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[WIP] Preparing release 3.0.28 #250

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merged 13 commits into from
Sep 27, 2024
Merged

[WIP] Preparing release 3.0.28 #250

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b715604
Open for development
egonw Sep 22, 2024
ccacd59
Newer MySQL driver
egonw Sep 21, 2024
4405518
Removed an unused dependency
egonw Sep 22, 2024
92eadef
Newer Apache CFX version
egonw Sep 22, 2024
425f691
Maven style
egonw Sep 22, 2024
596d2c4
Added a simple test
egonw Sep 22, 2024
2c6a62d
Restructured and added a mapping test
egonw Sep 22, 2024
022bb5c
Require minimal versions of Maven and Java
egonw Sep 22, 2024
ead0b3e
Set to Java8, bc even 'mvn -f pom-java8.xml' picks it up from pom.xml…
egonw Sep 22, 2024
3c4e2e9
Updated Maven Jar plugin
egonw Sep 22, 2024
0eb6f1a
Central, updated Felix maven plugin
egonw Sep 22, 2024
310a227
Updated more dependencies: Hamcrest 3.0, JUnit 5.11, and WSDL4J 1.6.3
egonw Sep 22, 2024
a8f5a2b
BridgeDb Datasources 20240925
egonw Sep 26, 2024
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16 changes: 2 additions & 14 deletions examples/pom.xml
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Expand Up @@ -3,7 +3,7 @@
<parent>
<artifactId>bridgedb-bundle</artifactId>
<groupId>org.bridgedb</groupId>
<version>3.0.27</version>
<version>3.0.28-SNAPSHOT</version>
</parent>
<modelVersion>4.0.0</modelVersion>
<groupId>org.bridgedb.examples</groupId>
Expand Down Expand Up @@ -65,22 +65,10 @@
<dependency>
<groupId>wsdl4j</groupId>
<artifactId>wsdl4j</artifactId>
<version>1.6.2</version>
<version>1.6.3</version>
<type>jar</type>
<scope>runtime</scope>
</dependency>
<dependency>
<groupId>org.apache.axis</groupId>
<artifactId>axis</artifactId>
<version>1.4</version>
<type>jar</type>
</dependency>
<dependency>
<groupId>org.apache.axis</groupId>
<artifactId>axis-jaxrpc</artifactId>
<version>1.4</version>
<type>jar</type>
</dependency>
</dependencies>

</project>
4 changes: 2 additions & 2 deletions org.bridgedb.bio/pom.xml
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Expand Up @@ -8,7 +8,7 @@
<parent>
<artifactId>bridgedb-bundle</artifactId>
<groupId>org.bridgedb</groupId>
<version>3.0.27</version>
<version>3.0.28-SNAPSHOT</version>
</parent>

<build>
Expand All @@ -32,7 +32,7 @@
<plugin>
<groupId>org.apache.felix</groupId>
<artifactId>maven-bundle-plugin</artifactId>
<version>5.1.2</version>
<version>${felix.version}</version>
<extensions>true</extensions>
<configuration>
<instructions>
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1 change: 0 additions & 1 deletion org.bridgedb.bio/resources/org/bridgedb/bio/datasources.tsv
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Expand Up @@ -55,7 +55,6 @@ Illumina Il http://www.illumina.com/ ILMN_5668 probe 0 Il ILMN_\d+ Illumina i
InChIKey Ik http://inchi.org/ QTBSBXVTEAMEQO-UHFFFAOYSA-N metabolite 1 urn:miriam:inchikey ^[A-Z]{14}\-[A-Z]{10}(\-[A-Z])? Standard InChIKey P235 inchikey metabolite
IntAct Ia http://www.ebi.ac.uk/intact/ http://www.ebi.ac.uk/intact/pages/details/details.xhtml?interactionAc=$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
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3 changes: 2 additions & 1 deletion org.bridgedb.bio/resources/org/bridgedb/bio/organisms.tsv
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Expand Up @@ -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
Expand Down
1 change: 0 additions & 1 deletion org.bridgedb.bio/src/main/resources/org/bridgedb/bio/datasources.tsv
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Expand Up @@ -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
Expand Down
3 changes: 2 additions & 1 deletion org.bridgedb.bio/src/main/resources/org/bridgedb/bio/organisms.tsv
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Expand Up @@ -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
Expand Down
2 changes: 1 addition & 1 deletion org.bridgedb.file.orthoxml/pom.xml
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Expand Up @@ -6,7 +6,7 @@
<parent>
<artifactId>bridgedb-bundle</artifactId>
<groupId>org.bridgedb</groupId>
<version>3.0.27</version>
<version>3.0.28-SNAPSHOT</version>
</parent>

<build>
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4 changes: 2 additions & 2 deletions org.bridgedb.gui/pom.xml
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Expand Up @@ -7,7 +7,7 @@
<parent>
<artifactId>bridgedb-bundle</artifactId>
<groupId>org.bridgedb</groupId>
<version>3.0.27</version>
<version>3.0.28-SNAPSHOT</version>
</parent>

<build>
Expand All @@ -32,7 +32,7 @@
<plugin>
<groupId>org.apache.felix</groupId>
<artifactId>maven-bundle-plugin</artifactId>
<version>5.1.2</version>
<version>${felix.version}</version>
<extensions>true</extensions>
<configuration>
<instructions>
Expand Down
8 changes: 4 additions & 4 deletions org.bridgedb.rdb.construct/pom.xml
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Expand Up @@ -7,7 +7,7 @@
<parent>
<artifactId>bridgedb-bundle</artifactId>
<groupId>org.bridgedb</groupId>
<version>3.0.27</version>
<version>3.0.28-SNAPSHOT</version>
</parent>

<build>
Expand All @@ -32,7 +32,7 @@
<plugin>
<groupId>org.apache.felix</groupId>
<artifactId>maven-bundle-plugin</artifactId>
<version>5.1.2</version>
<version>${felix.version}</version>
<extensions>true</extensions>
<configuration>
<instructions>
Expand Down Expand Up @@ -80,8 +80,8 @@
<scope>compile</scope>
</dependency>
<dependency>
<groupId>mysql</groupId>
<artifactId>mysql-connector-java</artifactId>
<groupId>com.mysql</groupId>
<artifactId>mysql-connector-j</artifactId>
<version>${mysql.version}</version>
<type>jar</type>
<scope>runtime</scope>
Expand Down
10 changes: 5 additions & 5 deletions org.bridgedb.rdb/pom.xml
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Expand Up @@ -7,7 +7,7 @@
<parent>
<artifactId>bridgedb-bundle</artifactId>
<groupId>org.bridgedb</groupId>
<version>3.0.27</version>
<version>3.0.28-SNAPSHOT</version>
</parent>

<build>
Expand All @@ -32,7 +32,7 @@
<plugin>
<groupId>org.apache.felix</groupId>
<artifactId>maven-bundle-plugin</artifactId>
<version>5.1.2</version>
<version>${felix.version}</version>
<extensions>true</extensions>
<configuration>
<instructions>
Expand Down Expand Up @@ -79,8 +79,8 @@
<scope>compile</scope>
</dependency>
<dependency>
<groupId>mysql</groupId>
<artifactId>mysql-connector-java</artifactId>
<groupId>com.mysql</groupId>
<artifactId>mysql-connector-j</artifactId>
<version>${mysql.version}</version>
<type>jar</type>
<scope>runtime</scope>
Expand Down Expand Up @@ -108,7 +108,7 @@
<dependency>
<groupId>org.junit.platform</groupId>
<artifactId>junit-platform-launcher</artifactId>
<version>1.10.1</version>
<version>${junit5.platform.launcher.version}</version>
<scope>test</scope>
</dependency>
<dependency>
Expand Down
2 changes: 1 addition & 1 deletion org.bridgedb.rdf/pom.xml
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Expand Up @@ -6,7 +6,7 @@
<parent>
<artifactId>bridgedb-bundle</artifactId>
<groupId>org.bridgedb</groupId>
<version>3.0.27</version>
<version>3.0.28-SNAPSHOT</version>
</parent>

<build>
Expand Down
6 changes: 3 additions & 3 deletions org.bridgedb.sql/pom.xml
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Expand Up @@ -7,7 +7,7 @@
<parent>
<artifactId>bridgedb-bundle</artifactId>
<groupId>org.bridgedb</groupId>
<version>3.0.27</version>
<version>3.0.28-SNAPSHOT</version>
</parent>

<build>
Expand Down Expand Up @@ -47,8 +47,8 @@
<scope>compile</scope>
</dependency>
<dependency>
<groupId>mysql</groupId>
<artifactId>mysql-connector-java</artifactId>
<groupId>com.mysql</groupId>
<artifactId>mysql-connector-j</artifactId>
<version>${mysql.version}</version>
<type>jar</type>
<scope>compile</scope>
Expand Down
8 changes: 4 additions & 4 deletions org.bridgedb.tools.batchmapper/pom.xml
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Expand Up @@ -6,7 +6,7 @@
<parent>
<artifactId>bridgedb-bundle</artifactId>
<groupId>org.bridgedb</groupId>
<version>3.0.27</version>
<version>3.0.28-SNAPSHOT</version>
</parent>

<build>
Expand All @@ -33,19 +33,19 @@
<dependency>
<groupId>org.bridgedb</groupId>
<artifactId>org.bridgedb</artifactId>
<version>3.0.27</version>
<version>3.0.28-SNAPSHOT</version>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>org.bridgedb</groupId>
<artifactId>org.bridgedb.bio</artifactId>
<version>3.0.27</version>
<version>3.0.28-SNAPSHOT</version>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>org.bridgedb</groupId>
<artifactId>org.bridgedb.rdb</artifactId>
<version>3.0.27</version>
<version>3.0.28-SNAPSHOT</version>
<scope>compile</scope>
</dependency>
</dependencies>
Expand Down
2 changes: 1 addition & 1 deletion org.bridgedb.tools.info/pom.xml
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Expand Up @@ -7,7 +7,7 @@
<parent>
<artifactId>bridgedb-bundle</artifactId>
<groupId>org.bridgedb</groupId>
<version>3.0.27</version>
<version>3.0.28-SNAPSHOT</version>
</parent>

<build>
Expand Down
10 changes: 5 additions & 5 deletions org.bridgedb.tools.qc/pom.xml
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Expand Up @@ -7,7 +7,7 @@
<parent>
<artifactId>bridgedb-bundle</artifactId>
<groupId>org.bridgedb</groupId>
<version>3.0.27</version>
<version>3.0.28-SNAPSHOT</version>
</parent>

<build>
Expand Down Expand Up @@ -71,8 +71,8 @@
<version>${project.parent.version}</version>
<exclusions>
<exclusion>
<groupId>mysql</groupId>
<artifactId>mysql-connector-java</artifactId>
<groupId>com.mysql</groupId>
<artifactId>mysql-connector-j</artifactId>
</exclusion>
</exclusions>
</dependency>
Expand All @@ -82,8 +82,8 @@
<version>${project.parent.version}</version>
<exclusions>
<exclusion>
<groupId>mysql</groupId>
<artifactId>mysql-connector-java</artifactId>
<groupId>com.mysql</groupId>
<artifactId>mysql-connector-j</artifactId>
</exclusion>
</exclusions>
</dependency>
Expand Down
10 changes: 5 additions & 5 deletions org.bridgedb.tools.voidtool/pom.xml
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Expand Up @@ -7,7 +7,7 @@
<parent>
<artifactId>bridgedb-bundle</artifactId>
<groupId>org.bridgedb</groupId>
<version>3.0.27</version>
<version>3.0.28-SNAPSHOT</version>
</parent>

<build>
Expand Down Expand Up @@ -71,8 +71,8 @@
<version>${project.parent.version}</version>
<exclusions>
<exclusion>
<groupId>mysql</groupId>
<artifactId>mysql-connector-java</artifactId>
<groupId>com.mysql</groupId>
<artifactId>mysql-connector-j</artifactId>
</exclusion>
</exclusions>
</dependency>
Expand All @@ -82,8 +82,8 @@
<version>${project.parent.version}</version>
<exclusions>
<exclusion>
<groupId>mysql</groupId>
<artifactId>mysql-connector-java</artifactId>
<groupId>com.mysql</groupId>
<artifactId>mysql-connector-j</artifactId>
</exclusion>
</exclusions>
</dependency>
Expand Down
2 changes: 1 addition & 1 deletion org.bridgedb.uri.api/pom.xml
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Expand Up @@ -7,7 +7,7 @@
<parent>
<artifactId>bridgedb-bundle</artifactId>
<groupId>org.bridgedb</groupId>
<version>3.0.27</version>
<version>3.0.28-SNAPSHOT</version>
</parent>

<build>
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2 changes: 1 addition & 1 deletion org.bridgedb.uri.loader/pom.xml
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Expand Up @@ -6,7 +6,7 @@
<parent>
<artifactId>bridgedb-bundle</artifactId>
<groupId>org.bridgedb</groupId>
<version>3.0.27</version>
<version>3.0.28-SNAPSHOT</version>
</parent>

<dependencies>
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6 changes: 3 additions & 3 deletions org.bridgedb.uri.sql/pom.xml
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Expand Up @@ -7,7 +7,7 @@
<parent>
<artifactId>bridgedb-bundle</artifactId>
<groupId>org.bridgedb</groupId>
<version>3.0.27</version>
<version>3.0.28-SNAPSHOT</version>
</parent>

<build>
Expand Down Expand Up @@ -64,8 +64,8 @@
<scope>compile</scope>
</dependency>
<dependency>
<groupId>mysql</groupId>
<artifactId>mysql-connector-java</artifactId>
<groupId>com.mysql</groupId>
<artifactId>mysql-connector-j</artifactId>
<version>${mysql.version}</version>
<type>jar</type>
<scope>compile</scope>
Expand Down
2 changes: 1 addition & 1 deletion org.bridgedb.uri.ws.client/pom.xml
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Expand Up @@ -8,7 +8,7 @@
<parent>
<artifactId>bridgedb-bundle</artifactId>
<groupId>org.bridgedb</groupId>
<version>3.0.27</version>
<version>3.0.28-SNAPSHOT</version>
</parent>

<build>
Expand Down
2 changes: 1 addition & 1 deletion org.bridgedb.uri.ws.core/pom.xml
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Expand Up @@ -8,7 +8,7 @@
<parent>
<artifactId>bridgedb-bundle</artifactId>
<groupId>org.bridgedb</groupId>
<version>3.0.27</version>
<version>3.0.28-SNAPSHOT</version>
</parent>

<build>
Expand Down
2 changes: 1 addition & 1 deletion org.bridgedb.uri.ws.server/pom.xml
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Expand Up @@ -8,7 +8,7 @@
<parent>
<artifactId>bridgedb-bundle</artifactId>
<groupId>org.bridgedb</groupId>
<version>3.0.27</version>
<version>3.0.28-SNAPSHOT</version>
</parent>

<build>
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2 changes: 1 addition & 1 deletion org.bridgedb.utils/pom.xml
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Expand Up @@ -7,7 +7,7 @@
<parent>
<artifactId>bridgedb-bundle</artifactId>
<groupId>org.bridgedb</groupId>
<version>3.0.27</version>
<version>3.0.28-SNAPSHOT</version>
</parent>

<build>
Expand Down
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