.gitignore

@@ -70,10 +70,4 @@ fabric.properties
 # Android studio 3.1+ serialized cache file
 .idea/caches/build_file_checksums.ser
 
-# VS Code settings
-.vscode
-
-# asdf-vm tool-versions file
-.tool-versions
-
 target/

CHANGELOG.md

@@ -1,15 +0,0 @@
-# Changelog
-All notable changes to this project will be documented in this file.
-
-The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
-and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
-
-## Unreleased
-### Updated
-- Update dependencies in `pom.xml`
-
-### Changed
-- Java compiler and target from JDK 7 to JDK 8
-
-### Added
-- New `FixLowQualityThumbnails` script to detect and remove more low-quality thumbnails

README.md

@@ -2,8 +2,7 @@
 DSpace curation tasks and other Java-based helpers used on the [CGSpace](https://cgspace.cgiar.org) institutional repository:
 
 - **CountryCodeTagger**: add ISO 3166-1 Alpha2 country codes to items based on their existing country metadata
-- **FixJpgJpgThumbnails**: fix low-quality ".jpg.jpg" thumbnails by replacing them with their originals
+- **FixJpgJpgThumbnails**: Fix low-quality ".jpg.jpg" thumbnails by replacing them with their originals
-- **FixLowQualityThumbnails**: remove low-quality thumbnails when PDF bitstreams are present
 
 Tested on DSpace 6.3. Read more about the [DSpace curation system](https://wiki.lyrasis.org/display/DSDOC5x/Curation+System).
 
@@ -25,13 +24,13 @@ The jar will be copied to all DSpace applications.
 ### Manual Build and Install
 To build the standalone jar:
 
-```console
+```
 $ mvn package
 ```
 
 Copy the resulting jar to the DSpace `lib` directory:
 
-```console
+```
 $ cp target/cgspace-java-helpers-6.1-SNAPSHOT.jar ~/dspace/lib/
 ```
 
@@ -41,7 +40,7 @@ Please refer to the appropriate README.md file:
 - Curation Tasks: [src/main/java/io/github/ilri/cgspace/ctasks/README.md](https://github.com/ilri/cgspace-java-helpers/blob/dspace6/src/main/java/io/github/ilri/cgspace/ctasks/README.md)
 - Scripts: [src/main/java/io/github/ilri/cgspace/scripts/README.md](https://github.com/ilri/cgspace-java-helpers/blob/dspace6/src/main/java/io/github/ilri/cgspace/scripts/README.md)
 
-## TODO
+## Todo
 
 - Add a curation task to normalize DOIs to "https://doi.org" format
 

pom.xml

@@ -28,15 +28,21 @@
 
   <properties>
     <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
-    <maven.compiler.source>1.8</maven.compiler.source>
+    <maven.compiler.source>1.7</maven.compiler.source>
-    <maven.compiler.target>1.8</maven.compiler.target>
+    <maven.compiler.target>1.7</maven.compiler.target>
   </properties>
 
   <dependencies>
+    <dependency>
+      <groupId>junit</groupId>
+      <artifactId>junit</artifactId>
+      <version>4.11</version>
+      <scope>test</scope>
+    </dependency>
     <dependency>
       <groupId>com.google.code.gson</groupId>
       <artifactId>gson</artifactId>
-      <version>2.9.1</version>
+      <version>2.6.1</version>
     </dependency>
     <dependency>
       <groupId>org.dspace</groupId>
@@ -69,41 +75,41 @@
         <!-- clean lifecycle, see https://maven.apache.org/ref/current/maven-core/lifecycles.html#clean_Lifecycle -->
         <plugin>
           <artifactId>maven-clean-plugin</artifactId>
-          <version>3.2.0</version>
+          <version>3.1.0</version>
         </plugin>
         <!-- default lifecycle, jar packaging: see https://maven.apache.org/ref/current/maven-core/default-bindings.html#Plugin_bindings_for_jar_packaging -->
         <plugin>
           <artifactId>maven-resources-plugin</artifactId>
-          <version>3.3.0</version>
+          <version>3.0.2</version>
         </plugin>
         <plugin>
           <artifactId>maven-compiler-plugin</artifactId>
-          <version>3.10.1</version>
+          <version>3.8.0</version>
         </plugin>
         <plugin>
           <artifactId>maven-surefire-plugin</artifactId>
-          <version>3.0.0-M7</version>
+          <version>2.22.1</version>
         </plugin>
         <plugin>
           <artifactId>maven-jar-plugin</artifactId>
-          <version>3.3.0</version>
+          <version>3.0.2</version>
         </plugin>
         <plugin>
           <artifactId>maven-install-plugin</artifactId>
-          <version>3.0.1</version>
+          <version>2.5.2</version>
         </plugin>
         <plugin>
           <artifactId>maven-deploy-plugin</artifactId>
-          <version>3.3.0</version>
+          <version>2.8.2</version>
         </plugin>
         <!-- site lifecycle, see https://maven.apache.org/ref/current/maven-core/lifecycles.html#site_Lifecycle -->
         <plugin>
           <artifactId>maven-site-plugin</artifactId>
-          <version>3.12.1</version>
+          <version>3.7.1</version>
         </plugin>
         <plugin>
           <artifactId>maven-project-info-reports-plugin</artifactId>
-          <version>3.4.1</version>
+          <version>3.0.0</version>
         </plugin>
       </plugins>
     </pluginManagement>

src/main/java/io/github/ilri/cgspace/ctasks/CGSpaceCountriesVocabulary.java

@@ -1,7 +1,19 @@
 /*
-* Copyright (C) 2020 Alan Orth
+DSpace Curation Tasks
-*
+Copyright (C) 2020  Alan Orth
-* SPDX-License-Identifier: GPL-3.0-or-later
+
+This program is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program.  If not, see <https://www.gnu.org/licenses/>.
 */
 
 package io.github.ilri.cgspace.ctasks;

src/main/java/io/github/ilri/cgspace/ctasks/CountriesVocabulary.java

@@ -1,7 +1,19 @@
 /*
-* Copyright (C) 2020 Alan Orth
+    DSpace Curation Tasks
-*
+    Copyright (C) 2020  Alan Orth
-* SPDX-License-Identifier: GPL-3.0-or-later
+
+    This program is free software: you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+
+    This program is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with this program.  If not, see <https://www.gnu.org/licenses/>.
 */
 
 package io.github.ilri.cgspace.ctasks;

src/main/java/io/github/ilri/cgspace/ctasks/CountryCodeTagger.java

@@ -1,7 +1,19 @@
 /*
-* Copyright (C) 2020 Alan Orth
+    DSpace Curation Tasks
-*
+    Copyright (C) 2020  Alan Orth
-* SPDX-License-Identifier: GPL-3.0-or-later
+
+    This program is free software: you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+
+    This program is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with this program.  If not, see <https://www.gnu.org/licenses/>.
 */
 
 package io.github.ilri.cgspace.ctasks;

src/main/java/io/github/ilri/cgspace/ctasks/ISO3166CountriesVocabulary.java

@@ -1,7 +1,19 @@
 /*
-* Copyright (C) 2020 Alan Orth
+DSpace Curation Tasks
-*
+Copyright (C) 2020  Alan Orth
-* SPDX-License-Identifier: GPL-3.0-or-later
+
+This program is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program.  If not, see <https://www.gnu.org/licenses/>.
 */
 
 package io.github.ilri.cgspace.ctasks;

src/main/java/io/github/ilri/cgspace/scripts/FixJpgJpgThumbnails.java

@@ -1,9 +1,3 @@
-/*
-* Copyright (C) 2020 Alan Orth
-*
-* SPDX-License-Identifier: GPL-3.0-or-later
-*/
-
 package io.github.ilri.cgspace.scripts;
 
 import org.apache.commons.lang.StringUtils;

src/main/java/io/github/ilri/cgspace/scripts/FixLowQualityThumbnails.java

@@ -1,270 +0,0 @@
-/*
-* Copyright (C) 2022 Alan Orth
-*
-* SPDX-License-Identifier: GPL-3.0-or-later
-*/
-
-package io.github.ilri.cgspace.scripts;
-
-import org.apache.commons.lang.StringUtils;
-import org.dspace.authorize.AuthorizeException;
-import org.dspace.content.*;
-import org.dspace.content.factory.ContentServiceFactory;
-import org.dspace.content.service.BundleService;
-import org.dspace.content.service.ItemService;
-import org.dspace.core.Constants;
-import org.dspace.core.Context;
-import org.dspace.handle.factory.HandleServiceFactory;
-import org.dspace.handle.service.HandleService;
-
-import java.io.IOException;
-import java.sql.SQLException;
-import java.util.Iterator;
-import java.util.List;
-
-/**
- * Fix low-quality thumbnails in a DSpace repository.
- *
- * <p>Search the DSpace repository for items containing bitstreams matching the following criteria:
- *
- * <ul>
- *   <li>If an item has an <code>IM Thumbnail</code> and a <code>Generated Thumbnail</code> in the
- *       <code>THUMBNAIL</code> bundle, remove the <code>Generated Thumbnail</code>.
- *   <li>If an item has a PDF bitstream and a JPEG bitstream with description "thumbnail" in the
- *       <code>ORIGINAL</code> bundle, remove the "thumbnail" bitstream in the ORIGINAL bundle.
- * </ul>
- *
- * <p>The general idea is that we should always prefer thumbnails generated from PDFs by ImageMagick
- * to manually uploaded JPEGs because ImageMagick Thumbnails can be regenerated with higher quality,
- * resolution, etc. Furthermore, if there are JPEG bitstreams in the ORIGINAL bundle DSpace will
- * automatically create ".jpg.jpg" thumbnails from them in the THUMBNAIL bundle so we should remove
- * those as well!
- *
- * @author Andrea Schweer schweer@waikato.ac.nz for the LCoNZ Institutional Research Repositories
- * @author Alan Orth for the International Livestock Research Institute
- * @version 6.1
- * @since 6.1
- * @see FixJpgJpgThumbnails
- */
-public class FixLowQualityThumbnails {
-    // note: static members belong to the class itself, not any one instance
-    public static ItemService itemService = ContentServiceFactory.getInstance().getItemService();
-    public static HandleService handleService =
-            HandleServiceFactory.getInstance().getHandleService();
-    public static BundleService bundleService =
-            ContentServiceFactory.getInstance().getBundleService();
-
-    public static void main(String[] args) {
-        String parentHandle = null;
-        if (args.length >= 1) {
-            parentHandle = args[0];
-        }
-
-        Context context = null;
-        try {
-            context = new Context();
-            context.turnOffAuthorisationSystem();
-
-            if (StringUtils.isBlank(parentHandle)) {
-                process(context, itemService.findAll(context));
-            } else {
-                DSpaceObject parent = handleService.resolveToObject(context, parentHandle);
-                if (parent != null) {
-                    switch (parent.getType()) {
-                        case Constants.COLLECTION:
-                            process(
-                                    context,
-                                    itemService.findByCollection(context, (Collection) parent));
-                            break;
-                        case Constants.COMMUNITY:
-                            List<Collection> collections = ((Community) parent).getCollections();
-                            for (Collection collection : collections) {
-                                process(
-                                        context,
-                                        itemService.findAllByCollection(context, collection));
-                            }
-                            break;
-                        case Constants.SITE:
-                            process(context, itemService.findAll(context));
-                            break;
-                        case Constants.ITEM:
-                            processItem(context, (Item) parent);
-                            context.commit();
-                            break;
-                    }
-                }
-            }
-        } catch (SQLException | AuthorizeException | IOException e) {
-            e.printStackTrace(System.err);
-        } finally {
-            if (context != null && context.isValid()) {
-                context.abort();
-            }
-        }
-    }
-
-    private static void process(Context context, Iterator<Item> items)
-            throws SQLException, IOException, AuthorizeException {
-        while (items.hasNext()) {
-            Item item = items.next();
-            processItem(context, item);
-            itemService.update(context, item);
-        }
-    }
-
-    private static void processItem(Context context, Item item)
-            throws SQLException, AuthorizeException, IOException {
-        // Set some state for the item before we iterate over the THUMBNAIL bundle
-        boolean itemHasImThumbnail = false;
-
-        // Iterate over the THUMBNAIL bundle to first identify if this item has an "IM Thumbnail"
-        List<Bundle> thumbnailBundles = item.getBundles("THUMBNAIL");
-        for (Bundle thumbnailBundle : thumbnailBundles) {
-            List<Bitstream> thumbnailBundleBitstreams = thumbnailBundle.getBitstreams();
-            for (Bitstream thumbnailBitstream : thumbnailBundleBitstreams) {
-                String thumbnailDescription = thumbnailBitstream.getDescription();
-
-                if (StringUtils.isEmpty(thumbnailDescription)) {
-                    continue;
-                }
-
-                // Check if this item has a bitstream in the THUMBNAIL bundle with description "IM
-                // Thumbnail", but only if we haven't already seen one in another iteration for this
-                // bundle.
-                if (!itemHasImThumbnail && "IM Thumbnail".equals(thumbnailDescription)) {
-                    itemHasImThumbnail = true;
-                }
-            }
-
-            // If this item has an IM Thumbnail we can be reasonably sure that there is a PDF
-            // in the ORIGINAL bundle and we don't need any other thumbnails.
-            if (itemHasImThumbnail) {
-                // Iterate over the bitstreams in the THUMBNAIL bundle again.
-                for (Bitstream thumbnailBitstream : thumbnailBundleBitstreams) {
-                    String thumbnailName = thumbnailBitstream.getName();
-                    String thumbnailDescription = thumbnailBitstream.getDescription();
-
-                    if (StringUtils.isEmpty(thumbnailDescription)) {
-                        continue;
-                    }
-
-                    // If this item has a "Generated Thumbnail" we can remove it, because those
-                    // typically come from other JPEGs in the ORIGINAL bundle and we would prefer
-                    // the IM Thumbnail generated from a PDF anyway. The DSpace-generated descri-
-                    // ption will *always* be "Generated Thumbnail".
-                    if ("Generated Thumbnail".equals(thumbnailDescription)) {
-                        System.out.print("\u001b[33m");
-                        System.out.println("Deleting (" + item.getHandle() + "):");
-                        System.out.println("> Name: »" + thumbnailName + "«");
-                        System.out.println("> Description: »" + thumbnailDescription + "«");
-                        System.out.print("\u001b[0m");
-
-                        // Remove the "Generated Thumbnail" bitstream from the THUMBNAIL bundle
-                        thumbnailBundle.removeBitstream(thumbnailBitstream);
-
-                        // If this item has a bitstream with the word "thumbnail" in it then we can
-                        // remove it because we already know this item has an IM Thumbnail and we
-                        // prefer that one.
-                    } else if (thumbnailDescription.toLowerCase().contains("thumbnail")
-                            && !"IM Thumbnail".equals(thumbnailDescription)) {
-                        System.out.print("\u001b[33m");
-                        System.out.println("Deleting (" + item.getHandle() + "):");
-                        System.out.println("> Name: »" + thumbnailName + "«");
-                        System.out.println("> Description: »" + thumbnailDescription + "«");
-                        System.out.print("\u001b[0m");
-
-                        // Remove the "thumbnail" bitstream from the THUMBNAIL bundle
-                        thumbnailBundle.removeBitstream(thumbnailBitstream);
-
-                        // Otherwise skip it because it might be something uploaded manually, like
-                        // a thumbnail for a journal or a limited access item.
-                    } else {
-                        System.out.print("\u001b[34m");
-                        System.out.println("Skipping (" + item.getHandle() + "):");
-                        System.out.println("> Name: »" + thumbnailName + "«");
-                        System.out.println("> Description: »" + thumbnailDescription + "«");
-                        System.out.print("\u001b[0m");
-                    }
-
-                    // Print a blank line
-                    System.out.println();
-                }
-            }
-        }
-
-        // Set some state before we iterate over the ORIGINAL bundle
-        boolean itemHasOriginalPdfBitstream = false;
-        boolean itemHasOriginalJpegBitstream = false;
-
-        // Iterate over the ORIGINAL bundle to delete manually-uploaded JPEG
-        // bitstreams labeled "Thumbnail" whenever we have a PDF because they
-        // don't belong in the ORIGINAL bundle and DSpace will automatically
-        // create a better thumbnail from the PDF anyway.
-        List<Bundle> originalBundles = item.getBundles("ORIGINAL");
-        for (Bundle originalBundle : originalBundles) {
-            List<Bitstream> originalBundleBitstreams = originalBundle.getBitstreams();
-            for (Bitstream originalBitstream : originalBundleBitstreams) {
-                String originalFormat = originalBitstream.getFormat(context).getMIMEType();
-
-                // Check if this item has a PDF bitstream in the ORIGINAL bundle,
-                // but only if we haven't already seen one in another iteration
-                // for this bundle. DSpace will return "format application/pdf"
-                // for the MIME type.
-                if (!itemHasOriginalPdfBitstream && originalFormat.contains("application/pdf")) {
-                    itemHasOriginalPdfBitstream = true;
-                }
-
-                // Check if this item has a JPEG bitstream in the ORIGINAL bundle,
-                // but only if we haven't already seen one in another iteration
-                // for this bundle. DSpace will return "format image/jpeg" for
-                // the MIME type.
-                if (!itemHasOriginalJpegBitstream && originalFormat.contains("image/jpeg")) {
-                    itemHasOriginalJpegBitstream = true;
-                }
-            }
-
-            // Check if we found a PDF *and* a JPEG in this item's ORIGINAL
-            // bundle.
-            if (itemHasOriginalPdfBitstream && itemHasOriginalJpegBitstream) {
-                // Yes! Now iterate over the bitstreams in the ORIGINAL bundle
-                // again to see if the JPEG is a manually uploaded "Thumbnail"
-                for (Bitstream originalBitstream : originalBundleBitstreams) {
-                    String originalName = originalBitstream.getName();
-                    String originalDescription = originalBitstream.getDescription();
-                    String originalFormat = originalBitstream.getFormat(context).getMIMEType();
-
-                    if (StringUtils.isEmpty(originalDescription)) {
-                        continue;
-                    }
-
-                    /*
-                    - check if the bitstream is a JPEG based on its MIME Type
-                    - check if the bitstream's name or description is "Thumbnail"
-                    */
-                    if (originalFormat.toLowerCase().contains("image/jpeg")
-                            && (originalName.toLowerCase().contains("thumbnail")
-                                    || originalDescription.toLowerCase().contains("thumbnail"))) {
-                        System.out.print("\u001b[33m");
-                        System.out.println("Removing (" + item.getHandle() + "):");
-                        System.out.println("> Name: »" + originalName + "«");
-                        System.out.println("> Description: »" + originalDescription + "«");
-                        System.out.print("\u001b[0m");
-
-                        // Remove the original bitstream from the ORIGINAL bundle
-                        originalBundle.removeBitstream(originalBitstream);
-
-                    } else {
-                        System.out.print("\u001b[34m");
-                        System.out.println("Skipping (" + item.getHandle() + "):");
-                        System.out.println("> Name: »" + originalName + "«");
-                        System.out.println("> Description: »" + originalDescription + "«");
-                        System.out.print("\u001b[0m");
-                    }
-
-                    // Print a blank line
-                    System.out.println();
-                }
-            }
-        }
-    }
-}

src/main/java/io/github/ilri/cgspace/scripts/README.md

@@ -1,17 +1,16 @@
 # Scripts
 Java-based helpers used on the [CGSpace](https://cgspace.cgiar.org) institutional repository:
 
-- **FixJpgJpgThumbnails**: fix low-quality ".jpg.jpg" thumbnails by replacing them with their originals
+- **FixJpgJpgThumbnails**: Fix low-quality ".jpg.jpg" thumbnails by replacing them with their originals
-- **FixLowQualityThumbnails**: remove low-quality thumbnails when PDF bitstreams are present
 
-Tested on DSpace 6.3. Read more about the [DSpace curation system](https://wiki.lyrasis.org/display/DSDOC6x/Curation+System).
+Tested on DSpace 6.3. Read more about the [DSpace curation system](https://wiki.lyrasis.org/display/DSDOC5x/Curation+System).
 
 ## Build and Install
 
 ### Integrate into DSpace Build
 To use these curation tasks in a DSpace project add the following dependency to `dspace/modules/additions/pom.xml`:
 
-```xml
+```
 <dependency>
   <groupId>io.github.ilri.cgspace</groupId>
   <artifactId>cgspace-java-helpers</artifactId>
@@ -24,19 +23,19 @@ The jar will be copied to all DSpace applications.
 ### Manual Build and Install
 To build the standalone jar:
 
-```console
+```
 $ mvn package
 ```
 
 Copy the resulting jar to the DSpace `lib` directory:
 
-```console
+```
 $ cp target/cgspace-java-helpers-6.1-SNAPSHOT.jar ~/dspace/lib/
 ```
 
 ## Invocation
-The scripts take only one argument, which is a community, collection, or item:
+The script only takes one argument, which is a community, collection, or item:
 
-```console
+```
 $ dspace dsrun io.github.ilri.cgspace.scripts.FixJpgJpgThumbnails 10568/83389
 ```