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Develop > Master #5

Merged
merged 12 commits into from
Oct 10, 2023
Merged

Develop > Master #5

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e923cda
updating poms for 2.0.13-SNAPSHOT development
noedelta Jan 18, 2019
b1d4ded
updating develop poms to master versions to avoid merge conflicts
noedelta Jan 18, 2019
f350369
Merge branch 'master' into develop
noedelta Jan 18, 2019
877f68d
Updating develop poms back to pre merge state
noedelta Jan 18, 2019
3f95cc3
:arrow_up: JAVA 11 upgrade
EliotRagueneau Aug 5, 2022
2229be7
Update to Java 11
jmedinaebi Nov 7, 2022
d0660f8
Remove disable doclint profile
jmedinaebi Nov 10, 2022
d1be29a
Update dependencies
jmedinaebi Nov 28, 2022
4ada7ca
Update nexus repo URLs
jmedinaebi Jan 9, 2023
d290119
Update version
jmedinaebi Jan 27, 2023
964cd17
Merge pull request #4 from HUPO-PSI/feature/juanjo-java-11-update
jmedinaebi Feb 1, 2023
e66860c
Merge branch 'master' into develop
jmedinaebi Oct 10, 2023
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2 changes: 1 addition & 1 deletion cv-rule-reader/pom.xml
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Expand Up @@ -4,7 +4,7 @@
<parent>
<groupId>psidev.psi.tools</groupId>
<artifactId>master-pom</artifactId>
<version>2.0.14-SNAPSHOT</version>
<version>2.1.0</version>
</parent>

<artifactId>cv-rule-reader</artifactId>
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2 changes: 1 addition & 1 deletion object-rule-reader/pom.xml
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Expand Up @@ -4,7 +4,7 @@
<parent>
<groupId>psidev.psi.tools</groupId>
<artifactId>master-pom</artifactId>
<version>2.0.14-SNAPSHOT</version>
<version>2.1.0</version>
</parent>

<artifactId>object-rule-reader</artifactId>
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2 changes: 1 addition & 1 deletion ontology-config-reader/pom.xml
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Expand Up @@ -4,7 +4,7 @@
<parent>
<groupId>psidev.psi.tools</groupId>
<artifactId>master-pom</artifactId>
<version>2.0.14-SNAPSHOT</version>
<version>2.1.0</version>
</parent>

<artifactId>ontology-config-reader</artifactId>
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33 changes: 32 additions & 1 deletion ontology-manager/pom.xml
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Expand Up @@ -4,7 +4,7 @@
<parent>
<groupId>psidev.psi.tools</groupId>
<artifactId>master-pom</artifactId>
<version>2.0.14-SNAPSHOT</version>
<version>2.1.0</version>
</parent>

<artifactId>ontology-manager</artifactId>
Expand Down Expand Up @@ -51,6 +51,18 @@
<version>${project.version}</version>
</dependency>

<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-web</artifactId>
<version>${spring.version}</version>
</dependency>

<dependency>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-databind</artifactId>
<version>2.13.3</version>
</dependency>

<!-- OBO parser -->
<dependency>
<groupId>uk.ac.ebi.ols</groupId>
Expand Down Expand Up @@ -151,6 +163,25 @@
<version>2.3</version>
</dependency>

<!-- Logging -->
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-api</artifactId>
<version>${org.slf4j-version}</version>
</dependency>
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>jcl-over-slf4j</artifactId>
<version>${org.slf4j-version}</version>
<scope>runtime</scope>
</dependency>
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-log4j12</artifactId>
<version>${org.slf4j-version}</version>
<scope>runtime</scope>
</dependency>

<!-- Tests -->
<dependency>
<groupId>junit</groupId>
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37 changes: 14 additions & 23 deletions pom.xml
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@@ -1,10 +1,11 @@
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>

<groupId>psidev.psi.tools</groupId>
<artifactId>master-pom</artifactId>
<packaging>pom</packaging>
<version>2.0.14-SNAPSHOT</version>
<version>2.1.0</version>

<name>PSI :: Tools :: Master pom</name>

Expand Down Expand Up @@ -52,6 +53,8 @@

<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<spring.version>4.3.30.RELEASE</spring.version>
<org.slf4j-version>1.6.6</org.slf4j-version>
</properties>

<modules>
Expand All @@ -76,18 +79,6 @@
<url>http://www.ebi.ac.uk/</url>
</organization>

<profiles>
<profile>
<id>disable-java8-doclint</id>
<activation>
<jdk>[1.8,)</jdk>
</activation>
<properties>
<additionalparam>-Xdoclint:none</additionalparam>
</properties>
</profile>
</profiles>

<build>
<defaultGoal>clean install</defaultGoal>
<plugins>
Expand All @@ -96,14 +87,14 @@
<artifactId>maven-compiler-plugin</artifactId>
<version>3.10.1</version>
<configuration>
<source>1.8</source>
<target>1.8</target>
<source>11</source>
<target>11</target>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-source-plugin</artifactId>
<version>3.0.1</version>
<version>3.2.1</version>
<executions>
<execution>
<id>attach-source</id>
Expand Down Expand Up @@ -146,9 +137,9 @@
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-javadoc-plugin</artifactId>
<version>2.10.3</version>
<version>3.2.0</version>
<configuration>
<source>1.8</source>
<source>11</source>
<aggregate>true</aggregate>
</configuration>
</plugin>
Expand Down Expand Up @@ -177,7 +168,7 @@
<artifactId>maven-pmd-plugin</artifactId>
<version>3.19.0</version>
<configuration>
<targetJdk>1.8</targetJdk>
<targetJdk>11</targetJdk>
<sourceEncoding>utf-8</sourceEncoding>
<linkXref>true</linkXref>
<rulesets>
Expand Down Expand Up @@ -251,7 +242,7 @@
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>4.3.1</version>
<version>4.13.2</version>
<scope>test</scope>
</dependency>
</dependencies>
Expand All @@ -273,14 +264,14 @@
<repository>
<id>pst-release</id>
<name>EBI Nexus Repository</name>
<url>https://www.ebi.ac.uk/Tools/maven/repos/content/repositories/pst-release</url>
<url>https://www.ebi.ac.uk/Tools/maven/repos/content/repositories/pst-release/</url>
</repository>
<!-- EBI SNAPSHOT repo -->
<snapshotRepository>
<uniqueVersion>false</uniqueVersion>
<id>pst-snapshots</id>
<name>EBI Nexus Snapshots Repository</name>
<url>http://www.ebi.ac.uk/Tools/maven/repos/content/repositories/pst-snapshots</url>
<url>https://www.ebi.ac.uk/Tools/maven/repos/content/repositories/pst-snapshots/</url>
</snapshotRepository>
</distributionManagement>

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6 changes: 3 additions & 3 deletions validator-tutorial/spe-model/pom.xml
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Expand Up @@ -15,7 +15,7 @@
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>4.3.1</version>
<version>4.13.2</version>
<scope>test</scope>
</dependency>
<dependency>
Expand All @@ -41,8 +41,8 @@
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<configuration>
<source>1.5</source>
<target>1.5</target>
<source>11</source>
<target>11</target>
</configuration>
</plugin>
</plugins>
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6 changes: 3 additions & 3 deletions validator-tutorial/spe-validator/pom.xml
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Expand Up @@ -15,7 +15,7 @@
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>4.3.1</version>
<version>4.13.2</version>
<scope>test</scope>
</dependency>

Expand All @@ -42,8 +42,8 @@
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<configuration>
<source>1.5</source>
<target>1.5</target>
<source>11</source>
<target>11</target>
</configuration>
</plugin>
</plugins>
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2 changes: 1 addition & 1 deletion validator/pom.xml
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Expand Up @@ -4,7 +4,7 @@
<parent>
<groupId>psidev.psi.tools</groupId>
<artifactId>master-pom</artifactId>
<version>2.0.14-SNAPSHOT</version>
<version>2.1.0</version>
</parent>

<artifactId>validator</artifactId>
Expand Down