Implementing library
This commit is contained in:
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@ -1,8 +1,10 @@
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package org.gcube.common.deposition;
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import java.io.File;
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import java.text.SimpleDateFormat;
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import org.gcube.com.fasterxml.jackson.databind.ObjectMapper;
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import org.gcube.com.fasterxml.jackson.databind.SerializationFeature;
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import org.gcube.common.deposition.model.Deposition;
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import org.gcube.common.deposition.model.DepositionVersion;
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import org.slf4j.Logger;
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@ -19,6 +21,10 @@ public class ElaborateDeposition {
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public ElaborateDeposition() {
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this.objectMapper = new ObjectMapper();
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SimpleDateFormat sdf = new SimpleDateFormat(DepositionVersion.DATETIME_PATTERN);
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this.objectMapper.setDateFormat(sdf);
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this.objectMapper.configure(SerializationFeature.INDENT_OUTPUT, true);
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}
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public void publish(File jsonFile) throws Exception {
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@ -43,7 +49,7 @@ public class ElaborateDeposition {
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name, depositionVersion.getVersion(),
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depositionVersion.getPrevious()!=null ? depositionVersion.getPrevious().getVersion(): null);
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ElaborateDepositionVersion elaborateDeposition = new ElaborateDepositionVersion(depositionVersion);
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ElaborateDepositionVersion elaborateDeposition = new ElaborateDepositionVersion(objectMapper, depositionVersion);
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elaborateDeposition.elaborate();
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previous = depositionVersion;
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@ -1,8 +1,16 @@
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package org.gcube.common.deposition;
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import java.net.MalformedURLException;
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import java.util.ArrayList;
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import java.util.Arrays;
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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.ObjectMapper;
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import org.gcube.common.deposition.config.Config;
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import org.gcube.common.deposition.executor.DepositionVersionExecutor;
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import org.gcube.common.deposition.model.Deposition;
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import org.gcube.common.deposition.model.DepositionFile;
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import org.gcube.common.deposition.model.DepositionVersion;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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@ -14,26 +22,89 @@ public class ElaborateDepositionVersion {
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private static final Logger logger = LoggerFactory.getLogger(ElaborateDeposition.class);
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protected ObjectMapper objectMapper;
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protected DepositionVersion depositionVersion;
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public ElaborateDepositionVersion(DepositionVersion depositionVersion) {
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public ElaborateDepositionVersion(ObjectMapper objectMapper, DepositionVersion depositionVersion) {
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this.objectMapper = objectMapper;
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this.depositionVersion = depositionVersion;
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}
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protected String replaceVariables(String stringToAnalise) {
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Deposition d = depositionVersion.getDeposition();
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String s = stringToAnalise.replaceAll("\\{\\{name\\}\\}", d.getName());
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s = s.replaceAll("\\{\\{version\\}\\}", depositionVersion.getVersion());
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s = s.replaceAll("\\{\\{date\\}\\}", DepositionVersion.getDateAsString(depositionVersion.getDate()));
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return s;
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}
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protected JsonNode getMetadata() {
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// TODO replace variables in metadata and add variables part is any
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// TODO replace variables in metadata and add variables part if any
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return null;
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}
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protected void addDefaultsToDepositionVersion() {
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// TODO add the missing content with
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protected List<DepositionFile> getDefaultFiles(){
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List<DepositionFile> defaultFiles = depositionVersion.getDeposition().getDefaultFiles();
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List<DepositionFile> files = new ArrayList<>();
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for(DepositionFile f : defaultFiles) {
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DepositionFile file = new DepositionFile();
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file.setDesiredName(replaceVariables(f.getDesiredName()));
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try {
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file.setURL(replaceVariables(f.getURL().toString()));
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} catch (MalformedURLException e) {
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throw new RuntimeException(e);
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}
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files.add(file);
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}
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return files;
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}
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public void elaborate() {
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protected void replaceVariablesInfiles() {
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List<DepositionFile> files = depositionVersion.getFiles();
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for(DepositionFile file : files) {
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file.setDesiredName(replaceVariables(file.getDesiredName()));
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try {
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file.setURL(replaceVariables(file.getURL().toString()));
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} catch (MalformedURLException e) {
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throw new RuntimeException(e);
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}
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}
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}
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protected String getDefaultCodeLocation() {
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String defaultCodeLocation = depositionVersion.getDeposition().getDefaultCodeLocation();
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return replaceVariables(defaultCodeLocation);
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}
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protected void addDefaultsToDepositionVersion() throws MalformedURLException {
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String version = depositionVersion.getVersion();
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if(version==null || version.length()==0) {
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throw new RuntimeException("Invalid version");
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}
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List<DepositionFile> files = depositionVersion.getFiles();
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if(files==null || files.size()==0) {
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depositionVersion.setFiles(getDefaultFiles());
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}else {
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replaceVariablesInfiles();
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}
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if(depositionVersion.getCodeLocation()==null && !depositionVersion.getNoCodeLocation()) {
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depositionVersion.setCodeLocation(getDefaultCodeLocation());
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}
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}
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public void elaborate() throws Exception {
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String name = depositionVersion.getDeposition().getName();
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logger.debug("DepositionVersion as is:\n{}", objectMapper.writeValueAsString(depositionVersion));
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addDefaultsToDepositionVersion();
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logger.debug("DepositionVersion wit defaults:\n{}", objectMapper.writeValueAsString(depositionVersion));
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DepositionVersionExecutor dve = DepositionVersionExecutor.getDefaultExecutor();
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dve.setMetadata(getMetadata());
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@ -64,6 +135,8 @@ public class ElaborateDepositionVersion {
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logger.info("Going to deposit {} {}",
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name , depositionVersion.getVersion());
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dve.setDepositionFiles(depositionVersion.getFiles());
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if(depositionVersion.getConceptDOIURL()==null) {
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dve.create();
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}else {
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@ -1,9 +1,11 @@
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package org.gcube.common.deposition.executor;
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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.common.deposition.executor.zenodo.ZenodoDepositionVersionExecutor;
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import org.gcube.common.deposition.model.DepositionFile;
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/**
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* @author Luca Frosini (ISTI - CNR)
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@ -16,6 +18,7 @@ public abstract class DepositionVersionExecutor {
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protected JsonNode metadata;
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protected URL doiURL;
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protected List<DepositionFile> depositionFiles;
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public JsonNode getMetadata() {
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return metadata;
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@ -33,10 +36,18 @@ public abstract class DepositionVersionExecutor {
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this.doiURL = doiURL;
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}
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public abstract void create();
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public List<DepositionFile> getDepositionFiles() {
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return depositionFiles;
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}
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public abstract void update();
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public void setDepositionFiles(List<DepositionFile> files) {
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this.depositionFiles = files;
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}
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public abstract void create() throws Exception;
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public abstract void update() throws Exception;
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public abstract void newVersion();
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public abstract void newVersion() throws Exception;
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}
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@ -1,9 +1,17 @@
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package org.gcube.common.deposition.executor.zenodo;
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import java.io.File;
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import java.io.IOException;
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import java.io.InputStream;
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import java.net.URL;
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import java.nio.file.Files;
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import java.nio.file.Path;
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import java.nio.file.Paths;
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import java.nio.file.StandardCopyOption;
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import org.gcube.common.deposition.config.Config;
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import org.gcube.common.deposition.executor.DepositionVersionExecutor;
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import org.gcube.common.deposition.model.DepositionFile;
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/**
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* @author Luca Frosini (ISTI - CNR)
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@ -22,28 +30,44 @@ public class ZenodoDepositionVersionExecutor extends DepositionVersionExecutor {
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}
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}
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protected void finalize() {
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// TODO Add files
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protected File downloadFile(DepositionFile df) throws IOException {
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Path path = Paths.get(df.getDesiredName());
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try (InputStream inputStream = df.getURL().openStream()) {
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Files.copy(inputStream, path, StandardCopyOption.REPLACE_EXISTING);
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}
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File file = new File(df.getDesiredName());
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if(!file.exists()) {
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throw new RuntimeException(file.getAbsolutePath() + "does not exist");
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}
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return file;
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}
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protected void finalize() throws IOException {
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for(DepositionFile df : depositionFiles) {
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downloadFile(df);
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}
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// TODO Add depositionFiles
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// TODO Update deposit metadata
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// TODO Publish the version
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}
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@Override
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public void create() {
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public void create() throws Exception {
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// TODO New deposit on Zenodo
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finalize();
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}
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@Override
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public void update() {
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public void update() throws Exception {
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// TODO edit a published version
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}
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@Override
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public void newVersion() {
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public void newVersion() throws Exception {
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// TODO New version on Zenodo from previous using the id in the DOI
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// TODO Remove previous files
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// TODO Remove previous depositionFiles
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finalize();
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}
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@JsonProperty(value = "metadata")
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protected JsonNode metadata;
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public static String parseRawString(String rawString, String name, String version, String date) {
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String s = rawString.replaceAll("{{name}}", name);
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s = s.replaceAll("{{version}}", version);
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s = s.replaceAll("{{date}}", date);
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return s;
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}
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public String getName() {
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return name;
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}
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@ -18,7 +18,7 @@ public class DepositionFile {
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protected String desiredName;
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public URL getUrl() {
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public URL getURL() {
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return url;
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}
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import java.net.MalformedURLException;
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import java.net.URL;
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import java.text.SimpleDateFormat;
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import java.util.Date;
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import java.util.List;
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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.annotation.JsonSetter;
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@ -13,6 +16,16 @@ import org.gcube.com.fasterxml.jackson.annotation.JsonSetter;
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*/
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public class DepositionVersion {
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/**
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* DateTime Pattern to be used to serialize Dates
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*/
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public static final String DATETIME_PATTERN = "yyyy-MM-dd";
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public static String getDateAsString(Date date) {
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SimpleDateFormat simpleDateFormat = new SimpleDateFormat(DATETIME_PATTERN);
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return simpleDateFormat.format(date);
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}
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@JsonIgnore
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protected Deposition deposition;
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protected String version;
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@JsonProperty(value = "date")
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protected String date;
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@JsonFormat(shape= JsonFormat.Shape.STRING, pattern=DepositionVersion.DATETIME_PATTERN)
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protected Date date;
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@JsonProperty(value = "files")
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protected List<DepositionFile> files;
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this.version = version;
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}
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public String getDate() {
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public Date getDate() {
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return date;
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}
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public void setDate(String date) {
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public void setDate(Date date) {
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this.date = date;
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}
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return files;
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}
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public void setFiles(List<DepositionFile> files) {
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this.files = files;
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}
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public String getgCubeReleaseVersion() {
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return gCubeReleaseVersion;
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}
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import java.net.URL;
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import org.junit.Test;
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import org.slf4j.Logger;
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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 ZenodoDepositTest {
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private static final Logger logger = LoggerFactory.getLogger(ZenodoDepositTest.class);
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protected static final String ZENODO_DEPOSIT_JSON_FILENAME = "zenodo-deposit.json";
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public File getZenodoDepositFile() throws Exception {
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zenodoDeposit.publish(getZenodoDepositFile());
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}
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@Test
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public void replateTest() {
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String test = "https://code-repo.d4science.org/gCubeSystem/{{name}}/archive/v{{version}}.tar.gz";
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test = test.replaceAll("\\{\\{name\\}\\}", "gcat");
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logger.info(test);
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}
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}
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}
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],
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"default_code_location": "https://code-repo.d4science.org/gCubeSystem/{{name}}/releases/tag/v{{version}}",
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"code_location_text": "\n\n<p>The official source code location of this software version is available at:</p>\n\n<p><a href=\"{{default_code_location}}\">{{default_code_location}}</a></p>",
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"code_location_text": "\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>",
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"versions": [
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{
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"version": "1.0.0",
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"concept_doi_url": "https://doi.org/10.5072/zenodo.1139445"
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}
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],
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"metadata":
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{
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"metadata": {
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"access_right": "open",
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"creators":
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[
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"creators": [
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{
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"affiliation": "Istituto di Scienza e Tecnologie dell'Informazione \"A. Faedo\" - CNR, Italy",
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"name": "Frosini, Luca",
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}
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],
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"description": "<p><a href=\"https://www.gcube-system.org/\">gCube</a> Catalogue (gCat) Service allows any client to publish on 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>",
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"grants":
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[
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"grants": [
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{
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"id": "283644"
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},
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"id": "10.13039/501100000780::654024"
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}
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],
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"keywords":
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[
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"keywords": [
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"gCube",
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"Catalogue",
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"D4Science"
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