README.md: Use correct version

I can't figure out how to publish releases on Maven central so let's
stick to SNAPSHOT releases for now.

CHANGELOG.md

@@ -0,0 +1,19 @@
+# Changelog
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## [5.3] - 2020-08-07
+### Changed
+- Make sure `FixJpgJpgThumbnails` only replaces thumbnails where the original is less than ~100KiB
+- Make sure `FixJpgJpgThumbnails` only replaces thumbnails if the item type is not `Infographic` (because the JPG in the ORIGINAL bundle is the "real" file and it's OK that the thumbnail is ".jpg.jpg")
+
+## [5.2] - 2020-08-06
+### Changed
+- Make `FixJpgJpgThumbnails` helper check for files named "JPG" as well as "jpg" (case insensitive)
+- Make `FixJpgJpgThumbnails` helper replace thumbnails with description `IM Thumbnail` as well as `Generated Thumbnail`
+
+## [5.1] - 2020-08-06
+### Added
+- Add `FixJpgJpgThumbnails` helper to replace ".jpg.jpg" thumbnails with their originals

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>5.1</version>
+  <version>5.4-SNAPSHOT</version>
 </dependency>
 ```
 
@@ -31,42 +31,14 @@ $ mvn package
 Copy the resulting jar to the DSpace `lib` directory:
 
 ```
-$ cp target/cgspace-java-helpers-5.1.jar ~/dspace/lib
+$ cp target/cgspace-java-helpers-5.4-SNAPSHOT.jar ~/dspace/lib
 ```
 
 ## Configuration
-Add the curation task to DSpace's `config/modules/curate.cfg`:
+Please refer to the appropriate README.md file:
 
-```
-plugin.named.org.dspace.curate.CurationTask = \
-...
-    io.github.ilri.cgspace.ctasks.CountryCodeTagger = countrycodetagger \
-    io.github.ilri.cgspace.ctasks.CountryCodeTagger = countrycodetagger.force
-```
-
-And then add a configuration file for the task in `config/modules/countrycodetagger.cfg`:
-
-```
-# name of the field containing ISO 3166-1 country names
-iso3166.field = cg.coverage.country
-
-# name of the field containing ISO 3166-1 Alpha2 country codes
-iso3166-alpha2.field = cg.coverage.iso3166-alpha2
-
-# only add country codes if an item doesn't have any (default false)
-#forceupdate = false
-```
-
-*Note*: DSpace's curation system supports "profiles" where you can use the same task with different options, for example above I have a normal country code tagger and a "force" variant. To use the "force" variant you create a new configuration file with the overridden options in `config/modules/countrycodetagger.force.cfg`. The "force" profile clears all existing country codes and updates everything.
-
-## Invocation
-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 - -l 500 -s object
-```
-
-*Note*: it is very important to set the cache limit (`-l`) and the database transaction scope to something sensible (`object`) if you're curating a community or collection with more than a few hundred items.
+- Curation Tasks: [src/main/java/io/github/ilri/cgspace/ctasks/README.md](https://github.com/ilri/cgspace-java-helpers/blob/dspace5/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/dspace5/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

@@ -6,7 +6,7 @@
 
   <groupId>io.github.ilri.cgspace</groupId>
   <artifactId>cgspace-java-helpers</artifactId>
-  <version>5.2</version>
+  <version>5.4-SNAPSHOT</version>
 
   <name>cgspace-java-helpers</name>
   <url>https://github.com/ilri/cgspace-java-helpers</url>

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

@@ -35,6 +35,11 @@ import java.sql.SQLException;
 import java.util.ArrayList;
 import java.util.List;
 
+/**
+ * @author Alan Orth for the International Livestock Research Institute
+ * @version 5.1
+ * @since 1.0
+*/
 public class CountryCodeTagger extends AbstractCurationTask
 {
     public class CountryCodeTaggerConfig {

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

@@ -0,0 +1,74 @@
+# Curation Tasks
+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
+
+Tested on DSpace 5.8. Read more about the [DSpace curation system](https://wiki.lyrasis.org/display/DSDOC5x/Curation+System).
+
+## Build and Install
+
+### Integrate into DSpace Build
+To use these curation tasks in a DSpace project add the following dependency to `dspace/modules/additions/pom.xml`:
+
+```
+<dependency>
+  <groupId>io.github.ilri.cgspace</groupId>
+  <artifactId>cgspace-java-helpers</artifactId>
+  <version>5.3</version>
+</dependency>
+```
+
+The jar will be copied to all DSpace applications.
+
+### Manual Build and Install
+To build the standalone jar:
+
+```
+$ mvn package
+```
+
+Copy the resulting jar to the DSpace `lib` directory:
+
+```
+$ cp target/cgspace-java-helpers-5.3.jar ~/dspace/lib
+```
+
+## Configuration
+Add the curation task to DSpace's `config/modules/curate.cfg`:
+
+```
+plugin.named.org.dspace.curate.CurationTask = \
+...
+    io.github.ilri.cgspace.ctasks.CountryCodeTagger = countrycodetagger \
+    io.github.ilri.cgspace.ctasks.CountryCodeTagger = countrycodetagger.force
+```
+
+And then add a configuration file for the task in `config/modules/countrycodetagger.cfg`:
+
+```
+# name of the field containing ISO 3166-1 country names
+iso3166.field = cg.coverage.country
+
+# name of the field containing ISO 3166-1 Alpha2 country codes
+iso3166-alpha2.field = cg.coverage.iso3166-alpha2
+
+# only add country codes if an item doesn't have any (default false)
+#forceupdate = false
+```
+
+*Note*: DSpace's curation system supports "profiles" where you can use the same task with different options, for example above I have a normal country code tagger and a "force" variant. To use the "force" variant you create a new configuration file with the overridden options in `config/modules/countrycodetagger.force.cfg`. The "force" profile clears all existing country codes and updates everything.
+
+## Invocation
+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 - -l 500 -s object
+```
+
+*Note*: it is very important to set the cache limit (`-l`) and the database transaction scope to something sensible (`object`) if you're curating a community or collection with more than a few hundred items.
+
+## TODO
+
+- Make sure this doesn't work on items in the workflow
+- Check for existence of metadata field before trying to add metadata
+- Add tests

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

@@ -13,8 +13,8 @@ import java.sql.SQLException;
 /**
  * @author Andrea Schweer schweer@waikato.ac.nz for the LCoNZ Institutional Research Repositories
  * @author Alan Orth for the International Livestock Research Institute
- * @version 5.1-SNAPSHOT
- * @since 5.1-SNAPSHOT
+ * @version 5.4
+ * @since 5.1
  */
 public class FixJpgJpgThumbnails {
 
@@ -73,6 +73,17 @@ public class FixJpgJpgThumbnails {
 	}
 
 	private static void processItem(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
+		// swap them.
+		Metadatum[] itemTypes = item.getMetadataByMetadataString("dc.type");
+		boolean itemHasInfographic = false;
+		for (Metadatum itemType: itemTypes) {
+			if (itemType.value.equals("Infographic")) {
+				itemHasInfographic = true;
+				break;
+			}
+		}
+
 		Bundle[] thumbnailBundles = item.getBundles("THUMBNAIL");
 		for (Bundle thumbnailBundle : thumbnailBundles) {
 			Bitstream[] thumbnailBundleBitstreams = thumbnailBundle.getBitstreams();
@@ -84,11 +95,25 @@ public class FixJpgJpgThumbnails {
 					for (Bundle originalBundle : originalBundles) {
 						Bitstream[] originalBundleBitstreams = originalBundle.getBitstreams();
 
-						for(Bitstream originalBitstream : originalBundleBitstreams) {
+						for (Bitstream originalBitstream : originalBundleBitstreams) {
 							String originalName = originalBitstream.getName();
 
-							//check if the original file name is the same as the thumbnail name minus the extra ".jpg"
-							if (originalName.equalsIgnoreCase(StringUtils.removeEndIgnoreCase(thumbnailName, ".jpg")) && ("Generated Thumbnail".equals(thumbnailBitstream.getDescription()) || "IM Thumbnail".equals(thumbnailBitstream.getDescription()))) {
+							long originalBitstreamBytes = originalBitstream.getSize();
+
+							/*
+							- 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);
 
 								//add the original bitstream to the THUMBNAIL bundle

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

@@ -0,0 +1,41 @@
+# Scripts
+Java-based helpers used on the [CGSpace](https://cgspace.cgiar.org) institutional repository:
+
+- **FixJpgJpgThumbnails**: Fix low-quality ".jpg.jpg" thumbnails by replacing them with their originals
+
+Tested on DSpace 5.8. Read more about the [DSpace curation system](https://wiki.lyrasis.org/display/DSDOC5x/Curation+System).
+
+## Build and Install
+
+### Integrate into DSpace Build
+To use these curation tasks in a DSpace project add the following dependency to `dspace/modules/additions/pom.xml`:
+
+```
+<dependency>
+  <groupId>io.github.ilri.cgspace</groupId>
+  <artifactId>cgspace-java-helpers</artifactId>
+  <version>5.3</version>
+</dependency>
+```
+
+The jar will be copied to all DSpace applications.
+
+### Manual Build and Install
+To build the standalone jar:
+
+```
+$ mvn package
+```
+
+Copy the resulting jar to the DSpace `lib` directory:
+
+```
+$ cp target/cgspace-java-helpers-5.3.jar ~/dspace/lib
+```
+
+### Invocation
+The script only takes one argument, which is a community, collection, or item:
+
+```
+$ dspace dsrun io.github.ilri.cgspace.scripts.FixJpgJpgThumbnails 10568/83389
+```