From 40161f91b374ca415fe5f3528b060dbfd821ccf6 Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Sun, 9 Nov 2025 14:17:22 +0100 Subject: [PATCH 01/16] Added Salvia fruticosa --- org.bridgedb.bio/src/main/java/org/bridgedb/bio/Organism.java | 1 + 1 file changed, 1 insertion(+) diff --git a/org.bridgedb.bio/src/main/java/org/bridgedb/bio/Organism.java b/org.bridgedb.bio/src/main/java/org/bridgedb/bio/Organism.java index 396c3bac..f3b6971a 100644 --- a/org.bridgedb.bio/src/main/java/org/bridgedb/bio/Organism.java +++ b/org.bridgedb.bio/src/main/java/org/bridgedb/bio/Organism.java @@ -97,6 +97,7 @@ public enum Organism { RattusNorvegicus("Rattus norvegicus", "Rn", "Rat", 10116), SaccharomycesCerevisiae("Saccharomyces cerevisiae", "Sc", "Yeast", 4932), + SalviaFruticosa("Salvia fruticosa", "Sf", "Greek sage", 268906), SolanumLycopersicum("Solanum lycopersicum", "Sl", "Tomato", 4081), SkeletonemaMarinoi("Skeletonema marinoi", "Sm", 267567), From 26f9f7fe0f5dd217e46c7b2f2eaa6cb29fb92c7d Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Sat, 28 Dec 2024 14:42:15 +0100 Subject: [PATCH 02/16] Open for development --- org.bridgedb/src/main/resources/version.props | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/org.bridgedb/src/main/resources/version.props b/org.bridgedb/src/main/resources/version.props index 0da9c3ac..62641760 100644 --- a/org.bridgedb/src/main/resources/version.props +++ b/org.bridgedb/src/main/resources/version.props @@ -1,2 +1,2 @@ # Current version of BridgeDb -bridgedb.version=3.1.3 +bridgedb.version=3.1.5 From 4269000b985c18652cc9357339573f3f3c7b2426 Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Sat, 28 Dec 2024 14:44:43 +0100 Subject: [PATCH 03/16] Don't forget to update the Java8 pom too --- README.md | 6 ++++-- pom-java8.xml | 2 +- 2 files changed, 5 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index fee8fd1b..60838684 100644 --- a/README.md +++ b/README.md @@ -135,7 +135,8 @@ To make the release, run the following commands. Mind you, this requires you to have an approved Sonatype (http://oss.sonatype.org/) account with push rights: ```shell -mvn versions:set -DnewVersion=3.1.4 +mvn versions:set -DnewVersion=3.1.5 +mvn -f pom-java8.xml versions:set -DnewVersion=3.1.5 mvn clean deploy ``` @@ -145,7 +146,8 @@ and everything. To make a development (SNAPSHOT) release, use: ```shell -mvn versions:set -DnewVersion=3.1.5-SNAPSHOT +mvn versions:set -DnewVersion=3.1.6-SNAPSHOT +mvn -f pom-java8.xml versions:set -DnewVersion=3.1.6-SNAPSHOT mvn clean deploy ``` diff --git a/pom-java8.xml b/pom-java8.xml index f0bd47b1..17cdb2ea 100644 --- a/pom-java8.xml +++ b/pom-java8.xml @@ -4,7 +4,7 @@ org.bridgedb bridgedb-bundle-pv pom - 3.1.4 + 3.1.5-SNAPSHOT BridgeDb 4 PathVisio bundle BridgeDb is a framework for finding and mapping equivalent database From d2653dc4a2ccb8648875ba0f32a6193f55043a33 Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Sat, 28 Dec 2024 14:02:15 +0100 Subject: [PATCH 04/16] Also handle old UniProt names here --- .../src/main/java/org/bridgedb/DataSource.java | 14 +++++++++++++- 1 file changed, 13 insertions(+), 1 deletion(-) diff --git a/org.bridgedb/src/main/java/org/bridgedb/DataSource.java b/org.bridgedb/src/main/java/org/bridgedb/DataSource.java index 1487399a..9a7737b2 100644 --- a/org.bridgedb/src/main/java/org/bridgedb/DataSource.java +++ b/org.bridgedb/src/main/java/org/bridgedb/DataSource.java @@ -666,6 +666,10 @@ public Builder description(String description){ * @return Builder that can be used for adding detailed information. */ public static Builder register(String sysCode, String fullName){ + if ("Uniprot-TrEMBL".equals(fullName) || "Uniprot-SwissProt".equals(fullName)) { + fullName = "UniProtKB"; + } + if (!isSuitableKey(sysCode)) { throw new IllegalArgumentException ("Unsuitable sysCode " + sysCode + " with " + fullName); } @@ -683,6 +687,10 @@ public static Builder register(String sysCode, String fullName){ * @return Builder that can be used for adding detailed information. */ public static Builder mock(String sysCode, String fullName){ + if ("Uniprot-TrEMBL".equals(fullName) || "Uniprot-SwissProt".equals(fullName)) { + fullName = "UniProtKB"; + } + return new Builder(new DataSource (sysCode, fullName)); } @@ -690,7 +698,11 @@ private static Builder findOrRegister(String sysCode, String fullName) { DataSource current = null; if (fullName == null && sysCode == null) throw new NullPointerException(); - + + if ("Uniprot-TrEMBL".equals(fullName) || "Uniprot-SwissProt".equals(fullName)) { + fullName = "UniProtKB"; + } + if (byFullName.containsKey(fullName)) { current = byFullName.get(fullName); From 470b04b0126bd739f506979f651c8bdb2874701f Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Sat, 28 Dec 2024 14:23:06 +0100 Subject: [PATCH 05/16] Updated for new UniProtKB data source full name --- org.bridgedb.ws.core/test/org/bridgedb/ws/core/Test.java | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/org.bridgedb.ws.core/test/org/bridgedb/ws/core/Test.java b/org.bridgedb.ws.core/test/org/bridgedb/ws/core/Test.java index 0777de0d..cc5d9d89 100644 --- a/org.bridgedb.ws.core/test/org/bridgedb/ws/core/Test.java +++ b/org.bridgedb.ws.core/test/org/bridgedb/ws/core/Test.java @@ -169,12 +169,12 @@ public void testListDataSourceBean() throws ClassNotFoundException, IDMapperExce assertEquals("class org.bridgedb.ws.bean.DataSourceBean",dsBean.getClass().toString()); assertEquals("S",dsBean.getIdExample()); assertEquals("S",dsBean.getSysCode()); - assertEquals("Uniprot-TrEMBL",dsBean.getFullName()); + assertEquals("UniProtKB",dsBean.getFullName()); assertEquals("http://www.uniprot.org/",dsBean.getMainUrl()); assertEquals("protein",dsBean.getType().toString()); assertEquals("http://www.uniprot.org/uniprot/$id", dsBean.getUrlPattern()); assertEquals("urn:miriam:uniprot", dsBean.getUrnBase()); - assertEquals("S:Uniprot-TrEMBL", dsBean.toString()); + assertEquals("S:UniProtKB", dsBean.toString()); assertEquals("sysCode = dsEnsembl", testdsBean.toString()); assertEquals("sysCode = Ensembl", testdsBean2.toString()); From 6314073f0f0988dd42fb9af77d960f23cef55283 Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Sat, 28 Dec 2024 15:47:09 +0100 Subject: [PATCH 06/16] Also backwards compatibility in fullNameExists() --- org.bridgedb/src/main/java/org/bridgedb/DataSource.java | 3 +++ org.bridgedb/src/test/java/org/bridgedb/DataSourceTest.java | 6 ++++++ 2 files changed, 9 insertions(+) diff --git a/org.bridgedb/src/main/java/org/bridgedb/DataSource.java b/org.bridgedb/src/main/java/org/bridgedb/DataSource.java index 9a7737b2..ea002998 100644 --- a/org.bridgedb/src/main/java/org/bridgedb/DataSource.java +++ b/org.bridgedb/src/main/java/org/bridgedb/DataSource.java @@ -835,6 +835,9 @@ public static DataSource getExistingByFullName(String fullName) * @since Version 2.0.0 */ public static boolean fullNameExists(String fullName){ + if ("Uniprot-TrEMBL".equals(fullName) || "Uniprot-SwissProt".equals(fullName)) { + fullName = "UniProtKB"; + } return byFullName.containsKey(fullName); } diff --git a/org.bridgedb/src/test/java/org/bridgedb/DataSourceTest.java b/org.bridgedb/src/test/java/org/bridgedb/DataSourceTest.java index c782b6a3..9cba1f63 100644 --- a/org.bridgedb/src/test/java/org/bridgedb/DataSourceTest.java +++ b/org.bridgedb/src/test/java/org/bridgedb/DataSourceTest.java @@ -505,4 +505,10 @@ public void testBioregistry() { assertFalse(DataSource.bioregistryPrefixExists("unifrot")); } + @Test + public void testFullNameExists() { + assertTrue(DataSource.fullNameExists("Uniprot-TrEMBL"));; + assertTrue(DataSource.fullNameExists("Uniprot-SwissProt"));; + assertTrue(DataSource.fullNameExists("UniProtKB"));; + } } From 70696b23451b4a9c83ad28177db888117eab01be Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Mon, 30 Dec 2024 14:40:18 +0100 Subject: [PATCH 07/16] Register the expected resource --- org.bridgedb/src/test/java/org/bridgedb/DataSourceTest.java | 3 +++ 1 file changed, 3 insertions(+) diff --git a/org.bridgedb/src/test/java/org/bridgedb/DataSourceTest.java b/org.bridgedb/src/test/java/org/bridgedb/DataSourceTest.java index 9cba1f63..9074537a 100644 --- a/org.bridgedb/src/test/java/org/bridgedb/DataSourceTest.java +++ b/org.bridgedb/src/test/java/org/bridgedb/DataSourceTest.java @@ -507,6 +507,9 @@ public void testBioregistry() { @Test public void testFullNameExists() { + DataSource.register("S", "UniProtKB") + .bioregistryPrefix("uniprot") + .asDataSource(); assertTrue(DataSource.fullNameExists("Uniprot-TrEMBL"));; assertTrue(DataSource.fullNameExists("Uniprot-SwissProt"));; assertTrue(DataSource.fullNameExists("UniProtKB"));; From d9d34eca7415d830e12759219f75a4cdbc18ad92 Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Mon, 30 Jun 2025 09:02:16 +0200 Subject: [PATCH 08/16] Open for development --- org.bridgedb/src/main/resources/version.props | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/org.bridgedb/src/main/resources/version.props b/org.bridgedb/src/main/resources/version.props index 62641760..946c3eca 100644 --- a/org.bridgedb/src/main/resources/version.props +++ b/org.bridgedb/src/main/resources/version.props @@ -1,2 +1,2 @@ # Current version of BridgeDb -bridgedb.version=3.1.5 +bridgedb.version=3.1.5-SNAPSHOT From 62bc8e894c04c3582760336d92ebbb0413f8499c Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Mon, 30 Jun 2025 09:25:51 +0200 Subject: [PATCH 09/16] Updated JUnit --- pom.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pom.xml b/pom.xml index 19568c16..1ce53e5c 100644 --- a/pom.xml +++ b/pom.xml @@ -59,7 +59,7 @@ 10.15.2.0 1.3.2 1.11.0 - 5.11.0 + 5.11.4 mysql From 299ebd52aab8b68c1c95a99acee6803d35d79769 Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Mon, 30 Jun 2025 09:26:28 +0200 Subject: [PATCH 10/16] Minimal Java and Maven versions --- pom.xml | 25 ++++++++++++++++++++++++- 1 file changed, 24 insertions(+), 1 deletion(-) diff --git a/pom.xml b/pom.xml index 1ce53e5c..10b9b558 100644 --- a/pom.xml +++ b/pom.xml @@ -95,7 +95,30 @@ - + + org.apache.maven.plugins + maven-enforcer-plugin + 3.5.0 + + + enforce-maven + + enforce + + + + + 3.6.3 + + + 1.11 + + + + + + + org.apache.maven.plugins maven-source-plugin 3.2.1 From f382d596c0b610e60ef335eebb099585a67d4da1 Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Tue, 1 Jul 2025 06:28:04 +0200 Subject: [PATCH 11/16] Proper Java version --- pom.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pom.xml b/pom.xml index 10b9b558..bfde9460 100644 --- a/pom.xml +++ b/pom.xml @@ -111,7 +111,7 @@ 3.6.3 - 1.11 + 11 From a49e7b7000bf98bcdd44d4f0ca85c860a0be7cd1 Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Tue, 1 Jul 2025 06:28:30 +0200 Subject: [PATCH 12/16] Take version from the top pom.xml to reduce duplication --- org.bridgedb.bio/pom.xml | 1 - org.bridgedb.gui/pom.xml | 1 - org.bridgedb.rdb.construct/pom.xml | 1 - org.bridgedb.rdb/pom.xml | 1 - org.bridgedb.sql/pom.xml | 1 - org.bridgedb.uri.api/pom.xml | 1 - org.bridgedb.uri.sql/pom.xml | 1 - org.bridgedb.uri.ws.core/pom.xml | 1 - org.bridgedb.utils/pom.xml | 1 - org.bridgedb.ws.core/pom.xml | 1 - 10 files changed, 10 deletions(-) diff --git a/org.bridgedb.bio/pom.xml b/org.bridgedb.bio/pom.xml index f8972e62..ff4f61a8 100644 --- a/org.bridgedb.bio/pom.xml +++ b/org.bridgedb.bio/pom.xml @@ -56,7 +56,6 @@ org.apache.maven.plugins maven-jar-plugin - 3.2.0 ${project.build.outputDirectory}/META-INF/MANIFEST.MF diff --git a/org.bridgedb.gui/pom.xml b/org.bridgedb.gui/pom.xml index 19e327f8..965b18f1 100644 --- a/org.bridgedb.gui/pom.xml +++ b/org.bridgedb.gui/pom.xml @@ -57,7 +57,6 @@ org.apache.maven.plugins maven-jar-plugin - 3.2.0 ${project.build.outputDirectory}/META-INF/MANIFEST.MF diff --git a/org.bridgedb.rdb.construct/pom.xml b/org.bridgedb.rdb.construct/pom.xml index 7f4a5888..d39e0095 100644 --- a/org.bridgedb.rdb.construct/pom.xml +++ b/org.bridgedb.rdb.construct/pom.xml @@ -57,7 +57,6 @@ org.apache.maven.plugins maven-jar-plugin - 3.2.0 ${project.build.outputDirectory}/META-INF/MANIFEST.MF diff --git a/org.bridgedb.rdb/pom.xml b/org.bridgedb.rdb/pom.xml index 9b1607f6..29222be8 100644 --- a/org.bridgedb.rdb/pom.xml +++ b/org.bridgedb.rdb/pom.xml @@ -56,7 +56,6 @@ org.apache.maven.plugins maven-jar-plugin - 3.2.0 ${project.build.outputDirectory}/META-INF/MANIFEST.MF diff --git a/org.bridgedb.sql/pom.xml b/org.bridgedb.sql/pom.xml index 4be335bf..5f5418ed 100644 --- a/org.bridgedb.sql/pom.xml +++ b/org.bridgedb.sql/pom.xml @@ -21,7 +21,6 @@ org.apache.maven.plugins maven-jar-plugin - 3.2.0 diff --git a/org.bridgedb.uri.api/pom.xml b/org.bridgedb.uri.api/pom.xml index 0c4aefdc..1f5478c6 100644 --- a/org.bridgedb.uri.api/pom.xml +++ b/org.bridgedb.uri.api/pom.xml @@ -32,7 +32,6 @@ org.apache.maven.plugins maven-jar-plugin - 3.2.0 diff --git a/org.bridgedb.uri.sql/pom.xml b/org.bridgedb.uri.sql/pom.xml index 34fc98b3..2bc147d8 100644 --- a/org.bridgedb.uri.sql/pom.xml +++ b/org.bridgedb.uri.sql/pom.xml @@ -32,7 +32,6 @@ org.apache.maven.plugins maven-jar-plugin - 3.2.0 diff --git a/org.bridgedb.uri.ws.core/pom.xml b/org.bridgedb.uri.ws.core/pom.xml index 26e10b89..9618fd01 100644 --- a/org.bridgedb.uri.ws.core/pom.xml +++ b/org.bridgedb.uri.ws.core/pom.xml @@ -33,7 +33,6 @@ org.apache.maven.plugins maven-jar-plugin - 3.2.0 diff --git a/org.bridgedb.utils/pom.xml b/org.bridgedb.utils/pom.xml index f5725b3c..fa8bc9ab 100644 --- a/org.bridgedb.utils/pom.xml +++ b/org.bridgedb.utils/pom.xml @@ -32,7 +32,6 @@ org.apache.maven.plugins maven-jar-plugin - 3.2.0 diff --git a/org.bridgedb.ws.core/pom.xml b/org.bridgedb.ws.core/pom.xml index de94c33f..128a33e7 100644 --- a/org.bridgedb.ws.core/pom.xml +++ b/org.bridgedb.ws.core/pom.xml @@ -33,7 +33,6 @@ org.apache.maven.plugins maven-jar-plugin - 3.2.0 From 0511a1c8096398556fe4241fdfbf1dc8de04a97a Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Tue, 1 Jul 2025 06:28:39 +0200 Subject: [PATCH 13/16] New log4j --- pom.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pom.xml b/pom.xml index bfde9460..76eedc2b 100644 --- a/pom.xml +++ b/pom.xml @@ -49,7 +49,7 @@ 5.1.9 3.0 1.10 - 2.22.0 + 2.25.0 9.0.0 Tomcat 3.4 From 95cc621e629a8ff4dd3429c01fafcbb618dca7dd Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Tue, 1 Jul 2025 07:00:29 +0200 Subject: [PATCH 14/16] Interferes with compiling the core with Java 8, which is also based on this pom.xml --- pom.xml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pom.xml b/pom.xml index 76eedc2b..f09d364a 100644 --- a/pom.xml +++ b/pom.xml @@ -110,9 +110,9 @@ 3.6.3 - + From 98ee29544533cccfc73a416fd4461aa4fe32a917 Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Sun, 16 Nov 2025 19:15:31 +0100 Subject: [PATCH 15/16] Use a more recent MySQL connector --- pom.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pom.xml b/pom.xml index f09d364a..b779b10d 100644 --- a/pom.xml +++ b/pom.xml @@ -50,7 +50,7 @@ 3.0 1.10 2.25.0 - 9.0.0 + 9.5.0 Tomcat 3.4 4.3.8 From e2c95523173dd21739909a96eafb5d3ad4505be6 Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Tue, 18 Nov 2025 15:01:16 +0100 Subject: [PATCH 16/16] Added potato --- org.bridgedb.bio/src/main/java/org/bridgedb/bio/Organism.java | 1 + 1 file changed, 1 insertion(+) diff --git a/org.bridgedb.bio/src/main/java/org/bridgedb/bio/Organism.java b/org.bridgedb.bio/src/main/java/org/bridgedb/bio/Organism.java index f3b6971a..2119ba20 100644 --- a/org.bridgedb.bio/src/main/java/org/bridgedb/bio/Organism.java +++ b/org.bridgedb.bio/src/main/java/org/bridgedb/bio/Organism.java @@ -99,6 +99,7 @@ public enum Organism { SaccharomycesCerevisiae("Saccharomyces cerevisiae", "Sc", "Yeast", 4932), SalviaFruticosa("Salvia fruticosa", "Sf", "Greek sage", 268906), SolanumLycopersicum("Solanum lycopersicum", "Sl", "Tomato", 4081), + SolanumTuberosum("Solanum tuberosum", "St", "potato", 4113), SkeletonemaMarinoi("Skeletonema marinoi", "Sm", 267567), SorexAraneus ("Sorex araneus", "Sa", "Shrew", 42254),