Release Notes
Get details on new features, changes, and bug fixes for each Platform and toolkit release.
- Security patching of Docker containers
- Fixes to the deletion queue services
- Apollo: Vizserver fixes
- Vulnerability patching for Docker containers and lambdas
- Expansion of the security ciphers for data in transit to includ 1.2 and 1.3
- Titan: Fixes to project spending limit reporting, dbclusters
- Apollo: upgrade to SQLAlchemy 1.4 and optimizations on the query builder for somatic variant analysis.
- Vulnerability patching for Docker containers and lambdas
- Support for canonical transcript annotation
- Efficiency optimization for the object deletion process, replacing open source code that is reaching end of life
- Apollo: internal changes to support new internal digital signatures (Supply Chain related)
- Vulnerability patching for Docker containers
- Disallowed executables will not disable any workflows containing these disallowed executables
- Fixes in the UI for Tool Runner
- Apollo: Performance enhancements for the Vizserver
- Vulnerability patching for Docker containers
- Fixes to long running jobs logs, refactoring logic for email arising from job notificiations and minor UI fixes
- Vulnerability patching for Docker containers
- Fixes for orphan projects, access to long running jobs, and minor UI fixes
- Apollo: security patching of libraries
- Vulnerability patches for Docker containers
- Fixes to airlock, granular long job notifications, access to long running jobs, fixes to spending limit controls and fixes for the file closer lambda
- Fixes to the Tool Runner UI for WDL workflows
- Patching known vulnerabilities in Docker containers and EC2 instances, workers, etc.
- Fixeds to the authentication token deleter and enforcement of egress limits
- Support for canonical transcripts, genomic data loading for somatic variants, CLI access for the somatic assay model. Project Level Usage Reports (limited release)
- Apollo fixes for: updated generates SQL queries and other fixes.
- Patching known vulnerabilities in Docker containers
- Batch runner and Tool Runner update on the web interface, resulting in a significant change in the UI and behavior
- Updated worker toolkits
- Project spend limitation reporting (licensed feature)
- Bugfixes in org-admin notifications, Azure cloud manager and other bugfixes
- Patching known vulnerabilities in Docker containers
- Fixes to egress and compute charge reporting
- Fixes to job restart functionality and long running job notifications
- Apollo: fixes to enforce the 5 minute query timeouts
- Airlock functionality added for Trusted Research Environments (TREs)
- Bug fixes to job restarts, project spend processes and fixes to the back button of the Community Portal
- Increase the size of the job log from 2M to 4M
- Security patches to Docker containers
- Apollo: minor bug fixes in the somatic variant functionality and error reporting
- Security patching of vulnerabilities on Docker containers and EC2 instances
- Detailed job metrics (limited release through the balance of the year)
- Apollo: bugfixes and infrastructure upgrades. Support for multi-assay support for Genetic Variant assays
- Security patching for Docker containers
- Better error messaging for users authenticating via SSO
- Project admins will be notified via email when their project has crossed thresholds of metadata capacity
- Preserve intermediate job outputs to aid in error tracking
- Fixes to job restart issues, better error mesages
- Security patching for Docker containers
- Fix for Community UI - after 15 minute timeout, the user is correctly redirected to the Community login page
- Apollo: Deprecate the apps association loader feature, extend the timeout for complext data fetches to 5 minutes
- Deprecate DNA_API_ORG-REPORT_HISTORICAL_CHARGES function
- Security patching for Docker containers, lambdas and EC2 instances
- Fixes to cloud manager and UI redirect issues
- Apollo: support for large scale database operations (important for handling WGS data)
- Security patching Docker containers
- Titan: fixes to known issues
- Apollo: fixes to issues, such as internal ID, return timeout errors from long running data fetches to vizserver
- Security patching of Docker containers
- Continuing the migration of the DNS to AWS' Route53, refactoring known issues
- Apollo: fixes to the query builder
- Security patching of Docker containers and applications
- Changes in the EBS swap volume with gp2 and SSD instances to fix known issues
- Apollo: fixes to the vizserver to allow more database access
- Security patching of Docker containers
- Ubuntu 22.04 AMIs available on both AWS and Azure execution planes
- Apollo: upgrades to the Spark server and related package updates
- Deprecating Javascript monitoring
- Security patching of Docker containers
- Changes to the User Interface to become CWAG 2.0 AA compliant
- Apollo: refactoring known issues, including large query handling by default
- Refactoring of the asynchronous archive services
- Refactoring of the job re-use and support workflow (e.g., WDL)
- Apollo: Refactoring of the geno filters for the command line interface
- Security patching for Docker and VMs
- Refactoring of job restart, asyncrhonous archival and UI backend changes
- Apollo: Spark server upgrades, Python upgrades
- Security patching on Docker containers and lambdas
- Fixes for job preservation functionality
- Security patching for Docker container, lambdas and Ubuntu instances
- Fixes to the Titan file uploader and cosmetic changes to the UI in the input components
- Apollo: deprecation of the Association Browser
- Monthly security patching for Ubuntu instances, patching of vulnerabilities for Docker containers and AWS lambdas
- Migration of platform service instances from Ubuntu 18.04 to 22.04 or 20.04 when not possible to fully migrate
- UI fix to SSO users who are confronted with separate MFA prompt
- Apollo: fix issues in dxfuse
- Granular wait time for spot instances for workflows (subscriber licensees only)
- Docker container security patching
- Refactoring of job refuse to support workflows (e.g., WDL)
- Refactoring of known issues in Titan including s3deleter, spot granlarity issues, expansion of the metadata capacity in the describe API call, UI fixes to SSO users
- Refactor of known issues in the initial login of the thrift cluster, more granularity in log reporting
- Patching of Docker container vulnerabilities
- Titan: Fixes to the UI and s3deleter functionality
- Apollo: fixes to enforcing region boundaries and API proxy issues
- Workflow Job Reuse will be deprecated completely, replaced with functionality elsewhere
- Change GiB to GB e in the job disk comparison
- Added new functionality to Titan, specifically:
- DNA_API_PROVIDER_PERMISSION_RESTRICTIONS - Project/org restrictions should be enforced based on the provider constraint options choice
- DNA_API_PROVIDER_DATA_CLONING_RESTRICTIONS - User is not able to clone data from restricted to unrestricted project or from restricted to restricted project with different studyID
- DNA_API_PROVIDER_JOB_RESTRICTIONS - Restriction on building tools into the project from the user's computer or analyses
- FastQC app (v2.2.3 and earlier) is deprecated
- NextFlow - GA to a limited set of users
- Added new functionality to Apollo, specifically:
- TIP_DATA_ACCESS_PROJECT_RESTRICTIONS - The system can limit users access to data based on project settings and license
- TIP_DATA_DISPENSAL - User is able to create project containing data specified by studyID
- New Titan Functionality
- DNA_API_INTERNET_JOB_RESTRICTIONS - Data providers are able restrict the internet access for jobs running in Trusted Research Environment (TRE) projects in order to prevent egress of sensitive data from the TRE
- DNA_API_EXTERNAL_UPLOAD_RESTRICTIONS - Project admin is able to restrict users ability to upload data into trusted research environment (TRE) projects outside of the jobs running in the TRE
- DNA_GUI_EXTERNAL_UPLOAD_ACCESS_RESTRICTED - User is not able to upload files into the External Upload restricted project
- DNA_GUI_EXTERNAL_UPLOAD_ALLOWED_FILE_UPLOAD - User is able to upload files into the External Upload allowed project
- DNA_GUI_EXTERNAL_UPLOAD_PROJECT_SETTING - User can change External Upload Access setting
- DNA_GUI_JUPYTERLAB_EXTERNAL_UPLOAD_RESTRICTED - External upload options are not available in JupyterLab job running over the External Upload restricted project
- DNA_API_OFH_PROJECT_CREATE - User is able to create new project with data dispense or without data dispense option
- DNA_GUI_OFH_PROJECT_CREATE - User is able to create new project with data dispense or without data dispense option
- DNA_GUI_OFH_CREATE_ACCOUNT - User is able to create new account via OFH Landing page
- DNA_GUI_OFH_USER_ASSOCIATION - User is able to make association of DNAnexus and AMS account
- DNA_GUI_OFH_USER_2FA - User is prompted to set 2FA and it is not possible to remove it
- DNA_GUI_OFH_USER_BILLING_INFO - User has XX GBP billing trial balance and default region is Azure OFH-TRE (London) after successful association
- G5 GPU workers available in specific cloud
- Apollo bug fixes: Fix for license and region checks
- New Apollo Functionality
- TIP_JOB_INTERNET_RESTRICTION - The system is able to restrict internet access in worker jobs
- TIP_EXTERNAL_UPLOAD_RESTRICTIONS - Upload restricted projects have limited access
- Titan bug fixes: Updates for the API server and Azure Cloud Manager. Fix of granularity for spot instances, fix of race condition for hard links updates; archival state fixes
- Docker Container vulnerability patching
- ​DNAnexus is on AWS' Marketplace, so if you have AWS-issued credits, you can consume them via this mechanism!
- Vulnerability patching of worker AMIs and Docker containers
- Fixes to the external uploader restrictions, code cleanup
- Apollo: Fixes to the Visualisation Server and API server. Cleanup of error messages
- Vulnerability remediation of Docker vulnerabilities
- Completion of the annual SSL cert rotation
- Apollo: fixes to the metastore, fixes to the clipboard functionality in the visualization module and other bugfixes
- Complete migration to new SSL certificates throughout the infrastructure
- Bugfixes for billing, upload restrictions and SSO logins will no longer be redirected to the Project Page
- Apollo: fixes to encryption of upload URLs in the API proxy and other minor fixes
- Security patching of the Titan User interface
- Upgrading upload restrictions at the project level
- Patching Docker containers to address new vulnerabilities
- Apollo: updating SSL certs and refacting app interactions
- Docker security patching and hardening
- User Interface security patching
- Apollo: bugfixes, library updates, security patching
- Update OpenSSL v3 to 3.0.7 patch level
- Patching Docker containers and CIS level 1 hardening
- Fixes of known Titan issues
- Apollo: bugfixes to known issues.
- Code optimization, bugfixes in the User Interface
- Vulnerability patching for docker containers
- Apollo: fix API proxy issues, regex fixes for routes and other fixes.
- Security patching of operating system and Docker containers
- Additional Nextflow functionality added to Titan and Apollo
​
- Bugfixes to Titan and Apollo
- Docker vulnerability patching
- Fix for 2FA prompt for existing SSO accounts
- Fix for Jupyter Notebook calls
- Fix to block archiving of object linked to applets
- Vulnerability patching of Docker containers
- Apollo: upgrades to the internal cache and related internal upgrades
- Filecloser, asynchronous archival function, and API proxy bug fixes
- Internal upgrades of the metadata database
- Apollo: fixes to the cohort browser and fixes to internal API routes
- End-to-end FIPS 140-2 validated ciphers within the FedRAMP boundary
- Bugfixes to the authentication server
- Apollo: bugfixes to known issues
- Hardening of routes behind the User Interface
- Vulnerability patches to the Docker containers
- Apollo: Additional granularity to the logging and billing. Cleanup of error messages.
- Added Monitoring and Restriction Controls regarding download and egress, ability to preview, IP addresses of users, etc.
- Bug fixes on streams containing gzipped files
- Apollo: Fixes to the 30K cohort browser encoding
- Complete migration to OpenSSL v3
- New functionality to restrict IP domains for certain API calls
- Updates to the NVIDIA drivers for GPU users
- Increase the partition sizes for LXC
- Security patching of Docker Containers
- Apollo: Restrictions to downloads from Apollo
- Security patching for Docker Container vulnerabilities
- Usage report fixes
- Hardening of routes in the User Interface
- Increases in timeout period for dxproxy
- Apollo: enhanced CLI based querying, fixes to HDFS filesystem
- Upgrade the metadata database to Mongo 4.4
- Upgrade node.js to v14
- fixes to Archiving in AWS regions
- Apollo: no release
- LXC filesystem limit increased
- Monthly security patching
- Upgrade for SSO users who switch accounts
- Apollo: CLI based data querying
- Security patching of Docker containers
- User Interface self-service billing functionality
- Improved clinical data ingestion experience
- Apollo: Refactoring of VizServer
- Fix of the "create" functionality of DBCluster (AWS deprecated previous engine on 25-Jun-2022)
- Refactoring of user interface issues
- Patching security vulnerabilities of EC2 and Docker containers
- Refactoring issues of the cloud manager on Azure
- Apollo: Enhance validations and experience around ingesting clinical data
- Internal refactoring of reported issues
- End-to-End FIPS 140-2 validated encryption throughout Titan
- Vulnerability patching of Docker containers
- Apollo: refactoring user interface issues
- Vulnerability patching for images and Docker Containers
- Titan new functionality: DNA_API_ORG_REPORT_HISTORICAL_CHARGES
- Apollo new functionality:
- TIP_VIZ_COHORT_COMBINE
- TIP_APPS_COHORT_COMBINE_REBASE
- DNA_GUI_COHORT_COMBINE
- Apollo: fixes on Azure deployment; upgrades to the Spark engine.
- Updates to the internal CloudManager and fixes to microservices
- Vulnerability patching of images and Docker containers
- UI fixes
- Refactoring of multiple analyses workflows, more info on the spending limits and updates to the cookie notice
- Security patching of the underlying operating systems and worker AMIs
- Apollo: no release
- FIPS 140-2 encryption implemented for uploading/downloading from the storage plane
- Apollo: no release
- Minor fixes and normal vulnerability patching of the User Interfaces and supporting libraries
- Apollo: minor fixes, including the ability to query without a primary key
- Security updates for the infrastructure
- Backend fixes to support upgrading the metadata database software version upgrades
- Apollo: Enhancements of existing functionalities to ease the creation of mixing multiple cohorts
- Restrictions for SSH functionality
- Refactoring of known issues related to container cleanup, caching, etc.
- Apollo: Ability to export up to 200 columns in a table; UI fixes
- Tuning to optimize workflow runs
- Updates to the documentation pages of the applications
- UI fixes to show app versions in descending order, other minor UI fixes
- Apollo: refactoring of known issues in the user interface
- Order pending jobs by rank
- Node.js updates
- Tuning of the thrift server throughput; facilitate the combination of cohorts in the cohort browser.
- Fixes to known issues, such as a fix to the scope of unarchiving to better control the scope, updated the internationalization library (fixes for text fields in the UI).
- Apollo: Refactoring of issues with field mapping and support for ordered fields.
- Refactoring the User Interface to address issues, including moving the workflow input to the Project workflow pages.
- Fixes to the unarchiving functionality, tighter control of scope of the unarchiving
- Apollo: Refactoring of issues arising from the visualization APIs
- Refactoring known issues in the dbcluster, internal changes to FIPS 140-2 validated ciphers, Cloud Manager, fixes to the app updater when archive resources are involved, etc.
- Updates to community portals - caching is now disabled
- Apollo: Refactoring of the issue involving model input.
- Vulnerability patching of operating systems
- Fixes to code compatibility to rush.js
- Support ticket generation will be tagged with the Platform page of origin
- Apollo: Enhanced support for bulk RNAseq data in a dataset
- Apollo: Security and version number upgrades of servers
- Apollo: Removal of autoloading a chart, so the user will be prompted to generate the chart
- Implemented FIPS 140-2 validated endpoints for archival functions
- Bugfixes, such as issues reported in unarchiving function and email org_invite function
- Updating reCaptcha functionality
- Apollo: Added functionality to allow a user to incorporate Molecular Expression data into a dataset
- Apollo: Fixes to issues in Thrift and VizServer.
- Update to Node.js v12 for the infrastructure
- Backend updates to rush.js version in some of the lambdas, revising metadata sharding approach, updates to s3_deleter and minor bugfixes to the User Interface
- Apollo: Address known bugs, including limiting the number of tiles in the dashboard to a maximum of 15
- Bug fixes on job restarts, rush.js updates and increased granularity of data in the audit trail
- Apollo: in addition to bugfixes, the following functionality was added: TIP_APPS_CLINICAL_DATASET_MERGER - Users will be able to merge phenotypic datasets and TIP_APPS_ASSAY_DATASET_MERGER - Users will be able to merge an assay dataset and a phenotypic dataset
- Update of security patches of identified vulnerabilities
- Spend limit enforcements
- Enhancements for job filters
- Updates to the email filters
- Apollo: fixes to address solution-exception messages, fixes of the update API calls, and removal of blank pages in the User Interface
- Service Provider Single Sign On (SSO)
- User Interface fixes
- CloudManager enhancements (internal)
- Apollo: updates and fixes of reported issues
- Fixes to Cloud Manager, visibility into the org license for the org-admins
- Remove all Ubuntu 16.04 instances from production. Ubuntu 16.04 is available at the app level
- UI fixes to the monitor pages; improve state transition with regard to Jupyter Notebooks
- Apollo: refactoring known issues, such as nametags, etc.
- User Interface fixes to cancel transfers
- Fixes for the initiation of nested workers and the API call for apprun worker limits
- Monthly Security patches
- Apollo: fixes for zero length files, security patches to packages and libraries
- Button changes on the Web User Interface
- Throttling renabled, refactoring of known issues
​
- Complete migration of the UI to React 17 with UI changes to the Data manager, removal of the Global Search button
- Refactoring of known issues, such as fixes to watermarks, etc.
- Additional metrics for spinup and interval time for instances
- User Interface infrastructure updates to React 17
- Infrastructure consolidation for load balancing
- Security patching
- Apollo: refactoring of known issues
- Org Admin can view each org member's userID and email address
- Refactoring minor bugs, including fixing timoues and fixes to allow additional flexibility for UKB dispensals
- Apollo: Refactoring known issues
- UI fix to https workers
- Refactoring of many reported UI issues
- Refactoring of unarchive issues
- Org Manager can access the org user's email addresses
- Refactoring of the UKB rate card
- Self-service billing for UKB RAP and PayGo customers only
- Apollo: no release
- Monthly Security Patching
- Deprecation of Global Search
- Apollo: no release
- Refactoring of CloudManager
- Additional heartbeat monitoring of the infrastructure
- Refactoring of user interface issues
- Apollo: Refactoring of known lissues and updating the version of tRNA to feed Apollo
- Changes to timeout on instance re-use
- Updates to the billing daemons
- Updates on data withdraw and refresh process
- Moving infrastructure components to node.js v12
- Apollo: Update of Spark to support v3.1.2 and fixes to database pointers
- Apollo available in AWS-Frankfurt
- Additional logging for cluster jobs
- Added additional time for reserve instances
- Efficiency enhancements for listing projects
- User Interface fixes to reported bugs
- Chef upgrade on the infrastructure
- Apollo: Deprecation of the legacy chort browser, efficiency enhancements of Spark and other fixes.
- Updates to Job Manager and Cloud Manager
- Refactoring of issues on the User Interface
- Apollo: refactoring of filter parameters, UI and Spark 3.x upgrades
- Audit logging updates
- Refactoring of the User Interface issues
- Sendgrid changes for event-based email notifications
- Apollo: refactoring reported issues
- London region archiving
- Refactoring of emall alerts
- Code efficiencies pertaining to audit trail generation
- Efficiencies added to the backend code to allow more efficient list of projects.
- Apollo: refactoring known issues, efficiency enhancements and deprecation of the legacy Cohort browser
- Cloud Manager caching implemented in regions that use autoscaling
- Refactoring of internal database to increase efficiency
- Opening AWS region in London, will be visible on the user interface and rate cards in UK currency
- Internal Splunk updated to v8.1.5
- OpenJDK v11 updated on Ubuntu 18.04 AMIs
- Apollo: No Release
- Switch to the Pannexin User Interface only
- Data master fixes in the User Interface
- Query optimizations
- Internal migration of the org-specific audit logs to a more efficient process
- Apollo: Refactoring of error messages, UI fixes to gene filter parsing an semiphore fixes for API calls
- Reset job fix
- jQuery update
- Master Daata UI fixes
- lambda functions update
- increase Cloud Manager Resilience
- Apollo: Refactoring known inssues, including updates for code efficiencies and documentation
- Restart job fix
- Internal update of jQuery to v3.6.0
- Monthly vulnerability patching implemented in production
- Apollo: Refactoring of known issues, including some minor refactor of UI for efficiencies
- Additions to ProjectDescribe API to include ranking field
- Visualization tab of the User Interface will be migrated to the newer version (Pannexin)
- Job Manager efficiences
- Apollo: Added TIP_VIZ_COHORT_ANDOR, DNA_GUI_COHORT_ANDOR_JOIN_FILTER, and DNA_GUI_COHORT_ANDOR_FILTER_GROUP functionality
- Archive API updates
- Platform refactoring: Fixes to the User Interface and error handling when project files do not exist
- UUbuntu 12.04 and 14.04 instances will be deprecated. Workers using Ubuntu from 16.04 to 20.04 will continue to be supported.
- Apollo: Refactoring of R functionality and fixes to license checks
- Updates to the billing page
- Fix to the GetDetails call, handling of incorrect API calls and code efficiencies
- Updating API servers to Ubuntu 18.04, security patching of infrastructure
- Fixes to getFileStatusURL, verify all filter values in an array, fixes in the data picker, fixes in the histogram functionality
- Upgrade of the dependencies of the Auth Server
- Titan bugfixes
- Org Page UI changes
- Apollo: UI fixes
- Refactoring for handling regions, fixes on cost limits, fixed prioritization and long-term fix for watermarking
- Egress Reporting
- Apollo: refactoring issues
- Apollo: TABBY release - moving sections to multiple tabs
- Fixes on Rush.js project dependencies
- Correction of defects in the JobManager and JobEvents
- DBCluster updates to the latest TypeScript
- React.js library upgrade, which may have slightly changes to the visual appearance as well as possibly behavior changes
- Corrections to UserDescribe functionality
- Fixes FileStatus calls, changes for efficiency of filesystem calls, tuning cache sizes
- Minor AMI changes for logging
- Revert of egress accounting change and some watermark functionality
- Additional information from file describe on watermarked files
- Functionality to allow org-admins to share projects across orgs
- dxcompile support for bash variables
- Ubuntu 14.04 deprecated
- Apollo: Fixing the total count number when multiple alleles are involved, performance enhancement on the underlying database access methods
- Job re-use with watermarking
- Cloud Manager updates
- Increase granularity in egress billing
- Apollo: fixes of known issues, such as retry logic on read conditions and efficiency changes in the User Interface
- Updates to the DBcluster monitoring process
- Re-deployment of dl-proxy modules to support ungraded infrastructure
- Application context ID now included in the profiled projects, workers handle watermarked APIs, etc.
- Implementing monthly vulnerability patching
- Apollo: Fixes of known issues within Apollo, including data filter conditions and fixes to the Locus filter
- Refactoring of watermarking code to address issues
- Refactoring of code performing bulk calls to reduce the volume of information returned
- Updated the user experience (UI) with a new root component error page. Formerly, an error would show a blank screen when the worker crashed.
- Implement Apollo on Azure West-US
- DBCluster services were updated to be more efficient.
- Okta updates on dependencies
- Fixes to the autoscaling of the Cloudmanager infrastructure
- Fixes to the timestamps on expired/destroyed containers to integrate correctly in the metadata database
- Expanded IP range on workers
- PHI flag implemented on Azure
- Implemented the 2FA authentication in the pannexin code (formerly only on the membrane UI code)
- Apollo: Updates to the metadata connect functionality
- Apollo: Fixes with the concurrency issues with API calls
- Apollo: Efficiency updates to reduce the number of API calls
- Fix to allow UKB RAP users to download from multiple resources
- Continued rollout of v6 to v12 upgrades to node.js in the APIproxy and CloudManager infrastructure
- Updates to allow the cloud manager to handle tagged AMIs
- Efficiency changes to the APIserver from the Monitor tab. UI fixes to the cohort browser where screen disappears and table crashes
- All AMIs on AWS will be Ubuntu 18.04. AMI updates on Azure will come later. Older AMIs will continue to be supported
- Apollo: Updates to the Vizserver to more efficiently use the API server and efficiencies implemented on the monitor badges.
- Apollo: Resolved access issues to non-DNAnexus S3 buckets.
- Apollo: Added DXDATA_CREATE_COHORT functionality to the product.
- Fix to userDescribe functionality
- Fix to DBClusters
- Okta SCIM update
- Vulnerability patching
- Refactoring of SSO token exchange
- Apollo: Resolving issues accessing data in public S3 buckets, fixes for the data filters, and increased the efficiency of displaying tables in the User Interface
- Refactoring user describe functionality to provide greater visbility to the org-admin
- Refactoring of minor User interface bugs
- Apollo: Minor fixes to the filters
- Refactoring of the watermarking and UKB withdraws