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release notes
michaelkain edited this page Jan 15, 2025
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183 revisions
(put latest release always on top of the page)
- Update to Angular 19, from 17 (technical roadmap to keep frameworks up-to-date)
- Spring Boot 3.4.0, from 3.2.2 (technical roadmap to keep frameworks up-to-date)
- Search (Solr) sorting index (== DICOM.seriesNumber) added to search table/filter
- Performance optimization on subject list loading (see Ican 3.000 subject list)
- FUNDINGS.md and CONTRIBUTORS.md added
- New tree view (GUI): refresh tree button added (if new data imported in between)
- Search (Solr) indexation: now in chunks of 100.000 documents and async (avoid bottlenecks)
- REST-API extension: in/output download from a list of processingIds (RHU PRIMUS)
- Fix for import mail (sent by Shanoir): order by seriesNumber now
- Fix for frameOfReferenceUID in pseudonymization module
- Fix for image preview with Papaya, opening dataset after dataset
- Feature: solr search detects keywords and switches automatically to expert mode
- Shorten acquisition names in tree (acquisitions with many datasets)
- Fix manual import of processed datasets and tree display
- Feature: delete subject: display list of linked studies and attention on consequences
- Feature: delete exam as async task in jobs and included fixes
- Ops: bootstrap.sh adapted for docker-compose-dev.yml
- New release of ShanoirUploader, see here: https://github.com/fli-iam/shanoir-ng/wiki/ShanoirUploader-Release-Notes
- Fix for create-subject (new) with ShUp (see issue https://github.com/fli-iam/shanoir-ng/issues/2497)
- New tree view: filter by subject name alphabetically, or by id, or by keyword
- Stats download export (OFSEP), now as async task in Job list, to avoid connection timeout in hospital env
- Ignore series, with BurnedInAnnotation == YES, by default and do not import them
- New releases of ShanoirUploader, see here: https://github.com/fli-iam/shanoir-ng/wiki/ShanoirUploader-Release-Notes
- We used to convert and store niftis at the import, this is not the case anymore. We are now able to delete, study by study, the existing niftis (for environmental, or financial purpose). Please send us an email in case you want the niftis of your study deleted.
- Fix: avoid empty subject names now in shanoir (create subject) and filter beginning/trailing spaces in subject names in the tree to show an even better alphabetical order
- Web GUI: New tree view: keep study tree always open and open details on the right (see more here: https://project.inria.fr/shanoir/new-study-tree-navigation/)
- OHIF-viewer migration from v2 to v3 (big step), now on latest v3.9.74 (see more here https://project.inria.fr/shanoir/new-version-of-viewer-ohif-integrated/)
- OHIF viewer: select 1-10 timepoints to compare examinations in one view (browser tab)
- In Chrome: new download options: all DICOM files (unzipped) in one folder
- Study's history: study-admins can now see all events, that happened on their study
- Important security hot fix on com.mysql:mysql-connector-j
- Security update: latest version of Keycloak migrated (v25.0.4)
- No more redirecting Users to homepage when opening a page requiring to be Expert or Admin
- Solr search: fix for import date filter in facets (left column)
- Solr search: show full content of cell in table with on-mouse-over
- Fix error message when creating an account with an already existing email address
- Fix for very big series with n-folders for their images (VHD + zip file import (not ShUp))
- Fix for Bruker import: select study card (as MR)
- Legacy architecture pattern: open-session-in-view removed from microservices import, users and studies
- Tag creation: auto-focus and validate with 'Enter' key
- Second migration to java 21
- Bugfix on tag on OFSEP server (study edition too slow)
- Bugfix on examination update (subject update)
- Bugfix on dataset-metadata for old datasets
- Technical upgrade
- Bugfix on processed datasets & processing (processing display and deletion, processed datasets in solr, etc..)
- Bugfix on study copy for preclinical subjects
- Bugfix on studycard with dicom fields multiplicity
- Tags on datasets (not from the interface yet)
- Tags are now displayed in solr
- Migration to java 21 (temurin)
- Update swagger (API interface) to make it functional
- Studycard policy (after import or only on demand)
- Mass NIfTI conversion: fix for /tmp space usage (disk saturation problem)
- Mass NIfTI conversion
- CoilType SYNERGY added for ofsep-import-bug-fix
- Add S to ScanningSequence for ofsep-import-bug-fix
- New properties API endpoints
- Add examination.comment to examination-list
- Filter tasks/jobs by user
- shanoir-issue#2155: improve delete of examination
- Migration Angular 15 to 17
- Filter processed datasets in Solr
- Security update: Keycloak, new version 23.0.5 from 20.0.0
- Mass downloads in Chrome, fixes for Windows
- Mass processing with VIP: corrections/extensions/logs
- Fixes + refactor for downloads (WADO-URLs)
- Migration to Spring Boot 3.2.2 (from 3.1.2)
- New import data type: XA DICOM Images
- WebGUI: error console, allow scrolling in Linux version, of Firefox
- Fix: manage subjects: create new subject (force selection of study)
- Fix for PACS query: StudyRootLevel
- Exam deletion: continue deletion, when images missing
- Study volume storage: performance optimization
- PACS Import: ShUp + webGUI: use wild cards again
- New API endpoint to expose study statistics
- ShUp: code integration v8.0.0 of ShUp (big refactor)
- ShUp: create equipment + center from ShUp
- Fix for ShUp import issue with raw data storage (fixed on server, applies for all new imports)
- Fix for PRIMUS: missing db connections
- PRIMUS: statistics export extensions
- Hot fix PRIMUS
- Hot fix downloads, single-dataset
- Hot fix PRIMUS
- Roadmap: derived studies!!!
- Create new study: better indicate must-have values with *
- Jobs table: fix for date format
- Download: duplicate dataset_files, avoid huge logs
- Statistics export: extended with dataset file size + series number (sorting index)
- vip-2-vip: mass processing extensions for PRIMUS
- shanoir-issue#1943: use dicom data to pre-fill center and acq equipment forms during imports
- Study cards: clean up for incomplete rules
- Shanoir hotfix missing sop uid
- Hotfix for processing
- Quality control/cards: pre-final version
- VIP integration: execMonitoring and more...
- Keycloak logs to named volume
- ShUp: rememberProfile flag added
- BIDS import : NIRS modality now implemented
- [CI]: auto-generated tagged docker-images
- Bug fix: all DICOMs download issue (multi-part header in files)
- Bug fix: Solr search: acquisition equipment errors
- Big refactoring on VIP-related operations
- Bug fix: some wrong exam dates in Solr search (correct format now)
- Bug fix: multi-frame download issue (via DICOMWeb-REST link)
- Bug fix: Fix some small issues on dataset view
- Auto-create release-version-tagged docker images per microservice (Kubernetes prepa)
- Chrome browser: mass downloads via web GUI + change on Firefox usage
- Fix for import-from-pacs with multiple DICOM studies
- import-from-pacs: performance optimization with query pacs
- Data user agreement (DUA): fixes and optimizations
- Refactor ShanoirUploader finished: now common code with MS Import and migrated to dcm4che3 library, imports from files and pacs working again
- Performance optimization: getAllSubjects from study details
- Infrastructure: migration to Debian Bookworm
- Migration to Spring Boot 3 and Java 17 (before 2 and Java 11)
- Beta-version for test: mass processing and integration with VIP
- Extension for ofsep-identification-pipeline value storage
- Multi-exam import: optimizations and fixes
- Storage volume: now as part of the list of studies, to have an overview
- Search extension (Solr): now filter by equipment and subject type
- WebGUI: re-introduction of measurement units
- WebGUI: imports (all) better error/ignore management + display
- BIDS-tree generation: fix for wrong subject prefix in dataset file names
- Fix for OFSEP: NPE with isSpectro on server
- Fix for EEG import
- Fixes for quality cards
- Fixes for preclinical subject management
- ShanoirUploader: big refactoring to share code with MS import + migration to dcm4che3 (before 2)
- Hot fix of hot fix: make new datasets again downloadable
- Hot fix: block some datasets within a time range from download/access
- Hot fix: edit study member and change rights
- Open data: DataCatalog and Datasets for bioschema and Google Dataset Search, by Pierre-Henri (https://github.com/fli-iam/shanoir-ng/pull/1726)
- Jobs menu: better import messages, by Youenn (https://github.com/fli-iam/shanoir-ng/pull/1727)
- Server log messages: better import logs (reduced)
- Fix for long center names, by Julien
- Fix for subject-prefix per center, by Pierre-Henri
- Fix for multi-exam-zip import, by Jean-Come
- Infrastructure: migration to Debian Bullseye (from Stretch), by Julien
- fix import bug ("body" in coil in studycards)
- Download datasets limit to 500 (https://github.com/fli-iam/shanoir-ng/pull/1661)
- New statistics procedure (export)
- Quality control fixes (https://github.com/fli-iam/shanoir-ng/pull/1654)
- Import summary logs back to work (https://github.com/fli-iam/shanoir-ng/pull/1677)
- Study volume counter: include extra file(s) size (on exams)
- Bug fix: white page issue (clean cache required) (https://github.com/fli-iam/shanoir-ng/issues/1678)
- Bug fix: create acquisition equipment from import (https://github.com/fli-iam/shanoir-ng/issues/1625)
- Bug fix: invite new user to study using userName
- Bug fix: allow blocked import for one user (related_datasets issue)
- Some GUI optimizations
- Quality control, v1 (retrospective data)
- Downloads (all) direct streaming of result
- New graphical interfaces: public catalog + home page + access requests
- Study volume counter (for new imported data)
- Bug fix: Solr selection tab: delete datasets from selection
- Bug fix: for parallel acquisition technique
- add subject name to single dataset download
- optimize VIP (Virtual Imaging Platform, CREATIS) integration
- massiveDownloadByExamId added (front + back)
- fixes on access requests (e.g. mail sending and mail content)
- Dataset search (Solr): directly open OHIF-Viewer added
- 2 fixes for examDate missing in Search datasets (Solr) + wrong version of OHIF viewer
- oneshot optimization + fix version of Angular docker image
- Fix for account extension request
- Fix for Solr search date filtering
- Roadmap issue: [NG-2021-16] Access Request
Study admins have already received an information email on the subject. users can now be invited by email address to join studies in Shanoir. If studies are "visible by default" anonymous users or any other user already in Shanoir can ask an access to a study. Once the access request "accepted" users are directly added to studies, what will save everybody a lot of time and give higher control to study admins.
Studies, that select "visible by default", are now display on a public catalog page, see screenshot, and expose very little meta-data publicly (no public access to the data!).
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Roadmap issue: Migration to version 20.0.0 of Keycloak (security update)
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Performance optimization: studies + subjects lists
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Minor fixes: examination list fix #1524
- Fix for 4D MULTIGRE
- Study detail: adds pseudonymization profile to study and displays it
- FAIR: FINDABLE: add schema.org data catalog header to login page for auto-indexation via web bots
- OHIF viewer: performance fix
- Multi-exam web import (ZIP)
- Some fixes
- OHIF viewer integration
- DICOMWeb implementation
- New WebGUI import (clinical context)
- Fix for shanoir-issue#1234 dataset download comment contains '/' bug
- Fix for Solr bug (can't use several keywords)
- Fix for Clinical context bug
- Fix for Solr Search and multiple word search
- Fix on study tabs
- Fix on downloads with "/"
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BIDS-Import! (raw NIfTI, no DICOM required)
- The import of a single-subject zip file in BIDS format is now possible using the web interface
- We have this limit, because of the too big file sizes otherwise
- With multi-modality (MR, CT, EEG) and multi-session (exams) support
- We are moving into the direction of mass imports:
- This development is the first step, to allow multi-subject imports on a local BIDS structure using ShanoirUploader in the next weeks
- Please do not forget, that we support already a mass import using a CSV file from a clinical PACS using ShanoirUploader (used for 800 patients in two days!)
- THX to Jean-Come!
- The import of a single-subject zip file in BIDS format is now possible using the web interface
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Multiple search optimisations
- Auto-completion and paging now in facets on all available data, not only the displayed facets
- THX to Julien!
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Tabs for View/Edit Study
- The information on View/Edit study has become more and more over the last months
- Now we have introduced a tab based structure, to better display the information
- THX to Julien!
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BIDS (Brain Imaging Data Structure v1.6.1) Auto-Export, v1.0 FINISHED (PR 852) Please see the very nice video of Jean-Come on shanoir.org: Upcoming imports, can now use the study cards in Shanoir-NG to generate automatically a compliant BIDS tree (raw NIfTIs). We can discuss for the future, if sharing rights dedicated to the BIDS tree could be interesting (not share the DICOMs, but the NIfTIs in BIDS format) When the re-application of study cards is implemented, this feature will apply on retrospective studies too.
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Subject-Name-Prefix per center (PR 1178) Concerns imports with the WebGUI only, no change for ShUp; Now in Edit Study you can configure a PREFIX for each center, that will be proposed for the Subject Name Creation during the import, to harmonise the subject naming.
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Shorter import: (PR 1185) you will save one click, as "Import now" is now on the clinical context page of the import, what avoids clicking on Next before.
- Import Processed Dataset (PR 1086)
- Papaya now full-screen (PR 1114)
- Email sent to user, when new user added to study (PR 1143)
All details under: PR List
- Set login options clearer : (PR 1098)
- Display correctly animal therapies / pathologies : (PR 1097)
- [Bug Fix] Remove unnecessary study-card warning : (PR 1095)
- Update statistics procedure to export dates : (PR 1089)
- Columns resizing feature : (PR 1082)
- Send a mail to the study admin when an import fails : (PR 1011)
- New Search and all other tables: configure column width with mouse drag In all tables with sh-ng an user can now manipulate the column settings for each table using the mouse, and for each table the configuration is stored in the browser.
- Receive Member Mail If a new member is added to a study, a study responsible can receive an email.
- Image preview online (Papaya) optimised Images are better centred now for preview in browser.
- Increase Keycloak access token lifetime to 15 minutes Token lifetime has been increased to 15min to avoid disturbance with very big file uploads.
- Direct links added to better navigate between entities Move better between the entity hierarchy: exam -> subject/acquisition, subject -> study/exam etc.
- Progress bar for the import/upload For very big uploads: now a upload progress bar is displayed.
- Automatic database updates db-changes contains numbered files now, that are automatically applied on the database, if missing, to perfectly trace the evolution of the database for everybody.
- GDPR text on account request form (PR GDPR) For each account request the Inria text for GDPR compliance is displayed.
- Tags on subjects (e.g. tag a subject with a clinical score value) (PR tags on subjects) Configure available "free text tags" on study level (expert) and select them during import for each subject.
- Migration to Spring Boot 2 and Java 11 (PR Spring Boot 2 Migration) Spring Boot 1.4.1 not supported anymore since 2019. Mandatory update!
- FIX: new search: subjects with "-" minus characters can be directly found in none-expert search! (PR custom solr config to fix "-" minus tokenizer issue)
- Import jobs overview: direct link to created exam (PR direct link to exam) When the list of import jobs is displayed, the created exam can now be accessed via a direct link to avoid searching it.
- FIX: Password reset allows usage of old password #192 (PR https://github.com/fli-iam/shanoir-ng/pull/1061)
- Last deployment done on the 20.09.2021