git-svn-id: https://svn.d4science.research-infrastructures.eu/gcube/trunk/data-analysis/dataminer-pool-manager@150801 82a268e6-3cf1-43bd-a215-b396298e98cf
This commit is contained in:
Nunzio Andrea Galante
parent
79f612e263
commit
3dabd84dad
282
pom.xml
282
pom.xml
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@ -1,169 +1,157 @@
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<project xmlns="http:***REMOVED***maven.apache.org/POM/4.0.0" xmlns:xsi="http:***REMOVED***www.w3.org/2001/XMLSchema-instance"
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xsi:schemaLocation="http:***REMOVED***maven.apache.org/POM/4.0.0 http:***REMOVED***maven.apache.org/xsd/maven-4.0.0.xsd">
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<modelVersion>4.0.0</modelVersion>
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xsi:schemaLocation="http:***REMOVED***maven.apache.org/POM/4.0.0 http:***REMOVED***maven.apache.org/xsd/maven-4.0.0.xsd">
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<modelVersion>4.0.0</modelVersion>
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<parent>
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<artifactId>maven-parent</artifactId>
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<groupId>org.gcube.tools</groupId>
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<version>1.0.0</version>
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<relativePath/>
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</parent>
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<parent>
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<artifactId>maven-parent</artifactId>
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<groupId>org.gcube.tools</groupId>
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<version>1.0.0</version>
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<relativePath />
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</parent>
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<groupId>org.gcube.dataAnalysis</groupId>
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<artifactId>dataminer-pool-manager</artifactId>
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<version>2.0.0-SNAPSHOT</version>
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<packaging>war</packaging>
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<groupId>org.gcube.dataAnalysis</groupId>
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<artifactId>dataminer-pool-manager</artifactId>
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<version>2.0.0-SNAPSHOT</version>
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<packaging>war</packaging>
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<name>dataminer-pool-manager</name>
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<description>
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<name>dataminer-pool-manager</name>
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<description>
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</description>
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<properties>
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<distroDirectory>distro</distroDirectory>
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<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
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<version.swagger>1.5.13</version.swagger>
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<version.jersey>2.25.1</version.jersey>
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</properties>
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<properties>
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<distroDirectory>distro</distroDirectory>
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<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
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<version.swagger>1.5.13</version.swagger>
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<version.jersey>2.25.1</version.jersey>
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</properties>
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<dependencies>
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<dependencies>
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<dependency>
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<groupId>org.gcube.core</groupId>
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<artifactId>common-smartgears</artifactId>
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<scope>provided</scope>
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</dependency>
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<dependency>
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<groupId>org.gcube.core</groupId>
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<artifactId>common-smartgears</artifactId>
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<scope>provided</scope>
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</dependency>
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<dependency>
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<groupId>org.gcube.resources.discovery</groupId>
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<artifactId>ic-client</artifactId>
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<scope>provided</scope>
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</dependency>
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<dependency>
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<groupId>org.gcube.resources.discovery</groupId>
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<artifactId>ic-client</artifactId>
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<scope>provided</scope>
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</dependency>
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<dependency>
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<groupId>commons-io</groupId>
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<artifactId>commons-io</artifactId>
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<version>[2.5.0,2.6.0)</version>
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</dependency>
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<dependency>
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<groupId>org.antlr</groupId>
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<artifactId>stringtemplate</artifactId>
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<version>[4.0.0, 4.1.0)</version>
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</dependency>
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<dependency>
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<groupId>org.tmatesoft.svnkit</groupId>
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<artifactId>svnkit</artifactId>
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<version>1.8.5</version>
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</dependency>
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<dependency>
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<groupId>commons-configuration</groupId>
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<artifactId>commons-configuration</artifactId>
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<version>1.10</version>
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</dependency>
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<dependency>
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<groupId>net.sf.opencsv</groupId>
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<artifactId>opencsv</artifactId>
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<version>2.3</version>
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</dependency>
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<dependency>
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<groupId>org.yaml</groupId>
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<artifactId>snakeyaml</artifactId>
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<version>1.16</version>
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</dependency>
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<dependency>
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<groupId>org.glassfish.jersey.media</groupId>
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<artifactId>jersey-media-json-jackson</artifactId>
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<version>$***REMOVED***version.jersey***REMOVED***</version>
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</dependency>
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<dependency>
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<groupId>org.glassfish.jersey.core</groupId>
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<artifactId>jersey-client</artifactId>
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<version>$***REMOVED***version.jersey***REMOVED***</version>
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</dependency>
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<dependency>
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<groupId>org.glassfish.jersey.containers</groupId>
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<artifactId>jersey-container-servlet</artifactId>
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<version>$***REMOVED***version.jersey***REMOVED***</version>
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</dependency>
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<!--
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<dependency>
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<groupId>io.swagger</groupId>
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<artifactId>swagger-jersey2-jaxrs</artifactId>
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<version>$***REMOVED***version.swagger***REMOVED***</version>
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</dependency>
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<dependency>
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<groupId>com.fasterxml.jackson.core</groupId>
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<artifactId>jackson-databind</artifactId>
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<version>2.6.0</version>
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<scope>provided</scope>
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</dependency>
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<dependency>
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<groupId>com.fasterxml.jackson.core</groupId>
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<artifactId>jackson-core</artifactId>
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<version>2.6.0</version>
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<scope>provided</scope>
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</dependency>
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<dependency>
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<groupId>io.swagger</groupId>
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<artifactId>swagger-annotations</artifactId>
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<version>$***REMOVED***version.swagger***REMOVED***</version>
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</dependency>
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-->
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<dependency>
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<groupId>org.slf4j</groupId>
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<artifactId>slf4j-api</artifactId>
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<scope>provided</scope>
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</dependency>
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<dependency>
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<groupId>commons-io</groupId>
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<artifactId>commons-io</artifactId>
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<version>[2.5.0,2.6.0)</version>
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</dependency>
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<dependency>
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<groupId>org.antlr</groupId>
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<artifactId>stringtemplate</artifactId>
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<version>[4.0.0, 4.1.0)</version>
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</dependency>
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<dependency>
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<groupId>org.gcube.dataanalysis</groupId>
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<artifactId>ecological-engine-smart-executor</artifactId>
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<version>1.4.0-SNAPSHOT</version>
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</dependency>
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</dependencies>
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<dependencyManagement>
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<dependencies>
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<dependency>
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<groupId>org.gcube.distribution</groupId>
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<artifactId>maven-smartgears-bom</artifactId>
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<version>LATEST</version>
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<type>pom</type>
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<scope>import</scope>
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</dependency>
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</dependencies>
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</dependencyManagement>
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<dependency>
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<groupId>org.tmatesoft.svnkit</groupId>
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<artifactId>svnkit</artifactId>
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<version>1.8.5</version>
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</dependency>
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<dependency>
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<groupId>commons-configuration</groupId>
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<artifactId>commons-configuration</artifactId>
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<version>1.10</version>
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</dependency>
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<build>
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<plugins>
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<dependency>
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<groupId>net.sf.opencsv</groupId>
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<artifactId>opencsv</artifactId>
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<version>2.3</version>
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</dependency>
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<plugin>
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<groupId>org.apache.maven.plugins</groupId>
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<artifactId>maven-assembly-plugin</artifactId>
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<configuration>
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<descriptors>
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<descriptor>$***REMOVED***distroDirectory***REMOVED***/descriptor.xml</descriptor>
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</descriptors>
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</configuration>
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<executions>
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<execution>
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<id>servicearchive</id>
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<phase>install</phase>
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<goals>
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<goal>single</goal>
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</goals>
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</execution>
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</executions>
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</plugin>
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<dependency>
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<groupId>org.yaml</groupId>
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<artifactId>snakeyaml</artifactId>
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<version>1.16</version>
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</dependency>
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<dependency>
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<groupId>org.glassfish.jersey.media</groupId>
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<artifactId>jersey-media-json-jackson</artifactId>
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<version>$***REMOVED***version.jersey***REMOVED***</version>
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</dependency>
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</plugins>
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</build>
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<dependency>
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<groupId>org.glassfish.jersey.core</groupId>
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<artifactId>jersey-client</artifactId>
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<version>$***REMOVED***version.jersey***REMOVED***</version>
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</dependency>
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<dependency>
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<groupId>org.glassfish.jersey.containers</groupId>
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<artifactId>jersey-container-servlet</artifactId>
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<version>$***REMOVED***version.jersey***REMOVED***</version>
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</dependency>
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<!-- <dependency> <groupId>io.swagger</groupId> <artifactId>swagger-jersey2-jaxrs</artifactId>
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<version>$***REMOVED***version.swagger***REMOVED***</version> </dependency> <dependency> <groupId>com.fasterxml.jackson.core</groupId>
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<artifactId>jackson-databind</artifactId> <version>2.6.0</version> <scope>provided</scope>
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</dependency> <dependency> <groupId>com.fasterxml.jackson.core</groupId>
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<artifactId>jackson-core</artifactId> <version>2.6.0</version> <scope>provided</scope>
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</dependency> <dependency> <groupId>io.swagger</groupId> <artifactId>swagger-annotations</artifactId>
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<version>$***REMOVED***version.swagger***REMOVED***</version> </dependency> -->
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<dependency>
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<groupId>org.slf4j</groupId>
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<artifactId>slf4j-api</artifactId>
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<scope>provided</scope>
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</dependency>
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</dependencies>
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<dependencyManagement>
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<dependencies>
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<dependency>
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<groupId>org.gcube.distribution</groupId>
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<artifactId>maven-smartgears-bom</artifactId>
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<version>LATEST</version>
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<type>pom</type>
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<scope>import</scope>
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</dependency>
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</dependencies>
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</dependencyManagement>
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<build>
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<plugins>
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<plugin>
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<groupId>org.apache.maven.plugins</groupId>
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<artifactId>maven-assembly-plugin</artifactId>
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<configuration>
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||||
<descriptors>
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<descriptor>$***REMOVED***distroDirectory***REMOVED***/descriptor.xml</descriptor>
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</descriptors>
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</configuration>
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<executions>
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<execution>
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<id>servicearchive</id>
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<phase>install</phase>
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<goals>
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<goal>single</goal>
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</goals>
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||||
</execution>
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||||
</executions>
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</plugin>
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</plugins>
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</build>
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</project>
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@ -9,8 +9,14 @@ import java.util.Vector;
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public class Algorithm ***REMOVED***
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private String username;
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private String fullname;
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private String email;
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private String language;
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private String name;
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private String description;
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@ -153,6 +159,42 @@ public class Algorithm ***REMOVED***
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this.skipJava = skipJava;
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***REMOVED***
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public String getUsername() ***REMOVED***
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return username;
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***REMOVED***
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public void setUsername(String username) ***REMOVED***
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this.username = username;
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***REMOVED***
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public String getFullname() ***REMOVED***
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return fullname;
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***REMOVED***
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public void setFullname(String fullname) ***REMOVED***
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this.fullname = fullname;
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***REMOVED***
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public String getEmail() ***REMOVED***
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return email;
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***REMOVED***
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public void setEmail(String email) ***REMOVED***
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this.email = email;
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***REMOVED***
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public String getLanguage() ***REMOVED***
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return language;
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***REMOVED***
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public void setLanguage(String language) ***REMOVED***
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this.language = language;
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***REMOVED***
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public void setActions(Collection<Action> actions) ***REMOVED***
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this.actions = actions;
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***REMOVED***
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|
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|
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***REMOVED***
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@ -22,6 +22,16 @@ public class AlgorithmPackageParser ***REMOVED***
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*/
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private static final String METADATA_FILE_NAME = "Info.txt";
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private static final String METADATA_USERNAME = "Username";
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||||
|
||||
private static final String METADATA_FULLNAME = "Full Name";
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||||
|
||||
private static final String METADATA_EMAIL = "Email";
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||||
|
||||
private static final String METADATA_LANGUAGE = "Language";
|
||||
|
||||
private static final String METADATA_CATEGORY = "Algorithm Category";
|
||||
|
||||
private static final String METADATA_ALGORITHM_NAME = "Algorithm Name";
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|
||||
private static final String METADATA_ALGORITHM_DESCRIPTION = "Algorithm Description";
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||||
|
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@ -145,73 +155,93 @@ public class AlgorithmPackageParser ***REMOVED***
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out.setName(extractSingleValue(metadata, METADATA_ALGORITHM_NAME));
|
||||
out.setDescription(extractSingleValue(metadata, METADATA_ALGORITHM_DESCRIPTION));
|
||||
out.setClazz(extractSingleValue(metadata, METADATA_CLASS_NAME));
|
||||
***REMOVED***List<String> dependencies = extractMultipleValues(metadata, METADATA_PACKAGES);
|
||||
out.setEmail(extractSingleValue(metadata, METADATA_EMAIL));
|
||||
out.setFullname(extractSingleValue(metadata, METADATA_FULLNAME));
|
||||
out.setUsername(extractSingleValue(metadata, METADATA_USERNAME));
|
||||
out.setLanguage(extractSingleValue(metadata, METADATA_LANGUAGE));
|
||||
out.setCategory(extractSingleValue(metadata, METADATA_CATEGORY));
|
||||
|
||||
|
||||
List<String> rdependencies = extractMultipleValues(metadata, "cran");
|
||||
if (rdependencies != null) ***REMOVED***
|
||||
for (String pkg : rdependencies) ***REMOVED***
|
||||
List<String> dependencies = extractMultipleValues(metadata, "Package Name");
|
||||
|
||||
if (dependencies != null) ***REMOVED***
|
||||
for (String pkg : dependencies) ***REMOVED***
|
||||
Dependency dep = new Dependency();
|
||||
|
||||
***REMOVED***if (pkg.startsWith("os:"))***REMOVED***
|
||||
dep.setName(pkg);
|
||||
dep.setType("cran");
|
||||
dep.setName(pkg);
|
||||
out.addDependency(dep);
|
||||
***REMOVED***
|
||||
***REMOVED***
|
||||
|
||||
|
||||
List<String> defdependencies = extractMultipleValues(metadata, "Packages");
|
||||
if (defdependencies != null) ***REMOVED***
|
||||
for (String pkg : defdependencies) ***REMOVED***
|
||||
Dependency dep = new Dependency();
|
||||
|
||||
***REMOVED***if (pkg.startsWith("os:"))***REMOVED***
|
||||
dep.setName(pkg);
|
||||
dep.setType("os");
|
||||
out.addDependency(dep);
|
||||
***REMOVED***
|
||||
***REMOVED***
|
||||
|
||||
List<String> osdependencies = extractMultipleValues(metadata, "os");
|
||||
if (osdependencies != null) ***REMOVED***
|
||||
for (String pkg : osdependencies) ***REMOVED***
|
||||
Dependency dep = new Dependency();
|
||||
|
||||
***REMOVED***if (pkg.startsWith("os:"))***REMOVED***
|
||||
dep.setName(pkg);
|
||||
dep.setType("os");
|
||||
out.addDependency(dep);
|
||||
***REMOVED***
|
||||
***REMOVED***
|
||||
|
||||
|
||||
|
||||
List<String> gitdependencies = extractMultipleValues(metadata, "github");
|
||||
if (gitdependencies != null) ***REMOVED***
|
||||
for (String pkg : gitdependencies) ***REMOVED***
|
||||
Dependency dep = new Dependency();
|
||||
|
||||
***REMOVED***if (pkg.startsWith("os:"))***REMOVED***
|
||||
dep.setName(pkg);
|
||||
dep.setType("github");
|
||||
out.addDependency(dep);
|
||||
***REMOVED***
|
||||
***REMOVED***
|
||||
|
||||
|
||||
|
||||
List<String> cdependencies = extractMultipleValues(metadata, "custom");
|
||||
if (cdependencies != null) ***REMOVED***
|
||||
for (String pkg : cdependencies) ***REMOVED***
|
||||
Dependency dep = new Dependency();
|
||||
|
||||
***REMOVED***if (pkg.startsWith("os:"))***REMOVED***
|
||||
dep.setName(pkg);
|
||||
dep.setType("custom");
|
||||
out.addDependency(dep);
|
||||
***REMOVED***
|
||||
***REMOVED***
|
||||
|
||||
|
||||
|
||||
***REMOVED*** List<String> rdependencies = extractMultipleValues(metadata, "cran");
|
||||
***REMOVED*** if (rdependencies != null) ***REMOVED***
|
||||
***REMOVED*** for (String pkg : rdependencies) ***REMOVED***
|
||||
***REMOVED*** Dependency dep = new Dependency();
|
||||
***REMOVED***
|
||||
***REMOVED*** ***REMOVED***if (pkg.startsWith("os:"))***REMOVED***
|
||||
***REMOVED*** dep.setName(pkg);
|
||||
***REMOVED*** dep.setType("cran");
|
||||
***REMOVED*** out.addDependency(dep);
|
||||
***REMOVED*** ***REMOVED***
|
||||
***REMOVED*** ***REMOVED***
|
||||
***REMOVED***
|
||||
***REMOVED***
|
||||
***REMOVED*** List<String> defdependencies = extractMultipleValues(metadata, "Packages");
|
||||
***REMOVED*** if (defdependencies != null) ***REMOVED***
|
||||
***REMOVED*** for (String pkg : defdependencies) ***REMOVED***
|
||||
***REMOVED*** Dependency dep = new Dependency();
|
||||
***REMOVED***
|
||||
***REMOVED*** ***REMOVED***if (pkg.startsWith("os:"))***REMOVED***
|
||||
***REMOVED*** dep.setName(pkg);
|
||||
***REMOVED*** dep.setType("os");
|
||||
***REMOVED*** out.addDependency(dep);
|
||||
***REMOVED*** ***REMOVED***
|
||||
***REMOVED*** ***REMOVED***
|
||||
***REMOVED***
|
||||
***REMOVED*** List<String> osdependencies = extractMultipleValues(metadata, "os");
|
||||
***REMOVED*** if (osdependencies != null) ***REMOVED***
|
||||
***REMOVED*** for (String pkg : osdependencies) ***REMOVED***
|
||||
***REMOVED*** Dependency dep = new Dependency();
|
||||
***REMOVED***
|
||||
***REMOVED*** ***REMOVED***if (pkg.startsWith("os:"))***REMOVED***
|
||||
***REMOVED*** dep.setName(pkg);
|
||||
***REMOVED*** dep.setType("os");
|
||||
***REMOVED*** out.addDependency(dep);
|
||||
***REMOVED*** ***REMOVED***
|
||||
***REMOVED*** ***REMOVED***
|
||||
***REMOVED***
|
||||
***REMOVED***
|
||||
***REMOVED***
|
||||
***REMOVED*** List<String> gitdependencies = extractMultipleValues(metadata, "github");
|
||||
***REMOVED*** if (gitdependencies != null) ***REMOVED***
|
||||
***REMOVED*** for (String pkg : gitdependencies) ***REMOVED***
|
||||
***REMOVED*** Dependency dep = new Dependency();
|
||||
***REMOVED***
|
||||
***REMOVED*** ***REMOVED***if (pkg.startsWith("os:"))***REMOVED***
|
||||
***REMOVED*** dep.setName(pkg);
|
||||
***REMOVED*** dep.setType("github");
|
||||
***REMOVED*** out.addDependency(dep);
|
||||
***REMOVED*** ***REMOVED***
|
||||
***REMOVED*** ***REMOVED***
|
||||
***REMOVED***
|
||||
***REMOVED***
|
||||
***REMOVED***
|
||||
***REMOVED*** List<String> cdependencies = extractMultipleValues(metadata, "custom");
|
||||
***REMOVED*** if (cdependencies != null) ***REMOVED***
|
||||
***REMOVED*** for (String pkg : cdependencies) ***REMOVED***
|
||||
***REMOVED*** Dependency dep = new Dependency();
|
||||
***REMOVED***
|
||||
***REMOVED*** ***REMOVED***if (pkg.startsWith("os:"))***REMOVED***
|
||||
***REMOVED*** dep.setName(pkg);
|
||||
***REMOVED*** dep.setType("custom");
|
||||
***REMOVED*** out.addDependency(dep);
|
||||
***REMOVED*** ***REMOVED***
|
||||
***REMOVED*** ***REMOVED***
|
||||
|
||||
|
||||
***REMOVED*** if (pkg.startsWith("r:"))***REMOVED***
|
||||
|
|
|
|||
|
|
@ -44,8 +44,8 @@ public interface PoolManager ***REMOVED***
|
|||
String addAlgorithmToHost(Algorithm algo, String host,boolean test) throws IOException, InterruptedException;
|
||||
|
||||
|
||||
String stageAlgorithm(String algorithmPackageURL, String category) throws IOException, InterruptedException;
|
||||
String publishAlgorithm(String algorithmPackageURL, String targetVREToken, String targetVRE, String category) throws IOException, InterruptedException;
|
||||
String stageAlgorithm(String algorithmPackageURL) throws IOException, InterruptedException;
|
||||
String publishAlgorithm(String algorithmPackageURL, String targetVREToken, String targetVRE) throws IOException, InterruptedException;
|
||||
|
||||
|
||||
Algorithm extractAlgorithm(String url) throws IOException;
|
||||
|
|
|
|||
|
|
@ -30,7 +30,7 @@ public class ProductionPublishingJob extends DMPMJob ***REMOVED***
|
|||
|
||||
this.svnUpdater.updateProdDeps(this.algorithm);
|
||||
|
||||
this.svnUpdater.updateSVNProdAlgorithmList(this.algorithm, this.targetVREName, "DataMiner Pool Manager", "Prod");
|
||||
this.svnUpdater.updateSVNProdAlgorithmList(this.algorithm, this.targetVREName, this.algorithm.getFullname(), "Prod");
|
||||
|
||||
***REMOVED***
|
||||
|
||||
|
|
|
|||
|
|
@ -36,25 +36,36 @@ public class StagingJob extends DMPMJob ***REMOVED***
|
|||
protected void execute() ***REMOVED***
|
||||
ServiceConfiguration a = new ServiceConfiguration();
|
||||
CheckMethod b = new CheckMethod();
|
||||
|
||||
try ***REMOVED***
|
||||
|
||||
int ret = this.executeAnsibleWorker(
|
||||
createWorker(this.algorithm, this.stagingCluster, true, "root"));
|
||||
|
||||
if(ret == 0)***REMOVED***
|
||||
|
||||
if (b.checkMethod(a.getStagingHost(), SecurityTokenProvider.instance.get()))***REMOVED***
|
||||
|
||||
this.svnUpdater.updateRPRotoDeps(this.algorithm);
|
||||
|
||||
this.svnUpdater.updateSVNRProtoAlgorithmList(this.algorithm, this.rProtoVREName, "DataMiner Pool Manager", "Proto");
|
||||
try ***REMOVED***
|
||||
|
||||
if (this.svnUpdater.checkIfAvaialable(this.algorithm.getLanguage(), this.algorithm.getDependencies())) ***REMOVED***
|
||||
int ret = this.executeAnsibleWorker(createWorker(this.algorithm, this.stagingCluster, false, "root"));
|
||||
|
||||
***REMOVED*** int ret2 = this.executeAnsibleWorker(
|
||||
***REMOVED*** createWorker(this.algorithm, this.rProtoCluster, false, "gcube"));
|
||||
|
||||
|
||||
|
||||
if (ret == 0) ***REMOVED***
|
||||
|
||||
if (b.checkMethod(a.getStagingHost(), SecurityTokenProvider.instance.get())
|
||||
&& (b.algoExists(this.algorithm))) ***REMOVED***
|
||||
|
||||
***REMOVED*** this.svnUpdater.updateRPRotoDeps(this.algorithm);
|
||||
|
||||
this.svnUpdater.updateSVNRProtoAlgorithmList(this.algorithm, this.rProtoVREName,
|
||||
this.algorithm.getFullname(), "Proto");
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
***REMOVED*** int ret2 = this.executeAnsibleWorker(
|
||||
***REMOVED*** createWorker(this.algorithm, this.rProtoCluster,
|
||||
***REMOVED*** false, "gcube"));
|
||||
***REMOVED***
|
||||
***REMOVED***
|
||||
***REMOVED***
|
||||
|
||||
|
||||
***REMOVED*** catch (Exception e) ***REMOVED***
|
||||
e.printStackTrace();
|
||||
***REMOVED***
|
||||
|
|
|
|||
|
|
@ -11,8 +11,8 @@ import org.gcube.dataanalysis.dataminer.poolmanager.process.AlgorithmPackagePars
|
|||
public class AlgorithmBuilder ***REMOVED***
|
||||
|
||||
|
||||
public static Algorithm create(String algorithmPackageURL, String category) throws IOException, InterruptedException ***REMOVED***
|
||||
return create(algorithmPackageURL, null, null, null, null, category, null, null);
|
||||
public static Algorithm create(String algorithmPackageURL) throws IOException, InterruptedException ***REMOVED***
|
||||
return create(algorithmPackageURL, null, null, null, null, null, null, null);
|
||||
***REMOVED***
|
||||
|
||||
public static Algorithm create(String algorithmPackageURL, String vre, String hostname, String name, String description,
|
||||
|
|
|
|||
|
|
@ -1,10 +1,13 @@
|
|||
package org.gcube.dataanalysis.dataminer.poolmanager.util;
|
||||
|
||||
import java.io.BufferedReader;
|
||||
import java.io.File;
|
||||
import java.io.FileWriter;
|
||||
import java.io.InputStreamReader;
|
||||
***REMOVED***
|
||||
|
||||
***REMOVED***
|
||||
|
||||
public class CheckMethod ***REMOVED***
|
||||
|
||||
public CheckMethod() ***REMOVED***
|
||||
|
|
@ -64,6 +67,20 @@ public class CheckMethod ***REMOVED***
|
|||
***REMOVED***
|
||||
return true;
|
||||
***REMOVED***
|
||||
|
||||
|
||||
|
||||
public boolean algoExists(Algorithm a)***REMOVED***
|
||||
File file = new File("/home/gcube/wps_algorithms/algorithms/"+a.getName()+".jar");
|
||||
File file2 = new File(" /home/gcube/wps_algorithms/algorithms/"+a.getName()+"interface_.jar");
|
||||
|
||||
if (file.exists()&&(file2.exists()))***REMOVED***
|
||||
return true;
|
||||
***REMOVED***
|
||||
else
|
||||
System.out.println("Algorithm"+a.getName()+".jar"+ " and "+a.getName()+"interface_.jar files are not present at the expected path");
|
||||
return false;
|
||||
***REMOVED***
|
||||
|
||||
|
||||
public static void main(String[] args) throws Exception ***REMOVED***
|
||||
|
|
|
|||
|
|
@ -0,0 +1,98 @@
|
|||
package org.gcube.dataanalysis.dataminer.poolmanager.util;
|
||||
|
||||
import java.text.SimpleDateFormat;
|
||||
import java.util.Calendar;
|
||||
|
||||
import org.apache.commons.lang.StringUtils;
|
||||
|
||||
import scala.actors.threadpool.Arrays;
|
||||
|
||||
public class NotificationHelper ***REMOVED***
|
||||
|
||||
private Calendar startTime;
|
||||
|
||||
private String taskId;
|
||||
|
||||
private String scope;
|
||||
|
||||
private Exception executionException;
|
||||
|
||||
public NotificationHelper() ***REMOVED***
|
||||
***REMOVED***
|
||||
|
||||
public void setStartTime(Calendar startTime) ***REMOVED***
|
||||
this.startTime = startTime;
|
||||
***REMOVED***
|
||||
|
||||
public void setTaskId(String taskId) ***REMOVED***
|
||||
this.taskId = taskId;
|
||||
***REMOVED***
|
||||
|
||||
public void setScope(String scope) ***REMOVED***
|
||||
this.scope = scope;
|
||||
***REMOVED***
|
||||
|
||||
private String getSubjectHeader() ***REMOVED***
|
||||
return "[[DataMinerGhostInstallationRequestReport]]";
|
||||
***REMOVED***
|
||||
|
||||
private String getSpecificVREName() ***REMOVED***
|
||||
if(this.scope!=null) ***REMOVED***
|
||||
String[] parts = this.scope.split("/");
|
||||
if(parts.length>=3) ***REMOVED***
|
||||
return StringUtils.join(Arrays.copyOfRange(parts, 3, parts.length), "/");
|
||||
***REMOVED***
|
||||
***REMOVED***
|
||||
return this.scope;
|
||||
***REMOVED***
|
||||
|
||||
private boolean isError() ***REMOVED***
|
||||
return this.executionException!=null;
|
||||
***REMOVED***
|
||||
|
||||
public void setExecutionException(Exception executionException) ***REMOVED***
|
||||
this.executionException = executionException;
|
||||
***REMOVED***
|
||||
|
||||
private String getSuccessSubject() ***REMOVED***
|
||||
return String.format("%s Results for your experiment '%s' are ready", this.getSubjectHeader(), this.taskId);
|
||||
***REMOVED***
|
||||
|
||||
private String getFailedSubject() ***REMOVED***
|
||||
return String.format("%s An error occurred while executing your experiment '%s'", this.getSubjectHeader(), this.taskId);
|
||||
***REMOVED***
|
||||
|
||||
private String getFormattedStartTime() ***REMOVED***
|
||||
SimpleDateFormat sdf = new SimpleDateFormat("EEE, d MMM yyyy HH:mm:ss Z");
|
||||
return sdf.format(this.startTime.getTime());
|
||||
***REMOVED***
|
||||
|
||||
private String getSuccessBody() ***REMOVED***
|
||||
String message = String.format("Your experiment '%s' submitted on %s in the '%s' VRE completed successfully.", this.taskId, this.getFormattedStartTime(), this.getSpecificVREName());
|
||||
message+="\n\nYou can retrieve experiment results under the '/DataMiner' e-Infrastructure Workspace folder or from the DataMiner interface.";
|
||||
return message;
|
||||
***REMOVED***
|
||||
|
||||
private String getFailedBody() ***REMOVED***
|
||||
String message = String.format("An error occurred while executing your experiment '%s' submitted on %s in the '%s' VRE.", this.taskId, this.getFormattedStartTime(), this.getSpecificVREName());
|
||||
message+= "\n\nHere are the error details:\n\n" + this.executionException;
|
||||
return message;
|
||||
***REMOVED***
|
||||
|
||||
public String getSubject() ***REMOVED***
|
||||
if(this.isError()) ***REMOVED***
|
||||
return this.getFailedSubject();
|
||||
***REMOVED*** else ***REMOVED***
|
||||
return this.getSuccessSubject();
|
||||
***REMOVED***
|
||||
***REMOVED***
|
||||
|
||||
public String getBody() ***REMOVED***
|
||||
if(this.isError()) ***REMOVED***
|
||||
return this.getFailedBody();
|
||||
***REMOVED*** else ***REMOVED***
|
||||
return this.getSuccessBody();
|
||||
***REMOVED***
|
||||
***REMOVED***
|
||||
|
||||
***REMOVED***
|
||||
|
|
@ -40,6 +40,71 @@ public class SVNUpdater ***REMOVED***
|
|||
this.updateSVN(this.configuration.getSVNRProtoCRANDepsList(), algorithm.getCranDependencies());
|
||||
this.updateSVN(this.configuration.getSVNRProtoGitHubDepsList(), algorithm.getGitHubDependencies());
|
||||
***REMOVED***
|
||||
|
||||
|
||||
|
||||
public void readRPRotoDeps(Algorithm algorithm) throws SVNException***REMOVED***
|
||||
if (algorithm.getLanguage().equals("R"))***REMOVED***
|
||||
this.checkIfAvaialable(this.configuration.getSVNRProtoCRANDepsList(), algorithm.getDependencies());
|
||||
***REMOVED***
|
||||
if (algorithm.getLanguage().equals("R-blackbox"))***REMOVED***
|
||||
this.checkIfAvaialable("", algorithm.getDependencies());
|
||||
***REMOVED***
|
||||
if (algorithm.getLanguage().equals("Java"))***REMOVED***
|
||||
this.checkIfAvaialable("", algorithm.getDependencies());
|
||||
***REMOVED***
|
||||
if (algorithm.getLanguage().equals("Knime-Workflow"))***REMOVED***
|
||||
this.checkIfAvaialable(this.configuration.getSVNRProtoCRANDepsList(), algorithm.getDependencies());
|
||||
***REMOVED***
|
||||
if (algorithm.getLanguage().equals("Linux-compiled"))***REMOVED***
|
||||
this.checkIfAvaialable("", algorithm.getDependencies());
|
||||
***REMOVED***
|
||||
if (algorithm.getLanguage().equals("Octave"))***REMOVED***
|
||||
this.checkIfAvaialable("", algorithm.getDependencies());
|
||||
***REMOVED***
|
||||
if (algorithm.getLanguage().equals("Python"))***REMOVED***
|
||||
this.checkIfAvaialable("", algorithm.getDependencies());
|
||||
***REMOVED***
|
||||
if (algorithm.getLanguage().equals("Windows-compiled"))***REMOVED***
|
||||
this.checkIfAvaialable("", algorithm.getDependencies());
|
||||
***REMOVED***
|
||||
if (algorithm.getLanguage().equals("Pre-Installed"))***REMOVED***
|
||||
this.checkIfAvaialable("", algorithm.getDependencies());
|
||||
***REMOVED***
|
||||
***REMOVED***
|
||||
|
||||
|
||||
public void readProdDeps(Algorithm algorithm) throws SVNException***REMOVED***
|
||||
if (algorithm.getLanguage().equals("R"))***REMOVED***
|
||||
this.checkIfAvaialable(this.configuration.getSVNRProdCRANDepsList(), algorithm.getDependencies());
|
||||
***REMOVED***
|
||||
if (algorithm.getLanguage().equals("R-blackbox"))***REMOVED***
|
||||
this.checkIfAvaialable("", algorithm.getDependencies());
|
||||
***REMOVED***
|
||||
if (algorithm.getLanguage().equals("Java"))***REMOVED***
|
||||
this.checkIfAvaialable("", algorithm.getDependencies());
|
||||
***REMOVED***
|
||||
if (algorithm.getLanguage().equals("Knime-Workflow"))***REMOVED***
|
||||
this.checkIfAvaialable("", algorithm.getDependencies());
|
||||
***REMOVED***
|
||||
if (algorithm.getLanguage().equals("Linux-compiled"))***REMOVED***
|
||||
this.checkIfAvaialable("", algorithm.getDependencies());
|
||||
***REMOVED***
|
||||
if (algorithm.getLanguage().equals("Octave"))***REMOVED***
|
||||
this.checkIfAvaialable("", algorithm.getDependencies());
|
||||
***REMOVED***
|
||||
if (algorithm.getLanguage().equals("Python"))***REMOVED***
|
||||
this.checkIfAvaialable("", algorithm.getDependencies());
|
||||
***REMOVED***
|
||||
if (algorithm.getLanguage().equals("Windows-compiled"))***REMOVED***
|
||||
this.checkIfAvaialable("", algorithm.getDependencies());
|
||||
***REMOVED***
|
||||
if (algorithm.getLanguage().equals("Pre-Installed"))***REMOVED***
|
||||
this.checkIfAvaialable("", algorithm.getDependencies());
|
||||
***REMOVED***
|
||||
***REMOVED***
|
||||
|
||||
|
||||
|
||||
public void updateProdDeps(Algorithm algorithm)***REMOVED***
|
||||
this.updateSVN(this.configuration.getSVNProdOSDepsList(), algorithm.getOSDependencies());
|
||||
|
|
@ -74,7 +139,7 @@ public class SVNUpdater ***REMOVED***
|
|||
|
||||
***REMOVED***the algorithm is not in the list. Add it
|
||||
List<String> newContent = new LinkedList<>(Arrays.asList(lines));
|
||||
newContent.add(this.generateAlgorithmEntry(algorithm, targetVRE, user, env));
|
||||
newContent.add(this.generateAlgorithmEntry(algorithm, targetVRE, env));
|
||||
***REMOVED***Collections.sort(newContent);
|
||||
|
||||
|
||||
|
|
@ -111,10 +176,10 @@ public class SVNUpdater ***REMOVED***
|
|||
***REMOVED*** ***REMOVED***
|
||||
|
||||
|
||||
public String generateAlgorithmEntry(Algorithm algorithm, String targetVRE, String user, String env)***REMOVED***
|
||||
public String generateAlgorithmEntry(Algorithm algorithm, String targetVRE, String env)***REMOVED***
|
||||
StringBuffer sb = new StringBuffer("| ");
|
||||
sb.append(algorithm.getName() +" | ");
|
||||
sb.append(user + " | ");
|
||||
sb.append(algorithm.getFullname() + " | ");
|
||||
sb.append(algorithm.getCategory() + " | ");
|
||||
sb.append(env + " | ");
|
||||
sb.append("<notextile>./addAlgorithm.sh "+ algorithm.getName()+" " + algorithm.getCategory() + " " + algorithm.getClazz() + " " + targetVRE + " " + algorithm.getAlgorithmType() + " N " + algorithm.getPackageURL() + " \"" + algorithm.getDescription() + "\" </notextile> | ");
|
||||
|
|
@ -123,6 +188,50 @@ public class SVNUpdater ***REMOVED***
|
|||
***REMOVED***
|
||||
|
||||
|
||||
|
||||
public boolean checkIfAvaialable(String file, Collection<Dependency> deps) throws SVNException ***REMOVED***
|
||||
boolean check = false;
|
||||
try***REMOVED***
|
||||
System.out.println("Checking dependencies list: " + file);
|
||||
final ByteArrayOutputStream byteArrayOutputStream = new ByteArrayOutputStream();
|
||||
svnRepository.getFile(file, SVNRepository.INVALID_REVISION, null, byteArrayOutputStream);
|
||||
String lines[] = byteArrayOutputStream.toString().split("\\r?\\n");
|
||||
|
||||
if(deps.isEmpty())***REMOVED***
|
||||
SendMail sm = new SendMail();
|
||||
NotificationHelper nh = new NotificationHelper();
|
||||
sm.sendNotification(nh.getSubject(), nh.getBody());
|
||||
***REMOVED***
|
||||
|
||||
|
||||
else if (!deps.isEmpty()) ***REMOVED***
|
||||
List<String> ldep = new LinkedList<>();
|
||||
for (Dependency d : deps) ***REMOVED***
|
||||
ldep.add(d.getName());
|
||||
***REMOVED***
|
||||
for (String a : lines) ***REMOVED***
|
||||
for (String b : ldep) ***REMOVED***
|
||||
if (b.equals(a)) ***REMOVED***
|
||||
System.out.println("The following dependency is correctly written: "+b);
|
||||
check = true;
|
||||
***REMOVED*** else
|
||||
check = false;
|
||||
***REMOVED***
|
||||
***REMOVED***
|
||||
***REMOVED***
|
||||
***REMOVED***catch (Exception a)***REMOVED***
|
||||
a.getMessage();
|
||||
***REMOVED***
|
||||
|
||||
return check;
|
||||
|
||||
***REMOVED***
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
public void updateSVN(String file, Collection<Dependency> deps) ***REMOVED***
|
||||
try ***REMOVED***
|
||||
System.out.println("Updating dependencies list: "+ file);
|
||||
|
|
|
|||
|
|
@ -0,0 +1,101 @@
|
|||
package org.gcube.dataanalysis.dataminer.poolmanager.util;
|
||||
|
||||
import java.net.URLEncoder;
|
||||
|
||||
import org.apache.activemq.transport.stomp.Stomp.Headers.Send;
|
||||
***REMOVED***
|
||||
***REMOVED***
|
||||
import org.gcube.contentmanagement.graphtools.utils.HttpRequest;
|
||||
import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger;
|
||||
import org.gcube.dataanalysis.ecoengine.interfaces.StandardLocalInfraAlgorithm;
|
||||
import org.gcube.dataanalysis.executor.util.InfraRetrieval;
|
||||
|
||||
public class SendMail extends StandardLocalInfraAlgorithm ***REMOVED***
|
||||
|
||||
public SendMail() ***REMOVED***
|
||||
***REMOVED*** TODO Auto-generated constructor stub
|
||||
***REMOVED***
|
||||
|
||||
public void sendNotification(String subject, String body) throws Exception ***REMOVED***
|
||||
|
||||
AnalysisLogger.getLogger().debug("Emailing System->Starting request of email in scope "+ScopeProvider.instance.get());
|
||||
|
||||
String serviceAddress = InfraRetrieval.findEmailingSystemAddress(ScopeProvider.instance.get());
|
||||
|
||||
if (!serviceAddress.endsWith("/"))
|
||||
serviceAddress = serviceAddress+"/";
|
||||
|
||||
String requestForMessage = serviceAddress + "messages/writeMessageToUsers" + "?gcube-token=" + SecurityTokenProvider.instance.get();
|
||||
requestForMessage = requestForMessage.replace("http:***REMOVED***", "https:***REMOVED***").replace(":80", ""); ***REMOVED*** remove the port (or set it to 443) otherwise you get an SSL error
|
||||
|
||||
AnalysisLogger.getLogger().debug("Emailing System->Request url is going to be " + requestForMessage);
|
||||
|
||||
***REMOVED*** put the sender, the recipients, subject and body of the mail here
|
||||
subject=URLEncoder.encode(subject,"UTF-8");
|
||||
body=URLEncoder.encode(body,"UTF-8");
|
||||
String requestParameters = "sender=dataminer&recipients="+SecurityTokenProvider.instance.get()+"&subject="+subject+"&body="+body;
|
||||
|
||||
String response = HttpRequest.sendPostRequest(requestForMessage, requestParameters);
|
||||
AnalysisLogger.getLogger().debug("Emailing System->Emailing response OK ");
|
||||
|
||||
if (response==null)***REMOVED***
|
||||
Exception e = new Exception("Error in email sending response");
|
||||
throw e;
|
||||
***REMOVED***
|
||||
***REMOVED***
|
||||
|
||||
***REMOVED*** public void notifySubmitter(String a, String b) throws Exception ***REMOVED***
|
||||
***REMOVED*** NotificationHelper nh = new NotificationHelper();
|
||||
***REMOVED*** super.sendNotification(nh.getSubject(),
|
||||
***REMOVED*** nh.getBody());
|
||||
***REMOVED*** ***REMOVED***
|
||||
|
||||
|
||||
|
||||
***REMOVED***
|
||||
public String getDescription() ***REMOVED***
|
||||
***REMOVED***
|
||||
***REMOVED***
|
||||
***REMOVED***
|
||||
|
||||
|
||||
|
||||
***REMOVED***
|
||||
public void init() throws Exception ***REMOVED***
|
||||
***REMOVED***
|
||||
|
||||
***REMOVED***
|
||||
|
||||
|
||||
|
||||
***REMOVED***
|
||||
protected void process() throws Exception ***REMOVED***
|
||||
***REMOVED***
|
||||
|
||||
***REMOVED***
|
||||
|
||||
|
||||
|
||||
***REMOVED***
|
||||
protected void setInputParameters() ***REMOVED***
|
||||
***REMOVED***
|
||||
|
||||
***REMOVED***
|
||||
|
||||
|
||||
|
||||
***REMOVED***
|
||||
public void shutdown() ***REMOVED***
|
||||
***REMOVED***
|
||||
|
||||
***REMOVED***
|
||||
|
||||
public static void main(String[] args) throws Exception ***REMOVED***
|
||||
ScopeProvider.instance.set("/d4science.research-infrastructures.eu/gCubeApps/RPrototypingLab");
|
||||
SecurityTokenProvider.instance.set("***REMOVED***");
|
||||
|
||||
NotificationHelper nh = new NotificationHelper();
|
||||
SendMail sm = new SendMail();
|
||||
sm.sendNotification(nh.getSubject(), nh.getBody());
|
||||
***REMOVED***
|
||||
***REMOVED***
|
||||
|
|
@ -21,7 +21,7 @@ public class JobTest ***REMOVED***
|
|||
ScopeProvider.instance.set("/d4science.research-infrastructures.eu/gCubeApps/RPrototypingLab");
|
||||
|
||||
SVNUpdater svnUpdater = new SVNUpdater(new ServiceConfiguration());
|
||||
Algorithm algo = AlgorithmBuilder.create("http:***REMOVED***data.d4science.org/dENQTTMxdjNZcGRpK0NHd2pvU0owMFFzN0VWemw3Zy9HbWJQNStIS0N6Yz0", "ICHTHYOP_MODEL");
|
||||
Algorithm algo = AlgorithmBuilder.create("http:***REMOVED***data.d4science.org/dENQTTMxdjNZcGRpK0NHd2pvU0owMFFzN0VWemw3Zy9HbWJQNStIS0N6Yz0");
|
||||
|
||||
***REMOVED***test phase
|
||||
Cluster stagingCluster = ClusterBuilder.getStagingDataminerCluster();
|
||||
|
|
|
|||
|
|
@ -17,11 +17,12 @@ public class SVNTests ***REMOVED***
|
|||
public static void main(String[] args) throws SVNException, IOException, InterruptedException ***REMOVED***
|
||||
|
||||
|
||||
SVNUpdater svnUpdater = new SVNUpdater(new ServiceConfiguration("/home/ggiammat/tmp/dmpm.properties"));
|
||||
Algorithm algo = AlgorithmBuilder.create("http:***REMOVED***data.d4science.org/dENQTTMxdjNZcGRpK0NHd2pvU0owMFFzN0VWemw3Zy9HbWJQNStIS0N6Yz0", "ICHTHYOP_MODEL");
|
||||
SVNUpdater svnUpdater = new SVNUpdater(new ServiceConfiguration("/home/ngalante/workspace/dataminer-pool-manager/src/main/resources/service.properties"));
|
||||
|
||||
Algorithm algo = AlgorithmBuilder.create("http:***REMOVED***data.d4science.org/cnFLNHYxR1ZDa1VNdEhrTUQyQlZjaWRBVVZlUHloUitHbWJQNStIS0N6Yz0");
|
||||
***REMOVED***algo.setClazz(algo.getClazz() + "TEST");
|
||||
|
||||
algo.setClazz(algo.getClazz() + "TEST");
|
||||
|
||||
svnUpdater.updateSVNRProtoAlgorithmList(algo, "/d4science.research-infrastructures.eu/gCubeApps/RPrototypingLab", "Dataminer Pool Manager", "Proto");
|
||||
***REMOVED***svnUpdater.updateSVNRProtoAlgorithmList(algo, "/d4science.research-infrastructures.eu/gCubeApps/RPrototypingLab", "Dataminer Pool Manager", "Proto");
|
||||
svnUpdater.readRPRotoDeps(algo);
|
||||
***REMOVED***
|
||||
***REMOVED***
|
||||
|
|
|
|||
Loading…
Reference in New Issue