdb-server/src/main/java/org/opencb/bionetdb/server/ws/PhysicalEntityWSServer.java
@@ -5,8 +5,8 @@
 import org.opencb.bionetdb.core.neo4j.Neo4JNetworkDBAdaptor;
 import org.opencb.bionetdb.server.exception.DatabaseException;
 import org.opencb.bionetdb.server.exception.VersionException;
-import org.opencb.datastore.core.Query;
-import org.opencb.datastore.core.QueryResult;
+import org.opencb.commons.datastore.core.Query;
+import org.opencb.commons.datastore.core.QueryResult;
 
 import javax.servlet.http.HttpServletRequest;
 import javax.ws.rs.GET;

diff --git a/pom.xml b/pom.xml
@@ -20,13 +20,12 @@
     </modules>
 
     <properties>
+        <java.version>1.8</java.version>
         <bionetdb.version>0.1.0</bionetdb.version>
-        <biodata.version>0.5-SNAPSHOT</biodata.version>
-        <datastore.version>0.4-SNAPSHOT</datastore.version>
-        <java-common-libs.version>3.0-SNAPSHOT</java-common-libs.version>
-        <jackson.version>2.5.4</jackson.version>
-        <jersey.version>2.19</jersey.version>
-        <compileSource>1.8</compileSource>
+        <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>
         <build.dir>build</build.dir>
     </properties>
 
@@ -79,22 +78,22 @@
             </dependency>
             <dependency>
                 <groupId>org.opencb.biodata</groupId>
-                <artifactId>biodata-models</artifactId>
+                <artifactId>biodata-formats</artifactId>
                 <version>${biodata.version}</version>
             </dependency>
             <dependency>
                 <groupId>org.opencb.biodata</groupId>
-                <artifactId>biodata-formats</artifactId>
+                <artifactId>biodata-models</artifactId>
                 <version>${biodata.version}</version>
             </dependency>
             <dependency>
-                <groupId>org.opencb.datastore</groupId>
-                <artifactId>datastore-core</artifactId>
-                <version>${datastore.version}</version>
+                <groupId>org.opencb.commons</groupId>
+                <artifactId>commons-lib</artifactId>
+                <version>${java-common-libs.version}</version>
             </dependency>
             <dependency>
                 <groupId>org.opencb.commons</groupId>
-                <artifactId>commons-lib</artifactId>
+                <artifactId>commons-datastore-core</artifactId>
                 <version>${java-common-libs.version}</version>
             </dependency>
 
@@ -180,8 +179,8 @@
                 <artifactId>maven-compiler-plugin</artifactId>
                 <version>3.2</version>
                 <configuration>
-                    <source>${compileSource}</source>
-                    <target>${compileSource}</target>
+                    <source>${java.version}</source>
+                    <target>${java.version}</target>
                     <showDeprecation>true</showDeprecation>
                     <showWarnings>true</showWarnings>
                     <encoding>UTF-8</encoding>