fix: correct process error handling and git security issues #1258
ivan-aksamentovbuild-and-deploy.yml
on: pull_request
build-and-deploy-datasets
2m 59s
Annotations
1 error and 10 warnings
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build-and-deploy-datasets:
data/community/itps/zikav/pathogen.json#L16
Misplaced 'placementMaskRanges' in pathogen.json. Placement masking not applied (belongs in tree.json at .meta.extensions.nextclade.placement_mask_ranges). Run migrations/migrate_016_fix_misplaced_placement_mask_ranges.py to fix locally. Fix in upstream pipeline (itps/zikav) to prevent recurrence.
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build-and-deploy-datasets:
data/nextstrain/mpox/lineage-b.1/pathogen.json#L20
Top-level 'deprecated' should be in 'attributes.deprecated'. Field may not be read correctly by Nextclade. Run migrations/migrate_017_unify_attributes.py to fix locally. Fix in upstream pipeline (nextstrain/mpox) to prevent recurrence.
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build-and-deploy-datasets:
data/nextstrain/mpox/lineage-b.1/pathogen.json#L107
Unknown field 'qc.missingData.scoreWeight'. No effect (use 'missingDataThreshold' and 'scoreBias' instead). Run migrations/migrate_011_remove_qc_score_weight.py to fix locally. Fix in upstream pipeline (nextstrain/mpox) to prevent recurrence.
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build-and-deploy-datasets:
data/nextstrain/mpox/all-clades/pathogen.json#L32
Field 'official' is obsolete (removed). No effect (official status derived from dataset path). Run migrations/migrate_017_unify_attributes.py to fix locally. Fix in upstream pipeline (nextstrain/mpox) to prevent recurrence.
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build-and-deploy-datasets:
data/nextstrain/mpox/all-clades/pathogen.json#L21
Field 'enabled' is obsolete (removed). No effect (field was never used). Run migrations/migrate_017_unify_attributes.py to fix locally. Fix in upstream pipeline (nextstrain/mpox) to prevent recurrence.
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build-and-deploy-datasets:
data/nextstrain/mpox/all-clades/pathogen.json#L22
Top-level 'experimental' should be in 'attributes.experimental'. Field may not be read correctly by Nextclade. Run migrations/migrate_017_unify_attributes.py to fix locally. Fix in upstream pipeline (nextstrain/mpox) to prevent recurrence.
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build-and-deploy-datasets:
data/nextstrain/mpox/all-clades/pathogen.json#L20
Top-level 'deprecated' should be in 'attributes.deprecated'. Field may not be read correctly by Nextclade. Run migrations/migrate_017_unify_attributes.py to fix locally. Fix in upstream pipeline (nextstrain/mpox) to prevent recurrence.
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build-and-deploy-datasets:
data/nextstrain/mpox/all-clades/pathogen.json#L157
Unknown field 'qc.missingData.scoreWeight'. No effect (use 'missingDataThreshold' and 'scoreBias' instead). Run migrations/migrate_011_remove_qc_score_weight.py to fix locally. Fix in upstream pipeline (nextstrain/mpox) to prevent recurrence.
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build-and-deploy-datasets:
data/community/itps/zikav/pathogen.json#L27
Field 'enabled' is obsolete (removed). No effect (field was never used). Run migrations/migrate_017_unify_attributes.py to fix locally. Fix in upstream pipeline (itps/zikav) to prevent recurrence.
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build-and-deploy-datasets:
data/community/itps/zikav/pathogen.json#L28
Top-level 'experimental' should be in 'attributes.experimental'. Field may not be read correctly by Nextclade. Run migrations/migrate_017_unify_attributes.py to fix locally. Fix in upstream pipeline (itps/zikav) to prevent recurrence.
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build-and-deploy-datasets:
data/community/itps/zikav/pathogen.json#L26
Top-level 'deprecated' should be in 'attributes.deprecated'. Field may not be read correctly by Nextclade. Run migrations/migrate_017_unify_attributes.py to fix locally. Fix in upstream pipeline (itps/zikav) to prevent recurrence.
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Artifacts
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server
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319 MB |
sha256:233391561e11944179650dd65f09c3e1890cb0da84989983b07bff801f3b3018
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zips
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9.01 MB |
sha256:3268d6b6eb6bc101e4b97fbde97fb0722eb836ecdb63a11471fa2974249e414c
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