Merge branch 'develop' into 2547

.github/workflows/docker.yml

@@ -107,13 +107,17 @@ jobs:
           # - we push the cache (cache_to) after development builds of the
           #   main branch only
           # - we never use the cache on production builds
+          #
+          # The image is exported in the OCI format ('image-manifest=true')
+          # to avoid a "failed to solve: not found" error when pushing to the
+          # github container registry.
           enable_cache_from = not env['PRODUCTION'] and not env['NO_CACHE']
           enable_cache_to   = not env['PRODUCTION'] and (
             main_branch_sha == env['IMAGE_TAG'] == env['SHA'])
           print(f"{enable_cache_from = }\n{enable_cache_to = }\n")
 
           def cache_arg(enabled: bool, image: str, extra=""):
-            return [f"type=registry,ref={env['DOCKER_REPOSITORY']}/{image}:cache{extra}"
+            return [f"type=registry,image-manifest=true,ref={env['DOCKER_REPOSITORY']}/{image}:cache{extra}"
                    ] if enabled else []
   
           # extract the list of images to be built from the docker-compose config

CONTRIBUTORS.md

@@ -0,0 +1,57 @@
+In alphabetic order:
+
+Alexandre Abadie, Anthony Baire, Elise Bannier, Emmanuel Barbier, Christian Barillot, Marjolaine Bodin, Olivier Commowick, Isabelle Corouge, Yao Chi, Pierre-Henri Dauvergne, Jean-Côme Douteau, Michel Dojat, Quentin Duché, Alae Es-Saki, Inès Fakhfakh, Adrien Férial, Bernard Gibaud, Justine Guillaumont, Malo Gaubert, Wefa Hakem, Guewen Hubert, Michael Kain, Khalil Kessa, Romain Lahaxe, Julien Lamy, Julien Louis, Simon Loury, Camille Maumet, Arthur Masson, Youenn Merel, Olivier Montignon, Aneta Morawin, Farid Ouhmich, Alexandre Pron, Guillaume Renard, Mathieu Simon, Arnaud Touboulic, Laurent Vallet, Nicolas Wiest Daessle.
+
+Inclusion of authors of research articles dealing with Shanoir [[1], [2]](https://www.zotero.org/google-docs/?Uc9jGd), [Inria BIL ](https://team.inria.fr/bilv2/fr/software/) (shanoir, shanoir-ng, qtshanoir, shanoirtk, shanoir-uploader, shanoir-uploader-ofsep) as well as all contributors to the Github code repositories shanoir-ng, shanoir-downloader, shanoir-deploy on January 7 th 2025,  sorted by surname in alphabetical order.
+
+[1]	C. Barillot et al., “Shanoir: Applying the Software as a Service Distribution Model to Manage Brain Imaging Research Repositories,” Front. ICT, vol. 3, Dec. 2016, doi: 10.3389/fict.2016.00025.
+
+[2]	M. Kain et al., “Small Animal Shanoir (SAS) A Cloud-Based Solution for Managing Preclinical MR Brain Imaging Studies,” Front. Neuroinformatics, vol. 14, p. 20, May 2020, doi: 10.3389/fninf.2020.00020.
+
+Contributions detailed following [https://allcontributors.org/docs/en/emoji-key](https://allcontributors.org/docs/en/emoji-key)
+All possible contributions ordered:
+
+🔊 ♿️ 🐛 📝 💼 💻 🖋 🔣 📖 🎨 💡 📋 💵 🔍 🤔 🚇 🚧 🧑‍🏫 📦 🔌 📆 📣 💬 🔬 👀 🛡️ 🔧 🌍 ⚠️ ✅ 📢 📓 📹
+
+|Contributor           | Contribution(s)                                                                                      |
+|----------------------|----------------------------------------------------------------------------------------------------- |
+|Alexandre Abadie      |                                                                                                      |
+|Anthony Baire         | ♿️ 🐛 💻 📖 🤔 🚇 🚧 🧑‍🏫 📦 🔌 💬 👀 🛡️ 🔧 ⚠️ ✅                                                        | 
+|Elise Bannier         | ♿️ 🐛 🖋 🔣 📖  💵 🔍 🤔 📆 📣 🔧 ✅ 📓                                                           |   
+|Emmanuel Barbier      |                                                                                                      | 
+|Christian Barillot    |                                                                                                      |
+|Marjolaine Bodin      |                                                                                                      |          
+|Olivier Commowick     |                                                                                                      |         
+|Isabelle Corouge      |                                                                                                      |          
+|Yao Chi               |                                                                                                      |     
+|Pierre-Henri Dauvergne| ♿️ 🐛 💻  📖 📋  🚧 🧑‍🏫  🔌  💬  👀 ⚠️ ✅  📓                                                     |
+|Jean Côme Douteau     | ♿️ 🐛 📝 💻 🖋 📖 📋 🤔 🚇 🚧 🧑‍🏫 📦 🔌 📣 💬  👀 🛡️ 🔧 ⚠️ ✅ 📢 📓                              |
+|Michel Dojat          |                                                                                                      |
+|Quentin Duché         | 🐛 💻 📖 💡 🤔 🧑‍🏫 👀 🔧 📢 📓                                                                       |
+|Alae Es-Saki          |                                                                                                      | 
+|Inès Fakhfakh         |                                                                                                      | 
+|Adrien Férial         |                                                                                                      | 
+|Bernard Gibaud        |                                                                                                      |            
+|Justine Guillaumont   |                                                                                                      | 
+|Malo Gaubert          | 🐛 💻 📖 💡 🤔 🧑‍🏫 👀 🔧 📢 📓                                                                       |              
+|Wefa Hakem            |                                                                                                      |                 
+|Guewen Hubert         | ♿️ 🐛 💻  📖  📋  🚧 🧑‍🏫  🔌  💬 👀 ⚠️ ✅  📓                                                        | 
+|Michael Kain          | ♿️ 🐛 📝 💻 🖋 🔣 📖 🎨 💡 📋 🔍 🤔 🚇 🚧 🧑‍🏫 📦 🔌 📆 📣 💬 🔬 👀 🛡️ 🔧 ⚠️ ✅ 📢 📓                |
+|Khalil Kessa          |                                                                                                      | 
+|Romain Lahaxe         |                                                                                                      | 
+|Julien Lamy           |                                                                                                      | 
+|Julien Louis          | ♿️ 🐛 💻 🖋 📖 🎨 💡 📋 🤔 🚇 🚧 🧑‍🏫 📦  💬 👀 🛡️ 🔧 ⚠️ ✅ 📢 📓                                     |
+|Simon Loury           |                                                                                                      | 
+|Camille Maumet        | ♿️ 🐛  🖋 🔣 📖 📋 🤔 🔌 📆 📣 💬 👀 🛡️ 🔧 📢 📓 |
+|Arthur Masson         |                                                                                                      |
+|Youenn Merel          | ♿️ 🐛 💻 🖋 📖 💡 📋 🤔 🚇 🚧 🧑‍🏫 📦 🔌  💬 👀 🛡️ 🔧 ⚠️ ✅ 📢 📓 📹 |
+|Olivier Montignon     |                                                                                                      | 
+|Aneta Morawin         |                                                                                                      | 
+|Farid Ouhmich         |                                                                                                      | 
+|Alexandre Pron        | ♿️ 🐛 💻  📖  🔌 ⚠️ ✅  📓 |
+|Guillaume Renard      |                                                                                                      | 
+|Mathieu Simon         |                                                                                                      | 
+|Arnaud Touboulic      |                                                                                                      | 
+|Laurent Vallet        |  ♿️ 🐛 💻 🖋 📖 💡 📋 🤔 🚧 🧑‍🏫 📦 🔌 💬 👀 🔧 ⚠️ 📓|
+|Nicolas Wiest Daessle |                                                                                                      | 
+

FUNDINGS.md

@@ -0,0 +1,8 @@
+# Fundings
+
+This page lists the funding that has contributed to the development of Shanoir and its software ecosystem.
+| Funding                                               |
+|: ----------------------------------------------------:|         
+| _Technological development program_ of Inria          |
+| Brittany region council                               |
+| _Investments for the Future program_: ANR-11-INBS-006 | 

shanoir-ng-back/pom.xml

@@ -21,7 +21,7 @@ along with this program. If not, see https://www.gnu.org/licenses/gpl-3.0.html
 	<parent>
 		<groupId>org.springframework.boot</groupId>
 		<artifactId>spring-boot-starter-parent</artifactId>
-		<version>3.2.2</version>
+		<version>3.4.0</version>
 		<relativePath/>
 	</parent>
 

shanoir-ng-datasets/src/main/java/org/shanoir/ng/importer/service/EegImporterService.java

@@ -33,6 +33,7 @@
 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.List;
+import java.util.Objects;
 
 @Service
 public class EegImporterService {
@@ -67,7 +68,12 @@ public class EegImporterService {
     public void createEegDataset(final EegImportJob importJob) throws IOException {
 
         Long userId = KeycloakUtil.getTokenUserId();
-        ShanoirEvent event = new ShanoirEvent(ShanoirEventType.IMPORT_DATASET_EVENT, importJob.getExaminationId().toString(), userId, "Starting import...", ShanoirEvent.IN_PROGRESS, 0f, importJob.getStudyId());
+        ShanoirEvent event;
+        if(Objects.isNull(importJob.getShanoirEvent())){
+            event = new ShanoirEvent(ShanoirEventType.IMPORT_DATASET_EVENT, importJob.getExaminationId().toString(), userId, "Starting import...", ShanoirEvent.IN_PROGRESS, 0f, importJob.getStudyId());
+        } else {
+            event = importJob.getShanoirEvent();
+        }
         eventService.publishEvent(event);
 
         if (importJob == null || importJob.getDatasets() == null || importJob.getDatasets().isEmpty()) {

shanoir-ng-front/src/app/import/clinical-context/clinical-context.component.css

@@ -20,4 +20,12 @@ a { text-decoration: underline; }
 .ct-warn i { color: orangered; }
 
 .global-loading { color: var(--color-b); }
-.global-loading i { font-size: 30px; color: var(--color-b-light2); }
+.global-loading i { font-size: 30px; color: var(--color-b-light2); }
+
+.new-subject { margin-left: 20px !important; }
+.new-subject:active,
+.new-subject:enabled:hover { cursor: pointer; }
+.secondary { font-size: 8px; margin-right: 7px; margin-left: 2px; }
+
+.subject-select { width: 185px; }
+.examination-select { width: 154px; }

shanoir-ng-front/src/app/import/clinical-context/clinical-context.component.html

@@ -143,14 +143,18 @@
         <li class="required">
             <label class="required-label">Select a subject</label>
             <span class="right-col">
-                <select-box
+                <select-box class="subject-select"
                         [disabled]="loading || !study || !acquisitionEquipment"
                         [(ngModel)]="subject"
                         (userChange)="onSelectSubject();"
-                        [viewRoute]="'/subject/details/' + subject?.id" [viewDisabled]="!subject"
-                        (onNewClick)="openCreateSubject()" [newDisabled]="!study || !acquisitionEquipment"
+                        [viewRoute]="'/subject/details/' + this.subject?.id" [viewDisabled]="!subject"
                         [optionArr]="subjects">
                 </select-box>
+                <button class="new-subject" (click)="openCreateSubject()" [disabled]="!study || !acquisitionEquipment">
+                    <i class="fa-solid fa-user"></i>
+                    <i class="fa-solid fa-plus secondary"></i>
+                    New subject
+                </button>
             </span>
         </li>
         <li *ngIf="editSubjectStudy" class="required">
@@ -209,10 +213,16 @@
         <li>
             <label class="required-label">Select an examination</label>
             <span class="right-col">
-                <select-box [disabled]="!study || !subject || loading" [(ngModel)]="examination" (userChange)="onSelectExam()"
-                        [viewRoute]="'/examination/details/' + examination?.id" [viewDisabled]="!examination"
-                        (onNewClick)="openCreateExam()" [newDisabled]="!study || !subject" [optionArr]="examinations" [pipe]="subjectExaminationLabelPipe">
+                <select-box class="examination-select" 
+                        [disabled]="!study || !subject || loading" [(ngModel)]="examination" (userChange)="onSelectExam()"
+                        [viewRoute]="'/examination/details/' + this.examination?.id" [viewDisabled]="!examination"
+                        [optionArr]="examinations" [pipe]="subjectExaminationLabelPipe">
                 </select-box>
+                <button class="new-subject" (click)="openCreateExam()" [disabled]="!study || !subject">
+                    <i class="fa-solid fa-stethoscope"></i>
+                    <i class="fa-solid fa-plus secondary"></i>
+                    New examination
+                </button>
             </span>
         </li>
     </ol>

shanoir-ng-front/src/app/shared/mass-download/download-setup-alt/download-setup-alt.component.css

@@ -9,4 +9,6 @@ input[type="number"] { width: 52px; }
 
 .msg { max-width: 600px; color: blue; line-height: 20px; text-align: left; background-color: lightsteelblue; padding: 10px 20px; border-radius: 2px; }
 .msg i { font-size: 20px; color: blue; opacity: 0.5; }
-.msg a { cursor: pointer; }
+.msg a { cursor: pointer; }
+
+.loading { margin-top: 15px; }

shanoir-ng-front/src/app/shared/mass-download/download-setup-alt/download-setup-alt.component.html

@@ -21,10 +21,10 @@ <h2 class="header">Download Datasets</h2>
             See the list of compatible browsers :
             <a href="https://developer.mozilla.org/en-US/docs/Web/API/Window/showDirectoryPicker#browser_compatibility" target="_blank">https://developer.mozilla.org/en-US/docs/Web/API/Window/showDirectoryPicker#browser_compatibility</a>
         </div>
-        <div *ngIf="loading">
+        <div class="loading" *ngIf="loading">
             <i *ngIf="loading" class="fas fa-cog fa-spin"></i> Retrieving download informations...
         </div>
-        <fieldset class="body" disabled="loading">            <ol>
+        <fieldset class="body" [disabled]="loading">            <ol>
                 <li *ngIf="hasDicom">
                     <label>Dataset files format</label>
                     <span class="right-col">
@@ -40,7 +40,7 @@ <h2 class="header">Download Datasets</h2>
             </ol>
         </fieldset>
         <div class="footer">
-            <button type="button" type="button" (click)="downloadNow()" class="alt left-icon" [disabled]="form.dirty && !form.valid">
+            <button type="button" type="button" (click)="downloadNow()" class="alt left-icon" [disabled]="loading || (form.dirty && !form.valid)">
                 <i class="fas fa-download"></i>Download zip
             </button>
             <button type="button" (click)="cancel()">Cancel</button>

shanoir-ng-front/src/app/shared/mass-download/mass-download.service.ts

@@ -117,7 +117,7 @@ export class MassDownloadService {
         }).catch(error => {
             if (error == this.BROWSER_COMPAT_ERROR_MSG) {
                     return this.openAltModal(inputIds).then(ret => {
-                        if (ret != 'cancel') {
+                        if (ret != 'cancel' && ret.datasets) {
                             return this._downloadAlt(ret.datasets.map(ds => ds.id), ret.format, ret.converter, downloadState).catch(error => {
                                 if (ret.datasets.length > this.datasetService.MAX_DATASETS_IN_ZIP_DL) {
                                     this.dialogService.error('Too many datasets', 'You are trying to download '

shanoir-ng-import/src/main/java/org/shanoir/ng/importer/ImporterApiController.java

@@ -610,6 +610,8 @@ public ResponseEntity<Void> startImportEEGJob(
 		// Comment: Anonymisation is not necessary for pure brainvision EEGs data
 		try {
 			importJob.setUsername(KeycloakUtil.getTokenUserName());
+			ShanoirEvent event = new ShanoirEvent(ShanoirEventType.IMPORT_DATASET_EVENT, importJob.getExaminationId().toString(), KeycloakUtil.getTokenUserId(), "Starting import...", ShanoirEvent.IN_PROGRESS, 0f, importJob.getStudyId());
+			importJob.setShanoirEvent(event);
 			Integer integg = (Integer) rabbitTemplate.convertSendAndReceive(RabbitMQConfiguration.IMPORT_EEG_QUEUE,  objectMapper.writeValueAsString(importJob));
 			return new ResponseEntity<Void>(HttpStatusCode.valueOf(integg.intValue()));			
 		} catch (Exception e) {

shanoir-ng-import/src/test/java/org/shanoir/ng/importer/ImporterApiControllerTest.java

@@ -137,6 +137,7 @@ public void testStartImportEEGJob() throws Exception {
 
 		EegImportJob importJob = new EegImportJob();
 		EegDataset dataset = new EegDataset();
+		importJob.setExaminationId(1L);
 		importJob.setDatasets(Collections.singletonList(dataset));
 		dataset.setName("Ceci est un nom bien particulier");
 

shanoir-uploader/src/main/java/org/shanoir/uploader/action/FindDicomActionListener.java

@@ -78,6 +78,7 @@ public void actionPerformed(ActionEvent event) {
 		mainWindow.birthDateTF.setText("");
 		mainWindow.mSexR.setSelected(true);
 		mainWindow.fSexR.setSelected(false);
+		mainWindow.oSexR.setSelected(false);
 
 		Media media = new Media();
 		// when the open file from CD/DVD menu is clicked
@@ -165,19 +166,7 @@ else if (!firstName1.equals(""))
 							+ firstName1.toUpperCase();
 				else
 					patientNameFinal = lastName.toUpperCase();
-
-					String modality = null;
-					if (!mainWindow.noRB.isSelected()) {
-						if (mainWindow.mrRB.isSelected()) {
-							modality = "MR";
-						} else if (mainWindow.ctRB.isSelected()) {
-							modality = "CT";
-						} else if (mainWindow.ptRB.isSelected()) {
-							modality = "PT";
-						} else if (mainWindow.nmRB.isSelected()) {
-							modality = "NM";
-						}
-					}
+					String modality = mainWindow.modality;
 					boolean studyRootQuery = false;
 					if (mainWindow.sRB.isSelected()) {
 						studyRootQuery = true;

shanoir-uploader/src/main/java/org/shanoir/uploader/dicom/DicomServerClient.java

@@ -232,7 +232,7 @@ private void readAndCopyDicomFilesToUploadFolder(String studyInstanceUID, List<S
 			} else {
 				downloadOrCopyReport.append("Error: Download: serie "
 					+ (serie.getSeriesNumber() != null ? "(No. " + serie.getSeriesNumber() + ") " : "")
-				 	+ serie.getSeriesDescription() + " downloaded with not existing serie folder.\n");
+				 	+ serie.getSeriesDescription() + " downloaded without an existing serie folder.\n");
 				logger.error(uploadFolder.getName() + ":\n\n Download of " + fileNamesForSerie.size()
 						+ " DICOM files for serie " + seriesInstanceUID + ": " + serie.getSeriesDescription()
 						+ " has failed.\n\n");