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Core Gen3 Release 2023.04 (Rhodonite)

uc-cdis/fence

Bug Fixes

  • Fix fence-create google-bucket-create when the project does not exist (#1077)
  • Fix "non-unique client name" migration to delete all the "unique client name" constraints it finds, instead of assuming there is exactly one (#1075)

Improvements

  • Add project id format check in usersync (#1067)

Dependency Updates

  • various updates to cryptography/future/pyjwt (#1073)

uc-cdis/guppy

Improvements

  • vulnerability fixes (#167)

uc-cdis/hatchery

Improvements

  • vulnerability fixes (#56)

uc-cdis/pelican

New Features

  • Pelican export: store the generated PFB files' _expires_at timestamp in MDS (set to 14 days after creation) so they can be deleted once expired (#69)

Breaking Changes

  • The Pelican export job now requires access to submit data in MDS. In cloud-automation setups, run kubectl delete secrets pelicanservice-g3auto, rm Gen3Secrets/g3auto/pelicanservice/config.json and gen3 kube-setup-pelicanjob. Then, grant the pelican-export-job client access to (resource=/mds_gateway, method=access, service=mds_gateway) in the user.yaml. (#69)

Deployment Changes

  • The Pelican export job should now be deployed alongside the metadata-delete-expired-objects cronjob: add "metadata-delete-expired-objects": "quay.io/cdis/metadata-delete-expired-objects:<version>" to the versions block of the manifest, run gen3 kube-setup-metadata-delete-expired-objects-cronjob and grant the metadata-delete-expired-objects-job client access to (resource=/mds_gateway, method=access, service=mds_gateway) and (resource=/programs, method=delete, service=fence) in the user.yaml. (#69)

uc-cdis/peregrine

New Features

  • Add the /coremetadata endpoint, replacing the pidgin service (#198)

Improvements

  • Improve the format of the citation automatically generated by the /coremetadata endpoint (#198)
  • Use central github workflow actions for image build and push (#192)

Deployment Changes

  • The pidgin service can be removed. Its functionalities are available at peregrine's /coremetadata endpoint (#198)
  • ASK AN ADMINISTRATOR TO DELETE THE PIDGIN DEPLOYMENT if you remove pidgin. This is NOT automatic (#198)

uc-cdis/pidgin

Deployment Changes

  • If you are seeing this message, you are deploying the Pidgin service after it has been deprecated. If you are using Peregrine version 3.2.0/2023.04 or newer, the Pidgin service can and should be removed. (#48)

Dependency Updates

  • Python 3.9 (#46)

uc-cdis/data-portal

Bug Fixes

  • Fixed a popup height issue (#1250)
  • Fixed an issue that some urls may have double slash in them (#1250)
  • fix for spinner for manifest button not showing until the count (#1234)

New Features

  • This adds 500ms debouncing to the HEAL search functionality following page load. This uses the lodash debounce API (this library is already included in the code base). (#1232)
  • This also adds a unit test for the debouncing functionality. (#1232)
  • Change workspace registration title and url location (#1249)
  • Fixed storybook for CustomDichotomousCovariates following the component's interface changes in uc-cdis/data-portal#1204 (#1246)
  • Adds unit tests for CohortsOverlapDiagram, including mocking of web-services (#1246)
  • This updates the Euler diagram to be more accessible, and include both a text version and a legend. (#1246)
  • Add uid query param to GWASJob.jsx endpoints to support archived workflows (#1246)
  • Add new temporary entry to VA QA, for testing the new GWAS Results Viewer App features (#1246)
  • Updates the code base associated with the GWASApp and GWASResults application by cleaning up unneeded CSS styles and changing the names of files and selectors from GWASV2 to GWASApp. (#1246)

Improvements

  • A utils folder has been added containing a Search folder to house the search functionality and to aid in code organization. The filtering functions associated with searching have been moved into this folder to help clean up Discovery.tsx. Unneeded imports were removed from Discovery.tsx. (#1232)
  • Added code to add new tab for COVID-19 Community Analysis tab in which we have three dashboards created in AWS Quicksight embed into Chicagoland Pandemic Response Commons (#1159)
  • changes the System Use message to a scrollable div with the accept button located at the bottom of the scrolled content. (#1219)
  • optionally show the System Use message after user login (#1219)

Screen Shots

  • With a 500ms debounce (#1232)
  • Note that when typing a longer query, such as "intersection" it only searches once (#1232)
  • output (#1232)

Changes

  • Moved COVID-19 Community Analysis Tab to the first position as requested by Bob (#1241)

uc-cdis/sower-jobs

Breaking Changes

  • update batch export job for MDS v3 AggMDS response syntax (#43)