diff --git a/.settings/org.eclipse.jdt.core.prefs b/.settings/org.eclipse.jdt.core.prefs
index b8947ec..2f5cc74 100644
--- a/.settings/org.eclipse.jdt.core.prefs
+++ b/.settings/org.eclipse.jdt.core.prefs
@@ -1,6 +1,8 @@
eclipse.preferences.version=1
org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.8
org.eclipse.jdt.core.compiler.compliance=1.8
+org.eclipse.jdt.core.compiler.problem.enablePreviewFeatures=disabled
org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning
+org.eclipse.jdt.core.compiler.problem.reportPreviewFeatures=ignore
org.eclipse.jdt.core.compiler.release=disabled
org.eclipse.jdt.core.compiler.source=1.8
diff --git a/CHANGELOG.md b/CHANGELOG.md
new file mode 100644
index 0000000..8b787fc
--- /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-access.sh-fuse-integration
+
+## Unreleased [v1.1.0-SNAPSHOT] 2020-09-07
+
+### Fixes
+
+- Solved issue on data download (https://support.d4science.org/issues/19651)
diff --git a/FUNDING.md b/FUNDING.md
new file mode 100644
index 0000000..6fa9eac
--- /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);
\ No newline at end of file
diff --git a/LICENCE.md b/LICENCE.md
new file mode 100644
index 0000000..3af0507
--- /dev/null
+++ b/LICENCE.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. Any use of
+the Work, other than as authorised under this Licence is prohibited (to the
+extent such use is covered by a right of the copyright holder of the Work).
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+The Original Work is provided under the terms of this Licence when the Licensor
+(as defined below) has placed the following notice immediately following the
+copyright notice for the Original Work:
+
+Licensed under the EUPL V.1.1
+
+or has expressed by any other mean his willingness to license under the EUPL.
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+
+
+## 1. Definitions
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+In this Licence, the following terms have the following meaning:
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+- The Original Work or the Software: the software distributed and/or
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+- The Executable Code: any code which has generally been compiled and which is
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+ the Work under the Licence.
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+Copyleft clause: If the Licensee distributes and/or communicates copies of the
+Original Works or Derivative Works based upon the Original Work, this
+Distribution and/or Communication will be done under the terms of this Licence
+or of a later version of this Licence unless the Original Work is expressly
+distributed only under this version of the Licence. The Licensee (becoming
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+“Compatible Licence” refers to the licences listed in the appendix attached to
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+
+## 6. Chain of Authorship
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+
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+power and authority to grant the Licence.
+
+Each time You accept the Licence, the original Licensor and subsequent
+Contributors grant You a licence to their contributions to the Work, under the
+terms of this Licence.
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+
+## 7. Disclaimer of Warranty
+
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+“bugs” inherent to this type of software development.
+
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+
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+for the grant of any rights to the Work.
+
+
+
+## 8. Disclaimer of Liability
+
+Except in the cases of wilful misconduct or damages directly caused to natural
+persons, the Licensor will in no event be liable for any direct or indirect,
+material or moral, damages of any kind, arising out of the Licence or of the use
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+stoppage, computer failure or malfunction, loss of data or any commercial
+damage, even if the Licensor has been advised of the possibility of such
+damage. However, the Licensor will be liable under statutory product liability
+laws as far such laws apply to the Work.
+
+
+
+## 9. Additional agreements
+
+While distributing the Original Work or Derivative Works, You may choose to
+conclude an additional agreement to offer, and charge a fee for, acceptance of
+support, warranty, indemnity, or other liability obligations and/or services
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+by, or claims asserted against such Contributor by the fact You have accepted
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+
+
+
+## 10. Acceptance of the Licence
+
+The provisions of this Licence can be accepted by clicking on an icon “I agree”
+placed under the bottom of a window displaying the text of this Licence or by
+affirming consent in any other similar way, in accordance with the rules of
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+acceptance of this Licence and all of its terms and conditions.
+
+Similarly, you irrevocably accept this Licence and all of its terms and
+conditions by exercising any rights granted to You by Article 2 of this Licence,
+such as the use of the Work, the creation by You of a Derivative Work or the
+Distribution and/or Communication by You of the Work or copies thereof.
+
+
+
+## 11. Information to the public
+
+In case of any Distribution and/or Communication of the Work by means of
+electronic communication by You (for example, by offering to download the Work
+from a remote location) the distribution channel or media (for example, a
+website) must at least provide to the public the information requested by the
+applicable law regarding the Licensor, the Licence and the way it may be
+accessible, concluded, stored and reproduced by the Licensee.
+
+
+
+## 12. Termination of the Licence
+
+The Licence and the rights granted hereunder will terminate automatically upon
+any breach by the Licensee of the terms of the Licence.
+
+Such a termination will not terminate the licences of any person who has
+received the Work from the Licensee under the Licence, provided such persons
+remain in full compliance with the Licence.
+
+
+
+## 13. Miscellaneous
+
+Without prejudice of Article 9 above, the Licence represents the complete
+agreement between the Parties as to the Work licensed hereunder.
+
+If any provision of the Licence is invalid or unenforceable under applicable
+law, this will not affect the validity or enforceability of the Licence as a
+whole. 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
new file mode 100644
index 0000000..a6a6b05
--- /dev/null
+++ b/README.md
@@ -0,0 +1,46 @@
+StorageHub Fuse Integration
+--------------------------------------------------
+
+
+## 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
+
+## 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
index 17d7627..40239ff 100644
--- a/pom.xml
+++ b/pom.xml
@@ -4,7 +4,7 @@
4.0.0
org.gcube.data-access
sh-fuse-integration
- 1.0.2
+ 1.1.0
SHFuseIntegration
diff --git a/src/main/java/org/gcube/data/access/storagehub/fs/FileDownload.java b/src/main/java/org/gcube/data/access/storagehub/fs/FileDownload.java
index bf66f2a..c4bbde8 100644
--- a/src/main/java/org/gcube/data/access/storagehub/fs/FileDownload.java
+++ b/src/main/java/org/gcube/data/access/storagehub/fs/FileDownload.java
@@ -1,16 +1,18 @@
package org.gcube.data.access.storagehub.fs;
-import java.io.IOException;
-import java.io.InputStream;
+import java.io.BufferedInputStream;
+import java.io.File;
+import java.io.FileOutputStream;
+import java.io.RandomAccessFile;
+import java.nio.file.Files;
+import org.gcube.common.storagehub.client.StreamDescriptor;
import org.gcube.common.storagehub.client.dsl.FileContainer;
import org.gcube.common.storagehub.model.items.AbstractFileItem;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import jnr.ffi.Pointer;
-import jnr.ffi.types.off_t;
-import jnr.ffi.types.size_t;
import ru.serce.jnrfuse.ErrorCodes;
import ru.serce.jnrfuse.struct.FileStat;
@@ -18,65 +20,55 @@ public class FileDownload implements SHFile{
public static Logger logger = LoggerFactory.getLogger(FileDownload.class);
- InputStream stream;
AbstractFileItem fileItem;
-
- Object monitor = new Object();
-
- long offset = 0;
-
- public FileDownload(FileContainer fileContainer) throws Exception {
- stream = fileContainer.download().getStream();
- fileItem = fileContainer.get();
- logger.trace("FILE-DOWNLOAD initialized with {} , {}", fileItem.getName(), fileItem.getContent().getSize());
- }
-
+ File output;
- public int read(Pointer buf, long size, long offset) {
- logger.trace("{} read called with size {} and offset {} ", fileItem.getName(), size, offset);
+
+ public FileDownload(FileContainer fileContainer) throws Exception {
+ StreamDescriptor stream = fileContainer.download();
- while (this.offset!=offset) {
- logger.trace("going in wait ({},{})",this.offset, offset);
- synchronized (monitor) {
- try {
- monitor.wait();
- logger.trace("waking up!!!");
- } catch (InterruptedException e2) {
- logger.warn("interrupt exception",e2);
- }
+ output = Files.createTempFile("down", stream.getFileName()).toFile();
+ try (BufferedInputStream bi = new BufferedInputStream(stream.getStream()); FileOutputStream fo = new FileOutputStream(output)){
+ byte[] buf = new byte[2046];
+ int read = -1;
+ while ((read=bi.read(buf))!=-1) {
+ fo.write(buf, 0, read);
}
}
-
+
+
+ fileItem = fileContainer.get();
+ logger.trace("FILE-DOWNLOAD with {} , {}", fileItem.getName(), fileItem.getContent().getSize());
+ }
+
+
+
+ @Override
+ public int read(Pointer buf, long size, long offset) {
+ RandomAccessFile raf = null;
int bytesToRead = (int) (size);
-
byte[] mybuf = new byte[bytesToRead];
int readTotal= 0;
try {
-
+ raf = new RandomAccessFile(output, "r");
int read =0;
logger.trace("{} BEFORE: bytes to read {} and read total {} and last read {}", fileItem.getName(), bytesToRead, readTotal, read);
- while ((read= stream.read(mybuf, 0 , bytesToRead-readTotal))!=-1 && bytesToRead>readTotal) {
+ while ((read= raf.read(mybuf, 0 , bytesToRead-readTotal))!=-1 && bytesToRead>readTotal) {
buf.put(readTotal, mybuf, 0, read);
readTotal+= read;
logger.trace("{} INSIDE: bytes to read {} and read total {} and last read {}", fileItem.getName() , bytesToRead, readTotal, read);
}
logger.trace("{} AFTER: bytes to read {} and read total {} and last read {}", fileItem.getName() , bytesToRead, readTotal, read);
-
}catch (Exception e) {
logger.error("error in read",e);
- try {
- stream.close();
- } catch (IOException e1) {}
return -ErrorCodes.ENOENT();
} finally {
- this.offset = readTotal+offset;
- logger.trace("setting offset to {}",this.offset);
- synchronized (monitor) {
- monitor.notifyAll();
- }
+ try{
+ if (raf!=null) raf.close();
+ }catch (Exception e) {}
}
logger.trace("{} work finished!!! {}",fileItem.getName() , readTotal);
- return readTotal;
+ return readTotal;
}
@@ -84,15 +76,7 @@ public class FileDownload implements SHFile{
public synchronized int flush() {
logger.trace("called flush");
- //logger.trace("file is ready "+mapPathUpload.get(path).toString());
- try {
- stream.close();
- synchronized (monitor) {
- monitor.notifyAll();
- }
- } catch (IOException e1) {
- logger.error("error closing stream",e1);
- }
+ output.delete();
return 0;
}
@@ -108,4 +92,8 @@ public class FileDownload implements SHFile{
return 0;
}
+ public File getOutputFile(){
+ return output;
+ }
+
}
diff --git a/src/main/java/org/gcube/data/access/storagehub/fs/StorageHubFS.java b/src/main/java/org/gcube/data/access/storagehub/fs/StorageHubFS.java
index 9ed0f07..18ca3e5 100644
--- a/src/main/java/org/gcube/data/access/storagehub/fs/StorageHubFS.java
+++ b/src/main/java/org/gcube/data/access/storagehub/fs/StorageHubFS.java
@@ -1,10 +1,12 @@
package org.gcube.data.access.storagehub.fs;
+import java.io.RandomAccessFile;
import java.nio.file.Paths;
import java.util.HashMap;
import java.util.List;
import java.util.Map.Entry;
import java.util.Objects;
+import java.util.Random;
import java.util.concurrent.TimeUnit;
import org.cache2k.Cache;
@@ -308,9 +310,10 @@ public class StorageHubFS extends FuseStubFS {
tempFiles.put(path, fileDownload);
}
}
-
+
+
int toReturn = fileDownload.read(buf, size, offset);
-
+
logger.trace("!!! read ---- returning {}",toReturn);
return toReturn;