From 987afa2f0e56add563534348dd01a5563a4da5b3 Mon Sep 17 00:00:00 2001 From: Ciro Formisano Date: Wed, 20 Dec 2017 11:01:01 +0000 Subject: [PATCH] git-svn-id: https://svn.d4science.research-infrastructures.eu/gcube/trunk/data-analysis/dataminer-pool-manager@160699 82a268e6-3cf1-43bd-a215-b396298e98cf --- .../template/AlgorithmPackage.java | 17 ++++-- .../template/CustomDependencyPackage.java | 16 +++--- .../template/CustomRoleManager.java | 4 -- .../template/DependencyPackage.java | 13 +++-- .../template/OSDependencyPackage.java | 4 +- .../template/StaticRoleManager.java | 1 - .../poolmanager/clients/HAProxy.java | 12 ++++- .../poolmanager/clients/ISClient.java | 52 ++++--------------- .../DMPMClientConfiguratorManager.java | 3 +- .../configurations/AbstractConfiguration.java | 19 +------ .../poolmanager/datamodel/Action.java | 2 - .../poolmanager/datamodel/Algorithm.java | 16 +----- .../poolmanager/datamodel/AlgorithmSet.java | 25 +++++---- .../poolmanager/datamodel/Cluster.java | 27 ++++++---- .../poolmanager/datamodel/Dependency.java | 4 +- .../dataminer/poolmanager/datamodel/Host.java | 2 +- .../process/AlgorithmPackageParser.java | 44 ++++++++-------- .../poolmanager/rest/PoolManager.java | 12 ++--- .../service/DataminerPoolManager.java | 2 +- .../poolmanager/util/CheckMethod.java | 8 +-- .../poolmanager/util/CheckPermission.java | 15 +++--- .../poolmanager/util/SVNUpdater.java | 14 ++--- .../dataminer/poolmanager/util/SendMail.java | 2 +- 23 files changed, 144 insertions(+), 170 deletions(-) diff --git a/src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/ansiblebridge/template/AlgorithmPackage.java b/src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/ansiblebridge/template/AlgorithmPackage.java index e00ffeb..d4a43e2 100644 --- a/src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/ansiblebridge/template/AlgorithmPackage.java +++ b/src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/ansiblebridge/template/AlgorithmPackage.java @@ -10,13 +10,19 @@ import java.util.Vector; import org.gcube.dataanalysis.dataminer.poolmanager.ansible.model.Role; ***REMOVED*** import org.gcube.dataanalysis.dataminer.poolmanager.datamodel.Dependency; +***REMOVED*** +***REMOVED*** public class AlgorithmPackage ***REMOVED*** private Algorithm algorithm; private boolean includeAlgorithmDependencies; - public AlgorithmPackage(Algorithm a,boolean includeAlgorithmDependencies) ***REMOVED*** - this.algorithm = a; + private Logger logger; + + public AlgorithmPackage(Algorithm a,boolean includeAlgorithmDependencies) + ***REMOVED*** + this.logger = LoggerFactory.getLogger(AlgorithmPackage.class); + this.algorithm = a; this.includeAlgorithmDependencies = includeAlgorithmDependencies; ***REMOVED*** @@ -61,12 +67,13 @@ public class AlgorithmPackage ***REMOVED*** Role r = tm.fillRoleTemplate(template, dictionary); r.setName(roleName); out.add(r); - ***REMOVED*** else ***REMOVED*** - System.out.println("WARNING: template is null"); + ***REMOVED*** else + ***REMOVED*** + this.logger.warn("WARNING: template is null"); ***REMOVED*** ***REMOVED*** catch (NoSuchElementException e) ***REMOVED*** ***REMOVED*** e.printStackTrace(); - System.out.println("WARNING: no template found for " + roleName); + this.logger.warn("WARNING: no template found for " + roleName); ***REMOVED*** ***REMOVED*** return out; diff --git a/src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/ansiblebridge/template/CustomDependencyPackage.java b/src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/ansiblebridge/template/CustomDependencyPackage.java index 4bd4b65..10f34e5 100644 --- a/src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/ansiblebridge/template/CustomDependencyPackage.java +++ b/src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/ansiblebridge/template/CustomDependencyPackage.java @@ -6,16 +6,20 @@ import java.util.Vector; import org.gcube.dataanalysis.dataminer.poolmanager.ansible.model.Role; import org.gcube.dataanalysis.dataminer.poolmanager.datamodel.Dependency; +***REMOVED*** public class CustomDependencyPackage extends DependencyPackage ***REMOVED*** - public CustomDependencyPackage(Dependency d) ***REMOVED*** - super(d); + private Logger logger; + + public CustomDependencyPackage(Dependency dependency) + ***REMOVED*** + super(dependency); ***REMOVED*** - private String getCustomRepositoryLocation(String ansibleRoot) ***REMOVED*** - return ansibleRoot+"/custom"; - ***REMOVED*** +***REMOVED*** private String getCustomRepositoryLocation(String ansibleRoot) ***REMOVED*** +***REMOVED*** return ansibleRoot+"/custom"; +***REMOVED*** ***REMOVED*** /* public void serializeTo(String ansibleRoot) ***REMOVED*** @@ -54,7 +58,7 @@ public class CustomDependencyPackage extends DependencyPackage ***REMOVED*** ***REMOVED*** ***REMOVED*** catch (NoSuchElementException e) ***REMOVED*** ***REMOVED*** e.printStackTrace(); - System.out.println("WARNING: no custom role found for " + roleName); + this.logger.warn("WARNING: no custom role found for " + roleName); ***REMOVED*** ***REMOVED*** return out; diff --git a/src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/ansiblebridge/template/CustomRoleManager.java b/src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/ansiblebridge/template/CustomRoleManager.java index c642469..3d59036 100644 --- a/src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/ansiblebridge/template/CustomRoleManager.java +++ b/src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/ansiblebridge/template/CustomRoleManager.java @@ -10,11 +10,7 @@ import org.gcube.dataanalysis.dataminer.poolmanager.ansiblebridge.AnsibleSeriali public class CustomRoleManager ***REMOVED*** - private String root; - public CustomRoleManager() ***REMOVED*** - - ***REMOVED*** public String getRoot() ***REMOVED*** String input = AnsibleBridge.class.getClassLoader().getResource("custom").getPath(); diff --git a/src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/ansiblebridge/template/DependencyPackage.java b/src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/ansiblebridge/template/DependencyPackage.java index 771afab..bb06412 100644 --- a/src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/ansiblebridge/template/DependencyPackage.java +++ b/src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/ansiblebridge/template/DependencyPackage.java @@ -8,13 +8,18 @@ import java.util.Vector; import org.gcube.dataanalysis.dataminer.poolmanager.ansible.model.Role; import org.gcube.dataanalysis.dataminer.poolmanager.datamodel.Dependency; +***REMOVED*** +***REMOVED*** public class DependencyPackage ***REMOVED*** + private Logger logger; + private Dependency dependency; - public DependencyPackage(Dependency d) ***REMOVED*** - this.dependency = d; + public DependencyPackage(Dependency dependency) ***REMOVED*** + this.dependency = dependency; + this.logger = LoggerFactory.getLogger(DependencyPackage.class); ***REMOVED*** protected Map getDictionary(Dependency d) ***REMOVED*** @@ -42,11 +47,11 @@ public class DependencyPackage ***REMOVED*** r.setName(roleName); out.add(r); ***REMOVED*** else ***REMOVED*** - System.out.println("WARNING: template is null"); + this.logger.warn("WARNING: template is null"); ***REMOVED*** ***REMOVED*** catch (NoSuchElementException e) ***REMOVED*** ***REMOVED*** e.printStackTrace(); - System.out.println("WARNING: no template found for " + roleName); + this.logger.warn("WARNING: no template found for " + roleName); ***REMOVED*** ***REMOVED*** return out; diff --git a/src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/ansiblebridge/template/OSDependencyPackage.java b/src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/ansiblebridge/template/OSDependencyPackage.java index 4eaa7e2..5540411 100644 --- a/src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/ansiblebridge/template/OSDependencyPackage.java +++ b/src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/ansiblebridge/template/OSDependencyPackage.java @@ -4,8 +4,8 @@ import org.gcube.dataanalysis.dataminer.poolmanager.datamodel.Dependency; public class OSDependencyPackage extends DependencyPackage ***REMOVED*** - public OSDependencyPackage(Dependency d) ***REMOVED*** - super(d); + public OSDependencyPackage(Dependency dependency) ***REMOVED*** + super(dependency); ***REMOVED*** ***REMOVED*** diff --git a/src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/ansiblebridge/template/StaticRoleManager.java b/src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/ansiblebridge/template/StaticRoleManager.java index 3eb4d3e..a11b6d4 100644 --- a/src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/ansiblebridge/template/StaticRoleManager.java +++ b/src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/ansiblebridge/template/StaticRoleManager.java @@ -2,7 +2,6 @@ package org.gcube.dataanalysis.dataminer.poolmanager.ansiblebridge.template; import java.io.File; ***REMOVED*** -import java.io.InputStream; import java.util.Collection; import java.util.Vector; diff --git a/src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/clients/HAProxy.java b/src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/clients/HAProxy.java index 36ca176..84a47f3 100644 --- a/src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/clients/HAProxy.java +++ b/src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/clients/HAProxy.java @@ -14,12 +14,20 @@ import org.gcube.dataanalysis.dataminer.poolmanager.datamodel.Cluster; import org.gcube.dataanalysis.dataminer.poolmanager.datamodel.Host; import org.gcube.dataanalysis.dataminer.poolmanager.util.CheckPermission; ***REMOVED*** +***REMOVED*** + import au.com.bytecode.opencsv.CSVReader; public class HAProxy ***REMOVED*** + private Logger logger; + private CSVReader reader; + public HAProxy() ***REMOVED*** + this.logger = LoggerFactory.getLogger(HAProxy.class); +***REMOVED*** + ***REMOVED*** public Cluster getClusterByHProxy() throws IOException ***REMOVED*** ***REMOVED*** Cluster cl = new Cluster(); ***REMOVED*** String HProxy = ISClient.getHProxy(); @@ -121,11 +129,11 @@ public class HAProxy ***REMOVED*** Host b = new Host(); b.setName(nextLine[1]); out.add(b); - System.out.println(b.getFullyQualifiedName()); + this.logger.info(b.getFullyQualifiedName()); ***REMOVED*** ***REMOVED*** ***REMOVED*** - System.out.println(out); + this.logger.info(out.toString()); return out; ***REMOVED*** diff --git a/src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/clients/ISClient.java b/src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/clients/ISClient.java index 489e33a..69a4010 100644 --- a/src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/clients/ISClient.java +++ b/src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/clients/ISClient.java @@ -3,29 +3,11 @@ package org.gcube.dataanalysis.dataminer.poolmanager.clients; 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; ***REMOVED*** -import java.io.InputStream; -import java.io.InputStreamReader; -import java.io.PrintStream; import java.io.StringWriter; -***REMOVED*** -***REMOVED*** -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; ***REMOVED*** -import java.util.Map; -import java.util.Scanner; -***REMOVED*** -import java.util.TreeMap; -import java.util.TreeSet; import java.util.Vector; ***REMOVED*** @@ -34,12 +16,7 @@ import org.gcube.common.resources.gcore.Resources; import org.gcube.common.resources.gcore.ServiceEndpoint; ***REMOVED*** ***REMOVED*** -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; -***REMOVED*** import org.gcube.informationsystem.publisher.AdvancedScopedPublisher; import org.gcube.informationsystem.publisher.RegistryPublisherFactory; import org.gcube.informationsystem.publisher.ScopedPublisher; @@ -48,24 +25,15 @@ import org.gcube.resources.discovery.client.api.DiscoveryClient; import org.gcube.resources.discovery.client.queries.api.SimpleQuery; ***REMOVED*** ***REMOVED*** -import org.tmatesoft.svn.core.SVNDepth; ***REMOVED*** -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; public class ISClient ***REMOVED*** - private static final Logger LOGGER = LoggerFactory.getLogger(ISClient.class); + private Logger logger; + public ISClient() ***REMOVED*** + this.logger = LoggerFactory.getLogger(ISClient.class); +***REMOVED*** + public Host getDataminer(String hostname) ***REMOVED*** Host h = new Host(); @@ -196,11 +164,11 @@ public class ISClient ***REMOVED*** ScopedPublisher scopedPublisher = RegistryPublisherFactory.scopedPublisher(); AdvancedScopedPublisher advancedScopedPublisher = new AdvancedScopedPublisher(scopedPublisher); String id = resource.id(); - LOGGER.debug("Trying to remove ***REMOVED******REMOVED*** with ID ***REMOVED******REMOVED*** from ***REMOVED******REMOVED***", resource.getClass().getSimpleName(), id, + this.logger.info("Trying to remove ***REMOVED******REMOVED*** with ID ***REMOVED******REMOVED*** from ***REMOVED******REMOVED***", resource.getClass().getSimpleName(), id, ScopeProvider.instance.get()); ***REMOVED*** scopedPublisher.remove(resource, scopes); advancedScopedPublisher.forceRemove(resource); - LOGGER.debug("***REMOVED******REMOVED*** with ID ***REMOVED******REMOVED*** removed successfully", resource.getClass().getSimpleName(), id); + this.logger.info("***REMOVED******REMOVED*** with ID ***REMOVED******REMOVED*** removed successfully", resource.getClass().getSimpleName(), id); ***REMOVED*** public void publishScopedResource(GenericResource a, List scopes) @@ -210,11 +178,11 @@ public class ISClient ***REMOVED*** ScopedPublisher scopedPublisher = RegistryPublisherFactory.scopedPublisher(); try ***REMOVED*** - System.out.println(scopes); - System.out.println(stringWriter); + this.logger.debug(scopes.toString()); + this.logger.debug(stringWriter.toString()); scopedPublisher.create(a, scopes); ***REMOVED*** catch (RegistryNotFoundException e) ***REMOVED*** - System.out.println(e); + this.logger.error("Registry not found",e); throw e; ***REMOVED*** ***REMOVED*** diff --git a/src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/clients/configuration/DMPMClientConfiguratorManager.java b/src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/clients/configuration/DMPMClientConfiguratorManager.java index 4b1cabb..7b86111 100755 --- a/src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/clients/configuration/DMPMClientConfiguratorManager.java +++ b/src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/clients/configuration/DMPMClientConfiguratorManager.java @@ -11,7 +11,8 @@ import org.gcube.dataanalysis.dataminer.poolmanager.clients.configuration.Config ***REMOVED*** ***REMOVED*** -public class DMPMClientConfiguratorManager***REMOVED*** +public class DMPMClientConfiguratorManager +***REMOVED*** private final Logger logger; private Properties defaultAdmins; private String admins; diff --git a/src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/clients/configurations/AbstractConfiguration.java b/src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/clients/configurations/AbstractConfiguration.java index acb64d6..df0d9f1 100755 --- a/src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/clients/configurations/AbstractConfiguration.java +++ b/src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/clients/configurations/AbstractConfiguration.java @@ -3,36 +3,21 @@ package org.gcube.dataanalysis.dataminer.poolmanager.clients.configurations; import javax.xml.bind.annotation.XmlElement; -public abstract class AbstractConfiguration ***REMOVED*** - - - - +public abstract class AbstractConfiguration +***REMOVED*** private String host; - private String algorithmsList; - private String softwareRepo; - private String ghostRepo; - private String depsLinuxCompiled; - private String depsPreInstalled; - private String depsRBlackbox; - private String depsR; - private String depsJava; - private String depsKnimeWorkflow; - private String depsOctave; - private String depsPython; - private String depsWindowsCompiled; diff --git a/src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/datamodel/Action.java b/src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/datamodel/Action.java index c4162f6..dadf22e 100644 --- a/src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/datamodel/Action.java +++ b/src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/datamodel/Action.java @@ -3,9 +3,7 @@ package org.gcube.dataanalysis.dataminer.poolmanager.datamodel; public class Action ***REMOVED*** private String name; - private String description; - private String script; public String getName() ***REMOVED*** diff --git a/src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/datamodel/Algorithm.java b/src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/datamodel/Algorithm.java index 8612c98..2218106 100644 --- a/src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/datamodel/Algorithm.java +++ b/src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/datamodel/Algorithm.java @@ -9,36 +9,24 @@ import java.util.Vector; public class Algorithm ***REMOVED*** - private String username; - + private String username; private String fullname; - private String email; - private String language; - private String name; - private String description; - private String clazz; - private String category; - private String algorithmType; - private String skipJava; - private String packageURL; - private Collection actions; - private Collection dependencies; public Algorithm() ***REMOVED*** this.actions = new Vector<>(); this.dependencies = new Vector<>(); - Dependency p = new Dependency(); + ***REMOVED*** Dependency p = new Dependency(); ***REMOVED***init with default values this.skipJava = "N"; diff --git a/src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/datamodel/AlgorithmSet.java b/src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/datamodel/AlgorithmSet.java index d209f89..7f9c9ed 100644 --- a/src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/datamodel/AlgorithmSet.java +++ b/src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/datamodel/AlgorithmSet.java @@ -6,39 +6,46 @@ import java.util.Vector; public class AlgorithmSet ***REMOVED*** private String name; - private Collection algorithms; - public AlgorithmSet() ***REMOVED*** + public AlgorithmSet() + ***REMOVED*** this.algorithms = new Vector<>(); ***REMOVED*** - public String getName() ***REMOVED*** + public String getName() + ***REMOVED*** return name; ***REMOVED*** - public void setName(String name) ***REMOVED*** + public void setName(String name) + ***REMOVED*** this.name = name; ***REMOVED*** - public Collection getAlgorithms() ***REMOVED*** + public Collection getAlgorithms() + ***REMOVED*** return new Vector<>(algorithms); ***REMOVED*** - public void addAlgorithm(Algorithm algoritm) ***REMOVED*** + public void addAlgorithm(Algorithm algoritm) + ***REMOVED*** this.algorithms.add(algoritm); ***REMOVED*** - public Boolean hasAlgorithm(Algorithm algorithm) ***REMOVED*** + public Boolean hasAlgorithm(Algorithm algorithm) + ***REMOVED*** for (Algorithm a : this.algorithms) ***REMOVED*** - if (a.getName().equals(algorithm.getName())) ***REMOVED*** + if (a.getName().equals(algorithm.getName())) + ***REMOVED*** return true; ***REMOVED*** ***REMOVED*** return false; ***REMOVED*** - public String toString() ***REMOVED*** + public String toString() + ***REMOVED*** String out = "ALGOSET: " + this.name + "\n"; for(Algorithm a:this.algorithms) ***REMOVED*** out+=a+"\n"; diff --git a/src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/datamodel/Cluster.java b/src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/datamodel/Cluster.java index 9432df4..914a688 100644 --- a/src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/datamodel/Cluster.java +++ b/src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/datamodel/Cluster.java @@ -25,40 +25,49 @@ public class Cluster ***REMOVED*** */ private Collection algoSets; - public Cluster() ***REMOVED*** + public Cluster() + ***REMOVED*** this.hosts = new Vector<>(); this.algoSets = new Vector<>(); ***REMOVED*** - public void addAlgorithmSet(AlgorithmSet set) ***REMOVED*** + public void addAlgorithmSet(AlgorithmSet set) + ***REMOVED*** this.algoSets.add(set); ***REMOVED*** - public void addHost(Host host) ***REMOVED*** + public void addHost(Host host) + ***REMOVED*** this.hosts.add(host); ***REMOVED*** - public Collection getHosts() ***REMOVED*** + public Collection getHosts() + ***REMOVED*** return hosts; ***REMOVED*** - public String getName() ***REMOVED*** + public String getName() + ***REMOVED*** return name; ***REMOVED*** - public void setName(String name) ***REMOVED*** + public void setName(String name) + ***REMOVED*** this.name = name; ***REMOVED*** - public String getDescription() ***REMOVED*** + public String getDescription() + ***REMOVED*** return description; ***REMOVED*** - public void setDescription(String description) ***REMOVED*** + public void setDescription(String description) + ***REMOVED*** this.description = description; ***REMOVED*** - public Collection getAlgorithmSets() ***REMOVED*** + public Collection getAlgorithmSets() + ***REMOVED*** return algoSets; ***REMOVED*** diff --git a/src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/datamodel/Dependency.java b/src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/datamodel/Dependency.java index b623c63..cb7ea89 100644 --- a/src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/datamodel/Dependency.java +++ b/src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/datamodel/Dependency.java @@ -3,10 +3,10 @@ package org.gcube.dataanalysis.dataminer.poolmanager.datamodel; public class Dependency ***REMOVED*** private String name; - private String type; - public String getName() ***REMOVED*** + public String getName() + ***REMOVED*** return name; ***REMOVED*** diff --git a/src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/datamodel/Host.java b/src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/datamodel/Host.java index 73b2090..e150476 100644 --- a/src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/datamodel/Host.java +++ b/src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/datamodel/Host.java @@ -11,7 +11,7 @@ public class Host ***REMOVED*** ***REMOVED*** public Host() ***REMOVED*** - ***REMOVED*** TODO Auto-generated constructor stub + ***REMOVED*** public String getFullyQualifiedName() ***REMOVED*** diff --git a/src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/process/AlgorithmPackageParser.java b/src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/process/AlgorithmPackageParser.java index a3367de..21ca2c2 100644 --- a/src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/process/AlgorithmPackageParser.java +++ b/src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/process/AlgorithmPackageParser.java @@ -10,9 +10,10 @@ import java.util.Vector; import java.util.zip.ZipEntry; import java.util.zip.ZipInputStream; -import org.apache.commons.lang.StringEscapeUtils; ***REMOVED*** import org.gcube.dataanalysis.dataminer.poolmanager.datamodel.Dependency; +***REMOVED*** +***REMOVED*** public class AlgorithmPackageParser ***REMOVED*** @@ -20,35 +21,32 @@ public class AlgorithmPackageParser ***REMOVED*** * The name of the file containing algorithm metadata. Expected in the root * directory of the package. */ - private static final String METADATA_FILE_NAME = "Info.txt"; + private final String METADATA_FILE_NAME = "Info.txt", + METADATA_USERNAME = "Username", + METADATA_FULLNAME = "Full Name", + METADATA_EMAIL = "Email", + METADATA_LANGUAGE = "Language", + METADATA_CATEGORY = "Algorithm Category", + METADATA_ALGORITHM_NAME = "Algorithm Name", + METADATA_ALGORITHM_DESCRIPTION = "Algorithm Description", + METADATA_CLASS_NAME = "Class Name", - private static final String METADATA_USERNAME = "Username"; + ***REMOVED*** private static final String METADATA_PACKAGES = "Packages"; - private static final String METADATA_FULLNAME = "Full Name"; + METADATA_KEY_VALUE_SEPARATOR = ":"; - private static final String METADATA_EMAIL = "Email"; + private final int BUFFER_SIZE = 4096; + + private Logger logger; - private static final String METADATA_LANGUAGE = "Language"; - - private static final String METADATA_CATEGORY = "Algorithm Category"; - - private static final String METADATA_ALGORITHM_NAME = "Algorithm Name"; - - private static final String METADATA_ALGORITHM_DESCRIPTION = "Algorithm Description"; - - private static final String METADATA_CLASS_NAME = "Class Name"; - - private static final String METADATA_PACKAGES = "Packages"; - - private static final String METADATA_KEY_VALUE_SEPARATOR = ":"; - - private static final int BUFFER_SIZE = 4096; - + public AlgorithmPackageParser() ***REMOVED*** + this.logger = LoggerFactory.getLogger(AlgorithmPackageParser.class); + ***REMOVED*** public Algorithm parsePackage(String url) throws IOException ***REMOVED*** String packageMetadata = this.getPackageMetadata(url); if (packageMetadata == null) ***REMOVED*** - System.out.println("WARNING: No metadata found for " + url); + this.logger.warn("WARNING: No metadata found for " + url); return null; ***REMOVED*** else ***REMOVED*** Map> parsedMetadata = this.parseMetadata(packageMetadata); @@ -125,7 +123,7 @@ public class AlgorithmPackageParser ***REMOVED*** out.put(key, values); ***REMOVED*** values.add(value); - System.out.println(key + METADATA_KEY_VALUE_SEPARATOR + " " + values); + this.logger.debug(key + METADATA_KEY_VALUE_SEPARATOR + " " + values); ***REMOVED*** ***REMOVED*** return out; diff --git a/src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/rest/PoolManager.java b/src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/rest/PoolManager.java index eb14280..68c7833 100644 --- a/src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/rest/PoolManager.java +++ b/src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/rest/PoolManager.java @@ -35,18 +35,17 @@ ***REMOVED*** ***REMOVED*** -import org.gcube.dataanalysis.dataminer.poolmanager.datamodel.AlgorithmSet; ***REMOVED*** -public interface PoolManager ***REMOVED*** - - String addAlgorithmToVRE(Algorithm algo, String vre, boolean test ) throws IOException, InterruptedException; - String addAlgorithmToHost(Algorithm algo, String host,boolean test) throws IOException, InterruptedException; +public interface PoolManager +***REMOVED*** + String addAlgorithmToVRE(Algorithm algo, String vre, boolean test ) throws IOException, InterruptedException; + String addAlgorithmToHost(Algorithm algo, String host,boolean test) throws IOException, InterruptedException; String stageAlgorithm(String algorithmPackageURL) throws IOException, InterruptedException; - String publishAlgorithm(String algorithmPackageURL, String targetVREToken, String targetVRE) throws IOException, InterruptedException; + String publishAlgorithm(String algorithmPackageURL, String targetVREToken, String targetVRE) throws IOException, InterruptedException; Algorithm extractAlgorithm(String url) throws IOException; @@ -61,6 +60,7 @@ public interface PoolManager ***REMOVED*** void addAlgToIs(Algorithm algo); Set getAlgoFromIs(); + List updateSVN(String file, List ldep) throws SVNException, IOException; diff --git a/src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/service/DataminerPoolManager.java b/src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/service/DataminerPoolManager.java index 65c94cb..523ee6d 100644 --- a/src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/service/DataminerPoolManager.java +++ b/src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/service/DataminerPoolManager.java @@ -30,7 +30,7 @@ public class DataminerPoolManager ***REMOVED*** this.svnUpdaterStaging = new SVNUpdaterStaging(); this.svnUpdaterProduction = new SVNUpdaterProduction(); ***REMOVED*** catch (SVNException e) ***REMOVED*** - e.printStackTrace(); + this.logger.error("SVN Exception",e); ***REMOVED*** ***REMOVED*** diff --git a/src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/util/CheckMethod.java b/src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/util/CheckMethod.java index 40302e6..52ffbdb 100644 --- a/src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/util/CheckMethod.java +++ b/src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/util/CheckMethod.java @@ -81,7 +81,6 @@ public abstract class CheckMethod ***REMOVED*** String operatorName = line.substring(line.indexOf(">") + 1); operatorName = operatorName.substring(0, operatorName.indexOf("<")); this.logger.debug("Operator "+operatorName); - System.out.println(" " + operatorName); URL innerRequestURL = new URL(baseDescriptionRequest + operatorName); BufferedReader innerBufferedReader = new BufferedReader( new InputStreamReader(innerRequestURL.openStream())); @@ -225,12 +224,9 @@ public abstract class CheckMethod ***REMOVED*** session.connect(); Channel channel = session.openChannel(SFTP_PROTOCOL); channel.connect(); - System.out.println("shell channel connected...."); - + this.logger.debug("shell channel connected...."); ChannelSftp c = (ChannelSftp) channel; - - - System.out.println(path); + this.logger.debug(path); try ***REMOVED*** c.lstat(path); diff --git a/src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/util/CheckPermission.java b/src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/util/CheckPermission.java index 269924e..e201384 100644 --- a/src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/util/CheckPermission.java +++ b/src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/util/CheckPermission.java @@ -4,21 +4,24 @@ import static org.gcube.common.authorization.client.Constants.authorizationServi ***REMOVED*** import org.gcube.common.authorization.library.AuthorizationEntry; +***REMOVED*** +***REMOVED*** public class CheckPermission ***REMOVED*** - public CheckPermission() ***REMOVED*** -***REMOVED*** + private static final Logger logger = LoggerFactory.getLogger(CheckPermission.class); + - public static boolean apply(String VREToken, String vre) throws ObjectNotFound, Exception ***REMOVED*** - + + public static boolean apply(String VREToken, String vre) throws ObjectNotFound, Exception + ***REMOVED*** AuthorizationEntry entry = authorizationService().get(VREToken); if (entry.getContext().equals(vre)) ***REMOVED*** - System.out.println("Authorization OK!"); + logger.info("Authorization OK!"); return true; ***REMOVED*** - System.out.println("Not a valid token recognized for the VRE: "+vre); + logger.info("Not a valid token recognized for the VRE: "+vre); return false; ***REMOVED*** diff --git a/src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/util/SVNUpdater.java b/src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/util/SVNUpdater.java index fd2d885..2fde62c 100644 --- a/src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/util/SVNUpdater.java +++ b/src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/util/SVNUpdater.java @@ -310,7 +310,7 @@ public abstract class SVNUpdater ***REMOVED*** sb.append("none | "); sb.append(this.getTimeZone() + " | "); - System.out.println("Algo details: "+sb.toString()); + this.logger.info("Algo details: "+sb.toString()); return sb.toString(); ***REMOVED*** @@ -419,7 +419,7 @@ public abstract class SVNUpdater ***REMOVED*** boolean check = false; try ***REMOVED*** - System.out.println("Checking dependencies list: " + file); + this.logger.info("Checking dependencies list: " + file); final ByteArrayOutputStream byteArrayOutputStream = new ByteArrayOutputStream(); svnRepository.getFile(file, SVNRepository.INVALID_REVISION, null, byteArrayOutputStream); String lines[] = byteArrayOutputStream.toString().split("\\r?\\n"); @@ -448,8 +448,10 @@ public abstract class SVNUpdater ***REMOVED*** ***REMOVED*** ***REMOVED*** ***REMOVED*** ***REMOVED*** - ***REMOVED*** catch (Exception a) ***REMOVED*** - a.getMessage(); + ***REMOVED*** catch (Exception a) + ***REMOVED*** + this.logger.error(a.getMessage(),a); + ***REMOVED*** return check; @@ -458,7 +460,7 @@ public abstract class SVNUpdater ***REMOVED*** public void updateSVN(String file, Collection deps) ***REMOVED*** try ***REMOVED*** - System.out.println("Updating dependencies list: " + file); + this.logger.info("Updating dependencies list: " + file); final ByteArrayOutputStream byteArrayOutputStream = new ByteArrayOutputStream(); svnRepository.getFile(file, SVNRepository.INVALID_REVISION, null, byteArrayOutputStream); @@ -537,7 +539,7 @@ public abstract class SVNUpdater ***REMOVED*** Date fromDate = formatter.parse(cal.getTime().toString()); TimeZone central = TimeZone.getTimeZone("UTC"); formatter.setTimeZone(central); - System.out.println(formatter.format(fromDate)); + this.logger.info(formatter.format(fromDate)); return formatter.format(fromDate); ***REMOVED*** diff --git a/src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/util/SendMail.java b/src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/util/SendMail.java index 7b65ecb..bca5b83 100644 --- a/src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/util/SendMail.java +++ b/src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/util/SendMail.java @@ -209,7 +209,7 @@ public class SendMail ***REMOVED*** HttpGet getReq = new HttpGet(serviceAddress); getReq.setHeader("accept", JSON_MIME_TYPE); getReq.setHeader("content-type", JSON_MIME_TYPE); - System.out.println(EntityUtils.toString(client.execute(getReq).getEntity())); + this.logger.info(EntityUtils.toString(client.execute(getReq).getEntity())); return EntityUtils.toString(client.execute(getReq).getEntity());