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Release Notes

June 29, 2022 - ICA v2.7.0 and CLI v2.4.0

Features and Enhancements
  • API - Added method to retrieve an analysis JSON input data
  • Added Analysis Details views in the UI
  • Added Analysis ID to the project analyses
  • Support deep links for direct navigation to Analysis Details view
  • Added support for multiple Nextflow versions when creating Nextflow pipeline
  • API - Added method to create multiple samples in batches
  • API - Improved response time performance of API that launches analysis with many data inputs
Bugs Fixed
  • Repaired issue where Pipeline-generated Sample Metadata is not picked up by platform
  • Restored Time to delete function; now executes file deletes at the specified time
  • Bench example code now lists project data and pagination correctly
  • Restored ability to link secondary data to primary data
  • Fixed issue where batch sample creation jobs get stuck in PARTIALLY_SUCCEEDED status
  • Resolved issue where batch sample creation is not completed if data items could not be linked
  • API - Fixed issue where mountPaths were ignored when launching analyses via API
  • Restored function so that bundle contributors can link assets to their bundle
  • Restored data linking to a sample in an ICA project
  • Resolved issue where child workflow configurations prevent termination of parent workflow
  • Removed incorrect error reported in cases where previous failure occurred
  • Restored pipeline linking for bundle contributors
  • Improved UI messaging for Storage Configuration permission errors
  • API - Updated GET /api/projects/{projectId}/data to returns correct file details

07 June 2022 - ICA v2.6.0 and CLI v2.3.0

Features and Enhancements
  • Re-labeled "Run" and "Runs" to “Analysis” and “Analyses” in the UI
  • Allow storage configuration to be disconnected from a hidden Project
  • Added support for a read-only view of Entitled Bundles and Bundles shared from another Tenant
  • Changed analysis timeouts for setting up environment, downloading inputs, pipeline runner (inclusive of all child steps), and finalizing output steps to 96 hours
  • API – Add idempotency key header to createAnalysis API
  • API – Analysis logs are available via getAnalysisSteps API; includes streamable via websocket endpoint during execution and downloadable S3 URL upon completion
  • JSON data with array field can be added in a Base table
  • Cohorts – Additional submenu items now available
  • CLI – Added support for setting the current Project ID to the value set in the ICA_PROJECT_UUID environment variable upon starting the CLI
  • CLI – Added support for mounting Project data to local operating system (Read-Only)
  • CLI – Added support for the outputParentFolderId flag for the ‘projectpripeline start’ command
  • CLI – Added support for customizing the filename/path of additional Pipeline files with the pipeline create commands
  • CLI – Added owning Project name/id attributes to the project data list output
  • CLI – Added owning Project name attribute to output for projectdata list command
  • CLI – Added commands to create and refresh API tokens (JWT)
  • CLI – Added support for CLI use without writing to disk by enabling API Key and Server flags for all commands
  • CLI – Added support for linking data to a Sample with projectdata upload command
Bugs Fixed
  • Fixed an issue with UI stability leading to slow response times
  • Fixed an issue causing data uploads via browser to hang without error
  • Fixed an issue with UI automatically refreshing upon load when many Projects are present in the Projects view
  • Fixed an issue where Accept Share pop-up remains on screen after pressing to Accept the share
  • Fixed an issue with uploading nested folders using the Windows Connector
  • Fixed an issue where path separators are misinterpreted in upload rules for Windows Connectors.
  • Fixed an issue where modifying a local file uploaded (tracked) using the Connector causes a Connector failure
  • A User with Contributor Role for Flow and a Viewer Role for a Project can start an Analysis using input data from a Sample
  • API – Fixed an issue where sampleDeepDelete API fails with 500 error response when Sample contains a linked folder in archived status
  • Fixed an issue where ICA_STARTING_USER_TENANT_NAME is not set to the correct value on initial start
  • API – Fixed an issue where upload rules are not deleted via the deleteUploadRule API despite a success response
  • Sensitive fields in metadata models are now shown in italics
  • Fixed an issue where filtering on the Data view gives incorrect results
  • All Contributors in a Bundle are allowed to link assets to the Bundle
  • Content of a Bundle shared via an entitlement in another Tenant is now visible
  • Fixed an externally managed Project Team to only allow adding members with "Viewer" and "Allow Download" permissions
  • API – Fixed an issue with project sample APIs returning 500 error response when sample is not linked to the project specified in the request
  • API – Fixed issues with cursor-based paging on listData and listBundleData APIs returning expected results
  • Fixed an issue where a User can create empty folders inside an externally managed Project with Viewer permission
  • Fix auto-detection of AVRO and PARQUET data formats
  • API – Fixed an issue where the API to link Samples to a Bundle incorrectly returns a 204 response when the Sample is not in Available status and the Sample is not actually linked
  • API - Fixed an issue where changing the Project owner causes unexpected error responses from the listProjects, listProjectPermissions, and getProjectPermission APIs
  • API – Fixed an issue where deleteDownloadRule API returns 204 responses but does not delete the specified download rule
  • Fixed an issue causing delays in operations performed on data
  • Fixed an intermittent permission error when writing to /scratch from a Pipeline
  • Fix to make tags optional (not required) with Pipeline launch requests
  • Fixed an issue causing Analyses to be incorrectly set to SUCCEEDED status when failure occurs
  • API – Possible to create a Pipeline with a metadata model via API
  • Fixed an issue where logs are not streamed during Analysis
  • Fixed an issue when a User tries to start an Analysis with missing required parameters, the analysis is stuck in "awaiting input"
  • Fixed an issue preventing renaming a pipeline after attempting to save and receiving error that a pipeline exists with the same name
  • API – Fixed an issue when a Pipeline is launched via API with no input value provided for a nonmandatory input parameter the analysis status remains in "Awaiting Input" indefinitely
  • API – Fixed an issue causing unpredictable error responses from createAnalysis API when many Analyses are launched in rapid succession
  • API – Added operationID to API spec for the listAnalysisStorages and getAnalysisRawOutput APIs
  • Fixed an issue when Analyses are queued and Aborted before they are Running, the status is not correctly updated in the API/UI, and they appear stuck in “Aborting”
  • API – Fixed an issue with createAnalysis API causing error responses when launching many Analyses in rapid succession
  • Possible to load JSON in Base with a repeated field (array)
  • Tables created by the meta and admin data Schedules are updated after a sync
  • Fixed an issue causing Base Table field names to be changed from lowercase to UPPERCASE during a manual sync
  • Fixed an intermittent issue with Base Administrative/Meta-data Schedules creating files in project Data when schedules are run
  • Fixed an intermittent issue with Base Administrative/Meta-data Schedules creating files in project Data when scheduled
  • Fixed an issue where the User receives an obscure error message when creating a Tool from a Bench Workspace with an image name that already exists
  • Fixed an error message upon attempting to save Bench Workspace when input values are invalid
  • Fixed an issue where the Bench Workspace is temporarily inaccessible and stuck in Starting status
  • CLI – Fixed an issue with list samples command output limited to 20 unique records

April 2022 - ICA v2.5.0

Features and Enhancements
  • The value of the "Show Hidden Projects" filter on the Project Overview page will be saved for each user
  • Change analysis task log names to be more human-readable
  • Analyses will queue when system load is high
  • Add owning project tenant name (ICA_PROJECT_TENANT_NAME) and the tenant name of the user which last started the Workspace (ICA_STARTING_USER_TENANT_NAME) environment variables to Bench Workspaces
  • Add Cohorts URL environment variable to Bench Workspaces
  • API - Add support for Cross Origin Resource Sharing (CORS) to the API
Bugs Fixed
  • Fixed an error message in UI when attempting to link a Sample that cannot be linked
  • API - Fix issue where API to update Sample metadata fields does not update the fields
  • Fixed error message when creating a Bundle with a name conflict
  • Fixed error message when a user attempts to view Bundle details without permission
  • API - Fix Project Bundle APIs to properly link, retrieve, and unlink entitled Bundles
  • Fixed to block ability to link data with Contributor role and no upload permission on the target project
  • Fixed an issue where the Owner of an externally managed Project cannot add Team members with Viewer or Download permission
  • Fixed field for providing an e-mail address when adding a Team member to a Project to be required
  • Removed temporary directory creation by service connector
  • Fix for configuring service connector to use proxy settings on Linux clients
  • Fixed an issue where data downloaded through Service Connector is incomplete
  • Fixed an issue causing errors in Service Connector when a directory is deleted in the UI but still present on the local machine. Data added to the folder on the local machine will not be uploaded if the corresponding folder is deleted in the UI.
  • Fix to display an error message when saving a Pipeline with invalid fields
  • Fix issue where CWL file/directory inputs are not mounted when provided within nested structures (ie, CommandInputRecordSchema, CommandInputArraySchema)
  • Fix to show error when attempting to run a graphical CWL pipeline with an invalid definition
  • Fix error when attempting to save a graphical CWL Pipeline with a Tool with an output folder and no specified format
  • API - Fix to ignore input JSON field when launching graphical CWL pipelines via API
  • API - Fix ignored default compute type (machine profile) defined in the Pipeline definition when launching a graphical CWL Pipeline via API
  • Fixed Base Query result export file format set to UNKNOWN
  • Fixed Base activity log to show Table associated with log event
  • API - Ignore unknown attributes in request bodies
  • API - Fixed API error responses formatted as HTML instead of JSON in error scenarios
  • API - Fix list analyses API not returning the "items[].analysisStorage" field

April 2022 - ICA v2.4.0, v2.4.1, v2.4.2

Features and Enhancements
  • Samples may only be linked when status is Available
  • Added Data ID to grid view in UI
  • Added ability to select and copy tag values to the clipboard
  • Added an indication of source domain in list of reference data sets when adding new data to Reference Data
  • Updated the service connector client icon
  • Added ability to filter projects by workgroup, including projects where user is a member of a workgroup added to the project
  • Added ability to specify output directory within a project when launching a pipeline
  • Added ability to Favorite Projects and filter the Projects view by Favorites
  • Remove obsolete commented text from auto-generated CWL Tool definitions
  • Scheduler displays the number of files to be loaded into a Base Table
  • Added an indication that Base Table previews display up to 50 columns and 100 rows
  • API - New endpoint to manage SecondaryData on Data objects
  • API - Added support for "mounts" parameter when launching a pipeline to provide input mount paths for file and folder inputs
  • API - Added fields to API error response schema: HTTP Method, User ID, Tenant Name, Tenant ID
  • API – Added new endpoints for retrieving Entitled Bundles and to manage Project Bundles
Bugs Fixed
  • Docker images available via entitled bundles are listed in green text in the Docker Repository view
  • Fixed an issue in OpenAPI spec causing invalid cURL requests in 'Try it Out' functionality for the create upload URL API
  • Fixed an issue that resulted in empty Workgroup listing via the API and when adding Workgroups to a Project Team
  • Fixed an intermittent error when navigating to Bundles view
  • Fixed an issue where Tools available via Bundles are not displayed in the Tool Repository
  • Fixed an issue where example JSON generation for root Metadata Model fails when the root Metadata Model is modified
  • Fixed an issue where incorrect reporting of compute start times resulted in incorrect compute billing
  • Fixed an issue where Nextflow analyses get stuck "In Progress" when output folder is deleted during an ongoing pipeline run
  • Fixed an issue where incorrect casing on the scatter method 'dotproduct' in CWL auto-generated from graphical pipelines results in failures in pipelines with scatter-gather steps
  • CLI - Fixed an issue with startAnalysis APIs no longer accepting the 'Accept' header with value "application/problem+json,application/vnd.illumina.v3+json”
  • API/CLI - Fixed issue where graphical CWL pipelines launched via API/CLI do not use machine profiles (compute types) specified in the pipeline definition
  • Fixed an issue where pipelines within shared bundles could not execute across regions
  • Fixed an issue where exported Base Tables with null values populate a CSV with 'N' values instead of empty values
  • Fixed an error when loading data into Base Tables with an invalid number of columns
  • Fixed an issue causing View Results in Base Query History to return an expiration error
  • Fixed an issue that caused JSON import into Base Tables to fail when sub-field (record type) is used in the Table schema
  • Updated the error message when invalid SQL is used in a Base Query
  • Fixed an issue with JSON import to Base Tables failing when reference data fields are enabled
  • Fixed an issue where updated Base Table fields in the UI do not update the underlying Snowflake Table
  • Fixed an issue resulting in "Unable to create file error" message when creating a Tool in a Bench Workspace
  • Fixed an issue where Bench Workspaces cannot be deleted
  • Fixed an intermittent issue where Bench Workspaces unexpectedly fail in an error state
  • Updated messaging for users without access to Variant Viewer and Cohorts
  • API - Fixed an issue where the API did not accept multiple 'Accept' header values
  • API - Fixed an issue where the create folder upload sessions API returns date and time with incorrect formatting
  • API - Fixed the 500 response on APIs when the user has not yet accessed the UI
  • API - Fixed missing version header in OpenAPI spec for APIs to link a pipeline to a Project or Bundle
  • API - Fixed the 500 response from create project API when the 'storageConfigurationSubfolder' value is invalid
  • API - Fixed a 500 response from the API to link data to a bundle when linking a Folder with child data records
  • API - Fixed an issue where the API to create File data record creates the data record at the root of the project data when a trailing forward slash ('/') is missing after the folder name
  • API - Fixed an issue where API to retrieve pipeline reference sets does not display linked reference data
  • API - Fixed an issue where APIs to initiate analysis perform validation of required properties in request body

March 2022 - ICA v2.3.1

Bugs Fixed
  • Fix issue where pipeline launch is blocked when a single file is used as the input to multiple pipeline inputs

March 2022 - ICA v2.3.0

Features and Enhancements
  • A Base query is now possible with null marker 'nan'
  • A user can search on Secondary Data tab
  • A user is allowed to run a pipeline from a shared project if the Billing mode is set as 'Tenant'
  • Add "application" field to Project API model to indicate whether a project is externally managed.
  • An error is shown when a user tries to build a workspace that is not running.
  • An error is thrown when the user uses the same name of an existing project connector rule in the same project
  • Base query can be exported as a view
  • Bug fix for allowing multiple files with same name but different paths to be passed as input; causes conflict when downloading inputs to pipeline filesystem, one file will be overwritten (random) causing unpredictable results
  • Data filters and columns now also apply to technical tags
  • Externally managed projects are now supported via API
  • Meta data schedule can be created on tenant level
  • New ICA notification for Data/Sample linked
  • Preview of the content of a Base table is available with null marker nan
  • Project connector permissions are aligned with manual linking permissions
  • Remove obsolete "BlueVantage" option from the Source drop down selections during Base schedule creation
  • Revert cwltool upgrade
  • Samples linked via a project connector are visible in the 'receiving' project
  • The 'Type of Files' field in the configuration of Upload Rules in a Connector is changed to 'Assign Format' so that its purpose is clear
  • The project connector rules are available across tenants when the user has Contributor rights
  • The user is able to use the filters 'Type' and 'Status' and sort the files
  • The yaks-scheduler used to check the pod-to-node fit, but will now defer to the kubernetes default-scheduler as the pod-placement authority. The assumption is that when the pod is not scheduled, there are no nodes available, and a node will be provisioned.
  • When a user links a sample from another project to the current project, the data will not be automatically linked to the current project as well. The user should explicitly add the data to the current project as well if the user wants to use it.
  • [Base] When selecting 'Include reference', you will see the record first and when you unfold the record, you will see the fields belonging to the record
  • When trying to populate the Sample Metadata, we now always use the Project Metadata Model if there is no Pipeline Metadata Model.
  • [API] Add ability to filter by region for list projects API
  • [API] Add psToken authorization type to enable creating JWT from psToken via the create token API
  • [Bench] Add ICA_PROJECT_UUID environment variable to the Jupyter Notebook Bench image.
Bugs Fixed
  • Fix 400 error response when launching an analysis with a pipeline from a bundle
  • Fix Base Query results file export set to format UNKNOWN
  • Fix Bench pricing calculation accuracy
  • Fix for Base table export unexpected failure
  • Fix for auto-linking pipeline outputs files to a sample when input files provided are linked to the sample
  • Fix for failed Base table import when imported data contains "nan" (null marker) for a column of type integer
  • Fix for linking Base Query templates to Bundles
  • Fix for modifying Bench Workspace image unless Workspace is in Stopped state
  • Fix for more informative API error response when EULA has not been accepted
  • Fix for preserving sample data links for samples linked from shared bundles
  • Fix for retrieving download URL for data in an externally managed project.
  • Fix for silent error when running Base schedule on Administrative Data or Metadata
  • Fix intermittent UI issue where checkbox for file selection during docker image add is partially visible
  • Fix issue where Base schedule for Metadata does not work when source is set to "Tenant"
  • Fix issue where Base table schema definition changes from record to string after sync
  • Fix issue where Project Connectors cannot link samples where the source project is owned by a different tenant
  • Fix issue where an analysis cannot be started when a metadata model is defined for the pipeline
  • Fix issue where data cannot be removed from a Sample using the "Remove Data" button from the sample details view.
  • Fix issue where pipelines from linked bundles do not show as available selections in the "Generated by Pipelines" drop down when creating a Base schedule
  • Fix issue where samples cannot be updated after configuring a Project Connector rule with the sample.
  • Fix issue where scroll bar is not shown in the metadata models list view
  • Fix issue where secondary data is not shown in the reference data view
  • Fix issue where team members added to eternally managed projects cannot be granted Contributor permissions, and cannot link data to other projects
  • Fix issue where user cannot use sample filtering when samples and files are manually linked to their project and the files do not appear associated with their sample in that project
  • Fix issue where user is unable to see their input files when using sample filtering if they are linked from another project without selecting the flat view option
  • Fix issue where workgroups cannot be added to project team of externally managed projects with Contributor permission
  • Handle K8s api timeouts by retrying query.
  • Improve pipeline analysis startup times to approximately 10 mins maximum (times may vary)
  • [API] Fix 500 response for getProjectDataLinkedProjects API
  • [API] Fix error response when invalid API Key is provided for authorization
  • [API] Fix get bundles API error response when user has access to a project with a linked bundle that the user does not have access to
  • [API] Fix getProjectData API to return correct results when using the "id" query param
  • [API] Fix incorrect error response for Project Data API to create folder upload session

February 2022 - ICA v2.2.0

Features and Enhancements
  • the cwl workflow engine logs now also show debug logs, these includes the javascript expressions evaluated etc. these logs are similar to running cwltool --debug locally
  • Show "username" of pipeline creator in Pipelines overview view
  • Removed excessive logging from the "Audit Trail" logging.
  • Various performance improvements - reuse of connections to Base instances
  • A particular storage configuration should only be available during project creation in case it is your own storage configuration, or when the owner (or a tenant administrator) gives explicit access to it for other users in their tenant.
  • Bench - when trying to get an access token through the API, access was denied in case Base was not enabled within the project.
  • Base - 'You are not allowed to modify data' was shown to the user when clicking the Sync button as a Contributor
  • Base - importing data with format JSON in a table was not possible.
  • Files within a sample will only show up in case the data is also explicitly linked to the project/bundle.
  • Bundles - a user with Contributor access did not have the necessary access rights for managing all resource of the bundle.
  • Project billing modes can be 'project' or 'tenant'. In case 'tenant', the users from another tenant than the owner of the project was not able to upload files.
  • Within the Activation Codes view, activation codes for access to the Variants/Cohorts modules were not listed.
  • It was not possible to add a bundle at project creation. The project had to be saved before the bundle could be added.
  • The roles explanation in the Team page on a permission record did not show the entire information.
  • Various stability improvements - In case of a database outage, ICA was not able to automatically reconnect.
  • When managing docker images, a partial docker image was not allowed to be deleted nor updated resulting in a stuck image.
  • When exporting the contents of a grid from the UI, the exported file contained tenant ids instead of tenant names.
  • Base - the export of query results to a json format resulted in a failure in case the query ended with ';'
  • A non-tenant-admin user was not able to create a metadata model.
  • Base - exporting query results, specifying a custom delimiter did not work.
  • When a user clicks the bundle card in the "Bundles" view, and the user has no access to manage the bundle because it is shared with the user by another tenant, the following notification will be displayed: "Details for a bundle from another tenant are not accessible" instead of "Bundle details unavailable"
  • When a user links a sample from another project to the current project, the data will not be automatically linked to the current project as well. The user should explicitly add the data to the current project as well if the user wants to use it.
  • Various performance improvements - linking a folder with a lot files to another project or bundle timed out.
  • Base - loading metadata into a table using a schedule resulted in the same data being added over and over again.
  • When trying to populate the Sample Metadata, we now always use the Project Metadata Model if there is no Pipeline Metadata Model.
  • Limit usable character set for the user reference of an analysis run
  • When an analysis was aborted, the output files which were generated so far were not visible in the details of the analysis, but only in the data view.
  • Base - schedule metadata population in a table did not work.
  • Added support for Docker Images to be added to Bundles
  • Added Project Connectors in the project connectivity section to enable creation of automatic sample and data linking rules between projects.
  • Added Queue Date to analysis Logs view to indicate when the specified job was submitted to the underlying infrastructure.
  • Added support for externally-managed projects for Illumina software applications built on top of ICA to manage resources inside ICA projects while limiting tenant users' direct access to the project to read-only capacity.
  • Improved performance of API calls when using API Key for authentication
  • Added tenantName to API resource DTOs
  • Add API to abort analysis run
  • Added APIs to share a storageConfiguration, share a storageCredential, update a storageCredential secret
  • Added mime-type field to the DataFormat DTO for the data APIs
  • Added "objectEtag" field to DataDto for Data APIs to expose e-tag from the cloud provider object store
  • Added Base APIs to retrieve Jobs, retrieve Tables, and load data into Table
  • API - POST‚/api/projects/{projectId}/samples:search was missing request parameters to browse through samples in a paged manner.
  • API - POST /api/projects/{projectId}/analysis:cwl - tags were not persisted when starting a CWL analysis run
  • The PUT /project/{projectid}/data/{dataid} gives the user the impression that all fields can be updated on the data, but it is a different set for files as for folders. This distinction is not properly documented.
  • API - GET /api/projects/{projectId}/analyses - when the pipeline did not belong to the tenant, but the user still has access to it (eg: through a bundle), the analysis details could not be retrieved through the API.
  • API - GET /api/projects/{projectId}/analyses/{analysisId} returned the details of an analysis, even if the projectid did not match the actual project the analysis ran in.
  • API - GET /projects/{projectId}/samples/{sampleId} did not expose metadata information
  • API - GET /projects/{projectsId}/data presented the user with an unclear error message in case providing invalid request parameters.
  • API - An unclear error was presented in the problem response in case an invalid json was provided as request body.
  • API - An unlcear error was presented in the problem response when creating a project using invalid uuids in the request body.
  • API - Removed deprecated "sample matching strategy" endpoint
  • [cli] Added command to update project data
  • [cli] Added command to retrieve a list of project samples
  • [cli] Added command to create a project sample
  • [cli] Added command to list available data formats
  • [cli] API Key encryption modified to use local value on machine where API Key is configured to prevent hijacking config.
  • [cli] Added command to get details of a project sample
  • [cli] Added command to list data linked to a project sample
  • [cli] Added command to update a project analysis
  • [cli] Added command to update a project sample
  • [cli] Added command to unlink data from a sample
  • [cli] Added commands to delete a project sample
  • [cli] Added command to link data to a sample
  • [cli] Added command to complete a sample
  • [cli] Removed unnecessary flags on the config command.
  • [cli] For starting CWL and Nextflow pipelines, the flag 'storage-size' was ignored by CLI, and the default storage size of the pipeline was taken.
Bugs Fixed
  • [bugfix] when CWL workflows failed or produced null as one of the outputs, all the outputs were incorrectly processed. in this case, the user may not be able to see the details of the analysis output in UI/API.
  • [Base] Fix error message when viewing a query from query history that no longer returns results
  • [bugfix] in some cases after aborting an analysis, it may remain stuck in aborting state indefinitely. Now more resources are explicitly cleaned to avoid this issue from happening.
  • Fixed bug when showing logfiles of steps in an analysis.
  • [bugfix] cwl workflow sometimes fails in spite of all steps in the workflows have succeeded. Made the workflow engine robust to detect and retry in this case
  • When linking a folder containing +2000 files to another project, only 2000 files were actually linked.
  • When a user did not choose a country when filling out the user account details, login to ICA could fail.
  • Fixed bug when handling custom output objects in CWL.
  • Fixes issue with compute type selection when launching CWL graphical pipelines
  • The Project > Team permissions showed a little pencil in front of the row indicating a modification. With this fix, the pencil will only show when there were actual modifications done to the row in particular.
  • API - All dates in API responses were formatted in 12 hours notation without AM/PM notation. This way a time in PM is presented as AM. With this fix, all time notations are in 24 hours.
  • When starting an analysis through the sample page, the start window is not closed after pressing start. Users would click it again, which would start the analysis multiple times. With this fix, the start window is closed after pressing start.
  • When starting an analysis fails because the backend service returns an error, the status of the analysis is "Awaiting Input". With this fix, the analysis goes to "Failed".
  • Base - in case the export of query results failed, an empty file was created and never cleaned up. With this fix, there are no leftovers in case of export failure.
  • When a sample was linked from another project to the current project, the details view of the sample shows all data linked to it, even of the current project does not have access to it. With this fix, only the data which is also linked to the current project will be shown on the details of the sample.
  • API - PUT /project/{projectid}/data/{dataid} update sometimes had to be done twice for it to persist. With this fix, all editable attributes can be updated at once.

Decemeber 2022 - ICA v2.1.0

Features and Enhancements
  • [CLI] Storage size can be entered by name
  • [CLI] Details of a project analysis can be retrieved by entering the analysis Id
  • [CLI] A list of metadata models can be retrieved
  • [CLI] A list of regions can be retrieved
  • [CLI] A list of storage configurations can be retrieved
  • [CLI] A pipeline can be linked to a project by using the name/id of the pipeline as an argument
  • [CLI] A pipeline can be unlinked from a project by defining the name/id as an argument
  • [CLI] A list of storage bundles can be retrieved
  • [API] Usability improvements for the list project data API:
    • Modify filePath query param to behave as prefix instead of exact match by default
    • Add filePathMatchMode query param
    • Add parentFolderPath query param
  • [API] Add API endpoint to refresh a JWT (POST /api/tokens:refresh)
  • [CLI] Add CLI command to create projects
  • [API] Support search by tags on samples search API
  • Renew macOS connector certificate
  • When a filter is applied and you select a folder, you can see the content from that folder without th* Connector rules for a project can only be changed when you are active in that project
  • It is possible to link more than 2000 files to a bundle or another project
  • Data coming from a project in another tenant can be linked when you are invite for collaboration
  • The error from a failed pipeline analysis is visible on the details page
  • Species and type are unique within a tenant, not across tenants
  • Sqs and sns test messages are aligned with the email test message
  • A collaborating user from another tenant is able to see the details view of a pipeline analysis run.
  • Bundle data can be used via API
  • When executing api/projects/{projectId}/data and a file already exist, there is an indication that thresponse.
  • Connector cancel button is renamed to delete to make its functionality more clearly
  • [CLI] Modify pipeline start command to use pipeline name or ID as an argument instead of a flag parameter
  • [API] Removed endpoint to POST on a sample metadata model
Bugs Fixed
  • [Base] Fix error message when viewing a query from query history that no longer returns results
  • [CLI] Fix for CLI upload command when uploading a folder with 0 bytes files
  • [API] Fix create bundle API to return error when bundle with existing name is attempted to be created
  • [API] Fix for non-functional If-Match header on PUT requests
  • [CLI] Fix folder upload "panic: close of closed channel" error
  • [API] Fix API for project creation returning success with invalid storage configuration provided
  • [Bench] Fix for docker build logs not showing when build is interrupted
  • Fix population of sample metadata from multiple analyses on the same sample
  • Fix error message for missing docker image on tool creation
  • [CLI] Fix pipeline create command to make pipeline code an argument instead of a flag parameter
  • Fix UI element for tags to remove active button appearance
  • Fix error when attempting to link pipeline with no pipeline selected
  • Fix error message when attempting to add field to Base table schema with invalid characters
  • Fix issue with analysis outputs files and logs not showing after analysis completion
  • Fix UI issue with pipeline selection in the Generated by Pipelines field of the view to create a Base s
  • Fix issue with a duplicate workspace being created while editing a workspace
  • Fix issue for table creation using schedule for metadata
  • Fix Base viewer role when applied to workgroups
  • Fixed Issue: optional parameters for Nextflow pipeline cause error when value not provided
  • Fixed issue when selecting data records to export from the Data overview page on a Bundle
  • Fix for Base saved queries not visible in shared project
  • Fix minor price calculation error (rounding) for Base storage

November 2022 - ICA v2.0.0

Features and Enhancements
  • API cursor-based and offset-set paging
  • Authorize calls using Illumina API key
  • Multiple reference data elements are possible when starting an analysis
  • APIs added for:
    • Account, User, Workgroup
    • Connector, Download Rule, Upload Rule
    • Data, Data Format, Data Transfer
    • Region
    • Download
    • Entitlement
    • Event Log
    • Project, Project Analysis, Project Data, Project Permission, Project Sample, Project Pipeline
    • Metadata model
    • Pipeline
    • Bundle
    • Notifications, Event Codes
    • Base
  • OpenAPI v3 API Spec published at https://ica.illumina.com/ica/api/swagger/index.html
  • Added sort parameter to several APIs
  • Custom event payload is defined as a json
  • Separate call to retrieve metadata model fields available
  • Add rclone temporary credentials support in the API to retrieve folder upload session details
  • Tokens API POST also contains basic authentication
  • Activation code endpoints are aligned with start analysis endpoints
  • Base templates cannot be deleted
  • Information can be written from Bench to Base
  • Viewer/Contributor permissions are introduced in Snowflake
  • Saved Template details can be edited
  • Access via Illumina authentication is available
  • Snowflake access token can be created
  • Added new Bundles feature for sharing data with other users
  • ICA allows the user to connect an S3 bucket as storage instead of an Illumina managed storage
  • An overview of all storage configurations is available
  • Secrets can be managed for the storage configuration
  • A new storage configuration can be added
  • The health status of a configuration can be monitored
  • A storage configuration can be deleted when not used in a project
  • Storage type and health are displayed in the overview
  • When selecting own storage ICA will return you a list of all BYOBs in the chosen region
  • A default bucket can be selected for every region
  • Data is automatically archived/deleted when the grace period (if present) is over
  • Data is archived/deleted automatically by a housekeeping mechanism
  • An admin user can change the date to be archived/deleted at any time
  • Data has a status
  • Data format is automatically detected at creation
  • Files can be grouped in a sample
  • Data can have additional linked projects
  • The data screen shows project data and data linked via a bundle
  • 3 new columns are present in the data grid: "Owning Project", "Linked Projects" and "Linked Bundles"
  • The record is displayed in the data grid depending on the data being linked or not
  • Filter on Status with checkboxes on status values is possible
  • Total Data Size is available
  • Data can be linked/unlinked to/from a project
  • Only root parent files and folders are shown when opening the data grid
  • Deleted status does not exist anymore
  • Data from projects with Data Sharing disabled cannot be linked
  • Project is hidden instead of (soft-)delete
  • Metadata models can be created for linking to a project
  • Add support for Nextflow pipeline language
  • A pipeline input can have multiple formats
  • Output JSON for CWL analysis is shown
  • Ongoing logfiles are available for the user
  • You have two options to define a CWL pipeline: Graphical editor or code
  • Test connection button is available for SQS
  • Checkbox is added to toggle view between all rules or only your own rules
  • Notification channels can be validated
  • Subscription can be edited
  • Custom subscriptions are possible
  • Notifications can be received via SQS, SNS, Mail, and Webhook
  • All users have an overview of all the notifications used in their tenant
  • Notification channels are only visible for tenant admins
  • Notifications can have a filter expression to only receive specific events
  • A project administrator can grant permission to a single user on a project
  • A project administrator can invite somebody unknown to ICA to his project
  • A contributor can manage reference data
  • A project administrator can define who pays for using my project
  • A project administrator can invite a workgroup to a project
  • When multiple project roles are given to a user/workgroup the correct project role is applied
  • Team-page in projects and bundles are aligned
  • Reference data can exist in multiple regions
  • Species and type are being populated per tenant
  • Data can become reference data
  • Data tree shows all the regions in which the reference data is available

Known Issues

  • Connector: Locally installed connectors not automatic upgraded when new ones are installed
  • Manual refresh on Data view required after archive/unarchive action to reflect new status
  • Project menu does not update when navigating into a Project in Chrome
  • Unable to get pre-signed URL or retrieve ObjectStore Credentials for files and with UTF-8 characters
  • User with ‘Data Provider’ role cannot view the Data page in the UI
  • Unable to add tags to sample during creation
  • Sample deleteDeep API fails with 500 error code when sample contains a linked folder in archived status
  • Unable to set file formats BedGraph, Bisulfite Converted Index, CNS.TAB, NextSeq/MiSeq/HiSeq RTA BCL, VCF.IDX - results in the UNKNOWN format when viewing file details
  • Workflows attempting to provision nodes of instance types with capacity issues may result in prolonged waiting periods and/or pipeline run failures
  • Graphical CWL pipelines containing Tools with any Input file with a populated "format" will always fail
  • Incorrect failure cause reported through error logs when infrastructure fails to spin up nodes for pipeline steps
  • Issue handling special characters in input file/folder paths
  • Unable to specify secondaryFiles when launching CWL pipeline runs via API
  • CWL file/directory pipeline inputs are not mounted when provided within nested structures (ie, CommandInputRecordSchema, CommandInputArraySchema)
  • No clear message in UI when invalid characters are entered when creating a new Bench Workspace
  • Unable to enter a Bench workspace stuck in Starting status
  • CLI – Fuse merges folders with the same names but different casing in local mount
  • CLI – CLI no longer allows pipeline linking to a project by name – requires UUID