issue https://support.d4science.org/issues/19651 solved
This commit is contained in:
parent
6d83dbe878
commit
f32b19ad7b
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@ -1,6 +1,8 @@
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eclipse.preferences.version=1
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org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.8
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org.eclipse.jdt.core.compiler.compliance=1.8
|
||||
org.eclipse.jdt.core.compiler.problem.enablePreviewFeatures=disabled
|
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org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning
|
||||
org.eclipse.jdt.core.compiler.problem.reportPreviewFeatures=ignore
|
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org.eclipse.jdt.core.compiler.release=disabled
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org.eclipse.jdt.core.compiler.source=1.8
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|
|
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@ -0,0 +1,9 @@
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This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
|
||||
|
||||
# Changelog for org.gcube.data-access.sh-fuse-integration
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||||
|
||||
## Unreleased [v1.1.0-SNAPSHOT] 2020-09-07
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||||
|
||||
### Fixes
|
||||
|
||||
- Solved issue on data download (https://support.d4science.org/issues/19651)
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@ -0,0 +1,26 @@
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|||
# 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);
|
||||
|
|
@ -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).
|
||||
|
||||
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.
|
||||
|
||||
|
||||
|
||||
## 1. Definitions
|
||||
|
||||
In this Licence, the following terms have the following meaning:
|
||||
|
||||
- The Licence: this Licence.
|
||||
|
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|
||||
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|
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|
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|
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|
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- The Work: the Original Work and/or its Derivative Works.
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## 2. Scope of the rights granted by the Licence
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The Licensor hereby grants You a world-wide, royalty-free, non-exclusive,
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Those rights can be exercised on any media, supports and formats, whether now
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In the countries where moral rights apply, the Licensor waives his right to
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## 3. Communication of the Source Code
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The Licensor may provide the Work either in its Source Code form, or as
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Executable Code. If the Work is provided as Executable Code, the Licensor
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## 4. Limitations on copyright
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Nothing in this Licence is intended to deprive the Licensee of the benefits from
|
||||
any exception or limitation to the exclusive rights of the rights owners in the
|
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Original Work or Software, of the exhaustion of those rights or of other
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## 5. Obligations of the Licensee
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The grant of the rights mentioned above is subject to some restrictions and
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Attribution right: the Licensee shall keep intact all copyright, patent or
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notices stating that the Work has been modified and the date of modification.
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Copyleft clause: If the Licensee distributes and/or communicates copies of the
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Original Works or Derivative Works based upon the Original Work, this
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Distribution and/or Communication will be done under the terms of this Licence
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or of a later version of this Licence unless the Original Work is expressly
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distributed only under this version of the Licence. The Licensee (becoming
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Licensor) cannot offer or impose any additional terms or conditions on the Work
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or Derivative Work that alter or restrict the terms of the Licence.
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|
||||
Compatibility clause: If the Licensee Distributes and/or Communicates Derivative
|
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Works or copies thereof based upon both the Original Work and another work
|
||||
licensed under a Compatible Licence, this Distribution and/or Communication can
|
||||
be done under the terms of this Compatible Licence. For the sake of this clause,
|
||||
“Compatible Licence” refers to the licences listed in the appendix attached to
|
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this Licence. Should the Licensee’s obligations under the Compatible Licence
|
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conflict with his/her obligations under this Licence, the obligations of the
|
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Compatible Licence shall prevail.
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Provision of Source Code: When distributing and/or communicating copies of the
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Work, the Licensee will provide a machine-readable copy of the Source Code or
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indicate a repository where this Source will be easily and freely available for
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as long as the Licensee continues to distribute and/or communicate the Work.
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Legal Protection: This Licence does not grant permission to use the trade names,
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trademarks, service marks, or names of the Licensor, except as required for
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reasonable and customary use in describing the origin of the Work and
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reproducing the content of the copyright notice.
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|
||||
|
||||
|
||||
## 6. Chain of Authorship
|
||||
|
||||
The original Licensor warrants that the copyright in the Original Work granted
|
||||
hereunder is owned by him/her or licensed to him/her and that he/she has the
|
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power and authority to grant the Licence.
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|
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Each Contributor warrants that the copyright in the modifications he/she brings
|
||||
to the Work are owned by him/her or licensed to him/her and that he/she has the
|
||||
power and authority to grant the Licence.
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|
||||
Each time You accept the Licence, the original Licensor and subsequent
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||||
Contributors grant You a licence to their contributions to the Work, under the
|
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terms of this Licence.
|
||||
|
||||
|
||||
|
||||
## 7. Disclaimer of Warranty
|
||||
|
||||
The Work is a work in progress, which is continuously improved by numerous
|
||||
contributors. It is not a finished work and may therefore contain defects or
|
||||
“bugs” inherent to this type of software development.
|
||||
|
||||
For the above reason, the Work is provided under the Licence on an “as is” basis
|
||||
and without warranties of any kind concerning the Work, including without
|
||||
limitation merchantability, fitness for a particular purpose, absence of defects
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or errors, accuracy, non-infringement of intellectual property rights other than
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||||
copyright as stated in Article 6 of this Licence.
|
||||
|
||||
This disclaimer of warranty is an essential part of the Licence and a condition
|
||||
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,
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||||
material or moral, damages of any kind, arising out of the Licence or of the use
|
||||
of the Work, including without limitation, damages for loss of goodwill, work
|
||||
stoppage, computer failure or malfunction, loss of data or any commercial
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||||
damage, even if the Licensor has been advised of the possibility of such
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damage. However, the Licensor will be liable under statutory product liability
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laws as far such laws apply to the Work.
|
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|
||||
|
||||
|
||||
## 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
|
||||
consistent with this Licence. However, in accepting such obligations, You may
|
||||
act only on your own behalf and on your sole responsibility, not on behalf of
|
||||
the original Licensor or any other Contributor, and only if You agree to
|
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indemnify, defend, and hold each Contributor harmless for any liability incurred
|
||||
by, or claims asserted against such Contributor by the fact You have accepted
|
||||
any such warranty or additional liability.
|
||||
|
||||
|
||||
|
||||
## 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
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||||
affirming consent in any other similar way, in accordance with the rules of
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||||
applicable law. Clicking on that icon indicates your clear and irrevocable
|
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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,
|
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such as the use of the Work, the creation by You of a Derivative Work or the
|
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Distribution and/or Communication by You of the Work or copies thereof.
|
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|
||||
|
||||
|
||||
## 11. Information to the public
|
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|
||||
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
|
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from a remote location) the distribution channel or media (for example, a
|
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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.
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|
||||
|
||||
|
||||
## 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
|
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|
||||
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
|
||||
|
||||
|
|
@ -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);
|
||||
|
||||
2
pom.xml
2
pom.xml
|
|
@ -4,7 +4,7 @@
|
|||
<modelVersion>4.0.0</modelVersion>
|
||||
<groupId>org.gcube.data-access</groupId>
|
||||
<artifactId>sh-fuse-integration</artifactId>
|
||||
<version>1.0.2</version>
|
||||
<version>1.1.0</version>
|
||||
<name>SHFuseIntegration</name>
|
||||
|
||||
<parent>
|
||||
|
|
|
|||
|
|
@ -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;
|
||||
}
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -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;
|
||||
|
|
|
|||
Loading…
Reference in New Issue