git-svn-id: https://svn.d4science.research-infrastructures.eu/gcube/trunk/data-analysis/dataminer-pool-manager@144447 82a268e6-3cf1-43bd-a215-b396298e98cf
This commit is contained in:
Nunzio Andrea Galante
parent
724d5376b6
commit
112e385179
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***REMOVED***
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import java.io.InputStream;
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***REMOVED***
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***REMOVED***
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import java.util.Vector;
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***REMOVED***
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import org.gcube.dataanalysis.dataminer.poolmanager.datamodel.AlgorithmSet;
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import org.gcube.dataanalysis.dataminer.poolmanager.process.AddAlgorithmCommand;
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import org.gcube.dataanalysis.dataminer.poolmanager.process.AlgorithmPackageParser;
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public class AlgorithmPackageParserTest ***REMOVED***
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private static int BUFFER_SIZE = 2048;
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public void extractAllAlgorithms() throws IOException ***REMOVED***
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String url = "http:***REMOVED***svn.research-infrastructures.eu/public/d4science/gcube/trunk/data-analysis/DataMinerConfiguration/algorithms/dev/algorithms";
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List<String> commands = this.extractAddAlgorithmCommands(url);
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AlgorithmSet algorithms = new AlgorithmSet();
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for (String cmd : commands) ***REMOVED***
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System.out.println("-----------------------------------------");
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System.out.println(cmd);
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AddAlgorithmCommand aac = new AddAlgorithmCommand(cmd);
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System.out.println(aac);
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***REMOVED*** start creating the algo from the command
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Algorithm algo = new Algorithm();
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algo.setAlgorithmType(aac.getAlgorithmType());
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algo.setCategory(aac.getCategory());
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algo.setClazz(aac.getClazz());
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algo.setDescription(aac.getDescription());
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algo.setName(aac.getName());
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algo.setPackageURL(aac.getUrl());
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algo.setSkipJava(aac.getSkipjava());
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***REMOVED*** then override with info from the package
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if (aac.getUrl().length() > 4) ***REMOVED***
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Algorithm packagedAlgo = this.extractAlgorithm(aac.getUrl());
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if (packagedAlgo != null) ***REMOVED***
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algo.setDependencies(packagedAlgo.getDependencies());
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***REMOVED***
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***REMOVED***
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algorithms.addAlgorithm(algo);
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break;
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***REMOVED***
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***REMOVED***to uncomment
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***REMOVED*** new DataminerPoolManager().addAlgorithmsToVRE(algorithms,
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***REMOVED*** "/gcube/devNext/NextNext");
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***REMOVED***
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/**
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* Extract 'addAlgorithm' commands from a file containing wiki-table-style
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* entries for algorithm.
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*
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* @return
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* @throws IOException
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*/
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private List<String> extractAddAlgorithmCommands(String listUrl)
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throws IOException ***REMOVED***
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URL url = new URL(listUrl);
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InputStream is = url.openStream();
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StringBuilder s = new StringBuilder();
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byte[] buffer = new byte[BUFFER_SIZE];
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int read = 0;
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while ((read = is.read(buffer)) != -1) ***REMOVED***
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s.append(new String(buffer, 0, read));
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***REMOVED***
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List<String> out = new Vector<>();
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String[] lines = s.toString().split("\n");
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for (String line : lines) ***REMOVED***
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System.out.println("--------------------");
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if (!line.isEmpty()) ***REMOVED***
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String[] parts = line.split("\\|");
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int c = 1;
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for (String part : parts) ***REMOVED***
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if (part == null || part.trim().isEmpty()) ***REMOVED***
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continue;
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***REMOVED***
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System.out.println(c + ". " + part);
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c++;
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if (part.contains("addAlgorithm.sh")) ***REMOVED***
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String cmd = part.trim();
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cmd = cmd.replaceAll("<notextile>", "");
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cmd = cmd.replaceAll("</notextile>", "");
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System.out.println(cmd);
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***REMOVED*** AddAlgorithmCommand aac = new AddAlgorithmCommand(cmd);
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***REMOVED*** System.out.println(aac);
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out.add(cmd);
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***REMOVED***
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***REMOVED***
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***REMOVED***
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***REMOVED***
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return out;
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***REMOVED***
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/**
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* Create an Algorithm starting from the algorithm jar.
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*
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* @param url
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* @return
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* @throws IOException
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*/
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private Algorithm extractAlgorithm(String url) throws IOException ***REMOVED***
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return new AlgorithmPackageParser().parsePackage(url);
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***REMOVED***
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public static void main(String[] args) throws Exception ***REMOVED***
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***REMOVED*** ProxySelector.setDefault(new PropertiesBasedProxySelector(
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***REMOVED*** "/home/ngalante/.proxy-settings"));
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new AlgorithmPackageParserTest().extractAllAlgorithms();
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***REMOVED***
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***REMOVED***
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@ -0,0 +1,33 @@
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import java.io.File;
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***REMOVED***
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import java.util.UUID;
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import org.gcube.dataanalysis.dataminer.poolmanager.ansible.AnsibleWorker;
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import org.gcube.dataanalysis.dataminer.poolmanager.ansible.model.Inventory;
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import org.gcube.dataanalysis.dataminer.poolmanager.ansible.model.Playbook;
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import org.gcube.dataanalysis.dataminer.poolmanager.ansible.model.Role;
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import org.gcube.dataanalysis.dataminer.poolmanager.ansible.model.RoleFile;
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public class AnsibleWorkerTest ***REMOVED***
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public static void main(String[] args) throws IOException ***REMOVED***
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AnsibleWorker worker = new AnsibleWorker(new File("/home/nagalante/gcube/dataminer-pool-manager/work/"+UUID.randomUUID().toString()));
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System.out.println("created worker named " + worker.getWorkerId());
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worker.setInventory(new Inventory());
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worker.setPlaybook(new Playbook());
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Role r = new Role();
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r.setName("latex");
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RoleFile tf = new RoleFile("main", "do something special for " + r.getName());
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r.addTaskFile(tf);
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worker.addRole(r);
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worker.apply();
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***REMOVED***
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***REMOVED***
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import java.net.ProxySelector;
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import java.util.UUID;
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***REMOVED***
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***REMOVED***
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import org.gcube.dataanalysis.dataminer.poolmanager.datamodel.AlgorithmSet;
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import org.gcube.dataanalysis.dataminer.poolmanager.datamodel.Dependency;
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***REMOVED***
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import org.gcube.dataanalysis.dataminer.poolmanager.util.PropertiesBasedProxySelector;
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public class DataminerPoolManagerTest ***REMOVED***
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/*
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private static Map<String, Domain> domains = new HashMap<>();
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private static Map<String, Cluster> clusters = new HashMap<>();
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private static Dependency createDependency(String depName) ***REMOVED***
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String[] parts = depName.split(":");
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Dependency out = new Dependency();
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if(parts.length>1) ***REMOVED***
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out.setType(parts[0]);
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out.setName(parts[1]);
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***REMOVED*** else ***REMOVED***
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out.setType("os");
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out.setName(depName);
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***REMOVED***
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return out;
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***REMOVED***
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private static Algorithm createAlgorithm(String name, String ... deps) ***REMOVED***
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Algorithm a = new Algorithm();
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a.setName(name);
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for(String dep:deps) ***REMOVED***
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a.addDependency(createDependency(dep));
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***REMOVED***
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return a;
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***REMOVED***
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private static AlgorithmSet createAlgorithmSet(String name, Algorithm ... algs) ***REMOVED***
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AlgorithmSet out = new AlgorithmSet();
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out.setName(name);
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for(Algorithm a:algs) ***REMOVED***
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out.addAlgorithm(a);
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***REMOVED***
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return out;
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***REMOVED***
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private static Domain getDomain(String name) ***REMOVED***
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if(domains.get(name)==null) ***REMOVED***
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Domain d = new Domain();
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d.setName(name);
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domains.put(name, d);
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return d;
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***REMOVED*** else ***REMOVED***
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return domains.get(name);
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***REMOVED***
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***REMOVED***
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private static Host createHost(String hostname, String domainName) ***REMOVED***
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Host out = new Host();
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out.setName(hostname);
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Domain d = getDomain(domainName);
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out.setDomain(d);
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return out;
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***REMOVED***
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private static Cluster getCluster(String name) ***REMOVED***
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if(clusters.get(name)==null) ***REMOVED***
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Cluster d = new Cluster();
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d.setName(name);
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clusters.put(name, d);
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return d;
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***REMOVED*** else ***REMOVED***
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return clusters.get(name);
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***REMOVED***
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***REMOVED***
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private static Collection<Dependency> extractDependencies() ***REMOVED***
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Collection<Dependency> out = new TreeSet<>(new DependencyComparator());
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for(Cluster c:clusters.values()) ***REMOVED***
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for(AlgorithmSet as:c.getAlgorithmSets()) ***REMOVED***
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for(Algorithm a:as.getAlgorithms()) ***REMOVED***
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for(Dependency d:a.getDependencies()) ***REMOVED***
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out.add(d);
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***REMOVED***
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***REMOVED***
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***REMOVED***
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***REMOVED***
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return out;
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***REMOVED***
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private static Collection<Algorithm> extractAlgorithms() ***REMOVED***
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Collection<Algorithm> out = new TreeSet<>(new AlgorithmComparator());
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for(Cluster c:clusters.values()) ***REMOVED***
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for(AlgorithmSet as:c.getAlgorithmSets()) ***REMOVED***
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for(Algorithm a:as.getAlgorithms()) ***REMOVED***
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out.add(a);
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***REMOVED***
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***REMOVED***
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***REMOVED***
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return out;
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***REMOVED***
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static ***REMOVED***
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Algorithm ewe = createAlgorithm("ewe", "mono", "latex", "cran:some_R_package", "custom:some_git_package");
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Algorithm ensemble = createAlgorithm("ensemble", "python");
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Algorithm voodoo = createAlgorithm("voodoo", "os:latex", "custom:blah");
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AlgorithmSet as1 = createAlgorithmSet("as1-fishes", ewe);
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AlgorithmSet as2 = createAlgorithmSet("as2-stat", ensemble);
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AlgorithmSet as3 = createAlgorithmSet("as3-blackmagic", voodoo, ewe);
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Cluster cluster1 = getCluster("cluster-1");
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cluster1.addHost(createHost("host1", "domain1"));
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cluster1.addHost(createHost("host2", "domain1"));
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cluster1.addHost(createHost("host3", "domain1"));
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cluster1.addHost(createHost("host1", "domain2"));
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cluster1.addHost(createHost("host2", "domain2"));
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Cluster cluster2 = getCluster("cluster-2");
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cluster2.addHost(createHost("host4", "domain1"));
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cluster2.addHost(createHost("host5", "domain1"));
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cluster2.addHost(createHost("host6", "domain1"));
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cluster2.addHost(createHost("host3", "domain2"));
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cluster2.addHost(createHost("host4", "domain2"));
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cluster2.addHost(createHost("host5", "domain2"));
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cluster1.addAlgorithmSet(as1);
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cluster1.addAlgorithmSet(as2);
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cluster2.addAlgorithmSet(as1);
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cluster2.addAlgorithmSet(as3);
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***REMOVED***
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*/
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public static void main(String[] args) throws Exception ***REMOVED***
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/*
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AnsibleBridge ab = new AnsibleBridge();
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ab.printInventoryByDomainAndSets(clusters.values());
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System.out.println("-----------");
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ab.printInventoryBySets(clusters.values());
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AnsibleWorker worker = ab.createWorker();
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for(Algorithm a:extractAlgorithms()) ***REMOVED***
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for(Role r:ab.generateRoles(a)) ***REMOVED***
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worker.addRole(r);
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***REMOVED***
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***REMOVED***
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for(Dependency d:extractDependencies()) ***REMOVED***
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for(Role r:ab.generateRoles(d)) ***REMOVED***
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worker.addRole(r);
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***REMOVED***
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***REMOVED***
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*/
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ScopeProvider.instance.set("/gcube/devNext/NextNext");
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ProxySelector.setDefault(new PropertiesBasedProxySelector("/home/ngalante/.proxy-settings"));
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***REMOVED***
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***REMOVED*** ***REMOVED*** create the algorithm (download it, etc etc)
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***REMOVED*** Algorithm algorithm = new Algorithm();
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***REMOVED*** algorithm.setName("ichtyop");
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***REMOVED*** algorithm.setClazz("org.gcube...");
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***REMOVED*** algorithm.setDescription("some description");
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***REMOVED***
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***REMOVED*** Dependency d = new Dependency();
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***REMOVED*** d.setName("libpng");
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***REMOVED*** d.setType("os");
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***REMOVED*** algorithm.addDependency(d);
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***REMOVED***
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***REMOVED*** d = new Dependency();
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***REMOVED*** d.setName("some-r-package");
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***REMOVED*** d.setType("cran");
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***REMOVED*** algorithm.addDependency(d);
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***REMOVED***
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***REMOVED*** d = new Dependency();
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***REMOVED*** d.setName("some-other-r-package");
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***REMOVED*** d.setType("cran");
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***REMOVED*** algorithm.addDependency(d);
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***REMOVED***
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***REMOVED*** d = new Dependency();
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***REMOVED*** d.setName("voodoo");
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***REMOVED*** d.setType("custom");
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***REMOVED*** algorithm.addDependency(d);
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***REMOVED***
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***REMOVED*** ***REMOVED*** create the algorithm (download it, etc etc)
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***REMOVED*** Algorithm ewe = new Algorithm();
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***REMOVED*** ewe.setName("ewe");
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***REMOVED***
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***REMOVED*** d = new Dependency();
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***REMOVED*** d.setName("voodoo");
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***REMOVED*** d.setType("custom");
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***REMOVED*** ewe.addDependency(d);
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AlgorithmSet algorithms = new AlgorithmSet();
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algorithms.setName("dummy-set");
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***REMOVED*** algorithms.addAlgorithm(algorithm);
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***REMOVED*** algorithms.addAlgorithm(ewe);
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Algorithm ensemble = new Algorithm();
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ensemble.setName("ewe");
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ensemble.setCategory("a");
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ensemble.setAlgorithmType("transducerers");
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ensemble.setPackageURL("http:***REMOVED***data.d4science.org/eDd5b2ovMmpSVEZaZWYvY3g2bDZNcGRFNUIxNi85UFlHbWJQNStIS0N6Yz0");
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ensemble.setClazz("org.gcube.dataanalysis.executor.rscripts.Ichthyopmodelonebyone");
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ensemble.setSkipJava("N");
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ensemble.setDescription("test");
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Dependency d = new Dependency();
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d.setName("libpng3");
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d.setType("os");
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ensemble.addDependency(d);
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algorithms.addAlgorithm(ensemble);
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new DataminerPoolManager().addAlgorithmsToVRE(algorithms, "/gcube/devNext/NextNext", "test"+UUID.randomUUID());
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***REMOVED***
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***REMOVED***
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@ -0,0 +1,17 @@
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import java.net.ProxySelector;
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***REMOVED***
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import org.gcube.dataanalysis.dataminer.poolmanager.clients.ISClient;
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import org.gcube.dataanalysis.dataminer.poolmanager.util.PropertiesBasedProxySelector;
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public class ISClientTest ***REMOVED***
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public static void main(String[] args) ***REMOVED***
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ProxySelector.setDefault(new PropertiesBasedProxySelector("/home/ngalante/.proxy-settings"));
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ScopeProvider.instance.set("/gcube/devNext/NextNext");
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System.out.println(new ISClient().listDataminersInVRE());
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***REMOVED***
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***REMOVED***
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Loading…
Reference in New Issue