From b263c80ee1adf8cece2ee651ea63c29304347011 Mon Sep 17 00:00:00 2001 From: Joel Weiser Date: Tue, 21 Jan 2025 19:52:56 -0500 Subject: [PATCH 1/7] updates pom.xml for sonatype --- pom.xml | 119 +++++++++++++++++++++++++++++++++++++++++++++++++++----- 1 file changed, 109 insertions(+), 10 deletions(-) diff --git a/pom.xml b/pom.xml index a96a2f0..de8766e 100644 --- a/pom.xml +++ b/pom.xml @@ -3,13 +3,16 @@ xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd"> - 4.0.0 + org.reactome.web.pwp analysis-client - jar 2.0.4 + jar + Analysis Client + Analysis Client for Reactome Analysis Service + https://github.com/reactome/pwp-analysis-client org.reactome.maven @@ -17,30 +20,45 @@ 1.0.3 - - Analysis Client for Reactome Analysis Service - - - The European Bioinformatics Institute - https://www.ebi.ac.uk/ + Reactome + https://reactome.org + + + The Apache Software License, Version 2.0 + https://www.apache.org/licenses/LICENSE-2.0.txt + + + fabregat Antonio Fabregat - fabregat@ebi.ac.uk + + alumni + + The European Bioinformatics Institute https://www.ebi.ac.uk/ ksidiro Kostas Sidiropoulos - ksidiro@ebi.ac.uk + + alumni + + The European Bioinformatics Institute https://www.ebi.ac.uk/ + + scm:git:git://github.com/reactome/pwp-analysis-client.git + scm:git:ssh://github.com/reactome/pwp-analysis-client.git + https://github.com/reactome/pwp-analysis-client/tree/master + + OBF @@ -53,6 +71,13 @@ org.reactome.web.analysis.Analysis ${appModule} + + + 3.2.7 + 3.11.2 + 3.3.1 + 3.3.1 + 1.7.0 @@ -240,6 +265,63 @@ ${maven.deploy.version} + + + org.sonatype.plugins + nexus-staging-maven-plugin + ${nexus-staging-maven-plugin} + true + + ossrh + https://s01.oss.sonatype.org/ + true + + + + + + org.apache.maven.plugins + maven-javadoc-plugin + ${maven.javadoc.version} + + + attach-javadocs + + jar + + + + + + + + org.apache.maven.plugins + maven-gpg-plugin + ${maven.gpg.version} + + + sign-artifacts + verify + + sign + + + + + + + + org.apache.maven.plugins + maven-release-plugin + ${maven.release.version} + + true + true + false + release + deploy + + @@ -252,6 +334,23 @@ + + + + + ossrh + Sonatype Release Repository + https://oss.sonatype.org/service/local/staging/deploy/maven2 + + + + + ossrh + Sonatype Snapshot Repository + https://oss.sonatype.org/content/repositories/snapshots + + + central From 278404b7a21140b2f8ff4cfe927468999ab5e222 Mon Sep 17 00:00:00 2001 From: Joel Weiser Date: Tue, 21 Jan 2025 19:59:01 -0500 Subject: [PATCH 2/7] updates JavaDocs --- .../java/org/reactome/web/analysis/client/AnalysisClient.java | 2 +- .../java/org/reactome/web/analysis/client/AnalysisHandler.java | 2 +- .../web/analysis/client/exceptions/AnalysisModelException.java | 2 +- .../org/reactome/web/analysis/client/model/AnalysisError.java | 2 +- .../org/reactome/web/analysis/client/model/AnalysisResult.java | 2 +- .../org/reactome/web/analysis/client/model/AnalysisSummary.java | 2 +- .../org/reactome/web/analysis/client/model/AnalysisType.java | 2 +- src/main/java/org/reactome/web/analysis/client/model/Bin.java | 2 +- .../java/org/reactome/web/analysis/client/model/DBInfo.java | 2 +- .../reactome/web/analysis/client/model/EntityStatistics.java | 2 +- .../reactome/web/analysis/client/model/ExpressionSummary.java | 2 +- .../org/reactome/web/analysis/client/model/FoundElements.java | 2 +- .../org/reactome/web/analysis/client/model/FoundEntities.java | 2 +- .../org/reactome/web/analysis/client/model/FoundEntity.java | 2 +- .../org/reactome/web/analysis/client/model/FoundInteractor.java | 2 +- .../reactome/web/analysis/client/model/FoundInteractors.java | 2 +- .../org/reactome/web/analysis/client/model/IdentifierMap.java | 2 +- .../reactome/web/analysis/client/model/IdentifierSummary.java | 2 +- .../reactome/web/analysis/client/model/InteractorEvidence.java | 2 +- .../org/reactome/web/analysis/client/model/PathwayBase.java | 2 +- .../org/reactome/web/analysis/client/model/PathwaySummary.java | 2 +- .../reactome/web/analysis/client/model/ReactionStatistics.java | 2 +- .../org/reactome/web/analysis/client/model/ResourceSummary.java | 2 +- .../web/analysis/client/model/SpeciesFilteredResult.java | 2 +- .../org/reactome/web/analysis/client/model/SpeciesSummary.java | 2 +- .../java/org/reactome/web/analysis/client/model/Statistics.java | 2 +- .../web/analysis/client/model/factory/AnalysisModelFactory.java | 2 +- src/main/java/org/reactome/web/analysis/test/AnalysisTest.java | 2 +- .../web/analysis/client/GwtTestInteractorsProjection.java | 2 +- 29 files changed, 29 insertions(+), 29 deletions(-) diff --git a/src/main/java/org/reactome/web/analysis/client/AnalysisClient.java b/src/main/java/org/reactome/web/analysis/client/AnalysisClient.java index 6be1c6d..044e218 100644 --- a/src/main/java/org/reactome/web/analysis/client/AnalysisClient.java +++ b/src/main/java/org/reactome/web/analysis/client/AnalysisClient.java @@ -17,7 +17,7 @@ /** * @author Antonio Fabregat (fabregat@ebi.ac.uk) - * @author Kostas Sidiropoulos + * @author Kostas Sidiropoulos (ksidiro@ebi.ac.uk) */ public abstract class AnalysisClient { diff --git a/src/main/java/org/reactome/web/analysis/client/AnalysisHandler.java b/src/main/java/org/reactome/web/analysis/client/AnalysisHandler.java index e036148..e68af2b 100755 --- a/src/main/java/org/reactome/web/analysis/client/AnalysisHandler.java +++ b/src/main/java/org/reactome/web/analysis/client/AnalysisHandler.java @@ -7,7 +7,7 @@ import java.util.Set; /** - * @author Antonio Fabregat + * @author Antonio Fabregat (fabregat@ebi.ac.uk) */ public interface AnalysisHandler { diff --git a/src/main/java/org/reactome/web/analysis/client/exceptions/AnalysisModelException.java b/src/main/java/org/reactome/web/analysis/client/exceptions/AnalysisModelException.java index fcc3930..b1da26a 100644 --- a/src/main/java/org/reactome/web/analysis/client/exceptions/AnalysisModelException.java +++ b/src/main/java/org/reactome/web/analysis/client/exceptions/AnalysisModelException.java @@ -1,7 +1,7 @@ package org.reactome.web.analysis.client.exceptions; /** - * @author Antonio Fabregat + * @author Antonio Fabregat (fabregat@ebi.ac.uk) */ public class AnalysisModelException extends Exception { diff --git a/src/main/java/org/reactome/web/analysis/client/model/AnalysisError.java b/src/main/java/org/reactome/web/analysis/client/model/AnalysisError.java index 53be968..663969e 100644 --- a/src/main/java/org/reactome/web/analysis/client/model/AnalysisError.java +++ b/src/main/java/org/reactome/web/analysis/client/model/AnalysisError.java @@ -3,7 +3,7 @@ import java.util.List; /** - * @author Antonio Fabregat + * @author Antonio Fabregat (fabregat@ebi.ac.uk) */ public interface AnalysisError { diff --git a/src/main/java/org/reactome/web/analysis/client/model/AnalysisResult.java b/src/main/java/org/reactome/web/analysis/client/model/AnalysisResult.java index 8e21fc9..0cce021 100644 --- a/src/main/java/org/reactome/web/analysis/client/model/AnalysisResult.java +++ b/src/main/java/org/reactome/web/analysis/client/model/AnalysisResult.java @@ -3,7 +3,7 @@ import java.util.List; /** - * @author Antonio Fabregat + * @author Antonio Fabregat (fabregat@ebi.ac.uk) */ public interface AnalysisResult { diff --git a/src/main/java/org/reactome/web/analysis/client/model/AnalysisSummary.java b/src/main/java/org/reactome/web/analysis/client/model/AnalysisSummary.java index 49cf065..16878c8 100644 --- a/src/main/java/org/reactome/web/analysis/client/model/AnalysisSummary.java +++ b/src/main/java/org/reactome/web/analysis/client/model/AnalysisSummary.java @@ -1,7 +1,7 @@ package org.reactome.web.analysis.client.model; /** - * @author Antonio Fabregat + * @author Antonio Fabregat (fabregat@ebi.ac.uk) */ public interface AnalysisSummary { diff --git a/src/main/java/org/reactome/web/analysis/client/model/AnalysisType.java b/src/main/java/org/reactome/web/analysis/client/model/AnalysisType.java index 7fbaf41..381f5f3 100755 --- a/src/main/java/org/reactome/web/analysis/client/model/AnalysisType.java +++ b/src/main/java/org/reactome/web/analysis/client/model/AnalysisType.java @@ -1,7 +1,7 @@ package org.reactome.web.analysis.client.model; /** - * @author Antonio Fabregat + * @author Antonio Fabregat (fabregat@ebi.ac.uk) */ public enum AnalysisType { diff --git a/src/main/java/org/reactome/web/analysis/client/model/Bin.java b/src/main/java/org/reactome/web/analysis/client/model/Bin.java index 583e4ba..c4e65c5 100644 --- a/src/main/java/org/reactome/web/analysis/client/model/Bin.java +++ b/src/main/java/org/reactome/web/analysis/client/model/Bin.java @@ -1,7 +1,7 @@ package org.reactome.web.analysis.client.model; /** - * @author Kostas Sidiropoulos + * @author Kostas Sidiropoulos (ksidiro@ebi.ac.uk) */ public interface Bin { diff --git a/src/main/java/org/reactome/web/analysis/client/model/DBInfo.java b/src/main/java/org/reactome/web/analysis/client/model/DBInfo.java index 718ecba..583ea29 100644 --- a/src/main/java/org/reactome/web/analysis/client/model/DBInfo.java +++ b/src/main/java/org/reactome/web/analysis/client/model/DBInfo.java @@ -1,7 +1,7 @@ package org.reactome.web.analysis.client.model; /** - * @author Antonio Fabregat + * @author Antonio Fabregat (fabregat@ebi.ac.uk) */ public interface DBInfo { diff --git a/src/main/java/org/reactome/web/analysis/client/model/EntityStatistics.java b/src/main/java/org/reactome/web/analysis/client/model/EntityStatistics.java index 2f84b65..d799590 100644 --- a/src/main/java/org/reactome/web/analysis/client/model/EntityStatistics.java +++ b/src/main/java/org/reactome/web/analysis/client/model/EntityStatistics.java @@ -3,7 +3,7 @@ import java.util.List; /** - * @author Antonio Fabregat + * @author Antonio Fabregat (fabregat@ebi.ac.uk) */ public interface EntityStatistics extends Statistics { diff --git a/src/main/java/org/reactome/web/analysis/client/model/ExpressionSummary.java b/src/main/java/org/reactome/web/analysis/client/model/ExpressionSummary.java index efea820..8f5f7c6 100644 --- a/src/main/java/org/reactome/web/analysis/client/model/ExpressionSummary.java +++ b/src/main/java/org/reactome/web/analysis/client/model/ExpressionSummary.java @@ -3,7 +3,7 @@ import java.util.List; /** - * @author Antonio Fabregat + * @author Antonio Fabregat (fabregat@ebi.ac.uk) */ public interface ExpressionSummary { List getColumnNames(); diff --git a/src/main/java/org/reactome/web/analysis/client/model/FoundElements.java b/src/main/java/org/reactome/web/analysis/client/model/FoundElements.java index ecb8b0e..dcc41f2 100644 --- a/src/main/java/org/reactome/web/analysis/client/model/FoundElements.java +++ b/src/main/java/org/reactome/web/analysis/client/model/FoundElements.java @@ -4,7 +4,7 @@ import java.util.Set; /** - * @author Antonio Fabregat + * @author Antonio Fabregat (fabregat@ebi.ac.uk) */ public interface FoundElements { diff --git a/src/main/java/org/reactome/web/analysis/client/model/FoundEntities.java b/src/main/java/org/reactome/web/analysis/client/model/FoundEntities.java index 24e61aa..7589a96 100644 --- a/src/main/java/org/reactome/web/analysis/client/model/FoundEntities.java +++ b/src/main/java/org/reactome/web/analysis/client/model/FoundEntities.java @@ -4,7 +4,7 @@ import java.util.Map; /** - * @author Antonio Fabregat + * @author Antonio Fabregat (fabregat@ebi.ac.uk) */ public interface FoundEntities { diff --git a/src/main/java/org/reactome/web/analysis/client/model/FoundEntity.java b/src/main/java/org/reactome/web/analysis/client/model/FoundEntity.java index 50e3727..7b4ee71 100644 --- a/src/main/java/org/reactome/web/analysis/client/model/FoundEntity.java +++ b/src/main/java/org/reactome/web/analysis/client/model/FoundEntity.java @@ -3,7 +3,7 @@ import java.util.Set; /** - * @author Antonio Fabregat + * @author Antonio Fabregat (fabregat@ebi.ac.uk) */ public interface FoundEntity extends IdentifierSummary { diff --git a/src/main/java/org/reactome/web/analysis/client/model/FoundInteractor.java b/src/main/java/org/reactome/web/analysis/client/model/FoundInteractor.java index a757a84..dd00ce1 100644 --- a/src/main/java/org/reactome/web/analysis/client/model/FoundInteractor.java +++ b/src/main/java/org/reactome/web/analysis/client/model/FoundInteractor.java @@ -3,7 +3,7 @@ import java.util.Set; /** - * @author Antonio Fabregat + * @author Antonio Fabregat (fabregat@ebi.ac.uk) */ public interface FoundInteractor extends IdentifierSummary { diff --git a/src/main/java/org/reactome/web/analysis/client/model/FoundInteractors.java b/src/main/java/org/reactome/web/analysis/client/model/FoundInteractors.java index 8067204..2a23d9e 100644 --- a/src/main/java/org/reactome/web/analysis/client/model/FoundInteractors.java +++ b/src/main/java/org/reactome/web/analysis/client/model/FoundInteractors.java @@ -4,7 +4,7 @@ import java.util.Set; /** - * @author Antonio Fabregat + * @author Antonio Fabregat (fabregat@ebi.ac.uk) */ public interface FoundInteractors { diff --git a/src/main/java/org/reactome/web/analysis/client/model/IdentifierMap.java b/src/main/java/org/reactome/web/analysis/client/model/IdentifierMap.java index 0b998ef..3c9f88c 100644 --- a/src/main/java/org/reactome/web/analysis/client/model/IdentifierMap.java +++ b/src/main/java/org/reactome/web/analysis/client/model/IdentifierMap.java @@ -3,7 +3,7 @@ import java.util.Set; /** - * @author Antonio Fabregat + * @author Antonio Fabregat (fabregat@ebi.ac.uk) */ public interface IdentifierMap { diff --git a/src/main/java/org/reactome/web/analysis/client/model/IdentifierSummary.java b/src/main/java/org/reactome/web/analysis/client/model/IdentifierSummary.java index 92581ae..5e68b17 100644 --- a/src/main/java/org/reactome/web/analysis/client/model/IdentifierSummary.java +++ b/src/main/java/org/reactome/web/analysis/client/model/IdentifierSummary.java @@ -3,7 +3,7 @@ import java.util.List; /** - * @author Antonio Fabregat + * @author Antonio Fabregat (fabregat@ebi.ac.uk) */ public interface IdentifierSummary { diff --git a/src/main/java/org/reactome/web/analysis/client/model/InteractorEvidence.java b/src/main/java/org/reactome/web/analysis/client/model/InteractorEvidence.java index a1aba0e..05474e1 100644 --- a/src/main/java/org/reactome/web/analysis/client/model/InteractorEvidence.java +++ b/src/main/java/org/reactome/web/analysis/client/model/InteractorEvidence.java @@ -1,7 +1,7 @@ package org.reactome.web.analysis.client.model; /** - * @author Antonio Fabregat + * @author Antonio Fabregat (fabregat@ebi.ac.uk) */ public interface InteractorEvidence extends IdentifierSummary { diff --git a/src/main/java/org/reactome/web/analysis/client/model/PathwayBase.java b/src/main/java/org/reactome/web/analysis/client/model/PathwayBase.java index cfb3baf..7551d70 100644 --- a/src/main/java/org/reactome/web/analysis/client/model/PathwayBase.java +++ b/src/main/java/org/reactome/web/analysis/client/model/PathwayBase.java @@ -1,7 +1,7 @@ package org.reactome.web.analysis.client.model; /** - * @author Antonio Fabregat + * @author Antonio Fabregat (fabregat@ebi.ac.uk) */ public interface PathwayBase { diff --git a/src/main/java/org/reactome/web/analysis/client/model/PathwaySummary.java b/src/main/java/org/reactome/web/analysis/client/model/PathwaySummary.java index f060a11..3b6b72d 100644 --- a/src/main/java/org/reactome/web/analysis/client/model/PathwaySummary.java +++ b/src/main/java/org/reactome/web/analysis/client/model/PathwaySummary.java @@ -1,7 +1,7 @@ package org.reactome.web.analysis.client.model; /** - * @author Antonio Fabregat + * @author Antonio Fabregat (fabregat@ebi.ac.uk) */ public interface PathwaySummary { String getStId(); diff --git a/src/main/java/org/reactome/web/analysis/client/model/ReactionStatistics.java b/src/main/java/org/reactome/web/analysis/client/model/ReactionStatistics.java index 2dd629f..4108d84 100644 --- a/src/main/java/org/reactome/web/analysis/client/model/ReactionStatistics.java +++ b/src/main/java/org/reactome/web/analysis/client/model/ReactionStatistics.java @@ -1,7 +1,7 @@ package org.reactome.web.analysis.client.model; /** - * @author Antonio Fabregat + * @author Antonio Fabregat (fabregat@ebi.ac.uk) */ public interface ReactionStatistics extends Statistics { } diff --git a/src/main/java/org/reactome/web/analysis/client/model/ResourceSummary.java b/src/main/java/org/reactome/web/analysis/client/model/ResourceSummary.java index 76a78ad..fd6b7a9 100644 --- a/src/main/java/org/reactome/web/analysis/client/model/ResourceSummary.java +++ b/src/main/java/org/reactome/web/analysis/client/model/ResourceSummary.java @@ -1,7 +1,7 @@ package org.reactome.web.analysis.client.model; /** - * @author Antonio Fabregat + * @author Antonio Fabregat (fabregat@ebi.ac.uk) */ public interface ResourceSummary { diff --git a/src/main/java/org/reactome/web/analysis/client/model/SpeciesFilteredResult.java b/src/main/java/org/reactome/web/analysis/client/model/SpeciesFilteredResult.java index 2c42ae2..1f9df37 100644 --- a/src/main/java/org/reactome/web/analysis/client/model/SpeciesFilteredResult.java +++ b/src/main/java/org/reactome/web/analysis/client/model/SpeciesFilteredResult.java @@ -3,7 +3,7 @@ import java.util.List; /** - * @author Antonio Fabregat + * @author Antonio Fabregat (fabregat@ebi.ac.uk) */ public interface SpeciesFilteredResult { diff --git a/src/main/java/org/reactome/web/analysis/client/model/SpeciesSummary.java b/src/main/java/org/reactome/web/analysis/client/model/SpeciesSummary.java index 1b4c955..2e463b3 100644 --- a/src/main/java/org/reactome/web/analysis/client/model/SpeciesSummary.java +++ b/src/main/java/org/reactome/web/analysis/client/model/SpeciesSummary.java @@ -1,7 +1,7 @@ package org.reactome.web.analysis.client.model; /** - * @author Antonio Fabregat + * @author Antonio Fabregat (fabregat@ebi.ac.uk) */ public interface SpeciesSummary { diff --git a/src/main/java/org/reactome/web/analysis/client/model/Statistics.java b/src/main/java/org/reactome/web/analysis/client/model/Statistics.java index 8d46d76..b724669 100644 --- a/src/main/java/org/reactome/web/analysis/client/model/Statistics.java +++ b/src/main/java/org/reactome/web/analysis/client/model/Statistics.java @@ -1,7 +1,7 @@ package org.reactome.web.analysis.client.model; /** - * @author Antonio Fabregat + * @author Antonio Fabregat (fabregat@ebi.ac.uk) */ public interface Statistics { diff --git a/src/main/java/org/reactome/web/analysis/client/model/factory/AnalysisModelFactory.java b/src/main/java/org/reactome/web/analysis/client/model/factory/AnalysisModelFactory.java index af7f56c..3b03240 100644 --- a/src/main/java/org/reactome/web/analysis/client/model/factory/AnalysisModelFactory.java +++ b/src/main/java/org/reactome/web/analysis/client/model/factory/AnalysisModelFactory.java @@ -15,7 +15,7 @@ import java.util.List; /** - * @author Antonio Fabregat + * @author Antonio Fabregat (fabregat@ebi.ac.uk) */ public abstract class AnalysisModelFactory { diff --git a/src/main/java/org/reactome/web/analysis/test/AnalysisTest.java b/src/main/java/org/reactome/web/analysis/test/AnalysisTest.java index ab53ae2..275b7e4 100644 --- a/src/main/java/org/reactome/web/analysis/test/AnalysisTest.java +++ b/src/main/java/org/reactome/web/analysis/test/AnalysisTest.java @@ -3,7 +3,7 @@ import com.google.gwt.core.client.EntryPoint; /** - * @author Antonio Fabregat + * @author Antonio Fabregat (fabregat@ebi.ac.uk) */ public class AnalysisTest implements EntryPoint { diff --git a/src/test/java/org/reactome/web/analysis/client/GwtTestInteractorsProjection.java b/src/test/java/org/reactome/web/analysis/client/GwtTestInteractorsProjection.java index 8077aea..036c9e8 100644 --- a/src/test/java/org/reactome/web/analysis/client/GwtTestInteractorsProjection.java +++ b/src/test/java/org/reactome/web/analysis/client/GwtTestInteractorsProjection.java @@ -6,7 +6,7 @@ import org.reactome.web.analysis.client.model.FoundInteractors; /** - * @author Antonio Fabregat + * @author Antonio Fabregat (fabregat@ebi.ac.uk) */ public class GwtTestInteractorsProjection extends GWTTestCase { From ffd39edb94e31698e78e29df9601cab5ffec2ef2 Mon Sep 17 00:00:00 2001 From: Joel Weiser Date: Thu, 23 Jan 2025 12:16:12 -0500 Subject: [PATCH 3/7] updates version to 2.0.5-SNAPSHOT --- pom.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pom.xml b/pom.xml index de8766e..5d3b58f 100644 --- a/pom.xml +++ b/pom.xml @@ -7,7 +7,7 @@ org.reactome.web.pwp analysis-client - 2.0.4 + 2.0.5-SNAPSHOT jar Analysis Client From b0b3443bd11111fec5db64397008f2111ef0f713 Mon Sep 17 00:00:00 2001 From: Joel Weiser Date: Thu, 23 Jan 2025 12:23:37 -0500 Subject: [PATCH 4/7] Create LICENSE --- LICENSE | 201 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 201 insertions(+) create mode 100644 LICENSE diff --git a/LICENSE b/LICENSE new file mode 100644 index 0000000..261eeb9 --- /dev/null +++ b/LICENSE @@ -0,0 +1,201 @@ + Apache License + Version 2.0, January 2004 + http://www.apache.org/licenses/ + + TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION + + 1. 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From 48626411e0ddb2385a46352c029050cd1f82f798 Mon Sep 17 00:00:00 2001 From: Joel Weiser Date: Fri, 11 Jul 2025 02:30:01 -0400 Subject: [PATCH 5/7] updates version and reactome-pwp-parent version --- pom.xml | 11 ++--------- 1 file changed, 2 insertions(+), 9 deletions(-) diff --git a/pom.xml b/pom.xml index 5d3b58f..6c507f8 100644 --- a/pom.xml +++ b/pom.xml @@ -7,7 +7,7 @@ org.reactome.web.pwp analysis-client - 2.0.5-SNAPSHOT + 2.0.5 jar Analysis Client @@ -17,7 +17,7 @@ org.reactome.maven reactome-pwp-parent - 1.0.3 + 1.0.4 @@ -71,13 +71,6 @@ org.reactome.web.analysis.Analysis ${appModule} - - - 3.2.7 - 3.11.2 - 3.3.1 - 3.3.1 - 1.7.0 From df8c4f2f8fce5733a135f907da8e57623271595b Mon Sep 17 00:00:00 2001 From: Joel Weiser Date: Wed, 16 Jul 2025 23:38:50 -0400 Subject: [PATCH 6/7] removes unneeded distr. management and plugins from pom.xml - now inherited --- pom.xml | 96 --------------------------------------------------------- 1 file changed, 96 deletions(-) diff --git a/pom.xml b/pom.xml index 6c507f8..0f734f6 100644 --- a/pom.xml +++ b/pom.xml @@ -236,85 +236,6 @@ ${webappDirectory} - - - org.apache.maven.plugins - maven-source-plugin - ${maven.source.version} - - - attach-sources - - jar - - - - - - - org.apache.maven.plugins - maven-deploy-plugin - true - ${maven.deploy.version} - - - - - org.sonatype.plugins - nexus-staging-maven-plugin - ${nexus-staging-maven-plugin} - true - - ossrh - https://s01.oss.sonatype.org/ - true - - - - - - org.apache.maven.plugins - maven-javadoc-plugin - ${maven.javadoc.version} - - - attach-javadocs - - jar - - - - - - - - org.apache.maven.plugins - maven-gpg-plugin - ${maven.gpg.version} - - - sign-artifacts - verify - - sign - - - - - - - - org.apache.maven.plugins - maven-release-plugin - ${maven.release.version} - - true - true - false - release - deploy - - @@ -327,23 +248,6 @@ - - - - - ossrh - Sonatype Release Repository - https://oss.sonatype.org/service/local/staging/deploy/maven2 - - - - - ossrh - Sonatype Snapshot Repository - https://oss.sonatype.org/content/repositories/snapshots - - - central From 7e4f4f6b784ef4cb214b9c14076d1e01ae62baf8 Mon Sep 17 00:00:00 2001 From: Joel Weiser Date: Thu, 17 Jul 2025 18:46:59 -0400 Subject: [PATCH 7/7] organizes pom.xml with mvn tidy --- pom.xml | 129 ++++++++++++++++++++++++++------------------------------ 1 file changed, 59 insertions(+), 70 deletions(-) diff --git a/pom.xml b/pom.xml index 0f734f6..3a183c3 100644 --- a/pom.xml +++ b/pom.xml @@ -1,10 +1,13 @@ - + 4.0.0 + + org.reactome.maven + reactome-pwp-parent + 1.0.4 + + org.reactome.web.pwp analysis-client 2.0.5 @@ -13,18 +16,10 @@ Analysis Client Analysis Client for Reactome Analysis Service https://github.com/reactome/pwp-analysis-client - - - org.reactome.maven - reactome-pwp-parent - 1.0.4 - - Reactome https://reactome.org - The Apache Software License, Version 2.0 @@ -84,17 +79,6 @@ - - - - dev - - org.reactome.web.AnalysisTest - widgettest - - - - com.google.gwt @@ -156,10 +140,49 @@ - - - ${webappDirectory}/WEB-INF/classes + + + + nexus-ebi-repo + The EBI internal repository + https://www.ebi.ac.uk/Tools/maven/repos/content/groups/ebi-repo/ + + true + + + false + + + + + nexus-ebi-snapshot-repo + The EBI internal snapshot repository + https://www.ebi.ac.uk/Tools/maven/repos/content/groups/ebi-snapshots/ + + false + + + true + + + + + + central + Central Repository + https://repo.maven.apache.org/maven2 + default + + false + + + never + + + + + ${webappDirectory}/WEB-INF/classes org.apache.maven.plugins @@ -237,7 +260,6 @@ - @@ -248,46 +270,13 @@ - - - central - Central Repository - https://repo.maven.apache.org/maven2 - default - - false - - - never - - - - - - - - nexus-ebi-repo - The EBI internal repository - https://www.ebi.ac.uk/Tools/maven/repos/content/groups/ebi-repo/ - - true - - - false - - - - - nexus-ebi-snapshot-repo - The EBI internal snapshot repository - https://www.ebi.ac.uk/Tools/maven/repos/content/groups/ebi-snapshots/ - - false - - - true - - - - - \ No newline at end of file + + + dev + + org.reactome.web.AnalysisTest + widgettest + + + +