Compare commits
9 Commits
3d3034fa4e
...
6c2588eba0
Author | SHA1 | Date |
---|---|---|
Fabio Sinibaldi | 6c2588eba0 | |
Fabio Sinibaldi | de4c509719 | |
Fabio Sinibaldi | f60c3b649c | |
Fabio Sinibaldi | 306c6723b8 | |
Fabio Sinibaldi | 5b969ac2cb | |
Fabio Sinibaldi | 70d7802cbe | |
Fabio Sinibaldi | 90466b296c | |
Fabio Sinibaldi | 7ce2c222e3 | |
Fabio Sinibaldi | d4799492a3 |
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@ -1,6 +1,11 @@
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This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
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# Changelog for org.gcube.data.publishing.ckan2zenodo-library
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## [v1.0.3] 2023-03-28
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- Extensions evaluated from URL [#22889](https://support.d4science.org/issues/22889)
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## [v1.0.2] 2021-07-30
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- Introduced environemnt check [#19990](https://support.d4science.org/issues/19990)
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5
pom.xml
5
pom.xml
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@ -8,7 +8,7 @@
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</parent>
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<groupId>org.gcube.data.publishing</groupId>
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<artifactId>ckan2zenodo-library</artifactId>
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<version>1.0.2</version>
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<version>1.0.3</version>
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<name>CKAN 2 Zenodo Library</name>
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<description>Library to publish d4science CKAN items into Zenodo</description>
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@ -31,7 +31,7 @@
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<dependency>
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<groupId>org.gcube.distribution</groupId>
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<artifactId>gcube-bom</artifactId>
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<version>2.0.1</version>
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<version>2.1.0</version>
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<type>pom</type>
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<scope>import</scope>
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</dependency>
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@ -59,6 +59,7 @@
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<version>1.14.8</version>
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</dependency>
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<dependency>
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<groupId>org.glassfish.jersey.media</groupId>
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<artifactId>jersey-media-json-jackson</artifactId>
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@ -35,8 +35,7 @@ public class TransformerManager {
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else return new Translator(m);
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}
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}
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throw new ConfigurationException("No specific mapping for the catalogue item has been configured. "
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+ "By continuing with the upload some metadata might not be upload to Zenodo.");
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return new Translator();
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}
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@ -1,10 +1,9 @@
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package org.gcube.data.publishing.ckan2zenodo.clients;
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import java.nio.file.Files;
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import java.util.Collection;
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import java.util.*;
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import java.util.concurrent.Callable;
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import org.gcube.data.publishing.ckan2zenodo.commons.Net;
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import org.gcube.data.publishing.ckan2zenodo.model.CkanResource;
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import org.gcube.data.publishing.ckan2zenodo.model.DownloadedFile;
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import org.gcube.data.publishing.ckan2zenodo.model.zenodo.FileDeposition;
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@ -40,64 +39,55 @@ public class UploadFilesCall implements Callable<ZenodoDeposition>{
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log.debug("Removing not referenced files..");
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HashMap<String,DownloadedFile> resourceMap=new HashMap<>();
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for(CkanResource r:toUpload) {
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DownloadedFile d=new DownloadedFile(r);
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resourceMap.put(d.getToUseFileName(),d);
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}
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Set<String> alreadyExistingFiles=new HashSet<>();
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for(FileDeposition f:dep.getFiles()) {
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CkanResource found=null;
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for(CkanResource r:toUpload)
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if(r.getName().equals(f.getFilename())) {
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found=r;
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break;
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}
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if(found==null) // File not present in current toUpload set
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if(resourceMap.containsKey(f.getFilename())){
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alreadyExistingFiles.add(f.getFilename());
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try{
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// check for update
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DownloadedFile downloaded = resourceMap.get(f.getFilename());
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if(!downloaded.getMD5().equals(f.getChecksum())) {
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log.debug("MD5 differ, going to update : "+downloaded+" - "+f);
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z.deleteFile(dep, f);
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z.uploadFile(dep, found.getName(), downloaded.getFile());
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}
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}catch (Throwable t){
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log.warn("Unable to update "+f,t);
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}
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}else {
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try{
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// remove File not present in current toUpload set
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log.debug("Remote file "+f+" is not in requested set. Deleting it..");
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z.deleteFile(dep, f);
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}catch(Throwable t) {
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log.warn("Unable to delete "+f,t);
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}
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else {
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// File present, checking for update
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DownloadedFile downloaded=null;
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try {
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log.debug("Found already existing remote file "+f);
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downloaded=Net.download(found);
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if(!downloaded.getMD5().equals(f.getChecksum())) {
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log.debug("MD5 differ, going to update : "+downloaded+" - "+f);
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z.deleteFile(dep, f);
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z.uploadFile(dep, found.getName(), downloaded.getF());
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}
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}catch(Throwable t) {
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log.warn("Unable to update "+f,t);
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}finally {
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if(downloaded!=null) Files.deleteIfExists(downloaded.getF().toPath());
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}
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}
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}
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log.debug("Going to push additional resources for "+deposition.getTitle()+" ID : "+deposition.getId());
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for(CkanResource r:toUpload) {
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DownloadedFile downloaded=null;
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try {
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boolean found=false;
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for(FileDeposition f:dep.getFiles())
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if(f.getFilename().equals(r.getName())) {
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found=true;
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break;
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}
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if(!found) {
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downloaded=Net.download(r);
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z.uploadFile(dep, r.getName(),downloaded.getF());
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}
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for(Map.Entry<String,DownloadedFile> e : resourceMap.entrySet()){
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DownloadedFile downloadedFile=e.getValue();
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if(!alreadyExistingFiles.contains(e.getKey()))
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try{
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// Upload new file
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z.uploadFile(dep,downloadedFile.getToUseFileName(),downloadedFile.getFile());
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}catch(Throwable t) {
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log.warn("Unable to upload "+r.getName()+".",t);
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log.warn("Unable to upload "+downloadedFile.getSource().getName(),t);
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}
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}
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return z.readDeposition(dep.getId());
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}
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}
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@ -129,8 +129,9 @@ public class Zenodo {
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}
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public FileDeposition uploadFile(ZenodoDeposition deposition, String toUploadName,File toUpload) throws ZenodoException {
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final ZenodoDeposition dep=(deposition.getSubmitted())?newVersion(deposition.getId()):deposition;
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log.info("Pushing File {} to Deposition {}",toUploadName,dep);
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Callable<Response> call=new Callable<Response>() {
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@Override
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|
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@ -1,56 +0,0 @@
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package org.gcube.data.publishing.ckan2zenodo.commons;
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import java.io.File;
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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.StandardCopyOption;
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import java.security.DigestInputStream;
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import java.security.MessageDigest;
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import org.gcube.data.publishing.ckan2zenodo.model.CkanResource;
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import org.gcube.data.publishing.ckan2zenodo.model.DownloadedFile;
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import lombok.extern.slf4j.Slf4j;
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@Slf4j
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public class Net {
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public static DownloadedFile download(CkanResource toDownload) throws Exception {
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String urlString=toDownload.getUrl();
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log.debug("Downloading "+urlString);
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//Download locally into temp
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URL url=new URL(urlString);
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File temp=File.createTempFile("zenodo_", ".tmp");
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MessageDigest md = MessageDigest.getInstance("MD5");
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// Multiple tries
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InputStream is=null;
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int attempt=0;
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Exception lastException=null;
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while(is==null&&attempt<5) {
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try {
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attempt++;
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is=url.openStream();
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}catch(Exception e) {
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lastException=e;
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try{
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Thread.sleep(500*attempt);
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}catch(InterruptedException e1) {}
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}
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}
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if(is==null) throw new Exception("Unable to download "+urlString,lastException);
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DigestInputStream dis = new DigestInputStream(is, md);
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// Download
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long size=Files.copy(is, temp.toPath(),StandardCopyOption.REPLACE_EXISTING);
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return new DownloadedFile(toDownload,temp,dis.getMessageDigest().toString());
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}
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}
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@ -1,20 +1,167 @@
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package org.gcube.data.publishing.ckan2zenodo.model;
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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.HttpURLConnection;
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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.StandardCopyOption;
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import java.security.DigestInputStream;
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import java.security.MessageDigest;
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import java.security.NoSuchAlgorithmException;
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import java.util.regex.Matcher;
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import java.util.regex.Pattern;
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import lombok.AllArgsConstructor;
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import lombok.Getter;
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import lombok.Setter;
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import lombok.ToString;
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import lombok.*;
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import lombok.extern.slf4j.Slf4j;
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@Getter
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@Setter
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@AllArgsConstructor
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@ToString
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@RequiredArgsConstructor
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@Slf4j
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public class DownloadedFile {
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private static final Pattern FILENAME_IN_DEPOSITION_REGEXP = Pattern.compile("(?<=filename\\=\\\").*(?=\\\")");
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@NonNull
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@Getter
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private CkanResource source;
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private File f;
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private String MD5;
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//private File f;
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private File f=null;
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private String MD5=null;
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private String remoteFileName=null;
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@Override
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public String toString() {
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return "DownloadedFile{" +
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"source=" + source +
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", f=" + f +
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", MD5='" + MD5 + '\'' +
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", remoteFileName='" + remoteFileName + '\'' +
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'}';
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}
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public String getToUseFileName() throws Exception {
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if (getExtension(source.getName())!=null){
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// source contains extension
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return source.getName();
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}else {
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if(remoteFileName == null){
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initRemoteFileName();
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}
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String evaluatedExtension=getExtension(remoteFileName);
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if(evaluatedExtension!=null)
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return source.getName()+evaluatedExtension;
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else return source.getName(); // No extension
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}
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}
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public File getFile() throws Exception {
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if(f==null){
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download();
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}
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return f;
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}
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public String getMD5() throws Exception {
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if(MD5==null){
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download();
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}
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return MD5;
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}
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static final String getExtension(String filename){
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int lastIndexOf = filename.lastIndexOf(".");
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if (lastIndexOf == -1) {
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return null; // no extension
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}
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return filename.substring(lastIndexOf);
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}
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/**
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* Actually downlaods the file INIT File, MD5 and remoteFilename.
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*/
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private void download() throws Exception {
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log.info("Downloading {} from {}",source.getName(),source.getUrl());
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URL url=new URL(source.getUrl());
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f=File.createTempFile("zenodo_", ".tmp");
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MessageDigest md = MessageDigest.getInstance("MD5");
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// Multiple tries
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InputStream is=null;
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int attempt=0;
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Exception lastException=null;
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||||
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while(is==null&&attempt<5) {
|
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try {
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attempt++;
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is=url.openStream();
|
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|
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if(remoteFileName == null)
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remoteFileName = getFilenameFromURL(url);
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}catch(Exception e) {
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lastException=e;
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try{
|
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Thread.sleep(500*attempt);
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}catch(InterruptedException e1) {}
|
||||
}
|
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}
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if(is==null) throw new Exception("Unable to download "+source.getUrl(),lastException);
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|
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if(remoteFileName == null)
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remoteFileName = ""; // Unable to evaluate from HEAD
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|
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|
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DigestInputStream dis = new DigestInputStream(is, md);
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MD5 = dis.getMessageDigest().toString();
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|
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// Download
|
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long size= Files.copy(is, f.toPath(), StandardCopyOption.REPLACE_EXISTING);
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log.info("Received {} bytes for {} ",size,source.getName());
|
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}
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|
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/**
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* Performs HTTP HEAD and INIT remoteFileName
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*/
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private void initRemoteFileName() throws Exception {
|
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int attempt =0;
|
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Exception lastException=null;
|
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URL url=new URL(source.getUrl());
|
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while(remoteFileName==null&&attempt<5) {
|
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try {
|
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attempt++;
|
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remoteFileName = getFilenameFromURL(url);
|
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}catch(Exception e) {
|
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lastException=e;
|
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try{
|
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Thread.sleep(500*attempt);
|
||||
}catch(InterruptedException e1) {}
|
||||
}
|
||||
}
|
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if(remoteFileName == null) {
|
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remoteFileName = ""; // Unable to evaluate from HEAD
|
||||
log.warn("Unable to get remote file name from {} [resource Name {}]",source.getUrl(),source.getName(),lastException);
|
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}
|
||||
}
|
||||
|
||||
|
||||
private static final String getFilenameFromURL(URL url) throws IOException {
|
||||
HttpURLConnection con = (HttpURLConnection) url.openConnection();
|
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con.setRequestMethod("GET");
|
||||
String contentDisp= con.getHeaderField("Content-Disposition");
|
||||
|
||||
Matcher m = FILENAME_IN_DEPOSITION_REGEXP.matcher(contentDisp);
|
||||
m.find();
|
||||
return m.group(0);
|
||||
}
|
||||
}
|
||||
|
|
|
@ -1,7 +1,5 @@
|
|||
package org.gcube.tests;
|
||||
package org.gcube.data.publishing.ckan2zenodo;
|
||||
|
||||
import org.gcube.data.publishing.ckan2zenodo.Ckan2Zenodo;
|
||||
import org.gcube.data.publishing.ckan2zenodo.Ckan2ZenodoImpl;
|
||||
import org.gcube.data.publishing.ckan2zenodo.model.faults.*;
|
||||
import org.gcube.data.publishing.ckan2zenodo.model.report.EnvironmentReport;
|
||||
import org.junit.Assume;
|
|
@ -1,4 +1,4 @@
|
|||
package org.gcube.tests;
|
||||
package org.gcube.data.publishing.ckan2zenodo;
|
||||
|
||||
import java.net.MalformedURLException;
|
||||
|
|
@ -1,4 +1,4 @@
|
|||
package org.gcube.tests;
|
||||
package org.gcube.data.publishing.ckan2zenodo;
|
||||
|
||||
import org.gcube.data.publishing.ckan2zenodo.clients.Zenodo;
|
||||
import org.gcube.data.publishing.ckan2zenodo.model.ZenodoCredentials;
|
|
@ -1,4 +1,4 @@
|
|||
package org.gcube.tests;
|
||||
package org.gcube.data.publishing.ckan2zenodo;
|
||||
|
||||
import java.net.MalformedURLException;
|
||||
import java.util.ArrayList;
|
||||
|
@ -7,8 +7,6 @@ import java.util.List;
|
|||
import java.util.concurrent.ExecutionException;
|
||||
import java.util.concurrent.Future;
|
||||
|
||||
import org.gcube.data.publishing.ckan2zenodo.Ckan2Zenodo;
|
||||
import org.gcube.data.publishing.ckan2zenodo.Ckan2ZenodoImpl;
|
||||
import org.gcube.data.publishing.ckan2zenodo.clients.GCat;
|
||||
import org.gcube.data.publishing.ckan2zenodo.model.CkanItemDescriptor;
|
||||
import org.gcube.data.publishing.ckan2zenodo.model.CkanResource;
|
|
@ -1,26 +1,19 @@
|
|||
package org.gcube.tests;
|
||||
package org.gcube.data.publishing.ckan2zenodo;
|
||||
|
||||
import java.io.IOException;
|
||||
import java.util.ArrayList;
|
||||
import java.util.Collection;
|
||||
import java.util.Collections;
|
||||
import java.util.HashMap;
|
||||
import java.util.List;
|
||||
|
||||
import org.gcube.data.publishing.ckan2zenodo.Fixer;
|
||||
import org.gcube.data.publishing.ckan2zenodo.commons.Parsing;
|
||||
import org.gcube.data.publishing.ckan2zenodo.model.CkanItemDescriptor;
|
||||
import org.gcube.data.publishing.ckan2zenodo.model.CkanRelatedIdentifier;
|
||||
import org.gcube.data.publishing.ckan2zenodo.model.faults.ConfigurationException;
|
||||
import org.gcube.data.publishing.ckan2zenodo.model.faults.InvalidItemException;
|
||||
import org.gcube.data.publishing.ckan2zenodo.model.zenodo.DepositionMetadata;
|
||||
import org.gcube.data.publishing.ckan2zenodo.model.zenodo.RelatedIdentifier;
|
||||
import org.gcube.data.publishing.ckan2zenodo.model.zenodo.ZenodoDeposition;
|
||||
import org.junit.Assert;
|
||||
import org.junit.BeforeClass;
|
||||
import org.junit.Test;
|
||||
|
||||
import com.fasterxml.jackson.annotation.JsonInclude.Include;
|
||||
import com.fasterxml.jackson.core.JsonParseException;
|
||||
import com.fasterxml.jackson.databind.JsonMappingException;
|
||||
import com.fasterxml.jackson.databind.ObjectMapper;
|
|
@ -1,14 +1,10 @@
|
|||
package org.gcube.tests;
|
||||
package org.gcube.data.publishing.ckan2zenodo;
|
||||
|
||||
import java.io.FileNotFoundException;
|
||||
import java.io.FileOutputStream;
|
||||
import java.io.IOException;
|
||||
|
||||
import org.gcube.common.resources.gcore.GenericResource;
|
||||
import org.gcube.common.resources.gcore.Resources;
|
||||
import org.gcube.data.publishing.ckan2zenodo.Translator;
|
||||
import org.gcube.data.publishing.ckan2zenodo.commons.IS;
|
||||
import org.gcube.data.publishing.ckan2zenodo.model.faults.ConfigurationException;
|
||||
import org.gcube.data.publishing.ckan2zenodo.model.parsing.Mappings;
|
||||
import org.junit.Test;
|
||||
|
|
@ -1,4 +1,4 @@
|
|||
package org.gcube.tests;
|
||||
package org.gcube.data.publishing.ckan2zenodo;
|
||||
|
||||
import java.io.IOException;
|
||||
import java.io.PrintStream;
|
||||
|
@ -7,8 +7,6 @@ import java.nio.file.Paths;
|
|||
import java.util.HashMap;
|
||||
import java.util.Map;
|
||||
|
||||
import org.gcube.data.publishing.ckan2zenodo.Fixer;
|
||||
import org.gcube.data.publishing.ckan2zenodo.Translator;
|
||||
import org.gcube.data.publishing.ckan2zenodo.model.CkanItemDescriptor;
|
||||
import org.gcube.data.publishing.ckan2zenodo.model.CkanResource;
|
||||
import org.gcube.data.publishing.ckan2zenodo.model.ZenodoCredentials;
|
|
@ -1,4 +1,4 @@
|
|||
package org.gcube.tests;
|
||||
package org.gcube.data.publishing.ckan2zenodo;
|
||||
|
||||
import java.util.Properties;
|
||||
|
|
@ -1,4 +1,4 @@
|
|||
package org.gcube.tests;
|
||||
package org.gcube.data.publishing.ckan2zenodo;
|
||||
|
||||
import static org.junit.Assert.assertTrue;
|
||||
|
||||
|
@ -9,7 +9,6 @@ import java.util.Map.Entry;
|
|||
|
||||
import org.gcube.common.resources.gcore.GenericResource;
|
||||
import org.gcube.common.resources.gcore.Resources;
|
||||
import org.gcube.data.publishing.ckan2zenodo.Translator;
|
||||
import org.gcube.data.publishing.ckan2zenodo.commons.IS;
|
||||
import org.gcube.data.publishing.ckan2zenodo.model.CkanItemDescriptor;
|
||||
import org.gcube.data.publishing.ckan2zenodo.model.CkanResource;
|
||||
|
@ -17,7 +16,6 @@ import org.gcube.data.publishing.ckan2zenodo.model.faults.ConfigurationException
|
|||
import org.gcube.data.publishing.ckan2zenodo.model.parsing.Filter;
|
||||
import org.gcube.data.publishing.ckan2zenodo.model.parsing.Mapping;
|
||||
import org.gcube.data.publishing.ckan2zenodo.model.parsing.Mappings;
|
||||
import org.gcube.data.publishing.ckan2zenodo.model.parsing.Regexp;
|
||||
import org.junit.BeforeClass;
|
||||
import org.junit.Test;
|
||||
|
|
@ -1,4 +1,4 @@
|
|||
package org.gcube.tests;
|
||||
package org.gcube.data.publishing.ckan2zenodo;
|
||||
|
||||
import java.io.IOException;
|
||||
import java.util.Arrays;
|
||||
|
@ -8,10 +8,8 @@ import java.util.Map.Entry;
|
|||
|
||||
import org.gcube.common.resources.gcore.GenericResource;
|
||||
import org.gcube.common.resources.gcore.Resources;
|
||||
import org.gcube.data.publishing.ckan2zenodo.Translator;
|
||||
import org.gcube.data.publishing.ckan2zenodo.clients.Zenodo;
|
||||
import org.gcube.data.publishing.ckan2zenodo.commons.IS;
|
||||
import org.gcube.data.publishing.ckan2zenodo.commons.Net;
|
||||
import org.gcube.data.publishing.ckan2zenodo.model.CkanItemDescriptor;
|
||||
import org.gcube.data.publishing.ckan2zenodo.model.CkanRelatedIdentifier;
|
||||
import org.gcube.data.publishing.ckan2zenodo.model.CkanResource;
|
||||
|
@ -89,8 +87,8 @@ public class ZenodoTests {
|
|||
CkanItemDescriptor desc=new CkanItemDescriptor(json);
|
||||
|
||||
for(CkanResource cRes:tran.filterResources(desc)) {
|
||||
DownloadedFile f=Net.download(cRes);
|
||||
FileDeposition file=z.uploadFile(dep, cRes.getName(), f.getF());
|
||||
DownloadedFile f=new DownloadedFile(cRes);
|
||||
FileDeposition file=z.uploadFile(dep, cRes.getName(), f.getFile());
|
||||
System.out.println("Published "+file);
|
||||
}
|
||||
|
||||
|
@ -117,9 +115,9 @@ public class ZenodoTests {
|
|||
CkanItemDescriptor desc=new CkanItemDescriptor(json);
|
||||
|
||||
for(CkanResource cRes:tran.filterResources(desc)) {
|
||||
DownloadedFile f=Net.download(cRes);
|
||||
DownloadedFile f=new DownloadedFile(cRes);
|
||||
|
||||
FileDeposition file=z.uploadFile(dep, cRes.getName(), f.getF());
|
||||
FileDeposition file=z.uploadFile(dep, cRes.getName(), f.getFile());
|
||||
System.out.println("Published "+file);
|
||||
}
|
||||
dep=z.publish(dep);
|
|
@ -0,0 +1,48 @@
|
|||
package org.gcube.data.publishing.ckan2zenodo.model;
|
||||
|
||||
import org.junit.Test;
|
||||
|
||||
import static junit.framework.TestCase.assertTrue;
|
||||
|
||||
public class NetTests {
|
||||
|
||||
@Test
|
||||
public void testfileNames() throws Exception {
|
||||
|
||||
CkanResource res=new CkanResource();
|
||||
res.setName("Deliverable");
|
||||
res.setDescription("My description");
|
||||
res.setId("resource_id");
|
||||
|
||||
// PDF URL
|
||||
res.setUrl("https://data-pre.d4science.net/RgA7");
|
||||
check(new DownloadedFile(res),"Deliverable.pdf",true);
|
||||
|
||||
|
||||
// Do not use HEAD if extension in resource name
|
||||
res.setName("Deliverable.rtf");
|
||||
check(new DownloadedFile(res),res.getName(),true);
|
||||
|
||||
//Check invalid urls i.e. folder url == UNABLE TO GET FILENAME FROM HEAD
|
||||
res.setUrl("http://data-pre.d4science.org/workspace-explorer-app?folderId=UjV1MTJ4K2lvQU5MRE1MT2NCOEVGWDkvMG5SL2dwY3A0QmpWZmdRVEFxR3Njd2cwcUxUQ3BBZzZxa1FhN3JQTQ");
|
||||
// Still should use resource name
|
||||
check(new DownloadedFile(res),res.getName(),true);
|
||||
|
||||
//Check invalid urls i.e. folder url == UNABLE TO GET FILENAME FROM HEAD
|
||||
res.setName("Deliverable");
|
||||
//Shouldn't have extension
|
||||
check(new DownloadedFile(res),res.getName(),false);
|
||||
}
|
||||
|
||||
|
||||
private static final void check(DownloadedFile f, String expectedFilename, boolean expectExtension) throws Exception {
|
||||
System.out.println(f);
|
||||
System.out.println("Resulting filename is : "+f.getToUseFileName());
|
||||
assertTrue(f.getToUseFileName()!=null);
|
||||
if(expectExtension)
|
||||
assertTrue(DownloadedFile.getExtension(f.getToUseFileName())!=null);
|
||||
else assertTrue(DownloadedFile.getExtension(f.getToUseFileName())==null);
|
||||
assertTrue(f.getToUseFileName().equals(expectedFilename));
|
||||
}
|
||||
|
||||
}
|
Loading…
Reference in New Issue