git-svn-id: https://svn.d4science.research-infrastructures.eu/gcube/trunk/data-analysis/dataminer-pool-manager@142567 82a268e6-3cf1-43bd-a215-b396298e98cf
This commit is contained in:
Paolo Fabriani
parent
a7a6dc91db
commit
d9a0e093dd
|
|
@ -0,0 +1,119 @@
|
||||||
|
package org.gcube.dataanalysis.dataminerpoolmanager;
|
||||||
|
|
||||||
|
***REMOVED***
|
||||||
|
import java.io.InputStream;
|
||||||
|
import java.net.ProxySelector;
|
||||||
|
***REMOVED***
|
||||||
|
***REMOVED***
|
||||||
|
import java.util.Vector;
|
||||||
|
|
||||||
|
import org.gcube.dataanalysys.dataminerpoolmanager.datamodel.Algorithm;
|
||||||
|
import org.gcube.dataanalysys.dataminerpoolmanager.datamodel.AlgorithmSet;
|
||||||
|
import org.gcube.dataanalysys.dataminerpoolmanager.process.AddAlgorithmCommand;
|
||||||
|
import org.gcube.dataanalysys.dataminerpoolmanager.process.AlgorithmPackageParser;
|
||||||
|
import org.gcube.dataanalysys.dataminerpoolmanager.service.DataminerPoolManager;
|
||||||
|
import org.gcube.dataanalysys.dataminerpoolmanager.util.PropertiesBasedProxySelector;
|
||||||
|
|
||||||
|
public class AlgorithmPackageParserTest ***REMOVED***
|
||||||
|
|
||||||
|
private static int BUFFER_SIZE = 2048;
|
||||||
|
|
||||||
|
private void extractAllAlgorithms() throws IOException ***REMOVED***
|
||||||
|
String url = "http:***REMOVED***svn.research-infrastructures.eu/public/d4science/gcube/trunk/data-analysis/DataMinerConfiguration/algorithms/dev/algorithms";
|
||||||
|
List<String> commands = this.extractAddAlgorithmCommands(url);
|
||||||
|
AlgorithmSet algorithms = new AlgorithmSet();
|
||||||
|
for (String cmd : commands) ***REMOVED***
|
||||||
|
System.out.println("-----------------------------------------");
|
||||||
|
System.out.println(cmd);
|
||||||
|
AddAlgorithmCommand aac = new AddAlgorithmCommand(cmd);
|
||||||
|
System.out.println(aac);
|
||||||
|
|
||||||
|
***REMOVED*** start creating the algo from the command
|
||||||
|
Algorithm algo = new Algorithm();
|
||||||
|
algo.setAlgorithmType(aac.getAlgorithmType());
|
||||||
|
algo.setCategory(aac.getCategory());
|
||||||
|
algo.setClazz(aac.getClazz());
|
||||||
|
algo.setDescription(aac.getDescription());
|
||||||
|
algo.setName(aac.getName());
|
||||||
|
algo.setPackageURL(aac.getUrl());
|
||||||
|
algo.setSkipJava(aac.getSkipjava());
|
||||||
|
|
||||||
|
***REMOVED*** then override with info from the package
|
||||||
|
if (aac.getUrl().length() > 4) ***REMOVED***
|
||||||
|
Algorithm packagedAlgo = this.extractAlgorithm(aac.getUrl());
|
||||||
|
if (packagedAlgo != null) ***REMOVED***
|
||||||
|
algo.setDependencies(packagedAlgo.getDependencies());
|
||||||
|
***REMOVED***
|
||||||
|
***REMOVED***
|
||||||
|
algorithms.addAlgorithm(algo);
|
||||||
|
break;
|
||||||
|
***REMOVED***
|
||||||
|
new DataminerPoolManager().addAlgorithmsToVRE(algorithms,
|
||||||
|
"/gcube/devNext/NextNext");
|
||||||
|
***REMOVED***
|
||||||
|
|
||||||
|
/**
|
||||||
|
* Extract 'addAlgorithm' commands from a file containing wiki-table-style
|
||||||
|
* entries for algorithm.
|
||||||
|
*
|
||||||
|
* @return
|
||||||
|
* @throws IOException
|
||||||
|
*/
|
||||||
|
private List<String> extractAddAlgorithmCommands(String listUrl)
|
||||||
|
throws IOException ***REMOVED***
|
||||||
|
URL url = new URL(listUrl);
|
||||||
|
InputStream is = url.openStream();
|
||||||
|
|
||||||
|
StringBuilder s = new StringBuilder();
|
||||||
|
byte[] buffer = new byte[BUFFER_SIZE];
|
||||||
|
int read = 0;
|
||||||
|
while ((read = is.read(buffer)) != -1) ***REMOVED***
|
||||||
|
s.append(new String(buffer, 0, read));
|
||||||
|
***REMOVED***
|
||||||
|
List<String> out = new Vector<>();
|
||||||
|
String[] lines = s.toString().split("\n");
|
||||||
|
for (String line : lines) ***REMOVED***
|
||||||
|
System.out.println("--------------------");
|
||||||
|
if (!line.isEmpty()) ***REMOVED***
|
||||||
|
String[] parts = line.split("\\|");
|
||||||
|
int c = 1;
|
||||||
|
for (String part : parts) ***REMOVED***
|
||||||
|
if (part == null || part.trim().isEmpty()) ***REMOVED***
|
||||||
|
continue;
|
||||||
|
***REMOVED***
|
||||||
|
System.out.println(c + ". " + part);
|
||||||
|
c++;
|
||||||
|
if (part.contains("addAlgorithm.sh")) ***REMOVED***
|
||||||
|
String cmd = part.trim();
|
||||||
|
cmd = cmd.replaceAll("<notextile>", "");
|
||||||
|
cmd = cmd.replaceAll("</notextile>", "");
|
||||||
|
System.out.println(cmd);
|
||||||
|
***REMOVED*** AddAlgorithmCommand aac = new AddAlgorithmCommand(cmd);
|
||||||
|
***REMOVED*** System.out.println(aac);
|
||||||
|
out.add(cmd);
|
||||||
|
***REMOVED***
|
||||||
|
***REMOVED***
|
||||||
|
***REMOVED***
|
||||||
|
***REMOVED***
|
||||||
|
return out;
|
||||||
|
***REMOVED***
|
||||||
|
|
||||||
|
/**
|
||||||
|
* Create an Algorithm starting from the algorithm jar.
|
||||||
|
*
|
||||||
|
* @param url
|
||||||
|
* @return
|
||||||
|
* @throws IOException
|
||||||
|
*/
|
||||||
|
private Algorithm extractAlgorithm(String url) throws IOException ***REMOVED***
|
||||||
|
return new AlgorithmPackageParser().parsePackage(url);
|
||||||
|
***REMOVED***
|
||||||
|
|
||||||
|
public static void main(String[] args) throws Exception ***REMOVED***
|
||||||
|
ProxySelector.setDefault(new PropertiesBasedProxySelector(
|
||||||
|
"/home/paolo/.proxy-settings"));
|
||||||
|
|
||||||
|
new AlgorithmPackageParserTest().extractAllAlgorithms();
|
||||||
|
***REMOVED***
|
||||||
|
|
||||||
|
***REMOVED***
|
||||||
|
|
@ -0,0 +1,33 @@
|
||||||
|
package org.gcube.dataanalysis.dataminerpoolmanager;
|
||||||
|
|
||||||
|
import java.io.File;
|
||||||
|
***REMOVED***
|
||||||
|
import java.util.UUID;
|
||||||
|
|
||||||
|
import org.gcube.dataanalysys.dataminerpoolmanager.ansible.AnsibleWorker;
|
||||||
|
import org.gcube.dataanalysys.dataminerpoolmanager.ansible.model.Inventory;
|
||||||
|
import org.gcube.dataanalysys.dataminerpoolmanager.ansible.model.Playbook;
|
||||||
|
import org.gcube.dataanalysys.dataminerpoolmanager.ansible.model.Role;
|
||||||
|
import org.gcube.dataanalysys.dataminerpoolmanager.ansible.model.RoleFile;
|
||||||
|
|
||||||
|
public class AnsibleWorkerTest ***REMOVED***
|
||||||
|
|
||||||
|
public static void main(String[] args) throws IOException ***REMOVED***
|
||||||
|
AnsibleWorker worker = new AnsibleWorker(new File("/tmp/dataminer-pool-manager/work/"+UUID.randomUUID().toString()));
|
||||||
|
|
||||||
|
System.out.println("created worker named " + worker.getWorkerId());
|
||||||
|
|
||||||
|
worker.setInventory(new Inventory());
|
||||||
|
worker.setPlaybook(new Playbook());
|
||||||
|
|
||||||
|
Role r = new Role();
|
||||||
|
r.setName("latex");
|
||||||
|
|
||||||
|
RoleFile tf = new RoleFile("main", "do something special for " + r.getName());
|
||||||
|
r.addTaskFile(tf);
|
||||||
|
worker.addRole(r);
|
||||||
|
|
||||||
|
worker.apply();
|
||||||
|
***REMOVED***
|
||||||
|
|
||||||
|
***REMOVED***
|
||||||
|
|
@ -0,0 +1,232 @@
|
||||||
|
package org.gcube.dataanalysis.dataminerpoolmanager;
|
||||||
|
|
||||||
|
import java.net.ProxySelector;
|
||||||
|
import java.util.Collection;
|
||||||
|
import java.util.HashMap;
|
||||||
|
import java.util.Map;
|
||||||
|
import java.util.TreeSet;
|
||||||
|
import java.util.Vector;
|
||||||
|
|
||||||
|
***REMOVED***
|
||||||
|
import org.gcube.dataanalysys.dataminerpoolmanager.ansible.AnsibleWorker;
|
||||||
|
import org.gcube.dataanalysys.dataminerpoolmanager.ansible.model.Role;
|
||||||
|
import org.gcube.dataanalysys.dataminerpoolmanager.ansiblebridge.AnsibleBridge;
|
||||||
|
import org.gcube.dataanalysys.dataminerpoolmanager.datamodel.Algorithm;
|
||||||
|
import org.gcube.dataanalysys.dataminerpoolmanager.datamodel.AlgorithmSet;
|
||||||
|
import org.gcube.dataanalysys.dataminerpoolmanager.datamodel.Cluster;
|
||||||
|
import org.gcube.dataanalysys.dataminerpoolmanager.datamodel.Dependency;
|
||||||
|
import org.gcube.dataanalysys.dataminerpoolmanager.datamodel.Domain;
|
||||||
|
import org.gcube.dataanalysys.dataminerpoolmanager.datamodel.Host;
|
||||||
|
import org.gcube.dataanalysys.dataminerpoolmanager.datamodel.comparator.AlgorithmComparator;
|
||||||
|
import org.gcube.dataanalysys.dataminerpoolmanager.datamodel.comparator.DependencyComparator;
|
||||||
|
import org.gcube.dataanalysys.dataminerpoolmanager.service.DataminerPoolManager;
|
||||||
|
import org.gcube.dataanalysys.dataminerpoolmanager.util.PropertiesBasedProxySelector;
|
||||||
|
|
||||||
|
public class DataminerPoolManagerTest ***REMOVED***
|
||||||
|
|
||||||
|
/*
|
||||||
|
private static Map<String, Domain> domains = new HashMap<>();
|
||||||
|
private static Map<String, Cluster> clusters = new HashMap<>();
|
||||||
|
|
||||||
|
private static Dependency createDependency(String depName) ***REMOVED***
|
||||||
|
String[] parts = depName.split(":");
|
||||||
|
Dependency out = new Dependency();
|
||||||
|
if(parts.length>1) ***REMOVED***
|
||||||
|
out.setType(parts[0]);
|
||||||
|
out.setName(parts[1]);
|
||||||
|
***REMOVED*** else ***REMOVED***
|
||||||
|
out.setType("os");
|
||||||
|
out.setName(depName);
|
||||||
|
***REMOVED***
|
||||||
|
return out;
|
||||||
|
***REMOVED***
|
||||||
|
|
||||||
|
private static Algorithm createAlgorithm(String name, String ... deps) ***REMOVED***
|
||||||
|
Algorithm a = new Algorithm();
|
||||||
|
a.setName(name);
|
||||||
|
for(String dep:deps) ***REMOVED***
|
||||||
|
a.addDependency(createDependency(dep));
|
||||||
|
***REMOVED***
|
||||||
|
return a;
|
||||||
|
***REMOVED***
|
||||||
|
|
||||||
|
private static AlgorithmSet createAlgorithmSet(String name, Algorithm ... algs) ***REMOVED***
|
||||||
|
AlgorithmSet out = new AlgorithmSet();
|
||||||
|
out.setName(name);
|
||||||
|
for(Algorithm a:algs) ***REMOVED***
|
||||||
|
out.addAlgorithm(a);
|
||||||
|
***REMOVED***
|
||||||
|
return out;
|
||||||
|
***REMOVED***
|
||||||
|
|
||||||
|
private static Domain getDomain(String name) ***REMOVED***
|
||||||
|
if(domains.get(name)==null) ***REMOVED***
|
||||||
|
Domain d = new Domain();
|
||||||
|
d.setName(name);
|
||||||
|
domains.put(name, d);
|
||||||
|
return d;
|
||||||
|
***REMOVED*** else ***REMOVED***
|
||||||
|
return domains.get(name);
|
||||||
|
***REMOVED***
|
||||||
|
***REMOVED***
|
||||||
|
|
||||||
|
private static Host createHost(String hostname, String domainName) ***REMOVED***
|
||||||
|
Host out = new Host();
|
||||||
|
out.setName(hostname);
|
||||||
|
Domain d = getDomain(domainName);
|
||||||
|
out.setDomain(d);
|
||||||
|
return out;
|
||||||
|
***REMOVED***
|
||||||
|
|
||||||
|
private static Cluster getCluster(String name) ***REMOVED***
|
||||||
|
if(clusters.get(name)==null) ***REMOVED***
|
||||||
|
Cluster d = new Cluster();
|
||||||
|
d.setName(name);
|
||||||
|
clusters.put(name, d);
|
||||||
|
return d;
|
||||||
|
***REMOVED*** else ***REMOVED***
|
||||||
|
return clusters.get(name);
|
||||||
|
***REMOVED***
|
||||||
|
***REMOVED***
|
||||||
|
|
||||||
|
private static Collection<Dependency> extractDependencies() ***REMOVED***
|
||||||
|
Collection<Dependency> out = new TreeSet<>(new DependencyComparator());
|
||||||
|
for(Cluster c:clusters.values()) ***REMOVED***
|
||||||
|
for(AlgorithmSet as:c.getAlgorithmSets()) ***REMOVED***
|
||||||
|
for(Algorithm a:as.getAlgorithms()) ***REMOVED***
|
||||||
|
for(Dependency d:a.getDependencies()) ***REMOVED***
|
||||||
|
out.add(d);
|
||||||
|
***REMOVED***
|
||||||
|
***REMOVED***
|
||||||
|
***REMOVED***
|
||||||
|
***REMOVED***
|
||||||
|
return out;
|
||||||
|
***REMOVED***
|
||||||
|
|
||||||
|
private static Collection<Algorithm> extractAlgorithms() ***REMOVED***
|
||||||
|
Collection<Algorithm> out = new TreeSet<>(new AlgorithmComparator());
|
||||||
|
for(Cluster c:clusters.values()) ***REMOVED***
|
||||||
|
for(AlgorithmSet as:c.getAlgorithmSets()) ***REMOVED***
|
||||||
|
for(Algorithm a:as.getAlgorithms()) ***REMOVED***
|
||||||
|
out.add(a);
|
||||||
|
***REMOVED***
|
||||||
|
***REMOVED***
|
||||||
|
***REMOVED***
|
||||||
|
return out;
|
||||||
|
***REMOVED***
|
||||||
|
|
||||||
|
static ***REMOVED***
|
||||||
|
|
||||||
|
Algorithm ewe = createAlgorithm("ewe", "mono", "latex", "cran:some_R_package", "custom:some_git_package");
|
||||||
|
Algorithm ensemble = createAlgorithm("ensemble", "python");
|
||||||
|
Algorithm voodoo = createAlgorithm("voodoo", "os:latex", "custom:blah");
|
||||||
|
|
||||||
|
AlgorithmSet as1 = createAlgorithmSet("as1-fishes", ewe);
|
||||||
|
AlgorithmSet as2 = createAlgorithmSet("as2-stat", ensemble);
|
||||||
|
AlgorithmSet as3 = createAlgorithmSet("as3-blackmagic", voodoo, ewe);
|
||||||
|
|
||||||
|
Cluster cluster1 = getCluster("cluster-1");
|
||||||
|
cluster1.addHost(createHost("host1", "domain1"));
|
||||||
|
cluster1.addHost(createHost("host2", "domain1"));
|
||||||
|
cluster1.addHost(createHost("host3", "domain1"));
|
||||||
|
cluster1.addHost(createHost("host1", "domain2"));
|
||||||
|
cluster1.addHost(createHost("host2", "domain2"));
|
||||||
|
|
||||||
|
Cluster cluster2 = getCluster("cluster-2");
|
||||||
|
cluster2.addHost(createHost("host4", "domain1"));
|
||||||
|
cluster2.addHost(createHost("host5", "domain1"));
|
||||||
|
cluster2.addHost(createHost("host6", "domain1"));
|
||||||
|
cluster2.addHost(createHost("host3", "domain2"));
|
||||||
|
cluster2.addHost(createHost("host4", "domain2"));
|
||||||
|
cluster2.addHost(createHost("host5", "domain2"));
|
||||||
|
|
||||||
|
cluster1.addAlgorithmSet(as1);
|
||||||
|
cluster1.addAlgorithmSet(as2);
|
||||||
|
|
||||||
|
cluster2.addAlgorithmSet(as1);
|
||||||
|
cluster2.addAlgorithmSet(as3);
|
||||||
|
|
||||||
|
***REMOVED***
|
||||||
|
*/
|
||||||
|
|
||||||
|
public static void main(String[] args) throws Exception ***REMOVED***
|
||||||
|
/*
|
||||||
|
AnsibleBridge ab = new AnsibleBridge();
|
||||||
|
ab.printInventoryByDomainAndSets(clusters.values());
|
||||||
|
System.out.println("-----------");
|
||||||
|
ab.printInventoryBySets(clusters.values());
|
||||||
|
|
||||||
|
AnsibleWorker worker = ab.createWorker();
|
||||||
|
|
||||||
|
for(Algorithm a:extractAlgorithms()) ***REMOVED***
|
||||||
|
for(Role r:ab.generateRoles(a)) ***REMOVED***
|
||||||
|
worker.addRole(r);
|
||||||
|
***REMOVED***
|
||||||
|
***REMOVED***
|
||||||
|
|
||||||
|
for(Dependency d:extractDependencies()) ***REMOVED***
|
||||||
|
for(Role r:ab.generateRoles(d)) ***REMOVED***
|
||||||
|
worker.addRole(r);
|
||||||
|
***REMOVED***
|
||||||
|
***REMOVED***
|
||||||
|
*/
|
||||||
|
|
||||||
|
ScopeProvider.instance.set("/gcube/devNext/NextNext");
|
||||||
|
|
||||||
|
ProxySelector.setDefault(new PropertiesBasedProxySelector("/home/paolo/.proxy-settings"));
|
||||||
|
|
||||||
|
***REMOVED*** create the algorithm (download it, etc etc)
|
||||||
|
Algorithm algorithm = new Algorithm();
|
||||||
|
algorithm.setName("ichtyop");
|
||||||
|
algorithm.setClazz("org.gcube...");
|
||||||
|
algorithm.setDescription("some description");
|
||||||
|
|
||||||
|
Dependency d = new Dependency();
|
||||||
|
d.setName("libpng");
|
||||||
|
d.setType("os");
|
||||||
|
algorithm.addDependency(d);
|
||||||
|
|
||||||
|
d = new Dependency();
|
||||||
|
d.setName("some-r-package");
|
||||||
|
d.setType("cran");
|
||||||
|
algorithm.addDependency(d);
|
||||||
|
|
||||||
|
d = new Dependency();
|
||||||
|
d.setName("some-other-r-package");
|
||||||
|
d.setType("cran");
|
||||||
|
algorithm.addDependency(d);
|
||||||
|
|
||||||
|
d = new Dependency();
|
||||||
|
d.setName("voodoo");
|
||||||
|
d.setType("custom");
|
||||||
|
algorithm.addDependency(d);
|
||||||
|
|
||||||
|
***REMOVED*** create the algorithm (download it, etc etc)
|
||||||
|
Algorithm ewe = new Algorithm();
|
||||||
|
ewe.setName("ewe");
|
||||||
|
|
||||||
|
d = new Dependency();
|
||||||
|
d.setName("voodoo");
|
||||||
|
d.setType("custom");
|
||||||
|
ewe.addDependency(d);
|
||||||
|
|
||||||
|
AlgorithmSet algorithms = new AlgorithmSet();
|
||||||
|
algorithms.setName("dummy-set");
|
||||||
|
|
||||||
|
algorithms.addAlgorithm(algorithm);
|
||||||
|
algorithms.addAlgorithm(ewe);
|
||||||
|
|
||||||
|
Algorithm ensemble = new Algorithm();
|
||||||
|
ensemble.setName("ensemble");
|
||||||
|
|
||||||
|
d = new Dependency();
|
||||||
|
d.setName("libpng");
|
||||||
|
d.setType("os");
|
||||||
|
ensemble.addDependency(d);
|
||||||
|
algorithms.addAlgorithm(ensemble);
|
||||||
|
|
||||||
|
new DataminerPoolManager().addAlgorithmsToVRE(algorithms, "/gcube/devNext/NextNext");
|
||||||
|
|
||||||
|
***REMOVED***
|
||||||
|
|
||||||
|
***REMOVED***
|
||||||
|
|
@ -0,0 +1,17 @@
|
||||||
|
package org.gcube.dataanalysis.dataminerpoolmanager;
|
||||||
|
|
||||||
|
import java.net.ProxySelector;
|
||||||
|
|
||||||
|
***REMOVED***
|
||||||
|
import org.gcube.dataanalysys.dataminerpoolmanager.clients.ISClient;
|
||||||
|
import org.gcube.dataanalysys.dataminerpoolmanager.util.PropertiesBasedProxySelector;
|
||||||
|
|
||||||
|
public class ISClientTest ***REMOVED***
|
||||||
|
|
||||||
|
public static void main(String[] args) ***REMOVED***
|
||||||
|
ProxySelector.setDefault(new PropertiesBasedProxySelector("/home/paolo/.proxy-settings"));
|
||||||
|
ScopeProvider.instance.set("/gcube/devNext/NextNext");
|
||||||
|
System.out.println(new ISClient().listDataminersInVRE());
|
||||||
|
***REMOVED***
|
||||||
|
|
||||||
|
***REMOVED***
|
||||||
Loading…
Reference in New Issue