CHANGELOG.rst

Changelog

v1.13.0 (25/02/2025)

Added

• Include movie count in returned foil holes @gmg29649

Changed

• hideUncollected renamed to hideSquares in /dataGroups/{dcgId}/grid-squares @gmg29649
• Grid squares with empty image paths are not returned if hideSquares is true @gmg29649

v1.12.0 (17/02/2025)

Added

• Endpoint for registering email alerts (dataGroups/{groupId}/alerts)
• Send out emails when appropriate message queue messages are received

Changed

• Grid square and foil hole models now accept null values for location fields

v1.11.2 (07/02/2025)

Changed

• Include image in grid square model

v1.11.1 (30/01/2025)

Fixed

• Movies with missing columns no longer throw internal server errors
• Data collections sorted on empty alignment quality columns now have predictable ordering

v1.11.0 (16/01/2025)

Added

• Added movie information endpoint (/movie/{movieId}) @gmg29649

v1.10.1 (14/01/2025)

Changed

• Coalesce null CTF values

v1.10.0 (10/12/2024)

Added

• Add GET /foil-holes/{foilHoleId}/movies endpoint
• Add GET /grid-squares/{gridSquareId}/foil-holes endpoint
• Add GET /grid-squares/{gridSquareId}/image endpoint
• Add GET /dataGroups/{groupId}/atlas/image endpoint
• Add GET /dataGroups/{groupId}/atlas endpoint
• Add GET /dataGroups/{groupId}/grid-squares endpoint

v1.9.0 (09/10/2024)

Added

• Include B-factor columns in particle classification data
• GZip support

v1.8.1 (23/09/2024)

Changed

• Semgented/denoised tomogram images are now sourced from the ProcessedTomogram table

v1.8.0 (28/08/2024)

Added

• Particle count per defocus value endpoint (/dataCollections/{collectionId}/ctf)
• Particle count per resolution bin endpoint (/dataCollections/{collectionId}/particleCountPerResolution)
• Custom model upload endpoint
• Sample handling redirect endpoint

v1.7.0 (20/06/2024)

Added

• Tomogram movie/thumbnail endpoints now support segmented movie/thumbnails

Changed

• Instead of setting denoised, requests to tomogram movie/thumbnail endpoints must set movieType to one of either "denoised" or "segmented"

v1.6.0 (14/05/2024)

Added

• B Factor fit plot (/{autoProcId}/bFactorFit)

v1.5.0 (25/03/2024)

Added

• Endpoint for getting angle distribution plots (/autoProc/{autoProcId}/classification/{classificationId}/angleDistribution)

Fixed

• Count of children in listing endpoints no longer return excess items for certain staff users

v1.4.1 (14/03/2024)

Fixed

• Session/proposal listings no longer show duplicate results

v1.4.0 (05/03/2024)

Added

• CTF endpoint for SPA now returns particle count for all image numbers
• Standard deviation is returned for average ice thickness

v1.3.2 (19/02/2024)

Changed

• Improved performance for /sessions endpoint, only returns eBIC sessions
• Fixed parameter generation for tomogram reprocessing
• CTF endpoint for autoprocessing programs now returns particle count

v1.3.1 (14/02/2024)

Changed

• "Reprocessing enabled" check moved to individual endpoint (/proposals/{proposalReference}/sessions/{visitNumber}/reprocessingEnabled)
• allowReprocessing removed from processing job parameters endpoint

v1.3.0 (07/02/2024)

Added

• Data collection creation endpoint (/proposals/{propId}/sessions/{sessionId}/dataCollections)
• sortBy argument to data collection listing endpoint

v1.2.3 (05/02/2024)

Changed

• Extract downscale is now true by default

Fixed

• Processing parameters now generate correct gain reference path

v1.2.2 (24/01/2024)

Fixed

• Fixed input validation on SPA reprocessing

v1.2.1 (23/01/2024)

Changed

• If there is no message queue user set, reprocessingAvailable is always false
• Updated database models

v1.2.0 (09/01/2024)

Changed

• Add single session endpoint (/proposals/{proposalReference}/sessions/{visitNumber})
• Fix data collections not showing up, due to table model mismatch

v1.1.11 (27/11/2023)

Changed

• Return pixel size on image in data collections in angstroms rather than nanometres

v1.1.10 (16/11/2023)

Changed

• Include image directory in dataCollectionGroups endpoint

v1.1.9 (31/10/2023)

Changed

• Phase plate status now accounts for column possibly being a string

v1.1.8 (30/10/2023)

Changed

• phasePlate field in data collection endpoints now returns a string rather than an integer value
• Drift plot X is read and passed down from file, rather than inferred from linear sequence generated from the range of the array's length

v1.1.7 (26/10/2023)

Removed

• User can no longer get motion correction drift data from table

v1.1.6 (05/10/2023)

Added

• Added option to disable CORS

v1.1.5 (27/09/2023)

Changed

• Consider recipe in processing job ordering

v1.1.4 (08/09/2023)

Changed

• Motion correction drift (/movies/{movieId}/drift) endpoint falls back to gathering data from file if database entries do not exist

v1.1.4 (08/09/2023)

Changed

• Motion correction drift (/movies/{movieId}/drift) endpoint falls back to gathering data from file if database entries do not exist

v1.1.3 (22/08/2023)

Changed

• Update internal dependencies due to vulnerabilities (certifi)

v1.1.2 (14/07/2023)

Changed

• Fix duplicate sessions for non-admin users
• Disable reprocessing on inactive visits

v1.1.1 (12/07/2023)

Added

• Virtual host can be set in message queue configs

v1.1.0 (11/07/2023)

Added

• GET endpoint for processing job parameters (dataCollections/{collectionId}/reprocessing)
• POST endpoint for firing off SPA reprocessing pipeline (dataCollections/{collectionId}/reprocessing/spa)

Changed

• Processing job list endpoint is now ordered by both processing job and autoprocessing job
• Tomogram reprocessing endpoint moved to dataCollections/{collectionId}/reprocessing/tomograms

v1.0.0 (20/06/2023)

Changed

• First public production release

v0.13.0 (13/06/2023)

Added

• Adds getMiddle option to tomogram motion correction endpoint

v0.12.1 (08/06/2023)

Changed

• Permission lists take in strings rather than integers

v0.12.0 (06/06/2023)

Added

• Adds denoised central slices
• countCollections option for session query

v0.11.0 (30/05/2023)

Added

• Logs HTTP exceptions server-side

Changed

• Classes are sorted in ascending order when estimated resolution is selected as sorting criterion

v0.10.0 (16/05/2023)

Added

• User can now filter classes by selection status

v0.9.0 (24/04/2023)

Added

• Tomogram endpoint now includes processing data information

v0.8.1 (31/03/2023)

Changed

• Tomogram endpoint returns refined tilt axis

v0.8.0 (28/03/2023)

Added

• Enables cookie authentication support

v0.7.0 (14/03/2023)

Changed

• Removes unused support for OIDC auth
• Fixes CTF data endpoint

v0.6.0 (28/02/2023)

Added

• Support for 3D classification in single particle analysis

Changed

• Performance improvements for session, data collection group and data collection listing queries

v0.5.0 (21/02/2023)

Added

• User can now initiate tomogram reprocessing for a given data collection dataCollections/{collectionId}/tomograms/reprocessing
• Collection/autoprocessing (/dataCollections/{collectionId} and /autoProc/{autoProcId}) program frequency data is available for total motion (/motion), estimated resolution (/resolution) and particle count (/particles)

Changed

• Fixes bug with histograms that omitted bins with no items

v0.4.0 (07/02/2023)

Added

• User can now retrieve tomogram that belongs to autoprocessing program (/autoProc/{autoProcId}/tomogram)
• Added max/min end date, max/min start date query parameters to sessions endpoint

Changed

• Collection can now return up to 3 tomograms, returns paged object for /tomograms (renamed from /tomogram)
• Proposal search also searches through title

v0.3.3 (03/02/2023)

Changed

• Adheres to new relations between data collections and tomograms, returns first tomogram instead of erroring out if there are more than 1

v0.3.2 (02/02/2023)

Changed

• Fixes error caused by lack of ProcessingJobId column
• Updates database model

v0.3.1 (01/02/2023)

Changed

• Fixed auth information mappings for user object causing 500s

v0.3.0 (01/02/2023)

Added

• Frequency data for ice thickness in data collections (/dataCollections/{id}/iceThickness) and autoprocessing programs (/dataCollections/{id}/iceThickness)

Changed

• Moves data collection listing from /dataCollections to /dataGroups/{groupId}/dataCollections
• Data collection also displays column with index relative to parent data collection group

v0.2.0 (24/01/2023)

Added

• New endpoint for getting ice thickness data (/movie/{id}/iceThickness)
• New endpoints for tomogram projection images (/tomograms/{id}/projection?axis={axis}) and movie (/tomograms/{id}/movie)
• Endpoints for additional tomogram projections

Changed

• Job status for autoprocessing is inferred from other columns and returned as status
• Tomogram endpoints for central slice and XY shift plot obtain paths from new tomogram columns instead of autoprocessing attachments
• Sessions can be searched through their visit numbers as well
• Sessions also return their parent proposals
• Improvements to session query performance

v0.1.0 (12/01/2023)

Added

• New endpoint for getting processing jobs in data collections (/collections/{id}/processingJobs)
• Autoprocessing program endpoints (/autoProc/{id}/ctf, /autoproc/{id}/classification, /autoProc/{id}/particlePicker and /autoProc/{id}/motion)
• Drift plot endpoint now support obtaining data directly from the DB instead of file (when fromDb is set)
• New endpoints for getting 2d classification and particle picker images (image suffix for both)
• Listing of data collections now supports filtering by data collections that contain valid tomograms (when onlyTomograms is set)

Changed

• Data collection groups now also include experiment type information
• Session has been moved from being a child of proposals to its own root endpoint (with proposal being a query parameter)
• Data collection groups have been moved from being a child of sessions to its own root endpoint (with proposal and session being query parameters)
• Data collections have been moved from being a child of dataGroups to its own root endpoint (with groupId being a query parameter)
• Overhaul of item count query; significant performance improvement
• Data collections now return all columns

v0.0.1 (06/12/2022)

Changed

• Search param s renamed to search for clarity
• Motion correction endpoints no longer return drift, and now support regular pagination. Drift is accessed through movies/{movieId}/drift
• Moved image endpoints to movies
• Moved visits to sessions

v0.0.1-rc4 (06/12/2022)

Changed

• Authorisation and authentication is done through a separate microservice
• Data collection listing moved from /collection?group={id} to dataGroups/{id}/collections
• Visit listing moved from /visit?prop={id} to proposals/{id}/visits
• Data collection groups listing from /dataCollectionGroups?visit={id} to visits/{id}/dataGroups

v0.0.1-rc3 (30/11/2022)

Added

• Motion has been split into tomogram motion correction (with the prefix /tomograms) and data collection motion correction (prefix /dataCollections)

Changed

• Shift plot moved from /shiftPlot to /tomograms/{tomogramId}/shiftPlot
• Central slice moved from /image/slice/{tomogramId} to /tomograms/{tomogramId}/centralSlice
• CTF moved from /ctf to /tomograms/{tomogramId}/ctf
• Listing of tomograms moved from /tomograms to /dataCollections/{collectionId}/tomogram
• Only a single tomogram is returned in the listing, as a one-to-one mapping between tomogram and collections is expected

v0.0.1-rc2 (25/11/2022)

Added

• Data collection group endpoint
• Support for configuration files
• Data collection groups and data collections are now searchable by comments
• Visits are now searchable by visit number
• Proposals are searchable by proposal code and proposal number
• User endpoint now also returns names, title and ID
• Model mapping for data collections and data collection groups

Changed

• Data collection moved from collection to dataCollection
• Data collections are now selected by group instead of visits

v0.0.1-rc1 (21/11/2022)

Initial version.