Generalised solution
This commit is contained in:
parent
de9066a4f7
commit
5c3209d07e
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@ -8,10 +8,9 @@ import java.util.concurrent.TimeUnit;
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import org.gcube.com.fasterxml.jackson.databind.JsonNode;
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import org.gcube.com.fasterxml.jackson.databind.ObjectMapper;
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import org.gcube.com.fasterxml.jackson.databind.node.ArrayNode;
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import org.gcube.com.fasterxml.jackson.databind.node.JsonNodeType;
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import org.gcube.com.fasterxml.jackson.databind.node.ObjectNode;
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import org.gcube.common.software.model.SoftwareConcept;
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import org.gcube.common.software.model.SoftwareVersion;
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import org.gcube.common.software.model.SoftwareGlobalConfig;
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import org.gcube.common.software.model.SoftwareVersionConfig;
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import org.gcube.common.software.model.Variables;
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import org.gcube.common.software.utils.Utils;
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import org.slf4j.Logger;
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@ -20,31 +19,29 @@ import org.slf4j.LoggerFactory;
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/**
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* @author Luca Frosini (ISTI - CNR)
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*/
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public class SoftwareConceptAnalyser {
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public class SoftwareConfigAnalyser {
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private static final Logger logger = LoggerFactory.getLogger(SoftwareConceptAnalyser.class);
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private static final Logger logger = LoggerFactory.getLogger(SoftwareConfigAnalyser.class);
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public static final String CONCEPT_FILENAME_EXTENSION = ".json";
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public static final String EXPORT_FILENAME_EXTENSION = ".json";
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public static final String CONCEPT_PROPERTY_NAME = "concept";
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public static final String GLOBAL_PROPERTY_NAME = "global";
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public static final String VERSIONS_PROPERTY_NAME = "versions";
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public static final String PUBLISHERS_PROPERTY_NAME = "publishers";
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public static final String EXPORTERS_PROPERTY_NAME = "exporters";
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protected ObjectMapper objectMapper;
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protected JsonNode jsonNode;
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public SoftwareConceptAnalyser(File jsonFile) throws Exception {
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public SoftwareConfigAnalyser(File jsonFile) throws Exception {
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this.objectMapper = Utils.getObjectMapper();
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this.jsonNode = objectMapper.readTree(jsonFile);
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}
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public SoftwareConceptAnalyser(String json) throws Exception {
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public SoftwareConfigAnalyser(String json) throws Exception {
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this.objectMapper = Utils.getObjectMapper();
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this.jsonNode = objectMapper.readTree(json);
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}
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protected SoftwareVersion actualize(JsonNode version) throws Exception {
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protected SoftwareVersionConfig actualize(JsonNode version) throws Exception {
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Variables variables = objectMapper.treeToValue(version, Variables.class);
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Set<String> missingVariables = variables.parse();
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int size = missingVariables.size();
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@ -53,18 +50,20 @@ public class SoftwareConceptAnalyser {
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missingVariables.toArray(new String[size]).toString());
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}
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JsonNode swVersion = objectMapper.convertValue(variables.getProperties(), JsonNode.class);
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SoftwareVersion softwareVersion = objectMapper.treeToValue(swVersion, SoftwareVersion.class);
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SoftwareVersionConfig softwareVersion = objectMapper.treeToValue(swVersion, SoftwareVersionConfig.class);
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// softwareVersion.setVariables(variables);
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return softwareVersion;
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}
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public void analyse() throws Exception {
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ObjectNode concept = (ObjectNode) jsonNode.get(CONCEPT_PROPERTY_NAME).deepCopy();
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SoftwareConcept softwareConcept = objectMapper.treeToValue(concept, SoftwareConcept.class);
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ObjectNode originalGlobal = (ObjectNode) jsonNode.get(GLOBAL_PROPERTY_NAME).deepCopy();
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SoftwareGlobalConfig softwareGlobalConfig = objectMapper.treeToValue(originalGlobal, SoftwareGlobalConfig.class);
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softwareGlobalConfig.setOriginalJson(originalGlobal);
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ArrayNode versions = (ArrayNode) jsonNode.get(VERSIONS_PROPERTY_NAME);
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String name = softwareConcept.getName();
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SoftwareVersion previous = null;
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String name = softwareGlobalConfig.getName();
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SoftwareVersionConfig previous = null;
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int i = 0;
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@ -73,9 +72,11 @@ public class SoftwareConceptAnalyser {
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for(i=0; i<versions.size(); i++) {
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ObjectNode originalVersion = (ObjectNode) versions.get(i).deepCopy();
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exportingVersions.add(originalVersion);
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JsonNode version = Utils.merge(concept, originalVersion);
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SoftwareVersion softwareVersion = actualize(version);
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JsonNode version = Utils.merge(originalGlobal, originalVersion);
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SoftwareVersionConfig softwareVersion = actualize(version);
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softwareVersion.setOriginalJson(originalVersion);
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boolean newDOI = false;
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if(softwareVersion.getDOIURL()==null) {
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@ -93,8 +94,8 @@ public class SoftwareConceptAnalyser {
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softwareVersion.getPrevious()!=null ? softwareVersion.getPrevious().getVersion(): null);
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try {
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SoftwareVersionAnalyser softwareVersionAnalyser = new SoftwareVersionAnalyser(softwareVersion);
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softwareVersionAnalyser.setOriginalJson(jsonNode);
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SoftwareVersionConfigAnalyser softwareVersionAnalyser = new SoftwareVersionConfigAnalyser(softwareVersion);
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softwareVersionAnalyser.setSoftwareGlobalConfig(softwareGlobalConfig);
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softwareVersionAnalyser.setFirst(i==0);
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softwareVersionAnalyser.analyse();
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@ -104,16 +105,16 @@ public class SoftwareConceptAnalyser {
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/* Need to export the original file with the DOI and Version DOI */
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URL doiURL = softwareVersion.getDOIURL();
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if(doiURL!=null) {
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originalVersion.put(SoftwareVersion.DOI_URL_PROPERTY_NAME, doiURL.toString());
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originalVersion.put(SoftwareVersionConfig.DOI_URL_PROPERTY_NAME, doiURL.toString());
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}
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if(softwareVersion.getVersionDOIURL()!=null) {
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originalVersion.put(SoftwareVersion.VERSION_DOI_URL_PROPERTY_NAME, softwareVersion.getVersionDOIURL().toString());
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originalVersion.put(SoftwareVersionConfig.VERSION_DOI_URL_PROPERTY_NAME, softwareVersion.getVersionDOIURL().toString());
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}
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if(newDOI) {
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softwareConcept.setDOIURL(doiURL);
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concept.put(SoftwareConcept.DOI_URL_PROPERTY_NAME, doiURL.toString());
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softwareGlobalConfig.setDOIURL(doiURL);
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originalGlobal.put(SoftwareGlobalConfig.DOI_URL_PROPERTY_NAME, doiURL.toString());
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}
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}
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Thread.sleep(TimeUnit.SECONDS.toMillis(2));
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@ -126,28 +127,27 @@ public class SoftwareConceptAnalyser {
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throw e;
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}finally {
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ObjectNode toBeExported = objectMapper.createObjectNode();
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toBeExported.replace(CONCEPT_PROPERTY_NAME, concept);
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toBeExported.replace(GLOBAL_PROPERTY_NAME, originalGlobal);
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// if(originalGlobal.has(SoftwareGlobalConfig.DOI_URL_PROPERTY_NAME)
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// && originalGlobal.get(SoftwareGlobalConfig.DOI_URL_PROPERTY_NAME).getNodeType()!=JsonNodeType.NULL) {
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// String conceptDOIURL = originalGlobal.get(SoftwareGlobalConfig.DOI_URL_PROPERTY_NAME).asText();
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//
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// for(i=0; i<exportingVersions.size(); i++) {
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// ObjectNode v = (ObjectNode) exportingVersions.get(i);
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// if(v.has(SoftwareVersionConfig.DOI_URL_PROPERTY_NAME)
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// && v.get(SoftwareVersionConfig.DOI_URL_PROPERTY_NAME).getNodeType()!=JsonNodeType.NULL){
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// String vDOI = v.get(SoftwareVersionConfig.DOI_URL_PROPERTY_NAME).asText();
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// if(conceptDOIURL.compareTo(vDOI)==0) {
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// v.remove(SoftwareVersionConfig.DOI_URL_PROPERTY_NAME);
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// }
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// }
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// }
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// }
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if(concept.has(SoftwareConcept.DOI_URL_PROPERTY_NAME)
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&& concept.get(SoftwareConcept.DOI_URL_PROPERTY_NAME).getNodeType()!=JsonNodeType.NULL) {
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String conceptDOIURL = concept.get(SoftwareConcept.DOI_URL_PROPERTY_NAME).asText();
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for(i=0; i<exportingVersions.size(); i++) {
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ObjectNode v = (ObjectNode) exportingVersions.get(i);
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if(v.has(SoftwareVersion.DOI_URL_PROPERTY_NAME)
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&& v.get(SoftwareVersion.DOI_URL_PROPERTY_NAME).getNodeType()!=JsonNodeType.NULL){
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String vDOI = v.get(SoftwareVersion.DOI_URL_PROPERTY_NAME).asText();
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if(conceptDOIURL.compareTo(vDOI)==0) {
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v.remove(SoftwareVersion.DOI_URL_PROPERTY_NAME);
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}
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}
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}
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}
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toBeExported.replace(VERSIONS_PROPERTY_NAME, exportingVersions);
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toBeExported.replace(PUBLISHERS_PROPERTY_NAME, jsonNode.get(PUBLISHERS_PROPERTY_NAME).deepCopy());
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toBeExported.replace(EXPORTERS_PROPERTY_NAME, jsonNode.get(EXPORTERS_PROPERTY_NAME).deepCopy());
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File file = new File(name+CONCEPT_FILENAME_EXTENSION);
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File file = new File(name+EXPORT_FILENAME_EXTENSION);
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objectMapper.writeValue(file, toBeExported);
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}
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@ -1,75 +0,0 @@
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package org.gcube.common.software.analyser;
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import java.net.URL;
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import java.util.List;
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import org.gcube.com.fasterxml.jackson.databind.JsonNode;
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import org.gcube.com.fasterxml.jackson.databind.node.ObjectNode;
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import org.gcube.common.software.model.SoftwareVersion;
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import org.gcube.common.software.model.SoftwareVersionFile;
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import org.gcube.common.software.model.Variables;
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import org.gcube.common.software.process.export.SoftwareVersionExporter;
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import org.gcube.common.software.process.publish.SoftwareVersionPublisher;
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/**
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* @author Luca Frosini (ISTI - CNR)
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*/
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public class SoftwareVersionAnalyser {
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protected JsonNode originalJson;
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protected SoftwareVersion softwareVersion;
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protected boolean first;
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public SoftwareVersionAnalyser(SoftwareVersion softwareVersion) {
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this.softwareVersion = softwareVersion;
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}
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public boolean isFirst() {
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return first;
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}
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public void setFirst(boolean first) {
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this.first = first;
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}
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public void setOriginalJson(JsonNode jsonNode) {
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this.originalJson = jsonNode;
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}
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public void analyse() throws Exception {
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Variables variables = softwareVersion.getVariables();
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List<SoftwareVersionFile> svfs = softwareVersion.getFiles();
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for(SoftwareVersionFile svf : svfs) {
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URL url = svf.getURL();
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String urlString = variables.replaceAllVariables(url.toString());
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svf.setURL(new URL(urlString));
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String desiredName = svf.getDesiredName();
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desiredName = variables.replaceAllVariables(desiredName);
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svf.setDesiredName(desiredName);
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}
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ObjectNode publishers = (ObjectNode) originalJson.get(SoftwareConceptAnalyser.PUBLISHERS_PROPERTY_NAME).deepCopy();
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List<SoftwareVersionPublisher> svps = SoftwareVersionPublisher.getPublishers();
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for(SoftwareVersionPublisher svp: svps) {
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JsonNode conf = publishers.get(svp.getClass().getSimpleName());
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svp.setSpecificConfiguration(conf);
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svp.setSoftwareVersion(softwareVersion);
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svp.setFirst(first);
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svp.publish();
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}
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ObjectNode exporters = (ObjectNode) originalJson.get(SoftwareConceptAnalyser.EXPORTERS_PROPERTY_NAME).deepCopy();
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List<SoftwareVersionExporter> sves = SoftwareVersionExporter.getExporters();
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for(SoftwareVersionExporter sve: sves) {
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JsonNode conf = publishers.get(exporters.getClass().getSimpleName());
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sve.setSpecificConfiguration(conf);
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sve.setSoftwareVersion(softwareVersion);
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sve.setFirst(first);
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sve.export();
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}
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}
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}
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@ -0,0 +1,89 @@
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package org.gcube.common.software.analyser;
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import java.net.URL;
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import java.util.List;
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import java.util.Map;
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import org.gcube.common.software.model.ProcessorConfig;
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import org.gcube.common.software.model.SoftwareGlobalConfig;
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import org.gcube.common.software.model.SoftwareVersionConfig;
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import org.gcube.common.software.model.SoftwareVersionFile;
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import org.gcube.common.software.model.Variables;
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import org.gcube.common.software.process.export.SoftwareVersionExporter;
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import org.gcube.common.software.process.publish.SoftwareVersionPublisher;
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/**
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* @author Luca Frosini (ISTI - CNR)
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*/
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public class SoftwareVersionConfigAnalyser {
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protected SoftwareGlobalConfig softwareGlobalConfig;
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protected SoftwareVersionConfig softwareVersionConfig;
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protected boolean first;
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public SoftwareVersionConfigAnalyser(SoftwareVersionConfig softwareVersionConfig) {
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this.softwareVersionConfig = softwareVersionConfig;
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}
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public SoftwareGlobalConfig getSoftwareGlobalConfig() {
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return softwareGlobalConfig;
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}
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public void setSoftwareGlobalConfig(SoftwareGlobalConfig softwareGlobalConfig) {
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this.softwareGlobalConfig = softwareGlobalConfig;
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}
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public SoftwareVersionConfig getSoftwareVersionConfig() {
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return softwareVersionConfig;
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}
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public void setSoftwareVersionConfig(SoftwareVersionConfig softwareVersionConfig) {
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this.softwareVersionConfig = softwareVersionConfig;
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}
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public boolean isFirst() {
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return first;
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}
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public void setFirst(boolean first) {
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this.first = first;
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}
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public void analyse() throws Exception {
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Variables variables = softwareVersionConfig.getVariables();
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List<SoftwareVersionFile> svfs = softwareVersionConfig.getFiles();
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for(SoftwareVersionFile svf : svfs) {
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URL url = svf.getURL();
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String urlString = variables.replaceAllVariables(url.toString());
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svf.setURL(new URL(urlString));
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String desiredName = svf.getDesiredName();
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desiredName = variables.replaceAllVariables(desiredName);
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svf.setDesiredName(desiredName);
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}
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Map<String,ProcessorConfig> processors = softwareVersionConfig.getPublishers();
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List<SoftwareVersionPublisher> svps = SoftwareVersionPublisher.getPublishers();
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for(SoftwareVersionPublisher svp: svps) {
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ProcessorConfig processorConfig = processors.get(svp.getClass().getSimpleName());
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svp.setProcessorConfig(processorConfig);
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svp.setSoftwareVersion(softwareVersionConfig);
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svp.setFirst(first);
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svp.publish();
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}
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Map<String,ProcessorConfig> exporters = softwareVersionConfig.getExporters();
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List<SoftwareVersionExporter> sves = SoftwareVersionExporter.getExporters();
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for(SoftwareVersionExporter sve: sves) {
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ProcessorConfig processorConfig = exporters.get(sve.getClass().getSimpleName());
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sve.setProcessorConfig(processorConfig);
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sve.setSoftwareVersion(softwareVersionConfig);
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sve.setFirst(first);
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sve.export();
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}
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}
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}
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@ -0,0 +1,49 @@
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package org.gcube.common.software.model;
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import java.util.LinkedHashMap;
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import java.util.Map;
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import org.gcube.com.fasterxml.jackson.annotation.JsonAnyGetter;
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import org.gcube.com.fasterxml.jackson.annotation.JsonAnySetter;
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import org.gcube.com.fasterxml.jackson.annotation.JsonFormat;
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import org.gcube.com.fasterxml.jackson.annotation.JsonIgnore;
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import org.gcube.com.fasterxml.jackson.annotation.JsonProperty;
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import org.gcube.com.fasterxml.jackson.databind.JsonNode;
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/**
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* @author Luca Frosini (ISTI - CNR)
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*/
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public class ProcessorConfig {
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public static final String ELABORATION_PROPERTY_NAME = "elaboration";
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@JsonProperty(ELABORATION_PROPERTY_NAME)
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@JsonFormat(shape=JsonFormat.Shape.STRING)
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protected ElaborationType elaboration;
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protected Map<String, JsonNode> properties;
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public ProcessorConfig() {
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properties = new LinkedHashMap<>();
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}
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public ElaborationType getElaboration() {
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return elaboration;
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}
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@JsonAnyGetter
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public Map<String, JsonNode> getProperties() {
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return properties;
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}
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@JsonAnySetter
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public void addProperty(String key, JsonNode value) {
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this.properties.put(key, value);
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}
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@JsonIgnore
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public JsonNode getProperty(String key) {
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return this.properties.get(key);
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}
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}
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@ -2,17 +2,19 @@ package org.gcube.common.software.model;
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import java.net.URL;
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import java.util.List;
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import java.util.Map;
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import java.util.Set;
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import org.gcube.com.fasterxml.jackson.annotation.JsonFormat;
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import org.gcube.com.fasterxml.jackson.annotation.JsonIgnore;
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import org.gcube.com.fasterxml.jackson.annotation.JsonProperty;
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import org.gcube.com.fasterxml.jackson.databind.JsonNode;
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import org.gcube.com.fasterxml.jackson.databind.node.ArrayNode;
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import org.gcube.com.fasterxml.jackson.databind.node.ObjectNode;
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/**
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* @author Luca Frosini (ISTI - CNR)
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*/
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public class SoftwareConcept {
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public class SoftwareGlobalConfig {
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public static final String NAME_PROPERTY_NAME = "name";
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public static final String GROUP_PROPERTY_NAME = "group";
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@ -25,9 +27,12 @@ public class SoftwareConcept {
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public static final String CODE_LOCATION_PROPERTY_NAME = "code_location";
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public static final String DOI_URL_PROPERTY_NAME = "doi_url";
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public static final String GRANTS_PROPERTY_NAME = "grants";
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public static final String PUBLISH_PROPERTY_NAME = "publish";
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public static final String EXPORT_PROPERTY_NAME = "export";
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public static final String PUBLISHERS_PROPERTY_NAME = "publishers";
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public static final String EXPORTERS_PROPERTY_NAME = "exporters";
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@JsonIgnore
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protected ObjectNode originalJson;
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@JsonProperty(NAME_PROPERTY_NAME)
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protected String name;
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@ -61,14 +66,22 @@ public class SoftwareConcept {
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@JsonProperty(GRANTS_PROPERTY_NAME)
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protected JsonNode grants;
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@JsonProperty(PUBLISH_PROPERTY_NAME)
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@JsonFormat(shape=JsonFormat.Shape.STRING)
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protected ElaborationType publish;
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@JsonProperty(PUBLISHERS_PROPERTY_NAME)
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protected Map<String,ProcessorConfig> publishers;
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@JsonProperty(EXPORT_PROPERTY_NAME)
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@JsonFormat(shape=JsonFormat.Shape.STRING)
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protected ElaborationType export;
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@JsonProperty(EXPORTERS_PROPERTY_NAME)
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protected Map<String,ProcessorConfig> exporters;
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@JsonIgnore
|
||||
public ObjectNode getOriginalJson() {
|
||||
return originalJson;
|
||||
}
|
||||
|
||||
@JsonIgnore
|
||||
public void setOriginalJson(ObjectNode originalJson) {
|
||||
this.originalJson = originalJson;
|
||||
}
|
||||
|
||||
public String getName() {
|
||||
return name;
|
||||
}
|
||||
|
|
@ -117,12 +130,12 @@ public class SoftwareConcept {
|
|||
return grants;
|
||||
}
|
||||
|
||||
public ElaborationType getPublish() {
|
||||
return publish;
|
||||
public Map<String,ProcessorConfig> getPublishers() {
|
||||
return publishers;
|
||||
}
|
||||
|
||||
public ElaborationType getExport() {
|
||||
return export;
|
||||
public Map<String,ProcessorConfig> getExporters() {
|
||||
return exporters;
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -16,7 +16,7 @@ import org.gcube.common.software.utils.Utils;
|
|||
/**
|
||||
* @author Luca Frosini (ISTI - CNR)
|
||||
*/
|
||||
public class SoftwareVersion extends SoftwareConcept {
|
||||
public class SoftwareVersionConfig extends SoftwareGlobalConfig {
|
||||
|
||||
public static final String VERSION_PROPERTY_NAME = "version";
|
||||
public static final String DATE_PROPERTY_NAME = "date";
|
||||
|
|
@ -25,10 +25,10 @@ public class SoftwareVersion extends SoftwareConcept {
|
|||
public static final String VERSION_DOI_URL_PROPERTY_NAME = "version_doi_url";
|
||||
|
||||
@JsonIgnore
|
||||
protected SoftwareVersion previous;
|
||||
protected SoftwareVersionConfig previous;
|
||||
|
||||
@JsonIgnore
|
||||
protected SoftwareVersion next;
|
||||
protected SoftwareVersionConfig next;
|
||||
|
||||
@JsonIgnore
|
||||
protected Boolean newDeposition;
|
||||
|
|
@ -50,27 +50,27 @@ public class SoftwareVersion extends SoftwareConcept {
|
|||
protected URL versionDOIURL;
|
||||
|
||||
|
||||
public SoftwareVersion() {
|
||||
public SoftwareVersionConfig() {
|
||||
this.newDeposition = false;
|
||||
}
|
||||
|
||||
@JsonIgnore
|
||||
public SoftwareVersion getPrevious() {
|
||||
public SoftwareVersionConfig getPrevious() {
|
||||
return previous;
|
||||
}
|
||||
|
||||
@JsonIgnore
|
||||
public void setPrevious(SoftwareVersion previous) {
|
||||
public void setPrevious(SoftwareVersionConfig previous) {
|
||||
this.previous = previous;
|
||||
}
|
||||
|
||||
@JsonIgnore
|
||||
public SoftwareVersion getNext() {
|
||||
public SoftwareVersionConfig getNext() {
|
||||
return next;
|
||||
}
|
||||
|
||||
@JsonIgnore
|
||||
public void setNext(SoftwareVersion next) {
|
||||
public void setNext(SoftwareVersionConfig next) {
|
||||
this.next = next;
|
||||
}
|
||||
|
||||
|
|
@ -54,14 +54,19 @@ public class Variables {
|
|||
Set<String> variableNames = findVariables(value);
|
||||
for(String variableName : variableNames) {
|
||||
if(properties.containsKey(variableName)) {
|
||||
String variableValue = properties.get(variableName).toString();
|
||||
value = Utils.replaceVariable(variableName, variableValue, value);
|
||||
try {
|
||||
String variableValue = properties.get(variableName).toString();
|
||||
value = Utils.replaceVariable(variableName, variableValue, value);
|
||||
}catch (Exception e) {
|
||||
missingVariables.add(variableName);
|
||||
}
|
||||
|
||||
}else {
|
||||
missingVariables.add(variableName);
|
||||
}
|
||||
}
|
||||
if(missingVariables.size()>0) {
|
||||
throw new Exception("The following varibles cannot be replaced because they don't exists " + missingVariables.toString());
|
||||
throw new Exception("The following variables cannot be replaced because they don't exists " + missingVariables.toString());
|
||||
}
|
||||
return value;
|
||||
}
|
||||
|
|
|
|||
|
|
@ -1,22 +1,23 @@
|
|||
package org.gcube.common.software.process;
|
||||
|
||||
import org.gcube.com.fasterxml.jackson.databind.JsonNode;
|
||||
import org.gcube.common.software.model.SoftwareVersion;
|
||||
import org.gcube.common.software.model.ProcessorConfig;
|
||||
import org.gcube.common.software.model.SoftwareVersionConfig;
|
||||
|
||||
/**
|
||||
* @author Luca Frosini (ISTI - CNR)
|
||||
*/
|
||||
public abstract class SoftwareVersionProcessor {
|
||||
|
||||
protected SoftwareVersion softwareVersion;
|
||||
protected JsonNode configuration;
|
||||
protected SoftwareVersionConfig softwareVersion;
|
||||
protected ProcessorConfig processorConfig;
|
||||
|
||||
protected boolean first;
|
||||
|
||||
public SoftwareVersion getSoftwareVersion() {
|
||||
public SoftwareVersionConfig getSoftwareVersion() {
|
||||
return softwareVersion;
|
||||
}
|
||||
|
||||
public void setSoftwareVersion(SoftwareVersion softwareVersion) {
|
||||
public void setSoftwareVersion(SoftwareVersionConfig softwareVersion) {
|
||||
this.softwareVersion = softwareVersion;
|
||||
}
|
||||
|
||||
|
|
@ -28,8 +29,12 @@ public abstract class SoftwareVersionProcessor {
|
|||
this.first = first;
|
||||
}
|
||||
|
||||
public void setSpecificConfiguration(JsonNode conf) {
|
||||
this.configuration = conf;
|
||||
public ProcessorConfig getProcessorConfig() {
|
||||
return processorConfig;
|
||||
}
|
||||
|
||||
public void setProcessorConfig(ProcessorConfig processorConfig) {
|
||||
this.processorConfig = processorConfig;
|
||||
}
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -30,7 +30,7 @@ public class BibLaTeXSoftwareVersionExporter extends SoftwareVersionExporter {
|
|||
public void export() throws Exception {
|
||||
String name = softwareVersion.getName();
|
||||
|
||||
ElaborationType export = softwareVersion.getExport();
|
||||
ElaborationType export = processorConfig.getElaboration();
|
||||
|
||||
switch (export) {
|
||||
case ALL:
|
||||
|
|
|
|||
|
|
@ -25,6 +25,7 @@ import javax.ws.rs.core.Response;
|
|||
import org.gcube.com.fasterxml.jackson.databind.JsonNode;
|
||||
import org.gcube.com.fasterxml.jackson.databind.ObjectMapper;
|
||||
import org.gcube.com.fasterxml.jackson.databind.node.ArrayNode;
|
||||
import org.gcube.com.fasterxml.jackson.databind.node.JsonNodeType;
|
||||
import org.gcube.com.fasterxml.jackson.databind.node.ObjectNode;
|
||||
import org.gcube.common.gxhttp.request.GXHTTPStringRequest;
|
||||
import org.gcube.common.software.config.Config;
|
||||
|
|
@ -48,13 +49,17 @@ public class ZenodoSoftwareVersionPublisher extends SoftwareVersionPublisher {
|
|||
|
||||
public static final String GUCBE_ZENODO_SOFTWARE_DEPOSIT = "gCubeSoftwareDeposit";
|
||||
|
||||
public static final String HTML_DESCRIPTION_CONFIG_FIELD_NAME = "html_description";
|
||||
public static final String HTML_CODE_LOCATION_CONFIG_FIELD_NAME = "html_code_location";
|
||||
public static final String SKIP_GRANTS_CONFIG_FIELD_NAME = "skip_grants";
|
||||
|
||||
public static final String METADATA_FIELD_NAME = "metadata";
|
||||
|
||||
private static final String SANDBOX_BASE_PATH = "https://sandbox.zenodo.org";
|
||||
private static final String SANDBOX_DOI_URL_BASE_PATH = "https://doi.org/10.5072/zenodo.";
|
||||
|
||||
private static final String PRODUCTION_BASE_PATH = "https://zenodo.org";
|
||||
private static final String PRODUCTION_DOI_URL_BASE_PATH = "https://doi.org/10.5281/zenodo.";
|
||||
// private static final String SANDBOX_BASE_PATH = "https://sandbox.zenodo.org";
|
||||
// private static final String SANDBOX_DOI_URL_BASE_PATH = "https://doi.org/10.5072/zenodo.";
|
||||
//
|
||||
// private static final String PRODUCTION_BASE_PATH = "https://zenodo.org";
|
||||
// private static final String PRODUCTION_DOI_URL_BASE_PATH = "https://doi.org/10.5281/zenodo.";
|
||||
|
||||
public static final String DEPOSITIONS_COLLECTION_PATH = "/api/deposit/depositions";
|
||||
public static final String DEPOSITION_PATH = DEPOSITIONS_COLLECTION_PATH + "/:id";
|
||||
|
|
@ -88,24 +93,7 @@ public class ZenodoSoftwareVersionPublisher extends SoftwareVersionPublisher {
|
|||
return map;
|
||||
}
|
||||
|
||||
public ZenodoSoftwareVersionPublisher() {
|
||||
try {
|
||||
this.zenodoBaseURL = new URL(Config.getProperties().getProperty("zenodo_base_url"));
|
||||
this.accessToken = Config.getProperties().getProperty("zenodo_access_token");
|
||||
this.doiBaseURL = Config.getProperties().getProperty("doi_base_url");
|
||||
if(doiBaseURL==null) {
|
||||
if(zenodoBaseURL.toString().compareTo(SANDBOX_BASE_PATH)==0) {
|
||||
doiBaseURL = SANDBOX_DOI_URL_BASE_PATH;
|
||||
}else if(zenodoBaseURL.toString().compareTo(PRODUCTION_BASE_PATH)==0) {
|
||||
doiBaseURL = PRODUCTION_DOI_URL_BASE_PATH;
|
||||
}else {
|
||||
throw new RuntimeException("Please set 'doi_base_url' in your config file");
|
||||
}
|
||||
}
|
||||
}catch (Exception e) {
|
||||
throw new RuntimeException(e);
|
||||
}
|
||||
}
|
||||
public ZenodoSoftwareVersionPublisher() {}
|
||||
|
||||
protected void addFilesToDeposition(List<File> files ) throws Exception {
|
||||
String depositID = getZenodoIDFromDOIURL(softwareVersion.getVersionDOIURL());
|
||||
|
|
@ -298,11 +286,11 @@ public class ZenodoSoftwareVersionPublisher extends SoftwareVersionPublisher {
|
|||
|
||||
private String getDescription() {
|
||||
StringBuffer stringBuffer = new StringBuffer();
|
||||
stringBuffer.append(configuration.get("html_description").asText());
|
||||
stringBuffer.append(processorConfig.getProperty(HTML_DESCRIPTION_CONFIG_FIELD_NAME).asText());
|
||||
|
||||
String codeLocation = softwareVersion.getCodeLocation();
|
||||
if(codeLocation!=null) {
|
||||
String htmlCodeLocation = configuration.get("html_code_location").asText();
|
||||
String htmlCodeLocation = processorConfig.getProperty(HTML_CODE_LOCATION_CONFIG_FIELD_NAME).asText();
|
||||
htmlCodeLocation = Utils.replaceVariable("code_location", codeLocation, htmlCodeLocation);
|
||||
stringBuffer.append(htmlCodeLocation);
|
||||
}
|
||||
|
|
@ -313,7 +301,7 @@ public class ZenodoSoftwareVersionPublisher extends SoftwareVersionPublisher {
|
|||
private ArrayNode getGrants(){
|
||||
ObjectMapper objectMapper = Utils.getObjectMapper();
|
||||
ArrayNode grants = objectMapper.createArrayNode();
|
||||
ArrayNode arrayNode = (ArrayNode) configuration.get("skip_grants");
|
||||
ArrayNode arrayNode = (ArrayNode) processorConfig.getProperty(SKIP_GRANTS_CONFIG_FIELD_NAME);
|
||||
Set<String> idToSkip = new HashSet<>();
|
||||
for(JsonNode idNode : arrayNode) {
|
||||
idToSkip.add(idNode.asText());
|
||||
|
|
@ -476,10 +464,31 @@ public class ZenodoSoftwareVersionPublisher extends SoftwareVersionPublisher {
|
|||
finalize();
|
||||
}
|
||||
|
||||
protected String getConfig(String propertyName) throws Exception {
|
||||
String conf = null;
|
||||
JsonNode node = processorConfig.getProperty(propertyName);
|
||||
if(node == null || node.getNodeType()==JsonNodeType.NULL) {
|
||||
conf = Config.getProperties().getProperty(propertyName);
|
||||
}
|
||||
if(conf==null) {
|
||||
throw new Exception("No configuration '" + propertyName + "' property found.");
|
||||
}
|
||||
return conf;
|
||||
}
|
||||
|
||||
protected void getZenodoConnectionConfig() throws Exception {
|
||||
this.zenodoBaseURL = new URL(getConfig("zenodo_base_url"));
|
||||
this.accessToken = getConfig("zenodo_access_token");
|
||||
this.doiBaseURL = getConfig("doi_base_url");
|
||||
}
|
||||
|
||||
@Override
|
||||
public void publish() throws Exception {
|
||||
getZenodoConnectionConfig();
|
||||
|
||||
String name = softwareVersion.getName();
|
||||
|
||||
ElaborationType publish = softwareVersion.getPublish();
|
||||
ElaborationType publish = processorConfig.getElaboration();
|
||||
|
||||
if(publish==ElaborationType.NONE) {
|
||||
logger.info("Deposit is disabled for {} {}.",
|
||||
|
|
|
|||
|
|
@ -17,7 +17,7 @@ public class SoftwareConceptAnalyserTest {
|
|||
@Test
|
||||
public void testUsingTestFile() throws Exception {
|
||||
File file = FileUtils.getFileFromFilename(FILENAME);
|
||||
SoftwareConceptAnalyser softwareConceptAnalyser = new SoftwareConceptAnalyser(file);
|
||||
SoftwareConfigAnalyser softwareConceptAnalyser = new SoftwareConfigAnalyser(file);
|
||||
softwareConceptAnalyser.analyse();
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -1,5 +1,5 @@
|
|||
{
|
||||
"concept":
|
||||
"global":
|
||||
{
|
||||
"name": "gcat",
|
||||
"group": "data-catalogue",
|
||||
|
|
@ -139,8 +139,19 @@
|
|||
"url": "https://cordis.europa.eu/project/id/871042"
|
||||
}
|
||||
],
|
||||
"publish": "NONE",
|
||||
"export": "ALL"
|
||||
"publishers": {
|
||||
"ZenodoSoftwareVersionPublisher": {
|
||||
"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> </p>",
|
||||
"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>",
|
||||
"skip_grants": ["004260"]
|
||||
}
|
||||
},
|
||||
"exporters": {
|
||||
"BibLaTeXSoftwareVersionExporter": {
|
||||
"elaboration": "ALL"
|
||||
}
|
||||
}
|
||||
},
|
||||
"versions":
|
||||
[
|
||||
|
|
@ -327,19 +338,5 @@
|
|||
"version_doi_url": "https://doi.org/10.5072/zenodo.1145788",
|
||||
"code_location": "https://code-repo.d4science.org/gCubeSystem/{{name}}/releases/tag/v{{version}}"
|
||||
}
|
||||
],
|
||||
"publishers":
|
||||
{
|
||||
"ZenodoSoftwareVersionPublisher":
|
||||
{
|
||||
"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> </p>",
|
||||
"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>",
|
||||
"skip_grants":
|
||||
[
|
||||
"004260"
|
||||
]
|
||||
}
|
||||
},
|
||||
"exporters":
|
||||
{}
|
||||
]
|
||||
}
|
||||
|
|
@ -1,5 +1,5 @@
|
|||
{
|
||||
"concept": {
|
||||
"global": {
|
||||
"name": "gcat",
|
||||
"group": "data-catalogue",
|
||||
"title": "gCube Catalogue (gCat) Service {{version}}",
|
||||
|
|
@ -129,8 +129,19 @@
|
|||
"url": "https://cordis.europa.eu/project/id/871042"
|
||||
}
|
||||
],
|
||||
"publish": "NONE",
|
||||
"export": "ALL"
|
||||
"publishers": {
|
||||
"ZenodoSoftwareVersionPublisher": {
|
||||
"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> </p>",
|
||||
"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>",
|
||||
"skip_grants": ["004260"]
|
||||
}
|
||||
},
|
||||
"exporters": {
|
||||
"BibLaTeXSoftwareVersionExporter": {
|
||||
"elaboration": "ALL"
|
||||
}
|
||||
}
|
||||
},
|
||||
"versions": [
|
||||
{
|
||||
|
|
@ -303,15 +314,5 @@
|
|||
"version_doi_url": null,
|
||||
"code_location": "https://code-repo.d4science.org/gCubeSystem/{{name}}/releases/tag/v{{version}}"
|
||||
}
|
||||
],
|
||||
"publishers": {
|
||||
"ZenodoSoftwareVersionPublisher" :{
|
||||
"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> </p>",
|
||||
"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>",
|
||||
"skip_grants": ["004260"]
|
||||
}
|
||||
},
|
||||
"exporters": {
|
||||
|
||||
}
|
||||
]
|
||||
}
|
||||
|
|
@ -1,6 +1,7 @@
|
|||
{
|
||||
"concept": {
|
||||
"global": {
|
||||
"name": "gcat",
|
||||
"group": "data-catalogue",
|
||||
"title": "gCube Catalogue (gCat) Service {{version}}",
|
||||
"license": {
|
||||
"id": "EUPL-1.1",
|
||||
|
|
@ -128,8 +129,19 @@
|
|||
"url": "https://cordis.europa.eu/project/id/871042"
|
||||
}
|
||||
],
|
||||
"publish": "NONE",
|
||||
"export": "ALL"
|
||||
"publishers": {
|
||||
"ZenodoSoftwareVersionPublisher": {
|
||||
"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> </p>",
|
||||
"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>",
|
||||
"skip_grants": ["004260"]
|
||||
}
|
||||
},
|
||||
"exporters": {
|
||||
"BibLaTeXSoftwareVersionExporter": {
|
||||
"elaboration": "ALL"
|
||||
}
|
||||
}
|
||||
},
|
||||
"versions": [
|
||||
{
|
||||
|
|
@ -312,15 +324,5 @@
|
|||
"version_doi_url" : "https://doi.org/10.5072/zenodo.1144799",
|
||||
"code_location": "https://code-repo.d4science.org/gCubeSystem/{{name}}/releases/tag/v{{version}}"
|
||||
}
|
||||
],
|
||||
"publishers": {
|
||||
"ZenodoSoftwareVersionPublisher" :{
|
||||
"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> </p>",
|
||||
"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>",
|
||||
"skip_grants": ["004260"]
|
||||
}
|
||||
},
|
||||
"exporters": {
|
||||
|
||||
}
|
||||
]
|
||||
}
|
||||
Loading…
Reference in New Issue