Merge discvr-22.3 to develop - #113

Merged

bbimber merged 69 commits into

fb_merge_22.3_to_develop

May 18, 2022

Commits on Mar 11, 2022

Restore FKs for MCC and dam/sire
bbimber
committed
dafa1c6
Update MCC ETL to use anonymized dam/sire
bbimber
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c8d3ab0
Update MCC ETL to ensure dam/sire have aliases
bbimber
committed
adeaf3e

Commits on Mar 12, 2022

Update MCC ETL to ensure dam/sire have aliases
bbimber
committed
30bdab1
Update MCC ETL to ensure dam/sire have aliases
bbimber
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866d44c
Allow aliasing of dam/site for MCC even when not present in primary animal table
bbimber
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6e40f5e
Add validation to customizer
bbimber
committed
95d25b4
Bugfix MCC alias FK
bbimber
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4975ca6
Allow MCC alias customizer to run during study import, when column might not exist yet
bbimber
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d5ce4f3
MCC: better support display of parents when not present in animal table
bbimber
committed
5e7b6c3

Commits on Mar 15, 2022

Convert CADD column to double (#54)
bbimber
authored
320f7b0

Commits on Mar 16, 2022

Add COVID samples to folder summary
bbimber
committed
09c33db

Commits on Mar 22, 2022

Allow MCC notifications to use combination of users and groups
bbimber
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f14ca2d
Add file missed with last commit
bbimber
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152ec9a
Fix typo
bbimber
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2daef99
Enforce cell hashing discordance in TCR import
bbimber
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2bc97f8
Add basic site management UI for MCC
bbimber
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85d83c8
MCC test fix
bbimber
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3eb720b

Commits on Mar 31, 2022

Add null check
bbimber
committed
a9c309d

Commits on Apr 1, 2022

Add support for standalone nimble run, and allow SRA to merge multiple input ReadData into one ReadData per accession
bbimber
committed
b0f07d9

Commits on Apr 2, 2022

Remove legacy lustre folder
bbimber
committed
ab8f03e

Commits on Apr 4, 2022

Fix typo in COVID import panel
bbimber
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f227900
Skip blank lines for COVID sample import
bbimber
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ae546eb

Commits on Apr 5, 2022

Bugfix state translation in COVID sample import
bbimber
committed
24e3e00
Add column for RQG_alt_ID
bbimber
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93ad4ac
Skip 'low counts' for VDJ hashing import
bbimber
committed
fd23bba

Commits on Apr 13, 2022

Ensure consistent case for status in MCC and add automatic selection of genomicsDB consolidate batch size
bbimber
committed
bf5d236

Commits on Apr 21, 2022

Allow mGAP releases to track when each new site/allele first appears
bbimber
committed
97c9d12

Commits on Apr 22, 2022

Commits on Apr 28, 2022

Commits on Apr 29, 2022

Bugfixes to MCC request (#62)
bbimber
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9272aec
Add returnURL to mcc columns
bbimber
committed
ba11ce2
Handful of small MCC form improvements
bbimber
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0fea03b
More minor MCC improvements
bbimber
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12fc73c
More minor MCC improvements
bbimber
committed
b3f5720
Non-admin users cannot write to requestscores, so use schema-layer for trigger script
bbimber
committed
d5fbdf3
Update field description
bbimber
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31af2d0
Add basic COVID candidate gene table
bbimber
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eff7bb2
Expand text description
bbimber
committed
19d0684
Improve formatting of text
bbimber
committed
dc12263

Commits on May 1, 2022

Merge discvr-21.11 to discvr-22.3
bbimber
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fa88724
Bump minimist from 1.2.5 to 1.2.6 in /mcc
dependabot[bot]
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86f1d46
Merge pull request #63 from bimberlabinternal/22.3_fb_merge
bbimber
authored
186cccc

Commits on May 2, 2022

Changes from npm audit
bbimber
committed
ee19441

Commits on May 3, 2022

Commits on May 4, 2022

Error handling for folder deletes
bbimber
committed
3b1c216
Minor improvements to MCC review form
bbimber
committed
236f2ba
Add columns to mGAP/MCC user request views
bbimber
committed
be0e74d

Commits on May 7, 2022

Misc improvements to MCC request forms (#65)
bbimber
authored
269ab29

Commits on May 8, 2022

Ensure consistent slash in MCC properties
bbimber
committed
597c344

Commits on May 9, 2022

Add returnURL to MCC display column URLs and show correct RowId
bbimber
committed
2618297

Commits on May 10, 2022

Bugfix to MCC request form
bbimber
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dd5785e
Add option to notify MCC reviewers
bbimber
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0a7caf7
Add file missed with last commit
bbimber
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b7ea83e
Test fix
bbimber
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19bf2f5
Correct MCC email URL
bbimber
committed
f5e0167

Commits on May 11, 2022

Commits on May 12, 2022

Introduce new more granular MCC permissions (#67)
bbimber
authored
8cf8f48

Commits on May 18, 2022

Merge discvr-22.3 to develop
bbimber
committed
d8e9508