Version 7.6.1.2

We don't need to print the Handle because some items can be in the
workflow still so this will be null, but also because DSpace will
already show the Handle in the log before printing the result.

CHANGELOG.md

@@ -4,9 +4,25 @@ 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
+## [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

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/DSDOC6x/Curation+System).
+Tested on DSpace 7.6. 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>6.2-SNAPSHOT</version>
+  <version>7.6.1.2-SNAPSHOT</version>
 </dependency>
 ```
 
@@ -32,18 +33,17 @@ $ mvn package
 Copy the resulting jar to the DSpace `lib` directory:
 
 ```console
-$ cp target/cgspace-java-helpers-6.2-SNAPSHOT.jar ~/dspace/lib/
+$ cp target/cgspace-java-helpers-7.6.1.2-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)
+- 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/dspace6/src/main/java/io/github/ilri/cgspace/scripts/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)
 
 ## 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
 

pom.xml

@@ -6,7 +6,7 @@
 
   <groupId>io.github.ilri.cgspace</groupId>
   <artifactId>cgspace-java-helpers</artifactId>
-  <version>6.2-SNAPSHOT</version>
+  <version>7.6.1.2-SNAPSHOT</version>
 
   <name>cgspace-java-helpers</name>
   <url>https://github.com/ilri/cgspace-java-helpers</url>
@@ -14,7 +14,7 @@
   <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>
 
@@ -28,15 +28,14 @@
 
   <properties>
     <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
-    <maven.compiler.source>1.8</maven.compiler.source>
+    <maven.compiler.release>11</maven.compiler.release>
-    <maven.compiler.target>1.8</maven.compiler.target>
   </properties>
 
   <dependencies>
     <dependency>
       <groupId>com.google.code.gson</groupId>
       <artifactId>gson</artifactId>
-      <version>2.10.1</version>
+      <version>2.9.0</version>
     </dependency>
     <dependency>
       <groupId>org.dspace</groupId>
@@ -48,8 +47,8 @@
 
   <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>
+      <developerConnection>scm:git:ssh://github.com:ilri/cgspace-java-helpers.git</developerConnection>
-      <url>http://github.com/ilri/cgspace-java-helpers</url>
+      <url>https://github.com/ilri/cgspace-java-helpers</url>
   </scm>
 
   <distributionManagement>
@@ -78,15 +77,15 @@
         </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>
@@ -108,4 +107,17 @@
       </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

@@ -1,7 +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;
@@ -10,14 +10,14 @@ import javax.annotation.Nullable;
 
 public class CountriesVocabulary {
 
-    class Country {
+    static class Country {
-        private String name; // required
+        private final String name; // required
-        private String common_name; // optional
+        private final String common_name; // optional
-        private String official_name; // optional
+        private final String official_name; // optional
-        private String cgspace_name; // optional
+        private final String cgspace_name; // optional
-        private String numeric; // required Hmmmm need to cast this...
+        private final String numeric; // required Hmmmm need to cast this...
-        private String alpha_2; // required
+        private final String alpha_2; // required
-        private String alpha_3; // required
+        private final String alpha_3; // required
 
         public Country(
                 String name,

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;
@@ -24,7 +24,15 @@ import java.io.InputStreamReader;
 import java.sql.SQLException;
 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";
@@ -37,7 +45,7 @@ public class CountryCodeTagger extends AbstractCurationTask {
         private final Logger log = LogManager.getLogger();
     }
 
-    public class CountryCodeTaggerResult {
+    public static class CountryCodeTaggerResult {
         private int status = Curator.CURATE_UNSET;
         private String result = null;
 
@@ -76,7 +84,6 @@ public class CountryCodeTagger extends AbstractCurationTask {
             }
 
             setResult(alpha2Result.getResult());
-            report(alpha2Result.getResult());
         }
 
         return alpha2Result.getStatus();
@@ -85,14 +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();
@@ -102,7 +108,7 @@ public class CountryCodeTagger extends AbstractCurationTask {
             BufferedReader reader =
                     new BufferedReader(
                             new InputStreamReader(
-                                    this.getClass().getResourceAsStream(config.isocodesJsonPath)));
+                                    Objects.requireNonNull(this.getClass().getResourceAsStream(config.isocodesJsonPath))));
             ISO3166CountriesVocabulary isocodesCountriesJson =
                     gson.fromJson(reader, ISO3166CountriesVocabulary.class);
             reader.close();
@@ -110,8 +116,8 @@ public class CountryCodeTagger extends AbstractCurationTask {
             reader =
                     new BufferedReader(
                             new InputStreamReader(
-                                    this.getClass()
+                                    Objects.requireNonNull(this.getClass()
-                                            .getResourceAsStream(config.cgspaceCountriesJsonPath)));
+                                            .getResourceAsStream(config.cgspaceCountriesJsonPath))));
             CGSpaceCountriesVocabulary cgspaceCountriesJson =
                     gson.fromJson(reader, CGSpaceCountriesVocabulary.class);
             reader.close();
@@ -171,21 +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 +1,96 @@
+/*
+ * 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 7.6.1.2
+ * @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) {
+        // 1. Convert to lowercase
+        String newDOI = itemDOI.getValue().toLowerCase();
+        // 2. Strip leading and trailing whitespace
+        newDOI = newDOI.strip();
+        // 3. Convert to HTTPS
+        newDOI = newDOI.replace("http://", "https://");
+        // 4. Prefer doi.org to dx.doi.org
+        newDOI = newDOI.replace("dx.doi.org", "doi.org");
+        // 5. Replace values like doi: 10.11648/j.jps.20140201.14
+        newDOI = newDOI.replaceAll("^doi: 10\\.", "https://doi.org/10.");
+        // 6. 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. Read more about the [DSpace curation system](https://wiki.lyrasis.org/display/DSDOC5x/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>6.2-SNAPSHOT</version>
+  <version>7.6.1.2-SNAPSHOT</version>
 </dependency>
 ```
 
@@ -30,15 +31,16 @@ $ mvn package
 Copy the resulting jar to the DSpace `lib` directory:
 
 ```
-$ cp target/cgspace-java-helpers-6.2-SNAPSHOT.jar ~/dspace/lib/
+$ cp target/cgspace-java-helpers-7.6.1.2-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):

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 6.3. Read more about the [DSpace curation system](https://wiki.lyrasis.org/display/DSDOC6x/Curation+System).
+Tested on DSpace 7.6. Read more about the [DSpace curation system](https://wiki.lyrasis.org/display/DSDOC6x/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>6.2-SNAPSHOT</version>
+  <version>7.6.1.2-SNAPSHOT</version>
 </dependency>
 ```
 
@@ -31,7 +31,7 @@ $ mvn package
 Copy the resulting jar to the DSpace `lib` directory:
 
 ```console
-$ cp target/cgspace-java-helpers-6.2-SNAPSHOT.jar ~/dspace/lib/
+$ cp target/cgspace-java-helpers-7.6.1.2-SNAPSHOT.jar ~/dspace/lib/
 ```
 
 ## Invocation

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

@@ -39,6 +39,6 @@
       "name": "Russian Federation",
       "cgspace_name": "Russia",
       "numeric": "643"
-    },
+    }
   ]
 }