Update gson to version used by dspace-api

Prevent dependency convergence.

CHANGELOG.md

@@ -4,6 +4,26 @@ 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 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

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 7.6. Read more about the [DSpace curation system](https://wiki.lyrasis.org/display/DSDOC7x/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>7.6.1-SNAPSHOT</version>
+  <version>7.6.1.4-SNAPSHOT</version>
 </dependency>
 ```
 
@@ -32,20 +33,14 @@ $ mvn package
 Copy the resulting jar to the DSpace `lib` directory:
 
 ```console
-$ cp target/cgspace-java-helpers-7.6.1-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
-- Migrate from maven-deploy-plugin to nexus-staging-maven-plugin, see: https://central.sonatype.org/publish/publish-maven/#nexus-staging-maven-plugin-for-deployment-and-release
-- Stop using oss-parent, see: https://central.sonatype.org/publish/publish-maven/#create-a-ticket-with-sonatype
+- 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/):

pom.xml

@@ -6,50 +6,57 @@
 
   <groupId>io.github.ilri.cgspace</groupId>
   <artifactId>cgspace-java-helpers</artifactId>
-  <version>7.6.1-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>2.9.0</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>7.6.1</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>
@@ -78,24 +85,20 @@
         </plugin>
         <plugin>
           <artifactId>maven-compiler-plugin</artifactId>
-          <version>3.12.1</version>
+          <version>3.13.0</version>
         </plugin>
         <plugin>
           <artifactId>maven-surefire-plugin</artifactId>
-          <version>3.2.3</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>3.1.1</version>
         </plugin>
-        <plugin>
-          <artifactId>maven-deploy-plugin</artifactId>
-          <version>3.1.1</version>
-        </plugin>
         <!-- site lifecycle, see https://maven.apache.org/ref/current/maven-core/lifecycles.html#site_Lifecycle -->
         <plugin>
           <artifactId>maven-site-plugin</artifactId>
@@ -105,6 +108,17 @@
           <artifactId>maven-project-info-reports-plugin</artifactId>
           <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>

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

@@ -1,7 +1,7 @@
 /*
  * Copyright (C) 2020 Alan Orth
  *
- * SPDX-License-Identifier: GPL-3.0-or-later
+ * SPDX-License-Identifier: GPL-3.0-only
  */
 
 package io.github.ilri.cgspace.ctasks;

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

@@ -1,7 +1,7 @@
 /*
  * Copyright (C) 2020 Alan Orth
  *
- * SPDX-License-Identifier: GPL-3.0-or-later
+ * SPDX-License-Identifier: GPL-3.0-only
  */
 
 package io.github.ilri.cgspace.ctasks;

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

@@ -1,7 +1,7 @@
 /*
  * Copyright (C) 2020 Alan Orth
  *
- * SPDX-License-Identifier: GPL-3.0-or-later
+ * SPDX-License-Identifier: GPL-3.0-only
  */
 
 package io.github.ilri.cgspace.ctasks;
@@ -26,6 +26,13 @@ import java.util.ArrayList;
 import java.util.List;
 import java.util.Objects;
 
+/*
+ * 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";
@@ -77,7 +84,6 @@ public class CountryCodeTagger extends AbstractCurationTask {
             }
 
             setResult(alpha2Result.getResult());
-            report(alpha2Result.getResult());
         }
 
         return alpha2Result.getStatus();
@@ -86,14 +92,13 @@ public class CountryCodeTagger extends AbstractCurationTask {
     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);
 
         // skip items that don't have country metadata
         if (itemCountries.isEmpty()) {
-            alpha2Result.setResult(itemHandle + ": no countries, skipping.");
+            alpha2Result.setResult("No countries, skipping.");
             alpha2Result.setStatus(Curator.CURATE_SKIP);
         } else {
             Gson gson = new Gson();
@@ -172,21 +177,20 @@ public class CountryCodeTagger extends AbstractCurationTask {
                         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 "
+                            "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

@@ -1,7 +1,7 @@
 /*
  * Copyright (C) 2020 Alan Orth
  *
- * SPDX-License-Identifier: GPL-3.0-or-later
+ * SPDX-License-Identifier: GPL-3.0-only
  */
 
 package io.github.ilri.cgspace.ctasks;

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 7.6. 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>7.6.1-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-7.6.1-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

@@ -1,7 +1,7 @@
 /*
  * Copyright (C) 2020 Alan Orth
  *
- * SPDX-License-Identifier: GPL-3.0-or-later
+ * SPDX-License-Identifier: GPL-3.0-only
  */
 
 package io.github.ilri.cgspace.scripts;

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

@@ -1,7 +1,7 @@
 /*
  * Copyright (C) 2022 Alan Orth
  *
- * SPDX-License-Identifier: GPL-3.0-or-later
+ * SPDX-License-Identifier: GPL-3.0-only
  */
 
 package io.github.ilri.cgspace.scripts;

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 7.6. 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>7.6.1-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-7.6.1-SNAPSHOT.jar ~/dspace/lib/
+$ cp target/cgspace-java-helpers-7.6.1.4-SNAPSHOT.jar ~/dspace/lib/
 ```
 
 ## Invocation