Update gson to version used by dspace-api

Prevent dependency convergence.

.github/workflows/maven.yml

@@ -5,20 +5,22 @@ name: Build
 
 on:
   push:
-    branches: [ dspace6 ]
+    branches: [ dspace7 ]
   pull_request:
-    branches: [ dspace6 ]
+    branches: [ dspace7 ]
 
 jobs:
   build:
 
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
 
     steps:
-    - uses: actions/checkout@v2
-    - name: Set up JDK 1.8
-      uses: actions/setup-java@v1
+    - uses: actions/checkout@v4
+    - name: Set up JDK 17
+      uses: actions/setup-java@v4
       with:
-        java-version: 1.8
+        java-version: 17
+        distribution: 'temurin'
+        cache: 'maven'
     - name: Build with Maven
       run: mvn -B package --file pom.xml

.idea/misc.xml

@@ -1,11 +1,13 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <project version="4">
+  <component name="ExternalStorageConfigurationManager" enabled="true" />
   <component name="MavenProjectsManager">
     <option name="originalFiles">
       <list>
         <option value="$PROJECT_DIR$/pom.xml" />
       </list>
     </option>
+    <option name="workspaceImportForciblyTurnedOn" value="true" />
   </component>
-  <component name="ProjectRootManager" version="2" languageLevel="JDK_11" project-jdk-name="11" project-jdk-type="JavaSDK" />
+  <component name="ProjectRootManager" version="2" languageLevel="JDK_11" project-jdk-name="17" project-jdk-type="JavaSDK" />
 </project>

CHANGELOG.md

@@ -5,11 +5,48 @@ 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 dspace-api dependency to 7.6.3
+- Update gson dependency to 2.11.0 to match dspace-api
+
+## [7.6.1.3] - 2024-06-26
+### Updated
+- Add more formats to `NormalizeDOIs` curation task
+
+## [7.6.1.2] - 2024-04-25
+### Changed
+- Remove reporting from curation tasks since "results" are enough
+
+## [7.6.1.1] - 2024-04-23
+### Added
+- New `NormalizeDOIs` curation task
+
 ### Updated
 - Update dependencies in `pom.xml`
 
+## [7.6.1] - 2024-01-02
+### Changed
+- Pin gson dependency to 2.9.0 to avoid dependency convergence issues with DSpace
+
+## [7.6] - 2024-01-02
+### Updated
+- `iso_3166-1.json` from iso-codes 4.13.0-SNAPSHOT, which [adds common names for Iran, Laos, and Syria](https://salsa.debian.org/iso-codes-team/iso-codes/-/merge_requests/32)
+- DSpace 7.6 compatibility
+
+## [6.2] - 2023-02-20
+### Updated
+- `iso_3166-1.json` from iso-codes 4.12.0, which updates the name for TR to "Türkiye"
+
+## [6.1] - 2022-10-31
+### Updated
+- Update dependencies in `pom.xml`
+- `iso_3166-1.json` from iso-codes 4.11.0
+
 ### Changed
 - Java compiler and target from JDK 7 to JDK 8
 
 ### Added
 - New `FixLowQualityThumbnails` script to detect and remove more low-quality thumbnails
+
+### Fixed
+- `FixJpgJpgThumbnails` and `FixLowQualityThumbnails` scripts not commiting changes when operating on a site, community, or collection

README.md

@@ -4,8 +4,9 @@ DSpace curation tasks and other Java-based helpers used on the [CGSpace](https:/
 - **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
 - **FixLowQualityThumbnails**: remove low-quality thumbnails when PDF bitstreams are present
+- **NormalizeDOIs**: normalize DOIs by stripping whitespace, lowercasing, and converting to https://doi.org/ format
 
-Tested on DSpace 6.3. Read more about the [DSpace curation system](https://wiki.lyrasis.org/display/DSDOC5x/Curation+System).
+Tested on DSpace 7.6.3. Read more about the [DSpace curation system](https://wiki.lyrasis.org/display/DSDOC7x/Curation+System).
 
 ## Build and Install
 
@@ -16,7 +17,7 @@ To use these curation tasks in a DSpace project add the following dependency to
 <dependency>
   <groupId>io.github.ilri.cgspace</groupId>
   <artifactId>cgspace-java-helpers</artifactId>
-  <version>6.1-SNAPSHOT</version>
+  <version>7.6.1.4-SNAPSHOT</version>
 </dependency>
 ```
 
@@ -32,18 +33,14 @@ $ mvn package
 Copy the resulting jar to the DSpace `lib` directory:
 
 ```console
-$ cp target/cgspace-java-helpers-6.1-SNAPSHOT.jar ~/dspace/lib/
+$ cp target/cgspace-java-helpers-7.6.1.4-SNAPSHOT.jar ~/dspace/lib/
 ```
 
 ## Configuration
 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
-
-- Add a curation task to normalize DOIs to "https://doi.org" format
+- Curation Tasks: [src/main/java/io/github/ilri/cgspace/ctasks/README.md](https://github.com/ilri/cgspace-java-helpers/blob/dspace7/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/dspace7/src/main/java/io/github/ilri/cgspace/scripts/README.md)
 
 ## Notes
 This project was initially created according to the [Maven Getting Started Guide](https://maven.apache.org/guides/getting-started/):
@@ -52,6 +49,14 @@ This project was initially created according to the [Maven Getting Started Guide
 $ mvn -B archetype:generate -DgroupId=io.github.ilri.cgspace -DartifactId=cgspace-java-helpers -DarchetypeArtifactId=maven-archetype-quickstart -DarchetypeVersion=1.4
 ```
 
+To deploy a new `-SNAPSHOT` release to Maven Central (make sure OSSHRH credentials are in `~/.m2/settings.xml`):
+
+```console
+$ mvn clean deploy
+```
+
+See: <a href="https://central.sonatype.org/publish/publish-maven/#performing-a-snapshot-deployment">Performing a Snapshot Deployment</a>
+
 ## License
 This work is licensed under the [GPLv3](https://www.gnu.org/licenses/gpl-3.0.en.html).
 

pom.xml

@@ -6,50 +6,57 @@
 
   <groupId>io.github.ilri.cgspace</groupId>
   <artifactId>cgspace-java-helpers</artifactId>
-  <version>6.1-SNAPSHOT</version>
+  <version>7.6.1.4-SNAPSHOT</version>
 
   <name>cgspace-java-helpers</name>
   <url>https://github.com/ilri/cgspace-java-helpers</url>
+  <description>Curation tasks and helper scripts for the CGSpace institutional repository</description>
+
+  <developers>
+    <developer>
+      <name>Alan Orth</name>
+      <email>maven@mjanja.mozmail.com</email>
+      <organizationUrl>https://mjanja.ch</organizationUrl>
+    </developer>
+  </developers>
 
   <licenses>
     <license>
         <name>GPL-3.0-only</name>
-        <url>https://spdx.org/licenses/GPL-3.0-or-later.html</url>
+        <url>https://spdx.org/licenses/GPL-3.0-only.html</url>
     </license>
   </licenses>
 
-  <!-- brings the sonatype snapshot repository and signing requirement on board -->
-  <parent>
-    <groupId>org.sonatype.oss</groupId>
-    <artifactId>oss-parent</artifactId>
-    <version>9</version>
-    <relativePath />
-  </parent>
-
   <properties>
     <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
-    <maven.compiler.source>1.8</maven.compiler.source>
-    <maven.compiler.target>1.8</maven.compiler.target>
+    <maven.compiler.release>11</maven.compiler.release>
   </properties>
 
   <dependencies>
     <dependency>
       <groupId>com.google.code.gson</groupId>
       <artifactId>gson</artifactId>
-      <version>2.9.1</version>
+      <version>2.11.0</version>
+      <!-- Ignore gson's dependency on error_prone_annotations because it causes dependency convergence with something pulled in by dspace-api -->
+      <exclusions>
+        <exclusion>
+          <groupId>com.google.errorprone</groupId>
+            <artifactId>error_prone_annotations</artifactId>
+          </exclusion>
+      </exclusions>
     </dependency>
     <dependency>
       <groupId>org.dspace</groupId>
       <artifactId>dspace-api</artifactId>
-      <version>6.3</version>
+      <version>7.6.3</version>
       <scope>provided</scope>
     </dependency>
   </dependencies>
 
   <scm>
       <connection>scm:git:git://github.com/ilri/cgspace-java-helpers.git</connection>
-      <developerConnection>scm:git:ssh://github.com:nanosai/cgspace-java-helpers.git</developerConnection>
-      <url>http://github.com/ilri/cgspace-java-helpers</url>
+      <developerConnection>scm:git:ssh://github.com:ilri/cgspace-java-helpers.git</developerConnection>
+      <url>https://github.com/ilri/cgspace-java-helpers</url>
   </scm>
 
   <distributionManagement>
@@ -69,32 +76,28 @@
         <!-- 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>3.3.2</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>3.3.1</version>
         </plugin>
         <plugin>
           <artifactId>maven-compiler-plugin</artifactId>
-          <version>3.10.1</version>
+          <version>3.13.0</version>
         </plugin>
         <plugin>
           <artifactId>maven-surefire-plugin</artifactId>
-          <version>3.0.0-M7</version>
+          <version>3.2.5</version>
         </plugin>
         <plugin>
           <artifactId>maven-jar-plugin</artifactId>
-          <version>3.3.0</version>
+          <version>3.4.1</version>
         </plugin>
         <plugin>
           <artifactId>maven-install-plugin</artifactId>
-          <version>3.0.1</version>
-        </plugin>
-        <plugin>
-          <artifactId>maven-deploy-plugin</artifactId>
-          <version>3.3.0</version>
+          <version>3.1.1</version>
         </plugin>
         <!-- site lifecycle, see https://maven.apache.org/ref/current/maven-core/lifecycles.html#site_Lifecycle -->
         <plugin>
@@ -103,9 +106,33 @@
         </plugin>
         <plugin>
           <artifactId>maven-project-info-reports-plugin</artifactId>
-          <version>3.4.1</version>
+          <version>3.5.0</version>
+        </plugin>
+        <plugin>
+          <groupId>org.sonatype.plugins</groupId>
+          <artifactId>nexus-staging-maven-plugin</artifactId>
+          <version>1.7.0</version>
+          <extensions>true</extensions>
+          <configuration>
+            <serverId>ossrh</serverId>
+            <nexusUrl>https://oss.sonatype.org/</nexusUrl>
+            <autoReleaseAfterClose>true</autoReleaseAfterClose>
+          </configuration>
         </plugin>
       </plugins>
     </pluginManagement>
   </build>
+
+  <repositories>
+    <!-- Check Maven Central first (before other repos below) -->
+    <repository>
+        <id>maven-central</id>
+        <url>https://repo.maven.apache.org/maven2</url>
+    </repository>
+    <!-- For Handle Server -->
+    <repository>
+        <id>handle.net</id>
+        <url>https://handle.net/maven</url>
+    </repository>
+  </repositories>
 </project>

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

@@ -1,8 +1,8 @@
 /*
-* Copyright (C) 2020 Alan Orth
-*
-* SPDX-License-Identifier: GPL-3.0-or-later
-*/
+ * Copyright (C) 2020 Alan Orth
+ *
+ * SPDX-License-Identifier: GPL-3.0-only
+ */
 
 package io.github.ilri.cgspace.ctasks;
 

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

@@ -1,8 +1,8 @@
 /*
-* Copyright (C) 2020 Alan Orth
-*
-* SPDX-License-Identifier: GPL-3.0-or-later
-*/
+ * Copyright (C) 2020 Alan Orth
+ *
+ * SPDX-License-Identifier: GPL-3.0-only
+ */
 
 package io.github.ilri.cgspace.ctasks;
 
@@ -10,16 +10,17 @@ import javax.annotation.Nullable;
 
 public class CountriesVocabulary {
 
-    class Country {
-        private String name;            //required
-        private String common_name;     //optional
-        private String official_name;   //optional
-        private String cgspace_name;    //optional
-        private String numeric;         //required Hmmmm need to cast this...
-        private String alpha_2;         //required
-        private String alpha_3;         //required
+    static class Country {
+        private final String name; // required
+        private final String common_name; // optional
+        private final String official_name; // optional
+        private final String cgspace_name; // optional
+        private final String numeric; // required Hmmmm need to cast this...
+        private final String alpha_2; // required
+        private final String alpha_3; // required
 
-        public Country(String name,
+        public Country(
+                String name,
                 @Nullable String common_name,
                 @Nullable String official_name,
                 @Nullable String cgspace_name,
@@ -30,7 +31,9 @@ public class CountriesVocabulary {
             this.common_name = common_name;
             this.official_name = official_name;
             this.cgspace_name = cgspace_name;
-            this.numeric = numeric; // fuuuuu this is a string and we can't cast to Integer because some values are zeropadded like "004"
+            this.numeric =
+                    numeric; // fuuuuu this is a string and we can't cast to Integer because some
+                             // values are zeropadded like "004"
             this.alpha_2 = alpha_2;
             this.alpha_3 = alpha_3;
         }

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

@@ -1,13 +1,15 @@
 /*
-* Copyright (C) 2020 Alan Orth
-*
-* SPDX-License-Identifier: GPL-3.0-or-later
-*/
+ * Copyright (C) 2020 Alan Orth
+ *
+ * SPDX-License-Identifier: GPL-3.0-only
+ */
 
 package io.github.ilri.cgspace.ctasks;
 
 import com.google.gson.Gson;
-import org.apache.log4j.Logger;
+
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
 import org.dspace.authorize.AuthorizeException;
 import org.dspace.content.DSpaceObject;
 import org.dspace.content.Item;
@@ -22,20 +24,28 @@ import java.io.InputStreamReader;
 import java.sql.SQLException;
 import java.util.ArrayList;
 import java.util.List;
+import java.util.Objects;
 
-public class CountryCodeTagger extends AbstractCurationTask
-{
+/*
+ * Add ISO 3166-1 Alpha2 country codes to items based on their existing country metadata.
+ *
+ * @author Alan Orth for the International Livestock Research Institute
+ * @version 7.6.1.2
+ * @since 5.1
+ */
+public class CountryCodeTagger extends AbstractCurationTask {
     public class CountryCodeTaggerConfig {
         private final String isocodesJsonPath = "/io/github/ilri/cgspace/ctasks/iso_3166-1.json";
-        private final String cgspaceCountriesJsonPath = "/io/github/ilri/cgspace/ctasks/cgspace-countries.json";
+        private final String cgspaceCountriesJsonPath =
+                "/io/github/ilri/cgspace/ctasks/cgspace-countries.json";
         private final String iso3166Field = taskProperty("iso3166.field");
         private final String iso3166Alpha2Field = taskProperty("iso3166-alpha2.field");
         private final boolean forceupdate = taskBooleanProperty("forceupdate", false);
 
-        private Logger log = Logger.getLogger(CountryCodeTagger.class);
+        private final Logger log = LogManager.getLogger();
     }
 
-    public class CountryCodeTaggerResult {
+    public static class CountryCodeTaggerResult {
         private int status = Curator.CURATE_UNSET;
         private String result = null;
 
@@ -57,17 +67,15 @@ public class CountryCodeTagger extends AbstractCurationTask
     }
 
     @Override
-    public int perform(DSpaceObject dso) throws IOException
-    {
+    public int perform(DSpaceObject dso) throws IOException {
         // gotta define this here so we can access it after the if context...
         CountryCodeTaggerResult alpha2Result = new CountryCodeTaggerResult();
 
-		if (dso.getType() == Constants.ITEM)
-        {
+        if (dso.getType() == Constants.ITEM) {
             // Load configuration
             CountryCodeTaggerConfig config = new CountryCodeTaggerConfig();
 
-            Item item = (Item)dso;
+            Item item = (Item) dso;
 
             try {
                 alpha2Result = performAlpha2(item, config);
@@ -76,55 +84,79 @@ public class CountryCodeTagger extends AbstractCurationTask
             }
 
             setResult(alpha2Result.getResult());
-            report(alpha2Result.getResult());
         }
 
         return alpha2Result.getStatus();
     }
 
-    public CountryCodeTaggerResult performAlpha2(Item item, CountryCodeTaggerConfig config) throws IOException, SQLException {
+    public CountryCodeTaggerResult performAlpha2(Item item, CountryCodeTaggerConfig config)
+            throws IOException, SQLException {
         CountryCodeTaggerResult alpha2Result = new CountryCodeTaggerResult();
-        String itemHandle = item.getHandle();
 
-        List<MetadataValue> itemCountries = itemService.getMetadataByMetadataString(item, config.iso3166Field);
+        List<MetadataValue> itemCountries =
+                itemService.getMetadataByMetadataString(item, config.iso3166Field);
 
         // skip items that don't have country metadata
-        if (itemCountries.size() == 0) {
-            alpha2Result.setResult(itemHandle + ": no countries, skipping.");
+        if (itemCountries.isEmpty()) {
+            alpha2Result.setResult("No countries, skipping.");
             alpha2Result.setStatus(Curator.CURATE_SKIP);
         } else {
             Gson gson = new Gson();
 
-            // TODO: convert to try: https://docs.oracle.com/javase/tutorial/essential/exceptions/tryResourceClose.html
-            BufferedReader reader = new BufferedReader(new InputStreamReader(this.getClass().getResourceAsStream(config.isocodesJsonPath)));
-            ISO3166CountriesVocabulary isocodesCountriesJson = gson.fromJson(reader, ISO3166CountriesVocabulary.class);
+            // TODO: convert to try:
+            // https://docs.oracle.com/javase/tutorial/essential/exceptions/tryResourceClose.html
+            BufferedReader reader =
+                    new BufferedReader(
+                            new InputStreamReader(
+                                    Objects.requireNonNull(this.getClass().getResourceAsStream(config.isocodesJsonPath))));
+            ISO3166CountriesVocabulary isocodesCountriesJson =
+                    gson.fromJson(reader, ISO3166CountriesVocabulary.class);
             reader.close();
 
-            reader = new BufferedReader(new InputStreamReader(this.getClass().getResourceAsStream(config.cgspaceCountriesJsonPath)));
-            CGSpaceCountriesVocabulary cgspaceCountriesJson = gson.fromJson(reader, CGSpaceCountriesVocabulary.class);
+            reader =
+                    new BufferedReader(
+                            new InputStreamReader(
+                                    Objects.requireNonNull(this.getClass()
+                                            .getResourceAsStream(config.cgspaceCountriesJsonPath))));
+            CGSpaceCountriesVocabulary cgspaceCountriesJson =
+                    gson.fromJson(reader, CGSpaceCountriesVocabulary.class);
             reader.close();
 
-            // split the alpha2 country code field into schema, element, and qualifier so we can use it with item.addMetadata()
+            // split the alpha2 country code field into schema, element, and qualifier so we can use
+            // it with item.addMetadata()
             String[] iso3166Alpha2FieldParts = config.iso3166Alpha2Field.split("\\.");
 
             if (config.forceupdate) {
-                itemService.clearMetadata(Curator.curationContext(), item, iso3166Alpha2FieldParts[0], iso3166Alpha2FieldParts[1], iso3166Alpha2FieldParts[2], Item.ANY);
+                itemService.clearMetadata(
+                        Curator.curationContext(),
+                        item,
+                        iso3166Alpha2FieldParts[0],
+                        iso3166Alpha2FieldParts[1],
+                        iso3166Alpha2FieldParts[2],
+                        Item.ANY);
             }
 
             // check the item's country codes, if any
-            List<MetadataValue> itemAlpha2CountryCodes = itemService.getMetadataByMetadataString(item, config.iso3166Alpha2Field);
+            List<MetadataValue> itemAlpha2CountryCodes =
+                    itemService.getMetadataByMetadataString(item, config.iso3166Alpha2Field);
 
-            if (itemAlpha2CountryCodes.size() == 0) {
+            if (itemAlpha2CountryCodes.isEmpty()) {
                 List<String> newAlpha2Codes = new ArrayList<String>();
                 for (MetadataValue itemCountry : itemCountries) {
-                    //check ISO 3166-1 countries
+                    // check ISO 3166-1 countries
                     for (CountriesVocabulary.Country country : isocodesCountriesJson.countries) {
-                        if (itemCountry.getValue().equalsIgnoreCase(country.getName()) || itemCountry.getValue().equalsIgnoreCase(country.get_official_name()) || itemCountry.getValue().equalsIgnoreCase(country.get_common_name())) {
+                        if (itemCountry.getValue().equalsIgnoreCase(country.getName())
+                                || itemCountry
+                                        .getValue()
+                                        .equalsIgnoreCase(country.get_official_name())
+                                || itemCountry
+                                        .getValue()
+                                        .equalsIgnoreCase(country.get_common_name())) {
                             newAlpha2Codes.add(country.getAlpha_2());
                         }
                     }
 
-                    //check CGSpace countries
+                    // check CGSpace countries
                     for (CountriesVocabulary.Country country : cgspaceCountriesJson.countries) {
                         if (itemCountry.getValue().equalsIgnoreCase(country.getCgspace_name())) {
                             newAlpha2Codes.add(country.getAlpha_2());
@@ -132,23 +164,33 @@ public class CountryCodeTagger extends AbstractCurationTask
                     }
                 }
 
-                if (newAlpha2Codes.size() > 0) {
+                if (!newAlpha2Codes.isEmpty()) {
                     try {
-                        itemService.addMetadata(Curator.curationContext(), item, iso3166Alpha2FieldParts[0], iso3166Alpha2FieldParts[1], iso3166Alpha2FieldParts[2], "en_US", newAlpha2Codes);
+                        itemService.addMetadata(
+                                Curator.curationContext(),
+                                item,
+                                iso3166Alpha2FieldParts[0],
+                                iso3166Alpha2FieldParts[1],
+                                iso3166Alpha2FieldParts[2],
+                                "en_US",
+                                newAlpha2Codes);
                         itemService.update(Curator.curationContext(), item);
                     } catch (SQLException | AuthorizeException sqle) {
                         config.log.debug(sqle.getMessage());
-                        alpha2Result.setResult(itemHandle + ": error");
+                        alpha2Result.setResult("Error");
                         alpha2Result.setStatus(Curator.CURATE_ERROR);
                     }
 
-                    alpha2Result.setResult(itemHandle + ": added " + newAlpha2Codes.size() + " alpha2 country code(s)");
+                    alpha2Result.setResult(
+                            "Added "
+                                    + newAlpha2Codes.size()
+                                    + " alpha2 country code(s)");
                 } else {
-                    alpha2Result.setResult(itemHandle + ": no matching countries found");
+                    alpha2Result.setResult("No matching countries found");
                 }
                 alpha2Result.setStatus(Curator.CURATE_SUCCESS);
             } else {
-                alpha2Result.setResult(itemHandle + ": item has country codes, skipping");
+                alpha2Result.setResult("Item already has country codes, skipping unless forced");
                 alpha2Result.setStatus(Curator.CURATE_SKIP);
             }
         }

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

@@ -1,15 +1,18 @@
 /*
-* Copyright (C) 2020 Alan Orth
-*
-* SPDX-License-Identifier: GPL-3.0-or-later
-*/
+ * Copyright (C) 2020 Alan Orth
+ *
+ * SPDX-License-Identifier: GPL-3.0-only
+ */
 
 package io.github.ilri.cgspace.ctasks;
 
 import com.google.gson.annotations.SerializedName;
+
 import java.util.List;
 
 public class ISO3166CountriesVocabulary extends CountriesVocabulary {
-    // support reading iso_3166-1.json from Debian's iso-codes package using SerializedName since our class needs to match the JSON exactly
-    @SerializedName("3166-1") List<Country> countries;
+    // support reading iso_3166-1.json from Debian's iso-codes package using SerializedName since
+    // our class needs to match the JSON exactly
+    @SerializedName("3166-1")
+    List<Country> countries;
 }

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

@@ -0,0 +1,100 @@
+/*
+ * Copyright (C) 2024 Alan Orth
+ *
+ * SPDX-License-Identifier: GPL-3.0-only
+ */
+
+package io.github.ilri.cgspace.ctasks;
+
+import org.dspace.content.DSpaceObject;
+import org.dspace.content.Item;
+import org.dspace.content.MetadataValue;
+import org.dspace.core.Constants;
+import org.dspace.curate.AbstractCurationTask;
+import org.dspace.curate.Curator;
+import org.dspace.curate.Suspendable;
+
+import java.io.IOException;
+import java.util.List;
+
+/**
+ * Attempt to normalize DOIs by stripping whitespace, lower casing, and
+ * converting to <code>https://doi.org</code> format. The reason is that DOIs are case
+ * insensitive and must be unique, which we can only guarantee if they are
+ * normalized to the same format.
+ *
+ * See: <a href="https://www.crossref.org/documentation/member-setup/constructing-your-dois/">https://www.crossref.org/documentation/member-setup/constructing-your-dois/</a>
+ *
+ * TODO: set curation to failed if invalid DOI submitted (and configure to reject in workflow)
+ * TODO: allow operation on communities and collections (currently only works on items)
+ *
+ * @author Alan Orth for the International Livestock Research Institute
+ * @version 7.6.1.3
+ * @since 7.6.1.1
+ */
+@Suspendable
+public class NormalizeDOIs extends AbstractCurationTask {
+    @Override
+    public int perform(DSpaceObject dso) throws IOException {
+        if (dso.getType() == Constants.ITEM) {
+            Item item = (Item) dso;
+            String result;
+
+            // Keep track of whether we change metadata, and how many
+            boolean metadataChanged = false;
+            int count = 0;
+
+            // Hard coding the metadata field for now since I can't figure out how to read the taskProperty
+            List<MetadataValue> itemDOIs = itemService.getMetadataByMetadataString(item, "cg.identifier.doi");
+
+            // skip items that don't have DOIs
+            if (itemDOIs.isEmpty()) {
+                setResult("No DOIs, skipping");
+                return Curator.CURATE_SKIP;
+            } else {
+                for (MetadataValue itemDOI : itemDOIs) {
+                    String newDOI = getNormalizedDOI(itemDOI);
+
+                    // Check if the normalized DOI is different than the original
+                    if (!newDOI.equals(itemDOI.getValue())) {
+                        itemDOI.setValue(newDOI);
+                        metadataChanged = true;
+                        count++;
+                    }
+                }
+            }
+            if (metadataChanged) {
+                result = "Normalized " + count + " DOI(s)";
+            } else {
+                result = "All DOIs already normalized";
+            }
+            setResult(result);
+
+            return Curator.CURATE_SUCCESS;
+        } else {
+            setResult("Object skipped");
+            return Curator.CURATE_SKIP;
+        }
+    }
+
+    private static String getNormalizedDOI(MetadataValue itemDOI) {
+        // Convert to lowercase
+        String newDOI = itemDOI.getValue().toLowerCase();
+        // Strip leading and trailing whitespace
+        newDOI = newDOI.strip();
+        // Convert to HTTPS
+        newDOI = newDOI.replace("http://", "https://");
+        // Prefer doi.org to dx.doi.org
+        newDOI = newDOI.replace("dx.doi.org", "doi.org");
+        // Prefer doi.org to www.doi.org
+        newDOI = newDOI.replace("www.doi.org", "doi.org");
+        // Fix URL encoded slashes (%2f)
+        newDOI = newDOI.replace("%2f", "/");
+        // Replace values like doi: 10.11648/j.jps.20140201.14
+        newDOI = newDOI.replaceAll("^doi: 10\\.", "https://doi.org/10.");
+        // Replace values like 10.3390/foods12010115
+        newDOI = newDOI.replaceAll("^10\\.", "https://doi.org/10.");
+
+        return newDOI;
+    }
+}

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

@@ -2,8 +2,9 @@
 DSpace curation tasks 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
+- **NormalizeDOIs**: normalize DOIs by stripping whitespace, lowercasing, and converting to https://doi.org/ format
 
-Tested on DSpace 6.3. Read more about the [DSpace curation system](https://wiki.lyrasis.org/display/DSDOC5x/Curation+System).
+Tested on DSpace 7.6.3. Read more about the [DSpace curation system](https://wiki.lyrasis.org/display/DSDOC7x/Curation+System).
 
 ## Build and Install
 
@@ -14,7 +15,7 @@ To use these curation tasks in a DSpace project add the following dependency to
 <dependency>
   <groupId>io.github.ilri.cgspace</groupId>
   <artifactId>cgspace-java-helpers</artifactId>
-  <version>6.1-SNAPSHOT</version>
+  <version>7.6.1.4-SNAPSHOT</version>
 </dependency>
 ```
 
@@ -30,18 +31,19 @@ $ mvn package
 Copy the resulting jar to the DSpace `lib` directory:
 
 ```
-$ cp target/cgspace-java-helpers-6.1-SNAPSHOT.jar ~/dspace/lib/
+$ cp target/cgspace-java-helpers-7.6.1.4-SNAPSHOT.jar ~/dspace/lib/
 ```
 
 ## Configuration
-Add the curation task to DSpace's `config/modules/curate.cfg`:
+Add the curation task(s) to DSpace's `config/modules/curate.cfg`:
 
 ```
 plugin.named.org.dspace.curate.CurationTask = io.github.ilri.cgspace.ctasks.CountryCodeTagger = countrycodetagger
 plugin.named.org.dspace.curate.CurationTask = io.github.ilri.cgspace.ctasks.CountryCodeTagger = countrycodetagger.force
+plugin.named.org.dspace.curate.CurationTask = io.github.ilri.cgspace.ctasks.NormalizeDOIs = normalizedois
 ```
 
-And then add the following variables to your `local.cfg` or some other [configuration file that is included](https://wiki.lyrasis.org/display/DSDOC6x/Configuration+Reference#ConfigurationReference-IncludingotherPropertyFiles):
+And then add the following variables to your `local.cfg` or some other [configuration file that is included](https://wiki.lyrasis.org/display/DSDOC7x/Configuration+Reference#ConfigurationReference-IncludingotherPropertyFiles):
 
 ```
 # name of the field containing ISO 3166-1 country names
@@ -60,7 +62,7 @@ countrycodetagger.iso3166-alpha2.field = cg.coverage.iso3166-alpha2
 Once the jar is installed and you have added appropriate configuration in `~/dspace/config/modules`:
 
 ```
-$ ~/dspace/bin/dspace curate -t countrycodetagger -i 10568/3 -r - -s object
+$ ~/dspace/bin/dspace curate -e eperson@repo.org -t countrycodetagger -i 10568/3 -r - -s object
 ```
 
 *Note*: it is very important to set the database transaction scope to something sensible (`object`) if you're curating a community or collection with more than a few hundred items.

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

@@ -1,21 +1,27 @@
 /*
-* Copyright (C) 2020 Alan Orth
-*
-* SPDX-License-Identifier: GPL-3.0-or-later
-*/
+ * Copyright (C) 2020 Alan Orth
+ *
+ * SPDX-License-Identifier: GPL-3.0-only
+ */
 
 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.Bitstream;
+import org.dspace.content.Bundle;
+import org.dspace.content.Collection;
+import org.dspace.content.Community;
+import org.dspace.content.DSpaceObject;
+import org.dspace.content.Item;
+import org.dspace.content.MetadataValue;
+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.content.factory.ContentServiceFactory;
-import org.dspace.content.service.ItemService;
 import org.dspace.handle.factory.HandleServiceFactory;
 import org.dspace.handle.service.HandleService;
-import org.dspace.content.service.BundleService;
 
 import java.io.IOException;
 import java.sql.SQLException;
@@ -29,10 +35,12 @@ import java.util.List;
  * @since 5.1
  */
 public class FixJpgJpgThumbnails {
-	//note: static members belong to the class itself, not any one instance
+    // 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 HandleService handleService =
+            HandleServiceFactory.getInstance().getHandleService();
+    public static BundleService bundleService =
+            ContentServiceFactory.getInstance().getBundleService();
 
     public static void main(String[] args) {
         String parentHandle = null;
@@ -51,17 +59,24 @@ public class FixJpgJpgThumbnails {
                 DSpaceObject parent = handleService.resolveToObject(context, parentHandle);
                 if (parent != null) {
                     switch (parent.getType()) {
-						case Constants.COLLECTION:
-							process(context, itemService.findByCollection(context, (Collection) parent));
+                        case Constants.SITE:
+                            process(context, itemService.findAll(context));
+                            context.commit();
                             break;
                         case Constants.COMMUNITY:
                             List<Collection> collections = ((Community) parent).getCollections();
                             for (Collection collection : collections) {
-								process(context, itemService.findAllByCollection(context, collection));
+                                process(
+                                        context,
+                                        itemService.findAllByCollection(context, collection));
                             }
+                            context.commit();
                             break;
-						case Constants.SITE:
-							process(context, itemService.findAll(context));
+                        case Constants.COLLECTION:
+                            process(
+                                    context,
+                                    itemService.findByCollection(context, (Collection) parent));
+                            context.commit();
                             break;
                         case Constants.ITEM:
                             processItem(context, (Item) parent);
@@ -79,7 +94,8 @@ public class FixJpgJpgThumbnails {
         }
     }
 
-	private static void process(Context context, Iterator<Item> items) throws SQLException, IOException, AuthorizeException {
+    private static void process(Context context, Iterator<Item> items)
+            throws SQLException, IOException, AuthorizeException {
         while (items.hasNext()) {
             Item item = items.next();
             processItem(context, item);
@@ -87,14 +103,18 @@ public class FixJpgJpgThumbnails {
         }
     }
 
-	private static void processItem(Context context, Item item) throws SQLException, AuthorizeException, IOException {
-		// Some bitstreams like Infographics are large JPGs and put in the ORIGINAL bundle on purpose so we shouldn't
+    private static void processItem(Context context, Item item)
+            throws SQLException, AuthorizeException, IOException {
+        // Some bitstreams like Infographics and Maps are large JPEGs and put in the ORIGINAL bundle
+        // on purpose so we shouldn't
         // swap them.
-		List<MetadataValue> itemTypes = itemService.getMetadataByMetadataString(item, "dcterms.type");
-		boolean itemHasInfographic = false;
-		for (MetadataValue itemType: itemTypes) {
-			if (itemType.getValue().equals("Infographic")) {
-				itemHasInfographic = true;
+        List<MetadataValue> itemTypes =
+                itemService.getMetadataByMetadataString(item, "dcterms.type");
+        for (MetadataValue itemType : itemTypes) {
+            if (itemType.getValue().equals("Infographic") || itemType.getValue().equals("Map")) {
+                System.out.println(
+                        item.getHandle() + ": item has an Infographic or Map, skipping.");
+                return;
             }
         }
 
@@ -103,6 +123,12 @@ public class FixJpgJpgThumbnails {
             List<Bitstream> thumbnailBundleBitstreams = thumbnailBundle.getBitstreams();
             for (Bitstream thumbnailBitstream : thumbnailBundleBitstreams) {
                 String thumbnailName = thumbnailBitstream.getName();
+                String thumbnailDescription = thumbnailBitstream.getDescription();
+
+                // There is no point continuing if the thumbnail's description is empty or null
+                if (StringUtils.isEmpty(thumbnailDescription)) {
+                    continue;
+                }
 
                 if (thumbnailName.toLowerCase().contains(".jpg.jpg")) {
                     List<Bundle> originalBundles = item.getBundles("ORIGINAL");
@@ -112,29 +138,33 @@ public class FixJpgJpgThumbnails {
                         for (Bitstream originalBitstream : originalBundleBitstreams) {
                             String originalName = originalBitstream.getName();
 
-							long originalBitstreamBytes = originalBitstream.getSize();
+                            long originalBitstreamBytes = originalBitstream.getSizeBytes();
 
                             /*
                             - check if the original file name is the same as the thumbnail name minus the extra ".jpg"
                             - check if the thumbnail description indicates it was automatically generated
-							- check if the item has dc.type Infographic (JPG could be the "real" item!)
                             - check if the original bitstream is less than ~100KiB
                                 - Note: in my tests there were 4022 items with ".jpg.jpg" thumbnails totaling 394549249
                                   bytes for an average of about 98KiB so ~100KiB seems like a good cut off
                             */
-							if (
-									originalName.equalsIgnoreCase(StringUtils.removeEndIgnoreCase(thumbnailName, ".jpg"))
-									&& ("Generated Thumbnail".equals(thumbnailBitstream.getDescription()) || "IM Thumbnail".equals(thumbnailBitstream.getDescription()))
-									&& !itemHasInfographic
-									&& originalBitstreamBytes < 100000
-							) {
-								System.out.println(item.getHandle() + ": replacing " + thumbnailName + " with " + originalName);
+                            if (originalName.equalsIgnoreCase(
+                                            StringUtils.removeEndIgnoreCase(thumbnailName, ".jpg"))
+                                    && ("Generated Thumbnail".equals(thumbnailDescription)
+                                            || "IM Thumbnail".equals(thumbnailDescription))
+                                    && originalBitstreamBytes < 100000) {
+                                System.out.println(
+                                        item.getHandle()
+                                                + ": replacing "
+                                                + thumbnailName
+                                                + " with "
+                                                + originalName);
 
-								//add the original bitstream to the THUMBNAIL bundle
-								bundleService.addBitstream(context, thumbnailBundle, originalBitstream);
-								//remove the original bitstream from the ORIGINAL bundle
+                                // add the original bitstream to the THUMBNAIL bundle
+                                bundleService.addBitstream(
+                                        context, thumbnailBundle, originalBitstream);
+                                // remove the original bitstream from the ORIGINAL bundle
                                 originalBundle.removeBitstream(originalBitstream);
-								//remove the JpgJpg bitstream from the THUMBNAIL bundle
+                                // remove the JpgJpg bitstream from the THUMBNAIL bundle
                                 thumbnailBundle.removeBitstream(thumbnailBitstream);
                             }
                         }

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

@@ -1,14 +1,19 @@
 /*
-* Copyright (C) 2022 Alan Orth
-*
-* SPDX-License-Identifier: GPL-3.0-or-later
-*/
+ * Copyright (C) 2022 Alan Orth
+ *
+ * SPDX-License-Identifier: GPL-3.0-only
+ */
 
 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.Bitstream;
+import org.dspace.content.Bundle;
+import org.dspace.content.Collection;
+import org.dspace.content.Community;
+import org.dspace.content.DSpaceObject;
+import org.dspace.content.Item;
 import org.dspace.content.factory.ContentServiceFactory;
 import org.dspace.content.service.BundleService;
 import org.dspace.content.service.ItemService;
@@ -71,10 +76,9 @@ public class FixLowQualityThumbnails {
                 DSpaceObject parent = handleService.resolveToObject(context, parentHandle);
                 if (parent != null) {
                     switch (parent.getType()) {
-                        case Constants.COLLECTION:
-                            process(
-                                    context,
-                                    itemService.findByCollection(context, (Collection) parent));
+                        case Constants.SITE:
+                            process(context, itemService.findAll(context));
+                            context.commit();
                             break;
                         case Constants.COMMUNITY:
                             List<Collection> collections = ((Community) parent).getCollections();
@@ -83,9 +87,13 @@ public class FixLowQualityThumbnails {
                                         context,
                                         itemService.findAllByCollection(context, collection));
                             }
+                            context.commit();
                             break;
-                        case Constants.SITE:
-                            process(context, itemService.findAll(context));
+                        case Constants.COLLECTION:
+                            process(
+                                    context,
+                                    itemService.findByCollection(context, (Collection) parent));
+                            context.commit();
                             break;
                         case Constants.ITEM:
                             processItem(context, (Item) parent);
@@ -114,6 +122,8 @@ public class FixLowQualityThumbnails {
 
     private static void processItem(Context context, Item item)
             throws SQLException, AuthorizeException, IOException {
+        System.out.println("FixLowQualityThumbnails: processing item: " + item.getHandle());
+
         // Set some state for the item before we iterate over the THUMBNAIL bundle
         boolean itemHasImThumbnail = false;
 
@@ -154,7 +164,7 @@ public class FixLowQualityThumbnails {
                     // 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("> Action: remove old thumbnail from THUMBNAIL bundle");
                         System.out.println("> Name: »" + thumbnailName + "«");
                         System.out.println("> Description: »" + thumbnailDescription + "«");
                         System.out.print("\u001b[0m");
@@ -168,7 +178,7 @@ public class FixLowQualityThumbnails {
                     } else if (thumbnailDescription.toLowerCase().contains("thumbnail")
                             && !"IM Thumbnail".equals(thumbnailDescription)) {
                         System.out.print("\u001b[33m");
-                        System.out.println("Deleting (" + item.getHandle() + "):");
+                        System.out.println("> Action: remove manually uploaded thumbnail from THUMBNAIL bundle");
                         System.out.println("> Name: »" + thumbnailName + "«");
                         System.out.println("> Description: »" + thumbnailDescription + "«");
                         System.out.print("\u001b[0m");
@@ -180,7 +190,7 @@ public class FixLowQualityThumbnails {
                         // 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("> Action: skip other thumbnail in THUMBNAIL bundle");
                         System.out.println("> Name: »" + thumbnailName + "«");
                         System.out.println("> Description: »" + thumbnailDescription + "«");
                         System.out.print("\u001b[0m");
@@ -245,7 +255,7 @@ public class FixLowQualityThumbnails {
                             && (originalName.toLowerCase().contains("thumbnail")
                                     || originalDescription.toLowerCase().contains("thumbnail"))) {
                         System.out.print("\u001b[33m");
-                        System.out.println("Removing (" + item.getHandle() + "):");
+                        System.out.println("> Action: remove thumbnail from ORIGINAL bundle");
                         System.out.println("> Name: »" + originalName + "«");
                         System.out.println("> Description: »" + originalDescription + "«");
                         System.out.print("\u001b[0m");
@@ -255,7 +265,7 @@ public class FixLowQualityThumbnails {
 
                     } else {
                         System.out.print("\u001b[34m");
-                        System.out.println("Skipping (" + item.getHandle() + "):");
+                        System.out.println("> Action: skip other bitstream in ORIGINAL bundle");
                         System.out.println("> Name: »" + originalName + "«");
                         System.out.println("> Description: »" + originalDescription + "«");
                         System.out.print("\u001b[0m");

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

@@ -4,7 +4,7 @@ Java-based helpers used on the [CGSpace](https://cgspace.cgiar.org) institutiona
 - **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 7.6.3. Read more about the [DSpace curation system](https://wiki.lyrasis.org/display/DSDOC7x/Curation+System).
 
 ## Build and Install
 
@@ -15,7 +15,7 @@ To use these curation tasks in a DSpace project add the following dependency to
 <dependency>
   <groupId>io.github.ilri.cgspace</groupId>
   <artifactId>cgspace-java-helpers</artifactId>
-  <version>6.1-SNAPSHOT</version>
+  <version>7.6.1.4-SNAPSHOT</version>
 </dependency>
 ```
 
@@ -31,7 +31,7 @@ $ mvn package
 Copy the resulting jar to the DSpace `lib` directory:
 
 ```console
-$ cp target/cgspace-java-helpers-6.1-SNAPSHOT.jar ~/dspace/lib/
+$ cp target/cgspace-java-helpers-7.6.1.4-SNAPSHOT.jar ~/dspace/lib/
 ```
 
 ## Invocation

src/main/resources/io/github/ilri/cgspace/ctasks/cgspace-countries.json

@@ -16,29 +16,15 @@
       "name": "Congo, The Democratic Republic of the",
       "numeric": "180"
     },
-    {
-      "alpha_2": "IR",
-      "alpha_3": "IRN",
-      "name": "Iran, Islamic Republic of",
-      "cgspace_name": "Iran",
-      "numeric": "364",
-      "official_name": "Islamic Republic of Iran"
-    },
     {
       "alpha_2": "KP",
       "alpha_3": "PRK",
+      "common_name": "North Korea",
       "name": "Korea, Democratic People's Republic of",
       "cgspace_name": "Korea, DPR",
       "numeric": "408",
       "official_name": "Democratic People's Republic of Korea"
     },
-    {
-      "alpha_2": "LA",
-      "alpha_3": "LAO",
-      "name": "Lao People's Democratic Republic",
-      "cgspace_name": "Laos",
-      "numeric": "418"
-    },
     {
       "alpha_2": "FM",
       "alpha_3": "FSM",
@@ -53,13 +39,6 @@
       "name": "Russian Federation",
       "cgspace_name": "Russia",
       "numeric": "643"
-    },
-    {
-      "alpha_2": "SY",
-      "alpha_3": "SYR",
-      "name": "Syrian Arab Republic",
-      "cgspace_name": "Syria",
-      "numeric": "760"
     }
   ]
 }