From 0838af6e794cc9c170efd5e56d5bfeff6d0e2733 Mon Sep 17 00:00:00 2001 From: Eduardo Pinho Date: Wed, 24 Jul 2024 17:01:17 +0100 Subject: [PATCH 01/10] Update project manifest and dependencies (sdk 3.4.1) - update project version to 3.1.0 (minor bump) - update dicoogle-sdk to 3.4.1 (latest SDK) - update build dependency maven-compiler-plugin to the latest version - update license-maven-plugin to v2.9 --- pom.xml | 12 +++++------- 1 file changed, 5 insertions(+), 7 deletions(-) diff --git a/pom.xml b/pom.xml index 45f3bae..ed82824 100644 --- a/pom.xml +++ b/pom.xml @@ -4,14 +4,14 @@ pt.ua.dicoogle.demo dicoogle-plugin-sample dicoogle-plugin-sample - 3.0.0 + 3.1.0 jar UTF-8 - 3.2.2 + 3.4.1 9.0.3.v20130506 @@ -38,7 +38,7 @@ org.apache.maven.plugins maven-compiler-plugin - 2.3.2 + 3.13.0 1.8 1.8 @@ -66,9 +66,9 @@ com.mycila license-maven-plugin - 2.4 + 2.9 -
./short-license.txt
+
short-license.txt
**/*.java @@ -140,7 +140,5 @@ jetty-webapp ${jetty.version} - - From 6811dde41cd69c9a37b5d9616333f78eb0bf04ad Mon Sep 17 00:00:00 2001 From: Eduardo Pinho Date: Wed, 24 Jul 2024 17:02:10 +0100 Subject: [PATCH 02/10] Update ghactions CI workflow - update actions/checkout to v4 - update actions/setup-java to v4 - use temurin for the JDK distro --- .github/workflows/maven.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/maven.yml b/.github/workflows/maven.yml index f087780..8d599df 100644 --- a/.github/workflows/maven.yml +++ b/.github/workflows/maven.yml @@ -19,11 +19,11 @@ jobs: java-version: ['8', '11'] steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - name: Set up Java (JDK ${{ matrix.java-version }}) - uses: actions/setup-java@v3 + uses: actions/setup-java@v4 with: - distribution: 'zulu' + distribution: 'temurin' java-version: ${{ matrix.java-version }} cache: 'maven' - name: Build with Maven From 01fe64f78ec93a38a3f6af0c7ed11b9da08e72e5 Mon Sep 17 00:00:00 2001 From: Eduardo Pinho Date: Wed, 24 Jul 2024 17:27:01 +0100 Subject: [PATCH 03/10] Fix URI creation logic at RSIQuery - URIs always use forward slashes regardless of platform OS --- .../dicoogle/plugin/demo/dicooglepluginsample/RSIQuery.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/main/java/pt/ieeta/dicoogle/plugin/demo/dicooglepluginsample/RSIQuery.java b/src/main/java/pt/ieeta/dicoogle/plugin/demo/dicooglepluginsample/RSIQuery.java index 5fb7522..da77cab 100644 --- a/src/main/java/pt/ieeta/dicoogle/plugin/demo/dicooglepluginsample/RSIQuery.java +++ b/src/main/java/pt/ieeta/dicoogle/plugin/demo/dicooglepluginsample/RSIQuery.java @@ -61,7 +61,7 @@ private SearchResult generateSearchResult() map.put("SeriesDate","20150120"); SearchResult r = new SearchResult( - URI.create("file:" + File.separatorChar + UUID.randomUUID().toString() ), 1, map); + URI.create("file://" + UUID.randomUUID().toString() ), 1, map); return r; } From a976c83bd97abfd2fd1af3d99365487c5dda1d18 Mon Sep 17 00:00:00 2001 From: Eduardo Pinho Date: Wed, 24 Jul 2024 17:27:41 +0100 Subject: [PATCH 04/10] Use maven-shade-plugin instead of maven-assembly-plugin - better practice --- pom.xml | 29 +++++++++++++++++++---------- 1 file changed, 19 insertions(+), 10 deletions(-) diff --git a/pom.xml b/pom.xml index ed82824..04f69aa 100644 --- a/pom.xml +++ b/pom.xml @@ -45,21 +45,30 @@ - maven-assembly-plugin - - - jar-with-dependencies - - - - + org.apache.maven.plugins + maven-shade-plugin + 3.6.0 - make-assembly package - single + shade + + + + *:* + + **/*.SF + **/*.DSA + **/*.RSA + **/module-info.class + **/module-info.java + + + + true + From f6b1a59b63f8d1027f6f64be263f9cce8ecb42da Mon Sep 17 00:00:00 2001 From: Eduardo Pinho Date: Wed, 24 Jul 2024 17:34:43 +0100 Subject: [PATCH 05/10] Update README - Update URLs - Ask user to have Java 8 or 11 installed - Suggest to use `mvn package` instead of `mvn install` - Update the resulting jar file name - Refer to Dicoogle learning pack - Suggest adding dicoogle-plugin-sample to the list of DIM providers - Tweak formatting a bit --- README.md | 53 ++++++++++++++++++++++++++++++++++++++--------------- 1 file changed, 38 insertions(+), 15 deletions(-) diff --git a/README.md b/README.md index 8bc77c1..a907005 100644 --- a/README.md +++ b/README.md @@ -9,8 +9,8 @@ Getting Started ### Installing and running Dicoogle -1. Go to http://www.dicoogle.com/downloads -2. Download version 2 (or later) of Dicoogle +1. Make sure that you have Java installed in your system. Versions 8 and 11 are known to work. +1. Go to https://www.dicoogle.com/downloads and get version 3 of Dicoogle 3. Extract your contents to its own directory (e.g. "~/dicoogle" or "C:\dicoogle", depending on the platform). 4. Run Dicoogle with: sh DicoogleClient.sh (OSX / Linux) or DicoogleClient.bat (Windows). 5. You should see your web browser opening the Dicoogle user interface. Is it running? You're ok! @@ -21,20 +21,26 @@ Maven is required in order to build the project. An IDE with Maven support such 1. Clone the git repository at https://github.com/bioinformatics-ua/dicoogle-plugin-sample.git -2. Go to the project's base directory in a command line and run `mvn install`. Alternatively, open - the Maven project of the plugin with your IDE, then force it to build your project. +2. Go to the project's base directory in a command line and run `mvn package`. + Alternatively, open the Maven project of the plugin with your IDE, then force it to build your project. -3. If the building task is successful, you will have a new jar with dependencies in the target - folder (target/dicoogle-plugin-sample-2.0-jar-with-dependencies.jar). +3. If the building task is successful, you will have a new shaded jar (with the necessary dependencies) + in the `target` folder (e.g. `target/dicoogle-plugin-sample-3.1.0.jar`) ### Developing your own plugin based on this sample -The first class to look into is RSIPluginSet. It is the main entry point for everything else. +The first class to look into is [`RSIPluginSet`][pluginset]. +It is the main entry point for everything else. Once modified to suit your needs, build the plugin again and re-deploy it to Dicoogle (see below). +Be sure to consult the [Dicoogle Learning Pack][learningpack] for more information. + +[pluginset]: src/main/java/pt/ieeta/dicoogle/plugin/demo/dicooglepluginsample/RSIPluginSet.java +[learningpack]: https://bioinformatics-ua.github.io/dicoogle-learning-pack/docs/developing-plugins/ + ### Using your plugin -1. Copy your plugin's package with dependencies (target/dicoogle-plugin-sample-2.0-jar-with-dependencies.jar) +1. Copy your plugin's built jar (`target/dicoogle-plugin-sample-3.1.0.jar`) to the "Plugins" folder inside the root folder of Dicoogle. 2. Run Dicoogle. The plugin will be automatically included. @@ -42,12 +48,12 @@ Once modified to suit your needs, build the plugin again and re-deploy it to Dic Available content ----------------- -- _RSIIndexer_ : a sample indexer, only logs the DIM contents of files -- _RSIStorage_ : a sample storage service, keeps files in memory buffers -- _RSIQuery_ : a sample query provider, returns random data on request -- _RSIJettyPlugin_ : a sample plugin for providing web services, holds `RSIWebService` -- _RSIWebService_ : a sample web service in the form of a servlet, serves a web page and a few other services -- _RSIRestPlugin_ : a sample Restlet server resource, provides dummy data +- `RSIIndexer` : a sample indexer, only logs the DIM contents of files +- `RSIStorage` : a sample storage service, keeps files in memory buffers +- `RSIQuery` : a sample query provider, returns random data on request +- `RSIJettyPlugin` : a sample plugin for providing web services, holds `RSIWebService` +- `RSIWebService` : a sample web service in the form of a servlet, serves a web page and a few other services +- `RSIRestPlugin` : a sample Restlet server resource, provides dummy data - Sample HTML5 content and consuming web service: helps you to build a web app Web service plugin sample and Web App: @@ -62,6 +68,23 @@ To test the webservice plugin, you may open your browser and navigate to these U You may also use the built-in Dicoogle services for testing other plugins: - GET `http://localhost:8080/search?query=test&provider=dicoogle-plugin-sample` to test the query provider + - Note: You will need to record `dicoogle-plugin-sample` + as a DIM provider first. In `confs/server.xml`, + add the query provider in `config/archive/dim-providers` + like this: + ```xml + + + + + + dicoogle-plugin-sample + + + ``` + Then restart Dicoogle. + Remember to remove the provider from the list after testing + if you do not want to keep it. - POST `http://localhost:8080/management/tasks/index?plugin=dicoogle-plugin-sample&uri=` to test the indexer Platforms @@ -73,5 +96,5 @@ Dicoogle has been tested in: - Linux - Mac OS X -For more information, please visit http://www.dicoogle.com +For more information, please visit https://www.dicoogle.com From 7caaa8b7b4a912a95a5f8790ee8ec6bb64bf6ccc Mon Sep 17 00:00:00 2001 From: Eduardo Pinho Date: Wed, 24 Jul 2024 17:39:52 +0100 Subject: [PATCH 06/10] Remove JsonWebService, extend RSIWebResource instead --- .../dicooglepluginsample/JsonWebService.java | 76 ------------------- .../dicooglepluginsample/RSIWebResource.java | 32 +++++++- 2 files changed, 30 insertions(+), 78 deletions(-) delete mode 100644 src/main/java/pt/ieeta/dicoogle/plugin/demo/dicooglepluginsample/JsonWebService.java diff --git a/src/main/java/pt/ieeta/dicoogle/plugin/demo/dicooglepluginsample/JsonWebService.java b/src/main/java/pt/ieeta/dicoogle/plugin/demo/dicooglepluginsample/JsonWebService.java deleted file mode 100644 index a201525..0000000 --- a/src/main/java/pt/ieeta/dicoogle/plugin/demo/dicooglepluginsample/JsonWebService.java +++ /dev/null @@ -1,76 +0,0 @@ -/** - * Copyright (C) 2014 Universidade de Aveiro, DETI/IEETA, Bioinformatics Group - http://bioinformatics.ua.pt/ - * - * This file is part of Dicoogle/dicoogle-plugin-sample. - * - * Dicoogle/dicoogle-plugin-sample 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. - * - * Dicoogle/dicoogle-plugin-sample 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 Dicoogle. If not, see . - */ - -package pt.ieeta.dicoogle.plugin.demo.dicooglepluginsample; - -import org.json.JSONException; -import org.restlet.data.MediaType; -import org.restlet.ext.json.JsonRepresentation; -import org.restlet.representation.Representation; -import org.restlet.representation.StringRepresentation; -import org.restlet.resource.Get; -import org.restlet.resource.Post; -import org.restlet.resource.ServerResource; - -/** - * - * @author Luís A. Bastião Silva - - */ -public class JsonWebService extends ServerResource { - - - @Get - public Representation testJson(){ - StringRepresentation sr = new StringRepresentation("{\"name\":\"dicoogle-plugin-sample\"}"); - - sr.setMediaType(MediaType.APPLICATION_JSON); - - return sr; - } - - - @Post("json") - public JsonRepresentation testJson(JsonRepresentation userJson){ - - org.json.JSONObject userObj = null; - try { - userObj = userJson.getJsonObject(); - System.out.println(userObj.getInt("id")); - System.out.println(userObj.getString("name")); - //return userObj.toString(); - } catch (JSONException e) { - e.printStackTrace(); - } - - - JsonRepresentation sr = new JsonRepresentation("{\"name\":\"rsi\"}"); - - sr.setMediaType(MediaType.APPLICATION_JSON); - - return sr; - } - - // You can handle all crud operations. Please, read the restlet documentation - - - - @Override - public String toString(){return "jsonDemo";} - -} diff --git a/src/main/java/pt/ieeta/dicoogle/plugin/demo/dicooglepluginsample/RSIWebResource.java b/src/main/java/pt/ieeta/dicoogle/plugin/demo/dicooglepluginsample/RSIWebResource.java index f12aa76..354528f 100644 --- a/src/main/java/pt/ieeta/dicoogle/plugin/demo/dicooglepluginsample/RSIWebResource.java +++ b/src/main/java/pt/ieeta/dicoogle/plugin/demo/dicooglepluginsample/RSIWebResource.java @@ -19,18 +19,25 @@ package pt.ieeta.dicoogle.plugin.demo.dicooglepluginsample; +import org.json.JSONException; import org.restlet.data.MediaType; +import org.restlet.data.Status; +import org.restlet.ext.json.JsonRepresentation; import org.restlet.representation.Representation; import org.restlet.representation.StringRepresentation; import org.restlet.resource.Get; +import org.restlet.resource.Post; import org.restlet.resource.ServerResource; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; /** Example of a Restlet-based server resource plugin. * - * @author Luís A. Bastião Silva - + * @author Luís A. Bastião Silva - */ public class RSIWebResource extends ServerResource { - + private static final Logger logger = LoggerFactory.getLogger(RSIWebResource.class); + @Get public Representation test(){ StringRepresentation sr = new StringRepresentation("{\"name\":\"dicoogle-plugin-sample\"}"); @@ -39,7 +46,28 @@ public Representation test(){ return sr; } + + @Post("json") + public JsonRepresentation testJson(JsonRepresentation userJson){ + + try { + org.json.JSONObject userObj = userJson.getJsonObject(); + logger.info("id = {} ; name = {}", userObj.getInt("id"), userObj.getString("name")); + + JsonRepresentation sr = new JsonRepresentation("{\"operation\":\"OK\"}"); + sr.setMediaType(MediaType.APPLICATION_JSON); + return sr; + } catch (JSONException e) { + logger.error("Could not retrieve JSON object", e); + setStatus(Status.CLIENT_ERROR_BAD_REQUEST); + + JsonRepresentation sr = new JsonRepresentation("{\"operation\":\"failed\"}"); + sr.setMediaType(MediaType.APPLICATION_JSON); + return sr; + } + } + // You can handle all crud operations. More information in the Restlet documentation. @Override From ff715dc4eef9f99fc7476e0ffcae2b35e5320842 Mon Sep 17 00:00:00 2001 From: Eduardo Pinho Date: Wed, 24 Jul 2024 17:58:52 +0100 Subject: [PATCH 07/10] Remove unused imports --- .../plugin/demo/dicooglepluginsample/RSIJettyPlugin.java | 1 - .../dicoogle/plugin/demo/dicooglepluginsample/RSIQuery.java | 1 - 2 files changed, 2 deletions(-) diff --git a/src/main/java/pt/ieeta/dicoogle/plugin/demo/dicooglepluginsample/RSIJettyPlugin.java b/src/main/java/pt/ieeta/dicoogle/plugin/demo/dicooglepluginsample/RSIJettyPlugin.java index 8985159..ae94bf4 100644 --- a/src/main/java/pt/ieeta/dicoogle/plugin/demo/dicooglepluginsample/RSIJettyPlugin.java +++ b/src/main/java/pt/ieeta/dicoogle/plugin/demo/dicooglepluginsample/RSIJettyPlugin.java @@ -19,7 +19,6 @@ package pt.ieeta.dicoogle.plugin.demo.dicooglepluginsample; import java.net.URL; -import javax.servlet.http.HttpServlet; import org.eclipse.jetty.server.handler.HandlerList; import org.eclipse.jetty.servlet.ServletContextHandler; import org.eclipse.jetty.servlet.ServletHolder; diff --git a/src/main/java/pt/ieeta/dicoogle/plugin/demo/dicooglepluginsample/RSIQuery.java b/src/main/java/pt/ieeta/dicoogle/plugin/demo/dicooglepluginsample/RSIQuery.java index da77cab..4f8c762 100644 --- a/src/main/java/pt/ieeta/dicoogle/plugin/demo/dicooglepluginsample/RSIQuery.java +++ b/src/main/java/pt/ieeta/dicoogle/plugin/demo/dicooglepluginsample/RSIQuery.java @@ -19,7 +19,6 @@ package pt.ieeta.dicoogle.plugin.demo.dicooglepluginsample; -import java.io.File; import java.net.URI; import java.util.ArrayList; import java.util.HashMap; From 198271f3b24ac2bf8cffcda682fb46916b6e7bc7 Mon Sep 17 00:00:00 2001 From: Eduardo Pinho Date: Wed, 24 Jul 2024 17:59:53 +0100 Subject: [PATCH 08/10] Fix reported scheme of RSIStorage - scheme should not include the "://" part --- .../dicoogle/plugin/demo/dicooglepluginsample/RSIStorage.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/main/java/pt/ieeta/dicoogle/plugin/demo/dicooglepluginsample/RSIStorage.java b/src/main/java/pt/ieeta/dicoogle/plugin/demo/dicooglepluginsample/RSIStorage.java index 54e4195..a1cd2b5 100644 --- a/src/main/java/pt/ieeta/dicoogle/plugin/demo/dicooglepluginsample/RSIStorage.java +++ b/src/main/java/pt/ieeta/dicoogle/plugin/demo/dicooglepluginsample/RSIStorage.java @@ -51,7 +51,7 @@ public class RSIStorage implements StorageInterface { @Override public String getScheme() { - return "mem://"; + return "mem"; } @Override From 8bb763226a65e45926a7479374ec0ff84dd98359 Mon Sep 17 00:00:00 2001 From: Eduardo Pinho Date: Wed, 24 Jul 2024 18:11:56 +0100 Subject: [PATCH 09/10] Refactor RSIStorage - do not use raw types - save byte arrays instead of dangling output streams --- .../demo/dicooglepluginsample/RSIStorage.java | 23 ++++++++----------- 1 file changed, 9 insertions(+), 14 deletions(-) diff --git a/src/main/java/pt/ieeta/dicoogle/plugin/demo/dicooglepluginsample/RSIStorage.java b/src/main/java/pt/ieeta/dicoogle/plugin/demo/dicooglepluginsample/RSIStorage.java index a1cd2b5..5cb7e47 100644 --- a/src/main/java/pt/ieeta/dicoogle/plugin/demo/dicooglepluginsample/RSIStorage.java +++ b/src/main/java/pt/ieeta/dicoogle/plugin/demo/dicooglepluginsample/RSIStorage.java @@ -28,8 +28,7 @@ import pt.ua.dicoogle.sdk.StorageInputStream; import pt.ua.dicoogle.sdk.StorageInterface; import pt.ua.dicoogle.sdk.settings.ConfigurationHolder; -import java.util.ArrayList; -import java.util.Collection; +import java.util.Collections; import java.util.HashMap; import java.util.Iterator; import java.util.Map; @@ -45,7 +44,7 @@ public class RSIStorage implements StorageInterface { private static final Logger logger = LoggerFactory.getLogger(RSIStorage.class); - private final Map mem = new HashMap<>(); + private final Map mem = new HashMap<>(); private boolean enabled = true; private ConfigurationHolder settings; @@ -67,7 +66,6 @@ public Iterable at(final URI location, Object... objects) { @Override public Iterator iterator() { - Collection c2 = new ArrayList<>(); StorageInputStream s = new StorageInputStream() { @Override @@ -77,18 +75,17 @@ public URI getURI() { @Override public InputStream getInputStream() throws IOException { - ByteArrayOutputStream bos = mem.get(location.toString()); - ByteArrayInputStream bin = new ByteArrayInputStream(bos.toByteArray()); + byte[] data = mem.get(location.toString()); + ByteArrayInputStream bin = new ByteArrayInputStream(data); return bin; } @Override public long getSize() throws IOException { - return mem.get(location.toString()).size(); + return mem.get(location.toString()).length; } }; - c2.add(s); - return c2.iterator(); + return Collections.singletonList(s).iterator(); } }; return c; @@ -97,16 +94,14 @@ public long getSize() throws IOException { @Override public URI store(DicomObject dicomObject, Object... objects) { ByteArrayOutputStream bos = new ByteArrayOutputStream(); - DicomOutputStream dos = new DicomOutputStream(bos); - try { + try (DicomOutputStream dos = new DicomOutputStream(bos)) { dos.writeDicomFile(dicomObject); } catch (IOException ex) { logger.warn("Failed to store object", ex); } - bos.toByteArray(); URI uri = URI.create("mem://" + UUID.randomUUID().toString()); - mem.put(uri.toString(), bos); - + mem.put(uri.toString(), bos.toByteArray()); + return uri; } From bd596cefc267f0b8ff4772d6734e0cde4ed36f20 Mon Sep 17 00:00:00 2001 From: Eduardo Pinho Date: Tue, 11 Mar 2025 15:01:00 +0000 Subject: [PATCH 10/10] Update webplugin - Instead of hello world, provide Dicoogle Health Check, the tutorial webplugin - use parcel to build the plugin --- pom.xml | 2 +- src/main/resources/webplugin-sample/.babelrc | 3 - .../resources/webplugin-sample/.gitignore | 3 +- src/main/resources/webplugin-sample/README.md | 8 +- .../webplugin-sample/build-package-json.js | 28 + .../resources/webplugin-sample/dist/module.js | 1 + .../webplugin-sample/dist/package.json | 13 + src/main/resources/webplugin-sample/module.js | 87 - .../webplugin-sample/package-lock.json | 3927 +++++++++++++++++ .../resources/webplugin-sample/package.json | 71 +- .../resources/webplugin-sample/src/index.js | 67 +- .../webplugin-sample/webpack.config.js | 20 - 12 files changed, 4087 insertions(+), 143 deletions(-) delete mode 100644 src/main/resources/webplugin-sample/.babelrc create mode 100644 src/main/resources/webplugin-sample/build-package-json.js create mode 100644 src/main/resources/webplugin-sample/dist/module.js create mode 100644 src/main/resources/webplugin-sample/dist/package.json delete mode 100644 src/main/resources/webplugin-sample/module.js create mode 100644 src/main/resources/webplugin-sample/package-lock.json delete mode 100644 src/main/resources/webplugin-sample/webpack.config.js diff --git a/pom.xml b/pom.xml index 04f69aa..9fdb8a0 100644 --- a/pom.xml +++ b/pom.xml @@ -24,7 +24,7 @@ src/main/resources/html5/ - src/main/resources/webplugin-sample + src/main/resources/webplugin-sample/dist WebPlugins/webplugin-sample false diff --git a/src/main/resources/webplugin-sample/.babelrc b/src/main/resources/webplugin-sample/.babelrc deleted file mode 100644 index c13c5f6..0000000 --- a/src/main/resources/webplugin-sample/.babelrc +++ /dev/null @@ -1,3 +0,0 @@ -{ - "presets": ["es2015"] -} diff --git a/src/main/resources/webplugin-sample/.gitignore b/src/main/resources/webplugin-sample/.gitignore index 3c3629e..26ade9b 100644 --- a/src/main/resources/webplugin-sample/.gitignore +++ b/src/main/resources/webplugin-sample/.gitignore @@ -1 +1,2 @@ -node_modules +.parcel-cache/ +node_modules/ diff --git a/src/main/resources/webplugin-sample/README.md b/src/main/resources/webplugin-sample/README.md index ec8135f..44c5c59 100644 --- a/src/main/resources/webplugin-sample/README.md +++ b/src/main/resources/webplugin-sample/README.md @@ -1,7 +1,9 @@ -# demo -> demo +# Dicoogle Health Check web UI plugin + +> Checks for issues in the Dicoogle archive. This is a web UI menu plugin for Dicoogle. +The development tutorial is available in the [Dicoogle Learning Pack](https://bioinformatics-ua.github.io/dicoogle-learning-pack/docs/webplugins/). ## Building @@ -11,4 +13,4 @@ npm install ## Deploying -Place `module.js` and `package.json` in a folder in the WebPlugins directory. +Place `dist/module.js` and `dist/package.json` in a folder in the `WebPlugins/` directory. diff --git a/src/main/resources/webplugin-sample/build-package-json.js b/src/main/resources/webplugin-sample/build-package-json.js new file mode 100644 index 0000000..48e6849 --- /dev/null +++ b/src/main/resources/webplugin-sample/build-package-json.js @@ -0,0 +1,28 @@ +// This build script updates the output package.json file. +// +// Although using the original package.json file works, +// it is better to provide a simple version to production, +// to reduce size and simplify the plugin. +const fs = require('fs'); +const packageJson = require('./package.json'); + +const { + name, + version, + private, + description, + license, + dicoogle, +} = packageJson; + +const out = { + name, + version, + private, + description, + license, + main: dicoogle['module-file'] || 'module.js', + dicoogle, +}; +fs.mkdirSync('dist', {recursive: true}); +fs.writeFileSync("dist/package.json", JSON.stringify(out, undefined, 2)); diff --git a/src/main/resources/webplugin-sample/dist/module.js b/src/main/resources/webplugin-sample/dist/module.js new file mode 100644 index 0000000..a36da81 --- /dev/null +++ b/src/main/resources/webplugin-sample/dist/module.js @@ -0,0 +1 @@ +var e=require("dicoogle-client");Object.defineProperty(module.exports,"__esModule",{value:!0,configurable:!0}),Object.defineProperty(module.exports,"default",{get:function(){return n},set:void 0,enumerable:!0,configurable:!0});const t=e();class n{constructor(){}render(e,n){let l=document.createElement("h3");l.innerText="Health Check",e.appendChild(l);let r=document.createElement("span");r.innerText="Checking Dicoogle health...",e.appendChild(r),t.getPlugins().then(({plugins:t,dead:n})=>{let l=[];if(0===t.filter(e=>"storage"===e.type).length&&l.push("No storage providers are installed"),0===t.filter(e=>"query"===e.type&&e.dim).length&&l.push("No DICOM data query providers are installed"),0===t.filter(e=>"index"===e.type&&e.dim).length&&l.push("No DICOM data indexers are installed"),n.length>0&&l.push("The following plugins are dead: "+n.map(e=>`${e.name} (${e.cause.message})`).join(", ")),0===l.length)r.innerText="✓ No issues were found!";else{r.innerText=`\u{26A0}\u{FE0F} There are ${l.length} ${1===l.length?"issue":"issues"} in this installation.`;let t=document.createElement("ul");for(let e of l){let n=document.createElement("li");n.innerText=e,t.appendChild(n)}e.appendChild(t)}})}} \ No newline at end of file diff --git a/src/main/resources/webplugin-sample/dist/package.json b/src/main/resources/webplugin-sample/dist/package.json new file mode 100644 index 0000000..5550989 --- /dev/null +++ b/src/main/resources/webplugin-sample/dist/package.json @@ -0,0 +1,13 @@ +{ + "name": "dicoogle-healthcheck", + "version": "1.0.0", + "private": true, + "description": "Example web UI plugin for Dicoogle", + "license": "MIT", + "main": "module.js", + "dicoogle": { + "slot-id": "menu", + "caption": "Health Check", + "module-file": "module.js" + } +} \ No newline at end of file diff --git a/src/main/resources/webplugin-sample/module.js b/src/main/resources/webplugin-sample/module.js deleted file mode 100644 index 09e1fd4..0000000 --- a/src/main/resources/webplugin-sample/module.js +++ /dev/null @@ -1,87 +0,0 @@ -module.exports = -/******/ (function(modules) { // webpackBootstrap -/******/ // The module cache -/******/ var installedModules = {}; - -/******/ // The require function -/******/ function __webpack_require__(moduleId) { - -/******/ // Check if module is in cache -/******/ if(installedModules[moduleId]) -/******/ return installedModules[moduleId].exports; - -/******/ // Create a new module (and put it into the cache) -/******/ var module = installedModules[moduleId] = { -/******/ exports: {}, -/******/ id: moduleId, -/******/ loaded: false -/******/ }; - -/******/ // Execute the module function -/******/ modules[moduleId].call(module.exports, module, module.exports, __webpack_require__); - -/******/ // Flag the module as loaded -/******/ module.loaded = true; - -/******/ // Return the exports of the module -/******/ return module.exports; -/******/ } - - -/******/ // expose the modules object (__webpack_modules__) -/******/ __webpack_require__.m = modules; - -/******/ // expose the module cache -/******/ __webpack_require__.c = installedModules; - -/******/ // __webpack_public_path__ -/******/ __webpack_require__.p = ""; - -/******/ // Load entry module and return exports -/******/ return __webpack_require__(0); -/******/ }) -/************************************************************************/ -/******/ ([ -/* 0 */ -/***/ function(module, exports) { - - 'use strict'; - - var _createClass = function () { function defineProperties(target, props) { for (var i = 0; i < props.length; i++) { var descriptor = props[i]; descriptor.enumerable = descriptor.enumerable || false; descriptor.configurable = true; if ("value" in descriptor) descriptor.writable = true; Object.defineProperty(target, descriptor.key, descriptor); } } return function (Constructor, protoProps, staticProps) { if (protoProps) defineProperties(Constructor.prototype, protoProps); if (staticProps) defineProperties(Constructor, staticProps); return Constructor; }; }(); - - Object.defineProperty(exports, "__esModule", { - value: true - }); - - function _classCallCheck(instance, Constructor) { if (!(instance instanceof Constructor)) { throw new TypeError("Cannot call a class as a function"); } } - - /* global Dicoogle */ - - var MyPlugin = function () { - function MyPlugin() { - _classCallCheck(this, MyPlugin); - } - // TODO initialize plugin here - - /** - * @param {DOMElement} parent - * @param {DOMElement} slot - */ - - _createClass(MyPlugin, [{ - key: 'render', - value: function render(parent, slot) { - // TODO mount a new web component here - var div = document.createElement('div'); - div.innerHTML = 'Hello, Dicoogle!'; - parent.appendChild(div); - } - }]); - - return MyPlugin; - }(); - - exports.default = MyPlugin; - -/***/ } -/******/ ]); \ No newline at end of file diff --git a/src/main/resources/webplugin-sample/package-lock.json b/src/main/resources/webplugin-sample/package-lock.json new file mode 100644 index 0000000..c9e08a6 --- /dev/null +++ b/src/main/resources/webplugin-sample/package-lock.json @@ -0,0 +1,3927 @@ +{ + "name": "dicoogle-healthcheck", + "version": "1.0.0", + "lockfileVersion": 3, + "requires": true, + "packages": { + "": { + "name": "dicoogle-healthcheck", + "version": "1.0.0", + "license": "MIT", + "dependencies": { + "dicoogle-client": "~5.2.0" + }, + "devDependencies": { + "parcel": "^2.13.3" + }, + "engines": { + 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"name": "demo", - "version": "0.1.0", - "description": "demo", - "files": [ - "module.js" + "name": "dicoogle-healthcheck", + "private": true, + "version": "1.0.0", + "description": "Example web UI plugin for Dicoogle", + "maintainers": [ + "Luís A. Bastião Silva ", + "Eduardo Pinho " ], - "scripts": { - "build": "webpack", - "build-debug": "webpack --devtool inline-source-map", - "prepublish": "npm run build" - }, - "author": "Luís A. Bastião Silva ", "license": "MIT", "repository": { "type": "git", - "url": "bastiao/demo" + "url": "bioinformatics-ua/dicoogle-plugin-sample" }, "keywords": [ "dicoogle", @@ -22,13 +18,54 @@ ], "dicoogle": { "slot-id": "menu", - "caption": "Webplugin-Sample", + "caption": "Health Check", "module-file": "module.js" }, + "engines": { + "node": ">=16", + "npm": ">=7" + }, + "source": "src/index.js", + "main": "dist/module.js", + "files": [ + "dist/module.js" + ], + "scripts": { + "build": "node build-package-json.js && parcel build --no-source-maps", + "build-debug": "node build-package-json.js && parcel build --no-optimize", + "build-watch": "node build-package-json.js && parcel watch --no-optimize", + "prepare": "npm run build" + }, + "targets": { + "main": { + "context": "browser", + "outputFormat": "commonjs", + "isLibrary": false, + "includeNodeModules": { + "@swc/helpers": true, + "react": false, + "react-dom": false, + "dicoogle-client": false, + "dicoogle-webcore": false, + "reflux": false, + "react-bootstrap": false, + "react-bootstrap-table": false, + "react-router": false, + "react-router-bootstrap": false + }, + "optimize": true, + "sourceMap": { + "inline": true + }, + "engines": { + "browsers": "> 1%, last 2 versions, not dead" + } + } + }, "devDependencies": { - "babel-core": "^6.4.0", - "babel-loader": "^6.2.1", - "babel-preset-es2015": "^6.3.13", - "webpack": "^1.12.11" + "parcel": "^2.13.3" + }, + "dependencies": { + "dicoogle-client": "~5.2.0" } } diff --git a/src/main/resources/webplugin-sample/src/index.js b/src/main/resources/webplugin-sample/src/index.js index b94937d..c8b3382 100644 --- a/src/main/resources/webplugin-sample/src/index.js +++ b/src/main/resources/webplugin-sample/src/index.js @@ -1,21 +1,66 @@ -/* global Dicoogle */ +const Dicoogle = require('dicoogle-client')(); export default class MyPlugin { - + constructor() { // TODO initialize plugin here } - + /** - * @param {DOMElement} parent - * @param {DOMElement} slot + * @param {HTMLDivElement} parent dedicated container div for this plugin + * @param {HTMLDivElement} slot the web UI plugin slot */ render(parent, slot) { - // TODO mount a new web component here - const div = document.createElement('div'); - div.innerHTML = 'Hello, Dicoogle!'; - parent.appendChild(div); - + // create header + const head = document.createElement('h3'); + head.innerText = 'Health Check'; + parent.appendChild(head); + + // create main info span + const baseInfo = document.createElement('span'); + baseInfo.innerText = 'Checking Dicoogle health...'; + parent.appendChild(baseInfo); + + // request for the full list of plugins + Dicoogle.getPlugins().then(({ plugins, dead }) => { + const problems = []; + + // check for no storage + if (plugins.filter(p => p.type === 'storage').length === 0) { + problems.push("No storage providers are installed"); + } + + // check for no DICOM query provider + if (plugins.filter(p => p.type === 'query' && p.dim).length === 0) { + problems.push("No DICOM data query providers are installed"); + } + + // check for no DICOM index provider + if (plugins.filter(p => p.type === 'index' && p.dim).length === 0) { + problems.push("No DICOM data indexers are installed"); + } + + if (dead.length > 0) { + problems.push("The following plugins are dead: " + dead + .map(p => `${p.name} (${p.cause.message})`).join(', ')) + } + + // update DOM with problems + if (problems.length === 0) { + baseInfo.innerText = "✓ No issues were found!"; + } else { + baseInfo.innerText = `⚠️ There are ${problems.length} ${problems.length === 1 ? "issue" : "issues"} in this installation.`; + + // create list of issues found + const ul = document.createElement('ul'); + for (const problem of problems) { + // one list item per problem + let problemItem = document.createElement('li'); + problemItem.innerText = problem; + ul.appendChild(problemItem); + } + parent.appendChild(ul); + } + }); } - } diff --git a/src/main/resources/webplugin-sample/webpack.config.js b/src/main/resources/webplugin-sample/webpack.config.js deleted file mode 100644 index 36e64d6..0000000 --- a/src/main/resources/webplugin-sample/webpack.config.js +++ /dev/null @@ -1,20 +0,0 @@ -module.exports = { - entry: './src/index.js', - output: { - filename: 'module.js', - libraryTarget: 'commonjs2' - }, - module: { - loaders: [ - { - test: /src\/.*\.js?$/, - exclude: /node_modules/, - loader: 'babel', - query: { - presets: ['es2015'] - } - } - ] - }, - externals: ['react', 'dicoogle-client', 'dicoogle-webcore'] -};