Refactoring library
This commit is contained in:
luca.frosini
parent
8897a25f4d
commit
85a36d12e5
|
|
@ -14,19 +14,29 @@ The library currently offers two processors:
|
|||
|
||||
Other processors can be easily added in the future by extending the ``SoftwareArtifactProcessor`` class.
|
||||
|
||||
|
||||
The Core of the Library
|
||||
=======================
|
||||
|
||||
The core class of the library is ``Analyser``, which must be initialized with:
|
||||
|
||||
* a configuration (JSON Object);
|
||||
* a list of software artifacts described by their metadata (JSON Array).
|
||||
|
||||
The configuration must contain at least the list of exporters to be used and their configuration parameters.
|
||||
The configuration must contain:
|
||||
|
||||
* The list of processors to be used and their configuration parameters (required);
|
||||
* A optional set of metadata which will be used as default metadata for all software artifacts defined in the list.
|
||||
|
||||
|
||||
|
||||
Exporter configuration requires at least the ``elaboration`` property, which can assume the following values
|
||||
(see ``ElaborationType`` enumerated):
|
||||
|
||||
* **ALL**: The exporter analyses all the software artifacts;
|
||||
* **UPDATE_ONLY**: The exporter analyes only the software artifact to be updated in the target;
|
||||
* **NEW**: The exporter analyses only the software artifact that does not yet exist in the target;
|
||||
* **NONE**: Does not export the software artifact in the target, but each software artifact is elaborated for the exporting without effectively doing it. It is a dry run.
|
||||
* **NONE**: Does not export the software artifact in the target, but each software artifact is elaborated without effectively exporting it. It is a dry run.
|
||||
|
||||
The processors are executed in the order they are defined.
|
||||
A processor could produce metadata itself (e.g., the obtained Zenodo DOI).
|
||||
|
|
@ -34,7 +44,6 @@ The input metadata + the metadata generated by a processor are made available to
|
|||
|
||||
At the end of the processing phase, the library produces the actualized output of all the software artifact metadata.
|
||||
|
||||
Moreover, the configuration can optionally include an arbitrary set of metadata used as default metadata for all software artifacts defined in the list.
|
||||
|
||||
The list of software artifacts contains an arbitrary set of metadata.
|
||||
It depends on the processor using certain metadata, among others.
|
||||
|
|
|
|||
|
|
@ -13,12 +13,12 @@ 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.ObjectNode;
|
||||
import org.gcube.common.software.export.SoftwareArtifactProcessor;
|
||||
import org.gcube.common.software.model.ExporterConfig;
|
||||
import org.gcube.common.software.model.ProcessorConfig;
|
||||
import org.gcube.common.software.model.GlobalConfig;
|
||||
import org.gcube.common.software.model.SoftwareArtifactConfig;
|
||||
import org.gcube.common.software.model.SoftwareArtifactMetadata;
|
||||
import org.gcube.common.software.model.SoftwareArtifactFile;
|
||||
import org.gcube.common.software.model.Variables;
|
||||
import org.gcube.common.software.processor.SoftwareArtifactProcessor;
|
||||
import org.gcube.common.software.utils.Utils;
|
||||
import org.slf4j.Logger;
|
||||
import org.slf4j.LoggerFactory;
|
||||
|
|
@ -34,7 +34,7 @@ public class Analyser {
|
|||
|
||||
protected File outputDirectory;
|
||||
protected ObjectNode globalConfiguration;
|
||||
protected ArrayNode versionConfigurations;
|
||||
protected ArrayNode artifactMetadataArray;
|
||||
|
||||
public Analyser() throws Exception {
|
||||
this.objectMapper = Utils.getObjectMapper();
|
||||
|
|
@ -52,16 +52,16 @@ public class Analyser {
|
|||
this.globalConfiguration = originalGlobal.deepCopy();
|
||||
}
|
||||
|
||||
public ArrayNode getVersionConfigurations() {
|
||||
return versionConfigurations;
|
||||
public ArrayNode getArtifactMetadataArray() {
|
||||
return artifactMetadataArray;
|
||||
}
|
||||
|
||||
public void setVersionConfigurations(ArrayNode originalVersions) {
|
||||
this.versionConfigurations = originalVersions.deepCopy();
|
||||
public void setArtifactMetadataArray(ArrayNode original) {
|
||||
this.artifactMetadataArray = original.deepCopy();
|
||||
}
|
||||
|
||||
protected SoftwareArtifactConfig actualizeSoftwareVersionConfig(JsonNode version) throws Exception {
|
||||
((ObjectNode) version).remove(GlobalConfig.EXPORTERS_PROPERTY_NAME);
|
||||
protected SoftwareArtifactMetadata actualizeSoftwareArtifactConfig(JsonNode version) throws Exception {
|
||||
((ObjectNode) version).remove(GlobalConfig.PROCESSORS_PROPERTY_NAME);
|
||||
Variables variables = objectMapper.treeToValue(version, Variables.class);
|
||||
Set<String> missingVariables = variables.parse();
|
||||
int size = missingVariables.size();
|
||||
|
|
@ -70,7 +70,7 @@ public class Analyser {
|
|||
missingVariables.toArray(new String[size]).toString());
|
||||
}
|
||||
JsonNode swVersion = objectMapper.convertValue(variables.getProperties(), JsonNode.class);
|
||||
SoftwareArtifactConfig softwareVersionConfig = objectMapper.treeToValue(swVersion, SoftwareArtifactConfig.class);
|
||||
SoftwareArtifactMetadata softwareVersionConfig = objectMapper.treeToValue(swVersion, SoftwareArtifactMetadata.class);
|
||||
|
||||
List<SoftwareArtifactFile> svfs = softwareVersionConfig.getFiles();
|
||||
for(SoftwareArtifactFile svf : svfs) {
|
||||
|
|
@ -94,22 +94,22 @@ public class Analyser {
|
|||
return globalConfig;
|
||||
}
|
||||
|
||||
protected ExporterConfig actualizeExporterConfig(ExporterConfig exporterConfig, SoftwareArtifactConfig softwareVersionConfig) throws Exception {
|
||||
ObjectNode versionNode = objectMapper.valueToTree(softwareVersionConfig);
|
||||
protected ProcessorConfig actualizeProcessorConfig(ProcessorConfig processorConfig, SoftwareArtifactMetadata softwareArtifactMetadata) throws Exception {
|
||||
ObjectNode versionNode = objectMapper.valueToTree(softwareArtifactMetadata);
|
||||
Variables versionVariables = objectMapper.treeToValue(versionNode, Variables.class);
|
||||
|
||||
ObjectNode node = objectMapper.valueToTree(exporterConfig);
|
||||
ObjectNode node = objectMapper.valueToTree(processorConfig);
|
||||
Variables variables = objectMapper.treeToValue(node, Variables.class);
|
||||
|
||||
variables.parseWith(versionVariables);
|
||||
JsonNode ec = objectMapper.convertValue(variables.getProperties(), JsonNode.class);
|
||||
return objectMapper.treeToValue(ec, ExporterConfig.class);
|
||||
return objectMapper.treeToValue(ec, ProcessorConfig.class);
|
||||
}
|
||||
|
||||
protected void checkExporters(Set<String> availableExporterNames, Set<String> requestedExporterNames) throws Exception {
|
||||
if(!availableExporterNames.containsAll(requestedExporterNames)) {
|
||||
requestedExporterNames.removeAll(availableExporterNames);
|
||||
throw new Exception("The following requested exporters does not exists " + requestedExporterNames);
|
||||
protected void checkProcessors(Set<String> availableProcessorNames, Set<String> requestedProcessorNames) throws Exception {
|
||||
if(!availableProcessorNames.containsAll(requestedProcessorNames)) {
|
||||
requestedProcessorNames.removeAll(availableProcessorNames);
|
||||
throw new Exception("The following requested exporters does not exists " + requestedProcessorNames);
|
||||
}
|
||||
}
|
||||
|
||||
|
|
@ -118,9 +118,9 @@ public class Analyser {
|
|||
|
||||
GlobalConfig globalConfig = getGlobalConfig(globalConfiguration);
|
||||
|
||||
Map<String, Class<? extends SoftwareArtifactProcessor>> availableExporters = SoftwareArtifactProcessor.getAvailableExporters();
|
||||
Map<String,ExporterConfig> requestedExporters = globalConfig.getExporters();
|
||||
checkExporters(availableExporters.keySet(), requestedExporters.keySet());
|
||||
Map<String, Class<? extends SoftwareArtifactProcessor>> availableProcessors = SoftwareArtifactProcessor.getAvailableProcessors();
|
||||
Map<String,ProcessorConfig> requestedProcessors = globalConfig.getProcessorConfigurations();
|
||||
checkProcessors(availableProcessors.keySet(), requestedProcessors.keySet());
|
||||
|
||||
if(outputDirectory==null) {
|
||||
outputDirectory = new File(globalConfig.getFileName());
|
||||
|
|
@ -130,37 +130,37 @@ public class Analyser {
|
|||
Files.createDirectories(outputDirectory.toPath());
|
||||
}
|
||||
|
||||
SoftwareArtifactConfig previous = null;
|
||||
SoftwareArtifactMetadata previous = null;
|
||||
int i = 0;
|
||||
|
||||
List<File> outputFiles = new ArrayList<>();
|
||||
|
||||
for(i=0; i<versionConfigurations.size(); i++) {
|
||||
ObjectNode versionConfig = (ObjectNode) versionConfigurations.get(i).deepCopy();
|
||||
JsonNode mergedVersionConfig = Utils.merge(globalConfiguration, versionConfig);
|
||||
for(i=0; i<artifactMetadataArray.size(); i++) {
|
||||
ObjectNode artifactMetadata = (ObjectNode) artifactMetadataArray.get(i).deepCopy();
|
||||
JsonNode mergedArtifactMetadata = Utils.merge(globalConfiguration, artifactMetadata);
|
||||
|
||||
SoftwareArtifactConfig softwareVersionConfig = actualizeSoftwareVersionConfig(mergedVersionConfig);
|
||||
softwareVersionConfig.setOriginalJson(versionConfig);
|
||||
softwareVersionConfig.setPrevious(previous);
|
||||
SoftwareArtifactMetadata softwareArtifactMetadata = actualizeSoftwareArtifactConfig(mergedArtifactMetadata);
|
||||
softwareArtifactMetadata.setOriginalJson(artifactMetadata);
|
||||
softwareArtifactMetadata.setPrevious(previous);
|
||||
|
||||
logger.trace("Going to process {}", softwareVersionConfig.getTitle());
|
||||
logger.trace("Going to process {}", softwareArtifactMetadata.getTitle());
|
||||
|
||||
|
||||
for(String className : requestedExporters.keySet()) {
|
||||
for(String className : requestedProcessors.keySet()) {
|
||||
logger.debug("Going to export with {}", className);
|
||||
Class<? extends SoftwareArtifactProcessor> exporterClass = availableExporters.get(className);
|
||||
Class<? extends SoftwareArtifactProcessor> processorClass = availableProcessors.get(className);
|
||||
|
||||
ExporterConfig exporterConfig = requestedExporters.get(className);
|
||||
exporterConfig = actualizeExporterConfig(exporterConfig, softwareVersionConfig);
|
||||
ProcessorConfig processorConfig = requestedProcessors.get(className);
|
||||
processorConfig = actualizeProcessorConfig(processorConfig, softwareArtifactMetadata);
|
||||
|
||||
SoftwareArtifactProcessor sve = exporterClass.newInstance();
|
||||
SoftwareArtifactProcessor sve = processorClass.newInstance();
|
||||
sve.setOutputDirectory(outputDirectory);
|
||||
sve.setGlobalConfig(globalConfig);
|
||||
sve.setSoftwareVersionConfig(softwareVersionConfig);
|
||||
sve.setExporterConfig(exporterConfig);
|
||||
sve.setSoftwareArtifactConfig(softwareArtifactMetadata);
|
||||
sve.setExporterConfig(processorConfig);
|
||||
sve.setFirst(i==0);
|
||||
|
||||
boolean last = i==(versionConfigurations.size()-1);
|
||||
boolean last = i==(artifactMetadataArray.size()-1);
|
||||
sve.setLast(last);
|
||||
sve.export();
|
||||
|
||||
|
|
@ -171,7 +171,7 @@ public class Analyser {
|
|||
|
||||
Thread.sleep(TimeUnit.SECONDS.toMillis(2));
|
||||
|
||||
previous = softwareVersionConfig;
|
||||
previous = softwareArtifactMetadata;
|
||||
}
|
||||
|
||||
return outputFiles;
|
||||
|
|
|
|||
|
|
@ -32,10 +32,10 @@ public class AnalyserFactory {
|
|||
|
||||
public static Analyser getAnalyser(JsonNode jsonNode) throws Exception {
|
||||
Analyser analyser = new Analyser();
|
||||
ObjectNode originalGlobal = (ObjectNode) jsonNode.get(CONFIGURATION_PROPERTY_NAME);
|
||||
analyser.setGlobalConfiguration(originalGlobal);
|
||||
ArrayNode originalVersions = (ArrayNode) jsonNode.get(ARTIFACTS_PROPERTY_NAME);
|
||||
analyser.setVersionConfigurations(originalVersions);
|
||||
ObjectNode originalGlobalConfiguration = (ObjectNode) jsonNode.get(CONFIGURATION_PROPERTY_NAME);
|
||||
analyser.setGlobalConfiguration(originalGlobalConfiguration);
|
||||
ArrayNode originalArtifactMetadataArray = (ArrayNode) jsonNode.get(ARTIFACTS_PROPERTY_NAME);
|
||||
analyser.setArtifactMetadataArray(originalArtifactMetadataArray);
|
||||
return analyser;
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -20,10 +20,10 @@ public class GlobalConfig {
|
|||
|
||||
public static final String EXPORT_FILENAME_PROPERTY_NAME = "export_filename";
|
||||
|
||||
public static final String EXPORTERS_PROPERTY_NAME = "exporters";
|
||||
public static final String PROCESSORS_PROPERTY_NAME = "processors";
|
||||
|
||||
@JsonProperty(EXPORTERS_PROPERTY_NAME)
|
||||
protected Map<String,ExporterConfig> exporters;
|
||||
@JsonProperty(PROCESSORS_PROPERTY_NAME)
|
||||
protected Map<String,ProcessorConfig> processorConfigurations;
|
||||
|
||||
protected Map<String, JsonNode> properties;
|
||||
|
||||
|
|
@ -34,8 +34,8 @@ public class GlobalConfig {
|
|||
this.properties = new LinkedHashMap<>();
|
||||
}
|
||||
|
||||
public Map<String,ExporterConfig> getExporters() {
|
||||
return exporters;
|
||||
public Map<String,ProcessorConfig> getProcessorConfigurations() {
|
||||
return processorConfigurations;
|
||||
}
|
||||
|
||||
@JsonIgnore
|
||||
|
|
|
|||
|
|
@ -13,7 +13,7 @@ import org.gcube.com.fasterxml.jackson.databind.JsonNode;
|
|||
/**
|
||||
* @author Luca Frosini (ISTI - CNR)
|
||||
*/
|
||||
public class ExporterConfig {
|
||||
public class ProcessorConfig {
|
||||
|
||||
public static final String ELABORATION_PROPERTY_NAME = "elaboration";
|
||||
|
||||
|
|
@ -23,11 +23,11 @@ public class ExporterConfig {
|
|||
|
||||
protected Map<String, JsonNode> properties;
|
||||
|
||||
public ExporterConfig() {
|
||||
public ProcessorConfig() {
|
||||
properties = new LinkedHashMap<>();
|
||||
}
|
||||
|
||||
public ElaborationType getElaboration() {
|
||||
public ElaborationType getElaborationType() {
|
||||
return elaboration;
|
||||
}
|
||||
|
||||
|
|
@ -21,7 +21,7 @@ import org.gcube.common.software.utils.Utils;
|
|||
* @author Luca Frosini (ISTI - CNR)
|
||||
* TO BE GENERALIZED
|
||||
*/
|
||||
public class SoftwareArtifactConfig {
|
||||
public class SoftwareArtifactMetadata {
|
||||
|
||||
public static final String PREVIOUS_CONCEPT_DOI_VALUE = "PREVIOUS";
|
||||
|
||||
|
|
@ -40,10 +40,10 @@ public class SoftwareArtifactConfig {
|
|||
public static final String GRANTS_PROPERTY_NAME = "grants";
|
||||
|
||||
@JsonIgnore
|
||||
protected SoftwareArtifactConfig previous;
|
||||
protected SoftwareArtifactMetadata previous;
|
||||
|
||||
@JsonIgnore
|
||||
protected SoftwareArtifactConfig next;
|
||||
protected SoftwareArtifactMetadata next;
|
||||
|
||||
@JsonIgnore
|
||||
protected Boolean newDeposition;
|
||||
|
|
@ -92,18 +92,18 @@ public class SoftwareArtifactConfig {
|
|||
|
||||
protected Map<String, JsonNode> additionalProperties;
|
||||
|
||||
public SoftwareArtifactConfig() {
|
||||
public SoftwareArtifactMetadata() {
|
||||
this.newDeposition = false;
|
||||
this.additionalProperties = new LinkedHashMap<>();
|
||||
}
|
||||
|
||||
@JsonIgnore
|
||||
public SoftwareArtifactConfig getPrevious() {
|
||||
public SoftwareArtifactMetadata getPrevious() {
|
||||
return previous;
|
||||
}
|
||||
|
||||
@JsonIgnore
|
||||
public void setPrevious(SoftwareArtifactConfig previous) {
|
||||
public void setPrevious(SoftwareArtifactMetadata previous) {
|
||||
this.previous = previous;
|
||||
if(previous!=null) {
|
||||
this.previous.next = this;
|
||||
|
|
@ -111,7 +111,7 @@ public class SoftwareArtifactConfig {
|
|||
}
|
||||
|
||||
@JsonIgnore
|
||||
public SoftwareArtifactConfig getNext() {
|
||||
public SoftwareArtifactMetadata getNext() {
|
||||
return next;
|
||||
}
|
||||
|
||||
|
|
@ -1,14 +1,14 @@
|
|||
package org.gcube.common.software.export;
|
||||
package org.gcube.common.software.processor;
|
||||
|
||||
import java.io.File;
|
||||
import java.util.HashMap;
|
||||
import java.util.Map;
|
||||
|
||||
import org.gcube.common.software.export.biblatex.BibLaTeXExporter;
|
||||
import org.gcube.common.software.export.zenodo.ZenodoExporter;
|
||||
import org.gcube.common.software.model.ExporterConfig;
|
||||
import org.gcube.common.software.model.ProcessorConfig;
|
||||
import org.gcube.common.software.model.GlobalConfig;
|
||||
import org.gcube.common.software.model.SoftwareArtifactConfig;
|
||||
import org.gcube.common.software.model.SoftwareArtifactMetadata;
|
||||
import org.gcube.common.software.processor.biblatex.BibLaTeXExporter;
|
||||
import org.gcube.common.software.processor.zenodo.ZenodoExporter;
|
||||
|
||||
/**
|
||||
* @author Luca Frosini (ISTI - CNR)
|
||||
|
|
@ -27,14 +27,14 @@ public abstract class SoftwareArtifactProcessor {
|
|||
availableProcessors.put(clz.getSimpleName(), clz);
|
||||
}
|
||||
|
||||
public static Map<String, Class<? extends SoftwareArtifactProcessor>> getAvailableExporters() {
|
||||
public static Map<String, Class<? extends SoftwareArtifactProcessor>> getAvailableProcessors() {
|
||||
return availableProcessors;
|
||||
}
|
||||
|
||||
protected File outputDirectory;
|
||||
protected GlobalConfig globalConfig;
|
||||
protected SoftwareArtifactConfig softwareVersionConfig;
|
||||
protected ExporterConfig exporterConfig;
|
||||
protected SoftwareArtifactMetadata softwareArtifactMetadata;
|
||||
protected ProcessorConfig processorConfig;
|
||||
|
||||
protected boolean first;
|
||||
protected boolean last;
|
||||
|
|
@ -57,20 +57,20 @@ public abstract class SoftwareArtifactProcessor {
|
|||
this.globalConfig = globalConfig;
|
||||
}
|
||||
|
||||
public SoftwareArtifactConfig getSoftwareVersionConfig() {
|
||||
return softwareVersionConfig;
|
||||
public SoftwareArtifactMetadata getSoftwareArtifactConfig() {
|
||||
return softwareArtifactMetadata;
|
||||
}
|
||||
|
||||
public void setSoftwareVersionConfig(SoftwareArtifactConfig softwareVersionConfig) {
|
||||
this.softwareVersionConfig = softwareVersionConfig;
|
||||
public void setSoftwareArtifactConfig(SoftwareArtifactMetadata softwareArtifactMetadata) {
|
||||
this.softwareArtifactMetadata = softwareArtifactMetadata;
|
||||
}
|
||||
|
||||
public ExporterConfig getExporterConfig() {
|
||||
return exporterConfig;
|
||||
public ProcessorConfig getExporterConfig() {
|
||||
return processorConfig;
|
||||
}
|
||||
|
||||
public void setExporterConfig(ExporterConfig processorConfig) {
|
||||
this.exporterConfig = processorConfig;
|
||||
public void setExporterConfig(ProcessorConfig processorConfig) {
|
||||
this.processorConfig = processorConfig;
|
||||
}
|
||||
|
||||
public void setFirst(boolean first) {
|
||||
|
|
@ -1,4 +1,4 @@
|
|||
package org.gcube.common.software.export.biblatex;
|
||||
package org.gcube.common.software.processor.biblatex;
|
||||
|
||||
import java.io.BufferedWriter;
|
||||
import java.io.File;
|
||||
|
|
@ -9,9 +9,9 @@ import java.util.Set;
|
|||
|
||||
import org.gcube.com.fasterxml.jackson.databind.JsonNode;
|
||||
import org.gcube.com.fasterxml.jackson.databind.node.ArrayNode;
|
||||
import org.gcube.common.software.export.SoftwareArtifactProcessor;
|
||||
import org.gcube.common.software.model.ElaborationType;
|
||||
import org.gcube.common.software.model.Variables;
|
||||
import org.gcube.common.software.processor.SoftwareArtifactProcessor;
|
||||
import org.gcube.common.software.utils.FileUtils;
|
||||
import org.gcube.common.software.utils.Utils;
|
||||
import org.slf4j.Logger;
|
||||
|
|
@ -41,9 +41,9 @@ public class BibLaTeXExporter extends SoftwareArtifactProcessor {
|
|||
exportFile.createNewFile();
|
||||
}
|
||||
|
||||
String title = softwareVersionConfig.getTitle();
|
||||
String title = softwareArtifactMetadata.getTitle();
|
||||
|
||||
ElaborationType export = exporterConfig.getElaboration();
|
||||
ElaborationType export = processorConfig.getElaborationType();
|
||||
|
||||
switch (export) {
|
||||
case ALL:
|
||||
|
|
@ -51,7 +51,7 @@ public class BibLaTeXExporter extends SoftwareArtifactProcessor {
|
|||
break;
|
||||
|
||||
case UPDATE_ONLY:
|
||||
if (softwareVersionConfig.isNewDeposition()) {
|
||||
if (softwareArtifactMetadata.isNewDeposition()) {
|
||||
logger.info("Skipping export for {}.", title);
|
||||
return;
|
||||
}
|
||||
|
|
@ -59,7 +59,7 @@ public class BibLaTeXExporter extends SoftwareArtifactProcessor {
|
|||
break;
|
||||
|
||||
case NEW:
|
||||
if (!softwareVersionConfig.isNewDeposition()) {
|
||||
if (!softwareArtifactMetadata.isNewDeposition()) {
|
||||
logger.info("Skipping export for {}.", title);
|
||||
return;
|
||||
}
|
||||
|
|
@ -157,10 +157,10 @@ public class BibLaTeXExporter extends SoftwareArtifactProcessor {
|
|||
|
||||
protected String parseTemplate(String template) throws Exception {
|
||||
String s = template;
|
||||
s = Utils.replaceVariable("author", getAuthors(softwareVersionConfig.getAuthors()), s);
|
||||
s = Utils.replaceVariable("keywords", getKeywords(softwareVersionConfig.getKeywords()), s);
|
||||
s = Utils.replaceVariable("author", getAuthors(softwareArtifactMetadata.getAuthors()), s);
|
||||
s = Utils.replaceVariable("keywords", getKeywords(softwareArtifactMetadata.getKeywords()), s);
|
||||
|
||||
Variables variables = softwareVersionConfig.getVariables();
|
||||
Variables variables = softwareArtifactMetadata.getVariables();
|
||||
s = variables.replaceAllVariables(s);
|
||||
// s = addNotes(s);
|
||||
|
||||
|
|
@ -168,8 +168,8 @@ public class BibLaTeXExporter extends SoftwareArtifactProcessor {
|
|||
}
|
||||
|
||||
protected void generate() throws Exception {
|
||||
String title = softwareVersionConfig.getTitle();
|
||||
if(softwareVersionConfig.getVersionDOIURL()==null) {
|
||||
String title = softwareArtifactMetadata.getTitle();
|
||||
if(softwareArtifactMetadata.getVersionDOIURL()==null) {
|
||||
logger.info("No Version DOI URL for {}. It will not be exported in BibLaTex format.", title);
|
||||
return;
|
||||
}
|
||||
|
|
@ -1,4 +1,4 @@
|
|||
package org.gcube.common.software.export.zenodo;
|
||||
package org.gcube.common.software.processor.zenodo;
|
||||
|
||||
import java.io.BufferedReader;
|
||||
import java.io.File;
|
||||
|
|
@ -30,9 +30,9 @@ import org.gcube.com.fasterxml.jackson.databind.node.ObjectNode;
|
|||
import org.gcube.common.gxhttp.request.GXHTTPStringRequest;
|
||||
import org.gcube.common.software.analyser.AnalyserFactory;
|
||||
import org.gcube.common.software.config.Config;
|
||||
import org.gcube.common.software.export.SoftwareArtifactProcessor;
|
||||
import org.gcube.common.software.model.ElaborationType;
|
||||
import org.gcube.common.software.model.SoftwareArtifactConfig;
|
||||
import org.gcube.common.software.model.SoftwareArtifactMetadata;
|
||||
import org.gcube.common.software.processor.SoftwareArtifactProcessor;
|
||||
import org.gcube.common.software.model.SoftwareArtifactFile;
|
||||
import org.gcube.common.software.utils.Utils;
|
||||
import org.glassfish.jersey.client.ClientProperties;
|
||||
|
|
@ -97,7 +97,7 @@ public class ZenodoExporter extends SoftwareArtifactProcessor {
|
|||
}
|
||||
|
||||
protected void addFilesToDeposition(List<File> files ) throws Exception {
|
||||
String depositID = getZenodoIDFromDOIURL(softwareVersionConfig.getVersionDOIURL());
|
||||
String depositID = getZenodoIDFromDOIURL(softwareArtifactMetadata.getVersionDOIURL());
|
||||
String newFilePath = DEPOSTION_FILES_PATH.replace(":id", depositID);
|
||||
URL url = new URL(zenodoBaseURL, newFilePath);
|
||||
|
||||
|
|
@ -132,7 +132,7 @@ public class ZenodoExporter extends SoftwareArtifactProcessor {
|
|||
gxHTTPStringRequest.header("Content-Type", "application/json");
|
||||
gxHTTPStringRequest.header("Accept", "application/json");
|
||||
|
||||
String id = getZenodoIDFromDOIURL(softwareVersionConfig.getVersionDOIURL());
|
||||
String id = getZenodoIDFromDOIURL(softwareArtifactMetadata.getVersionDOIURL());
|
||||
gxHTTPStringRequest.path(DEPOSITION_PATH.replace(":id", id));
|
||||
|
||||
ObjectNode metadata = generateMetadata();
|
||||
|
|
@ -149,7 +149,7 @@ public class ZenodoExporter extends SoftwareArtifactProcessor {
|
|||
gxHTTPStringRequest.header("Content-Type", "application/json");
|
||||
gxHTTPStringRequest.header("Accept", "application/json");
|
||||
|
||||
String id = getZenodoIDFromDOIURL(softwareVersionConfig.getVersionDOIURL());
|
||||
String id = getZenodoIDFromDOIURL(softwareArtifactMetadata.getVersionDOIURL());
|
||||
gxHTTPStringRequest.path(DEPOSTION_PUBLISH_PATH.replace(":id", id));
|
||||
|
||||
HttpURLConnection httpURLConnection = gxHTTPStringRequest.post();
|
||||
|
|
@ -158,7 +158,7 @@ public class ZenodoExporter extends SoftwareArtifactProcessor {
|
|||
|
||||
protected void finalize() throws Exception {
|
||||
List<File> files = new ArrayList<>();
|
||||
for(SoftwareArtifactFile svf : softwareVersionConfig.getFiles()) {
|
||||
for(SoftwareArtifactFile svf : softwareArtifactMetadata.getFiles()) {
|
||||
File file = svf.downloadFile();
|
||||
files.add(file);
|
||||
Thread.sleep(TimeUnit.SECONDS.toMillis(1));
|
||||
|
|
@ -273,23 +273,23 @@ public class ZenodoExporter extends SoftwareArtifactProcessor {
|
|||
response = getResponse(httpURLConnection);
|
||||
|
||||
String conceptDOIURL = createZenodoDOIURLFromID(response.get("conceptrecid").asText());
|
||||
softwareVersionConfig.setConceptDOIURL(conceptDOIURL);
|
||||
softwareArtifactMetadata.setConceptDOIURL(conceptDOIURL);
|
||||
String versionDOIURL = createZenodoDOIURLFromID(response.get("id").asText());
|
||||
softwareVersionConfig.setVersionDOIURL(versionDOIURL);
|
||||
softwareArtifactMetadata.setVersionDOIURL(versionDOIURL);
|
||||
finalize();
|
||||
}
|
||||
|
||||
private ArrayNode getAuthors(){
|
||||
ArrayNode authors = softwareVersionConfig.getAuthors().deepCopy();
|
||||
ArrayNode authors = softwareArtifactMetadata.getAuthors().deepCopy();
|
||||
return authors;
|
||||
}
|
||||
|
||||
private String getDescription() {
|
||||
StringBuffer stringBuffer = new StringBuffer();
|
||||
stringBuffer.append(softwareVersionConfig.getAdditionalProperty(HTML_DESCRIPTION_CONFIG_FIELD_NAME).asText());
|
||||
stringBuffer.append(softwareArtifactMetadata.getAdditionalProperty(HTML_DESCRIPTION_CONFIG_FIELD_NAME).asText());
|
||||
|
||||
if(exporterConfig.getProperty(ADDITIONAL_HTML_DESCRIPTION_CONFIG_FIELD_NAME)!=null) {
|
||||
String additionalHTMLDescription = exporterConfig.getProperty(ADDITIONAL_HTML_DESCRIPTION_CONFIG_FIELD_NAME).asText();
|
||||
if(processorConfig.getProperty(ADDITIONAL_HTML_DESCRIPTION_CONFIG_FIELD_NAME)!=null) {
|
||||
String additionalHTMLDescription = processorConfig.getProperty(ADDITIONAL_HTML_DESCRIPTION_CONFIG_FIELD_NAME).asText();
|
||||
stringBuffer.append(additionalHTMLDescription);
|
||||
}
|
||||
|
||||
|
|
@ -299,12 +299,12 @@ public class ZenodoExporter extends SoftwareArtifactProcessor {
|
|||
private ArrayNode getGrants(){
|
||||
ObjectMapper objectMapper = Utils.getObjectMapper();
|
||||
ArrayNode grants = objectMapper.createArrayNode();
|
||||
ArrayNode arrayNode = (ArrayNode) exporterConfig.getProperty(SKIP_GRANTS_CONFIG_FIELD_NAME);
|
||||
ArrayNode arrayNode = (ArrayNode) processorConfig.getProperty(SKIP_GRANTS_CONFIG_FIELD_NAME);
|
||||
Set<String> idToSkip = new HashSet<>();
|
||||
for(JsonNode idNode : arrayNode) {
|
||||
idToSkip.add(idNode.asText());
|
||||
}
|
||||
for(JsonNode g : softwareVersionConfig.getGrants()) {
|
||||
for(JsonNode g : softwareArtifactMetadata.getGrants()) {
|
||||
String id = g.get("id").asText();
|
||||
if(idToSkip.contains(id)) {
|
||||
continue;
|
||||
|
|
@ -317,7 +317,7 @@ public class ZenodoExporter extends SoftwareArtifactProcessor {
|
|||
}
|
||||
|
||||
private ArrayNode getKeywords(){
|
||||
Set<String> keywords = softwareVersionConfig.getKeywords();
|
||||
Set<String> keywords = softwareArtifactMetadata.getKeywords();
|
||||
ObjectMapper objectMapper = Utils.getObjectMapper();
|
||||
ArrayNode keywordsArrayNode = objectMapper.createArrayNode();
|
||||
for(String keyword : keywords) {
|
||||
|
|
@ -327,15 +327,15 @@ public class ZenodoExporter extends SoftwareArtifactProcessor {
|
|||
}
|
||||
|
||||
private ArrayNode getCommunities() {
|
||||
return (ArrayNode) softwareVersionConfig.getAdditionalProperty(COMMUNITIES_FIELD_NAME);
|
||||
return (ArrayNode) softwareArtifactMetadata.getAdditionalProperty(COMMUNITIES_FIELD_NAME);
|
||||
}
|
||||
|
||||
private String getLicense() {
|
||||
return softwareVersionConfig.getLicense().get("id").asText();
|
||||
return softwareArtifactMetadata.getLicense().get("id").asText();
|
||||
}
|
||||
|
||||
private String getDate() {
|
||||
return Utils.getDateAsString(softwareVersionConfig.getDate());
|
||||
return Utils.getDateAsString(softwareArtifactMetadata.getDate());
|
||||
}
|
||||
|
||||
private ObjectNode generateMetadata() {
|
||||
|
|
@ -352,8 +352,8 @@ public class ZenodoExporter extends SoftwareArtifactProcessor {
|
|||
metadata.replace("keywords", getKeywords());
|
||||
metadata.put("license", getLicense());
|
||||
metadata.put("publication_date", getDate());
|
||||
metadata.put("title", softwareVersionConfig.getTitle());
|
||||
metadata.put("version", softwareVersionConfig.getVersion());
|
||||
metadata.put("title", softwareArtifactMetadata.getTitle());
|
||||
metadata.put("version", softwareArtifactMetadata.getVersion());
|
||||
|
||||
metadatWrapper.set(METADATA_FIELD_NAME, metadata);
|
||||
return metadatWrapper;
|
||||
|
|
@ -366,7 +366,7 @@ public class ZenodoExporter extends SoftwareArtifactProcessor {
|
|||
gxHTTPStringRequest.from(GUCBE_ZENODO_SOFTWARE_DEPOSIT);
|
||||
gxHTTPStringRequest.queryParams(getAccessTokenQueryParamters());
|
||||
gxHTTPStringRequest.header("Accept", "application/json");
|
||||
String id = getZenodoIDFromDOIURL(softwareVersionConfig.getVersionDOIURL());
|
||||
String id = getZenodoIDFromDOIURL(softwareArtifactMetadata.getVersionDOIURL());
|
||||
gxHTTPStringRequest.path(DEPOSTION_EDIT_PATH.replace(":id", id));
|
||||
HttpURLConnection httpURLConnection = gxHTTPStringRequest.post();
|
||||
getResponse(httpURLConnection);
|
||||
|
|
@ -406,7 +406,7 @@ public class ZenodoExporter extends SoftwareArtifactProcessor {
|
|||
gxHTTPStringRequest.header("Content-Type", "application/json");
|
||||
gxHTTPStringRequest.header("Accept", "application/json");
|
||||
|
||||
String conceptDOIURL = softwareVersionConfig.getConceptDOIURL();
|
||||
String conceptDOIURL = softwareArtifactMetadata.getConceptDOIURL();
|
||||
String conceptID = getZenodoIDFromDOIURL(conceptDOIURL);
|
||||
gxHTTPStringRequest.path(RECORD_PATH.replace(":id", conceptID));
|
||||
HttpURLConnection httpURLConnection = gxHTTPStringRequest.get();
|
||||
|
|
@ -419,13 +419,13 @@ public class ZenodoExporter extends SoftwareArtifactProcessor {
|
|||
* this should avoid errors on softwareConcept.
|
||||
*/
|
||||
String latestVersionDOI = jsonNode.get("links").get("doi").asText();
|
||||
String previousVersionDOI = softwareVersionConfig.getPrevious().getVersionDOIURL().toString();
|
||||
String previousVersionDOI = softwareArtifactMetadata.getPrevious().getVersionDOIURL().toString();
|
||||
if(previousVersionDOI.compareTo(latestVersionDOI)!=0) {
|
||||
logger.error("Zenodo obtained latest DOI {} != {} DOI from previous version", latestVersionDOI, previousVersionDOI);
|
||||
throw new RuntimeException("It seems that your json is not up to date with Zenodo.");
|
||||
}
|
||||
String latestVersionVersion = jsonNode.get("metadata").get("version").asText();
|
||||
String previousVersionVersion = softwareVersionConfig.getPrevious().getVersion().toString();
|
||||
String previousVersionVersion = softwareArtifactMetadata.getPrevious().getVersion().toString();
|
||||
if(latestVersionVersion.compareTo(previousVersionVersion)!=0) {
|
||||
logger.error("Zenodo obtained latest Version {} != {} Version from previous version", latestVersionVersion, previousVersionVersion);
|
||||
throw new RuntimeException("It seems that your json is not up to date with Zenodo.");
|
||||
|
|
@ -461,7 +461,7 @@ public class ZenodoExporter extends SoftwareArtifactProcessor {
|
|||
|
||||
// The reserved DOI of this created new version will be
|
||||
String newVersionDOIURL = response.get("doi_url").asText();
|
||||
softwareVersionConfig.setVersionDOIURL(newVersionDOIURL);
|
||||
softwareArtifactMetadata.setVersionDOIURL(newVersionDOIURL);
|
||||
|
||||
// Remove previous depositionFiles
|
||||
deletePreviousFiles();
|
||||
|
|
@ -471,7 +471,7 @@ public class ZenodoExporter extends SoftwareArtifactProcessor {
|
|||
|
||||
protected String getConfig(String propertyName) throws Exception {
|
||||
String conf = null;
|
||||
JsonNode node = exporterConfig.getProperty(propertyName);
|
||||
JsonNode node = processorConfig.getProperty(propertyName);
|
||||
if(node == null || node.getNodeType()==JsonNodeType.NULL) {
|
||||
conf = Config.getProperties().getProperty(propertyName);
|
||||
}
|
||||
|
|
@ -499,18 +499,18 @@ public class ZenodoExporter extends SoftwareArtifactProcessor {
|
|||
|
||||
getZenodoConnectionConfig();
|
||||
|
||||
String title = softwareVersionConfig.getTitle();
|
||||
String title = softwareArtifactMetadata.getTitle();
|
||||
|
||||
ElaborationType publish = exporterConfig.getElaboration();
|
||||
ElaborationType publish = processorConfig.getElaborationType();
|
||||
|
||||
if(publish==ElaborationType.NONE) {
|
||||
logger.info("Zenodo Deposit is disabled for {}.",title);
|
||||
return;
|
||||
}
|
||||
|
||||
if(softwareVersionConfig.getVersionDOIURL()!=null) {
|
||||
if(softwareArtifactMetadata.getVersionDOIURL()!=null) {
|
||||
|
||||
softwareVersionConfig.setNewDeposition(false);
|
||||
softwareArtifactMetadata.setNewDeposition(false);
|
||||
|
||||
if(publish==ElaborationType.ALL ||
|
||||
publish==ElaborationType.UPDATE_ONLY) {
|
||||
|
|
@ -525,9 +525,9 @@ public class ZenodoExporter extends SoftwareArtifactProcessor {
|
|||
publish==ElaborationType.NEW) {
|
||||
logger.info("Going to deposit {}", title);
|
||||
|
||||
softwareVersionConfig.setNewDeposition(true);
|
||||
softwareArtifactMetadata.setNewDeposition(true);
|
||||
|
||||
if(softwareVersionConfig.getConceptDOIURL()==null) {
|
||||
if(softwareArtifactMetadata.getConceptDOIURL()==null) {
|
||||
create();
|
||||
}else {
|
||||
newVersion();
|
||||
|
|
@ -542,16 +542,16 @@ public class ZenodoExporter extends SoftwareArtifactProcessor {
|
|||
ObjectNode toBeExported = objectMapper.createObjectNode();
|
||||
toBeExported.replace(AnalyserFactory.CONFIGURATION_PROPERTY_NAME, globalConfig.getOriginalJson().deepCopy());
|
||||
ArrayNode array = objectMapper.createArrayNode();
|
||||
SoftwareArtifactConfig previous = softwareVersionConfig;
|
||||
SoftwareArtifactMetadata previous = softwareArtifactMetadata;
|
||||
boolean firstNode = true;
|
||||
while(previous!=null){
|
||||
ObjectNode node = previous.getOriginalJson().deepCopy();
|
||||
node.put(SoftwareArtifactConfig.CONCEPT_DOI_URL_PROPERTY_NAME, previous.getConceptDOIURL());
|
||||
node.put(SoftwareArtifactMetadata.CONCEPT_DOI_URL_PROPERTY_NAME, previous.getConceptDOIURL());
|
||||
if(firstNode) {
|
||||
toBeExported.put(SoftwareArtifactConfig.CONCEPT_DOI_URL_PROPERTY_NAME, previous.getConceptDOIURL());
|
||||
toBeExported.put(SoftwareArtifactMetadata.CONCEPT_DOI_URL_PROPERTY_NAME, previous.getConceptDOIURL());
|
||||
firstNode = false;
|
||||
}
|
||||
node.put(SoftwareArtifactConfig.VERSION_DOI_URL_PROPERTY_NAME, previous.getVersionDOIURL());
|
||||
node.put(SoftwareArtifactMetadata.VERSION_DOI_URL_PROPERTY_NAME, previous.getVersionDOIURL());
|
||||
array.insert(0, node);
|
||||
previous = previous.getPrevious();
|
||||
}
|
||||
|
|
@ -3,7 +3,7 @@ package org.gcube.common.software.utils;
|
|||
import java.io.File;
|
||||
import java.net.URL;
|
||||
|
||||
import org.gcube.common.software.export.biblatex.BibLaTeXExporter;
|
||||
import org.gcube.common.software.processor.biblatex.BibLaTeXExporter;
|
||||
import org.slf4j.Logger;
|
||||
import org.slf4j.LoggerFactory;
|
||||
|
||||
|
|
|
|||
|
|
@ -135,7 +135,7 @@
|
|||
}
|
||||
],
|
||||
"export_filename": "{{name}}",
|
||||
"exporters": {
|
||||
"processors": {
|
||||
"ZenodoExporter": {
|
||||
"elaboration": "NONE",
|
||||
"skip_grants": ["004260"],
|
||||
|
|
|
|||
|
|
@ -136,7 +136,7 @@
|
|||
}
|
||||
],
|
||||
"export_filename": "{{name}}",
|
||||
"exporters": {
|
||||
"processors": {
|
||||
"ZenodoExporter": {
|
||||
"elaboration": "NONE",
|
||||
"skip_grants": ["004260"],
|
||||
|
|
|
|||
Loading…
Reference in New Issue