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release 0.1.0.beta.1.7 (#101)
* continuous integration serves #59 * JobProxy Local implemented close #63 * add maven enforcer plugin close #69 * remove consumes annotation close #57 * logger level added #70 * fix for local java docker close #87 * add batch * fix circle configuration * fix tests * remove jar packaging in DRMAA * try not to run mvn go-offline * remove jobproxy commit * fix(JobProxyLocal): states endpoint * continuous integration service #59 * JobProxy Local implemented close #63 * add maven enforcer plugin close #69 * remove consumes annotation close #57 * fix developer section for importing artifacts close #79 * test logging with logback * feat(development): add reference to bibiserv development guide (#99) * Fix/versioning (#100) * feat(development): add reference to bibiserv development guide * fix(versioning): release number fixed * docs(versioning): mvn version plugin usage
1 parent dddb503 commit e46802c

18 files changed

Lines changed: 291 additions & 86 deletions

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‎.gitignore‎

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@@ -5,3 +5,14 @@ target/
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target/
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/.target
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dependency-reduced-pom.xml
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pom.xml.tag
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pom.xml.releaseBackup
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pom.xml.versionsBackup
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pom.xml.next
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release.properties
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dependency-reduced-pom.xml
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buildNumber.properties
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.mvn/timing.properties
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# Exclude maven wrapper
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!/.mvn/wrapper/maven-wrapper.jar

‎JobProxyChronos/pom.xml‎

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@@ -5,7 +5,7 @@
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<parent>
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<artifactId>JobProxy</artifactId>
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<groupId>de.unibi.cebitec.bibiserv</groupId>
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<version>beta.1.2.release</version>
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<version>0.1.0.beta.1.7</version>
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</parent>
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<modelVersion>4.0.0</modelVersion>
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@@ -14,7 +14,7 @@
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<dependency>
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<groupId>de.unibi.cebitec.bibiserv</groupId>
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<artifactId>JobProxyModel</artifactId>
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<version>beta.1.2.release</version>
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<version>${project.version}</version>
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</dependency>
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<dependency>
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<groupId>com.fasterxml.jackson.dataformat</groupId>

‎JobProxyDRMAA/pom.xml‎

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@@ -4,10 +4,9 @@
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<parent>
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<groupId>de.unibi.cebitec.bibiserv</groupId>
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<artifactId>JobProxy</artifactId>
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<version>beta.1.2.release</version>
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<version>0.1.0.beta.1.7</version>
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</parent>
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<artifactId>JobProxyDRMAA</artifactId>
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<packaging>jar</packaging>
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<dependencies>
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<dependency>
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<groupId>${project.groupId}</groupId>
@@ -20,4 +19,4 @@
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<version>6.2u5</version>
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</dependency>
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</dependencies>
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</project>
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</project>

JobProxyJavaDocker/pom.xml renamed to JobProxyLocal/pom.xml

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@@ -5,25 +5,20 @@
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<parent>
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<artifactId>JobProxy</artifactId>
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<groupId>de.unibi.cebitec.bibiserv</groupId>
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<version>beta.1.2.release</version>
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<version>0.1.0.beta.1.7</version>
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</parent>
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<modelVersion>4.0.0</modelVersion>
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<artifactId>JobProxyJavaDocker</artifactId>
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<artifactId>JobProxyLocal</artifactId>
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<dependencies>
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<dependency>
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<groupId>de.unibi.cebitec.bibiserv</groupId>
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<artifactId>JobProxyModel</artifactId>
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<version>beta.1.2.release</version>
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<version>${project.version}</version>
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</dependency>
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<dependency>
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<groupId>com.spotify</groupId>
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<artifactId>docker-client</artifactId>
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<version>5.0.2</version>
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</dependency>
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<dependency>
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<groupId>com.google.guava</groupId>
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<artifactId>guava</artifactId>
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<version>19.0</version>
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</dependency>
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</dependencies>
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</project>

JobProxyJavaDocker/src/main/java/de/unibi/cebitec/bibiserv/jobproxy/javadocker/JavaDocker.java renamed to JobProxyLocal/src/main/java/de/unibi/cebitec/bibiserv/jobproxy/local/Local.java

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@@ -1,6 +1,7 @@
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package de.unibi.cebitec.bibiserv.jobproxy.javadocker;
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package de.unibi.cebitec.bibiserv.jobproxy.local;
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33
import com.spotify.docker.client.DefaultDockerClient;
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import com.spotify.docker.client.DockerClient;
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import com.spotify.docker.client.exceptions.DockerException;
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import com.spotify.docker.client.messages.*;
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import de.unibi.cebitec.bibiserv.jobproxy.model.JobProxyInterface;
@@ -12,24 +13,22 @@
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import de.unibi.cebitec.bibiserv.jobproxy.model.task.Task;
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import java.util.Arrays;
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import java.io.IOException;
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import java.util.List;
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import java.util.Properties;
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import java.util.stream.Collectors;
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public class JavaDocker extends JobProxyInterface {
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public class Local extends JobProxyInterface {
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private final DefaultDockerClient dockerClient;
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25-
public JavaDocker(Properties properties) {
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public Local(Properties properties) {
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super(properties);
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dockerClient = new DefaultDockerClient("unix:///var/run/docker.sock");
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}
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30-
@Override
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public String addTask(Task task) throws FrameworkException {
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private String handleDockerTask(Task task){
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HostConfig.Builder hostConfigBuilder = HostConfig.builder();
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task.getContainer().getMounts().forEach(mounts -> {
@@ -82,6 +81,27 @@ public String addTask(Task task) throws FrameworkException {
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return id;
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}
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private String handleLocalCommand(Task task) throws FrameworkException {
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try {
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Runtime.getRuntime().exec(task.getCmd());
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} catch (IOException e) {
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e.printStackTrace();
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throw new FrameworkException(e.getMessage());
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}
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return "";
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}
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@Override
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public String addTask(Task task) throws FrameworkException {
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if (task.getContainer() == null) {
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return handleLocalCommand(task);
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} else {
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return handleDockerTask(task);
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}
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}
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@Override
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public Task getTask(String id) throws FrameworkException {
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@@ -128,7 +148,6 @@ public Task getTask(String id) throws FrameworkException {
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tmounts.setMount(mount);
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container.getMounts().add(tmounts);
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});
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task.setContainer(container);
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return task;
@@ -150,9 +169,9 @@ public void delTask(String id) throws FrameworkException {
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@Override
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public State getState(String id) throws FrameworkException {
153-
ExecState inspect;
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ContainerInfo container;
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try {
155-
inspect = dockerClient.execInspect(id);
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container = dockerClient.inspectContainer(id);
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} catch (DockerException e) {
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e.printStackTrace();
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throw new FrameworkException(e.getMessage());
@@ -161,24 +180,27 @@ public State getState(String id) throws FrameworkException {
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throw new FrameworkException(e.getMessage());
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}
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State state = new State();
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state.setId(inspect.container().id());
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if (!inspect.running()) {
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state.setCode(String.valueOf(inspect.exitCode()));
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state.setId(container.id());
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state.setDescription(container.name());
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if (!container.state().running()) {
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state.setCode(String.valueOf(container.state().exitCode()));
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}
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state.setDescription(inspect.container().name());
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state.setDescription(container.name());
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return state;
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}
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@Override
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public States getState() throws FrameworkException {
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States states = new States();
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try {
176-
List<Container> containers = dockerClient.listContainers();
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List<Container> containers = dockerClient.listContainers(DockerClient.ListContainersParam.allContainers());
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for (Container container : containers) {
178199
states.getState().add(getState(container.id()));
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}
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} catch (FrameworkException e) {
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202+
e.printStackTrace();
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throw new FrameworkException(e.getMessage());
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} catch (DockerException e) {
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e.printStackTrace();
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throw new FrameworkException(e.getMessage());
@@ -191,12 +213,15 @@ public States getState() throws FrameworkException {
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@Override
193215
public String getName() {
194-
return "JavaDocker";
216+
return "JobProxyLocal";
195217
}
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@Override
198220
public String help() {
199-
throw new UnsupportedOperationException("Not supported yet."); //To change body of generated methods, choose Tools | Templates.
221+
return "Simple Jobproxy implementation for executing commands and docker container on the local system.\n" +
222+
"Note!: \n " +
223+
"Ressources for system native commands can not be restricted! This means that fields like mem,cpu and cputime are ignored\n" +
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"Executed native commands are not reported by using the 'state' or 'states' endpoint.";
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}
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}
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‎JobProxyModel/pom.xml‎

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<parent>
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<artifactId>JobProxy</artifactId>
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<groupId>de.unibi.cebitec.bibiserv</groupId>
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<version>beta.1.2.release</version>
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<version>0.1.0.beta.1.7</version>
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</parent>
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<modelVersion>4.0.0</modelVersion>
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@@ -32,6 +32,12 @@
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<groupId>org.glassfish.jersey.core</groupId>
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<artifactId>jersey-client</artifactId>
3434
<version>2.23.1</version>
35+
<exclusions>
36+
<exclusion>
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<groupId>org.javassist</groupId>
38+
<artifactId>javassist</artifactId>
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</exclusion>
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</exclusions>
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</dependency>
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<dependency>
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<groupId>org.glassfish.jersey.ext</groupId>

‎JobProxyModel/src/main/java/de/unibi/cebitec/bibiserv/jobproxy/model/JobProxyFactory.java‎

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import java.util.Map;
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import java.util.Properties;
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import java.util.Set;
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import org.reflections.Reflections;
11+
import org.slf4j.Logger;
12+
import org.slf4j.LoggerFactory;
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1114
/**
1215
* Provides a list of all FRAMEWORKS found within the classpath
@@ -18,6 +21,7 @@
1821
public class JobProxyFactory {
1922

2023
private static final Map<String, Class<? extends de.unibi.cebitec.bibiserv.jobproxy.model.JobProxyInterface>> FRAMEWORKS = new HashMap<>();
24+
private static final Logger LOGGER = LoggerFactory.getLogger(JobProxyFactory.class);
2125

2226
static {
2327
Reflections reflections = new Reflections("de.unibi.cebitec.bibiserv.jobproxy");
@@ -71,17 +75,17 @@ public static JobProxyInterface getFramework(String name, Properties properties)
7175
framework = FRAMEWORKS.get(name).getConstructor(Properties.class).newInstance(properties);
7276
return framework;
7377
}
74-
throw new FrameworkException("Unknown framework '"+name+"'!");
78+
throw new FrameworkException("Unknown framework '"+name+"'!");
7579
} catch (NoSuchMethodException | InstantiationException | IllegalAccessException e) {
7680
throw new FrameworkException("Error instantiating framework '"+name+"'!",e);
7781
} catch (InvocationTargetException e) {
7882
throw new FrameworkException("InvocationTargetException while instantiating framework '"+name+"'!");
7983
}
8084
}
8185

82-
/**
86+
/**
8387
* Return a set of found FRAMEWORKS.
84-
* @return
88+
* @return
8589
*/
8690
public static Set<String> list() {
8791
return FRAMEWORKS.keySet();

‎JobProxyModel/src/main/java/de/unibi/cebitec/bibiserv/jobproxy/model/rest/Delete.java‎

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4747
@DELETE
4848
@Path("/{id}")
49-
@Consumes({MediaType.TEXT_PLAIN})
5049
public void delete(@PathParam("id")String id){
5150
try {
5251
JobProxyFactory.getFramework().delTask(id);

‎JobProxyServer/pom.xml‎

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<parent>
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<groupId>de.unibi.cebitec.bibiserv</groupId>
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<artifactId>JobProxy</artifactId>
8-
<version>beta.1.2.release</version>
8+
<version>0.1.0.beta.1.7</version>
99
</parent>
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<modelVersion>4.0.0</modelVersion>
1111

@@ -14,29 +14,39 @@
1414
<dependency>
1515
<groupId>de.unibi.cebitec.bibiserv</groupId>
1616
<artifactId>JobProxyModel</artifactId>
17-
<version>beta.1.2.release</version>
17+
<version>${project.version}</version>
18+
<exclusions>
19+
<exclusion>
20+
<artifactId>jackson-core</artifactId>
21+
<groupId>com.fasterxml.jackson.core</groupId>
22+
</exclusion>
23+
<exclusion>
24+
<artifactId>guava</artifactId>
25+
<groupId>com.fasterxml.jackson.core</groupId>
26+
</exclusion>
27+
</exclusions>
1828
</dependency>
1929
<dependency>
2030
<groupId>de.unibi.cebitec.bibiserv</groupId>
2131
<artifactId>JobProxyModel</artifactId>
22-
<version>beta.1.2.release</version>
32+
<version>${project.version}</version>
2333
<type>test-jar</type>
2434
<scope>test</scope>
2535
</dependency>
2636
<dependency>
2737
<groupId>de.unibi.cebitec.bibiserv</groupId>
2838
<artifactId>JobProxyDRMAA</artifactId>
29-
<version>beta.1.2.release</version>
39+
<version>${project.version}</version>
3040
</dependency>
3141
<dependency>
3242
<groupId>de.unibi.cebitec.bibiserv</groupId>
3343
<artifactId>JobProxyChronos</artifactId>
34-
<version>beta.1.2.release</version>
44+
<version>${project.version}</version>
3545
</dependency>
3646
<dependency>
3747
<groupId>de.unibi.cebitec.bibiserv</groupId>
38-
<artifactId>JobProxyJavaDocker</artifactId>
39-
<version>beta.1.2.release</version>
48+
<artifactId>JobProxyLocal</artifactId>
49+
<version>${project.version}</version>
4050
</dependency>
4151
<dependency>
4252
<groupId>junit</groupId>

‎JobProxyServer/src/main/java/de/unibi/cebitec/bibiserv/jobproxy/server/JobProxyServer.java‎

Lines changed: 3 additions & 1 deletion
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@@ -1,4 +1,4 @@
1-
package de.unibi.cebitec.bibiserv.jobproxy.model;
1+
package de.unibi.cebitec.bibiserv.jobproxy.server;
22

33
/*
44
* Copyright 2016 Jan Krueger.
@@ -16,6 +16,8 @@
1616
* limitations under the License.
1717
*/
1818
import com.sun.net.httpserver.HttpServer;
19+
import de.unibi.cebitec.bibiserv.jobproxy.model.JobProxyFactory;
20+
import de.unibi.cebitec.bibiserv.jobproxy.model.JobProxyInterface;
1921
import de.unibi.cebitec.bibiserv.jobproxy.model.exceptions.FrameworkException;
2022
import de.unibi.cebitec.bibiserv.jobproxy.model.rest.Delete;
2123
import de.unibi.cebitec.bibiserv.jobproxy.model.rest.Ping;

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