BMDSoftware · Jul 16, 2015 · Jul 16, 2015 · Jul 16, 2015 · Nov 25, 2015 · Nov 25, 2015
Showing 580 changed files with 58,347 additions and 101,237 deletions.
diff --git a/.github/workflows/maven.yml b/.github/workflows/maven.yml
@@ -0,0 +1,36 @@
+# This workflow builds the full Java project using Maven.
+# The webapp is not included.
+name: Build Dicoogle with Maven
+
+on:
+  push:
+    branches: [ dev ]
+  pull_request:
+    branches: [ dev ]
+    paths:
+     - 'pom.xml'
+     - 'short-license.txt'
+     - 'dicoogle/**'
+     - 'sdk/**'
+     - '.github/workflows/maven.yml'
+     - '!dicoogle/src/main/resources/webapp/**'
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    strategy:
+      matrix:
+        java-version: ['8', '11']
+
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Java (JDK ${{ matrix.java-version }})
+      uses: actions/setup-java@v3
+      with:
+        distribution: 'zulu'
+        java-version: ${{ matrix.java-version }}
+        cache: 'maven'
+    - name: Build with Maven
+      run: mvn -B package license:check -Dskip.installnodenpm -Dskip.npm -Dskip.format --file pom.xml
diff --git a/.github/workflows/node.yml b/.github/workflows/node.yml
@@ -0,0 +1,40 @@
+# This workflow validates and builds the Dicoogle web application.
+name: Build Webapp with Node.js
+
+on:
+  push:
+    branches: [ dev ]
+  pull_request:
+    branches: [ dev ]
+    paths:
+     - 'dicoogle/src/main/resources/webapp/**'
+     - 'webcore/**'
+     - '.github/workflows/node.yml'
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    strategy:
+      matrix:
+        node-version: [16.x, lts/*, latest]
+        # See supported Node.js release schedule at https://nodejs.org/en/about/releases/
+        # Recommended versions to include:
+        # - minimum supported version
+        # - latest LTS
+        # - latest stable
+
+    steps:
+    - uses: actions/checkout@v3
+    - name: Use Node.js ${{ matrix.node-version }}
+      uses: actions/setup-node@v3
+      with:
+        node-version: ${{ matrix.node-version }}
+        cache: 'npm'
+        cache-dependency-path: '**/package-lock.json'
+    - working-directory: ./dicoogle/src/main/resources/webapp
+      run: npm ci
+    - name: Check & build webapp
+      working-directory: ./dicoogle/src/main/resources/webapp
+      run: npm run check && npm run build
diff --git a/.gitignore b/.gitignore
@@ -1,20 +1,37 @@
+/target
+/dicoogle/.classpath
+/dicoogle/.settings/*
+/sdk-ext/.classpath
+/sdk-ext/.settings/*
+/sdk/.classpath
+/sdk/.project
+/sdk/.settings/*
+/webcore/lib/
 node_modules/
-dist
+**/webapp/dist
 .tmp
 .sass-cache/
-app/bower_components
 
 #eclipse
 .project
 .settings/*
-dicoogle/.classpath
-dicoogle/.settings/*
-sdk-ext/.classpath
-sdk-ext/.settings/*
-sdk/.classpath
-sdk/.project
-sdk/.settings/*
-webcore/lib/
+# IDEA
 .idea
+
+# Visual Studio Code
 .vscode/
+
 *.iml
+
+
+#MacOS
+.DS_Store
+.AppleDouble
+.LSOverride
+._*
+
+.AppleDB
+.AppleDesktop
+Network Trash Folder
+Temporary Items
+.apdisk
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -0,0 +1,190 @@
+# CHANGELOG
+This document intends to keep track of the changes performed on the various releases of Dicoogle.
+
+## 3.4
+
+### 3.4.0 (2024-08-27)
+
+* New: Introduced bulk unindexing functionality for IndexerInterface. (#598)
+* Enhancement: Added a kill switch for dead plugin sets in the core. (#686) 
+* Enhancement: Improved logging around indexing tasks. (#691)
+* Enhancement: Added robustness to DIMGeneric against BodyPartThickness. (#694) 
+* Enhancement: Improved StorageInterface by adding a `get` method. (#660)
+* Enhancement: Undeprecated StorageInterface#handles in the SDK. (#695)
+
+## 3.3
+
+### 3.3.6 (2024-04-24)
+
+- Fix application of task cleaning hook in `RunningIndexTasks` (#687)
+
+### 3.3.5 (2024-02-28)
+
+- Change DICOM storage stop behavior to soft stop (#684)
+
+### 3.3.4 (2023-12-15)
+
+- New (webui): Pass Web UI Plugin settings to webapp and expose identifiers in study view entries (#680)
+- Chore: Update links to use scheme https (#678)
+- Chore: Webapp maintenance (#674)
+
+### 3.3.3 (2023-10-23)
+
+* New: Include submitted query and provider in "result-selection-ready" event (#673)
+* Enhancement: Remove advanced search UI (#672)
+* Chore: Update Maven plugins (#669)
+* Chore: Update Bcrypt dependency and password hash service (#670)
+
+### 3.3.2 (2023-09-25)
+
+- New: Provide full search results on result-batch plugin mount event (#666)
+   - **This is a Web UI plugin API change!** Upon a `result-selection-ready` event
+     (plugins for the `result-batch` slot only),
+     the additional event argument is now an object with
+     both the full list of results and the list of results selected by the user
+     (rather than just the latter):
+     ```jsonc
+     {
+        "selected": [ /* selected results */ ],
+        "search": [ /* all results */ ]
+     }
+     ```
+- Fix: Fix cast in SeriesNumber mostly affecting C-FIND and C-MOVE services (#662)
+- Enhancement: Improve indexer queue worker thread handling (#664)
+- Enhancement: Make Find SCP resilient to missing query-retrievel level (#665)
+- Chore: Bump word-wrap from 1.2.3 to 1.2.4 in `/webcore`` (#659)
+- Chore: [CI] Update setup-java action in maven.yml (#661)
+
+### 3.3.1  (2023-07-07)
+
+- Fix: QueryInterface to QueryDimInterface (#646)
+
+### 3.3.0  (2023-07-06)
+
+- New: extensions to the SOP classes and Transfer Syntaxes hardcoded lists (#516)
+- Enhancement: Transfer Options - improve web service and UI (#649)
+- Enhancement: Save transfer options to server settings (#650)
+- Chore: Update logging dependencies and add jul-to-slf4j (#643)
+- Enhancement: URI from default search servlet fields (#644)
+- Fix: URI can be dumped in meta table (#655)
+- Chore: Remove aclmanager (#640)
+- Chore: Remove dependency on commons-codec (#639)
+- Chore: Switch to new maven repo dicoogle-public (#647)
+- Chore: Update CI workflows (#645)
+
+## 3.2
+
+### 3.2.2  (2023-02-13)
+
+- Fix: [C-MOVE] Fix problem related with infinite loop if skip IS returns zero
+
+### 3.2.1 (2023-02-08)
+
+- Enhancement: DicomStorage - add guards on unexpected exceptions (#637)
+
+### 3.2.0 (2022-11-23)
+
+- New: Add opt-in `call-shutdown` setting to call plugin shutdown routines on Dicoogle shutdown (#606)
+- Enhancement: Replace DcmSend with custom DICOM sender (#604)
+- Enhancement: Fix and update OpenAPI specification (#591)
+- Enhancement: [webcore] Update example webplugins (#585)
+- Enhancement: [webapp] Added capability to export dump of metadata to CSV  (#593)
+- Enhancement: [webapp] Show URI on image meta-data dump  (#592)
+- Enhancement: [webapp] Improve aligments in the about page (#616)
+- Enhancement: Remove duplicate SOP classes in transfer options (#607)
+- [openapi] Fix user management endpoint API specification (#603)
+- Chore: Update npm dependencies (#608, #570, #612, #613, #614, #596)
+- Chore: Update README/remove not used files (#611, #615)
+
+
+## 3.1
+
+### 3.1.0 (2022-06-24)
+
+- Enhancement: Bring back depth and paging to searchDIM (#509)
+- Enhancement: Add Instance Number to search results (#584)
+- Enhancement: Add creation time to running tasks (#511)
+- Enhancement: Encode text files and server text responses in UTF-8 (#583)
+- Enhancement: Change DICOM logging and deprecate XML log (#577)
+- Enhancement: Update commons-collections4 to 4.4 (#561)
+- Fix: Set key in dicoogle-slot element (#587)
+- Chore: Improve CI Java Maven workflow (#588)
+
+## 3.0
+
+### 3.0.7 (2022-03-17)
+
+- Fix: [UI] Prevent default on export modal button click (#568)
+- Chore: Update webapp dependencies (#569)
+- Chore: Update contributors in README (#565)
+
+### 3.0.6 (2022-01-14)
+
+- Fix: categorization of plugins in management page (#554)
+- Enhancement: Adjust webapp readme for Dicoogle 3 (#548)
+- Chore: Update log4j to 2.17.1 (#556)
+- Chore: Drop console.log in webapp js bundle (#551)
+
+### 3.0.5 (2021-12-15)
+
+- Fix: ExportCSVToFILEServlet query expansion handling (#550)
+- Chore: Bump log4j-core to 2.16.0 (#546) 
+
+### 3.0.4 (2021-12-06)
+
+- Fix Queries using the platform for query plugins that implements QueryInterface (#541)
+- Fix: Check whether confs dir exists before creating (#538)
+- Enhancement: improve web UI manager asset fetching (#540)
+
+### 3.0.3 (2021-11-29)
+
+- Fix: Make WebUI plugins visible to admin (#497)
+- Fix: DICOM storage priority improvement (#468)
+- Fix: Added missing SOPClasses UIDs for VLWholeSlideMicroscopyImageStorage, BreastTomosynthesisImageStorage and XRayRadiationDoseSRStorage (#474)
+- Fix: Add missing StudyInstanceUID in DIMGeneric JSON output (#507)
+- Fix: Async DICOM Storage SCP indexing + independent task pool for queries (#503)
+- Fix: Add encrypt-users-file to server settings (#504)
+- Fix: Fix zip settings property and remove it from UI (#515)
+- Fix: Fix server error on /webui without user session (#517)
+- Fix: Consider all properties of move destination in web API (#526)
+- Fix: Add missing plugin info properties in /plugins (#529)
+- Fix: Replace service status signal implementation  (#521)
+- Fix: Save move destination properties as XML attributes (#525)
+- Fix: Check roles before loading plugins, warn about missing roles (#518)
+- Fix: Remove sdk-ext (#493)
+- Fix: Fix the image loader when the thumbnail is a larger image (#514)
+- Chore: Use HTTPS URLs to Maven repositories (#461)
+- Chore: Update important dependencies (dicoogle-client, devdeps) (#523)
+- Chore: Server code cleanup (#500)
+
+### 3.0.2 (2021-04-03)
+
+- Fix: exportToCSV modal on webapp (#450)
+- Fix: StackOverflowError and users settings folder issues (#451)
+- Enhancement: DICOM services - bring patches from 2.5.X releases to main stream (#453)
+
+### 3.0.1 (2021-02-08)
+
+* Fix: Webcore plugins was not able to load 
+* Fix: WebUI Plugins: emit events for result-batch slot plugins
+* Enhancement: [UI] small improvements in button UI for search result slot. (#447)
+
+### 3.0.0 (2020-12-31)
+
+* New: configuration format (config.xml now lives in confs/server.xml)
+* New: [SDK] expansion to better support DIM (DICOM Information Modal).
+* New: docker support
+* New: API documentation
+* New: [UI] supports list of loaded plugins
+* New: [UI] supports to search and index in multiple plugins with possibility to choose them.
+* Fix: When getting defaults, the number of admins was not incremented in the UsersStruct, voiding the deletion of admin users
+* Fix: problem with SOP Class Transfer Syntaxes to be loaded in DICOM C-STORE SCP.
+* Fix: [UI] logins/logout and user session handling
+* Enhancement: [SDK] better error handling
+* Enhancement: [SDK] Webcore update structure and dependency of dicoogle-client-js
+* Enhancement: [UI] new look and support for small screen devices
+* Enhancement: User credentials (hash and encryption improvements)
+* Enhancement: Change list of providers to multiselect
+* Enhancement: CFindServiceSCP performs log string manipulation only when required.
+* Enhancement: Update core libraries (server and UI) and use of webpack.
+* Enhancement: Removed deprecated code from oldest RMI GUI.
diff --git a/Dockerfile b/Dockerfile
@@ -0,0 +1,11 @@
+FROM openjdk:8
+
+WORKDIR /root
+
+RUN apt-get update && \
+    apt-get install -y software-properties-common build-essential git maven
+
+RUN git clone https://github.com/bioinformatics-ua/dicoogle
+RUN ( cd dicoogle && mvn install && ln -s /root/dicoogle/dicoogle/target/dicoogle.jar /root/ )
+
+CMD ["java","-jar","dicoogle.jar","-s"]