Skip to content

Commit 709be4c

Browse files
juanfeSanahujajuanfeSanahuja
authored
Merge pull request #734 from opencb/TASK-7843
Portpatch 6.6.0 -> 7.1.0-SNAPSHOT
2 parents f9e0e51 + 03d0267 commit 709be4c

9 files changed

Lines changed: 49 additions & 21 deletions

File tree

‎.github/workflows/pull-request-merge.yml‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -14,4 +14,4 @@ jobs:
1414
uses: opencb/cellbase/.github/workflows/reusable-delete-docker.yml@develop
1515
with:
1616
task: ${{ github.head_ref }}
17-
secrets: inherit
17+
secrets: inherit

‎.github/workflows/release.yml‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -36,4 +36,4 @@ jobs:
3636

3737
release:
3838
uses: opencb/java-common-libs/.github/workflows/release-github-workflow.yml@develop
39-
needs: [deploy-maven, deploy-docker, deploy-python]
39+
needs: [deploy-maven, deploy-zetta-docker, deploy-python]

‎cellbase-app/pom.xml‎

Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -12,6 +12,7 @@
1212

1313
<artifactId>cellbase-app</artifactId>
1414
<packaging>jar</packaging>
15+
<name>OpenCB CellBase Application</name>
1516

1617
<properties>
1718
<build.dir>${project.basedir}/../build</build.dir>

‎cellbase-client/pom.xml‎

Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -12,6 +12,7 @@
1212

1313
<artifactId>cellbase-client</artifactId>
1414
<packaging>jar</packaging>
15+
<name>OpenCB CellBase Client</name>
1516

1617
<dependencies>
1718
<dependency>

‎cellbase-core/pom.xml‎

Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -12,6 +12,7 @@
1212

1313
<artifactId>cellbase-core</artifactId>
1414
<packaging>jar</packaging>
15+
<name>OpenCB CellBase Core</name>
1516

1617
<dependencies>
1718
<dependency>

‎cellbase-lib/pom.xml‎

Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -12,6 +12,7 @@
1212

1313
<artifactId>cellbase-lib</artifactId>
1414
<packaging>jar</packaging>
15+
<name>OpenCB CellBase Library</name>
1516

1617
<dependencies>
1718
<dependency>

‎cellbase-lib/src/main/java/org/opencb/cellbase/lib/builders/clinical/variant/CosmicIndexer.java‎

Lines changed: 0 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -19,7 +19,6 @@
1919
import org.opencb.biodata.formats.io.FileFormatException;
2020
import org.opencb.biodata.formats.variant.cosmic.CosmicParser;
2121
import org.opencb.cellbase.core.exception.CellBaseException;
22-
2322
import org.opencb.cellbase.lib.EtlCommons;
2423
import org.rocksdb.RocksDB;
2524
import org.rocksdb.RocksDBException;

‎cellbase-server/pom.xml‎

Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -12,6 +12,7 @@
1212

1313
<artifactId>cellbase-server</artifactId>
1414
<packaging>war</packaging>
15+
<name>OpenCB CellBase Server</name>
1516

1617
<dependencies>
1718
<dependency>

‎pom.xml‎

Lines changed: 42 additions & 18 deletions
Original file line numberDiff line numberDiff line change
@@ -40,7 +40,8 @@
4040
<swagger-annotations.version>1.6.5</swagger-annotations.version>
4141
<javax.servlet-api.version>3.1.0</javax.servlet-api.version>
4242
<poi.version>4.1.2</poi.version>
43-
<mongodb.version>4.11.4</mongodb.version>
43+
<mongodb.version>4.11.5</mongodb.version>
44+
4445
<junit.version>4.12</junit.version>
4546
<commons-codec.version>1.13</commons-codec.version>
4647
<jakarta.xml.bind-api.version>2.3.3</jakarta.xml.bind-api.version>
@@ -108,7 +109,7 @@
108109
<repositories>
109110
<repository>
110111
<id>ossrh</id>
111-
<url>https://oss.sonatype.org/content/repositories/snapshots</url>
112+
<url>https://central.sonatype.com/repository/maven-snapshots/</url>
112113
<snapshots>
113114
<enabled>true</enabled>
114115
<updatePolicy>daily</updatePolicy>
@@ -650,30 +651,57 @@
650651
<profile>
651652
<id>deploy-maven</id>
652653
<distributionManagement>
654+
<!-- Releases repository using the Sonatype OSSRH Staging API for staging and deployment -->
653655
<repository>
654656
<id>ossrh</id>
655-
<url>https://oss.sonatype.org/service/local/staging/deploy/maven2/</url>
657+
<name>OSSRH Staging API Releases</name>
658+
<url>https://ossrh-staging-api.central.sonatype.com/service/local/staging/deploy/maven2/</url>
656659
</repository>
660+
661+
<!-- Snapshots repository pointing to Maven Central’s snapshot feed for ongoing development versions -->
657662
<snapshotRepository>
658663
<id>ossrh</id>
659-
<url>https://oss.sonatype.org/content/repositories/snapshots</url>
664+
<name>Central Portal Snapshots</name>
665+
<url>https://central.sonatype.com/repository/maven-snapshots/</url>
660666
</snapshotRepository>
661667
</distributionManagement>
662668
<build>
663669
<plugins>
670+
<!-- Central Publishing Plugin: handles both snapshots and releases via the Sonatype Central API -->
671+
<plugin>
672+
<groupId>org.sonatype.central</groupId>
673+
<artifactId>central-publishing-maven-plugin</artifactId>
674+
<version>0.8.0</version>
675+
<!-- extensions=true allows this plugin to hook into the build lifecycle -->
676+
<extensions>true</extensions>
677+
<configuration>
678+
<!-- ID of the <server> in your settings.xml containing your Sonatype credentials -->
679+
<publishingServerId>ossrh</publishingServerId>
680+
<!-- autoPublish=true will automatically close and release the staging repository after deploy -->
681+
<autoPublish>true</autoPublish>
682+
<!-- waitUntil=published makes the build wait until the artifacts are fully available in Central -->
683+
<waitUntil>published</waitUntil>
684+
<!-- ignorePublishedComponents skips already-published modules in multimodule builds -->
685+
<ignorePublishedComponents>true</ignorePublishedComponents>
686+
</configuration>
687+
</plugin>
688+
<!-- Source Plugin: generates and attaches a -sources.jar containing all your project’s source files -->
664689
<plugin>
665690
<groupId>org.apache.maven.plugins</groupId>
666691
<artifactId>maven-source-plugin</artifactId>
667-
<version>3.2.0</version>
692+
<version>3.2.1</version>
668693
<executions>
669694
<execution>
670695
<id>attach-sources</id>
671696
<goals>
697+
<!-- jar-no-fork: create the sources jar without running the default lifecycle again -->
672698
<goal>jar-no-fork</goal>
673699
</goals>
674700
</execution>
675701
</executions>
676702
</plugin>
703+
704+
<!-- Javadoc Plugin: generates and attaches a -javadoc.jar containing your project’s API documentation -->
677705
<plugin>
678706
<groupId>org.apache.maven.plugins</groupId>
679707
<artifactId>maven-javadoc-plugin</artifactId>
@@ -682,27 +710,34 @@
682710
<execution>
683711
<id>attach-javadocs</id>
684712
<goals>
713+
<!-- jar: package the generated Javadocs into a jar file -->
685714
<goal>jar</goal>
686715
</goals>
687716
</execution>
688717
</executions>
689718
<configuration>
719+
<!-- disable strict checking of HTML tags in comments -->
690720
<doclint>none</doclint>
721+
<!-- do not fail the build if Javadoc generation issues errors -->
722+
<failOnError>false</failOnError>
691723
</configuration>
692724
</plugin>
725+
726+
<!-- GPG Plugin: signs all deployable artifacts (.jar, .pom, sources, javadoc) with your GPG key -->
693727
<plugin>
694728
<groupId>org.apache.maven.plugins</groupId>
695729
<artifactId>maven-gpg-plugin</artifactId>
696730
<version>1.6</version>
697731
<executions>
698732
<execution>
699733
<id>sign-artifacts</id>
700-
<phase>deploy</phase>
734+
<!-- bind signing to the verify phase, so signatures are created before deploy -->
735+
<phase>verify</phase>
701736
<goals>
702737
<goal>sign</goal>
703738
</goals>
704739
<configuration>
705-
<!-- Prevent `gpg` from using pinentry programs -->
740+
<!-- Use loopback pinentry to allow unattended signing in CI -->
706741
<gpgArguments>
707742
<arg>--pinentry-mode</arg>
708743
<arg>loopback</arg>
@@ -711,17 +746,6 @@
711746
</execution>
712747
</executions>
713748
</plugin>
714-
<plugin>
715-
<groupId>org.sonatype.plugins</groupId>
716-
<artifactId>nexus-staging-maven-plugin</artifactId>
717-
<version>1.6.8</version>
718-
<extensions>true</extensions>
719-
<configuration>
720-
<serverId>ossrh</serverId>
721-
<nexusUrl>https://oss.sonatype.org/</nexusUrl>
722-
<autoReleaseAfterClose>true</autoReleaseAfterClose>
723-
</configuration>
724-
</plugin>
725749
</plugins>
726750
</build>
727751
</profile>

0 commit comments

Comments
 (0)