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gcat
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Merge remote-tracking branch 'origin/feature/20225'

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Luca Frosini 2023-02-01 09:51:29 +01:00
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commit b01fdcb81c
7 changed files with 373 additions and 53 deletions
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18
CHANGELOG.md
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@ -9,7 +9,7 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm
- Set resource-registry-publisher dependency scope to provided
- Switching to Facet Based IS [#20225]
## [v2.4.1]
## [v2.4.1] [r5.14.0] - 2022-12-07
- Integrating Sphinx for documentation [#23833]
- Migrated Social service interaction to social-service-client [#23151]
@ -17,7 +17,7 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm
- Fixed item listing [#23901]
## [v2.4.0]
## [v2.4.0] [r5.13.1] - 2022-09-16
- Added moderation link in moderation message [#23142]
- Added query parameter in item listing to get the whole item instead of just the name [#23691]
@ -25,13 +25,13 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm
- Explict request for approved items return only moderated and approved [#23696]
## [v2.3.0]
## [v2.3.0] [r5.13.0] - 2022-07-22
- Switched moderation messages to notification [#23317]
- Item listing returns items in the default organization and not in all supported organization
## [v2.2.0]
## [v2.2.0] [r5.11.0] - 2022-05-12
- Switched gcat credentials to new IAM authz [#21628][#22727]
- Added support to manage configurations [#22658][#22742]
@ -44,7 +44,7 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm
- ClientID requests are now properly supported [#21903]
## [v2.1.0]
## [v2.1.0] [r5.7.0] - 2022-01-27
- Added query parameter social_post_notification to override default VRE behaviour [#21345]
- Users are created/referenced in the form <Surname Name> and not vice-versa [#21479]
@ -79,7 +79,7 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm
- Switched JSON management to gcube-jackson [#19735]
## [v1.4.3] [r4.23.0] - 2020-06-19
## [v1.4.3] [r4.23.0] - 2020-06-16
- Social Post is disabled if not explicitly enabled by the client [#19295]
- Solved null pointer exception while creating the JSON object to send to CKAN to create the user [#19395]
@ -110,7 +110,7 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm
- Resource URL existence is not checked anymore [#16748]
## [v1.2.0]
## [v1.2.0-SNAPSHOT] - 2019-05-20
- Separated REST class for Profile management from the logic which effectively manage profile on IS
- Tags are now properly created/added according to profile definition [#16182]
@ -137,7 +137,7 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm
- Refactored to use gcat-api library
## [v1.0.0]
## [v1.0.0-SNAPSHOT] - 2019-01-10
- First Release
- First Version

26
FUNDING.md Normal file
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@ -0,0 +1,26 @@
# Acknowledgments
The projects leading to this software have received funding from a series of European Union programmes including:
- the Sixth Framework Programme for Research and Technological Development
- [DILIGENT](https://cordis.europa.eu/project/id/004260) (grant no. 004260).
- the Seventh Framework Programme for research, technological development and demonstration
- [D4Science](https://cordis.europa.eu/project/id/212488) (grant no. 212488);
- [D4Science-II](https://cordis.europa.eu/project/id/239019) (grant no.239019);
- [ENVRI](https://cordis.europa.eu/project/id/283465) (grant no. 283465);
- [iMarine](https://cordis.europa.eu/project/id/283644) (grant no. 283644);
- [EUBrazilOpenBio](https://cordis.europa.eu/project/id/288754) (grant no. 288754).
- the H2020 research and innovation programme
- [SoBigData](https://cordis.europa.eu/project/id/654024) (grant no. 654024);
- [PARTHENOS](https://cordis.europa.eu/project/id/654119) (grant no. 654119);
- [EGI-Engage](https://cordis.europa.eu/project/id/654142) (grant no. 654142);
- [ENVRI PLUS](https://cordis.europa.eu/project/id/654182) (grant no. 654182);
- [BlueBRIDGE](https://cordis.europa.eu/project/id/675680) (grant no. 675680);
- [PerformFISH](https://cordis.europa.eu/project/id/727610) (grant no. 727610);
- [AGINFRA PLUS](https://cordis.europa.eu/project/id/731001) (grant no. 731001);
- [DESIRA](https://cordis.europa.eu/project/id/818194) (grant no. 818194);
- [ARIADNEplus](https://cordis.europa.eu/project/id/823914) (grant no. 823914);
- [RISIS 2](https://cordis.europa.eu/project/id/824091) (grant no. 824091);
- [EOSC-Pillar](https://cordis.europa.eu/project/id/857650) (grant no. 857650);
- [Blue Cloud](https://cordis.europa.eu/project/id/862409) (grant no. 862409);
- [SoBigData-PlusPlus](https://cordis.europa.eu/project/id/871042) (grant no. 871042);

41
README.md
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@ -13,7 +13,7 @@ This service allows any client to publish on the gCube Catalogue.
## Change log
See [Releases](https://code-repo.d4science.org/gCubeSystem/gcat/releases).
See [CHANGELOG.md](CHANGELOG.md).
## Authors
@ -25,15 +25,13 @@ Tell people how to cite this software.
* Cite an associated paper?
* Use a specific BibTeX entry for the software?
@Manual{,
title = {gCube Catalogue (gCat) Service},
author = {{Frosini, Luca}},
organization = {ISTI - CNR},
address = {Pisa, Italy},
year = 2019,
url = {http://www.gcube-system.org/}
}
@software{gcat,
author = {{Luca Frosini}},
title = {gCube Catalogue (gCat) Service},
abstract = {gCube Catalogue (gCat) Service allows the publication of items in the gCube Catalogue.},
url = {https://doi.org/10.5281/zenodo.7446641},
keywords = {Catalogue, D4Science, gCube}
}
## License
@ -46,26 +44,5 @@ 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);
The projects leading to this software have received funding from a series of European Union programmes see [FUNDING.md](FUNDING.md)

4
docs/conf.py
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@ -17,12 +17,12 @@
# -- Project information -----------------------------------------------------
project = 'gCube Catalogue Service (aka gCat)'
project = 'gCube Catalogue (gCat) Service'
copyright = '2022, Luca Frosini (ISTI-CNR)'
author = 'Luca Frosini (ISTI-CNR)'
# The full version, including alpha/beta/rc tags
release = '2.4.1-SNAPSHOT'
release = '2.5.0-SNAPSHOT'
# -- General configuration ---------------------------------------------------

321
gcube/gcat-export.json Normal file
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@ -0,0 +1,321 @@
{
"global": {
"name": "gcat",
"group": "data-catalogue",
"title": "gCube Catalogue (gCat) Service {{version}}",
"license": {
"id": "EUPL-1.1",
"url": "https://opensource.org/licenses/EUPL-1.1"
},
"keywords": ["gCube", "Catalogue", "D4Science"],
"description": "gCube Catalogue (gCat) Service allows the publication of items in the gCube Catalogue.",
"html_description": "<p><a href=\"https://www.gcube-system.org/\">gCube</a> Catalogue (gCat) Service allows any client to publish items in the gCube Catalogue.</p>",
"authors": [
{
"affiliation": "Istituto di Scienza e Tecnologie dell'Informazione \"A. Faedo\" - CNR, Italy",
"name": "Frosini, Luca",
"orcid": "0000-0003-3183-2291"
}
],
"files": [
{
"url": "https://code-repo.d4science.org/gCubeSystem/{{name}}/archive/v{{version}}.zip",
"desired_name": "{{name}}-v{{version}}.zip"
},
{
"url": "https://code-repo.d4science.org/gCubeSystem/{{name}}/archive/v{{version}}.tar.gz",
"desired_name": "{{name}}-v{{version}}.tar.gz"
},
{
"url": "https://nexus.d4science.org/nexus/service/local/repo_groups/gcube-releases-all/content/org/gcube/{{group}}/{{name}}/{{version}}/{{name}}-{{version}}.war",
"desired_name": "{{name}}-v{{version}}.war"
}
],
"code_location": "https://code-repo.d4science.org/gCubeSystem/{{name}}/releases/tag/v{{version}}",
"grants": [
{
"id": "004260",
"name": "DILIGENT",
"url": "https://cordis.europa.eu/project/id/004260"
},
{
"id": "212488",
"name": "D4Science",
"url": "https://cordis.europa.eu/project/id/212488"
},
{
"id": "239019",
"name": "D4Science-II",
"url": "https://cordis.europa.eu/project/id/239019"
},
{
"id": "283465",
"name": "ENVRI",
"url": "https://cordis.europa.eu/project/id/283465"
},
{
"id": "283644",
"name": "iMarine",
"url": "https://cordis.europa.eu/project/id/283644"
},
{
"id": "288754",
"name": "EUBrazilOpenBio",
"url": "https://cordis.europa.eu/project/id/288754"
},
{
"id": "654024",
"name": "SoBigData",
"url": "https://cordis.europa.eu/project/id/654024"
},
{
"id": "654119",
"name": "PARTHENOS",
"url": "https://cordis.europa.eu/project/id/654119"
},
{
"id": "654142",
"name": "EGI-Engage",
"url": "https://cordis.europa.eu/project/id/654142"
},
{
"id": "654182",
"name": "ENVRI PLUS",
"url": "https://cordis.europa.eu/project/id/654182"
},
{
"id": "675680",
"name": "BlueBRIDGE",
"url": "https://cordis.europa.eu/project/id/675680"
},
{
"id": "727610",
"name": "PerformFISH",
"url": "https://cordis.europa.eu/project/id/727610"
},
{
"id": "731001",
"name": "AGINFRA PLUS",
"url": "https://cordis.europa.eu/project/id/731001"
},
{
"id": "818194",
"name": "DESIRA",
"url": "https://cordis.europa.eu/project/id/818194"
},
{
"id": "823914",
"name": "ARIADNEplus",
"url": "https://cordis.europa.eu/project/id/823914"
},
{
"id": "824091",
"name": "RISIS 2",
"url": "https://cordis.europa.eu/project/id/824091"
},
{
"id": "857650",
"name": "EOSC-Pillar",
"url": "https://cordis.europa.eu/project/id/857650"
},
{
"id": "862409",
"name": "Blue Cloud",
"url": "https://cordis.europa.eu/project/id/862409"
},
{
"id": "871042",
"name": "SoBigData-PlusPlus",
"url": "https://cordis.europa.eu/project/id/871042"
}
],
"publishers": {
"ZenodoSoftwareVersionPublisher": {
"elaboration": "NONE",
"additional_html_description": "\n\n<p><a href=\"https://www.gcube-system.org/\">gCube</a> is an open-source software toolkit used for building and operating Hybrid Data Infrastructures enabling the dynamic deployment of Virtual Research Environments, such as the <a href=\"https://www.d4science.org/\">D4Science Infrastructure</a>, by favouring the realisation of reuse-oriented policies.</p>\n\n<p><a href=\"https://www.gcube-system.org/\">gCube</a> has been used to successfully build and operate infrastructures and virtual research environments for application domains ranging from biodiversity to environmental data management and cultural heritage.</p>\n\n<p><a href=\"https://www.gcube-system.org/\">gCube</a> offers components supporting typical data management workflows including data access, curation, processing, and visualisation on a large set of data typologies ranging from primary biodiversity data to geospatial and tabular data.</p>\n\n<p><a href=\"https://www.d4science.org/\">D4Science</a> is a Hybrid Data Infrastructure combining over 500 software components and integrating data from more than 50 different data providers into a coherent and managed system of hardware, software, and data resources. The D4Science infrastructure drastically reduces the cost of ownership, maintenance, and operation thanks to the exploitation of gCube.</p>\n\n<p>&nbsp;</p>\n\n<p>The official source code location of this software version is available at:</p>\n\n<p><a href=\"{{code_location}}\">{{code_location}}</a></p>",
"skip_grants": ["004260"]
}
},
"exporters": {
"BibLaTeXSoftwareVersionExporter": {
"elaboration": "ALL"
}
},
"export_filename": "{{name}}"
},
"versions": [
{
"version": "1.0.0",
"date": "2019-01-10",
"group": "data-publishing",
"files": [
{
"url": "https://nexus.d4science.org/nexus/service/local/repositories/gcube-snapshots/content/org/gcube/data-publishing/gcat/1.0.0-SNAPSHOT/gcat-1.0.0-20190109.172827-2.war",
"desired_name": "{{name}}-v{{version}}.war"
}
],
"gcube_release_version": null,
"gcube_release_ticket": null,
"concept_doi_url": null,
"version_doi_url": null,
"code_location": "https://code-repo.d4science.org/gCubeSystem/{{name}}"
},
{
"version": "1.1.0",
"date": "2019-02-26",
"group": "data-publishing",
"files": [
{
"url": "https://nexus.d4science.org/nexus/service/local/repo_groups/gcube-releases-all/content/org/gcube/data-publishing/gcat/1.1.0-4.13.1-177071/gcat-1.1.0-4.13.1-177071-src.zip",
"desired_name": "{{name}}-v{{version}}.zip"
},
{
"url": "https://nexus.d4science.org/nexus/service/local/repo_groups/gcube-releases-all/content/org/gcube/data-publishing/gcat/1.1.0-4.13.1-177071/gcat-1.1.0-4.13.1-177071.war",
"desired_name": "{{name}}-v{{version}}.war"
}
],
"gcube_release_version": "4.13.1",
"gcube_release_ticket": "https://support.d4science.org/issues/12988",
"concept_doi_url": "PREVIOUS",
"version_doi_url": null,
"code_location": "https://code-repo.d4science.org/gCubeSystem/{{name}}"
},
{
"version": "1.2.0",
"date": "2019-05-20",
"group": "data-publishing",
"files": [
{
"url": "https://nexus.d4science.org/nexus/service/local/repositories/gcube-snapshots/content/org/gcube/data-publishing/gcat/1.2.0-SNAPSHOT/gcat-1.2.0-20190520.132914-10.war",
"desired_name": "{{name}}-v{{version}}.war"
}
],
"gcube_release_version": null,
"gcube_release_ticket": null,
"concept_doi_url": "PREVIOUS",
"version_doi_url": null,
"code_location": "https://code-repo.d4science.org/gCubeSystem/{{name}}"
},
{
"version": "1.3.0",
"date": "2019-06-27",
"group": "data-publishing",
"files": [
{
"url": "https://nexus.d4science.org/nexus/service/local/repo_groups/gcube-releases-all/content/org/gcube/data-publishing/gcat/1.3.0-4.14.0-179505/gcat-1.3.0-4.14.0-179505-src.zip",
"desired_name": "{{name}}-v{{version}}.zip"
},
{
"url": "https://nexus.d4science.org/nexus/service/local/repo_groups/gcube-releases-all/content/org/gcube/data-publishing/gcat/1.3.0-4.14.0-179505/gcat-1.3.0-4.14.0-179505.war",
"desired_name": "{{name}}-v{{version}}.war"
}
],
"gcube_release_version": "4.14.0",
"gcube_release_ticket": "https://support.d4science.org/issues/16743",
"concept_doi_url": "PREVIOUS",
"version_doi_url": null,
"code_location": "https://code-repo.d4science.org/gCubeSystem/{{name}}"
},
{
"version": "1.4.0",
"date": "2019-11-06",
"group": "data-publishing",
"gcube_release_version": "4.15.0",
"gcube_release_ticket": "https://support.d4science.org/issues/17294",
"concept_doi_url": "PREVIOUS",
"version_doi_url": null
},
{
"version": "1.4.1",
"date": "2019-12-20",
"group": "data-publishing",
"gcube_release_version": "4.18.0",
"gcube_release_ticket": "https://support.d4science.org/issues/18335",
"concept_doi_url": "PREVIOUS",
"version_doi_url": null
},
{
"version": "1.4.2",
"date": "2020-02-14",
"group": "data-publishing",
"gcube_release_version": "4.20.0",
"gcube_release_ticket": "https://support.d4science.org/issues/18507",
"concept_doi_url": "PREVIOUS",
"version_doi_url": null
},
{
"version": "1.4.3",
"date": "2020-06-16",
"group": "data-publishing",
"gcube_release_version": "4.23.0",
"gcube_release_ticket": "https://support.d4science.org/issues/19322",
"concept_doi_url": "PREVIOUS",
"version_doi_url": null
},
{
"version": "1.4.4",
"date": "2021-02-24",
"group": "data-publishing",
"gcube_release_version": "5.0.0",
"gcube_release_ticket": "https://support.d4science.org/issues/20648",
"concept_doi_url": "PREVIOUS",
"version_doi_url": null
},
{
"version": "1.4.5",
"date": "2021-03-31",
"group": "data-publishing",
"gcube_release_version": "5.1.0",
"gcube_release_ticket": "https://support.d4science.org/issues/20920",
"concept_doi_url": "PREVIOUS",
"version_doi_url": null
},
{
"version": "2.0.0",
"date": "2021-05-04",
"gcube_release_version": "5.2.0",
"concept_doi_url": "https://doi.org/10.5281/zenodo.7446641",
"version_doi_url": "https://doi.org/10.5281/zenodo.7446642"
},
{
"version": "2.1.0",
"date": "2022-01-27",
"gcube_release_version": "5.7.0",
"gcube_release_ticket": "https://support.d4science.org/issues/21685/",
"concept_doi_url": "https://doi.org/10.5281/zenodo.7446641",
"version_doi_url": "https://doi.org/10.5281/zenodo.7447405"
},
{
"version": "2.2.0",
"date": "2022-05-12",
"gcube_release_version": "5.11.0",
"gcube_release_ticket": "https://support.d4science.org/issues/22943",
"concept_doi_url": "https://doi.org/10.5281/zenodo.7446641",
"version_doi_url": "https://doi.org/10.5281/zenodo.7447427"
},
{
"version": "2.3.0",
"date": "2022-07-22",
"gcube_release_version": "5.13.0",
"gcube_release_ticket": "https://support.d4science.org/issues/23374",
"concept_doi_url": "https://doi.org/10.5281/zenodo.7446641",
"version_doi_url": "https://doi.org/10.5281/zenodo.7448628"
},
{
"version": "2.4.0",
"date": "2022-09-16",
"gcube_release_version": "5.13.1",
"gcube_release_ticket": "https://support.d4science.org/issues/23650",
"concept_doi_url": "https://doi.org/10.5281/zenodo.7446641",
"version_doi_url": "https://doi.org/10.5281/zenodo.7448730"
},
{
"version": "2.4.1",
"date": "2022-12-07",
"gcube_release_version": "5.14.0",
"gcube_release_ticket": "https://support.d4science.org/issues/23885",
"concept_doi_url": "https://doi.org/10.5281/zenodo.7446641",
"version_doi_url": "https://doi.org/10.5281/zenodo.7467222"
}
]
}

4
src/main/java/org/gcube/gcat/rest/RequestFilter.java
View File

@ -32,7 +32,7 @@ public class RequestFilter implements ContainerRequestFilter, ContainerResponseF
public void filter(ContainerRequestContext requestContext) throws IOException {
logger.trace("PreMatching RequestFilter");
SecretManagerProvider.instance.reset();
SecretManagerProvider.instance.remove();
SecretManager secretManager = new SecretManager();
String token = AccessTokenProvider.instance.get();
@ -55,7 +55,7 @@ public class RequestFilter implements ContainerRequestFilter, ContainerResponseF
public void filter(ContainerRequestContext requestContext, ContainerResponseContext responseContext)
throws IOException {
logger.trace("ResponseFilter");
SecretManagerProvider.instance.reset();
SecretManagerProvider.instance.remove();
}
}

12
src/main/java/org/gcube/gcat/rest/administration/User.java
View File

@ -141,13 +141,8 @@ public class User extends REST<CKANUser> implements org.gcube.gcat.api.interface
@DELETE
// @AuthorizationControl(allowedRoles={Role.CATALOGUE_MANAGER}, exception=NotAuthorizedException.class)
public Response removeCallerFromCache() {
SecretManager secretManager = SecretManagerProvider.instance.get();
org.gcube.common.authorization.utils.user.User user = secretManager.getUser();
if(user.getRoles().contains(Role.MANAGER.getPortalRole())) {
CKANUserCache.removeUserFromCache();
}else {
throw new ForbiddenException("Only " + Role.MANAGER.getPortalRole() + "s are authorized to remove an user from the cache");
}
// Any user can remove self from cache
CKANUserCache.removeUserFromCache();
return Response.status(Status.NO_CONTENT).build();
}
@ -157,7 +152,8 @@ public class User extends REST<CKANUser> implements org.gcube.gcat.api.interface
public Response removeUserFromCache(@PathParam(GCUBE_USERNAME_PARAMETER) String username) {
SecretManager secretManager = SecretManagerProvider.instance.get();
org.gcube.common.authorization.utils.user.User user = secretManager.getUser();
if(user.getRoles().contains(Role.MANAGER.getPortalRole())) {
if(user.getRoles().contains(Role.MANAGER.getPortalRole()) || user.getUsername().compareTo(username)==0) {
// Any user can remove self from cache
CKANUserCache.removeUserFromCache(username);
}else {
throw new ForbiddenException("Only " + Role.MANAGER.getPortalRole() + "s are authorized to remove an user from the cache");