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
parent
e57b57e59c
commit
5018f51090
5
pom.xml
5
pom.xml
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@ -41,6 +41,11 @@
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<version>[4.0.0, 4.1.0)</version>
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</dependency>
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<dependency>
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<groupId>org.tmatesoft.svnkit</groupId>
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<artifactId>svnkit</artifactId>
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<version>1.8.5</version>
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</dependency>
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<dependency>
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<groupId>commons-configuration</groupId>
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<artifactId>commons-configuration</artifactId>
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<version>1.10</version>
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@ -70,15 +70,24 @@ import static org.gcube.resources.discovery.icclient.ICFactory.clientFor;
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import static org.gcube.resources.discovery.icclient.ICFactory.queryFor;
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***REMOVED***
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import java.io.ByteArrayOutputStream;
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import java.io.File;
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***REMOVED***
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import java.io.InputStream;
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***REMOVED***
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import java.io.PrintStream;
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import java.net.MalformedURLException;
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***REMOVED***
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import java.util.ArrayList;
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import java.util.Arrays;
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import java.util.Collection;
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import java.util.Collections;
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import java.util.HashSet;
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import java.util.LinkedHashMap;
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***REMOVED***
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***REMOVED***
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import java.util.Map;
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import java.util.Scanner;
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import java.util.Set;
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import java.util.TreeMap;
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import java.util.TreeSet;
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@ -87,11 +96,24 @@ import java.util.Vector;
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import org.gcube.common.resources.gcore.ServiceEndpoint;
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***REMOVED***
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***REMOVED***
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import org.gcube.dataanalysis.dataminer.poolmanager.datamodel.Dependency;
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import org.gcube.dataanalysis.dataminer.poolmanager.datamodel.Domain;
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***REMOVED***
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import org.gcube.dataanalysis.dataminer.poolmanager.datamodel.comparator.HostComparator;
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import org.gcube.resources.discovery.client.api.DiscoveryClient;
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import org.gcube.resources.discovery.client.queries.api.SimpleQuery;
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import org.tmatesoft.svn.core.SVNDepth;
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import org.tmatesoft.svn.core.SVNException;
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import org.tmatesoft.svn.core.SVNURL;
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import org.tmatesoft.svn.core.auth.ISVNAuthenticationManager;
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import org.tmatesoft.svn.core.internal.io.dav.DAVRepositoryFactory;
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import org.tmatesoft.svn.core.io.SVNRepository;
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import org.tmatesoft.svn.core.io.SVNRepositoryFactory;
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import org.tmatesoft.svn.core.wc.ISVNOptions;
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import org.tmatesoft.svn.core.wc.SVNClientManager;
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import org.tmatesoft.svn.core.wc.SVNRevision;
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import org.tmatesoft.svn.core.wc.SVNUpdateClient;
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import org.tmatesoft.svn.core.wc.SVNWCUtil;
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***REMOVED***
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@ -168,6 +190,8 @@ public Cluster getClusterByHProxy() throws IOException {
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***REMOVED***
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/**
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* Return the list of hosts (dataminers) in a given VRE
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*
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@ -210,12 +234,25 @@ public Cluster getClusterByHProxy() throws IOException {
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***REMOVED***
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***REMOVED***
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public static void main(String[] args) throws IOException {
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public static void main(String[] args) throws IOException, SVNException {
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ISClient a = new ISClient();
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ScopeProvider.instance.set("/gcube/devNext/NextNext");
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***REMOVED***System.out.println(a.getHProxy());
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System.out.println(a.getClusterByHProxy());
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System.out.println(a.listDataMinersByCluster());
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***REMOVED***System.out.println(a.getClusterByHProxy());
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***REMOVED***System.out.println(a.listDataMinersByCluster());
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***REMOVED***List<Dependency> list = new LinkedList<Dependency>();
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***REMOVED***Dependency aa = new Dependency();
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***REMOVED***aa.setName("testnunzio");
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***REMOVED***aa.setType("cran:");
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***REMOVED***list.add(aa);
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***REMOVED***a.checkSVNdep();
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***REMOVED***System.out.println(a.getDataminer("dataminer1-devnext.d4science.org").getDomain());
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***REMOVED***System.out.println(a.listDataminersInVRE());
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***REMOVED***
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@ -31,9 +31,11 @@ package org.gcube.dataanalysis.dataminer.poolmanager.rest;
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import java.net.MalformedURLException;
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***REMOVED***
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import java.net.UnknownHostException;
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***REMOVED***
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import java.util.Set;
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import org.gcube.dataanalysis.dataminer.poolmanager.datamodel.Algorithm;
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import org.tmatesoft.svn.core.SVNException;
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public interface PoolManager {
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@ -53,6 +55,7 @@ public interface PoolManager {
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void addAlgToIs(Algorithm algo);
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Set<Algorithm> getAlgoFromIs();
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List<String> getOriginalContents(String file, List<String> ldep) throws SVNException;
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***REMOVED***
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@ -142,11 +142,14 @@
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***REMOVED******REMOVED***
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package org.gcube.dataanalysis.dataminer.poolmanager.rest;
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import java.awt.color.ICC_ColorSpace;
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***REMOVED***
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import java.net.MalformedURLException;
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import java.net.ProxySelector;
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***REMOVED***
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import java.net.UnknownHostException;
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***REMOVED***
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***REMOVED***
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import java.util.Random;
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import java.util.Set;
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import java.util.UUID;
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@ -159,11 +162,14 @@ import javax.ws.rs.QueryParam;
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import org.apache.commons.lang.math.RandomUtils;
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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.datamodel.Algorithm;
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import org.gcube.dataanalysis.dataminer.poolmanager.datamodel.Dependency;
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import org.gcube.dataanalysis.dataminer.poolmanager.service.DataminerPoolManager;
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import org.gcube.dataanalysis.dataminer.poolmanager.util.PropertiesBasedProxySelector;
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***REMOVED***
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***REMOVED***
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import org.tmatesoft.svn.core.SVNException;
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@ -191,12 +197,39 @@ public class RestPoolManager implements PoolManager {
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@QueryParam("category") String category,
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@DefaultValue("transducerers") @QueryParam("algorithmType") String algorithmType,
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@DefaultValue("N") @QueryParam("skipJava") String skipJava,
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@DefaultValue("false") @QueryParam("publish") boolean publish) throws IOException, InterruptedException {
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@DefaultValue("false") @QueryParam("publish") boolean publish) throws IOException, InterruptedException, SVNException {
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Algorithm algo= this.getAlgorithm(algorithm, vre, null, name, description, category, algorithmType, skipJava);
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***REMOVED***publish algo
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if (publish){
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service.addAlgToIs(algo);
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***REMOVED***
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***REMOVED***update svn
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for (Dependency d : algo.getDependencies()){
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if (d.getType().equals("os")){
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List<String> ls = new LinkedList<String>();
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ls.add(d.getName());
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service.getOriginalContents("r_deb_pkgs.txt", ls);
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***REMOVED***
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if (d.getType().equals("cran")){
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List<String> ls = new LinkedList<String>();
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ls.add(d.getName());
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service.getOriginalContents("r_cran_pkgs.txt", ls);
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***REMOVED***
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if (d.getType().equals("custom")){
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List<String> ls = new LinkedList<String>();
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ls.add(d.getName());
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service.getOriginalContents("r_github_pkgs.txt", ls);
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***REMOVED***
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if (d.getType().equals("")){
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List<String> ls = new LinkedList<String>();
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ls.add(d.getName());
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service.getOriginalContents("r_deb_pkgs.txt", ls);
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***REMOVED***
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***REMOVED***
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return service.addAlgorithmToVRE(algo, vre);
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***REMOVED***
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@ -210,8 +243,38 @@ public class RestPoolManager implements PoolManager {
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@QueryParam("description") String description,
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@QueryParam("category") String category,
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@DefaultValue("transducerers") @QueryParam("algorithmType") String algorithmType,
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@DefaultValue("N") @QueryParam("skipJava") String skipJava) throws IOException, InterruptedException {
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@DefaultValue("N") @QueryParam("skipJava") String skipJava,
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@DefaultValue("false") @QueryParam("publish") boolean publish) throws IOException, InterruptedException, SVNException {
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Algorithm algo= this.getAlgorithm(algorithm, null, hostname, name, description, category, algorithmType, skipJava);
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***REMOVED***publish algo
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if (publish){
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service.addAlgToIs(algo);
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***REMOVED***
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***REMOVED***update svn
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for (Dependency d : algo.getDependencies()){
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if (d.getType().equals("os")){
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List<String> ls = new LinkedList<String>();
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ls.add(d.getName());
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service.getOriginalContents("r_deb_pkgs.txt", ls);
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***REMOVED***
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if (d.getType().equals("cran")){
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List<String> ls = new LinkedList<String>();
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ls.add(d.getName());
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service.getOriginalContents("r_cran_pkgs.txt", ls);
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***REMOVED***
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if (d.getType().equals("custom")){
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List<String> ls = new LinkedList<String>();
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ls.add(d.getName());
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service.getOriginalContents("r_github_pkgs.txt", ls);
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***REMOVED***
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if (d.getType().equals("")){
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List<String> ls = new LinkedList<String>();
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ls.add(d.getName());
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service.getOriginalContents("r_deb_pkgs.txt", ls);
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***REMOVED***
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***REMOVED***
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return service.addAlgorithmToHost(algo, hostname);
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***REMOVED***
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@ -274,7 +337,7 @@ public class RestPoolManager implements PoolManager {
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***REMOVED***
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public static void main(String[] args) throws IOException, InterruptedException {
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public static void main(String[] args) throws IOException, InterruptedException, SVNException {
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***REMOVED***System.out.println(System.getProperty("user.home")+File.separator+"/gcube/dataminer-pool-manager");
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***REMOVED***ProxySelector.setDefault(new PropertiesBasedProxySelector("/home/ngalante/.proxy-settings"));
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@ -285,16 +348,27 @@ public class RestPoolManager implements PoolManager {
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***REMOVED***System.out.println(aa.getAlgoFromIs());
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RestPoolManager a = new RestPoolManager();
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***REMOVED***RestPoolManager a = new RestPoolManager();
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***REMOVED***a.addAlgorithmToVRE(
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***REMOVED***"http:***REMOVED***data.d4science.org/S2h1RHZGd0JpWnBjZk9qTytQTndqcDRLVHNrQUt6QjhHbWJQNStIS0N6Yz0",
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***REMOVED***"/gcube/devNext/NextNext",
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***REMOVED***null, null, "test", "transducerers", "N");
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a.addAlgorithmToHost(
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"http:***REMOVED***data.d4science.org/dENQTTMxdjNZcGRpK0NHd2pvU0owMFFzN0VWemw3Zy9HbWJQNStIS0N6Yz0",
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"dataminer1-devnext.d4science.org",
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"ICHTHYOP_MODEL_ONE_BY_ONE", null, "ICHTHYOP_MODEL", "transducerers", "N");
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***REMOVED*** a.addAlgorithmToHost(
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***REMOVED*** "http:***REMOVED***data.d4science.org/dENQTTMxdjNZcGRpK0NHd2pvU0owMFFzN0VWemw3Zy9HbWJQNStIS0N6Yz0",
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***REMOVED*** "dataminer1-devnext.d4science.org",
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***REMOVED*** "ICHTHYOP_MODEL_ONE_BY_ONE", null, "ICHTHYOP_MODEL", "transducerers", "N",false);
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***REMOVED***
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***REMOVED***
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PoolManager aa = new DataminerPoolManager();
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List<String> ls = new LinkedList<String>();
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String afa = "nunzio";
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String b = "galante";
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ls.add(b);
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ls.add(afa);
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System.out.println(aa.getOriginalContents("r_deb_pkgs.txt",ls));
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***REMOVED***
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@ -344,6 +418,12 @@ public class RestPoolManager implements PoolManager {
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return null;
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***REMOVED***
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@Override
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public List<String> getOriginalContents(String file, List<String> ldep) throws SVNException {
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***REMOVED*** TODO Auto-generated method stub
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return null;
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***REMOVED***
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@ -266,6 +266,7 @@ import static org.gcube.resources.discovery.icclient.ICFactory.clientFor;
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import static org.gcube.resources.discovery.icclient.ICFactory.queryFor;
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***REMOVED***
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import java.io.ByteArrayOutputStream;
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import java.io.File;
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***REMOVED***
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***REMOVED***
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@ -274,6 +275,7 @@ import java.net.MalformedURLException;
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***REMOVED***
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import java.net.URLConnection;
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import java.net.UnknownHostException;
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import java.util.ArrayList;
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import java.util.Arrays;
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import java.util.HashSet;
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***REMOVED***
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@ -302,6 +304,12 @@ import org.gcube.resources.discovery.client.queries.api.SimpleQuery;
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***REMOVED***
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***REMOVED***
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import org.tmatesoft.svn.core.SVNException;
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import org.tmatesoft.svn.core.SVNURL;
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import org.tmatesoft.svn.core.auth.ISVNAuthenticationManager;
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import org.tmatesoft.svn.core.io.SVNRepository;
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import org.tmatesoft.svn.core.io.SVNRepositoryFactory;
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import org.tmatesoft.svn.core.wc.SVNWCUtil;
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public class DataminerPoolManager implements PoolManager {
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@ -549,6 +557,64 @@ public class DataminerPoolManager implements PoolManager {
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***REMOVED***
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private SVNRepository getSvnRepository(String url) throws SVNException {
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String usr = "nunzioandrea.galante";
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String pwd = "Newuser1";
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SVNRepository repository = SVNRepositoryFactory.create(SVNURL.parseURIEncoded(url));
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ISVNAuthenticationManager authManager = SVNWCUtil.createDefaultAuthenticationManager(
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usr, pwd);
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repository.setAuthenticationManager(authManager);
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System.out.println(repository.getLocation());
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return repository;
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***REMOVED***
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@Override
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public List<String> getOriginalContents(String file, List<String> ldep) throws SVNException {
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final SVNRepository svnRepository = this.getSvnRepository("https:***REMOVED***svn.d4science.research-infrastructures.eu/gcube/trunk/data-analysis/RConfiguration/RPackagesManagement/");
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try {
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final ByteArrayOutputStream byteArrayOutputStream = new ByteArrayOutputStream();
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svnRepository.getFile(file, SVNRepository.INVALID_REVISION, null, byteArrayOutputStream);
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String lines[] = byteArrayOutputStream.toString().split("\\r?\\n");
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List<String> aa = this.checkMatch(lines, ldep);
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return aa;
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***REMOVED*** finally {
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svnRepository.closeSession();
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***REMOVED***
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***REMOVED***
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public List<String> checkMatch(String[] lines, List<String> ls) {
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Set<String> ss = new HashSet<String>(ls);
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ss.addAll(Arrays.asList(lines));
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***REMOVED*** for (int z = 0; z < aa.size(); z++) {
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***REMOVED*** for (int i = 0; i < ls.size(); i++) {
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***REMOVED*** if (!ls.get(i).equals(aa.get(z))) {
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***REMOVED*** aa.add(ls.get(i));
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***REMOVED*** ***REMOVED***
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***REMOVED*** ***REMOVED***
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***REMOVED******REMOVED***
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return new ArrayList<>(ss);
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***REMOVED***
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public void checkSVNdeps(/*List<Dependency> listdep*/) throws IOException{
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***REMOVED***take svn page (one for each kind of dep)
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***REMOVED***take deps from metadata
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***REMOVED***if dep.typology available in svn.typology nothing to do
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***REMOVED***else add dep to svn page
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***REMOVED***
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public Algorithm extractAlgorithm(String url) throws IOException {
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return new AlgorithmPackageParser().parsePackage(url);
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***REMOVED***
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