From 90466296b8812f66dcef47b2cae002530e629de8 Mon Sep 17 00:00:00 2001 From: Fabio Sinibaldi Date: Mon, 7 Sep 2020 11:42:02 +0200 Subject: [PATCH] Initial Commit --- CHANGELOG.md | 9 + FUNDING.md | 26 ++ LICENSE.md | 312 ++++++++++++++++++ README.md | 51 ++- pom.xml | 89 +++++ .../plugins/decompress/DecompressPlugin.java | 147 +++++++++ .../decompress/DecompressPluginFactory.java | 115 +++++++ ...data.transfer.plugin.AbstractPluginFactory | 1 + .../plugin/decompress/PluginTest.java | 36 ++ .../transfer/plugin/decompress/UnzipTest.java | 58 ++++ src/test/resources/log4j.properties | 25 ++ 11 files changed, 868 insertions(+), 1 deletion(-) create mode 100644 CHANGELOG.md create mode 100644 FUNDING.md create mode 100644 LICENSE.md create mode 100644 pom.xml create mode 100644 src/main/java/org/gcube/data/transfer/plugins/decompress/DecompressPlugin.java create mode 100644 src/main/java/org/gcube/data/transfer/plugins/decompress/DecompressPluginFactory.java create mode 100644 src/main/resources/META-INF/services/org.gcube.data.transfer.plugin.AbstractPluginFactory create mode 100644 src/test/java/org/gcube/data/transfer/plugin/decompress/PluginTest.java create mode 100644 src/test/java/org/gcube/data/transfer/plugin/decompress/UnzipTest.java create mode 100644 src/test/resources/log4j.properties diff --git a/CHANGELOG.md b/CHANGELOG.md new file mode 100644 index 0000000..4937b73 --- /dev/null +++ b/CHANGELOG.md @@ -0,0 +1,9 @@ +This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). + +# Changelog for org.gcube.data.transfer.decompress-archive-plugin + +## Unreleased [v1.0.2-SNAPSHOT] 2020-09-07 + +### Fixes + +- Integration with gcube distribution (https://support.d4science.org/issues/19612) diff --git a/FUNDING.md b/FUNDING.md new file mode 100644 index 0000000..9e48b94 --- /dev/null +++ b/FUNDING.md @@ -0,0 +1,26 @@ +# Acknowledgments + +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 + - [DILIGENT](https://cordis.europa.eu/project/id/004260) (grant no. 004260). +- the Seventh Framework Programme for research, technological development and demonstration + - [D4Science](https://cordis.europa.eu/project/id/212488) (grant no. 212488); + - [D4Science-II](https://cordis.europa.eu/project/id/239019) (grant no.239019); + - [ENVRI](https://cordis.europa.eu/project/id/283465) (grant no. 283465); + - [iMarine](https://cordis.europa.eu/project/id/283644) (grant no. 283644); + - [EUBrazilOpenBio](https://cordis.europa.eu/project/id/288754) (grant no. 288754). +- the H2020 research and innovation programme + - [SoBigData](https://cordis.europa.eu/project/id/654024) (grant no. 654024); + - [PARTHENOS](https://cordis.europa.eu/project/id/654119) (grant no. 654119); + - [EGI-Engage](https://cordis.europa.eu/project/id/654142) (grant no. 654142); + - [ENVRI PLUS](https://cordis.europa.eu/project/id/654182) (grant no. 654182); + - [BlueBRIDGE](https://cordis.europa.eu/project/id/675680) (grant no. 675680); + - [PerformFISH](https://cordis.europa.eu/project/id/727610) (grant no. 727610); + - [AGINFRA PLUS](https://cordis.europa.eu/project/id/731001) (grant no. 731001); + - [DESIRA](https://cordis.europa.eu/project/id/818194) (grant no. 818194); + - [ARIADNEplus](https://cordis.europa.eu/project/id/823914) (grant no. 823914); + - [RISIS 2](https://cordis.europa.eu/project/id/824091) (grant no. 824091); + - [EOSC-Pillar](https://cordis.europa.eu/project/id/857650) (grant no. 857650); + - [Blue Cloud](https://cordis.europa.eu/project/id/862409) (grant no. 862409); + - [SoBigData-PlusPlus](https://cordis.europa.eu/project/id/871042) (grant no. 871042); diff --git a/LICENSE.md b/LICENSE.md new file mode 100644 index 0000000..3af0507 --- /dev/null +++ b/LICENSE.md @@ -0,0 +1,312 @@ +# European Union Public Licence V. 1.1 + + +EUPL © the European Community 2007 + + +This European Union Public Licence (the “EUPL”) applies to the Work or Software +(as defined below) which is provided under the terms of this Licence. 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Such provision will be construed and/or reformed so as necessary to make +it valid and enforceable. + +The European Commission may publish other linguistic versions and/or new +versions of this Licence, so far this is required and reasonable, without +reducing the scope of the rights granted by the Licence. New versions of the +Licence will be published with a unique version number. + +All linguistic versions of this Licence, approved by the European Commission, +have identical value. Parties can take advantage of the linguistic version of +their choice. + + + +## 14. Jurisdiction + +Any litigation resulting from the interpretation of this License, arising +between the European Commission, as a Licensor, and any Licensee, will be +subject to the jurisdiction of the Court of Justice of the European Communities, +as laid down in article 238 of the Treaty establishing the European Community. + +Any litigation arising between Parties, other than the European Commission, and +resulting from the interpretation of this License, will be subject to the +exclusive jurisdiction of the competent court where the Licensor resides or +conducts its primary business. + + + +## 15. Applicable Law + +This Licence shall be governed by the law of the European Union country where +the Licensor resides or has his registered office. + +This licence shall be governed by the Belgian law if: + +- a litigation arises between the European Commission, as a Licensor, and any +- Licensee; the Licensor, other than the European Commission, has no residence +- or registered office inside a European Union country. + + + +## Appendix + + + +“Compatible Licences” according to article 5 EUPL are: + + +- GNU General Public License (GNU GPL) v. 2 + +- Open Software License (OSL) v. 2.1, v. 3.0 + +- Common Public License v. 1.0 + +- Eclipse Public License v. 1.0 + +- Cecill v. 2.0 + diff --git a/README.md b/README.md index abcef08..edf6a27 100644 --- a/README.md +++ b/README.md @@ -1,2 +1,51 @@ -# decompress-archive-plugin +Data Transfer - Plugin Framework +-------------------------------------------------- + +Data Transfer Plugin Framework is one of the subsystems forming the gCube Data Transfer Facilities. It aims to provide gCube Applications a common layer for efficient and transparent data transfer towards gCube SmartGear nodes. It's designed as a client service architecture exploiting plugin design pattern. + +## Built with +* [OpenJDK](https://openjdk.java.net/) - The JDK used +* [JAX-RS](https://github.com/eclipse-ee4j/jaxrs-api) - Java™ API for RESTful Web Services +* [Jersey](https://jersey.github.io/) - JAX-RS runtime +* [Maven](https://maven.apache.org/) - Dependency Management + +## Documentation + +Documentation can be found [here](https://gcube.wiki.gcube-system.org/gcube/Data_Transfer_2). + +## Change log + +See [CHANGELOG.md](CHANGELOG.md). + +## License + +This project is licensed under the EUPL V.1.1 License - see the [LICENSE.md](LICENSE.md) file for details. + +## About the gCube Framework +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 +Infrastructures enabling the dynamic deployment of Virtual Research Environments +by favouring the realisation of reuse oriented policies. + +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 + - DILIGENT (grant no. 004260). +- the Seventh Framework Programme for research, technological development and demonstration + - D4Science (grant no. 212488); + - D4Science-II (grant no.239019); + - ENVRI (grant no. 283465); + - iMarine(grant no. 283644); + - EUBrazilOpenBio (grant no. 288754). +- the H2020 research and innovation programme + - SoBigData (grant no. 654024); + - PARTHENOS (grant no. 654119); + - EGIEngage (grant no. 654142); + - ENVRIplus (grant no. 654182); + - BlueBRIDGE (grant no. 675680); + - PerformFish (grant no. 727610); + - AGINFRAplus (grant no. 731001); + - DESIRA (grant no. 818194); + - ARIADNEplus (grant no. 823914); + - RISIS2 (grant no. 824091); diff --git a/pom.xml b/pom.xml new file mode 100644 index 0000000..e051f0c --- /dev/null +++ b/pom.xml @@ -0,0 +1,89 @@ + + 4.0.0 + + org.gcube.tools + maven-parent + 1.1.0 + + org.gcube.data.transfer + decompress-archive-plugin + 1.0.2-SNAPSHOT + decompress-archive-plugin + Data Transfer Plugin that decompress archive files + + + https://code-repo.d4science.org/gCubeSystem + + + + + + + scm:git:${gitBaseUrl}/${project.artifactId}.git + scm:git:${gitBaseUrl}/${project.artifactId}.git + ${gitBaseUrl}/${project.artifactId}.git + + + + + + + org.gcube.distribution + gcube-smartgears-bom + 2.0.0-SNAPSHOT + pom + import + + + org.gcube.distribution + gcube-bom + 2.0.0-SNAPSHOT + pom + import + + + + + + + + org.gcube.data.transfer + data-transfer-plugin-framework + [1.0.0-SNAPSHOT,2.0.0-SNAPSHOT) + + + org.slf4j + slf4j-log4j12 + 1.6.4 + test + + + junit + junit + 4.11 + test + + + + + + + + org.apache.maven.plugins + maven-assembly-plugin + + + make-uberjar + package + + + make-servicearchive + package + + + + + + + + \ No newline at end of file diff --git a/src/main/java/org/gcube/data/transfer/plugins/decompress/DecompressPlugin.java b/src/main/java/org/gcube/data/transfer/plugins/decompress/DecompressPlugin.java new file mode 100644 index 0000000..cd41865 --- /dev/null +++ b/src/main/java/org/gcube/data/transfer/plugins/decompress/DecompressPlugin.java @@ -0,0 +1,147 @@ +package org.gcube.data.transfer.plugins.decompress; + +import java.io.File; +import java.io.FileInputStream; +import java.io.FileOutputStream; +import java.io.IOException; +import java.util.Map; +import java.util.zip.ZipEntry; +import java.util.zip.ZipInputStream; + +import org.gcube.data.transfer.model.ExecutionReport; +import org.gcube.data.transfer.model.ExecutionReport.ExecutionReportFlag; +import org.gcube.data.transfer.model.PluginInvocation; +import org.gcube.data.transfer.plugin.AbstractPlugin; +import org.gcube.data.transfer.plugin.fails.PluginCleanupException; +import org.gcube.data.transfer.plugin.fails.PluginExecutionException; + +import lombok.extern.slf4j.Slf4j; + +@Slf4j +public class DecompressPlugin extends AbstractPlugin { + + public DecompressPlugin(PluginInvocation invocation) { + super(invocation); + } + + @Override + public void cleanup() throws PluginCleanupException { + + + } + + + + @Override + public ExecutionReport run() throws PluginExecutionException { + try{ + log.debug("Getting parameters from {} ",invocation); + Map params=invocation.getParameters(); + File source=new File(params.get(DecompressPluginFactory.SOURCE_PARAMETER)); + String destinationPath=source.getParent() +( + params.containsKey(DecompressPluginFactory.DESTINATION_PARAMETER)? File.separator+params.get(DecompressPluginFactory.DESTINATION_PARAMETER):""); + Boolean overwrite=params.containsKey(DecompressPluginFactory.OVERWRITE_DESTINATION)?Boolean.parseBoolean(params.get(DecompressPluginFactory.OVERWRITE_DESTINATION)):Boolean.FALSE; + log.trace("Unzipping {} to {} OVERWRITE= {} ",source.getAbsolutePath(),destinationPath,overwrite); + unzip(source,destinationPath,overwrite); + Boolean deleteArchive=params.containsKey(DecompressPluginFactory.DELETE_ARCHIVE)?Boolean.parseBoolean(params.get(DecompressPluginFactory.DELETE_ARCHIVE)):Boolean.FALSE; + if(deleteArchive){ + log.trace("Deleting source {}",source.getAbsolutePath()); + deleteQuietly(source); + } + return new ExecutionReport(invocation,"Successfully decompressed to "+destinationPath,ExecutionReportFlag.SUCCESS); + }catch(IOException e){ + log.error("Unable to unzip ",e); + throw new PluginExecutionException("Unable to extract content, "+e.getMessage()); + } + } + + + + public static final void unzip(File source,String destination,Boolean overwrite) throws IOException{ + log.debug("Creating destination folder {}",destination); + + File folder = new File(destination); + if(!folder.exists()){ + folder.mkdir(); + } + + log.debug("Reading zip file ",source.getAbsolutePath()); + //get the zip file content + ZipInputStream zis = + new ZipInputStream(new FileInputStream(source)); + //get the zipped file list entry + ZipEntry ze = zis.getNextEntry(); + + + byte[] buffer = new byte[1024]; + + while(ze!=null){ + + String fileName = ze.getName(); + if(fileName.endsWith(File.separator)) { + // folder + fileName=fileName.substring(0, fileName.length()-1); + + }else { + log.debug("Extracting {} ",fileName); + + String newFileBase=destination + File.separator + fileName; + File newFile = new File(newFileBase); + + int suffixCounter=1; + while(newFile.exists()){ + log.debug("File {} already exists, overwrite policy is {} ",newFile.getAbsolutePath(),overwrite); + if(overwrite){ + log.debug("Deleting existing content"); + deleteQuietly(newFile); + }else { + newFile=new File(newFileBase+"("+suffixCounter+")"); + suffixCounter++; + } + } + log.debug("Destination file is {}",newFile.getAbsolutePath()); + //create all non exists folders + //else you will hit FileNotFoundException for compressed folder + new File(newFile.getParent()).mkdirs(); + + FileOutputStream fos = new FileOutputStream(newFile); + + int len; + while ((len = zis.read(buffer)) > 0) { + fos.write(buffer, 0, len); + } + + fos.close(); + } + ze = zis.getNextEntry(); + } + + zis.closeEntry(); + zis.close(); + + + + + + + } + + + private static final boolean deleteQuietly(File path){ + if( path.exists() ) { + if(!path.isDirectory()) return path.delete(); + File[] files = path.listFiles(); + for(int i=0; i { + + static final String PLUGIN_ID="DECOMPRESS"; + + + public static final String SOURCE_PARAMETER="SOURCE_ARCHIVE"; + public static final String DESTINATION_PARAMETER="DESTINATION"; + public static final String OVERWRITE_DESTINATION="OVERWITE_DESTINATION"; + public static final String DELETE_ARCHIVE="DELETE_ARCHIVE"; + public static final String ARCHIVE_TYPE="ARCHIVE_TYPE"; + + static final Map PARAMETERS_DESCRIPTION= new HashMap(); + + static{ + PARAMETERS_DESCRIPTION.put(DESTINATION_PARAMETER, "[String value] The folder destination of uncompressed content expressed as a path relative to <"+SOURCE_PARAMETER+">. Default is same directory of <"+SOURCE_PARAMETER+">."); + PARAMETERS_DESCRIPTION.put(OVERWRITE_DESTINATION, "[Boolean value] Set true in order to overwrite <"+DESTINATION_PARAMETER+"> content. Default is false"); + PARAMETERS_DESCRIPTION.put(DELETE_ARCHIVE, "[Boolean value] Set true in order to delete <"+SOURCE_PARAMETER+"> after extracting content. Default is false"); + // PARAMETERS_DESCRIPTION.put(ARCHIVE_TYPE, "[String value] <"+SOURCE_PARAMETER+"> archive type. Supported types are : "); + + + } + + + + + @Override + public String getID() { + return PLUGIN_ID; + } + + @Override + public String getDescription() { + return String.format("Decompress a <%s> archive file to a given <%s>.",SOURCE_PARAMETER,DESTINATION_PARAMETER); + } + + @Override + public Map getParameters() { + return PARAMETERS_DESCRIPTION; + } + + @Override + public boolean init(DataTransferContext ctx) throws PluginInitializationException { + return true; + } + + @Override + public DecompressPlugin createWorker(PluginInvocation invocation) { + return new DecompressPlugin(invocation); + } + + + @Override + public PluginInvocation checkInvocation(PluginInvocation invocation,String transferredFile) throws ParameterException { + try{ + Map params=invocation.getParameters(); + if(params == null || params.isEmpty()) params=new HashMap(); + if(!params.containsKey(SOURCE_PARAMETER)) params.put(SOURCE_PARAMETER, transferredFile); + if(!params.containsKey(OVERWRITE_DESTINATION)) params.put(OVERWRITE_DESTINATION, "false"); + if(!params.containsKey(DELETE_ARCHIVE)) params.put(DELETE_ARCHIVE, "false"); + + + + File source=new File(params.get(SOURCE_PARAMETER)); + if (!source.exists()) + throw new ParameterException("Source file "+params.get(SOURCE_PARAMETER)+" not found."); + if(!source.canRead()) + throw new ParameterException("Cannot read Source file "+params.get(SOURCE_PARAMETER)+"."); + + + String destinationPath=source.getParent() +( + params.containsKey(DecompressPluginFactory.DESTINATION_PARAMETER)? File.pathSeparator+params.get(DecompressPluginFactory.DESTINATION_PARAMETER):""); + new File(destinationPath); + + + try{ + Boolean.parseBoolean(params.get(OVERWRITE_DESTINATION)); + }catch(Throwable t){ + throw new ParameterException("Unable to evaluate parameter "+OVERWRITE_DESTINATION,t); + } + + try{ + Boolean.parseBoolean(params.get(DELETE_ARCHIVE)); + }catch(Throwable t){ + throw new ParameterException("Unable to evaluate parameter "+DELETE_ARCHIVE,t); + } + invocation.setParameters(params); + return invocation; + }catch(ParameterException e){ + throw e; + }catch (Throwable t){ + throw new ParameterException ("Unable to check invocation parameters ",t); + } + + } + + + @Override + public boolean shutDown() throws PluginShutDownException { + return true; + } + +} diff --git a/src/main/resources/META-INF/services/org.gcube.data.transfer.plugin.AbstractPluginFactory b/src/main/resources/META-INF/services/org.gcube.data.transfer.plugin.AbstractPluginFactory new file mode 100644 index 0000000..bf543bd --- /dev/null +++ b/src/main/resources/META-INF/services/org.gcube.data.transfer.plugin.AbstractPluginFactory @@ -0,0 +1 @@ +org.gcube.data.transfer.plugins.decompress.DecompressPluginFactory \ No newline at end of file diff --git a/src/test/java/org/gcube/data/transfer/plugin/decompress/PluginTest.java b/src/test/java/org/gcube/data/transfer/plugin/decompress/PluginTest.java new file mode 100644 index 0000000..feefe9b --- /dev/null +++ b/src/test/java/org/gcube/data/transfer/plugin/decompress/PluginTest.java @@ -0,0 +1,36 @@ +package org.gcube.data.transfer.plugin.decompress; + +import java.io.IOException; +import java.util.HashMap; +import java.util.Map; + +import org.gcube.data.transfer.model.PluginInvocation; +import org.gcube.data.transfer.plugin.fails.ParameterException; +import org.gcube.data.transfer.plugins.decompress.DecompressPluginFactory; +import org.junit.Assert; +import org.junit.Test; + +public class PluginTest { + + @Test + public void factoryTest() throws ParameterException, IOException{ + + + + DecompressPluginFactory factory=new DecompressPluginFactory(); + Assert.assertNotNull(factory.getDescription()); + Assert.assertNotNull(factory.getID()); + Assert.assertNotNull(factory.getParameters()); + + Map params=new HashMap<>(); + params.put(DecompressPluginFactory.DESTINATION_PARAMETER, "here"); + params.put(DecompressPluginFactory.SOURCE_PARAMETER, UnzipTest.urlToFile("https://goo.gl/r5jFZ9")); + + PluginInvocation invocation=new PluginInvocation(factory.getID(), params); + + factory.checkInvocation(invocation,""); + Assert.assertNotNull(factory.createWorker(invocation)); + } + + +} diff --git a/src/test/java/org/gcube/data/transfer/plugin/decompress/UnzipTest.java b/src/test/java/org/gcube/data/transfer/plugin/decompress/UnzipTest.java new file mode 100644 index 0000000..ad2dd95 --- /dev/null +++ b/src/test/java/org/gcube/data/transfer/plugin/decompress/UnzipTest.java @@ -0,0 +1,58 @@ +package org.gcube.data.transfer.plugin.decompress; + +import java.io.File; +import java.io.FileOutputStream; +import java.io.IOException; +import java.io.InputStream; +import java.net.MalformedURLException; +import java.net.URL; +import java.net.URLConnection; +import java.util.HashMap; +import java.util.Map; + +import org.gcube.data.transfer.model.PluginInvocation; +import org.gcube.data.transfer.plugins.decompress.DecompressPluginFactory; + +public class UnzipTest { + + public static void main(String[] args) throws IOException { +// DecompressPlugin.unzip(new File("/home/fabio/workspaces/home-library-jcr-PRE-PROD.jar"), "/home/fabio/workspaces/unzips/hl", true); + + + + + Map params=new HashMap<>(); + params.put(DecompressPluginFactory.DESTINATION_PARAMETER, "here"); + params.put(DecompressPluginFactory.SOURCE_PARAMETER, urlToFile("https://goo.gl/r5jFZ9")); + PluginInvocation invocation=new PluginInvocation("", params); + + + new DecompressPluginFactory().createWorker(invocation).execute(); + + + + + } + + + public static String urlToFile(String urlString) throws IOException{ + URL url = new URL(urlString); + URLConnection connection = url.openConnection(); + InputStream in = connection.getInputStream(); + File outputFile=File.createTempFile("archive_", ".zip"); + FileOutputStream fos = new FileOutputStream(outputFile); + byte[] buf = new byte[512]; + while (true) { + int len = in.read(buf); + if (len == -1) { + break; + } + fos.write(buf, 0, len); + } + in.close(); + fos.flush(); + fos.close(); + return outputFile.getAbsolutePath(); + } + +} diff --git a/src/test/resources/log4j.properties b/src/test/resources/log4j.properties new file mode 100644 index 0000000..0bfe651 --- /dev/null +++ b/src/test/resources/log4j.properties @@ -0,0 +1,25 @@ +log4j.rootLogger=AQS +log4j.appender.A1=org.apache.log4j.RollingFileAppender +log4j.appender.A1.File=log.txt +log4j.appender.A1.layout=org.apache.log4j.PatternLayout +log4j.appender.A1.layout.ConversionPattern=%-4r [%t] %-5p %c %x - %m%n +# ***** Max file size is set to 100KB +log4j.appender.A1.MaxFileSize=100MB +# ***** Keep one backup file +log4j.appender.A1.MaxBackupIndex=1 + +#CONSOLE +#log4j.appender.stdout=org.apache.log4j.ConsoleAppender +#log4j.appender.stdout.Threshold=DEBUG +#log4j.appender.stdout.layout=org.apache.log4j.PatternLayout +#log4j.appender.stdout.layout.ConversionPattern=[%t] %-5p %c %d{dd MMM yyyy ;HH:mm:ss.SSS} - %m%n + +#CONSOLE-TOOLS +log4j.logger.org.gcube=DEBUG, AQS +log4j.appender.AQS=org.apache.log4j.ConsoleAppender +log4j.appender.AQS.layout=org.apache.log4j.PatternLayout +log4j.appender.AQS.layout.ConversionPattern=%d{ISO8601} %-5p %c{2} [%t,%M:%L] %m%n + + + +