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V111 egonw #30

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merged 5 commits into from
Sep 16, 2024
Merged

V111 egonw #30

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715b63b
bridgedb version
tabbassidaloii Sep 11, 2024
a3c4545
gdb4 to 3
tabbassidaloii Sep 11, 2024
04cac28
Update pom.xml
tabbassidaloii Sep 12, 2024
cbbcc1c
Tweaks: remove Derby 10.15 and BridgeDb 3.0.27 (use the 3.0.27-java8 …
egonw Sep 15, 2024
bd96677
add code loading the driver
tabbassidaloii Sep 16, 2024
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35 changes: 31 additions & 4 deletions pom.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -69,22 +69,44 @@
<dependency>
<groupId>org.bridgedb</groupId>
<artifactId>org.bridgedb.bio</artifactId>
<version>3.0.6</version>
<version>3.0.27-java8</version>
</dependency>
<dependency>
<groupId>org.bridgedb</groupId>
<artifactId>org.bridgedb.rdb</artifactId>
<version>3.0.6</version>
<version>3.0.27-java8</version>
</dependency>
<dependency>
<groupId>org.bridgedb</groupId>
<artifactId>org.bridgedb.rdb.construct</artifactId>
<version>3.0.6</version>
<version>3.0.27-java8</version>
</dependency>
<dependency>
<groupId>org.bridgedb</groupId>
<artifactId>org.bridgedb.tools.qc</artifactId>
<version>3.0.6</version>
<version>3.0.27</version>
<exclusions>
<exclusion>
<groupId>org.bridgedb</groupId>
<artifactId>org.bridgedb</artifactId>
</exclusion>
<exclusion>
<groupId>org.bridgedb</groupId>
<artifactId>org.bridgedb.bio</artifactId>
</exclusion>
<exclusion>
<groupId>org.bridgedb</groupId>
<artifactId>org.bridgedb.rdb</artifactId>
</exclusion>
<exclusion>
<groupId>org.bridgedb</groupId>
<artifactId>org.bridgedb.rdb.construct</artifactId>
</exclusion>
<exclusion>
<groupId>org.apache.derby</groupId>
<artifactId>derbyshared</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.apache.derby</groupId>
Expand All @@ -98,5 +120,10 @@
<artifactId>derbyclient</artifactId>
<version>10.4.2.0</version>
</dependency>
<dependency>
<groupId>org.apache.derby</groupId>
<artifactId>derbytools</artifactId>
<version>10.4.2.0</version>
</dependency>
</dependencies>
</project>
4 changes: 2 additions & 2 deletions src/main/java/org/bridgedb/creator/DbBuilder.java
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Expand Up @@ -41,7 +41,7 @@
import org.bridgedb.rdb.construct.DBConnector;
import org.bridgedb.rdb.construct.DataDerby;
import org.bridgedb.rdb.construct.GdbConstruct;
import org.bridgedb.rdb.construct.GdbConstructImpl4;
import org.bridgedb.rdb.construct.GdbConstructImpl3;

/**
* The class that performs the actual work on the database, used by
Expand Down Expand Up @@ -71,7 +71,7 @@ public DbBuilder(BridgeDbCreator creator) {
* @throws IDMapperException when it cannot write to the output file
*/
public void createNewDb() throws IDMapperException {
newDb = new GdbConstructImpl4(creator.getOutputFilePath(), new DataDerby(), DBConnector.PROP_RECREATE);
newDb = new GdbConstructImpl3(creator.getOutputFilePath(), new DataDerby(), DBConnector.PROP_RECREATE);
newDb.createGdbTables();
newDb.preInsert();

Expand Down
1 change: 1 addition & 0 deletions src/main/java/org/bridgedb/creator/Main.java
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Expand Up @@ -63,6 +63,7 @@ public static void main(String[] args) throws ClassNotFoundException, IDMapperEx

logInit();
DataSourceTxt.init(); // Initialize BrideDb data source
Class.forName("org.apache.derby.jdbc.EmbeddedDriver");
File dir = null;
String datasourceName = null;
String version = null;
Expand Down
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