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dataminer-pool-manager
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git-svn-id: https://svn.d4science.research-infrastructures.eu/gcube/trunk/data-analysis/dataminer-pool-manager@146587 82a268e6-3cf1-43bd-a215-b396298e98cf

This commit is contained in:
Nunzio Andrea Galante 2017-04-05 15:14:18 +00:00
parent e99eccffb3
commit f41d1cb5d5
5 changed files with 202 additions and 11 deletions
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5
pom.xml
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@ -41,6 +41,11 @@
<version>[4.0.0, 4.1.0)</version>
</dependency>
<dependency>
<groupId>org.tmatesoft.svnkit</groupId>
<artifactId>svnkit</artifactId>
<version>1.8.5</version>
</dependency>
<dependency>
<groupId>commons-configuration</groupId>
<artifactId>commons-configuration</artifactId>
<version>1.10</version>

43
src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/clients/ISClient.java
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@ -70,15 +70,24 @@ import static org.gcube.resources.discovery.icclient.ICFactory.clientFor;
import static org.gcube.resources.discovery.icclient.ICFactory.queryFor;
import java.io.BufferedReader;
import java.io.ByteArrayOutputStream;
import java.io.File;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.io.PrintStream;
import java.net.MalformedURLException;
import java.net.URL;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collection;
import java.util.Collections;
import java.util.HashSet;
import java.util.LinkedHashMap;
import java.util.LinkedList;
import java.util.List;
import java.util.Map;
import java.util.Scanner;
import java.util.Set;
import java.util.TreeMap;
import java.util.TreeSet;
@ -87,11 +96,24 @@ import java.util.Vector;
import org.gcube.common.resources.gcore.ServiceEndpoint;
import org.gcube.common.scope.api.ScopeProvider;
import org.gcube.dataanalysis.dataminer.poolmanager.datamodel.Cluster;
import org.gcube.dataanalysis.dataminer.poolmanager.datamodel.Dependency;
import org.gcube.dataanalysis.dataminer.poolmanager.datamodel.Domain;
import org.gcube.dataanalysis.dataminer.poolmanager.datamodel.Host;
import org.gcube.dataanalysis.dataminer.poolmanager.datamodel.comparator.HostComparator;
import org.gcube.resources.discovery.client.api.DiscoveryClient;
import org.gcube.resources.discovery.client.queries.api.SimpleQuery;
import org.tmatesoft.svn.core.SVNDepth;
import org.tmatesoft.svn.core.SVNException;
import org.tmatesoft.svn.core.SVNURL;
import org.tmatesoft.svn.core.auth.ISVNAuthenticationManager;
import org.tmatesoft.svn.core.internal.io.dav.DAVRepositoryFactory;
import org.tmatesoft.svn.core.io.SVNRepository;
import org.tmatesoft.svn.core.io.SVNRepositoryFactory;
import org.tmatesoft.svn.core.wc.ISVNOptions;
import org.tmatesoft.svn.core.wc.SVNClientManager;
import org.tmatesoft.svn.core.wc.SVNRevision;
import org.tmatesoft.svn.core.wc.SVNUpdateClient;
import org.tmatesoft.svn.core.wc.SVNWCUtil;
import au.com.bytecode.opencsv.CSVReader;
@ -168,6 +190,8 @@ public Cluster getClusterByHProxy() throws IOException {
}
/**
* Return the list of hosts (dataminers) in a given VRE
*
@ -210,12 +234,25 @@ public Cluster getClusterByHProxy() throws IOException {
}
}
public static void main(String[] args) throws IOException {
public static void main(String[] args) throws IOException, SVNException {
ISClient a = new ISClient();
ScopeProvider.instance.set("/gcube/devNext/NextNext");
//System.out.println(a.getHProxy());
System.out.println(a.getClusterByHProxy());
System.out.println(a.listDataMinersByCluster());
//System.out.println(a.getClusterByHProxy());
//System.out.println(a.listDataMinersByCluster());
//List<Dependency> list = new LinkedList<Dependency>();
//Dependency aa = new Dependency();
//aa.setName("testnunzio");
//aa.setType("cran:");
//list.add(aa);
//a.checkSVNdep();
//System.out.println(a.getDataminer("dataminer1-devnext.d4science.org").getDomain());
//System.out.println(a.listDataminersInVRE());
}

3
src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/rest/PoolManager.java
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@ -31,9 +31,11 @@ import java.io.IOException;
import java.net.MalformedURLException;
import java.net.URL;
import java.net.UnknownHostException;
import java.util.List;
import java.util.Set;
import org.gcube.dataanalysis.dataminer.poolmanager.datamodel.Algorithm;
import org.tmatesoft.svn.core.SVNException;
public interface PoolManager {
@ -53,6 +55,7 @@ public interface PoolManager {
void addAlgToIs(Algorithm algo);
Set<Algorithm> getAlgoFromIs();
List<String> getOriginalContents(String file, List<String> ldep) throws SVNException;
}

96
src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/rest/RestPoolManager.java
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@ -142,11 +142,14 @@
//}
package org.gcube.dataanalysis.dataminer.poolmanager.rest;
import java.awt.color.ICC_ColorSpace;
import java.io.IOException;
import java.net.MalformedURLException;
import java.net.ProxySelector;
import java.net.URL;
import java.net.UnknownHostException;
import java.util.LinkedList;
import java.util.List;
import java.util.Random;
import java.util.Set;
import java.util.UUID;
@ -159,11 +162,14 @@ import javax.ws.rs.QueryParam;
import org.apache.commons.lang.math.RandomUtils;
import org.gcube.common.scope.api.ScopeProvider;
import org.gcube.dataanalysis.dataminer.poolmanager.clients.ISClient;
import org.gcube.dataanalysis.dataminer.poolmanager.datamodel.Algorithm;
import org.gcube.dataanalysis.dataminer.poolmanager.datamodel.Dependency;
import org.gcube.dataanalysis.dataminer.poolmanager.service.DataminerPoolManager;
import org.gcube.dataanalysis.dataminer.poolmanager.util.PropertiesBasedProxySelector;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.tmatesoft.svn.core.SVNException;
@ -191,12 +197,39 @@ public class RestPoolManager implements PoolManager {
@QueryParam("category") String category,
@DefaultValue("transducerers") @QueryParam("algorithmType") String algorithmType,
@DefaultValue("N") @QueryParam("skipJava") String skipJava,
@DefaultValue("false") @QueryParam("publish") boolean publish) throws IOException, InterruptedException {
@DefaultValue("false") @QueryParam("publish") boolean publish) throws IOException, InterruptedException, SVNException {
Algorithm algo= this.getAlgorithm(algorithm, vre, null, name, description, category, algorithmType, skipJava);
//publish algo
if (publish){
service.addAlgToIs(algo);
}
//update svn
for (Dependency d : algo.getDependencies()){
if (d.getType().equals("os")){
List<String> ls = new LinkedList<String>();
ls.add(d.getName());
service.getOriginalContents("r_deb_pkgs.txt", ls);
}
if (d.getType().equals("cran")){
List<String> ls = new LinkedList<String>();
ls.add(d.getName());
service.getOriginalContents("r_cran_pkgs.txt", ls);
}
if (d.getType().equals("custom")){
List<String> ls = new LinkedList<String>();
ls.add(d.getName());
service.getOriginalContents("r_github_pkgs.txt", ls);
}
if (d.getType().equals("")){
List<String> ls = new LinkedList<String>();
ls.add(d.getName());
service.getOriginalContents("r_deb_pkgs.txt", ls);
}
}
return service.addAlgorithmToVRE(algo, vre);
}
@ -210,8 +243,38 @@ public class RestPoolManager implements PoolManager {
@QueryParam("description") String description,
@QueryParam("category") String category,
@DefaultValue("transducerers") @QueryParam("algorithmType") String algorithmType,
@DefaultValue("N") @QueryParam("skipJava") String skipJava) throws IOException, InterruptedException {
@DefaultValue("N") @QueryParam("skipJava") String skipJava,
@DefaultValue("false") @QueryParam("publish") boolean publish) throws IOException, InterruptedException, SVNException {
Algorithm algo= this.getAlgorithm(algorithm, null, hostname, name, description, category, algorithmType, skipJava);
//publish algo
if (publish){
service.addAlgToIs(algo);
}
//update svn
for (Dependency d : algo.getDependencies()){
if (d.getType().equals("os")){
List<String> ls = new LinkedList<String>();
ls.add(d.getName());
service.getOriginalContents("r_deb_pkgs.txt", ls);
}
if (d.getType().equals("cran")){
List<String> ls = new LinkedList<String>();
ls.add(d.getName());
service.getOriginalContents("r_cran_pkgs.txt", ls);
}
if (d.getType().equals("custom")){
List<String> ls = new LinkedList<String>();
ls.add(d.getName());
service.getOriginalContents("r_github_pkgs.txt", ls);
}
if (d.getType().equals("")){
List<String> ls = new LinkedList<String>();
ls.add(d.getName());
service.getOriginalContents("r_deb_pkgs.txt", ls);
}
}
return service.addAlgorithmToHost(algo, hostname);
}
@ -274,7 +337,7 @@ public class RestPoolManager implements PoolManager {
}
public static void main(String[] args) throws IOException, InterruptedException {
public static void main(String[] args) throws IOException, InterruptedException, SVNException {
//System.out.println(System.getProperty("user.home")+File.separator+"/gcube/dataminer-pool-manager");
//ProxySelector.setDefault(new PropertiesBasedProxySelector("/home/ngalante/.proxy-settings"));
@ -285,16 +348,27 @@ public class RestPoolManager implements PoolManager {
//System.out.println(aa.getAlgoFromIs());
RestPoolManager a = new RestPoolManager();
//RestPoolManager a = new RestPoolManager();
//a.addAlgorithmToVRE(
//"http://data.d4science.org/S2h1RHZGd0JpWnBjZk9qTytQTndqcDRLVHNrQUt6QjhHbWJQNStIS0N6Yz0",
//"/gcube/devNext/NextNext",
//null, null, "test", "transducerers", "N");
a.addAlgorithmToHost(
"http://data.d4science.org/dENQTTMxdjNZcGRpK0NHd2pvU0owMFFzN0VWemw3Zy9HbWJQNStIS0N6Yz0",
"dataminer1-devnext.d4science.org",
"ICHTHYOP_MODEL_ONE_BY_ONE", null, "ICHTHYOP_MODEL", "transducerers", "N");
// a.addAlgorithmToHost(
// "http://data.d4science.org/dENQTTMxdjNZcGRpK0NHd2pvU0owMFFzN0VWemw3Zy9HbWJQNStIS0N6Yz0",
// "dataminer1-devnext.d4science.org",
// "ICHTHYOP_MODEL_ONE_BY_ONE", null, "ICHTHYOP_MODEL", "transducerers", "N",false);
//
//
PoolManager aa = new DataminerPoolManager();
List<String> ls = new LinkedList<String>();
String afa = "nunzio";
String b = "galante";
ls.add(b);
ls.add(afa);
System.out.println(aa.getOriginalContents("r_deb_pkgs.txt",ls));
}
@ -344,6 +418,12 @@ public class RestPoolManager implements PoolManager {
return null;
}
@Override
public List<String> getOriginalContents(String file, List<String> ldep) throws SVNException {
// TODO Auto-generated method stub
return null;
}

66
src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/service/DataminerPoolManager.java
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@ -266,6 +266,7 @@ import static org.gcube.resources.discovery.icclient.ICFactory.clientFor;
import static org.gcube.resources.discovery.icclient.ICFactory.queryFor;
import java.io.BufferedReader;
import java.io.ByteArrayOutputStream;
import java.io.File;
import java.io.IOException;
import java.io.InputStreamReader;
@ -274,6 +275,7 @@ import java.net.MalformedURLException;
import java.net.URL;
import java.net.URLConnection;
import java.net.UnknownHostException;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.HashSet;
import java.util.List;
@ -302,6 +304,12 @@ import org.gcube.resources.discovery.client.queries.api.SimpleQuery;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.tmatesoft.svn.core.SVNException;
import org.tmatesoft.svn.core.SVNURL;
import org.tmatesoft.svn.core.auth.ISVNAuthenticationManager;
import org.tmatesoft.svn.core.io.SVNRepository;
import org.tmatesoft.svn.core.io.SVNRepositoryFactory;
import org.tmatesoft.svn.core.wc.SVNWCUtil;
public class DataminerPoolManager implements PoolManager {
@ -549,6 +557,64 @@ public class DataminerPoolManager implements PoolManager {
}
private SVNRepository getSvnRepository(String url) throws SVNException {
String usr = "nunzioandrea.galante";
String pwd = "Newuser1";
SVNRepository repository = SVNRepositoryFactory.create(SVNURL.parseURIEncoded(url));
ISVNAuthenticationManager authManager = SVNWCUtil.createDefaultAuthenticationManager(
usr, pwd);
repository.setAuthenticationManager(authManager);
System.out.println(repository.getLocation());
return repository;
}
@Override
public List<String> getOriginalContents(String file, List<String> ldep) throws SVNException {
final SVNRepository svnRepository = this.getSvnRepository("https://svn.d4science.research-infrastructures.eu/gcube/trunk/data-analysis/RConfiguration/RPackagesManagement/");
try {
final ByteArrayOutputStream byteArrayOutputStream = new ByteArrayOutputStream();
svnRepository.getFile(file, SVNRepository.INVALID_REVISION, null, byteArrayOutputStream);
String lines[] = byteArrayOutputStream.toString().split("\\r?\\n");
List<String> aa = this.checkMatch(lines, ldep);
return aa;
} finally {
svnRepository.closeSession();
}
}
public List<String> checkMatch(String[] lines, List<String> ls) {
Set<String> ss = new HashSet<String>(ls);
ss.addAll(Arrays.asList(lines));
// for (int z = 0; z < aa.size(); z++) {
// for (int i = 0; i < ls.size(); i++) {
// if (!ls.get(i).equals(aa.get(z))) {
// aa.add(ls.get(i));
// }
// }
//}
return new ArrayList<>(ss);
}
public void checkSVNdeps(/*List<Dependency> listdep*/) throws IOException{
//take svn page (one for each kind of dep)
//take deps from metadata
//if dep.typology available in svn.typology nothing to do
//else add dep to svn page
}
public Algorithm extractAlgorithm(String url) throws IOException {
return new AlgorithmPackageParser().parsePackage(url);
}