Changelog

All notable user-facing changes to the Trakka platform will be documented here.

Release notes for the Trakka CLI can be found in the CLI changelog.

2026-03-23​

Added​

• It is now possible to assign usernames to users. These are unique strings which will be useable to refer to users via the CLI or web interface. Usernames will be assigned for all users and made mandatory in a future release.
• Dashboard templates for public health reporting

Changed​

• Date filters on the samples table now have the behaviour of On and After and On and Before which has replaced the functionality of just After and Before
• Help Text of the Sequence Upload Page has been updated, to be more structured and clear.
• Certain large bulk operations on samples will now be processed in batches, to avoid issues in logging. These are sample sharing and unsharing, and sample disable or re-enable.

Fixed​

• Fixed issue where ProjectAnalysts could not disable/re-enable trees.
• Fixed issue affecting feedback submission via the UI.
• Fixed issue where multiple successive updates to large projects could slow down the system.
• Fixed issue where CSV export could fail for large projects.

2026-03-11​

Added​

• FASTA upload (fasta-asm and fasta-cns) is now available via the UI as well as the CLI.
• Project, organisation, and admin views now contain logs of recent activity. These logs track events since Jan-Feb 2026. Note that permissions-related events, such as users being assigned roles in projects, are not yet displayed. Logs can also be accessed via the CLI.
• For admins, V2 roles will now automatically shadow V1 roles to simplify management during the transition.

Changed​

• When uploading sequence data via the UI, the pipe character (|) will be treated as a separator in detecting the Seq_ID. This is particularly useful for consensus FASTA files, where the contig name may use a pipe character to separate the sample name from other information.
• When uploading sequence data via the UI, "snackbar" alerts can now be clicked to dismiss them prior to their automatic dismissal.

Fixed​

• When uploading sequence data via the UI, changing the sequence data type after selecting files could sometimes cause the interface to hang. Changing the sequence data type will now reset the file selection.

2026-03-06​

Changed​

• In the tree viewer, legends for metadata variables will now only include values present in the currently-viewed tree, rather than the project as a whole.

2026-02-09​

Added​

• Headers in the project Samples table can now be coloured to indicate the data source (submitted org-owned sample metadata, or project-managed metadata).
• Either short names (e.g. project abbreviations, proforma abbreviations) or global IDs are now accepted interchangeably for most commands; this will be reflected in CLI functionality.
• All new projects and groups now contain Seq_ID by default.
• Logging added for actions which do not succeed.
• Logging added for "proforma update" and "organisation update" events.
• Admin-only functionality to regenerate user-facing logs from source logs.

Changed​

• Proforma detail pages now have a more intelligible and predictable URL

Fixed​

• Login session persistence across tabs is now maintained and users no longer need to re-login when opening a new tab or accessing a shared search query URL.
• Tree SVG export now preserves whitespace used for metadata column alignment, independent of software utilised to open the downloaded SVG.

2026-02-02​

Fixed​

• Improvements to performance of overview widget on main dashboard, and overall system performance.
• Removed a bug which could cause sequence upload events to be logged with incorrect information.

2026-01-30​

Fixed​

• Fixed issue where users with no access to samples, such as newly-added users, would get an error message on the main dashboard.

2026-01-28​

Changed​

• The "basic" dashboard has been renamed to "default" and will function as the default if a project dashboard is not specified. The old "default" dashboard layout has been renamed to "public-health".
• When selecting projects to share uploaded samples and sequences with, the project selector will now show the full names of projects.

2025-12-15​

Added​

• Users can now unshare samples from projects via the web interface, from their organisation's sample listing page. Users will require the Viewer and Uploader roles within their organisation to use this feature.

2025-12-10​

Fixed​

• Fixed an issue where non-admin users submitting sequence data would get an error if trying to create new sample records during submission.
• Fixed an issue where customised download quotas would be ignored in favour of the default download quota.

2025-12-05​

• Users can now share samples into projects via the web interface, from their organisation's sample listing page. Users will require the Viewer and Uploader roles within their organisation to use this feature.

2025-12-02​

Added​

• In the sequence upload page, the table of uploaded files will now consolidate errors and warnings for review.

Fixed​

• Issue where tree legend was not correctly exported.

2025-11-24​

Added​

• Species names are now displayed in italics in metadata table.
• In the Fields table, field types now render with colours for easy identification.

Fixed​

• Issue where the sequence count widget on project dashboards incorrectly displayed missing for all samples.
• Issue where tree labels were not correctly exported to SVG.

2025-11-10​

Added​

• Organisation abbreviated names, and all associated entities, can now be edited by admins.

2025-11-05​

Changed​

• CSV exports now reflect the user's current table view, including hidden columns and applied filters, so only visible data is exported. This includes rows manually deselected via checkboxes in e.g. the tree samples table.
• The Fields table now displays data more clearly, and the table has been made more compact by not initially displaying all allowed values for a field if there are a large number of allowed values. The user can expand the cell to see all allowed values if desired.

Added​

• It is now easier for admins to update organisation names, in particular the abbreviated name used for data-sharing.

2025-10-21​

Added​

• Users can now navigate to their own user profile page by clicking on their name in the sidebar.

Changed​

• CSV exports of data will now have more informative filenames.

Fixed​

• Fixed a bug where maps might not display properly on page refresh.
• Fixed a bug where epi curve faceting into rows could be added but not removed.

2025-10-19​

Changed​

• On the metadata upload page, users can now select the data-owning organisation for the upload, and any projects to share with. These settings will apply to all sample records in the upload. The Owner_group and Shared_groups columns in the upload file are no longer required and will be ignored if present.
• On the sequence upload page, users must now always select the data-owning organisation for the upload, even if no new sample records are being created.
• The project Summary tab has been renamed to Dashboard.
• Admins can now edit user download quota settings via the UI.

Added​

• The table filter component now supports 'in' and 'not in' operators for categorical fields, allowing users to filter by multiple values at once.
• Users now have a "Position" field in their profile, which can be set to indicate their role or position in their home organisation.

Fixed​

• Certain date fields were displaying timestamps when shown in tree labels; this has been fixed.

2025-10-08​

Changed​

• Map visualisations (choropleths) have been upgraded with better visuals, more features on tooltip and legend, and listing of aggregated data.

2025-09-22​

Added​

• Metadata fields can now be marked as "geographic" fields, which will be used to assign samples to geographic regions on maps.
• Dynamically-defined roles can now be deleted.
• When multiple metadata fields are added to tree node labels, their padding will now dynamically adjust as the tree is navigated, so that the minimum possible width is used that fits in all metadata values in just the currently-viewed subtree.
• Epi curve and cluster timeline plots now have an option to rotate the x-axis labels for better readability.
• A "demo" dashboard layout has been added and can be assigned to projects.

2025-09-05​

Changed​

• In the tree viewer, it is now possible to deselect Seq_ID as a node label while still selecting other metadata fields to display against nodes.

2025-08-26​

Changed​

• The data filter widget on tables, plots and trees has been restyled to make the add-filter button easier to find and the reset button more difficult to accidentally hit.
• The default filter comparator for string fields is now contains rather than equals.
• Performance improvements for switching tabs in large projects.
• Trees in a project are now sorted in reverse chronological order by default, based on their last updated date.
• Under the new permissions system, a better error message will now be returned when the user does not have permission to take an action.

2025-08-20​

Changed​

• ResultWriter role deprecated and merged with the ProjectAnalyst role. ProjectAnalysts may now manage trees as well as project datasets.

2025-08-12​

Added​

• Configurable sequence download quotas have been added for users.
• When filtering sample records on a categorical field, and using an equality operator, the text input box will now show an autocomplete/dropdown for available metadata values for that field. This makes it easier to search for categorical values.

Fixed​

• When no tree versions (newick files) have yet been provided for a particular tree in a project, a sensible error message will be displayed.
• Fixed issue where newick strings would be unnecessarily retrieved for historical tree versions.

2025-07-29​

Fixed​

• Fixed an issue where changing visualisation options on a plot could break an existing date filter.
• Increased loading speed of the widgets on the master dashboard / landing page; this addresses lag on this page observed following the database migration.

2025-07-21​

Fixed​

• Fixed an issue to allow using dataset-sourced metadata fields in maps.

2025-07-14​

Changed​

• Increased the vertical height of the sample tables when possible, to occupy all available space.
• Performance improvement for loading projects which have many datasets.

2025-07-08​

Added​

• Tabs in the Project and Organisation views are now scrollable; this allows access on narrow screens.

2025-07-02​

Added​

• Added prototype maps: these are choropleths which may be added to projects under the Plots tab.
• Added a QC pie chart widget which may be configured for project dashboards.

2025-06-19​

Added​

• Added new 'Examples' column for metadata fields, to guide recommended usage of fields including unvalidated string fields. Can be viewed and edited in the the fields UI, subject to privileges.
• Added the ability to hide columns on the fields page.
• Admins can now see when users were most recently active on the platform.

Changed​

• Changed styling of vertical headers to be more space effecient.
• New users will always have the 'User' role, admins do not need to set this.
• Admin uploads of metadata to existing sample records, specifying a different sample owner, are no longer allowed. See the new CLI command for sample ownership changes.

2025-05-20​

Added​

• Improvements to the user dashboard, including addition of latest sequence date and latest tree date for each project.
• Added support for hiding empty columns in the Samples table. The hide/show column picker has also been updated with better visuals, and the user no longer has to click Submit to put changes into effect.
• The project proformas tab will now list all configured proforma validation specs for the project, regardless of whether they have a downloadable proforma template. Proformas with no attached template file are shown and styled differently.

Changed​

• Clicking on an older version of a proforma in the project proformas tab will now navigate to the corresponding older version of that proforma on the proforma page.
• Fields with the same column ordering value will now be sorted in alphabetical order in the Samples table.

Fixed​

• Fixed a bug causing FASTQ files not to validate correctly in the sequence upload page for some Windows users.
• Fixed a bug where if a plot control was changed with an active data filter, the filter would be lost.
• Fixed a bug where the ST count dashboard widget would break if the legend had many values.
• Fixed a bug where any project dashboard containing an epi curve would crash if the project had the Date_coll field but it contained no valid dates.
• Fixed a bug where plots on the project dashboard sometimes would be blank after navigating to another project tab and back.
• Disabled plots will no longer be listed for non-admins.
• The project type selector on the projects listing no longer overflows visually when in use.
• The validation success message on project dataset upload now correctly reports Success rather than Warning.

2025-04-07​

Changed​

• Projects will now be listed in reverse chronological order by default, based on their creation date.

2025-03-25​

Added​

• New dashboard templated and widgets available for config, including a pie chart widget for metadata values, table widgets for any metadata values, and more configurable metadata/sequence count widgets. The epi curve widget colour field is now more configurable.

Changed​

• The quick search in tables will now have a larger clickable area for accessibility reasons.

Fixed​

• If a dataset is uploaded with duplicate column headers, the uploader will now receive a useful error message.
• Newick parsing is now more robust and can handle more corner cases for uploaded trees.

2025-02-25​

Added​

• The sequence data upload page now supports single-end FASTQ upload: Illumina and ONT.

2025-02-19​

Added​

• FASTQ sequence data may now be uploaded via the web UI. For now, this is restricted to paired-end Illumina FASTQ.

2025-02-14​

Added​

• Basic version of project dashboard available for use by projects; this dashboard is dependent only on system fields and not user-supplied metadata.

2025-02-11​

Added​

• Admin UI for managing role assignments in new permissions system
• Dashboard widgets for sequence and metadata availability added to default project dashboard
• Colour scheme for Australian and NZ jurisdictions added for use in plots
• Project dashboard epi curve widget will colour by Owner_group if other jurisdiction fields are not available

Fixed​

• Fixed privilege escalation bug affecting admin users in the new permissions system
• Fixed bug where a user with no privileges would not see the web UI at all

2025-01-28​

Added​

• Introduced a type property to projects, enabling better organisation and filtering.
• Added a filter on the project list page to allow filtering by project type.
• Sequence listings, for instance via the CLI, will now include information on sequence file sizes.

2025-01-17​

Fixed​

• Fixed bug where a project dashboard would not display properly if the project contained no sample records.

2025-01-13​

Added​

• New widgets are now available for project dashboards:
  • Accession counts (reads accession and assembly accession) availability per organisation.
  • Counts of samples with and without sequences, per organisation.
  • Counts of samples with a Date_coll value, per organisation. The date of collection is a proxy for a sample having any metadata; samples without a date of collection generally have no metadata values uploaded at all, as this field is mandatory.

Changed​

• The project dashboard Organisation sample count widget is now sorted by counts.

2024-12-17​

Added​

• A new slice for managing users and their roles, with a warning to signify that it is a work-in-progress system (admin only).
• Splash loading screen on initial load.
• UI elements in the client are now able to reflect the permissions assigned to users via dynamically-created roles. This means that assigning fine-grained permissions to users will now enable, disable, or display the relevant UI elements as appropriate.

Fixed​

• In sample metadata tables, filtering by is-null-or-empty or not-null-or-empty on a date field now works correctly again.
• User list export to CSV is fixed (admin only).
• Deleting a user's role in the user detail page will not now trigger reordering (admin only).

Changed​

• Quick Search in tables will stay open if it contains an input, so that the filter state is visible.
• In the project proformas tab, clicking on a proforma will now take the user to the proforma detail page, rather than opening a modal. It is still possible to download a pro forma template directly from the project proformas view.
• An Admin is now able to select multiple group targets for their role selections for a user (admin only).
• Users now require explicit permission for core functionality, and the client makes use of this updated functionality. This means that in order to use the Trakka front-end, a user must be assigned an User or similar role granting them these basic permissions.
• Larger page sizes for table pagination may now be selected, so that more rows may be displayed in Samples tables and the Fields table.

2024-12-11​

Added​

• Link to the Trakka documentation

2024-11-21​

Fixed​

• Removed reference to unsupported .xls files on the upload page.
• Fixed issue where clicking on a user would not navigate correctly to the user details page.
• In the admin view for editing user roles, selections will now clear after changes are submitted.

Changed​

• The default colour scheme for heatmaps is now a sequential scheme (greens).

2024-10-24​

Added​

• Trakka deployed instances now support configurable themes.
• Project fields can now be configured to be initially hidden, and will be hidden by default in the project sample table view.
• The default project dashboard now includes an epi curve chart. If ANZ jurisdictions or states are present in the project metadata, an appropriate colour scheme will be applied to this chart.

Changed​

• The default colour scheme in plots is now Set3.
• Epi curve plots will now select a reasonable date bin size when first loaded. This bin size may still be adjusted by the user.

Fixed​

• Project dashboards can no longer filter on upload date if Date_created is not included as a project field.
• If a field with too many unique values is selected for the facets of a plot, resulting in the plot being too large to render, the plot will now display an error message instead of crashing.

2024-09-17​

Added​

• Ability to submit support requests in the UI.

2024-09-12​

Fixed​

• Filtered sample counts now display correctly when the filters are loaded from the URL.

2024-09-11​

Added​

• Added new discrete colour schemes for plots and trees, includes a colourblind-friendly scheme.

Changed​

• Colour Scheme Selector now groups colour schemes by type and has a more organised look.

Fixed​

• Fixed an issue where applying a date filter could cause a crash.
• Fixed an issue where the "after" date filter filtered to timestamps after 00:00:00 on the selected date, rather than after 23:59:59.
• Fixed an issue where boolean filters such as is-null-or-empty were not parsed correctly from the URL.
• Improved reliability of sequence upload by requiring the client to send the file hash at the start of upload.

2024-09-05​

Added​

• A Fields page, listing all defined Trakka fields, is now available to all users.

Changed​

• Minor plot tweaks: update preferred fields, smaller cluster timeline point size
• The condition on and after and on and before have been changed to just be After and Before respectively. This is due to a change in available table component filters.
• Table column layout and appearance improvements, including darker cell separator lines for accessibility.

Fixed​

• Plots in projects in show-all mode will select their preferred fields when they exist, independent of dataset analysis label.

2024-08-16​

Changed​

• Org page now appears at org-specific URL rather than a universal /org URL.

2024-08-07​

Added​

• Display Analysis Server Username for users.
• Clicking on the Trakka logo will navigate home.

2024-08-01​

Added​

• Added filter information to the url of all queryable table pages. This allows users to share a link to a table or plot with the current filter settings applied.
• Plot colour legends are now interactive; click a legend item to highlight the corresponding data in the plot.
• Cluster timeline plots are now able to bin samples by date and represent the number of samples via point size.
• Cluster timeline plots now have the option of setting the colour to None.
• Epi curve plots with a row facet now allow independent Y axes (and X axes) for each row.

2024-07-08​

Added​

• Server-side support for more sequence data types: ONT FASTQ and multi-contig FASTA assemblies (fastq-ont and fasta-asm).

Changed​

• The existing fastq sequence data type is now split explicitly into fastq-ill-pe and fastq-ill-se; the existing fasta sequence data type, representing single-contig consensus genomes, is now named fasta-cns. Existing data has been migrated to the new types.

2024-06-27​

Added​

• A colour scheme selector has been added to plots
• Plot settings such as fields and colours will update the URL dynamically; they will persist on page reload and can be shared with others via URL
• Sample tables in projects now show the field source (sourced from organisation sample metadata, or project datasets)
• Hide all / show all columns buttons have been added to the column selector for the sample metadata tables
• Admin UI for editing field details

Fixed​

• Fix to admin functionality to search users by name

2024-06-06​

Added​

• Colour scheme is now selectable per field on the tree view.

2024-05-28​

Fixed​

• Fixed broken sample view

2024-05-21​

Added​

• Admin view of all Trakka field details.

Fixed​

• Organisation sample table view now correctly shows all rows.
• User's name in the sidebar now draws on the Trakka-set display name, which we can update, rather than drawing directly on the Azure display name.

2024-05-11​

Fixed​

• SVG export of trees now correctly renders the tree nodes in the SVG file.

2024-05-06​

Added​

• Admin user management interface added. Admins can now view and edit user details, including display name, contact email, organisation, group-role assignments, and activation status. Easier access for admins to a user's objectID.

2024-05-03​

Changed​

• All legends (trees and plots) now list only values present in the data itself, even if the field is a categorical field with additional valid values.
• Plot and tree legends will now be sorted in natural sort order (ST1, ST5, ST11 rather than ST1, ST11, ST5).
• Plot colouring now uses a neutral (grey) value for null metadata values.

Fixed​

• Has_sequences field will no longer display "false" values while the field is still loading; instead it will appear, correctly, as empty
• Reinstate using a neutral (grey) value for null metadata values on trees.

2024-04-23​

Fixed​

• Performance issues when loading users page

Changed​

• Plots may now optionally be specified as Vega, instead of Vega-Lite.

2024-04-12​

Added​

• User management page for admins.

Fixed​

• Bug with quick search in tree view.

2024-04-11​

Fixed​

• Dashboard table rows are now clickable.

2024-04-04​

Fixed​

• Fixes an issue where the Projects table did not occupy the full height of the browser window, and adds a minimum height regardless of window size.

2024-03-27​

Added​

• The functionality of tabular displays has been updated:
  • Tables containing many rows, for instance sample table views for large projects, will now have significantly improved performance.
  • CSV export of sample data should now correctly escape values containing quotes.
  • A control is now available to toggle vertical rendering of table columns in the sample table. This allows column widths to be made very narrow, if desired, without hiding column headers.
  • Default column widths now better adapt to the data.
  • Column sort controls are now a toggle, rather than a dropdown, and are quicker to use.
  • The pagination controls have been moved to the bottom-left of the table to make it more obvious when the current table view does not show all available items.

Fixed​

• The data filter component on tables, plots and trees now correctly makes available numerical operators (e.g. greater than, less than) for floating-point numerical fields. Previously numerical operators were only appearing for integer numerical fields.

2024-03-21​

Added​

• Override mode for project analysis metadata is now available. In the case of multiple active project datasets containing calculated values for the same field, Trakka will display only the most recent values of the metadata for that field. All values for a field (including nulls) will be sourced from the latest project dataset containing that field.

Changed​

• The project merge algorithm ("override" or "show all") is now shown on the Datasets tab.
• When a project is in "show all" mode, and no datasets have yet been uploaded for a particular metadata field, no columns will be displayed for that field. Previously, an empty column would display.

2024-03-15​

Added​

• Release of project analysis metadata (show-all mode):
  • A new project role, ProjectAnalyst, has been added. This role manages analysis-generated result data for the project.
  • The Trakka backend now supports new CLI commands for configuring project settings and field sources, and for uploading and managing datasets.
  • A Datasets tab has been added, visible to ProjectAnalysts and Viewers. This shows the analysis metadata datasets currently active within the project. Viewers may list datasets, but not alter them.
  • Each project field will now be configured to be sourced from either organisation-owned sample metadata (usually epi sample/case metadata, or sequence metadata), or project-owned dataset metadata. Seq_ID is always be sourced from both, as it is used to merge sample and dataset metadata; no other field in a project may be sourced from both.
  • The project Samples table, all trees, and all plots, will display metadata fields derived from both organisation-owned metadata and project-owned analysis metadata as a unified view.
  • Projects may now be configured to preferentially load high-priority fields by defining "project provisions" of a specified subset of fields, to improve client performance. Any client functionality which requires only certain fields will be available as soon as the relevant fields are loaded; for instance search on Seq_ID is available as soon as Seq_ID is loaded, and rendering of an epi curve should occur as soon as the relevant date field is loaded.
  • In the case of multiple active project datasets containing calculated values for the same field, Trakka will display a version of the field for each dataset, with the analysis label added to the field name to disambiguate results. This project mode is "show-all", intended primarily for research use. An "override" mode for public health will be implemented in a future release.

Changed​

• As a part of the project analysis metadata release, project data is now retrieved as a whole and queried client-side, and cached as the user navigates between pages. As a part of this change:
  • Users may see longer load times on the initial load of large projects.
  • Users should see faster page loads on all successive page views for a project, including any tree or plot pages.
  • It is now possible to sort columns in natural sort order (ST1, ST5, ST11 rather than ST1, ST11, ST5).
  • Quick search is now available on sample metadata tables.
• Tree colouring of nodes or metadata blocks now uses a neutral (grey) value for null metadata values. This improvement has not yet been made for plots.
• Allowed values are now returned when listing available metadata fields. As a result, the trakka field list CLI command will now display allowed values for categorical (i.e. controlled) fields.

Fixed​

• Additional checks have been added to guard against simultaneous upload of sequences to the same Seq_ID, which could previously, in rare cases, lead to more than one active version of a sequence or sequence file pair for the same Seq_ID.

2024-02-14​

Changed​

• Performance improvements when navigating between project tabs in large projects; this will make only a small difference to current behaviour but will support future changes.

Fixed​

• Buxfix display of booleans (Has_sequences) on the sample detail page; do not display timestamps on dates which should not have timestamps on the sample detail page (e.g. date of collection).