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Core Gen3 Release (Uptown)

uc-cdis/fence

New Features

  • Expose /ga4gh/drs/v1/objects/{object_id}/access/{access_id} GA4GH DRS Access API via Fence (#957)
  • Use RAS v1.1 Passport instead of RAS v1.0 passport (#956)
  • Validate RAS v1.1 Passports (#956)
  • Added logic to create Gen3 Passports (#956)
  • Add registration endpoints (registration form endpoint and admin-only list endpoint) (#906)
  • Use Azure Blob Storage with Fence (#946)

Bug Fixes

  • A change in the gen3cirrus package for the get_signed_url function was made, the function parameters were not updated in fence and returned an invalid parameter error. Adding missing parameters to the function in Fence resolved error. (#955)
  • Bug fix in checking email claims for Azure AD (in case the email claim is missing from the AAD response) (#946)

Improvements

  • remove deprecated project access from cookies (making them smaller) (#958)
  • update to latest python base image (#959)
  • Improvements around CSRF handling (#906)
  • Test suite update (#946)

Dependency Updates

  • New dependency Flask-WTF (#906)
  • Python (#946)
  • azure-storage-blob=^12.6.0 (#946)
  • azure-core==1.13.0 (#946)
  • cryptography==2.8 (#946)
  • isodate==0.6.0 (#946)
  • msrest==0.6.21 (#946)
  • oauth==3.1.0 (#946)
  • requests-oauthlib==1.3.0 (#946)
  • six==1.16.0 (#946)

Deployment Changes

uc-cdis/indexd

New Features

  • Add indexd settings files for PostgreSQL SSL support (#317)

Bug Fixes

  • Clean up test settings (#317)

Improvements

  • update to latest python base image (#322)
  • Add notes for local development (#315)
  • Add example Azure DevOps pipeline and Documentation (#316)

Deployment Changes

  • Include example secrets to load PostgreSQL settings for indexd (#317)

uc-cdis/pelican

Bug Fixes

  • adding aligned_reads_index to the extra nodes on VCF file exports to make them inline with CRAM files (#58)

New Features

  • Fix encoding issue when exporting (#57)

uc-cdis/peregrine

Bug Fixes

  • Handle exceptions without 'message' attribute (#178)

Improvements

  • update to latest python base image (#179)

uc-cdis/pidgin

Improvements

  • Do not crash when Peregrine returns a non-200 code, and try to parse the data anyway (#40)

uc-cdis/data-portal

New Features

  • add vaccine map layer (#908)
  • Add contentSecurityPolicyConnectSRCWhiteList to portal config to allow for urls to be whitelisted by Content-Security-Policy (#919)
  • Explorer: Redirects users to the login page if they try to download the data without logging in. (#912)
  • Closable banner at the top of workspace page to remind users to link account to other data commons (#916)
  • add an R logo for workspaces with titles formatted " *R Notebook *" (#915)
  • Screenshot 2021-08-20 at 14-06-55 Generic Data Commons (#915)
  • NCT: Add a web form component to allow signing up for email lists at govdelivery.com (#911)
  • A user can select one or more studies to request for download. This dispatches a sower job which is monitored until it either sends back an s3 presigned url, or fails with an error description. (#906)

Bug Fixes

  • Mitigated PFB export bug (PXP-8400) by increasing timeout before checking for status of PFB export job (#871)
  • Fix occ data bucket from being blocked by Content Security Policy (#919)
  • Workspace: fixed a bug causing workspace be putting into incorrect Launching state if some containers has already been terminated (#903)

Improvements

  • refactor map data handling logic (#908)
  • update colors of Mobility Data layers (#908)
  • Misc: add the optional Discovery page to nct and covid19 bundles (note the workspace bundle still don't have it) (#918)
  • New configurable subtitle helper text under the Discovery page search box in the gitops.json attribute inputSubtitle. (#909)
  • UX improvements in the Discovery page's Data Availability column header -- 3 filter options, remove sort icon (#909)
  • Removing AccessLevel.UNACCESSIBLE from table sorting and filtering options (#909)
  • Core metadata / download page: remove empty values from the header (#910)

Deployment Changes

  • Misc: add option for bundle name: ecosystem, which is the same as heal bundle under the hood (#918)
  • Requires loginForDownload flag set to true in gitops (#912)
  • User registration before download feature depends on uc-cdis/fence#906 (#912)
  • Requires the configuration of the batch-export sower job: uc-cdis/sower-jobs#29 in the environment's manifest. This job also has its own setup in cloud automation: uc-cdis/cloud-automation#1708 (#906)
  • 2 new fields in gitops.json: discoveryconfig.features.exportToWorkspace.[enableDownloadZip (bool) downloadZipButtonText (string)] (#906)

uc-cdis/sheepdog

New Features

  • Update for PostgreSQL SSL support (#351)

Bug Fixes

Improvements

  • update to latest python base image (#356)
  • Update uwsgi.ini and Dockerfile to support python dependency installs (#351)
  • Update test suite (#351)
  • Add debug log when unable to parse JSON input (#354)
  • Handle TSV/CSV data for program/project creation (#354)

Dependency Updates

  • Included python dependency updates in requirements.txt for datamodelutils==1.0.0, dictionaryutils==3.2.0, gen3authz==0.4.0, six>=1.15.0, py2neo, and google-crc32==1.1.2. (#351)

  • Note that dictionaryutils==3.4.0 is the current sheepdog python dependency but is not available for download from pypi (at least with a wsl / windows release). The lower version 3.2.0 is a workaround. (#351)

  • Included python dependency updates in dev-requirements.txt for coverage==5.3.0 and codacy-coverage==1.3.11 (#351)

uc-cdis/sower

New Features

  • add filtering of list of jobs/outputs based on the user email (#23)

uc-cdis/tube

Improvements

  • Refactor and improve documentation: split the readme into several smaller files and add etlMapping.yaml configuration details (#156)
  • Add example Azure DevOps pipeline and documentation (#151)

uc-cdis/indexs3client

Bug Fixes

  • This change will include parsing logic of uuid. (#33)

uc-cdis/metadata-service

New Features

  • Use env and config for populate script rather than passing parameters (#33)
  • Add aggregate metadata adapters to talk to third party metadata services (#29)

Improvements

  • Better name for the defaulted index namespace (#33)
  • Update documentation (#33)
  • More verbose logging for populate (#31)
  • Timeout retry via tenacity (#31)
  • Remove aggregate MDS configs from source control (#30)

Deployment Changes

  • A job has been created to make aggregate MDS population more robust uc-cdis/cloud-automation#1722 (#33)
  • Must set the appropriate AGG_MDS_NAMESPACE value in metadata.env (#29)
  • Per #3332 a metadata/aggregate_config.json file should be created as part of the manifest config for a commons and the appropriate environment vars for metadata should be defined in the manifest JSON (#30)
  • The new command to populate an aggregate MDS is kubectl exec $(gen3 pod metadata) -- python /src/src/mds/populate.py --config /aggregate_config.json --hostname esproxy-service --port 9200 (#30)

Dependency Updates

  • Bumps fastapi from 0.54.2 to 0.65.2. (#32)

Breaking Changes

  • ES indices will not be namespaced per environment (#29)

Bug Fixes

  • Scope ES indices to a namespace so they don't conflict with other environments (#29)
  • This fixes an issue that prevents populating a AggMDS if one or more of the remote commons is down or unavailable. Instead of throwing an exception, the error is logged and the remote commons is skipped. (#31)

Dependency Updates

  • Python package: tenacity (#31)

uc-cdis/cloud-automation

New Features

  • gen3 job for syncing aggregate metadata to a metadata service (#1722)
  • Added netnolimit for indexd (#1725)
  • Added jenkins-ci cleanup to jenkins cronjob (#1712)
  • save-failed-pod-logs now will save both initContainer and container logs for specific pod (#1711)

Bug Fixes

  • Increased header buffer size to prevent header too large error (#1724)

Improvements

  • Hatchery: mount HOSTNAME from manifest-global (#1717)