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cherry-pick clarin v7 into dtq dev (#820)
* cherry-picked DataCite related changes from customer/uk * Add a script that adds a file from url to an item intended for large file workflows * Add ways to influence the bitstream name * add more options to specify an item * Expose resourceId (#1134) A BE part of #1127 - this exposes the resourceId so it can be used in the handle mgmt table * fixes #1135 - findEpersonByNetId should stop searching when it finds an eperson - moved the `return eperson` inside the for cycle (after eperson non null check). - removed the eperson param (both callers were passing in `null`)
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dspace-api/src/main/java/org/dspace/administer/FileDownloader.java
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| /** | ||
| * The contents of this file are subject to the license and copyright | ||
| * detailed in the LICENSE and NOTICE files at the root of the source | ||
| * tree and available online at | ||
| * | ||
| * http://www.dspace.org/license/ | ||
| */ | ||
| package org.dspace.administer; | ||
|
|
||
| import java.io.IOException; | ||
| import java.io.InputStream; | ||
| import java.net.URI; | ||
| import java.net.URISyntaxException; | ||
| import java.net.http.HttpClient; | ||
| import java.net.http.HttpRequest; | ||
| import java.net.http.HttpResponse; | ||
| import java.sql.SQLException; | ||
| import java.util.List; | ||
| import java.util.UUID; | ||
| import java.util.stream.Stream; | ||
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|
||
| import org.apache.commons.cli.ParseException; | ||
| import org.dspace.authorize.AuthorizeException; | ||
| import org.dspace.content.Bitstream; | ||
| import org.dspace.content.BitstreamFormat; | ||
| import org.dspace.content.Bundle; | ||
| import org.dspace.content.DSpaceObject; | ||
| import org.dspace.content.Item; | ||
| import org.dspace.content.factory.ContentServiceFactory; | ||
| import org.dspace.content.service.BitstreamFormatService; | ||
| import org.dspace.content.service.BitstreamService; | ||
| import org.dspace.content.service.ItemService; | ||
| import org.dspace.content.service.WorkspaceItemService; | ||
| import org.dspace.core.Context; | ||
| import org.dspace.eperson.EPerson; | ||
| import org.dspace.eperson.factory.EPersonServiceFactory; | ||
| import org.dspace.eperson.service.EPersonService; | ||
| import org.dspace.identifier.IdentifierNotFoundException; | ||
| import org.dspace.identifier.IdentifierNotResolvableException; | ||
| import org.dspace.identifier.factory.IdentifierServiceFactory; | ||
| import org.dspace.identifier.service.IdentifierService; | ||
| import org.dspace.scripts.DSpaceRunnable; | ||
| import org.dspace.scripts.configuration.ScriptConfiguration; | ||
| import org.dspace.utils.DSpace; | ||
| import org.slf4j.Logger; | ||
| import org.slf4j.LoggerFactory; | ||
|
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| public class FileDownloader extends DSpaceRunnable<FileDownloaderConfiguration> { | ||
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| private static final Logger log = LoggerFactory.getLogger(FileDownloader.class); | ||
| private boolean help = false; | ||
| private UUID itemUUID; | ||
| private int workspaceID; | ||
| private String pid; | ||
| private URI uri; | ||
| private String epersonMail; | ||
| private String bitstreamName; | ||
| private EPersonService epersonService; | ||
| private ItemService itemService; | ||
| private WorkspaceItemService workspaceItemService; | ||
| private IdentifierService identifierService; | ||
| private BitstreamService bitstreamService; | ||
| private BitstreamFormatService bitstreamFormatService; | ||
| private final HttpClient httpClient = HttpClient.newBuilder() | ||
| .followRedirects(HttpClient.Redirect.NORMAL) | ||
| .build(); | ||
|
|
||
| /** | ||
| * This method will return the Configuration that the implementing DSpaceRunnable uses | ||
| * | ||
| * @return The {@link ScriptConfiguration} that this implementing DspaceRunnable uses | ||
| */ | ||
| @Override | ||
| public FileDownloaderConfiguration getScriptConfiguration() { | ||
| return new DSpace().getServiceManager().getServiceByName("file-downloader", | ||
| FileDownloaderConfiguration.class); | ||
| } | ||
|
|
||
| /** | ||
| * This method has to be included in every script and handles the setup of the script by parsing the CommandLine | ||
| * and setting the variables | ||
| * | ||
| * @throws ParseException If something goes wrong | ||
| */ | ||
| @Override | ||
| public void setup() throws ParseException { | ||
| log.debug("Setting up {}", FileDownloader.class.getName()); | ||
| if (commandLine.hasOption("h")) { | ||
| help = true; | ||
| return; | ||
| } | ||
|
|
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| if (!commandLine.hasOption("u")) { | ||
| throw new ParseException("No URL option has been provided"); | ||
| } | ||
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| if (!commandLine.hasOption("i") && !commandLine.hasOption("w") && !commandLine.hasOption("p")) { | ||
| throw new ParseException("No item id option has been provided"); | ||
| } | ||
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| if (getEpersonIdentifier() == null && !commandLine.hasOption("e")) { | ||
| throw new ParseException("No eperson option has been provided"); | ||
| } | ||
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| this.epersonService = EPersonServiceFactory.getInstance().getEPersonService(); | ||
| this.itemService = ContentServiceFactory.getInstance().getItemService(); | ||
| this.workspaceItemService = ContentServiceFactory.getInstance().getWorkspaceItemService(); | ||
| this.bitstreamService = ContentServiceFactory.getInstance().getBitstreamService(); | ||
| this.bitstreamFormatService = ContentServiceFactory.getInstance().getBitstreamFormatService(); | ||
| this.identifierService = IdentifierServiceFactory.getInstance().getIdentifierService(); | ||
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| try { | ||
| uri = new URI(commandLine.getOptionValue("u")); | ||
| } catch (URISyntaxException e) { | ||
| throw new ParseException("The provided URL is not a valid URL"); | ||
| } | ||
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| if (commandLine.hasOption("i")) { | ||
| itemUUID = UUID.fromString(commandLine.getOptionValue("i")); | ||
| } else if (commandLine.hasOption("w")) { | ||
| workspaceID = Integer.parseInt(commandLine.getOptionValue("w")); | ||
| } else if (commandLine.hasOption("p")) { | ||
| pid = commandLine.getOptionValue("p"); | ||
| } | ||
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| epersonMail = commandLine.getOptionValue("e"); | ||
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| if (commandLine.hasOption("n")) { | ||
| bitstreamName = commandLine.getOptionValue("n"); | ||
| } | ||
| } | ||
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| /** | ||
| * This method has to be included in every script and this will be the main execution block for the script that'll | ||
| * contain all the logic needed | ||
| * | ||
| * @throws Exception If something goes wrong | ||
| */ | ||
| @Override | ||
| public void internalRun() throws Exception { | ||
| log.debug("Running {}", FileDownloader.class.getName()); | ||
| if (help) { | ||
| printHelp(); | ||
| return; | ||
| } | ||
|
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| Context context = new Context(); | ||
| context.setCurrentUser(getEperson(context)); | ||
|
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| //find the item by the given id | ||
| Item item = findItem(context); | ||
| if (item == null) { | ||
| throw new IllegalArgumentException("No item found for the given ID"); | ||
| } | ||
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| HttpRequest request = HttpRequest.newBuilder() | ||
| .uri(uri) | ||
| .build(); | ||
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| HttpResponse<InputStream> response = httpClient.send(request, HttpResponse.BodyHandlers.ofInputStream()); | ||
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| if (response.statusCode() >= 400) { | ||
| throw new IllegalArgumentException("The provided URL returned a status code of " + response.statusCode()); | ||
| } | ||
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| //use the provided value, the content-disposition header, the last part of the uri | ||
| if (bitstreamName == null) { | ||
| bitstreamName = response.headers().firstValue("Content-Disposition") | ||
| .filter(value -> value.contains("filename=")).flatMap(value -> Stream.of(value.split(";")) | ||
| .filter(v -> v.contains("filename=")) | ||
| .findFirst() | ||
| .map(fvalue -> fvalue.replaceFirst("filename=", "").replaceAll("\"", ""))) | ||
| .orElse(uri.getPath().substring(uri.getPath().lastIndexOf('/') + 1)); | ||
| } | ||
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| try (InputStream is = response.body()) { | ||
| saveFileToItem(context, item, is, bitstreamName); | ||
| } | ||
|
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| context.commit(); | ||
| } | ||
|
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| private Item findItem(Context context) throws SQLException { | ||
| if (itemUUID != null) { | ||
| return itemService.find(context, itemUUID); | ||
| } else if (workspaceID != 0) { | ||
| return workspaceItemService.find(context, workspaceID).getItem(); | ||
| } else { | ||
| try { | ||
| DSpaceObject dso = identifierService.resolve(context, pid); | ||
| if (dso instanceof Item) { | ||
| return (Item) dso; | ||
| } else { | ||
| throw new IllegalArgumentException("The provided identifier does not resolve to an item"); | ||
| } | ||
| } catch (IdentifierNotFoundException | IdentifierNotResolvableException e) { | ||
| throw new IllegalArgumentException(e); | ||
| } | ||
| } | ||
| } | ||
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| private void saveFileToItem(Context context, Item item, InputStream is, String name) | ||
| throws SQLException, AuthorizeException, IOException { | ||
| log.debug("Saving file to item {}", item.getID()); | ||
| List<Bundle> originals = item.getBundles("ORIGINAL"); | ||
| Bitstream b; | ||
| if (originals.isEmpty()) { | ||
| b = itemService.createSingleBitstream(context, is, item); | ||
| } else { | ||
| Bundle bundle = originals.get(0); | ||
| b = bitstreamService.create(context, bundle, is); | ||
| } | ||
| b.setName(context, name); | ||
| //now guess format of the bitstream | ||
| BitstreamFormat bf = bitstreamFormatService.guessFormat(context, b); | ||
| b.setFormat(context, bf); | ||
| } | ||
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| private EPerson getEperson(Context context) throws SQLException { | ||
| if (getEpersonIdentifier() != null) { | ||
| return epersonService.find(context, getEpersonIdentifier()); | ||
| } else { | ||
| return epersonService.findByEmail(context, epersonMail); | ||
| } | ||
| } | ||
| } | ||
|
|
73 changes: 73 additions & 0 deletions
73
dspace-api/src/main/java/org/dspace/administer/FileDownloaderConfiguration.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,73 @@ | ||
| /** | ||
| * The contents of this file are subject to the license and copyright | ||
| * detailed in the LICENSE and NOTICE files at the root of the source | ||
| * tree and available online at | ||
| * | ||
| * http://www.dspace.org/license/ | ||
| */ | ||
| package org.dspace.administer; | ||
|
|
||
| import org.apache.commons.cli.OptionGroup; | ||
| import org.apache.commons.cli.Options; | ||
| import org.dspace.scripts.configuration.ScriptConfiguration; | ||
|
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| public class FileDownloaderConfiguration extends ScriptConfiguration<FileDownloader> { | ||
|
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| private Class<FileDownloader> dspaceRunnableClass; | ||
|
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| /** | ||
| * Generic getter for the dspaceRunnableClass | ||
| * | ||
| * @return the dspaceRunnableClass value of this ScriptConfiguration | ||
| */ | ||
| @Override | ||
| public Class<FileDownloader> getDspaceRunnableClass() { | ||
| return dspaceRunnableClass; | ||
| } | ||
|
|
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| /** | ||
| * Generic setter for the dspaceRunnableClass | ||
| * | ||
| * @param dspaceRunnableClass The dspaceRunnableClass to be set on this IndexDiscoveryScriptConfiguration | ||
| */ | ||
| @Override | ||
| public void setDspaceRunnableClass(Class<FileDownloader> dspaceRunnableClass) { | ||
| this.dspaceRunnableClass = dspaceRunnableClass; | ||
| } | ||
|
|
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| /** | ||
| * The getter for the options of the Script | ||
| * | ||
| * @return the options value of this ScriptConfiguration | ||
| */ | ||
| @Override | ||
| public Options getOptions() { | ||
| if (options == null) { | ||
|
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| Options options = new Options(); | ||
| OptionGroup ids = new OptionGroup(); | ||
|
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| options.addOption("h", "help", false, "help"); | ||
|
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| options.addOption("u", "url", true, "source url"); | ||
| options.getOption("u").setRequired(true); | ||
|
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| options.addOption("i", "uuid", true, "item uuid"); | ||
| options.addOption("w", "wsid", true, "workspace id"); | ||
| options.addOption("p", "pid", true, "item pid (e.g. handle or doi)"); | ||
| ids.addOption(options.getOption("i")); | ||
| ids.addOption(options.getOption("w")); | ||
| ids.addOption(options.getOption("p")); | ||
| ids.setRequired(true); | ||
|
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| options.addOption("e", "eperson", true, "eperson email"); | ||
| options.getOption("e").setRequired(false); | ||
|
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| options.addOption("n", "name", true, "name of the file/bitstream"); | ||
| options.getOption("n").setRequired(false); | ||
|
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| super.options = options; | ||
| } | ||
| return options; | ||
| } | ||
| } |
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