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feature/19
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target
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||||
.classpath
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||||
.project
|
||||
/.DS_Store
|
||||
|
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@ -1 +0,0 @@
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/org.eclipse.jdt.core.prefs
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@ -1,6 +1,4 @@
|
|||
eclipse.preferences.version=1
|
||||
encoding//src/main/java=UTF-8
|
||||
encoding//src/main/resources=UTF-8
|
||||
encoding//src/test/java=UTF-8
|
||||
encoding//src/test/resources=UTF-8
|
||||
encoding/<project>=UTF-8
|
||||
|
|
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@ -0,0 +1,5 @@
|
|||
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.forbiddenReference=warning
|
||||
org.eclipse.jdt.core.compiler.source=1.8
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@ -1,23 +1,12 @@
|
|||
<?xml version="1.0" encoding="UTF-8"?><project-modules id="moduleCoreId" project-version="1.5.0">
|
||||
|
||||
<wb-module deploy-name="grsf-publisher-ws-1.12.1-SNAPSHOT">
|
||||
|
||||
<wb-module deploy-name="grsf-publisher-ws">
|
||||
<wb-resource deploy-path="/" source-path="/target/m2e-wtp/web-resources"/>
|
||||
|
||||
<wb-resource deploy-path="/" source-path="/src/main/webapp" tag="defaultRootSource"/>
|
||||
|
||||
<wb-resource deploy-path="/WEB-INF/classes" source-path="/src/main/java"/>
|
||||
<dependent-module archiveName="storagehub-model-1.1.0.jar" deploy-path="/WEB-INF/lib" handle="module:/resource/storagehub-model/storagehub-model">
|
||||
<dependent-module archiveName="grsf-common-library-1.0.3-SNAPSHOT.jar" deploy-path="/WEB-INF/lib" handle="module:/resource/grsf-common-library/grsf-common-library">
|
||||
<dependency-type>uses</dependency-type>
|
||||
</dependent-module>
|
||||
<dependent-module archiveName="common-gcube-calls-1.3.1-SNAPSHOT.jar" deploy-path="/WEB-INF/lib" handle="module:/resource/common-gcube-calls/common-gcube-calls">
|
||||
<dependency-type>uses</dependency-type>
|
||||
</dependent-module>
|
||||
|
||||
<property name="context-root" value="grsf-publisher-ws"/>
|
||||
|
||||
<property name="java-output-path" value="/grsf-publisher-ws/target/classes"/>
|
||||
|
||||
</wb-module>
|
||||
|
||||
</project-modules>
|
||||
|
|
139
CHANGELOG.md
139
CHANGELOG.md
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@ -1,139 +0,0 @@
|
|||
# Changelog
|
||||
|
||||
All notable changes to this project will be documented in this file.
|
||||
This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
|
||||
|
||||
## [v1.13.3]
|
||||
|
||||
- Adding support for "FAO SDG 14.4.1 Questionnaire" source [#23670]
|
||||
|
||||
|
||||
## [v1.13.2]
|
||||
|
||||
- Migrated request to social-service-client [#23679]
|
||||
- Added "Assessment Methods" as Group [#23409]
|
||||
|
||||
|
||||
## [v1.13.1]
|
||||
|
||||
- Aligned code and wiki to the new requirements [#23167]
|
||||
- Changed group assign strategy [#23211] [#23215]
|
||||
- Tag are added also to legacy records [#23216]
|
||||
- Fixed code which generated groups id from name [#23215]
|
||||
|
||||
|
||||
## [v1.13.0]
|
||||
|
||||
### Added
|
||||
|
||||
- Added support to not include in records time dependant metadata [#21995]
|
||||
|
||||
### Changed
|
||||
|
||||
- Switched dependency management to gcube-bom 2.0.0
|
||||
- Migrated code to storagehub [#21432]
|
||||
|
||||
|
||||
## [v1.12.0] - 2020-06-19
|
||||
|
||||
### Added
|
||||
|
||||
**Features**
|
||||
|
||||
- [#19166] Added support for GRSF_pre VRE with the behaviour of GRSF Admin
|
||||
|
||||
## [v1.11.0] - 2020-03-30
|
||||
|
||||
### Changed
|
||||
|
||||
- [#18293] Traceability flag is assigned only to Fishery records
|
||||
|
||||
## [v1.10.0] - 2019-11-11
|
||||
|
||||
### Changed
|
||||
|
||||
- [#17965] Tags longer than 100 characters are truncated instead of skipped
|
||||
|
||||
## [v1.9.0] - 2019-05-27
|
||||
|
||||
### Changed
|
||||
|
||||
- [#13347] refers_to can be null while publishing legacy records
|
||||
|
||||
- [#12421] Removed the non-ascii clean from extra fields
|
||||
|
||||
- [#12421] Properly supporting UTF-8 characters
|
||||
|
||||
- [#16395] Title is updated according to Stock/Fishery Name
|
||||
|
||||
## [v1.8.0] - 2019-02-26
|
||||
|
||||
### Changed
|
||||
|
||||
- [#12861] The sources in GRSF VRE are calculated using 'database_sources' field
|
||||
|
||||
## [v1.7.0] - 2018-10-10
|
||||
|
||||
### Changed
|
||||
|
||||
- [#12510] Fixed pom to exclude libraries already provided by the container
|
||||
|
||||
## [v1.6.0] - 2018-07-18
|
||||
|
||||
### Changed
|
||||
|
||||
- [#11464] Added biomass timeseries support to stock data
|
||||
- [#11749] Added 'With Similarities'-'No Similarities' tag to GRSF Records
|
||||
- [#11748] Added Tag for 'Fishing Gears' and 'Flag State' fields
|
||||
- [#11766] Added 'Connected'-'Not Connected' tag to GRSF Records
|
||||
- [#11767] Added group for SDG flag
|
||||
- [#11811] Added citation field
|
||||
- [#11832] Added sub-groups support for available time series related to GRSF Type "Assessment Unit"
|
||||
- [#11967] Added Biomass group
|
||||
- [#11968] Changed 'State and trend of Marine Resource' to 'State and Trend'
|
||||
- [#11969] Changed 'Scientific advice' to 'Scientific Advice'
|
||||
|
||||
## [v1.5.0] - 2017-01-10
|
||||
|
||||
### Changed
|
||||
|
||||
- Model enhancements
|
||||
|
||||
## [v1.4.0] - 2017-11-02
|
||||
|
||||
### Changed
|
||||
|
||||
- Some fixes and improvements: added a common library between service and management widget
|
||||
|
||||
## [v1.3.0] - 2017-08-01
|
||||
|
||||
### Changed
|
||||
|
||||
- Model upgrade
|
||||
|
||||
## [v1.2.0] - 2017-07-01
|
||||
|
||||
### Changed
|
||||
|
||||
- [#8719] Model changed
|
||||
|
||||
## [v1.1.2] - 2017-05-15
|
||||
|
||||
- [#8719] Updates for ticket
|
||||
- Minor fixes
|
||||
|
||||
## [v1.1.1] - 2017-04-02
|
||||
|
||||
- Minor fixes
|
||||
|
||||
## [v1.1.0] - 2017-02-28
|
||||
|
||||
- Model update
|
||||
|
||||
## [v1.0.1] - 2017-02-10
|
||||
|
||||
- Minor fixes
|
||||
|
||||
## [v1.0.0] - 2016-12-10
|
||||
|
||||
- First Release
|
312
LICENSE.md
312
LICENSE.md
|
@ -1,312 +0,0 @@
|
|||
# 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
|
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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
|
||||
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|
||||
|
||||
Licensed under the EUPL V.1.1
|
||||
|
||||
or has expressed by any other mean his willingness to license under the EUPL.
|
||||
|
||||
|
||||
|
||||
## 1. Definitions
|
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|
||||
In this Licence, the following terms have the following meaning:
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||||
|
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- The Licence: this Licence.
|
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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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## 3. Communication of the Source Code
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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
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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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Works or copies thereof based upon both the Original Work and another work
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Legal Protection: This Licence does not grant permission to use the trade names,
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|
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## 6. Chain of Authorship
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|
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The original Licensor warrants that the copyright in the Original Work granted
|
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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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|
||||
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|
||||
## 7. Disclaimer of Warranty
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|
||||
The Work is a work in progress, which is continuously improved by numerous
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For the above reason, the Work is provided under the Licence on an “as is” basis
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This disclaimer of warranty is an essential part of the Licence and a condition
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||||
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||||
|
||||
|
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## 8. Disclaimer of Liability
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|
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Except in the cases of wilful misconduct or damages directly caused to natural
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|
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## 9. Additional agreements
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|
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While distributing the Original Work or Derivative Works, You may choose to
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|
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## 10. Acceptance of the Licence
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|
||||
The provisions of this Licence can be accepted by clicking on an icon “I agree”
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Similarly, you irrevocably accept this Licence and all of its terms and
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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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|
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In case of any Distribution and/or Communication of the Work by means of
|
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|
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|
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accessible, concluded, stored and reproduced by the Licensee.
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|
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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.
|
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|
||||
Such a termination will not terminate the licences of any person who has
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|
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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.
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|
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If any provision of the Licence is invalid or unenforceable under applicable
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|
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|
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|
||||
The European Commission may publish other linguistic versions and/or new
|
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|
||||
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|
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|
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All linguistic versions of this Licence, approved by the European Commission,
|
||||
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||||
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|
||||
|
||||
|
||||
|
||||
## 14. Jurisdiction
|
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|
||||
Any litigation resulting from the interpretation of this License, arising
|
||||
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|
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|
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|
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|
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|
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|
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|
||||
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|
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|
||||
|
||||
|
||||
## 15. Applicable Law
|
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|
||||
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
|
||||
|
69
README.md
69
README.md
|
@ -1,69 +0,0 @@
|
|||
# GRSF Publisher Service
|
||||
|
||||
This service allows any client to publish on GRSF Catalogue.
|
||||
|
||||
## Built With
|
||||
|
||||
* [OpenJDK](https://openjdk.java.net/) - The JDK used
|
||||
* [Maven](https://maven.apache.org/) - Dependency Management
|
||||
|
||||
## Documentation
|
||||
|
||||
[GRSF Publisher Service](https://wiki.gcube-system.org/gcube/GCube_Data_Catalogue_for_GRSF)
|
||||
|
||||
## Change log
|
||||
|
||||
See [Releases](https://code-repo.d4science.org/gCubeSystem/grsf-publisher-ws/releases).
|
||||
|
||||
## Authors
|
||||
|
||||
* **Luca Frosini** ([ORCID](https://orcid.org/0000-0003-3183-2291)) - [ISTI-CNR Infrascience Group](http://nemis.isti.cnr.it/groups/infrascience)
|
||||
|
||||
## How to Cite this Software
|
||||
|
||||
Tell people how to cite this software.
|
||||
* Cite an associated paper?
|
||||
* Use a specific BibTeX entry for the software?
|
||||
|
||||
|
||||
@Manual{,
|
||||
title = {GRSF Publisher Service},
|
||||
author = {{Perciante, Costantino}, {Frosini, Luca}},
|
||||
organization = {ISTI - CNR},
|
||||
address = {Pisa, Italy},
|
||||
year = 2019,
|
||||
url = {http://www.gcube-system.org/}
|
||||
}
|
||||
|
||||
## 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);
|
|
@ -0,0 +1 @@
|
|||
${gcube.license}
|
|
@ -0,0 +1,62 @@
|
|||
The gCube System - ${name}
|
||||
--------------------------------------------------
|
||||
|
||||
${description}
|
||||
|
||||
|
||||
${gcube.description}
|
||||
|
||||
${gcube.funding}
|
||||
|
||||
|
||||
Version
|
||||
--------------------------------------------------
|
||||
|
||||
${version} (${buildDate})
|
||||
|
||||
Please see the file named "changelog.xml" in this directory for the release notes.
|
||||
|
||||
|
||||
Authors
|
||||
--------------------------------------------------
|
||||
|
||||
* Costantino Perciante (costantino.perciante-AT-isti.cnr.it), Istituto di Scienza e Tecnologie dell'Informazione "A. Faedo" - CNR, Pisa (Italy).
|
||||
|
||||
Maintainers
|
||||
-----------
|
||||
|
||||
* Costantino Perciante (costantino.perciante-AT-isti.cnr.it), Istituto di Scienza e Tecnologie dell'Informazione "A. Faedo" - CNR, Pisa (Italy).
|
||||
|
||||
Download information
|
||||
--------------------------------------------------
|
||||
|
||||
Source code is available from SVN:
|
||||
${scm.url}
|
||||
|
||||
Binaries can be downloaded from the gCube website:
|
||||
${gcube.website}
|
||||
|
||||
|
||||
Installation
|
||||
--------------------------------------------------
|
||||
|
||||
Installation documentation is available on-line in the gCube Wiki:
|
||||
${gcube.wikiRoot}
|
||||
|
||||
Documentation
|
||||
--------------------------------------------------
|
||||
|
||||
Documentation is available on-line in the gCube Wiki:
|
||||
${gcube.wikiRoot}
|
||||
|
||||
Support
|
||||
--------------------------------------------------
|
||||
|
||||
Bugs and support requests can be reported in the gCube issue tracking tool:
|
||||
${gcube.issueTracking}
|
||||
|
||||
|
||||
Licensing
|
||||
--------------------------------------------------
|
||||
|
||||
This software is licensed under the terms you may find in the file named "LICENSE" in this directory.
|
|
@ -13,10 +13,10 @@
|
|||
<outputDirectory>/</outputDirectory>
|
||||
<useDefaultExcludes>true</useDefaultExcludes>
|
||||
<includes>
|
||||
<include>LICENSE.md</include>
|
||||
<include>README.md</include>
|
||||
<include>CHANGELOG.md</include>
|
||||
<include>gcube-app.xml</include>
|
||||
<include>README</include>
|
||||
<include>LICENSE</include>
|
||||
<include>changelog.xml</include>
|
||||
<include>profile.xml</include>
|
||||
</includes>
|
||||
<fileMode>755</fileMode>
|
||||
<filtered>true</filtered>
|
|
@ -0,0 +1,25 @@
|
|||
<?xml version="1.0" encoding="UTF-8"?>
|
||||
<Resource xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
|
||||
<ID></ID>
|
||||
<Type>Library</Type>
|
||||
<Profile>
|
||||
<Description>${description}</Description>
|
||||
<Class>DataCatalogue</Class>
|
||||
<Name>${artifactId}</Name>
|
||||
<Version>1.0.0</Version>
|
||||
<Packages>
|
||||
<Software>
|
||||
<Name>${artifactId}</Name>
|
||||
<Version>${version}</Version>
|
||||
<MavenCoordinates>
|
||||
<groupId>${groupId}</groupId>
|
||||
<artifactId>${artifactId}</artifactId>
|
||||
<version>${version}</version>
|
||||
</MavenCoordinates>
|
||||
<Files>
|
||||
<File>${build.finalName}.war</File>
|
||||
</Files>
|
||||
</Software>
|
||||
</Packages>
|
||||
</Profile>
|
||||
</Resource>
|
|
@ -1,10 +0,0 @@
|
|||
<?xml version="1.0" encoding="UTF-8"?>
|
||||
<!DOCTYPE xml>
|
||||
<application mode='online'>
|
||||
<name>GRSFPublisher</name>
|
||||
<group>Data-Catalogue</group>
|
||||
<version>${project.version}</version>
|
||||
<description>${project.description}</description>
|
||||
<local-persistence location='target' />
|
||||
</application>
|
||||
|
125
pom.xml
125
pom.xml
|
@ -11,7 +11,7 @@
|
|||
|
||||
<groupId>org.gcube.data-catalogue</groupId>
|
||||
<artifactId>grsf-publisher-ws</artifactId>
|
||||
<version>1.13.3</version>
|
||||
<version>1.12.0</version>
|
||||
<packaging>war</packaging>
|
||||
<name>grsf-publisher-ws</name>
|
||||
<description>Utility library to publish GRSF products on GRSF catalogue.</description>
|
||||
|
@ -19,14 +19,12 @@
|
|||
<properties>
|
||||
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
|
||||
<version.jersey>2.22.4</version.jersey>
|
||||
<version.jackson>2.8.11</version.jackson>
|
||||
<version.jackson>2.6.0</version.jackson>
|
||||
<distroDirectory>${project.basedir}/distro</distroDirectory>
|
||||
<webappDirectory>${project.build.directory}/${project.build.finalName}</webappDirectory>
|
||||
<distroDirectory>distro</distroDirectory>
|
||||
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
|
||||
<jsoup.version>1.10.1</jsoup.version>
|
||||
<serviceClass>DataPublishing</serviceClass>
|
||||
<maven.compiler.release>8</maven.compiler.release>
|
||||
</properties>
|
||||
|
||||
<scm>
|
||||
|
@ -37,10 +35,17 @@
|
|||
|
||||
<dependencyManagement>
|
||||
<dependencies>
|
||||
<dependency>
|
||||
<groupId>org.gcube.distribution</groupId>
|
||||
<artifactId>gcube-bom</artifactId>
|
||||
<version>1.3.1</version>
|
||||
<type>pom</type>
|
||||
<scope>import</scope>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>org.gcube.distribution</groupId>
|
||||
<artifactId>gcube-smartgears-bom</artifactId>
|
||||
<version>2.2.0</version>
|
||||
<version>1.0.2</version>
|
||||
<type>pom</type>
|
||||
<scope>import</scope>
|
||||
</dependency>
|
||||
|
@ -51,16 +56,7 @@
|
|||
<dependency>
|
||||
<groupId>org.gcube.data-catalogue</groupId>
|
||||
<artifactId>grsf-common-library</artifactId>
|
||||
<version>[2.0.0, 3.0.0-SNAPSHOT)</version>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>org.gcube.common</groupId>
|
||||
<artifactId>storagehub-client-library</artifactId>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>org.gcube.social-networking</groupId>
|
||||
<artifactId>social-service-client</artifactId>
|
||||
<version>[1.0.0, 2.0.0-SNAPSHOT)</version>
|
||||
<version>[1-0-0-SNAPSHOT, 2.0.0-SNAPSHOT)</version>
|
||||
</dependency>
|
||||
<!-- jsoup HTML parser library @ http://jsoup.org/ -->
|
||||
<dependency>
|
||||
|
@ -110,7 +106,12 @@
|
|||
<artifactId>authorization-client</artifactId>
|
||||
<scope>provided</scope>
|
||||
</dependency>
|
||||
|
||||
<dependency>
|
||||
<groupId>org.gcube.common</groupId>
|
||||
<artifactId>home-library-jcr</artifactId>
|
||||
<version>[2.0.0-SNAPSHOT, 3.0.0-SNAPSHOT)</version>
|
||||
<scope>compile</scope>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>org.gcube.common</groupId>
|
||||
<artifactId>common-authorization</artifactId>
|
||||
|
@ -119,26 +120,32 @@
|
|||
<dependency>
|
||||
<groupId>org.glassfish.jersey.containers</groupId>
|
||||
<artifactId>jersey-container-servlet-core</artifactId>
|
||||
<version>${version.jersey}</version>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>org.glassfish.jersey.media</groupId>
|
||||
<artifactId>jersey-media-json-jackson</artifactId>
|
||||
<version>${version.jersey}</version>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>org.glassfish.jersey.media</groupId>
|
||||
<artifactId>jersey-media-json-processing</artifactId>
|
||||
<version>${version.jersey}</version>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>org.glassfish.jersey.media</groupId>
|
||||
<artifactId>jersey-media-multipart</artifactId>
|
||||
<version>${version.jersey}</version>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>org.glassfish.jersey.media</groupId>
|
||||
<artifactId>jersey-media-sse</artifactId>
|
||||
<version>${version.jersey}</version>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>org.glassfish.jersey.ext</groupId>
|
||||
<artifactId>jersey-bean-validation</artifactId>
|
||||
<version>${version.jersey}</version>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>javax.servlet</groupId>
|
||||
|
@ -156,37 +163,99 @@
|
|||
<artifactId>jackson-jaxrs-json-provider</artifactId>
|
||||
<version>${version.jackson}</version>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>com.fasterxml.jackson.core</groupId>
|
||||
<artifactId>jackson-databind</artifactId>
|
||||
<scope>provided</scope>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>com.fasterxml.jackson.core</groupId>
|
||||
<artifactId>jackson-annotations</artifactId>
|
||||
<scope>provided</scope>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>com.fasterxml.jackson.core</groupId>
|
||||
<artifactId>jackson-core</artifactId>
|
||||
<scope>provided</scope>
|
||||
</dependency>
|
||||
<!-- SmartGears -->
|
||||
<dependency>
|
||||
<groupId>org.gcube.core</groupId>
|
||||
<artifactId>common-smartgears</artifactId>
|
||||
<scope>provided</scope>
|
||||
</dependency>
|
||||
|
||||
<dependency>
|
||||
<groupId>org.gcube.common</groupId>
|
||||
<artifactId>home-library</artifactId>
|
||||
<version>[2.0.0-SNAPSHOT, 3.0.0-SNAPSHOT)</version>
|
||||
<scope>compile</scope>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>org.glassfish.jersey.test-framework.providers</groupId>
|
||||
<artifactId>jersey-test-framework-provider-jetty</artifactId>
|
||||
<version>2.23.2</version>
|
||||
<scope>test</scope>
|
||||
</dependency>
|
||||
|
||||
<!-- Added to support Java 11 JDK -->
|
||||
<dependency>
|
||||
<groupId>org.projectlombok</groupId>
|
||||
<artifactId>lombok</artifactId>
|
||||
<scope>provided</scope>
|
||||
</dependency>
|
||||
<!-- END Added to support Java 11 JDK -->
|
||||
</dependencies>
|
||||
|
||||
<build>
|
||||
<finalName>${name}</finalName>
|
||||
<plugins>
|
||||
<plugin>
|
||||
<groupId>org.apache.maven.plugins</groupId>
|
||||
<artifactId>maven-assembly-plugin</artifactId>
|
||||
<artifactId>maven-war-plugin</artifactId>
|
||||
<version>2.1.1</version>
|
||||
<executions>
|
||||
<execution>
|
||||
<id>make-servicearchive</id>
|
||||
<phase>package</phase>
|
||||
<phase>compile</phase>
|
||||
</execution>
|
||||
</executions>
|
||||
<configuration>
|
||||
<webappDirectory>${webappDirectory}</webappDirectory>
|
||||
</configuration>
|
||||
</plugin>
|
||||
<!-- SA Plugin -->
|
||||
<plugin>
|
||||
<groupId>org.apache.maven.plugins</groupId>
|
||||
<artifactId>maven-assembly-plugin</artifactId>
|
||||
<configuration>
|
||||
<descriptors>
|
||||
<descriptor>${distroDirectory}/descriptor.xml</descriptor>
|
||||
</descriptors>
|
||||
</configuration>
|
||||
<executions>
|
||||
<execution>
|
||||
<id>servicearchive</id>
|
||||
<phase>install</phase>
|
||||
<goals>
|
||||
<goal>single</goal>
|
||||
</goals>
|
||||
</execution>
|
||||
</executions>
|
||||
</plugin>
|
||||
<plugin>
|
||||
<groupId>org.apache.maven.plugins</groupId>
|
||||
<artifactId>maven-resources-plugin</artifactId>
|
||||
<version>2.5</version>
|
||||
<executions>
|
||||
<execution>
|
||||
<id>copy-profile</id>
|
||||
<phase>install</phase>
|
||||
<goals>
|
||||
<goal>copy-resources</goal>
|
||||
</goals>
|
||||
<configuration>
|
||||
<outputDirectory>target</outputDirectory>
|
||||
<resources>
|
||||
<resource>
|
||||
<directory>${distroDirectory}</directory>
|
||||
<filtering>true</filtering>
|
||||
<includes>
|
||||
<include>profile.xml</include>
|
||||
</includes>
|
||||
</resource>
|
||||
</resources>
|
||||
</configuration>
|
||||
</execution>
|
||||
</executions>
|
||||
</plugin>
|
||||
|
|
|
@ -21,8 +21,8 @@ public @interface Group {
|
|||
String condition() default "";
|
||||
|
||||
/**
|
||||
* If this value is set, it is used as name of the group in place of the filed value.
|
||||
* (apart the source, i.e. "grsf", "ram", "firms", "fishsource" that will be prepended depending on prependSourceToGroupName)
|
||||
* If this value is set, it is the name of the group (apart the source, i.e. "grsf", "ram", "firms", "fishsource" that will be prepended) to which the
|
||||
* record needs to be put.
|
||||
* @return
|
||||
*/
|
||||
String groupNameOverValue() default "";
|
||||
|
@ -32,6 +32,6 @@ public @interface Group {
|
|||
* Set to false to avoid source prepending
|
||||
* @return
|
||||
*/
|
||||
boolean prependSourceToGroupName() default false;
|
||||
boolean prependSourceToGroupName() default true;
|
||||
|
||||
}
|
||||
|
|
|
@ -202,18 +202,12 @@ public abstract class Base {
|
|||
|
||||
@Override
|
||||
public String toString() {
|
||||
return "Base ["
|
||||
+ "catalogId=" + catalogId
|
||||
+ ", description=" + description
|
||||
+ ", license=" + license
|
||||
+ ", author=" + author
|
||||
+ ", authorContact=" + authorContact
|
||||
+ ", version=" + version
|
||||
+ ", maintainer=" + maintainer
|
||||
+ ", maintainerContact=" + maintainerContact
|
||||
+ ", extrasFields=" + extrasFields
|
||||
+ ", extrasResources=" + extrasResources
|
||||
+ "]";
|
||||
return "Base [catalogId=" + catalogId + ", description=" + description
|
||||
+ ", license=" + license + ", author=" + author
|
||||
+ ", authorContact=" + authorContact + ", version=" + version
|
||||
+ ", maintainer=" + maintainer + ", maintainerContact="
|
||||
+ maintainerContact + ", extrasFields=" + extrasFields
|
||||
+ ", extrasResources=" + extrasResources + "]";
|
||||
}
|
||||
|
||||
}
|
|
@ -35,7 +35,6 @@ public abstract class Common extends Base {
|
|||
private List<String> dataOwner;
|
||||
|
||||
@JsonProperty(Constants.DATABASE_SOURCES_JSON_KEY)
|
||||
@CustomField(key=Constants.DATABASE_SOURCES_CUSTOM_KEY)
|
||||
@CkanResource
|
||||
@Valid
|
||||
private List<Resource<Sources>> databaseSources;
|
||||
|
@ -55,7 +54,7 @@ public abstract class Common extends Base {
|
|||
|
||||
@JsonProperty(Constants.SDG_FLAG_JSON_KEY)
|
||||
@CustomField(key=Constants.SDG_FLAG_CUSTOM_KEY)
|
||||
@Group(condition="true", groupNameOverValue=Constants.SDG_FLAG_GROUP_NAME, prependSourceToGroupName=false) // record is added to group grsf-sdg-flag if sdg Flag is true
|
||||
@Group(condition="true", groupNameOverValue=Constants.SDG_FLAG_GROUP_NAME) // record is added to group grsf-sdg-flag if sdg Flag is true
|
||||
private Boolean sdgFlag;
|
||||
|
||||
@JsonProperty(Constants.STATUS_OF_THE_GRSF_RECORD_JSON_KEY)
|
||||
|
@ -89,6 +88,10 @@ public abstract class Common extends Base {
|
|||
@CustomField(key=Constants.SIMILAR_GRSF_RECORDS_CUSTOM_KEY)
|
||||
private List<SimilarRecordBean> similarGRSFRecords;
|
||||
|
||||
@JsonProperty(Constants.SIMILAR_SOURCE_RECORDS_JSON_KEY)
|
||||
@CustomField(key=Constants.SIMILAR_SOURCE_RECORDS_CUSTOM_KEY)
|
||||
private List<SimilarRecordBean> similarSourceRecords;
|
||||
|
||||
// automatically set
|
||||
@CustomField(key=Constants.DOMAIN_CUSTOM_KEY)
|
||||
private String domain;
|
||||
|
@ -111,10 +114,6 @@ public abstract class Common extends Base {
|
|||
@CustomField(key=Constants.CONNECTED_CUSTOM_KEY)
|
||||
private List<String> connectedBeans;
|
||||
|
||||
@JsonProperty(Constants.CONNECTIONS_INDICATOR)
|
||||
@Tag
|
||||
private String connectionsIndicator;
|
||||
|
||||
@JsonProperty(Constants.ANNOTATION_PUBLISHER_JSON_KEY)
|
||||
@CustomField(key=Constants.ANNOTATION_PUBLISHER_CUSTOM_KEY)
|
||||
private List<AnnotationBean> annotations;
|
||||
|
@ -123,6 +122,10 @@ public abstract class Common extends Base {
|
|||
@Tag
|
||||
private String similaritiesIndicator;
|
||||
|
||||
@JsonProperty(Constants.CONNECTIONS_INDICATOR)
|
||||
@Tag
|
||||
private String connectionsIndicator;
|
||||
|
||||
@JsonProperty(Constants.CITATION_JSON_KEY)
|
||||
@CustomField(key=Constants.CITATION_CUSTOM_KEY)
|
||||
private String citation;
|
||||
|
@ -177,6 +180,7 @@ public abstract class Common extends Base {
|
|||
this.landings = landings;
|
||||
this.species = species;
|
||||
this.similarGRSFRecords = similarGRSFRecords;
|
||||
this.similarSourceRecords = similarSourceRecords;
|
||||
this.domain = domain;
|
||||
this.uuid = uuid;
|
||||
this.managementBodyAuthorities = managementBodyAuthorities;
|
||||
|
@ -224,7 +228,6 @@ public abstract class Common extends Base {
|
|||
public void setRefersTo(List<RefersToBean> refersTo) {
|
||||
this.refersTo = refersTo;
|
||||
}
|
||||
|
||||
public List<Resource<Sources>> getDatabaseSources() {
|
||||
return databaseSources;
|
||||
}
|
||||
|
@ -297,6 +300,14 @@ public abstract class Common extends Base {
|
|||
this.similarGRSFRecords = similarGRSFRecords;
|
||||
}
|
||||
|
||||
public List<SimilarRecordBean> getSimilarSourceRecords() {
|
||||
return similarSourceRecords;
|
||||
}
|
||||
|
||||
public void setSimilarSourceRecords(List<SimilarRecordBean> similarSourceRecords) {
|
||||
this.similarSourceRecords = similarSourceRecords;
|
||||
}
|
||||
|
||||
public String getSpatial() {
|
||||
return spatial;
|
||||
}
|
||||
|
@ -356,28 +367,17 @@ public abstract class Common extends Base {
|
|||
|
||||
@Override
|
||||
public String toString() {
|
||||
return super.toString() + " - Common ["
|
||||
+ " dataOwner=" + dataOwner
|
||||
+ ", databaseSources=" + databaseSources
|
||||
+ ", sourceOfInformation=" + sourceOfInformation
|
||||
+ ", refersTo=" + refersTo
|
||||
+ ", shortName=" + shortName
|
||||
+ ", sdgFlag=" + sdgFlag
|
||||
+ ", status=" + status
|
||||
+ ", systemType=" + systemType
|
||||
+ ", catches=" + catches
|
||||
+ ", landings=" + landings
|
||||
+ ", species=" + species
|
||||
return "Common [dataOwner=" + dataOwner + ", databaseSources="
|
||||
+ databaseSources + ", sourceOfInformation="
|
||||
+ sourceOfInformation + ", refersTo=" + refersTo
|
||||
+ ", shortName=" + shortName + ", sdgFlag=" + sdgFlag + ", status="
|
||||
+ status + ", systemType=" + systemType + ", catches="
|
||||
+ catches + ", landings=" + landings + ", species=" + species
|
||||
+ ", similarGRSFRecords=" + similarGRSFRecords
|
||||
+ ", domain=" + domain
|
||||
+ ", uuid=" + uuid
|
||||
+ ", similarSourceRecords=" + similarSourceRecords
|
||||
+ ", domain=" + domain + ", uuid=" + uuid
|
||||
+ ", managementBodyAuthorities=" + managementBodyAuthorities
|
||||
+ ", spatial=" + spatial
|
||||
+ ", connectedBeans=" + connectedBeans
|
||||
+ ", annotations=" + annotations
|
||||
+ ", similaritiesIndicator=" + similaritiesIndicator
|
||||
+ ", connectionsIndicator=" + connectionsIndicator
|
||||
+ ", citation=" + citation
|
||||
+ "]";
|
||||
+ ", spatial=" + spatial + ", connectedBeans=" + connectedBeans
|
||||
+ ", annotations=" + annotations + "]";
|
||||
}
|
||||
}
|
|
@ -21,35 +21,38 @@ import com.fasterxml.jackson.annotation.JsonProperty;
|
|||
*/
|
||||
public class FisheryRecord extends Common {
|
||||
|
||||
@JsonProperty(Constants.TRACEABILITY_FLAG_JSON_KEY)
|
||||
@CustomField(key=Constants.TRACEABILITY_FLAG_CUSTOM_KEY)
|
||||
@Group(condition="true", groupNameOverValue=Constants.TRACEABILITY_FLAG_GROUP_NAME) // record is added to group grsf-traceability-flag if Traceability Flag is true
|
||||
private Boolean traceabilityFlag;
|
||||
|
||||
@JsonProperty(Constants.FISHERY_NAME_JSON_KEY)
|
||||
@CustomField(key=Constants.FISHERY_NAME_CUSTOM_KEY)
|
||||
@NotNull(message="fishery_name cannot be null")
|
||||
@Size(min=1, message="fishery_name cannot be empty")
|
||||
@CustomField(key=Constants.FISHERY_NAME_CUSTOM_KEY)
|
||||
private String fisheryName;
|
||||
|
||||
@JsonProperty(Constants.GRSF_SEMANTIC_IDENTIFIER_JSON_KEY)
|
||||
@CustomField(key=Constants.GRSF_SEMANTIC_IDENTIFIER_CUSTOM_KEY)
|
||||
private String fisheryId;
|
||||
|
||||
@JsonProperty(Constants.TRACEABILITY_FLAG_JSON_KEY)
|
||||
@CustomField(key=Constants.TRACEABILITY_FLAG_CUSTOM_KEY)
|
||||
@Group(condition="true", groupNameOverValue=Constants.TRACEABILITY_FLAG_GROUP_NAME, prependSourceToGroupName=false) // record is added to group grsf-traceability-flag if Traceability Flag is true
|
||||
private Boolean traceabilityFlag;
|
||||
|
||||
@JsonProperty(Constants.FISHING_AREA_JSON_KEY)
|
||||
@CustomField(key=Constants.FISHING_AREA_CUSTOM_KEY)
|
||||
@Tag
|
||||
private List<String> fishingArea;
|
||||
|
||||
@JsonProperty(Constants.JURISDICTION_AREA_JSON_KEY)
|
||||
@CustomField(key=Constants.JURISDICTION_AREA_CUSTOM_KEY)
|
||||
@Tag
|
||||
private List<String> jurisdictionArea;
|
||||
|
||||
@JsonProperty(Constants.RESOURCES_EXPLOITED_JSON_KEY)
|
||||
@CustomField(key=Constants.RESOURCES_EXPLOITED_CUSTOM_KEY)
|
||||
private List<String> resourcesExploited;
|
||||
|
||||
@JsonProperty(Constants.JURISDICTION_AREA_JSON_KEY)
|
||||
@CustomField(key=Constants.JURISDICTION_AREA_CUSTOM_KEY)
|
||||
private List<String> jurisdictionArea;
|
||||
|
||||
@JsonProperty(Constants.PRODUCTION_SYSTEM_TYPE_JSON_KEY)
|
||||
@CustomField(key=Constants.PRODUCTION_SYSTEM_TYPE_CUSTOM_KEY)
|
||||
private List<Production_System_Type> productionSystemType;
|
||||
|
||||
@JsonProperty(Constants.FLAG_STATE_JSON_KEY)
|
||||
@CustomField(key=Constants.FLAG_STATE_CUSTOM_KEY)
|
||||
@Tag
|
||||
|
@ -62,6 +65,7 @@ public class FisheryRecord extends Common {
|
|||
|
||||
@JsonProperty(Constants.GRSF_TYPE_JSON_KEY)
|
||||
@CustomField(key=Constants.GRSF_TYPE_CUSTOM_KEY)
|
||||
@Group
|
||||
@Tag
|
||||
private Fishery_Type type;
|
||||
|
||||
|
@ -93,6 +97,7 @@ public class FisheryRecord extends Common {
|
|||
this.fishingArea = fishingArea;
|
||||
this.resourcesExploited = resourcesExploited;
|
||||
this.jurisdictionArea = jurisdictionArea;
|
||||
this.productionSystemType = productionSystemType;
|
||||
this.flagState = flagState;
|
||||
this.fishingGear = fishingGear;
|
||||
this.type = type;
|
||||
|
@ -160,6 +165,15 @@ public class FisheryRecord extends Common {
|
|||
this.resourcesExploited = resourcesExploited;
|
||||
}
|
||||
|
||||
public List<Production_System_Type> getProductionSystemType() {
|
||||
return productionSystemType;
|
||||
}
|
||||
|
||||
public void setProductionSystemType(
|
||||
List<Production_System_Type> productionSystemType) {
|
||||
this.productionSystemType = productionSystemType;
|
||||
}
|
||||
|
||||
public List<String> getFlagState() {
|
||||
return flagState;
|
||||
}
|
||||
|
@ -183,6 +197,7 @@ public class FisheryRecord extends Common {
|
|||
+ ", traceabilityFlag=" + traceabilityFlag
|
||||
+ ", resourcesExploited=" + resourcesExploited
|
||||
+ ", jurisdictionArea=" + jurisdictionArea
|
||||
+ ", productionSystemType=" + productionSystemType
|
||||
+ ", flagState=" + flagState + ", fishingGear=" + fishingGear
|
||||
+ ", type=" + type + "]";
|
||||
}
|
||||
|
|
|
@ -26,9 +26,9 @@ import com.fasterxml.jackson.annotation.JsonProperty;
|
|||
public class StockRecord extends Common{
|
||||
|
||||
@JsonProperty(Constants.STOCK_NAME_JSON_KEY)
|
||||
@CustomField(key=Constants.STOCK_NAME_CUSTOM_KEY)
|
||||
@NotNull(message=Constants.STOCK_NAME_JSON_KEY + " cannot be null")
|
||||
@Size(min=2, message=Constants.STOCK_NAME_JSON_KEY + " cannot be empty")
|
||||
@CustomField(key=Constants.STOCK_NAME_CUSTOM_KEY)
|
||||
private String stockName;
|
||||
|
||||
@JsonProperty(Constants.GRSF_SEMANTIC_IDENTIFIER_JSON_KEY)
|
||||
|
@ -46,7 +46,6 @@ public class StockRecord extends Common{
|
|||
|
||||
@JsonProperty(Constants.ASSESSMENT_METHODS_JSON_KEY)
|
||||
@CustomField(key=Constants.ASSESSMENT_METHODS_CUSTOM_KEY)
|
||||
@Group(groupNameOverValue=Constants.ASSESSMENT_METHODS_CUSTOM_KEY, prependSourceToGroupName=false)
|
||||
private List<String> assessmentMethods;
|
||||
|
||||
@JsonProperty(Constants.FIRMS_ABUNDANCE_LEVEL_JSON_KEY)
|
||||
|
@ -100,9 +99,8 @@ public class StockRecord extends Common{
|
|||
|
||||
@JsonProperty(Constants.SCIENTIFIC_ADVICE_JSON_KEY)
|
||||
@CustomField(key=Constants.SCIENTIFIC_ADVICE_CUSTOM_KEY)
|
||||
@TimeSeries
|
||||
@Group(groupNameOverValue=Constants.SCIENTIFIC_ADVICE_CUSTOM_KEY, prependSourceToGroupName=false)
|
||||
private List<TimeSeriesBean<String, Void>> scientificAdvice;
|
||||
private List<String> scientificAdvice;
|
||||
|
||||
@JsonProperty(Constants.ASSESSOR_JSON_KEY)
|
||||
@CustomField(key=Constants.ASSESSOR_CUSTOM_KEY)
|
||||
|
@ -110,6 +108,7 @@ public class StockRecord extends Common{
|
|||
|
||||
@JsonProperty(Constants.GRSF_TYPE_JSON_KEY)
|
||||
@CustomField(key=Constants.GRSF_TYPE_CUSTOM_KEY)
|
||||
@Group
|
||||
@Tag
|
||||
private Stock_Type type;
|
||||
|
||||
|
@ -147,7 +146,7 @@ public class StockRecord extends Common{
|
|||
List<TimeSeriesBean<String, String>> fishingPressure,
|
||||
List<TimeSeriesBean<String, Void>> narrativeState,
|
||||
List<TimeSeriesBean<String, Void>> faoState,
|
||||
List<TimeSeriesBean<String, Void>> scientificAdvice, String assessor, Stock_Type type) {
|
||||
List<String> scientificAdvice, String assessor, Stock_Type type) {
|
||||
super();
|
||||
this.stockName = stockName;
|
||||
this.stockId = stockId;
|
||||
|
@ -263,11 +262,11 @@ public class StockRecord extends Common{
|
|||
this.narrativeState = narrativeState;
|
||||
}
|
||||
|
||||
public List<TimeSeriesBean<String, Void>> getScientificAdvice() {
|
||||
public List<String> getScientificAdvice() {
|
||||
return scientificAdvice;
|
||||
}
|
||||
|
||||
public void setScientificAdvice(List<TimeSeriesBean<String, Void>> scientificAdvice) {
|
||||
public void setScientificAdvice(List<String> scientificAdvice) {
|
||||
this.scientificAdvice = scientificAdvice;
|
||||
}
|
||||
|
||||
|
|
|
@ -51,7 +51,7 @@ import eu.trentorise.opendata.jackan.model.CkanDataset;
|
|||
* @author Costantino Perciante (ISTI - CNR)
|
||||
* @author Luca Frosini (ISTI - CNR)
|
||||
*/
|
||||
@Path("{source:firms|FIRMS|grsf|GRSF|FishSource|fishsource|sdg|SDG}/fishery/")
|
||||
@Path("{source:firms|FIRMS|grsf|GRSF|FishSource|fishsource}/fishery/")
|
||||
public class GrsfPublisherFisheryService {
|
||||
|
||||
// the context
|
||||
|
@ -61,13 +61,17 @@ public class GrsfPublisherFisheryService {
|
|||
// Logger
|
||||
private static final org.slf4j.Logger logger = LoggerFactory.getLogger(GrsfPublisherFisheryService.class);
|
||||
|
||||
/*
|
||||
@GET
|
||||
@Path("hello")
|
||||
@Produces(MediaType.TEXT_PLAIN)
|
||||
public Response hello() {
|
||||
return Response.ok("Hello.. Fishery service is here").build();
|
||||
}
|
||||
*/
|
||||
|
||||
/*
|
||||
* Already Managed By gCat
|
||||
@GET
|
||||
@Path("get-licenses")
|
||||
@Produces(MediaType.APPLICATION_JSON)
|
||||
|
@ -88,6 +92,7 @@ public class GrsfPublisherFisheryService {
|
|||
.build();
|
||||
}
|
||||
}
|
||||
*/
|
||||
|
||||
@POST
|
||||
@Path("publish-product")
|
||||
|
@ -257,7 +262,7 @@ public class GrsfPublisherFisheryService {
|
|||
String type = fisheryInCkan.getExtrasAsHashMap().get(Constants.DOMAIN_CUSTOM_KEY);
|
||||
|
||||
if((fisheryInCkan.getOrganization().getName().equalsIgnoreCase(source)
|
||||
|| fisheryInCkan.getOrganization().getName().toLowerCase().startsWith(source.toLowerCase()))
|
||||
|| fisheryInCkan.getOrganization().getName().toLowerCase().contains(source))
|
||||
&& Product_Type.FISHERY.getOrigName().equals(type)) {
|
||||
|
||||
logger.debug("Ok, this is a fishery of the right source, removing it");
|
||||
|
@ -551,7 +556,7 @@ public class GrsfPublisherFisheryService {
|
|||
|
||||
// check system type
|
||||
boolean isGRSF = !record.getExtrasAsHashMap().get(Constants.SYSTEM_TYPE_CUSTOM_KEY)
|
||||
.equals(Constants.SYSTEM_TYPE_LEGACY_RECORD);
|
||||
.equals(Constants.SYSTEM_TYPE_FOR_SOURCES_VALUE);
|
||||
|
||||
if(!isGRSF)
|
||||
throw new Exception("You are trying to modify a Legacy record!");
|
||||
|
|
|
@ -51,7 +51,7 @@ import eu.trentorise.opendata.jackan.model.CkanDataset;
|
|||
* @author Costantino Perciante (ISTI - CNR)
|
||||
* @author Luca Frosini (ISTI - CNR)
|
||||
*/
|
||||
@Path("{source:firms|FIRMS|ram|RAM|grsf|GRSF|FishSource|fishsource|sdg|SDG}/stock/")
|
||||
@Path("{source:firms|FIRMS|ram|RAM|grsf|GRSF|FishSource|fishsource}/stock/")
|
||||
public class GrsfPublisherStockService {
|
||||
|
||||
// the context
|
||||
|
@ -260,7 +260,7 @@ public class GrsfPublisherStockService {
|
|||
// check it is in the right source and it is a stock
|
||||
String type = stockInCkan.getExtrasAsHashMap().get(Constants.DOMAIN_CUSTOM_KEY);
|
||||
if((stockInCkan.getOrganization().getName().equalsIgnoreCase(source)
|
||||
|| stockInCkan.getOrganization().getName().toLowerCase().startsWith(source.toLowerCase()))
|
||||
|| stockInCkan.getOrganization().getName().toLowerCase().contains(source))
|
||||
&& Product_Type.STOCK.getOrigName().equals(type)) {
|
||||
|
||||
logger.debug("Ok, this is a stock of the right type, removing it");
|
||||
|
@ -554,7 +554,7 @@ public class GrsfPublisherStockService {
|
|||
|
||||
// check system type
|
||||
boolean isGRSF = !record.getExtrasAsHashMap().get(Constants.SYSTEM_TYPE_CUSTOM_KEY)
|
||||
.equals(Constants.SYSTEM_TYPE_LEGACY_RECORD);
|
||||
.equals(Constants.SYSTEM_TYPE_FOR_SOURCES_VALUE);
|
||||
|
||||
if(!isGRSF)
|
||||
throw new Exception("You are trying to modify a Legacy record!");
|
||||
|
|
|
@ -4,6 +4,7 @@ import java.beans.PropertyDescriptor;
|
|||
import java.lang.reflect.Field;
|
||||
import java.util.ArrayList;
|
||||
import java.util.Arrays;
|
||||
import java.util.Collections;
|
||||
import java.util.HashMap;
|
||||
import java.util.HashSet;
|
||||
import java.util.List;
|
||||
|
@ -35,6 +36,7 @@ import org.gcube.datacatalogue.common.Constants;
|
|||
import org.gcube.datacatalogue.common.enums.Product_Type;
|
||||
import org.gcube.datacatalogue.common.enums.Sources;
|
||||
import org.gcube.datacatalogue.common.enums.Status;
|
||||
import org.gcube.datacatalogue.common.enums.Stock_Type;
|
||||
import org.json.simple.JSONObject;
|
||||
import org.slf4j.LoggerFactory;
|
||||
|
||||
|
@ -217,90 +219,6 @@ public class CommonServiceUtils {
|
|||
}
|
||||
}
|
||||
|
||||
public static final String GROUP_SUFFIX = "-group";
|
||||
|
||||
/**
|
||||
* Convert a group name to its id on ckan
|
||||
* @param origName
|
||||
* @return
|
||||
*/
|
||||
private static String getGroupIDOnCkan(String origName){
|
||||
if(origName == null) {
|
||||
throw new IllegalArgumentException("origName cannot be null");
|
||||
}
|
||||
String modified = origName.replaceAll("\\(", "");
|
||||
modified = modified.replaceAll("\\)", "");
|
||||
modified = modified.trim().toLowerCase().replaceAll("[^A-Za-z0-9-]", "-");
|
||||
if(modified.startsWith("-")) {
|
||||
modified = modified.substring(1);
|
||||
}
|
||||
if(modified.endsWith("-")) {
|
||||
modified = modified.substring(0, modified.length() -1);
|
||||
}
|
||||
return modified;
|
||||
}
|
||||
|
||||
public static String getGroupId(String groupName) {
|
||||
StringBuffer stringBuffer = new StringBuffer();
|
||||
stringBuffer.append(groupName);
|
||||
/*
|
||||
* The "_group" suffix is added to all groups to
|
||||
* avoid issues on groups and organizations having the same name
|
||||
* e.g. RAM organization (id=ram) and RAM group (id=ram_group)
|
||||
*/
|
||||
if(!groupName.endsWith(GROUP_SUFFIX)) {
|
||||
stringBuffer.append(GROUP_SUFFIX);
|
||||
}
|
||||
return getGroupIDOnCkan(stringBuffer.toString());
|
||||
}
|
||||
|
||||
private static void addGroup(Group group, Sources source, String value, Set<String> groups) {
|
||||
String conditionToCheck = group.condition();
|
||||
String groupNameOverValue = group.groupNameOverValue();
|
||||
boolean prependSource = group.prependSourceToGroupName();
|
||||
|
||||
boolean match = conditionToCheck.isEmpty() ? true
|
||||
: value.matches(conditionToCheck);
|
||||
|
||||
if(match) {
|
||||
StringBuffer stringBuffer = new StringBuffer();
|
||||
if(prependSource) {
|
||||
stringBuffer.append(source.getURLPath());
|
||||
stringBuffer.append(" ");
|
||||
}
|
||||
if(groupNameOverValue.isEmpty()) {
|
||||
stringBuffer.append(value);
|
||||
}else {
|
||||
stringBuffer.append(groupNameOverValue);
|
||||
}
|
||||
String groupId = getGroupId(stringBuffer.toString());
|
||||
groups.add(groupId);
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
/**
|
||||
* Add the record to the group of sources
|
||||
* @param groups
|
||||
* @param sourcesList
|
||||
* @param productType
|
||||
* @param sourceInPath
|
||||
*/
|
||||
private static void addRecordToGroups(Set<String> groups, Set<String> sourcesList, Product_Type productType, Sources sourceInPath) {
|
||||
if(sourceInPath == Sources.GRSF) {
|
||||
groups.add(getGroupId(Sources.GRSF.getURLPath())); // i.e. grsf_group
|
||||
}else {
|
||||
groups.add(getGroupId(Constants.SYSTEM_TYPE_LEGACY_RECORD)); // i.e. legacy_group
|
||||
}
|
||||
|
||||
// evaluate the custom fields/tags, resources and groups
|
||||
groups.add(getGroupId(productType.getOrigName())); //i.e. stock_group or fishery_group
|
||||
|
||||
for(String source : sourcesList) {
|
||||
groups.add(getGroupId(source)); // i.e. firms_group, fishsource_group, ram_group
|
||||
}
|
||||
}
|
||||
|
||||
/**
|
||||
* Retrieve the list of groups' names for this object
|
||||
*/
|
||||
|
@ -308,22 +226,74 @@ public class CommonServiceUtils {
|
|||
Sources source) {
|
||||
if(field.isAnnotationPresent(Group.class)) {
|
||||
Group group = field.getAnnotation(Group.class);
|
||||
String conditionToCheck = group.condition();
|
||||
String groupNameOverValue = group.groupNameOverValue();
|
||||
|
||||
|
||||
|
||||
// See https://support.d4science.org/issues/11832
|
||||
boolean assessmentUnit = false;
|
||||
boolean prependSource = group.prependSourceToGroupName();
|
||||
if(record instanceof StockRecord) {
|
||||
StockRecord stockRecord = (StockRecord) record;
|
||||
Stock_Type stock_Type = stockRecord.getType();
|
||||
if(stock_Type != Stock_Type.Assessment_Unit) {
|
||||
prependSource = false;
|
||||
}else {
|
||||
assessmentUnit = true;
|
||||
}
|
||||
}
|
||||
// end patch for https://support.d4science.org/issues/11832
|
||||
|
||||
try {
|
||||
Object f = new PropertyDescriptor(field.getName(), current).getReadMethod().invoke(record);
|
||||
if(f != null) {
|
||||
if(f instanceof List<?>) {
|
||||
List asList = ((List) f);
|
||||
if(!asList.isEmpty()) {
|
||||
|
||||
logger.debug("The object annotated with @Group is a list. Adding ... ");
|
||||
// add all the available elements
|
||||
|
||||
// else add all the available elements
|
||||
for(int i = 0; i < asList.size(); i++) {
|
||||
String value = asList.get(i).toString().trim();
|
||||
addGroup(group, source, value, groups);
|
||||
}
|
||||
}
|
||||
boolean match = conditionToCheck.isEmpty() ? true
|
||||
: asList.get(i).toString().trim().matches(conditionToCheck);
|
||||
if(match) {
|
||||
String groupName = groupNameOverValue.isEmpty()
|
||||
? HelperMethods.getGroupNameOnCkan(source.toString().toLowerCase() + "-"
|
||||
+ asList.get(i).toString().trim())
|
||||
: source.toString().toLowerCase() + "-" + groupNameOverValue;
|
||||
if(assessmentUnit && !prependSource) {
|
||||
groups.add(groupNameOverValue);
|
||||
}else {
|
||||
String value = f.toString().trim();
|
||||
addGroup(group, source, value, groups);
|
||||
groups.add(groupName);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
} else {
|
||||
|
||||
// also convert to the group name that should be on ckan
|
||||
boolean match = conditionToCheck.isEmpty() ? true
|
||||
: f.toString().trim().matches(conditionToCheck);
|
||||
if(match) {
|
||||
|
||||
String groupName = groupNameOverValue.isEmpty()
|
||||
? HelperMethods.getGroupNameOnCkan(
|
||||
source.toString().toLowerCase() + "-" + f.toString().trim())
|
||||
: source.toString().toLowerCase() + "-" + groupNameOverValue;
|
||||
|
||||
if(assessmentUnit && !prependSource) {
|
||||
groups.add(groupNameOverValue);
|
||||
}else {
|
||||
groups.add(groupName);
|
||||
}
|
||||
|
||||
|
||||
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
|
@ -331,6 +301,7 @@ public class CommonServiceUtils {
|
|||
logger.error("Failed to read value for field " + field.getName() + " skipping", e);
|
||||
}
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
/**
|
||||
|
@ -514,7 +485,7 @@ public class CommonServiceUtils {
|
|||
|
||||
// validate the record if it is a GRSF one and set the record type and in manage context
|
||||
// Status field is needed only in the Manage context for GRSF records
|
||||
if( (context.equals((String) contextServlet.getInitParameter(HelperMethods.MANAGE_CONTEX_KEY))) || (context.equals((String) contextServlet.getInitParameter(HelperMethods.PREVALIDATE_CONTEX_KEY)))) {
|
||||
if(context.equals((String) contextServlet.getInitParameter(HelperMethods.MANAGE_CONTEX_KEY))) {
|
||||
if(sourceInPath.equals(Sources.GRSF)) {
|
||||
|
||||
List<RefersToBean> refersTo = record.getRefersTo();
|
||||
|
@ -542,13 +513,13 @@ public class CommonServiceUtils {
|
|||
if(databaseSources!=null) {
|
||||
for(Resource<Sources> source : databaseSources) {
|
||||
Sources sourceName = source.getName();
|
||||
sourcesList.add(sourceName.getURLPath());
|
||||
sourcesList.add(sourceName.getOrigName().toLowerCase());
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
addRecordToGroups(groups, sourcesList, productType, sourceInPath);
|
||||
|
||||
// append to groups: we need to add this record to the correspondent group of the sources
|
||||
addRecordToGroupSources(groups, new ArrayList(sourcesList), productType, sourceInPath);
|
||||
|
||||
// validate
|
||||
CommonServiceUtils.validateAggregatedRecord(record, sourceInPath);
|
||||
|
@ -561,41 +532,57 @@ public class CommonServiceUtils {
|
|||
sourceInPath.equals(Sources.GRSF)
|
||||
? productType.equals(Product_Type.FISHERY) ? ((FisheryRecord) record).getType().getOrigName()
|
||||
: ((StockRecord) record).getType().getOrigName()
|
||||
: Constants.SYSTEM_TYPE_LEGACY_RECORD);
|
||||
: Constants.SYSTEM_TYPE_FOR_SOURCES_VALUE);
|
||||
|
||||
logger.debug("Domain is " + productType.getOrigName() + " and system type " + record.getSystemType());
|
||||
|
||||
|
||||
/*
|
||||
* It has been decided to add tags also for legacy records see #23216
|
||||
* boolean skipTags = !sourceInPath.equals(Sources.GRSF); // no tags for the Original records
|
||||
*/
|
||||
CommonServiceUtils.getTagsGroupsResourcesExtrasByRecord(tags, false, groups, false, resources, false,
|
||||
// evaluate the custom fields/tags, resources and groups
|
||||
groups.add(sourceInPath.getOrigName().toLowerCase() + "-" + productType.getOrigName().toLowerCase()); //e.g. grsf-fishery
|
||||
boolean skipTags = !sourceInPath.equals(Sources.GRSF); // no tags for the Original records
|
||||
CommonServiceUtils.getTagsGroupsResourcesExtrasByRecord(tags, skipTags, groups, false, resources, false,
|
||||
customFields, record, username, sourceInPath);
|
||||
|
||||
}
|
||||
|
||||
// /**
|
||||
// * Fetch the system:type property from a record
|
||||
// * @param itemIdOrName
|
||||
// * @param apiKey
|
||||
// * @return null on error
|
||||
// * @throws Exception
|
||||
// */
|
||||
// public static String getSystemTypeValue(String itemIdOrName, String apiKey, String context) throws Exception {
|
||||
// DataCatalogue catalog = HelperMethods.getDataCatalogueRunningInstance(context);
|
||||
// CkanDataset dataset = catalog.getDataset(itemIdOrName, apiKey);
|
||||
// if(dataset == null) {
|
||||
// throw new Exception("Unable to find record with id or name " + itemIdOrName);
|
||||
// }
|
||||
// String systemTypeValue = dataset.getExtrasAsHashMap().get(Constants.SYSTEM_TYPE_CUSTOM_KEY);
|
||||
// if(systemTypeValue == null || systemTypeValue.isEmpty()) {
|
||||
// throw new Exception(Constants.SYSTEM_TYPE_CUSTOM_KEY + " property not set in record " + itemIdOrName);
|
||||
// }else {
|
||||
// return systemTypeValue;
|
||||
// }
|
||||
//
|
||||
// }
|
||||
/**
|
||||
* Add the record to the group of sources
|
||||
* @param groups
|
||||
* @param sourcesList
|
||||
* @param productType
|
||||
* @param sourceInPath
|
||||
*/
|
||||
private static void addRecordToGroupSources(Set<String> groups, List<String> sourcesList, Product_Type productType,
|
||||
Sources sourceInPath) {
|
||||
|
||||
Collections.sort(sourcesList); // be sure the name are sorted because the groups have been generated this way
|
||||
String groupName = sourceInPath.getOrigName().toLowerCase() + "-" + productType.getOrigName().toLowerCase();
|
||||
for(String source : sourcesList) {
|
||||
groupName += "-" + source;
|
||||
}
|
||||
|
||||
groups.add(groupName);
|
||||
}
|
||||
|
||||
/**
|
||||
* Fetch the system:type property from a record
|
||||
* @param itemIdOrName
|
||||
* @param apiKey
|
||||
* @return null on error
|
||||
* @throws Exception
|
||||
*/
|
||||
public static String getSystemTypeValue(String itemIdOrName, String apiKey, String context) throws Exception {
|
||||
|
||||
DataCatalogue catalog = HelperMethods.getDataCatalogueRunningInstance(context);
|
||||
CkanDataset dataset = catalog.getDataset(itemIdOrName, apiKey);
|
||||
if(dataset == null)
|
||||
throw new Exception("Unable to find record with id or name " + itemIdOrName);
|
||||
String systemTypeValue = dataset.getExtrasAsHashMap().get(Constants.SYSTEM_TYPE_CUSTOM_KEY);
|
||||
if(systemTypeValue == null || systemTypeValue.isEmpty())
|
||||
throw new Exception(Constants.SYSTEM_TYPE_CUSTOM_KEY + " property not set in record " + itemIdOrName);
|
||||
else
|
||||
return systemTypeValue;
|
||||
|
||||
}
|
||||
|
||||
public static String getRecordOrganization(String itemIdOrName, String apiKey, String context) throws Exception {
|
||||
DataCatalogue catalog = HelperMethods.getDataCatalogueRunningInstance(context);
|
||||
|
@ -718,6 +705,6 @@ public class CommonServiceUtils {
|
|||
return Constants.GRSF_PRE_ORGANIZATION_NAME;
|
||||
}
|
||||
}else
|
||||
return sourceInPath.getURLPath();
|
||||
return sourceInPath.getOrigName().toLowerCase();
|
||||
}
|
||||
}
|
|
@ -5,6 +5,7 @@ import static org.gcube.resources.discovery.icclient.ICFactory.client;
|
|||
import java.io.BufferedReader;
|
||||
import java.io.File;
|
||||
import java.io.FileInputStream;
|
||||
import java.io.FileNotFoundException;
|
||||
import java.io.InputStream;
|
||||
import java.io.InputStreamReader;
|
||||
import java.io.StringReader;
|
||||
|
@ -19,11 +20,15 @@ import javax.xml.parsers.DocumentBuilder;
|
|||
import javax.xml.parsers.DocumentBuilderFactory;
|
||||
|
||||
import org.gcube.common.authorization.library.provider.SecurityTokenProvider;
|
||||
import org.gcube.common.homelibrary.home.exceptions.InternalErrorException;
|
||||
import org.gcube.common.homelibrary.home.workspace.WorkspaceFolder;
|
||||
import org.gcube.common.homelibrary.home.workspace.WorkspaceItem;
|
||||
import org.gcube.common.homelibrary.home.workspace.exceptions.InsufficientPrivilegesException;
|
||||
import org.gcube.common.homelibrary.home.workspace.exceptions.ItemAlreadyExistException;
|
||||
import org.gcube.common.homelibrary.home.workspace.exceptions.ItemNotFoundException;
|
||||
import org.gcube.common.homelibrary.home.workspace.folder.items.ExternalFile;
|
||||
import org.gcube.common.resources.gcore.utils.XPathHelper;
|
||||
import org.gcube.common.scope.api.ScopeProvider;
|
||||
import org.gcube.common.storagehub.client.dsl.FileContainer;
|
||||
import org.gcube.common.storagehub.client.dsl.FolderContainer;
|
||||
import org.gcube.common.storagehub.model.exceptions.StorageHubException;
|
||||
import org.gcube.datacatalogue.ckanutillibrary.server.DataCatalogue;
|
||||
import org.gcube.datacatalogue.ckanutillibrary.server.DataCatalogueFactory;
|
||||
import org.gcube.datacatalogue.common.caches.CacheImpl;
|
||||
|
@ -31,7 +36,6 @@ import org.gcube.datacatalogue.common.caches.CacheInterface;
|
|||
import org.gcube.resources.discovery.client.api.DiscoveryClient;
|
||||
import org.gcube.resources.discovery.client.queries.api.Query;
|
||||
import org.gcube.resources.discovery.client.queries.impl.QueryBox;
|
||||
import org.gcube.social_networking.social_networking_client_library.UserClient;
|
||||
import org.jsoup.Jsoup;
|
||||
import org.jsoup.safety.Whitelist;
|
||||
import org.slf4j.LoggerFactory;
|
||||
|
@ -68,19 +72,37 @@ public abstract class HelperMethods {
|
|||
|
||||
// to be retrieved from the web.xml
|
||||
public static final String MANAGE_CONTEX_KEY = "ManageVRE";
|
||||
public static final String PREVALIDATE_CONTEX_KEY = "PreValidateVRE";
|
||||
public static final String PUBLIC_CONTEX_KEY = "PublicVRE";
|
||||
private static final String CSV_MIME = "text/csv";
|
||||
private static final String PATH_SEPARATOR = "/";
|
||||
|
||||
// This key is used in replaceFieldsKey() function to indicate to remove the metadata field
|
||||
private static final String NONE_KEY = "none:none";
|
||||
|
||||
// caches
|
||||
private static CacheInterface<String, String> userEmailCache = new CacheImpl<String, String>(1000 * 60 * 60 * 24);
|
||||
private static CacheInterface<String, String> userFullnameCache = new CacheImpl<String, String>(1000 * 60 * 60 * 24);
|
||||
private static CacheInterface<String, Map<String, String>> namespacesCache = new CacheImpl<String, Map<String, String>>(1000 * 60 * 60 * 24);
|
||||
private static CacheInterface<String, DataCatalogue> catalogueCache = new CacheImpl<String, DataCatalogue>(1000 * 60 * 60 * 24);
|
||||
|
||||
/**
|
||||
* Convert a group name to its id on ckan
|
||||
* @param origName
|
||||
* @return
|
||||
*/
|
||||
public static String getGroupNameOnCkan(String origName){
|
||||
|
||||
if(origName == null)
|
||||
throw new IllegalArgumentException("origName cannot be null");
|
||||
|
||||
String modified = origName.trim().toLowerCase().replaceAll("[^A-Za-z0-9-]", "-");
|
||||
if(modified.startsWith("-"))
|
||||
modified = modified.substring(1);
|
||||
if(modified.endsWith("-"))
|
||||
modified = modified.substring(0, modified.length() -1);
|
||||
|
||||
logger.info("Group name generated is " + modified);
|
||||
|
||||
return modified;
|
||||
}
|
||||
|
||||
/**
|
||||
* Retrieve the running instance of the data catalogue for this scope
|
||||
* @return
|
||||
|
@ -135,18 +157,21 @@ public abstract class HelperMethods {
|
|||
* @return
|
||||
* @throws Exception
|
||||
*/
|
||||
public static String getUserEmail(String context, String token) throws Exception{
|
||||
public static String getUserEmail(String context, String token){
|
||||
|
||||
// check in cache
|
||||
String email = null;
|
||||
if((email = (String) userEmailCache.get(token)) != null){
|
||||
return email;
|
||||
String result = null;
|
||||
if((result = (String) userEmailCache.get(token)) != null){
|
||||
return result;
|
||||
}else{
|
||||
UserClient userClient = new UserClient();
|
||||
email = userClient.getEmail();
|
||||
userEmailCache.insert(token, email);
|
||||
String baseUrl = new GcoreEndPointReaderSocial(context).getBasePath();
|
||||
String url = baseUrl.endsWith("/") ? baseUrl + "users/getUserEmail?gcube-token=" + token :
|
||||
baseUrl + "/users/getUserEmail?gcube-token=" + token;
|
||||
logger.debug("Request url is " + url);
|
||||
result = executGETHttpRequest(url, 200);
|
||||
userEmailCache.insert(token, result);
|
||||
}
|
||||
return email;
|
||||
return result;
|
||||
}
|
||||
|
||||
/**
|
||||
|
@ -156,18 +181,21 @@ public abstract class HelperMethods {
|
|||
* @return
|
||||
* @throws Exception
|
||||
*/
|
||||
public static String getUserFullname(String context, String token) throws Exception{
|
||||
public static String getUserFullname(String context, String token){
|
||||
|
||||
// check in cache
|
||||
String fullName = null;
|
||||
if((fullName = (String) userFullnameCache.get(token)) != null){
|
||||
return fullName;
|
||||
String result = null;
|
||||
if((result = (String) userFullnameCache.get(token)) != null){
|
||||
return result;
|
||||
}else{
|
||||
UserClient userClient = new UserClient();
|
||||
fullName = userClient.getFullName();
|
||||
userFullnameCache.insert(token, fullName);
|
||||
String baseUrl = new GcoreEndPointReaderSocial(context).getBasePath();
|
||||
String url = baseUrl.endsWith("/") ? baseUrl + "users/getUserFullname?gcube-token=" + token :
|
||||
baseUrl + "/users/getUserFullname?gcube-token=" + token;
|
||||
logger.debug("Request url is " + url);
|
||||
result = executGETHttpRequest(url, 200);
|
||||
userFullnameCache.insert(token, result);
|
||||
}
|
||||
return fullName;
|
||||
return result;
|
||||
}
|
||||
|
||||
/**
|
||||
|
@ -229,17 +257,26 @@ public abstract class HelperMethods {
|
|||
* @param csvFile
|
||||
* @return
|
||||
*/
|
||||
public static FileContainer uploadExternalFile(FolderContainer resourceFormatFolder, String resourceToAttachName, String description, File csvFile) {
|
||||
public static ExternalFile uploadExternalFile(WorkspaceFolder resourceFormatFolder, String resourceToAttachName, String description, File csvFile) {
|
||||
try {
|
||||
|
||||
try (InputStream is= new FileInputStream(csvFile)) {
|
||||
FileContainer fileContainer = resourceFormatFolder.uploadFile(is , resourceToAttachName, description);
|
||||
return fileContainer;
|
||||
WorkspaceItem existsFile = resourceFormatFolder.find(resourceToAttachName);
|
||||
|
||||
if(existsFile == null)
|
||||
return resourceFormatFolder.createExternalFileItem(resourceToAttachName, description, CSV_MIME, csvFile);
|
||||
else{
|
||||
InputStream targetStream = new FileInputStream(csvFile);
|
||||
existsFile.updateItem(targetStream);
|
||||
return (ExternalFile)existsFile;
|
||||
}
|
||||
|
||||
} catch (StorageHubException she) {
|
||||
logger.error("Failed to upload the file into the workspace shared folder for " + resourceToAttachName, she);
|
||||
} catch (Exception e) {
|
||||
} catch (InsufficientPrivilegesException | ItemAlreadyExistException
|
||||
| InternalErrorException e) {
|
||||
logger.error("Failed to upload the file into the workspace shared folder for " + resourceToAttachName, e);
|
||||
} catch (FileNotFoundException e) {
|
||||
// TODO Auto-generated catch block
|
||||
e.printStackTrace();
|
||||
} catch (ItemNotFoundException e) {
|
||||
// TODO Auto-generated catch block
|
||||
e.printStackTrace();
|
||||
}
|
||||
|
@ -253,10 +290,9 @@ public abstract class HelperMethods {
|
|||
* @param subPath
|
||||
* @return null if an error occurred
|
||||
*/
|
||||
public static FolderContainer createOrGetSubFoldersByPath(FolderContainer folder, String subPath){
|
||||
|
||||
FolderContainer parentFolder = folder;
|
||||
public static WorkspaceFolder createOrGetSubFoldersByPath(WorkspaceFolder folder, String subPath){
|
||||
|
||||
WorkspaceFolder parentFolder = folder;
|
||||
if(folder == null)
|
||||
throw new IllegalArgumentException("Root folder is null!");
|
||||
|
||||
|
@ -275,9 +311,8 @@ public abstract class HelperMethods {
|
|||
String[] splittedPaths = subPath.split(PATH_SEPARATOR);
|
||||
|
||||
for (String path : splittedPaths) {
|
||||
|
||||
FolderContainer createdFolder = getFolderOrCreate(parentFolder, path, "");
|
||||
logger.debug("Created subfolder with path " + createdFolder.get().getPath());
|
||||
WorkspaceFolder createdFolder = getFolderOrCreate(parentFolder, path, "");
|
||||
logger.debug("Created subfolder with path " + createdFolder.getPath());
|
||||
parentFolder = createdFolder;
|
||||
}
|
||||
|
||||
|
@ -293,18 +328,23 @@ public abstract class HelperMethods {
|
|||
* Get a folder within the catalogue folder or create it if it doesn't exist.
|
||||
* @return
|
||||
*/
|
||||
public static FolderContainer getFolderOrCreate(FolderContainer folder, String relativePath, String descriptionFolder){
|
||||
|
||||
FolderContainer result = null;
|
||||
public static WorkspaceFolder getFolderOrCreate(WorkspaceFolder folder, String relativePath, String descriptionFolder){
|
||||
WorkspaceFolder result = null;
|
||||
try {
|
||||
result = folder.openByRelativePath(relativePath).asFolder();
|
||||
WorkspaceItem foundFolder = folder.find(relativePath);
|
||||
if(foundFolder != null && foundFolder.isFolder())
|
||||
result = (WorkspaceFolder)foundFolder;
|
||||
|
||||
if(result != null)
|
||||
logger.debug("Folder found with name " + result.getName() + ", it has id " + result.getId());
|
||||
else
|
||||
throw new Exception("There is no folder with name " + relativePath + " under folder " + folder.getName());
|
||||
} catch (Exception e) {
|
||||
logger.debug("Probably the folder doesn't exist");
|
||||
try{
|
||||
result = folder.newFolder(relativePath, descriptionFolder);
|
||||
} catch (StorageHubException se) {
|
||||
logger.error("Failed to get or generate this folder", se);
|
||||
result = folder.createFolder(relativePath, descriptionFolder);
|
||||
} catch (InsufficientPrivilegesException | InternalErrorException | ItemAlreadyExistException e2) {
|
||||
logger.error("Failed to get or generate this folder", e2);
|
||||
}
|
||||
}
|
||||
return result;
|
||||
|
@ -548,18 +588,16 @@ public abstract class HelperMethods {
|
|||
|
||||
if(namespaces.containsKey(entry.getKey())){
|
||||
usedKey = namespaces.get(entry.getKey());
|
||||
} else{
|
||||
}
|
||||
else{
|
||||
usedKey = entry.getKey();
|
||||
}
|
||||
|
||||
if(isSourceRecord) {
|
||||
if(isSourceRecord)
|
||||
usedKey = usedKey.replace("GRSF", "").trim();
|
||||
}
|
||||
|
||||
// When the replaced key is none the metadata field must be removed
|
||||
if(usedKey.compareTo(NONE_KEY)!=0) {
|
||||
toReturn.put(usedKey, entry.getValue());
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
return toReturn;
|
||||
|
|
|
@ -1,5 +1,6 @@
|
|||
package org.gcube.data_catalogue.grsf_publish_ws.utils.csv;
|
||||
|
||||
import java.beans.IntrospectionException;
|
||||
import java.beans.PropertyDescriptor;
|
||||
import java.io.File;
|
||||
import java.lang.reflect.Field;
|
||||
|
@ -7,11 +8,18 @@ import java.lang.reflect.InvocationTargetException;
|
|||
import java.util.List;
|
||||
|
||||
import org.gcube.common.authorization.library.provider.SecurityTokenProvider;
|
||||
import org.gcube.common.homelibrary.home.HomeLibrary;
|
||||
import org.gcube.common.homelibrary.home.exceptions.HomeNotFoundException;
|
||||
import org.gcube.common.homelibrary.home.exceptions.InternalErrorException;
|
||||
import org.gcube.common.homelibrary.home.exceptions.UserNotFoundException;
|
||||
import org.gcube.common.homelibrary.home.workspace.Workspace;
|
||||
import org.gcube.common.homelibrary.home.workspace.WorkspaceFolder;
|
||||
import org.gcube.common.homelibrary.home.workspace.WorkspaceSharedFolder;
|
||||
import org.gcube.common.homelibrary.home.workspace.catalogue.WorkspaceCatalogue;
|
||||
import org.gcube.common.homelibrary.home.workspace.exceptions.ItemNotFoundException;
|
||||
import org.gcube.common.homelibrary.home.workspace.exceptions.WorkspaceFolderNotFoundException;
|
||||
import org.gcube.common.homelibrary.home.workspace.folder.items.ExternalFile;
|
||||
import org.gcube.common.scope.api.ScopeProvider;
|
||||
import org.gcube.common.storagehub.client.dsl.FileContainer;
|
||||
import org.gcube.common.storagehub.client.dsl.FolderContainer;
|
||||
import org.gcube.common.storagehub.client.dsl.StorageHubClient;
|
||||
import org.gcube.common.storagehub.model.exceptions.StorageHubException;
|
||||
import org.gcube.data_catalogue.grsf_publish_ws.custom_annotations.CustomField;
|
||||
import org.gcube.data_catalogue.grsf_publish_ws.custom_annotations.TimeSeries;
|
||||
import org.gcube.data_catalogue.grsf_publish_ws.json.input.record.Common;
|
||||
|
@ -34,15 +42,13 @@ public class ManageTimeSeriesThread extends Thread{
|
|||
|
||||
private static final String PATH_SEPARATOR = "/";
|
||||
|
||||
private static final String CATALOGUE_FOLDER = ".catalogue";
|
||||
|
||||
// Logger
|
||||
private static final org.slf4j.Logger logger = LoggerFactory.getLogger(ManageTimeSeriesThread.class);
|
||||
|
||||
// try to attach the source at most CHANCES times ..
|
||||
private static final int CHANCES = 10;
|
||||
|
||||
private static CacheInterface<String, FolderContainer> vreFolderCache = new CacheImpl<String, FolderContainer>(1000 * 60 * 60 * 24);
|
||||
private static CacheInterface<String, WorkspaceCatalogue> vreFolderCache = new CacheImpl<String, WorkspaceCatalogue>(1000 * 60 * 60 * 24);
|
||||
|
||||
private static final int MAX_NAME_CSV_FILE_WITHOUT_MEASURE = 50;
|
||||
|
||||
|
@ -90,7 +96,17 @@ public class ManageTimeSeriesThread extends Thread{
|
|||
logger.error("Error was " + e.getMessage());
|
||||
} catch (InvocationTargetException e) {
|
||||
logger.error("Error was " + e.getMessage());
|
||||
} catch (StorageHubException e) {
|
||||
} catch (WorkspaceFolderNotFoundException e) {
|
||||
logger.error("Error was " + e.getMessage());
|
||||
} catch (ItemNotFoundException e) {
|
||||
logger.error("Error was " + e.getMessage());
|
||||
} catch (IntrospectionException e) {
|
||||
logger.error("Error was " + e.getMessage());
|
||||
} catch (InternalErrorException e) {
|
||||
logger.error("Error was " + e.getMessage());
|
||||
} catch (HomeNotFoundException e) {
|
||||
logger.error("Error was " + e.getMessage());
|
||||
} catch (UserNotFoundException e) {
|
||||
logger.error("Error was " + e.getMessage());
|
||||
} catch (Exception e) {
|
||||
logger.error("Error was " + e.getMessage());
|
||||
|
@ -114,26 +130,17 @@ public class ManageTimeSeriesThread extends Thread{
|
|||
if(record == null)
|
||||
throw new IllegalArgumentException("The given record is null!!");
|
||||
|
||||
StorageHubClient shClient = new StorageHubClient();
|
||||
|
||||
String token = SecurityTokenProvider.instance.get();
|
||||
|
||||
FolderContainer catalogueFolder = null;
|
||||
|
||||
//WorkspaceCatalogue catalogueFolder = null;
|
||||
WorkspaceCatalogue catalogueFolder = null;
|
||||
if((catalogueFolder = vreFolderCache.get(token)) == null){
|
||||
//Workspace ws = HomeLibrary.getHomeManagerFactory().getHomeManager().getHome().getWorkspace();
|
||||
FolderContainer vreFolder = shClient.openVREFolder();
|
||||
try {
|
||||
catalogueFolder = vreFolder.openByRelativePath(CATALOGUE_FOLDER).asFolder();
|
||||
}catch (StorageHubException e) {
|
||||
catalogueFolder = vreFolder.newHiddenFolder(CATALOGUE_FOLDER, "catalogue folder");
|
||||
}
|
||||
|
||||
Workspace ws = HomeLibrary.getHomeManagerFactory().getHomeManager().getHome().getWorkspace();
|
||||
WorkspaceSharedFolder vreFolder = ws.getVREFolderByScope(ScopeProvider.instance.get());
|
||||
catalogueFolder = vreFolder.getVRECatalogue();
|
||||
vreFolderCache.insert(token, catalogueFolder);
|
||||
}
|
||||
|
||||
logger.debug("Catalogue folder in vre has path " + catalogueFolder.get().getPath());
|
||||
logger.debug("Catalogue folder in vre has path " + catalogueFolder.getPath());
|
||||
|
||||
// the structure under the .catalogue will be as follows:
|
||||
// .catalogue:
|
||||
|
@ -160,7 +167,7 @@ public class ManageTimeSeriesThread extends Thread{
|
|||
// the whole path of the directory is going to be...
|
||||
String csvDirectoryForThisProduct = recordTypeFolderName + PATH_SEPARATOR + firstLetter + PATH_SEPARATOR + replaceIllegalChars(uuidKB, "_") + PATH_SEPARATOR + CSVUtils.CSV_EXTENSION.replace(".", "");
|
||||
logger.debug("The path under which the time series are going to be saved is " + csvDirectoryForThisProduct);
|
||||
FolderContainer csvFolder = HelperMethods.createOrGetSubFoldersByPath(catalogueFolder, csvDirectoryForThisProduct);
|
||||
WorkspaceFolder csvFolder = HelperMethods.createOrGetSubFoldersByPath(catalogueFolder, csvDirectoryForThisProduct);
|
||||
|
||||
if(csvFolder == null)
|
||||
logger.error("Failed to create directory where csv files will be deployed in the workspace!!");
|
||||
|
@ -185,7 +192,7 @@ public class ManageTimeSeriesThread extends Thread{
|
|||
String resourceToAttachOnCkanDescription = productName;
|
||||
|
||||
CkanResourceBase ckanResource = null;
|
||||
FileContainer createdFileOnWorkspace = null;
|
||||
ExternalFile createdFileOnWorkspace = null;
|
||||
String[] relevantSources = new String[1];
|
||||
File csvFile = CSVUtils.listToCSV(asList, relevantSources);
|
||||
if(csvFile != null){
|
||||
|
@ -205,7 +212,7 @@ public class ManageTimeSeriesThread extends Thread{
|
|||
+ customAnnotation.key() + CSVUtils.CSV_EXTENSION, resourceToAttachOnCkanDescription, csvFile);
|
||||
|
||||
if(createdFileOnWorkspace != null){
|
||||
String publicUrlToSetOnCkan = createdFileOnWorkspace.getPublicLink().toString();
|
||||
String publicUrlToSetOnCkan = createdFileOnWorkspace.getPublicLink(true);
|
||||
|
||||
// wait for patching..
|
||||
Thread.sleep(1500);
|
||||
|
|
|
@ -1,94 +0,0 @@
|
|||
<Resource version="0.4.x">
|
||||
<ID>85480b75-62f5-4708-acd9-382b22cffc90</ID>
|
||||
<Type>GenericResource</Type>
|
||||
<Scopes>
|
||||
<Scope>/d4science.research-infrastructures.eu/FARM/GRSF</Scope>
|
||||
</Scopes>
|
||||
<Profile>
|
||||
<SecondaryType>ApplicationProfile</SecondaryType>
|
||||
<Name>GRSF Fishery</Name>
|
||||
<Description>GRSF mapping between fields and namespaces for Fishery
|
||||
records</Description>
|
||||
<Body>
|
||||
<fields>
|
||||
<field>
|
||||
<originalKey>Data Owner</originalKey>
|
||||
<modifiedKey>none:none</modifiedKey>
|
||||
</field>
|
||||
<field>
|
||||
<originalKey>Database Source</originalKey>
|
||||
<modifiedKey>fishery_identity:Database Source</modifiedKey>
|
||||
</field>
|
||||
<field>
|
||||
<originalKey>Short Name</originalKey>
|
||||
<modifiedKey>fishery_identity:Short Name</modifiedKey>
|
||||
</field>
|
||||
<field>
|
||||
<originalKey>Catch</originalKey>
|
||||
<modifiedKey>none:none</modifiedKey>
|
||||
</field>
|
||||
<field>
|
||||
<originalKey>Landing</originalKey>
|
||||
<modifiedKey>none:none</modifiedKey>
|
||||
</field>
|
||||
<field>
|
||||
<originalKey>Species</originalKey>
|
||||
<modifiedKey>fishery_identity:Species</modifiedKey>
|
||||
</field>
|
||||
<field>
|
||||
<originalKey>Similar GRSF Record</originalKey>
|
||||
<modifiedKey>fishery_identity:Similar GRSF Record</modifiedKey>
|
||||
</field>
|
||||
<field>
|
||||
<originalKey>Management Body/Authority</originalKey>
|
||||
<modifiedKey>fishery_identity:Management Body/Authority</modifiedKey>
|
||||
</field>
|
||||
<field>
|
||||
<originalKey>Connected Record</originalKey>
|
||||
<modifiedKey>fishery_identity:Connected Record</modifiedKey>
|
||||
</field>
|
||||
<field>
|
||||
<originalKey>Annotation</originalKey>
|
||||
<modifiedKey>none:none</modifiedKey>
|
||||
</field>
|
||||
<field>
|
||||
<originalKey>GRSF Fishery Name</originalKey>
|
||||
<modifiedKey>fishery_identity:GRSF Fishery Name</modifiedKey>
|
||||
</field>
|
||||
<field>
|
||||
<originalKey>GRSF Semantic Identifier</originalKey>
|
||||
<modifiedKey>fishery_identity:GRSF Semantic Identifier
|
||||
</modifiedKey>
|
||||
</field>
|
||||
<field>
|
||||
<originalKey>Traceability Flag</originalKey>
|
||||
<modifiedKey>fishery_identity:Traceability Flag</modifiedKey>
|
||||
</field>
|
||||
<field>
|
||||
<originalKey>Fishing Area</originalKey>
|
||||
<modifiedKey>fishery_identity:Fishing Area</modifiedKey>
|
||||
</field>
|
||||
<field>
|
||||
<originalKey>Jurisdiction Area</originalKey>
|
||||
<modifiedKey>fishery_identity:Jurisdiction Area</modifiedKey>
|
||||
</field>
|
||||
<field>
|
||||
<originalKey>Resources Exploited</originalKey>
|
||||
<modifiedKey>fishery_identity:Resources Exploited</modifiedKey>
|
||||
</field>
|
||||
<field>
|
||||
<originalKey>Flag State</originalKey>
|
||||
<modifiedKey>fishery_identity:Flag State</modifiedKey>
|
||||
</field>
|
||||
<field>
|
||||
<originalKey>Fishing Gear</originalKey>
|
||||
<modifiedKey>fishery_identity:Fishing Gear</modifiedKey>
|
||||
</field>
|
||||
<field>
|
||||
<originalKey>GRSF Type</originalKey>
|
||||
<modifiedKey>fishery_identity:GRSF Type</modifiedKey>
|
||||
</field>
|
||||
</fields>
|
||||
</Body>
|
||||
</Profile>
|
||||
</Resource>
|
|
@ -1,91 +0,0 @@
|
|||
<Resource version="0.4.x">
|
||||
<ID>c3326373-c620-45e8-a7e3-a25a1a2a970b</ID>
|
||||
<Type>GenericResource</Type>
|
||||
<Scopes>
|
||||
<Scope>/d4science.research-infrastructures.eu/FARM/GRSF_Admin</Scope>
|
||||
<Scope>/d4science.research-infrastructures.eu/FARM</Scope>
|
||||
</Scopes>
|
||||
<Profile>
|
||||
<SecondaryType>ApplicationProfile</SecondaryType>
|
||||
<Name>GRSF Fishery</Name>
|
||||
<Description>GRSF mapping between fields and namespaces for Fishery
|
||||
records</Description>
|
||||
<Body>
|
||||
<fields>
|
||||
<field>
|
||||
<originalKey>Data Owner</originalKey>
|
||||
<modifiedKey>fishery_data:Data Owner</modifiedKey>
|
||||
</field>
|
||||
<field>
|
||||
<originalKey>Database Source</originalKey>
|
||||
<modifiedKey>fishery_identity:Database Source</modifiedKey>
|
||||
</field>
|
||||
<field>
|
||||
<originalKey>Short Name</originalKey>
|
||||
<modifiedKey>fishery_identity:Short Name</modifiedKey>
|
||||
</field>
|
||||
<field>
|
||||
<originalKey>Catch</originalKey>
|
||||
<modifiedKey>fishery_data:Catch</modifiedKey>
|
||||
</field>
|
||||
<field>
|
||||
<originalKey>Landing</originalKey>
|
||||
<modifiedKey>fishery_data:Landing</modifiedKey>
|
||||
</field>
|
||||
<field>
|
||||
<originalKey>Species</originalKey>
|
||||
<modifiedKey>fishery_identity:Species</modifiedKey>
|
||||
</field>
|
||||
<field>
|
||||
<originalKey>Similar GRSF Record</originalKey>
|
||||
<modifiedKey>fishery_identity:Similar GRSF Record</modifiedKey>
|
||||
</field>
|
||||
<field>
|
||||
<originalKey>Management Body/Authority</originalKey>
|
||||
<modifiedKey>fishery_identity:Management Body/Authority</modifiedKey>
|
||||
</field>
|
||||
<field>
|
||||
<originalKey>Connected Record</originalKey>
|
||||
<modifiedKey>fishery_identity:Connected Record</modifiedKey>
|
||||
</field>
|
||||
<field>
|
||||
<originalKey>GRSF Fishery Name</originalKey>
|
||||
<modifiedKey>fishery_identity:GRSF Fishery Name</modifiedKey>
|
||||
</field>
|
||||
<field>
|
||||
<originalKey>GRSF Semantic Identifier</originalKey>
|
||||
<modifiedKey>fishery_identity:GRSF Semantic Identifier
|
||||
</modifiedKey>
|
||||
</field>
|
||||
<field>
|
||||
<originalKey>Traceability Flag</originalKey>
|
||||
<modifiedKey>fishery_identity:Traceability Flag</modifiedKey>
|
||||
</field>
|
||||
<field>
|
||||
<originalKey>Fishing Area</originalKey>
|
||||
<modifiedKey>fishery_identity:Fishing Area</modifiedKey>
|
||||
</field>
|
||||
<field>
|
||||
<originalKey>Jurisdiction Area</originalKey>
|
||||
<modifiedKey>fishery_identity:Jurisdiction Area</modifiedKey>
|
||||
</field>
|
||||
<field>
|
||||
<originalKey>Resources Exploited</originalKey>
|
||||
<modifiedKey>fishery_identity:Resources Exploited</modifiedKey>
|
||||
</field>
|
||||
<field>
|
||||
<originalKey>Flag State</originalKey>
|
||||
<modifiedKey>fishery_identity:Flag State</modifiedKey>
|
||||
</field>
|
||||
<field>
|
||||
<originalKey>Fishing Gear</originalKey>
|
||||
<modifiedKey>fishery_identity:Fishing Gear</modifiedKey>
|
||||
</field>
|
||||
<field>
|
||||
<originalKey>GRSF Type</originalKey>
|
||||
<modifiedKey>fishery_identity:GRSF Type</modifiedKey>
|
||||
</field>
|
||||
</fields>
|
||||
</Body>
|
||||
</Profile>
|
||||
</Resource>
|
|
@ -1,118 +0,0 @@
|
|||
<Resource version="0.4.x">
|
||||
<ID>512cca02-e178-420c-a766-b47171e154e2</ID>
|
||||
<Type>GenericResource</Type>
|
||||
<Scopes>
|
||||
<Scope>/d4science.research-infrastructures.eu/FARM/GRSF</Scope>
|
||||
</Scopes>
|
||||
<Profile>
|
||||
<SecondaryType>ApplicationProfile</SecondaryType>
|
||||
<Name>GRSF Stock</Name>
|
||||
<Description>GRSF mapping between fields and namespaces for Stock
|
||||
records
|
||||
</Description>
|
||||
<Body>
|
||||
<fields>
|
||||
<field>
|
||||
<originalKey>Data Owner</originalKey>
|
||||
<modifiedKey>none:none</modifiedKey>
|
||||
</field>
|
||||
<field>
|
||||
<originalKey>Database Source</originalKey>
|
||||
<modifiedKey>stock_identity:Database Source</modifiedKey>
|
||||
</field>
|
||||
<field>
|
||||
<originalKey>Short Name</originalKey>
|
||||
<modifiedKey>stock_identity:Short Name</modifiedKey>
|
||||
</field>
|
||||
<field>
|
||||
<originalKey>Catch</originalKey>
|
||||
<modifiedKey>none:none</modifiedKey>
|
||||
</field>
|
||||
<field>
|
||||
<originalKey>Landing</originalKey>
|
||||
<modifiedKey>none:none</modifiedKey>
|
||||
</field>
|
||||
<field>
|
||||
<originalKey>Species</originalKey>
|
||||
<modifiedKey>stock_identity:Species</modifiedKey>
|
||||
</field>
|
||||
<field>
|
||||
<originalKey>Similar GRSF Record</originalKey>
|
||||
<modifiedKey>stock_identity:Similar GRSF Record</modifiedKey>
|
||||
</field>
|
||||
<field>
|
||||
<originalKey>Management Body/Authority</originalKey>
|
||||
<modifiedKey>stock_identity:Management Body/Authority</modifiedKey>
|
||||
</field>
|
||||
<field>
|
||||
<originalKey>Connected Record</originalKey>
|
||||
<modifiedKey>stock_identity:Connected Record</modifiedKey>
|
||||
</field>
|
||||
<field>
|
||||
<originalKey>Annotation</originalKey>
|
||||
<modifiedKey>none:none</modifiedKey>
|
||||
</field>
|
||||
<field>
|
||||
<originalKey>GRSF Stock Name</originalKey>
|
||||
<modifiedKey>stock_identity:GRSF Stock Name</modifiedKey>
|
||||
</field>
|
||||
<field>
|
||||
<originalKey>GRSF Semantic Identifier</originalKey>
|
||||
<modifiedKey>stock_identity:GRSF Semantic Identifier</modifiedKey>
|
||||
</field>
|
||||
<field>
|
||||
<originalKey>Assessment Area</originalKey>
|
||||
<modifiedKey>stock_identity:Assessment Area</modifiedKey>
|
||||
</field>
|
||||
<field>
|
||||
<originalKey>Exploiting Fishery</originalKey>
|
||||
<modifiedKey>stock_identity:Exploiting Fishery</modifiedKey>
|
||||
</field>
|
||||
<field>
|
||||
<originalKey>Assessment Method</originalKey>
|
||||
<modifiedKey>none:none</modifiedKey>
|
||||
</field>
|
||||
<field>
|
||||
<originalKey>Abundance Level (FIRMS Standard)</originalKey>
|
||||
<modifiedKey>none:none</modifiedKey>
|
||||
</field>
|
||||
<field>
|
||||
<originalKey>Abundance Level</originalKey>
|
||||
<modifiedKey>none:none</modifiedKey>
|
||||
</field>
|
||||
<field>
|
||||
<originalKey>Biomass</originalKey>
|
||||
<modifiedKey>none:none</modifiedKey>
|
||||
</field>
|
||||
<field>
|
||||
<originalKey>Fishing Pressure (FIRMS Standard)</originalKey>
|
||||
<modifiedKey>none:none</modifiedKey>
|
||||
</field>
|
||||
<field>
|
||||
<originalKey>Fishing Pressure</originalKey>
|
||||
<modifiedKey>none:none</modifiedKey>
|
||||
</field>
|
||||
<field>
|
||||
<originalKey>State and Trend</originalKey>
|
||||
<modifiedKey>none:none</modifiedKey>
|
||||
</field>
|
||||
<field>
|
||||
<originalKey>FAO Stock Status Category</originalKey>
|
||||
<modifiedKey>none:none</modifiedKey>
|
||||
</field>
|
||||
<field>
|
||||
<originalKey>Scientific Advice</originalKey>
|
||||
<modifiedKey>none:none</modifiedKey>
|
||||
</field>
|
||||
<field>
|
||||
<originalKey>Assessor</originalKey>
|
||||
<modifiedKey>none:none</modifiedKey>
|
||||
</field>
|
||||
<field>
|
||||
<originalKey>GRSF Type</originalKey>
|
||||
<modifiedKey>stock_identity:GRSF Type</modifiedKey>
|
||||
</field>
|
||||
</fields>
|
||||
</Body>
|
||||
</Profile>
|
||||
</Resource>
|
|
@ -1,115 +0,0 @@
|
|||
<Resource version="0.4.x">
|
||||
<ID>c9cad3f8-5773-4ca7-95a5-4692db5eae2e</ID>
|
||||
<Type>GenericResource</Type>
|
||||
<Scopes>
|
||||
<Scope>/d4science.research-infrastructures.eu/FARM</Scope>
|
||||
<Scope>/d4science.research-infrastructures.eu/FARM/GRSF_Admin</Scope>
|
||||
</Scopes>
|
||||
<Profile>
|
||||
<SecondaryType>ApplicationProfile</SecondaryType>
|
||||
<Name>GRSF Stock</Name>
|
||||
<Description>GRSF mapping between fields and namespaces for Stock
|
||||
records</Description>
|
||||
<Body>
|
||||
<fields>
|
||||
<field>
|
||||
<originalKey>Data Owner</originalKey>
|
||||
<modifiedKey>stock_data:Data Owner</modifiedKey>
|
||||
</field>
|
||||
<field>
|
||||
<originalKey>Database Source</originalKey>
|
||||
<modifiedKey>stock_identity:Database Source</modifiedKey>
|
||||
</field>
|
||||
<field>
|
||||
<originalKey>Short Name</originalKey>
|
||||
<modifiedKey>stock_identity:Short Name</modifiedKey>
|
||||
</field>
|
||||
<field>
|
||||
<originalKey>Catch</originalKey>
|
||||
<modifiedKey>stock_data:Catch</modifiedKey>
|
||||
</field>
|
||||
<field>
|
||||
<originalKey>Landing</originalKey>
|
||||
<modifiedKey>stock_data:Landing</modifiedKey>
|
||||
</field>
|
||||
<field>
|
||||
<originalKey>Species</originalKey>
|
||||
<modifiedKey>stock_identity:Species</modifiedKey>
|
||||
</field>
|
||||
<field>
|
||||
<originalKey>Similar GRSF Record</originalKey>
|
||||
<modifiedKey>stock_identity:Similar GRSF Record</modifiedKey>
|
||||
</field>
|
||||
<field>
|
||||
<originalKey>Management Body/Authority</originalKey>
|
||||
<modifiedKey>stock_identity:Management Body/Authority</modifiedKey>
|
||||
</field>
|
||||
<field>
|
||||
<originalKey>Connected Record</originalKey>
|
||||
<modifiedKey>stock_identity:Connected Record</modifiedKey>
|
||||
</field>
|
||||
<field>
|
||||
<originalKey>GRSF Stock Name</originalKey>
|
||||
<modifiedKey>stock_identity:GRSF Stock Name</modifiedKey>
|
||||
</field>
|
||||
<field>
|
||||
<originalKey>GRSF Semantic Identifier</originalKey>
|
||||
<modifiedKey>stock_identity:GRSF Semantic Identifier</modifiedKey>
|
||||
</field>
|
||||
<field>
|
||||
<originalKey>Assessment Area</originalKey>
|
||||
<modifiedKey>stock_identity:Assessment Area</modifiedKey>
|
||||
</field>
|
||||
<field>
|
||||
<originalKey>Exploiting Fishery</originalKey>
|
||||
<modifiedKey>stock_identity:Exploiting Fishery</modifiedKey>
|
||||
</field>
|
||||
<field>
|
||||
<originalKey>Assessment Method</originalKey>
|
||||
<modifiedKey>stock_data:Assessment Method</modifiedKey>
|
||||
</field>
|
||||
<field>
|
||||
<originalKey>Abundance Level (FIRMS Standard)</originalKey>
|
||||
<modifiedKey>stock_data:Abundance Level (FIRMS Standard)
|
||||
</modifiedKey>
|
||||
</field>
|
||||
<field>
|
||||
<originalKey>Abundance Level</originalKey>
|
||||
<modifiedKey>stock_data:Abundance Level</modifiedKey>
|
||||
</field>
|
||||
<field>
|
||||
<originalKey>Biomass</originalKey>
|
||||
<modifiedKey>stock_data:Biomass</modifiedKey>
|
||||
</field>
|
||||
<field>
|
||||
<originalKey>Fishing Pressure (FIRMS Standard)</originalKey>
|
||||
<modifiedKey>stock_data:Fishing Pressure (FIRMS Standard)</modifiedKey>
|
||||
</field>
|
||||
<field>
|
||||
<originalKey>Fishing Pressure</originalKey>
|
||||
<modifiedKey>stock_data:Fishing Pressure</modifiedKey>
|
||||
</field>
|
||||
<field>
|
||||
<originalKey>State and Trend</originalKey>
|
||||
<modifiedKey>stock_data:State and Trend</modifiedKey>
|
||||
</field>
|
||||
<field>
|
||||
<originalKey>FAO Stock Status Category</originalKey>
|
||||
<modifiedKey>stock_data:FAO Stock Status Category</modifiedKey>
|
||||
</field>
|
||||
<field>
|
||||
<originalKey>Scientific Advice</originalKey>
|
||||
<modifiedKey>stock_data:Scientific Advice</modifiedKey>
|
||||
</field>
|
||||
<field>
|
||||
<originalKey>Assessor</originalKey>
|
||||
<modifiedKey>stock_data:Assessor</modifiedKey>
|
||||
</field>
|
||||
<field>
|
||||
<originalKey>GRSF Type</originalKey>
|
||||
<modifiedKey>stock_identity:GRSF Type</modifiedKey>
|
||||
</field>
|
||||
</fields>
|
||||
</Body>
|
||||
</Profile>
|
||||
</Resource>
|
|
@ -1,40 +0,0 @@
|
|||
<Resource version="0.4.x">
|
||||
|
||||
<ID>7ee9c6e9-ff73-4428-88e4-185aeb4b3742</ID>
|
||||
|
||||
<Type>GenericResource</Type>
|
||||
|
||||
<Scopes>
|
||||
|
||||
<Scope>/d4science.research-infrastructures.eu/FARM/GRSF_Pre</Scope>
|
||||
|
||||
<Scope>/d4science.research-infrastructures.eu/FARM/GRSF_Admin</Scope>
|
||||
|
||||
</Scopes>
|
||||
|
||||
<Profile>
|
||||
|
||||
<SecondaryType>ApplicationProfile</SecondaryType>
|
||||
|
||||
<Name>GRSFManageEntries</Name>
|
||||
|
||||
<Description>A list of extras metadata to be looked up and prompted by the GRSF Manage widget. The body reports the key values.</Description>
|
||||
|
||||
<Body>
|
||||
fishery_identity:GRSF Type,
|
||||
fishery_identity:Short Name,
|
||||
fishery_identity:Database Source,
|
||||
fishery_identity:GRSF Semantic Identifier,
|
||||
fishery_data:Catch,
|
||||
fishery_data:Landing,
|
||||
stock_identity:GRSF Type,
|
||||
stock_identity:Short Name,
|
||||
stock_identity:Database Source,
|
||||
stock_identity:GRSF Semantic Identifier,
|
||||
stock_data:Catch,
|
||||
stock_data:Landing
|
||||
</Body>
|
||||
|
||||
</Profile>
|
||||
|
||||
</Resource>
|
|
@ -1,7 +1,7 @@
|
|||
<application mode='online'>
|
||||
<name>GRSFPublisher</name>
|
||||
<group>Data-Catalogue</group>
|
||||
<version>1.13.0</version>
|
||||
<version>1.5.0</version>
|
||||
<description>Data Catalogue Service</description>
|
||||
<local-persistence location='target' />
|
||||
<exclude>/rest/</exclude>
|
||||
|
|
|
@ -32,12 +32,6 @@
|
|||
<param-name>PublicVRE</param-name>
|
||||
<!-- <param-value>/gcube/devsec/devVRE</param-value> -->
|
||||
<param-value>/d4science.research-infrastructures.eu/FARM/GRSF</param-value>
|
||||
</context-param>
|
||||
<context-param>
|
||||
<description>Context of pending products under manage activities for prevalidation VRE</description>
|
||||
<param-name>PreValidateVRE</param-name>
|
||||
<!-- <param-value>/gcube/devNext/NextNext</param-value> -->
|
||||
<param-value>/d4science.research-infrastructures.eu/FARM/GRSF_Pre</param-value>
|
||||
</context-param>
|
||||
<welcome-file-list>
|
||||
<welcome-file>index.jsp</welcome-file>
|
||||
|
|
|
@ -13,6 +13,17 @@ import java.util.HashMap;
|
|||
import java.util.List;
|
||||
import java.util.Map;
|
||||
|
||||
import org.gcube.common.authorization.library.provider.SecurityTokenProvider;
|
||||
import org.gcube.common.homelibrary.home.HomeLibrary;
|
||||
import org.gcube.common.homelibrary.home.exceptions.InternalErrorException;
|
||||
import org.gcube.common.homelibrary.home.workspace.Workspace;
|
||||
import org.gcube.common.homelibrary.home.workspace.WorkspaceFolder;
|
||||
import org.gcube.common.homelibrary.home.workspace.WorkspaceItem;
|
||||
import org.gcube.common.homelibrary.home.workspace.WorkspaceSharedFolder;
|
||||
import org.gcube.common.homelibrary.home.workspace.catalogue.WorkspaceCatalogue;
|
||||
import org.gcube.common.homelibrary.home.workspace.exceptions.InsufficientPrivilegesException;
|
||||
import org.gcube.common.homelibrary.home.workspace.exceptions.ItemAlreadyExistException;
|
||||
import org.gcube.common.scope.api.ScopeProvider;
|
||||
import org.gcube.data_catalogue.grsf_publish_ws.custom_annotations.CustomField;
|
||||
import org.gcube.data_catalogue.grsf_publish_ws.custom_annotations.Group;
|
||||
import org.gcube.data_catalogue.grsf_publish_ws.custom_annotations.Tag;
|
||||
|
@ -227,8 +238,129 @@ public class JTests {
|
|||
instance.uploadResourceFile(csvFile, datasetName, instance.getApiKeyFromUsername("costantino.perciante"), "random_name.csv", null, null, null);
|
||||
}
|
||||
|
||||
// @Test
|
||||
public void sharedVREFolderWriteTest() throws Exception{
|
||||
|
||||
String token = "";
|
||||
String context = "/gcube/devNext/NextNext";
|
||||
|
||||
ScopeProvider.instance.set(context);
|
||||
SecurityTokenProvider.instance.set(token);
|
||||
|
||||
Workspace ws = HomeLibrary.getHomeManagerFactory().getHomeManager().getHome().getWorkspace();
|
||||
|
||||
// Get a VRE folder by scope
|
||||
WorkspaceSharedFolder vreFolder = ws.getVREFolderByScope(context);
|
||||
|
||||
//Get the VRE Folder catalogue
|
||||
WorkspaceCatalogue catalogueFolder = vreFolder.getVRECatalogue();
|
||||
|
||||
logger.debug("Catalogue folder retrieved " + catalogueFolder.getName());
|
||||
|
||||
// WorkspaceItem stockFolder = catalogueFolder.find("stock");
|
||||
|
||||
// vreFolder.removeChild(stockFolder);
|
||||
|
||||
/**
|
||||
* Test is
|
||||
* .catalogue:
|
||||
* -test
|
||||
* - a
|
||||
* -aproductwiththisname
|
||||
* - csv
|
||||
* - testfile.csv
|
||||
*/
|
||||
|
||||
String allSubPath = "/test/a/aproductwiththisname/";
|
||||
//WorkspaceFolder lastFolder = createGetSubFoldersByPath(catalogueFolder, allSubPath);
|
||||
// WorkspaceFolder recordFolder = (WorkspaceFolder)getFolderOrCreate(catalogueFolder, "test", "");
|
||||
// String firstLetter = "a";
|
||||
// WorkspaceFolder firstLetterFolder = (WorkspaceFolder)getFolderOrCreate(recordFolder, firstLetter, "");
|
||||
// String folderPath = "aproductwiththisname";
|
||||
// WorkspaceFolder productFolder = (WorkspaceFolder)getFolderOrCreate(firstLetterFolder, folderPath, "");
|
||||
//logger.debug("Test folder created/get..its path is " + lastFolder.getPath());
|
||||
// String ccsvUnderProductFolderName = productFolderName + "/" + "csv";
|
||||
// WorkspaceFolder csvUnderProductFolder = (WorkspaceFolder)getFolderOrCreate(catalogueFolder, ccsvUnderProductFolderName, "");
|
||||
//
|
||||
// logger.debug("FOLDERS created " + csvUnderProductFolder.getPath());
|
||||
// treeCheck(catalogueFolder);
|
||||
|
||||
}
|
||||
|
||||
public void treeCheck(WorkspaceFolder rootFolder) throws InternalErrorException{
|
||||
List<WorkspaceItem> children = rootFolder.getChildren();
|
||||
for (WorkspaceItem workspaceItem : children) {
|
||||
if(workspaceItem.isFolder()){
|
||||
logger.debug("children folder is " + workspaceItem.getName());
|
||||
treeCheck((WorkspaceFolder)workspaceItem);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/**
|
||||
* Create subfolders in cascade, returning the last created ones
|
||||
* It could be also used for getting them if they already exists
|
||||
* @param folder
|
||||
* @param subPath
|
||||
* @return
|
||||
*/
|
||||
private static WorkspaceFolder createGetSubFoldersByPath(WorkspaceFolder folder, String subPath){
|
||||
|
||||
String pathSeparator = "/";
|
||||
WorkspaceFolder parentFolder = folder;
|
||||
if(folder == null)
|
||||
throw new IllegalArgumentException("Root folder is null!");
|
||||
|
||||
if(subPath == null || subPath.isEmpty())
|
||||
throw new IllegalArgumentException("subPath is null/empty!");
|
||||
|
||||
try{
|
||||
if(subPath.startsWith(pathSeparator))
|
||||
subPath = subPath.replaceFirst(pathSeparator, "");
|
||||
|
||||
if(subPath.endsWith(subPath))
|
||||
subPath = subPath.substring(0, subPath.length() - 1);
|
||||
|
||||
logger.debug("Splitting path " + subPath);
|
||||
|
||||
String[] splittedPaths = subPath.split(pathSeparator);
|
||||
|
||||
for (String path : splittedPaths) {
|
||||
WorkspaceFolder createdFolder = getFolderOrCreate(parentFolder, path, "");
|
||||
logger.debug("Created subfolder with path " + createdFolder.getPath());
|
||||
parentFolder = createdFolder;
|
||||
}
|
||||
|
||||
}catch(Exception e){
|
||||
logger.error("Failed to create the subfolders by path " + subPath);
|
||||
}
|
||||
|
||||
return parentFolder;
|
||||
}
|
||||
|
||||
/**
|
||||
* Get a folder within the catalogue folder or create it if it doesn't exist.
|
||||
* @return
|
||||
*/
|
||||
private static WorkspaceFolder getFolderOrCreate(WorkspaceFolder folder, String relativePath, String descriptionFolder){
|
||||
WorkspaceFolder result = null;
|
||||
try {
|
||||
if(folder.exists(relativePath) && folder.find(relativePath).isFolder())
|
||||
result = (WorkspaceFolder) folder.find(relativePath);
|
||||
if(result != null)
|
||||
logger.debug("Folder found with name " + result.getName() + ", it has id " + result.getId());
|
||||
else
|
||||
throw new Exception("There is no folder with name " + relativePath + " under foler " + folder.getName());
|
||||
} catch (Exception e) {
|
||||
logger.debug("Probably the folder doesn't exist", e);
|
||||
try{
|
||||
result = folder.createFolder(relativePath, descriptionFolder);
|
||||
} catch (InsufficientPrivilegesException | InternalErrorException | ItemAlreadyExistException e2) {
|
||||
logger.error("Failed to get or generate this folder", e2);
|
||||
}
|
||||
}
|
||||
return result;
|
||||
}
|
||||
|
||||
//@Test
|
||||
public void GRSFServiceUrl() throws Exception{
|
||||
|
@ -270,7 +402,7 @@ public class JTests {
|
|||
}
|
||||
|
||||
//@Test
|
||||
public void testCaches() throws Exception{
|
||||
public void testCaches(){
|
||||
|
||||
String context = "/gcube/devNext/NextNext";
|
||||
String token = "";
|
||||
|
|
|
@ -1,38 +0,0 @@
|
|||
package org.gcube.data_catalogue.grsf_publish_ws;
|
||||
|
||||
import java.io.File;
|
||||
import java.net.URL;
|
||||
|
||||
import org.gcube.data_catalogue.grsf_publish_ws.json.input.record.StockRecord;
|
||||
import org.junit.Test;
|
||||
import org.slf4j.Logger;
|
||||
import org.slf4j.LoggerFactory;
|
||||
|
||||
import com.fasterxml.jackson.databind.JsonNode;
|
||||
import com.fasterxml.jackson.databind.ObjectMapper;
|
||||
|
||||
/**
|
||||
* @author Luca Frosini (ISTI - CNR)
|
||||
*/
|
||||
public class TestJson {
|
||||
|
||||
private static final Logger logger = LoggerFactory.getLogger(Test.class);
|
||||
|
||||
public File getResourcesDirectory() throws Exception {
|
||||
URL logbackFileURL = TestJson.class.getClassLoader().getResource("logback-test.xml");
|
||||
File logbackFile = new File(logbackFileURL.toURI());
|
||||
File resourcesDirectory = logbackFile.getParentFile();
|
||||
return resourcesDirectory;
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testJsonDeserialization() throws Exception {
|
||||
File jsonQueryFile = new File(getResourcesDirectory(), "70ae6895-7d3d-4f4a-86f9-bcb17d41bff6.json");
|
||||
ObjectMapper objectMapper = new ObjectMapper();
|
||||
JsonNode jsonNode = objectMapper.readTree(jsonQueryFile);
|
||||
logger.debug("{}", jsonNode);
|
||||
StockRecord sr = objectMapper.readValue(jsonQueryFile, StockRecord.class);
|
||||
logger.debug("{}", sr);
|
||||
}
|
||||
|
||||
}
|
|
@ -1,34 +0,0 @@
|
|||
{
|
||||
"stock_name" : "European hake - Southern Adriatic",
|
||||
"license_id" : "CC-BY-SA-4.0",
|
||||
"version" : 1.0,
|
||||
"database_sources" : [ {
|
||||
"name" : "FAO SDG 14.4.1 questionnaire",
|
||||
"description" : "FAO SDG 14.4.1 questionnaire",
|
||||
"url" : "https://www.fao.org/sustainable-development-goals/indicators/14.4.1/en/"
|
||||
} ],
|
||||
"stock_uri" : "https://github.com/grsf/resource/sdg_14_4_1/stock/70ae6895-7d3d-4f4a-86f9-bcb17d41bff6",
|
||||
"grsf_uuid" : "70ae6895-7d3d-4f4a-86f9-bcb17d41bff6",
|
||||
"short_name" : "European hake - Southern Adriatic",
|
||||
"description" : "European hake - Southern Adriatic",
|
||||
"grsf_type" : "assessment unit",
|
||||
"species" : [ "Code: HKE, Classification System: ASFIS, Scientific Name: Merluccius merluccius" ],
|
||||
"assessment_area" : [ "Code: 18, System: gfcm, Name: Southern Adriatic " ],
|
||||
"source_of_information" : [ {
|
||||
"name" : "https://www.fao.org/sustainable-development-goals/indicators/14.4.1/en/sdg-alb-1",
|
||||
"description" : "",
|
||||
"url" : "https://www.fao.org/sustainable-development-goals/indicators/14.4.1/en/sdg-alb-1"
|
||||
} ],
|
||||
"data_owner" : [ "Albania" ],
|
||||
"assessment_methods" : [ "The official stock assessment concludes 'Overfished' with respect to abundance reference points. [Rep. Year or Assessment ID: 2019, Ref. Year: 2018]" ],
|
||||
"connections_indicator" : "not connected",
|
||||
"similarities_indicator" : "without similar records",
|
||||
"landings" : [ {
|
||||
"value" : "872",
|
||||
"unit" : "Tonnes",
|
||||
"reference_year" : 2018,
|
||||
"reporting_year_or_assessment_id" : "2020",
|
||||
"data_owner" : "Albania"
|
||||
} ],
|
||||
"citation" : "citation TBD"
|
||||
}
|
|
@ -1,19 +0,0 @@
|
|||
<?xml version="1.0" encoding="UTF-8"?>
|
||||
<!DOCTYPE xml>
|
||||
<configuration>
|
||||
|
||||
<appender name="STDOUT" class="ch.qos.logback.core.ConsoleAppender">
|
||||
<encoder>
|
||||
<pattern>%d{HH:mm:ss.SSS} [%thread] %-5level %logger{0}: %msg%n</pattern>
|
||||
</encoder>
|
||||
</appender>
|
||||
|
||||
|
||||
<logger name="org.gcube" level="INFO" />
|
||||
<logger name="org.gcube.data_catalogue.grsf_publish_ws" level="TRACE" />
|
||||
|
||||
<root level="WARN">
|
||||
<appender-ref ref="STDOUT" />
|
||||
</root>
|
||||
|
||||
</configuration>
|
Loading…
Reference in New Issue