CHANGELOG.md

@@ -4,17 +4,6 @@ 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).
 
-## [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

@@ -4,7 +4,6 @@ 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).
 
@@ -17,7 +16,7 @@ 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>7.6.1.2-SNAPSHOT</version>
+  <version>7.6.1-SNAPSHOT</version>
 </dependency>
 ```
 
@@ -33,17 +32,18 @@ $ mvn package
 Copy the resulting jar to the DSpace `lib` directory:
 
 ```console
-$ cp target/cgspace-java-helpers-7.6.1.2-SNAPSHOT.jar ~/dspace/lib/
+$ cp target/cgspace-java-helpers-7.6.1-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/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)
+- 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
 

pom.xml

@@ -6,7 +6,7 @@
 
   <groupId>io.github.ilri.cgspace</groupId>
   <artifactId>cgspace-java-helpers</artifactId>
-  <version>7.6.1.2-SNAPSHOT</version>
+  <version>7.6.1-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-only.html</url>
+        <url>https://spdx.org/licenses/GPL-3.0-or-later.html</url>
     </license>
   </licenses>
 
@@ -28,7 +28,8 @@
 
   <properties>
     <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
-    <maven.compiler.release>11</maven.compiler.release>
+    <maven.compiler.source>1.8</maven.compiler.source>
+    <maven.compiler.target>1.8</maven.compiler.target>
   </properties>
 
   <dependencies>
@@ -47,8 +48,8 @@
 
   <scm>
       <connection>scm:git:git://github.com/ilri/cgspace-java-helpers.git</connection>
-      <developerConnection>scm:git:ssh://github.com:ilri/cgspace-java-helpers.git</developerConnection>
-      <url>https://github.com/ilri/cgspace-java-helpers</url>
+      <developerConnection>scm:git:ssh://github.com:nanosai/cgspace-java-helpers.git</developerConnection>
+      <url>http://github.com/ilri/cgspace-java-helpers</url>
   </scm>
 
   <distributionManagement>
@@ -77,15 +78,15 @@
         </plugin>
         <plugin>
           <artifactId>maven-compiler-plugin</artifactId>
-          <version>3.13.0</version>
+          <version>3.12.1</version>
         </plugin>
         <plugin>
           <artifactId>maven-surefire-plugin</artifactId>
-          <version>3.2.5</version>
+          <version>3.2.3</version>
         </plugin>
         <plugin>
           <artifactId>maven-jar-plugin</artifactId>
-          <version>3.4.1</version>
+          <version>3.3.0</version>
         </plugin>
         <plugin>
           <artifactId>maven-install-plugin</artifactId>

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-only
+ * SPDX-License-Identifier: GPL-3.0-or-later
  */
 
 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-only
+ * SPDX-License-Identifier: GPL-3.0-or-later
  */
 
 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-only
+ * SPDX-License-Identifier: GPL-3.0-or-later
  */
 
 package io.github.ilri.cgspace.ctasks;
@@ -26,13 +26,6 @@ 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";
@@ -84,6 +77,7 @@ public class CountryCodeTagger extends AbstractCurationTask {
             }
 
             setResult(alpha2Result.getResult());
+            report(alpha2Result.getResult());
         }
 
         return alpha2Result.getStatus();
@@ -92,13 +86,14 @@ 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("No countries, skipping.");
+            alpha2Result.setResult(itemHandle + ": no countries, skipping.");
             alpha2Result.setStatus(Curator.CURATE_SKIP);
         } else {
             Gson gson = new Gson();
@@ -177,20 +172,21 @@ public class CountryCodeTagger extends AbstractCurationTask {
                         itemService.update(Curator.curationContext(), item);
                     } catch (SQLException | AuthorizeException sqle) {
                         config.log.debug(sqle.getMessage());
-                        alpha2Result.setResult("Error");
+                        alpha2Result.setResult(itemHandle + ": error");
                         alpha2Result.setStatus(Curator.CURATE_ERROR);
                     }
 
                     alpha2Result.setResult(
-                            "Added "
+                            itemHandle
+                                    + ": added "
                                     + newAlpha2Codes.size()
                                     + " alpha2 country code(s)");
                 } else {
-                    alpha2Result.setResult("No matching countries found");
+                    alpha2Result.setResult(itemHandle + ": no matching countries found");
                 }
                 alpha2Result.setStatus(Curator.CURATE_SUCCESS);
             } else {
-                alpha2Result.setResult("Item already has country codes, skipping unless forced");
+                alpha2Result.setResult(itemHandle + ": item has country codes, skipping");
                 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-only
+ * SPDX-License-Identifier: GPL-3.0-or-later
  */
 
 package io.github.ilri.cgspace.ctasks;

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

@@ -1,96 +0,0 @@
-/*
- * 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

@@ -2,7 +2,6 @@
 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).
 
@@ -15,7 +14,7 @@ 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>7.6.1.2-SNAPSHOT</version>
+  <version>7.6.1-SNAPSHOT</version>
 </dependency>
 ```
 
@@ -31,16 +30,15 @@ $ mvn package
 Copy the resulting jar to the DSpace `lib` directory:
 
 ```
-$ cp target/cgspace-java-helpers-7.6.1.2-SNAPSHOT.jar ~/dspace/lib/
+$ cp target/cgspace-java-helpers-7.6.1-SNAPSHOT.jar ~/dspace/lib/
 ```
 
 ## Configuration
-Add the curation task(s) to DSpace's `config/modules/curate.cfg`:
+Add the curation task 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):
@@ -62,7 +60,7 @@ 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 -e eperson@repo.org -t countrycodetagger -i 10568/3 -r - -s object
+$ ~/dspace/bin/dspace curate -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-only
+ * SPDX-License-Identifier: GPL-3.0-or-later
  */
 
 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-only
+ * SPDX-License-Identifier: GPL-3.0-or-later
  */
 
 package io.github.ilri.cgspace.scripts;

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

@@ -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>7.6.1.2-SNAPSHOT</version>
+  <version>7.6.1-SNAPSHOT</version>
 </dependency>
 ```
 
@@ -31,7 +31,7 @@ $ mvn package
 Copy the resulting jar to the DSpace `lib` directory:
 
 ```console
-$ cp target/cgspace-java-helpers-7.6.1.2-SNAPSHOT.jar ~/dspace/lib/
+$ cp target/cgspace-java-helpers-7.6.1-SNAPSHOT.jar ~/dspace/lib/
 ```
 
 ## Invocation