From 1b6f47e6404ff84d080936d1f5c0169f928cf785 Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Sat, 21 Sep 2024 09:10:48 +0200 Subject: [PATCH 01/16] Open for development --- examples/pom.xml | 2 +- org.bridgedb.bio/pom.xml | 2 +- org.bridgedb.file.orthoxml/pom.xml | 2 +- org.bridgedb.gui/pom.xml | 2 +- org.bridgedb.rdb.construct/pom.xml | 2 +- org.bridgedb.rdb/pom.xml | 2 +- org.bridgedb.rdf/pom.xml | 2 +- org.bridgedb.sql/pom.xml | 2 +- org.bridgedb.tools.batchmapper/pom.xml | 8 ++++---- org.bridgedb.tools.info/pom.xml | 2 +- org.bridgedb.tools.qc/pom.xml | 2 +- org.bridgedb.tools.voidtool/pom.xml | 2 +- org.bridgedb.uri.api/pom.xml | 2 +- org.bridgedb.uri.loader/pom.xml | 2 +- org.bridgedb.uri.sql/pom.xml | 2 +- org.bridgedb.uri.ws.client/pom.xml | 2 +- org.bridgedb.uri.ws.core/pom.xml | 2 +- org.bridgedb.uri.ws.server/pom.xml | 2 +- org.bridgedb.utils/pom.xml | 2 +- org.bridgedb.webservice.biomart/pom.xml | 2 +- org.bridgedb.webservice.bridgerest/pom.xml | 2 +- org.bridgedb.ws.client/pom.xml | 2 +- org.bridgedb.ws.core/pom.xml | 2 +- org.bridgedb.ws.server/pom.xml | 2 +- org.bridgedb/pom.xml | 2 +- pom.xml | 2 +- 26 files changed, 29 insertions(+), 29 deletions(-) diff --git a/examples/pom.xml b/examples/pom.xml index 0c490e85b..a2c683fc1 100644 --- a/examples/pom.xml +++ b/examples/pom.xml @@ -3,7 +3,7 @@ bridgedb-bundle org.bridgedb - 3.1.2 + 3.1.3-SNAPSHOT 4.0.0 org.bridgedb.examples diff --git a/org.bridgedb.bio/pom.xml b/org.bridgedb.bio/pom.xml index d92cfc8fe..211fb58f8 100644 --- a/org.bridgedb.bio/pom.xml +++ b/org.bridgedb.bio/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.1.2 + 3.1.3-SNAPSHOT diff --git a/org.bridgedb.file.orthoxml/pom.xml b/org.bridgedb.file.orthoxml/pom.xml index 2cd2f9413..88b5d884f 100644 --- a/org.bridgedb.file.orthoxml/pom.xml +++ b/org.bridgedb.file.orthoxml/pom.xml @@ -6,7 +6,7 @@ bridgedb-bundle org.bridgedb - 3.1.2 + 3.1.3-SNAPSHOT diff --git a/org.bridgedb.gui/pom.xml b/org.bridgedb.gui/pom.xml index a2e97b835..a3e041099 100644 --- a/org.bridgedb.gui/pom.xml +++ b/org.bridgedb.gui/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.2 + 3.1.3-SNAPSHOT diff --git a/org.bridgedb.rdb.construct/pom.xml b/org.bridgedb.rdb.construct/pom.xml index feb7e76d3..fe55c4414 100644 --- a/org.bridgedb.rdb.construct/pom.xml +++ b/org.bridgedb.rdb.construct/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.2 + 3.1.3-SNAPSHOT diff --git a/org.bridgedb.rdb/pom.xml b/org.bridgedb.rdb/pom.xml index 88c3a389e..fdeffdc43 100644 --- a/org.bridgedb.rdb/pom.xml +++ b/org.bridgedb.rdb/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.2 + 3.1.3-SNAPSHOT diff --git a/org.bridgedb.rdf/pom.xml b/org.bridgedb.rdf/pom.xml index 50eec5bc7..14e4863d9 100644 --- a/org.bridgedb.rdf/pom.xml +++ b/org.bridgedb.rdf/pom.xml @@ -6,7 +6,7 @@ bridgedb-bundle org.bridgedb - 3.1.2 + 3.1.3-SNAPSHOT diff --git a/org.bridgedb.sql/pom.xml b/org.bridgedb.sql/pom.xml index 763f300fe..5ccd3e6d0 100644 --- a/org.bridgedb.sql/pom.xml +++ b/org.bridgedb.sql/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.2 + 3.1.3-SNAPSHOT diff --git a/org.bridgedb.tools.batchmapper/pom.xml b/org.bridgedb.tools.batchmapper/pom.xml index 4d26f9632..4a489cede 100644 --- a/org.bridgedb.tools.batchmapper/pom.xml +++ b/org.bridgedb.tools.batchmapper/pom.xml @@ -6,7 +6,7 @@ bridgedb-bundle org.bridgedb - 3.1.2 + 3.1.3-SNAPSHOT @@ -33,19 +33,19 @@ org.bridgedb org.bridgedb - 3.1.2 + 3.1.3-SNAPSHOT compile org.bridgedb org.bridgedb.bio - 3.1.2 + 3.1.3-SNAPSHOT compile org.bridgedb org.bridgedb.rdb - 3.1.2 + 3.1.3-SNAPSHOT compile diff --git a/org.bridgedb.tools.info/pom.xml b/org.bridgedb.tools.info/pom.xml index dcd850997..b5ecac8a0 100644 --- a/org.bridgedb.tools.info/pom.xml +++ b/org.bridgedb.tools.info/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.2 + 3.1.3-SNAPSHOT diff --git a/org.bridgedb.tools.qc/pom.xml b/org.bridgedb.tools.qc/pom.xml index 9dd9273a2..d9145e1d0 100644 --- a/org.bridgedb.tools.qc/pom.xml +++ b/org.bridgedb.tools.qc/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.2 + 3.1.3-SNAPSHOT diff --git a/org.bridgedb.tools.voidtool/pom.xml b/org.bridgedb.tools.voidtool/pom.xml index 32b8fdd5a..96e160566 100644 --- a/org.bridgedb.tools.voidtool/pom.xml +++ b/org.bridgedb.tools.voidtool/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.2 + 3.1.3-SNAPSHOT diff --git a/org.bridgedb.uri.api/pom.xml b/org.bridgedb.uri.api/pom.xml index 7203717ab..8b74b4eea 100644 --- a/org.bridgedb.uri.api/pom.xml +++ b/org.bridgedb.uri.api/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.2 + 3.1.3-SNAPSHOT diff --git a/org.bridgedb.uri.loader/pom.xml b/org.bridgedb.uri.loader/pom.xml index 99572ef6c..4fc3d983e 100644 --- a/org.bridgedb.uri.loader/pom.xml +++ b/org.bridgedb.uri.loader/pom.xml @@ -6,7 +6,7 @@ bridgedb-bundle org.bridgedb - 3.1.2 + 3.1.3-SNAPSHOT diff --git a/org.bridgedb.uri.sql/pom.xml b/org.bridgedb.uri.sql/pom.xml index c1ea354c8..f671bda7d 100644 --- a/org.bridgedb.uri.sql/pom.xml +++ b/org.bridgedb.uri.sql/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.2 + 3.1.3-SNAPSHOT diff --git a/org.bridgedb.uri.ws.client/pom.xml b/org.bridgedb.uri.ws.client/pom.xml index dc097d6e5..2beeba819 100644 --- a/org.bridgedb.uri.ws.client/pom.xml +++ b/org.bridgedb.uri.ws.client/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.1.2 + 3.1.3-SNAPSHOT diff --git a/org.bridgedb.uri.ws.core/pom.xml b/org.bridgedb.uri.ws.core/pom.xml index 6b615cf78..a1349048c 100644 --- a/org.bridgedb.uri.ws.core/pom.xml +++ b/org.bridgedb.uri.ws.core/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.1.2 + 3.1.3-SNAPSHOT diff --git a/org.bridgedb.uri.ws.server/pom.xml b/org.bridgedb.uri.ws.server/pom.xml index 4638f2530..f3672d4e3 100644 --- a/org.bridgedb.uri.ws.server/pom.xml +++ b/org.bridgedb.uri.ws.server/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.1.2 + 3.1.3-SNAPSHOT diff --git a/org.bridgedb.utils/pom.xml b/org.bridgedb.utils/pom.xml index 6d769698e..f8ac233e2 100644 --- a/org.bridgedb.utils/pom.xml +++ b/org.bridgedb.utils/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.2 + 3.1.3-SNAPSHOT diff --git a/org.bridgedb.webservice.biomart/pom.xml b/org.bridgedb.webservice.biomart/pom.xml index eaf9b5248..c5ac195d8 100644 --- a/org.bridgedb.webservice.biomart/pom.xml +++ b/org.bridgedb.webservice.biomart/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.1.2 + 3.1.3-SNAPSHOT diff --git a/org.bridgedb.webservice.bridgerest/pom.xml b/org.bridgedb.webservice.bridgerest/pom.xml index afb7fe1aa..394f3fd18 100644 --- a/org.bridgedb.webservice.bridgerest/pom.xml +++ b/org.bridgedb.webservice.bridgerest/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.1.2 + 3.1.3-SNAPSHOT diff --git a/org.bridgedb.ws.client/pom.xml b/org.bridgedb.ws.client/pom.xml index ccd78fba1..ea57e2096 100644 --- a/org.bridgedb.ws.client/pom.xml +++ b/org.bridgedb.ws.client/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.1.2 + 3.1.3-SNAPSHOT diff --git a/org.bridgedb.ws.core/pom.xml b/org.bridgedb.ws.core/pom.xml index 9aed75286..d39248962 100644 --- a/org.bridgedb.ws.core/pom.xml +++ b/org.bridgedb.ws.core/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.1.2 + 3.1.3-SNAPSHOT diff --git a/org.bridgedb.ws.server/pom.xml b/org.bridgedb.ws.server/pom.xml index 3ac9a6a9b..ebbe3b200 100644 --- a/org.bridgedb.ws.server/pom.xml +++ b/org.bridgedb.ws.server/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.1.2 + 3.1.3-SNAPSHOT diff --git a/org.bridgedb/pom.xml b/org.bridgedb/pom.xml index d641b271f..a4f99bee8 100644 --- a/org.bridgedb/pom.xml +++ b/org.bridgedb/pom.xml @@ -33,7 +33,7 @@ bridgedb-bundle org.bridgedb - 3.1.2 + 3.1.3-SNAPSHOT diff --git a/pom.xml b/pom.xml index e8c9507fc..d19e892e8 100644 --- a/pom.xml +++ b/pom.xml @@ -4,7 +4,7 @@ org.bridgedb bridgedb-bundle pom - 3.1.2 + 3.1.3-SNAPSHOT BridgeDb bundle BridgeDb is a framework for finding and mapping equivalent database From a76888fb91f52296d58a54c135ded3b9de079de3 Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Sat, 21 Sep 2024 10:23:01 +0200 Subject: [PATCH 02/16] Newer MySQL driver --- org.bridgedb.rdb.construct/pom.xml | 4 ++-- org.bridgedb.rdb/pom.xml | 4 ++-- org.bridgedb.sql/pom.xml | 4 ++-- org.bridgedb.tools.qc/pom.xml | 8 ++++---- org.bridgedb.tools.voidtool/pom.xml | 8 ++++---- org.bridgedb.uri.sql/pom.xml | 4 ++-- pom.xml | 9 ++++++++- 7 files changed, 24 insertions(+), 17 deletions(-) diff --git a/org.bridgedb.rdb.construct/pom.xml b/org.bridgedb.rdb.construct/pom.xml index fe55c4414..dc64e183c 100644 --- a/org.bridgedb.rdb.construct/pom.xml +++ b/org.bridgedb.rdb.construct/pom.xml @@ -80,8 +80,8 @@ compile - mysql - mysql-connector-java + com.mysql + mysql-connector-j ${mysql.version} jar runtime diff --git a/org.bridgedb.rdb/pom.xml b/org.bridgedb.rdb/pom.xml index fdeffdc43..bb546516b 100644 --- a/org.bridgedb.rdb/pom.xml +++ b/org.bridgedb.rdb/pom.xml @@ -79,8 +79,8 @@ compile - mysql - mysql-connector-java + com.mysql + mysql-connector-j ${mysql.version} jar runtime diff --git a/org.bridgedb.sql/pom.xml b/org.bridgedb.sql/pom.xml index 5ccd3e6d0..e33449052 100644 --- a/org.bridgedb.sql/pom.xml +++ b/org.bridgedb.sql/pom.xml @@ -47,8 +47,8 @@ compile - mysql - mysql-connector-java + com.mysql + mysql-connector-j ${mysql.version} jar compile diff --git a/org.bridgedb.tools.qc/pom.xml b/org.bridgedb.tools.qc/pom.xml index d9145e1d0..04e125150 100644 --- a/org.bridgedb.tools.qc/pom.xml +++ b/org.bridgedb.tools.qc/pom.xml @@ -71,8 +71,8 @@ ${project.parent.version} - mysql - mysql-connector-java + com.mysql + mysql-connector-j @@ -82,8 +82,8 @@ ${project.parent.version} - mysql - mysql-connector-java + com.mysql + mysql-connector-j diff --git a/org.bridgedb.tools.voidtool/pom.xml b/org.bridgedb.tools.voidtool/pom.xml index 96e160566..e592e3388 100644 --- a/org.bridgedb.tools.voidtool/pom.xml +++ b/org.bridgedb.tools.voidtool/pom.xml @@ -71,8 +71,8 @@ ${project.parent.version} - mysql - mysql-connector-java + com.mysql + mysql-connector-j @@ -82,8 +82,8 @@ ${project.parent.version} - mysql - mysql-connector-java + com.mysql + mysql-connector-j diff --git a/org.bridgedb.uri.sql/pom.xml b/org.bridgedb.uri.sql/pom.xml index f671bda7d..00a76920c 100644 --- a/org.bridgedb.uri.sql/pom.xml +++ b/org.bridgedb.uri.sql/pom.xml @@ -64,8 +64,8 @@ compile - mysql - mysql-connector-java + com.mysql + mysql-connector-j ${mysql.version} jar compile diff --git a/pom.xml b/pom.xml index d19e892e8..e3887cf7b 100644 --- a/pom.xml +++ b/pom.xml @@ -49,7 +49,7 @@ 2.2 1.10 2.22.0 - 8.0.33 + 9.0.0 Tomcat 3.4 4.3.8 @@ -317,4 +317,11 @@ https://github.com/bridgedb/BridgeDb/issues + + + mvnrepository + https://mvnrepository.com/artifact/ + + + From 3c1f57a9748e590735d96b0dc1db7bc0f73b7d89 Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Sun, 22 Sep 2024 09:10:32 +0200 Subject: [PATCH 03/16] Removed an unused dependency --- examples/pom.xml | 12 ------------ 1 file changed, 12 deletions(-) diff --git a/examples/pom.xml b/examples/pom.xml index a2c683fc1..477368ef7 100644 --- a/examples/pom.xml +++ b/examples/pom.xml @@ -69,18 +69,6 @@ jar runtime - - org.apache.axis - axis - 1.4 - jar - - - org.apache.axis - axis-jaxrpc - 1.4 - jar - From b78a5a52c2eb0537f12249f14dc8227471da06ef Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Sun, 22 Sep 2024 09:18:49 +0200 Subject: [PATCH 04/16] Newer Apache CFX version --- pom.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pom.xml b/pom.xml index e3887cf7b..de58ae97d 100644 --- a/pom.xml +++ b/pom.xml @@ -45,7 +45,7 @@ UTF-8 UTF-8 1.2 - 3.2.14 + 3.6.4 2.2 1.10 2.22.0 From 1ae2751f1b64a5cf2ec8a7a20d6c5e7b2bbdd167 Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Sun, 22 Sep 2024 09:36:50 +0200 Subject: [PATCH 05/16] Maven style --- org.bridgedb.webservice.bridgerest/pom.xml | 8 ++++---- .../org/bridgedb/webservice/bridgerest/BridgeRest.java | 0 2 files changed, 4 insertions(+), 4 deletions(-) rename org.bridgedb.webservice.bridgerest/src/{ => main/java}/org/bridgedb/webservice/bridgerest/BridgeRest.java (100%) diff --git a/org.bridgedb.webservice.bridgerest/pom.xml b/org.bridgedb.webservice.bridgerest/pom.xml index 394f3fd18..b8cd705a4 100644 --- a/org.bridgedb.webservice.bridgerest/pom.xml +++ b/org.bridgedb.webservice.bridgerest/pom.xml @@ -16,17 +16,17 @@ target/classes ${project.artifactId}-${project.version} target/test-classes - src + src/main/java scripts - test + src/test/main - resources + src/main/resources - test-resources + src/test/resources diff --git a/org.bridgedb.webservice.bridgerest/src/org/bridgedb/webservice/bridgerest/BridgeRest.java b/org.bridgedb.webservice.bridgerest/src/main/java/org/bridgedb/webservice/bridgerest/BridgeRest.java similarity index 100% rename from org.bridgedb.webservice.bridgerest/src/org/bridgedb/webservice/bridgerest/BridgeRest.java rename to org.bridgedb.webservice.bridgerest/src/main/java/org/bridgedb/webservice/bridgerest/BridgeRest.java From d250241c2c44e2cd5ef6c5b7eaab068342e0ba82 Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Sun, 22 Sep 2024 10:01:24 +0200 Subject: [PATCH 06/16] Added a simple test --- org.bridgedb.webservice.bridgerest/pom.xml | 26 +++++++++++++- .../webservice/bridgerest/BridgeRestTest.java | 35 +++++++++++++++++++ 2 files changed, 60 insertions(+), 1 deletion(-) create mode 100644 org.bridgedb.webservice.bridgerest/src/test/java/org/bridgedb/webservice/bridgerest/BridgeRestTest.java diff --git a/org.bridgedb.webservice.bridgerest/pom.xml b/org.bridgedb.webservice.bridgerest/pom.xml index b8cd705a4..25f704fa9 100644 --- a/org.bridgedb.webservice.bridgerest/pom.xml +++ b/org.bridgedb.webservice.bridgerest/pom.xml @@ -18,7 +18,7 @@ target/test-classes src/main/java scripts - src/test/main + src/test/java src/main/resources @@ -80,5 +80,29 @@ ${project.parent.version} compile + + org.junit.platform + junit-platform-surefire-provider + 1.3.2 + test + + + org.junit.jupiter + junit-jupiter-engine + ${junit5.jupiter.version} + test + + + org.junit.vintage + junit-vintage-engine + ${junit5.jupiter.version} + test + + + org.junit.jupiter + junit-jupiter-api + ${junit5.jupiter.version} + test + diff --git a/org.bridgedb.webservice.bridgerest/src/test/java/org/bridgedb/webservice/bridgerest/BridgeRestTest.java b/org.bridgedb.webservice.bridgerest/src/test/java/org/bridgedb/webservice/bridgerest/BridgeRestTest.java new file mode 100644 index 000000000..610b00f88 --- /dev/null +++ b/org.bridgedb.webservice.bridgerest/src/test/java/org/bridgedb/webservice/bridgerest/BridgeRestTest.java @@ -0,0 +1,35 @@ +// Copyright 2024 Egon Willighagen +// +// Licensed under the Apache License, Version 2.0 (the "License"); +// you may not use this file except in compliance with the License. +// You may obtain a copy of the License at +// +// http://www.apache.org/licenses/LICENSE-2.0 +// +// Unless required by applicable law or agreed to in writing, software +// distributed under the License is distributed on an "AS IS" BASIS, +// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +// See the License for the specific language governing permissions and +// limitations under the License. +// +package org.bridgedb.webservice.bridgerest; + +import static org.junit.jupiter.api.Assertions.assertNotNull; + +import org.bridgedb.IDMapperException; +import org.junit.jupiter.api.BeforeAll; +import org.junit.jupiter.api.Test; + +public class BridgeRestTest { + + @BeforeAll + public static void init() { + + } + + @Test + public void test() throws IDMapperException { + BridgeRest service = new BridgeRest("https://webservice.bridgedb.org/Human"); + assertNotNull(service); + } +} From 07d37b082965b655e2970b09c3143f5dd0014f07 Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Sun, 22 Sep 2024 10:14:42 +0200 Subject: [PATCH 07/16] Restructured and added a mapping test --- org.bridgedb.webservice.bridgerest/pom.xml | 6 +++++ .../webservice/bridgerest/BridgeRestTest.java | 22 +++++++++++++++---- 2 files changed, 24 insertions(+), 4 deletions(-) diff --git a/org.bridgedb.webservice.bridgerest/pom.xml b/org.bridgedb.webservice.bridgerest/pom.xml index 25f704fa9..d5bc08fef 100644 --- a/org.bridgedb.webservice.bridgerest/pom.xml +++ b/org.bridgedb.webservice.bridgerest/pom.xml @@ -80,6 +80,12 @@ ${project.parent.version} compile + + org.bridgedb + org.bridgedb.bio + ${project.parent.version} + test + org.junit.platform junit-platform-surefire-provider diff --git a/org.bridgedb.webservice.bridgerest/src/test/java/org/bridgedb/webservice/bridgerest/BridgeRestTest.java b/org.bridgedb.webservice.bridgerest/src/test/java/org/bridgedb/webservice/bridgerest/BridgeRestTest.java index 610b00f88..645f2e75d 100644 --- a/org.bridgedb.webservice.bridgerest/src/test/java/org/bridgedb/webservice/bridgerest/BridgeRestTest.java +++ b/org.bridgedb.webservice.bridgerest/src/test/java/org/bridgedb/webservice/bridgerest/BridgeRestTest.java @@ -14,22 +14,36 @@ // package org.bridgedb.webservice.bridgerest; +import static org.junit.Assert.assertNotSame; +import static org.junit.Assert.assertTrue; import static org.junit.jupiter.api.Assertions.assertNotNull; +import java.util.Set; + +import org.bridgedb.DataSource; import org.bridgedb.IDMapperException; +import org.bridgedb.Xref; +import org.bridgedb.bio.DataSourceTxt; import org.junit.jupiter.api.BeforeAll; import org.junit.jupiter.api.Test; public class BridgeRestTest { + private static BridgeRest service; + @BeforeAll - public static void init() { - + public static void init() throws IDMapperException { + if (DataSource.getDataSources().size() == 0) DataSourceTxt.init(); + BridgeRestTest.service = new BridgeRest("https://webservice.bridgedb.org/Human"); + assertNotNull(service); + assertTrue(service.isConnected()); } @Test - public void test() throws IDMapperException { - BridgeRest service = new BridgeRest("https://webservice.bridgedb.org/Human"); + public void testMap() throws IDMapperException { assertNotNull(service); + assertTrue(service.isConnected()); + Set mappings = service.mapID(new Xref("CHEBI:123", DataSource.getExistingBySystemCode("Ce"))); + assertNotSame(0, mappings.size()); } } From e86b179f3f4760be60926ef7e4054c0732276806 Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Sun, 22 Sep 2024 10:34:47 +0200 Subject: [PATCH 08/16] Updated Maven Jar plugin --- org.bridgedb.webservice.bridgerest/pom.xml | 2 +- org.bridgedb/pom.xml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/org.bridgedb.webservice.bridgerest/pom.xml b/org.bridgedb.webservice.bridgerest/pom.xml index d5bc08fef..1546e20f2 100644 --- a/org.bridgedb.webservice.bridgerest/pom.xml +++ b/org.bridgedb.webservice.bridgerest/pom.xml @@ -57,7 +57,7 @@ org.apache.maven.plugins maven-jar-plugin - 3.2.2 + 3.4.2 ${project.build.outputDirectory}/META-INF/MANIFEST.MF diff --git a/org.bridgedb/pom.xml b/org.bridgedb/pom.xml index a4f99bee8..f363b121d 100644 --- a/org.bridgedb/pom.xml +++ b/org.bridgedb/pom.xml @@ -81,7 +81,7 @@ org.apache.maven.plugins maven-jar-plugin - 3.2.2 + 3.4.2 ${project.build.outputDirectory}/META-INF/MANIFEST.MF From 3a054e32c76bd693efb33840674e3b2ab2ee741d Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Sun, 22 Sep 2024 10:52:15 +0200 Subject: [PATCH 09/16] Central, updated Felix maven plugin --- org.bridgedb.bio/pom.xml | 2 +- org.bridgedb.gui/pom.xml | 2 +- org.bridgedb.rdb.construct/pom.xml | 2 +- org.bridgedb.rdb/pom.xml | 2 +- org.bridgedb.webservice.bridgerest/pom.xml | 2 +- org.bridgedb/pom.xml | 2 +- pom.xml | 1 + 7 files changed, 7 insertions(+), 6 deletions(-) diff --git a/org.bridgedb.bio/pom.xml b/org.bridgedb.bio/pom.xml index 211fb58f8..cbcc44086 100644 --- a/org.bridgedb.bio/pom.xml +++ b/org.bridgedb.bio/pom.xml @@ -32,7 +32,7 @@ org.apache.felix maven-bundle-plugin - 5.1.2 + ${felix.version} true diff --git a/org.bridgedb.gui/pom.xml b/org.bridgedb.gui/pom.xml index a3e041099..22a091701 100644 --- a/org.bridgedb.gui/pom.xml +++ b/org.bridgedb.gui/pom.xml @@ -32,7 +32,7 @@ org.apache.felix maven-bundle-plugin - 5.1.2 + ${felix.version} true diff --git a/org.bridgedb.rdb.construct/pom.xml b/org.bridgedb.rdb.construct/pom.xml index dc64e183c..2fdee3665 100644 --- a/org.bridgedb.rdb.construct/pom.xml +++ b/org.bridgedb.rdb.construct/pom.xml @@ -32,7 +32,7 @@ org.apache.felix maven-bundle-plugin - 5.1.2 + ${felix.version} true diff --git a/org.bridgedb.rdb/pom.xml b/org.bridgedb.rdb/pom.xml index bb546516b..94b5cd35b 100644 --- a/org.bridgedb.rdb/pom.xml +++ b/org.bridgedb.rdb/pom.xml @@ -32,7 +32,7 @@ org.apache.felix maven-bundle-plugin - 5.1.2 + ${felix.version} true diff --git a/org.bridgedb.webservice.bridgerest/pom.xml b/org.bridgedb.webservice.bridgerest/pom.xml index 1546e20f2..6726e0633 100644 --- a/org.bridgedb.webservice.bridgerest/pom.xml +++ b/org.bridgedb.webservice.bridgerest/pom.xml @@ -33,7 +33,7 @@ org.apache.felix maven-bundle-plugin - 5.1.1 + ${felix.version} true diff --git a/org.bridgedb/pom.xml b/org.bridgedb/pom.xml index f363b121d..7b96e71fb 100644 --- a/org.bridgedb/pom.xml +++ b/org.bridgedb/pom.xml @@ -57,7 +57,7 @@ org.apache.felix maven-bundle-plugin - 5.1.2 + ${felix.version} true diff --git a/pom.xml b/pom.xml index de58ae97d..5bdf16cd2 100644 --- a/pom.xml +++ b/pom.xml @@ -46,6 +46,7 @@ UTF-8 1.2 3.6.4 + 5.1.9 2.2 1.10 2.22.0 From b8184a06fd4650c2572708acd3da3a174bb4de7a Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Sun, 22 Sep 2024 11:32:08 +0200 Subject: [PATCH 10/16] Updated more dependencies: Hamcrest 3.0, JUnit 5.11, and WSDL4J 1.6.3 --- examples/pom.xml | 2 +- org.bridgedb.rdb/pom.xml | 2 +- pom.xml | 5 +++-- 3 files changed, 5 insertions(+), 4 deletions(-) diff --git a/examples/pom.xml b/examples/pom.xml index 477368ef7..3fe355949 100644 --- a/examples/pom.xml +++ b/examples/pom.xml @@ -65,7 +65,7 @@ wsdl4j wsdl4j - 1.6.2 + 1.6.3 jar runtime diff --git a/org.bridgedb.rdb/pom.xml b/org.bridgedb.rdb/pom.xml index 94b5cd35b..75ea6d092 100644 --- a/org.bridgedb.rdb/pom.xml +++ b/org.bridgedb.rdb/pom.xml @@ -108,7 +108,7 @@ org.junit.platform junit-platform-launcher - 1.10.1 + ${junit5.platform.launcher.version} test diff --git a/pom.xml b/pom.xml index 5bdf16cd2..502cb7f58 100644 --- a/pom.xml +++ b/pom.xml @@ -47,7 +47,7 @@ 1.2 3.6.4 5.1.9 - 2.2 + 3.0 1.10 2.22.0 9.0.0 @@ -58,7 +58,8 @@ 2.0.9 10.15.2.0 1.3.2 - 5.10.1 + 1.11.0 + 5.11.0 mysql From 5b2a6d8960fdca5dc3d5d4ee2c9bbe73069cc001 Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Thu, 26 Sep 2024 04:42:57 +0200 Subject: [PATCH 11/16] BridgeDb Datasources 20240925 --- org.bridgedb.bio/resources/org/bridgedb/bio/datasources.tsv | 1 - org.bridgedb.bio/resources/org/bridgedb/bio/organisms.tsv | 3 ++- .../src/main/resources/org/bridgedb/bio/datasources.tsv | 1 - .../src/main/resources/org/bridgedb/bio/organisms.tsv | 3 ++- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/org.bridgedb.bio/resources/org/bridgedb/bio/datasources.tsv b/org.bridgedb.bio/resources/org/bridgedb/bio/datasources.tsv index 289fb0957..655878bd4 100644 --- a/org.bridgedb.bio/resources/org/bridgedb/bio/datasources.tsv +++ b/org.bridgedb.bio/resources/org/bridgedb/bio/datasources.tsv @@ -55,7 +55,6 @@ Illumina Il http://www.illumina.com/ ILMN_5668 probe 0 Il ILMN_\d+ Illumina i InChIKey Ik http://inchi.org/ QTBSBXVTEAMEQO-UHFFFAOYSA-N metabolite 1 urn:miriam:inchikey ^[A-Z]{14}\-[A-Z]{10}(\-[A-Z])? Standard InChIKey P235 inchikey metabolite IntAct Ia http://www.ebi.ac.uk/intact/ http://www.ebi.ac.uk/intact/pages/details/details.xhtml?interactionAc=$id EBI-2307691 interaction 1 urn:miriam:intact ^EBI\-[0-9]+$ IntAct intact interaction InterPro I http://www.ebi.ac.uk/interpro/ https://www.ebi.ac.uk/interpro/entry/InterPro/$id IPR000100 protein 1 urn:miriam:interpro ^IPR\d{6}$ InterPro P2926 interpro protein -IPI Ip http://www.ebi.ac.uk/IPI http://www.ebi.ac.uk/cgi-bin/dbfetch?db=IPI&id=$id&format=default IPI00000001 protein 1 ^IPI\d{8}$ IPI interpro protein IRGSP Gene Ir http://rgp.dna.affrc.go.jp/IRGSP/ https://rapdb.dna.affrc.go.jp/viewer/gbrowse_details/irgsp1?name=$id Os12g0561000 gene 1 Ir Os\d{2}g\d+ IRGSP Gene rapdb.locus gene ISBN isbn http://isbndb.com/ http://isbndb.com/search-all.html?kw=$id 9781584885658 publication 1 urn:miriam:isbn ^(ISBN)?(-13|-10)?[:]?[ ]?(\d{2,3}[ -]?)?\d{1,5}[ -]?\d{1,7}[ -]?\d{1,6}[ -]?(\d|X)$ ISBN P212 isbn publication ISSN issn https://portal.issn.org https://portal.issn.org/resource/ISSN/$id 1776-3045 publication 1 urn:miriam:issn ^\d{4}-\d{3}[\dX]$ ISSN P236 issn publication diff --git a/org.bridgedb.bio/resources/org/bridgedb/bio/organisms.tsv b/org.bridgedb.bio/resources/org/bridgedb/bio/organisms.tsv index 560d65f42..940d8117d 100644 --- a/org.bridgedb.bio/resources/org/bridgedb/bio/organisms.tsv +++ b/org.bridgedb.bio/resources/org/bridgedb/bio/organisms.tsv @@ -40,10 +40,11 @@ Plasmodium falciparum Malaria parasite Pf 5833 Prymnesium parvum Pp 97485 Populus trichocarpa Western Balsam Poplar Pi 3694 Rattus norvegicus Rat Rn 10116 +Rosmarinus officinalis Rosemary Ro 39367 Saccharomyces cerevisiae Yeast Sc 4932 Skeletonema marinoi Sm 267567 Solanum lycopersicum Tomato Sl 4081 -Solanum tuberosum St 4113 +Solanum tuberosum St 4113 Sorex araneus Shrew Sa 42254 Sorghum bicolor Sorghum Sb 4558 Sus scrofa Pig Ss 9823 diff --git a/org.bridgedb.bio/src/main/resources/org/bridgedb/bio/datasources.tsv b/org.bridgedb.bio/src/main/resources/org/bridgedb/bio/datasources.tsv index 66cb63176..4b50c0d78 100644 --- a/org.bridgedb.bio/src/main/resources/org/bridgedb/bio/datasources.tsv +++ b/org.bridgedb.bio/src/main/resources/org/bridgedb/bio/datasources.tsv @@ -55,7 +55,6 @@ Illumina Il http://www.illumina.com/ ILMN_5668 probe 0 Il ILMN_\d+ Illumina i InChIKey Ik http://inchi.org/ QTBSBXVTEAMEQO-UHFFFAOYSA-N metabolite 1 urn:miriam:inchikey ^[A-Z]{14}\-[A-Z]{10}(\-[A-Z])? Standard InChIKey P235 inchikey metabolite IntAct Ia http://www.ebi.ac.uk/intact/ http://www.ebi.ac.uk/intact/pages/details/details.xhtml?interactionAc=$id EBI-2307691 interaction 1 urn:miriam:intact ^EBI\-[0-9]+$ IntAct intact interaction InterPro I http://www.ebi.ac.uk/interpro/ https://www.ebi.ac.uk/interpro/entry/InterPro/$id IPR000100 protein 1 urn:miriam:interpro ^IPR\d{6}$ InterPro P2926 interpro protein -IPI Ip http://www.ebi.ac.uk/IPI http://www.ebi.ac.uk/cgi-bin/dbfetch?db=IPI&id=$id&format=default IPI00000001 protein 1 ^IPI\d{8}$ IPI interpro protein IRGSP Gene Ir http://rgp.dna.affrc.go.jp/IRGSP/ https://rapdb.dna.affrc.go.jp/viewer/gbrowse_details/irgsp1?name=$id Os12g0561000 gene 1 Ir Os\d{2}g\d+ IRGSP Gene rapdb.locus gene ISBN isbn http://isbndb.com/ http://isbndb.com/search-all.html?kw=$id 9781584885658 publication 1 urn:miriam:isbn ^(ISBN)?(-13|-10)?[:]?[ ]?(\d{2,3}[ -]?)?\d{1,5}[ -]?\d{1,7}[ -]?\d{1,6}[ -]?(\d|X)$ ISBN P212 isbn publication ISSN issn https://portal.issn.org https://portal.issn.org/resource/ISSN/$id 1776-3045 publication 1 urn:miriam:issn ^\d{4}-\d{3}[\dX]$ ISSN P236 issn publication diff --git a/org.bridgedb.bio/src/main/resources/org/bridgedb/bio/organisms.tsv b/org.bridgedb.bio/src/main/resources/org/bridgedb/bio/organisms.tsv index 560d65f42..940d8117d 100644 --- a/org.bridgedb.bio/src/main/resources/org/bridgedb/bio/organisms.tsv +++ b/org.bridgedb.bio/src/main/resources/org/bridgedb/bio/organisms.tsv @@ -40,10 +40,11 @@ Plasmodium falciparum Malaria parasite Pf 5833 Prymnesium parvum Pp 97485 Populus trichocarpa Western Balsam Poplar Pi 3694 Rattus norvegicus Rat Rn 10116 +Rosmarinus officinalis Rosemary Ro 39367 Saccharomyces cerevisiae Yeast Sc 4932 Skeletonema marinoi Sm 267567 Solanum lycopersicum Tomato Sl 4081 -Solanum tuberosum St 4113 +Solanum tuberosum St 4113 Sorex araneus Shrew Sa 42254 Sorghum bicolor Sorghum Sb 4558 Sus scrofa Pig Ss 9823 From fc5c436f22cb82bc1b1519309120dff21e8ef616 Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Tue, 1 Oct 2024 07:41:49 +0200 Subject: [PATCH 12/16] Release 3.1.3 --- CITATION.cff | 4 ++-- README.md | 14 +++++++------- examples/pom.xml | 2 +- org.bridgedb.bio/pom.xml | 2 +- org.bridgedb.file.orthoxml/pom.xml | 2 +- org.bridgedb.gui/pom.xml | 2 +- org.bridgedb.rdb.construct/pom.xml | 2 +- org.bridgedb.rdb/pom.xml | 2 +- org.bridgedb.rdf/pom.xml | 2 +- org.bridgedb.sql/pom.xml | 2 +- org.bridgedb.tools.batchmapper/pom.xml | 8 ++++---- org.bridgedb.tools.info/pom.xml | 2 +- org.bridgedb.tools.qc/pom.xml | 2 +- org.bridgedb.tools.voidtool/pom.xml | 2 +- org.bridgedb.uri.api/pom.xml | 2 +- org.bridgedb.uri.loader/pom.xml | 2 +- org.bridgedb.uri.sql/pom.xml | 2 +- org.bridgedb.uri.ws.client/pom.xml | 2 +- org.bridgedb.uri.ws.core/pom.xml | 2 +- org.bridgedb.uri.ws.server/pom.xml | 2 +- org.bridgedb.utils/pom.xml | 2 +- org.bridgedb.webservice.biomart/pom.xml | 2 +- org.bridgedb.webservice.bridgerest/pom.xml | 2 +- org.bridgedb.ws.client/pom.xml | 2 +- org.bridgedb.ws.core/pom.xml | 2 +- org.bridgedb.ws.server/pom.xml | 2 +- org.bridgedb/pom.xml | 2 +- org.bridgedb/src/main/resources/version.props | 2 +- pom-java8.xml | 2 +- pom.xml | 2 +- 30 files changed, 40 insertions(+), 40 deletions(-) diff --git a/CITATION.cff b/CITATION.cff index cdd95bc91..1c035e2b9 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -2,8 +2,8 @@ cff-version: 1.2.0 title: BridgeDb message: 'If you use this software, please cite it as below.' type: software -version: 3.1.2 -date-released: '2024-07-30' +version: 3.1.3 +date-released: '2024-10-01' authors: - given-names: Manas family-names: Awasthi diff --git a/README.md b/README.md index 555e3e9a8..83fbdba8e 100644 --- a/README.md +++ b/README.md @@ -15,7 +15,7 @@ Using BridgeDb dependencies The [BridgeDb releases](https://github.com/bridgedb/BridgeDb/releases) are published to [Maven Central](http://central.maven.org/maven2/org/bridgedb/), which means you can use the BridgeDb JARs without needing to compile BridgeDb. -Usage depends on which module you require. The examples below assumes artifact `org.bridgedb.bio` and version `3.1.2`: +Usage depends on which module you require. The examples below assumes artifact `org.bridgedb.bio` and version `3.1.3`: For [Maven](https://maven.apache.org/): @@ -24,7 +24,7 @@ For [Maven](https://maven.apache.org/): org.bridgedb org.bridgedb.bio - 3.1.2 + 3.1.3 ``` @@ -32,19 +32,19 @@ For [Maven](https://maven.apache.org/): For [Gradle](https://gradle.org/): ```gradle -compile group: 'org.bridgedb', name: 'org.bridgedb.bio', version: '3.1.2' +compile group: 'org.bridgedb', name: 'org.bridgedb.bio', version: '3.1.3' ``` For [Ivy](http://ant.apache.org/ivy/): ```xml - + ``` For [Buildr](https://buildr.apache.org/): ```buildr -'org.bridgedb:org.bridgedb.bio:jar:3.1.2' +'org.bridgedb:org.bridgedb.bio:jar:3.1.3' ``` @@ -135,7 +135,7 @@ 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=3.1.2 +mvn versions:set -DnewVersion=3.1.3 mvn clean deploy ``` @@ -145,7 +145,7 @@ and everything. To make a development (SNAPSHOT) release, use: ```shell -mvn versions:set -DnewVersion=3.1.3-SNAPSHOT +mvn versions:set -DnewVersion=3.1.4-SNAPSHOT mvn clean deploy ``` diff --git a/examples/pom.xml b/examples/pom.xml index 3fe355949..046535746 100644 --- a/examples/pom.xml +++ b/examples/pom.xml @@ -3,7 +3,7 @@ bridgedb-bundle org.bridgedb - 3.1.3-SNAPSHOT + 3.1.3 4.0.0 org.bridgedb.examples diff --git a/org.bridgedb.bio/pom.xml b/org.bridgedb.bio/pom.xml index cbcc44086..32af86677 100644 --- a/org.bridgedb.bio/pom.xml +++ b/org.bridgedb.bio/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.1.3-SNAPSHOT + 3.1.3 diff --git a/org.bridgedb.file.orthoxml/pom.xml b/org.bridgedb.file.orthoxml/pom.xml index 88b5d884f..609362c96 100644 --- a/org.bridgedb.file.orthoxml/pom.xml +++ b/org.bridgedb.file.orthoxml/pom.xml @@ -6,7 +6,7 @@ bridgedb-bundle org.bridgedb - 3.1.3-SNAPSHOT + 3.1.3 diff --git a/org.bridgedb.gui/pom.xml b/org.bridgedb.gui/pom.xml index 22a091701..e4e9c498a 100644 --- a/org.bridgedb.gui/pom.xml +++ b/org.bridgedb.gui/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.3-SNAPSHOT + 3.1.3 diff --git a/org.bridgedb.rdb.construct/pom.xml b/org.bridgedb.rdb.construct/pom.xml index 2fdee3665..1ee0d0da8 100644 --- a/org.bridgedb.rdb.construct/pom.xml +++ b/org.bridgedb.rdb.construct/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.3-SNAPSHOT + 3.1.3 diff --git a/org.bridgedb.rdb/pom.xml b/org.bridgedb.rdb/pom.xml index 75ea6d092..169b5be78 100644 --- a/org.bridgedb.rdb/pom.xml +++ b/org.bridgedb.rdb/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.3-SNAPSHOT + 3.1.3 diff --git a/org.bridgedb.rdf/pom.xml b/org.bridgedb.rdf/pom.xml index 14e4863d9..d7a497f28 100644 --- a/org.bridgedb.rdf/pom.xml +++ b/org.bridgedb.rdf/pom.xml @@ -6,7 +6,7 @@ bridgedb-bundle org.bridgedb - 3.1.3-SNAPSHOT + 3.1.3 diff --git a/org.bridgedb.sql/pom.xml b/org.bridgedb.sql/pom.xml index e33449052..22fec0bd2 100644 --- a/org.bridgedb.sql/pom.xml +++ b/org.bridgedb.sql/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.3-SNAPSHOT + 3.1.3 diff --git a/org.bridgedb.tools.batchmapper/pom.xml b/org.bridgedb.tools.batchmapper/pom.xml index 4a489cede..be079f4b8 100644 --- a/org.bridgedb.tools.batchmapper/pom.xml +++ b/org.bridgedb.tools.batchmapper/pom.xml @@ -6,7 +6,7 @@ bridgedb-bundle org.bridgedb - 3.1.3-SNAPSHOT + 3.1.3 @@ -33,19 +33,19 @@ org.bridgedb org.bridgedb - 3.1.3-SNAPSHOT + 3.1.3 compile org.bridgedb org.bridgedb.bio - 3.1.3-SNAPSHOT + 3.1.3 compile org.bridgedb org.bridgedb.rdb - 3.1.3-SNAPSHOT + 3.1.3 compile diff --git a/org.bridgedb.tools.info/pom.xml b/org.bridgedb.tools.info/pom.xml index b5ecac8a0..26c9f2308 100644 --- a/org.bridgedb.tools.info/pom.xml +++ b/org.bridgedb.tools.info/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.3-SNAPSHOT + 3.1.3 diff --git a/org.bridgedb.tools.qc/pom.xml b/org.bridgedb.tools.qc/pom.xml index 04e125150..3fafb090e 100644 --- a/org.bridgedb.tools.qc/pom.xml +++ b/org.bridgedb.tools.qc/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.3-SNAPSHOT + 3.1.3 diff --git a/org.bridgedb.tools.voidtool/pom.xml b/org.bridgedb.tools.voidtool/pom.xml index e592e3388..a7e5b5a3b 100644 --- a/org.bridgedb.tools.voidtool/pom.xml +++ b/org.bridgedb.tools.voidtool/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.3-SNAPSHOT + 3.1.3 diff --git a/org.bridgedb.uri.api/pom.xml b/org.bridgedb.uri.api/pom.xml index 8b74b4eea..f8d17ca80 100644 --- a/org.bridgedb.uri.api/pom.xml +++ b/org.bridgedb.uri.api/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.3-SNAPSHOT + 3.1.3 diff --git a/org.bridgedb.uri.loader/pom.xml b/org.bridgedb.uri.loader/pom.xml index 4fc3d983e..3fe0993f3 100644 --- a/org.bridgedb.uri.loader/pom.xml +++ b/org.bridgedb.uri.loader/pom.xml @@ -6,7 +6,7 @@ bridgedb-bundle org.bridgedb - 3.1.3-SNAPSHOT + 3.1.3 diff --git a/org.bridgedb.uri.sql/pom.xml b/org.bridgedb.uri.sql/pom.xml index 00a76920c..523efff03 100644 --- a/org.bridgedb.uri.sql/pom.xml +++ b/org.bridgedb.uri.sql/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.3-SNAPSHOT + 3.1.3 diff --git a/org.bridgedb.uri.ws.client/pom.xml b/org.bridgedb.uri.ws.client/pom.xml index 2beeba819..5f0f5b744 100644 --- a/org.bridgedb.uri.ws.client/pom.xml +++ b/org.bridgedb.uri.ws.client/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.1.3-SNAPSHOT + 3.1.3 diff --git a/org.bridgedb.uri.ws.core/pom.xml b/org.bridgedb.uri.ws.core/pom.xml index a1349048c..2027b7914 100644 --- a/org.bridgedb.uri.ws.core/pom.xml +++ b/org.bridgedb.uri.ws.core/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.1.3-SNAPSHOT + 3.1.3 diff --git a/org.bridgedb.uri.ws.server/pom.xml b/org.bridgedb.uri.ws.server/pom.xml index f3672d4e3..f6ae18627 100644 --- a/org.bridgedb.uri.ws.server/pom.xml +++ b/org.bridgedb.uri.ws.server/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.1.3-SNAPSHOT + 3.1.3 diff --git a/org.bridgedb.utils/pom.xml b/org.bridgedb.utils/pom.xml index f8ac233e2..468fcf5cb 100644 --- a/org.bridgedb.utils/pom.xml +++ b/org.bridgedb.utils/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.3-SNAPSHOT + 3.1.3 diff --git a/org.bridgedb.webservice.biomart/pom.xml b/org.bridgedb.webservice.biomart/pom.xml index c5ac195d8..0ad3609ea 100644 --- a/org.bridgedb.webservice.biomart/pom.xml +++ b/org.bridgedb.webservice.biomart/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.1.3-SNAPSHOT + 3.1.3 diff --git a/org.bridgedb.webservice.bridgerest/pom.xml b/org.bridgedb.webservice.bridgerest/pom.xml index 6726e0633..820d4039a 100644 --- a/org.bridgedb.webservice.bridgerest/pom.xml +++ b/org.bridgedb.webservice.bridgerest/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.1.3-SNAPSHOT + 3.1.3 diff --git a/org.bridgedb.ws.client/pom.xml b/org.bridgedb.ws.client/pom.xml index ea57e2096..05d56cc59 100644 --- a/org.bridgedb.ws.client/pom.xml +++ b/org.bridgedb.ws.client/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.1.3-SNAPSHOT + 3.1.3 diff --git a/org.bridgedb.ws.core/pom.xml b/org.bridgedb.ws.core/pom.xml index d39248962..6494251c5 100644 --- a/org.bridgedb.ws.core/pom.xml +++ b/org.bridgedb.ws.core/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.1.3-SNAPSHOT + 3.1.3 diff --git a/org.bridgedb.ws.server/pom.xml b/org.bridgedb.ws.server/pom.xml index ebbe3b200..378d6371a 100644 --- a/org.bridgedb.ws.server/pom.xml +++ b/org.bridgedb.ws.server/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.1.3-SNAPSHOT + 3.1.3 diff --git a/org.bridgedb/pom.xml b/org.bridgedb/pom.xml index 7b96e71fb..29cd03789 100644 --- a/org.bridgedb/pom.xml +++ b/org.bridgedb/pom.xml @@ -33,7 +33,7 @@ bridgedb-bundle org.bridgedb - 3.1.3-SNAPSHOT + 3.1.3 diff --git a/org.bridgedb/src/main/resources/version.props b/org.bridgedb/src/main/resources/version.props index 6cc9da92d..0da9c3ac6 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=3.1.2 +bridgedb.version=3.1.3 diff --git a/pom-java8.xml b/pom-java8.xml index 4b568673d..e994adb9a 100644 --- a/pom-java8.xml +++ b/pom-java8.xml @@ -4,7 +4,7 @@ org.bridgedb bridgedb-bundle-pv pom - 3.1.2 + 3.1.3-java8 BridgeDb 4 PathVisio bundle BridgeDb is a framework for finding and mapping equivalent database diff --git a/pom.xml b/pom.xml index 502cb7f58..d95abc4a0 100644 --- a/pom.xml +++ b/pom.xml @@ -4,7 +4,7 @@ org.bridgedb bridgedb-bundle pom - 3.1.3-SNAPSHOT + 3.1.3 BridgeDb bundle BridgeDb is a framework for finding and mapping equivalent database From dddd78f035f14331b9e424b344d78044ade51521 Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Tue, 1 Oct 2024 08:13:10 +0200 Subject: [PATCH 13/16] Use Derby 10.4 --- pom-java8.xml | 12 ++++++++++-- 1 file changed, 10 insertions(+), 2 deletions(-) diff --git a/pom-java8.xml b/pom-java8.xml index e994adb9a..6728dfff4 100644 --- a/pom-java8.xml +++ b/pom-java8.xml @@ -4,7 +4,7 @@ org.bridgedb bridgedb-bundle-pv pom - 3.1.3-java8 + 3.1.3 BridgeDb 4 PathVisio bundle BridgeDb is a framework for finding and mapping equivalent database @@ -36,7 +36,7 @@ 3.7.7 2.5 1.6.4 - 10.15.2.0 + 10.4.2.0 1.3.2 5.10.0 mysql @@ -110,4 +110,12 @@ + + + mvnrepository + MVN Repository + https://mvnrepository.com/artifact/ + + + From 336dab4bd844d23a67c762afa1a353eca7b427ae Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Tue, 1 Oct 2024 08:30:10 +0200 Subject: [PATCH 14/16] Make sure we have data sources defined --- .../src/test/java/org/bridgedb/bio/DataSourceTxtTest.java | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/org.bridgedb.bio/src/test/java/org/bridgedb/bio/DataSourceTxtTest.java b/org.bridgedb.bio/src/test/java/org/bridgedb/bio/DataSourceTxtTest.java index 67f06fba0..6825e1a4f 100644 --- a/org.bridgedb.bio/src/test/java/org/bridgedb/bio/DataSourceTxtTest.java +++ b/org.bridgedb.bio/src/test/java/org/bridgedb/bio/DataSourceTxtTest.java @@ -33,6 +33,7 @@ import java.util.Set; import org.bridgedb.DataSource; +import org.junit.jupiter.api.BeforeAll; /** @@ -41,6 +42,11 @@ */ public class DataSourceTxtTest { + @BeforeAll + public static void setUpSources() { + if (DataSource.getDataSources().size() < 20) DataSourceTxt.init(); + } + @org.junit.jupiter.api.Test public void testUniqueSystemCodes() { Set codes = new HashSet(); From 73e1115969565ab5955fc61cd08fcf391e97c319 Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Tue, 1 Oct 2024 08:40:44 +0200 Subject: [PATCH 15/16] Make sure we don't define data source twice --- .../src/test/java/org/bridgedb/bio/UniProtKBTest.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/org.bridgedb.bio/src/test/java/org/bridgedb/bio/UniProtKBTest.java b/org.bridgedb.bio/src/test/java/org/bridgedb/bio/UniProtKBTest.java index 67cec09d7..1e639458b 100644 --- a/org.bridgedb.bio/src/test/java/org/bridgedb/bio/UniProtKBTest.java +++ b/org.bridgedb.bio/src/test/java/org/bridgedb/bio/UniProtKBTest.java @@ -21,7 +21,7 @@ public class UniProtKBTest { @BeforeAll public static void setUpSources() { - DataSourceTxt.init(); + if (DataSource.getDataSources().size() < 20) DataSourceTxt.init(); } @Test From 90bf94734f51f81e687c27075bbd7d18ff6454f5 Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Tue, 1 Oct 2024 09:12:47 +0200 Subject: [PATCH 16/16] Synched the versions with the main pom.xml --- pom-java8.xml | 15 ++++++++------- 1 file changed, 8 insertions(+), 7 deletions(-) diff --git a/pom-java8.xml b/pom-java8.xml index 6728dfff4..59e8db953 100644 --- a/pom-java8.xml +++ b/pom-java8.xml @@ -26,19 +26,20 @@ UTF-8 UTF-8 1.2 - 3.2.14 - 2.2 + 3.6.4 + 3.0 1.10 - 2.20.0 - 8.0.33 + 2.22.0 + 9.0.0 Tomcat 3.4 - 3.7.7 + 4.3.8 2.5 - 1.6.4 + 2.0.9 10.4.2.0 1.3.2 - 5.10.0 + 1.11.0 + 5.11.0 mysql