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 index 2559917..826a607 100644 --- 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 index dffbfc0..8b5fb6d 100644 --- 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 index 84a2bf2..f98db3d 100644 --- a/bionetdb-core/pom.xml +++ b/bionetdb-core/pom.xml @@ -21,12 +21,12 @@ biodata-formats - org.opencb.datastore - datastore-core + org.opencb.commons + commons-lib org.opencb.commons - commons-lib + commons-datastore-core 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 index 4d0cd4d..48a9176 100644 --- 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 index be5c411..6a22397 100644 --- 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 index 2ca911e..5e18fd5 100644 --- 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 index 6765b2f..43b89f6 100644 --- 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 index 19c7431..632147b 100644 --- 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 index cb48ca7..a88cebe 100644 --- a/bionetdb-server/pom.xml +++ b/bionetdb-server/pom.xml @@ -21,8 +21,8 @@ bionetdb-core - org.opencb.datastore - datastore-core + org.opencb.commons + commons-datastore-core org.sbml.libsbml 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 index ed1b6a6..2a81860 100644 --- 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 index 9ece118..125c8d2 100644 --- 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 index a0b78cc..9066a99 100644 --- a/pom.xml +++ b/pom.xml @@ -20,13 +20,12 @@ + 1.8 0.1.0 - 0.5-SNAPSHOT - 0.4-SNAPSHOT - 3.0-SNAPSHOT - 2.5.4 - 2.19 - 1.8 + 3.3.0-SNAPSHOT + 0.8.0-SNAPSHOT + 2.6.4 + 2.22.1 build @@ -79,22 +78,22 @@ org.opencb.biodata - biodata-models + biodata-formats ${biodata.version} org.opencb.biodata - biodata-formats + biodata-models ${biodata.version} - org.opencb.datastore - datastore-core - ${datastore.version} + org.opencb.commons + commons-lib + ${java-common-libs.version} org.opencb.commons - commons-lib + commons-datastore-core ${java-common-libs.version} @@ -180,8 +179,8 @@ maven-compiler-plugin 3.2 - ${compileSource} - ${compileSource} + ${java.version} + ${java.version} true true UTF-8