All pull requests

Pull requests

• chore: add Dockerfile and threat model for Anthropic OSS Scanner

  #7534·theosanderson-agent opened Oct 11, 2026Collaborator·

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• feat(raw-reads,prepro): centralize error logging in raw reads processing service

  preprocessing
  #7533·maverbiest opened Oct 9, 2026Contributor·3 tasks·

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  1

  6

• fix(deposition): stop warning about directories and binaries in webin-cli output

  deposition
  #7532·corneliusroemer opened Oct 9, 2026Contributor·2 tasks done·

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  1

  3

• feat(website): RU prompt for individual sequence download

  previewwebsite
  #7506·theosanderson-agent opened Oct 7, 2026Collaborator·

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  4

• test(ingest): add tests for attaching raw reads from ENA

  depositioningestpreview
  #7496·theosanderson-agent opened Oct 6, 2026Collaborator·4/4·3 tasks·

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  1

• feat(ingest): attach raw reads hosted at ENA to ingested entries

  deploymentdepositioningest
  #7495·theosanderson-agent opened Oct 6, 2026Collaborator·3/4·

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• test(backend): add tests for linking external files

  backendpreprocessing
  #7494·theosanderson-agent opened Oct 6, 2026Collaborator·2/4·

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• feat(backend): allow linking files hosted in trusted external archives

  backenddeploymentpreprocessing
  #7493·theosanderson-agent opened Oct 6, 2026Collaborator·1/4·

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• feat(backend, deployment): daily write quotas per group and instance-wide

  backenddeployment
  #7492·corneliusroemer-agent opened Oct 6, 2026Collaborator·3 tasks·

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  1

• feat(action):add oropouche virus

  #7491·arthurshem86 opened Oct 6, 2026Contributor·1 of 3 tasks·

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• fix(backend): don't issue file IDs whose S3 object already exists

  preprocessing
  #7441·corneliusroemer-agent opened Sep 28, 2026Collaborator·

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  1

• DON'T MERGE: query engine review fixes preview (stacked on #7431)

  backenddeploymentdon't mergepreviewupdate_db_schema
  #7435·corneliusroemer-agent opened Sep 28, 2026Collaborator·

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• fix(taxonomy): accept NCBI synonyms and common names as hosts, strip whitespace

  preprocessing
  #7433·corneliusroemer-agent opened Sep 28, 2026Collaborator·

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  1

• query experiments, not to merge

  backendpreview
  #7431·theosanderson opened Sep 27, 2026Member·3 tasks·

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  1

• ci(integration-tests): retry firefox tests only after a browser crash, and record why it died

  #7430·corneliusroemer-agent opened Sep 27, 2026Collaborator·

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  4

• fix(kubernetes): allow extra Keycloak env vars, disable the gzip resource encoder in e2e/dev

  deploymente2ekeycloak
  #7429·corneliusroemer-agent opened Sep 27, 2026Collaborator·

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  4

• ci(ena-submission): fail fast with an explanation when ENA secrets are missing

  #7428·corneliusroemer-agent opened Sep 27, 2026Collaborator·

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  2

• perf(website,backend): load review card data in one request

  backendpreviewwebsite
  #7427·clonder opened Sep 27, 2026Contributor·4 of 5 tasks·

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  8

• feat: add opt-in restricted instance access

  backenddeploymentpreviewwebsite
  #7426·snehasaisneha opened Sep 27, 2026Member·

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  2

• test(deployment): rehearse OIDC upgrade on a persistent preview

  deploymentpreview
  #7424·snehasaisneha opened Sep 26, 2026Member·

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• fix/refactor(website): sequence upload fixes: accept re-dropped files with the same fastaID, don't show rejected files, and undo restores the original header/label

  website
  #7420·tombch opened Sep 25, 2026Collaborator·3 tasks·

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  2

• feat!(prepro): validate user-submitted external accessions

  deploymentdepositionpreprocessing
  #7413·maverbiest opened Sep 24, 2026Contributor·3 tasks done·

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  1

  7

• feat(deposition): derive raw reads library fields from sequencingApproach

  preprocessing
  #7411·theosanderson-agent opened Sep 24, 2026Collaborator·

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  2

• chor(raw-reads-processing): hide warnings

  preprocessing
  #7396·anna-parker opened Sep 23, 2026Contributor·

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  1

  3

• ci(integration-tests): run Playwright with 3 workers instead of 2, allowlist unused keycloak font 404

  #7393·corneliusroemer-agent opened Sep 23, 2026Collaborator·

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  5