Example usage for org.apache.commons.configuration BaseConfiguration getStringArray

Introduction

In this page you can find the example usage for org.apache.commons.configuration BaseConfiguration getStringArray.

Prototype

public String[] getStringArray(String key) 

Source Link

Document

Get an array of strings associated with the given configuration key.

Usage

From source file:uk.ac.sanger.cgp.wwdocker.daemon.PrimaryDaemon.java

private void hostSet(BaseConfiguration config, Map<String, String> hosts) {
    // first remove the killed off hosts
    List toRemove = new ArrayList();
    for (Map.Entry<String, String> e : hosts.entrySet()) {
        if (e.getValue().equals("DELETE")) {
            toRemove.add(e.getKey());/*  w w  w  .j a  v a2 s .  c  o m*/
        }
    }
    hosts.keySet().removeAll(toRemove);

    // add the new hosts
    BaseConfiguration workerConf = Config.loadWorkers(config.getString("workerCfg"));
    String[] rawHosts = workerConf.getStringArray("hosts");
    if (rawHosts.length == 1 && rawHosts[0].equals(new String())) {
        rawHosts = new String[0];
    }
    Set<String> tmp = new LinkedHashSet<>();
    for (String h : rawHosts) {
        if (!hosts.containsKey(h)) {
            hosts.put(h, "TO_PROVISION");
        }
        tmp.add(h);
    }

    // identify which hosts need to be killed
    for (Map.Entry<String, String> e : hosts.entrySet()) {
        if (!tmp.contains(e.getKey())) {
            hosts.replace(e.getKey(), "KILL");
        }
    }
}

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From source file:uk.ac.sanger.cgp.wwdocker.interfaces.Workflow.java

default String seqwareWhiteStarImage(BaseConfiguration config) {
    String[] pullImages = config.getStringArray("pullDockerImages");
    String whitestar = null;//from  w w  w  .  j a  va  2  s .c  o  m
    for (String i : pullImages) {
        if (i.contains("seqware_whitestar_pancancer")) {
            whitestar = i;
            break;
        }
    }
    return whitestar;
}

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From source file:uk.ac.sanger.cgp.wwdocker.workflow.DEWorkflow.java

@Override
public boolean provisionHost(String host, BaseConfiguration config, File thisJar, File tmpConf, String mode,
        Map<String, String> envs) throws InterruptedException {
    boolean provisioned = false;
    String remoteWorkflowDir = config.getString("workflowDir");
    String localSeqwareJar = config.getString("seqware");
    String localWorkflowZip = config.getString("workflow");
    File jreDist = Utils.expandUserFile(config, "jreDist", true);
    File remoteSeqwareJar = new File(
            remoteWorkflowDir.concat("/").concat(localSeqwareJar.replaceAll(".*/", "")));
    File remoteWorkflowZip = new File(
            remoteWorkflowDir.concat("/").concat(localWorkflowZip.replaceAll(".*/", "")));
    String[] pullDockerImages = config.getStringArray("pullDockerImages");
    String[] curlDockerImages = config.getStringArray("curlDockerImages");
    String[] pushDockerImages = config.getStringArray("pushDockerImages");
    String optDir = "/opt/wwdocker";
    String workerLog = config.getString("log4-worker");
    File localTmp = Utils.expandUserDirPath(config, "primaryLargeTmp", true);

    List<String> createPaths = new ArrayList();
    createPaths.add("/opt/wwdocker");
    createPaths.add("/opt/wwdocker/jre");
    createPaths.add(remoteWorkflowDir);//from  ww  w.ja v  a 2s.co  m
    createPaths.add(config.getString("datastoreDir"));

    Session ssh = Remote.getSession(config, host);

    Remote.createPaths(ssh, createPaths);
    Remote.chmodPaths(ssh, "a+wrx", createPaths, true);
    Remote.cleanFiles(ssh, new String[] { config.getString("log4-delete") });

    Remote.cleanupOldImages(ssh); // incase lots of stale ones are already present

    if (Local.pushFileSetToHost(pushDockerImages, host, "/opt/wwdocker", envs, ssh, null) != 0) {
        return provisioned;
    }
    String[] pushedDockerImages = new String[pushDockerImages.length];
    for (int i = 0; i < pushDockerImages.length; i++) {
        pushedDockerImages[i] = Paths.get("/opt/wwdocker", new File(pushDockerImages[i]).getName()).toFile()
                .getPath();
    }

    if (Remote.dockerPull(ssh, pullDockerImages) != 0
            || Remote.dockerLoad(ssh, curlDockerImages, remoteWorkflowDir) != 0
            || Remote.dockerLoad(ssh, pushedDockerImages, remoteWorkflowDir) != 0) {
        return provisioned;
    }
    Remote.cleanupOldImages(ssh); // incase lots of stale ones are already present

    if (Remote.curl(ssh, localSeqwareJar, remoteWorkflowDir) == null) {
        return provisioned;
    }

    Local.pushToHost(jreDist.getAbsolutePath(), host, optDir, envs, ssh, localTmp);
    if (Remote.expandJre(ssh, jreDist) != 0) {
        return provisioned;
    }
    Remote.curl(ssh, localWorkflowZip, remoteWorkflowDir);
    if (Remote.expandWorkflow(ssh, remoteWorkflowZip, remoteSeqwareJar, remoteWorkflowDir) != 0) {
        return provisioned;
    }
    //String workflowBase = remoteWorkflowZip.getName().replaceAll("\\.zip$", "");
    //Path gnosDest = Paths.get(remoteWorkflowDir, workflowBase);
    if (Local.pushToHost(thisJar.getAbsolutePath(), host, optDir, envs, ssh, localTmp) != 0 // this jar file
            || Local.pushToHost(workerLog, host, optDir, envs, ssh, localTmp) != 0 // worker log config
            || Local.pushToHost(tmpConf.getAbsolutePath(), host, optDir, envs, ssh, localTmp) != 0 // config file
            || Remote.chmodPath(ssh, "go-wrx", optDir.concat("/*"), true) != 0 // file will have passwords
            || Local.pushFileSetToHost(Utils.getGnosKeys(config), host, config.getString("datastoreDir"), envs,
                    ssh, localTmp) != 0 // GNOS keys, note DATASTORE
            || Remote.chmodPath(ssh, "a+r", config.getString("datastoreDir").concat("/*.pem"), false) != 0 // need to ensure these are readable within the image
            || Remote.startWorkerDaemon(ssh, thisJar.getName(), tmpConf.getName(), mode) != 0) {
        return provisioned;
    }
    provisioned = true;
    return provisioned;
}

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From source file:uk.ac.sanger.cgp.wwdocker.workflow.SangerWorkflow.java

@Override
public boolean provisionHost(String host, BaseConfiguration config, File thisJar, File tmpConf, String mode,
        Map<String, String> envs) throws InterruptedException {
    boolean provisioned = false;
    String remoteWorkflowDir = config.getString("workflowDir");
    String localSeqwareJar = config.getString("seqware");
    String localWorkflowZip = config.getString("workflow");
    File jreDist = Utils.expandUserFile(config, "jreDist", true);
    File remoteSeqwareJar = new File(
            remoteWorkflowDir.concat("/").concat(localSeqwareJar.replaceAll(".*/", "")));
    File remoteWorkflowZip = new File(
            remoteWorkflowDir.concat("/").concat(localWorkflowZip.replaceAll(".*/", "")));
    String[] pullDockerImages = config.getStringArray("pullDockerImages");
    String optDir = "/opt/wwdocker";
    String workerLog = config.getString("log4-worker");
    File localTmp = Utils.expandUserDirPath(config, "primaryLargeTmp", true);

    List<String> createPaths = new ArrayList();
    createPaths.add("/opt/wwdocker");
    createPaths.add("/opt/wwdocker/jre");
    createPaths.add(remoteWorkflowDir);/*from w w  w  .j ava  2  s.c o m*/
    createPaths.add(config.getString("datastoreDir"));

    Session ssh = Remote.getSession(config, host);

    Remote.createPaths(ssh, createPaths);
    Remote.chmodPaths(ssh, "a+wrx", createPaths, true);
    Remote.cleanFiles(ssh, new String[] { config.getString("log4-delete") });

    if (Remote.dockerPull(ssh, pullDockerImages) != 0) {
        return provisioned;
    }

    if (Remote.curl(ssh, localSeqwareJar, remoteWorkflowDir) == null) {
        return provisioned;
    }

    Local.pushToHost(jreDist.getAbsolutePath(), host, optDir, envs, ssh, localTmp);
    if (Remote.expandJre(ssh, jreDist) != 0) {
        return provisioned;
    }

    if (Remote.curl(ssh, localWorkflowZip, remoteWorkflowDir) == null
            || Remote.expandWorkflow(ssh, remoteWorkflowZip, remoteSeqwareJar, remoteWorkflowDir) != 0) {
        return provisioned;
    }
    String workflowBase = remoteWorkflowZip.getName().replaceAll("\\.zip$", "");
    Path gnosDest = Paths.get(remoteWorkflowDir, workflowBase);
    if (Local.pushToHost(thisJar.getAbsolutePath(), host, optDir, envs, ssh, localTmp) != 0 // this jar file
            || Local.pushToHost(workerLog, host, optDir, envs, ssh, localTmp) != 0 // worker log config
            || Local.pushToHost(tmpConf.getAbsolutePath(), host, optDir, envs, ssh, localTmp) != 0 // config file
            || Remote.chmodPath(ssh, "go-wrx", optDir.concat("/*"), true) != 0 // file will have passwords
            || Local.pushFileSetToHost(Utils.getGnosKeys(config), host, gnosDest.toString(), envs, ssh,
                    localTmp) != 0 // GNOS keys
            || Remote.startWorkerDaemon(ssh, thisJar.getName(), tmpConf.getName(), mode) != 0) {
        return provisioned;
    }
    provisioned = true;
    return provisioned;
}

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From source file:uk.ac.sanger.cgp.wwdocker.workflow.TestWorkflow.java

@Override
public boolean provisionHost(String host, BaseConfiguration config, File thisJar, File tmpConf, String mode,
        Map<String, String> envs) throws InterruptedException {
    boolean provisioned = false;
    String remoteWorkflowDir = config.getString("workflowDir");
    String localSeqwareJar = config.getString("seqware");
    File jreDist = Utils.expandUserFile(config, "jreDist", true);
    String[] pullDockerImages = config.getStringArray("pullDockerImages");
    String optDir = "/opt/wwdocker";
    String workerLog = config.getString("log4-worker");
    File localTmp = Utils.expandUserDirPath(config, "primaryLargeTmp", true);

    List<String> createPaths = new ArrayList();
    createPaths.add("/opt/wwdocker");
    createPaths.add("/opt/wwdocker/jre");
    createPaths.add(remoteWorkflowDir);/*  w  ww  . j a v a  2  s  .c  om*/
    createPaths.add(config.getString("datastoreDir"));

    Session ssh = Remote.getSession(config, host);

    Remote.createPaths(ssh, createPaths);
    Remote.chmodPaths(ssh, "a+wrx", createPaths, true);
    Remote.cleanFiles(ssh, new String[] { config.getString("log4-delete") });

    if (Remote.dockerPull(ssh, pullDockerImages) != 0) {
        return provisioned;
    }

    if (Remote.curl(ssh, localSeqwareJar, remoteWorkflowDir) == null) {
        return provisioned;
    }

    Local.pushToHost(jreDist.getAbsolutePath(), host, optDir, envs, ssh, localTmp);
    if (Remote.expandJre(ssh, jreDist) != 0) {
        return provisioned;
    }

    Local.pushToHost("testData/run.pl", host, config.getString("datastoreDir"), envs, ssh, localTmp);

    if (Local.pushToHost(thisJar.getAbsolutePath(), host, optDir, envs, ssh, localTmp) != 0 // this jar file
            || Local.pushToHost(workerLog, host, optDir, envs, ssh, localTmp) != 0 // worker log config
            || Local.pushToHost(tmpConf.getAbsolutePath(), host, optDir, envs, ssh, localTmp) != 0 // config file
            || Remote.chmodPath(ssh, "go-wrx", optDir.concat("/*"), true) != 0 // file will have passwords
            || Remote.startWorkerDaemon(ssh, thisJar.getName(), tmpConf.getName(), mode) != 0) {
        return provisioned;
    }
    provisioned = true;
    return provisioned;
}

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