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 0c490e85b..046535746 100644 --- a/examples/pom.xml +++ b/examples/pom.xml @@ -3,7 +3,7 @@ bridgedb-bundle org.bridgedb - 3.1.2 + 3.1.3 4.0.0 org.bridgedb.examples @@ -65,22 +65,10 @@ wsdl4j wsdl4j - 1.6.2 + 1.6.3 jar runtime - - org.apache.axis - axis - 1.4 - jar - - - org.apache.axis - axis-jaxrpc - 1.4 - jar - diff --git a/org.bridgedb.bio/pom.xml b/org.bridgedb.bio/pom.xml index d92cfc8fe..32af86677 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 @@ -32,7 +32,7 @@ org.apache.felix maven-bundle-plugin - 5.1.2 + ${felix.version} true diff --git a/org.bridgedb.bio/resources/org/bridgedb/bio/datasources.tsv b/org.bridgedb.bio/resources/org/bridgedb/bio/datasources.tsv index 289fb0957..655878bd4 100644 --- a/org.bridgedb.bio/resources/org/bridgedb/bio/datasources.tsv +++ b/org.bridgedb.bio/resources/org/bridgedb/bio/datasources.tsv @@ -55,7 +55,6 @@ Illumina Il http://www.illumina.com/ ILMN_5668 probe 0 Il ILMN_\d+ Illumina i InChIKey Ik http://inchi.org/ QTBSBXVTEAMEQO-UHFFFAOYSA-N metabolite 1 urn:miriam:inchikey ^[A-Z]{14}\-[A-Z]{10}(\-[A-Z])? Standard InChIKey P235 inchikey metabolite IntAct Ia http://www.ebi.ac.uk/intact/ http://www.ebi.ac.uk/intact/pages/details/details.xhtml?interactionAc=$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 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(); 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 diff --git a/org.bridgedb.file.orthoxml/pom.xml b/org.bridgedb.file.orthoxml/pom.xml index 2cd2f9413..609362c96 100644 --- a/org.bridgedb.file.orthoxml/pom.xml +++ b/org.bridgedb.file.orthoxml/pom.xml @@ -6,7 +6,7 @@ bridgedb-bundle org.bridgedb - 3.1.2 + 3.1.3 diff --git a/org.bridgedb.gui/pom.xml b/org.bridgedb.gui/pom.xml index a2e97b835..e4e9c498a 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 @@ -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 feb7e76d3..1ee0d0da8 100644 --- a/org.bridgedb.rdb.construct/pom.xml +++ b/org.bridgedb.rdb.construct/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.2 + 3.1.3 @@ -32,7 +32,7 @@ org.apache.felix maven-bundle-plugin - 5.1.2 + ${felix.version} true @@ -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 88c3a389e..169b5be78 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 @@ -32,7 +32,7 @@ org.apache.felix maven-bundle-plugin - 5.1.2 + ${felix.version} true @@ -79,8 +79,8 @@ compile - mysql - mysql-connector-java + com.mysql + mysql-connector-j ${mysql.version} jar runtime @@ -108,7 +108,7 @@ org.junit.platform junit-platform-launcher - 1.10.1 + ${junit5.platform.launcher.version} test diff --git a/org.bridgedb.rdf/pom.xml b/org.bridgedb.rdf/pom.xml index 50eec5bc7..d7a497f28 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 diff --git a/org.bridgedb.sql/pom.xml b/org.bridgedb.sql/pom.xml index 763f300fe..22fec0bd2 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 @@ -47,8 +47,8 @@ compile - mysql - mysql-connector-java + com.mysql + mysql-connector-j ${mysql.version} jar compile diff --git a/org.bridgedb.tools.batchmapper/pom.xml b/org.bridgedb.tools.batchmapper/pom.xml index 4d26f9632..be079f4b8 100644 --- a/org.bridgedb.tools.batchmapper/pom.xml +++ b/org.bridgedb.tools.batchmapper/pom.xml @@ -6,7 +6,7 @@ bridgedb-bundle org.bridgedb - 3.1.2 + 3.1.3 @@ -33,19 +33,19 @@ org.bridgedb org.bridgedb - 3.1.2 + 3.1.3 compile org.bridgedb org.bridgedb.bio - 3.1.2 + 3.1.3 compile org.bridgedb org.bridgedb.rdb - 3.1.2 + 3.1.3 compile diff --git a/org.bridgedb.tools.info/pom.xml b/org.bridgedb.tools.info/pom.xml index dcd850997..26c9f2308 100644 --- a/org.bridgedb.tools.info/pom.xml +++ b/org.bridgedb.tools.info/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.2 + 3.1.3 diff --git a/org.bridgedb.tools.qc/pom.xml b/org.bridgedb.tools.qc/pom.xml index 9dd9273a2..3fafb090e 100644 --- a/org.bridgedb.tools.qc/pom.xml +++ b/org.bridgedb.tools.qc/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.2 + 3.1.3 @@ -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 32b8fdd5a..a7e5b5a3b 100644 --- a/org.bridgedb.tools.voidtool/pom.xml +++ b/org.bridgedb.tools.voidtool/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.2 + 3.1.3 @@ -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.api/pom.xml b/org.bridgedb.uri.api/pom.xml index 7203717ab..f8d17ca80 100644 --- a/org.bridgedb.uri.api/pom.xml +++ b/org.bridgedb.uri.api/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.2 + 3.1.3 diff --git a/org.bridgedb.uri.loader/pom.xml b/org.bridgedb.uri.loader/pom.xml index 99572ef6c..3fe0993f3 100644 --- a/org.bridgedb.uri.loader/pom.xml +++ b/org.bridgedb.uri.loader/pom.xml @@ -6,7 +6,7 @@ bridgedb-bundle org.bridgedb - 3.1.2 + 3.1.3 diff --git a/org.bridgedb.uri.sql/pom.xml b/org.bridgedb.uri.sql/pom.xml index c1ea354c8..523efff03 100644 --- a/org.bridgedb.uri.sql/pom.xml +++ b/org.bridgedb.uri.sql/pom.xml @@ -7,7 +7,7 @@ bridgedb-bundle org.bridgedb - 3.1.2 + 3.1.3 @@ -64,8 +64,8 @@ compile - mysql - mysql-connector-java + com.mysql + mysql-connector-j ${mysql.version} jar compile diff --git a/org.bridgedb.uri.ws.client/pom.xml b/org.bridgedb.uri.ws.client/pom.xml index dc097d6e5..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 - 3.1.2 + 3.1.3 diff --git a/org.bridgedb.uri.ws.core/pom.xml b/org.bridgedb.uri.ws.core/pom.xml index 6b615cf78..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 - 3.1.2 + 3.1.3 diff --git a/org.bridgedb.uri.ws.server/pom.xml b/org.bridgedb.uri.ws.server/pom.xml index 4638f2530..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 - 3.1.2 + 3.1.3 diff --git a/org.bridgedb.utils/pom.xml b/org.bridgedb.utils/pom.xml index 6d769698e..468fcf5cb 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 diff --git a/org.bridgedb.webservice.biomart/pom.xml b/org.bridgedb.webservice.biomart/pom.xml index eaf9b5248..0ad3609ea 100644 --- a/org.bridgedb.webservice.biomart/pom.xml +++ b/org.bridgedb.webservice.biomart/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.1.2 + 3.1.3 diff --git a/org.bridgedb.webservice.bridgerest/pom.xml b/org.bridgedb.webservice.bridgerest/pom.xml index afb7fe1aa..820d4039a 100644 --- a/org.bridgedb.webservice.bridgerest/pom.xml +++ b/org.bridgedb.webservice.bridgerest/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.1.2 + 3.1.3 @@ -16,24 +16,24 @@ target/classes ${project.artifactId}-${project.version} target/test-classes - src + src/main/java scripts - test + src/test/java - resources + src/main/resources - test-resources + src/test/resources org.apache.felix maven-bundle-plugin - 5.1.1 + ${felix.version} true @@ -57,7 +57,7 @@ org.apache.maven.plugins maven-jar-plugin - 3.2.2 + 3.4.2 ${project.build.outputDirectory}/META-INF/MANIFEST.MF @@ -80,5 +80,35 @@ ${project.parent.version} compile + + org.bridgedb + org.bridgedb.bio + ${project.parent.version} + test + + + 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/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 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..645f2e75d --- /dev/null +++ b/org.bridgedb.webservice.bridgerest/src/test/java/org/bridgedb/webservice/bridgerest/BridgeRestTest.java @@ -0,0 +1,49 @@ +// 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.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() 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 testMap() throws IDMapperException { + assertNotNull(service); + assertTrue(service.isConnected()); + Set mappings = service.mapID(new Xref("CHEBI:123", DataSource.getExistingBySystemCode("Ce"))); + assertNotSame(0, mappings.size()); + } +} diff --git a/org.bridgedb.ws.client/pom.xml b/org.bridgedb.ws.client/pom.xml index ccd78fba1..05d56cc59 100644 --- a/org.bridgedb.ws.client/pom.xml +++ b/org.bridgedb.ws.client/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.1.2 + 3.1.3 diff --git a/org.bridgedb.ws.core/pom.xml b/org.bridgedb.ws.core/pom.xml index 9aed75286..6494251c5 100644 --- a/org.bridgedb.ws.core/pom.xml +++ b/org.bridgedb.ws.core/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.1.2 + 3.1.3 diff --git a/org.bridgedb.ws.server/pom.xml b/org.bridgedb.ws.server/pom.xml index 3ac9a6a9b..378d6371a 100644 --- a/org.bridgedb.ws.server/pom.xml +++ b/org.bridgedb.ws.server/pom.xml @@ -8,7 +8,7 @@ bridgedb-bundle org.bridgedb - 3.1.2 + 3.1.3 diff --git a/org.bridgedb/pom.xml b/org.bridgedb/pom.xml index d641b271f..29cd03789 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 @@ -57,7 +57,7 @@ org.apache.felix maven-bundle-plugin - 5.1.2 + ${felix.version} true @@ -81,7 +81,7 @@ 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/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..59e8db953 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 BridgeDb 4 PathVisio bundle BridgeDb is a framework for finding and mapping equivalent database @@ -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 - 10.15.2.0 + 2.0.9 + 10.4.2.0 1.3.2 - 5.10.0 + 1.11.0 + 5.11.0 mysql @@ -110,4 +111,12 @@ + + + mvnrepository + MVN Repository + https://mvnrepository.com/artifact/ + + + diff --git a/pom.xml b/pom.xml index e8c9507fc..d95abc4a0 100644 --- a/pom.xml +++ b/pom.xml @@ -4,7 +4,7 @@ org.bridgedb bridgedb-bundle pom - 3.1.2 + 3.1.3 BridgeDb bundle BridgeDb is a framework for finding and mapping equivalent database @@ -45,11 +45,12 @@ UTF-8 UTF-8 1.2 - 3.2.14 - 2.2 + 3.6.4 + 5.1.9 + 3.0 1.10 2.22.0 - 8.0.33 + 9.0.0 Tomcat 3.4 4.3.8 @@ -57,7 +58,8 @@ 2.0.9 10.15.2.0 1.3.2 - 5.10.1 + 1.11.0 + 5.11.0 mysql @@ -317,4 +319,11 @@ https://github.com/bridgedb/BridgeDb/issues + + + mvnrepository + https://mvnrepository.com/artifact/ + + +