2024
2024 December 13 - ICA v2.31.2
Fixed Issues
When creating a new cohort, the disease filter’s tree hierarchy was not showing up, meaning it was not possible to add disease filter into the cohort definition. This has been resolved.
2024 December 12 - ICA v2.31.1
Fixed Issues
Flow
Fixed an issue which caused service degradation where analysis steps were not properly updated until analyses were finished, and log files only became available after completion.
2024 December 4 - ICA v2.31.0
Features and Enhancements
General
General usability improvements for the project overview screen
The timing for when jobs are deleted has been updated so that:
SUCCEEDED remains 7 days
FAILED and PARTIALLY_SUCCEEDED are increased to 90 days
Data Management
Data can now be uploaded into the BaseSpace-managed project
Flow
Analyses can now be started from the pipeline details screen
The analysis details now contain two additional tabs displaying timeline and execution reports for Nextflow analyses to aid in troubleshooting errors
Introduced a start command for starting a Nextflow pipeline with a JSON-based input form
Added new API endpoints to create a new CWL pipeline and start an analysis from a CWL pipeline with JSON-based input forms:
POST/api/projects/{projectId}/pipelines:createCwlJsonPipeline
POST/api/projects/{projectId}/analysis:cwlJson
Pipelines with JSON-based input forms can now pre-determine and validate storage sizes
Added support for tree structures in dropdown boxes on JSON-based input forms to simplify searching for specific values
Introduced a new filtering option on the analyses gid to enable filtering for values which differ from, or do not equal (!=), a given value (such as exit codes in the pipeline steps in the analysis details screen)
The analysis output folder format will now be user reference-analysis id
Cohorts
The side panel now displays the Boolean logic used for a query with ‘AND’, ‘OR’ notations
The needle plot visualization now drives the content of the variant list table below it. By default, the list displays variants in the visualization and can be toggled to display all variants with subsequent filtering
For diagnostic hierarchies, concept children count and descendant count for each disease name is displayed
The measurement/lab value can be removed when creating query criteria
Fixed Issues
General
Notification channels are not created at the tenant level and are not visible to members of external tenants working on the same project
Data Management
Fixed an issue where move jobs fail when the destination is set to the user’s S3 bucket where the root of the bucket mapped to ICA as storage configuration and volume
Fixed a data synchronization issue when restoring an already restored object from a project configured with S3 storage
Flow
Corrected the status of deleted Docker images from incorrect ‘Available’ to ‘Deleted’
The reference for an analysis has changed to userReference-UUID, where the UUID matches the ID from the analysis. (The previous format was userReference-pipelineCode-UUID.)
Pipeline files are limited to a file size of 20 Megabytes
Bench
Fixed an issue which caused ‘ICA_PROJECT_UUID not found in workspaceSettings.EnvironmentVariables’ when creating a new Workspace
Cohorts
Fixed an issue where the system displays ALL/partial filter chips when the top level tree node is selected in a hierarchical search
Fixed an issue where the system displays 400 bad request error despite valid input of metadata files during import jobs
Fixed an issue where the system displays inconsistent hierarchical disease filter results
Fixed an issue where the system changes the layout when displaying the p-value column
Fixed an issue where the system disables the next blutton when there is no study available in the dropdown menu
Fixed an issue where studies could not be selected when a project has one study to ingest data into
2024 October 31 - ICA v2.30.1
Fixed Issues
Mitigated an issue causing intermittent system authentication request failures. Impact includes analysis failures with "createFolderSessionForbidden" error
2024 October 30 - ICA v2.30.0
Features and Enhancements
General
The projectdata upload CLI command will from now on give you the credentials to access the data
Data Management
Introduced a limit to the number of data elements that can be put in POST /api/projects/{projectId}/dataUpdateBatch to 100.000 entries
Flow
Users can now access json-based pipeline input forms for both Nextflow and CWL pipelines. API access is not yet available for CWL pipelines
Added GPU compute types (gpu-small, gpu-medium) for use in workflows
Users can now sort analyses by request date instead of start date, which was not always available
The analysis details page has been upgraded with the following features:
The progress bar which could be found on the analyses overview page will now also appear in the details page
A maximum of 5 rows of output are shown for each output parameter, but the output can be displayed in a large popup to have a better overview
Orchestrated analyses are shown in a separate tab
Cohorts
Users can now use the Measurement concept API to create cohorts based on lab measurement data and harmonize their values to perform downstream analysis
Users can now access the Hierarchical concept search API to view the phenotype ontologies
Fixed Issues
General
The mail option is now automatically filtered out for those events that do not support it
Fixed an issue where there was no email sent after rerunning a workflow session
Fixed an issue which caused authentication failures when using a direct link
Made file and folder selection more consistent
Fixed an issue with the CLI where using the “projectsamples get” command to retrieve a sample shared via an entitled bundle in another tenant failed
Fixed filtering so you can only see subscriptions and channels from your own tenant
Improved GUI handling for smaller display sizes
Fixed the workflow session user reference and output folder naming to use BaseSpace Experiment Name when available
Data Management
The unlink action is now greyed out if data not linked is in the selection
Fixed an issue that when deleting folders, the parent folders were deleted first, giving the impression that the parent folder is deleted but not the subfolders and files
Fixed an issue where the connector downloads only downloaded the main folder, not the folder contents
For consistency, it is no longer possible to link to folders or files from within subfolders. Previously, you could link, but the files and folders are always linked to top level instead of the subfolder from where linking was done
Updated error handling for dataUpdateBatch API endpoint
Moving small files (>8Mb) will not trigger a "moving" event, only that the move has completed as out-of-order events caused issues and moving small files happens fast enough to not need the status of being moved, only the completion of the move
Improved error handling when encountering issues during cancellation of data copy/move
Improved error message when trying to unlink data from a project via the API when this data is native to that project and not linked
Fixed issue where analysis can proceed to download input data when any of the inputs are in status other than AVAILABLE, including records within folder data inputs
Flow
Redesigned UI component to prevent issues with Analysis summary display
Fixed an issue where the field content was not set to empty when the field input forms have changed between the original analysis and a rerun
Replaced retry exhaustion message, "External Service failed to process after max retries 503 Unique Reference ID: 1234" with a more useful message to end users that advises them to contact Illumina support: "Attempt to launch ICA workflow session failed after max retries. Please contact Illumina Tech Support for assistance. Unique Reference ID: 1234". This does not replace more specific error messages that provide corrective advice to the user, such as "projectId cannot be null"
For efficiency reasons, pipeline files are limited to a file size of 100 Megabytes
Bench
Fixed an issue which caused .bash_profile to no longer source .bashrc
Fixed the status of deleted docker images which previously were displayed as available
After creating a tool, the Information tab and Create Tool are now no longer accessible to prevent erroneous selection
Cohorts
Fixed layout issue where buttons were moved up when the user selected the option
Fixed issue where user was not able to view PheWas plot when multiple cohorts are open and same gene is searched
Fixed issue where the user was not able to view GWAS plot when multiple cohorts are open and user switched forth and back between cohorts
Fixed issue where users were not able to see the cryogenic map in the gene summary page for gene associated with the chromosome
2024 September 27 - ICA v2.29.1
Fixed Issues
General
Fixed an issue where various Data Transfer Ownership API calls were failing with a 'countryView' constraint violation error
2024 September 25 - ICA v2.29.0
Features and Enhancements
General
Dynamically linked folders and files now have their own icon type, which is a folder/file symbol with a link symbol consisting of three connected circles
Data Management
With the move from static to dynamic data linking, unlinking data is now only possible from the project top level to prevent inconsistencies
The user can now manually, dynamically link a folder
The icav2 project data mount command now supports the “--allow-other” option to allow other users access to the data
The user can now set a time to be archived or deleted for files and folders with the “timeToBeArchived” and “timeToBeDeleted” parameter on the “POST/api/projects/{projectId}/dataUpdateBatch” command
Added 4 new API endpoints which combine the create and retrieve upload information
Flow
The default Nextflow version is now 22.04.03, from 20.10.0
The user can now specify the Nextflow version when deploying a pipeline via the CLI with the “--nextflow-version” flag
Bench
The user now has the option to choose either a tool or bench as a docker image when adding new docker images
It is now possible to open contents of a Bench workspace in a new tab from the Bench details tab > access section
Fixed Issues
General
Improved handling of API calls with an invalid or expired JWT or API token
Data Management
Renamed the "New storage credential" button to "Create storage credential"
Removed the "Edit storage credential" button. The user can now edit the column directly in the open dialog when clicking on the name
Performance improvements to scheduled data download
Fixed an issue where data records were shown more than once when updating the tags\
The data details were erroneously labeled with "size in bytes" while the size was in a variable unit
Fixed an issue where trying to download files could result in the error "Href must not be null" when the file was not available
Fixed an issue where existing data catalog views would return an empty screen caused by a mismatch in role naming
Flow
Fixed an issue that caused opening a pipeline in the read-only view to incorrectly detect there were unsaved changes to the pipeline
Fixed an issue when having different pipeline bundles with the same (name) resource models would result in duplicate listing of these resources
Improved error handling when encountering output folder creation failure, which previously could result in analysis being stuck in REQUESTED status
By default Nextflow will no longer generate the trace report. If you want to enable generating the report, add the section below to your userNextflow.config file:
trace.enabled = true
trace.file = '.ica/user/trace-report.txt'
trace.fields = 'task_id,hash,native_id,process,tag,name,status,exit,module,container,cpus,time,disk,memory,attempt,submit,start,complete,duration,realtime,queue,%cpu,%mem,rss,vmem,peak_rss,peak_vmem,rchar,wchar,syscr,syscw,read_bytes,write_bytes,vol_ctxt,inv_ctxt,env,workdir,script,scratch,error_action'
Fixed the issue where users not allowed to run or rerun workflows could start them from the API or BaseSpace SequenceHub. Now, users that cannot start workflows cannot rerun them.
Cohorts
Fixed issue where the users can select the lower needles despite the overlap of multiple needles at the same location in the needle plot
Fixed issue where the user would not be able to view the cryogenic map in the gene summary page for gene associated with the chromosome
Fixed issue where the user would not be able to view the PheWas plot when multiple cohorts are open and same gene is searched
2024 September 5 - ICA v2.28.1
Features and Enhancements
Data Management
Improved performance of data linking jobs
Fixed Issues
General
Fixed an issue causing slow API responses and 500 errors
2024 August 28 - ICA v2.28.0
Features and Enhancements
General
The CLI readme file will now additionally contain the CLI build number
Data Management
Fixed an issue where there was a discrepancy between the Run Input tags shown to the user and what was stored on the data
Added a 25,000-item limit to the v3 endpoint for batch data linking. Using the v4 endpoint, which does not have this limitation, is recommended
Flow
Analyses and workflow sessions can now be resubmitted, and parameters can be updated upon resubmission
Changed the default image used for CWL pipeline processes with undefined image from docker.io/bash:5 to public.ecr.aws/docker/library/bash:5
Updated the choice of default nextflow docker image which is used when no docker image is defined. It is now public.ecr.aws/lts/ubuntu:22.04_stable
The analysis logs in the analysis details page can be refreshed
The user is now able to write a pipeline which executes files located in the /data/bin folder of the runtime environment
Pipeline files are now shown in a tree structure for easier overview
Cohorts
Updated GWAS UK Biobank data base gives users access to more phenotype information
Users can now incrementally ingest their molecular data for germline, CNV, structural variants, and somatic mutation data
Fixed Issues
General
Added an "All" option to the workgroup selection box in the projects view to reset the filter, which previously required you to delete all characters from the filter
Fixed an issue where updating two base permissions at the same time would sometimes not execute correctly
Fixed an issue where creating grid filters could result in a nullpointer error
Fixed an issue where 'Copy to Clipboard' button did not work anymore
After searching for a folder in the search box and going into that folder, the search box is now cleared
Improved the project permissions API to correctly handle empty values
Previously, when attempting to save and send a message from the Websolutions section without a unique subject, the system would report an error and still send the message. Now the non-unique message subject error is reported and no message is sent
Fixed an issue where linking samples in the sample screen would result in receiving the same "sample(s) linked" message twice
Improved error handling for CLI FUSE driver
Hardened log streaming for ongoing runs to better handle network issues which previously would result in missing log streaming
Add retries for "connected reset by peer" network-related errors during analysis upload tasks
Fixed an issue where inviting a user to collaborate on a project containing base would result in the error "entity not managed" if that user did not have base enabled in any project or if base was not enabled in the project tenant
Data Management
Fixed an issue where data could be moved to a restricted location called /analyses/ and no longer be visible after the move. Please contact Illumina Support with your data move job information to recover your data if you have encountered this issue
Fixed an issue where sorting on data format did not work correctly
Copying empty folders no longer results in a partially copied status
ICA now performs an automatic refresh after unlinking or deleting a sample
Improved handling of file path collisions when handling linked projects during data copy / move
Fixed an issue where, even though uploading a file in a linked folder is not permitted, this would erroneously present a success message without copying the file
Analysis-events which are too large for SQS (256KB) are now truncated at the first 1000 characters when using SQS
Improved error handling when trying to upload files which no longer exist
Fix system degradation under load by introducing rate limit for spawning tasks for a given analysis to 25 per 1 min
The createUploadUrl endpoint can now be used to upload a file directly from the region where it is located. The user can create both new files and overwrite files in status "partial"
Improved the project data list command with wildcard support. For example:
/ or /* will return the contents of the root
/folder/ will return the folder
/folder/* will return the contents of the folder
To optimize performance, a limit has been set to prevent concurrent uploading of more than 100 files
Fixed an issue where folder syncing functionality would sometimes result in “Unhandled exception in scheduling worker”
Flow
Fixed an issue where writing a pipeline which executes files in the /data/bin folder wasn't functioning properly with larger storage classes
Nextflow pipelines no longer require pipeline inputs when starting them via the CLI
Improved error handling when using an unsupported data format in the XML input forms during pipeline creation
Fixed the issue where it was not possible to add links in the detail page for pipelines and bundles
Sorting is no longer supported on duration and average duration columns for analysis grids
In situations where the user would previously get the error "zero choices with weight >= 1" after the first attempt, additional retries will execute to prevent this from occurring
Cohorts
Fixed an issue resulting in a blank error when a cohort with hundreds of diagnostic concepts was created
2024 July 10 - ICA v2.27.1
Features and Enhancements
Flow
Improved analysis queue times during periods of limited compute resource availability
2024 June 25 - ICA v2.27.0
Features and Enhancements
General
New notification to the user when a copy job finishes running
Updated the "GET analysis storage" API endpoint to account for the billing mode of the project. If the billing mode of the project is set to tenant, then the analysis storage of the user's tenant will be returned. If the billing mode of the project is set to project, then the analysis storage of the project's owner tenant will be returned
A ReadMe file containing used libraries and licenses is now available for ICA CLI
Data Management
New DataFormats YAML (.yaml, .cwl), JAVASCRIPT (.js, .javascript), GROOVY (.groovy, .nf), DIFF (.diff), SH (.sh), SQL (.sql) to determine the used syntax highlighting when displaying/editing new pipeline files in the UI
ICAv2 CLI supports moving data both between and within projects
Added an alert to notify users when data sharing or data move is disabled for the project
A new version of the Event Log endpoint has been developed to support paging, retrieval of previous events, and resolution of inconsistencies in date formats. This new endpoint introduces the EventLogListV4 data transfer object
The user is now able to select a single file and download it from the browser directly. This does not apply for folders and multiple files selected at once
User can subscribe to notifications when data is unarchived
The BaseSpace Sequencing Run Experiment name will now be added to the technical tags when a workflow session is launched
Flow
Fastqs with the .ora extension are now supported when staging these for secondary analysis, either as a list of fastqs or as fastq_list_s3.csv files
Before, users had to click on the pipeline on the pipeline overview screen to start a new analysis. Now, you will enter the pipeline in edit mode when you click on the pipeline name. If you want to select a pipeline to start an analysis, you need to check the checkbox
Fixed Issues
General
Removed the refresh button from the workspace detail view as it was superfluous
Fixed an issue where searching for certain characters in the search field of the Projects or Data overviews screen would result in an indecipherable error
Improved security handling around tenant admin-level users in the context of data move
Data Management
Fixed a bug so folders copied from another previously copied folder no longer results in a corrupted file
Fixed an issue where creating a new bundle would result in an error if a project with the same name already exists
Data move between projects from different tenants is now supported
Fixed an issue where not selecting files before using the copy or move commands would result in EmptyDataId errors
For the CLI, Improved notifications when files can not be downloaded correctly
Fixed an issue where scheduled downloads of linked data would fail without warning
Corrected an issue where the tenant billing mode would be erroneously set to Illumina after a data copy
Fixed an issue where BatchCopy on linked data did not work
Flow
Resolved an issue to ensure that when a user creates a pipeline using a docker image shared from an entitled bundle, their analyses utilizing that pipeline can pull the docker image without errors
Removed superfluous options from the analysis status filter
Awaiting input
Pending request
Awaiting previous unit
Fixed an issue where writing a pipeline which executes files in the /data/bin folder wasn't functioning properly with larger storage classes
Fixed an issue where many-step analyses are getting stuck in "In Progress" status
Fixed an issue where the wrapper scripts when running a CommandLineTool in CWL would return a warning
Fixed the issue which caused the "Save as" option not to work when saving pipelines
Base
Fixed an issue where the ICA reference fields in the schema definition had the wrong casing. As a result of this update you might end up with 2 different versions of the reference data (one with keys written with an uppercase letter at the start, another one with keys written entirely in lowercase letters). To fix this:
Update your queries and use the Snowflake function : GET_IGNORE_CASE (ex: select GET_IGNORE_CASE( to_object(ica) , 'data_name' ) from testtableref)
Update the 'old' field names to the new ones (ex: update testtableref_orig set ica = object_delete(object_insert(ica, 'data_name', ica:Data_name), 'Data_name'))
Fixed an issue where using an expression to filter the "Base Job Success" event is not working
2024 June 6 - ICA v2.26.1
Fixed Issues
Flow
Resolved an issue to ensure that when a user creates a pipeline using a docker image shared from an entitled bundle, their analyses utilizing that pipeline can pull the docker image without errors.
2024 June 5 - ICA v2.26.0
Features and Enhancements
General
The left side navigation bar will collapse by default for screen smaller than 800 pixels. The user can expand it by hovering over it
The browser URL may be copied to share analyses, pipelines, samples, tools, workspaces and data in various contexts (project, bundle)
Data Management
Users are now able to move data within and across projects:
The user can:
Move available data
Move up to 1000 files and/or folders in 1 move operation
Retain links to entities (sample, sequencing run, etc.) and other meta-data (tags, app-info) when moving
Move data within a project if the user is a contributor
Move data across projects if (1) in the source project the user has download rights, has at least contributor rights, and data sharing is enabled, and (2) the user has upload rights and at least viewer rights in the target project
Move data across projects with different types of storage configurations (user-defined or default ICA-managed storage)
Select and move data to the folder they are currently in through the graphical UI
Select and move data in a destination project and/or folder through the API
The user cannot:
Move linked data. Only the source data can be moved
Move data to linked data. Can only move data to the source data location
Move data to a folder that is in the process of being moved
Move data which is in the first level of the destination folder
Move data to a destination folder which would create a naming conflict such as a file name duplicate
Move data across regions
New Event Log entries are provided when a user links (ICA_BASE_100) or unlinks (ICA_BASE_101) a Cohorts data set to a bundle
Added support for the following data formats: ora, adat, zarr, tiff and wsi
Flow
New compute types (Transfer Small, Transfer Medium, Transfer Large) are supported and can be used in upload and download tasks to significantly reduce overall analysis runtimes (and overall cost)
API: All the endpoints containing pipeline information now contain the status from the pipeline(s) as well
Bench
External Docker images will no longer display a status as they consistently showed 'Available,' even when the URL is not functional
Cohorts
Performance improvements to needle plot by refactoring its API endpoint to return only sample IDs
Users now click a cancel button that returns them to the landing page
Users can now perform time series analysis for a single patient view
Refresh of PrimateAI data now drives data in variant tables
Users can now access the structural variant tab in the Marker frequency section
Fixed Issues
General
Fixed an issue where, when a user is added to or removed from a workgroup, they could be stuck on an infinite redirect loop when logging in
Fixed syncing discrepancy issues about deleted files in user-managed storage projects with Lifecycle rules & Versioning
Data Access & Management
Sorting API responses for the endpoint GET /api/jobs is possible on the following criteria: timeCreated, timeStarted and timeFinished
Improved the error message when trying to link a bundle which is in a different region than the project
More documentation has been added to the GET /eventLog regarding the order of rows to fetch
Fixed an issue where the API call - POST api/projects/{projectId}/permissions would return an error when DATA_PROVIDER was set for roleProject
Fixed an issue stemming from attempts to copy files from the same source to the same destination, which incorrectly updated file statuses to Partial
CLI: Fixed an issue where the environment variable ICAV2_X_API_KEY did not work
Flow
The analysis is no longer started from the API if error 400 ( 'Content-Type' and 'Accept' do not match) occurs
Base
Fixed an issue where the Base schedule would not run automatically in some cases when files are present in the schedule
Bench
Improved error handling when trying to create a tool with insufficient permissions
Fixed an issue where the user is unable to download docker-image with adhoc-subscription
The "version":"string" field is now included in the API response GET /api/referenceSets. If no version is specified, the field is set to "Not Specified"
Fixed an issue where, under some conditions, fetching a job by id would throw an error if the job was in pending status
2024 April 24 - ICA v2.25.0
Features and Enhancements
Data Management
The GUI now has a limit of 100 characters for the name and 2048 characters for the URL for links in pipelines and bundles
Added a link to create a new connector if needed when scheduling a data download
Improved the data view with additional filtering in the side panel
Flow
New CLI environment variable ICA_NO_RETRY_RATE_LIMITING allows users to disable the retry mechanism. When it is set to "1”, no retries are performed. For any other value, http code 429 will result in 4 retry attempts after 0.5, 2, 10, and 30 seconds * Code-based pipelines will alphabetically order additional files next to the main.nf or workflow.cwl file
When the Compute Type is unspecified, it will be determined automatically based on CPU and Memory values using a "best fit" strategy to meet the minimum specified requirements
Bench
Paths can be whitelisted to allowed URLs on restricted settings
Fixed Issues
General
Fixed an issue where the online help button does not work upon clicking on it
Data Access & Management
Improved automatic resource cleanup when hiding a project
Fixed an issue with the service connector where leading blanks in the path of an upload/download rule would result in errors. It is no longer possible to define rules with leading or trailing blanks
Fixed an issue where a folder copy job fails if the source folder doesn't have metadata set
Linking data to sample has been made consistent between API and GUI
Improved resource handling when uploading large amounts of files via the GUI
Fixed an issue where the API endpoint to retrieve input parameters for a project pipeline linked to a bundle would fail when the user is not entitled on the bundle
Fixed an issue where deleting and adding a bundle to a project in one action does not work
Flow
The event sending protocol was rewritten to limit prematurely exhausting event retries and potentially leaving workflows stuck when experiencing high server loads or outages
Fixed an issue where specifying the minimum number of CPUs using coresMin in a CWL workflow would always result in the allocation of a standard-small instance, regardless of the coresMin value specified
Fixed an issue in the API endpoint to create a Nextflow analysis where tags were incorrectly marked as mandatory inputs in the request body
Fixed an issue with intermittent failures following completion of a workflow session
Base
Improved syntax highlighting in Base queries by making the different colors more distinguishable
Bench
Fixed an issue where the Bench workspace disk size cannot be adjusted when the workspace is stopped. Now, the adjusted size is reflected when the workspace is resumed
Fixed an issue where regions were not populating correctly for Docker images
Fixed an issue where API keys do not get cleaned up after failed workspace starts, leading to unusable workspaces once the API key limit is reached
2024 April 15 - ICA v2.24.2
Features and Enhancements
Cohorts
Users can now query variant lists with a large number of associated phenotypes
Users can now perform multiple concurrent data import jobs
Fixed Issues:
Cohorts
Fixed an issue with displaying shared views when refreshing a Bundle’s shared database in Base
2024 April 4 - ICA v2.24.1
Fixed Issues
Fixed an issue where autolaunch is broken for any users utilizing run and samplesheet inputs stored in BSSH and operating in a personal context, rather than a workgroup.
2024 March 27 - ICA v2.24.0
Features and Enhancements
Data Management
Data (files and folders) may be copied from one folder to another within the same Project
The empty ‘URN’ field in the Project details at Project creation is now removed
The ‘Linked Bundles’ area in the Project details at Project creation is now removed as you are only allowed to link Bundles after Project creation
The card or grid view selected will become the default view when navigating back to the Projects or Bundles views
Added a new API endpoints to retrieve and accept the Terms & Conditions of an entitled bundle:
/api/entitledbundles{entitledBundleId}/termsOfUse
/api/entitledbundles/{entitledBundleId}/termsOfUse/userAcceptance/currentUser
/api/entitledbundles/{entitledBundleId}/termsOfUse:accept
Flow
Added a new API endpoint to retrieve orchestrated analyses of a workflow session
GET /api/projects/{ProjectID}/workflowSessoins/{WorkflowSessionID}/analyses
Code-based pipelines will alphabetically order additional files next to the main.nf or workflow.cwl file
Bench
New JupyterLab - 1.0.19 image published for Bench using the Ubuntu 22.04 base image
Resources have been expanded to include more options for compute families when configuring a workspace. See ICA help documentation for more details
Cohorts
Sample count for an individual cohort may be viewed in the variants table
Filter the variants list table through the filter setting in the needle plot
Execute concurrent jobs from a single tenant
Improved the display of error and warning messages for import jobs
Structural variant tab may be accessed from the Marker frequency section
Fixed Issues
Data Access & Management
Bundles now reflect the correct status when they are released instead of the draft status
Double clicking a file opens the data details popup only once instead of multiple times
Improved performance to prevent timeouts during list generation which resulted in Error 500
The counter is now accurately updated when selecting refresh in the Projects view
Fixed an issue resulting in one job to succeed and one to fail when running two or more file copy jobs at the same time to copy files from same project to same destination folder
Fixed an issue resulting in an error in a sample when linking nested files with the same name
Added a new column to the Source Data tab of the Table view which indicates the upload status of the source data
Removed the unused ‘storage-bundle’ field from the Data details window
Fixed an issue where the Project menu does not update when navigating into a Project in Chrome browsers
(CLI) Fixed an issue where deleting a file/folder via path would result in an error on Windows CLI
Base
Improved schedule handling to prevent an issue where some files were not correctly picked up by the scheduler in exceptional circumstances
Fixed an issue where an incorrect owning tenant is set on a schedule when running it before saving
The number of returned results which is displayed on the scheduler when trying to load files now reflects the total number of files instead of the maximum number of files which could be displayed per page
Fixed an issue where Null Pointer Exception is observed when deleting Base within a Project
Bench
Fixed an issue where users were unable to delete their own Bench image(s) from the docker repository
Cohorts
Fixed an issue where the value in the tumor_or_normal field, in the phenotype table in database, would not set properly for germline and somatic mutation data
Fixed an issue where large genes with subjects containing large sets of diagnostic concepts caused a 503 error
2024 March 7 - ICA v2.23.1
Fixed Issues
Fixed an issue where automated analysis after sequencing run in non-US regions may fail for certain analysis configurations
2024 February 28 - ICA v2.23.0
Features and Enhancements
Data Management
The --exclude-source-path flag has been added to the ‘project data download’ command so that subfolders can be downloaded to the target path without including the parent path
The system automatically re-validates storage credentials updated in the graphical UI
Added a new API endpoint to validate storage configurations after credentials are changed: /api/storageConfigurations/{storageConfigurationId}:validate
Notifications
Added support for multi-version notification event payloads corresponding to versioned API response models
Flow
(API) Improved the analysis-dto by adding a new POST search endpoint as a replacement for the search analysis GET endpoint. The GET endpoint will keep working but we advise using the new POST endpoint.
Improved analysis statuses to reflect the actual status more accurately
Parallelized analysis input data downloads and output data uploads to reduce overall analysis time
No scratch size is allocated if tmpdirMin is not specified
Cohorts
Performance improvements of the ingestion pipeline
Performance improvements to subject list retrieval
Increased the character limit of ingestion log messages to the user
Fixed Issues
Data Access & Management
Fixed an issue where the target user cannot see analysis outputs after a successful transfer of analysis ownership in BaseSpace Sequence Hub
Update the API Swagger documentation to include paging information for: /projects/{projectId}/samples/{sampleId}/data
Fixed an issue resulting in errors when creating a new bundle version
Fixed an issue where the GET API call with the ‘Sort’ parameter returns an error when multiple values are separated by commas followed by a space
Fixed an issue where adding the –eligible-link flag to the ‘projectdata list’ API endpoint caused other flags to not work correctly
Added cursor-based pagination for the ‘projectdata list’ API endpoint
Fixed an issue with the entitled bundles cards view where the region is cut off when the Status is not present
Fixed an issue where bundle filtering on categories did not work as expected
Fixed an issue where file copy across tenants did not work as expected
Added a cross-account permission check so that file copy jobs fail when the cross-account set up is missing instead of being retried indefinitely
Fixed an issue where ‘Get Projects’ API endpoint returns an error when too many projects are in the tenant
Fixed an issue where the UpdateProject API call (PUT /api/projects/{projectId}) returns an error when technical tags are removed from the request
Fixed an issue where users need to confirm they want to cancel an action multiple times when clicking the back button in the graphical UI
Fixed an issue where clicking into a new version of a bundle from the details view does not open the new version, and instead directs to the bundle card view
Flow
Fixed an issue where the analysis logs are returned in the analysis screen “outputs” section and included in the getAnalysisOutputs API response. The log output is no longer considered as part of the analysis outputs
Analysis history screen has been removed
Fixed an issue resulting in inability to retrieve pipeline files via the API when the pipeline is shared cross-tenant
Fixed an issue where the API endpoint to retrieve files for a project pipeline would not return all files for pipelines created via CLI or API
Fixed an issue where the API does not check the proprietary flag of a pipeline before retrieving or downloading the pipeline files
Base
The ‘Download’ button is available to download Base activity data locally (and replaces the non-functional ‘Export’ button for restricted bundles)
Fixed an issue resulting in missing ICA reference fields in table records if the file was loaded into the table with no metadata
Improved consistency of the references included in the scheduler
Bench
Users are now logged out from a terminal window opened in a workspace after a period of inactivity
Fixed an issue where permissions could not be enabled after a workspaces has been created
Fixed an issue where a Contributor could not start/stop a workspace
Cohorts
Fixed an issue where large genes with subjects with large sets of diagnostic concepts cause a 503 error
Fixed an issue where the value in tumor_or_normal field in the phenotype table in the database is not set properly for germline and somatic mutation data
Resolved a discrepancy between the number of samples reported when hovering over the needle plot and the variant list
2024 January 31 - ICA v2.22.0
Features and Enhancements
General
Data Management
Users are now able to revalidate storage configurations in an Error state
Improved existing endpoints and added new endpoints to link and unlink data to a bundle or a project in batch:
POST /api/projects/{projectId}/dataUnlinkingBatch
GET /api/projects/{projectId}/dataUnlinkingBatch/{batchId}
GET /api/projects/{projectId}/dataUnlinkingBatch/{batchId}/items
GET /api/projects/{projectId}/dataUnlinkingBatch/{batchId}/items/{itemId}
Flow
Analyses started via the API can now leverage data stored in BaseSpace Sequence Hub as input
ICA now supports auto-launching analysis pipelines upon sequencing run completion with run data stored in BaseSpace Sequence Hub (instead of ICA)
Updated the API for creating pipelines to include "proprietary" setting, which hides pipeline scripts and details from users who do not belong to the tenant which owns the pipeline and prevents pipeline cloning.
Cohorts
Added support for partial matches against a single input string to the “Search subjects” flexible filtering logic
Users can now view an overview page for a gene when they search for it or click on a gene in the marker frequency charts
ICA Cohorts includes access to both pathogenic and benign variants, which are plotted in the “Pathogenic variants” track underneath the needle plot
Ingestion: UI notifications and/or errors will be displayed in the event of partially completed ingestions
Users can share cohort comparisons with any other users with access to the same project
Fixed Issues
General
Improved the project card view in the UI
Fixed an issue with user administration where changing the permissions of multiple users at the same time would result in users receiving Invalid OAuth access token messages
Data Access & Management
Improved the error message when downloading project data if the storage configuration is not ready for use
Fixed an issue causing Folder Copy jobs to time out and restart, resulting in delays in copy operations
Fixed an issue where only the Docker image of the first restricted bundle that was added could be selected
Improved the performance of folder linking with "api/projects/{ProjectID}/dataLinkingBatch"
The URL for links for "post/api/bundles" endpoint can be up to 2048 characters long
Improved the error response when using offset-based paging on API responses which contain too much data and require cursor-based paging
Fixed an issue resulting in failures downloading data from CLI using a path
The correct error message is displayed if the user does not have a valid subscription when creating a new project
Fixed an issue where changing ownership of a project does not change previous owner access for Base tables
Flow
Input parameters of pipelines are now displayed in the "label (code)" format unless there is no label available or the label equals the code, in which case only the code is shown
Fixed an issue where multiple folders were created upon starting new analyses
Fixed an issue preventing analyses from using inputs with BaseSpace v1pre3 APIs
Fixed an issue causing analyses with a specified output path to incorrectly return an error stating that the data does not exist
The following endpoint "/api/projects/{projectId}/workflowSessions/{workflowSessionId}/inputs" now supports using external data as input
Any value other than "economy" or "standard" for submitted analysis jobs will default to "standard" and use "standard"
The parameter to pass an activationcode is now optional for start-analysis API endpoints
Base
Improved the display of errors in the activity jobs screen if a Meta Data schedule fails
If an error occurs when processing metadata a failed job entry will be added in the Base Activity screen
Fixed an issue where records ingested via schedules from the same file could be duplicated
Fixed an issue where exporting the view shared via bundle would show an error 'Could not find data with ID (fol. ....)'
Resolved a NullPointerException error when clicking on Format and Status filters in the details screen of a Schedule in the Results tab
Fixed an issue where a schedule download would fail when performed by different user than the initial user
Bench
Fixed an issue when trying to query a Base table with a high limit within a workspace
Fixed an apt-get error when building images due to an outdated repository
Fixed an issue where a stopped workspace would display "Workspace paused" instead of "Workspace stopped"
Fixed an issue where large files (e.g., 150GB+) could not be downloaded to a fuse-driver location from a Workspace, and set the new limit to 500GB
Cohorts
Fixed an issue where split Nirvana JSON files are not recognized during ingestion
Fixed an issue causing the UI hangs on large genes and returns a 502 error
Fixed an issue where OMOP files are not correctly converted to CAM data model, preventing OMOP data ingestions
Fixed an issue where OMOP large drug ingestions led to memory issues and preventing further drug data ingestion
Fixed an issue where users from a different tenant accessing a shared project could not ingest data
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