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Commit 72b74a59 authored by Lukas Jelonek's avatar Lukas Jelonek
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Merge branch 'release/2.0.1'

parents f46177d9 002091ff
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.gitlab-ci.yml 0 → 100644
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variables:
# This will supress any download for dependencies and plugins or upload messages which would clutter the console log.
# `showDateTime` will show the passed time in milliseconds. You need to specify `--batch-mode` to make this work.
MAVEN_OPTS: "-Dorg.slf4j.simpleLogger.log.org.apache.maven.cli.transfer.Slf4jMavenTransferListener=WARN -Dorg.slf4j.simpleLogger.showDateTime=true -Djava.awt.headless=true"
# As of Maven 3.3.0 instead of this you may define these options in `.mvn/maven.config` so the same config is used
# when running from the command line.
# `installAtEnd` and `deployAtEnd`are only effective with recent version of the corresponding plugins.
MAVEN_CLI_OPTS: "--batch-mode --errors --fail-at-end --show-version -DinstallAtEnd=true -DdeployAtEnd=true --settings .mvn/artifactory-settings.xml"
# Cache downloaded dependencies and plugins between builds.
cache:
paths:
- /root/.m2/repository/
# Validate merge requests using JDK8, e.g. check for compile errors
validate:jdk8:
stage: build
script:
- 'mvn $MAVEN_CLI_OPTS test-compile'
image: maven:3.3.9-jdk-8
# Verify merge requests using JDK8, e.g. run the tests
verify:jdk8:
stage: test
script:
- 'mvn $MAVEN_CLI_OPTS deploy site'
artifacts:
paths:
- target/site
expire_in: 6h
image: maven:3.3.9-jdk-8
.mvn/artifactory-settings.xml 0 → 100644
View file @ 72b74a59
<settings xmlns:profile="http://maven.apache.org/SETTINGS/1.0.0">
<profiles>
<profile>
<id>artifactory-giessen</id>
<repositories>
<repository>
<snapshots>
<enabled>false</enabled>
</snapshots>
<id>central-giessen</id>
<name>libs-release</name>
<url>https://artifactory.computational.bio.uni-giessen.de/artifactory/libs-release</url>
</repository>
<repository>
<snapshots>
<enabled>true</enabled>
</snapshots>
<releases>
<enabled>false</enabled>
</releases>
<id>snapshots-giessen</id>
<name>libs-snapshot</name>
<url>https://artifactory.computational.bio.uni-giessen.de/artifactory/libs-snapshot</url>
</repository>
</repositories>
<pluginRepositories>
<pluginRepository>
<snapshots>
<enabled>false</enabled>
</snapshots>
<id>central-giessen</id>
<name>plugins-release</name>
<url>https://artifactory.computational.bio.uni-giessen.de/artifactory/plugins-release</url>
</pluginRepository>
<pluginRepository>
<snapshots>
<enabled>true</enabled>
</snapshots>
<releases>
<enabled>false</enabled>
</releases>
<id>snapshots-giessen</id>
<name>plugins-snapshot</name>
<url>https://artifactory.computational.bio.uni-giessen.de/artifactory/plugins-snapshot</url>
</pluginRepository>
</pluginRepositories>
</profile>
</profiles>
<servers>
<server>
<id>central-giessen</id>
<username>${env.ARTIFACTORY_USER}</username>
<password>${env.ARTIFACTORY_PASSWORD}</password>
</server>
<server>
<id>snapshots-giessen</id>
<username>${env.ARTIFACTORY_USER}</username>
<password>${env.ARTIFACTORY_PASSWORD}</password>
</server>
</servers>
<activeProfiles>
<activeProfile>artifactory-giessen</activeProfile>
</activeProfiles>
</settings>
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.mvn/jvm.config 0 → 100644
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-Djava.awt.headless=true
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.mvn/maven.config 0 → 100644
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--fail-at-end
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pom.xml
View file @ 72b74a59
<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>de.cebitec.common</groupId>
<artifactId>dbxref</artifactId>
<version>2.0.0</version>
<packaging>bundle</packaging>
<name>DbXRef library</name>
<licenses>
<license>
<url>http://www.gnu.org/licenses/gpl-3.0.html</url>
</license>
</licenses>
<description>
Library for resolving of database cross references (dbxrefs) to urls.
</description>
<scm>
<developerConnection>scm:git:https://git.computational.bio.uni-giessen.de/gendb3/lib-dbxref.git</developerConnection>
<tag>HEAD</tag>
</scm>
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
</properties>
<dependencies>
<dependency>
<groupId>org.hibernate.javax.persistence</groupId>
<artifactId>hibernate-jpa-2.1-api</artifactId>
<version>1.0.0.Final</version>
</dependency>
<dependency>
<groupId>org.hibernate</groupId>
<artifactId>hibernate-jpamodelgen</artifactId>
<version>1.2.0.Final</version>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>org.kohsuke.metainf-services</groupId>
<artifactId>metainf-services</artifactId>
<version>1.5</version>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>com.google.guava</groupId>
<artifactId>guava</artifactId>
<version>16.0.1</version>
</dependency>
<!-- Test dependencies -->
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>4.11</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.hamcrest</groupId>
<artifactId>hamcrest-all</artifactId>
<version>1.3</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.hibernate</groupId>
<artifactId>hibernate-entitymanager</artifactId>
<version>4.2.2.Final</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>com.h2database</groupId>
<artifactId>h2</artifactId>
<version>[1.3.171,)</version>
<scope>test</scope>
</dependency>
<!-- Additional debuging dependencies -->
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-jdk14</artifactId>
<version>1.7.5</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>p6spy</groupId>
<artifactId>p6spy</artifactId>
<version>1.3</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>commons-io</groupId>
<artifactId>commons-io</artifactId>
<version>2.4</version>
</dependency>
<dependency>
<groupId>com.google.code.gson</groupId>
<artifactId>gson</artifactId>
<version>2.6.2</version>
</dependency>
</dependencies>
<build>
<plugins>
<plugin>
<groupId>org.apache.felix</groupId>
<artifactId>maven-bundle-plugin</artifactId>
<version>2.3.7</version>
<extensions>true</extensions>
<configuration>
<instructions>
<Include-Resource>{maven-resources},
META-INF/services=${project.build.outputDirectory}/META-INF/services</Include-Resource>
<SPI-Consumer>*</SPI-Consumer>
<SPI-Provider>*</SPI-Provider>
</instructions>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.1</version>
<configuration>
<source>1.8</source>
<target>1.8</target>
<encoding>${project.build.sourceEncoding}</encoding>
<compilerArgument>-Xlint:unchecked</compilerArgument>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-resources-plugin</artifactId>
<version>2.4.3</version>
<configuration>
<encoding>${project.build.sourceEncoding}</encoding>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-failsafe-plugin</artifactId>
<version>2.17</version>
<executions>
<execution>
<goals>
<goal>integration-test</goal>
<goal>verify</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<groupId>external.atlassian.jgitflow</groupId>
<artifactId>jgitflow-maven-plugin</artifactId>
<version>1.0-m5.1</version>
<configuration>
<autoVersionSubmodules>true</autoVersionSubmodules>
<localOnly>true</localOnly>
<noDeploy>true</noDeploy>
</configuration>
</plugin>
</plugins>
</build>
<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>de.cebitec.common</groupId>
<artifactId>dbxref</artifactId>
<version>2.0.1</version>
<packaging>bundle</packaging>
<name>DbXRef library</name>
<licenses>
<license>
<url>http://www.gnu.org/licenses/gpl-3.0.html</url>
</license>
</licenses>
<description>
Library for resolving of database cross references (dbxrefs) to urls.
</description>
<scm>
<developerConnection>scm:git:https://git.computational.bio.uni-giessen.de/gendb3/lib-dbxref.git</developerConnection>
<tag>HEAD</tag>
</scm>
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
</properties>
<dependencies>
<dependency>
<groupId>org.hibernate.javax.persistence</groupId>
<artifactId>hibernate-jpa-2.1-api</artifactId>
<version>1.0.0.Final</version>
</dependency>
<dependency>
<groupId>org.hibernate</groupId>
<artifactId>hibernate-jpamodelgen</artifactId>
<version>1.2.0.Final</version>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>org.kohsuke.metainf-services</groupId>
<artifactId>metainf-services</artifactId>
<version>1.5</version>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>com.google.guava</groupId>
<artifactId>guava</artifactId>
<version>16.0.1</version>
</dependency>
<!-- Test dependencies -->
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>4.11</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.hamcrest</groupId>
<artifactId>hamcrest-all</artifactId>
<version>1.3</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.hibernate</groupId>
<artifactId>hibernate-entitymanager</artifactId>
<version>4.2.2.Final</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>com.h2database</groupId>
<artifactId>h2</artifactId>
<version>[1.3.171,)</version>
<scope>test</scope>
</dependency>
<!-- Additional debuging dependencies -->
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-jdk14</artifactId>
<version>1.7.5</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>p6spy</groupId>
<artifactId>p6spy</artifactId>
<version>1.3</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>commons-io</groupId>
<artifactId>commons-io</artifactId>
<version>2.4</version>
</dependency>
<dependency>
<groupId>com.google.code.gson</groupId>
<artifactId>gson</artifactId>
<version>2.6.2</version>
</dependency>
</dependencies>
<build>
<plugins>
<plugin>
<groupId>org.apache.felix</groupId>
<artifactId>maven-bundle-plugin</artifactId>
<version>2.3.7</version>
<extensions>true</extensions>
<configuration>
<instructions>
<Include-Resource>{maven-resources},
META-INF/services=${project.build.outputDirectory}/META-INF/services</Include-Resource>
<SPI-Consumer>*</SPI-Consumer>
<SPI-Provider>*</SPI-Provider>
</instructions>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.1</version>
<configuration>
<source>1.8</source>
<target>1.8</target>
<encoding>${project.build.sourceEncoding}</encoding>
<compilerArgument>-Xlint:unchecked</compilerArgument>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-resources-plugin</artifactId>
<version>2.4.3</version>
<configuration>
<encoding>${project.build.sourceEncoding}</encoding>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-failsafe-plugin</artifactId>
<version>2.17</version>
<executions>
<execution>
<goals>
<goal>integration-test</goal>
<goal>verify</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.jfrog.buildinfo</groupId>
<artifactId>artifactory-maven-plugin</artifactId>
<version>2.6.1</version>
<inherited>false</inherited>
<executions>
<execution>
<id>build-info</id>
<goals>
<goal>publish</goal>
</goals>
<configuration>
<deployProperties>
</deployProperties>
<publisher>
<!-- Define user and password as environment variables. -->
<username>{{ARTIFACTORY_USER}}</username>
<password>{{ARTIFACTORY_PASSWORD}}</password>
<contextUrl>https://artifactory.computational.bio.uni-giessen.de/artifactory</contextUrl>
<repoKey>libs-release-local</repoKey>
<snapshotRepoKey>libs-snapshot-local</snapshotRepoKey>
</publisher>
</configuration>
</execution>
</executions>
</plugin>
<plugin>
<groupId>external.atlassian.jgitflow</groupId>
<artifactId>jgitflow-maven-plugin</artifactId>
<version>1.0-m5.1</version>
<configuration>
<autoVersionSubmodules>true</autoVersionSubmodules>
<localOnly>true</localOnly>
<noDeploy>true</noDeploy>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-site-plugin</artifactId>
<version>3.6</version>
</plugin>
</plugins>
</build>
<reporting>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-report-plugin</artifactId>
<version>2.20</version>
</plugin>
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>jdepend-maven-plugin</artifactId>
<version>2.0</version>
</plugin>
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>cobertura-maven-plugin</artifactId>
<version>2.7</version>
<configuration>
<formats>
<format>html</format>
<format>xml</format>
</formats>
</configuration>
</plugin>
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>findbugs-maven-plugin</artifactId>
<version>3.0.4</version>
<configuration>
<argLine>-Xmx512m</argLine>
<argLine>-XX:MaxPermSize=512zm</argLine>
</configuration>
</plugin>
</plugins>
</reporting>
</project>
\ No newline at end of file
src/main/resources/de/cebitec/common/dbxref/providers/providers.json
View file @ 72b74a59
......@@ -24,8 +24,8 @@
},
{
"prefixes": ["RFAM"],
"html": ["http://rfam.sanger.ac.uk/family/%i"],
"xml": ["http://rfam.sanger.ac.uk/family/%i?content-type=text%2Fxml"]
"html": ["http://rfam.xfam.org/family/%i"],
"xml": ["http://rfam.xfam.org/family/%i?content-type=text%2Fxml"]
},
{
"prefixes": ["pubmed", "Pubmed"],
......
src/test/java/de/cebitec/common/dbxref/providers/ValidResourceAvailableTest.java
View file @ 72b74a59
......@@ -38,7 +38,7 @@ import org.junit.runners.Parameterized.Parameters;
@RunWith(Parameterized.class)
public class ValidResourceAvailableTest {
@Parameters
@Parameters(name = "{index}: {1}")
public static Collection<Object[]> data() {
return Arrays.asList(new Object[][]{
{new CompositeProvider(), "UniProtKB/Swiss-Prot:P12345"},
......
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