Dev - #5466

Merged

hanars merged 180 commits into

May 29, 2026

Commits on May 4, 2026

first pass format manual variants for response
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169677d
clean up
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0b7cc43
clean up setting saved variant json
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1d82f81
drop saved variant json
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c86a123
update test fixtures
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b63feed
update test fixtures
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0ed1912
update matchmaker saved variant json usage
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437ccb6
test clean up
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ca4c0d6
test clean up
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3d84ad6
fix saved variant tests
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fa0bf2c
fix test
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98fe671
update set key command
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6a03abb

Commits on May 5, 2026

correctly return end for manual SVs
hanars
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e81dfd7
fix manual sv response
hanars
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17dd63c
genome version difff cleanup
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ae10fb1
loftee cleanup
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bac2004
remiove callset pop support
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8abbcf5
pathogenicity clean up
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9c9ff44
predictor clean up
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1d6f55d
sort export cleanup
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96431c7
clean up genotype
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4576018

Commits on May 6, 2026

clean up
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b296883
fix linting
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1a06aa7

Commits on May 8, 2026

caid test coverage
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e94aaf4
relaod clinvar type sepcific helper function
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c99964d
manager clean up
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30e51d5
caid error handling clean up
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6eadb02
caid error handling clean up
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0ccc1e8
search coverage
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afe878a
panel app cleanup
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f309583
debug
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a42533c
clean up export
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a69144b
fix test
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03475e8
debug
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fe4c30b
reference data prase gene record cleanup
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85b68f9
fix error
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af19142
debug
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7d30d30
fix multi dt bug
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68e0fe0
add coverage
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b9cc8a3
clean up parent hpo mapping
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c1f6bff

Commits on May 11, 2026

fix hpo update
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df837d6
debug
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c7c70b7
fix test
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26ab1f9
sample cleanup
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1627ea1
debug
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b722fb9
remove deprecated family structure notation
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5012fc9
fix hpo update
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dadf38d
fix search error
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4efd973
test csv file iter
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6d0aeea
clean up
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a8b190b
clean up usage
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a09ec58
fix typo
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dc5e1ff
fix typo
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4189a60
clean up
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6eff66e
Merge branch 'dev' of https://github.com/broadinstitute/seqr into coverage-cleanup
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887734c
fix genotype sorting
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19872c8

Commits on May 12, 2026

Merge branch 'dev' of https://github.com/broadinstitute/seqr into coverage-cleanup
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5fa15ed

Commits on May 13, 2026

Merge branch 'dev' of https://github.com/broadinstitute/seqr into coverage-cleanup
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afdf810
test split pdo warning
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115de32
update qc coverage
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7dfe8a2
clean up
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8348e3e
test error handling for failed email send
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6dc86d9
dont over mock social auth logging
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2102647
better mocking
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ed7cf13
test success validating other data types
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1ec8227
test successful wait for service account grant
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7af90da
add edge case test
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67d91ad
update fixture
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2d7911a
gregor paternal id mapping
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975e230
remove phenotips json upload support
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e91de03
fix project test mock
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23a86eb
test edge case
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6bc9269

Commits on May 14, 2026

report edge case test
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5aa8754
cleaner logic
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2ddb7a2
Merge branch 'dev' of https://github.com/broadinstitute/seqr into coverage-cleanup
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5beec21
clean up
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20a1dee
test alerting when fetch for patch fails
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9c98219
pedigee util cleanup
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be9a14b
first pass new postgres dicts
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723c579
allow additional genotype fields
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5581acc
fix dictionary defs
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4ff7eff
load individual metadata from clickhouse
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1de880c
add contact info to metadata
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75e740c
use clickhosue metadata instead of postgres
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51f033b
fix metadata for other sv lookup
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cb51890

Commits on May 15, 2026

Merge pull request #5438 from broadinstitute/clivar-no-update-slack
hanars
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fd846e6
shared helper for cached variant formatting
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ca6c425
no access missing indiv
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9e6254d
add reload to migration
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183b818
pr feedback
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2c1ebd3
add discovery tags to snv indel variants
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b64895e
Merge branch 'dev' of https://github.com/broadinstitute/seqr into vlm-clickhouse-views
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966c0f7
fix variant tables
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b65fb97
Merge pull request #5426 from broadinstitute/saved-variant-ui-cleanup
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1a5441a
Merge pull request #5429 from broadinstitute/coverage-cleanup
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92a0c9a
Merge branch 'dev' of https://github.com/broadinstitute/seqr into saved-variant-json-cleanup
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4c1e1f4
Merge branch 'saved-variant-json-cleanup' of https://github.com/broadinstitute/seqr into saved-variant-json-cleanup
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478d6d8
Merge branch 'vlm-clickhouse-views' of https://github.com/broadinstitute/seqr into discovery-families-all-projects
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613fb7c
use dataset tpe for varant dict get key
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57924a4
Merge pull request #5424 from broadinstitute/saved-variant-json-cleanup
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c8a6282
Merge branch 'dev' of https://github.com/broadinstitute/seqr into vlm-clickhouse-views
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23a28e3
Merge branch 'vlm-clickhouse-views' of https://github.com/broadinstitute/seqr into discovery-families-all-projects
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1e5f1bd
add sv discovery families
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0892033
handle other data types
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f8a1815
add replace missing import
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7147e6d
update discovery tests
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f974aaf
fix dataset type key conflicts
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85d6e34
fix anvil call test
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0208cca
test fix
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6711ed3
todo
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c6e8609

Commits on May 18, 2026

fix tests
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661661c
fix no access project bug
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dbed324
test search context
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5901b35
return discovery family mapping in lookup
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557efd7
fix flappy test
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895bda5
clean up
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8a3fe70
test discovery fixtures
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df65987
update lookup discovery fixtures
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02be7cb

Commits on May 19, 2026

discovery lookup test fixture
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6d128f0
cached variant formatting
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3c3cc8c
cached variant formatting
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128b738
fix test order
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9778412
clean up global tags
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aa4e819
debug
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6b3ca8a
split fixture data
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764c94c
more fixture fixes
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322b90d
more fixture fixes
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ab3cb05
new fixture updates
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5ceefe4
fix fixture data
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3bfeaa7
shared helper
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093a725
handle exclude tags
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1fc1cf1
use actual db query for context discovery tags
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a52eee1
show no access discovery families
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7be5139
restructure lookup tags response
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f571915
display lookup tags
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8720ebf
better ui linitng
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12b35b0
Merge pull request #5440 from broadinstitute/vlm-clickhouse-views
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78b9ab9
Merge branch 'dev' of https://github.com/broadinstitute/seqr into discovery-families-all-projects
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78335a3
return additional metadata lookup fields
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ea3954c
display additional fields
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0d0da24
fix tag display
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7032c5e

Commits on May 20, 2026

Apply suggestions from code review

hanars
and
Copilot
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3e2d9f1
Merge branch 'discovery-families-all-projects' of https://github.com/broadinstitute/seqr into discovery-families-all-projects
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bbddc6a
fix varianst with multiple discovery tags in same family
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826dd37
correctly test all project family filters
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b99e784
fixture updates
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a7dab1c
specify correct data type in metadata tuple
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6ee0b81
add instructions for running old npm on new macs
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c1387b6
Merge pull request #5446 from broadinstitute/node-install-instructions
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7b89e69
accordian display for fq
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6d45ef5
add processing assitance q to faq
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7e27449
use pyliftover
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645d368
remove hail validation
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2917f4d
fix typo
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90a0dea
debug
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0eb5ce3
fix test
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9806d7a
coverage report
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1f69b6b
real requiment files
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24f2f45
no hail dockerfile
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f8c4e7f
update test image;
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6f5483d
fix requiremnts
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a979ec8
fix dependency install path
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d645344
add dependency
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6ee1583
correct jwt package
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5718fb9
clean up
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79365c4
pr feedback
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91aa892
only initialize liftover once
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56c6b67
fix
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1800d58

Commits on May 22, 2026

Bump qs and express in /ui
dependabot[bot]
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69fd265

Commits on May 26, 2026

Commits on May 27, 2026

Merge pull request #5447 from broadinstitute/faq-update
hanars
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ba586c7

Commits on May 28, 2026

Commits on May 29, 2026