gCubeSystem
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software-versions-processor-lib
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improved solution

This commit is contained in:
Luca Frosini 2023-01-31 14:25:31 +01:00
parent 2ee0e60530
commit 18e77c9089
8 changed files with 81 additions and 54 deletions
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30
src/main/java/org/gcube/common/software/analyser/Analyser.java
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@ -61,6 +61,7 @@ public class Analyser {
} }
protected SoftwareVersionConfig actualizeSoftwareVersionConfig(JsonNode version) throws Exception { protected SoftwareVersionConfig actualizeSoftwareVersionConfig(JsonNode version) throws Exception {
((ObjectNode) version).remove(GlobalConfig.EXPORTERS_PROPERTY_NAME);
Variables variables = objectMapper.treeToValue(version, Variables.class); Variables variables = objectMapper.treeToValue(version, Variables.class);
Set<String> missingVariables = variables.parse(); Set<String> missingVariables = variables.parse();
int size = missingVariables.size(); int size = missingVariables.size();
@ -84,13 +85,26 @@ public class Analyser {
return softwareVersionConfig; return softwareVersionConfig;
} }
protected GlobalConfig actualizeGlobalConfig(JsonNode node) throws Exception { protected GlobalConfig getGlobalConfig(JsonNode node) throws Exception {
Variables variables = objectMapper.treeToValue(node, Variables.class); Variables variables = objectMapper.treeToValue(node, Variables.class);
variables.parse(); variables.parse();
JsonNode sc = objectMapper.convertValue(variables.getProperties(), JsonNode.class); JsonNode sc = objectMapper.convertValue(variables.getProperties(), JsonNode.class);
return objectMapper.treeToValue(sc, GlobalConfig.class); GlobalConfig globalConfig = objectMapper.treeToValue(sc, GlobalConfig.class);
globalConfig.setOriginalJson(globalConfiguration);
return globalConfig;
} }
protected ExporterConfig actualizeExporterConfig(ExporterConfig exporterConfig, SoftwareVersionConfig softwareVersionConfig) throws Exception {
ObjectNode versionNode = objectMapper.valueToTree(softwareVersionConfig);
Variables versionVariables = objectMapper.treeToValue(versionNode, Variables.class);
ObjectNode node = objectMapper.valueToTree(exporterConfig);
Variables variables = objectMapper.treeToValue(node, Variables.class);
variables.parseWith(versionVariables);
JsonNode ec = objectMapper.convertValue(variables.getProperties(), JsonNode.class);
return objectMapper.treeToValue(ec, ExporterConfig.class);
}
protected void checkExporters(Set<String> availableExporterNames, Set<String> requestedExporterNames) throws Exception { protected void checkExporters(Set<String> availableExporterNames, Set<String> requestedExporterNames) throws Exception {
if(!availableExporterNames.containsAll(requestedExporterNames)) { if(!availableExporterNames.containsAll(requestedExporterNames)) {
@ -102,9 +116,8 @@ public class Analyser {
public List<File> analyse() throws Exception { public List<File> analyse() throws Exception {
GlobalConfig globalConfig = actualizeGlobalConfig(globalConfiguration); GlobalConfig globalConfig = getGlobalConfig(globalConfiguration);
globalConfig.setOriginalJson(globalConfiguration);
Map<String, Class<? extends SoftwareVersionExporter>> availableExporters = SoftwareVersionExporter.getAvailableExporters(); Map<String, Class<? extends SoftwareVersionExporter>> availableExporters = SoftwareVersionExporter.getAvailableExporters();
Map<String,ExporterConfig> requestedExporters = globalConfig.getExporters(); Map<String,ExporterConfig> requestedExporters = globalConfig.getExporters();
checkExporters(availableExporters.keySet(), requestedExporters.keySet()); checkExporters(availableExporters.keySet(), requestedExporters.keySet());
@ -124,9 +137,9 @@ public class Analyser {
for(i=0; i<versionConfigurations.size(); i++) { for(i=0; i<versionConfigurations.size(); i++) {
ObjectNode versionConfig = (ObjectNode) versionConfigurations.get(i).deepCopy(); ObjectNode versionConfig = (ObjectNode) versionConfigurations.get(i).deepCopy();
JsonNode actualizedVersionConfig = Utils.merge(globalConfiguration, versionConfig); JsonNode mergedVersionConfig = Utils.merge(globalConfiguration, versionConfig);
SoftwareVersionConfig softwareVersionConfig = actualizeSoftwareVersionConfig(actualizedVersionConfig); SoftwareVersionConfig softwareVersionConfig = actualizeSoftwareVersionConfig(mergedVersionConfig);
softwareVersionConfig.setOriginalJson(versionConfig); softwareVersionConfig.setOriginalJson(versionConfig);
softwareVersionConfig.setPrevious(previous); softwareVersionConfig.setPrevious(previous);
@ -138,7 +151,8 @@ public class Analyser {
Class<? extends SoftwareVersionExporter> exporterClass = availableExporters.get(className); Class<? extends SoftwareVersionExporter> exporterClass = availableExporters.get(className);
ExporterConfig exporterConfig = requestedExporters.get(className); ExporterConfig exporterConfig = requestedExporters.get(className);
exporterConfig = actualizeExporterConfig(exporterConfig, softwareVersionConfig);
SoftwareVersionExporter sve = exporterClass.newInstance(); SoftwareVersionExporter sve = exporterClass.newInstance();
sve.setOutputDirectory(outputDirectory); sve.setOutputDirectory(outputDirectory);
sve.setGlobalConfig(globalConfig); sve.setGlobalConfig(globalConfig);

6
src/main/java/org/gcube/common/software/export/zenodo/ZenodoSoftwareVersionExporter.java
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@ -58,6 +58,7 @@ public class ZenodoSoftwareVersionExporter extends SoftwareVersionExporter {
public static final String SKIP_GRANTS_CONFIG_FIELD_NAME = "skip_grants"; public static final String SKIP_GRANTS_CONFIG_FIELD_NAME = "skip_grants";
public static final String METADATA_FIELD_NAME = "metadata"; public static final String METADATA_FIELD_NAME = "metadata";
public static final String COMMUNITIES_FIELD_NAME = "communities";
public static final String PREVIOUS = "PREVIOUS"; public static final String PREVIOUS = "PREVIOUS";
@ -326,6 +327,10 @@ public class ZenodoSoftwareVersionExporter extends SoftwareVersionExporter {
} }
return keywordsArrayNode; return keywordsArrayNode;
} }
private ArrayNode getCommunities() {
return (ArrayNode) softwareVersionConfig.getAdditionalProperty(COMMUNITIES_FIELD_NAME);
}
private String getLicense() { private String getLicense() {
return softwareVersionConfig.getLicense().get("id").asText(); return softwareVersionConfig.getLicense().get("id").asText();
@ -344,6 +349,7 @@ public class ZenodoSoftwareVersionExporter extends SoftwareVersionExporter {
metadata.put("upload_type", "software"); metadata.put("upload_type", "software");
metadata.replace("creators", getAuthors()); metadata.replace("creators", getAuthors());
metadata.put("description", getDescription()); metadata.put("description", getDescription());
metadata.replace("communities", getCommunities());
metadata.replace("grants", getGrants()); metadata.replace("grants", getGrants());
metadata.replace("keywords", getKeywords()); metadata.replace("keywords", getKeywords());
metadata.put("license", getLicense()); metadata.put("license", getLicense());

7
src/main/java/org/gcube/common/software/model/SoftwareVersionConfig.java
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@ -50,6 +50,9 @@ public class SoftwareVersionConfig {
@JsonIgnore @JsonIgnore
protected ObjectNode originalJson; protected ObjectNode originalJson;
@JsonProperty(NAME_PROPERTY_NAME)
protected String name;
@JsonProperty(VERSION_PROPERTY_NAME) @JsonProperty(VERSION_PROPERTY_NAME)
protected String version; protected String version;
@ -145,6 +148,10 @@ public class SoftwareVersionConfig {
this.originalJson = originalJson; this.originalJson = originalJson;
} }
public String getName() {
return name;
}
public String getVersion() { public String getVersion() {
return version; return version;
} }

12
src/main/java/org/gcube/common/software/utils/Utils.java
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@ -44,14 +44,14 @@ public class Utils {
/* /*
* Merge all the properties contained in version in concept * Merge all the properties contained in version in concept
*/ */
public static JsonNode merge(JsonNode concept, JsonNode version) { public static JsonNode merge(JsonNode node1, JsonNode node2) {
ObjectNode clonedConcept = concept.deepCopy(); ObjectNode cloned = node1.deepCopy();
Iterator<String> iterator = version.fieldNames(); Iterator<String> iterator = node2.fieldNames();
while (iterator.hasNext()) { while (iterator.hasNext()) {
String fieldName = iterator.next(); String fieldName = iterator.next();
JsonNode value = version.get(fieldName); JsonNode value = node2.get(fieldName);
clonedConcept.replace(fieldName, value.deepCopy()); cloned.replace(fieldName, value.deepCopy());
} }
return clonedConcept; return cloned;
} }
} }

4
src/test/java/org/gcube/common/software/analyser/AnalyserTest.java
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@ -15,8 +15,8 @@ public class AnalyserTest {
private static final Logger logger = LoggerFactory.getLogger(Analyser.class); private static final Logger logger = LoggerFactory.getLogger(Analyser.class);
// public static final String FILENAME = "gcat-test-sandbox.json"; public static final String FILENAME = "gcat-test-sandbox.json";
public static final String FILENAME = "gcat-from-scratch.json"; // public static final String FILENAME = "gcat-from-scratch.json";
@Test @Test
public void testUsingTestFile() throws Exception { public void testUsingTestFile() throws Exception {

1
src/test/resources/.gitignore vendored
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@ -1,2 +1,3 @@
/config.properties /config.properties
/zenodo.properties /zenodo.properties
/config.properties.prod

62
src/test/resources/gcat-from-scratch.json
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@ -9,6 +9,7 @@
}, },
"keywords": ["gCube", "Catalogue", "D4Science"], "keywords": ["gCube", "Catalogue", "D4Science"],
"description": "gCube Catalogue (gCat) Service allows the publication of items in the gCube Catalogue.", "description": "gCube Catalogue (gCat) Service allows the publication of items in the gCube Catalogue.",
"html_description": "<p>{{description}}</p>",
"authors": [ "authors": [
{ {
"affiliation": "Istituto di Scienza e Tecnologie dell'Informazione \"A. Faedo\" - CNR, Italy", "affiliation": "Istituto di Scienza e Tecnologie dell'Informazione \"A. Faedo\" - CNR, Italy",
@ -30,7 +31,12 @@
"desired_name": "{{name}}-v{{version}}.war" "desired_name": "{{name}}-v{{version}}.war"
} }
], ],
"code_location": "https://code-repo.d4science.org/gCubeSystem/{{name}}", "code_location": "https://code-repo.d4science.org/gCubeSystem/{{name}}/releases/tag/v{{version}}",
"communities": [
{
"identifier": "gcube-system"
}
],
"grants": [ "grants": [
{ {
"id": "004260", "id": "004260",
@ -129,12 +135,11 @@
} }
], ],
"export_filename": "{{name}}", "export_filename": "{{name}}",
"exporters": { "exporters": {
"ZenodoSoftwareVersionExporter": { "ZenodoSoftwareVersionExporter": {
"elaboration": "NONE", "elaboration": "NONE",
"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>\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>", "skip_grants": ["004260"],
"html_code_location": "\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>", "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"]
}, },
"BibLaTeXSoftwareVersionExporter": { "BibLaTeXSoftwareVersionExporter": {
"elaboration": "ALL" "elaboration": "ALL"
@ -156,7 +161,7 @@
"gcube_release_ticket": null, "gcube_release_ticket": null,
"concept_doi_url": null, "concept_doi_url": null,
"version_doi_url": null, "version_doi_url": null,
"code_location": null "code_location": "https://code-repo.d4science.org/gCubeSystem/{{name}}"
}, },
{ {
"version": "1.1.0", "version": "1.1.0",
@ -176,7 +181,7 @@
"gcube_release_ticket": "https://support.d4science.org/issues/12988", "gcube_release_ticket": "https://support.d4science.org/issues/12988",
"concept_doi_url": "PREVIOUS", "concept_doi_url": "PREVIOUS",
"version_doi_url": null, "version_doi_url": null,
"code_location": null "code_location": "https://code-repo.d4science.org/gCubeSystem/{{name}}"
}, },
{ {
"version": "1.2.0", "version": "1.2.0",
@ -192,7 +197,7 @@
"gcube_release_ticket": null, "gcube_release_ticket": null,
"concept_doi_url": "PREVIOUS", "concept_doi_url": "PREVIOUS",
"version_doi_url": null, "version_doi_url": null,
"code_location": null "code_location": "https://code-repo.d4science.org/gCubeSystem/{{name}}"
}, },
{ {
"version": "1.3.0", "version": "1.3.0",
@ -212,7 +217,7 @@
"gcube_release_ticket": "https://support.d4science.org/issues/16743", "gcube_release_ticket": "https://support.d4science.org/issues/16743",
"concept_doi_url": "PREVIOUS", "concept_doi_url": "PREVIOUS",
"version_doi_url": null, "version_doi_url": null,
"code_location": null "code_location": "https://code-repo.d4science.org/gCubeSystem/{{name}}"
}, },
{ {
"version": "1.4.0", "version": "1.4.0",
@ -221,8 +226,7 @@
"gcube_release_version": "4.15.0", "gcube_release_version": "4.15.0",
"gcube_release_ticket": "https://support.d4science.org/issues/17294", "gcube_release_ticket": "https://support.d4science.org/issues/17294",
"concept_doi_url": "PREVIOUS", "concept_doi_url": "PREVIOUS",
"version_doi_url": null, "version_doi_url": null
"code_location": "https://code-repo.d4science.org/gCubeSystem/{{name}}/releases/tag/v{{version}}"
}, },
{ {
"version": "1.4.1", "version": "1.4.1",
@ -231,8 +235,7 @@
"gcube_release_version": "4.18.0", "gcube_release_version": "4.18.0",
"gcube_release_ticket": "https://support.d4science.org/issues/18335", "gcube_release_ticket": "https://support.d4science.org/issues/18335",
"concept_doi_url": "PREVIOUS", "concept_doi_url": "PREVIOUS",
"version_doi_url": null, "version_doi_url": null
"code_location": "https://code-repo.d4science.org/gCubeSystem/{{name}}/releases/tag/v{{version}}"
}, },
{ {
"version": "1.4.2", "version": "1.4.2",
@ -241,8 +244,7 @@
"gcube_release_version": "4.20.0", "gcube_release_version": "4.20.0",
"gcube_release_ticket": "https://support.d4science.org/issues/18507", "gcube_release_ticket": "https://support.d4science.org/issues/18507",
"concept_doi_url": "PREVIOUS", "concept_doi_url": "PREVIOUS",
"version_doi_url": null, "version_doi_url": null
"code_location": "https://code-repo.d4science.org/gCubeSystem/{{name}}/releases/tag/v{{version}}"
}, },
{ {
"version": "1.4.3", "version": "1.4.3",
@ -251,8 +253,7 @@
"gcube_release_version": "4.23.0", "gcube_release_version": "4.23.0",
"gcube_release_ticket": "https://support.d4science.org/issues/19322", "gcube_release_ticket": "https://support.d4science.org/issues/19322",
"concept_doi_url": "PREVIOUS", "concept_doi_url": "PREVIOUS",
"version_doi_url": null, "version_doi_url": null
"code_location": "https://code-repo.d4science.org/gCubeSystem/{{name}}/releases/tag/v{{version}}"
}, },
{ {
"version": "1.4.4", "version": "1.4.4",
@ -261,8 +262,7 @@
"gcube_release_version": "5.0.0", "gcube_release_version": "5.0.0",
"gcube_release_ticket": "https://support.d4science.org/issues/20648", "gcube_release_ticket": "https://support.d4science.org/issues/20648",
"concept_doi_url": "PREVIOUS", "concept_doi_url": "PREVIOUS",
"version_doi_url": null, "version_doi_url": null
"code_location": "https://code-repo.d4science.org/gCubeSystem/{{name}}/releases/tag/v{{version}}"
}, },
{ {
"version": "1.4.5", "version": "1.4.5",
@ -271,16 +271,14 @@
"gcube_release_version": "5.1.0", "gcube_release_version": "5.1.0",
"gcube_release_ticket": "https://support.d4science.org/issues/20920", "gcube_release_ticket": "https://support.d4science.org/issues/20920",
"concept_doi_url": "PREVIOUS", "concept_doi_url": "PREVIOUS",
"version_doi_url": null, "version_doi_url": null
"code_location": "https://code-repo.d4science.org/gCubeSystem/{{name}}/releases/tag/v{{version}}"
}, },
{ {
"version": "2.0.0", "version": "2.0.0",
"date": "2021-05-04", "date": "2021-05-04",
"gcube_release_version": "5.2.0", "gcube_release_version": "5.2.0",
"concept_doi_url": null, "concept_doi_url": null,
"version_doi_url": null, "version_doi_url": null
"code_location": "https://code-repo.d4science.org/gCubeSystem/{{name}}/releases/tag/v{{version}}"
}, },
{ {
"version": "2.1.0", "version": "2.1.0",
@ -288,16 +286,15 @@
"gcube_release_version": "5.7.0", "gcube_release_version": "5.7.0",
"gcube_release_ticket": "https://support.d4science.org/issues/21685/", "gcube_release_ticket": "https://support.d4science.org/issues/21685/",
"concept_doi_url": "PREVIOUS", "concept_doi_url": "PREVIOUS",
"version_doi_url": null, "version_doi_url": null
"code_location": "https://code-repo.d4science.org/gCubeSystem/{{name}}/releases/tag/v{{version}}"
}, },
{ {
"version": "2.2.0", "version": "2.2.0",
"date": "2022-05-12", "date": "2022-05-12",
"gcube_release_version": "5.11.0", "gcube_release_version": "5.11.0",
"gcube_release_ticket": "https://support.d4science.org/issues/22943", "gcube_release_ticket": "https://support.d4science.org/issues/22943",
"version_doi_url": null, "concept_doi_url": "PREVIOUS",
"code_location": "https://code-repo.d4science.org/gCubeSystem/{{name}}/releases/tag/v{{version}}" "version_doi_url": null
}, },
{ {
"version": "2.3.0", "version": "2.3.0",
@ -305,8 +302,7 @@
"gcube_release_version": "5.13.0", "gcube_release_version": "5.13.0",
"gcube_release_ticket": "https://support.d4science.org/issues/23374", "gcube_release_ticket": "https://support.d4science.org/issues/23374",
"concept_doi_url": "PREVIOUS", "concept_doi_url": "PREVIOUS",
"version_doi_url": null, "version_doi_url": null
"code_location": "https://code-repo.d4science.org/gCubeSystem/{{name}}/releases/tag/v{{version}}"
}, },
{ {
"version": "2.4.0", "version": "2.4.0",
@ -314,8 +310,7 @@
"gcube_release_version": "5.13.1", "gcube_release_version": "5.13.1",
"gcube_release_ticket": "https://support.d4science.org/issues/23650", "gcube_release_ticket": "https://support.d4science.org/issues/23650",
"concept_doi_url": "PREVIOUS", "concept_doi_url": "PREVIOUS",
"version_doi_url": null, "version_doi_url": null
"code_location": "https://code-repo.d4science.org/gCubeSystem/{{name}}/releases/tag/v{{version}}"
}, },
{ {
"version": "2.4.1", "version": "2.4.1",
@ -323,8 +318,7 @@
"gcube_release_version": "5.14.0", "gcube_release_version": "5.14.0",
"gcube_release_ticket": "https://support.d4science.org/issues/23885", "gcube_release_ticket": "https://support.d4science.org/issues/23885",
"concept_doi_url": "PREVIOUS", "concept_doi_url": "PREVIOUS",
"version_doi_url": null, "version_doi_url": null
"code_location": "https://code-repo.d4science.org/gCubeSystem/{{name}}/releases/tag/v{{version}}"
} }
] ]
} }

13
src/test/resources/gcat-test-sandbox.json
View File

@ -9,7 +9,7 @@
}, },
"keywords": ["gCube", "Catalogue", "D4Science"], "keywords": ["gCube", "Catalogue", "D4Science"],
"description": "gCube Catalogue (gCat) Service allows the publication of items in the gCube Catalogue.", "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>", "html_description": "<p>{{description}}</p>",
"authors": [ "authors": [
{ {
"affiliation": "Istituto di Scienza e Tecnologie dell'Informazione \"A. Faedo\" - CNR, Italy", "affiliation": "Istituto di Scienza e Tecnologie dell'Informazione \"A. Faedo\" - CNR, Italy",
@ -31,8 +31,13 @@
"desired_name": "{{name}}-v{{version}}.war" "desired_name": "{{name}}-v{{version}}.war"
} }
], ],
"code_location": "https://code-repo.d4science.org/gCubeSystem/{{name}}/releases/tag/v{{version}}",
"concept_doi_url": "https://doi.org/10.5072/zenodo.1139068", "concept_doi_url": "https://doi.org/10.5072/zenodo.1139068",
"code_location": "https://code-repo.d4science.org/gCubeSystem/{{name}}/releases/tag/v{{version}}",
"communities": [
{
"identifier": "gcube-system"
}
],
"grants": [ "grants": [
{ {
"id": "004260", "id": "004260",
@ -133,9 +138,9 @@
"export_filename": "{{name}}", "export_filename": "{{name}}",
"exporters": { "exporters": {
"ZenodoSoftwareVersionExporter": { "ZenodoSoftwareVersionExporter": {
"elaboration": "NONE", "elaboration": "UPDATE_ONLY",
"skip_grants": ["004260"], "skip_grants": ["004260"],
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