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https://github.com/ilri/cgspace-java-helpers.git
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26
.github/workflows/maven.yml
vendored
26
.github/workflows/maven.yml
vendored
@ -1,26 +0,0 @@
|
||||
# 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: [ dspace7 ]
|
||||
pull_request:
|
||||
branches: [ dspace7 ]
|
||||
|
||||
jobs:
|
||||
build:
|
||||
|
||||
runs-on: ubuntu-22.04
|
||||
|
||||
steps:
|
||||
- uses: actions/checkout@v4
|
||||
- name: Set up JDK 17
|
||||
uses: actions/setup-java@v4
|
||||
with:
|
||||
java-version: 17
|
||||
distribution: 'temurin'
|
||||
cache: 'maven'
|
||||
- name: Build with Maven
|
||||
run: mvn -B package --file pom.xml
|
||||
6
.gitignore
vendored
6
.gitignore
vendored
@ -70,10 +70,4 @@ 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/
|
||||
|
||||
@ -1,13 +1,11 @@
|
||||
<?xml version="1.0" encoding="UTF-8"?>
|
||||
<project version="4">
|
||||
<component name="ExternalStorageConfigurationManager" enabled="true" />
|
||||
<component name="MavenProjectsManager">
|
||||
<option name="originalFiles">
|
||||
<list>
|
||||
<option value="$PROJECT_DIR$/pom.xml" />
|
||||
</list>
|
||||
</option>
|
||||
<option name="workspaceImportForciblyTurnedOn" value="true" />
|
||||
</component>
|
||||
<component name="ProjectRootManager" version="2" languageLevel="JDK_11" project-jdk-name="17" project-jdk-type="JavaSDK" />
|
||||
<component name="ProjectRootManager" version="2" languageLevel="JDK_11" project-jdk-name="11" project-jdk-type="JavaSDK" />
|
||||
</project>
|
||||
8
.travis.yml
Normal file
8
.travis.yml
Normal file
@ -0,0 +1,8 @@
|
||||
dist: bionic
|
||||
language: java
|
||||
jdk:
|
||||
- openjdk8
|
||||
script:
|
||||
- mvn package -B
|
||||
|
||||
# vim: ts=2 sw=2 et
|
||||
49
CHANGELOG.md
49
CHANGELOG.md
@ -1,49 +0,0 @@
|
||||
# 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
|
||||
|
||||
## [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
|
||||
|
||||
## [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
|
||||
- `iso_3166-1.json` from iso-codes 4.12.0, which updates the name for TR to "Türkiye"
|
||||
|
||||
## [6.1] - 2022-10-31
|
||||
### Updated
|
||||
- Update dependencies in `pom.xml`
|
||||
- `iso_3166-1.json` from iso-codes 4.11.0
|
||||
|
||||
### Changed
|
||||
- Java compiler and target from JDK 7 to JDK 8
|
||||
|
||||
### Added
|
||||
- New `FixLowQualityThumbnails` script to detect and remove more low-quality thumbnails
|
||||
|
||||
### Fixed
|
||||
- `FixJpgJpgThumbnails` and `FixLowQualityThumbnails` scripts not commiting changes when operating on a site, community, or collection
|
||||
60
README.md
60
README.md
@ -1,12 +1,10 @@
|
||||
# CGSpace Java Helpers [](https://github.com/ilri/cgspace-java-helpers/actions)
|
||||
# CGSpace Java Helpers [](https://travis-ci.org/ilri/dspace-curation-tasks)
|
||||
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
|
||||
- **FixLowQualityThumbnails**: remove low-quality thumbnails when PDF bitstreams are present
|
||||
- **NormalizeDOIs**: normalize DOIs by stripping whitespace, lowercasing, and converting to https://doi.org/ format
|
||||
- **FixJpgJpgThumbnails**: Fix low-quality ".jpg.jpg" thumbnails by replacing them with their originals
|
||||
|
||||
Tested on DSpace 7.6.1. Read more about the [DSpace curation system](https://wiki.lyrasis.org/display/DSDOC7x/Curation+System).
|
||||
Tested on DSpace 5.8. Read more about the [DSpace curation system](https://wiki.lyrasis.org/display/DSDOC5x/Curation+System).
|
||||
|
||||
## Build and Install
|
||||
|
||||
@ -17,7 +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>7.6.1.4-SNAPSHOT</version>
|
||||
<version>5.1</version>
|
||||
</dependency>
|
||||
```
|
||||
|
||||
@ -26,21 +24,49 @@ 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-7.6.1.4-SNAPSHOT.jar ~/dspace/lib/
|
||||
```
|
||||
$ cp target/cgspace-java-helpers-5.1.jar ~/dspace/lib
|
||||
```
|
||||
|
||||
## Configuration
|
||||
Please refer to the appropriate README.md file:
|
||||
Add the curation task to DSpace's `config/modules/curate.cfg`:
|
||||
|
||||
- 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)
|
||||
```
|
||||
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.
|
||||
|
||||
## Notes
|
||||
This project was initially created according to the [Maven Getting Started Guide](https://maven.apache.org/guides/getting-started/):
|
||||
@ -49,13 +75,11 @@ 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
|
||||
```
|
||||
|
||||
To deploy a new `-SNAPSHOT` release to Maven Central (make sure OSSHRH credentials are in `~/.m2/settings.xml`):
|
||||
## TODO
|
||||
|
||||
```console
|
||||
$ mvn clean deploy
|
||||
```
|
||||
|
||||
See: <a href="https://central.sonatype.org/publish/publish-maven/#performing-a-snapshot-deployment">Performing a Snapshot Deployment</a>
|
||||
- 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).
|
||||
|
||||
82
pom.xml
82
pom.xml
@ -6,50 +6,56 @@
|
||||
|
||||
<groupId>io.github.ilri.cgspace</groupId>
|
||||
<artifactId>cgspace-java-helpers</artifactId>
|
||||
<version>7.6.1.4-SNAPSHOT</version>
|
||||
<version>5.1</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-only.html</url>
|
||||
<url>https://spdx.org/licenses/GPL-3.0-or-later.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.release>11</maven.compiler.release>
|
||||
<maven.compiler.source>1.7</maven.compiler.source>
|
||||
<maven.compiler.target>1.7</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>2.9.0</version>
|
||||
<version>2.2.1</version>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>org.dspace</groupId>
|
||||
<artifactId>dspace-api</artifactId>
|
||||
<version>7.6.1</version>
|
||||
<version>5.8</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: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>
|
||||
@ -69,63 +75,43 @@
|
||||
<!-- clean lifecycle, see https://maven.apache.org/ref/current/maven-core/lifecycles.html#clean_Lifecycle -->
|
||||
<plugin>
|
||||
<artifactId>maven-clean-plugin</artifactId>
|
||||
<version>3.3.2</version>
|
||||
<version>3.1.0</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>3.3.1</version>
|
||||
<version>3.0.2</version>
|
||||
</plugin>
|
||||
<plugin>
|
||||
<artifactId>maven-compiler-plugin</artifactId>
|
||||
<version>3.13.0</version>
|
||||
<version>3.8.0</version>
|
||||
</plugin>
|
||||
<plugin>
|
||||
<artifactId>maven-surefire-plugin</artifactId>
|
||||
<version>3.2.5</version>
|
||||
<version>2.22.1</version>
|
||||
</plugin>
|
||||
<plugin>
|
||||
<artifactId>maven-jar-plugin</artifactId>
|
||||
<version>3.4.1</version>
|
||||
<version>3.0.2</version>
|
||||
</plugin>
|
||||
<plugin>
|
||||
<artifactId>maven-install-plugin</artifactId>
|
||||
<version>3.1.1</version>
|
||||
<version>2.5.2</version>
|
||||
</plugin>
|
||||
<plugin>
|
||||
<artifactId>maven-deploy-plugin</artifactId>
|
||||
<version>2.8.2</version>
|
||||
</plugin>
|
||||
<!-- site lifecycle, see https://maven.apache.org/ref/current/maven-core/lifecycles.html#site_Lifecycle -->
|
||||
<plugin>
|
||||
<artifactId>maven-site-plugin</artifactId>
|
||||
<version>3.12.1</version>
|
||||
<version>3.7.1</version>
|
||||
</plugin>
|
||||
<plugin>
|
||||
<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>
|
||||
<version>3.0.0</version>
|
||||
</plugin>
|
||||
</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>
|
||||
|
||||
@ -1,8 +1,20 @@
|
||||
/*
|
||||
* Copyright (C) 2020 Alan Orth
|
||||
*
|
||||
* SPDX-License-Identifier: GPL-3.0-only
|
||||
*/
|
||||
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/>.
|
||||
*/
|
||||
|
||||
package io.github.ilri.cgspace.ctasks;
|
||||
|
||||
|
||||
@ -1,8 +1,20 @@
|
||||
/*
|
||||
* Copyright (C) 2020 Alan Orth
|
||||
*
|
||||
* SPDX-License-Identifier: GPL-3.0-only
|
||||
*/
|
||||
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/>.
|
||||
*/
|
||||
|
||||
package io.github.ilri.cgspace.ctasks;
|
||||
|
||||
@ -10,17 +22,16 @@ import javax.annotation.Nullable;
|
||||
|
||||
public class CountriesVocabulary {
|
||||
|
||||
static class Country {
|
||||
private final String name; // required
|
||||
private final String common_name; // optional
|
||||
private final String official_name; // optional
|
||||
private final String cgspace_name; // optional
|
||||
private final String numeric; // required Hmmmm need to cast this...
|
||||
private final String alpha_2; // required
|
||||
private final String alpha_3; // required
|
||||
class Country {
|
||||
private String name; //required
|
||||
private String common_name; //optional
|
||||
private String official_name; //optional
|
||||
private String cgspace_name; //optional
|
||||
private String numeric; //required Hmmmm need to cast this...
|
||||
private String alpha_2; //required
|
||||
private String alpha_3; //required
|
||||
|
||||
public Country(
|
||||
String name,
|
||||
public Country(String name,
|
||||
@Nullable String common_name,
|
||||
@Nullable String official_name,
|
||||
@Nullable String cgspace_name,
|
||||
@ -31,9 +42,7 @@ public class CountriesVocabulary {
|
||||
this.common_name = common_name;
|
||||
this.official_name = official_name;
|
||||
this.cgspace_name = cgspace_name;
|
||||
this.numeric =
|
||||
numeric; // fuuuuu this is a string and we can't cast to Integer because some
|
||||
// values are zeropadded like "004"
|
||||
this.numeric = numeric; // fuuuuu this is a string and we can't cast to Integer because some values are zeropadded like "004"
|
||||
this.alpha_2 = alpha_2;
|
||||
this.alpha_3 = alpha_3;
|
||||
}
|
||||
|
||||
@ -1,19 +1,29 @@
|
||||
/*
|
||||
* Copyright (C) 2020 Alan Orth
|
||||
*
|
||||
* SPDX-License-Identifier: GPL-3.0-only
|
||||
*/
|
||||
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/>.
|
||||
*/
|
||||
|
||||
package io.github.ilri.cgspace.ctasks;
|
||||
|
||||
import com.google.gson.Gson;
|
||||
|
||||
import org.apache.logging.log4j.LogManager;
|
||||
import org.apache.logging.log4j.Logger;
|
||||
import org.apache.log4j.Logger;
|
||||
import org.dspace.authorize.AuthorizeException;
|
||||
import org.dspace.content.DSpaceObject;
|
||||
import org.dspace.content.Item;
|
||||
import org.dspace.content.MetadataValue;
|
||||
import org.dspace.content.Metadatum;
|
||||
import org.dspace.core.Constants;
|
||||
import org.dspace.curate.AbstractCurationTask;
|
||||
import org.dspace.curate.Curator;
|
||||
@ -24,28 +34,20 @@ 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 CountryCodeTagger extends AbstractCurationTask
|
||||
{
|
||||
public class CountryCodeTaggerConfig {
|
||||
private final String isocodesJsonPath = "/io/github/ilri/cgspace/ctasks/iso_3166-1.json";
|
||||
private final String cgspaceCountriesJsonPath =
|
||||
"/io/github/ilri/cgspace/ctasks/cgspace-countries.json";
|
||||
private final String cgspaceCountriesJsonPath = "/io/github/ilri/cgspace/ctasks/cgspace-countries.json";
|
||||
private final String iso3166Field = taskProperty("iso3166.field");
|
||||
private final String iso3166Alpha2Field = taskProperty("iso3166-alpha2.field");
|
||||
private final boolean forceupdate = taskBooleanProperty("forceupdate", false);
|
||||
|
||||
private final Logger log = LogManager.getLogger();
|
||||
private Logger log = Logger.getLogger(CountryCodeTagger.class);
|
||||
}
|
||||
|
||||
public static class CountryCodeTaggerResult {
|
||||
public class CountryCodeTaggerResult {
|
||||
private int status = Curator.CURATE_UNSET;
|
||||
private String result = null;
|
||||
|
||||
@ -67,130 +69,96 @@ public class CountryCodeTagger extends AbstractCurationTask {
|
||||
}
|
||||
|
||||
@Override
|
||||
public int perform(DSpaceObject dso) throws IOException {
|
||||
public int perform(DSpaceObject dso) throws IOException
|
||||
{
|
||||
// gotta define this here so we can access it after the if context...
|
||||
CountryCodeTaggerResult alpha2Result = new CountryCodeTaggerResult();
|
||||
|
||||
if (dso.getType() == Constants.ITEM) {
|
||||
if (dso.getType() == Constants.ITEM)
|
||||
{
|
||||
// Load configuration
|
||||
CountryCodeTaggerConfig config = new CountryCodeTaggerConfig();
|
||||
|
||||
Item item = (Item) dso;
|
||||
Item item = (Item)dso;
|
||||
|
||||
try {
|
||||
alpha2Result = performAlpha2(item, config);
|
||||
} catch (SQLException throwables) {
|
||||
throwables.printStackTrace();
|
||||
}
|
||||
|
||||
setResult(alpha2Result.getResult());
|
||||
report(alpha2Result.getResult());
|
||||
}
|
||||
|
||||
return alpha2Result.getStatus();
|
||||
}
|
||||
|
||||
public CountryCodeTaggerResult performAlpha2(Item item, CountryCodeTaggerConfig config)
|
||||
throws IOException, SQLException {
|
||||
public CountryCodeTaggerResult performAlpha2(Item item, CountryCodeTaggerConfig config) throws IOException
|
||||
{
|
||||
CountryCodeTaggerResult alpha2Result = new CountryCodeTaggerResult();
|
||||
String itemHandle = item.getHandle();
|
||||
|
||||
List<MetadataValue> itemCountries =
|
||||
itemService.getMetadataByMetadataString(item, config.iso3166Field);
|
||||
Metadatum[] itemCountries = item.getMetadataByMetadataString(config.iso3166Field);
|
||||
|
||||
// skip items that don't have country metadata
|
||||
if (itemCountries.isEmpty()) {
|
||||
alpha2Result.setResult("No countries, skipping.");
|
||||
if (itemCountries.length == 0) {
|
||||
alpha2Result.setResult(itemHandle + ": no countries, skipping.");
|
||||
alpha2Result.setStatus(Curator.CURATE_SKIP);
|
||||
} else {
|
||||
Gson gson = new Gson();
|
||||
|
||||
// TODO: convert to try:
|
||||
// https://docs.oracle.com/javase/tutorial/essential/exceptions/tryResourceClose.html
|
||||
BufferedReader reader =
|
||||
new BufferedReader(
|
||||
new InputStreamReader(
|
||||
Objects.requireNonNull(this.getClass().getResourceAsStream(config.isocodesJsonPath))));
|
||||
ISO3166CountriesVocabulary isocodesCountriesJson =
|
||||
gson.fromJson(reader, ISO3166CountriesVocabulary.class);
|
||||
// TODO: convert to try: https://docs.oracle.com/javase/tutorial/essential/exceptions/tryResourceClose.html
|
||||
BufferedReader reader = new BufferedReader(new InputStreamReader(this.getClass().getResourceAsStream(config.isocodesJsonPath)));
|
||||
ISO3166CountriesVocabulary isocodesCountriesJson = gson.fromJson(reader, ISO3166CountriesVocabulary.class);
|
||||
reader.close();
|
||||
|
||||
reader =
|
||||
new BufferedReader(
|
||||
new InputStreamReader(
|
||||
Objects.requireNonNull(this.getClass()
|
||||
.getResourceAsStream(config.cgspaceCountriesJsonPath))));
|
||||
CGSpaceCountriesVocabulary cgspaceCountriesJson =
|
||||
gson.fromJson(reader, CGSpaceCountriesVocabulary.class);
|
||||
reader = new BufferedReader(new InputStreamReader(this.getClass().getResourceAsStream(config.cgspaceCountriesJsonPath)));
|
||||
CGSpaceCountriesVocabulary cgspaceCountriesJson = gson.fromJson(reader, CGSpaceCountriesVocabulary.class);
|
||||
reader.close();
|
||||
|
||||
// split the alpha2 country code field into schema, element, and qualifier so we can use
|
||||
// it with item.addMetadata()
|
||||
// split the alpha2 country code field into schema, element, and qualifier so we can use it with item.addMetadata()
|
||||
String[] iso3166Alpha2FieldParts = config.iso3166Alpha2Field.split("\\.");
|
||||
|
||||
if (config.forceupdate) {
|
||||
itemService.clearMetadata(
|
||||
Curator.curationContext(),
|
||||
item,
|
||||
iso3166Alpha2FieldParts[0],
|
||||
iso3166Alpha2FieldParts[1],
|
||||
iso3166Alpha2FieldParts[2],
|
||||
Item.ANY);
|
||||
item.clearMetadata(iso3166Alpha2FieldParts[0], iso3166Alpha2FieldParts[1], iso3166Alpha2FieldParts[2], Item.ANY);
|
||||
}
|
||||
|
||||
// check the item's country codes, if any
|
||||
List<MetadataValue> itemAlpha2CountryCodes =
|
||||
itemService.getMetadataByMetadataString(item, config.iso3166Alpha2Field);
|
||||
Metadatum[] itemAlpha2CountryCodes = item.getMetadataByMetadataString(config.iso3166Alpha2Field);
|
||||
|
||||
if (itemAlpha2CountryCodes.isEmpty()) {
|
||||
if (itemAlpha2CountryCodes.length == 0) {
|
||||
List<String> newAlpha2Codes = new ArrayList<String>();
|
||||
for (MetadataValue itemCountry : itemCountries) {
|
||||
// check ISO 3166-1 countries
|
||||
for (Metadatum itemCountry : itemCountries) {
|
||||
//check ISO 3166-1 countries
|
||||
for (CountriesVocabulary.Country country : isocodesCountriesJson.countries) {
|
||||
if (itemCountry.getValue().equalsIgnoreCase(country.getName())
|
||||
|| itemCountry
|
||||
.getValue()
|
||||
.equalsIgnoreCase(country.get_official_name())
|
||||
|| itemCountry
|
||||
.getValue()
|
||||
.equalsIgnoreCase(country.get_common_name())) {
|
||||
if (itemCountry.value.equalsIgnoreCase(country.getName()) || itemCountry.value.equalsIgnoreCase(country.get_official_name()) || itemCountry.value.equalsIgnoreCase(country.get_common_name())) {
|
||||
newAlpha2Codes.add(country.getAlpha_2());
|
||||
}
|
||||
}
|
||||
|
||||
// check CGSpace countries
|
||||
//check CGSpace countries
|
||||
for (CountriesVocabulary.Country country : cgspaceCountriesJson.countries) {
|
||||
if (itemCountry.getValue().equalsIgnoreCase(country.getCgspace_name())) {
|
||||
if (itemCountry.value.equalsIgnoreCase(country.getCgspace_name())) {
|
||||
newAlpha2Codes.add(country.getAlpha_2());
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
if (!newAlpha2Codes.isEmpty()) {
|
||||
if (newAlpha2Codes.size() > 0) {
|
||||
try {
|
||||
itemService.addMetadata(
|
||||
Curator.curationContext(),
|
||||
item,
|
||||
iso3166Alpha2FieldParts[0],
|
||||
iso3166Alpha2FieldParts[1],
|
||||
iso3166Alpha2FieldParts[2],
|
||||
"en_US",
|
||||
newAlpha2Codes);
|
||||
itemService.update(Curator.curationContext(), item);
|
||||
// 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();
|
||||
} catch (SQLException | AuthorizeException sqle) {
|
||||
config.log.debug(sqle.getMessage());
|
||||
alpha2Result.setResult("Error");
|
||||
alpha2Result.setResult(itemHandle + ": error");
|
||||
alpha2Result.setStatus(Curator.CURATE_ERROR);
|
||||
}
|
||||
|
||||
alpha2Result.setResult(
|
||||
"Added "
|
||||
+ newAlpha2Codes.size()
|
||||
+ " alpha2 country code(s)");
|
||||
alpha2Result.setResult(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);
|
||||
}
|
||||
}
|
||||
|
||||
@ -1,18 +1,27 @@
|
||||
/*
|
||||
* Copyright (C) 2020 Alan Orth
|
||||
*
|
||||
* SPDX-License-Identifier: GPL-3.0-only
|
||||
*/
|
||||
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/>.
|
||||
*/
|
||||
|
||||
package io.github.ilri.cgspace.ctasks;
|
||||
|
||||
import com.google.gson.annotations.SerializedName;
|
||||
|
||||
import java.util.List;
|
||||
|
||||
public class ISO3166CountriesVocabulary extends CountriesVocabulary {
|
||||
// support reading iso_3166-1.json from Debian's iso-codes package using SerializedName since
|
||||
// our class needs to match the JSON exactly
|
||||
@SerializedName("3166-1")
|
||||
List<Country> countries;
|
||||
// support reading iso_3166-1.json from Debian's iso-codes package using SerializedName since our class needs to match the JSON exactly
|
||||
@SerializedName("3166-1") List<Country> countries;
|
||||
}
|
||||
@ -1,100 +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 7.6.1.3
|
||||
* @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;
|
||||
}
|
||||
}
|
||||
@ -1,74 +0,0 @@
|
||||
# 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
|
||||
- **NormalizeDOIs**: normalize DOIs by stripping whitespace, lowercasing, and converting to https://doi.org/ format
|
||||
|
||||
Tested on DSpace 7.6.1. 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>7.6.1.4-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-7.6.1.4-SNAPSHOT.jar ~/dspace/lib/
|
||||
```
|
||||
|
||||
## Configuration
|
||||
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):
|
||||
|
||||
```
|
||||
# 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 -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.
|
||||
|
||||
## 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
|
||||
@ -1,46 +1,22 @@
|
||||
/*
|
||||
* Copyright (C) 2020 Alan Orth
|
||||
*
|
||||
* SPDX-License-Identifier: GPL-3.0-only
|
||||
*/
|
||||
|
||||
package io.github.ilri.cgspace.scripts;
|
||||
|
||||
import org.apache.commons.lang.StringUtils;
|
||||
import org.dspace.authorize.AuthorizeException;
|
||||
import org.dspace.content.Bitstream;
|
||||
import org.dspace.content.Bundle;
|
||||
import org.dspace.content.Collection;
|
||||
import org.dspace.content.Community;
|
||||
import org.dspace.content.DSpaceObject;
|
||||
import org.dspace.content.Item;
|
||||
import org.dspace.content.MetadataValue;
|
||||
import org.dspace.content.factory.ContentServiceFactory;
|
||||
import org.dspace.content.service.BundleService;
|
||||
import org.dspace.content.service.ItemService;
|
||||
import org.dspace.content.*;
|
||||
import org.dspace.core.Constants;
|
||||
import org.dspace.core.Context;
|
||||
import org.dspace.handle.factory.HandleServiceFactory;
|
||||
import org.dspace.handle.service.HandleService;
|
||||
import org.dspace.handle.HandleManager;
|
||||
|
||||
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 6.1
|
||||
* @since 5.1
|
||||
* @version 5.1-SNAPSHOT
|
||||
* @since 5.1-SNAPSHOT
|
||||
*/
|
||||
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;
|
||||
@ -54,32 +30,25 @@ public class FixJpgJpgThumbnails {
|
||||
context.turnOffAuthorisationSystem();
|
||||
|
||||
if (StringUtils.isBlank(parentHandle)) {
|
||||
process(context, itemService.findAll(context));
|
||||
process(context, Item.findAll(context));
|
||||
} else {
|
||||
DSpaceObject parent = handleService.resolveToObject(context, parentHandle);
|
||||
DSpaceObject parent = HandleManager.resolveToObject(context, parentHandle);
|
||||
if (parent != null) {
|
||||
switch (parent.getType()) {
|
||||
case Constants.SITE:
|
||||
process(context, itemService.findAll(context));
|
||||
context.commit();
|
||||
case Constants.COLLECTION:
|
||||
process(context, ((Collection) parent).getAllItems()); // getAllItems because we want to work on non-archived ones as well
|
||||
break;
|
||||
case Constants.COMMUNITY:
|
||||
List<Collection> collections = ((Community) parent).getCollections();
|
||||
Collection[] collections = ((Community) parent).getCollections();
|
||||
for (Collection collection : collections) {
|
||||
process(
|
||||
context,
|
||||
itemService.findAllByCollection(context, collection));
|
||||
process(context, collection.getAllItems()); // getAllItems because we want to work on non-archived ones as well
|
||||
}
|
||||
context.commit();
|
||||
break;
|
||||
case Constants.COLLECTION:
|
||||
process(
|
||||
context,
|
||||
itemService.findByCollection(context, (Collection) parent));
|
||||
context.commit();
|
||||
case Constants.SITE:
|
||||
process(context, Item.findAll(context));
|
||||
break;
|
||||
case Constants.ITEM:
|
||||
processItem(context, (Item) parent);
|
||||
processItem((Item) parent);
|
||||
context.commit();
|
||||
break;
|
||||
}
|
||||
@ -94,77 +63,39 @@ public class FixJpgJpgThumbnails {
|
||||
}
|
||||
}
|
||||
|
||||
private static void process(Context context, Iterator<Item> items)
|
||||
throws SQLException, IOException, AuthorizeException {
|
||||
private static void process(Context context, ItemIterator items) throws SQLException, IOException, AuthorizeException {
|
||||
while (items.hasNext()) {
|
||||
Item item = items.next();
|
||||
processItem(context, item);
|
||||
itemService.update(context, item);
|
||||
processItem(item);
|
||||
context.commit();
|
||||
item.decache();
|
||||
}
|
||||
}
|
||||
|
||||
private static void processItem(Context context, Item item)
|
||||
throws SQLException, AuthorizeException, IOException {
|
||||
// Some bitstreams like Infographics and Maps are large JPEGs and put in the ORIGINAL bundle
|
||||
// on purpose so we shouldn't
|
||||
// swap them.
|
||||
List<MetadataValue> itemTypes =
|
||||
itemService.getMetadataByMetadataString(item, "dcterms.type");
|
||||
for (MetadataValue itemType : itemTypes) {
|
||||
if (itemType.getValue().equals("Infographic") || itemType.getValue().equals("Map")) {
|
||||
System.out.println(
|
||||
item.getHandle() + ": item has an Infographic or Map, skipping.");
|
||||
return;
|
||||
}
|
||||
}
|
||||
|
||||
List<Bundle> thumbnailBundles = item.getBundles("THUMBNAIL");
|
||||
private static void processItem(Item item) throws SQLException, AuthorizeException, IOException {
|
||||
Bundle[] thumbnailBundles = item.getBundles("THUMBNAIL");
|
||||
for (Bundle thumbnailBundle : thumbnailBundles) {
|
||||
List<Bitstream> thumbnailBundleBitstreams = thumbnailBundle.getBitstreams();
|
||||
Bitstream[] thumbnailBundleBitstreams = thumbnailBundle.getBitstreams();
|
||||
for (Bitstream thumbnailBitstream : thumbnailBundleBitstreams) {
|
||||
String thumbnailName = thumbnailBitstream.getName();
|
||||
String thumbnailDescription = thumbnailBitstream.getDescription();
|
||||
|
||||
// There is no point continuing if the thumbnail's description is empty or null
|
||||
if (StringUtils.isEmpty(thumbnailDescription)) {
|
||||
continue;
|
||||
}
|
||||
|
||||
if (thumbnailName.toLowerCase().contains(".jpg.jpg")) {
|
||||
List<Bundle> originalBundles = item.getBundles("ORIGINAL");
|
||||
if (thumbnailName.contains(".jpg.jpg")) {
|
||||
Bundle[] originalBundles = item.getBundles("ORIGINAL");
|
||||
for (Bundle originalBundle : originalBundles) {
|
||||
List<Bitstream> originalBundleBitstreams = originalBundle.getBitstreams();
|
||||
Bitstream[] originalBundleBitstreams = originalBundle.getBitstreams();
|
||||
|
||||
for (Bitstream originalBitstream : originalBundleBitstreams) {
|
||||
for(Bitstream originalBitstream : originalBundleBitstreams) {
|
||||
String originalName = originalBitstream.getName();
|
||||
|
||||
long originalBitstreamBytes = originalBitstream.getSizeBytes();
|
||||
//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())) {
|
||||
System.out.println(item.getHandle() + ": replacing " + thumbnailName + " with " + originalName);
|
||||
|
||||
/*
|
||||
- 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 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(thumbnailDescription)
|
||||
|| "IM Thumbnail".equals(thumbnailDescription))
|
||||
&& originalBitstreamBytes < 100000) {
|
||||
System.out.println(
|
||||
item.getHandle()
|
||||
+ ": replacing "
|
||||
+ thumbnailName
|
||||
+ " with "
|
||||
+ originalName);
|
||||
|
||||
// add the original bitstream to the THUMBNAIL bundle
|
||||
bundleService.addBitstream(
|
||||
context, thumbnailBundle, originalBitstream);
|
||||
// remove the original bitstream from the ORIGINAL bundle
|
||||
//add the original bitstream to the THUMBNAIL bundle
|
||||
thumbnailBundle.addBitstream(originalBitstream);
|
||||
//remove the original bitstream from the ORIGINAL bundle
|
||||
originalBundle.removeBitstream(originalBitstream);
|
||||
// remove the JpgJpg bitstream from the THUMBNAIL bundle
|
||||
//remove the JpgJpg bitstream from the THUMBNAIL bundle
|
||||
thumbnailBundle.removeBitstream(thumbnailBitstream);
|
||||
}
|
||||
}
|
||||
|
||||
@ -1,280 +0,0 @@
|
||||
/*
|
||||
* Copyright (C) 2022 Alan Orth
|
||||
*
|
||||
* SPDX-License-Identifier: GPL-3.0-only
|
||||
*/
|
||||
|
||||
package io.github.ilri.cgspace.scripts;
|
||||
|
||||
import org.apache.commons.lang.StringUtils;
|
||||
import org.dspace.authorize.AuthorizeException;
|
||||
import org.dspace.content.Bitstream;
|
||||
import org.dspace.content.Bundle;
|
||||
import org.dspace.content.Collection;
|
||||
import org.dspace.content.Community;
|
||||
import org.dspace.content.DSpaceObject;
|
||||
import org.dspace.content.Item;
|
||||
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.SITE:
|
||||
process(context, itemService.findAll(context));
|
||||
context.commit();
|
||||
break;
|
||||
case Constants.COMMUNITY:
|
||||
List<Collection> collections = ((Community) parent).getCollections();
|
||||
for (Collection collection : collections) {
|
||||
process(
|
||||
context,
|
||||
itemService.findAllByCollection(context, collection));
|
||||
}
|
||||
context.commit();
|
||||
break;
|
||||
case Constants.COLLECTION:
|
||||
process(
|
||||
context,
|
||||
itemService.findByCollection(context, (Collection) parent));
|
||||
context.commit();
|
||||
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 {
|
||||
System.out.println("FixLowQualityThumbnails: processing item: " + item.getHandle());
|
||||
|
||||
// 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("> Action: remove old thumbnail from THUMBNAIL bundle");
|
||||
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("> Action: remove manually uploaded thumbnail from THUMBNAIL bundle");
|
||||
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("> Action: skip other thumbnail in THUMBNAIL bundle");
|
||||
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("> Action: remove thumbnail from ORIGINAL bundle");
|
||||
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("> Action: skip other bitstream in ORIGINAL bundle");
|
||||
System.out.println("> Name: »" + originalName + "«");
|
||||
System.out.println("> Description: »" + originalDescription + "«");
|
||||
System.out.print("\u001b[0m");
|
||||
}
|
||||
|
||||
// Print a blank line
|
||||
System.out.println();
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
@ -1,42 +0,0 @@
|
||||
# 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 7.6.1. 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>7.6.1.4-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-7.6.1.4-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
|
||||
```
|
||||
@ -16,15 +16,29 @@
|
||||
"name": "Congo, The Democratic Republic of the",
|
||||
"numeric": "180"
|
||||
},
|
||||
{
|
||||
"alpha_2": "IR",
|
||||
"alpha_3": "IRN",
|
||||
"name": "Iran, Islamic Republic of",
|
||||
"cgspace_name": "Iran",
|
||||
"numeric": "364",
|
||||
"official_name": "Islamic Republic of Iran"
|
||||
},
|
||||
{
|
||||
"alpha_2": "KP",
|
||||
"alpha_3": "PRK",
|
||||
"common_name": "North Korea",
|
||||
"name": "Korea, Democratic People's Republic of",
|
||||
"cgspace_name": "Korea, DPR",
|
||||
"numeric": "408",
|
||||
"official_name": "Democratic People's Republic of Korea"
|
||||
},
|
||||
{
|
||||
"alpha_2": "LA",
|
||||
"alpha_3": "LAO",
|
||||
"name": "Lao People's Democratic Republic",
|
||||
"cgspace_name": "Laos",
|
||||
"numeric": "418"
|
||||
},
|
||||
{
|
||||
"alpha_2": "FM",
|
||||
"alpha_3": "FSM",
|
||||
@ -39,6 +53,13 @@
|
||||
"name": "Russian Federation",
|
||||
"cgspace_name": "Russia",
|
||||
"numeric": "643"
|
||||
},
|
||||
{
|
||||
"alpha_2": "SY",
|
||||
"alpha_3": "SYR",
|
||||
"name": "Syrian Arab Republic",
|
||||
"cgspace_name": "Syria",
|
||||
"numeric": "760"
|
||||
}
|
||||
]
|
||||
}
|
||||
|
||||
File diff suppressed because it is too large
Load Diff
Loading…
Reference in New Issue
Block a user