From 94e9edd55065b8e70dff5dfdc0d4dd9827df69b9 Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Sat, 28 Dec 2024 14:42:15 +0100 Subject: [PATCH 1/6] 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 +- org.bridgedb/src/main/resources/version.props | 2 +- pom.xml | 2 +- 27 files changed, 30 insertions(+), 30 deletions(-) diff --git a/examples/pom.xml b/examples/pom.xml index d2a705db..ca9bc140 100644 --- a/examples/pom.xml +++ b/examples/pom.xml @@ -3,7 +3,7 @@ bridgedb-bundle org.bridgedb - 3.1.4 + 3.1.5-SNAPSHOT 4.0.0 org.bridgedb.examples diff --git a/org.bridgedb.bio/pom.xml b/org.bridgedb.bio/pom.xml index c0f0be58..f8972e62 100644 --- a/org.bridgedb.bio/pom.xml +++ b/org.bridgedb.bio/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.1.4 + 3.1.5-SNAPSHOT diff --git a/org.bridgedb.file.orthoxml/pom.xml b/org.bridgedb.file.orthoxml/pom.xml index 3433845a..68a5d324 100644 --- a/org.bridgedb.file.orthoxml/pom.xml +++ b/org.bridgedb.file.orthoxml/pom.xml @@ -6,7 +6,7 @@ bridgedb-bundle org.bridgedb - 3.1.4 + 3.1.5-SNAPSHOT diff --git a/org.bridgedb.gui/pom.xml b/org.bridgedb.gui/pom.xml index 6b21739b..19e327f8 100644 --- a/org.bridgedb.gui/pom.xml +++ b/org.bridgedb.gui/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.4 + 3.1.5-SNAPSHOT diff --git a/org.bridgedb.rdb.construct/pom.xml b/org.bridgedb.rdb.construct/pom.xml index 026adc09..7f4a5888 100644 --- a/org.bridgedb.rdb.construct/pom.xml +++ b/org.bridgedb.rdb.construct/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.4 + 3.1.5-SNAPSHOT diff --git a/org.bridgedb.rdb/pom.xml b/org.bridgedb.rdb/pom.xml index fdc99624..9b1607f6 100644 --- a/org.bridgedb.rdb/pom.xml +++ b/org.bridgedb.rdb/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.4 + 3.1.5-SNAPSHOT diff --git a/org.bridgedb.rdf/pom.xml b/org.bridgedb.rdf/pom.xml index e56013aa..9c9d0649 100644 --- a/org.bridgedb.rdf/pom.xml +++ b/org.bridgedb.rdf/pom.xml @@ -6,7 +6,7 @@ bridgedb-bundle org.bridgedb - 3.1.4 + 3.1.5-SNAPSHOT diff --git a/org.bridgedb.sql/pom.xml b/org.bridgedb.sql/pom.xml index d8ed5f76..4be335bf 100644 --- a/org.bridgedb.sql/pom.xml +++ b/org.bridgedb.sql/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.4 + 3.1.5-SNAPSHOT diff --git a/org.bridgedb.tools.batchmapper/pom.xml b/org.bridgedb.tools.batchmapper/pom.xml index d65a4d9a..ce883272 100644 --- a/org.bridgedb.tools.batchmapper/pom.xml +++ b/org.bridgedb.tools.batchmapper/pom.xml @@ -6,7 +6,7 @@ bridgedb-bundle org.bridgedb - 3.1.4 + 3.1.5-SNAPSHOT @@ -33,19 +33,19 @@ org.bridgedb org.bridgedb - 3.1.4 + 3.1.5-SNAPSHOT compile org.bridgedb org.bridgedb.bio - 3.1.4 + 3.1.5-SNAPSHOT compile org.bridgedb org.bridgedb.rdb - 3.1.4 + 3.1.5-SNAPSHOT compile diff --git a/org.bridgedb.tools.info/pom.xml b/org.bridgedb.tools.info/pom.xml index 91adf6d8..6ae994ec 100644 --- a/org.bridgedb.tools.info/pom.xml +++ b/org.bridgedb.tools.info/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.4 + 3.1.5-SNAPSHOT diff --git a/org.bridgedb.tools.qc/pom.xml b/org.bridgedb.tools.qc/pom.xml index 327225ea..89d9076d 100644 --- a/org.bridgedb.tools.qc/pom.xml +++ b/org.bridgedb.tools.qc/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.4 + 3.1.5-SNAPSHOT diff --git a/org.bridgedb.tools.voidtool/pom.xml b/org.bridgedb.tools.voidtool/pom.xml index f195a05c..19aaa167 100644 --- a/org.bridgedb.tools.voidtool/pom.xml +++ b/org.bridgedb.tools.voidtool/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.4 + 3.1.5-SNAPSHOT diff --git a/org.bridgedb.uri.api/pom.xml b/org.bridgedb.uri.api/pom.xml index 6f74e8c7..0c4aefdc 100644 --- a/org.bridgedb.uri.api/pom.xml +++ b/org.bridgedb.uri.api/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.4 + 3.1.5-SNAPSHOT diff --git a/org.bridgedb.uri.loader/pom.xml b/org.bridgedb.uri.loader/pom.xml index 867d9321..aca4fc19 100644 --- a/org.bridgedb.uri.loader/pom.xml +++ b/org.bridgedb.uri.loader/pom.xml @@ -6,7 +6,7 @@ bridgedb-bundle org.bridgedb - 3.1.4 + 3.1.5-SNAPSHOT diff --git a/org.bridgedb.uri.sql/pom.xml b/org.bridgedb.uri.sql/pom.xml index 8a83fe0c..34fc98b3 100644 --- a/org.bridgedb.uri.sql/pom.xml +++ b/org.bridgedb.uri.sql/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.4 + 3.1.5-SNAPSHOT diff --git a/org.bridgedb.uri.ws.client/pom.xml b/org.bridgedb.uri.ws.client/pom.xml index fcaa8242..91e1db33 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 - 3.1.4 + 3.1.5-SNAPSHOT diff --git a/org.bridgedb.uri.ws.core/pom.xml b/org.bridgedb.uri.ws.core/pom.xml index b39522c7..26e10b89 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 - 3.1.4 + 3.1.5-SNAPSHOT diff --git a/org.bridgedb.uri.ws.server/pom.xml b/org.bridgedb.uri.ws.server/pom.xml index f20a4091..cfa35ac1 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 - 3.1.4 + 3.1.5-SNAPSHOT diff --git a/org.bridgedb.utils/pom.xml b/org.bridgedb.utils/pom.xml index 2d406643..f5725b3c 100644 --- a/org.bridgedb.utils/pom.xml +++ b/org.bridgedb.utils/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.4 + 3.1.5-SNAPSHOT diff --git a/org.bridgedb.webservice.biomart/pom.xml b/org.bridgedb.webservice.biomart/pom.xml index d6b1d7ca..8bf5c06b 100644 --- a/org.bridgedb.webservice.biomart/pom.xml +++ b/org.bridgedb.webservice.biomart/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.1.4 + 3.1.5-SNAPSHOT diff --git a/org.bridgedb.webservice.bridgerest/pom.xml b/org.bridgedb.webservice.bridgerest/pom.xml index d00d424d..df3edbd2 100644 --- a/org.bridgedb.webservice.bridgerest/pom.xml +++ b/org.bridgedb.webservice.bridgerest/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.1.4 + 3.1.5-SNAPSHOT diff --git a/org.bridgedb.ws.client/pom.xml b/org.bridgedb.ws.client/pom.xml index e98637f2..1bf92376 100644 --- a/org.bridgedb.ws.client/pom.xml +++ b/org.bridgedb.ws.client/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.1.4 + 3.1.5-SNAPSHOT diff --git a/org.bridgedb.ws.core/pom.xml b/org.bridgedb.ws.core/pom.xml index a4f29eb9..de94c33f 100644 --- a/org.bridgedb.ws.core/pom.xml +++ b/org.bridgedb.ws.core/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.1.4 + 3.1.5-SNAPSHOT diff --git a/org.bridgedb.ws.server/pom.xml b/org.bridgedb.ws.server/pom.xml index bda968c5..796c6a57 100644 --- a/org.bridgedb.ws.server/pom.xml +++ b/org.bridgedb.ws.server/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.1.4 + 3.1.5-SNAPSHOT diff --git a/org.bridgedb/pom.xml b/org.bridgedb/pom.xml index 15c9a564..59751d6a 100644 --- a/org.bridgedb/pom.xml +++ b/org.bridgedb/pom.xml @@ -33,7 +33,7 @@ bridgedb-bundle org.bridgedb - 3.1.4 + 3.1.5-SNAPSHOT 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 diff --git a/pom.xml b/pom.xml index d7ab84f3..3c1f581a 100644 --- a/pom.xml +++ b/pom.xml @@ -4,7 +4,7 @@ org.bridgedb bridgedb-bundle pom - 3.1.4 + 3.1.5-SNAPSHOT BridgeDb bundle BridgeDb is a framework for finding and mapping equivalent database From 82e3996cfc825bf615e47b7a94e5241ba51ff95a Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Sat, 28 Dec 2024 14:44:43 +0100 Subject: [PATCH 2/6] 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 f3445dbb0709d04c85ef52069455c1b122af7023 Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Sat, 28 Dec 2024 14:02:15 +0100 Subject: [PATCH 3/6] 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 c83bce17103727ebfe0021ff44fda31f77dc4180 Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Sat, 28 Dec 2024 14:23:06 +0100 Subject: [PATCH 4/6] 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 e6e730e5..cc1b875c 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 @@ -172,12 +172,12 @@ 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 2532a861669df67d4cb49d3e7290fca2414eb857 Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Sat, 28 Dec 2024 15:47:09 +0100 Subject: [PATCH 5/6] 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 d75afa20bc0d1a3bc638aa3e5790b0500f19eda0 Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Mon, 30 Dec 2024 14:40:18 +0100 Subject: [PATCH 6/6] 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"));;