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24
.github/workflows/maven.yml
vendored
Normal file
24
.github/workflows/maven.yml
vendored
Normal file
@ -0,0 +1,24 @@
|
||||
# This workflow will build a Java project with Maven
|
||||
# For more information see: https://help.github.com/actions/language-and-framework-guides/building-and-testing-java-with-maven
|
||||
|
||||
name: Build
|
||||
|
||||
on:
|
||||
push:
|
||||
branches: [ dspace6 ]
|
||||
pull_request:
|
||||
branches: [ dspace6 ]
|
||||
|
||||
jobs:
|
||||
build:
|
||||
|
||||
runs-on: ubuntu-latest
|
||||
|
||||
steps:
|
||||
- uses: actions/checkout@v2
|
||||
- name: Set up JDK 1.8
|
||||
uses: actions/setup-java@v1
|
||||
with:
|
||||
java-version: 1.8
|
||||
- name: Build with Maven
|
||||
run: mvn -B package --file pom.xml
|
||||
6
.gitignore
vendored
6
.gitignore
vendored
@ -70,4 +70,10 @@ fabric.properties
|
||||
# Android studio 3.1+ serialized cache file
|
||||
.idea/caches/build_file_checksums.ser
|
||||
|
||||
# VS Code settings
|
||||
.vscode
|
||||
|
||||
# asdf-vm tool-versions file
|
||||
.tool-versions
|
||||
|
||||
target/
|
||||
|
||||
@ -1,8 +0,0 @@
|
||||
dist: bionic
|
||||
language: java
|
||||
jdk:
|
||||
- openjdk8
|
||||
script:
|
||||
- mvn package -B
|
||||
|
||||
# vim: ts=2 sw=2 et
|
||||
15
CHANGELOG.md
Normal file
15
CHANGELOG.md
Normal file
@ -0,0 +1,15 @@
|
||||
# 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).
|
||||
|
||||
## Unreleased
|
||||
### Updated
|
||||
- Update dependencies in `pom.xml`
|
||||
|
||||
### Changed
|
||||
- Java compiler and target from JDK 7 to JDK 8
|
||||
|
||||
### Added
|
||||
- New `FixLowQualityThumbnails` script to detect and remove more low-quality thumbnails
|
||||
55
README.md
55
README.md
@ -1,10 +1,11 @@
|
||||
# CGSpace Java Helpers [](https://travis-ci.org/ilri/dspace-curation-tasks)
|
||||
# CGSpace Java Helpers [](https://github.com/ilri/cgspace-java-helpers/actions)
|
||||
DSpace curation tasks and other Java-based helpers 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
|
||||
- **FixJpgJpgThumbnails**: Fix low-quality ".jpg.jpg" thumbnails by replacing them with their originals
|
||||
- **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 5.8. Read more about the [DSpace curation system](https://wiki.lyrasis.org/display/DSDOC5x/Curation+System).
|
||||
Tested on DSpace 6.3. Read more about the [DSpace curation system](https://wiki.lyrasis.org/display/DSDOC5x/Curation+System).
|
||||
|
||||
## Build and Install
|
||||
|
||||
@ -15,7 +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>5.1</version>
|
||||
<version>6.1-SNAPSHOT</version>
|
||||
</dependency>
|
||||
```
|
||||
|
||||
@ -24,49 +25,25 @@ The jar will be copied to all DSpace applications.
|
||||
### Manual Build and Install
|
||||
To build the standalone jar:
|
||||
|
||||
```
|
||||
```console
|
||||
$ mvn package
|
||||
```
|
||||
|
||||
Copy the resulting jar to the DSpace `lib` directory:
|
||||
|
||||
```
|
||||
$ cp target/cgspace-java-helpers-5.1.jar ~/dspace/lib
|
||||
```console
|
||||
$ cp target/cgspace-java-helpers-6.1-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
|
||||
```
|
||||
- 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)
|
||||
|
||||
And then add a configuration file for the task in `config/modules/countrycodetagger.cfg`:
|
||||
## TODO
|
||||
|
||||
```
|
||||
# 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.
|
||||
- Add a curation task to normalize DOIs to "https://doi.org" format
|
||||
|
||||
## Notes
|
||||
This project was initially created according to the [Maven Getting Started Guide](https://maven.apache.org/guides/getting-started/):
|
||||
@ -75,12 +52,6 @@ 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
|
||||
```
|
||||
|
||||
## 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
|
||||
|
||||
## License
|
||||
This work is licensed under the [GPLv3](https://www.gnu.org/licenses/gpl-3.0.en.html).
|
||||
|
||||
|
||||
34
pom.xml
34
pom.xml
@ -6,7 +6,7 @@
|
||||
|
||||
<groupId>io.github.ilri.cgspace</groupId>
|
||||
<artifactId>cgspace-java-helpers</artifactId>
|
||||
<version>5.1</version>
|
||||
<version>6.1-SNAPSHOT</version>
|
||||
|
||||
<name>cgspace-java-helpers</name>
|
||||
<url>https://github.com/ilri/cgspace-java-helpers</url>
|
||||
@ -28,26 +28,20 @@
|
||||
|
||||
<properties>
|
||||
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
|
||||
<maven.compiler.source>1.7</maven.compiler.source>
|
||||
<maven.compiler.target>1.7</maven.compiler.target>
|
||||
<maven.compiler.source>1.8</maven.compiler.source>
|
||||
<maven.compiler.target>1.8</maven.compiler.target>
|
||||
</properties>
|
||||
|
||||
<dependencies>
|
||||
<dependency>
|
||||
<groupId>junit</groupId>
|
||||
<artifactId>junit</artifactId>
|
||||
<version>4.11</version>
|
||||
<scope>test</scope>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>com.google.code.gson</groupId>
|
||||
<artifactId>gson</artifactId>
|
||||
<version>2.2.1</version>
|
||||
<version>2.9.1</version>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>org.dspace</groupId>
|
||||
<artifactId>dspace-api</artifactId>
|
||||
<version>5.8</version>
|
||||
<version>6.3</version>
|
||||
<scope>provided</scope>
|
||||
</dependency>
|
||||
</dependencies>
|
||||
@ -75,41 +69,41 @@
|
||||
<!-- clean lifecycle, see https://maven.apache.org/ref/current/maven-core/lifecycles.html#clean_Lifecycle -->
|
||||
<plugin>
|
||||
<artifactId>maven-clean-plugin</artifactId>
|
||||
<version>3.1.0</version>
|
||||
<version>3.2.0</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>3.0.2</version>
|
||||
<version>3.3.0</version>
|
||||
</plugin>
|
||||
<plugin>
|
||||
<artifactId>maven-compiler-plugin</artifactId>
|
||||
<version>3.8.0</version>
|
||||
<version>3.10.1</version>
|
||||
</plugin>
|
||||
<plugin>
|
||||
<artifactId>maven-surefire-plugin</artifactId>
|
||||
<version>2.22.1</version>
|
||||
<version>3.0.0-M7</version>
|
||||
</plugin>
|
||||
<plugin>
|
||||
<artifactId>maven-jar-plugin</artifactId>
|
||||
<version>3.0.2</version>
|
||||
<version>3.3.0</version>
|
||||
</plugin>
|
||||
<plugin>
|
||||
<artifactId>maven-install-plugin</artifactId>
|
||||
<version>2.5.2</version>
|
||||
<version>3.0.1</version>
|
||||
</plugin>
|
||||
<plugin>
|
||||
<artifactId>maven-deploy-plugin</artifactId>
|
||||
<version>2.8.2</version>
|
||||
<version>3.3.0</version>
|
||||
</plugin>
|
||||
<!-- site lifecycle, see https://maven.apache.org/ref/current/maven-core/lifecycles.html#site_Lifecycle -->
|
||||
<plugin>
|
||||
<artifactId>maven-site-plugin</artifactId>
|
||||
<version>3.7.1</version>
|
||||
<version>3.12.1</version>
|
||||
</plugin>
|
||||
<plugin>
|
||||
<artifactId>maven-project-info-reports-plugin</artifactId>
|
||||
<version>3.0.0</version>
|
||||
<version>3.4.1</version>
|
||||
</plugin>
|
||||
</plugins>
|
||||
</pluginManagement>
|
||||
|
||||
@ -1,19 +1,7 @@
|
||||
/*
|
||||
DSpace Curation Tasks
|
||||
Copyright (C) 2020 Alan Orth
|
||||
|
||||
This program is free software: you can redistribute it and/or modify
|
||||
it under the terms of the GNU General Public License as published by
|
||||
the Free Software Foundation, either version 3 of the License, or
|
||||
(at your option) any later version.
|
||||
|
||||
This program is distributed in the hope that it will be useful,
|
||||
but WITHOUT ANY WARRANTY; without even the implied warranty of
|
||||
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
|
||||
GNU General Public License for more details.
|
||||
|
||||
You should have received a copy of the GNU General Public License
|
||||
along with this program. If not, see <https://www.gnu.org/licenses/>.
|
||||
* Copyright (C) 2020 Alan Orth
|
||||
*
|
||||
* SPDX-License-Identifier: GPL-3.0-or-later
|
||||
*/
|
||||
|
||||
package io.github.ilri.cgspace.ctasks;
|
||||
|
||||
@ -1,19 +1,7 @@
|
||||
/*
|
||||
DSpace Curation Tasks
|
||||
Copyright (C) 2020 Alan Orth
|
||||
|
||||
This program is free software: you can redistribute it and/or modify
|
||||
it under the terms of the GNU General Public License as published by
|
||||
the Free Software Foundation, either version 3 of the License, or
|
||||
(at your option) any later version.
|
||||
|
||||
This program is distributed in the hope that it will be useful,
|
||||
but WITHOUT ANY WARRANTY; without even the implied warranty of
|
||||
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
|
||||
GNU General Public License for more details.
|
||||
|
||||
You should have received a copy of the GNU General Public License
|
||||
along with this program. If not, see <https://www.gnu.org/licenses/>.
|
||||
* Copyright (C) 2020 Alan Orth
|
||||
*
|
||||
* SPDX-License-Identifier: GPL-3.0-or-later
|
||||
*/
|
||||
|
||||
package io.github.ilri.cgspace.ctasks;
|
||||
|
||||
@ -1,19 +1,7 @@
|
||||
/*
|
||||
DSpace Curation Tasks
|
||||
Copyright (C) 2020 Alan Orth
|
||||
|
||||
This program is free software: you can redistribute it and/or modify
|
||||
it under the terms of the GNU General Public License as published by
|
||||
the Free Software Foundation, either version 3 of the License, or
|
||||
(at your option) any later version.
|
||||
|
||||
This program is distributed in the hope that it will be useful,
|
||||
but WITHOUT ANY WARRANTY; without even the implied warranty of
|
||||
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
|
||||
GNU General Public License for more details.
|
||||
|
||||
You should have received a copy of the GNU General Public License
|
||||
along with this program. If not, see <https://www.gnu.org/licenses/>.
|
||||
* Copyright (C) 2020 Alan Orth
|
||||
*
|
||||
* SPDX-License-Identifier: GPL-3.0-or-later
|
||||
*/
|
||||
|
||||
package io.github.ilri.cgspace.ctasks;
|
||||
@ -23,7 +11,7 @@ import org.apache.log4j.Logger;
|
||||
import org.dspace.authorize.AuthorizeException;
|
||||
import org.dspace.content.DSpaceObject;
|
||||
import org.dspace.content.Item;
|
||||
import org.dspace.content.Metadatum;
|
||||
import org.dspace.content.MetadataValue;
|
||||
import org.dspace.core.Constants;
|
||||
import org.dspace.curate.AbstractCurationTask;
|
||||
import org.dspace.curate.Curator;
|
||||
@ -81,7 +69,11 @@ public class CountryCodeTagger extends AbstractCurationTask
|
||||
|
||||
Item item = (Item)dso;
|
||||
|
||||
alpha2Result = performAlpha2(item, config);
|
||||
try {
|
||||
alpha2Result = performAlpha2(item, config);
|
||||
} catch (SQLException throwables) {
|
||||
throwables.printStackTrace();
|
||||
}
|
||||
|
||||
setResult(alpha2Result.getResult());
|
||||
report(alpha2Result.getResult());
|
||||
@ -90,15 +82,14 @@ public class CountryCodeTagger extends AbstractCurationTask
|
||||
return alpha2Result.getStatus();
|
||||
}
|
||||
|
||||
public CountryCodeTaggerResult performAlpha2(Item item, CountryCodeTaggerConfig config) throws IOException
|
||||
{
|
||||
public CountryCodeTaggerResult performAlpha2(Item item, CountryCodeTaggerConfig config) throws IOException, SQLException {
|
||||
CountryCodeTaggerResult alpha2Result = new CountryCodeTaggerResult();
|
||||
String itemHandle = item.getHandle();
|
||||
|
||||
Metadatum[] itemCountries = item.getMetadataByMetadataString(config.iso3166Field);
|
||||
List<MetadataValue> itemCountries = itemService.getMetadataByMetadataString(item, config.iso3166Field);
|
||||
|
||||
// skip items that don't have country metadata
|
||||
if (itemCountries.length == 0) {
|
||||
if (itemCountries.size() == 0) {
|
||||
alpha2Result.setResult(itemHandle + ": no countries, skipping.");
|
||||
alpha2Result.setStatus(Curator.CURATE_SKIP);
|
||||
} else {
|
||||
@ -117,25 +108,25 @@ public class CountryCodeTagger extends AbstractCurationTask
|
||||
String[] iso3166Alpha2FieldParts = config.iso3166Alpha2Field.split("\\.");
|
||||
|
||||
if (config.forceupdate) {
|
||||
item.clearMetadata(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
|
||||
Metadatum[] itemAlpha2CountryCodes = item.getMetadataByMetadataString(config.iso3166Alpha2Field);
|
||||
List<MetadataValue> itemAlpha2CountryCodes = itemService.getMetadataByMetadataString(item, config.iso3166Alpha2Field);
|
||||
|
||||
if (itemAlpha2CountryCodes.length == 0) {
|
||||
if (itemAlpha2CountryCodes.size() == 0) {
|
||||
List<String> newAlpha2Codes = new ArrayList<String>();
|
||||
for (Metadatum itemCountry : itemCountries) {
|
||||
for (MetadataValue itemCountry : itemCountries) {
|
||||
//check ISO 3166-1 countries
|
||||
for (CountriesVocabulary.Country country : isocodesCountriesJson.countries) {
|
||||
if (itemCountry.value.equalsIgnoreCase(country.getName()) || itemCountry.value.equalsIgnoreCase(country.get_official_name()) || itemCountry.value.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
|
||||
for (CountriesVocabulary.Country country : cgspaceCountriesJson.countries) {
|
||||
if (itemCountry.value.equalsIgnoreCase(country.getCgspace_name())) {
|
||||
if (itemCountry.getValue().equalsIgnoreCase(country.getCgspace_name())) {
|
||||
newAlpha2Codes.add(country.getAlpha_2());
|
||||
}
|
||||
}
|
||||
@ -143,9 +134,8 @@ public class CountryCodeTagger extends AbstractCurationTask
|
||||
|
||||
if (newAlpha2Codes.size() > 0) {
|
||||
try {
|
||||
// add metadata values (casting the List<String> to an array)
|
||||
item.addMetadata(iso3166Alpha2FieldParts[0], iso3166Alpha2FieldParts[1], iso3166Alpha2FieldParts[2], "en_US", newAlpha2Codes.toArray(new String[0]));
|
||||
item.update();
|
||||
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");
|
||||
|
||||
@ -1,19 +1,7 @@
|
||||
/*
|
||||
DSpace Curation Tasks
|
||||
Copyright (C) 2020 Alan Orth
|
||||
|
||||
This program is free software: you can redistribute it and/or modify
|
||||
it under the terms of the GNU General Public License as published by
|
||||
the Free Software Foundation, either version 3 of the License, or
|
||||
(at your option) any later version.
|
||||
|
||||
This program is distributed in the hope that it will be useful,
|
||||
but WITHOUT ANY WARRANTY; without even the implied warranty of
|
||||
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
|
||||
GNU General Public License for more details.
|
||||
|
||||
You should have received a copy of the GNU General Public License
|
||||
along with this program. If not, see <https://www.gnu.org/licenses/>.
|
||||
* Copyright (C) 2020 Alan Orth
|
||||
*
|
||||
* SPDX-License-Identifier: GPL-3.0-or-later
|
||||
*/
|
||||
|
||||
package io.github.ilri.cgspace.ctasks;
|
||||
|
||||
72
src/main/java/io/github/ilri/cgspace/ctasks/README.md
Normal file
72
src/main/java/io/github/ilri/cgspace/ctasks/README.md
Normal file
@ -0,0 +1,72 @@
|
||||
# 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 6.3. 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>6.1-SNAPSHOT</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-6.1-SNAPSHOT.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
|
||||
plugin.named.org.dspace.curate.CurationTask = io.github.ilri.cgspace.ctasks.CountryCodeTagger = countrycodetagger.force
|
||||
```
|
||||
|
||||
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):
|
||||
|
||||
```
|
||||
# name of the field containing ISO 3166-1 country names
|
||||
countrycodetagger.iso3166.field = cg.coverage.country
|
||||
|
||||
# name of the field containing ISO 3166-1 Alpha2 country codes
|
||||
countrycodetagger.iso3166-alpha2.field = cg.coverage.iso3166-alpha2
|
||||
|
||||
# only add country codes if an item doesn't have any (default false)
|
||||
#countrycodetagger.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 task and a "force" variant. The "force" variant is the same task, but it looks for configuration variables using the `countrycodetagger.force` instead. To use the "force" variant you simply need to add these new variables with the `forceupdate` parameter overridden to the same configuration file where you put the other variables. 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 - -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.
|
||||
|
||||
## 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
|
||||
@ -1,3 +1,9 @@
|
||||
/*
|
||||
* Copyright (C) 2020 Alan Orth
|
||||
*
|
||||
* SPDX-License-Identifier: GPL-3.0-or-later
|
||||
*/
|
||||
|
||||
package io.github.ilri.cgspace.scripts;
|
||||
|
||||
import org.apache.commons.lang.StringUtils;
|
||||
@ -5,18 +11,28 @@ import org.dspace.authorize.AuthorizeException;
|
||||
import org.dspace.content.*;
|
||||
import org.dspace.core.Constants;
|
||||
import org.dspace.core.Context;
|
||||
import org.dspace.handle.HandleManager;
|
||||
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;
|
||||
import java.util.Iterator;
|
||||
import java.util.List;
|
||||
|
||||
/**
|
||||
* @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 6.1
|
||||
* @since 5.1
|
||||
*/
|
||||
public class FixJpgJpgThumbnails {
|
||||
//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 void main(String[] args) {
|
||||
String parentHandle = null;
|
||||
@ -30,25 +46,25 @@ public class FixJpgJpgThumbnails {
|
||||
context.turnOffAuthorisationSystem();
|
||||
|
||||
if (StringUtils.isBlank(parentHandle)) {
|
||||
process(context, Item.findAll(context));
|
||||
process(context, itemService.findAll(context));
|
||||
} else {
|
||||
DSpaceObject parent = HandleManager.resolveToObject(context, parentHandle);
|
||||
DSpaceObject parent = handleService.resolveToObject(context, parentHandle);
|
||||
if (parent != null) {
|
||||
switch (parent.getType()) {
|
||||
case Constants.COLLECTION:
|
||||
process(context, ((Collection) parent).getAllItems()); // getAllItems because we want to work on non-archived ones as well
|
||||
process(context, itemService.findByCollection(context, (Collection) parent));
|
||||
break;
|
||||
case Constants.COMMUNITY:
|
||||
Collection[] collections = ((Community) parent).getCollections();
|
||||
List<Collection> collections = ((Community) parent).getCollections();
|
||||
for (Collection collection : collections) {
|
||||
process(context, collection.getAllItems()); // getAllItems because we want to work on non-archived ones as well
|
||||
process(context, itemService.findAllByCollection(context, collection));
|
||||
}
|
||||
break;
|
||||
case Constants.SITE:
|
||||
process(context, Item.findAll(context));
|
||||
process(context, itemService.findAll(context));
|
||||
break;
|
||||
case Constants.ITEM:
|
||||
processItem((Item) parent);
|
||||
processItem(context, (Item) parent);
|
||||
context.commit();
|
||||
break;
|
||||
}
|
||||
@ -63,36 +79,59 @@ public class FixJpgJpgThumbnails {
|
||||
}
|
||||
}
|
||||
|
||||
private static void process(Context context, ItemIterator 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(item);
|
||||
context.commit();
|
||||
item.decache();
|
||||
processItem(context, item);
|
||||
itemService.update(context, item);
|
||||
}
|
||||
}
|
||||
|
||||
private static void processItem(Item item) throws SQLException, AuthorizeException, IOException {
|
||||
Bundle[] thumbnailBundles = item.getBundles("THUMBNAIL");
|
||||
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
|
||||
// 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<Bundle> thumbnailBundles = item.getBundles("THUMBNAIL");
|
||||
for (Bundle thumbnailBundle : thumbnailBundles) {
|
||||
Bitstream[] thumbnailBundleBitstreams = thumbnailBundle.getBitstreams();
|
||||
List<Bitstream> thumbnailBundleBitstreams = thumbnailBundle.getBitstreams();
|
||||
for (Bitstream thumbnailBitstream : thumbnailBundleBitstreams) {
|
||||
String thumbnailName = thumbnailBitstream.getName();
|
||||
|
||||
if (thumbnailName.contains(".jpg.jpg")) {
|
||||
Bundle[] originalBundles = item.getBundles("ORIGINAL");
|
||||
if (thumbnailName.toLowerCase().contains(".jpg.jpg")) {
|
||||
List<Bundle> originalBundles = item.getBundles("ORIGINAL");
|
||||
for (Bundle originalBundle : originalBundles) {
|
||||
Bitstream[] originalBundleBitstreams = originalBundle.getBitstreams();
|
||||
List<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.equals(StringUtils.removeEndIgnoreCase(thumbnailName, ".jpg")) && "Generated 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
|
||||
thumbnailBundle.addBitstream(originalBitstream);
|
||||
bundleService.addBitstream(context, thumbnailBundle, originalBitstream);
|
||||
//remove the original bitstream from the ORIGINAL bundle
|
||||
originalBundle.removeBitstream(originalBitstream);
|
||||
//remove the JpgJpg bitstream from the THUMBNAIL bundle
|
||||
|
||||
@ -0,0 +1,270 @@
|
||||
/*
|
||||
* Copyright (C) 2022 Alan Orth
|
||||
*
|
||||
* SPDX-License-Identifier: GPL-3.0-or-later
|
||||
*/
|
||||
|
||||
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.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.handle.factory.HandleServiceFactory;
|
||||
import org.dspace.handle.service.HandleService;
|
||||
|
||||
import java.io.IOException;
|
||||
import java.sql.SQLException;
|
||||
import java.util.Iterator;
|
||||
import java.util.List;
|
||||
|
||||
/**
|
||||
* Fix low-quality thumbnails in a DSpace repository.
|
||||
*
|
||||
* <p>Search the DSpace repository for items containing bitstreams matching the following criteria:
|
||||
*
|
||||
* <ul>
|
||||
* <li>If an item has an <code>IM Thumbnail</code> and a <code>Generated Thumbnail</code> in the
|
||||
* <code>THUMBNAIL</code> bundle, remove the <code>Generated Thumbnail</code>.
|
||||
* <li>If an item has a PDF bitstream and a JPEG bitstream with description "thumbnail" in the
|
||||
* <code>ORIGINAL</code> bundle, remove the "thumbnail" bitstream in the ORIGINAL bundle.
|
||||
* </ul>
|
||||
*
|
||||
* <p>The general idea is that we should always prefer thumbnails generated from PDFs by ImageMagick
|
||||
* to manually uploaded JPEGs because ImageMagick Thumbnails can be regenerated with higher quality,
|
||||
* resolution, etc. Furthermore, if there are JPEG bitstreams in the ORIGINAL bundle DSpace will
|
||||
* automatically create ".jpg.jpg" thumbnails from them in the THUMBNAIL bundle so we should remove
|
||||
* those as well!
|
||||
*
|
||||
* @author Andrea Schweer schweer@waikato.ac.nz for the LCoNZ Institutional Research Repositories
|
||||
* @author Alan Orth for the International Livestock Research Institute
|
||||
* @version 6.1
|
||||
* @since 6.1
|
||||
* @see FixJpgJpgThumbnails
|
||||
*/
|
||||
public class FixLowQualityThumbnails {
|
||||
// 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 void main(String[] args) {
|
||||
String parentHandle = null;
|
||||
if (args.length >= 1) {
|
||||
parentHandle = args[0];
|
||||
}
|
||||
|
||||
Context context = null;
|
||||
try {
|
||||
context = new Context();
|
||||
context.turnOffAuthorisationSystem();
|
||||
|
||||
if (StringUtils.isBlank(parentHandle)) {
|
||||
process(context, itemService.findAll(context));
|
||||
} else {
|
||||
DSpaceObject parent = handleService.resolveToObject(context, parentHandle);
|
||||
if (parent != null) {
|
||||
switch (parent.getType()) {
|
||||
case Constants.COLLECTION:
|
||||
process(
|
||||
context,
|
||||
itemService.findByCollection(context, (Collection) parent));
|
||||
break;
|
||||
case Constants.COMMUNITY:
|
||||
List<Collection> collections = ((Community) parent).getCollections();
|
||||
for (Collection collection : collections) {
|
||||
process(
|
||||
context,
|
||||
itemService.findAllByCollection(context, collection));
|
||||
}
|
||||
break;
|
||||
case Constants.SITE:
|
||||
process(context, itemService.findAll(context));
|
||||
break;
|
||||
case Constants.ITEM:
|
||||
processItem(context, (Item) parent);
|
||||
context.commit();
|
||||
break;
|
||||
}
|
||||
}
|
||||
}
|
||||
} catch (SQLException | AuthorizeException | IOException e) {
|
||||
e.printStackTrace(System.err);
|
||||
} finally {
|
||||
if (context != null && context.isValid()) {
|
||||
context.abort();
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
private static void process(Context context, Iterator<Item> items)
|
||||
throws SQLException, IOException, AuthorizeException {
|
||||
while (items.hasNext()) {
|
||||
Item item = items.next();
|
||||
processItem(context, item);
|
||||
itemService.update(context, item);
|
||||
}
|
||||
}
|
||||
|
||||
private static void processItem(Context context, Item item)
|
||||
throws SQLException, AuthorizeException, IOException {
|
||||
// Set some state for the item before we iterate over the THUMBNAIL bundle
|
||||
boolean itemHasImThumbnail = false;
|
||||
|
||||
// Iterate over the THUMBNAIL bundle to first identify if this item has an "IM Thumbnail"
|
||||
List<Bundle> thumbnailBundles = item.getBundles("THUMBNAIL");
|
||||
for (Bundle thumbnailBundle : thumbnailBundles) {
|
||||
List<Bitstream> thumbnailBundleBitstreams = thumbnailBundle.getBitstreams();
|
||||
for (Bitstream thumbnailBitstream : thumbnailBundleBitstreams) {
|
||||
String thumbnailDescription = thumbnailBitstream.getDescription();
|
||||
|
||||
if (StringUtils.isEmpty(thumbnailDescription)) {
|
||||
continue;
|
||||
}
|
||||
|
||||
// Check if this item has a bitstream in the THUMBNAIL bundle with description "IM
|
||||
// Thumbnail", but only if we haven't already seen one in another iteration for this
|
||||
// bundle.
|
||||
if (!itemHasImThumbnail && "IM Thumbnail".equals(thumbnailDescription)) {
|
||||
itemHasImThumbnail = true;
|
||||
}
|
||||
}
|
||||
|
||||
// If this item has an IM Thumbnail we can be reasonably sure that there is a PDF
|
||||
// in the ORIGINAL bundle and we don't need any other thumbnails.
|
||||
if (itemHasImThumbnail) {
|
||||
// Iterate over the bitstreams in the THUMBNAIL bundle again.
|
||||
for (Bitstream thumbnailBitstream : thumbnailBundleBitstreams) {
|
||||
String thumbnailName = thumbnailBitstream.getName();
|
||||
String thumbnailDescription = thumbnailBitstream.getDescription();
|
||||
|
||||
if (StringUtils.isEmpty(thumbnailDescription)) {
|
||||
continue;
|
||||
}
|
||||
|
||||
// If this item has a "Generated Thumbnail" we can remove it, because those
|
||||
// typically come from other JPEGs in the ORIGINAL bundle and we would prefer
|
||||
// the IM Thumbnail generated from a PDF anyway. The DSpace-generated descri-
|
||||
// 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("> Name: »" + thumbnailName + "«");
|
||||
System.out.println("> Description: »" + thumbnailDescription + "«");
|
||||
System.out.print("\u001b[0m");
|
||||
|
||||
// Remove the "Generated Thumbnail" bitstream from the THUMBNAIL bundle
|
||||
thumbnailBundle.removeBitstream(thumbnailBitstream);
|
||||
|
||||
// If this item has a bitstream with the word "thumbnail" in it then we can
|
||||
// remove it because we already know this item has an IM Thumbnail and we
|
||||
// prefer that one.
|
||||
} else if (thumbnailDescription.toLowerCase().contains("thumbnail")
|
||||
&& !"IM Thumbnail".equals(thumbnailDescription)) {
|
||||
System.out.print("\u001b[33m");
|
||||
System.out.println("Deleting (" + item.getHandle() + "):");
|
||||
System.out.println("> Name: »" + thumbnailName + "«");
|
||||
System.out.println("> Description: »" + thumbnailDescription + "«");
|
||||
System.out.print("\u001b[0m");
|
||||
|
||||
// Remove the "thumbnail" bitstream from the THUMBNAIL bundle
|
||||
thumbnailBundle.removeBitstream(thumbnailBitstream);
|
||||
|
||||
// Otherwise skip it because it might be something uploaded manually, like
|
||||
// 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("> Name: »" + thumbnailName + "«");
|
||||
System.out.println("> Description: »" + thumbnailDescription + "«");
|
||||
System.out.print("\u001b[0m");
|
||||
}
|
||||
|
||||
// Print a blank line
|
||||
System.out.println();
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
// Set some state before we iterate over the ORIGINAL bundle
|
||||
boolean itemHasOriginalPdfBitstream = false;
|
||||
boolean itemHasOriginalJpegBitstream = false;
|
||||
|
||||
// Iterate over the ORIGINAL bundle to delete manually-uploaded JPEG
|
||||
// bitstreams labeled "Thumbnail" whenever we have a PDF because they
|
||||
// don't belong in the ORIGINAL bundle and DSpace will automatically
|
||||
// create a better thumbnail from the PDF anyway.
|
||||
List<Bundle> originalBundles = item.getBundles("ORIGINAL");
|
||||
for (Bundle originalBundle : originalBundles) {
|
||||
List<Bitstream> originalBundleBitstreams = originalBundle.getBitstreams();
|
||||
for (Bitstream originalBitstream : originalBundleBitstreams) {
|
||||
String originalFormat = originalBitstream.getFormat(context).getMIMEType();
|
||||
|
||||
// Check if this item has a PDF bitstream in the ORIGINAL bundle,
|
||||
// but only if we haven't already seen one in another iteration
|
||||
// for this bundle. DSpace will return "format application/pdf"
|
||||
// for the MIME type.
|
||||
if (!itemHasOriginalPdfBitstream && originalFormat.contains("application/pdf")) {
|
||||
itemHasOriginalPdfBitstream = true;
|
||||
}
|
||||
|
||||
// Check if this item has a JPEG bitstream in the ORIGINAL bundle,
|
||||
// but only if we haven't already seen one in another iteration
|
||||
// for this bundle. DSpace will return "format image/jpeg" for
|
||||
// the MIME type.
|
||||
if (!itemHasOriginalJpegBitstream && originalFormat.contains("image/jpeg")) {
|
||||
itemHasOriginalJpegBitstream = true;
|
||||
}
|
||||
}
|
||||
|
||||
// Check if we found a PDF *and* a JPEG in this item's ORIGINAL
|
||||
// bundle.
|
||||
if (itemHasOriginalPdfBitstream && itemHasOriginalJpegBitstream) {
|
||||
// Yes! Now iterate over the bitstreams in the ORIGINAL bundle
|
||||
// again to see if the JPEG is a manually uploaded "Thumbnail"
|
||||
for (Bitstream originalBitstream : originalBundleBitstreams) {
|
||||
String originalName = originalBitstream.getName();
|
||||
String originalDescription = originalBitstream.getDescription();
|
||||
String originalFormat = originalBitstream.getFormat(context).getMIMEType();
|
||||
|
||||
if (StringUtils.isEmpty(originalDescription)) {
|
||||
continue;
|
||||
}
|
||||
|
||||
/*
|
||||
- check if the bitstream is a JPEG based on its MIME Type
|
||||
- check if the bitstream's name or description is "Thumbnail"
|
||||
*/
|
||||
if (originalFormat.toLowerCase().contains("image/jpeg")
|
||||
&& (originalName.toLowerCase().contains("thumbnail")
|
||||
|| originalDescription.toLowerCase().contains("thumbnail"))) {
|
||||
System.out.print("\u001b[33m");
|
||||
System.out.println("Removing (" + item.getHandle() + "):");
|
||||
System.out.println("> Name: »" + originalName + "«");
|
||||
System.out.println("> Description: »" + originalDescription + "«");
|
||||
System.out.print("\u001b[0m");
|
||||
|
||||
// Remove the original bitstream from the ORIGINAL bundle
|
||||
originalBundle.removeBitstream(originalBitstream);
|
||||
|
||||
} else {
|
||||
System.out.print("\u001b[34m");
|
||||
System.out.println("Skipping (" + item.getHandle() + "):");
|
||||
System.out.println("> Name: »" + originalName + "«");
|
||||
System.out.println("> Description: »" + originalDescription + "«");
|
||||
System.out.print("\u001b[0m");
|
||||
}
|
||||
|
||||
// Print a blank line
|
||||
System.out.println();
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
42
src/main/java/io/github/ilri/cgspace/scripts/README.md
Normal file
42
src/main/java/io/github/ilri/cgspace/scripts/README.md
Normal file
@ -0,0 +1,42 @@
|
||||
# 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
|
||||
- **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).
|
||||
|
||||
## 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`:
|
||||
|
||||
```xml
|
||||
<dependency>
|
||||
<groupId>io.github.ilri.cgspace</groupId>
|
||||
<artifactId>cgspace-java-helpers</artifactId>
|
||||
<version>6.1-SNAPSHOT</version>
|
||||
</dependency>
|
||||
```
|
||||
|
||||
The jar will be copied to all DSpace applications.
|
||||
|
||||
### Manual Build and Install
|
||||
To build the standalone jar:
|
||||
|
||||
```console
|
||||
$ mvn package
|
||||
```
|
||||
|
||||
Copy the resulting jar to the DSpace `lib` directory:
|
||||
|
||||
```console
|
||||
$ cp target/cgspace-java-helpers-6.1-SNAPSHOT.jar ~/dspace/lib/
|
||||
```
|
||||
|
||||
## Invocation
|
||||
The scripts take only one argument, which is a community, collection, or item:
|
||||
|
||||
```console
|
||||
$ dspace dsrun io.github.ilri.cgspace.scripts.FixJpgJpgThumbnails 10568/83389
|
||||
```
|
||||
Reference in New Issue
Block a user