From 4db678b3113ef741b93e431d2043135121ad43ea Mon Sep 17 00:00:00 2001 From: Julien Louis Date: Fri, 15 Nov 2024 15:28:28 +0100 Subject: [PATCH 01/14] separate add subject button --- .../import/clinical-context/clinical-context.component.css | 6 +++++- .../import/clinical-context/clinical-context.component.html | 5 ++++- 2 files changed, 9 insertions(+), 2 deletions(-) diff --git a/shanoir-ng-front/src/app/import/clinical-context/clinical-context.component.css b/shanoir-ng-front/src/app/import/clinical-context/clinical-context.component.css index 58b0506ca6..c7e9ff0c5a 100644 --- a/shanoir-ng-front/src/app/import/clinical-context/clinical-context.component.css +++ b/shanoir-ng-front/src/app/import/clinical-context/clinical-context.component.css @@ -20,4 +20,8 @@ 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); } \ No newline at end of file +.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; } \ No newline at end of file diff --git a/shanoir-ng-front/src/app/import/clinical-context/clinical-context.component.html b/shanoir-ng-front/src/app/import/clinical-context/clinical-context.component.html index cb789fc42a..8a07b90256 100644 --- a/shanoir-ng-front/src/app/import/clinical-context/clinical-context.component.html +++ b/shanoir-ng-front/src/app/import/clinical-context/clinical-context.component.html @@ -148,9 +148,12 @@ [(ngModel)]="subject" (userChange)="onSelectSubject();" [viewRoute]="'/subject/details/' + this.subject?.id" [viewDisabled]="!subject" - (onNewClick)="openCreateSubject()" [newDisabled]="!study || !acquisitionEquipment" [optionArr]="subjects"> +
  • From 78b989b9c785260a662d7e556aea8b1a025432b6 Mon Sep 17 00:00:00 2001 From: Julien Louis Date: Mon, 18 Nov 2024 10:04:42 +0100 Subject: [PATCH 02/14] new exam button --- .../clinical-context.component.css | 6 +++++- .../clinical-context.component.html | 19 +++++++++++++------ 2 files changed, 18 insertions(+), 7 deletions(-) diff --git a/shanoir-ng-front/src/app/import/clinical-context/clinical-context.component.css b/shanoir-ng-front/src/app/import/clinical-context/clinical-context.component.css index c7e9ff0c5a..e66434fdd0 100644 --- a/shanoir-ng-front/src/app/import/clinical-context/clinical-context.component.css +++ b/shanoir-ng-front/src/app/import/clinical-context/clinical-context.component.css @@ -24,4 +24,8 @@ a { text-decoration: underline; } .new-subject { margin-left: 20px !important; } .new-subject:active, -.new-subject:enabled:hover { cursor: pointer; } \ No newline at end of file +.new-subject:enabled:hover { cursor: pointer; } +.secondary { font-size: 8px; margin-right: 7px; margin-left: 2px; } + +.subject-select { width: 185px; } +.examination-select { width: 154px; } \ No newline at end of file diff --git a/shanoir-ng-front/src/app/import/clinical-context/clinical-context.component.html b/shanoir-ng-front/src/app/import/clinical-context/clinical-context.component.html index 8a07b90256..a63c3c33f0 100644 --- a/shanoir-ng-front/src/app/import/clinical-context/clinical-context.component.html +++ b/shanoir-ng-front/src/app/import/clinical-context/clinical-context.component.html @@ -143,16 +143,17 @@
  • - -
    • @@ -212,10 +213,16 @@
  • - + [optionArr]="examinations" [pipe]="subjectExaminationLabelPipe"> +
    • From 0173c1c8f67256568b8874f5518e638468dd5117 Mon Sep 17 00:00:00 2001 From: Duckflip Date: Thu, 5 Dec 2024 10:16:59 +0100 Subject: [PATCH 03/14] #1874 : import job working properly with eeg (logged as jobs) --- .../shanoir/ng/importer/service/EegImporterService.java | 8 +++++++- .../org/shanoir/ng/importer/ImporterApiController.java | 2 ++ 2 files changed, 9 insertions(+), 1 deletion(-) diff --git a/shanoir-ng-datasets/src/main/java/org/shanoir/ng/importer/service/EegImporterService.java b/shanoir-ng-datasets/src/main/java/org/shanoir/ng/importer/service/EegImporterService.java index de03339894..10e43d057e 100644 --- a/shanoir-ng-datasets/src/main/java/org/shanoir/ng/importer/service/EegImporterService.java +++ b/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()) { diff --git a/shanoir-ng-import/src/main/java/org/shanoir/ng/importer/ImporterApiController.java b/shanoir-ng-import/src/main/java/org/shanoir/ng/importer/ImporterApiController.java index 19efab9b6f..6b32dbed85 100644 --- a/shanoir-ng-import/src/main/java/org/shanoir/ng/importer/ImporterApiController.java +++ b/shanoir-ng-import/src/main/java/org/shanoir/ng/importer/ImporterApiController.java @@ -610,6 +610,8 @@ public ResponseEntity 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(HttpStatusCode.valueOf(integg.intValue())); } catch (Exception e) { From c663135cb930caedf109855a01b5ea750d8608b2 Mon Sep 17 00:00:00 2001 From: Duckflip Date: Thu, 5 Dec 2024 11:09:58 +0100 Subject: [PATCH 04/14] 1874 : test update linked to eeg import correction --- .../java/org/shanoir/ng/importer/ImporterApiControllerTest.java | 1 + 1 file changed, 1 insertion(+) diff --git a/shanoir-ng-import/src/test/java/org/shanoir/ng/importer/ImporterApiControllerTest.java b/shanoir-ng-import/src/test/java/org/shanoir/ng/importer/ImporterApiControllerTest.java index 6ea656eb13..acf9df2832 100644 --- a/shanoir-ng-import/src/test/java/org/shanoir/ng/importer/ImporterApiControllerTest.java +++ b/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"); From 8315f2bd4be10997f496504d509a829e870d6d7c Mon Sep 17 00:00:00 2001 From: Duckflip Date: Mon, 9 Dec 2024 11:33:11 +0100 Subject: [PATCH 05/14] #2527 : Springboot 3.2.2 -> 3.4.0 --- shanoir-ng-back/pom.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/shanoir-ng-back/pom.xml b/shanoir-ng-back/pom.xml index 2966734662..bc5ae4fd23 100644 --- a/shanoir-ng-back/pom.xml +++ b/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 org.springframework.boot spring-boot-starter-parent - 3.2.2 + 3.4.0 From bb0d61e4df90c77f9cc5e52d17a94e64680121bd Mon Sep 17 00:00:00 2001 From: LaurentPV Date: Tue, 7 Jan 2025 15:18:28 +0100 Subject: [PATCH 06/14] minor adjustments and modifications of UI --- .../action/FindDicomActionListener.java | 15 +- .../uploader/dicom/DicomServerClient.java | 2 +- .../org/shanoir/uploader/gui/MainWindow.java | 173 +++++++----------- .../src/main/resources/messages_en.properties | 9 +- .../src/main/resources/messages_fr.properties | 17 +- 5 files changed, 92 insertions(+), 124 deletions(-) diff --git a/shanoir-uploader/src/main/java/org/shanoir/uploader/action/FindDicomActionListener.java b/shanoir-uploader/src/main/java/org/shanoir/uploader/action/FindDicomActionListener.java index d114e1fce3..83369e36ce 100644 --- a/shanoir-uploader/src/main/java/org/shanoir/uploader/action/FindDicomActionListener.java +++ b/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; diff --git a/shanoir-uploader/src/main/java/org/shanoir/uploader/dicom/DicomServerClient.java b/shanoir-uploader/src/main/java/org/shanoir/uploader/dicom/DicomServerClient.java index bd9df40636..412ae60880 100644 --- a/shanoir-uploader/src/main/java/org/shanoir/uploader/dicom/DicomServerClient.java +++ b/shanoir-uploader/src/main/java/org/shanoir/uploader/dicom/DicomServerClient.java @@ -213,7 +213,7 @@ private void readAndCopyDicomFilesToUploadFolder(String studyInstanceUID, List modalityCB = new JComboBox(modalityList); + modalityCB.setSelectedIndex(0); + GridBagConstraints gBC_modality = new GridBagConstraints(); + gBC_modality.anchor = GridBagConstraints.WEST; + gBC_modality.insets = new Insets(5, 5, 0, 0); + gBC_modality.gridx = 1; + gBC_modality.gridy = 7; + queryPanel.add(modalityCB, gBC_modality); + + modalityCB.addActionListener(new ActionListener() { + @Override + public void actionPerformed(ActionEvent e) { + // If None is selected we set back to null + if (modalityList[modalityList.length - 1].equals(modalityCB.getSelectedItem())) { + modality = null; + } else { + modality = (String) modalityCB.getSelectedItem(); + } + } + }); queryButton = new JButton(resourceBundle.getString("shanoir.uploader.queryButton"), searchIcon); GridBagConstraints gbc_queryButton = new GridBagConstraints(); @@ -703,10 +679,11 @@ public void actionPerformed(ActionEvent e) { .getResource("images/copyLastNameToBirthName.16x16.png")); birthNameCopyButton = new JButton(copyIcon); GridBagConstraints gBCBithNameCopyButton = new GridBagConstraints(); - gBCBithNameCopyButton.anchor = GridBagConstraints.EAST; - gBCBithNameCopyButton.insets = new Insets(10, 10, 10, 10); + gBCBithNameCopyButton.anchor = GridBagConstraints.WEST; + gBCBithNameCopyButton.insets = new Insets(10, 0, 10, 10); gBCBithNameCopyButton.gridx = 3; - gBCBithNameCopyButton.gridy = 2; + gBCBithNameCopyButton.gridy = 3; + birthNameCopyButton.setToolTipText(resourceBundle.getString("shanoir.uploader.copyLastNameToBirthName")); birthNameCopyButton.setEnabled(false); editPanel.add(birthNameCopyButton, gBCBithNameCopyButton); @@ -785,50 +762,42 @@ public void actionPerformed(ActionEvent e) { new RSDocumentListener(this)); /** - * Radio buttons for sex: F, M or O + * Radio buttons for sex: Female, Male or Other */ + GridBagConstraints sexGBconstraints = new GridBagConstraints(); + sexGBconstraints.insets = new Insets(10, 0, 10, 10); + JLabel sexLabel = new JLabel(resourceBundle.getString("shanoir.uploader.sexLabel")); sexLabel.setHorizontalAlignment(SwingConstants.RIGHT); - GridBagConstraints gBCSexLabel = new GridBagConstraints(); - gBCSexLabel.anchor = GridBagConstraints.EAST; - gBCSexLabel.insets = new Insets(10, 10, 10, 10); - gBCSexLabel.gridx = 0; - gBCSexLabel.gridy = 5; - editPanel.add(sexLabel, gBCSexLabel); + sexGBconstraints.anchor = GridBagConstraints.EAST; + sexGBconstraints.gridx = 0; + sexGBconstraints.gridy = 5; + editPanel.add(sexLabel, sexGBconstraints); + + JPanel sexRadioPanel = new JPanel(new FlowLayout(FlowLayout.LEFT, 10, 0)); sexRG = new ButtonGroup(); - fSexR = new JRadioButton("F"); + + fSexR = new JRadioButton(resourceBundle.getString("shanoir.uploader.sex.F")); fSexR.setEnabled(false); sexRG.add(fSexR); - editPanel.add(fSexR); - mSexR = new JRadioButton("M"); + sexRadioPanel.add(fSexR); + + mSexR = new JRadioButton(resourceBundle.getString("shanoir.uploader.sex.M")); mSexR.setEnabled(false); sexRG.add(mSexR); - editPanel.add(mSexR); - oSexR = new JRadioButton("O"); + sexRadioPanel.add(mSexR); + + oSexR = new JRadioButton(resourceBundle.getString("shanoir.uploader.sex.O")); oSexR.setEnabled(false); sexRG.add(oSexR); - editPanel.add(oSexR); - GridBagConstraints gBCFSexR = new GridBagConstraints(); - gBCFSexR.insets = new Insets(10, 10, 10, 10); - gBCFSexR.fill = GridBagConstraints.HORIZONTAL; - gBCFSexR.gridx = 1; - gBCFSexR.gridy = 5; - gBCFSexR.weightx = 1.0; - editPanel.add(fSexR, gBCFSexR); - GridBagConstraints gBCMSexR = new GridBagConstraints(); - gBCMSexR.insets = new Insets(10, 10, 10, 10); - gBCMSexR.fill = GridBagConstraints.HORIZONTAL; - gBCMSexR.gridx = 2; - gBCMSexR.gridy = 5; - gBCMSexR.weightx = 1.0; - editPanel.add(mSexR, gBCMSexR); - GridBagConstraints gBCOSexR = new GridBagConstraints(); - gBCOSexR.insets = new Insets(10, 10, 10, 10); - gBCOSexR.fill = GridBagConstraints.HORIZONTAL; - gBCOSexR.gridx = 3; - gBCOSexR.gridy = 5; - gBCOSexR.weightx = 1.0; - editPanel.add(oSexR, gBCOSexR); + sexRadioPanel.add(oSexR); + + sexGBconstraints.gridx = 1; + sexGBconstraints.gridy = 5; + sexGBconstraints.gridwidth = 3; + sexGBconstraints.anchor = GridBagConstraints.WEST; + sexGBconstraints.fill = GridBagConstraints.HORIZONTAL; + editPanel.add(sexRadioPanel, sexGBconstraints); /** * Last button for download or copy action: diff --git a/shanoir-uploader/src/main/resources/messages_en.properties b/shanoir-uploader/src/main/resources/messages_en.properties index 8ffaccd57d..f23715feaf 100644 --- a/shanoir-uploader/src/main/resources/messages_en.properties +++ b/shanoir-uploader/src/main/resources/messages_en.properties @@ -1,5 +1,6 @@ shanoir.uploader.BirthDateLabel=Birth date: shanoir.uploader.BirthNameLabel=Birth name: +shanoir.uploader.copyLastNameToBirthName=Copy last name as birth name shanoir.uploader.cancel=Cancel shanoir.uploader.configurationMenu.dicomServer.aetLabel=AET: shanoir.uploader.configurationMenu.dicomServer.checkFormEchoParameters.mandatoryFields.message=Fill in all mandatory fields: AET, Host Name and Port @@ -31,7 +32,7 @@ shanoir.uploader.configurationMenu.dicomServer.localPortLabel=Local Port: shanoir.uploader.configurationMenu.dicomServer.portLabel=Port: shanoir.uploader.configurationMenu.dicomServer.title=PACS (DICOM Server) Configuration shanoir.uploader.configurationMenu.dicomServer=PACS (DICOM Server) Configuration -shanoir.uploader.configurationMenu.dicomServer.cmoveLabel=Attention: please verify with your PACS admin, that c-move is enabled for this connection!!! +shanoir.uploader.configurationMenu.dicomServer.cmoveLabel=Attention: please verify with your PACS admin, that c-move is enabled for this connection !!! shanoir.uploader.configurationMenu.language.configure.english.message.part1= Congratulation! ShanoirUploader language is set to ENGLISH shanoir.uploader.configurationMenu.language.configure.english.message.part2= Please restart ShanoirUploader application shanoir.uploader.configurationMenu.language.configure.french.message.part1= Congratulation! ShanoirUploader language is set to FRENCH @@ -61,7 +62,7 @@ shanoir.uploader.configurationMenu.shanoirServer.userName=User Name: shanoir.uploader.configurationMenu.shanoirServer=Shanoir Server Configuration shanoir.uploader.configurationMenu=Configuration shanoir.uploader.connect=Connect -shanoir.uploader.connect.later=Connect later +shanoir.uploader.connect.later=Offline Mode shanoir.uploader.contact.admin=Please contact your administrator : imagerie@ofsep.fr shanoir.uploader.createSubjectButton=Create Subject shanoir.uploader.currentCopyOrDownloadSummary=Current copies or downloads: @@ -233,12 +234,16 @@ shanoir.uploader.proxy.ssl=Secure SSL shanoir.uploader.queryBoxMessage=Query PACS (DICOM Server) shanoir.uploader.queryButton=Query PACS shanoir.uploader.queryLevelLabel=Query level: +shanoir.uploader.queryLevelStudy=Study shanoir.uploader.select.error.message.study=Please select only one study at a time. shanoir.uploader.select.error.message.subject=Please select only one subject at a time. shanoir.uploader.select.error.title=Data error shanoir.uploader.sendBoxMessage=Patient Data Verification shanoir.uploader.separatorMrExaminationLabel=Examination info shanoir.uploader.sexLabel=Sex: +shanoir.uploader.sex.F=Female +shanoir.uploader.sex.M=Male +shanoir.uploader.sex.O=Other shanoir.uploader.startedUploadsSummary=Started uploads: shanoir.uploader.startup.remote.server.down=Shanoir server is not running shanoir.uploader.startup.test.connection.fail=Shanoir test connection ... FAIL diff --git a/shanoir-uploader/src/main/resources/messages_fr.properties b/shanoir-uploader/src/main/resources/messages_fr.properties index 948cb6bec9..ec7ce50f1f 100644 --- a/shanoir-uploader/src/main/resources/messages_fr.properties +++ b/shanoir-uploader/src/main/resources/messages_fr.properties @@ -1,5 +1,6 @@ shanoir.uploader.BirthDateLabel=Date de naissance : shanoir.uploader.BirthNameLabel=Nom de naissance : +shanoir.uploader.copyLastNameToBirthName=Copier le nom en tant que nom de naissance shanoir.uploader.cancel=Annuler shanoir.uploader.configurationMenu.dicomServer.aetLabel=AET : shanoir.uploader.configurationMenu.dicomServer.checkFormEchoParameters.mandatoryFields.message=Remplissez tous les champs obligatoires : AET, Nom du Host and Port @@ -31,7 +32,7 @@ shanoir.uploader.configurationMenu.dicomServer.localPortLabel=Port local: shanoir.uploader.configurationMenu.dicomServer.portLabel=Port: shanoir.uploader.configurationMenu.dicomServer.title=Configuration du serveur DICOM shanoir.uploader.configurationMenu.dicomServer=Configuration du serveur DICOM -shanoir.uploader.configurationMenu.dicomServer.cmoveLabel=Attention : \u00E0 bien verifier avec le administrator de PACS : c-move est activ\u00E9 pour la connexion!!! +shanoir.uploader.configurationMenu.dicomServer.cmoveLabel=Attention : verifiez avec l'administrateur du PACS que le DICOM C-MOVE est activ\u00E9 pour la connexion !!! shanoir.uploader.configurationMenu.language.configure.english.message.part1= F\u00E9licitation! La langue est r\u00E9gl\u00E9e sur ANGLAIS shanoir.uploader.configurationMenu.language.configure.english.message.part2= Red\u00E9marrez l'application ShanoirUploader shanoir.uploader.configurationMenu.language.configure.french.message.part1= F\u00E9licitation! La langue est r\u00E9gl\u00E9e sur FRANCAIS @@ -60,8 +61,8 @@ shanoir.uploader.configurationMenu.shanoirServer.title=Configuration du serveur shanoir.uploader.configurationMenu.shanoirServer.userName=Nom d'utilisateur: shanoir.uploader.configurationMenu.shanoirServer=Configuration du serveur Shanoir shanoir.uploader.configurationMenu=Configuration -shanoir.uploader.connect=Connection -shanoir.uploader.connect.later=Connection plus tard +shanoir.uploader.connect=Connexion +shanoir.uploader.connect.later=Mode hors ligne shanoir.uploader.contact.admin=Veuillez contacter votre administrateur : imagerie@ofsep.fr shanoir.uploader.createSubjectButton=Cre\u00E9r le sujet shanoir.uploader.currentCopyOrDownloadSummary=Copies ou t\u00e9l\u00e9chargements actuels : @@ -234,17 +235,21 @@ shanoir.uploader.proxy.save=Enregistrer les changements shanoir.uploader.proxy.ssl=SSL actif ? shanoir.uploader.queryBoxMessage=Requ\u00eater le PACS (serveur DICOM) shanoir.uploader.queryButton=Requ\u00eater le PACS -shanoir.uploader.queryLevelLabel=Niveau de requete : +shanoir.uploader.queryLevelLabel=Niveau de requ\u00eate : +shanoir.uploader.queryLevelStudy=Etude shanoir.uploader.select.error.message.study=Veuillez s\u00E9lectionner une seule \u00E9tude \u00E0 la fois. shanoir.uploader.select.error.message.subject=Veuillez s\u00E9lectionnez un seul sujet \u00E0 la fois. shanoir.uploader.select.error.title=Erreur shanoir.uploader.sendBoxMessage=Verification du patient shanoir.uploader.separatorMrExaminationLabel=Infos Examen shanoir.uploader.sexLabel=Sexe : +shanoir.uploader.sex.F=F\u00E9minin +shanoir.uploader.sex.M=Masculin +shanoir.uploader.sex.O=Autre shanoir.uploader.startedUploadsSummary=Imports commenc\u00E9s : shanoir.uploader.startup.remote.server.down=Le serveur Shanoir ne r\u00E9pond pas. -shanoir.uploader.startup.test.connection.fail=Shanoir test de connection ... ERREUR -shanoir.uploader.startup.test.connection.success=Shanoir test de connection ... OK +shanoir.uploader.startup.test.connection.fail=Shanoir test de connexion ... ERREUR +shanoir.uploader.startup.test.connection.success=Shanoir test de connexion ... OK shanoir.uploader.startup.test.login.fail=Shanoir test login/mot de passe ... ERREUR shanoir.uploader.startup.test.login.success=Shanoir test login/mot de passe ... OK shanoir.uploader.startup.test.proxy.fail=Test de proxy ... ERREUR From f36b3089e1586e64f963df132623f9c3d7cb5bdd Mon Sep 17 00:00:00 2001 From: LaurentPV Date: Tue, 7 Jan 2025 15:56:39 +0100 Subject: [PATCH 07/14] setting vertically query level Radio buttons --- .../src/main/java/org/shanoir/uploader/gui/MainWindow.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/shanoir-uploader/src/main/java/org/shanoir/uploader/gui/MainWindow.java b/shanoir-uploader/src/main/java/org/shanoir/uploader/gui/MainWindow.java index db1738b0b7..4c08a8c9aa 100644 --- a/shanoir-uploader/src/main/java/org/shanoir/uploader/gui/MainWindow.java +++ b/shanoir-uploader/src/main/java/org/shanoir/uploader/gui/MainWindow.java @@ -339,7 +339,7 @@ public void actionPerformed(ActionEvent arg0) { queryRadioPanel.add(sRB); GridBagConstraints gbc_radioPanel = new GridBagConstraints(); - gbc_radioPanel.insets = new Insets(2, 0, 2, 0); + gbc_radioPanel.insets = new Insets(2, 0, 0, 0); gbc_radioPanel.gridx = 1; gbc_radioPanel.gridy = 1; gbc_radioPanel.gridwidth = 2; From f595eac10a00a4c90f4988ea39812e1e8a9a6a49 Mon Sep 17 00:00:00 2001 From: Alexandre Pron Date: Mon, 13 Jan 2025 15:47:51 +0100 Subject: [PATCH 08/14] [ENH]: add CONTRIBUTORS.md file relying on wiki --- CONTRIBUTORS.md | 57 +++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 57 insertions(+) create mode 100644 CONTRIBUTORS.md diff --git a/CONTRIBUTORS.md b/CONTRIBUTORS.md new file mode 100644 index 0000000000..3b1fee7005 --- /dev/null +++ b/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 | | + From 04fbd98ea517bfccfb48e1cd09461c9040c47da9 Mon Sep 17 00:00:00 2001 From: Alexandre Pron Date: Tue, 14 Jan 2025 10:28:17 +0100 Subject: [PATCH 09/14] [ENH]: add FUNDINS.md (first draft) --- FUNDINGS.md | 8 ++++++++ 1 file changed, 8 insertions(+) create mode 100644 FUNDINGS.md diff --git a/FUNDINGS.md b/FUNDINGS.md new file mode 100644 index 0000000000..d0cd625868 --- /dev/null +++ b/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 | From 0f0b72d54e876f8c144d43f5c09d68bc1c6535ce Mon Sep 17 00:00:00 2001 From: Julien Louis Date: Tue, 14 Jan 2025 14:27:32 +0100 Subject: [PATCH 10/14] disabled ff dl button when loading info --- .../download-setup-alt/download-setup-alt.component.css | 4 +++- .../download-setup-alt/download-setup-alt.component.html | 6 +++--- .../src/app/shared/mass-download/mass-download.service.ts | 2 +- 3 files changed, 7 insertions(+), 5 deletions(-) diff --git a/shanoir-ng-front/src/app/shared/mass-download/download-setup-alt/download-setup-alt.component.css b/shanoir-ng-front/src/app/shared/mass-download/download-setup-alt/download-setup-alt.component.css index 2df0cac129..92f55caeec 100644 --- a/shanoir-ng-front/src/app/shared/mass-download/download-setup-alt/download-setup-alt.component.css +++ b/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; } \ No newline at end of file +.msg a { cursor: pointer; } + +.loading { margin-top: 15px; } \ No newline at end of file diff --git a/shanoir-ng-front/src/app/shared/mass-download/download-setup-alt/download-setup-alt.component.html b/shanoir-ng-front/src/app/shared/mass-download/download-setup-alt/download-setup-alt.component.html index 0782bcd0cc..0cda96dc97 100644 --- a/shanoir-ng-front/src/app/shared/mass-download/download-setup-alt/download-setup-alt.component.html +++ b/shanoir-ng-front/src/app/shared/mass-download/download-setup-alt/download-setup-alt.component.html @@ -21,10 +21,10 @@

    Download Datasets

    See the list of compatible browsers : https://developer.mozilla.org/en-US/docs/Web/API/Window/showDirectoryPicker#browser_compatibility -
    +
    Retrieving download informations...
    -
      +
      1. @@ -40,7 +40,7 @@

        Download Datasets

      - diff --git a/shanoir-ng-front/src/app/shared/mass-download/mass-download.service.ts b/shanoir-ng-front/src/app/shared/mass-download/mass-download.service.ts index 10a49b64d9..2734bda330 100644 --- a/shanoir-ng-front/src/app/shared/mass-download/mass-download.service.ts +++ b/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 ' From e2486ac05be111dc96167b4e17d6abce77300534 Mon Sep 17 00:00:00 2001 From: Anthony Baire Date: Wed, 15 Jan 2025 11:40:36 +0100 Subject: [PATCH 11/14] push buildkit cache images in the OCI format --- .github/workflows/docker.yml | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/.github/workflows/docker.yml b/.github/workflows/docker.yml index 4c73f39506..358d03cd22 100644 --- a/.github/workflows/docker.yml +++ b/.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 From a2bef3cf4612e3ce10ac817e96a7c4c33a5efdf1 Mon Sep 17 00:00:00 2001 From: michaelkain Date: Wed, 15 Jan 2025 16:01:15 +0100 Subject: [PATCH 12/14] Update CONTRIBUTORS.md --- CONTRIBUTORS.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CONTRIBUTORS.md b/CONTRIBUTORS.md index 3b1fee7005..f10babc9b4 100644 --- a/CONTRIBUTORS.md +++ b/CONTRIBUTORS.md @@ -1,6 +1,6 @@ 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. +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. From bf6ab2a3e728d649b657497f790cfc71cf55e19d Mon Sep 17 00:00:00 2001 From: LaurentPV Date: Thu, 16 Jan 2025 16:23:38 +0100 Subject: [PATCH 13/14] applying code review comment --- .../src/main/java/org/shanoir/uploader/gui/MainWindow.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/shanoir-uploader/src/main/java/org/shanoir/uploader/gui/MainWindow.java b/shanoir-uploader/src/main/java/org/shanoir/uploader/gui/MainWindow.java index 4c08a8c9aa..fa3ba9f35d 100644 --- a/shanoir-uploader/src/main/java/org/shanoir/uploader/gui/MainWindow.java +++ b/shanoir-uploader/src/main/java/org/shanoir/uploader/gui/MainWindow.java @@ -126,7 +126,7 @@ public class MainWindow extends JFrame { public UtilDateModel studyDateModel; public String birthDate = ""; public String studyDate = ""; - public String modality = ""; + public String modality; JScrollPane scrollPaneUpload; public JLabel startedDownloadsLB; From 12a187d8d7d8355a5058903b96c6b6aea7102139 Mon Sep 17 00:00:00 2001 From: Duckflip Date: Wed, 15 Jan 2025 09:34:37 +0100 Subject: [PATCH 14/14] 2547 : back to initial transaction state (not splitted transaction) --- .../ng/solr/service/SolrServiceImpl.java | 25 +++++-------------- 1 file changed, 6 insertions(+), 19 deletions(-) diff --git a/shanoir-ng-datasets/src/main/java/org/shanoir/ng/solr/service/SolrServiceImpl.java b/shanoir-ng-datasets/src/main/java/org/shanoir/ng/solr/service/SolrServiceImpl.java index 892fbe4b8b..e42d13be64 100644 --- a/shanoir-ng-datasets/src/main/java/org/shanoir/ng/solr/service/SolrServiceImpl.java +++ b/shanoir-ng-datasets/src/main/java/org/shanoir/ng/solr/service/SolrServiceImpl.java @@ -94,16 +94,6 @@ public class SolrServiceImpl implements SolrService { @Autowired private ShanoirEventService eventService; - //This attribute is a bean of the class itself. - //Its goal is to avoid transactional self-invocation issue, - //which appears when a transactional method calls another transactional method, - //and both are defined in the same class. - //When the issue occurs, Spring might have difficulties to manage the transactions, - //which is not the case anymore when methods are called with various beans of the class. - @Lazy - @Autowired - private SolrServiceImpl solrServiceImpl; - private static final Logger LOG = LoggerFactory.getLogger(SolrServiceImpl.class); public void addToIndex (final ShanoirSolrDocument document) throws SolrServerException, IOException { @@ -129,17 +119,17 @@ public void deleteAll() throws SolrServerException, IOException { @Override @Async - @Scheduled(cron = "0 0 6 * * *", zone="Europe/Paris") + @Transactional public void indexAll() { List documents = new ArrayList<>(); Map> tags = new HashMap<>(); ShanoirEvent event; try { - event = solrServiceImpl.beginIndexationProcess(); - solrServiceImpl.cleanOldIndex(event); - solrServiceImpl.fetchDatasToIndex(event, documents, tags); - solrServiceImpl.indexDatas(event, documents, tags); + event = beginIndexationProcess(); + cleanOldIndex(event); + fetchDatasToIndex(event, documents, tags); + indexDatas(event, documents, tags); } catch (SolrServerException | IOException ignored) { } } @@ -151,7 +141,7 @@ protected void indexDatas(ShanoirEvent event, List documents, M for (List partition : ListUtils.partition(documents, 100000)) { indexedData += partition.size(); event.setProgress((float) Math.floor(30F + ((indexedData / (float) totalData) * 70F)) / 100F); - solrServiceImpl.indexDataPartition(event, partition, tags, indexedData); + indexDataPartition(event, partition, tags, indexedData); } } catch (Exception e) { LOG.error("Error indexing datasets into Solr.", e); @@ -159,7 +149,6 @@ protected void indexDatas(ShanoirEvent event, List documents, M } } - @Transactional protected void indexDataPartition(ShanoirEvent event, List documents, Map> tags, int indexedSize) throws SolrServerException, IOException { indexDocumentsInSolr(documents, tags); if(Objects.equals(1f, event.getProgress())){ @@ -169,7 +158,6 @@ protected void indexDataPartition(ShanoirEvent event, List docu } } - @Transactional protected void fetchDatasToIndex(ShanoirEvent event, List documents, Map> tags) { try { documents.addAll(shanoirMetadataRepository.findAllAsSolrDoc()); @@ -183,7 +171,6 @@ protected void fetchDatasToIndex(ShanoirEvent event, List docum } } - @Transactional protected void cleanOldIndex(ShanoirEvent event) throws SolrServerException, IOException { try { deleteAll();