gCubeSystem
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dataminer-pool-manager
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Removed sensitive data

This commit is contained in:
Giancarlo Panichi 2023-01-18 17:56:48 +01:00
parent 65ef56ad78
commit a5667a7c57
100 changed files with 2884 additions and 2639 deletions
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8
.settings/org.eclipse.core.resources.prefs
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@ -1,6 +1,6 @@
eclipse.preferences.version=1 eclipse.preferences.version=1
encoding***REMOVED***src/main/java=UTF-8 encoding//src/main/java=UTF-8
encoding***REMOVED***src/main/resources=UTF-8 encoding//src/main/resources=UTF-8
encoding***REMOVED***src/test/java=UTF-8 encoding//src/test/java=UTF-8
encoding***REMOVED***src/test/resources=UTF-8 encoding//src/test/resources=UTF-8
encoding/<project>=UTF-8 encoding/<project>=UTF-8

2
CHANGELOG.md
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@ -55,4 +55,4 @@
- First Release - First Release
This project adheres to [Semantic Versioning](https:***REMOVED***semver.org/spec/v2.0.0.html). This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).

38
FUNDING.md
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@ -3,24 +3,24 @@
The projects leading to this software have received funding from a series of European Union programmes including: The projects leading to this software have received funding from a series of European Union programmes including:
- the Sixth Framework Programme for Research and Technological Development - the Sixth Framework Programme for Research and Technological Development
- [DILIGENT](https:***REMOVED***cordis.europa.eu/project/id/004260) (grant no. 004260). - [DILIGENT](https://cordis.europa.eu/project/id/004260) (grant no. 004260).
- the Seventh Framework Programme for research, technological development and demonstration - the Seventh Framework Programme for research, technological development and demonstration
- [D4Science](https:***REMOVED***cordis.europa.eu/project/id/212488) (grant no. 212488); - [D4Science](https://cordis.europa.eu/project/id/212488) (grant no. 212488);
- [D4Science-II](https:***REMOVED***cordis.europa.eu/project/id/239019) (grant no.239019); - [D4Science-II](https://cordis.europa.eu/project/id/239019) (grant no.239019);
- [ENVRI](https:***REMOVED***cordis.europa.eu/project/id/283465) (grant no. 283465); - [ENVRI](https://cordis.europa.eu/project/id/283465) (grant no. 283465);
- [iMarine](https:***REMOVED***cordis.europa.eu/project/id/283644) (grant no. 283644); - [iMarine](https://cordis.europa.eu/project/id/283644) (grant no. 283644);
- [EUBrazilOpenBio](https:***REMOVED***cordis.europa.eu/project/id/288754) (grant no. 288754). - [EUBrazilOpenBio](https://cordis.europa.eu/project/id/288754) (grant no. 288754).
- the H2020 research and innovation programme - the H2020 research and innovation programme
- [SoBigData](https:***REMOVED***cordis.europa.eu/project/id/654024) (grant no. 654024); - [SoBigData](https://cordis.europa.eu/project/id/654024) (grant no. 654024);
- [PARTHENOS](https:***REMOVED***cordis.europa.eu/project/id/654119) (grant no. 654119); - [PARTHENOS](https://cordis.europa.eu/project/id/654119) (grant no. 654119);
- [EGI-Engage](https:***REMOVED***cordis.europa.eu/project/id/654142) (grant no. 654142); - [EGI-Engage](https://cordis.europa.eu/project/id/654142) (grant no. 654142);
- [ENVRI PLUS](https:***REMOVED***cordis.europa.eu/project/id/654182) (grant no. 654182); - [ENVRI PLUS](https://cordis.europa.eu/project/id/654182) (grant no. 654182);
- [BlueBRIDGE](https:***REMOVED***cordis.europa.eu/project/id/675680) (grant no. 675680); - [BlueBRIDGE](https://cordis.europa.eu/project/id/675680) (grant no. 675680);
- [PerformFISH](https:***REMOVED***cordis.europa.eu/project/id/727610) (grant no. 727610); - [PerformFISH](https://cordis.europa.eu/project/id/727610) (grant no. 727610);
- [AGINFRA PLUS](https:***REMOVED***cordis.europa.eu/project/id/731001) (grant no. 731001); - [AGINFRA PLUS](https://cordis.europa.eu/project/id/731001) (grant no. 731001);
- [DESIRA](https:***REMOVED***cordis.europa.eu/project/id/818194) (grant no. 818194); - [DESIRA](https://cordis.europa.eu/project/id/818194) (grant no. 818194);
- [ARIADNEplus](https:***REMOVED***cordis.europa.eu/project/id/823914) (grant no. 823914); - [ARIADNEplus](https://cordis.europa.eu/project/id/823914) (grant no. 823914);
- [RISIS 2](https:***REMOVED***cordis.europa.eu/project/id/824091) (grant no. 824091); - [RISIS 2](https://cordis.europa.eu/project/id/824091) (grant no. 824091);
- [EOSC-Pillar](https:***REMOVED***cordis.europa.eu/project/id/857650) (grant no. 857650); - [EOSC-Pillar](https://cordis.europa.eu/project/id/857650) (grant no. 857650);
- [Blue Cloud](https:***REMOVED***cordis.europa.eu/project/id/862409) (grant no. 862409); - [Blue Cloud](https://cordis.europa.eu/project/id/862409) (grant no. 862409);
- [SoBigData-PlusPlus](https:***REMOVED***cordis.europa.eu/project/id/871042) (grant no. 871042); - [SoBigData-PlusPlus](https://cordis.europa.eu/project/id/871042) (grant no. 871042);

14
README.md
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@ -8,12 +8,12 @@ DataMiner Pool Manager is a service to support the integration of algorithms in
## Built With ## Built With
* [OpenJDK](https:***REMOVED***openjdk.java.net/) - The JDK used * [OpenJDK](https://openjdk.java.net/) - The JDK used
* [Maven](https:***REMOVED***maven.apache.org/) - Dependency Management * [Maven](https://maven.apache.org/) - Dependency Management
## Documentation ## Documentation
* Use of this widget is is described on [Wiki](https:***REMOVED***wiki.gcube-system.org/gcube/How_to_use_the_DataMiner_Pool_Manager). * Use of this widget is is described on [Wiki](https://wiki.gcube-system.org/gcube/How_to_use_the_DataMiner_Pool_Manager).
## Change log ## Change log
@ -21,9 +21,9 @@ See [CHANGELOG.md](CHANGELOG.md).
## Authors ## Authors
* **Paolo Fabriani** - [Engineering Ingegneria Informatica S.p.A., Italy](https:***REMOVED***www.eng.it/) * **Paolo Fabriani** - [Engineering Ingegneria Informatica S.p.A., Italy](https://www.eng.it/)
* **Nunzio Andrea Galante** - [Engineering Ingegneria Informatica S.p.A., Italy](https:***REMOVED***www.eng.it/) * **Nunzio Andrea Galante** - [Engineering Ingegneria Informatica S.p.A., Italy](https://www.eng.it/)
* **Ciro Formisano** - [Engineering Ingegneria Informatica S.p.A., Italy](https:***REMOVED***www.eng.it/) * **Ciro Formisano** - [Engineering Ingegneria Informatica S.p.A., Italy](https://www.eng.it/)
## License ## License
@ -32,7 +32,7 @@ This project is licensed under the EUPL V.1.1 License - see the [LICENSE.md](LIC
## About the gCube Framework ## About the gCube Framework
This software is part of the [gCubeFramework](https:***REMOVED***www.gcube-system.org/ "gCubeFramework"): an This software is part of the [gCubeFramework](https://www.gcube-system.org/ "gCubeFramework"): an
open-source software toolkit used for building and operating Hybrid Data open-source software toolkit used for building and operating Hybrid Data
Infrastructures enabling the dynamic deployment of Virtual Research Environments Infrastructures enabling the dynamic deployment of Virtual Research Environments
by favouring the realisation of reuse oriented policies. by favouring the realisation of reuse oriented policies.

10
descriptor.xml
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@ -1,7 +1,7 @@
<assembly <assembly
xmlns="http:***REMOVED***maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.0" xmlns="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.0"
xmlns:xsi="http:***REMOVED***www.w3.org/2001/XMLSchema-instance" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http:***REMOVED***maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.0 http:***REMOVED***maven.apache.org/xsd/assembly-1.1.0.xsd"> xsi:schemaLocation="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.0 http://maven.apache.org/xsd/assembly-1.1.0.xsd">
<id>servicearchive</id> <id>servicearchive</id>
<formats> <formats>
<format>tar.gz</format> <format>tar.gz</format>
@ -24,8 +24,8 @@
</fileSets> </fileSets>
<files> <files>
<file> <file>
<source>target/$***REMOVED***build.finalName***REMOVED***.$***REMOVED***project.packaging***REMOVED***</source> <source>target/${build.finalName}.${project.packaging}</source>
<outputDirectory>/$***REMOVED***artifactId***REMOVED***</outputDirectory> <outputDirectory>/${artifactId}</outputDirectory>
</file> </file>
</files> </files>
</assembly> </assembly>

8
gcube-app.xml
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@ -1,9 +1,9 @@
<?xml version="1.0" encoding="UTF-8"?> <?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE xml> <!DOCTYPE xml>
<application mode="online"> <application mode="online">
<name>$***REMOVED***serviceName***REMOVED***</name> <name>${serviceName}</name>
<group>$***REMOVED***serviceClass***REMOVED***</group> <group>${serviceClass}</group>
<version>$***REMOVED***version***REMOVED***</version> <version>${version}</version>
<description>$***REMOVED***description***REMOVED***</description> <description>${description}</description>
<exclude>/api/swagger.*</exclude> <exclude>/api/swagger.*</exclude>
</application> </application>

18
pom.xml
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@ -1,5 +1,5 @@
<project xmlns="http:***REMOVED***maven.apache.org/POM/4.0.0" xmlns:xsi="http:***REMOVED***www.w3.org/2001/XMLSchema-instance" <project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http:***REMOVED***maven.apache.org/POM/4.0.0 http:***REMOVED***maven.apache.org/xsd/maven-4.0.0.xsd"> xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion> <modelVersion>4.0.0</modelVersion>
<parent> <parent>
@ -18,9 +18,9 @@
<description>DataMiner Pool Manager is a service to support the integration of algorithms in D4Science Infrastructure</description> <description>DataMiner Pool Manager is a service to support the integration of algorithms in D4Science Infrastructure</description>
<scm> <scm>
<connection>scm:git:https:***REMOVED***code-repo.d4science.org/gCubeSystem/$***REMOVED***project.artifactId***REMOVED***.git</connection> <connection>scm:git:https://code-repo.d4science.org/gCubeSystem/${project.artifactId}.git</connection>
<developerConnection>scm:git:https:***REMOVED***code-repo.d4science.org/gCubeSystem/$***REMOVED***project.artifactId***REMOVED***.git</developerConnection> <developerConnection>scm:git:https://code-repo.d4science.org/gCubeSystem/${project.artifactId}.git</developerConnection>
<url>https:***REMOVED***code-repo.d4science.org/gCubeSystem/$***REMOVED***project.artifactId***REMOVED***</url> <url>https://code-repo.d4science.org/gCubeSystem/${project.artifactId}</url>
</scm> </scm>
@ -28,7 +28,7 @@
<serviceName>dataminer-pool-manager</serviceName> <serviceName>dataminer-pool-manager</serviceName>
<serviceClass>DataAnalysis</serviceClass> <serviceClass>DataAnalysis</serviceClass>
<webappDirectory>$***REMOVED***project.basedir***REMOVED***/src/main/webapp/WEB-INF</webappDirectory> <webappDirectory>${project.basedir}/src/main/webapp/WEB-INF</webappDirectory>
<distroDirectory>distro</distroDirectory> <distroDirectory>distro</distroDirectory>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding> <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<version.swagger>1.5.13</version.swagger> <version.swagger>1.5.13</version.swagger>
@ -103,7 +103,7 @@
<version>1.10</version> <version>1.10</version>
</dependency> </dependency>
<!-- https:***REMOVED***mvnrepository.com/artifact/com.jcraft/jsch --> <!-- https://mvnrepository.com/artifact/com.jcraft/jsch -->
<dependency> <dependency>
<groupId>com.jcraft</groupId> <groupId>com.jcraft</groupId>
<artifactId>jsch</artifactId> <artifactId>jsch</artifactId>
@ -172,10 +172,10 @@
</goals> </goals>
<phase>process-resources</phase> <phase>process-resources</phase>
<configuration> <configuration>
<outputDirectory>$***REMOVED***webappDirectory***REMOVED***</outputDirectory> <outputDirectory>${webappDirectory}</outputDirectory>
<resources> <resources>
<resource> <resource>
<directory>$***REMOVED***project.basedir***REMOVED***</directory> <directory>${project.basedir}</directory>
<filtering>true</filtering> <filtering>true</filtering>
<excludes> <excludes>
<exclude>src</exclude> <exclude>src</exclude>

18
profile.xml
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@ -1,23 +1,23 @@
<?xml version="1.0" encoding="UTF-8"?> <?xml version="1.0" encoding="UTF-8"?>
<Resource xmlns:xsi="http:***REMOVED***www.w3.org/2001/XMLSchema-instance"> <Resource xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
<ID /> <ID />
<Type>Service</Type> <Type>Service</Type>
<Profile> <Profile>
<Description>$***REMOVED***description***REMOVED***</Description> <Description>${description}</Description>
<Class>DataminerPoolManager</Class> <Class>DataminerPoolManager</Class>
<Name>$***REMOVED***artifactId***REMOVED***</Name> <Name>${artifactId}</Name>
<Version>1.0.0</Version> <Version>1.0.0</Version>
<Packages> <Packages>
<Software> <Software>
<Name>$***REMOVED***artifactId***REMOVED***</Name> <Name>${artifactId}</Name>
<Version>$***REMOVED***version***REMOVED***</Version> <Version>${version}</Version>
<MavenCoordinates> <MavenCoordinates>
<groupId>$***REMOVED***groupId***REMOVED***</groupId> <groupId>${groupId}</groupId>
<artifactId>$***REMOVED***artifactId***REMOVED***</artifactId> <artifactId>${artifactId}</artifactId>
<version>$***REMOVED***version***REMOVED***</version> <version>${version}</version>
</MavenCoordinates> </MavenCoordinates>
<Files> <Files>
<File>$***REMOVED***build.finalName***REMOVED***.jar</File> <File>${build.finalName}.jar</File>
</Files> </Files>
</Software> </Software>
</Packages> </Packages>

98
src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/ansible/AnsibleWorker.java
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@ -1,7 +1,7 @@
package org.gcube.dataanalysis.dataminer.poolmanager.ansible; package org.gcube.dataanalysis.dataminer.poolmanager.ansible;
import java.io.File; import java.io.File;
***REMOVED*** import java.io.IOException;
import java.io.InputStream; import java.io.InputStream;
import java.io.PrintStream; import java.io.PrintStream;
import java.util.Scanner; import java.util.Scanner;
@ -10,7 +10,7 @@ import org.gcube.dataanalysis.dataminer.poolmanager.ansible.model.Inventory;
import org.gcube.dataanalysis.dataminer.poolmanager.ansible.model.Playbook; import org.gcube.dataanalysis.dataminer.poolmanager.ansible.model.Playbook;
import org.gcube.dataanalysis.dataminer.poolmanager.ansible.model.Role; import org.gcube.dataanalysis.dataminer.poolmanager.ansible.model.Role;
import org.gcube.dataanalysis.dataminer.poolmanager.ansiblebridge.AnsibleSerializeHelper; import org.gcube.dataanalysis.dataminer.poolmanager.ansiblebridge.AnsibleSerializeHelper;
***REMOVED*** import org.tmatesoft.svn.core.SVNException;
/** /**
* This class is responsible for the interface with ansible, retrieving log, * This class is responsible for the interface with ansible, retrieving log,
@ -20,7 +20,7 @@ import org.gcube.dataanalysis.dataminer.poolmanager.ansiblebridge.AnsibleSeriali
* @author paolo * @author paolo
* *
*/ */
public class AnsibleWorker ***REMOVED*** public class AnsibleWorker {
/** /**
* The name of the inventory * The name of the inventory
@ -42,99 +42,99 @@ public class AnsibleWorker ***REMOVED***
*/ */
private File workerRoot; private File workerRoot;
public AnsibleWorker(File root) ***REMOVED*** public AnsibleWorker(File root) {
this.workerRoot = root; this.workerRoot = root;
this.ensureWorkStructure(); this.ensureWorkStructure();
***REMOVED*** }
***REMOVED*** public File getWorkdir() ***REMOVED*** // public File getWorkdir() {
***REMOVED*** return this.workerRoot; // return this.workerRoot;
***REMOVED*** ***REMOVED*** // }
public File getRolesDir() ***REMOVED*** public File getRolesDir() {
return new File(this.workerRoot, ROLES_DIR); return new File(this.workerRoot, ROLES_DIR);
***REMOVED*** }
public String getWorkerId() ***REMOVED*** public String getWorkerId() {
return this.workerRoot.getName(); return this.workerRoot.getName();
***REMOVED*** }
public void ensureWorkStructure() ***REMOVED*** public void ensureWorkStructure() {
***REMOVED*** generate root // generate root
this.workerRoot.mkdirs(); this.workerRoot.mkdirs();
***REMOVED*** }
public void removeWorkStructure() ***REMOVED*** public void removeWorkStructure() {
***REMOVED*** remove the working dir // remove the working dir
this.workerRoot.delete(); this.workerRoot.delete();
***REMOVED*** }
public File getPlaybookFile() ***REMOVED*** public File getPlaybookFile() {
return new File(this.workerRoot, PLAYBOOK_NAME); return new File(this.workerRoot, PLAYBOOK_NAME);
***REMOVED*** }
public File getInventoryFile() ***REMOVED*** public File getInventoryFile() {
return new File(this.workerRoot, INVENTORY_NAME); return new File(this.workerRoot, INVENTORY_NAME);
***REMOVED*** }
public void setInventory(Inventory inventory) throws IOException ***REMOVED*** public void setInventory(Inventory inventory) throws IOException {
***REMOVED*** serialize the string to the 'inventory' file // serialize the string to the 'inventory' file
AnsibleSerializeHelper.serialize(inventory, this.getInventoryFile()); AnsibleSerializeHelper.serialize(inventory, this.getInventoryFile());
***REMOVED*** }
public void setPlaybook(Playbook playbook) throws IOException ***REMOVED*** public void setPlaybook(Playbook playbook) throws IOException {
***REMOVED*** serialize the string to the 'playbook' file // serialize the string to the 'playbook' file
AnsibleSerializeHelper.serialize(playbook, this.getPlaybookFile()); AnsibleSerializeHelper.serialize(playbook, this.getPlaybookFile());
***REMOVED*** }
public void addRole(Role r) throws IOException ***REMOVED*** public void addRole(Role r) throws IOException {
***REMOVED*** Serialize role in the workdir // Serialize role in the workdir
AnsibleSerializeHelper.serializeRole(r, this.getRolesDir()); AnsibleSerializeHelper.serializeRole(r, this.getRolesDir());
***REMOVED*** }
public int execute(PrintStream ps) public int execute(PrintStream ps)
throws IOException, InterruptedException, SVNException ***REMOVED*** throws IOException, InterruptedException, SVNException {
System.out.println(this.workerRoot); System.out.println(this.workerRoot);
try ***REMOVED*** try {
Process p = Runtime.getRuntime().exec("ansible-playbook -v -i " + this.getInventoryFile().getAbsolutePath() Process p = Runtime.getRuntime().exec("ansible-playbook -v -i " + this.getInventoryFile().getAbsolutePath()
+ " " + this.getPlaybookFile().getAbsolutePath()); + " " + this.getPlaybookFile().getAbsolutePath());
inheritIO(p.getInputStream(), ps); inheritIO(p.getInputStream(), ps);
inheritIO(p.getErrorStream(), ps); inheritIO(p.getErrorStream(), ps);
***REMOVED*** writer.println(this.getStatus(p.waitFor())); // writer.println(this.getStatus(p.waitFor()));
***REMOVED*** writer.close(); // writer.close();
return p.waitFor(); return p.waitFor();
***REMOVED*** catch (IOException e) ***REMOVED*** } catch (IOException e) {
e.printStackTrace(); e.printStackTrace();
***REMOVED*** }
return -1; return -1;
***REMOVED*** }
private static void inheritIO(final InputStream src, final PrintStream dest) ***REMOVED*** private static void inheritIO(final InputStream src, final PrintStream dest) {
new Thread(new Runnable() ***REMOVED*** new Thread(new Runnable() {
public void run() ***REMOVED*** public void run() {
Scanner sc = new Scanner(src); Scanner sc = new Scanner(src);
while (sc.hasNextLine()) ***REMOVED*** while (sc.hasNextLine()) {
dest.println(sc.nextLine()); dest.println(sc.nextLine());
***REMOVED*** }
sc.close(); sc.close();
***REMOVED*** }
***REMOVED***).start(); }).start();
***REMOVED*** }
/** /**
* Destroy the worker: * Destroy the worker:
* - remove the working dir * - remove the working dir
*/ */
public void destroy() ***REMOVED*** public void destroy() {
this.removeWorkStructure(); this.removeWorkStructure();
***REMOVED*** }
***REMOVED*** }

16
src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/ansible/model/AnsibleHost.java
View File

@ -1,19 +1,19 @@
package org.gcube.dataanalysis.dataminer.poolmanager.ansible.model; package org.gcube.dataanalysis.dataminer.poolmanager.ansible.model;
public class AnsibleHost ***REMOVED*** public class AnsibleHost {
private String name; private String name;
public AnsibleHost(String name) ***REMOVED*** public AnsibleHost(String name) {
this.name = name; this.name = name;
***REMOVED*** }
public String getName() ***REMOVED*** public String getName() {
return name; return name;
***REMOVED*** }
public void setName(String name) ***REMOVED*** public void setName(String name) {
this.name = name; this.name = name;
***REMOVED*** }
***REMOVED*** }

20
src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/ansible/model/HostGroup.java
View File

@ -3,27 +3,27 @@ package org.gcube.dataanalysis.dataminer.poolmanager.ansible.model;
import java.util.Collection; import java.util.Collection;
import java.util.Vector; import java.util.Vector;
public class HostGroup ***REMOVED*** public class HostGroup {
private String name; private String name;
private Collection<AnsibleHost> hosts; private Collection<AnsibleHost> hosts;
public HostGroup(String name) ***REMOVED*** public HostGroup(String name) {
this.name = name; this.name = name;
this.hosts = new Vector<>(); this.hosts = new Vector<>();
***REMOVED*** }
public void addHost(AnsibleHost h) ***REMOVED*** public void addHost(AnsibleHost h) {
this.hosts.add(h); this.hosts.add(h);
***REMOVED*** }
public String getName() ***REMOVED*** public String getName() {
return this.name; return this.name;
***REMOVED*** }
public Collection<AnsibleHost> getHosts() ***REMOVED*** public Collection<AnsibleHost> getHosts() {
return new Vector<>(this.hosts); return new Vector<>(this.hosts);
***REMOVED*** }
***REMOVED*** }

32
src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/ansible/model/Inventory.java
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@ -3,35 +3,35 @@ package org.gcube.dataanalysis.dataminer.poolmanager.ansible.model;
import java.util.Collection; import java.util.Collection;
import java.util.Vector; import java.util.Vector;
public class Inventory ***REMOVED*** public class Inventory {
private Collection<HostGroup> groups; private Collection<HostGroup> groups;
public Inventory() ***REMOVED*** public Inventory() {
this.groups = new Vector<>(); this.groups = new Vector<>();
***REMOVED*** }
public void addGroup(HostGroup group) ***REMOVED*** public void addGroup(HostGroup group) {
this.groups.add(group); this.groups.add(group);
***REMOVED*** }
public void addHost(AnsibleHost h, String groupName) ***REMOVED*** public void addHost(AnsibleHost h, String groupName) {
this.getGroup(groupName).addHost(h); this.getGroup(groupName).addHost(h);
***REMOVED*** }
private HostGroup getGroup(String groupName) ***REMOVED*** private HostGroup getGroup(String groupName) {
for (HostGroup hg : this.groups) ***REMOVED*** for (HostGroup hg : this.groups) {
if (groupName.equals(hg.getName())) ***REMOVED*** if (groupName.equals(hg.getName())) {
return hg; return hg;
***REMOVED*** }
***REMOVED*** }
HostGroup hg = new HostGroup(groupName); HostGroup hg = new HostGroup(groupName);
this.groups.add(hg); this.groups.add(hg);
return hg; return hg;
***REMOVED*** }
public Collection<HostGroup> getHostGroups() ***REMOVED*** public Collection<HostGroup> getHostGroups() {
return new Vector<>(this.groups); return new Vector<>(this.groups);
***REMOVED*** }
***REMOVED*** }

42
src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/ansible/model/Playbook.java
View File

@ -1,9 +1,9 @@
package org.gcube.dataanalysis.dataminer.poolmanager.ansible.model; package org.gcube.dataanalysis.dataminer.poolmanager.ansible.model;
***REMOVED*** import java.util.List;
import java.util.Vector; import java.util.Vector;
public class Playbook ***REMOVED*** public class Playbook {
private String hostGroupName; private String hostGroupName;
@ -11,40 +11,40 @@ public class Playbook ***REMOVED***
private String remote_user; private String remote_user;
public Playbook() ***REMOVED*** public Playbook() {
this.roles = new Vector<>(); this.roles = new Vector<>();
***REMOVED*** }
public void addRole(String role) ***REMOVED*** public void addRole(String role) {
roles.add(role); roles.add(role);
***REMOVED*** }
public void applyTo(String hostGroupName) ***REMOVED*** public void applyTo(String hostGroupName) {
this.hostGroupName = hostGroupName; this.hostGroupName = hostGroupName;
***REMOVED*** }
public String getHostGroupName() ***REMOVED*** public String getHostGroupName() {
return hostGroupName; return hostGroupName;
***REMOVED*** }
public List<String> getRoles() ***REMOVED*** public List<String> getRoles() {
return new Vector<>(roles); return new Vector<>(roles);
***REMOVED*** }
public String getRemote_user() ***REMOVED*** public String getRemote_user() {
return remote_user; return remote_user;
***REMOVED*** }
public void setRemote_user(String remote_user) ***REMOVED*** public void setRemote_user(String remote_user) {
this.remote_user = remote_user; this.remote_user = remote_user;
***REMOVED*** }
public void setHostGroupName(String hostGroupName) ***REMOVED*** public void setHostGroupName(String hostGroupName) {
this.hostGroupName = hostGroupName; this.hostGroupName = hostGroupName;
***REMOVED*** }
public void setRoles(List<String> roles) ***REMOVED*** public void setRoles(List<String> roles) {
this.roles = roles; this.roles = roles;
***REMOVED*** }
***REMOVED*** }

36
src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/ansible/model/Role.java
View File

@ -3,7 +3,7 @@ package org.gcube.dataanalysis.dataminer.poolmanager.ansible.model;
import java.util.Collection; import java.util.Collection;
import java.util.Vector; import java.util.Vector;
public class Role ***REMOVED*** public class Role {
/** /**
* The name of the role * The name of the role
@ -14,38 +14,38 @@ public class Role ***REMOVED***
private Collection<RoleFile> meta; private Collection<RoleFile> meta;
public Role() ***REMOVED*** public Role() {
this.tasks = new Vector<>(); this.tasks = new Vector<>();
this.meta = new Vector<>(); this.meta = new Vector<>();
***REMOVED*** }
public Role(String name) ***REMOVED*** public Role(String name) {
this(); this();
this.name = name; this.name = name;
***REMOVED*** }
public void addTaskFile(RoleFile tf) ***REMOVED*** public void addTaskFile(RoleFile tf) {
this.tasks.add(tf); this.tasks.add(tf);
***REMOVED*** }
public void addMeta(RoleFile tf) ***REMOVED*** public void addMeta(RoleFile tf) {
this.meta.add(tf); this.meta.add(tf);
***REMOVED*** }
public String getName() ***REMOVED*** public String getName() {
return name; return name;
***REMOVED*** }
public void setName(String name) ***REMOVED*** public void setName(String name) {
this.name = name; this.name = name;
***REMOVED*** }
public Collection<RoleFile> getTaskFiles() ***REMOVED*** public Collection<RoleFile> getTaskFiles() {
return new Vector<>(this.tasks); return new Vector<>(this.tasks);
***REMOVED*** }
public Collection<RoleFile> getMeta() ***REMOVED*** public Collection<RoleFile> getMeta() {
return new Vector<>(this.meta); return new Vector<>(this.meta);
***REMOVED*** }
***REMOVED*** }

36
src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/ansible/model/RoleFile.java
View File

@ -1,6 +1,6 @@
package org.gcube.dataanalysis.dataminer.poolmanager.ansible.model; package org.gcube.dataanalysis.dataminer.poolmanager.ansible.model;
public class RoleFile ***REMOVED*** public class RoleFile {
/** /**
* The path to the file, starting from the role root * The path to the file, starting from the role root
@ -18,37 +18,37 @@ public class RoleFile ***REMOVED***
*/ */
private String content; private String content;
public RoleFile() ***REMOVED*** public RoleFile() {
***REMOVED*** }
public RoleFile(String name, String content) ***REMOVED*** public RoleFile(String name, String content) {
this(); this();
this.setName(name); this.setName(name);
this.setContent(content); this.setContent(content);
***REMOVED*** }
public String getName() ***REMOVED*** public String getName() {
return name; return name;
***REMOVED*** }
public void setName(String name) ***REMOVED*** public void setName(String name) {
this.name = name; this.name = name;
***REMOVED*** }
public String getContent() ***REMOVED*** public String getContent() {
return content; return content;
***REMOVED*** }
public void setContent(String content) ***REMOVED*** public void setContent(String content) {
this.content = content; this.content = content;
***REMOVED*** }
public String getPath() ***REMOVED*** public String getPath() {
return path; return path;
***REMOVED*** }
public void setPath(String path) ***REMOVED*** public void setPath(String path) {
this.path = path; this.path = path;
***REMOVED*** }
***REMOVED*** }

394
src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/ansiblebridge/AnsibleBridge.java
View File

@ -1,11 +1,11 @@
package org.gcube.dataanalysis.dataminer.poolmanager.ansiblebridge; package org.gcube.dataanalysis.dataminer.poolmanager.ansiblebridge;
import java.io.File; import java.io.File;
***REMOVED*** import java.io.IOException;
import java.util.Collection; import java.util.Collection;
***REMOVED*** import java.util.List;
import java.util.Map; import java.util.Map;
***REMOVED*** import java.util.Set;
import java.util.TreeMap; import java.util.TreeMap;
import java.util.TreeSet; import java.util.TreeSet;
import java.util.UUID; import java.util.UUID;
@ -23,302 +23,302 @@ import org.gcube.dataanalysis.dataminer.poolmanager.ansiblebridge.template.Custo
import org.gcube.dataanalysis.dataminer.poolmanager.ansiblebridge.template.OSDependencyPackage; import org.gcube.dataanalysis.dataminer.poolmanager.ansiblebridge.template.OSDependencyPackage;
import org.gcube.dataanalysis.dataminer.poolmanager.ansiblebridge.template.StaticRoleManager; import org.gcube.dataanalysis.dataminer.poolmanager.ansiblebridge.template.StaticRoleManager;
import org.gcube.dataanalysis.dataminer.poolmanager.ansiblebridge.template.TemplateManager; import org.gcube.dataanalysis.dataminer.poolmanager.ansiblebridge.template.TemplateManager;
***REMOVED*** import org.gcube.dataanalysis.dataminer.poolmanager.datamodel.Algorithm;
import org.gcube.dataanalysis.dataminer.poolmanager.datamodel.AlgorithmSet; import org.gcube.dataanalysis.dataminer.poolmanager.datamodel.AlgorithmSet;
import org.gcube.dataanalysis.dataminer.poolmanager.datamodel.Cluster; import org.gcube.dataanalysis.dataminer.poolmanager.datamodel.Cluster;
import org.gcube.dataanalysis.dataminer.poolmanager.datamodel.Dependency; import org.gcube.dataanalysis.dataminer.poolmanager.datamodel.Dependency;
import org.gcube.dataanalysis.dataminer.poolmanager.datamodel.Host; import org.gcube.dataanalysis.dataminer.poolmanager.datamodel.Host;
import org.gcube.dataanalysis.dataminer.poolmanager.datamodel.comparator.HostComparator; import org.gcube.dataanalysis.dataminer.poolmanager.datamodel.comparator.HostComparator;
public class AnsibleBridge ***REMOVED*** public class AnsibleBridge {
***REMOVED*** private static final org.slf4j.Logger LOGGER = // private static final org.slf4j.Logger LOGGER =
***REMOVED*** LoggerFactory.getLogger(AnsibleBridge.class); // LoggerFactory.getLogger(AnsibleBridge.class);
private String dpmRoot; private String dpmRoot;
***REMOVED*** public AnsibleBridge() ***REMOVED*** // public AnsibleBridge() {
***REMOVED*** this(System.getProperty("user.home")+File.separator+"dataminer-pool-manager"); // this(System.getProperty("user.home")+File.separator+"dataminer-pool-manager");
***REMOVED*** ***REMOVED***this(System.getProperty("/home/gcube/dataminer-pool-manager")); // //this(System.getProperty("/home/gcube/dataminer-pool-manager"));
***REMOVED*** //
***REMOVED*** ***REMOVED*** // }
public AnsibleBridge(String root) ***REMOVED*** public AnsibleBridge(String root) {
this.dpmRoot = root; this.dpmRoot = root;
this.ensureServiceRoot(); this.ensureServiceRoot();
***REMOVED*** }
private void ensureServiceRoot() ***REMOVED*** private void ensureServiceRoot() {
***REMOVED*** generate root // generate root
new File(dpmRoot).mkdirs(); new File(dpmRoot).mkdirs();
***REMOVED*** 'template' is for template roles // 'template' is for template roles
***REMOVED*** this.getTemplatesDir().mkdirs(); // this.getTemplatesDir().mkdirs();
***REMOVED*** 'static' is for custom roles // 'static' is for custom roles
***REMOVED*** this.getCustomDir().mkdirs(); // this.getCustomDir().mkdirs();
***REMOVED*** 'work' is for temporary working directories // 'work' is for temporary working directories
this.getWorkDir().mkdirs(); this.getWorkDir().mkdirs();
***REMOVED*** }
private File getWorkDir() ***REMOVED*** private File getWorkDir() {
return new File(this.dpmRoot, "work"); return new File(this.dpmRoot, "work");
***REMOVED*** }
***REMOVED*** private String getTemplatesDir() ***REMOVED*** // private String getTemplatesDir() {
***REMOVED*** String input = null; // String input = null;
***REMOVED*** input = // input =
***REMOVED*** AnsibleBridge.class.getClassLoader().getResource("templates").getPath(); // AnsibleBridge.class.getClassLoader().getResource("templates").getPath();
***REMOVED*** return input; // return input;
***REMOVED*** ***REMOVED*** // }
***REMOVED*** //
***REMOVED*** //
***REMOVED*** private String getCustomDir() ***REMOVED*** // private String getCustomDir() {
***REMOVED*** String input = null; // String input = null;
***REMOVED*** input = // input =
***REMOVED*** AnsibleBridge.class.getClassLoader().getResource("custom").getPath(); // AnsibleBridge.class.getClassLoader().getResource("custom").getPath();
***REMOVED*** return input; // return input;
***REMOVED*** ***REMOVED*** // }
public AnsibleWorker createWorker(Algorithm algorithm, Cluster dataminerCluster, public AnsibleWorker createWorker(Algorithm algorithm, Cluster dataminerCluster,
boolean includeAlgorithmDependencies, String user) throws IOException ***REMOVED*** boolean includeAlgorithmDependencies, String user) throws IOException {
File workerRoot = new File(this.getWorkDir(), UUID.randomUUID().toString()); File workerRoot = new File(this.getWorkDir(), UUID.randomUUID().toString());
AnsibleWorker worker = new AnsibleWorker(workerRoot); AnsibleWorker worker = new AnsibleWorker(workerRoot);
List<Role> algoRoles = new Vector<>(); List<Role> algoRoles = new Vector<>();
***REMOVED*** add algorithms and dependencies to the worker // add algorithms and dependencies to the worker
for (Role r : this.generateRoles(algorithm, includeAlgorithmDependencies)) ***REMOVED*** for (Role r : this.generateRoles(algorithm, includeAlgorithmDependencies)) {
algoRoles.add(r); algoRoles.add(r);
worker.addRole(r); worker.addRole(r);
***REMOVED*** }
***REMOVED*** to comment the for in case of just install algo // to comment the for in case of just install algo
if (includeAlgorithmDependencies) ***REMOVED*** if (includeAlgorithmDependencies) {
for (Dependency d : algorithm.getDependencies()) ***REMOVED*** for (Dependency d : algorithm.getDependencies()) {
for (Role r : this.generateRoles(d)) ***REMOVED*** for (Role r : this.generateRoles(d)) {
worker.addRole(r); worker.addRole(r);
***REMOVED*** }
***REMOVED*** }
***REMOVED*** }
***REMOVED*** add static roles // add static roles
for (Role r : this.getStaticRoleManager().getStaticRoles()) ***REMOVED*** for (Role r : this.getStaticRoleManager().getStaticRoles()) {
worker.addRole(r); worker.addRole(r);
***REMOVED*** }
***REMOVED*** generate the inventory // generate the inventory
Inventory inventory = new Inventory(); Inventory inventory = new Inventory();
for (Host h : dataminerCluster.getHosts()) ***REMOVED*** for (Host h : dataminerCluster.getHosts()) {
AnsibleHost ah = new AnsibleHost(h.getName()); AnsibleHost ah = new AnsibleHost(h.getName());
inventory.addHost(ah, "universe"); inventory.addHost(ah, "universe");
inventory.addHost(ah, "d4science"); inventory.addHost(ah, "d4science");
***REMOVED*** }
worker.setInventory(inventory); worker.setInventory(inventory);
***REMOVED*** generate the playbook // generate the playbook
Playbook playbook = new Playbook(); Playbook playbook = new Playbook();
playbook.setRemote_user(user); playbook.setRemote_user(user);
playbook.applyTo("universe"); playbook.applyTo("universe");
for (Role r : algoRoles) ***REMOVED*** for (Role r : algoRoles) {
***REMOVED*** add only 'add' roles // add only 'add' roles
if (!r.getName().endsWith("remove")) ***REMOVED*** if (!r.getName().endsWith("remove")) {
playbook.addRole(r.getName()); playbook.addRole(r.getName());
***REMOVED*** }
***REMOVED*** }
worker.setPlaybook(playbook); worker.setPlaybook(playbook);
return worker; return worker;
***REMOVED*** }
public void printInventoryByDomainAndSets(Collection<Cluster> clusters) ***REMOVED*** public void printInventoryByDomainAndSets(Collection<Cluster> clusters) {
Map<String, Set<Host>> inventory = new TreeMap<>(); Map<String, Set<Host>> inventory = new TreeMap<>();
for (Cluster cluster : clusters) ***REMOVED*** for (Cluster cluster : clusters) {
for (AlgorithmSet as : cluster.getAlgorithmSets()) ***REMOVED*** for (AlgorithmSet as : cluster.getAlgorithmSets()) {
String asName = as.getName(); String asName = as.getName();
for (Host h : cluster.getHosts()) ***REMOVED*** for (Host h : cluster.getHosts()) {
String domain = h.getDomain().getName(); String domain = h.getDomain().getName();
String key = String.format("[%s@%s]", asName, domain); String key = String.format("[%s@%s]", asName, domain);
Set<Host> hosts = inventory.get(key); Set<Host> hosts = inventory.get(key);
if (hosts == null) ***REMOVED*** if (hosts == null) {
hosts = new TreeSet<>(new HostComparator()); hosts = new TreeSet<>(new HostComparator());
inventory.put(key, hosts); inventory.put(key, hosts);
***REMOVED*** }
hosts.add(h); hosts.add(h);
***REMOVED*** }
***REMOVED*** }
***REMOVED*** }
for (String key : inventory.keySet()) ***REMOVED*** for (String key : inventory.keySet()) {
System.out.println(key); System.out.println(key);
Collection<Host> hosts = inventory.get(key); Collection<Host> hosts = inventory.get(key);
for (Host h : hosts) ***REMOVED*** for (Host h : hosts) {
System.out.println(h.getName() + "." + h.getDomain().getName()); System.out.println(h.getName() + "." + h.getDomain().getName());
***REMOVED*** }
System.out.println(); System.out.println();
***REMOVED*** }
***REMOVED*** }
public void printInventoryBySets(Collection<Cluster> clusters) ***REMOVED*** public void printInventoryBySets(Collection<Cluster> clusters) {
Map<String, Set<Host>> inventory = new TreeMap<>(); Map<String, Set<Host>> inventory = new TreeMap<>();
for (Cluster cluster : clusters) ***REMOVED*** for (Cluster cluster : clusters) {
for (AlgorithmSet as : cluster.getAlgorithmSets()) ***REMOVED*** for (AlgorithmSet as : cluster.getAlgorithmSets()) {
String asName = as.getName(); String asName = as.getName();
for (Host h : cluster.getHosts()) ***REMOVED*** for (Host h : cluster.getHosts()) {
String key = String.format("[%s]", asName); String key = String.format("[%s]", asName);
Set<Host> hosts = inventory.get(key); Set<Host> hosts = inventory.get(key);
if (hosts == null) ***REMOVED*** if (hosts == null) {
hosts = new TreeSet<>(new HostComparator()); hosts = new TreeSet<>(new HostComparator());
inventory.put(key, hosts); inventory.put(key, hosts);
***REMOVED*** }
hosts.add(h); hosts.add(h);
***REMOVED*** }
***REMOVED*** }
***REMOVED*** }
for (String key : inventory.keySet()) ***REMOVED*** for (String key : inventory.keySet()) {
System.out.println(key); System.out.println(key);
Collection<Host> hosts = inventory.get(key); Collection<Host> hosts = inventory.get(key);
for (Host h : hosts) ***REMOVED*** for (Host h : hosts) {
System.out.println(h.getName() + "." + h.getDomain().getName()); System.out.println(h.getName() + "." + h.getDomain().getName());
***REMOVED*** }
System.out.println(); System.out.println();
***REMOVED*** }
***REMOVED*** }
***REMOVED*** public AnsibleWorker applyAlgorithmSetToCluster(AlgorithmSet as, Cluster // public AnsibleWorker applyAlgorithmSetToCluster(AlgorithmSet as, Cluster
***REMOVED*** cluster, /*boolean updateSVN,*/ boolean test) throws IOException, // cluster, /*boolean updateSVN,*/ boolean test) throws IOException,
***REMOVED*** InterruptedException, SVNException ***REMOVED*** // InterruptedException, SVNException {
***REMOVED*** //
***REMOVED*** //
***REMOVED*** return applyAlgorithmSetToCluster // return applyAlgorithmSetToCluster
***REMOVED*** (as,cluster,UUID.randomUUID().toString(),/*updateSVN,*/ test); // (as,cluster,UUID.randomUUID().toString(),/*updateSVN,*/ test);
***REMOVED*** ***REMOVED*** // }
***REMOVED*** public AnsibleWorker applyAlgorithmSetToCluster(AlgorithmSet as, Cluster // public AnsibleWorker applyAlgorithmSetToCluster(AlgorithmSet as, Cluster
***REMOVED*** cluster,String uuid, /*boolean updateSVN,*/ boolean test) throws // cluster,String uuid, /*boolean updateSVN,*/ boolean test) throws
***REMOVED*** IOException, InterruptedException, SVNException ***REMOVED*** // IOException, InterruptedException, SVNException {
***REMOVED*** AnsibleWorker worker = new AnsibleWorker(new File(this.getWorkDir(), // AnsibleWorker worker = new AnsibleWorker(new File(this.getWorkDir(),
***REMOVED*** uuid)); // uuid));
***REMOVED*** //
***REMOVED*** //
***REMOVED*** List<Role> algoRoles = new Vector<>(); // List<Role> algoRoles = new Vector<>();
***REMOVED*** //
***REMOVED*** ***REMOVED*** add algorithms and dependencies to the worker // // add algorithms and dependencies to the worker
***REMOVED*** for (Algorithm a : as.getAlgorithms()) ***REMOVED*** // for (Algorithm a : as.getAlgorithms()) {
***REMOVED*** for (Role r : this.generateRoles(a)) ***REMOVED*** // for (Role r : this.generateRoles(a)) {
***REMOVED*** algoRoles.add(r); // algoRoles.add(r);
***REMOVED*** worker.addRole(r); // worker.addRole(r);
***REMOVED*** ***REMOVED*** // }
***REMOVED*** ***REMOVED***to comment the for in case of just install algo // //to comment the for in case of just install algo
***REMOVED*** if(test)***REMOVED*** // if(test){
***REMOVED*** for (Dependency d : a.getDependencies()) ***REMOVED*** // for (Dependency d : a.getDependencies()) {
***REMOVED*** for (Role r : this.generateRoles(d)) ***REMOVED*** // for (Role r : this.generateRoles(d)) {
***REMOVED*** worker.addRole(r); // worker.addRole(r);
***REMOVED*** ***REMOVED*** // }
***REMOVED*** ***REMOVED*** // }
***REMOVED*** ***REMOVED*** // }
***REMOVED*** ***REMOVED*** // }
***REMOVED*** //
***REMOVED*** ***REMOVED*** add static roles // // add static roles
***REMOVED*** for(Role r:this.getStaticRoleManager().getStaticRoles()) ***REMOVED*** // for(Role r:this.getStaticRoleManager().getStaticRoles()) {
***REMOVED*** worker.addRole(r); // worker.addRole(r);
***REMOVED*** ***REMOVED*** // }
***REMOVED*** //
***REMOVED*** ***REMOVED*** generate the inventory // // generate the inventory
***REMOVED*** Inventory inventory = new Inventory(); // Inventory inventory = new Inventory();
***REMOVED*** for (Host h : cluster.getHosts()) ***REMOVED*** // for (Host h : cluster.getHosts()) {
***REMOVED*** AnsibleHost ah = new AnsibleHost(h.getName()); // AnsibleHost ah = new AnsibleHost(h.getName());
***REMOVED*** inventory.addHost(ah, "universe"); // inventory.addHost(ah, "universe");
***REMOVED*** inventory.addHost(ah, "d4science"); // inventory.addHost(ah, "d4science");
***REMOVED*** ***REMOVED*** // }
***REMOVED*** worker.setInventory(inventory); // worker.setInventory(inventory);
***REMOVED*** //
***REMOVED*** ***REMOVED*** generate the playbook // // generate the playbook
***REMOVED*** Playbook playbook = new Playbook(); // Playbook playbook = new Playbook();
***REMOVED*** if(test)***REMOVED*** // if(test){
***REMOVED*** playbook.setRemote_user("root");***REMOVED*** // playbook.setRemote_user("root");}
***REMOVED*** playbook.setRemote_user("gcube"); // playbook.setRemote_user("gcube");
***REMOVED*** playbook.applyTo("universe"); // playbook.applyTo("universe");
***REMOVED*** for(Role r:algoRoles) ***REMOVED*** // for(Role r:algoRoles) {
***REMOVED*** ***REMOVED*** add only 'add' roles // // add only 'add' roles
***REMOVED*** if(!r.getName().endsWith("remove")) ***REMOVED*** // if(!r.getName().endsWith("remove")) {
***REMOVED*** playbook.addRole(r.getName()); // playbook.addRole(r.getName());
***REMOVED*** ***REMOVED*** // }
***REMOVED*** ***REMOVED*** // }
***REMOVED*** //
***REMOVED*** worker.setPlaybook(playbook); // worker.setPlaybook(playbook);
***REMOVED*** //
***REMOVED*** ***REMOVED*** execute and save log locally // // execute and save log locally
***REMOVED*** ***REMOVED***PrintStream console = System.out; // //PrintStream console = System.out;
***REMOVED*** File path = new File(worker.getWorkdir() + File.separator + "logs"); // File path = new File(worker.getWorkdir() + File.separator + "logs");
***REMOVED*** path.mkdirs(); // path.mkdirs();
***REMOVED*** File n = new File(path + File.separator + worker.getWorkerId()); // File n = new File(path + File.separator + worker.getWorkerId());
***REMOVED*** FileOutputStream fos = new FileOutputStream(n); // FileOutputStream fos = new FileOutputStream(n);
***REMOVED*** PrintStream ps = new PrintStream(fos); // PrintStream ps = new PrintStream(fos);
***REMOVED*** //
***REMOVED*** ***REMOVED***System.setErr(console); // //System.setErr(console);
***REMOVED*** //
***REMOVED*** worker.apply(as,ps,test); // worker.apply(as,ps,test);
***REMOVED*** ***REMOVED***System.setOut(console); // //System.setOut(console);
***REMOVED*** ***REMOVED***worker.apply(); // //worker.apply();
***REMOVED*** System.out.println("Log stored to to " + n.getAbsolutePath()); // System.out.println("Log stored to to " + n.getAbsolutePath());
***REMOVED*** //
***REMOVED*** ***REMOVED*** destroy the worker // // destroy the worker
***REMOVED*** worker.destroy(); // worker.destroy();
***REMOVED*** return worker; // return worker;
***REMOVED*** ***REMOVED*** // }
private TemplateManager getTemplateManager() ***REMOVED*** private TemplateManager getTemplateManager() {
return new TemplateManager(); return new TemplateManager();
***REMOVED*** }
private CustomRoleManager getCustomRoleManager() ***REMOVED*** private CustomRoleManager getCustomRoleManager() {
return new CustomRoleManager(); return new CustomRoleManager();
***REMOVED*** }
private StaticRoleManager getStaticRoleManager() ***REMOVED*** private StaticRoleManager getStaticRoleManager() {
return new StaticRoleManager(); return new StaticRoleManager();
***REMOVED*** }
***REMOVED**** /**
* Generate all roles for this dependency * Generate all roles for this dependency
* *
* @param dep * @param dep
* Dependency * Dependency
* @return Collection of Roles * @return Collection of Roles
***REMOVED*** */
public Collection<Role> generateRoles(Dependency dep) ***REMOVED*** public Collection<Role> generateRoles(Dependency dep) {
Collection<Role> roles = new Vector<>(); Collection<Role> roles = new Vector<>();
if ("os".equalsIgnoreCase(dep.getType())) ***REMOVED*** if ("os".equalsIgnoreCase(dep.getType())) {
OSDependencyPackage pkg = new OSDependencyPackage(dep); OSDependencyPackage pkg = new OSDependencyPackage(dep);
if (pkg != null) ***REMOVED*** if (pkg != null) {
roles.addAll(pkg.getRoles(this.getTemplateManager())); roles.addAll(pkg.getRoles(this.getTemplateManager()));
***REMOVED*** }
***REMOVED*** else if ("custom".equalsIgnoreCase(dep.getType())) ***REMOVED*** } else if ("custom".equalsIgnoreCase(dep.getType())) {
CustomDependencyPackage pkg = new CustomDependencyPackage(dep); CustomDependencyPackage pkg = new CustomDependencyPackage(dep);
if (pkg != null) ***REMOVED*** if (pkg != null) {
roles.addAll(pkg.getRoles(this.getCustomRoleManager())); roles.addAll(pkg.getRoles(this.getCustomRoleManager()));
***REMOVED*** }
***REMOVED*** else if ("github".equalsIgnoreCase(dep.getType())) ***REMOVED*** } else if ("github".equalsIgnoreCase(dep.getType())) {
CranDependencyPackage pkg = new CranDependencyPackage(dep); CranDependencyPackage pkg = new CranDependencyPackage(dep);
if (pkg != null) ***REMOVED*** if (pkg != null) {
roles.addAll(pkg.getRoles(this.getTemplateManager())); roles.addAll(pkg.getRoles(this.getTemplateManager()));
***REMOVED*** }
***REMOVED*** else if ("cran".equalsIgnoreCase(dep.getType())) ***REMOVED*** } else if ("cran".equalsIgnoreCase(dep.getType())) {
CranDependencyPackage pkg = new CranDependencyPackage(dep); CranDependencyPackage pkg = new CranDependencyPackage(dep);
if (pkg != null) ***REMOVED*** if (pkg != null) {
roles.addAll(pkg.getRoles(this.getTemplateManager())); roles.addAll(pkg.getRoles(this.getTemplateManager()));
***REMOVED*** }
***REMOVED*** }
return roles; return roles;
***REMOVED*** }
public Collection<Role> generateRoles(Algorithm a, boolean includeAlgorithmDependencies) ***REMOVED*** public Collection<Role> generateRoles(Algorithm a, boolean includeAlgorithmDependencies) {
AlgorithmPackage pkg = new AlgorithmPackage(a, includeAlgorithmDependencies); AlgorithmPackage pkg = new AlgorithmPackage(a, includeAlgorithmDependencies);
return pkg.getRoles(this.getTemplateManager()); return pkg.getRoles(this.getTemplateManager());
***REMOVED*** }
***REMOVED*** }

96
src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/ansiblebridge/AnsibleSerializeHelper.java
View File

@ -3,7 +3,7 @@ package org.gcube.dataanalysis.dataminer.poolmanager.ansiblebridge;
import java.io.File; import java.io.File;
import java.io.FileInputStream; import java.io.FileInputStream;
import java.io.FileNotFoundException; import java.io.FileNotFoundException;
***REMOVED*** import java.io.IOException;
import java.io.PrintWriter; import java.io.PrintWriter;
import org.apache.commons.io.IOUtils; import org.apache.commons.io.IOUtils;
@ -14,106 +14,106 @@ import org.gcube.dataanalysis.dataminer.poolmanager.ansible.model.Playbook;
import org.gcube.dataanalysis.dataminer.poolmanager.ansible.model.Role; import org.gcube.dataanalysis.dataminer.poolmanager.ansible.model.Role;
import org.gcube.dataanalysis.dataminer.poolmanager.ansible.model.RoleFile; import org.gcube.dataanalysis.dataminer.poolmanager.ansible.model.RoleFile;
public class AnsibleSerializeHelper ***REMOVED*** public class AnsibleSerializeHelper {
public static void serialize(Inventory inventory, File inventoryFile) throws IOException ***REMOVED*** public static void serialize(Inventory inventory, File inventoryFile) throws IOException {
String out = ""; String out = "";
for(HostGroup hg:inventory.getHostGroups()) ***REMOVED*** for(HostGroup hg:inventory.getHostGroups()) {
out+=String.format("[%s]\n", hg.getName()); out+=String.format("[%s]\n", hg.getName());
for(AnsibleHost h:hg.getHosts()) ***REMOVED*** for(AnsibleHost h:hg.getHosts()) {
out+=h.getName()+"\n"; out+=h.getName()+"\n";
***REMOVED*** }
out+="\n"; out+="\n";
***REMOVED*** }
out = out.trim(); out = out.trim();
serialize(out, inventoryFile); serialize(out, inventoryFile);
***REMOVED*** }
public static void serialize(Playbook playbook, File playbookFile) throws IOException ***REMOVED*** public static void serialize(Playbook playbook, File playbookFile) throws IOException {
String out = "- hosts: " + playbook.getHostGroupName() + "\n"; String out = "- hosts: " + playbook.getHostGroupName() + "\n";
out += " remote_user: "+playbook.getRemote_user()+"\n"; out += " remote_user: "+playbook.getRemote_user()+"\n";
out+=" roles:\n"; out+=" roles:\n";
for(String r:playbook.getRoles()) ***REMOVED*** for(String r:playbook.getRoles()) {
out+=" - " + r+"\n"; out+=" - " + r+"\n";
***REMOVED*** }
out+=" vars:\n"; out+=" vars:\n";
out+=" os_package_state: present\n"; out+=" os_package_state: present\n";
out = out.trim(); out = out.trim();
serialize(out, playbookFile); serialize(out, playbookFile);
***REMOVED*** }
public static void serializeRole(Role r, File dir) throws IOException ***REMOVED*** public static void serializeRole(Role r, File dir) throws IOException {
***REMOVED*** create root // create root
File root = new File(dir, r.getName()); File root = new File(dir, r.getName());
root.mkdirs(); root.mkdirs();
***REMOVED*** create tasks // create tasks
if(r.getTaskFiles().size()>0) ***REMOVED*** if(r.getTaskFiles().size()>0) {
File tasks = new File(root, "tasks"); File tasks = new File(root, "tasks");
tasks.mkdirs(); tasks.mkdirs();
for(RoleFile tf: r.getTaskFiles()) ***REMOVED*** for(RoleFile tf: r.getTaskFiles()) {
serializeTask(tf, tasks); serializeTask(tf, tasks);
***REMOVED*** }
***REMOVED*** }
***REMOVED*** create meta // create meta
if(r.getMeta().size()>0) ***REMOVED*** if(r.getMeta().size()>0) {
File meta = new File(root, "meta"); File meta = new File(root, "meta");
meta.mkdirs(); meta.mkdirs();
for(RoleFile tf: r.getMeta()) ***REMOVED*** for(RoleFile tf: r.getMeta()) {
serializeTask(tf, meta); serializeTask(tf, meta);
***REMOVED*** }
***REMOVED*** }
***REMOVED*** }
public static void serializeTask(RoleFile tf, File dir) throws IOException ***REMOVED*** public static void serializeTask(RoleFile tf, File dir) throws IOException {
File f = new File(dir, tf.getName()); File f = new File(dir, tf.getName());
serialize(tf.getContent().trim(), f); serialize(tf.getContent().trim(), f);
***REMOVED*** }
public static void serialize(String s, File f) throws IOException ***REMOVED*** public static void serialize(String s, File f) throws IOException {
PrintWriter out = new PrintWriter(f); PrintWriter out = new PrintWriter(f);
out.println(s); out.println(s);
out.close(); out.close();
***REMOVED*** }
public static Role deserializeRoleFromFilesystem(File roleDir) throws IOException ***REMOVED*** public static Role deserializeRoleFromFilesystem(File roleDir) throws IOException {
Role out = new Role(); Role out = new Role();
out.setName(roleDir.getName()); out.setName(roleDir.getName());
if(!roleDir.exists()) ***REMOVED*** if(!roleDir.exists()) {
throw new FileNotFoundException(); throw new FileNotFoundException();
***REMOVED*** }
try ***REMOVED*** try {
File tasksDir = new File(roleDir, "tasks"); File tasksDir = new File(roleDir, "tasks");
if(tasksDir.exists()) ***REMOVED*** if(tasksDir.exists()) {
for(File main:tasksDir.listFiles()) ***REMOVED*** for(File main:tasksDir.listFiles()) {
String content = IOUtils.toString(new FileInputStream(main), "UTF-8"); String content = IOUtils.toString(new FileInputStream(main), "UTF-8");
RoleFile tf = new RoleFile(main.getName(), content); RoleFile tf = new RoleFile(main.getName(), content);
tf.setPath(main.getAbsolutePath().substring(roleDir.getAbsolutePath().length()+1)); tf.setPath(main.getAbsolutePath().substring(roleDir.getAbsolutePath().length()+1));
out.addTaskFile(tf); out.addTaskFile(tf);
***REMOVED*** }
***REMOVED*** }
***REMOVED*** catch(FileNotFoundException e) ***REMOVED*** } catch(FileNotFoundException e) {
e.printStackTrace(); e.printStackTrace();
***REMOVED*** }
try ***REMOVED*** try {
File metaDir = new File(roleDir, "meta"); File metaDir = new File(roleDir, "meta");
if(metaDir.exists()) ***REMOVED*** if(metaDir.exists()) {
for(File main:metaDir.listFiles()) ***REMOVED*** for(File main:metaDir.listFiles()) {
String content = IOUtils.toString(new FileInputStream(main), "UTF-8"); String content = IOUtils.toString(new FileInputStream(main), "UTF-8");
RoleFile tf = new RoleFile(main.getName(), content); RoleFile tf = new RoleFile(main.getName(), content);
tf.setPath(main.getAbsolutePath().substring(roleDir.getAbsolutePath().length()+1)); tf.setPath(main.getAbsolutePath().substring(roleDir.getAbsolutePath().length()+1));
out.addMeta(tf); out.addMeta(tf);
***REMOVED*** }
***REMOVED*** }
***REMOVED*** catch(FileNotFoundException e) ***REMOVED*** } catch(FileNotFoundException e) {
e.printStackTrace(); e.printStackTrace();
***REMOVED*** }
return out; return out;
***REMOVED*** }
***REMOVED*** }

62
src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/ansiblebridge/template/AlgorithmPackage.java
View File

@ -6,29 +6,29 @@ import java.util.Map;
import java.util.NoSuchElementException; import java.util.NoSuchElementException;
import java.util.Vector; import java.util.Vector;
***REMOVED*** import org.gcube.common.scope.api.ScopeProvider;
import org.gcube.dataanalysis.dataminer.poolmanager.ansible.model.Role; import org.gcube.dataanalysis.dataminer.poolmanager.ansible.model.Role;
***REMOVED*** import org.gcube.dataanalysis.dataminer.poolmanager.datamodel.Algorithm;
import org.gcube.dataanalysis.dataminer.poolmanager.datamodel.Dependency; import org.gcube.dataanalysis.dataminer.poolmanager.datamodel.Dependency;
***REMOVED*** import org.slf4j.Logger;
***REMOVED*** import org.slf4j.LoggerFactory;
public class AlgorithmPackage ***REMOVED*** public class AlgorithmPackage {
private Algorithm algorithm; private Algorithm algorithm;
private boolean includeAlgorithmDependencies; private boolean includeAlgorithmDependencies;
private Logger logger; private Logger logger;
public AlgorithmPackage(Algorithm a,boolean includeAlgorithmDependencies) public AlgorithmPackage(Algorithm a,boolean includeAlgorithmDependencies)
***REMOVED*** {
this.logger = LoggerFactory.getLogger(AlgorithmPackage.class); this.logger = LoggerFactory.getLogger(AlgorithmPackage.class);
this.algorithm = a; this.algorithm = a;
this.includeAlgorithmDependencies = includeAlgorithmDependencies; this.includeAlgorithmDependencies = includeAlgorithmDependencies;
***REMOVED*** }
protected Map<String, String> getDictionary(Algorithm a) ***REMOVED*** protected Map<String, String> getDictionary(Algorithm a) {
Map<String, String> out = new HashMap<String, String>(); Map<String, String> out = new HashMap<String, String>();
out.put("name", a.getName()); out.put("name", a.getName());
out.put("category", a.getCategory()); out.put("category", a.getCategory());
@ -36,47 +36,47 @@ public class AlgorithmPackage ***REMOVED***
out.put("atype", a.getAlgorithmType()); out.put("atype", a.getAlgorithmType());
out.put("skipjava", a.getSkipJava()); out.put("skipjava", a.getSkipJava());
out.put("vre", ScopeProvider.instance.get()); out.put("vre", ScopeProvider.instance.get());
***REMOVED***out.put("vre", "FAKE_VRE"); //out.put("vre", "FAKE_VRE");
out.put("packageurl", a.getPackageURL()); out.put("packageurl", a.getPackageURL());
out.put("description", a.getDescription()); out.put("description", a.getDescription());
String deps = ""; String deps = "";
if(includeAlgorithmDependencies)***REMOVED*** if(includeAlgorithmDependencies){
for(Dependency d:a.getDependencies()) ***REMOVED*** for(Dependency d:a.getDependencies()) {
deps+=String.format("- ***REMOVED*** role: %s ***REMOVED***\n", d.getType()+"-"+d.getName().replaceAll("/", "-")); deps+=String.format("- { role: %s }\n", d.getType()+"-"+d.getName().replaceAll("/", "-"));
***REMOVED******REMOVED*** }}
deps = deps.trim(); deps = deps.trim();
out.put("dependencies", deps); out.put("dependencies", deps);
return out; return out;
***REMOVED*** }
protected Algorithm getAlgorithm() ***REMOVED*** protected Algorithm getAlgorithm() {
return this.algorithm; return this.algorithm;
***REMOVED*** }
public Collection<Role> getRoles(TemplateManager tm) ***REMOVED*** public Collection<Role> getRoles(TemplateManager tm) {
Collection<Role> out = new Vector<>(); Collection<Role> out = new Vector<>();
for(String mode:new String[]***REMOVED***"add"***REMOVED***) ***REMOVED*** ***REMOVED*** "remove", "update" for(String mode:new String[]{"add"}) { // "remove", "update"
String roleName = "gcube-algorithm-"+this.getAlgorithm().getName()+("add".equals(mode) ? "" : "-"+mode); String roleName = "gcube-algorithm-"+this.getAlgorithm().getName()+("add".equals(mode) ? "" : "-"+mode);
try ***REMOVED*** try {
***REMOVED*** find template // find template
Role template = tm.getRoleTemplate("gcube-algorithm-" + mode); Role template = tm.getRoleTemplate("gcube-algorithm-" + mode);
***REMOVED*** //
if(template!=null) ***REMOVED*** if(template!=null) {
Map<String, String> dictionary = this.getDictionary(this.getAlgorithm()); Map<String, String> dictionary = this.getDictionary(this.getAlgorithm());
Role r = tm.fillRoleTemplate(template, dictionary); Role r = tm.fillRoleTemplate(template, dictionary);
r.setName(roleName); r.setName(roleName);
out.add(r); out.add(r);
***REMOVED*** else } else
***REMOVED*** {
this.logger.warn("WARNING: template is null"); this.logger.warn("WARNING: template is null");
***REMOVED*** }
***REMOVED*** catch (NoSuchElementException e) ***REMOVED*** } catch (NoSuchElementException e) {
***REMOVED*** e.printStackTrace(); // e.printStackTrace();
this.logger.warn("WARNING: no template found for " + roleName); this.logger.warn("WARNING: no template found for " + roleName);
***REMOVED*** }
***REMOVED*** }
return out; return out;
***REMOVED*** }
***REMOVED*** }

8
src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/ansiblebridge/template/CranDependencyPackage.java
View File

@ -2,10 +2,10 @@ package org.gcube.dataanalysis.dataminer.poolmanager.ansiblebridge.template;
import org.gcube.dataanalysis.dataminer.poolmanager.datamodel.Dependency; import org.gcube.dataanalysis.dataminer.poolmanager.datamodel.Dependency;
public class CranDependencyPackage extends DependencyPackage ***REMOVED*** public class CranDependencyPackage extends DependencyPackage {
public CranDependencyPackage(Dependency d) ***REMOVED*** public CranDependencyPackage(Dependency d) {
super(d); super(d);
***REMOVED*** }
***REMOVED*** }

68
src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/ansiblebridge/template/CustomDependencyPackage.java
View File

@ -6,64 +6,64 @@ import java.util.Vector;
import org.gcube.dataanalysis.dataminer.poolmanager.ansible.model.Role; import org.gcube.dataanalysis.dataminer.poolmanager.ansible.model.Role;
import org.gcube.dataanalysis.dataminer.poolmanager.datamodel.Dependency; import org.gcube.dataanalysis.dataminer.poolmanager.datamodel.Dependency;
***REMOVED*** import org.slf4j.Logger;
public class CustomDependencyPackage extends DependencyPackage ***REMOVED*** public class CustomDependencyPackage extends DependencyPackage {
private Logger logger; private Logger logger;
public CustomDependencyPackage(Dependency dependency) public CustomDependencyPackage(Dependency dependency)
***REMOVED*** {
super(dependency); super(dependency);
***REMOVED*** }
***REMOVED*** private String getCustomRepositoryLocation(String ansibleRoot) ***REMOVED*** // private String getCustomRepositoryLocation(String ansibleRoot) {
***REMOVED*** return ansibleRoot+"/custom"; // return ansibleRoot+"/custom";
***REMOVED*** ***REMOVED*** // }
/* /*
public void serializeTo(String ansibleRoot) ***REMOVED*** public void serializeTo(String ansibleRoot) {
for(String mode:new String[]***REMOVED***"add", "remove", "update"***REMOVED***) ***REMOVED*** for(String mode:new String[]{"add", "remove", "update"}) {
***REMOVED*** look for roles in the 'custom' repository // look for roles in the 'custom' repository
try ***REMOVED*** try {
***REMOVED*** role name // role name
String roleName = this.getDependency().getType()+"-"+this.getDependency().getName()+("add".equals(mode) ? "" : "-"+mode); String roleName = this.getDependency().getType()+"-"+this.getDependency().getName()+("add".equals(mode) ? "" : "-"+mode);
***REMOVED*** look for the custom role // look for the custom role
File src = new File(this.getCustomRepositoryLocation(ansibleRoot)+"/"+roleName); File src = new File(this.getCustomRepositoryLocation(ansibleRoot)+"/"+roleName);
System.out.println("** CUSTOM ** " + src); System.out.println("** CUSTOM ** " + src);
if(src.exists()) ***REMOVED*** if(src.exists()) {
***REMOVED*** do copy // do copy
System.out.println("copying CUSTOM role"); System.out.println("copying CUSTOM role");
File dest = new File(ansibleRoot+"/work/"+roleName); File dest = new File(ansibleRoot+"/work/"+roleName);
FileUtils.copyDirectory(src, dest); FileUtils.copyDirectory(src, dest);
***REMOVED*** }
***REMOVED*** catch(IOException e) ***REMOVED*** } catch(IOException e) {
e.printStackTrace(); e.printStackTrace();
***REMOVED*** }
***REMOVED*** }
***REMOVED*** }
*/ */
public Collection<Role> getRoles(CustomRoleManager crm) ***REMOVED*** public Collection<Role> getRoles(CustomRoleManager crm) {
Collection<Role> out = new Vector<>(); Collection<Role> out = new Vector<>();
***REMOVED*** for(String mode:new String[]***REMOVED***"add", "remove", "update"***REMOVED***) ***REMOVED*** // for(String mode:new String[]{"add", "remove", "update"}) {
for(String mode:new String[]***REMOVED***"add"***REMOVED***) ***REMOVED*** ***REMOVED*** "remove", "update" for(String mode:new String[]{"add"}) { // "remove", "update"
***REMOVED*** role name // role name
String roleName = this.getDependency().getType()+"-"+this.getDependency().getName()+("add".equals(mode) ? "" : "-"+mode); String roleName = this.getDependency().getType()+"-"+this.getDependency().getName()+("add".equals(mode) ? "" : "-"+mode);
try ***REMOVED*** try {
***REMOVED*** look for custom role // look for custom role
Role role = crm.getRole(roleName); Role role = crm.getRole(roleName);
if(role!=null) ***REMOVED*** if(role!=null) {
out.add(role); out.add(role);
***REMOVED*** }
***REMOVED*** catch (NoSuchElementException e) ***REMOVED*** } catch (NoSuchElementException e) {
***REMOVED*** e.printStackTrace(); // e.printStackTrace();
this.logger.warn("WARNING: no custom role found for " + roleName); this.logger.warn("WARNING: no custom role found for " + roleName);
***REMOVED*** }
***REMOVED*** }
return out; return out;
***REMOVED*** }
***REMOVED*** }

22
src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/ansiblebridge/template/CustomRoleManager.java
View File

@ -1,31 +1,31 @@
package org.gcube.dataanalysis.dataminer.poolmanager.ansiblebridge.template; package org.gcube.dataanalysis.dataminer.poolmanager.ansiblebridge.template;
import java.io.File; import java.io.File;
***REMOVED*** import java.io.IOException;
import java.util.NoSuchElementException; import java.util.NoSuchElementException;
import org.gcube.dataanalysis.dataminer.poolmanager.ansible.model.Role; import org.gcube.dataanalysis.dataminer.poolmanager.ansible.model.Role;
import org.gcube.dataanalysis.dataminer.poolmanager.ansiblebridge.AnsibleBridge; import org.gcube.dataanalysis.dataminer.poolmanager.ansiblebridge.AnsibleBridge;
import org.gcube.dataanalysis.dataminer.poolmanager.ansiblebridge.AnsibleSerializeHelper; import org.gcube.dataanalysis.dataminer.poolmanager.ansiblebridge.AnsibleSerializeHelper;
public class CustomRoleManager ***REMOVED*** public class CustomRoleManager {
public String getRoot() ***REMOVED*** public String getRoot() {
String input = AnsibleBridge.class.getClassLoader().getResource("custom").getPath(); String input = AnsibleBridge.class.getClassLoader().getResource("custom").getPath();
return input; return input;
***REMOVED*** }
public Role getRole(String roleName) throws NoSuchElementException ***REMOVED*** public Role getRole(String roleName) throws NoSuchElementException {
File f = new File(this.getRoot(), roleName); File f = new File(this.getRoot(), roleName);
try ***REMOVED*** try {
return AnsibleSerializeHelper.deserializeRoleFromFilesystem(f); return AnsibleSerializeHelper.deserializeRoleFromFilesystem(f);
***REMOVED*** catch (IOException e) ***REMOVED*** } catch (IOException e) {
***REMOVED*** e.printStackTrace(); // e.printStackTrace();
throw new NoSuchElementException("unable to find " + roleName); throw new NoSuchElementException("unable to find " + roleName);
***REMOVED*** }
***REMOVED*** }
***REMOVED*** }

46
src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/ansiblebridge/template/DependencyPackage.java
View File

@ -8,53 +8,53 @@ import java.util.Vector;
import org.gcube.dataanalysis.dataminer.poolmanager.ansible.model.Role; import org.gcube.dataanalysis.dataminer.poolmanager.ansible.model.Role;
import org.gcube.dataanalysis.dataminer.poolmanager.datamodel.Dependency; import org.gcube.dataanalysis.dataminer.poolmanager.datamodel.Dependency;
***REMOVED*** import org.slf4j.Logger;
***REMOVED*** import org.slf4j.LoggerFactory;
public class DependencyPackage ***REMOVED*** public class DependencyPackage {
private Logger logger; private Logger logger;
private Dependency dependency; private Dependency dependency;
public DependencyPackage(Dependency dependency) ***REMOVED*** public DependencyPackage(Dependency dependency) {
this.dependency = dependency; this.dependency = dependency;
this.logger = LoggerFactory.getLogger(DependencyPackage.class); this.logger = LoggerFactory.getLogger(DependencyPackage.class);
***REMOVED*** }
protected Map<String, String> getDictionary(Dependency d) ***REMOVED*** protected Map<String, String> getDictionary(Dependency d) {
Map<String, String> out = new HashMap<String, String>(); Map<String, String> out = new HashMap<String, String>();
out.put("name", d.getName()); out.put("name", d.getName());
out.put("type", d.getType()); out.put("type", d.getType());
return out; return out;
***REMOVED*** }
protected Dependency getDependency() ***REMOVED*** protected Dependency getDependency() {
return this.dependency; return this.dependency;
***REMOVED*** }
public Collection<Role> getRoles(TemplateManager tm) ***REMOVED*** public Collection<Role> getRoles(TemplateManager tm) {
Collection<Role> out = new Vector<>(); Collection<Role> out = new Vector<>();
for(String mode:new String[]***REMOVED***"add"***REMOVED***) ***REMOVED*** ***REMOVED*** "remove", "update" for(String mode:new String[]{"add"}) { // "remove", "update"
String roleName = this.getDependency().getType()+"-"+this.getDependency().getName().replaceAll("/", "-")+("add".equals(mode) ? "" : "-"+mode); String roleName = this.getDependency().getType()+"-"+this.getDependency().getName().replaceAll("/", "-")+("add".equals(mode) ? "" : "-"+mode);
try ***REMOVED*** try {
***REMOVED*** find template // find template
Role template = tm.getRoleTemplate(this.getDependency().getType()+"-package-"+mode); Role template = tm.getRoleTemplate(this.getDependency().getType()+"-package-"+mode);
***REMOVED*** //
if(template!=null) ***REMOVED*** if(template!=null) {
Map<String, String> dictionary = this.getDictionary(this.getDependency()); Map<String, String> dictionary = this.getDictionary(this.getDependency());
Role r = tm.fillRoleTemplate(template, dictionary); Role r = tm.fillRoleTemplate(template, dictionary);
r.setName(roleName); r.setName(roleName);
out.add(r); out.add(r);
***REMOVED*** else ***REMOVED*** } else {
this.logger.warn("WARNING: template is null"); this.logger.warn("WARNING: template is null");
***REMOVED*** }
***REMOVED*** catch (NoSuchElementException e) ***REMOVED*** } catch (NoSuchElementException e) {
***REMOVED*** e.printStackTrace(); // e.printStackTrace();
this.logger.warn("WARNING: no template found for " + roleName); this.logger.warn("WARNING: no template found for " + roleName);
***REMOVED*** }
***REMOVED*** }
return out; return out;
***REMOVED*** }
***REMOVED*** }

8
src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/ansiblebridge/template/OSDependencyPackage.java
View File

@ -2,10 +2,10 @@ package org.gcube.dataanalysis.dataminer.poolmanager.ansiblebridge.template;
import org.gcube.dataanalysis.dataminer.poolmanager.datamodel.Dependency; import org.gcube.dataanalysis.dataminer.poolmanager.datamodel.Dependency;
public class OSDependencyPackage extends DependencyPackage ***REMOVED*** public class OSDependencyPackage extends DependencyPackage {
public OSDependencyPackage(Dependency dependency) ***REMOVED*** public OSDependencyPackage(Dependency dependency) {
super(dependency); super(dependency);
***REMOVED*** }
***REMOVED*** }

28
src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/ansiblebridge/template/StaticRoleManager.java
View File

@ -1,7 +1,7 @@
package org.gcube.dataanalysis.dataminer.poolmanager.ansiblebridge.template; package org.gcube.dataanalysis.dataminer.poolmanager.ansiblebridge.template;
import java.io.File; import java.io.File;
***REMOVED*** import java.io.IOException;
import java.util.Collection; import java.util.Collection;
import java.util.Vector; import java.util.Vector;
@ -9,30 +9,30 @@ import org.gcube.dataanalysis.dataminer.poolmanager.ansible.model.Role;
import org.gcube.dataanalysis.dataminer.poolmanager.ansiblebridge.AnsibleBridge; import org.gcube.dataanalysis.dataminer.poolmanager.ansiblebridge.AnsibleBridge;
import org.gcube.dataanalysis.dataminer.poolmanager.ansiblebridge.AnsibleSerializeHelper; import org.gcube.dataanalysis.dataminer.poolmanager.ansiblebridge.AnsibleSerializeHelper;
public class StaticRoleManager ***REMOVED*** public class StaticRoleManager {
public StaticRoleManager() ***REMOVED*** public StaticRoleManager() {
***REMOVED*** }
public String getRoot() ***REMOVED*** public String getRoot() {
String input = AnsibleBridge.class.getClassLoader().getResource("static").getPath(); String input = AnsibleBridge.class.getClassLoader().getResource("static").getPath();
return input; return input;
***REMOVED*** }
public Collection<Role> getStaticRoles() ***REMOVED*** public Collection<Role> getStaticRoles() {
Collection<Role> out = new Vector<>(); Collection<Role> out = new Vector<>();
for(File f: new File(this.getRoot()).listFiles()) ***REMOVED*** for(File f: new File(this.getRoot()).listFiles()) {
try ***REMOVED*** try {
out.add(AnsibleSerializeHelper.deserializeRoleFromFilesystem(f)); out.add(AnsibleSerializeHelper.deserializeRoleFromFilesystem(f));
***REMOVED*** catch(IOException e) ***REMOVED*** } catch(IOException e) {
e.printStackTrace(); e.printStackTrace();
***REMOVED*** }
***REMOVED*** }
return out; return out;
***REMOVED*** }
***REMOVED*** }

84
src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/ansiblebridge/template/TemplateManager.java
View File

@ -1,7 +1,7 @@
package org.gcube.dataanalysis.dataminer.poolmanager.ansiblebridge.template; package org.gcube.dataanalysis.dataminer.poolmanager.ansiblebridge.template;
import java.io.File; import java.io.File;
***REMOVED*** import java.io.IOException;
import java.util.Map; import java.util.Map;
import java.util.NoSuchElementException; import java.util.NoSuchElementException;
@ -11,75 +11,75 @@ import org.gcube.dataanalysis.dataminer.poolmanager.ansiblebridge.AnsibleBridge;
import org.gcube.dataanalysis.dataminer.poolmanager.ansiblebridge.AnsibleSerializeHelper; import org.gcube.dataanalysis.dataminer.poolmanager.ansiblebridge.AnsibleSerializeHelper;
import org.stringtemplate.v4.ST; import org.stringtemplate.v4.ST;
public class TemplateManager ***REMOVED*** public class TemplateManager {
public TemplateManager() ***REMOVED*** public TemplateManager() {
***REMOVED*** }
public String getTemplateRoot() ***REMOVED*** public String getTemplateRoot() {
String input = AnsibleBridge.class.getClassLoader().getResource("templates").getPath(); String input = AnsibleBridge.class.getClassLoader().getResource("templates").getPath();
return input; return input;
***REMOVED*** }
***REMOVED*** private String readTemplate(String templateName) throws IOException ***REMOVED*** // private String readTemplate(String templateName) throws IOException {
***REMOVED*** File templateFile = new File(this.getTemplateRoot(), templateName + ".yaml"); // File templateFile = new File(this.getTemplateRoot(), templateName + ".yaml");
***REMOVED*** System.out.println("looking for file " + templateFile.getName()); // System.out.println("looking for file " + templateFile.getName());
***REMOVED*** String out = IOUtils.toString(new FileInputStream(templateFile), "UTF-8"); // String out = IOUtils.toString(new FileInputStream(templateFile), "UTF-8");
***REMOVED*** return out; // return out;
***REMOVED*** ***REMOVED*** // }
***REMOVED*** public String getTemplate(String templateName) throws NoSuchElementException ***REMOVED*** // public String getTemplate(String templateName) throws NoSuchElementException {
***REMOVED*** String template = null; // String template = null;
***REMOVED*** try ***REMOVED*** // try {
***REMOVED*** template = this.readTemplate(templateName); // template = this.readTemplate(templateName);
***REMOVED*** ***REMOVED*** catch (IOException e) ***REMOVED*** // } catch (IOException e) {
***REMOVED*** throw new NoSuchElementException(); // throw new NoSuchElementException();
***REMOVED*** ***REMOVED*** // }
***REMOVED*** return template; // return template;
***REMOVED*** ***REMOVED*** // }
public Role fillRoleTemplate(Role template, Map<String, String> dictionary) ***REMOVED*** public Role fillRoleTemplate(Role template, Map<String, String> dictionary) {
Role out = new Role(); Role out = new Role();
out.setName(template.getName()); out.setName(template.getName());
for(RoleFile tf:template.getTaskFiles()) ***REMOVED*** for(RoleFile tf:template.getTaskFiles()) {
out.addTaskFile(this.fillTaskTemplate(tf, dictionary)); out.addTaskFile(this.fillTaskTemplate(tf, dictionary));
***REMOVED*** }
for(RoleFile tf:template.getMeta()) ***REMOVED*** for(RoleFile tf:template.getMeta()) {
out.addMeta(this.fillTaskTemplate(tf, dictionary)); out.addMeta(this.fillTaskTemplate(tf, dictionary));
***REMOVED*** }
return out; return out;
***REMOVED*** }
private RoleFile fillTaskTemplate(RoleFile template, Map<String, String> dictionary) ***REMOVED*** private RoleFile fillTaskTemplate(RoleFile template, Map<String, String> dictionary) {
RoleFile out = new RoleFile(); RoleFile out = new RoleFile();
out.setName(template.getName()); out.setName(template.getName());
out.setContent(this.fillTemplate(template.getContent(), dictionary)); out.setContent(this.fillTemplate(template.getContent(), dictionary));
return out; return out;
***REMOVED*** }
private String fillTemplate(String template, Map<String, String> dictionary) ***REMOVED*** private String fillTemplate(String template, Map<String, String> dictionary) {
if (template != null) ***REMOVED*** if (template != null) {
ST t = new ST(template); ST t = new ST(template);
for (String key : dictionary.keySet()) ***REMOVED*** for (String key : dictionary.keySet()) {
t.add(key, dictionary.get(key)); t.add(key, dictionary.get(key));
***REMOVED*** }
String output = t.render(); String output = t.render();
return output; return output;
***REMOVED*** }
return template; return template;
***REMOVED*** }
public Role getRoleTemplate(String roleName) throws NoSuchElementException ***REMOVED*** public Role getRoleTemplate(String roleName) throws NoSuchElementException {
File f = new File(this.getTemplateRoot(), roleName); File f = new File(this.getTemplateRoot(), roleName);
try ***REMOVED*** try {
return AnsibleSerializeHelper.deserializeRoleFromFilesystem(f); return AnsibleSerializeHelper.deserializeRoleFromFilesystem(f);
***REMOVED*** catch (IOException e) ***REMOVED*** } catch (IOException e) {
***REMOVED*** e.printStackTrace(); // e.printStackTrace();
throw new NoSuchElementException("unable to find " + roleName); throw new NoSuchElementException("unable to find " + roleName);
***REMOVED*** }
***REMOVED*** }
***REMOVED*** }

204
src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/clients/HAProxy.java
View File

@ -1,167 +1,167 @@
package org.gcube.dataanalysis.dataminer.poolmanager.clients; package org.gcube.dataanalysis.dataminer.poolmanager.clients;
import java.io.BufferedReader; import java.io.BufferedReader;
***REMOVED*** import java.io.IOException;
import java.io.InputStreamReader; import java.io.InputStreamReader;
***REMOVED*** import java.net.URL;
import java.util.LinkedList; import java.util.LinkedList;
***REMOVED*** import java.util.List;
***REMOVED*** import org.gcube.common.authorization.client.exceptions.ObjectNotFound;
***REMOVED*** import org.gcube.common.authorization.library.provider.SecurityTokenProvider;
***REMOVED*** import org.gcube.common.scope.api.ScopeProvider;
import org.gcube.dataanalysis.dataminer.poolmanager.datamodel.Cluster; import org.gcube.dataanalysis.dataminer.poolmanager.datamodel.Cluster;
import org.gcube.dataanalysis.dataminer.poolmanager.datamodel.Host; import org.gcube.dataanalysis.dataminer.poolmanager.datamodel.Host;
import org.gcube.dataanalysis.dataminer.poolmanager.util.CheckPermission; import org.gcube.dataanalysis.dataminer.poolmanager.util.CheckPermission;
***REMOVED*** import org.slf4j.Logger;
***REMOVED*** import org.slf4j.LoggerFactory;
import au.com.bytecode.opencsv.CSVReader; import au.com.bytecode.opencsv.CSVReader;
public class HAProxy ***REMOVED*** public class HAProxy {
private Logger logger; private Logger logger;
private CSVReader reader; private CSVReader reader;
public HAProxy() ***REMOVED*** public HAProxy() {
this.logger = LoggerFactory.getLogger(HAProxy.class); this.logger = LoggerFactory.getLogger(HAProxy.class);
***REMOVED*** }
***REMOVED*** public Cluster getClusterByHProxy() throws IOException ***REMOVED*** // public Cluster getClusterByHProxy() throws IOException {
***REMOVED*** Cluster cl = new Cluster(); // Cluster cl = new Cluster();
***REMOVED*** String HProxy = ISClient.getHProxy(); // String HProxy = ISClient.getHProxy();
***REMOVED*** URL stockURL = new URL("http:***REMOVED***data.d4science.org/Yk4zSFF6V3JOSytNd3JkRDlnRFpDUUR5TnRJZEw2QjRHbWJQNStIS0N6Yz0"); // URL stockURL = new URL("http://data.d4science.org/Yk4zSFF6V3JOSytNd3JkRDlnRFpDUUR5TnRJZEw2QjRHbWJQNStIS0N6Yz0");
***REMOVED*** BufferedReader in = new BufferedReader(new InputStreamReader(stockURL.openStream())); // BufferedReader in = new BufferedReader(new InputStreamReader(stockURL.openStream()));
***REMOVED*** reader = new CSVReader(in); // reader = new CSVReader(in);
***REMOVED*** String[] nextLine; // String[] nextLine;
***REMOVED*** while ((nextLine = reader.readNext()) != null) ***REMOVED*** // while ((nextLine = reader.readNext()) != null) {
***REMOVED*** ***REMOVED*** rules to add // // rules to add
***REMOVED*** if (HProxy.contains(nextLine[0])) ***REMOVED*** // if (HProxy.contains(nextLine[0])) {
***REMOVED*** cl.setName(nextLine[0]); // cl.setName(nextLine[0]);
***REMOVED*** ***REMOVED*** // }
***REMOVED*** ***REMOVED*** // }
***REMOVED*** return cl; // return cl;
***REMOVED*** //
***REMOVED******REMOVED*** // }
public Cluster MapCluster() throws IOException ***REMOVED*** public Cluster MapCluster() throws IOException {
Cluster cl = new Cluster(); Cluster cl = new Cluster();
String HProxy = ISClient.getHProxy(); String HProxy = ISClient.getHProxy();
***REMOVED***Prod HAproxy //Prod HAproxy
if (HProxy.equals("dataminer-cluster1.d4science.org")) ***REMOVED*** if (HProxy.equals("dataminer-cluster1.d4science.org")) {
cl.setName("dataminer_cluster1"); cl.setName("dataminer_cluster1");
***REMOVED*** }
if (HProxy.equals("dataminer-bigdata.d4science.org")) ***REMOVED*** if (HProxy.equals("dataminer-bigdata.d4science.org")) {
cl.setName("bigdata"); cl.setName("bigdata");
***REMOVED*** }
if (HProxy.equals("dataminer-cluster1.d4science.org")) ***REMOVED*** if (HProxy.equals("dataminer-cluster1.d4science.org")) {
cl.setName("dataminer_cluster1"); cl.setName("dataminer_cluster1");
***REMOVED*** }
if (HProxy.equals("dataminer-cloud1.d4science.org")) ***REMOVED*** if (HProxy.equals("dataminer-cloud1.d4science.org")) {
cl.setName("dataminer_cloud1"); cl.setName("dataminer_cloud1");
***REMOVED*** }
if (HProxy.equals("dataminer-prototypes.d4science.org")) ***REMOVED*** if (HProxy.equals("dataminer-prototypes.d4science.org")) {
cl.setName("prototypes"); cl.setName("prototypes");
***REMOVED*** }
if (HProxy.equals("dataminer.d4science.org")) ***REMOVED*** if (HProxy.equals("dataminer.d4science.org")) {
cl.setName("gcubeapps"); cl.setName("gcubeapps");
***REMOVED*** }
if (HProxy.equals("dataminer-genericworkers.d4science.org")) ***REMOVED*** if (HProxy.equals("dataminer-genericworkers.d4science.org")) {
cl.setName("genericworkers"); cl.setName("genericworkers");
***REMOVED*** }
if (HProxy.equals("dataminer-genericworkers-proto.d4science.org")) ***REMOVED*** if (HProxy.equals("dataminer-genericworkers-proto.d4science.org")) {
cl.setName("genericworkers_proto"); cl.setName("genericworkers_proto");
***REMOVED*** }
***REMOVED***dev HAProxy //dev HAProxy
if (HProxy.equals("dataminer-d-workers.d4science.org")||(HProxy.equals("dataminer-d-d4s.d4science.org"))) ***REMOVED*** if (HProxy.equals("dataminer-d-workers.d4science.org")||(HProxy.equals("dataminer-d-d4s.d4science.org"))) {
cl.setName("devnext_backend"); cl.setName("devnext_backend");
***REMOVED*** }
***REMOVED***preProd HAProxy //preProd HAProxy
***REMOVED*** if (HProxy.equals("dataminer1-pre.d4science.org")) ***REMOVED*** // if (HProxy.equals("dataminer1-pre.d4science.org")) {
***REMOVED*** cl.setName("dataminer1-pre.d4science.org"); // cl.setName("dataminer1-pre.d4science.org");
***REMOVED*** ***REMOVED*** // }
return cl; return cl;
***REMOVED*** }
public List<Host> listDataMinersByCluster(String targetVREToken,String targetVRE) throws IOException ***REMOVED*** public List<Host> listDataMinersByCluster(String targetVREToken,String targetVRE) throws IOException {
SecurityTokenProvider.instance.set(targetVREToken); SecurityTokenProvider.instance.set(targetVREToken);
ScopeProvider.instance.set(targetVRE); ScopeProvider.instance.set(targetVRE);
***REMOVED*** next op to use when Cluster info available in the IS // next op to use when Cluster info available in the IS
***REMOVED*** Cluster cluster = this.getClusterByHProxy(); // Cluster cluster = this.getClusterByHProxy();
Cluster cluster = this.MapCluster(); Cluster cluster = this.MapCluster();
List<Host> out = new LinkedList<Host>(); List<Host> out = new LinkedList<Host>();
Host a = new Host(); Host a = new Host();
***REMOVED***no proxy dataminer (preprod) //no proxy dataminer (preprod)
if (cluster.getName() == null)***REMOVED*** if (cluster.getName() == null){
a.setName(ISClient.getHProxy()); a.setName(ISClient.getHProxy());
out.add(a); out.add(a);
***REMOVED*** }
***REMOVED*** if preprod, just one dm available // if preprod, just one dm available
***REMOVED*** if (cluster.getName().equals("dataminer1-pre.d4science.org")) ***REMOVED*** // if (cluster.getName().equals("dataminer1-pre.d4science.org")) {
***REMOVED*** a.setName("dataminer1-pre.d4science.org"); // a.setName("dataminer1-pre.d4science.org");
***REMOVED*** out.add(a); // out.add(a);
***REMOVED******REMOVED*** //}
else ***REMOVED*** else {
***REMOVED*** prod // prod
***REMOVED***URL stockURL = new //URL stockURL = new
***REMOVED***URL("http:***REMOVED***data.d4science.org/Yk4zSFF6V3JOSytNd3JkRDlnRFpDUUR5TnRJZEw2QjRHbWJQNStIS0N6Yz0"); //URL("http://data.d4science.org/Yk4zSFF6V3JOSytNd3JkRDlnRFpDUUR5TnRJZEw2QjRHbWJQNStIS0N6Yz0");
URL stockURL = new URL("http:***REMOVED***"+ ISClient.getHProxy() +":8880/;csv"); URL stockURL = new URL("http://"+ ISClient.getHProxy() +":8880/;csv");
***REMOVED***URL stockURL = new URL("http:***REMOVED***data.d4science.org/c29KTUluTkZnRlB0WXE5NVNaZnRoR0dtYThUSmNTVlhHbWJQNStIS0N6Yz0"); //URL stockURL = new URL("http://data.d4science.org/c29KTUluTkZnRlB0WXE5NVNaZnRoR0dtYThUSmNTVlhHbWJQNStIS0N6Yz0");
***REMOVED***System.out.println(stockURL); //System.out.println(stockURL);
***REMOVED*** dev // dev
***REMOVED***URL stockURL = new //URL stockURL = new
***REMOVED***URL("http:***REMOVED***data.d4science.org/c29KTUluTkZnRlB0WXE5NVNaZnRoR0dtYThUSmNTVlhHbWJQNStIS0N6Yz0"); //URL("http://data.d4science.org/c29KTUluTkZnRlB0WXE5NVNaZnRoR0dtYThUSmNTVlhHbWJQNStIS0N6Yz0");
BufferedReader in = new BufferedReader(new InputStreamReader(stockURL.openStream())); BufferedReader in = new BufferedReader(new InputStreamReader(stockURL.openStream()));
reader = new CSVReader(in, ','); reader = new CSVReader(in, ',');
String[] nextLine; String[] nextLine;
while ((nextLine = reader.readNext()) != null) ***REMOVED*** while ((nextLine = reader.readNext()) != null) {
if (nextLine[1].equals("BACKEND") || (nextLine[1].equals("FRONTEND"))) ***REMOVED*** if (nextLine[1].equals("BACKEND") || (nextLine[1].equals("FRONTEND"))) {
continue; continue;
***REMOVED*** }
if (nextLine[0].equals(cluster.getName())) ***REMOVED*** if (nextLine[0].equals(cluster.getName())) {
Host b = new Host(); Host b = new Host();
b.setName(nextLine[1]); b.setName(nextLine[1]);
out.add(b); out.add(b);
this.logger.info(b.getFullyQualifiedName()); this.logger.info(b.getFullyQualifiedName());
***REMOVED*** }
***REMOVED*** }
***REMOVED*** }
this.logger.info(out.toString()); this.logger.info(out.toString());
return out; return out;
***REMOVED*** }
public static void main(String[] args) throws ObjectNotFound, Exception ***REMOVED*** public static void main(String[] args) throws ObjectNotFound, Exception {
HAProxy a = new HAProxy(); HAProxy a = new HAProxy();
***REMOVED***ScopeProvider.instance.set("/gcube/devNext/NextNext"); //ScopeProvider.instance.set("/gcube/devNext/NextNext");
***REMOVED***ScopeProvider.instance.set("/d4science.research-infrastructures.eu/gCubeApps/RPrototypingLab"); //ScopeProvider.instance.set("/d4science.research-infrastructures.eu/gCubeApps/RPrototypingLab");
SecurityTokenProvider.instance.set("***REMOVED***"); SecurityTokenProvider.instance.set("3a23bfa4-4dfe-44fc-988f-194b91071dd2-843339462");
CheckPermission test = new CheckPermission(); CheckPermission test = new CheckPermission();
CheckPermission.apply("***REMOVED***", "/gcube/devNext/NextNext"); CheckPermission.apply("708e7eb8-11a7-4e9a-816b-c9ed7e7e99fe-98187548", "/gcube/devNext/NextNext");
***REMOVED***ScopeProvider.instance.set("/d4science.research-infrastructures.eu/gCubeApps/RPrototypingLab"); //ScopeProvider.instance.set("/d4science.research-infrastructures.eu/gCubeApps/RPrototypingLab");
***REMOVED*** System.out.println(a.getHProxy()); // System.out.println(a.getHProxy());
***REMOVED*** System.out.println(a.MapCluster()); // System.out.println(a.MapCluster());
***REMOVED***System.out.println(a.listDataMinersByCluster("***REMOVED***","/gcube/devNext/NextNext")); //System.out.println(a.listDataMinersByCluster("708e7eb8-11a7-4e9a-816b-c9ed7e7e99fe-98187548","/gcube/devNext/NextNext"));
***REMOVED*** System.out.println(a.listDataMinersByCluster()); // System.out.println(a.listDataMinersByCluster());
***REMOVED*** List<Dependency> list = new LinkedList<Dependency>(); // List<Dependency> list = new LinkedList<Dependency>();
***REMOVED*** Dependency aa = new Dependency(); // Dependency aa = new Dependency();
***REMOVED*** aa.setName("testnunzio"); // aa.setName("testnunzio");
***REMOVED*** aa.setType("cran:"); // aa.setType("cran:");
***REMOVED*** list.add(aa); // list.add(aa);
***REMOVED*** a.checkSVNdep(); // a.checkSVNdep();
***REMOVED*** System.out.println(a.getDataminer("dataminer1-devnext.d4science.org").getDomain()); // System.out.println(a.getDataminer("dataminer1-devnext.d4science.org").getDomain());
***REMOVED*** System.out.println(a.listDataminersInVRE()); // System.out.println(a.listDataminersInVRE());
***REMOVED*** }
***REMOVED*** }

246
src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/clients/ISClient.java
View File

@ -3,19 +3,19 @@ package org.gcube.dataanalysis.dataminer.poolmanager.clients;
import static org.gcube.resources.discovery.icclient.ICFactory.clientFor; import static org.gcube.resources.discovery.icclient.ICFactory.clientFor;
import static org.gcube.resources.discovery.icclient.ICFactory.queryFor; import static org.gcube.resources.discovery.icclient.ICFactory.queryFor;
***REMOVED*** import java.io.IOException;
import java.io.StringWriter; import java.io.StringWriter;
import java.util.Arrays; import java.util.Arrays;
import java.util.Collection; import java.util.Collection;
***REMOVED*** import java.util.List;
import java.util.Vector; import java.util.Vector;
***REMOVED*** import org.gcube.common.authorization.library.provider.SecurityTokenProvider;
import org.gcube.common.resources.gcore.GenericResource; import org.gcube.common.resources.gcore.GenericResource;
import org.gcube.common.resources.gcore.Resources; import org.gcube.common.resources.gcore.Resources;
import org.gcube.common.resources.gcore.ServiceEndpoint; import org.gcube.common.resources.gcore.ServiceEndpoint;
***REMOVED*** import org.gcube.common.scope.api.ScopeProvider;
***REMOVED*** import org.gcube.dataanalysis.dataminer.poolmanager.datamodel.Algorithm;
import org.gcube.dataanalysis.dataminer.poolmanager.datamodel.Host; import org.gcube.dataanalysis.dataminer.poolmanager.datamodel.Host;
import org.gcube.informationsystem.publisher.AdvancedScopedPublisher; import org.gcube.informationsystem.publisher.AdvancedScopedPublisher;
import org.gcube.informationsystem.publisher.RegistryPublisherFactory; import org.gcube.informationsystem.publisher.RegistryPublisherFactory;
@ -23,40 +23,40 @@ import org.gcube.informationsystem.publisher.ScopedPublisher;
import org.gcube.informationsystem.publisher.exception.RegistryNotFoundException; import org.gcube.informationsystem.publisher.exception.RegistryNotFoundException;
import org.gcube.resources.discovery.client.api.DiscoveryClient; import org.gcube.resources.discovery.client.api.DiscoveryClient;
import org.gcube.resources.discovery.client.queries.api.SimpleQuery; import org.gcube.resources.discovery.client.queries.api.SimpleQuery;
***REMOVED*** import org.slf4j.Logger;
***REMOVED*** import org.slf4j.LoggerFactory;
***REMOVED*** import org.tmatesoft.svn.core.SVNException;
public class ISClient ***REMOVED*** public class ISClient {
private Logger logger; private Logger logger;
public ISClient() ***REMOVED*** public ISClient() {
this.logger = LoggerFactory.getLogger(ISClient.class); this.logger = LoggerFactory.getLogger(ISClient.class);
***REMOVED*** }
public Host getDataminer(String hostname) ***REMOVED*** public Host getDataminer(String hostname) {
Host h = new Host(); Host h = new Host();
boolean remote2 = true; boolean remote2 = true;
if (!remote2) ***REMOVED*** if (!remote2) {
h.setName("dataminer1-devnext.d4science.org"); h.setName("dataminer1-devnext.d4science.org");
return h; return h;
***REMOVED*** else ***REMOVED*** } else {
***REMOVED***SimpleQuery query = queryFor(ServiceEndpoint.class); //SimpleQuery query = queryFor(ServiceEndpoint.class);
***REMOVED***query.addCondition("$resource/Profile/RunTime/HostedOn/text() eq '" + hostname + "'"); //query.addCondition("$resource/Profile/RunTime/HostedOn/text() eq '" + hostname + "'");
***REMOVED***DiscoveryClient<ServiceEndpoint> client = clientFor(ServiceEndpoint.class); //DiscoveryClient<ServiceEndpoint> client = clientFor(ServiceEndpoint.class);
***REMOVED***List<ServiceEndpoint> resources = client.submit(query); //List<ServiceEndpoint> resources = client.submit(query);
***REMOVED***ServiceEndpoint a = resources.get(0); //ServiceEndpoint a = resources.get(0);
***REMOVED***h.setName(a.profile().runtime().hostedOn()); //h.setName(a.profile().runtime().hostedOn());
h.setName(hostname); h.setName(hostname);
***REMOVED*** }
return h; return h;
***REMOVED*** }
***REMOVED*** return the HProxy hostname in the VRE // return the HProxy hostname in the VRE
public static String getHProxy() ***REMOVED*** public static String getHProxy() {
Host h = new Host(); Host h = new Host();
SimpleQuery query = queryFor(ServiceEndpoint.class); SimpleQuery query = queryFor(ServiceEndpoint.class);
query.addCondition("$resource/Profile/Name/text() eq 'DataMiner'"); query.addCondition("$resource/Profile/Name/text() eq 'DataMiner'");
@ -64,29 +64,29 @@ public class ISClient ***REMOVED***
List<ServiceEndpoint> resources = client.submit(query); List<ServiceEndpoint> resources = client.submit(query);
h.setName(resources.get(0).profile().runtime().hostedOn()); h.setName(resources.get(0).profile().runtime().hostedOn());
return h.getName(); return h.getName();
***REMOVED*** }
public Collection<Host> listDataminersInVRE() ***REMOVED*** public Collection<Host> listDataminersInVRE() {
boolean remote = false; boolean remote = false;
if (!remote) ***REMOVED*** if (!remote) {
Collection<Host> out = new Vector<>(); Collection<Host> out = new Vector<>();
Host h = new Host(); Host h = new Host();
***REMOVED*** h.setName("bb-dataminer.res.eng.it"); // h.setName("bb-dataminer.res.eng.it");
***REMOVED*** h.setName("vm101.ui.savba.sk"); // h.setName("vm101.ui.savba.sk");
h.setName("dataminer1-devnext.d4science.org"); h.setName("dataminer1-devnext.d4science.org");
out.add(h); out.add(h);
return out; return out;
***REMOVED*** else ***REMOVED*** } else {
SimpleQuery query = queryFor(ServiceEndpoint.class); SimpleQuery query = queryFor(ServiceEndpoint.class);
***REMOVED*** old version // old version
***REMOVED*** query.addCondition("$resource/Profile/Category/text() eq // query.addCondition("$resource/Profile/Category/text() eq
***REMOVED*** 'DataAnalysis'") // 'DataAnalysis'")
***REMOVED*** .addCondition("$resource/Profile/Name/text() eq 'DataMiner'"); // .addCondition("$resource/Profile/Name/text() eq 'DataMiner'");
query.addCondition("$resource/Profile/Platform/Name/text() eq 'DataMiner'"); query.addCondition("$resource/Profile/Platform/Name/text() eq 'DataMiner'");
@ -95,17 +95,17 @@ public class ISClient ***REMOVED***
List<ServiceEndpoint> resources = client.submit(query); List<ServiceEndpoint> resources = client.submit(query);
Collection<Host> out = new Vector<>(); Collection<Host> out = new Vector<>();
for (ServiceEndpoint r : resources) ***REMOVED*** for (ServiceEndpoint r : resources) {
Host h = new Host(); Host h = new Host();
h.setName(r.profile().runtime().hostedOn()); h.setName(r.profile().runtime().hostedOn());
out.add(h); out.add(h);
***REMOVED*** }
return out; return out;
***REMOVED*** }
***REMOVED*** }
public void updateAlg(Algorithm algo) ***REMOVED*** public void updateAlg(Algorithm algo) {
ScopedPublisher scopedPublisher = RegistryPublisherFactory.scopedPublisher(); ScopedPublisher scopedPublisher = RegistryPublisherFactory.scopedPublisher();
@ -113,137 +113,137 @@ public class ISClient ***REMOVED***
query.addCondition("$resource/Profile/Name/text() eq '" + algo.getName() + "'").setResult("$resource"); query.addCondition("$resource/Profile/Name/text() eq '" + algo.getName() + "'").setResult("$resource");
DiscoveryClient<GenericResource> client = clientFor(GenericResource.class); DiscoveryClient<GenericResource> client = clientFor(GenericResource.class);
List<GenericResource> ds = client.submit(query); List<GenericResource> ds = client.submit(query);
if (ds.isEmpty()) ***REMOVED*** if (ds.isEmpty()) {
return; return;
***REMOVED*** }
GenericResource a = ds.get(0); GenericResource a = ds.get(0);
a.profile().newBody(this.getAlgoBody(algo)); a.profile().newBody(this.getAlgoBody(algo));
try ***REMOVED*** try {
scopedPublisher.update(a); scopedPublisher.update(a);
***REMOVED*** catch (RegistryNotFoundException e) ***REMOVED*** } catch (RegistryNotFoundException e) {
e.printStackTrace(); e.printStackTrace();
***REMOVED*** }
***REMOVED*** }
private String getAlgoBody(Algorithm algo) ***REMOVED*** private String getAlgoBody(Algorithm algo) {
return "<category>" + algo.getCategory() + "</category>" + "\n" + "<clazz>" + algo.getClazz() + "</clazz>" return "<category>" + algo.getCategory() + "</category>" + "\n" + "<clazz>" + algo.getClazz() + "</clazz>"
+ "\n" + "<algorithmType>" + algo.getAlgorithmType() + "</algorithmType>" + "\n" + "<skipJava>" + "\n" + "<algorithmType>" + algo.getAlgorithmType() + "</algorithmType>" + "\n" + "<skipJava>"
+ algo.getSkipJava() + "</skipJava>" + "\n" + "<packageURL>" + algo.getPackageURL() + "</packageURL>" + algo.getSkipJava() + "</skipJava>" + "\n" + "<packageURL>" + algo.getPackageURL() + "</packageURL>"
+ "\n" + "<dependencies>" + algo.getDependencies() + "</dependencies>"; + "\n" + "<dependencies>" + algo.getDependencies() + "</dependencies>";
***REMOVED*** }
***REMOVED*** public void addAlgToIs(Algorithm algo) ***REMOVED*** // public void addAlgToIs(Algorithm algo) {
***REMOVED*** GenericResource a = new GenericResource(); // GenericResource a = new GenericResource();
***REMOVED*** a.newProfile().name(algo.getName()).type("StatisticalManagerAlgorithm").description(algo.getDescription()); // a.newProfile().name(algo.getName()).type("StatisticalManagerAlgorithm").description(algo.getDescription());
***REMOVED*** a.profile().newBody(this.getAlgoBody(algo)); // a.profile().newBody(this.getAlgoBody(algo));
***REMOVED*** try ***REMOVED*** // try {
***REMOVED*** publishScopedResource(a, Arrays.asList(new String[] ***REMOVED*** ScopeProvider.instance.get() ***REMOVED***)); // publishScopedResource(a, Arrays.asList(new String[] { ScopeProvider.instance.get() }));
***REMOVED*** ***REMOVED*** catch (Exception e) ***REMOVED*** // } catch (Exception e) {
***REMOVED*** e.printStackTrace(); // e.printStackTrace();
***REMOVED*** ***REMOVED*** // }
***REMOVED******REMOVED*** // }
public void addAlgToIs(Algorithm algo, String token) ***REMOVED*** public void addAlgToIs(Algorithm algo, String token) {
GenericResource a = new GenericResource(); GenericResource a = new GenericResource();
a.newProfile().name(algo.getName()).type("StatisticalManagerAlgorithm").description(algo.getDescription()); a.newProfile().name(algo.getName()).type("StatisticalManagerAlgorithm").description(algo.getDescription());
a.profile().newBody(this.getAlgoBody(algo)); a.profile().newBody(this.getAlgoBody(algo));
try ***REMOVED*** try {
SecurityTokenProvider.instance.set(token); SecurityTokenProvider.instance.set(token);
publishScopedResource(a, Arrays.asList(new String[] ***REMOVED*** SecurityTokenProvider.instance.get() ***REMOVED***)); publishScopedResource(a, Arrays.asList(new String[] { SecurityTokenProvider.instance.get() }));
***REMOVED*** catch (Exception e) ***REMOVED*** } catch (Exception e) {
e.printStackTrace(); e.printStackTrace();
***REMOVED*** }
***REMOVED*** }
public void unPublishScopedResource(GenericResource resource) throws RegistryNotFoundException, Exception ***REMOVED*** public void unPublishScopedResource(GenericResource resource) throws RegistryNotFoundException, Exception {
ScopedPublisher scopedPublisher = RegistryPublisherFactory.scopedPublisher(); ScopedPublisher scopedPublisher = RegistryPublisherFactory.scopedPublisher();
AdvancedScopedPublisher advancedScopedPublisher = new AdvancedScopedPublisher(scopedPublisher); AdvancedScopedPublisher advancedScopedPublisher = new AdvancedScopedPublisher(scopedPublisher);
String id = resource.id(); String id = resource.id();
this.logger.info("Trying to remove ***REMOVED******REMOVED*** with ID ***REMOVED******REMOVED*** from ***REMOVED******REMOVED***", resource.getClass().getSimpleName(), id, this.logger.info("Trying to remove {} with ID {} from {}", resource.getClass().getSimpleName(), id,
ScopeProvider.instance.get()); ScopeProvider.instance.get());
***REMOVED*** scopedPublisher.remove(resource, scopes); // scopedPublisher.remove(resource, scopes);
advancedScopedPublisher.forceRemove(resource); advancedScopedPublisher.forceRemove(resource);
this.logger.info("***REMOVED******REMOVED*** with ID ***REMOVED******REMOVED*** removed successfully", resource.getClass().getSimpleName(), id); this.logger.info("{} with ID {} removed successfully", resource.getClass().getSimpleName(), id);
***REMOVED*** }
public void publishScopedResource(GenericResource a, List<String> scopes) public void publishScopedResource(GenericResource a, List<String> scopes)
throws RegistryNotFoundException, Exception ***REMOVED*** throws RegistryNotFoundException, Exception {
StringWriter stringWriter = new StringWriter(); StringWriter stringWriter = new StringWriter();
Resources.marshal(a, stringWriter); Resources.marshal(a, stringWriter);
ScopedPublisher scopedPublisher = RegistryPublisherFactory.scopedPublisher(); ScopedPublisher scopedPublisher = RegistryPublisherFactory.scopedPublisher();
try ***REMOVED*** try {
this.logger.debug(scopes.toString()); this.logger.debug(scopes.toString());
this.logger.debug(stringWriter.toString()); this.logger.debug(stringWriter.toString());
scopedPublisher.create(a, scopes); scopedPublisher.create(a, scopes);
***REMOVED*** catch (RegistryNotFoundException e) ***REMOVED*** } catch (RegistryNotFoundException e) {
this.logger.error("Registry not found",e); this.logger.error("Registry not found",e);
throw e; throw e;
***REMOVED*** }
***REMOVED*** }
***REMOVED*** public Set<Algorithm> getAlgoFromIs() ***REMOVED*** // public Set<Algorithm> getAlgoFromIs() {
***REMOVED******REMOVED*** // // TODO Auto-generated method stub
***REMOVED*** //
***REMOVED*** Set<Algorithm> out = new HashSet<Algorithm>(); // Set<Algorithm> out = new HashSet<Algorithm>();
***REMOVED*** SimpleQuery query = queryFor(GenericResource.class); // SimpleQuery query = queryFor(GenericResource.class);
***REMOVED*** query.addCondition("$resource/Profile/SecondaryType/text() eq 'StatisticalManagerAlgorithm'") // query.addCondition("$resource/Profile/SecondaryType/text() eq 'StatisticalManagerAlgorithm'")
***REMOVED*** .setResult("$resource"); // .setResult("$resource");
***REMOVED*** DiscoveryClient<GenericResource> client = clientFor(GenericResource.class); // DiscoveryClient<GenericResource> client = clientFor(GenericResource.class);
***REMOVED*** List<GenericResource> ds = client.submit(query); // List<GenericResource> ds = client.submit(query);
***REMOVED*** for (GenericResource a : ds) ***REMOVED*** // for (GenericResource a : ds) {
***REMOVED*** out.add(this.convertAlgo(a)); // out.add(this.convertAlgo(a));
***REMOVED*** ***REMOVED*** // }
***REMOVED*** return out; // return out;
***REMOVED******REMOVED*** // }
***REMOVED*** private Algorithm convertAlgo(GenericResource a) ***REMOVED*** // private Algorithm convertAlgo(GenericResource a) {
***REMOVED*** Algorithm out = new Algorithm(); // Algorithm out = new Algorithm();
***REMOVED*** //
***REMOVED*** ***REMOVED*** out.setId(a.profile().body().getElementsByTagName("id").item(0).getTextContent()); // // out.setId(a.profile().body().getElementsByTagName("id").item(0).getTextContent());
***REMOVED*** out.setAlgorithmType(a.profile().body().getElementsByTagName("algorithmType").item(0).getTextContent()); // out.setAlgorithmType(a.profile().body().getElementsByTagName("algorithmType").item(0).getTextContent());
***REMOVED*** out.setCategory(a.profile().body().getElementsByTagName("category").item(0).getTextContent()); // out.setCategory(a.profile().body().getElementsByTagName("category").item(0).getTextContent());
***REMOVED*** out.setClazz(a.profile().body().getElementsByTagName("clazz").item(0).getTextContent()); // out.setClazz(a.profile().body().getElementsByTagName("clazz").item(0).getTextContent());
***REMOVED*** out.setName(a.profile().name()); // out.setName(a.profile().name());
***REMOVED*** out.setPackageURL(a.profile().body().getElementsByTagName("packageURL").item(0).getTextContent()); // out.setPackageURL(a.profile().body().getElementsByTagName("packageURL").item(0).getTextContent());
***REMOVED*** out.setSkipJava(a.profile().body().getElementsByTagName("skipJava").item(0).getTextContent()); // out.setSkipJava(a.profile().body().getElementsByTagName("skipJava").item(0).getTextContent());
***REMOVED*** out.setDescription(a.profile().description()); // out.setDescription(a.profile().description());
***REMOVED*** //
***REMOVED*** Set<org.gcube.dataanalysis.dataminer.poolmanager.datamodel.Dependency> deps = new HashSet<org.gcube.dataanalysis.dataminer.poolmanager.datamodel.Dependency>(); // Set<org.gcube.dataanalysis.dataminer.poolmanager.datamodel.Dependency> deps = new HashSet<org.gcube.dataanalysis.dataminer.poolmanager.datamodel.Dependency>();
***REMOVED*** for (int i = 0; i < a.profile().body().getElementsByTagName("dependencies").getLength(); i++) ***REMOVED*** // for (int i = 0; i < a.profile().body().getElementsByTagName("dependencies").getLength(); i++) {
***REMOVED*** org.gcube.dataanalysis.dataminer.poolmanager.datamodel.Dependency d1 = new org.gcube.dataanalysis.dataminer.poolmanager.datamodel.Dependency(); // org.gcube.dataanalysis.dataminer.poolmanager.datamodel.Dependency d1 = new org.gcube.dataanalysis.dataminer.poolmanager.datamodel.Dependency();
***REMOVED*** d1.setName(a.profile().body().getElementsByTagName("dependencies").item(i).getTextContent()); // d1.setName(a.profile().body().getElementsByTagName("dependencies").item(i).getTextContent());
***REMOVED*** deps.add(d1); // deps.add(d1);
***REMOVED*** ***REMOVED*** // }
***REMOVED*** out.setDependencies(deps); // out.setDependencies(deps);
***REMOVED*** return out; // return out;
***REMOVED******REMOVED*** // }
public static void main(String[] args) throws IOException, SVNException ***REMOVED*** public static void main(String[] args) throws IOException, SVNException {
ISClient a = new ISClient(); ISClient a = new ISClient();
ScopeProvider.instance.set("/gcube/devNext/NextNext"); ScopeProvider.instance.set("/gcube/devNext/NextNext");
***REMOVED*** System.out.println(a.getHProxy()); // System.out.println(a.getHProxy());
***REMOVED*** System.out.println(a.MapCluster()); // System.out.println(a.MapCluster());
***REMOVED*** System.out.println(a.listDataMinersByCluster()); // System.out.println(a.listDataMinersByCluster());
***REMOVED*** System.out.println(a.listDataMinersByCluster()); // System.out.println(a.listDataMinersByCluster());
***REMOVED*** List<Dependency> list = new LinkedList<Dependency>(); // List<Dependency> list = new LinkedList<Dependency>();
***REMOVED*** Dependency aa = new Dependency(); // Dependency aa = new Dependency();
***REMOVED*** aa.setName("testnunzio"); // aa.setName("testnunzio");
***REMOVED*** aa.setType("cran:"); // aa.setType("cran:");
***REMOVED*** list.add(aa); // list.add(aa);
***REMOVED*** a.checkSVNdep(); // a.checkSVNdep();
***REMOVED***System.out.println(a.getDataminer("dataminer1-d-d4s.d4science.org").getDomain()); //System.out.println(a.getDataminer("dataminer1-d-d4s.d4science.org").getDomain());
***REMOVED*** System.out.println(a.listDataminersInVRE()); // System.out.println(a.listDataminersInVRE());
***REMOVED*** }
***REMOVED*** }

8
src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/clients/ScopedCacheMap.java
View File

@ -4,15 +4,15 @@ import java.util.HashMap;
import org.gcube.dataanalysis.dataminer.poolmanager.clients.configuration.ClientConfigurationCache; import org.gcube.dataanalysis.dataminer.poolmanager.clients.configuration.ClientConfigurationCache;
public class ScopedCacheMap extends HashMap<String, ClientConfigurationCache> ***REMOVED*** public class ScopedCacheMap extends HashMap<String, ClientConfigurationCache> {
***REMOVED**** /**
* *
***REMOVED*** */
private static final long serialVersionUID = 1L; private static final long serialVersionUID = 1L;
***REMOVED*** }

56
src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/clients/configuration/ClientConfigurationCache.java
View File

@ -6,7 +6,7 @@ import static org.gcube.resources.discovery.icclient.ICFactory.queryFor;
import java.util.Date; import java.util.Date;
import java.util.HashMap; import java.util.HashMap;
import java.util.Iterator; import java.util.Iterator;
***REMOVED*** import java.util.List;
import java.util.Map; import java.util.Map;
import org.gcube.common.resources.gcore.GenericResource; import org.gcube.common.resources.gcore.GenericResource;
@ -14,11 +14,11 @@ import org.gcube.dataanalysis.dataminer.poolmanager.clients.configuration.Config
import org.gcube.dataanalysis.dataminer.poolmanager.clients.configurations.AbstractConfiguration; import org.gcube.dataanalysis.dataminer.poolmanager.clients.configurations.AbstractConfiguration;
import org.gcube.resources.discovery.client.api.DiscoveryClient; import org.gcube.resources.discovery.client.api.DiscoveryClient;
import org.gcube.resources.discovery.client.queries.api.SimpleQuery; import org.gcube.resources.discovery.client.queries.api.SimpleQuery;
***REMOVED*** import org.slf4j.Logger;
***REMOVED*** import org.slf4j.LoggerFactory;
public class ClientConfigurationCache public class ClientConfigurationCache
***REMOVED*** {
private Logger logger; private Logger logger;
private SVNRepository svnRepository; private SVNRepository svnRepository;
@ -26,48 +26,48 @@ public class ClientConfigurationCache
private long svnRepositoryTimeout; private long svnRepositoryTimeout;
private Map<String, Long> configurationsTimeouts; private Map<String, Long> configurationsTimeouts;
private final long duration = 120000; ***REMOVED***2 minutes private final long duration = 120000; //2 minutes
ClientConfigurationCache () ClientConfigurationCache ()
***REMOVED*** {
this.logger = LoggerFactory.getLogger(ClientConfigurationCache.class); this.logger = LoggerFactory.getLogger(ClientConfigurationCache.class);
this.svnRepository = null; this.svnRepository = null;
this.configurations = new HashMap<>(); this.configurations = new HashMap<>();
this.svnRepositoryTimeout = 0; this.svnRepositoryTimeout = 0;
this.configurationsTimeouts = new HashMap<>(); this.configurationsTimeouts = new HashMap<>();
***REMOVED*** }
public AbstractConfiguration getConfiguration (CONFIGURATIONS configuration) public AbstractConfiguration getConfiguration (CONFIGURATIONS configuration)
***REMOVED*** {
Long time = this.configurationsTimeouts.get(configuration.toString()); Long time = this.configurationsTimeouts.get(configuration.toString());
long currentTime = new Date().getTime(); long currentTime = new Date().getTime();
if (time == null || currentTime > time+this.duration) if (time == null || currentTime > time+this.duration)
***REMOVED*** {
this.configurations.put(configuration.toString(), getConfiguration (configuration.getType())); this.configurations.put(configuration.toString(), getConfiguration (configuration.getType()));
this.configurationsTimeouts.put(configuration.toString(), currentTime); this.configurationsTimeouts.put(configuration.toString(), currentTime);
***REMOVED*** }
return this.configurations.get(configuration.toString()); return this.configurations.get(configuration.toString());
***REMOVED*** }
public SVNRepository getSVNRepository () public SVNRepository getSVNRepository ()
***REMOVED*** {
long currentTime = new Date().getTime(); long currentTime = new Date().getTime();
if (this.svnRepositoryTimeout == 0 || currentTime > this.svnRepositoryTimeout+this.duration) if (this.svnRepositoryTimeout == 0 || currentTime > this.svnRepositoryTimeout+this.duration)
***REMOVED*** {
this.svnRepository = queryForRepository(); this.svnRepository = queryForRepository();
this.svnRepositoryTimeout = currentTime; this.svnRepositoryTimeout = currentTime;
***REMOVED*** }
return this.svnRepository; return this.svnRepository;
***REMOVED*** }
private SVNRepository queryForRepository() private SVNRepository queryForRepository()
***REMOVED*** {
SimpleQuery query = queryFor(GenericResource.class); SimpleQuery query = queryFor(GenericResource.class);
query.addCondition("$resource/Profile/SecondaryType/text() eq 'DMPMConfigurator'").setResult("$resource"); query.addCondition("$resource/Profile/SecondaryType/text() eq 'DMPMConfigurator'").setResult("$resource");
DiscoveryClient<GenericResource> client = clientFor(GenericResource.class); DiscoveryClient<GenericResource> client = clientFor(GenericResource.class);
@ -76,12 +76,12 @@ public class ClientConfigurationCache
SVNRepository response = null; SVNRepository response = null;
while (resourcesIterator.hasNext() && response == null) while (resourcesIterator.hasNext() && response == null)
***REMOVED*** {
GenericResource resource = resourcesIterator.next(); GenericResource resource = resourcesIterator.next();
String repositoryURL = resource.profile().body().getElementsByTagName(SVNRepository.REPOSITORY_URL).item(0).getTextContent(); String repositoryURL = resource.profile().body().getElementsByTagName(SVNRepository.REPOSITORY_URL).item(0).getTextContent();
if (repositoryURL != null) if (repositoryURL != null)
***REMOVED*** {
String repositoryPath = resource.profile().body().getElementsByTagName(SVNRepository.REPOSITORY_PATH).item(0).getTextContent(); String repositoryPath = resource.profile().body().getElementsByTagName(SVNRepository.REPOSITORY_PATH).item(0).getTextContent();
String repositoryUsername = null; String repositoryUsername = null;
@ -89,7 +89,7 @@ public class ClientConfigurationCache
try try
***REMOVED*** {
repositoryUsername = resource.profile().body().getElementsByTagName(SVNRepository.REPOSITORY_USERNAME).item(0).getTextContent(); repositoryUsername = resource.profile().body().getElementsByTagName(SVNRepository.REPOSITORY_USERNAME).item(0).getTextContent();
repositoryPassword = resource.profile().body().getElementsByTagName(SVNRepository.REPOSITORY_PASSWORD).item(0).getTextContent(); repositoryPassword = resource.profile().body().getElementsByTagName(SVNRepository.REPOSITORY_PASSWORD).item(0).getTextContent();
@ -100,31 +100,31 @@ public class ClientConfigurationCache
this.logger.debug("Repository username "+repositoryUsername); this.logger.debug("Repository username "+repositoryUsername);
this.logger.debug("Repository password "+repositoryPassword); this.logger.debug("Repository password "+repositoryPassword);
***REMOVED*** catch (Exception e) } catch (Exception e)
***REMOVED*** {
this.logger.debug("SVN Username and password not present"); this.logger.debug("SVN Username and password not present");
***REMOVED*** }
this.logger.debug("SVN Repository URL: "+repositoryURL); this.logger.debug("SVN Repository URL: "+repositoryURL);
this.logger.debug("SVN Repository path: "+repositoryPath); this.logger.debug("SVN Repository path: "+repositoryPath);
response = new SVNRepository(repositoryURL, repositoryPath,repositoryUsername, repositoryPassword); response = new SVNRepository(repositoryURL, repositoryPath,repositoryUsername, repositoryPassword);
***REMOVED*** }
***REMOVED*** }
return response; return response;
***REMOVED*** }
private AbstractConfiguration getConfiguration (AbstractConfiguration type) private AbstractConfiguration getConfiguration (AbstractConfiguration type)
***REMOVED*** {
SimpleQuery query = queryFor(GenericResource.class); SimpleQuery query = queryFor(GenericResource.class);
query.addCondition("$resource/Profile/SecondaryType/text() eq 'DMPMConfigurator'").setResult(type.getXMLModel()); query.addCondition("$resource/Profile/SecondaryType/text() eq 'DMPMConfigurator'").setResult(type.getXMLModel());
DiscoveryClient<? extends AbstractConfiguration> client = clientFor(type.getClass()); DiscoveryClient<? extends AbstractConfiguration> client = clientFor(type.getClass());
List<? extends AbstractConfiguration> configurations = client.submit(query); List<? extends AbstractConfiguration> configurations = client.submit(query);
if (configurations != null && !configurations.isEmpty()) return configurations.get(0); if (configurations != null && !configurations.isEmpty()) return configurations.get(0);
else return null; else return null;
***REMOVED*** }
***REMOVED*** }

4
src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/clients/configuration/Configuration.java
View File

@ -1,6 +1,6 @@
package org.gcube.dataanalysis.dataminer.poolmanager.clients.configuration; package org.gcube.dataanalysis.dataminer.poolmanager.clients.configuration;
public interface Configuration ***REMOVED*** public interface Configuration {
public String getHost(); public String getHost();
@ -35,4 +35,4 @@ public interface Configuration ***REMOVED***
public String getGhostAlgoDirectory(); public String getGhostAlgoDirectory();
***REMOVED*** }

152
src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/clients/configuration/ConfigurationImpl.java
View File

@ -4,155 +4,155 @@ import org.gcube.dataanalysis.dataminer.poolmanager.clients.configurations.Abstr
import org.gcube.dataanalysis.dataminer.poolmanager.clients.configurations.Prod; import org.gcube.dataanalysis.dataminer.poolmanager.clients.configurations.Prod;
import org.gcube.dataanalysis.dataminer.poolmanager.clients.configurations.Stage; import org.gcube.dataanalysis.dataminer.poolmanager.clients.configurations.Stage;
public class ConfigurationImpl implements Configuration ***REMOVED*** public class ConfigurationImpl implements Configuration {
enum CONFIGURATIONS ***REMOVED*** enum CONFIGURATIONS {
STAGE (new Stage ()), STAGE (new Stage ()),
PROD (new Prod ()); PROD (new Prod ());
private AbstractConfiguration type; private AbstractConfiguration type;
private CONFIGURATIONS(AbstractConfiguration type) ***REMOVED*** private CONFIGURATIONS(AbstractConfiguration type) {
this.type = type; this.type = type;
***REMOVED*** }
***REMOVED*** @Override
public String toString() ***REMOVED*** public String toString() {
return this.type.getType(); return this.type.getType();
***REMOVED*** }
public AbstractConfiguration getType () public AbstractConfiguration getType ()
***REMOVED*** {
return this.type; return this.type;
***REMOVED*** }
***REMOVED*** }
***REMOVED*** enum REPOSITORIES ***REMOVED*** // enum REPOSITORIES {
***REMOVED*** REPO ("svn.repository"), // REPO ("svn.repository"),
***REMOVED*** MAIN_ALGO ("svn.algo.main.repo"); // MAIN_ALGO ("svn.algo.main.repo");
***REMOVED*** //
***REMOVED*** private String type; // private String type;
***REMOVED*** //
***REMOVED*** private REPOSITORIES(String type) ***REMOVED*** // private REPOSITORIES(String type) {
***REMOVED*** this.type = type; // this.type = type;
***REMOVED*** ***REMOVED*** // }
***REMOVED*** //
***REMOVED******REMOVED*** // @Override
***REMOVED*** public String toString() ***REMOVED*** // public String toString() {
***REMOVED*** return this.type; // return this.type;
***REMOVED*** ***REMOVED*** // }
***REMOVED******REMOVED*** // }
private CONFIGURATIONS type; private CONFIGURATIONS type;
private ClientConfigurationCache cache; private ClientConfigurationCache cache;
public ConfigurationImpl(CONFIGURATIONS type,ClientConfigurationCache cache) ***REMOVED*** public ConfigurationImpl(CONFIGURATIONS type,ClientConfigurationCache cache) {
this.type = type; this.type = type;
this.cache = cache; this.cache = cache;
***REMOVED*** }
***REMOVED*** @Override
public String getHost() ***REMOVED*** public String getHost() {
return this.cache.getConfiguration(this.type).getHost (); return this.cache.getConfiguration(this.type).getHost ();
***REMOVED*** }
***REMOVED*** @Override
public String getSVNAlgorithmsList() ***REMOVED*** public String getSVNAlgorithmsList() {
return this.cache.getConfiguration(this.type).getAlgorithmsList(); return this.cache.getConfiguration(this.type).getAlgorithmsList();
***REMOVED*** }
***REMOVED*** @Override
public String getRepository() ***REMOVED*** public String getRepository() {
return this.cache.getConfiguration(this.type).getSoftwareRepo(); return this.cache.getConfiguration(this.type).getSoftwareRepo();
***REMOVED*** }
***REMOVED*** @Override
public String getSVNLinuxCompiledDepsList() public String getSVNLinuxCompiledDepsList()
***REMOVED*** {
return this.cache.getConfiguration(this.type).getDepsLinuxCompiled(); return this.cache.getConfiguration(this.type).getDepsLinuxCompiled();
***REMOVED*** }
***REMOVED*** @Override
public String getSVNPreInstalledDepsList() ***REMOVED*** public String getSVNPreInstalledDepsList() {
return this.cache.getConfiguration(this.type).getDepsPreInstalled(); return this.cache.getConfiguration(this.type).getDepsPreInstalled();
***REMOVED*** }
***REMOVED*** @Override
public String getSVNRBDepsList() public String getSVNRBDepsList()
***REMOVED*** {
return this.cache.getConfiguration(this.type).getDepsRBlackbox(); return this.cache.getConfiguration(this.type).getDepsRBlackbox();
***REMOVED*** }
***REMOVED*** @Override
public String getSVNCRANDepsList() ***REMOVED*** public String getSVNCRANDepsList() {
return this.cache.getConfiguration(this.type).getDepsR(); return this.cache.getConfiguration(this.type).getDepsR();
***REMOVED*** }
***REMOVED*** @Override
public String getSVNJavaDepsList() ***REMOVED*** public String getSVNJavaDepsList() {
return this.cache.getConfiguration(this.type).getDepsJava(); return this.cache.getConfiguration(this.type).getDepsJava();
***REMOVED*** }
***REMOVED*** @Override
public String getSVNKWDepsList() ***REMOVED*** public String getSVNKWDepsList() {
return this.cache.getConfiguration(this.type).getDepsKnimeWorkflow(); return this.cache.getConfiguration(this.type).getDepsKnimeWorkflow();
***REMOVED*** }
***REMOVED*** @Override
public String getSVNKW4_1DepsList() ***REMOVED*** public String getSVNKW4_1DepsList() {
return this.cache.getConfiguration(this.type).getDepsKnimeWorkflow4_1(); return this.cache.getConfiguration(this.type).getDepsKnimeWorkflow4_1();
***REMOVED*** }
***REMOVED*** @Override
public String getSVNOctaveDepsList() ***REMOVED*** public String getSVNOctaveDepsList() {
return this.cache.getConfiguration(this.type).getDepsOctave(); return this.cache.getConfiguration(this.type).getDepsOctave();
***REMOVED*** }
***REMOVED*** @Override
public String getSVNPythonDepsList() ***REMOVED*** public String getSVNPythonDepsList() {
return this.cache.getConfiguration(this.type).getDepsPython(); return this.cache.getConfiguration(this.type).getDepsPython();
***REMOVED*** }
***REMOVED*** @Override
public String getSVNPython3_6DepsList() ***REMOVED*** public String getSVNPython3_6DepsList() {
return this.cache.getConfiguration(this.type).getDepsPython3_6(); return this.cache.getConfiguration(this.type).getDepsPython3_6();
***REMOVED*** }
***REMOVED*** @Override
public String getSVNWCDepsList() ***REMOVED*** public String getSVNWCDepsList() {
return this.cache.getConfiguration(this.type).getDepsWindowsCompiled(); return this.cache.getConfiguration(this.type).getDepsWindowsCompiled();
***REMOVED*** }
***REMOVED*** @Override
public SVNRepository getSVNRepository() public SVNRepository getSVNRepository()
***REMOVED*** {
return this.cache.getSVNRepository(); return this.cache.getSVNRepository();
***REMOVED*** }
***REMOVED*** @Override
public String getGhostAlgoDirectory() ***REMOVED*** public String getGhostAlgoDirectory() {
return this.cache.getConfiguration(this.type).getGhostRepo(); return this.cache.getConfiguration(this.type).getGhostRepo();
***REMOVED*** }
***REMOVED*** }

74
src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/clients/configuration/DMPMClientConfiguratorManager.java
View File

@ -1,102 +1,102 @@
package org.gcube.dataanalysis.dataminer.poolmanager.clients.configuration; package org.gcube.dataanalysis.dataminer.poolmanager.clients.configuration;
***REMOVED*** import java.io.IOException;
import java.util.ArrayList; import java.util.ArrayList;
import java.util.Iterator; import java.util.Iterator;
***REMOVED*** import java.util.List;
import java.util.Properties; import java.util.Properties;
***REMOVED*** import org.gcube.common.scope.api.ScopeProvider;
import org.gcube.dataanalysis.dataminer.poolmanager.clients.ScopedCacheMap; import org.gcube.dataanalysis.dataminer.poolmanager.clients.ScopedCacheMap;
import org.gcube.dataanalysis.dataminer.poolmanager.clients.configuration.ConfigurationImpl.CONFIGURATIONS; import org.gcube.dataanalysis.dataminer.poolmanager.clients.configuration.ConfigurationImpl.CONFIGURATIONS;
***REMOVED*** import org.slf4j.Logger;
***REMOVED*** import org.slf4j.LoggerFactory;
***REMOVED*** import org.tmatesoft.svn.core.SVNException;
public class DMPMClientConfiguratorManager ***REMOVED*** public class DMPMClientConfiguratorManager {
***REMOVED*** private final Logger logger;
private Properties defaultAdmins; private Properties defaultAdmins;
static DMPMClientConfiguratorManager instance; static DMPMClientConfiguratorManager instance;
private ScopedCacheMap cacheMap; private ScopedCacheMap cacheMap;
private DMPMClientConfiguratorManager() ***REMOVED*** private DMPMClientConfiguratorManager() {
this.cacheMap = new ScopedCacheMap(); this.cacheMap = new ScopedCacheMap();
this.logger = LoggerFactory.getLogger(DMPMClientConfiguratorManager.class); this.logger = LoggerFactory.getLogger(DMPMClientConfiguratorManager.class);
this.defaultAdmins = new Properties(); this.defaultAdmins = new Properties();
try ***REMOVED*** try {
this.defaultAdmins.load(this.getClass().getResourceAsStream("/default.admins")); this.defaultAdmins.load(this.getClass().getResourceAsStream("/default.admins"));
this.logger.debug("Default users successfully loaded"); this.logger.debug("Default users successfully loaded");
***REMOVED*** catch (Exception e) ***REMOVED*** } catch (Exception e) {
this.logger.error("Unable to get default users", e); this.logger.error("Unable to get default users", e);
***REMOVED*** }
***REMOVED*** }
private ClientConfigurationCache getCurrentCache() ***REMOVED*** private ClientConfigurationCache getCurrentCache() {
String currentScope = ScopeProvider.instance.get(); String currentScope = ScopeProvider.instance.get();
this.logger.debug("Current scope = " + currentScope); this.logger.debug("Current scope = " + currentScope);
this.logger.debug("Getting current configuration cache"); this.logger.debug("Getting current configuration cache");
ClientConfigurationCache cache = this.cacheMap.get(currentScope); ClientConfigurationCache cache = this.cacheMap.get(currentScope);
if (cache == null) ***REMOVED*** if (cache == null) {
this.logger.debug("Cache not created yet, creating..."); this.logger.debug("Cache not created yet, creating...");
cache = new ClientConfigurationCache(); cache = new ClientConfigurationCache();
this.cacheMap.put(currentScope, cache); this.cacheMap.put(currentScope, cache);
***REMOVED*** }
return cache; return cache;
***REMOVED*** }
public static DMPMClientConfiguratorManager getInstance() ***REMOVED*** public static DMPMClientConfiguratorManager getInstance() {
if (instance == null) if (instance == null)
instance = new DMPMClientConfiguratorManager(); instance = new DMPMClientConfiguratorManager();
return instance; return instance;
***REMOVED*** }
public Configuration getProductionConfiguration() ***REMOVED*** public Configuration getProductionConfiguration() {
return new ConfigurationImpl(CONFIGURATIONS.PROD, getCurrentCache()); return new ConfigurationImpl(CONFIGURATIONS.PROD, getCurrentCache());
***REMOVED*** }
public Configuration getStagingConfiguration() ***REMOVED*** public Configuration getStagingConfiguration() {
return new ConfigurationImpl(CONFIGURATIONS.STAGE, getCurrentCache()); return new ConfigurationImpl(CONFIGURATIONS.STAGE, getCurrentCache());
***REMOVED*** }
public List<String> getDefaultAdmins() ***REMOVED*** public List<String> getDefaultAdmins() {
List<String> admins = new ArrayList<String>(); List<String> admins = new ArrayList<String>();
if (defaultAdmins == null || defaultAdmins.isEmpty()) ***REMOVED*** if (defaultAdmins == null || defaultAdmins.isEmpty()) {
admins.add("statistical.manager"); admins.add("statistical.manager");
***REMOVED*** else ***REMOVED*** } else {
Iterator<Object> keys = this.defaultAdmins.keySet().iterator(); Iterator<Object> keys = this.defaultAdmins.keySet().iterator();
while (keys.hasNext()) ***REMOVED*** while (keys.hasNext()) {
String key = (String) keys.next(); String key = (String) keys.next();
admins.add(defaultAdmins.getProperty(key)); admins.add(defaultAdmins.getProperty(key));
***REMOVED*** }
***REMOVED*** }
this.logger.debug("Default admins list: " + admins); this.logger.debug("Default admins list: " + admins);
return admins; return admins;
***REMOVED*** }
public static void main(String[] args) throws IOException, SVNException ***REMOVED*** public static void main(String[] args) throws IOException, SVNException {
DMPMClientConfiguratorManager a = new DMPMClientConfiguratorManager(); DMPMClientConfiguratorManager a = new DMPMClientConfiguratorManager();
ScopeProvider.instance.set("/gcube/devNext/NextNext"); ScopeProvider.instance.set("/gcube/devNext/NextNext");
***REMOVED*** SecurityTokenProvider.instance.set("***REMOVED***"); // SecurityTokenProvider.instance.set("708e7eb8-11a7-4e9a-816b-c9ed7e7e99fe-98187548");
System.out.println("RESULT 1" + a.getStagingConfiguration().getSVNCRANDepsList()); System.out.println("RESULT 1" + a.getStagingConfiguration().getSVNCRANDepsList());
System.out.println("RESULT 2" + a.getProductionConfiguration().getRepository()); System.out.println("RESULT 2" + a.getProductionConfiguration().getRepository());
System.out.println("RESULT 3" + a.getStagingConfiguration().getSVNRepository().getPath()); System.out.println("RESULT 3" + a.getStagingConfiguration().getSVNRepository().getPath());
***REMOVED*** System.out.println(a.getRepo()); // System.out.println(a.getRepo());
***REMOVED*** System.out.println(a.getAlgoRepo()); // System.out.println(a.getAlgoRepo());
***REMOVED*** System.out.println(a.getSVNRepo()); // System.out.println(a.getSVNRepo());
***REMOVED*** }
***REMOVED*** }

36
src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/clients/configuration/SVNRepository.java
View File

@ -1,7 +1,7 @@
package org.gcube.dataanalysis.dataminer.poolmanager.clients.configuration; package org.gcube.dataanalysis.dataminer.poolmanager.clients.configuration;
public class SVNRepository public class SVNRepository
***REMOVED*** {
static final String REPOSITORY_URL = "svn.repository", static final String REPOSITORY_URL = "svn.repository",
REPOSITORY_PATH = "svn.algo.main.repo", REPOSITORY_PATH = "svn.algo.main.repo",
@ -13,41 +13,41 @@ public class SVNRepository
username, username,
password; password;
SVNRepository(String baseUrl, String path, String username, String password) ***REMOVED*** SVNRepository(String baseUrl, String path, String username, String password) {
this.baseUrl = baseUrl; this.baseUrl = baseUrl;
this.path = path; this.path = path;
this.username = username; this.username = username;
this.password = password; this.password = password;
***REMOVED*** }
SVNRepository(String baseUrl, String path) ***REMOVED*** SVNRepository(String baseUrl, String path) {
this (baseUrl, path, null, null); this (baseUrl, path, null, null);
***REMOVED*** }
public String getUsername() ***REMOVED*** public String getUsername() {
return username; return username;
***REMOVED*** }
public void setUsername(String username) ***REMOVED*** public void setUsername(String username) {
this.username = username; this.username = username;
***REMOVED*** }
public String getPassword() ***REMOVED*** public String getPassword() {
return password; return password;
***REMOVED*** }
public void setPassword(String password) ***REMOVED*** public void setPassword(String password) {
this.password = password; this.password = password;
***REMOVED*** }
public String getBaseUrl() ***REMOVED*** public String getBaseUrl() {
return baseUrl; return baseUrl;
***REMOVED*** }
public String getPath() ***REMOVED*** public String getPath() {
return path; return path;
***REMOVED*** }
***REMOVED*** }

158
src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/clients/configurations/AbstractConfiguration.java
View File

@ -4,7 +4,7 @@ import javax.xml.bind.annotation.XmlElement;
public abstract class AbstractConfiguration public abstract class AbstractConfiguration
***REMOVED*** {
private String host; private String host;
private String algorithmsList; private String algorithmsList;
@ -24,154 +24,154 @@ public abstract class AbstractConfiguration
@XmlElement (name="host") @XmlElement (name="host")
public String getHost() ***REMOVED*** public String getHost() {
return host; return host;
***REMOVED*** }
public void setHost(String host) ***REMOVED*** public void setHost(String host) {
this.host = host; this.host = host;
***REMOVED*** }
@XmlElement (name="algorithms-list") @XmlElement (name="algorithms-list")
public String getAlgorithmsList() ***REMOVED*** public String getAlgorithmsList() {
return algorithmsList; return algorithmsList;
***REMOVED*** }
public void setAlgorithmsList(String algorithmsList) ***REMOVED*** public void setAlgorithmsList(String algorithmsList) {
this.algorithmsList = algorithmsList; this.algorithmsList = algorithmsList;
***REMOVED*** }
@XmlElement (name="software-repo") @XmlElement (name="software-repo")
public String getSoftwareRepo() ***REMOVED*** public String getSoftwareRepo() {
return softwareRepo; return softwareRepo;
***REMOVED*** }
public void setSoftwareRepo(String softwareRepo) ***REMOVED*** public void setSoftwareRepo(String softwareRepo) {
this.softwareRepo = softwareRepo; this.softwareRepo = softwareRepo;
***REMOVED*** }
@XmlElement (name="ghost-repo") @XmlElement (name="ghost-repo")
public String getGhostRepo() ***REMOVED*** public String getGhostRepo() {
return ghostRepo; return ghostRepo;
***REMOVED*** }
public void setGhostRepo(String ghostRepo) ***REMOVED*** public void setGhostRepo(String ghostRepo) {
this.ghostRepo = ghostRepo; this.ghostRepo = ghostRepo;
***REMOVED*** }
@XmlElement (name="deps-linux-compiled") @XmlElement (name="deps-linux-compiled")
public String getDepsLinuxCompiled() ***REMOVED*** public String getDepsLinuxCompiled() {
return depsLinuxCompiled; return depsLinuxCompiled;
***REMOVED*** }
public void setDepsLinuxCompiled(String depsLinuxCompiled) ***REMOVED*** public void setDepsLinuxCompiled(String depsLinuxCompiled) {
this.depsLinuxCompiled = depsLinuxCompiled; this.depsLinuxCompiled = depsLinuxCompiled;
***REMOVED*** }
@XmlElement (name="deps-pre-installed") @XmlElement (name="deps-pre-installed")
public String getDepsPreInstalled() ***REMOVED*** public String getDepsPreInstalled() {
return depsPreInstalled; return depsPreInstalled;
***REMOVED*** }
public void setDepsPreInstalled(String depsPreInstalled) ***REMOVED*** public void setDepsPreInstalled(String depsPreInstalled) {
this.depsPreInstalled = depsPreInstalled; this.depsPreInstalled = depsPreInstalled;
***REMOVED*** }
@XmlElement (name="deps-r-blackbox") @XmlElement (name="deps-r-blackbox")
public String getDepsRBlackbox() ***REMOVED*** public String getDepsRBlackbox() {
return depsRBlackbox; return depsRBlackbox;
***REMOVED*** }
public void setDepsRBlackbox(String depsRBlackbox) ***REMOVED*** public void setDepsRBlackbox(String depsRBlackbox) {
this.depsRBlackbox = depsRBlackbox; this.depsRBlackbox = depsRBlackbox;
***REMOVED*** }
@XmlElement (name="deps-r") @XmlElement (name="deps-r")
public String getDepsR() ***REMOVED*** public String getDepsR() {
return depsR; return depsR;
***REMOVED*** }
public void setDepsR(String depsR) ***REMOVED*** public void setDepsR(String depsR) {
this.depsR = depsR; this.depsR = depsR;
***REMOVED*** }
@XmlElement (name="deps-java") @XmlElement (name="deps-java")
public String getDepsJava() ***REMOVED*** public String getDepsJava() {
return depsJava; return depsJava;
***REMOVED*** }
public void setDepsJava(String depsJava) ***REMOVED*** public void setDepsJava(String depsJava) {
this.depsJava = depsJava; this.depsJava = depsJava;
***REMOVED*** }
@XmlElement (name="deps-knime-workflow") @XmlElement (name="deps-knime-workflow")
public String getDepsKnimeWorkflow() ***REMOVED*** public String getDepsKnimeWorkflow() {
return depsKnimeWorkflow; return depsKnimeWorkflow;
***REMOVED*** }
public void setDepsKnimeWorkflow(String depsKnimeWorkflow) ***REMOVED*** public void setDepsKnimeWorkflow(String depsKnimeWorkflow) {
this.depsKnimeWorkflow = depsKnimeWorkflow; this.depsKnimeWorkflow = depsKnimeWorkflow;
***REMOVED*** }
@XmlElement (name="deps-knime-workflow4_1") @XmlElement (name="deps-knime-workflow4_1")
public String getDepsKnimeWorkflow4_1() ***REMOVED*** public String getDepsKnimeWorkflow4_1() {
return depsKnimeWorkflow4_1; return depsKnimeWorkflow4_1;
***REMOVED*** }
public void setDepsKnimeWorkflow4_1(String depsKnimeWorkflow4_1) ***REMOVED*** public void setDepsKnimeWorkflow4_1(String depsKnimeWorkflow4_1) {
this.depsKnimeWorkflow4_1 = depsKnimeWorkflow4_1; this.depsKnimeWorkflow4_1 = depsKnimeWorkflow4_1;
***REMOVED*** }
@XmlElement (name="deps-octave") @XmlElement (name="deps-octave")
public String getDepsOctave() ***REMOVED*** public String getDepsOctave() {
return depsOctave; return depsOctave;
***REMOVED*** }
public void setDepsOctave(String depsOctave) ***REMOVED*** public void setDepsOctave(String depsOctave) {
this.depsOctave = depsOctave; this.depsOctave = depsOctave;
***REMOVED*** }
@XmlElement (name="deps-python") @XmlElement (name="deps-python")
public String getDepsPython() ***REMOVED*** public String getDepsPython() {
return depsPython; return depsPython;
***REMOVED*** }
public void setDepsPython(String depsPython) ***REMOVED*** public void setDepsPython(String depsPython) {
this.depsPython = depsPython; this.depsPython = depsPython;
***REMOVED*** }
@XmlElement (name="deps-python3_6") @XmlElement (name="deps-python3_6")
public String getDepsPython3_6() ***REMOVED*** public String getDepsPython3_6() {
return depsPython3_6; return depsPython3_6;
***REMOVED*** }
public void setDepsPython3_6(String depsPython3_6) ***REMOVED*** public void setDepsPython3_6(String depsPython3_6) {
this.depsPython3_6 = depsPython3_6; this.depsPython3_6 = depsPython3_6;
***REMOVED*** }
@XmlElement (name="deps-windows-compiled") @XmlElement (name="deps-windows-compiled")
public String getDepsWindowsCompiled() ***REMOVED*** public String getDepsWindowsCompiled() {
return depsWindowsCompiled; return depsWindowsCompiled;
***REMOVED*** }
public void setDepsWindowsCompiled(String depsWindowsCompiled) ***REMOVED*** public void setDepsWindowsCompiled(String depsWindowsCompiled) {
this.depsWindowsCompiled = depsWindowsCompiled; this.depsWindowsCompiled = depsWindowsCompiled;
***REMOVED*** }
protected String getXML (String type) protected String getXML (String type)
***REMOVED*** {
return "<"+type+"><host>***REMOVED***$resource/Profile/Body/"+type+"/ghost/text()***REMOVED***</host>"+ return "<"+type+"><host>{$resource/Profile/Body/"+type+"/ghost/text()}</host>"+
"<algorithms-list>***REMOVED***$resource/Profile/Body/"+type+"/algorithms-list/text()***REMOVED***</algorithms-list>"+ "<algorithms-list>{$resource/Profile/Body/"+type+"/algorithms-list/text()}</algorithms-list>"+
" <software-repo>***REMOVED***$resource/Profile/Body/"+type+"/software.repo/text()***REMOVED***</software-repo>"+ " <software-repo>{$resource/Profile/Body/"+type+"/software.repo/text()}</software-repo>"+
"<ghost-repo>***REMOVED***$resource/Profile/Body/"+type+"/algo.ghost.repo/text()***REMOVED***</ghost-repo>"+ "<ghost-repo>{$resource/Profile/Body/"+type+"/algo.ghost.repo/text()}</ghost-repo>"+
"<deps-linux-compiled>***REMOVED***$resource/Profile/Body/"+type+"/deps-linux-compiled/text()***REMOVED***</deps-linux-compiled>"+ "<deps-linux-compiled>{$resource/Profile/Body/"+type+"/deps-linux-compiled/text()}</deps-linux-compiled>"+
"<deps-pre-installed>***REMOVED***$resource/Profile/Body/"+type+"/deps-pre-installed/text()***REMOVED***</deps-pre-installed>"+ "<deps-pre-installed>{$resource/Profile/Body/"+type+"/deps-pre-installed/text()}</deps-pre-installed>"+
"<deps-r-blackbox>***REMOVED***$resource/Profile/Body/"+type+"/deps-r-blackbox/text()***REMOVED***</deps-r-blackbox>"+ "<deps-r-blackbox>{$resource/Profile/Body/"+type+"/deps-r-blackbox/text()}</deps-r-blackbox>"+
"<deps-r>***REMOVED***$resource/Profile/Body/"+type+"/deps-r/text()***REMOVED***</deps-r>"+ "<deps-r>{$resource/Profile/Body/"+type+"/deps-r/text()}</deps-r>"+
"<deps-java>***REMOVED***$resource/Profile/Body/"+type+"/deps-java/text()***REMOVED***</deps-java>"+ "<deps-java>{$resource/Profile/Body/"+type+"/deps-java/text()}</deps-java>"+
"<deps-knime-workflow>***REMOVED***$resource/Profile/Body/"+type+"/deps-knime-workflow/text()***REMOVED***</deps-knime-workflow >"+ "<deps-knime-workflow>{$resource/Profile/Body/"+type+"/deps-knime-workflow/text()}</deps-knime-workflow >"+
"<deps-knime-workflow4_1>***REMOVED***$resource/Profile/Body/"+type+"/deps-knime-workflow4_1/text()***REMOVED***</deps-knime-workflow4_1>"+ "<deps-knime-workflow4_1>{$resource/Profile/Body/"+type+"/deps-knime-workflow4_1/text()}</deps-knime-workflow4_1>"+
"<deps-octave>***REMOVED***$resource/Profile/Body/"+type+"/deps-octave/text()***REMOVED***</deps-octave>"+ "<deps-octave>{$resource/Profile/Body/"+type+"/deps-octave/text()}</deps-octave>"+
"<deps-python>***REMOVED***$resource/Profile/Body/"+type+"/deps-python/text()***REMOVED***</deps-python>"+ "<deps-python>{$resource/Profile/Body/"+type+"/deps-python/text()}</deps-python>"+
"<deps-python3_6>***REMOVED***$resource/Profile/Body/"+type+"/deps-python3_6/text()***REMOVED***</deps-python3_6>"+ "<deps-python3_6>{$resource/Profile/Body/"+type+"/deps-python3_6/text()}</deps-python3_6>"+
"<deps-windows-compiled>***REMOVED***$resource/Profile/Body/"+type+"/deps-windows-compiled/text()***REMOVED***</deps-windows-compiled></"+type+">"; "<deps-windows-compiled>{$resource/Profile/Body/"+type+"/deps-windows-compiled/text()}</deps-windows-compiled></"+type+">";
***REMOVED*** }
abstract public String getXMLModel (); abstract public String getXMLModel ();
abstract public String getType (); abstract public String getType ();
***REMOVED*** }

16
src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/clients/configurations/Prod.java
View File

@ -3,21 +3,21 @@ package org.gcube.dataanalysis.dataminer.poolmanager.clients.configurations;
import javax.xml.bind.annotation.XmlRootElement; import javax.xml.bind.annotation.XmlRootElement;
@XmlRootElement(name="prod") @XmlRootElement(name="prod")
public class Prod extends AbstractConfiguration ***REMOVED*** public class Prod extends AbstractConfiguration {
private final String TYPE = "prod"; private final String TYPE = "prod";
***REMOVED*** @Override
public String getXMLModel () public String getXMLModel ()
***REMOVED*** {
return super.getXML(TYPE); return super.getXML(TYPE);
***REMOVED*** }
***REMOVED*** @Override
public String getType() ***REMOVED*** public String getType() {
return TYPE; return TYPE;
***REMOVED*** }
***REMOVED*** }

16
src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/clients/configurations/Stage.java
View File

@ -3,21 +3,21 @@ package org.gcube.dataanalysis.dataminer.poolmanager.clients.configurations;
import javax.xml.bind.annotation.XmlRootElement; import javax.xml.bind.annotation.XmlRootElement;
@XmlRootElement(name="stage") @XmlRootElement(name="stage")
public class Stage extends AbstractConfiguration ***REMOVED*** public class Stage extends AbstractConfiguration {
private final String TYPE = "stage"; private final String TYPE = "stage";
***REMOVED*** @Override
public String getXMLModel () public String getXMLModel ()
***REMOVED*** {
return super.getXML(TYPE); return super.getXML(TYPE);
***REMOVED*** }
***REMOVED*** @Override
public String getType() ***REMOVED*** public String getType() {
return TYPE; return TYPE;
***REMOVED*** }
***REMOVED*** }

28
src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/datamodel/Action.java
View File

@ -1,33 +1,33 @@
package org.gcube.dataanalysis.dataminer.poolmanager.datamodel; package org.gcube.dataanalysis.dataminer.poolmanager.datamodel;
public class Action ***REMOVED*** public class Action {
private String name; private String name;
private String description; private String description;
private String script; private String script;
public String getName() ***REMOVED*** public String getName() {
return name; return name;
***REMOVED*** }
public void setName(String name) ***REMOVED*** public void setName(String name) {
this.name = name; this.name = name;
***REMOVED*** }
public String getDescription() ***REMOVED*** public String getDescription() {
return description; return description;
***REMOVED*** }
public void setDescription(String description) ***REMOVED*** public void setDescription(String description) {
this.description = description; this.description = description;
***REMOVED*** }
public String getScript() ***REMOVED*** public String getScript() {
return script; return script;
***REMOVED*** }
public void setScript(String script) ***REMOVED*** public void setScript(String script) {
this.script = script; this.script = script;
***REMOVED*** }
***REMOVED*** }

20
src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/datamodel/AlgoResource.java
View File

@ -1,22 +1,22 @@
package org.gcube.dataanalysis.dataminer.poolmanager.datamodel; package org.gcube.dataanalysis.dataminer.poolmanager.datamodel;
public class AlgoResource ***REMOVED*** public class AlgoResource {
protected String id; protected String id;
public AlgoResource() ***REMOVED*** public AlgoResource() {
***REMOVED*** }
public AlgoResource(String id) ***REMOVED*** public AlgoResource(String id) {
this.id = id; this.id = id;
***REMOVED*** }
public String getId() ***REMOVED*** public String getId() {
return this.id; return this.id;
***REMOVED*** }
public void setId(String id) ***REMOVED*** public void setId(String id) {
this.id = id; this.id = id;
***REMOVED*** }
***REMOVED*** }

166
src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/datamodel/Algorithm.java
View File

@ -2,11 +2,11 @@ package org.gcube.dataanalysis.dataminer.poolmanager.datamodel;
import java.util.Collection; import java.util.Collection;
import java.util.HashSet; import java.util.HashSet;
***REMOVED*** import java.util.Set;
import java.util.Vector; import java.util.Vector;
public class Algorithm ***REMOVED*** public class Algorithm {
private String username; private String username;
@ -23,166 +23,166 @@ public class Algorithm ***REMOVED***
private Collection<Action> actions; private Collection<Action> actions;
private Collection<Dependency> dependencies; private Collection<Dependency> dependencies;
public Algorithm() ***REMOVED*** public Algorithm() {
this.actions = new Vector<>(); this.actions = new Vector<>();
this.dependencies = new Vector<>(); this.dependencies = new Vector<>();
***REMOVED*** Dependency p = new Dependency(); // Dependency p = new Dependency();
***REMOVED***init with default values //init with default values
this.skipJava = "N"; this.skipJava = "N";
this.algorithmType = "transducerers"; this.algorithmType = "transducerers";
***REMOVED*** }
public void addDependency(Dependency dep) ***REMOVED*** public void addDependency(Dependency dep) {
this.dependencies.add(dep); this.dependencies.add(dep);
***REMOVED*** }
public void addAction(Action action) ***REMOVED*** public void addAction(Action action) {
this.actions.add(action); this.actions.add(action);
***REMOVED*** }
public String getName() ***REMOVED*** public String getName() {
return name; return name;
***REMOVED*** }
public void setName(String name) ***REMOVED*** public void setName(String name) {
this.name = name; this.name = name;
***REMOVED*** }
public String getDescription() ***REMOVED*** public String getDescription() {
return description; return description;
***REMOVED*** }
public void setDescription(String description) ***REMOVED*** public void setDescription(String description) {
this.description = description.replace(": ", " "); this.description = description.replace(": ", " ");
***REMOVED*** }
public String getCategory() ***REMOVED*** public String getCategory() {
return category; return category;
***REMOVED*** }
public void setCategory(String category) ***REMOVED*** public void setCategory(String category) {
this.category = category; this.category = category;
***REMOVED*** }
public Collection<Action> getActions() ***REMOVED*** public Collection<Action> getActions() {
return actions; return actions;
***REMOVED*** }
public Collection<Dependency> getDependencies() ***REMOVED*** public Collection<Dependency> getDependencies() {
return dependencies; return dependencies;
***REMOVED*** }
public Collection<Dependency> getOSDependencies()***REMOVED*** public Collection<Dependency> getOSDependencies(){
Set<Dependency> deps = new HashSet<>(); Set<Dependency> deps = new HashSet<>();
for(Dependency d: this.getDependencies())***REMOVED*** for(Dependency d: this.getDependencies()){
if(d.getType().equals("os"))***REMOVED*** if(d.getType().equals("os")){
deps.add(d); deps.add(d);
***REMOVED*** }
***REMOVED*** }
return deps; return deps;
***REMOVED*** }
public Collection<Dependency> getCranDependencies()***REMOVED*** public Collection<Dependency> getCranDependencies(){
Set<Dependency> deps = new HashSet<>(); Set<Dependency> deps = new HashSet<>();
for(Dependency d: this.getDependencies())***REMOVED*** for(Dependency d: this.getDependencies()){
if(d.getType().equals("cran"))***REMOVED*** if(d.getType().equals("cran")){
deps.add(d); deps.add(d);
***REMOVED*** }
***REMOVED*** }
return deps; return deps;
***REMOVED*** }
public Collection<Dependency> getGitHubDependencies()***REMOVED*** public Collection<Dependency> getGitHubDependencies(){
Set<Dependency> deps = new HashSet<>(); Set<Dependency> deps = new HashSet<>();
for(Dependency d: this.getDependencies())***REMOVED*** for(Dependency d: this.getDependencies()){
if(d.getType().equals("github"))***REMOVED*** if(d.getType().equals("github")){
deps.add(d); deps.add(d);
***REMOVED*** }
***REMOVED*** }
return deps; return deps;
***REMOVED*** }
public void setDependencies(Collection<Dependency> deps) ***REMOVED*** public void setDependencies(Collection<Dependency> deps) {
this.dependencies = deps; this.dependencies = deps;
***REMOVED*** }
public String toString() ***REMOVED*** public String toString() {
String out = "Algorithm: " + this.getName()+"\n"; String out = "Algorithm: " + this.getName()+"\n";
out+=" Class Name: " + this.getClazz()+"\n"; out+=" Class Name: " + this.getClazz()+"\n";
out+=" Description: " + this.getDescription()+"\n"; out+=" Description: " + this.getDescription()+"\n";
out+=" Dependencies: " + this.getDependencies()+"\n"; out+=" Dependencies: " + this.getDependencies()+"\n";
return out; return out;
***REMOVED*** }
public String getClazz() ***REMOVED*** public String getClazz() {
return clazz; return clazz;
***REMOVED*** }
public void setClazz(String clazz) ***REMOVED*** public void setClazz(String clazz) {
this.clazz = clazz; this.clazz = clazz;
***REMOVED*** }
public String getPackageURL() ***REMOVED*** public String getPackageURL() {
return packageURL; return packageURL;
***REMOVED*** }
public void setPackageURL(String packageURL) ***REMOVED*** public void setPackageURL(String packageURL) {
this.packageURL = packageURL; this.packageURL = packageURL;
***REMOVED*** }
public String getAlgorithmType() ***REMOVED*** public String getAlgorithmType() {
return algorithmType; return algorithmType;
***REMOVED*** }
public void setAlgorithmType(String algorithmType) ***REMOVED*** public void setAlgorithmType(String algorithmType) {
this.algorithmType = algorithmType; this.algorithmType = algorithmType;
***REMOVED*** }
public String getSkipJava() ***REMOVED*** public String getSkipJava() {
return skipJava; return skipJava;
***REMOVED*** }
public void setSkipJava(String skipJava) ***REMOVED*** public void setSkipJava(String skipJava) {
this.skipJava = skipJava; this.skipJava = skipJava;
***REMOVED*** }
public String getUsername() ***REMOVED*** public String getUsername() {
return username; return username;
***REMOVED*** }
public void setUsername(String username) ***REMOVED*** public void setUsername(String username) {
this.username = username; this.username = username;
***REMOVED*** }
public String getFullname() ***REMOVED*** public String getFullname() {
return fullname; return fullname;
***REMOVED*** }
public void setFullname(String fullname) ***REMOVED*** public void setFullname(String fullname) {
this.fullname = fullname; this.fullname = fullname;
***REMOVED*** }
public String getEmail() ***REMOVED*** public String getEmail() {
return email; return email;
***REMOVED*** }
public void setEmail(String email) ***REMOVED*** public void setEmail(String email) {
this.email = email; this.email = email;
***REMOVED*** }
public String getLanguage() ***REMOVED*** public String getLanguage() {
return language; return language;
***REMOVED*** }
public void setLanguage(String language) ***REMOVED*** public void setLanguage(String language) {
this.language = language; this.language = language;
***REMOVED*** }
public void setActions(Collection<Action> actions) ***REMOVED*** public void setActions(Collection<Action> actions) {
this.actions = actions; this.actions = actions;
***REMOVED*** }
***REMOVED*** }

44
src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/datamodel/AlgorithmSet.java
View File

@ -3,54 +3,54 @@ package org.gcube.dataanalysis.dataminer.poolmanager.datamodel;
import java.util.Collection; import java.util.Collection;
import java.util.Vector; import java.util.Vector;
public class AlgorithmSet ***REMOVED*** public class AlgorithmSet {
private String name; private String name;
private Collection<Algorithm> algorithms; private Collection<Algorithm> algorithms;
public AlgorithmSet() public AlgorithmSet()
***REMOVED*** {
this.algorithms = new Vector<>(); this.algorithms = new Vector<>();
***REMOVED*** }
public String getName() public String getName()
***REMOVED*** {
return name; return name;
***REMOVED*** }
public void setName(String name) public void setName(String name)
***REMOVED*** {
this.name = name; this.name = name;
***REMOVED*** }
public Collection<Algorithm> getAlgorithms() public Collection<Algorithm> getAlgorithms()
***REMOVED*** {
return new Vector<>(algorithms); return new Vector<>(algorithms);
***REMOVED*** }
public void addAlgorithm(Algorithm algoritm) public void addAlgorithm(Algorithm algoritm)
***REMOVED*** {
this.algorithms.add(algoritm); this.algorithms.add(algoritm);
***REMOVED*** }
public Boolean hasAlgorithm(Algorithm algorithm) public Boolean hasAlgorithm(Algorithm algorithm)
***REMOVED*** {
for (Algorithm a : this.algorithms) ***REMOVED*** for (Algorithm a : this.algorithms) {
if (a.getName().equals(algorithm.getName())) if (a.getName().equals(algorithm.getName()))
***REMOVED*** {
return true; return true;
***REMOVED*** }
***REMOVED*** }
return false; return false;
***REMOVED*** }
public String toString() public String toString()
***REMOVED*** {
String out = "ALGOSET: " + this.name + "\n"; String out = "ALGOSET: " + this.name + "\n";
for(Algorithm a:this.algorithms) ***REMOVED*** for(Algorithm a:this.algorithms) {
out+=a+"\n"; out+=a+"\n";
***REMOVED*** }
return out; return out;
***REMOVED*** }
***REMOVED*** }

48
src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/datamodel/Cluster.java
View File

@ -3,7 +3,7 @@ package org.gcube.dataanalysis.dataminer.poolmanager.datamodel;
import java.util.Collection; import java.util.Collection;
import java.util.Vector; import java.util.Vector;
public class Cluster ***REMOVED*** public class Cluster {
/** /**
* The set of hosts belonging to the cluster. * The set of hosts belonging to the cluster.
@ -26,57 +26,57 @@ public class Cluster ***REMOVED***
private Collection<AlgorithmSet> algoSets; private Collection<AlgorithmSet> algoSets;
public Cluster() public Cluster()
***REMOVED*** {
this.hosts = new Vector<>(); this.hosts = new Vector<>();
this.algoSets = new Vector<>(); this.algoSets = new Vector<>();
***REMOVED*** }
public void addAlgorithmSet(AlgorithmSet set) public void addAlgorithmSet(AlgorithmSet set)
***REMOVED*** {
this.algoSets.add(set); this.algoSets.add(set);
***REMOVED*** }
public void addHost(Host host) public void addHost(Host host)
***REMOVED*** {
this.hosts.add(host); this.hosts.add(host);
***REMOVED*** }
public Collection<Host> getHosts() public Collection<Host> getHosts()
***REMOVED*** {
return hosts; return hosts;
***REMOVED*** }
public String getName() public String getName()
***REMOVED*** {
return name; return name;
***REMOVED*** }
public void setName(String name) public void setName(String name)
***REMOVED*** {
this.name = name; this.name = name;
***REMOVED*** }
public String getDescription() public String getDescription()
***REMOVED*** {
return description; return description;
***REMOVED*** }
public void setDescription(String description) public void setDescription(String description)
***REMOVED*** {
this.description = description; this.description = description;
***REMOVED*** }
public Collection<AlgorithmSet> getAlgorithmSets() public Collection<AlgorithmSet> getAlgorithmSets()
***REMOVED*** {
return algoSets; return algoSets;
***REMOVED*** }
public String toString() ***REMOVED*** public String toString() {
String out = "Cluster: "+this.name+"\n"; String out = "Cluster: "+this.name+"\n";
for(Host h:this.getHosts()) ***REMOVED*** for(Host h:this.getHosts()) {
out+=" "+h+"\n"; out+=" "+h+"\n";
***REMOVED*** }
return out; return out;
***REMOVED*** }
***REMOVED*** }

24
src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/datamodel/Dependency.java
View File

@ -1,29 +1,29 @@
package org.gcube.dataanalysis.dataminer.poolmanager.datamodel; package org.gcube.dataanalysis.dataminer.poolmanager.datamodel;
public class Dependency ***REMOVED*** public class Dependency {
private String name; private String name;
private String type; private String type;
public String getName() public String getName()
***REMOVED*** {
return name; return name;
***REMOVED*** }
public void setName(String name) ***REMOVED*** public void setName(String name) {
this.name = name; this.name = name;
***REMOVED*** }
public String getType() ***REMOVED*** public String getType() {
return type; return type;
***REMOVED*** }
public void setType(String type) ***REMOVED*** public void setType(String type) {
this.type = type; this.type = type;
***REMOVED*** }
public String toString() ***REMOVED*** public String toString() {
return this.type+":"+this.name; return this.type+":"+this.name;
***REMOVED*** }
***REMOVED*** }

12
src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/datamodel/Domain.java
View File

@ -1,15 +1,15 @@
package org.gcube.dataanalysis.dataminer.poolmanager.datamodel; package org.gcube.dataanalysis.dataminer.poolmanager.datamodel;
public class Domain ***REMOVED*** public class Domain {
private String name; private String name;
public String getName() ***REMOVED*** public String getName() {
return name; return name;
***REMOVED*** }
public void setName(String name) ***REMOVED*** public void setName(String name) {
this.name = name; this.name = name;
***REMOVED*** }
***REMOVED*** }

42
src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/datamodel/Host.java
View File

@ -1,48 +1,48 @@
package org.gcube.dataanalysis.dataminer.poolmanager.datamodel; package org.gcube.dataanalysis.dataminer.poolmanager.datamodel;
public class Host ***REMOVED*** public class Host {
private String name; private String name;
private Domain domain; private Domain domain;
public Host(String hostname) ***REMOVED*** public Host(String hostname) {
this.setName(hostname); this.setName(hostname);
***REMOVED*** }
public Host() ***REMOVED*** public Host() {
***REMOVED*** }
public String getFullyQualifiedName() ***REMOVED*** public String getFullyQualifiedName() {
if(this.domain!=null && this.domain.getName()!=null) if(this.domain!=null && this.domain.getName()!=null)
return this.getName()+"."+this.getDomain().getName(); return this.getName()+"."+this.getDomain().getName();
else else
return this.getName(); return this.getName();
***REMOVED*** }
public String getName() ***REMOVED*** public String getName() {
return name; return name;
***REMOVED*** }
public void setName(String name) ***REMOVED*** public void setName(String name) {
this.name = name; this.name = name;
***REMOVED*** }
public Domain getDomain() ***REMOVED*** public Domain getDomain() {
return domain; return domain;
***REMOVED*** }
public void setDomain(Domain domain) ***REMOVED*** public void setDomain(Domain domain) {
this.domain = domain; this.domain = domain;
***REMOVED*** }
***REMOVED*** public String toString() ***REMOVED*** // public String toString() {
***REMOVED*** return this.name + "@" + this.domain; // return this.name + "@" + this.domain;
***REMOVED*** ***REMOVED*** // }
public String toString() ***REMOVED*** public String toString() {
return this.name; return this.name;
***REMOVED*** }
***REMOVED*** }

10
src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/datamodel/comparator/AlgorithmComparator.java
View File

@ -2,14 +2,14 @@ package org.gcube.dataanalysis.dataminer.poolmanager.datamodel.comparator;
import java.util.Comparator; import java.util.Comparator;
***REMOVED*** import org.gcube.dataanalysis.dataminer.poolmanager.datamodel.Algorithm;
public class AlgorithmComparator implements Comparator<Algorithm> ***REMOVED*** public class AlgorithmComparator implements Comparator<Algorithm> {
@Override @Override
public int compare(Algorithm a1, Algorithm a2) ***REMOVED*** public int compare(Algorithm a1, Algorithm a2) {
return a1.getName().compareTo(a2.getName()); return a1.getName().compareTo(a2.getName());
***REMOVED*** }
***REMOVED*** }

8
src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/datamodel/comparator/DependencyComparator.java
View File

@ -4,15 +4,15 @@ import java.util.Comparator;
import org.gcube.dataanalysis.dataminer.poolmanager.datamodel.Dependency; import org.gcube.dataanalysis.dataminer.poolmanager.datamodel.Dependency;
public class DependencyComparator implements Comparator<Dependency> ***REMOVED*** public class DependencyComparator implements Comparator<Dependency> {
@Override @Override
public int compare(Dependency a1, Dependency a2) ***REMOVED*** public int compare(Dependency a1, Dependency a2) {
int out = a1.getType().compareTo(a2.getType()); int out = a1.getType().compareTo(a2.getType());
if(out!=0) if(out!=0)
return out; return out;
return a1.getName().compareTo(a2.getName()); return a1.getName().compareTo(a2.getName());
***REMOVED*** }
***REMOVED*** }

8
src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/datamodel/comparator/HostComparator.java
View File

@ -4,14 +4,14 @@ import java.util.Comparator;
import org.gcube.dataanalysis.dataminer.poolmanager.datamodel.Host; import org.gcube.dataanalysis.dataminer.poolmanager.datamodel.Host;
public class HostComparator implements Comparator<Host> ***REMOVED*** public class HostComparator implements Comparator<Host> {
@Override @Override
public int compare(Host h1, Host h2) ***REMOVED*** public int compare(Host h1, Host h2) {
int out = h1.getDomain().getName().compareTo(h2.getDomain().getName()); int out = h1.getDomain().getName().compareTo(h2.getDomain().getName());
if(out!=0) if(out!=0)
return out; return out;
return h1.getName().compareTo(h2.getName()); return h1.getName().compareTo(h2.getName());
***REMOVED*** }
***REMOVED*** }

60
src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/process/AddAlgorithmCommand.java
View File

@ -2,7 +2,7 @@ package org.gcube.dataanalysis.dataminer.poolmanager.process;
import java.util.StringTokenizer; import java.util.StringTokenizer;
public class AddAlgorithmCommand ***REMOVED*** public class AddAlgorithmCommand {
private String command; private String command;
private String name; private String name;
@ -14,7 +14,7 @@ public class AddAlgorithmCommand ***REMOVED***
private String url; private String url;
private String description; private String description;
public AddAlgorithmCommand(String cmd) ***REMOVED*** public AddAlgorithmCommand(String cmd) {
StringTokenizer st = new StringTokenizer(cmd, " "); StringTokenizer st = new StringTokenizer(cmd, " ");
if (st.hasMoreElements()) if (st.hasMoreElements())
command = st.nextToken(); command = st.nextToken();
@ -38,55 +38,55 @@ public class AddAlgorithmCommand ***REMOVED***
d = d + st.nextToken() + " "; d = d + st.nextToken() + " ";
this.setDescription(d); this.setDescription(d);
***REMOVED*** }
public void setDescription(String d) ***REMOVED*** public void setDescription(String d) {
if(d!=null) ***REMOVED*** if(d!=null) {
d = d.trim(); d = d.trim();
if(d.startsWith("\"") && d.endsWith("\"")) ***REMOVED*** if(d.startsWith("\"") && d.endsWith("\"")) {
d = d.substring(1, d.length()-1).trim(); d = d.substring(1, d.length()-1).trim();
***REMOVED*** }
***REMOVED*** }
this.description = d; this.description = d;
***REMOVED*** }
public String getCommand() ***REMOVED*** public String getCommand() {
return command; return command;
***REMOVED*** }
public String getName() ***REMOVED*** public String getName() {
return name; return name;
***REMOVED*** }
public String getCategory() ***REMOVED*** public String getCategory() {
return category; return category;
***REMOVED*** }
public String getClazz() ***REMOVED*** public String getClazz() {
return clazz; return clazz;
***REMOVED*** }
public String getVRE() ***REMOVED*** public String getVRE() {
return scope; return scope;
***REMOVED*** }
public String getAlgorithmType() ***REMOVED*** public String getAlgorithmType() {
return algorithmType; return algorithmType;
***REMOVED*** }
public String getSkipjava() ***REMOVED*** public String getSkipjava() {
return skipJava; return skipJava;
***REMOVED*** }
public String getUrl() ***REMOVED*** public String getUrl() {
return url; return url;
***REMOVED*** }
public String getDescription() ***REMOVED*** public String getDescription() {
return description; return description;
***REMOVED*** }
public String toString() ***REMOVED*** public String toString() {
String out = ""; String out = "";
out += String.format("%-12s: %s\n", "command", command); out += String.format("%-12s: %s\n", "command", command);
out += String.format("%-12s: %s\n", "algo name", name); out += String.format("%-12s: %s\n", "algo name", name);
@ -98,6 +98,6 @@ public class AddAlgorithmCommand ***REMOVED***
out += String.format("%-12s: %s\n", "url", url); out += String.format("%-12s: %s\n", "url", url);
out += String.format("%-12s: %s\n", "description", this.description); out += String.format("%-12s: %s\n", "description", this.description);
return out; return out;
***REMOVED*** }
***REMOVED*** }

320
src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/process/AlgorithmPackageParser.java
View File

@ -1,21 +1,21 @@
package org.gcube.dataanalysis.dataminer.poolmanager.process; package org.gcube.dataanalysis.dataminer.poolmanager.process;
***REMOVED*** import java.io.IOException;
import java.io.InputStream; import java.io.InputStream;
***REMOVED*** import java.net.URL;
import java.util.HashMap; import java.util.HashMap;
***REMOVED*** import java.util.List;
import java.util.Map; import java.util.Map;
import java.util.Vector; import java.util.Vector;
import java.util.zip.ZipEntry; import java.util.zip.ZipEntry;
import java.util.zip.ZipInputStream; import java.util.zip.ZipInputStream;
***REMOVED*** import org.gcube.dataanalysis.dataminer.poolmanager.datamodel.Algorithm;
import org.gcube.dataanalysis.dataminer.poolmanager.datamodel.Dependency; import org.gcube.dataanalysis.dataminer.poolmanager.datamodel.Dependency;
***REMOVED*** import org.slf4j.Logger;
***REMOVED*** import org.slf4j.LoggerFactory;
public class AlgorithmPackageParser ***REMOVED*** public class AlgorithmPackageParser {
/** /**
* The name of the file containing algorithm metadata. Expected in the root * The name of the file containing algorithm metadata. Expected in the root
@ -31,7 +31,7 @@ public class AlgorithmPackageParser ***REMOVED***
METADATA_ALGORITHM_DESCRIPTION = "Algorithm Description", METADATA_ALGORITHM_DESCRIPTION = "Algorithm Description",
METADATA_CLASS_NAME = "Class Name", METADATA_CLASS_NAME = "Class Name",
***REMOVED*** private static final String METADATA_PACKAGES = "Packages"; // private static final String METADATA_PACKAGES = "Packages";
METADATA_KEY_VALUE_SEPARATOR = ":"; METADATA_KEY_VALUE_SEPARATOR = ":";
@ -39,116 +39,116 @@ public class AlgorithmPackageParser ***REMOVED***
private Logger logger; private Logger logger;
public AlgorithmPackageParser() ***REMOVED*** public AlgorithmPackageParser() {
this.logger = LoggerFactory.getLogger(AlgorithmPackageParser.class); this.logger = LoggerFactory.getLogger(AlgorithmPackageParser.class);
***REMOVED*** }
public Algorithm parsePackage(String url) throws IOException ***REMOVED*** public Algorithm parsePackage(String url) throws IOException {
String packageMetadata = this.getPackageMetadata(url); String packageMetadata = this.getPackageMetadata(url);
if (packageMetadata == null) ***REMOVED*** if (packageMetadata == null) {
this.logger.warn("WARNING: No metadata found for " + url); this.logger.warn("WARNING: No metadata found for " + url);
return null; return null;
***REMOVED*** else ***REMOVED*** } else {
Map<String, List<String>> parsedMetadata = this.parseMetadata(packageMetadata); Map<String, List<String>> parsedMetadata = this.parseMetadata(packageMetadata);
Algorithm a = this.createAlgorithm(parsedMetadata); Algorithm a = this.createAlgorithm(parsedMetadata);
a.setPackageURL(url); a.setPackageURL(url);
return a; return a;
***REMOVED*** }
***REMOVED*** }
private String getPackageMetadata(String url) throws IOException ***REMOVED*** private String getPackageMetadata(String url) throws IOException {
InputStream is = new URL(url).openStream(); InputStream is = new URL(url).openStream();
ZipInputStream zipIs = new ZipInputStream(is); ZipInputStream zipIs = new ZipInputStream(is);
ZipEntry entry = zipIs.getNextEntry(); ZipEntry entry = zipIs.getNextEntry();
String out = null; String out = null;
while (entry != null) ***REMOVED*** while (entry != null) {
if (METADATA_FILE_NAME.equalsIgnoreCase(entry.getName())) ***REMOVED*** if (METADATA_FILE_NAME.equalsIgnoreCase(entry.getName())) {
out = this.getEntryContent(zipIs); out = this.getEntryContent(zipIs);
break; break;
***REMOVED*** }
entry = zipIs.getNextEntry(); entry = zipIs.getNextEntry();
***REMOVED*** }
is.close(); is.close();
zipIs.close(); zipIs.close();
return out; return out;
***REMOVED*** }
private String getEntryContent(ZipInputStream zipIn) throws IOException ***REMOVED*** private String getEntryContent(ZipInputStream zipIn) throws IOException {
StringBuilder s = new StringBuilder(); StringBuilder s = new StringBuilder();
byte[] buffer = new byte[BUFFER_SIZE]; byte[] buffer = new byte[BUFFER_SIZE];
int read = 0; int read = 0;
while ((read = zipIn.read(buffer)) != -1) ***REMOVED*** while ((read = zipIn.read(buffer)) != -1) {
s.append(new String(buffer, 0, read)); s.append(new String(buffer, 0, read));
***REMOVED*** }
return s.toString(); return s.toString();
***REMOVED*** }
private Map<String, List<String>> parseMetadata(String metadata) ***REMOVED*** private Map<String, List<String>> parseMetadata(String metadata) {
Map<String, List<String>> out = new HashMap<String, List<String>>(); Map<String, List<String>> out = new HashMap<String, List<String>>();
String[] lines = metadata.split("\n"); String[] lines = metadata.split("\n");
String key = null; String key = null;
String value = null; String value = null;
for (String line : lines) ***REMOVED*** for (String line : lines) {
***REMOVED*** skip empty lines // skip empty lines
if (line.trim().isEmpty()) ***REMOVED*** if (line.trim().isEmpty()) {
continue; continue;
***REMOVED*** }
***REMOVED*** scan lines one by one, looking for key and values // scan lines one by one, looking for key and values
String[] parts = line.split(METADATA_KEY_VALUE_SEPARATOR); String[] parts = line.split(METADATA_KEY_VALUE_SEPARATOR);
if (parts.length > 1) ***REMOVED*** if (parts.length > 1) {
***REMOVED*** key and value on the same line // key and value on the same line
key = parts[0].trim(); key = parts[0].trim();
value = line.substring(parts[0].length() + 1).trim(); value = line.substring(parts[0].length() + 1).trim();
***REMOVED*** else if (parts.length == 1) ***REMOVED*** } else if (parts.length == 1) {
***REMOVED*** either a key or a value // either a key or a value
if (line.trim().endsWith(METADATA_KEY_VALUE_SEPARATOR)) ***REMOVED*** if (line.trim().endsWith(METADATA_KEY_VALUE_SEPARATOR)) {
***REMOVED*** key // key
key = parts[0].trim(); key = parts[0].trim();
value = null; value = null;
***REMOVED*** else ***REMOVED*** } else {
***REMOVED*** value // value
value = line.trim(); value = line.trim();
***REMOVED*** }
***REMOVED*** }
***REMOVED*** add key+value to the map // add key+value to the map
if (key != null && value != null) ***REMOVED*** if (key != null && value != null) {
List<String> values = out.get(key); List<String> values = out.get(key);
if (values == null) ***REMOVED*** if (values == null) {
values = new Vector<>(); values = new Vector<>();
out.put(key, values); out.put(key, values);
***REMOVED*** }
values.add(value); values.add(value);
this.logger.debug(key + METADATA_KEY_VALUE_SEPARATOR + " " + values); this.logger.debug(key + METADATA_KEY_VALUE_SEPARATOR + " " + values);
***REMOVED*** }
***REMOVED*** }
return out; return out;
***REMOVED*** }
***REMOVED*** private Algorithm createAlgorithm(Map<String, List<String>> metadata) ***REMOVED*** // private Algorithm createAlgorithm(Map<String, List<String>> metadata) {
***REMOVED*** Algorithm out = new Algorithm(); // Algorithm out = new Algorithm();
***REMOVED*** out.setName(extractSingleValue(metadata, METADATA_ALGORITHM_NAME)); // out.setName(extractSingleValue(metadata, METADATA_ALGORITHM_NAME));
***REMOVED*** out.setDescription(extractSingleValue(metadata, METADATA_ALGORITHM_DESCRIPTION)); // out.setDescription(extractSingleValue(metadata, METADATA_ALGORITHM_DESCRIPTION));
***REMOVED*** out.setClazz(extractSingleValue(metadata, METADATA_CLASS_NAME)); // out.setClazz(extractSingleValue(metadata, METADATA_CLASS_NAME));
***REMOVED*** List<String> dependencies = extractMultipleValues(metadata, METADATA_PACKAGES); // List<String> dependencies = extractMultipleValues(metadata, METADATA_PACKAGES);
***REMOVED*** if (dependencies != null) ***REMOVED*** // if (dependencies != null) {
***REMOVED*** for (String pkg : dependencies) ***REMOVED*** // for (String pkg : dependencies) {
***REMOVED*** Dependency dep = new Dependency(); // Dependency dep = new Dependency();
***REMOVED*** dep.setName(pkg); // dep.setName(pkg);
***REMOVED*** dep.setType("os"); // dep.setType("os");
***REMOVED*** out.addDependency(dep); // out.addDependency(dep);
***REMOVED*** ***REMOVED*** // }
***REMOVED*** ***REMOVED*** // }
***REMOVED*** return out; // return out;
***REMOVED*** ***REMOVED*** // }
private Algorithm createAlgorithm(Map<String, List<String>> metadata) ***REMOVED*** private Algorithm createAlgorithm(Map<String, List<String>> metadata) {
Algorithm out = new Algorithm(); Algorithm out = new Algorithm();
out.setName(extractSingleValue(metadata, METADATA_ALGORITHM_NAME)); out.setName(extractSingleValue(metadata, METADATA_ALGORITHM_NAME));
out.setDescription(extractSingleValue(metadata, METADATA_ALGORITHM_DESCRIPTION)); out.setDescription(extractSingleValue(metadata, METADATA_ALGORITHM_DESCRIPTION));
@ -161,13 +161,13 @@ public class AlgorithmPackageParser ***REMOVED***
List<String> dependencies = extractMultipleValues(metadata, "Package Name"); List<String> dependencies = extractMultipleValues(metadata, "Package Name");
if (dependencies != null) ***REMOVED*** if (dependencies != null) {
for (String pkg : dependencies) ***REMOVED*** for (String pkg : dependencies) {
Dependency dep = new Dependency(); Dependency dep = new Dependency();
dep.setName(pkg); dep.setName(pkg);
out.addDependency(dep); out.addDependency(dep);
***REMOVED*** }
***REMOVED*** }
@ -176,119 +176,119 @@ public class AlgorithmPackageParser ***REMOVED***
***REMOVED*** List<String> rdependencies = extractMultipleValues(metadata, "cran"); // List<String> rdependencies = extractMultipleValues(metadata, "cran");
***REMOVED*** if (rdependencies != null) ***REMOVED*** // if (rdependencies != null) {
***REMOVED*** for (String pkg : rdependencies) ***REMOVED*** // for (String pkg : rdependencies) {
***REMOVED*** Dependency dep = new Dependency(); // Dependency dep = new Dependency();
***REMOVED*** //
***REMOVED*** ***REMOVED***if (pkg.startsWith("os:"))***REMOVED*** // //if (pkg.startsWith("os:")){
***REMOVED*** dep.setName(pkg); // dep.setName(pkg);
***REMOVED*** dep.setType("cran"); // dep.setType("cran");
***REMOVED*** out.addDependency(dep); // out.addDependency(dep);
***REMOVED*** ***REMOVED*** // }
***REMOVED*** ***REMOVED*** // }
***REMOVED*** //
***REMOVED*** //
***REMOVED*** List<String> defdependencies = extractMultipleValues(metadata, "Packages"); // List<String> defdependencies = extractMultipleValues(metadata, "Packages");
***REMOVED*** if (defdependencies != null) ***REMOVED*** // if (defdependencies != null) {
***REMOVED*** for (String pkg : defdependencies) ***REMOVED*** // for (String pkg : defdependencies) {
***REMOVED*** Dependency dep = new Dependency(); // Dependency dep = new Dependency();
***REMOVED*** //
***REMOVED*** ***REMOVED***if (pkg.startsWith("os:"))***REMOVED*** // //if (pkg.startsWith("os:")){
***REMOVED*** dep.setName(pkg); // dep.setName(pkg);
***REMOVED*** dep.setType("os"); // dep.setType("os");
***REMOVED*** out.addDependency(dep); // out.addDependency(dep);
***REMOVED*** ***REMOVED*** // }
***REMOVED*** ***REMOVED*** // }
***REMOVED*** //
***REMOVED*** List<String> osdependencies = extractMultipleValues(metadata, "os"); // List<String> osdependencies = extractMultipleValues(metadata, "os");
***REMOVED*** if (osdependencies != null) ***REMOVED*** // if (osdependencies != null) {
***REMOVED*** for (String pkg : osdependencies) ***REMOVED*** // for (String pkg : osdependencies) {
***REMOVED*** Dependency dep = new Dependency(); // Dependency dep = new Dependency();
***REMOVED*** //
***REMOVED*** ***REMOVED***if (pkg.startsWith("os:"))***REMOVED*** // //if (pkg.startsWith("os:")){
***REMOVED*** dep.setName(pkg); // dep.setName(pkg);
***REMOVED*** dep.setType("os"); // dep.setType("os");
***REMOVED*** out.addDependency(dep); // out.addDependency(dep);
***REMOVED*** ***REMOVED*** // }
***REMOVED*** ***REMOVED*** // }
***REMOVED*** //
***REMOVED*** //
***REMOVED*** //
***REMOVED*** List<String> gitdependencies = extractMultipleValues(metadata, "github"); // List<String> gitdependencies = extractMultipleValues(metadata, "github");
***REMOVED*** if (gitdependencies != null) ***REMOVED*** // if (gitdependencies != null) {
***REMOVED*** for (String pkg : gitdependencies) ***REMOVED*** // for (String pkg : gitdependencies) {
***REMOVED*** Dependency dep = new Dependency(); // Dependency dep = new Dependency();
***REMOVED*** //
***REMOVED*** ***REMOVED***if (pkg.startsWith("os:"))***REMOVED*** // //if (pkg.startsWith("os:")){
***REMOVED*** dep.setName(pkg); // dep.setName(pkg);
***REMOVED*** dep.setType("github"); // dep.setType("github");
***REMOVED*** out.addDependency(dep); // out.addDependency(dep);
***REMOVED*** ***REMOVED*** // }
***REMOVED*** ***REMOVED*** // }
***REMOVED*** //
***REMOVED*** //
***REMOVED*** //
***REMOVED*** List<String> cdependencies = extractMultipleValues(metadata, "custom"); // List<String> cdependencies = extractMultipleValues(metadata, "custom");
***REMOVED*** if (cdependencies != null) ***REMOVED*** // if (cdependencies != null) {
***REMOVED*** for (String pkg : cdependencies) ***REMOVED*** // for (String pkg : cdependencies) {
***REMOVED*** Dependency dep = new Dependency(); // Dependency dep = new Dependency();
***REMOVED*** //
***REMOVED*** ***REMOVED***if (pkg.startsWith("os:"))***REMOVED*** // //if (pkg.startsWith("os:")){
***REMOVED*** dep.setName(pkg); // dep.setName(pkg);
***REMOVED*** dep.setType("custom"); // dep.setType("custom");
***REMOVED*** out.addDependency(dep); // out.addDependency(dep);
***REMOVED*** ***REMOVED*** // }
***REMOVED*** ***REMOVED*** // }
***REMOVED*** if (pkg.startsWith("r:"))***REMOVED*** // if (pkg.startsWith("r:")){
***REMOVED*** ***REMOVED***String results = StringEscapeUtils.escapeJava(pkg); // //String results = StringEscapeUtils.escapeJava(pkg);
***REMOVED*** dep.setName(pkg); // dep.setName(pkg);
***REMOVED*** dep.setType("cran"); // dep.setType("cran");
***REMOVED*** ***REMOVED*** // }
***REMOVED*** if (pkg.startsWith("custom:"))***REMOVED*** // if (pkg.startsWith("custom:")){
***REMOVED*** dep.setName(pkg); // dep.setName(pkg);
***REMOVED*** dep.setType("custom"); // dep.setType("custom");
***REMOVED*** ***REMOVED*** // }
***REMOVED*** if (!pkg.startsWith("os:")&&!pkg.startsWith("r:")&&!pkg.startsWith("custom:"))***REMOVED*** // if (!pkg.startsWith("os:")&&!pkg.startsWith("r:")&&!pkg.startsWith("custom:")){
***REMOVED*** dep.setName(pkg); // dep.setName(pkg);
***REMOVED*** dep.setType("os"); // dep.setType("os");
***REMOVED*** ***REMOVED*** // }
return out; return out;
***REMOVED*** }
private static String extractSingleValue(Map<String, List<String>> metadata, private static String extractSingleValue(Map<String, List<String>> metadata,
String key) ***REMOVED*** String key) {
List<String> l = metadata.get(key); List<String> l = metadata.get(key);
if (l != null && l.size() == 1) ***REMOVED*** if (l != null && l.size() == 1) {
return l.get(0); return l.get(0);
***REMOVED*** else ***REMOVED*** } else {
return null; return null;
***REMOVED*** }
***REMOVED*** }
private static List<String> extractMultipleValues( private static List<String> extractMultipleValues(
Map<String, List<String>> metadata, String key) ***REMOVED*** Map<String, List<String>> metadata, String key) {
List<String> l = metadata.get(key); List<String> l = metadata.get(key);
if (l != null) ***REMOVED*** if (l != null) {
return new Vector<>(l); return new Vector<>(l);
***REMOVED*** else ***REMOVED*** } else {
return null; return null;
***REMOVED*** }
***REMOVED*** }
public static void main(String[] args) ***REMOVED*** public static void main(String[] args) {
AlgorithmPackageParser ap = new AlgorithmPackageParser(); AlgorithmPackageParser ap = new AlgorithmPackageParser();
String txt = String txt =
"Username: giancarlo.panichi\n"+ "Username: giancarlo.panichi\n"+
@ -312,6 +312,6 @@ public class AlgorithmPackageParser ***REMOVED***
ap.parseMetadata(txt); ap.parseMetadata(txt);
***REMOVED*** }
***REMOVED*** }

70
src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/rest/PoolManager.java
View File

@ -1,44 +1,44 @@
***REMOVED******REMOVED*** //package org.gcube.dataanalysis.dataminer.poolmanager.rest;
***REMOVED*** //
***REMOVED******REMOVED*** //import java.io.IOException;
***REMOVED******REMOVED*** //import java.net.MalformedURLException;
***REMOVED******REMOVED*** //import java.net.URL;
***REMOVED******REMOVED*** //import java.net.UnknownHostException;
***REMOVED*** //
***REMOVED******REMOVED*** //import org.gcube.dataanalysis.dataminer.poolmanager.datamodel.Algorithm;
***REMOVED*** //
***REMOVED***public interface PoolManager ***REMOVED*** //public interface PoolManager {
***REMOVED*** //
***REMOVED*** String addAlgorithmToVRE(Algorithm algo, String vre) throws IOException, InterruptedException; // String addAlgorithmToVRE(Algorithm algo, String vre) throws IOException, InterruptedException;
***REMOVED*** //
***REMOVED*** Algorithm extractAlgorithm(String url) throws IOException; // Algorithm extractAlgorithm(String url) throws IOException;
***REMOVED*** //
***REMOVED*** String getLogById(String logId) throws IOException; // String getLogById(String logId) throws IOException;
***REMOVED*** //
***REMOVED*** void getLogId(Algorithm algo, String vre); // void getLogId(Algorithm algo, String vre);
***REMOVED*** //
***REMOVED*** String getScriptFromURL(URL logId) throws IOException; // String getScriptFromURL(URL logId) throws IOException;
***REMOVED*** //
***REMOVED*** URL getURLfromWorkerLog(String logUrl) throws MalformedURLException, UnknownHostException; // URL getURLfromWorkerLog(String logUrl) throws MalformedURLException, UnknownHostException;
***REMOVED*** //
***REMOVED******REMOVED*** //}
***REMOVED*** package org.gcube.dataanalysis.dataminer.poolmanager.rest;
***REMOVED*** import java.io.IOException;
***REMOVED*** import java.net.MalformedURLException;
***REMOVED*** import java.net.URL;
***REMOVED*** import java.net.UnknownHostException;
***REMOVED*** import java.util.List;
***REMOVED*** import java.util.Set;
***REMOVED*** import org.gcube.dataanalysis.dataminer.poolmanager.datamodel.Algorithm;
***REMOVED*** import org.tmatesoft.svn.core.SVNException;
public interface PoolManager public interface PoolManager
***REMOVED*** {
String addAlgorithmToVRE(Algorithm algo, String vre, boolean test ) throws IOException, InterruptedException; String addAlgorithmToVRE(Algorithm algo, String vre, boolean test ) throws IOException, InterruptedException;
String addAlgorithmToHost(Algorithm algo, String host,boolean test) throws IOException, InterruptedException; String addAlgorithmToHost(Algorithm algo, String host,boolean test) throws IOException, InterruptedException;
@ -64,4 +64,4 @@ public interface PoolManager
List<String> updateSVN(String file, List<String> ldep) throws SVNException, IOException; List<String> updateSVN(String file, List<String> ldep) throws SVNException, IOException;
***REMOVED*** }

245
src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/rest/RestPoolManager.java Executable file
View File

@ -0,0 +1,245 @@
package org.gcube.dataanalysis.dataminer.poolmanager.rest;
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 javax.ws.rs.GET;
import javax.ws.rs.Path;
import javax.ws.rs.Produces;
import javax.ws.rs.QueryParam;
import org.gcube.common.authorization.client.exceptions.ObjectNotFound;
import org.gcube.common.authorization.library.provider.SecurityTokenProvider;
import org.gcube.common.scope.api.ScopeProvider;
import org.gcube.dataanalysis.dataminer.poolmanager.datamodel.Algorithm;
import org.gcube.dataanalysis.dataminer.poolmanager.service.DataminerPoolManager;
import org.gcube.dataanalysis.dataminer.poolmanager.util.AlgorithmBuilder;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.tmatesoft.svn.core.SVNException;
@Path("/")
public class RestPoolManager implements PoolManager
{
//@Context ServletContext context;
private final Logger logger;
private DataminerPoolManager service;
//@Context
//private ApplicationContext context = ContextProvider.get();
public RestPoolManager()
{
this.logger = LoggerFactory.getLogger(RestPoolManager.class);
this.service = new DataminerPoolManager();
}
@GET
@Path("/algorithm/stage")
@Produces("text/plain")
public String stageAlgorithm(
@QueryParam("algorithmPackageURL") String algorithmPackageURL,
@QueryParam("targetVRE") String targetVRE,
@QueryParam("category") String category,
@QueryParam("algorithm_type") String algorithm_type) throws IOException, InterruptedException {
this.logger.debug("Stage algorithm method called");
Algorithm algo = AlgorithmBuilder.create(algorithmPackageURL);
//String env = context.application().getInitParameter("Environment");
return this.service.stageAlgorithm(algo,targetVRE,category,algorithm_type/*,env*/);
}
@GET
@Path("/algorithm/add")
@Produces("text/plain")
public String publishAlgorithm(
@QueryParam("algorithmPackageURL") String algorithmPackageURL,
//@QueryParam("targetVREToken") String targetVREToken,
@QueryParam("targetVRE") String targetVRE,
@QueryParam("category") String category,
@QueryParam("algorithm_type") String algorithm_type) throws IOException, InterruptedException {
this.logger.debug("Publish algorithm method called");
Algorithm algo = AlgorithmBuilder.create(algorithmPackageURL);
//String env = context.application().getInitParameter("Environment");
return this.service.publishAlgorithm(algo, /*targetVREToken,*/ targetVRE,category,algorithm_type/*,env*/);
}
/*
* /scopes/<scope> POST // add an algorithm to all dataminers in the scope
* /hosts/<hostname> POST // add an algorithm to the given host
*/
@GET
@Path("/log")
@Produces("text/plain")
public String getLogById(@QueryParam("logUrl") String logUrl) throws IOException {
// TODO Auto-generated method stub
this.logger.debug("Get log by id method called");
this.logger.debug("Returning Log =" + logUrl);
return service.getLogById(logUrl);
}
@GET
@Path("/monitor")
@Produces("text/plain")
public String getMonitorById(@QueryParam("logUrl") String logUrl) throws IOException {
// TODO Auto-generated method stub
this.logger.debug("Get monitor by id method called");
this.logger.debug("Returning Log =" + logUrl);
return service.getMonitorById(logUrl);
}
@Override
public Algorithm extractAlgorithm(String url) throws IOException {
// TODO Auto-generated method stub
return null;
}
public static void main(String[] args) throws ObjectNotFound, Exception {
// System.out.println(System.getProperty("user.home")+File.separator+"/gcube/dataminer-pool-manager");
// // ProxySelector.setDefault(new
// // PropertiesBasedProxySelector("/home/ngalante/.proxy-settings"));
//
// ScopeProvider.instance.set("/d4science.research-infrastructures.eu/gCubeApps/RPrototypingLab");
// SecurityTokenProvider.instance.set("xxxx-xxx-xxx-xxx");
ScopeProvider.instance.set("/gcube/devNext");
SecurityTokenProvider.instance.set("xxx-xxx-xxx-xxx");
// AuthorizationEntry entry = authorizationService().get("xxx-xxx-xxx-xxx");
// System.out.println(entry.getContext());
RestPoolManager a = new RestPoolManager();
a.stageAlgorithm("http://data-d.d4science.org/TSt3cUpDTG1teUJMemxpcXplVXYzV1lBelVHTTdsYjlHbWJQNStIS0N6Yz0");
// //a.publishAlgorithm("http://data.d4science.org/MnovRjZIdGV5WlB0WXE5NVNaZnRoRVg0SU8xZWpWQlFHbWJQNStIS0N6Yz0", "xxxx-xxx-xxx-xxx","/gcube/devNext/NextNext");
// // PoolManager aa = new DataminerPoolManager();
//
}
//Production Testing
/*
stageAlgorithm(Rproto caller token,pacchetto, category)
http://node2-d-d4s.d4science.org:8080/dataminer-pool-manager-1.0.0-SNAPSHOT/rest/algorithm/stage?gcube-token=xxx-xxx-xxx-xxx&algorithmPackageURL=http://data.d4science.org/dENQTTMxdjNZcGRpK0NHd2pvU0owMFFzN0VWemw3Zy9HbWJQNStIS0N6Yz0&category=ICHTHYOP_MODEL
publishAlgorithm(Rproto caller token, pacchetto, category, target token, target prod vre)
node2-d-d4s.d4science.org:8080/dataminer-pool-manager-1.0.0-SNAPSHOT/rest/algorithm/add?gcube-token=xxx-xxx-xxx-xxx&algorithmPackageURL=http://data.d4science.org/dENQTTMxdjNZcGRpK0NHd2pvU0owMFFzN0VWemw3Zy9HbWJQNStIS0N6Yz0&category=ICHTHYOP_MODEL&targetVREToken=xxxx-xxx-xxx-xxx&targetVRE=/d4science.research-infrastructures.eu/gCubeApps/RPrototypingLab
getLogById(Rproto caller token, logid)
http://node2-d-d4s.d4science.org:8080/dataminer-pool-manager-1.0.0-SNAPSHOT/rest/log?gcube-token=xxxx-xxxx-xxx-xxx&logUrl=
*/
//dev Testing
/*
stageAlgorithm(dev_caller_vre_token,pacchetto, category)
http://node2-d-d4s.d4science.org:8080/dataminer-pool-manager-1.0.0-SNAPSHOT/rest/algorithm/stage?gcube-token=xxx-xxxx-xxxx-xxx-xxxx&algorithmPackageURL=http://data.d4science.org/dENQTTMxdjNZcGRpK0NHd2pvU0owMFFzN0VWemw3Zy9HbWJQNStIS0N6Yz0&category=ICHTHYOP_MODEL
publishAlgorithm(dev_caller_vre_token, pacchetto, category, target token, target prod vre)
http://node2-d-d4s.d4science.org:8080/dataminer-pool-manager-1.0.0-SNAPSHOT/rest/log?gcube-token=xxx-xxx-xxx-xxx&logUrl=450bb7f9-9e38-4bde-8f4d-f3296f95deba
getLogById(dev_caller_vre_token, logid)
http://node2-d-d4s.d4science.org:8080/dataminer-pool-manager-1.0.0-SNAPSHOT/rest/log?gcube-token=xxx-xxx-xxx-xxx&logUrl=426c8e35-a624-4710-b612-c90929c32c27 */
@Override
public void getLogId(Algorithm algo, String vre) {
// TODO Auto-generated method stub
}
@Override
public String getScriptFromURL(URL logId) throws IOException {
// TODO Auto-generated method stub
return null;
}
@Override
public URL getURLfromWorkerLog(String logUrl) throws MalformedURLException, UnknownHostException {
// TODO Auto-generated method stub
return null;
}
@Override
public void addAlgToIs(Algorithm algo) {
// TODO Auto-generated method stub
}
@Override
public Set<Algorithm> getAlgoFromIs() {
// TODO Auto-generated method stub
return null;
}
@Override
public List<String> updateSVN(String file, List<String> ldep) throws SVNException {
// TODO Auto-generated method stub
return null;
}
@Override
public String addAlgorithmToHost(Algorithm algo, String host, boolean test)
throws IOException, InterruptedException {
// TODO Auto-generated method stub
return null;
}
@Override
public String addAlgorithmToVRE(Algorithm algo, String vre, boolean test)
throws IOException, InterruptedException {
// TODO Auto-generated method stub
return null;
}
@Override
public String stageAlgorithm(String algorithmPackageURL) throws IOException, InterruptedException {
// TODO Auto-generated method stub
return null;
}
@Override
public String publishAlgorithm(String algorithmPackageURL, String targetVREToken, String targetVRE)
throws IOException, InterruptedException {
// TODO Auto-generated method stub
return null;
}
}

146
src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/service/DMPMJob.java
View File

@ -2,18 +2,18 @@ package org.gcube.dataanalysis.dataminer.poolmanager.service;
import java.io.File; import java.io.File;
import java.io.FileOutputStream; import java.io.FileOutputStream;
***REMOVED*** import java.io.IOException;
import java.io.PrintStream; import java.io.PrintStream;
import java.io.PrintWriter; import java.io.PrintWriter;
import java.util.Collection; import java.util.Collection;
import java.util.UUID; import java.util.UUID;
***REMOVED*** import org.gcube.common.authorization.library.provider.SecurityTokenProvider;
***REMOVED*** import org.gcube.common.scope.api.ScopeProvider;
import org.gcube.dataanalysis.dataminer.poolmanager.ansible.AnsibleWorker; import org.gcube.dataanalysis.dataminer.poolmanager.ansible.AnsibleWorker;
import org.gcube.dataanalysis.dataminer.poolmanager.ansiblebridge.AnsibleBridge; import org.gcube.dataanalysis.dataminer.poolmanager.ansiblebridge.AnsibleBridge;
import org.gcube.dataanalysis.dataminer.poolmanager.clients.configuration.Configuration; import org.gcube.dataanalysis.dataminer.poolmanager.clients.configuration.Configuration;
***REMOVED*** import org.gcube.dataanalysis.dataminer.poolmanager.datamodel.Algorithm;
import org.gcube.dataanalysis.dataminer.poolmanager.datamodel.Cluster; import org.gcube.dataanalysis.dataminer.poolmanager.datamodel.Cluster;
import org.gcube.dataanalysis.dataminer.poolmanager.service.exceptions.AnsibleException; import org.gcube.dataanalysis.dataminer.poolmanager.service.exceptions.AnsibleException;
import org.gcube.dataanalysis.dataminer.poolmanager.service.exceptions.UndefinedDependenciesException; import org.gcube.dataanalysis.dataminer.poolmanager.service.exceptions.UndefinedDependenciesException;
@ -24,11 +24,11 @@ import org.gcube.dataanalysis.dataminer.poolmanager.util.SendMail;
import org.gcube.dataanalysis.dataminer.poolmanager.util.exception.DMPMException; import org.gcube.dataanalysis.dataminer.poolmanager.util.exception.DMPMException;
import org.gcube.dataanalysis.dataminer.poolmanager.util.exception.EMailException; import org.gcube.dataanalysis.dataminer.poolmanager.util.exception.EMailException;
import org.gcube.dataanalysis.dataminer.poolmanager.util.exception.GenericException; import org.gcube.dataanalysis.dataminer.poolmanager.util.exception.GenericException;
***REMOVED*** import org.slf4j.Logger;
***REMOVED*** import org.slf4j.LoggerFactory;
public abstract class DMPMJob ***REMOVED*** public abstract class DMPMJob {
private Configuration configuration; private Configuration configuration;
private String dmpmHomeDirectory; private String dmpmHomeDirectory;
@ -43,7 +43,7 @@ public abstract class DMPMJob ***REMOVED***
private Logger logger; private Logger logger;
private enum STATUS private enum STATUS
***REMOVED*** {
PROGRESS ("IN PROGRESS"), PROGRESS ("IN PROGRESS"),
COMPLETED ("COMPLETED"), COMPLETED ("COMPLETED"),
FAILED ("FAILED"); FAILED ("FAILED");
@ -51,13 +51,13 @@ public abstract class DMPMJob ***REMOVED***
private String status; private String status;
STATUS (String status) STATUS (String status)
***REMOVED*** {
this.status = status; this.status = status;
***REMOVED*** }
***REMOVED*** }
public DMPMJob(SVNUpdater svnUpdater,Configuration configuration,Algorithm algorithm, Cluster cluster,String vREName, public DMPMJob(SVNUpdater svnUpdater,Configuration configuration,Algorithm algorithm, Cluster cluster,String vREName,
String category, String algorithm_type)***REMOVED*** String category, String algorithm_type){
this.logger = LoggerFactory.getLogger(DMPMJob.class); this.logger = LoggerFactory.getLogger(DMPMJob.class);
this.configuration = configuration; this.configuration = configuration;
@ -71,82 +71,82 @@ public abstract class DMPMJob ***REMOVED***
this.dmpmHomeDirectory = new String (System.getProperty("user.home")+File.separator+"dataminer-pool-manager"); this.dmpmHomeDirectory = new String (System.getProperty("user.home")+File.separator+"dataminer-pool-manager");
this.id = UUID.randomUUID().toString(); this.id = UUID.randomUUID().toString();
***REMOVED***TODO: dmpm work directory should be loaded from configuration file //TODO: dmpm work directory should be loaded from configuration file
this.jobLogs = new File(this.dmpmHomeDirectory+File.separator+"jobs"); this.jobLogs = new File(this.dmpmHomeDirectory+File.separator+"jobs");
this.jobLogs.mkdirs(); this.jobLogs.mkdirs();
***REMOVED*** }
public String start() public String start()
***REMOVED*** {
setStatusInformation(STATUS.PROGRESS); setStatusInformation(STATUS.PROGRESS);
new Thread(new Runnable() ***REMOVED*** new Thread(new Runnable() {
***REMOVED*** @Override
public void run() ***REMOVED*** public void run() {
try ***REMOVED*** try {
execute(); execute();
***REMOVED*** catch (Exception e) ***REMOVED*** } catch (Exception e) {
e.printStackTrace(); e.printStackTrace();
***REMOVED*** }
***REMOVED*** }
***REMOVED***).start(); }).start();
return this.id; return this.id;
***REMOVED*** }
protected AnsibleWorker createWorker(Algorithm algo, protected AnsibleWorker createWorker(Algorithm algo,
Cluster dataminerCluster, Cluster dataminerCluster,
boolean includeAlgorithmDependencies, boolean includeAlgorithmDependencies,
String user)***REMOVED*** String user){
AnsibleBridge ansibleBridge = new AnsibleBridge(this.dmpmHomeDirectory); AnsibleBridge ansibleBridge = new AnsibleBridge(this.dmpmHomeDirectory);
try ***REMOVED*** try {
return ansibleBridge.createWorker(algo, dataminerCluster, includeAlgorithmDependencies, user); return ansibleBridge.createWorker(algo, dataminerCluster, includeAlgorithmDependencies, user);
***REMOVED*** catch (IOException e) ***REMOVED*** } catch (IOException e) {
e.printStackTrace(); e.printStackTrace();
***REMOVED*** }
***REMOVED*** return null;
***REMOVED*** }
public void setStatusInformation(STATUS exitStatus) ***REMOVED*** public void setStatusInformation(STATUS exitStatus) {
try try
***REMOVED*** {
File statusFile = new File (this.jobLogs,this.id + "_exitStatus"); File statusFile = new File (this.jobLogs,this.id + "_exitStatus");
***REMOVED***File m = new File ( this.jobLogs + File.separator + this.id + "_exitStatus"); //File m = new File ( this.jobLogs + File.separator + this.id + "_exitStatus");
PrintWriter writer = new PrintWriter(statusFile, "UTF-8"); PrintWriter writer = new PrintWriter(statusFile, "UTF-8");
writer.println(exitStatus.status); writer.println(exitStatus.status);
writer.close(); writer.close();
***REMOVED*** catch (Exception e) } catch (Exception e)
***REMOVED*** {
this.logger.error ("Unable to update exit status file with status "+exitStatus.status,e); this.logger.error ("Unable to update exit status file with status "+exitStatus.status,e);
***REMOVED*** }
***REMOVED*** }
private void updateLogFile (File logFile, String message) private void updateLogFile (File logFile, String message)
***REMOVED*** {
try try
***REMOVED*** {
PrintWriter writer = new PrintWriter(logFile,"UTF-8"); PrintWriter writer = new PrintWriter(logFile,"UTF-8");
writer.print(message); writer.print(message);
writer.close(); writer.close();
***REMOVED*** catch (Exception e) } catch (Exception e)
***REMOVED*** {
this.logger.error("Unable to log the error message: "+message,e); this.logger.error("Unable to log the error message: "+message,e);
***REMOVED*** }
***REMOVED*** }
protected abstract void execute (); protected abstract void execute ();
private void preInstallation (SendMail sm,NotificationHelper nh, File logFile ) throws GenericException, EMailException,UndefinedDependenciesException private void preInstallation (SendMail sm,NotificationHelper nh, File logFile ) throws GenericException, EMailException,UndefinedDependenciesException
***REMOVED*** {
this.logger.debug("Checking dependencies..."); this.logger.debug("Checking dependencies...");
Collection<String> undefinedDependencies = this.svnUpdater.getUndefinedDependencies( Collection<String> undefinedDependencies = this.svnUpdater.getUndefinedDependencies(
@ -154,16 +154,16 @@ public abstract class DMPMJob ***REMOVED***
this.algorithm.getDependencies()); this.algorithm.getDependencies());
if (!undefinedDependencies.isEmpty()) if (!undefinedDependencies.isEmpty())
***REMOVED*** {
this.logger.debug("Some dependencies are not defined"); this.logger.debug("Some dependencies are not defined");
throw new UndefinedDependenciesException(undefinedDependencies); throw new UndefinedDependenciesException(undefinedDependencies);
***REMOVED*** }
***REMOVED*** }
private String installation (SendMail sm,NotificationHelper nh,CheckMethod methodChecker,File logFile ) throws DMPMException private String installation (SendMail sm,NotificationHelper nh,CheckMethod methodChecker,File logFile ) throws DMPMException
***REMOVED*** {
this.logger.debug("Installation process started"); this.logger.debug("Installation process started");
methodChecker.deleteFiles(this.algorithm/*, env*/); methodChecker.deleteFiles(this.algorithm/*, env*/);
int ret = this.executeAnsibleWorker(createWorker(this.algorithm, this.cluster, false, "root"),logFile); int ret = this.executeAnsibleWorker(createWorker(this.algorithm, this.cluster, false, "root"),logFile);
@ -172,9 +172,9 @@ public abstract class DMPMJob ***REMOVED***
if (ret != 0) throw new AnsibleException(ret); if (ret != 0) throw new AnsibleException(ret);
else else
***REMOVED*** {
this.logger.debug("Operation completed"); this.logger.debug("Operation completed");
***REMOVED***this.setStatusInformation(STATUS.PROGRESS); //this.setStatusInformation(STATUS.PROGRESS);
this.logger.debug("Checking the method..."); this.logger.debug("Checking the method...");
methodChecker.checkMethod(this.configuration.getHost(), SecurityTokenProvider.instance.get()); methodChecker.checkMethod(this.configuration.getHost(), SecurityTokenProvider.instance.get());
methodChecker.copyAlgorithms(this.algorithm); methodChecker.copyAlgorithms(this.algorithm);
@ -185,20 +185,20 @@ public abstract class DMPMJob ***REMOVED***
this.algorithm.getFullname()); this.algorithm.getFullname());
this.setStatusInformation(STATUS.COMPLETED); this.setStatusInformation(STATUS.COMPLETED);
return algorithmListResult ?"":"\nWARNING: algorithm list could not be updated on SVN"; return algorithmListResult ?"":"\nWARNING: algorithm list could not be updated on SVN";
***REMOVED*** }
***REMOVED*** }
protected void execute(NotificationHelper nh, CheckMethod methodChecker) protected void execute(NotificationHelper nh, CheckMethod methodChecker)
***REMOVED*** {
SendMail sm = new SendMail(); SendMail sm = new SendMail();
File logFile = new File(this.jobLogs,this.id); File logFile = new File(this.jobLogs,this.id);
try try
***REMOVED*** {
try ***REMOVED*** try {
this.logger.debug("Pre installation operations"); this.logger.debug("Pre installation operations");
preInstallation(sm, nh, logFile); preInstallation(sm, nh, logFile);
@ -213,8 +213,8 @@ public abstract class DMPMJob ***REMOVED***
***REMOVED*** catch (DMPMException dmpme) } catch (DMPMException dmpme)
***REMOVED*** {
this.logger.error("Operation failed: "+dmpme.getMessage()); this.logger.error("Operation failed: "+dmpme.getMessage());
this.logger.error("Exception: ",dmpme); this.logger.error("Exception: ",dmpme);
this.setStatusInformation(STATUS.FAILED); this.setStatusInformation(STATUS.FAILED);
@ -222,41 +222,41 @@ public abstract class DMPMJob ***REMOVED***
this.updateLogFile(logFile, errorMessage); this.updateLogFile(logFile, errorMessage);
sm.sendNotification(nh.getFailedSubject() +" for "+this.algorithm.getName()+ " algorithm", errorMessage); sm.sendNotification(nh.getFailedSubject() +" for "+this.algorithm.getName()+ " algorithm", errorMessage);
***REMOVED*** }
***REMOVED*** catch (EMailException eme) } catch (EMailException eme)
***REMOVED*** {
this.logger.error("Unable to send notification email",eme); this.logger.error("Unable to send notification email",eme);
***REMOVED*** }
***REMOVED*** }
protected int executeAnsibleWorker(AnsibleWorker worker, File logFile) throws GenericException protected int executeAnsibleWorker(AnsibleWorker worker, File logFile) throws GenericException
***REMOVED*** {
try try
***REMOVED*** {
FileOutputStream fos = new FileOutputStream(logFile, true); FileOutputStream fos = new FileOutputStream(logFile, true);
PrintStream ps = new PrintStream(fos); PrintStream ps = new PrintStream(fos);
***REMOVED*** File m = new File(this.jobLogs + File.separator + this.id + "_exitStatus"); // File m = new File(this.jobLogs + File.separator + this.id + "_exitStatus");
***REMOVED*** PrintWriter fos2 = new PrintWriter(m, "UTF-8"); // PrintWriter fos2 = new PrintWriter(m, "UTF-8");
return worker.execute(ps); return worker.execute(ps);
***REMOVED*** catch (Exception e) } catch (Exception e)
***REMOVED*** {
throw new GenericException(e); throw new GenericException(e);
***REMOVED*** }
***REMOVED*** }
public String buildInfo() ***REMOVED*** public String buildInfo() {
return return
"\n"+ "\n"+
@ -266,8 +266,8 @@ public abstract class DMPMJob ***REMOVED***
"Staging DataMiner Host: "+ this.configuration.getHost()+"\n"+ "Staging DataMiner Host: "+ this.configuration.getHost()+"\n"+
"Caller VRE: "+ScopeProvider.instance.get()+"\n"+ "Caller VRE: "+ScopeProvider.instance.get()+"\n"+
"Target VRE: "+this.vREName+"\n"; "Target VRE: "+this.vREName+"\n";
***REMOVED*** }
***REMOVED*** }

52
src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/service/DataminerPoolManager.java
View File

@ -2,55 +2,55 @@ package org.gcube.dataanalysis.dataminer.poolmanager.service;
import java.io.File; import java.io.File;
import java.io.FileNotFoundException; import java.io.FileNotFoundException;
***REMOVED*** import java.io.IOException;
import java.util.Scanner; import java.util.Scanner;
***REMOVED*** import org.gcube.dataanalysis.dataminer.poolmanager.datamodel.Algorithm;
import org.gcube.dataanalysis.dataminer.poolmanager.datamodel.Cluster; import org.gcube.dataanalysis.dataminer.poolmanager.datamodel.Cluster;
import org.gcube.dataanalysis.dataminer.poolmanager.util.ClusterBuilder; import org.gcube.dataanalysis.dataminer.poolmanager.util.ClusterBuilder;
import org.gcube.dataanalysis.dataminer.poolmanager.util.impl.ClusterBuilderProduction; import org.gcube.dataanalysis.dataminer.poolmanager.util.impl.ClusterBuilderProduction;
import org.gcube.dataanalysis.dataminer.poolmanager.util.impl.ClusterBuilderStaging; import org.gcube.dataanalysis.dataminer.poolmanager.util.impl.ClusterBuilderStaging;
import org.gcube.dataanalysis.dataminer.poolmanager.util.impl.SVNUpdaterProduction; import org.gcube.dataanalysis.dataminer.poolmanager.util.impl.SVNUpdaterProduction;
import org.gcube.dataanalysis.dataminer.poolmanager.util.impl.SVNUpdaterStaging; import org.gcube.dataanalysis.dataminer.poolmanager.util.impl.SVNUpdaterStaging;
***REMOVED*** import org.slf4j.Logger;
***REMOVED*** import org.slf4j.LoggerFactory;
***REMOVED*** import org.tmatesoft.svn.core.SVNException;
public class DataminerPoolManager ***REMOVED*** public class DataminerPoolManager {
private Logger logger; private Logger logger;
private SVNUpdaterStaging svnUpdaterStaging; private SVNUpdaterStaging svnUpdaterStaging;
private SVNUpdaterProduction svnUpdaterProduction; private SVNUpdaterProduction svnUpdaterProduction;
public DataminerPoolManager() ***REMOVED*** public DataminerPoolManager() {
this.logger = LoggerFactory.getLogger(this.getClass()); this.logger = LoggerFactory.getLogger(this.getClass());
try ***REMOVED*** try {
***REMOVED***TODO: read this from configuration //TODO: read this from configuration
this.svnUpdaterStaging = new SVNUpdaterStaging(); this.svnUpdaterStaging = new SVNUpdaterStaging();
this.svnUpdaterProduction = new SVNUpdaterProduction(); this.svnUpdaterProduction = new SVNUpdaterProduction();
***REMOVED*** catch (SVNException e) ***REMOVED*** } catch (SVNException e) {
this.logger.error("SVN Exception",e); this.logger.error("SVN Exception",e);
***REMOVED*** }
***REMOVED*** }
***REMOVED***Algorithm algo,String targetVRE, String category, String algorithm_type/*,String env*/) throws IOException, InterruptedException public String stageAlgorithm(Algorithm algo,String targetVRE, String category, String algorithm_type/*,String env*/) throws IOException, InterruptedException
***REMOVED*** {
this.logger.debug("Stage algorithm"); this.logger.debug("Stage algorithm");
this.logger.debug("Algo "+algo); this.logger.debug("Algo "+algo);
this.logger.debug("Category "+category); this.logger.debug("Category "+category);
this.logger.debug("Algo type "+algorithm_type); this.logger.debug("Algo type "+algorithm_type);
ClusterBuilder stagingClusterBuilder = new ClusterBuilderStaging(); ClusterBuilder stagingClusterBuilder = new ClusterBuilderStaging();
Cluster stagingCluster = stagingClusterBuilder.getDataminerCluster(); Cluster stagingCluster = stagingClusterBuilder.getDataminerCluster();
***REMOVED***Cluster rProtoCluster = ClusterBuilder.getRProtoCluster(); //Cluster rProtoCluster = ClusterBuilder.getRProtoCluster();
DMPMJob job = new StagingJob(this.svnUpdaterStaging, algo, stagingCluster, /*rProtoCluster,*/ targetVRE, category, algorithm_type/*,env*/); DMPMJob job = new StagingJob(this.svnUpdaterStaging, algo, stagingCluster, /*rProtoCluster,*/ targetVRE, category, algorithm_type/*,env*/);
String id = job.start(); String id = job.start();
return id; return id;
***REMOVED*** }
***REMOVED***Algorithm algo, String targetVRE, String category, String algorithm_type/*, String env*/) throws IOException, InterruptedException public String publishAlgorithm(Algorithm algo, String targetVRE, String category, String algorithm_type/*, String env*/) throws IOException, InterruptedException
***REMOVED*** {
this.logger.debug("publish algorithm"); this.logger.debug("publish algorithm");
this.logger.debug("Algo "+algo); this.logger.debug("Algo "+algo);
this.logger.debug("Category "+category); this.logger.debug("Category "+category);
@ -60,12 +60,12 @@ public class DataminerPoolManager ***REMOVED***
DMPMJob job = new ProductionPublishingJob(this.svnUpdaterProduction, algo, prodCluster, targetVRE, category, algorithm_type/*,env*/); DMPMJob job = new ProductionPublishingJob(this.svnUpdaterProduction, algo, prodCluster, targetVRE, category, algorithm_type/*,env*/);
String id = job.start(); String id = job.start();
return id; return id;
***REMOVED*** }
public String getLogById(String id) throws FileNotFoundException***REMOVED*** public String getLogById(String id) throws FileNotFoundException{
***REMOVED***TODO: load dir from configuration file //TODO: load dir from configuration file
this.logger.debug("Getting log by id "+id); this.logger.debug("Getting log by id "+id);
File path = new File(System.getProperty("user.home") + File.separator + "dataminer-pool-manager/jobs/" File path = new File(System.getProperty("user.home") + File.separator + "dataminer-pool-manager/jobs/"
+ id); + id);
@ -75,13 +75,13 @@ public class DataminerPoolManager ***REMOVED***
this.logger.debug("Response "+response); this.logger.debug("Response "+response);
scanner.close(); scanner.close();
return response; return response;
***REMOVED*** }
public String getMonitorById(String id) throws FileNotFoundException***REMOVED*** public String getMonitorById(String id) throws FileNotFoundException{
this.logger.debug("Getting monitor by id "+id); this.logger.debug("Getting monitor by id "+id);
***REMOVED***TODO: load dir from configuration file //TODO: load dir from configuration file
File path = new File(System.getProperty("user.home") + File.separator + "dataminer-pool-manager/jobs/" File path = new File(System.getProperty("user.home") + File.separator + "dataminer-pool-manager/jobs/"
+ id + "_exitStatus"); + id + "_exitStatus");
Scanner scanner = new Scanner(path); Scanner scanner = new Scanner(path);
@ -89,9 +89,9 @@ public class DataminerPoolManager ***REMOVED***
this.logger.debug("Response "+response); this.logger.debug("Response "+response);
scanner.close(); scanner.close();
return response; return response;
***REMOVED*** }
***REMOVED*** }

26
src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/service/ProductionPublishingJob.java
View File

@ -4,34 +4,34 @@ import java.io.FileNotFoundException;
import java.io.UnsupportedEncodingException; import java.io.UnsupportedEncodingException;
import org.gcube.dataanalysis.dataminer.poolmanager.clients.configuration.DMPMClientConfiguratorManager; import org.gcube.dataanalysis.dataminer.poolmanager.clients.configuration.DMPMClientConfiguratorManager;
***REMOVED*** import org.gcube.dataanalysis.dataminer.poolmanager.datamodel.Algorithm;
import org.gcube.dataanalysis.dataminer.poolmanager.datamodel.Cluster; import org.gcube.dataanalysis.dataminer.poolmanager.datamodel.Cluster;
import org.gcube.dataanalysis.dataminer.poolmanager.util.SVNUpdater; import org.gcube.dataanalysis.dataminer.poolmanager.util.SVNUpdater;
import org.gcube.dataanalysis.dataminer.poolmanager.util.impl.CheckMethodProduction; import org.gcube.dataanalysis.dataminer.poolmanager.util.impl.CheckMethodProduction;
import org.gcube.dataanalysis.dataminer.poolmanager.util.impl.NotificationHelperProduction; import org.gcube.dataanalysis.dataminer.poolmanager.util.impl.NotificationHelperProduction;
***REMOVED*** import org.slf4j.Logger;
***REMOVED*** import org.slf4j.LoggerFactory;
public class ProductionPublishingJob extends DMPMJob ***REMOVED*** public class ProductionPublishingJob extends DMPMJob {
***REMOVED***private String targetVREToken; //private String targetVREToken;
***REMOVED***private String env; //private String env;
private Logger logger; private Logger logger;
public ProductionPublishingJob(SVNUpdater svnUpdater, Algorithm algorithm, public ProductionPublishingJob(SVNUpdater svnUpdater, Algorithm algorithm,
Cluster prodCluster, String targetVREName, String category,String algorithm_type/*, String env*/) throws FileNotFoundException, UnsupportedEncodingException ***REMOVED*** Cluster prodCluster, String targetVREName, String category,String algorithm_type/*, String env*/) throws FileNotFoundException, UnsupportedEncodingException {
super(svnUpdater,DMPMClientConfiguratorManager.getInstance().getProductionConfiguration(),algorithm,prodCluster,targetVREName,category,algorithm_type); super(svnUpdater,DMPMClientConfiguratorManager.getInstance().getProductionConfiguration(),algorithm,prodCluster,targetVREName,category,algorithm_type);
this.logger = LoggerFactory.getLogger(StagingJob.class);***REMOVED*** this.jobLogs = new File( this.logger = LoggerFactory.getLogger(StagingJob.class);// this.jobLogs = new File(
***REMOVED*** }
***REMOVED*** @Override
protected void execute() ***REMOVED*** protected void execute() {
this.logger.debug("Executing staging job..."); this.logger.debug("Executing staging job...");
super.execute(new NotificationHelperProduction(), new CheckMethodProduction()); super.execute(new NotificationHelperProduction(), new CheckMethodProduction());
***REMOVED*** }
@ -42,4 +42,4 @@ public class ProductionPublishingJob extends DMPMJob ***REMOVED***
***REMOVED*** }

20
src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/service/StagingJob.java
View File

@ -4,15 +4,15 @@ import java.io.FileNotFoundException;
import java.io.UnsupportedEncodingException; import java.io.UnsupportedEncodingException;
import org.gcube.dataanalysis.dataminer.poolmanager.clients.configuration.DMPMClientConfiguratorManager; import org.gcube.dataanalysis.dataminer.poolmanager.clients.configuration.DMPMClientConfiguratorManager;
***REMOVED*** import org.gcube.dataanalysis.dataminer.poolmanager.datamodel.Algorithm;
import org.gcube.dataanalysis.dataminer.poolmanager.datamodel.Cluster; import org.gcube.dataanalysis.dataminer.poolmanager.datamodel.Cluster;
import org.gcube.dataanalysis.dataminer.poolmanager.util.SVNUpdater; import org.gcube.dataanalysis.dataminer.poolmanager.util.SVNUpdater;
import org.gcube.dataanalysis.dataminer.poolmanager.util.impl.CheckMethodStaging; import org.gcube.dataanalysis.dataminer.poolmanager.util.impl.CheckMethodStaging;
import org.gcube.dataanalysis.dataminer.poolmanager.util.impl.NotificationHelperStaging; import org.gcube.dataanalysis.dataminer.poolmanager.util.impl.NotificationHelperStaging;
***REMOVED*** import org.slf4j.Logger;
***REMOVED*** import org.slf4j.LoggerFactory;
public class StagingJob extends DMPMJob ***REMOVED*** public class StagingJob extends DMPMJob {
@ -20,18 +20,18 @@ public class StagingJob extends DMPMJob ***REMOVED***
public StagingJob(SVNUpdater svnUpdater, Algorithm algorithm, public StagingJob(SVNUpdater svnUpdater, Algorithm algorithm,
Cluster stagingCluster, /* Cluster rProtoCluster, */ Cluster stagingCluster, /* Cluster rProtoCluster, */
String rProtoVREName, String category, String algorithm_type/*, String env*/) throws FileNotFoundException, UnsupportedEncodingException ***REMOVED*** String rProtoVREName, String category, String algorithm_type/*, String env*/) throws FileNotFoundException, UnsupportedEncodingException {
super(svnUpdater,DMPMClientConfiguratorManager.getInstance().getStagingConfiguration(),algorithm,stagingCluster,rProtoVREName,category,algorithm_type); super(svnUpdater,DMPMClientConfiguratorManager.getInstance().getStagingConfiguration(),algorithm,stagingCluster,rProtoVREName,category,algorithm_type);
this.logger = LoggerFactory.getLogger(StagingJob.class); this.logger = LoggerFactory.getLogger(StagingJob.class);
***REMOVED*** }
***REMOVED*** @Override
protected void execute() ***REMOVED*** protected void execute() {
this.logger.debug("Executing staging job..."); this.logger.debug("Executing staging job...");
super.execute(new NotificationHelperStaging(), new CheckMethodStaging()); super.execute(new NotificationHelperStaging(), new CheckMethodStaging());
***REMOVED*** }
@ -40,4 +40,4 @@ public class StagingJob extends DMPMJob ***REMOVED***
***REMOVED*** }

18
src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/service/exceptions/AnsibleException.java
View File

@ -2,24 +2,24 @@ package org.gcube.dataanalysis.dataminer.poolmanager.service.exceptions;
import org.gcube.dataanalysis.dataminer.poolmanager.util.exception.DMPMException; import org.gcube.dataanalysis.dataminer.poolmanager.util.exception.DMPMException;
public class AnsibleException extends DMPMException ***REMOVED*** public class AnsibleException extends DMPMException {
***REMOVED**** /**
* *
***REMOVED*** */
private static final long serialVersionUID = 6772009633547404120L; private static final long serialVersionUID = 6772009633547404120L;
private int returnCode; private int returnCode;
public AnsibleException(int returnCode) ***REMOVED*** public AnsibleException(int returnCode) {
super ("Ansible work failed"); super ("Ansible work failed");
this.returnCode =returnCode; this.returnCode =returnCode;
***REMOVED*** }
***REMOVED*** @Override
public String getErrorMessage() ***REMOVED*** public String getErrorMessage() {
return "Installation failed. Return code=" + this.returnCode; return "Installation failed. Return code=" + this.returnCode;
***REMOVED*** }
***REMOVED*** }

22
src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/service/exceptions/UndefinedDependenciesException.java
View File

@ -4,26 +4,26 @@ import java.util.Collection;
import org.gcube.dataanalysis.dataminer.poolmanager.util.exception.DMPMException; import org.gcube.dataanalysis.dataminer.poolmanager.util.exception.DMPMException;
public class UndefinedDependenciesException extends DMPMException ***REMOVED*** public class UndefinedDependenciesException extends DMPMException {
private String message; private String message;
***REMOVED**** /**
* *
***REMOVED*** */
private static final long serialVersionUID = 4504593796352609191L; private static final long serialVersionUID = 4504593796352609191L;
public UndefinedDependenciesException(Collection<String> undefinedDependencies) ***REMOVED*** public UndefinedDependenciesException(Collection<String> undefinedDependencies) {
super ("Some dependencies are not defined"); super ("Some dependencies are not defined");
this.message = "Following dependencies are not defined:\n"; this.message = "Following dependencies are not defined:\n";
for (String n : undefinedDependencies) ***REMOVED*** for (String n : undefinedDependencies) {
message += "\n" + n +"\n"; message += "\n" + n +"\n";
***REMOVED*** }
***REMOVED*** }
***REMOVED*** @Override
public String getErrorMessage() ***REMOVED*** public String getErrorMessage() {
return this.message; return this.message;
***REMOVED*** }
***REMOVED*** }

40
src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/util/AlgorithmBuilder.java
View File

@ -1,47 +1,47 @@
package org.gcube.dataanalysis.dataminer.poolmanager.util; package org.gcube.dataanalysis.dataminer.poolmanager.util;
***REMOVED*** import org.gcube.dataanalysis.dataminer.poolmanager.datamodel.Algorithm;
import org.gcube.dataanalysis.dataminer.poolmanager.process.AlgorithmPackageParser; import org.gcube.dataanalysis.dataminer.poolmanager.process.AlgorithmPackageParser;
***REMOVED*** import java.io.IOException;
/** /**
* Created by ggiammat on 5/9/17. * Created by ggiammat on 5/9/17.
*/ */
public class AlgorithmBuilder ***REMOVED*** public class AlgorithmBuilder {
public static Algorithm create(String algorithmPackageURL) throws IOException, InterruptedException ***REMOVED*** public static Algorithm create(String algorithmPackageURL) throws IOException, InterruptedException {
return create(algorithmPackageURL, null, null, null, null, null, null, null); return create(algorithmPackageURL, null, null, null, null, null, null, null);
***REMOVED*** }
public static Algorithm create(String algorithmPackageURL, String vre, String hostname, String name, String description, public static Algorithm create(String algorithmPackageURL, String vre, String hostname, String name, String description,
String category, String algorithmType, String skipJava) throws IOException, InterruptedException ***REMOVED*** String category, String algorithmType, String skipJava) throws IOException, InterruptedException {
Algorithm algo = new AlgorithmPackageParser().parsePackage(algorithmPackageURL); Algorithm algo = new AlgorithmPackageParser().parsePackage(algorithmPackageURL);
if(category != null)***REMOVED*** if(category != null){
algo.setCategory(category); algo.setCategory(category);
***REMOVED*** }
if(algorithmType != null)***REMOVED*** if(algorithmType != null){
algo.setAlgorithmType(algorithmType); algo.setAlgorithmType(algorithmType);
***REMOVED*** }
if(skipJava != null)***REMOVED*** if(skipJava != null){
algo.setSkipJava(skipJava); algo.setSkipJava(skipJava);
***REMOVED*** }
if(skipJava != null)***REMOVED*** if(skipJava != null){
algo.setSkipJava(skipJava); algo.setSkipJava(skipJava);
***REMOVED*** }
if(name != null)***REMOVED*** if(name != null){
algo.setName(name); algo.setName(name);
***REMOVED*** }
if(description != null)***REMOVED*** if(description != null){
algo.setDescription(description); algo.setDescription(description);
***REMOVED*** }
return algo; return algo;
***REMOVED*** }
***REMOVED*** }

144
src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/util/CheckMethod.java
View File

@ -4,21 +4,21 @@ import java.io.BufferedReader;
import java.io.File; import java.io.File;
import java.io.FileWriter; import java.io.FileWriter;
import java.io.InputStreamReader; import java.io.InputStreamReader;
***REMOVED*** import java.net.URL;
import java.util.ArrayList; import java.util.ArrayList;
import java.util.Arrays; import java.util.Arrays;
import java.util.LinkedList; import java.util.LinkedList;
***REMOVED*** import java.util.List;
import java.util.Properties; import java.util.Properties;
import org.gcube.dataanalysis.dataminer.poolmanager.clients.configuration.Configuration; import org.gcube.dataanalysis.dataminer.poolmanager.clients.configuration.Configuration;
***REMOVED*** import org.gcube.dataanalysis.dataminer.poolmanager.datamodel.Algorithm;
import org.gcube.dataanalysis.dataminer.poolmanager.util.exception.AlgorithmException; import org.gcube.dataanalysis.dataminer.poolmanager.util.exception.AlgorithmException;
import org.gcube.dataanalysis.dataminer.poolmanager.util.exception.GenericException; import org.gcube.dataanalysis.dataminer.poolmanager.util.exception.GenericException;
import org.gcube.dataanalysis.dataminer.poolmanager.util.exception.SVNCommitException; import org.gcube.dataanalysis.dataminer.poolmanager.util.exception.SVNCommitException;
***REMOVED*** import org.slf4j.Logger;
***REMOVED*** import org.slf4j.LoggerFactory;
***REMOVED*** import org.tmatesoft.svn.core.SVNException;
import com.jcraft.jsch.Channel; import com.jcraft.jsch.Channel;
import com.jcraft.jsch.ChannelSftp; import com.jcraft.jsch.ChannelSftp;
@ -27,7 +27,7 @@ import com.jcraft.jsch.JSchException;
import com.jcraft.jsch.Session; import com.jcraft.jsch.Session;
import com.jcraft.jsch.SftpException; import com.jcraft.jsch.SftpException;
public abstract class CheckMethod ***REMOVED*** public abstract class CheckMethod {
private Logger logger; private Logger logger;
private Configuration configuration; private Configuration configuration;
@ -40,27 +40,27 @@ public abstract class CheckMethod ***REMOVED***
private final Properties sshConfig; private final Properties sshConfig;
public CheckMethod(Configuration configuration) public CheckMethod(Configuration configuration)
***REMOVED*** {
this.logger = LoggerFactory.getLogger(CheckMethod.class); this.logger = LoggerFactory.getLogger(CheckMethod.class);
this.configuration = configuration; this.configuration = configuration;
sshConfig = new java.util.Properties(); sshConfig = new java.util.Properties();
sshConfig.put("StrictHostKeyChecking", "no"); sshConfig.put("StrictHostKeyChecking", "no");
***REMOVED*** }
public void checkMethod(String machine, String token) throws AlgorithmException ***REMOVED*** public void checkMethod(String machine, String token) throws AlgorithmException {
try ***REMOVED*** try {
this.logger.debug("Checking method for machine "+machine); this.logger.debug("Checking method for machine "+machine);
this.logger.debug("By using tocken "+token); this.logger.debug("By using tocken "+token);
this.logger.debug("Machine: " + machine); this.logger.debug("Machine: " + machine);
***REMOVED*** String getCapabilitesRequest = new String(); // String getCapabilitesRequest = new String();
***REMOVED*** String getCapabilitesResponse = new String(); // String getCapabilitesResponse = new String();
this.logger.debug(" Token: " + token); this.logger.debug(" Token: " + token);
String request = "http:***REMOVED***" + machine String request = "http://" + machine
+ "/wps/WebProcessingService?Request=GetCapabilities&Service=WPS&gcube-token=" + token; + "/wps/WebProcessingService?Request=GetCapabilities&Service=WPS&gcube-token=" + token;
String response = machine + "___" + token + ".xml"; String response = machine + "___" + token + ".xml";
***REMOVED*** getCapabilitesRequest = request; // getCapabilitesRequest = request;
***REMOVED*** getCapabilitesResponse = response; // getCapabilitesResponse = response;
String baseDescriptionRequest = "http:***REMOVED***" + machine String baseDescriptionRequest = "http://" + machine
+ "/wps/WebProcessingService?Request=DescribeProcess&Service=WPS&Version=1.0.0" + "&gcube-token=" + "/wps/WebProcessingService?Request=DescribeProcess&Service=WPS&Version=1.0.0" + "&gcube-token="
+ token + "&Identifier="; + token + "&Identifier=";
URL requestURL = new URL(request); URL requestURL = new URL(request);
@ -70,13 +70,13 @@ public abstract class CheckMethod ***REMOVED***
String line; String line;
boolean flag = true; boolean flag = true;
this.logger.debug("Writing file"); this.logger.debug("Writing file");
while (flag && (line = bufferedReader.readLine()) != null) ***REMOVED*** while (flag && (line = bufferedReader.readLine()) != null) {
this.logger.debug(line); this.logger.debug(line);
fileWriter.write(line); fileWriter.write(line);
fileWriter.write(System.lineSeparator()); fileWriter.write(System.lineSeparator());
if (line.contains("ows:Identifier")) if (line.contains("ows:Identifier"))
***REMOVED*** {
this.logger.debug("Identifier found"); this.logger.debug("Identifier found");
String operatorName = line.substring(line.indexOf(">") + 1); String operatorName = line.substring(line.indexOf(">") + 1);
operatorName = operatorName.substring(0, operatorName.indexOf("<")); operatorName = operatorName.substring(0, operatorName.indexOf("<"));
@ -88,45 +88,45 @@ public abstract class CheckMethod ***REMOVED***
this.logger.debug("Inner line "+innerLine); this.logger.debug("Inner line "+innerLine);
boolean innerFlag = true; boolean innerFlag = true;
while (innerFlag && (innerLine = innerBufferedReader.readLine()) != null) while (innerFlag && (innerLine = innerBufferedReader.readLine()) != null)
***REMOVED*** {
if (innerLine.contains("ows:Abstract")) if (innerLine.contains("ows:Abstract"))
***REMOVED*** {
this.logger.debug("Abstract found"); this.logger.debug("Abstract found");
String operatorDescription = innerLine.substring(innerLine.indexOf(">") + 1); String operatorDescription = innerLine.substring(innerLine.indexOf(">") + 1);
operatorDescription = operatorDescription.substring(0, operatorDescription.indexOf("<")); operatorDescription = operatorDescription.substring(0, operatorDescription.indexOf("<"));
this.logger.debug("Operator descriptor "+operatorDescription); this.logger.debug("Operator descriptor "+operatorDescription);
this.logger.debug(" " + operatorDescription); this.logger.debug(" " + operatorDescription);
innerFlag = false; innerFlag = false;
***REMOVED*** else if (innerLine.contains("ows:ExceptionText")) } else if (innerLine.contains("ows:ExceptionText"))
***REMOVED*** {
this.logger.debug("Exception found"); this.logger.debug("Exception found");
this.logger.debug(" " + "error retrieving operator description"); this.logger.debug(" " + "error retrieving operator description");
innerFlag = false; innerFlag = false;
flag = false; flag = false;
***REMOVED*** else } else
***REMOVED*** {
innerLine = innerBufferedReader.readLine(); innerLine = innerBufferedReader.readLine();
this.logger.debug("Inner line completed "+innerLine); this.logger.debug("Inner line completed "+innerLine);
***REMOVED*** }
***REMOVED*** }
***REMOVED*** }
***REMOVED*** }
this.logger.debug("Operation successful"); this.logger.debug("Operation successful");
fileWriter.close(); fileWriter.close();
***REMOVED*** catch (Exception e) ***REMOVED*** } catch (Exception e) {
throw new AlgorithmException("Error "+e.getMessage(),e); throw new AlgorithmException("Error "+e.getMessage(),e);
***REMOVED*** }
***REMOVED*** }
public void copyAlgorithms(Algorithm algo/*, String env*/) throws SVNCommitException, GenericException, AlgorithmException public void copyAlgorithms(Algorithm algo/*, String env*/) throws SVNCommitException, GenericException, AlgorithmException
***REMOVED*** {
this.logger.debug("Looking if algo "+algo.getName()+ " exists"); this.logger.debug("Looking if algo "+algo.getName()+ " exists");
File file = new File(this.configuration.getGhostAlgoDirectory()+"/"+algo.getName()+".jar"); File file = new File(this.configuration.getGhostAlgoDirectory()+"/"+algo.getName()+".jar");
@ -135,45 +135,45 @@ public abstract class CheckMethod ***REMOVED***
boolean fileExists = false; boolean fileExists = false;
try try
***REMOVED*** {
fileExists = (this.doesExist(file.getPath()/*,env*/)) && (this.doesExist(file2.getPath()/*,env*/)); fileExists = (this.doesExist(file.getPath()/*,env*/)) && (this.doesExist(file2.getPath()/*,env*/));
***REMOVED*** catch (Exception e) } catch (Exception e)
***REMOVED*** {
throw new GenericException(e); throw new GenericException(e);
***REMOVED*** }
if (fileExists) if (fileExists)
***REMOVED*** {
try try
***REMOVED*** {
this.logger.debug("Files found"); this.logger.debug("Files found");
this.copyFromDmToSVN(file/*,env*/); this.copyFromDmToSVN(file/*,env*/);
this.copyFromDmToSVN(file2/*,env*/); this.copyFromDmToSVN(file2/*,env*/);
this.logger.debug("Files have been copied to SVN"); this.logger.debug("Files have been copied to SVN");
***REMOVED*** catch (Exception e) } catch (Exception e)
***REMOVED*** {
throw new GenericException(e); throw new GenericException(e);
***REMOVED*** }
***REMOVED*** }
else else
***REMOVED*** {
this.logger.debug("Files not found"); this.logger.debug("Files not found");
this.logger.debug("Algorithm "+algo.getName()+".jar"+ " and "+algo.getName()+"_interface.jar files are not present at the expected path"); this.logger.debug("Algorithm "+algo.getName()+".jar"+ " and "+algo.getName()+"_interface.jar files are not present at the expected path");
throw new AlgorithmException("Algorithm "+algo.getName()+".jar"+ " and "+algo.getName()+"_interface.jar files are not present at the expected path"); throw new AlgorithmException("Algorithm "+algo.getName()+".jar"+ " and "+algo.getName()+"_interface.jar files are not present at the expected path");
***REMOVED*** }
***REMOVED*** }
public void deleteFiles(Algorithm a/*,String env*/) throws GenericException public void deleteFiles(Algorithm a/*,String env*/) throws GenericException
***REMOVED*** {
try try
***REMOVED*** {
Session session = generateSession(); Session session = generateSession();
this.logger.debug("checking existing in env: " + this.configuration.getHost()); this.logger.debug("checking existing in env: " + this.configuration.getHost());
@ -195,29 +195,29 @@ public abstract class CheckMethod ***REMOVED***
ChannelSftp c = (ChannelSftp) channel; ChannelSftp c = (ChannelSftp) channel;
if(doesExist(file.getPath()/*,env*/)&&(doesExist(file2.getPath()/*,env*/)))***REMOVED*** if(doesExist(file.getPath()/*,env*/)&&(doesExist(file2.getPath()/*,env*/))){
c.rm(file.getPath()); c.rm(file.getPath());
c.rm(file2.getPath()); c.rm(file2.getPath());
this.logger.debug("Both the files have been deleted"); this.logger.debug("Both the files have been deleted");
***REMOVED*** }
else this.logger.debug("Files not found"); else this.logger.debug("Files not found");
channel.disconnect(); channel.disconnect();
c.disconnect(); c.disconnect();
session.disconnect(); session.disconnect();
***REMOVED*** catch (Exception e) } catch (Exception e)
***REMOVED*** {
throw new GenericException(e); throw new GenericException(e);
***REMOVED*** }
***REMOVED*** }
public boolean doesExist(String path/*, String env*/) throws Exception ***REMOVED*** public boolean doesExist(String path/*, String env*/) throws Exception {
Session session = generateSession(); Session session = generateSession();
boolean success = false; boolean success = false;
@ -228,29 +228,29 @@ public abstract class CheckMethod ***REMOVED***
ChannelSftp c = (ChannelSftp) channel; ChannelSftp c = (ChannelSftp) channel;
this.logger.debug(path); this.logger.debug(path);
try ***REMOVED*** try {
c.lstat(path); c.lstat(path);
success = true; success = true;
***REMOVED*** catch (SftpException e) ***REMOVED*** } catch (SftpException e) {
if (e.id == ChannelSftp.SSH_FX_NO_SUCH_FILE) ***REMOVED*** if (e.id == ChannelSftp.SSH_FX_NO_SUCH_FILE) {
***REMOVED*** file doesn't exist // file doesn't exist
success = false; success = false;
***REMOVED*** }
***REMOVED***success = true; ***REMOVED*** something else went wrong //success = true; // something else went wrong
***REMOVED*** }
channel.disconnect(); channel.disconnect();
c.disconnect(); c.disconnect();
session.disconnect(); session.disconnect();
this.logger.debug("Operation result "+success); this.logger.debug("Operation result "+success);
return success; return success;
***REMOVED*** }
protected abstract void copyFromDmToSVN(File a) throws SVNCommitException, Exception; protected abstract void copyFromDmToSVN(File a) throws SVNCommitException, Exception;
protected void copyFromDmToSVN(File algorithmsFile/*,String env*/,SVNUpdater svnUpdater) throws SVNException, SVNCommitException, JSchException, SftpException ***REMOVED*** protected void copyFromDmToSVN(File algorithmsFile/*,String env*/,SVNUpdater svnUpdater) throws SVNException, SVNCommitException, JSchException, SftpException {
this.logger.debug("Copying algorithm file from Data Miner to SVN"); this.logger.debug("Copying algorithm file from Data Miner to SVN");
String fileName = algorithmsFile.getName(); String fileName = algorithmsFile.getName();
@ -271,10 +271,10 @@ public abstract class CheckMethod ***REMOVED***
File f = new File(localFile); File f = new File(localFile);
svnUpdater.updateAlgorithmFiles(f); svnUpdater.updateAlgorithmFiles(f);
f.delete(); f.delete();
***REMOVED*** }
private Session generateSession () throws JSchException private Session generateSession () throws JSchException
***REMOVED*** {
JSch jsch = new JSch(); JSch jsch = new JSch();
jsch.setKnownHosts(KNOWN_HOSTS); jsch.setKnownHosts(KNOWN_HOSTS);
jsch.addIdentity(PRIVATE_KEY); jsch.addIdentity(PRIVATE_KEY);
@ -283,23 +283,23 @@ public abstract class CheckMethod ***REMOVED***
this.logger.debug("session created."); this.logger.debug("session created.");
session.setConfig(this.sshConfig); session.setConfig(this.sshConfig);
return session; return session;
***REMOVED*** }
public static List<String> getFiles(String a)***REMOVED*** public static List<String> getFiles(String a){
String[] array = a.split(","); String[] array = a.split(",");
ArrayList<String> list = new ArrayList<>(Arrays.asList(array)); ArrayList<String> list = new ArrayList<>(Arrays.asList(array));
List<String> ls = new LinkedList<String>(); List<String> ls = new LinkedList<String>();
for (String s: list)***REMOVED*** for (String s: list){
ls.add(s.trim()); ls.add(s.trim());
***REMOVED*** }
return ls; return ls;
***REMOVED*** }
***REMOVED*** }

18
src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/util/CheckPermission.java
View File

@ -2,27 +2,27 @@ package org.gcube.dataanalysis.dataminer.poolmanager.util;
import static org.gcube.common.authorization.client.Constants.authorizationService; import static org.gcube.common.authorization.client.Constants.authorizationService;
***REMOVED*** import org.gcube.common.authorization.client.exceptions.ObjectNotFound;
import org.gcube.common.authorization.library.AuthorizationEntry; import org.gcube.common.authorization.library.AuthorizationEntry;
***REMOVED*** import org.slf4j.Logger;
***REMOVED*** import org.slf4j.LoggerFactory;
public class CheckPermission ***REMOVED*** public class CheckPermission {
private static final Logger logger = LoggerFactory.getLogger(CheckPermission.class); private static final Logger logger = LoggerFactory.getLogger(CheckPermission.class);
public static boolean apply(String VREToken, String vre) throws ObjectNotFound, Exception public static boolean apply(String VREToken, String vre) throws ObjectNotFound, Exception
***REMOVED*** {
AuthorizationEntry entry = authorizationService().get(VREToken); AuthorizationEntry entry = authorizationService().get(VREToken);
if (entry.getContext().equals(vre)) ***REMOVED*** if (entry.getContext().equals(vre)) {
logger.info("Authorization OK!"); logger.info("Authorization OK!");
return true; return true;
***REMOVED*** }
logger.info("Not a valid token recognized for the VRE: "+vre); logger.info("Not a valid token recognized for the VRE: "+vre);
return false; return false;
***REMOVED*** }
***REMOVED*** }

34
src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/util/ClusterBuilder.java
View File

@ -1,26 +1,26 @@
package org.gcube.dataanalysis.dataminer.poolmanager.util; package org.gcube.dataanalysis.dataminer.poolmanager.util;
import java.io.FileNotFoundException; import java.io.FileNotFoundException;
***REMOVED*** import java.io.IOException;
***REMOVED*** import org.gcube.common.authorization.library.provider.SecurityTokenProvider;
***REMOVED*** import org.gcube.common.scope.api.ScopeProvider;
import org.gcube.dataanalysis.dataminer.poolmanager.clients.HAProxy; import org.gcube.dataanalysis.dataminer.poolmanager.clients.HAProxy;
import org.gcube.dataanalysis.dataminer.poolmanager.clients.configuration.Configuration; import org.gcube.dataanalysis.dataminer.poolmanager.clients.configuration.Configuration;
import org.gcube.dataanalysis.dataminer.poolmanager.datamodel.Cluster; import org.gcube.dataanalysis.dataminer.poolmanager.datamodel.Cluster;
import org.gcube.dataanalysis.dataminer.poolmanager.datamodel.Host; import org.gcube.dataanalysis.dataminer.poolmanager.datamodel.Host;
public abstract class ClusterBuilder ***REMOVED*** public abstract class ClusterBuilder {
private Configuration configuration; private Configuration configuration;
public ClusterBuilder (Configuration configuration) public ClusterBuilder (Configuration configuration)
***REMOVED*** {
this.configuration = configuration; this.configuration = configuration;
***REMOVED*** }
***REMOVED***1. to complete //1. to complete
public Cluster getDataminerCluster() throws FileNotFoundException***REMOVED*** public Cluster getDataminerCluster() throws FileNotFoundException{
Cluster cluster = new Cluster(); Cluster cluster = new Cluster();
Host h = new Host(); Host h = new Host();
@ -30,29 +30,29 @@ public abstract class ClusterBuilder ***REMOVED***
return cluster; return cluster;
***REMOVED*** }
public Cluster getVRECluster(String targetVREToken, String targetVRE) throws IOException***REMOVED*** public Cluster getVRECluster(String targetVREToken, String targetVRE) throws IOException{
Cluster cluster = new Cluster(); Cluster cluster = new Cluster();
for (Host h : new HAProxy().listDataMinersByCluster(targetVREToken,targetVRE)) ***REMOVED*** for (Host h : new HAProxy().listDataMinersByCluster(targetVREToken,targetVRE)) {
cluster.addHost(h); cluster.addHost(h);
***REMOVED*** }
return cluster; return cluster;
***REMOVED*** }
public Cluster getRProtoCluster() throws IOException***REMOVED*** public Cluster getRProtoCluster() throws IOException{
***REMOVED***Assumes the service is running in RPrototypingLab //Assumes the service is running in RPrototypingLab
String token = SecurityTokenProvider.instance.get(); String token = SecurityTokenProvider.instance.get();
String targetVRE = ScopeProvider.instance.get(); String targetVRE = ScopeProvider.instance.get();
return this.getVRECluster(token, targetVRE); return this.getVRECluster(token, targetVRE);
***REMOVED*** }
***REMOVED*** }

92
src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/util/NotificationHelper.java
View File

@ -1,79 +1,79 @@
package org.gcube.dataanalysis.dataminer.poolmanager.util; package org.gcube.dataanalysis.dataminer.poolmanager.util;
***REMOVED***import scala.actors.threadpool.Arrays; //import scala.actors.threadpool.Arrays;
public abstract class NotificationHelper ***REMOVED*** public abstract class NotificationHelper {
private String subjectHeader; private String subjectHeader;
protected NotificationHelper (String subjectHeader) protected NotificationHelper (String subjectHeader)
***REMOVED*** {
this.subjectHeader = subjectHeader; this.subjectHeader = subjectHeader;
***REMOVED*** }
***REMOVED*** private Exception executionException; // private Exception executionException;
***REMOVED*** private boolean isError() ***REMOVED*** // private boolean isError() {
***REMOVED*** return this.executionException!=null; // return this.executionException!=null;
***REMOVED*** ***REMOVED*** // }
***REMOVED*** public void setExecutionException(Exception executionException) ***REMOVED*** // public void setExecutionException(Exception executionException) {
***REMOVED*** this.executionException = executionException; // this.executionException = executionException;
***REMOVED*** ***REMOVED*** // }
public String getSuccessSubject() ***REMOVED*** public String getSuccessSubject() {
return this.subjectHeader+" is SUCCESS"; return this.subjectHeader+" is SUCCESS";
***REMOVED*** }
public String getFailedSubject() ***REMOVED*** public String getFailedSubject() {
return String.format(this.subjectHeader+" is FAILED"); return String.format(this.subjectHeader+" is FAILED");
***REMOVED*** }
public static String getSuccessBody(String info) ***REMOVED*** public static String getSuccessBody(String info) {
String message = String.format("The installation of the algorithm is completed successfully."); String message = String.format("The installation of the algorithm is completed successfully.");
message+="\n\nYou can retrieve experiment results under the '/DataMiner' e-Infrastructure Workspace folder or from the DataMiner interface.\n\n"+ info; message+="\n\nYou can retrieve experiment results under the '/DataMiner' e-Infrastructure Workspace folder or from the DataMiner interface.\n\n"+ info;
return message; return message;
***REMOVED*** }
public static String getFailedBody(String message) ***REMOVED*** public static String getFailedBody(String message) {
String body = String.format("An error occurred while deploying your algorithm"); String body = String.format("An error occurred while deploying your algorithm");
body+= "\n\nHere are the error details:\n\n" + message; body+= "\n\nHere are the error details:\n\n" + message;
return body; return body;
***REMOVED*** }
***REMOVED*** public String getSuccessBodyRelease(String info) ***REMOVED*** // public String getSuccessBodyRelease(String info) {
***REMOVED*** String message = String.format("SVN REPOSITORY CORRECTLY UPDATED."); // String message = String.format("SVN REPOSITORY CORRECTLY UPDATED.");
***REMOVED*** message+="\n\n The CRON job will install the algorithm in the target VRE \n\n"+ info; // message+="\n\n The CRON job will install the algorithm in the target VRE \n\n"+ info;
***REMOVED*** return message; // return message;
***REMOVED*** ***REMOVED*** // }
***REMOVED*** //
***REMOVED*** public String getFailedBodyRelease(String info) ***REMOVED*** // public String getFailedBodyRelease(String info) {
***REMOVED*** String message = String.format("SVN REPOSITORY UPDATE FAILED."); // String message = String.format("SVN REPOSITORY UPDATE FAILED.");
***REMOVED*** message+="\n\n The CRON job will NOT be able to install the algorithm in the target VRE \n\n"+ info; // message+="\n\n The CRON job will NOT be able to install the algorithm in the target VRE \n\n"+ info;
***REMOVED*** return message; // return message;
***REMOVED*** ***REMOVED*** // }
***REMOVED*** public String getSubject() ***REMOVED*** // public String getSubject() {
***REMOVED*** if(this.isError()) ***REMOVED*** // if(this.isError()) {
***REMOVED*** return this.getFailedSubject(); // return this.getFailedSubject();
***REMOVED*** ***REMOVED*** else ***REMOVED*** // } else {
***REMOVED*** return this.getSuccessSubject(); // return this.getSuccessSubject();
***REMOVED*** ***REMOVED*** // }
***REMOVED*** ***REMOVED*** // }
***REMOVED*** //
***REMOVED*** public String getBody() ***REMOVED*** // public String getBody() {
***REMOVED*** if(this.isError()) ***REMOVED*** // if(this.isError()) {
***REMOVED*** return this.getFailedBody(); // return this.getFailedBody();
***REMOVED*** ***REMOVED*** else ***REMOVED*** // } else {
***REMOVED*** return this.getSuccessBody(); // return this.getSuccessBody();
***REMOVED*** ***REMOVED*** // }
***REMOVED*** ***REMOVED*** // }
***REMOVED*** }

108
src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/util/PropertiesBasedProxySelector.java
View File

@ -1,6 +1,6 @@
package org.gcube.dataanalysis.dataminer.poolmanager.util; package org.gcube.dataanalysis.dataminer.poolmanager.util;
***REMOVED*** import java.io.IOException;
import java.net.Authenticator; import java.net.Authenticator;
import java.net.InetSocketAddress; import java.net.InetSocketAddress;
import java.net.PasswordAuthentication; import java.net.PasswordAuthentication;
@ -10,13 +10,13 @@ import java.net.SocketAddress;
import java.net.URI; import java.net.URI;
import java.util.ArrayList; import java.util.ArrayList;
import java.util.Arrays; import java.util.Arrays;
***REMOVED*** import java.util.List;
import org.apache.commons.configuration.ConfigurationException; import org.apache.commons.configuration.ConfigurationException;
import org.apache.commons.configuration.PropertiesConfiguration; import org.apache.commons.configuration.PropertiesConfiguration;
import org.apache.commons.configuration.reloading.FileChangedReloadingStrategy; import org.apache.commons.configuration.reloading.FileChangedReloadingStrategy;
interface NetworkConfiguration ***REMOVED*** interface NetworkConfiguration {
public String getProxyHost(); public String getProxyHost();
@ -28,118 +28,118 @@ interface NetworkConfiguration ***REMOVED***
public String getNonProxyHosts(); public String getNonProxyHosts();
***REMOVED*** }
class FileBasedProxyConfiguration implements NetworkConfiguration ***REMOVED*** class FileBasedProxyConfiguration implements NetworkConfiguration {
private static PropertiesConfiguration configuration; private static PropertiesConfiguration configuration;
public FileBasedProxyConfiguration(String path) ***REMOVED*** public FileBasedProxyConfiguration(String path) {
try ***REMOVED*** try {
***REMOVED*** load the configuration // load the configuration
configuration = new PropertiesConfiguration(path); configuration = new PropertiesConfiguration(path);
***REMOVED*** set the reloading strategy to enable hot-configuration // set the reloading strategy to enable hot-configuration
FileChangedReloadingStrategy fcrs = new FileChangedReloadingStrategy(); FileChangedReloadingStrategy fcrs = new FileChangedReloadingStrategy();
configuration.setReloadingStrategy(fcrs); configuration.setReloadingStrategy(fcrs);
***REMOVED*** catch (ConfigurationException e) ***REMOVED*** } catch (ConfigurationException e) {
e.printStackTrace(); e.printStackTrace();
***REMOVED*** }
***REMOVED*** }
@Override @Override
public String getProxyHost() ***REMOVED*** public String getProxyHost() {
return configuration.getString("proxyHost"); return configuration.getString("proxyHost");
***REMOVED*** }
@Override @Override
public String getProxyPort() ***REMOVED*** public String getProxyPort() {
return configuration.getString("proxyPort"); return configuration.getString("proxyPort");
***REMOVED*** }
@Override @Override
public String getProxyUser() ***REMOVED*** public String getProxyUser() {
return configuration.getString("proxyUser"); return configuration.getString("proxyUser");
***REMOVED*** }
@Override @Override
public String getProxyPassword() ***REMOVED*** public String getProxyPassword() {
return configuration.getString("proxyPassword"); return configuration.getString("proxyPassword");
***REMOVED*** }
@Override @Override
public String getNonProxyHosts() ***REMOVED*** public String getNonProxyHosts() {
return configuration.getString("nonProxyHosts"); return configuration.getString("nonProxyHosts");
***REMOVED*** }
***REMOVED*** }
public class PropertiesBasedProxySelector extends ProxySelector ***REMOVED*** public class PropertiesBasedProxySelector extends ProxySelector {
List<Proxy> proxies = null; List<Proxy> proxies = null;
List<String> nonProxyHosts = null; List<String> nonProxyHosts = null;
public PropertiesBasedProxySelector(String proxySettingsPath) ***REMOVED*** public PropertiesBasedProxySelector(String proxySettingsPath) {
this(new FileBasedProxyConfiguration(proxySettingsPath)); this(new FileBasedProxyConfiguration(proxySettingsPath));
***REMOVED*** }
public PropertiesBasedProxySelector(NetworkConfiguration config) ***REMOVED*** public PropertiesBasedProxySelector(NetworkConfiguration config) {
if (config == null || config.getProxyHost() == null) ***REMOVED*** if (config == null || config.getProxyHost() == null) {
this.proxies = null; this.proxies = null;
return; return;
***REMOVED*** }
String host = config.getProxyHost(); String host = config.getProxyHost();
int port = 80; int port = 80;
if (config.getProxyPort() != null) ***REMOVED*** if (config.getProxyPort() != null) {
port = Integer.valueOf(config.getProxyPort()); port = Integer.valueOf(config.getProxyPort());
***REMOVED*** }
if (config.getNonProxyHosts() != null) ***REMOVED*** if (config.getNonProxyHosts() != null) {
this.nonProxyHosts = Arrays this.nonProxyHosts = Arrays
.asList(config.getNonProxyHosts().split("\\|")); .asList(config.getNonProxyHosts().split("\\|"));
***REMOVED*** }
this.proxies = new ArrayList<Proxy>(); this.proxies = new ArrayList<Proxy>();
this.proxies.add(new Proxy(Proxy.Type.HTTP, new InetSocketAddress(host, this.proxies.add(new Proxy(Proxy.Type.HTTP, new InetSocketAddress(host,
port))); port)));
if (config.getProxyUser() != null) ***REMOVED*** if (config.getProxyUser() != null) {
final String username = config.getProxyUser(); final String username = config.getProxyUser();
final String password = config.getProxyPassword(); final String password = config.getProxyPassword();
Authenticator.setDefault(new Authenticator() ***REMOVED*** Authenticator.setDefault(new Authenticator() {
@Override @Override
protected PasswordAuthentication getPasswordAuthentication() ***REMOVED*** protected PasswordAuthentication getPasswordAuthentication() {
return new PasswordAuthentication(username, password.toCharArray()); return new PasswordAuthentication(username, password.toCharArray());
***REMOVED*** }
***REMOVED***); });
***REMOVED*** }
***REMOVED*** }
@Override @Override
public List<Proxy> select(URI uri) ***REMOVED*** public List<Proxy> select(URI uri) {
if (this.nonProxyHosts == null) ***REMOVED*** if (this.nonProxyHosts == null) {
return Arrays.asList(Proxy.NO_PROXY); return Arrays.asList(Proxy.NO_PROXY);
***REMOVED*** else ***REMOVED*** } else {
for (String entry : this.nonProxyHosts) ***REMOVED*** for (String entry : this.nonProxyHosts) {
entry = entry.trim(); entry = entry.trim();
if (entry.startsWith("*") && uri.getHost().endsWith(entry.substring(1))) ***REMOVED*** if (entry.startsWith("*") && uri.getHost().endsWith(entry.substring(1))) {
return Arrays.asList(Proxy.NO_PROXY); return Arrays.asList(Proxy.NO_PROXY);
***REMOVED*** }
if (uri.getHost().equals(entry)) ***REMOVED*** if (uri.getHost().equals(entry)) {
return Arrays.asList(Proxy.NO_PROXY); return Arrays.asList(Proxy.NO_PROXY);
***REMOVED*** }
***REMOVED*** }
return this.proxies; return this.proxies;
***REMOVED*** }
***REMOVED*** }
@Override @Override
public void connectFailed(URI uri, SocketAddress socketAddress, IOException e) ***REMOVED*** public void connectFailed(URI uri, SocketAddress socketAddress, IOException e) {
***REMOVED*** }
***REMOVED*** }

30
src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/util/SVNRepositoryManager.java
View File

@ -1,56 +1,56 @@
package org.gcube.dataanalysis.dataminer.poolmanager.util; package org.gcube.dataanalysis.dataminer.poolmanager.util;
import org.gcube.dataanalysis.dataminer.poolmanager.clients.configuration.Configuration; import org.gcube.dataanalysis.dataminer.poolmanager.clients.configuration.Configuration;
***REMOVED*** import org.slf4j.Logger;
***REMOVED*** import org.slf4j.LoggerFactory;
***REMOVED*** import org.tmatesoft.svn.core.SVNException;
import org.tmatesoft.svn.core.SVNURL; import org.tmatesoft.svn.core.SVNURL;
import org.tmatesoft.svn.core.auth.ISVNAuthenticationManager; import org.tmatesoft.svn.core.auth.ISVNAuthenticationManager;
import org.tmatesoft.svn.core.io.SVNRepository; import org.tmatesoft.svn.core.io.SVNRepository;
import org.tmatesoft.svn.core.io.SVNRepositoryFactory; import org.tmatesoft.svn.core.io.SVNRepositoryFactory;
import org.tmatesoft.svn.core.wc.SVNWCUtil; import org.tmatesoft.svn.core.wc.SVNWCUtil;
public class SVNRepositoryManager ***REMOVED*** public class SVNRepositoryManager {
private SVNRepository svnRepository; private SVNRepository svnRepository;
private static SVNRepositoryManager instance; private static SVNRepositoryManager instance;
private Logger logger; private Logger logger;
private SVNRepositoryManager (Configuration configuration) throws SVNException private SVNRepositoryManager (Configuration configuration) throws SVNException
***REMOVED*** {
this.logger = LoggerFactory.getLogger(SVNRepositoryManager.class); this.logger = LoggerFactory.getLogger(SVNRepositoryManager.class);
org.gcube.dataanalysis.dataminer.poolmanager.clients.configuration.SVNRepository repository = configuration.getSVNRepository(); org.gcube.dataanalysis.dataminer.poolmanager.clients.configuration.SVNRepository repository = configuration.getSVNRepository();
this.svnRepository = SVNRepositoryFactory.create(SVNURL.parseURIEncoded(repository.getBaseUrl())); this.svnRepository = SVNRepositoryFactory.create(SVNURL.parseURIEncoded(repository.getBaseUrl()));
ISVNAuthenticationManager authManager = null; ISVNAuthenticationManager authManager = null;
if (repository.getUsername() == null) if (repository.getUsername() == null)
***REMOVED*** {
this.logger.debug("Using SVN default credentials"); this.logger.debug("Using SVN default credentials");
authManager = SVNWCUtil.createDefaultAuthenticationManager(); authManager = SVNWCUtil.createDefaultAuthenticationManager();
***REMOVED*** }
else else
***REMOVED*** {
this.logger.debug("Using IS credentials"); this.logger.debug("Using IS credentials");
authManager = SVNWCUtil.createDefaultAuthenticationManager(repository.getUsername(),repository.getPassword()); authManager = SVNWCUtil.createDefaultAuthenticationManager(repository.getUsername(),repository.getPassword());
***REMOVED*** }
this.svnRepository.setAuthenticationManager(authManager); this.svnRepository.setAuthenticationManager(authManager);
***REMOVED*** }
public static SVNRepositoryManager getInstance (Configuration configuration) throws SVNException public static SVNRepositoryManager getInstance (Configuration configuration) throws SVNException
***REMOVED*** {
if (instance == null) instance = new SVNRepositoryManager(configuration); if (instance == null) instance = new SVNRepositoryManager(configuration);
return instance; return instance;
***REMOVED*** }
public SVNRepository getSvnRepository() ***REMOVED*** public SVNRepository getSvnRepository() {
return svnRepository; return svnRepository;
***REMOVED*** }
***REMOVED*** }

422
src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/util/SVNUpdater.java
View File

@ -5,7 +5,7 @@ import java.io.ByteArrayOutputStream;
import java.io.File; import java.io.File;
import java.io.FileInputStream; import java.io.FileInputStream;
import java.io.FileNotFoundException; import java.io.FileNotFoundException;
***REMOVED*** import java.io.IOException;
import java.text.DateFormat; import java.text.DateFormat;
import java.text.ParseException; import java.text.ParseException;
import java.text.SimpleDateFormat; import java.text.SimpleDateFormat;
@ -17,20 +17,20 @@ import java.util.Collections;
import java.util.Date; import java.util.Date;
import java.util.HashSet; import java.util.HashSet;
import java.util.LinkedList; import java.util.LinkedList;
***REMOVED*** import java.util.List;
***REMOVED*** import java.util.Set;
import java.util.TimeZone; import java.util.TimeZone;
import org.gcube.dataanalysis.dataminer.poolmanager.clients.configuration.Configuration; import org.gcube.dataanalysis.dataminer.poolmanager.clients.configuration.Configuration;
***REMOVED*** import org.gcube.dataanalysis.dataminer.poolmanager.datamodel.Algorithm;
import org.gcube.dataanalysis.dataminer.poolmanager.datamodel.Dependency; import org.gcube.dataanalysis.dataminer.poolmanager.datamodel.Dependency;
import org.gcube.dataanalysis.dataminer.poolmanager.util.exception.GenericException; import org.gcube.dataanalysis.dataminer.poolmanager.util.exception.GenericException;
import org.gcube.dataanalysis.dataminer.poolmanager.util.exception.SVNCommitException; import org.gcube.dataanalysis.dataminer.poolmanager.util.exception.SVNCommitException;
***REMOVED*** import org.slf4j.Logger;
***REMOVED*** import org.slf4j.LoggerFactory;
import org.tmatesoft.svn.core.SVNCommitInfo; import org.tmatesoft.svn.core.SVNCommitInfo;
import org.tmatesoft.svn.core.SVNErrorMessage; import org.tmatesoft.svn.core.SVNErrorMessage;
***REMOVED*** import org.tmatesoft.svn.core.SVNException;
import org.tmatesoft.svn.core.SVNNodeKind; import org.tmatesoft.svn.core.SVNNodeKind;
import org.tmatesoft.svn.core.internal.wc.SVNFileUtil; import org.tmatesoft.svn.core.internal.wc.SVNFileUtil;
import org.tmatesoft.svn.core.internal.wc.admin.SVNChecksumInputStream; import org.tmatesoft.svn.core.internal.wc.admin.SVNChecksumInputStream;
@ -41,41 +41,41 @@ import org.tmatesoft.svn.core.io.diff.SVNDeltaGenerator;
/** /**
* Created by ggiammat on 5/9/17. * Created by ggiammat on 5/9/17.
*/ */
public abstract class SVNUpdater ***REMOVED*** public abstract class SVNUpdater {
private SVNRepository svnRepository; private SVNRepository svnRepository;
private Configuration configuration; private Configuration configuration;
private Logger logger; private Logger logger;
public SVNUpdater(Configuration configuration) throws SVNException ***REMOVED*** public SVNUpdater(Configuration configuration) throws SVNException {
this.configuration = configuration; this.configuration = configuration;
this.svnRepository = SVNRepositoryManager.getInstance(configuration).getSvnRepository(); this.svnRepository = SVNRepositoryManager.getInstance(configuration).getSvnRepository();
this.logger = LoggerFactory.getLogger(SVNUpdater.class); this.logger = LoggerFactory.getLogger(SVNUpdater.class);
***REMOVED*** }
***REMOVED*** public void updateRPRotoDeps(Algorithm algorithm) ***REMOVED*** // public void updateRPRotoDeps(Algorithm algorithm) {
***REMOVED*** this.updateSVN(this.configuration.getSVNRProtoOSDepsList(), algorithm.getOSDependencies()); // this.updateSVN(this.configuration.getSVNRProtoOSDepsList(), algorithm.getOSDependencies());
***REMOVED*** this.updateSVN(this.configuration.getSVNRProtoCRANDepsList(), algorithm.getCranDependencies()); // this.updateSVN(this.configuration.getSVNRProtoCRANDepsList(), algorithm.getCranDependencies());
***REMOVED*** this.updateSVN(this.configuration.getSVNRProtoGitHubDepsList(), algorithm.getGitHubDependencies()); // this.updateSVN(this.configuration.getSVNRProtoGitHubDepsList(), algorithm.getGitHubDependencies());
***REMOVED******REMOVED*** // }
public String getDependencyFile(String language/*, String env*/) public String getDependencyFile(String language/*, String env*/)
***REMOVED*** {
return getDependencyFile(this.configuration,language); return getDependencyFile(this.configuration,language);
***REMOVED*** }
private String getDependencyFile (Configuration configuration, String language) private String getDependencyFile (Configuration configuration, String language)
***REMOVED*** {
this.logger.debug("Getting dependency file for language "+language); this.logger.debug("Getting dependency file for language "+language);
switch (language) switch (language)
***REMOVED*** {
case "R": case "R":
return configuration.getSVNCRANDepsList(); return configuration.getSVNCRANDepsList();
case "R-blackbox": case "R-blackbox":
@ -99,22 +99,22 @@ public abstract class SVNUpdater ***REMOVED***
case "Windows-compiled": case "Windows-compiled":
return configuration.getSVNWCDepsList(); return configuration.getSVNWCDepsList();
default: default:
***REMOVED*** return null;
***REMOVED*** }
***REMOVED*** }
public boolean updateSVNAlgorithmList(Algorithm algorithm, String targetVRE, String category, String algorithm_type, String user/*, String env*/) public boolean updateSVNAlgorithmList(Algorithm algorithm, String targetVRE, String category, String algorithm_type, String user/*, String env*/)
***REMOVED*** {
return this.updateSVNAlgorithmList(this.configuration.getSVNAlgorithmsList(), algorithm, targetVRE, category, algorithm_type, user); return this.updateSVNAlgorithmList(this.configuration.getSVNAlgorithmsList(), algorithm, targetVRE, category, algorithm_type, user);
***REMOVED*** }
public void updateAlgorithmFiles(File a) throws SVNException, SVNCommitException***REMOVED*** public void updateAlgorithmFiles(File a) throws SVNException, SVNCommitException{
***REMOVED***this.updateAlgorithmList(this.configuration.getSVNMainAlgoRepo(), a); //this.updateAlgorithmList(this.configuration.getSVNMainAlgoRepo(), a);
this.updateAlgorithmList(this.configuration.getRepository(), a); this.updateAlgorithmList(this.configuration.getRepository(), a);
***REMOVED*** }
@ -122,33 +122,33 @@ public abstract class SVNUpdater ***REMOVED***
private void updateAlgorithmList(String svnMainAlgoRepo, File algorithmsFile) throws SVNException, SVNCommitException private void updateAlgorithmList(String svnMainAlgoRepo, File algorithmsFile) throws SVNException, SVNCommitException
***REMOVED*** {
this.logger.debug("Adding .jar file: " + algorithmsFile + " to repository " + svnMainAlgoRepo); this.logger.debug("Adding .jar file: " + algorithmsFile + " to repository " + svnMainAlgoRepo);
try try
***REMOVED*** {
if (fileExists(svnMainAlgoRepo+File.separator+algorithmsFile.getName(), -1)) if (fileExists(svnMainAlgoRepo+File.separator+algorithmsFile.getName(), -1))
***REMOVED*** {
this.updateFile(new FileInputStream(algorithmsFile), svnMainAlgoRepo, algorithmsFile.getName()); this.updateFile(new FileInputStream(algorithmsFile), svnMainAlgoRepo, algorithmsFile.getName());
***REMOVED*** }
else this.putFile(new FileInputStream(algorithmsFile), svnMainAlgoRepo,algorithmsFile.getName()); else this.putFile(new FileInputStream(algorithmsFile), svnMainAlgoRepo,algorithmsFile.getName());
***REMOVED*** }
catch (FileNotFoundException e) catch (FileNotFoundException e)
***REMOVED*** {
this.logger.error("Temporary algorithm file not found: this exception should not happen",e); this.logger.error("Temporary algorithm file not found: this exception should not happen",e);
***REMOVED*** }
finally finally
***REMOVED*** {
this.svnRepository.closeSession(); this.svnRepository.closeSession();
***REMOVED*** }
***REMOVED*** }
public void putFile(FileInputStream fileInputSreeam, String destinationFolder, String fileName) throws SVNException, SVNCommitException public void putFile(FileInputStream fileInputSreeam, String destinationFolder, String fileName) throws SVNException, SVNCommitException
***REMOVED*** {
this.logger.debug("Putting new file on the SVN repository"); this.logger.debug("Putting new file on the SVN repository");
final ISVNEditor commitEditor = svnRepository.getCommitEditor("Add algorithm to list", null); final ISVNEditor commitEditor = svnRepository.getCommitEditor("Add algorithm to list", null);
commitEditor.openRoot(-1); commitEditor.openRoot(-1);
@ -165,27 +165,27 @@ public abstract class SVNUpdater ***REMOVED***
SVNErrorMessage errorMessage = info.getErrorMessage(); SVNErrorMessage errorMessage = info.getErrorMessage();
if (errorMessage != null) if (errorMessage != null)
***REMOVED*** {
this.logger.error("Operation failed: "+errorMessage.getFullMessage()); this.logger.error("Operation failed: "+errorMessage.getFullMessage());
throw new SVNCommitException(errorMessage,fileName); throw new SVNCommitException(errorMessage,fileName);
***REMOVED*** }
this.logger.debug("Operation completed"); this.logger.debug("Operation completed");
***REMOVED*** }
public void updateFile(FileInputStream fileInputStream, String destinationFolder, String fileName) throws SVNException, SVNCommitException ***REMOVED*** public void updateFile(FileInputStream fileInputStream, String destinationFolder, String fileName) throws SVNException, SVNCommitException {
this.logger.debug("Updating existing file on the SVN repository"); this.logger.debug("Updating existing file on the SVN repository");
final ISVNEditor commitEditor = svnRepository.getCommitEditor("Updating algorithm", null); final ISVNEditor commitEditor = svnRepository.getCommitEditor("Updating algorithm", null);
commitEditor.openRoot(-1); commitEditor.openRoot(-1);
commitEditor.openDir(destinationFolder, -1); commitEditor.openDir(destinationFolder, -1);
String filePath = destinationFolder + "/" + fileName; String filePath = destinationFolder + "/" + fileName;
***REMOVED*** if (fileExists(filePath, -1)) ***REMOVED*** ***REMOVED*** updating existing file // if (fileExists(filePath, -1)) { // updating existing file
commitEditor.openFile(filePath, -1); commitEditor.openFile(filePath, -1);
***REMOVED******REMOVED*** else ***REMOVED*** ***REMOVED*** creating new file //} else { // creating new file
***REMOVED***commitEditor.addFile(filePath, null, -1); //commitEditor.addFile(filePath, null, -1);
***REMOVED******REMOVED*** //}
commitEditor.applyTextDelta(filePath, null); commitEditor.applyTextDelta(filePath, null);
SVNDeltaGenerator deltaGenerator = new SVNDeltaGenerator(); SVNDeltaGenerator deltaGenerator = new SVNDeltaGenerator();
String checksum = deltaGenerator.sendDelta(filePath, fileInputStream, commitEditor, true); String checksum = deltaGenerator.sendDelta(filePath, fileInputStream, commitEditor, true);
@ -196,41 +196,41 @@ public abstract class SVNUpdater ***REMOVED***
SVNErrorMessage errorMessage = info.getErrorMessage(); SVNErrorMessage errorMessage = info.getErrorMessage();
if (errorMessage != null) if (errorMessage != null)
***REMOVED*** {
this.logger.error("Operation failed: "+errorMessage.getFullMessage()); this.logger.error("Operation failed: "+errorMessage.getFullMessage());
throw new SVNCommitException(errorMessage,fileName+" to be updated"); throw new SVNCommitException(errorMessage,fileName+" to be updated");
***REMOVED*** }
this.logger.debug("Operation completed"); this.logger.debug("Operation completed");
***REMOVED*** }
public boolean fileExists(String path, long revision) throws SVNException ***REMOVED*** public boolean fileExists(String path, long revision) throws SVNException {
SVNNodeKind kind = svnRepository.checkPath(path, revision); SVNNodeKind kind = svnRepository.checkPath(path, revision);
if (kind == SVNNodeKind.FILE) ***REMOVED*** if (kind == SVNNodeKind.FILE) {
return true; return true;
***REMOVED*** }
return false; return false;
***REMOVED*** }
***REMOVED*** public static ByteArrayInputStream reteriveByteArrayInputStream(File file) throws IOException // public static ByteArrayInputStream reteriveByteArrayInputStream(File file) throws IOException
***REMOVED*** ***REMOVED*** // {
***REMOVED*** //
***REMOVED*** return new ByteArrayInputStream(FileUtils.readFileToByteArray(file)); // return new ByteArrayInputStream(FileUtils.readFileToByteArray(file));
***REMOVED******REMOVED*** // }
private boolean updateSVNAlgorithmList(String file, Algorithm algorithm, String targetVRE, String category, String algorithm_type, String user/*, String env*/) private boolean updateSVNAlgorithmList(String file, Algorithm algorithm, String targetVRE, String category, String algorithm_type, String user/*, String env*/)
***REMOVED*** {
boolean response = false; boolean response = false;
try ***REMOVED*** try {
this.logger.debug("Updating algorithm list: " + file); this.logger.debug("Updating algorithm list: " + file);
final ByteArrayOutputStream byteArrayOutputStream = new ByteArrayOutputStream(); final ByteArrayOutputStream byteArrayOutputStream = new ByteArrayOutputStream();
svnRepository.getFile(file, SVNRepository.INVALID_REVISION, null, byteArrayOutputStream); svnRepository.getFile(file, SVNRepository.INVALID_REVISION, null, byteArrayOutputStream);
@ -238,18 +238,18 @@ public abstract class SVNUpdater ***REMOVED***
List<String> newContent = new LinkedList<>(Arrays.asList(lines)); List<String> newContent = new LinkedList<>(Arrays.asList(lines));
***REMOVED*** check if the algorithm is already in the list (match the class name) and delete the content // check if the algorithm is already in the list (match the class name) and delete the content
for (String l : lines) ***REMOVED*** for (String l : lines) {
if (l.contains(algorithm.getClazz())) ***REMOVED*** if (l.contains(algorithm.getClazz())) {
newContent.remove(l); newContent.remove(l);
***REMOVED***System.out.println("Not updating algorithm list beacuse already present"); //System.out.println("Not updating algorithm list beacuse already present");
***REMOVED***return; //return;
***REMOVED*** }
***REMOVED*** }
***REMOVED*** the algorithm is not in the list or must be overwritten cause some modification. Add it // the algorithm is not in the list or must be overwritten cause some modification. Add it
newContent.add(this.generateAlgorithmEntry(algorithm, targetVRE, category,algorithm_type/*, env*/)); newContent.add(this.generateAlgorithmEntry(algorithm, targetVRE, category,algorithm_type/*, env*/));
***REMOVED*** Collections.sort(newContent); // Collections.sort(newContent);
final SVNDeltaGenerator deltaGenerator = new SVNDeltaGenerator(); final SVNDeltaGenerator deltaGenerator = new SVNDeltaGenerator();
@ -261,10 +261,10 @@ public abstract class SVNUpdater ***REMOVED***
ByteArrayOutputStream baos = new ByteArrayOutputStream(); ByteArrayOutputStream baos = new ByteArrayOutputStream();
for (String line : newContent) ***REMOVED*** for (String line : newContent) {
baos.write(line.getBytes()); baos.write(line.getBytes());
baos.write("\n".getBytes()); baos.write("\n".getBytes());
***REMOVED*** }
byte[] bytes = baos.toByteArray(); byte[] bytes = baos.toByteArray();
commitEditor.applyTextDelta(file, md5(originalContents)); commitEditor.applyTextDelta(file, md5(originalContents));
@ -276,32 +276,32 @@ public abstract class SVNUpdater ***REMOVED***
SVNErrorMessage errorMessage = info.getErrorMessage(); SVNErrorMessage errorMessage = info.getErrorMessage();
if (errorMessage != null) if (errorMessage != null)
***REMOVED*** {
this.logger.error("Operation failed: "+errorMessage.getFullMessage()); this.logger.error("Operation failed: "+errorMessage.getFullMessage());
response = false; response = false;
***REMOVED*** }
else response = true; else response = true;
***REMOVED*** }
catch (Exception ex) catch (Exception ex)
***REMOVED*** {
this.logger.error("Unable to commit algorithm list",ex); this.logger.error("Unable to commit algorithm list",ex);
response = false; response = false;
***REMOVED*** }
finally finally
***REMOVED*** {
svnRepository.closeSession(); svnRepository.closeSession();
***REMOVED*** }
return response; return response;
***REMOVED*** }
public String generateAlgorithmEntry(Algorithm algorithm, String targetVRE, String category, String algorithm_type/*,String env*/) throws ParseException ***REMOVED*** public String generateAlgorithmEntry(Algorithm algorithm, String targetVRE, String category, String algorithm_type/*,String env*/) throws ParseException {
***REMOVED***Timestamp timestamp = new Timestamp(System.currentTimeMillis()); //Timestamp timestamp = new Timestamp(System.currentTimeMillis());
***REMOVED***long unixTime = System.currentTimeMillis() / 1000L; //long unixTime = System.currentTimeMillis() / 1000L;
StringBuffer sb = new StringBuffer("| "); StringBuffer sb = new StringBuffer("| ");
sb.append(algorithm.getName() + " | "); sb.append(algorithm.getName() + " | ");
@ -317,24 +317,24 @@ public abstract class SVNUpdater ***REMOVED***
this.logger.info("Algo details: "+sb.toString()); this.logger.info("Algo details: "+sb.toString());
return sb.toString(); return sb.toString();
***REMOVED*** }
public Collection<String> getUndefinedDependencies(String file, Collection<Dependency> deps) throws GenericException public Collection<String> getUndefinedDependencies(String file, Collection<Dependency> deps) throws GenericException
***REMOVED*** {
try try
***REMOVED*** {
***REMOVED*** SendMail sm = new SendMail(); // SendMail sm = new SendMail();
***REMOVED*** NotificationHelper nh = new NotificationHelper(); // NotificationHelper nh = new NotificationHelper();
List<String> undefined = new LinkedList<String>(); List<String> undefined = new LinkedList<String>();
***REMOVED***to fix in next release: if the file is not present for that language in the service.properties then skip and return null list of string //to fix in next release: if the file is not present for that language in the service.properties then skip and return null list of string
***REMOVED***just to uncomment the following lines //just to uncomment the following lines
if(file.isEmpty())***REMOVED*** if(file.isEmpty()){
return undefined; return undefined;
***REMOVED*** }
this.logger.debug("Checking dependencies list: " + file); this.logger.debug("Checking dependencies list: " + file);
@ -342,128 +342,128 @@ public abstract class SVNUpdater ***REMOVED***
List<String> validDependencies = new LinkedList<String>(); List<String> validDependencies = new LinkedList<String>();
for (String singlefile: CheckMethod.getFiles(file))***REMOVED*** for (String singlefile: CheckMethod.getFiles(file)){
final ByteArrayOutputStream byteArrayOutputStream = new ByteArrayOutputStream(); final ByteArrayOutputStream byteArrayOutputStream = new ByteArrayOutputStream();
svnRepository.getFile(singlefile, SVNRepository.INVALID_REVISION, null, byteArrayOutputStream); svnRepository.getFile(singlefile, SVNRepository.INVALID_REVISION, null, byteArrayOutputStream);
for(String l: byteArrayOutputStream.toString().split("\\r?\\n"))***REMOVED*** for(String l: byteArrayOutputStream.toString().split("\\r?\\n")){
validDependencies.add(l.trim()); validDependencies.add(l.trim());
***REMOVED******REMOVED*** }}
this.logger.debug("Valid dependencies are: "+validDependencies); this.logger.debug("Valid dependencies are: "+validDependencies);
for(Dependency d: deps)***REMOVED*** for(Dependency d: deps){
String depName = d.getName(); String depName = d.getName();
if(!validDependencies.contains(depName))***REMOVED*** if(!validDependencies.contains(depName)){
undefined.add(depName); undefined.add(depName);
***REMOVED*** }
***REMOVED*** }
return undefined; return undefined;
***REMOVED*** //
***REMOVED*** //
***REMOVED*** for (String a : lines) ***REMOVED*** // for (String a : lines) {
***REMOVED*** for (String b : ldep) ***REMOVED*** // for (String b : ldep) {
***REMOVED*** if (b.equals(a)) ***REMOVED*** // if (b.equals(a)) {
***REMOVED*** System.out.println("The following dependency is correctly written: " + b); // System.out.println("The following dependency is correctly written: " + b);
***REMOVED*** ***REMOVED*** else // } else
***REMOVED*** //
***REMOVED*** ***REMOVED*** // }
***REMOVED*** ***REMOVED*** // }
***REMOVED*** //
***REMOVED*** boolean check = false; // boolean check = false;
***REMOVED*** try ***REMOVED*** // try {
***REMOVED*** System.out.println("Checking dependencies list: " + file); // System.out.println("Checking dependencies list: " + file);
***REMOVED*** final ByteArrayOutputStream byteArrayOutputStream = new ByteArrayOutputStream(); // final ByteArrayOutputStream byteArrayOutputStream = new ByteArrayOutputStream();
***REMOVED*** svnRepository.getFile(file, SVNRepository.INVALID_REVISION, null, byteArrayOutputStream); // svnRepository.getFile(file, SVNRepository.INVALID_REVISION, null, byteArrayOutputStream);
***REMOVED*** String lines[] = byteArrayOutputStream.toString().split("\\r?\\n"); // String lines[] = byteArrayOutputStream.toString().split("\\r?\\n");
***REMOVED*** //
***REMOVED*** ***REMOVED*** if(deps.isEmpty())***REMOVED*** // // if(deps.isEmpty()){
***REMOVED*** ***REMOVED*** sm.sendNotification(nh.getFailedSubject(), nh.getFailedBody()); // // sm.sendNotification(nh.getFailedSubject(), nh.getFailedBody());
***REMOVED*** ***REMOVED*** Exception e = new Exception("No dependency specified for this // // Exception e = new Exception("No dependency specified for this
***REMOVED*** ***REMOVED*** algorithm"); // // algorithm");
***REMOVED*** ***REMOVED*** throw e; // // throw e;
***REMOVED*** ***REMOVED*** // //
***REMOVED*** ***REMOVED*** ***REMOVED*** // // }
***REMOVED*** //
***REMOVED*** ***REMOVED*** else if (!deps.isEmpty()) ***REMOVED*** // // else if (!deps.isEmpty()) {
***REMOVED*** List<String> ldep = new LinkedList<>(); // List<String> ldep = new LinkedList<>();
***REMOVED*** for (Dependency d : deps) ***REMOVED*** // for (Dependency d : deps) {
***REMOVED*** ldep.add(d.getName()); // ldep.add(d.getName());
***REMOVED*** ***REMOVED*** // }
***REMOVED*** for (String a : lines) ***REMOVED*** // for (String a : lines) {
***REMOVED*** for (String b : ldep) ***REMOVED*** // for (String b : ldep) {
***REMOVED*** if (b.equals(a)) ***REMOVED*** // if (b.equals(a)) {
***REMOVED*** System.out.println("The following dependency is correctly written: " + b); // System.out.println("The following dependency is correctly written: " + b);
***REMOVED*** check = true; // check = true;
***REMOVED*** ***REMOVED*** else // } else
***REMOVED*** check = false; // check = false;
***REMOVED*** //
***REMOVED*** ***REMOVED*** // }
***REMOVED*** ***REMOVED*** // }
***REMOVED*** ***REMOVED*** ***REMOVED*** // // }
***REMOVED*** ***REMOVED*** catch (Exception a) ***REMOVED*** // } catch (Exception a) {
***REMOVED*** a.getMessage(); // a.getMessage();
***REMOVED*** ***REMOVED*** // }
***REMOVED*** //
***REMOVED*** return check; // return check;
***REMOVED*** catch (SVNException e) } catch (SVNException e)
***REMOVED*** {
throw new GenericException(e); throw new GenericException(e);
***REMOVED*** }
***REMOVED*** }
public boolean checkIfAvaialable(String file, Collection<Dependency> deps) throws SVNException ***REMOVED*** public boolean checkIfAvaialable(String file, Collection<Dependency> deps) throws SVNException {
***REMOVED***SendMail sm = new SendMail(); //SendMail sm = new SendMail();
***REMOVED***NotificationHelper nh = new NotificationHelper(); //NotificationHelper nh = new NotificationHelper();
boolean check = false; boolean check = false;
try ***REMOVED*** try {
this.logger.info("Checking dependencies list: " + file); this.logger.info("Checking dependencies list: " + file);
final ByteArrayOutputStream byteArrayOutputStream = new ByteArrayOutputStream(); final ByteArrayOutputStream byteArrayOutputStream = new ByteArrayOutputStream();
svnRepository.getFile(file, SVNRepository.INVALID_REVISION, null, byteArrayOutputStream); svnRepository.getFile(file, SVNRepository.INVALID_REVISION, null, byteArrayOutputStream);
String lines[] = byteArrayOutputStream.toString().split("\\r?\\n"); String lines[] = byteArrayOutputStream.toString().split("\\r?\\n");
***REMOVED*** if(deps.isEmpty())***REMOVED*** // if(deps.isEmpty()){
***REMOVED*** sm.sendNotification(nh.getFailedSubject(), nh.getFailedBody()); // sm.sendNotification(nh.getFailedSubject(), nh.getFailedBody());
***REMOVED*** Exception e = new Exception("No dependency specified for this // Exception e = new Exception("No dependency specified for this
***REMOVED*** algorithm"); // algorithm");
***REMOVED*** throw e; // throw e;
***REMOVED*** //
***REMOVED*** ***REMOVED*** // }
***REMOVED*** else if (!deps.isEmpty()) ***REMOVED*** // else if (!deps.isEmpty()) {
List<String> ldep = new LinkedList<>(); List<String> ldep = new LinkedList<>();
for (Dependency d : deps) ***REMOVED*** for (Dependency d : deps) {
ldep.add(d.getName()); ldep.add(d.getName());
***REMOVED*** }
for (String a : lines) ***REMOVED*** for (String a : lines) {
for (String b : ldep) ***REMOVED*** for (String b : ldep) {
if (b.equals(a)) ***REMOVED*** if (b.equals(a)) {
System.out.println("The following dependency is correctly written: " + b); System.out.println("The following dependency is correctly written: " + b);
check = true; check = true;
***REMOVED*** else } else
check = false; check = false;
***REMOVED*** }
***REMOVED*** }
***REMOVED*** ***REMOVED*** // }
***REMOVED*** catch (Exception a) } catch (Exception a)
***REMOVED*** {
this.logger.error(a.getMessage(),a); this.logger.error(a.getMessage(),a);
***REMOVED*** }
return check; return check;
***REMOVED*** }
public void updateSVN(String file, Collection<Dependency> deps) ***REMOVED*** public void updateSVN(String file, Collection<Dependency> deps) {
try ***REMOVED*** try {
this.logger.info("Updating dependencies list: " + file); this.logger.info("Updating dependencies list: " + file);
final ByteArrayOutputStream byteArrayOutputStream = new ByteArrayOutputStream(); final ByteArrayOutputStream byteArrayOutputStream = new ByteArrayOutputStream();
@ -471,9 +471,9 @@ public abstract class SVNUpdater ***REMOVED***
String lines[] = byteArrayOutputStream.toString().split("\\r?\\n"); String lines[] = byteArrayOutputStream.toString().split("\\r?\\n");
List<String> ldep = new LinkedList<>(); List<String> ldep = new LinkedList<>();
for (Dependency d : deps) ***REMOVED*** for (Dependency d : deps) {
ldep.add(d.getName()); ldep.add(d.getName());
***REMOVED*** }
List<String> aa = this.checkMatch(lines, ldep); List<String> aa = this.checkMatch(lines, ldep);
Collections.sort(aa); Collections.sort(aa);
@ -487,11 +487,11 @@ public abstract class SVNUpdater ***REMOVED***
ByteArrayOutputStream baos = new ByteArrayOutputStream(); ByteArrayOutputStream baos = new ByteArrayOutputStream();
for (String line : aa) ***REMOVED*** for (String line : aa) {
baos.write(line.getBytes()); baos.write(line.getBytes());
baos.write("\n".getBytes()); baos.write("\n".getBytes());
***REMOVED*** }
byte[] bytes = baos.toByteArray(); byte[] bytes = baos.toByteArray();
commitEditor.applyTextDelta(file, md5(originalContents)); commitEditor.applyTextDelta(file, md5(originalContents));
@ -503,40 +503,40 @@ public abstract class SVNUpdater ***REMOVED***
commitEditor.closeFile(file, checksum); commitEditor.closeFile(file, checksum);
commitEditor.closeEdit(); commitEditor.closeEdit();
***REMOVED*** catch (Exception ex) ***REMOVED*** } catch (Exception ex) {
ex.printStackTrace(); ex.printStackTrace();
***REMOVED*** }
finally ***REMOVED*** finally {
svnRepository.closeSession(); svnRepository.closeSession();
***REMOVED*** }
***REMOVED*** }
public static String md5(byte[] contents) ***REMOVED*** public static String md5(byte[] contents) {
final byte[] tmp = new byte[1024]; final byte[] tmp = new byte[1024];
final SVNChecksumInputStream checksumStream = new SVNChecksumInputStream(new ByteArrayInputStream(contents), final SVNChecksumInputStream checksumStream = new SVNChecksumInputStream(new ByteArrayInputStream(contents),
"md5"); "md5");
try ***REMOVED*** try {
while (checksumStream.read(tmp) > 0) ***REMOVED*** while (checksumStream.read(tmp) > 0) {
***REMOVED*** //
***REMOVED*** }
return checksumStream.getDigest(); return checksumStream.getDigest();
***REMOVED*** catch (IOException e) ***REMOVED*** } catch (IOException e) {
***REMOVED*** never happens // never happens
e.printStackTrace(); e.printStackTrace();
***REMOVED*** return null;
***REMOVED*** finally ***REMOVED*** } finally {
SVNFileUtil.closeFile(checksumStream); SVNFileUtil.closeFile(checksumStream);
***REMOVED*** }
***REMOVED*** }
public List<String> checkMatch(String[] lines, List<String> ls) ***REMOVED*** public List<String> checkMatch(String[] lines, List<String> ls) {
Set<String> ss = new HashSet<String>(ls); Set<String> ss = new HashSet<String>(ls);
ss.addAll(Arrays.asList(lines)); ss.addAll(Arrays.asList(lines));
return new ArrayList<>(ss); return new ArrayList<>(ss);
***REMOVED*** }
public String getTimeZone() throws ParseException***REMOVED*** public String getTimeZone() throws ParseException{
Calendar cal = Calendar.getInstance(); Calendar cal = Calendar.getInstance();
cal.getTime(); cal.getTime();
DateFormat formatter = new SimpleDateFormat("EEE MMM dd HH:mm:ss zzz yyyy"); DateFormat formatter = new SimpleDateFormat("EEE MMM dd HH:mm:ss zzz yyyy");
@ -545,21 +545,21 @@ public abstract class SVNUpdater ***REMOVED***
formatter.setTimeZone(central); formatter.setTimeZone(central);
this.logger.info(formatter.format(fromDate)); this.logger.info(formatter.format(fromDate));
return formatter.format(fromDate); return formatter.format(fromDate);
***REMOVED*** }
public static void main(String[] args) throws SVNException, ParseException ***REMOVED*** public static void main(String[] args) throws SVNException, ParseException {
***REMOVED*** SVNUpdater c = new SVNUpdater(); // SVNUpdater c = new SVNUpdater();
***REMOVED***File a = new File("/home/ngalante/Desktop/testCiro"); //File a = new File("/home/ngalante/Desktop/testCiro");
***REMOVED***File b = new File ("/home/ngalante/Desktop/testB"); //File b = new File ("/home/ngalante/Desktop/testB");
***REMOVED***long unixTime = System.currentTimeMillis() / 1000L; //long unixTime = System.currentTimeMillis() / 1000L;
***REMOVED***System.out.println(unixTime); //System.out.println(unixTime);
***REMOVED***c.updateAlgorithmFiles(a); //c.updateAlgorithmFiles(a);
***REMOVED***c.updateAlgorithmFiles(b); //c.updateAlgorithmFiles(b);
***REMOVED***Timestamp timestamp = new Timestamp(System.currentTimeMillis()); //Timestamp timestamp = new Timestamp(System.currentTimeMillis());
Calendar cal = Calendar.getInstance(); Calendar cal = Calendar.getInstance();
cal.getTime(); cal.getTime();
@ -571,9 +571,9 @@ public abstract class SVNUpdater ***REMOVED***
***REMOVED*** }
***REMOVED*** }

178
src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/util/SendMail.java
View File

@ -5,23 +5,23 @@ import static org.gcube.resources.discovery.icclient.ICFactory.clientFor;
import static org.gcube.resources.discovery.icclient.ICFactory.queryFor; import static org.gcube.resources.discovery.icclient.ICFactory.queryFor;
import java.io.BufferedReader; import java.io.BufferedReader;
***REMOVED*** import java.io.IOException;
import java.io.InputStreamReader; import java.io.InputStreamReader;
import java.io.OutputStreamWriter; import java.io.OutputStreamWriter;
***REMOVED*** import java.net.MalformedURLException;
***REMOVED*** import java.net.URL;
import java.net.URLConnection; import java.net.URLConnection;
import java.util.ArrayList; import java.util.ArrayList;
import java.util.Iterator; import java.util.Iterator;
***REMOVED*** import java.util.List;
import org.apache.http.client.methods.HttpGet; import org.apache.http.client.methods.HttpGet;
import org.apache.http.impl.client.CloseableHttpClient; import org.apache.http.impl.client.CloseableHttpClient;
import org.apache.http.impl.client.HttpClientBuilder; import org.apache.http.impl.client.HttpClientBuilder;
import org.apache.http.util.EntityUtils; import org.apache.http.util.EntityUtils;
***REMOVED*** import org.gcube.common.authorization.client.exceptions.ObjectNotFound;
import org.gcube.common.authorization.library.AuthorizationEntry; import org.gcube.common.authorization.library.AuthorizationEntry;
***REMOVED*** import org.gcube.common.authorization.library.provider.SecurityTokenProvider;
import org.gcube.common.encryption.encrypter.StringEncrypter; import org.gcube.common.encryption.encrypter.StringEncrypter;
import org.gcube.common.resources.gcore.GCoreEndpoint; import org.gcube.common.resources.gcore.GCoreEndpoint;
import org.gcube.common.resources.gcore.ServiceEndpoint; import org.gcube.common.resources.gcore.ServiceEndpoint;
@ -35,10 +35,10 @@ import org.gcube.resources.discovery.client.queries.api.SimpleQuery;
import org.json.JSONArray; import org.json.JSONArray;
import org.json.JSONException; import org.json.JSONException;
import org.json.JSONObject; import org.json.JSONObject;
***REMOVED*** import org.slf4j.Logger;
***REMOVED*** import org.slf4j.LoggerFactory;
public class SendMail ***REMOVED*** public class SendMail {
private static final Logger logger = LoggerFactory.getLogger(SendMail.class); private static final Logger logger = LoggerFactory.getLogger(SendMail.class);
@ -52,11 +52,11 @@ public class SendMail ***REMOVED***
private String socialServiceAddress; private String socialServiceAddress;
private String applicationToken; private String applicationToken;
public SendMail() ***REMOVED*** public SendMail() {
***REMOVED*** }
public void sendNotification(String subject, String body) throws EMailException ***REMOVED*** public void sendNotification(String subject, String body) throws EMailException {
logger.debug("SendNotification"); logger.debug("SendNotification");
logger.debug("Notification Subject: " + subject); logger.debug("Notification Subject: " + subject);
logger.debug("Notification Body: " + body); logger.debug("Notification Body: " + body);
@ -69,63 +69,63 @@ public class SendMail ***REMOVED***
sendPostRequest(postBody); sendPostRequest(postBody);
***REMOVED*** }
private String createPostBody(String subject, String body) throws EMailException ***REMOVED*** private String createPostBody(String subject, String body) throws EMailException {
try ***REMOVED*** try {
List<String> recipientsList = getRecipients(); List<String> recipientsList = getRecipients();
if (recipientsList == null || recipientsList.isEmpty()) ***REMOVED*** if (recipientsList == null || recipientsList.isEmpty()) {
logger.error("Invalid recipient list: " + recipientsList); logger.error("Invalid recipient list: " + recipientsList);
throw new EMailException("Unable to send email notification. Invalid recipient list:" + recipientsList); throw new EMailException("Unable to send email notification. Invalid recipient list:" + recipientsList);
***REMOVED*** }
***REMOVED*** ***REMOVED***"subject": "subject-content", "body": "body-content", // {"subject": "subject-content", "body": "body-content",
***REMOVED*** "recipients":[***REMOVED***"id":"userid"***REMOVED***]***REMOVED*** // "recipients":[{"id":"userid"}]}
JSONObject data = new JSONObject(); JSONObject data = new JSONObject();
data.put("subject", subject); data.put("subject", subject);
data.put("body", body); data.put("body", body);
JSONArray recipients = new JSONArray(); JSONArray recipients = new JSONArray();
for (String recipient : recipientsList) ***REMOVED*** for (String recipient : recipientsList) {
JSONObject d = new JSONObject(); JSONObject d = new JSONObject();
d.put("id", recipient); d.put("id", recipient);
recipients.put(d); recipients.put(d);
***REMOVED*** }
data.put("recipients", recipients); data.put("recipients", recipients);
logger.debug("Post Body: " + data); logger.debug("Post Body: " + data);
return data.toString(); return data.toString();
***REMOVED*** catch (EMailException e) ***REMOVED*** } catch (EMailException e) {
throw e; throw e;
***REMOVED*** catch (Throwable e) ***REMOVED*** } catch (Throwable e) {
logger.error("Error creating the notification body: " + e.getLocalizedMessage(), e); logger.error("Error creating the notification body: " + e.getLocalizedMessage(), e);
throw new EMailException(e); throw new EMailException(e);
***REMOVED*** }
***REMOVED*** }
private String retrieveApplicationToken() throws EMailException ***REMOVED*** private String retrieveApplicationToken() throws EMailException {
try ***REMOVED*** try {
logger.info("Retrieve Application Token"); logger.info("Retrieve Application Token");
SimpleQuery query = queryFor(ServiceEndpoint.class); SimpleQuery query = queryFor(ServiceEndpoint.class);
query.addCondition(DMPOOLMANAGER_SERVICE_QUERY_CONDITION); query.addCondition(DMPOOLMANAGER_SERVICE_QUERY_CONDITION);
DiscoveryClient<ServiceEndpoint> client = clientFor(ServiceEndpoint.class); DiscoveryClient<ServiceEndpoint> client = clientFor(ServiceEndpoint.class);
List<ServiceEndpoint> resources = client.submit(query); List<ServiceEndpoint> resources = client.submit(query);
if (resources.isEmpty()) ***REMOVED*** if (resources.isEmpty()) {
logger.error("No services resource found on IS!"); logger.error("No services resource found on IS!");
***REMOVED*** else ***REMOVED*** } else {
logger.debug("Retrieved: " + resources.get(0)); logger.debug("Retrieved: " + resources.get(0));
***REMOVED*** }
Group<AccessPoint> accessPoints = resources.get(0).profile().accessPoints(); Group<AccessPoint> accessPoints = resources.get(0).profile().accessPoints();
if (!accessPoints.isEmpty()) ***REMOVED*** if (!accessPoints.isEmpty()) {
Iterator<AccessPoint> iterator = accessPoints.iterator(); Iterator<AccessPoint> iterator = accessPoints.iterator();
AccessPoint ap = iterator.next(); AccessPoint ap = iterator.next();
Group<Property> props = ap.properties(); Group<Property> props = ap.properties();
if (!props.isEmpty()) ***REMOVED*** if (!props.isEmpty()) {
Iterator<Property> iteratorProps = props.iterator(); Iterator<Property> iteratorProps = props.iterator();
Property p = iteratorProps.next(); Property p = iteratorProps.next();
String applicationToken = StringEncrypter.getEncrypter().decrypt(p.value()); String applicationToken = StringEncrypter.getEncrypter().decrypt(p.value());
@ -133,55 +133,55 @@ public class SendMail ***REMOVED***
logger.info("Application Token retrieved"); logger.info("Application Token retrieved");
return applicationToken; return applicationToken;
***REMOVED*** else ***REMOVED*** } else {
String error = "DMPoolManager application token not found in service resource on IS!"; String error = "DMPoolManager application token not found in service resource on IS!";
logger.error(error); logger.error(error);
throw new EMailException(error); throw new EMailException(error);
***REMOVED*** }
***REMOVED*** else ***REMOVED*** } else {
String error = "DMPoolManager invalid service resource on IS!"; String error = "DMPoolManager invalid service resource on IS!";
logger.error(error); logger.error(error);
throw new EMailException(error); throw new EMailException(error);
***REMOVED*** }
***REMOVED*** catch (Throwable e) ***REMOVED*** } catch (Throwable e) {
logger.error("DMPoolManager application token not found: " + e.getLocalizedMessage(), e); logger.error("DMPoolManager application token not found: " + e.getLocalizedMessage(), e);
throw new EMailException("DMPoolManager application token not found: " + e.getLocalizedMessage(), e); throw new EMailException("DMPoolManager application token not found: " + e.getLocalizedMessage(), e);
***REMOVED*** }
***REMOVED*** }
private void retrieveSocialService() throws EMailException ***REMOVED*** private void retrieveSocialService() throws EMailException {
try ***REMOVED*** try {
SimpleQuery query = queryFor(GCoreEndpoint.class); SimpleQuery query = queryFor(GCoreEndpoint.class);
query.addCondition(SOCIAL_SERVICE_QUERY_CONDITION); query.addCondition(SOCIAL_SERVICE_QUERY_CONDITION);
DiscoveryClient<GCoreEndpoint> client = clientFor(GCoreEndpoint.class); DiscoveryClient<GCoreEndpoint> client = clientFor(GCoreEndpoint.class);
List<GCoreEndpoint> resources = client.submit(query); List<GCoreEndpoint> resources = client.submit(query);
socialServiceAddress = resources.get(0).profile().endpointMap().get(SOCIAL_SERVICE_URI).uri().toString(); socialServiceAddress = resources.get(0).profile().endpointMap().get(SOCIAL_SERVICE_URI).uri().toString();
logger.info("Retrieved Social Service Address: " + socialServiceAddress); logger.info("Retrieved Social Service Address: " + socialServiceAddress);
if (socialServiceAddress == null || socialServiceAddress.isEmpty()) ***REMOVED*** if (socialServiceAddress == null || socialServiceAddress.isEmpty()) {
throw new EMailException( throw new EMailException(
"Unable to send email notification. Invalid address in GCoreEndpoint resource on IS."); "Unable to send email notification. Invalid address in GCoreEndpoint resource on IS.");
***REMOVED*** }
***REMOVED*** catch (EMailException e) ***REMOVED*** } catch (EMailException e) {
logger.error(e.getLocalizedMessage(), e); logger.error(e.getLocalizedMessage(), e);
throw e; throw e;
***REMOVED*** catch (Throwable e) ***REMOVED*** } catch (Throwable e) {
logger.error(e.getLocalizedMessage(), e); logger.error(e.getLocalizedMessage(), e);
throw new EMailException(e); throw new EMailException(e);
***REMOVED*** }
***REMOVED*** }
private String username(String token) throws ObjectNotFound, Exception ***REMOVED*** private String username(String token) throws ObjectNotFound, Exception {
AuthorizationEntry entry = authorizationService().get(token); AuthorizationEntry entry = authorizationService().get(token);
logger.debug(entry.getClientInfo().getId()); logger.debug(entry.getClientInfo().getId());
return entry.getClientInfo().getId(); return entry.getClientInfo().getId();
***REMOVED*** }
private void sendPostRequest(String postBody) throws EMailException ***REMOVED*** private void sendPostRequest(String postBody) throws EMailException {
try ***REMOVED*** try {
logger.info("Execute Post Body:" + postBody); logger.info("Execute Post Body:" + postBody);
StringBuilder requestMessageBuilder = new StringBuilder(socialServiceAddress); StringBuilder requestMessageBuilder = new StringBuilder(socialServiceAddress);
@ -194,7 +194,7 @@ public class SendMail ***REMOVED***
requestMessageBuilder.append(applicationToken); requestMessageBuilder.append(applicationToken);
String endpoint = requestMessageBuilder.toString(); String endpoint = requestMessageBuilder.toString();
***REMOVED*** Send the request // Send the request
URL url = new URL(endpoint); URL url = new URL(endpoint);
URLConnection conn = url.openConnection(); URLConnection conn = url.openConnection();
conn.setRequestProperty("Accept", JSON_MIME_TYPE); conn.setRequestProperty("Accept", JSON_MIME_TYPE);
@ -205,13 +205,13 @@ public class SendMail ***REMOVED***
writer.write(postBody); writer.write(postBody);
writer.flush(); writer.flush();
***REMOVED*** Get the response // Get the response
StringBuffer answer = new StringBuffer(); StringBuffer answer = new StringBuffer();
BufferedReader reader = new BufferedReader(new InputStreamReader(conn.getInputStream())); BufferedReader reader = new BufferedReader(new InputStreamReader(conn.getInputStream()));
String line; String line;
while ((line = reader.readLine()) != null) ***REMOVED*** while ((line = reader.readLine()) != null) {
answer.append(line); answer.append(line);
***REMOVED*** }
writer.close(); writer.close();
reader.close(); reader.close();
@ -220,76 +220,76 @@ public class SendMail ***REMOVED***
logger.info("Notification Response: " + response); logger.info("Notification Response: " + response);
checkResponse(response); checkResponse(response);
***REMOVED*** catch (EMailException e) ***REMOVED*** } catch (EMailException e) {
throw e; throw e;
***REMOVED*** catch (MalformedURLException e) ***REMOVED*** } catch (MalformedURLException e) {
logger.error("Invalid URL: " + e.getLocalizedMessage(), e); logger.error("Invalid URL: " + e.getLocalizedMessage(), e);
throw new EMailException(e); throw new EMailException(e);
***REMOVED*** catch (IOException e) ***REMOVED*** } catch (IOException e) {
logger.error("Error in the IO process: " + e.getLocalizedMessage(), e); logger.error("Error in the IO process: " + e.getLocalizedMessage(), e);
throw new EMailException(e); throw new EMailException(e);
***REMOVED*** catch (Throwable e) ***REMOVED*** } catch (Throwable e) {
logger.error("Error executing post:" + e.getLocalizedMessage(), e); logger.error("Error executing post:" + e.getLocalizedMessage(), e);
throw new EMailException(e); throw new EMailException(e);
***REMOVED*** }
***REMOVED*** }
private void checkResponse(String response) throws EMailException ***REMOVED*** private void checkResponse(String response) throws EMailException {
if (response == null) ***REMOVED*** if (response == null) {
logger.error("Invalid notification response: " + response); logger.error("Invalid notification response: " + response);
throw new EMailException(); throw new EMailException();
***REMOVED*** else ***REMOVED*** } else {
try ***REMOVED*** try {
JSONObject res = new JSONObject(response); JSONObject res = new JSONObject(response);
boolean success = res.getBoolean("success"); boolean success = res.getBoolean("success");
if (!success) ***REMOVED*** if (!success) {
String message = res.getString("message"); String message = res.getString("message");
logger.error("Error in send email notification: " + message); logger.error("Error in send email notification: " + message);
throw new EMailException("Error in send email notification: " + message); throw new EMailException("Error in send email notification: " + message);
***REMOVED*** }
***REMOVED*** catch (JSONException e) ***REMOVED*** } catch (JSONException e) {
logger.error("Invalid notification response: " + response); logger.error("Invalid notification response: " + response);
throw new EMailException(e); throw new EMailException(e);
***REMOVED*** }
***REMOVED*** }
***REMOVED*** }
private List<String> getRecipients() ***REMOVED*** private List<String> getRecipients() {
try ***REMOVED*** try {
List<String> recipients = new ArrayList<String>(); List<String> recipients = new ArrayList<String>();
String dataMinerManagers = retrieveDataMinerManagers(); String dataMinerManagers = retrieveDataMinerManagers();
logger.debug("Retrieved DataMiner Managers: " + dataMinerManagers); logger.debug("Retrieved DataMiner Managers: " + dataMinerManagers);
if (dataMinerManagers != null && !dataMinerManagers.isEmpty()) ***REMOVED*** if (dataMinerManagers != null && !dataMinerManagers.isEmpty()) {
JSONObject obj = new JSONObject(dataMinerManagers); JSONObject obj = new JSONObject(dataMinerManagers);
JSONArray data = obj.getJSONArray("result"); JSONArray data = obj.getJSONArray("result");
if (data != null) ***REMOVED*** if (data != null) {
for (int i = 0; i < data.length(); i++) ***REMOVED*** for (int i = 0; i < data.length(); i++) {
recipients.add(data.getString(i)); recipients.add(data.getString(i));
***REMOVED*** }
***REMOVED*** }
***REMOVED*** else ***REMOVED*** } else {
logger.info("Use the default admins how workaround "); logger.info("Use the default admins how workaround ");
List<String> defaultManagers = DMPMClientConfiguratorManager.getInstance().getDefaultAdmins(); List<String> defaultManagers = DMPMClientConfiguratorManager.getInstance().getDefaultAdmins();
recipients.addAll(defaultManagers); recipients.addAll(defaultManagers);
***REMOVED*** }
recipients.add(this.username(SecurityTokenProvider.instance.get())); recipients.add(this.username(SecurityTokenProvider.instance.get()));
logger.info("Retrieved Recipients: " + recipients); logger.info("Retrieved Recipients: " + recipients);
return recipients; return recipients;
***REMOVED*** catch (Exception e) ***REMOVED*** } catch (Exception e) {
logger.error("Error retrieving recipients: " + e.getLocalizedMessage(), e); logger.error("Error retrieving recipients: " + e.getLocalizedMessage(), e);
logger.info("Use the default admins how workaround "); logger.info("Use the default admins how workaround ");
return DMPMClientConfiguratorManager.getInstance().getDefaultAdmins(); return DMPMClientConfiguratorManager.getInstance().getDefaultAdmins();
***REMOVED*** }
***REMOVED*** }
private String retrieveDataMinerManagers() throws Exception ***REMOVED*** private String retrieveDataMinerManagers() throws Exception {
***REMOVED*** Try to retrieve a url like this: // Try to retrieve a url like this:
***REMOVED*** https:***REMOVED***api.d4science.org/social-networking-library-ws/rest/2/users/get-usernames-by-role?role-name=DataMiner-Manager&gcube-token=xxx-xxxx-xxxx-xxx // https://api.d4science.org/social-networking-library-ws/rest/2/users/get-usernames-by-role?role-name=DataMiner-Manager&gcube-token=xxx-xxxx-xxxx-xxx
StringBuilder requestMessageBuilder = new StringBuilder(socialServiceAddress); StringBuilder requestMessageBuilder = new StringBuilder(socialServiceAddress);
@ -298,7 +298,7 @@ public class SendMail ***REMOVED***
requestMessageBuilder.append(USER_ROLES_ADDRESS_PATH); requestMessageBuilder.append(USER_ROLES_ADDRESS_PATH);
logger.info("Request Admins Url: " + requestMessageBuilder.toString()); logger.info("Request Admins Url: " + requestMessageBuilder.toString());
***REMOVED*** SecurityTokenProvider.instance.get() // SecurityTokenProvider.instance.get()
requestMessageBuilder.append(applicationToken); requestMessageBuilder.append(applicationToken);
String requestAdminsUrl = requestMessageBuilder.toString(); String requestAdminsUrl = requestMessageBuilder.toString();
@ -311,6 +311,6 @@ public class SendMail ***REMOVED***
return EntityUtils.toString(client.execute(getReq).getEntity()); return EntityUtils.toString(client.execute(getReq).getEntity());
***REMOVED*** }
***REMOVED*** }

22
src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/util/exception/AlgorithmException.java
View File

@ -1,35 +1,35 @@
package org.gcube.dataanalysis.dataminer.poolmanager.util.exception; package org.gcube.dataanalysis.dataminer.poolmanager.util.exception;
public class AlgorithmException extends DMPMException***REMOVED*** public class AlgorithmException extends DMPMException{
***REMOVED**** /**
* *
***REMOVED*** */
private static final long serialVersionUID = -5678597187512954288L; private static final long serialVersionUID = -5678597187512954288L;
private String algorithmName; private String algorithmName;
public AlgorithmException (String algorithmName) public AlgorithmException (String algorithmName)
***REMOVED*** {
super ("Algorithm exception"); super ("Algorithm exception");
this.algorithmName = algorithmName; this.algorithmName = algorithmName;
***REMOVED*** }
public AlgorithmException (String algorithmName, Throwable cause) public AlgorithmException (String algorithmName, Throwable cause)
***REMOVED*** {
super ("Algorithm exception", cause); super ("Algorithm exception", cause);
this.algorithmName = algorithmName; this.algorithmName = algorithmName;
***REMOVED*** }
***REMOVED*** @Override
public String getErrorMessage() ***REMOVED*** public String getErrorMessage() {
return "Installation completed but DataMiner Interface not working correctly or files " return "Installation completed but DataMiner Interface not working correctly or files "
+ this.algorithmName + ".jar and " + this.algorithmName + this.algorithmName + ".jar and " + this.algorithmName
+ "_interface.jar not availables at the expected path"; + "_interface.jar not availables at the expected path";
***REMOVED*** }
***REMOVED*** }

16
src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/util/exception/DMPMException.java
View File

@ -1,20 +1,20 @@
package org.gcube.dataanalysis.dataminer.poolmanager.util.exception; package org.gcube.dataanalysis.dataminer.poolmanager.util.exception;
public abstract class DMPMException extends Exception***REMOVED*** public abstract class DMPMException extends Exception{
***REMOVED**** /**
* *
***REMOVED*** */
private static final long serialVersionUID = 1L; private static final long serialVersionUID = 1L;
public DMPMException (String errorMessage) public DMPMException (String errorMessage)
***REMOVED*** {
super (errorMessage); super (errorMessage);
***REMOVED*** }
public DMPMException(String errorMessage,Throwable cause) ***REMOVED*** public DMPMException(String errorMessage,Throwable cause) {
super (errorMessage,cause); super (errorMessage,cause);
***REMOVED*** }
public abstract String getErrorMessage (); public abstract String getErrorMessage ();
***REMOVED*** }

24
src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/util/exception/EMailException.java
View File

@ -1,28 +1,28 @@
package org.gcube.dataanalysis.dataminer.poolmanager.util.exception; package org.gcube.dataanalysis.dataminer.poolmanager.util.exception;
public class EMailException extends Exception ***REMOVED*** public class EMailException extends Exception {
private static final String MESSAGE = "Unable to send email notification"; private static final String MESSAGE = "Unable to send email notification";
***REMOVED**** /**
* *
***REMOVED*** */
private static final long serialVersionUID = 1L; private static final long serialVersionUID = 1L;
public EMailException() ***REMOVED*** public EMailException() {
super(MESSAGE); super(MESSAGE);
***REMOVED*** }
public EMailException(String message) ***REMOVED*** public EMailException(String message) {
super(message); super(message);
***REMOVED*** }
public EMailException(String message, Throwable e) ***REMOVED*** public EMailException(String message, Throwable e) {
super(message, e); super(message, e);
***REMOVED*** }
public EMailException(Throwable e) ***REMOVED*** public EMailException(Throwable e) {
super(MESSAGE, e); super(MESSAGE, e);
***REMOVED*** }
***REMOVED*** }

18
src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/util/exception/GenericException.java
View File

@ -1,26 +1,26 @@
package org.gcube.dataanalysis.dataminer.poolmanager.util.exception; package org.gcube.dataanalysis.dataminer.poolmanager.util.exception;
public class GenericException extends DMPMException ***REMOVED*** public class GenericException extends DMPMException {
***REMOVED**** /**
* *
***REMOVED*** */
private static final long serialVersionUID = 6772009633547404120L; private static final long serialVersionUID = 6772009633547404120L;
public GenericException(Throwable cause) ***REMOVED*** public GenericException(Throwable cause) {
super ("Generic exception",cause); super ("Generic exception",cause);
***REMOVED*** }
***REMOVED*** @Override
public String getErrorMessage() ***REMOVED*** public String getErrorMessage() {
return this.getCause().getMessage(); return this.getCause().getMessage();
***REMOVED*** }
***REMOVED*** }

26
src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/util/exception/SVNCommitException.java
View File

@ -2,43 +2,43 @@ package org.gcube.dataanalysis.dataminer.poolmanager.util.exception;
import org.tmatesoft.svn.core.SVNErrorMessage; import org.tmatesoft.svn.core.SVNErrorMessage;
public class SVNCommitException extends DMPMException ***REMOVED*** public class SVNCommitException extends DMPMException {
***REMOVED**** /**
* *
***REMOVED*** */
private static final long serialVersionUID = -5225403308313619585L; private static final long serialVersionUID = -5225403308313619585L;
private SVNErrorMessage svnErrorMessage; private SVNErrorMessage svnErrorMessage;
private String fileName; private String fileName;
public SVNCommitException(SVNErrorMessage errorMessage, String fileName) ***REMOVED*** public SVNCommitException(SVNErrorMessage errorMessage, String fileName) {
super ("Unable to commit"); super ("Unable to commit");
this.svnErrorMessage = errorMessage; this.svnErrorMessage = errorMessage;
this.fileName = fileName; this.fileName = fileName;
***REMOVED*** }
public SVNCommitException(String message,SVNErrorMessage errorMessage,String fileName) ***REMOVED*** public SVNCommitException(String message,SVNErrorMessage errorMessage,String fileName) {
super (message); super (message);
this.svnErrorMessage = errorMessage; this.svnErrorMessage = errorMessage;
this.fileName = fileName; this.fileName = fileName;
***REMOVED*** }
public SVNErrorMessage getSvnErrorMessage() ***REMOVED*** public SVNErrorMessage getSvnErrorMessage() {
return svnErrorMessage; return svnErrorMessage;
***REMOVED*** }
***REMOVED*** @Override
public String getErrorMessage() ***REMOVED*** public String getErrorMessage() {
return "Commit operation failed for "+this.fileName return "Commit operation failed for "+this.fileName
+ "the message of the SVN Server is the following:\n"+this.svnErrorMessage.getMessage(); + "the message of the SVN Server is the following:\n"+this.svnErrorMessage.getMessage();
***REMOVED*** }
***REMOVED*** }

110
src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/util/impl/CheckMethodProduction.java
View File

@ -5,101 +5,101 @@ import java.io.File;
import org.gcube.dataanalysis.dataminer.poolmanager.clients.configuration.DMPMClientConfiguratorManager; import org.gcube.dataanalysis.dataminer.poolmanager.clients.configuration.DMPMClientConfiguratorManager;
import org.gcube.dataanalysis.dataminer.poolmanager.util.CheckMethod; import org.gcube.dataanalysis.dataminer.poolmanager.util.CheckMethod;
import org.gcube.dataanalysis.dataminer.poolmanager.util.exception.SVNCommitException; import org.gcube.dataanalysis.dataminer.poolmanager.util.exception.SVNCommitException;
***REMOVED*** import org.tmatesoft.svn.core.SVNException;
import com.jcraft.jsch.JSchException; import com.jcraft.jsch.JSchException;
import com.jcraft.jsch.SftpException; import com.jcraft.jsch.SftpException;
public class CheckMethodProduction extends CheckMethod***REMOVED*** public class CheckMethodProduction extends CheckMethod{
public CheckMethodProduction() public CheckMethodProduction()
***REMOVED*** {
super (DMPMClientConfiguratorManager.getInstance().getProductionConfiguration()); super (DMPMClientConfiguratorManager.getInstance().getProductionConfiguration());
***REMOVED*** }
***REMOVED*** @Override
protected void copyFromDmToSVN(File a) throws SVNException, SVNCommitException, JSchException, SftpException ***REMOVED*** protected void copyFromDmToSVN(File a) throws SVNException, SVNCommitException, JSchException, SftpException {
super.copyFromDmToSVN(a, new SVNUpdaterProduction()); super.copyFromDmToSVN(a, new SVNUpdaterProduction());
***REMOVED*** }
public static void main(String[] args) throws Exception ***REMOVED*** public static void main(String[] args) throws Exception {
***REMOVED*** ServiceConfiguration a = new ServiceConfiguration(); // ServiceConfiguration a = new ServiceConfiguration();
***REMOVED*** System.out.println(a.getStagingHost()); // System.out.println(a.getStagingHost());
CheckMethodProduction a = new CheckMethodProduction(); CheckMethodProduction a = new CheckMethodProduction();
***REMOVED***a.getFiles("/trunk/data-analysis/RConfiguration/RPackagesManagement/r_deb_pkgs.txt, /trunk/data-analysis/RConfiguration/RPackagesManagement/r_cran_pkgs.txt, /trunk/data-analysis/RConfiguration/RPackagesManagement/r_github_pkgs.txt"); //a.getFiles("/trunk/data-analysis/RConfiguration/RPackagesManagement/r_deb_pkgs.txt, /trunk/data-analysis/RConfiguration/RPackagesManagement/r_cran_pkgs.txt, /trunk/data-analysis/RConfiguration/RPackagesManagement/r_github_pkgs.txt");
***REMOVED*** File aa = new File("OCTAVEBLACKBOX.jar"); // File aa = new File("OCTAVEBLACKBOX.jar");
***REMOVED*** System.out.println(aa.getName()); // System.out.println(aa.getName());
***REMOVED*** System.out.println(aa.getPath()); // System.out.println(aa.getPath());
***REMOVED***a.copyFromDmToSVN(aa); //a.copyFromDmToSVN(aa);
***REMOVED*** if (a.checkMethod("dataminer-ghost-d.dev.d4science.org", "***REMOVED***"))***REMOVED*** // if (a.checkMethod("dataminer-ghost-d.dev.d4science.org", "xxx-xxx-xxx-xxx")){
***REMOVED*** System.out.println("AAA");***REMOVED*** // System.out.println("AAA"); }
***REMOVED*** //
***REMOVED*** if (a.doesExist("/home/gcube/wps_algorithms/algorithms/WINDOWS_BLACK_BOX_EXAMPLE.jar"))***REMOVED*** // if (a.doesExist("/home/gcube/wps_algorithms/algorithms/WINDOWS_BLACK_BOX_EXAMPLE.jar")){
***REMOVED*** System.out.println("BBBB"); // System.out.println("BBBB");
***REMOVED*** //
***REMOVED******REMOVED*** // }
***REMOVED*** if (a.doesExist("/home/gcube/wps_algorithms/algorithms/WINDOWS_BLACK_BOX_EXAMPLE_interface.jar"))***REMOVED*** // if (a.doesExist("/home/gcube/wps_algorithms/algorithms/WINDOWS_BLACK_BOX_EXAMPLE_interface.jar")){
***REMOVED*** System.out.println("CCCC");***REMOVED*** // System.out.println("CCCC");}
***REMOVED*** //
***REMOVED*** File aa = new File("/home/gcube/wps_algorithms/algorithms/RBLACKBOX_interface.jar"); // File aa = new File("/home/gcube/wps_algorithms/algorithms/RBLACKBOX_interface.jar");
***REMOVED*** a.copyFromDmToSVN(aa, "Dev"); // a.copyFromDmToSVN(aa, "Dev");
***REMOVED*** //
***REMOVED***System.out.println(a.checkMethod("dataminer-ghost-t.pre.d4science.org", //System.out.println(a.checkMethod("dataminer-ghost-t.pre.d4science.org",
***REMOVED*** "2eceaf27-0e22-4dbe-8075-e09eff199bf9-98187548")); // "xxxx-xxx-xxx-xxx"));
***REMOVED***System.out.println(a.checkMethod("dataminer-proto-ghost.d4science.org", //System.out.println(a.checkMethod("dataminer-proto-ghost.d4science.org",
***REMOVED*** "***REMOVED***")); // "xxx-xxxx-xxx-xxx"));
try try
***REMOVED*** {
a.checkMethod("dataminer-ghost-d.dev.d4science.org", a.checkMethod("dataminer-ghost-d.dev.d4science.org",
"***REMOVED***"); "xxx-xxx-xxx-xxx");
***REMOVED*** catch (Exception e) } catch (Exception e)
***REMOVED*** {
e.printStackTrace(); e.printStackTrace();
***REMOVED*** }
***REMOVED***Algorithm aa = new Algorithm(); //Algorithm aa = new Algorithm();
***REMOVED***aa.setName("UDPIPE_WRAPPER"); //aa.setName("UDPIPE_WRAPPER");
***REMOVED***System.out.println(a.algoExists(aa)); //System.out.println(a.algoExists(aa));
***REMOVED******REMOVED*** ////
***REMOVED***ServiceConfiguration bp = new ServiceConfiguration(); //ServiceConfiguration bp = new ServiceConfiguration();
***REMOVED******REMOVED*** ////
***REMOVED***SecurityTokenProvider.instance.set("***REMOVED***"); //SecurityTokenProvider.instance.set("xxxx-xxx-xxx-xxx");
***REMOVED******REMOVED*** ////
***REMOVED***if (a.checkMethod(bp.getStagingHost(), SecurityTokenProvider.instance.get())&&a.algoExists(aa)); ***REMOVED*** //if (a.checkMethod(bp.getStagingHost(), SecurityTokenProvider.instance.get())&&a.algoExists(aa)); {
***REMOVED***System.out.println("ciao"); //System.out.println("ciao");
***REMOVED*** //
***REMOVED******REMOVED*** //}
***REMOVED*** //
***REMOVED***Algorithm al = new Algorithm(); //Algorithm al = new Algorithm();
***REMOVED*** al.setName("UDPIPE_WRAPPER"); // al.setName("UDPIPE_WRAPPER");
***REMOVED*** a.deleteFiles(al); // a.deleteFiles(al);
***REMOVED*** }
***REMOVED*** }

108
src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/util/impl/CheckMethodStaging.java
View File

@ -5,93 +5,93 @@ import java.io.File;
import org.gcube.dataanalysis.dataminer.poolmanager.clients.configuration.DMPMClientConfiguratorManager; import org.gcube.dataanalysis.dataminer.poolmanager.clients.configuration.DMPMClientConfiguratorManager;
import org.gcube.dataanalysis.dataminer.poolmanager.util.CheckMethod; import org.gcube.dataanalysis.dataminer.poolmanager.util.CheckMethod;
public class CheckMethodStaging extends CheckMethod***REMOVED*** public class CheckMethodStaging extends CheckMethod{
public CheckMethodStaging() public CheckMethodStaging()
***REMOVED*** {
super (DMPMClientConfiguratorManager.getInstance().getStagingConfiguration()); super (DMPMClientConfiguratorManager.getInstance().getStagingConfiguration());
***REMOVED*** }
***REMOVED*** @Override
protected void copyFromDmToSVN(File a) throws Exception***REMOVED*** protected void copyFromDmToSVN(File a) throws Exception{
super.copyFromDmToSVN(a, new SVNUpdaterStaging()); super.copyFromDmToSVN(a, new SVNUpdaterStaging());
***REMOVED*** }
public static void main(String[] args) throws Exception ***REMOVED*** public static void main(String[] args) throws Exception {
***REMOVED*** ServiceConfiguration a = new ServiceConfiguration(); // ServiceConfiguration a = new ServiceConfiguration();
***REMOVED*** System.out.println(a.getStagingHost()); // System.out.println(a.getStagingHost());
CheckMethodStaging a = new CheckMethodStaging(); CheckMethodStaging a = new CheckMethodStaging();
***REMOVED***a.getFiles("/trunk/data-analysis/RConfiguration/RPackagesManagement/r_deb_pkgs.txt, /trunk/data-analysis/RConfiguration/RPackagesManagement/r_cran_pkgs.txt, /trunk/data-analysis/RConfiguration/RPackagesManagement/r_github_pkgs.txt"); //a.getFiles("/trunk/data-analysis/RConfiguration/RPackagesManagement/r_deb_pkgs.txt, /trunk/data-analysis/RConfiguration/RPackagesManagement/r_cran_pkgs.txt, /trunk/data-analysis/RConfiguration/RPackagesManagement/r_github_pkgs.txt");
***REMOVED*** File aa = new File("OCTAVEBLACKBOX.jar"); // File aa = new File("OCTAVEBLACKBOX.jar");
***REMOVED*** System.out.println(aa.getName()); // System.out.println(aa.getName());
***REMOVED*** System.out.println(aa.getPath()); // System.out.println(aa.getPath());
***REMOVED***a.copyFromDmToSVN(aa); //a.copyFromDmToSVN(aa);
***REMOVED*** if (a.checkMethod("dataminer-ghost-d.dev.d4science.org", "***REMOVED***"))***REMOVED*** // if (a.checkMethod("dataminer-ghost-d.dev.d4science.org", "xxxx-xxx-xxx-xxx")){
***REMOVED*** System.out.println("AAA");***REMOVED*** // System.out.println("AAA"); }
***REMOVED*** //
***REMOVED*** if (a.doesExist("/home/gcube/wps_algorithms/algorithms/WINDOWS_BLACK_BOX_EXAMPLE.jar"))***REMOVED*** // if (a.doesExist("/home/gcube/wps_algorithms/algorithms/WINDOWS_BLACK_BOX_EXAMPLE.jar")){
***REMOVED*** System.out.println("BBBB"); // System.out.println("BBBB");
***REMOVED*** //
***REMOVED******REMOVED*** // }
***REMOVED*** if (a.doesExist("/home/gcube/wps_algorithms/algorithms/WINDOWS_BLACK_BOX_EXAMPLE_interface.jar"))***REMOVED*** // if (a.doesExist("/home/gcube/wps_algorithms/algorithms/WINDOWS_BLACK_BOX_EXAMPLE_interface.jar")){
***REMOVED*** System.out.println("CCCC");***REMOVED*** // System.out.println("CCCC");}
***REMOVED*** //
***REMOVED*** File aa = new File("/home/gcube/wps_algorithms/algorithms/RBLACKBOX_interface.jar"); // File aa = new File("/home/gcube/wps_algorithms/algorithms/RBLACKBOX_interface.jar");
***REMOVED*** a.copyFromDmToSVN(aa, "Dev"); // a.copyFromDmToSVN(aa, "Dev");
***REMOVED*** //
***REMOVED***System.out.println(a.checkMethod("dataminer-ghost-t.pre.d4science.org", //System.out.println(a.checkMethod("dataminer-ghost-t.pre.d4science.org",
***REMOVED*** "2eceaf27-0e22-4dbe-8075-e09eff199bf9-98187548")); // "xxxx-xxx-xxx-xxx"));
***REMOVED***System.out.println(a.checkMethod("dataminer-proto-ghost.d4science.org", //System.out.println(a.checkMethod("dataminer-proto-ghost.d4science.org",
***REMOVED*** "***REMOVED***")); // "xxx-xxx-xxx-xxx"));
try try
***REMOVED*** {
a.checkMethod("dataminer-ghost-d.dev.d4science.org", a.checkMethod("dataminer-ghost-d.dev.d4science.org",
"***REMOVED***"); "xxx-xxx-xxxx-xxx");
***REMOVED*** catch (Exception e) } catch (Exception e)
***REMOVED*** {
e.printStackTrace(); e.printStackTrace();
***REMOVED*** }
***REMOVED***Algorithm aa = new Algorithm(); //Algorithm aa = new Algorithm();
***REMOVED***aa.setName("UDPIPE_WRAPPER"); //aa.setName("UDPIPE_WRAPPER");
***REMOVED***System.out.println(a.algoExists(aa)); //System.out.println(a.algoExists(aa));
***REMOVED******REMOVED*** ////
***REMOVED***ServiceConfiguration bp = new ServiceConfiguration(); //ServiceConfiguration bp = new ServiceConfiguration();
***REMOVED******REMOVED*** ////
***REMOVED***SecurityTokenProvider.instance.set("***REMOVED***"); //SecurityTokenProvider.instance.set("xxxx-xxx-xxx-xxx");
***REMOVED******REMOVED*** ////
***REMOVED***if (a.checkMethod(bp.getStagingHost(), SecurityTokenProvider.instance.get())&&a.algoExists(aa)); ***REMOVED*** //if (a.checkMethod(bp.getStagingHost(), SecurityTokenProvider.instance.get())&&a.algoExists(aa)); {
***REMOVED***System.out.println("ciao"); //System.out.println("ciao");
***REMOVED*** //
***REMOVED******REMOVED*** //}
***REMOVED*** //
***REMOVED***Algorithm al = new Algorithm(); //Algorithm al = new Algorithm();
***REMOVED*** al.setName("UDPIPE_WRAPPER"); // al.setName("UDPIPE_WRAPPER");
***REMOVED*** a.deleteFiles(al); // a.deleteFiles(al);
***REMOVED*** }
***REMOVED*** }

8
src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/util/impl/ClusterBuilderProduction.java
View File

@ -3,12 +3,12 @@ package org.gcube.dataanalysis.dataminer.poolmanager.util.impl;
import org.gcube.dataanalysis.dataminer.poolmanager.clients.configuration.DMPMClientConfiguratorManager; import org.gcube.dataanalysis.dataminer.poolmanager.clients.configuration.DMPMClientConfiguratorManager;
import org.gcube.dataanalysis.dataminer.poolmanager.util.ClusterBuilder; import org.gcube.dataanalysis.dataminer.poolmanager.util.ClusterBuilder;
public class ClusterBuilderProduction extends ClusterBuilder***REMOVED*** public class ClusterBuilderProduction extends ClusterBuilder{
public ClusterBuilderProduction() ***REMOVED*** public ClusterBuilderProduction() {
super (DMPMClientConfiguratorManager.getInstance().getProductionConfiguration()); super (DMPMClientConfiguratorManager.getInstance().getProductionConfiguration());
***REMOVED*** }
***REMOVED*** }

8
src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/util/impl/ClusterBuilderStaging.java
View File

@ -3,11 +3,11 @@ package org.gcube.dataanalysis.dataminer.poolmanager.util.impl;
import org.gcube.dataanalysis.dataminer.poolmanager.clients.configuration.DMPMClientConfiguratorManager; import org.gcube.dataanalysis.dataminer.poolmanager.clients.configuration.DMPMClientConfiguratorManager;
import org.gcube.dataanalysis.dataminer.poolmanager.util.ClusterBuilder; import org.gcube.dataanalysis.dataminer.poolmanager.util.ClusterBuilder;
public class ClusterBuilderStaging extends ClusterBuilder***REMOVED*** public class ClusterBuilderStaging extends ClusterBuilder{
public ClusterBuilderStaging() ***REMOVED*** public ClusterBuilderStaging() {
super (DMPMClientConfiguratorManager.getInstance().getStagingConfiguration()); super (DMPMClientConfiguratorManager.getInstance().getStagingConfiguration());
***REMOVED*** }
***REMOVED*** }

12
src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/util/impl/NotificationHelperProduction.java
View File

@ -2,18 +2,18 @@ package org.gcube.dataanalysis.dataminer.poolmanager.util.impl;
import org.gcube.dataanalysis.dataminer.poolmanager.util.NotificationHelper; import org.gcube.dataanalysis.dataminer.poolmanager.util.NotificationHelper;
***REMOVED***import scala.actors.threadpool.Arrays; //import scala.actors.threadpool.Arrays;
public class NotificationHelperProduction extends NotificationHelper***REMOVED*** public class NotificationHelperProduction extends NotificationHelper{
***REMOVED*** private Exception executionException; // private Exception executionException;
public NotificationHelperProduction() ***REMOVED*** public NotificationHelperProduction() {
super ("[DataMinerGhostProductionInstallationRequestReport]"); super ("[DataMinerGhostProductionInstallationRequestReport]");
***REMOVED*** }
***REMOVED*** }

12
src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/util/impl/NotificationHelperStaging.java
View File

@ -2,17 +2,17 @@ package org.gcube.dataanalysis.dataminer.poolmanager.util.impl;
import org.gcube.dataanalysis.dataminer.poolmanager.util.NotificationHelper; import org.gcube.dataanalysis.dataminer.poolmanager.util.NotificationHelper;
***REMOVED***import scala.actors.threadpool.Arrays; //import scala.actors.threadpool.Arrays;
public class NotificationHelperStaging extends NotificationHelper ***REMOVED*** public class NotificationHelperStaging extends NotificationHelper {
***REMOVED*** private Exception executionException; // private Exception executionException;
public NotificationHelperStaging() ***REMOVED*** public NotificationHelperStaging() {
super ("[DataMinerGhostStagingInstallationRequestReport]"); super ("[DataMinerGhostStagingInstallationRequestReport]");
***REMOVED*** }
***REMOVED*** }

10
src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/util/impl/SVNUpdaterProduction.java
View File

@ -2,20 +2,20 @@ package org.gcube.dataanalysis.dataminer.poolmanager.util.impl;
import org.gcube.dataanalysis.dataminer.poolmanager.clients.configuration.DMPMClientConfiguratorManager; import org.gcube.dataanalysis.dataminer.poolmanager.clients.configuration.DMPMClientConfiguratorManager;
import org.gcube.dataanalysis.dataminer.poolmanager.util.SVNUpdater; import org.gcube.dataanalysis.dataminer.poolmanager.util.SVNUpdater;
***REMOVED*** import org.tmatesoft.svn.core.SVNException;
/** /**
* Created by ggiammat on 5/9/17. * Created by ggiammat on 5/9/17.
*/ */
public class SVNUpdaterProduction extends SVNUpdater***REMOVED*** public class SVNUpdaterProduction extends SVNUpdater{
public SVNUpdaterProduction() throws SVNException ***REMOVED*** public SVNUpdaterProduction() throws SVNException {
super (DMPMClientConfiguratorManager.getInstance().getProductionConfiguration()); super (DMPMClientConfiguratorManager.getInstance().getProductionConfiguration());
***REMOVED*** }
***REMOVED*** }

10
src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/util/impl/SVNUpdaterStaging.java
View File

@ -2,20 +2,20 @@ package org.gcube.dataanalysis.dataminer.poolmanager.util.impl;
import org.gcube.dataanalysis.dataminer.poolmanager.clients.configuration.DMPMClientConfiguratorManager; import org.gcube.dataanalysis.dataminer.poolmanager.clients.configuration.DMPMClientConfiguratorManager;
import org.gcube.dataanalysis.dataminer.poolmanager.util.SVNUpdater; import org.gcube.dataanalysis.dataminer.poolmanager.util.SVNUpdater;
***REMOVED*** import org.tmatesoft.svn.core.SVNException;
/** /**
* Created by ggiammat on 5/9/17. * Created by ggiammat on 5/9/17.
*/ */
public class SVNUpdaterStaging extends SVNUpdater***REMOVED*** public class SVNUpdaterStaging extends SVNUpdater{
public SVNUpdaterStaging() throws SVNException ***REMOVED*** public SVNUpdaterStaging() throws SVNException {
super (DMPMClientConfiguratorManager.getInstance().getStagingConfiguration()); super (DMPMClientConfiguratorManager.getInstance().getStagingConfiguration());
***REMOVED*** }
***REMOVED*** }

2
src/main/resources/custom/custom-flr-Flash/meta/main.yaml
View File

@ -1,4 +1,4 @@
#--- #---
#dependencies: #dependencies:
# <dependencies> # <dependencies>
# - ***REMOVED*** role: digest ***REMOVED*** # - { role: digest }

4
src/main/resources/service.properties
View File

@ -1,7 +1,7 @@
#YML node file #YML node file
SVN_REPO = https:***REMOVED***svn.d4science.research-infrastructures.eu/gcube/trunk/data-analysis/RConfiguration/RPackagesManagement/ SVN_REPO = https://svn.d4science.research-infrastructures.eu/gcube/trunk/data-analysis/RConfiguration/RPackagesManagement/
svn.repository = https:***REMOVED***svn.d4science.research-infrastructures.eu/gcube svn.repository = https://svn.d4science.research-infrastructures.eu/gcube
svn.algo.main.repo = /trunk/data-analysis/DataMinerConfiguration/algorithms svn.algo.main.repo = /trunk/data-analysis/DataMinerConfiguration/algorithms

6
src/main/resources/static/gcube-algorithm-installer/meta/main.yaml
View File

@ -1,4 +1,4 @@
dependencies: dependencies:
# - ***REMOVED*** role: gcube-dataminer ***REMOVED*** # - { role: gcube-dataminer }
# - ***REMOVED*** role: os-unzip ***REMOVED*** # - { role: os-unzip }
# - ***REMOVED*** role: os-java-1.7.0 ***REMOVED*** # - { role: os-java-1.7.0 }

6
src/main/resources/static/gcube-algorithm-installer/tasks/main.yaml
View File

@ -12,14 +12,14 @@
#- name: download the installer zip #- name: download the installer zip
# get_url: # get_url:
# url: https:***REMOVED***svn.research-infrastructures.eu/public/d4science/gcube/trunk/data-analysis/DataminerAlgorithmsInstaller/package/algorithmInstaller.zip # url: https://svn.research-infrastructures.eu/public/d4science/gcube/trunk/data-analysis/DataminerAlgorithmsInstaller/package/algorithmInstaller.zip
# dest: /home/dpm/algorithmInstaller.zip # dest: /home/dpm/algorithmInstaller.zip
# validate_certs: no # validate_certs: no
#- name: download and unzip the package #- name: download and unzip the package
# unarchive: # unarchive:
# src: https:***REMOVED***svn.research-infrastructures.eu/public/d4science/gcube/trunk/data-analysis/DataminerAlgorithmsInstaller/package/algorithmInstaller1_1.zip # src: https://svn.research-infrastructures.eu/public/d4science/gcube/trunk/data-analysis/DataminerAlgorithmsInstaller/package/algorithmInstaller1_1.zip
## src: http:***REMOVED***maven.research-infrastructures.eu:8081/nexus/service/local/artifact/maven/redirect?r=gcube-snapshots&g=org.gcube.dataanalysis&a=dataminer-algorithms-importer&v=1.1.1-SNAPSHOT&e=tar.gz ## src: http://maven.research-infrastructures.eu:8081/nexus/service/local/artifact/maven/redirect?r=gcube-snapshots&g=org.gcube.dataanalysis&a=dataminer-algorithms-importer&v=1.1.1-SNAPSHOT&e=tar.gz
# dest: /home/gcube # dest: /home/gcube
# remote_src: yes # remote_src: yes
# validate_certs: no # validate_certs: no

2
src/main/resources/static/gcube-dataminer/meta/main.yaml
View File

@ -1,2 +1,2 @@
dependencies: dependencies:
- ***REMOVED*** role: gcube-ghn ***REMOVED*** - { role: gcube-ghn }

2
src/main/resources/static/os-java-1.7.0/tasks/main.yaml
View File

@ -3,5 +3,5 @@
- name: adding OS Package java-1.7.0 - name: adding OS Package java-1.7.0
package: package:
name: java-1.7.0-openjdk name: java-1.7.0-openjdk
state: "***REMOVED******REMOVED***os_package_state***REMOVED******REMOVED***" state: "{{os_package_state}}"
become: true become: true

2
src/main/resources/static/os-unzip/tasks/main.yaml
View File

@ -3,5 +3,5 @@
- name: adding OS Package unzip - name: adding OS Package unzip
package: package:
name: unzip name: unzip
state: "***REMOVED******REMOVED***os_package_state***REMOVED******REMOVED***" state: "{{os_package_state}}"
become: true become: true

2
src/main/resources/templates/cran-package-add/meta/main.yaml
View File

@ -1,4 +1,4 @@
--- ---
#dependencies: #dependencies:
# <dependencies> # <dependencies>
# - ***REMOVED*** role: os-r ***REMOVED*** # - { role: os-r }

2
src/main/resources/templates/cran-package-add/tasks/main.yaml
View File

@ -1,4 +1,4 @@
# tasks file for r # tasks file for r
--- ---
- name: Install algorithm <name> - name: Install algorithm <name>
command: Rscript -e "install.packages('<name>', repos=c('http:***REMOVED***ftp.heanet.ie/mirrors/cran.r-project.org/'))" command: Rscript -e "install.packages('<name>', repos=c('http://ftp.heanet.ie/mirrors/cran.r-project.org/'))"

2
src/main/resources/templates/gcube-algorithm-add/meta/main.yaml
View File

@ -1,4 +1,4 @@
--- ---
dependencies: dependencies:
<dependencies> <dependencies>
- ***REMOVED*** role: gcube-algorithm-installer ***REMOVED*** - { role: gcube-algorithm-installer }

2
src/main/resources/templates/github-package-add/meta/main.yaml
View File

@ -1,4 +1,4 @@
--- ---
#dependencies: #dependencies:
# <dependencies> # <dependencies>
# - ***REMOVED*** role: os-r ***REMOVED*** # - { role: os-r }

2
src/main/resources/templates/os-package-add/tasks/main.yaml
View File

@ -3,6 +3,6 @@
- name: adding OS Package <name> - name: adding OS Package <name>
package: package:
name: <name> name: <name>
state: "***REMOVED******REMOVED***os_package_state***REMOVED******REMOVED***" state: "{{os_package_state}}"
become: true become: true

6
src/main/webapp/WEB-INF/web.xml
View File

@ -1,6 +1,6 @@
<!DOCTYPE web-app PUBLIC <!DOCTYPE web-app PUBLIC
"-***REMOVED***Sun Microsystems, Inc.***REMOVED***DTD Web Application 2.3***REMOVED***EN" "-//Sun Microsystems, Inc.//DTD Web Application 2.3//EN"
"http:***REMOVED***java.sun.com/dtd/web-app_2_3.dtd" > "http://java.sun.com/dtd/web-app_2_3.dtd" >
<web-app> <web-app>
<display-name>Archetype Created Web Application</display-name> <display-name>Archetype Created Web Application</display-name>
@ -41,7 +41,7 @@
<!-- <servlet> <servlet-name>Jersey2Config</servlet-name> <servlet-class>io.swagger.jersey.config.JerseyJaxrsConfig</servlet-class> <!-- <servlet> <servlet-name>Jersey2Config</servlet-name> <servlet-class>io.swagger.jersey.config.JerseyJaxrsConfig</servlet-class>
<init-param> <param-name>api.version</param-name> <param-value>1.0.0</param-value> <init-param> <param-name>api.version</param-name> <param-value>1.0.0</param-value>
</init-param> <init-param> <param-name>swagger.api.basepath</param-name> </init-param> <init-param> <param-name>swagger.api.basepath</param-name>
<param-value>http:***REMOVED***localhost:8080/api</param-value> </init-param> <load-on-startup>2</load-on-startup> <param-value>http://localhost:8080/api</param-value> </init-param> <load-on-startup>2</load-on-startup>
</servlet> --> </servlet> -->

90
src/test/java/org/gcube/dataanalysis/dataminerpoolmanager/AlgorithmPackageParserTest.java
View File

@ -1,31 +1,31 @@
package org.gcube.dataanalysis.dataminerpoolmanager; package org.gcube.dataanalysis.dataminerpoolmanager;
***REMOVED*** import java.io.IOException;
import java.io.InputStream; import java.io.InputStream;
***REMOVED*** import java.net.URL;
***REMOVED*** import java.util.List;
import java.util.Vector; import java.util.Vector;
***REMOVED*** import org.gcube.dataanalysis.dataminer.poolmanager.datamodel.Algorithm;
import org.gcube.dataanalysis.dataminer.poolmanager.datamodel.AlgorithmSet; import org.gcube.dataanalysis.dataminer.poolmanager.datamodel.AlgorithmSet;
import org.gcube.dataanalysis.dataminer.poolmanager.process.AddAlgorithmCommand; import org.gcube.dataanalysis.dataminer.poolmanager.process.AddAlgorithmCommand;
import org.gcube.dataanalysis.dataminer.poolmanager.process.AlgorithmPackageParser; import org.gcube.dataanalysis.dataminer.poolmanager.process.AlgorithmPackageParser;
public class AlgorithmPackageParserTest ***REMOVED*** public class AlgorithmPackageParserTest {
private static int BUFFER_SIZE = 2048; private static int BUFFER_SIZE = 2048;
public void extractAllAlgorithms() throws IOException ***REMOVED*** public void extractAllAlgorithms() throws IOException {
String url = "http:***REMOVED***svn.research-infrastructures.eu/public/d4science/gcube/trunk/data-analysis/DataMinerConfiguration/algorithms/dev/algorithms"; String url = "http://svn.research-infrastructures.eu/public/d4science/gcube/trunk/data-analysis/DataMinerConfiguration/algorithms/dev/algorithms";
List<String> commands = this.extractAddAlgorithmCommands(url); List<String> commands = this.extractAddAlgorithmCommands(url);
AlgorithmSet algorithms = new AlgorithmSet(); AlgorithmSet algorithms = new AlgorithmSet();
for (String cmd : commands) ***REMOVED*** for (String cmd : commands) {
System.out.println("-----------------------------------------"); System.out.println("-----------------------------------------");
System.out.println(cmd); System.out.println(cmd);
AddAlgorithmCommand aac = new AddAlgorithmCommand(cmd); AddAlgorithmCommand aac = new AddAlgorithmCommand(cmd);
System.out.println(aac); System.out.println(aac);
***REMOVED*** start creating the algo from the command // start creating the algo from the command
Algorithm algo = new Algorithm(); Algorithm algo = new Algorithm();
algo.setAlgorithmType(aac.getAlgorithmType()); algo.setAlgorithmType(aac.getAlgorithmType());
algo.setCategory(aac.getCategory()); algo.setCategory(aac.getCategory());
@ -35,20 +35,20 @@ public class AlgorithmPackageParserTest ***REMOVED***
algo.setPackageURL(aac.getUrl()); algo.setPackageURL(aac.getUrl());
algo.setSkipJava(aac.getSkipjava()); algo.setSkipJava(aac.getSkipjava());
***REMOVED*** then override with info from the package // then override with info from the package
if (aac.getUrl().length() > 4) ***REMOVED*** if (aac.getUrl().length() > 4) {
Algorithm packagedAlgo = this.extractAlgorithm(aac.getUrl()); Algorithm packagedAlgo = this.extractAlgorithm(aac.getUrl());
if (packagedAlgo != null) ***REMOVED*** if (packagedAlgo != null) {
algo.setDependencies(packagedAlgo.getDependencies()); algo.setDependencies(packagedAlgo.getDependencies());
***REMOVED*** }
***REMOVED*** }
algorithms.addAlgorithm(algo); algorithms.addAlgorithm(algo);
break; break;
***REMOVED*** }
***REMOVED***to uncomment //to uncomment
***REMOVED*** new DataminerPoolManager().addAlgorithmsToVRE(algorithms, // new DataminerPoolManager().addAlgorithmsToVRE(algorithms,
***REMOVED*** "/gcube/devNext/NextNext"); // "/gcube/devNext/NextNext");
***REMOVED*** }
/** /**
* Extract 'addAlgorithm' commands from a file containing wiki-table-style * Extract 'addAlgorithm' commands from a file containing wiki-table-style
@ -58,43 +58,43 @@ public class AlgorithmPackageParserTest ***REMOVED***
* @throws IOException * @throws IOException
*/ */
private List<String> extractAddAlgorithmCommands(String listUrl) private List<String> extractAddAlgorithmCommands(String listUrl)
throws IOException ***REMOVED*** throws IOException {
URL url = new URL(listUrl); URL url = new URL(listUrl);
InputStream is = url.openStream(); InputStream is = url.openStream();
StringBuilder s = new StringBuilder(); StringBuilder s = new StringBuilder();
byte[] buffer = new byte[BUFFER_SIZE]; byte[] buffer = new byte[BUFFER_SIZE];
int read = 0; int read = 0;
while ((read = is.read(buffer)) != -1) ***REMOVED*** while ((read = is.read(buffer)) != -1) {
s.append(new String(buffer, 0, read)); s.append(new String(buffer, 0, read));
***REMOVED*** }
List<String> out = new Vector<>(); List<String> out = new Vector<>();
String[] lines = s.toString().split("\n"); String[] lines = s.toString().split("\n");
for (String line : lines) ***REMOVED*** for (String line : lines) {
System.out.println("--------------------"); System.out.println("--------------------");
if (!line.isEmpty()) ***REMOVED*** if (!line.isEmpty()) {
String[] parts = line.split("\\|"); String[] parts = line.split("\\|");
int c = 1; int c = 1;
for (String part : parts) ***REMOVED*** for (String part : parts) {
if (part == null || part.trim().isEmpty()) ***REMOVED*** if (part == null || part.trim().isEmpty()) {
continue; continue;
***REMOVED*** }
System.out.println(c + ". " + part); System.out.println(c + ". " + part);
c++; c++;
if (part.contains("addAlgorithm.sh")) ***REMOVED*** if (part.contains("addAlgorithm.sh")) {
String cmd = part.trim(); String cmd = part.trim();
cmd = cmd.replaceAll("<notextile>", ""); cmd = cmd.replaceAll("<notextile>", "");
cmd = cmd.replaceAll("</notextile>", ""); cmd = cmd.replaceAll("</notextile>", "");
System.out.println(cmd); System.out.println(cmd);
***REMOVED*** AddAlgorithmCommand aac = new AddAlgorithmCommand(cmd); // AddAlgorithmCommand aac = new AddAlgorithmCommand(cmd);
***REMOVED*** System.out.println(aac); // System.out.println(aac);
out.add(cmd); out.add(cmd);
***REMOVED*** }
***REMOVED*** }
***REMOVED*** }
***REMOVED*** }
return out; return out;
***REMOVED*** }
/** /**
* Create an Algorithm starting from the algorithm jar. * Create an Algorithm starting from the algorithm jar.
@ -103,18 +103,18 @@ public class AlgorithmPackageParserTest ***REMOVED***
* @return * @return
* @throws IOException * @throws IOException
*/ */
private Algorithm extractAlgorithm(String url) throws IOException ***REMOVED*** private Algorithm extractAlgorithm(String url) throws IOException {
return new AlgorithmPackageParser().parsePackage(url); return new AlgorithmPackageParser().parsePackage(url);
***REMOVED*** }
public static void main(String[] args) throws Exception ***REMOVED*** public static void main(String[] args) throws Exception {
***REMOVED*** ProxySelector.setDefault(new PropertiesBasedProxySelector( // ProxySelector.setDefault(new PropertiesBasedProxySelector(
***REMOVED*** "/home/ngalante/.proxy-settings")); // "/home/ngalante/.proxy-settings"));
new AlgorithmPackageParserTest().extractAllAlgorithms(); new AlgorithmPackageParserTest().extractAllAlgorithms();
***REMOVED*** AlgorithmPackageParserTest at = new AlgorithmPackageParserTest(); // AlgorithmPackageParserTest at = new AlgorithmPackageParserTest();
***REMOVED*** Algorithm a = at.extractAlgorithm("http:***REMOVED***data.d4science.org/YjJ3TmJab1dqYzVoTmppdjlsK0l0b1ZXWGtzWlQ1NHNHbWJQNStIS0N6Yz0"); // Algorithm a = at.extractAlgorithm("http://data.d4science.org/YjJ3TmJab1dqYzVoTmppdjlsK0l0b1ZXWGtzWlQ1NHNHbWJQNStIS0N6Yz0");
***REMOVED*** System.out.println(a.getFullname()); // System.out.println(a.getFullname());
***REMOVED*** }
***REMOVED*** }

12
src/test/java/org/gcube/dataanalysis/dataminerpoolmanager/AnsibleWorkerTest.java
View File

@ -1,7 +1,7 @@
package org.gcube.dataanalysis.dataminerpoolmanager; package org.gcube.dataanalysis.dataminerpoolmanager;
import java.io.File; import java.io.File;
***REMOVED*** import java.io.IOException;
import java.util.UUID; import java.util.UUID;
import org.gcube.dataanalysis.dataminer.poolmanager.ansible.AnsibleWorker; import org.gcube.dataanalysis.dataminer.poolmanager.ansible.AnsibleWorker;
@ -10,9 +10,9 @@ import org.gcube.dataanalysis.dataminer.poolmanager.ansible.model.Playbook;
import org.gcube.dataanalysis.dataminer.poolmanager.ansible.model.Role; import org.gcube.dataanalysis.dataminer.poolmanager.ansible.model.Role;
import org.gcube.dataanalysis.dataminer.poolmanager.ansible.model.RoleFile; import org.gcube.dataanalysis.dataminer.poolmanager.ansible.model.RoleFile;
public class AnsibleWorkerTest ***REMOVED*** public class AnsibleWorkerTest {
public static void main(String[] args) throws IOException ***REMOVED*** public static void main(String[] args) throws IOException {
AnsibleWorker worker = new AnsibleWorker(new File("/home/nagalante/gcube/dataminer-pool-manager/work/"+UUID.randomUUID().toString())); AnsibleWorker worker = new AnsibleWorker(new File("/home/nagalante/gcube/dataminer-pool-manager/work/"+UUID.randomUUID().toString()));
System.out.println("created worker named " + worker.getWorkerId()); System.out.println("created worker named " + worker.getWorkerId());
@ -27,7 +27,7 @@ public class AnsibleWorkerTest ***REMOVED***
r.addTaskFile(tf); r.addTaskFile(tf);
worker.addRole(r); worker.addRole(r);
***REMOVED***worker.apply(); //worker.apply();
***REMOVED*** }
***REMOVED*** }

42
src/test/java/org/gcube/dataanalysis/dataminerpoolmanager/ApplicationTokenTest.java
View File

@ -4,66 +4,66 @@ import static org.gcube.resources.discovery.icclient.ICFactory.clientFor;
import static org.gcube.resources.discovery.icclient.ICFactory.queryFor; import static org.gcube.resources.discovery.icclient.ICFactory.queryFor;
import java.util.Iterator; import java.util.Iterator;
***REMOVED*** import java.util.List;
***REMOVED*** import org.gcube.common.authorization.library.provider.SecurityTokenProvider;
import org.gcube.common.encryption.encrypter.StringEncrypter; import org.gcube.common.encryption.encrypter.StringEncrypter;
import org.gcube.common.resources.gcore.ServiceEndpoint; import org.gcube.common.resources.gcore.ServiceEndpoint;
import org.gcube.common.resources.gcore.ServiceEndpoint.AccessPoint; import org.gcube.common.resources.gcore.ServiceEndpoint.AccessPoint;
import org.gcube.common.resources.gcore.ServiceEndpoint.Property; import org.gcube.common.resources.gcore.ServiceEndpoint.Property;
import org.gcube.common.resources.gcore.utils.Group; import org.gcube.common.resources.gcore.utils.Group;
***REMOVED*** import org.gcube.common.scope.api.ScopeProvider;
import org.gcube.resources.discovery.client.api.DiscoveryClient; import org.gcube.resources.discovery.client.api.DiscoveryClient;
import org.gcube.resources.discovery.client.queries.api.SimpleQuery; import org.gcube.resources.discovery.client.queries.api.SimpleQuery;
public class ApplicationTokenTest ***REMOVED*** public class ApplicationTokenTest {
private static final String DMPOOLMANAGER_SERVICE_QUERY_CONDITION = "$resource/Profile/Name/text() eq 'DMPoolManager'"; private static final String DMPOOLMANAGER_SERVICE_QUERY_CONDITION = "$resource/Profile/Name/text() eq 'DMPoolManager'";
public static void main(String[] args) ***REMOVED*** public static void main(String[] args) {
ScopeProvider.instance.set("/gcube/devsec/devVRE"); ScopeProvider.instance.set("/gcube/devsec/devVRE");
SecurityTokenProvider.instance.set("xxxx-xxxx-xxx"); SecurityTokenProvider.instance.set("xxxx-xxxx-xxx");
decryptToken(); decryptToken();
***REMOVED*** }
private static void decryptToken() ***REMOVED*** private static void decryptToken() {
try ***REMOVED*** try {
SimpleQuery query = queryFor(ServiceEndpoint.class); SimpleQuery query = queryFor(ServiceEndpoint.class);
query.addCondition(DMPOOLMANAGER_SERVICE_QUERY_CONDITION); query.addCondition(DMPOOLMANAGER_SERVICE_QUERY_CONDITION);
DiscoveryClient<ServiceEndpoint> client = clientFor(ServiceEndpoint.class); DiscoveryClient<ServiceEndpoint> client = clientFor(ServiceEndpoint.class);
List<ServiceEndpoint> resources = client.submit(query); List<ServiceEndpoint> resources = client.submit(query);
if (resources.isEmpty()) ***REMOVED*** if (resources.isEmpty()) {
System.out.println("No services resource found on IS!"); System.out.println("No services resource found on IS!");
***REMOVED*** else ***REMOVED*** } else {
System.out.println("Retrieved: " + resources.get(0)); System.out.println("Retrieved: " + resources.get(0));
***REMOVED*** }
Group<AccessPoint> accessPoints = resources.get(0).profile().accessPoints(); Group<AccessPoint> accessPoints = resources.get(0).profile().accessPoints();
if (!accessPoints.isEmpty()) ***REMOVED*** if (!accessPoints.isEmpty()) {
Iterator<AccessPoint> iterator = accessPoints.iterator(); Iterator<AccessPoint> iterator = accessPoints.iterator();
AccessPoint ap = iterator.next(); AccessPoint ap = iterator.next();
Group<Property> props = ap.properties(); Group<Property> props = ap.properties();
if (!props.isEmpty()) ***REMOVED*** if (!props.isEmpty()) {
Iterator<Property> iteratorProps = props.iterator(); Iterator<Property> iteratorProps = props.iterator();
Property p = iteratorProps.next(); Property p = iteratorProps.next();
String applicationToken = StringEncrypter.getEncrypter().decrypt(p.value()); String applicationToken = StringEncrypter.getEncrypter().decrypt(p.value());
System.out.println("Application token found: " + applicationToken); System.out.println("Application token found: " + applicationToken);
***REMOVED*** else ***REMOVED*** } else {
System.out.println("No application token found in service resource on IS!"); System.out.println("No application token found in service resource on IS!");
***REMOVED*** }
***REMOVED*** else ***REMOVED*** } else {
System.out.println("Invalid service resource on IS!"); System.out.println("Invalid service resource on IS!");
***REMOVED*** }
***REMOVED*** catch (Exception e) ***REMOVED*** } catch (Exception e) {
e.printStackTrace(); e.printStackTrace();
***REMOVED*** }
***REMOVED*** }
***REMOVED*** }

196
src/test/java/org/gcube/dataanalysis/dataminerpoolmanager/DataminerPoolManagerTest.java
View File

@ -2,106 +2,106 @@ package org.gcube.dataanalysis.dataminerpoolmanager;
import java.net.ProxySelector; import java.net.ProxySelector;
***REMOVED*** import org.gcube.common.scope.api.ScopeProvider;
***REMOVED*** import org.gcube.dataanalysis.dataminer.poolmanager.datamodel.Algorithm;
import org.gcube.dataanalysis.dataminer.poolmanager.datamodel.AlgorithmSet; import org.gcube.dataanalysis.dataminer.poolmanager.datamodel.AlgorithmSet;
import org.gcube.dataanalysis.dataminer.poolmanager.datamodel.Dependency; import org.gcube.dataanalysis.dataminer.poolmanager.datamodel.Dependency;
import org.gcube.dataanalysis.dataminer.poolmanager.util.PropertiesBasedProxySelector; import org.gcube.dataanalysis.dataminer.poolmanager.util.PropertiesBasedProxySelector;
public class DataminerPoolManagerTest ***REMOVED*** public class DataminerPoolManagerTest {
/* /*
private static Map<String, Domain> domains = new HashMap<>(); private static Map<String, Domain> domains = new HashMap<>();
private static Map<String, Cluster> clusters = new HashMap<>(); private static Map<String, Cluster> clusters = new HashMap<>();
private static Dependency createDependency(String depName) ***REMOVED*** private static Dependency createDependency(String depName) {
String[] parts = depName.split(":"); String[] parts = depName.split(":");
Dependency out = new Dependency(); Dependency out = new Dependency();
if(parts.length>1) ***REMOVED*** if(parts.length>1) {
out.setType(parts[0]); out.setType(parts[0]);
out.setName(parts[1]); out.setName(parts[1]);
***REMOVED*** else ***REMOVED*** } else {
out.setType("os"); out.setType("os");
out.setName(depName); out.setName(depName);
***REMOVED*** }
return out; return out;
***REMOVED*** }
private static Algorithm createAlgorithm(String name, String ... deps) ***REMOVED*** private static Algorithm createAlgorithm(String name, String ... deps) {
Algorithm a = new Algorithm(); Algorithm a = new Algorithm();
a.setName(name); a.setName(name);
for(String dep:deps) ***REMOVED*** for(String dep:deps) {
a.addDependency(createDependency(dep)); a.addDependency(createDependency(dep));
***REMOVED*** }
return a; return a;
***REMOVED*** }
private static AlgorithmSet createAlgorithmSet(String name, Algorithm ... algs) ***REMOVED*** private static AlgorithmSet createAlgorithmSet(String name, Algorithm ... algs) {
AlgorithmSet out = new AlgorithmSet(); AlgorithmSet out = new AlgorithmSet();
out.setName(name); out.setName(name);
for(Algorithm a:algs) ***REMOVED*** for(Algorithm a:algs) {
out.addAlgorithm(a); out.addAlgorithm(a);
***REMOVED*** }
return out; return out;
***REMOVED*** }
private static Domain getDomain(String name) ***REMOVED*** private static Domain getDomain(String name) {
if(domains.get(name)==null) ***REMOVED*** if(domains.get(name)==null) {
Domain d = new Domain(); Domain d = new Domain();
d.setName(name); d.setName(name);
domains.put(name, d); domains.put(name, d);
return d; return d;
***REMOVED*** else ***REMOVED*** } else {
return domains.get(name); return domains.get(name);
***REMOVED*** }
***REMOVED*** }
private static Host createHost(String hostname, String domainName) ***REMOVED*** private static Host createHost(String hostname, String domainName) {
Host out = new Host(); Host out = new Host();
out.setName(hostname); out.setName(hostname);
Domain d = getDomain(domainName); Domain d = getDomain(domainName);
out.setDomain(d); out.setDomain(d);
return out; return out;
***REMOVED*** }
private static Cluster getCluster(String name) ***REMOVED*** private static Cluster getCluster(String name) {
if(clusters.get(name)==null) ***REMOVED*** if(clusters.get(name)==null) {
Cluster d = new Cluster(); Cluster d = new Cluster();
d.setName(name); d.setName(name);
clusters.put(name, d); clusters.put(name, d);
return d; return d;
***REMOVED*** else ***REMOVED*** } else {
return clusters.get(name); return clusters.get(name);
***REMOVED*** }
***REMOVED*** }
private static Collection<Dependency> extractDependencies() ***REMOVED*** private static Collection<Dependency> extractDependencies() {
Collection<Dependency> out = new TreeSet<>(new DependencyComparator()); Collection<Dependency> out = new TreeSet<>(new DependencyComparator());
for(Cluster c:clusters.values()) ***REMOVED*** for(Cluster c:clusters.values()) {
for(AlgorithmSet as:c.getAlgorithmSets()) ***REMOVED*** for(AlgorithmSet as:c.getAlgorithmSets()) {
for(Algorithm a:as.getAlgorithms()) ***REMOVED*** for(Algorithm a:as.getAlgorithms()) {
for(Dependency d:a.getDependencies()) ***REMOVED*** for(Dependency d:a.getDependencies()) {
out.add(d); out.add(d);
***REMOVED*** }
***REMOVED*** }
***REMOVED*** }
***REMOVED*** }
return out; return out;
***REMOVED*** }
private static Collection<Algorithm> extractAlgorithms() ***REMOVED*** private static Collection<Algorithm> extractAlgorithms() {
Collection<Algorithm> out = new TreeSet<>(new AlgorithmComparator()); Collection<Algorithm> out = new TreeSet<>(new AlgorithmComparator());
for(Cluster c:clusters.values()) ***REMOVED*** for(Cluster c:clusters.values()) {
for(AlgorithmSet as:c.getAlgorithmSets()) ***REMOVED*** for(AlgorithmSet as:c.getAlgorithmSets()) {
for(Algorithm a:as.getAlgorithms()) ***REMOVED*** for(Algorithm a:as.getAlgorithms()) {
out.add(a); out.add(a);
***REMOVED*** }
***REMOVED*** }
***REMOVED*** }
return out; return out;
***REMOVED*** }
static ***REMOVED*** static {
Algorithm ewe = createAlgorithm("ewe", "mono", "latex", "cran:some_R_package", "custom:some_git_package"); Algorithm ewe = createAlgorithm("ewe", "mono", "latex", "cran:some_R_package", "custom:some_git_package");
Algorithm ensemble = createAlgorithm("ensemble", "python"); Algorithm ensemble = createAlgorithm("ensemble", "python");
@ -132,10 +132,10 @@ public class DataminerPoolManagerTest ***REMOVED***
cluster2.addAlgorithmSet(as1); cluster2.addAlgorithmSet(as1);
cluster2.addAlgorithmSet(as3); cluster2.addAlgorithmSet(as3);
***REMOVED*** }
*/ */
public static void main(String[] args) throws Exception ***REMOVED*** public static void main(String[] args) throws Exception {
/* /*
AnsibleBridge ab = new AnsibleBridge(); AnsibleBridge ab = new AnsibleBridge();
ab.printInventoryByDomainAndSets(clusters.values()); ab.printInventoryByDomainAndSets(clusters.values());
@ -144,70 +144,70 @@ public class DataminerPoolManagerTest ***REMOVED***
AnsibleWorker worker = ab.createWorker(); AnsibleWorker worker = ab.createWorker();
for(Algorithm a:extractAlgorithms()) ***REMOVED*** for(Algorithm a:extractAlgorithms()) {
for(Role r:ab.generateRoles(a)) ***REMOVED*** for(Role r:ab.generateRoles(a)) {
worker.addRole(r); worker.addRole(r);
***REMOVED*** }
***REMOVED*** }
for(Dependency d:extractDependencies()) ***REMOVED*** for(Dependency d:extractDependencies()) {
for(Role r:ab.generateRoles(d)) ***REMOVED*** for(Role r:ab.generateRoles(d)) {
worker.addRole(r); worker.addRole(r);
***REMOVED*** }
***REMOVED*** }
*/ */
ScopeProvider.instance.set("/gcube/devNext/NextNext"); ScopeProvider.instance.set("/gcube/devNext/NextNext");
ProxySelector.setDefault(new PropertiesBasedProxySelector("/home/ngalante/.proxy-settings")); ProxySelector.setDefault(new PropertiesBasedProxySelector("/home/ngalante/.proxy-settings"));
***REMOVED*** //
***REMOVED*** ***REMOVED*** create the algorithm (download it, etc etc) // // create the algorithm (download it, etc etc)
***REMOVED*** Algorithm algorithm = new Algorithm(); // Algorithm algorithm = new Algorithm();
***REMOVED*** algorithm.setName("ichtyop"); // algorithm.setName("ichtyop");
***REMOVED*** algorithm.setClazz("org.gcube..."); // algorithm.setClazz("org.gcube...");
***REMOVED*** algorithm.setDescription("some description"); // algorithm.setDescription("some description");
***REMOVED*** //
***REMOVED*** Dependency d = new Dependency(); // Dependency d = new Dependency();
***REMOVED*** d.setName("libpng"); // d.setName("libpng");
***REMOVED*** d.setType("os"); // d.setType("os");
***REMOVED*** algorithm.addDependency(d); // algorithm.addDependency(d);
***REMOVED*** //
***REMOVED*** d = new Dependency(); // d = new Dependency();
***REMOVED*** d.setName("some-r-package"); // d.setName("some-r-package");
***REMOVED*** d.setType("cran"); // d.setType("cran");
***REMOVED*** algorithm.addDependency(d); // algorithm.addDependency(d);
***REMOVED*** //
***REMOVED*** d = new Dependency(); // d = new Dependency();
***REMOVED*** d.setName("some-other-r-package"); // d.setName("some-other-r-package");
***REMOVED*** d.setType("cran"); // d.setType("cran");
***REMOVED*** algorithm.addDependency(d); // algorithm.addDependency(d);
***REMOVED*** //
***REMOVED*** d = new Dependency(); // d = new Dependency();
***REMOVED*** d.setName("voodoo"); // d.setName("voodoo");
***REMOVED*** d.setType("custom"); // d.setType("custom");
***REMOVED*** algorithm.addDependency(d); // algorithm.addDependency(d);
***REMOVED*** //
***REMOVED*** ***REMOVED*** create the algorithm (download it, etc etc) // // create the algorithm (download it, etc etc)
***REMOVED*** Algorithm ewe = new Algorithm(); // Algorithm ewe = new Algorithm();
***REMOVED*** ewe.setName("ewe"); // ewe.setName("ewe");
***REMOVED*** //
***REMOVED*** d = new Dependency(); // d = new Dependency();
***REMOVED*** d.setName("voodoo"); // d.setName("voodoo");
***REMOVED*** d.setType("custom"); // d.setType("custom");
***REMOVED*** ewe.addDependency(d); // ewe.addDependency(d);
AlgorithmSet algorithms = new AlgorithmSet(); AlgorithmSet algorithms = new AlgorithmSet();
algorithms.setName("dummy-set"); algorithms.setName("dummy-set");
***REMOVED*** algorithms.addAlgorithm(algorithm); // algorithms.addAlgorithm(algorithm);
***REMOVED*** algorithms.addAlgorithm(ewe); // algorithms.addAlgorithm(ewe);
Algorithm ensemble = new Algorithm(); Algorithm ensemble = new Algorithm();
ensemble.setName("ensemble"); ensemble.setName("ensemble");
ensemble.setCategory("ICHTHYOP_MODEL"); ensemble.setCategory("ICHTHYOP_MODEL");
ensemble.setAlgorithmType("transducerers"); ensemble.setAlgorithmType("transducerers");
ensemble.setPackageURL("http:***REMOVED***data.d4science.org/R0FqV2lNOW1jMkxuUEIrWXY4aUhvSENHSmVMQks4NjdHbWJQNStIS0N6Yz0"); ensemble.setPackageURL("http://data.d4science.org/R0FqV2lNOW1jMkxuUEIrWXY4aUhvSENHSmVMQks4NjdHbWJQNStIS0N6Yz0");
ensemble.setClazz("org.gcube.dataanalysis.executor.rscripts.Ichthyopmodelonebyone"); ensemble.setClazz("org.gcube.dataanalysis.executor.rscripts.Ichthyopmodelonebyone");
ensemble.setSkipJava("N"); ensemble.setSkipJava("N");
ensemble.setDescription("test"); ensemble.setDescription("test");
@ -218,8 +218,8 @@ public class DataminerPoolManagerTest ***REMOVED***
ensemble.addDependency(d); ensemble.addDependency(d);
algorithms.addAlgorithm(ensemble); algorithms.addAlgorithm(ensemble);
***REMOVED***new DataminerPoolManager().addAlgorithmsToVRE(algorithms, "/gcube/devNext/NextNext", "test"+UUID.randomUUID(), false); //new DataminerPoolManager().addAlgorithmsToVRE(algorithms, "/gcube/devNext/NextNext", "test"+UUID.randomUUID(), false);
***REMOVED*** }
***REMOVED*** }

10
src/test/java/org/gcube/dataanalysis/dataminerpoolmanager/ISClientTest.java
View File

@ -2,16 +2,16 @@ package org.gcube.dataanalysis.dataminerpoolmanager;
import java.net.ProxySelector; import java.net.ProxySelector;
***REMOVED*** import org.gcube.common.scope.api.ScopeProvider;
import org.gcube.dataanalysis.dataminer.poolmanager.clients.ISClient; import org.gcube.dataanalysis.dataminer.poolmanager.clients.ISClient;
import org.gcube.dataanalysis.dataminer.poolmanager.util.PropertiesBasedProxySelector; import org.gcube.dataanalysis.dataminer.poolmanager.util.PropertiesBasedProxySelector;
public class ISClientTest ***REMOVED*** public class ISClientTest {
public static void main(String[] args) ***REMOVED*** public static void main(String[] args) {
ProxySelector.setDefault(new PropertiesBasedProxySelector("/home/ngalante/.proxy-settings")); ProxySelector.setDefault(new PropertiesBasedProxySelector("/home/ngalante/.proxy-settings"));
ScopeProvider.instance.set("/gcube/devNext/NextNext"); ScopeProvider.instance.set("/gcube/devNext/NextNext");
System.out.println(new ISClient().listDataminersInVRE()); System.out.println(new ISClient().listDataminersInVRE());
***REMOVED*** }
***REMOVED*** }

38
src/test/java/org/gcube/dataanalysis/dataminerpoolmanager/JobTest.java
View File

@ -1,34 +1,34 @@
package org.gcube.dataanalysis.dataminerpoolmanager; package org.gcube.dataanalysis.dataminerpoolmanager;
***REMOVED*** import java.io.IOException;
***REMOVED*** import org.gcube.common.scope.api.ScopeProvider;
***REMOVED*** import org.gcube.dataanalysis.dataminer.poolmanager.datamodel.Algorithm;
***REMOVED*** import org.gcube.dataanalysis.dataminer.poolmanager.util.AlgorithmBuilder;
import org.gcube.dataanalysis.dataminer.poolmanager.util.SVNUpdater; import org.gcube.dataanalysis.dataminer.poolmanager.util.SVNUpdater;
import org.gcube.dataanalysis.dataminer.poolmanager.util.impl.SVNUpdaterProduction; import org.gcube.dataanalysis.dataminer.poolmanager.util.impl.SVNUpdaterProduction;
***REMOVED*** import org.tmatesoft.svn.core.SVNException;
public class JobTest ***REMOVED*** public class JobTest {
public static void main(String[] args) throws SVNException, IOException, InterruptedException***REMOVED*** public static void main(String[] args) throws SVNException, IOException, InterruptedException{
ScopeProvider.instance.set("/d4science.research-infrastructures.eu/gCubeApps/RPrototypingLab"); ScopeProvider.instance.set("/d4science.research-infrastructures.eu/gCubeApps/RPrototypingLab");
SVNUpdater svnUpdater = new SVNUpdaterProduction(); SVNUpdater svnUpdater = new SVNUpdaterProduction();
Algorithm algo = AlgorithmBuilder.create("http:***REMOVED***data.d4science.org/dENQTTMxdjNZcGRpK0NHd2pvU0owMFFzN0VWemw3Zy9HbWJQNStIS0N6Yz0"); Algorithm algo = AlgorithmBuilder.create("http://data.d4science.org/dENQTTMxdjNZcGRpK0NHd2pvU0owMFFzN0VWemw3Zy9HbWJQNStIS0N6Yz0");
***REMOVED***test phase //test phase
***REMOVED***Cluster stagingCluster = ClusterBuilder.getStagingDataminerCluster(); //Cluster stagingCluster = ClusterBuilder.getStagingDataminerCluster();
***REMOVED***Cluster rProtoCluster = ClusterBuilder.getRProtoCluster(); //Cluster rProtoCluster = ClusterBuilder.getRProtoCluster();
***REMOVED***DMPMJob job = new StagingJob(svnUpdater, algo, stagingCluster, /*rProtoCluster,*/ ScopeProvider.instance.get()); //DMPMJob job = new StagingJob(svnUpdater, algo, stagingCluster, /*rProtoCluster,*/ ScopeProvider.instance.get());
***REMOVED***job.start(); //job.start();
***REMOVED***release phase //release phase
***REMOVED***Cluster prodCluster = ClusterBuilder.getVRECluster(targetVREToken, targetVRE); //Cluster prodCluster = ClusterBuilder.getVRECluster(targetVREToken, targetVRE);
***REMOVED***DMPMJob job2 = new ProductionPublishingJob(svnUpdater, algo, prodCluster); //DMPMJob job2 = new ProductionPublishingJob(svnUpdater, algo, prodCluster);
***REMOVED***job2.start(); //job2.start();
***REMOVED*** }
***REMOVED*** }

30
src/test/java/org/gcube/dataanalysis/dataminerpoolmanager/SVNTests.java
View File

@ -1,36 +1,36 @@
package org.gcube.dataanalysis.dataminerpoolmanager; package org.gcube.dataanalysis.dataminerpoolmanager;
***REMOVED*** import java.io.IOException;
***REMOVED*** import org.gcube.dataanalysis.dataminer.poolmanager.datamodel.Algorithm;
***REMOVED*** import org.gcube.dataanalysis.dataminer.poolmanager.util.AlgorithmBuilder;
import org.gcube.dataanalysis.dataminer.poolmanager.util.SVNUpdater; import org.gcube.dataanalysis.dataminer.poolmanager.util.SVNUpdater;
import org.gcube.dataanalysis.dataminer.poolmanager.util.impl.SVNUpdaterStaging; import org.gcube.dataanalysis.dataminer.poolmanager.util.impl.SVNUpdaterStaging;
***REMOVED*** import org.tmatesoft.svn.core.SVNException;
/** /**
* Created by ggiammat on 5/17/17. * Created by ggiammat on 5/17/17.
*/ */
public class SVNTests ***REMOVED*** public class SVNTests {
public static void main(String[] args) throws SVNException, IOException, InterruptedException ***REMOVED*** public static void main(String[] args) throws SVNException, IOException, InterruptedException {
SVNUpdater svnUpdater = new SVNUpdaterStaging(); SVNUpdater svnUpdater = new SVNUpdaterStaging();
Algorithm algo = AlgorithmBuilder.create("http:***REMOVED***data.d4science.org/YjJ3TmJab1dqYzVoTmppdjlsK0l0b1ZXWGtzWlQ1NHNHbWJQNStIS0N6Yz0"); Algorithm algo = AlgorithmBuilder.create("http://data.d4science.org/YjJ3TmJab1dqYzVoTmppdjlsK0l0b1ZXWGtzWlQ1NHNHbWJQNStIS0N6Yz0");
***REMOVED***algo.setClazz(algo.getClazz() + "TEST"); //algo.setClazz(algo.getClazz() + "TEST");
algo.setAlgorithmType("transducerers"); algo.setAlgorithmType("transducerers");
algo.setCategory("NLP"); algo.setCategory("NLP");
algo.setFullname("Ondřej Košarko"); algo.setFullname("Ondřej Košarko");
***REMOVED***System.out.println(algo.getCategory()); //System.out.println(algo.getCategory());
***REMOVED***System.out.println(algo.getSkipJava()); //System.out.println(algo.getSkipJava());
***REMOVED***svnUpdater.updateSVNAlgorithmList("/trunk/data-analysis/DataMinerConfiguration/algorithms/dev/algorithms", algo, "/gcube/devNext/NextNext", algo.getCategory(), algo.getAlgorithmType(), ""); //svnUpdater.updateSVNAlgorithmList("/trunk/data-analysis/DataMinerConfiguration/algorithms/dev/algorithms", algo, "/gcube/devNext/NextNext", algo.getCategory(), algo.getAlgorithmType(), "");
***REMOVED***svnUpdater.updateSVNRProtoAlgorithmList(algo, "/d4science.research-infrastructures.eu/gCubeApps/RPrototypingLab", "Dataminer Pool Manager", "Proto"); //svnUpdater.updateSVNRProtoAlgorithmList(algo, "/d4science.research-infrastructures.eu/gCubeApps/RPrototypingLab", "Dataminer Pool Manager", "Proto");
***REMOVED***svnUpdater.readRPRotoDeps(algo); //svnUpdater.readRPRotoDeps(algo);
***REMOVED*** }
***REMOVED*** }

44
src/test/java/org/gcube/dataanalysis/dataminerpoolmanager/SendMailTest.java
View File

@ -1,38 +1,38 @@
package org.gcube.dataanalysis.dataminerpoolmanager; package org.gcube.dataanalysis.dataminerpoolmanager;
***REMOVED*** import org.gcube.common.authorization.library.provider.SecurityTokenProvider;
***REMOVED*** import org.gcube.common.scope.api.ScopeProvider;
import org.gcube.dataanalysis.dataminer.poolmanager.util.SendMail; import org.gcube.dataanalysis.dataminer.poolmanager.util.SendMail;
public class SendMailTest ***REMOVED*** public class SendMailTest {
public static void main(String[] args) ***REMOVED*** public static void main(String[] args) {
try ***REMOVED*** try {
***REMOVED*** NotificationHelper nh = new NotificationHelper(); // NotificationHelper nh = new NotificationHelper();
SendMail sm = new SendMail(); SendMail sm = new SendMail();
ScopeProvider.instance.set("/gcube/devNext/NextNext"); ScopeProvider.instance.set("/gcube/devNext/NextNext");
SecurityTokenProvider.instance.set("xxxx-xxxx-xxx"); SecurityTokenProvider.instance.set("xxxx-xxxx-xxx");
***REMOVED*** System.out.println(sm.getRootToken()); // System.out.println(sm.getRootToken());
***REMOVED*** sm.getGenericResourceByName(""); // sm.getGenericResourceByName("");
***REMOVED***ScopeProvider.instance.set("/gcube/devsec/devVRE"); //ScopeProvider.instance.set("/gcube/devsec/devVRE");
***REMOVED***SecurityTokenProvider.instance.set("xxxx-xxxx-xxxx"); //SecurityTokenProvider.instance.set("xxxx-xxxx-xxxx");
***REMOVED*** sm.sendNotification(nh.getFailedSubject(), nh.getFailedBody("test // sm.sendNotification(nh.getFailedSubject(), nh.getFailedBody("test
***REMOVED*** failed")); // failed"));
***REMOVED*** sm.username(SecurityTokenProvider.instance.get()); // sm.username(SecurityTokenProvider.instance.get());
***REMOVED*** sm.retrieveAdminRole(); // sm.retrieveAdminRole();
***REMOVED*** sm.getAdminRoles(); // sm.getAdminRoles();
sm.sendNotification("Test DMPoolManager Notification", "This is only a test please cancel this message."); sm.sendNotification("Test DMPoolManager Notification", "This is only a test please cancel this message.");
***REMOVED*** System.out.println(sm.getAdmins()); // System.out.println(sm.getAdmins());
***REMOVED*** sm.sendNotification("test", "test"); // sm.sendNotification("test", "test");
***REMOVED*** System.out.println(sm.getSocialService()); // System.out.println(sm.getSocialService());
***REMOVED*** catch (Exception e) ***REMOVED*** } catch (Exception e) {
System.out.println("Error in sent mail: "+e.getLocalizedMessage()); System.out.println("Error in sent mail: "+e.getLocalizedMessage());
e.printStackTrace(); e.printStackTrace();
***REMOVED*** }
***REMOVED*** }
***REMOVED*** }