Refine gene phenotype detail #210
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resize lavaa plot
results helm configuration
…heweb into 215-remove-random-page
215 remove random page
2. fix sort on region 3. fix clinvar error
remove lock on region
214 logout
multiple threads are causing the gene page go fail this is an emergency patch.
* fix: fixed gene pheno path in react router * refactor: open gene pheno in the same page as gene instead of a separate window
…fetching colocalization table if needed (#362)
fix: fixed formatting of y-axis ticks in the plot.
* support for quantitative table columns * remove notes --------- Co-authored-by: major seitan <majorseitan@gmail.com>
Co-authored-by: major seitan <majorseitan@gmail.com>
javascript treats empty spaces at zero for e.g. +"" == 0 string representations of numeric values should be checked for empty string. Co-authored-by: major seitan <majorseitan@gmail.com>
* Fix merging columns in autoreporting backend Merging columns resulted in ";" when having no values. Fixed that so either empty strings or "NA" are filtered out, so columns are merged correctly. * fill in NA for empty strings in autoreporting group data
fix field returning supplementary data.
Update gene loss of function empty message
fix optional formatter
Fixed faulty conversion to boolean causing all credsets to have good_…
Risteys link has changed
… results) and pheno (credible set tab) pages.
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Hi, can you change some settings to avoid sending these PRs?
…On Tue, Jul 11, 2023 at 3:12 PM major seitan ***@***.***> wrote:
------------------------------
You can view, comment on, or merge this pull request online at:
#210
Commit Summary
- 177ec8b
<177ec8b>
fix staging
- 085b9c8
<085b9c8>
added roles
- a7210a3
<a7210a3>
fixes
- ffc98f4
<ffc98f4>
bump staging default version
- 800b750
<800b750>
resize lavaa plot
- f1ad5b5
<f1ad5b5>
results helm configuration
- 668cd3a
<668cd3a>
Merge pull request #219 from FINNGEN/211-size-volcano-plot
- 78bb16d
<78bb16d>
Merge pull request #218 from FINNGEN/217-create-helm-results-finngen-fi
- 861ce5c
<861ce5c>
added pips
- 36538f7
<36538f7>
backend changes
- ee32d76
<ee32d76>
backend changes
- 412f0f3
<412f0f3>
changes
- 80c096c
<80c096c>
Merge branch '215-remove-random-page' of
https://github.com/FINNGEN/pheweb into 215-remove-random-page
- e7dee8a
<e7dee8a>
Merge pull request #221 from FINNGEN/215-remove-random-page
- 5389ca7
<5389ca7>
switch staging to r9
- 7417149
<7417149>
remove unused functions
- d8cfeab
<d8cfeab>
1. remove lock on region
- f04f456
<f04f456>
Merge pull request #222 from FINNGEN/213-remove-lock-on-region
- b2f7623
<b2f7623>
improve gene banner
- 0c59b2c
<0c59b2c>
fixes to gene
- 7b01f77
<7b01f77>
fix buttons
- 30202c6
<30202c6>
clean up gene
- f252cd9
<f252cd9>
remove templates
- a952acc
<a952acc>
fix filter
- 66885fe
<66885fe>
fix filter
- 6940ad2
<6940ad2>
code clean up
- a595a00
<a595a00>
wip logout
- 622d051
<622d051>
fix redirect
- 5f80878
<5f80878>
Merge pull request #223 from FINNGEN/214-logout
- 4ba8895
<4ba8895>
bump package
- 7f600f8
<7f600f8>
emergency patch for threading issue
- 98f22bd
<98f22bd>
Update README.md
- 02553e9
<02553e9>
Update README.md
- 34d8284
<34d8284>
clean build
- c2399ee
<c2399ee>
parameters for bad load. r6 fixes
- 0f98611
<0f98611>
fix mlog p
- f2e490c
<f2e490c>
make fields maf_cases maf_controls options
- ade5b24
<ade5b24>
add cli support to augment_phenos.py
- feb01bc
<feb01bc>
fix args
- b0a8c85
<b0a8c85>
setup for meds
- 24fe7b9
<24fe7b9>
fix contention issues
- a99d1f2
<a99d1f2>
Merge pull request #227 from FINNGEN/212-resource-contention
- 4ecc7c3
<4ecc7c3>
parameters for bad load. r6 fixes
- 297f72a
<297f72a>
fix mlog p
- e3790f9
<e3790f9>
make fields maf_cases maf_controls options
- e2fa76e
<e2fa76e>
add cli support to augment_phenos.py
- 680b1fa
<680b1fa>
fix args
- f511b24
<f511b24>
setup for meds
- 04ae60b
<04ae60b>
update readme.txt
- 9c7d110
<9c7d110>
add ansible for meta
- 52d2e53
<52d2e53>
wip:meta import
- acd4bcb
<acd4bcb>
wip:228-only-push-master-to-bstaging
- dff4e68
<dff4e68>
wip:228-only-push-master-to-bstaging
- efe9530
<efe9530>
wip:228-only-push-master-to-bstaging
- 5b66dd4
<5b66dd4>
wip:228-only-push-master-to-bstaging
- f1cfdf1
<f1cfdf1>
wip:228-only-push-master-to-bstaging
- 8531704
<8531704>
import error message
- 2f2b0f9
<2f2b0f9>
allow additional fields
- 4024d1f
<4024d1f>
deal with affix
- 8c49ab4
<8c49ab4>
fix contention issues
- 366dc65
<366dc65>
bump container version for meds
- 7b6a0aa
<7b6a0aa>
correct import fields
- fcdb938
<fcdb938>
increase size
- a461b3d
<a461b3d>
add additional columns
- d923b81
<d923b81>
fix:add support for non standard fields
- 69dfa7f
<69dfa7f>
locus zoom parameters for genes
- 87e8189
<87e8189>
locus zoom parameters for region
- 5dc720b
<5dc720b>
wip:228-only-push-master-to-bstaging
- e93617f
<e93617f>
wip:228-only-push-master-to-bstaging
- 4f98374
<4f98374>
fix mlog calculation
- 0ef6b2a
<0ef6b2a>
setup production scripts
- 29dfa66
<29dfa66>
bump wdl
- a5ab8d3
<a5ab8d3>
disable calculate m log p from beta
- 89815c1
<89815c1>
bump version
- 960b8bb
<960b8bb>
r9.production wdl
- 698ef97
<698ef97>
r9.development wdl
- 494677e
<494677e>
remove best phenos by gene
- ff13944
<ff13944>
add version
- c9758eb
<c9758eb>
Merge pull request #235 from FINNGEN/234-cleanup-import-scripts
- 6ce25b5
<6ce25b5>
document wdl version
- cfe2767
<cfe2767>
bump version
- 52996d5
<52996d5>
address tabix threading issue
- 72aee90
<72aee90>
Merge pull request #236 from FINNGEN/225-meds-finngen-fi
- 0315934
<0315934>
fix autocomplete
- 1633efd
<1633efd>
fix: typo + helm
- bbf3150
<bbf3150>
Merge branch '229-import-meta-analysis' of
https://github.com/FINNGEN/pheweb into 229-import-meta-analysis
- 3d1e686
<3d1e686>
meta ukbb deployment
- c8c20b0
<c8c20b0>
deploy to bstaging only when committed to master
- d94be8b
<d94be8b>
increase number of pods on bstaging
- caf1326
<caf1326>
Merge pull request #246 from FINNGEN/244-r9-to-bstaging
- 9c50514
<9c50514>
Conditional backend changes
- 7369a2a
<7369a2a>
don't create tabix for all variants in gene page
- ad5b361
<ad5b361>
Conditional analysis front end changes
- 8e42ae5
<8e42ae5>
Merge branch 'conditional_front_mk' into conditional_mk
- a3bb9b2
<a3bb9b2>
Merge branch 'master' into conditional_mk
- 7913a32
<7913a32>
Removed deployment files dragged along from deploy branch
- 89ed94b
<89ed94b>
Remove all remnants from reusing tabix files and always create new tabix
- 04327a7
<04327a7>
Removed more remnants of the newer import branch
- fe1cf36
<fe1cf36>
Merge pull request #254 from FINNGEN/conditional_mk
- 8797691
<8797691>
fix autocomplete
- fa8c631
<fa8c631>
fix autocomplete
- 4e6a271
<4e6a271>
fix autocomplete
- 0466a41
<0466a41>
switch feature flag for lavaa plot default to on
- 3c859f1
<3c859f1>
upgrade to new version of lavaa plot
- a633128
<a633128>
Merge pull request #259 from FINNGEN/258-change-default-on-lava-plot
- 36c358a
<36c358a>
migrate r9 nfs
- 362d8dd
<362d8dd>
switch feature flag for lavaa plot default to on
- c6299d1
<c6299d1>
restore default port
- 1e910d9
<1e910d9>
migrate r8 nfs
- 7e86514
<7e86514>
migrate drugwas nfs
- 9cf56b6
<9cf56b6>
migrate meds nfs
- 24192b3
<24192b3>
migrate drugwas nfs
- 3795430
<3795430>
migrate userresults
- f648cbc
<f648cbc>
remove r9 legacy nfs
- 1b7d4a0
<1b7d4a0>
switch feature flag for lavaa plot default to on
- 45d4b6e
<45d4b6e>
update r9 bucket
- db1fa28
<db1fa28>
use default in development configuration
- b3d1409
<b3d1409>
improve default
- 744bde3
<744bde3>
improve defaults
- 6e2ff76
<6e2ff76>
Merge pull request #262 from FINNGEN/258-change-default-on-lava-plot-fix
- 6a76145
<6a76145>
Merge pull request #261 from FINNGEN/250-migrate-from-google-nfs
- 69e4b96
<69e4b96>
r10 release
- cd0a82a
<cd0a82a>
provision r10
- e3829e7
<e3829e7>
bump image
- 413a396
<413a396>
bump r10 image
- dae9ae5
<dae9ae5>
type alias
- de45334
<de45334>
log import
- 5c08f71
<5c08f71>
update instructions
- adadcfe
<adadcfe>
additional chrom
- 4d9f66b
<4d9f66b>
imporve docs
- 814210e
<814210e>
Merge pull request #266 from FINNGEN/255-import-r10-wip
- a81aa38
<a81aa38>
229 import meta analysis (#267)
- cd87005
<cd87005>
bump r10 version
- 16097a5
<16097a5>
269 error on userresults variant page (#270)
- f9c1d3e
<f9c1d3e>
resized columns (#273)
- 53ad27f
<53ad27f>
fix finemapping (#274)
- ce92c27
<ce92c27>
fix download locus zoom (#275)
- 973f2d7
<973f2d7>
chore:remove logging
- 39846a5
<39846a5>
fix x chromosome when using finemapped_regions (#277)
- 720c022
<720c022>
Update README.md
- 871a175
<871a175>
285 region gene track chrom x (#286)
- a8ed8f5
<a8ed8f5>
biobank url optional (#287)
- c406a7c
<c406a7c>
Update augment_phenos.py
- 870b638
<870b638>
ld lookup fix for chr 23 (#288)
- 138e539
<138e539>
bump gcloud
- cfe26b4
<cfe26b4>
fix chrom x site file (#290)
- 11c9c2a
<11c9c2a>
smaller patch (#291)
- c65a363
<c65a363>
revert cli changes
- 2858f21
<2858f21>
fix annotation
- 19a20e5
<19a20e5>
improve font . display af and info values
- bd0aeeb
<bd0aeeb>
variant page fixes
- 1a7140c
<1a7140c>
fix add genes
- 5f245ca
<5f245ca>
fix gene tuple
- 51b4241
<51b4241>
fix add genes
- 31348a8
<31348a8>
swap bstaging from r9 to r10
- 46a2b1b
<46a2b1b>
ui fixes
- 1deecc7
<1deecc7>
fix:remove logging
- dea6c01
<dea6c01>
switch to release
- 0ba52ff
<0ba52ff>
fix meds
- f7490ae
<f7490ae>
bump results
- a2ebf09
<a2ebf09>
266 userresults deployment (#295)
- a9764a6
<a9764a6>
gene lof optional (#299)
- a1ec364
<a1ec364>
Update Gene.tsx
- 7392d12
<7392d12>
Update main.yml
- da293c9
<da293c9>
update red targets
- a6da2a5
<a6da2a5>
gene links target blank . variant lz hover fix . variant tooltip width
fixed (#300)
- c44a772
<c44a772>
hotfix (#302)
- a13e412
<a13e412>
resize gene columns
- 4d81c1b
<4d81c1b>
bump lavaa version
- 9416345
<9416345>
X search (#303)
- 339eccc
<339eccc>
empty rsid variant fix
- f8dc4af
<f8dc4af>
306 remove non docker deploy (#307)
- 9ec7c77
<9ec7c77>
304 search backend (#308)
- 4b38905
<4b38905>
remove ukbb from autoreporting prereqs, remove pandas from group report
function
- 3ab40ff
<3ab40ff>
restrict to variant
- b9f5893
<b9f5893>
305 variant page fixes (#310)
- c9c4986
<c9c4986>
add na checks for values
- 568a201
<568a201>
fix typo
- 8c48929
<8c48929>
fix typo
- 2d50846
<2d50846>
fix
- 2f5bbde
<2f5bbde>
282 x chr fixes (#311)
- b8008bd
<b8008bd>
separate assoc merging to lambda
- 0ef2f5b
<0ef2f5b>
rm unnecessary variable annotation
- e5cc0b3
<e5cc0b3>
region fix locus zoom
- ef855ea
<ef855ea>
Merge pull request #312 from FINNGEN/309-decouple-autorep-ukbb
- 50fb9c1
<50fb9c1>
fix x issue on gene page
- ee814ca
<ee814ca>
add gene name in gene drug name table banner (#316)
- e6ab39b
<e6ab39b>
use strict matching for gene names (#318)
- acc0a7f
<acc0a7f>
added gene report template (#320)
- 593dfe2
<593dfe2>
toggle lavaa plot (#321)
- 9d3f9d9
<9d3f9d9>
drop pandas and strict req for annotation dbv
- d7441c2
<d7441c2>
small changes
- 1d568cd
<1d568cd>
column changes (#328)
- 5ddc75a
<5ddc75a>
Update tableColumn.tsx
- f8555e7
<f8555e7>
Merge pull request #326 from FINNGEN/323-autoreport-group-variants
- 8f856b4
<8f856b4>
variant page fix (#329)
- bc45fba
<bc45fba>
331 coding variant (#335)
- 8ad6010
<8ad6010>
336 fix css issues (#337)
- 8b2fe75
<8b2fe75>
Update ResultTable.tsx
- ad79bbc
<ad79bbc>
fix build
- 6c9e1f0
<6c9e1f0>
fix build
- fa21635
<fa21635>
chip config changes
- 66c2c5a
<66c2c5a>
338 rename chip to coding (#339)
- cb05add
<cb05add>
add coding db dao
- 225f7e0
<225f7e0>
add coding banner
- d3a4383
<d3a4383>
mysql autocomplete dao (#342)
- 313d24d
<313d24d>
fix spacing in lof variants
- e4216bd
<e4216bd>
pip and sex difference (#344)
- 447377a
<447377a>
add sql statements
- 23f4d8c
<23f4d8c>
Merge branch 'master' of https://github.com/FINNGEN/pheweb
- 8f8175f
<8f8175f>
fix typescript bug
- c309192
<c309192>
remove ui settings from backend
- 58a67b4
<58a67b4>
add supplementary status
- 8aa0bdf
<8aa0bdf>
fix build warnings and overflow errors
- 9d58d31
<9d58d31>
349 ld configuration (#354)
- bf3e53d
<bf3e53d>
349 ld configuration (#355)
- 9179474
<9179474>
add husky
- c8d69c0
<c8d69c0>
test husky
- e6b2d41
<e6b2d41>
setup husky
- 7d1890b
<7d1890b>
fix build
- 37a934d
<37a934d>
fix husky
- 9864811
<9864811>
add space to variant list
- 5e1c0f8
<5e1c0f8>
Gene pqtl coloc table (#356)
- 6fad4c7
<6fad4c7>
fix coding only chip label
- 60325d5
<60325d5>
meta fix
- f38ec53
<f38ec53>
fix lz configuration
- 1164cad
<1164cad>
fix lz configuration
- 03cad88
<03cad88>
support multiple nearest genes
- eff5f66
<eff5f66>
add delimiters
- e907fe8
<e907fe8>
fix delimiter
- c54d345
<c54d345>
360 gene page does not change phenotype when clicking (#361)
- ef9847e
<ef9847e>
fix: updated server side code to accept precise db specification for
fetching colocalization table if needed (#362)
- 477af59
<477af59>
fix: fixed formatting of y-axis ticks in the plot.
- 3c3c806
<3c3c806>
Merge pull request #368 from FINNGEN/363-manhattan-plot-lost-y-axis
- 99b653d
<99b653d>
366 quantitative traits columns (#372)
- 6b970f3
<6b970f3>
fix download coding variant table (#379)
- 2fc079c
<2fc079c>
Risteys link has changed
- 4dfae72
<4dfae72>
fix parsing of strings representing numbers (#382)
- 5719bfa
<5719bfa>
Risteys link has changed (#381)
- d8dd694
<d8dd694>
Fix merging columns in autoreporting backend (#378)
- aca1325
<aca1325>
fix supplementary
- 21feefe
<21feefe>
Update gene loss of function empty message
- cd0d6ce
<cd0d6ce>
Update commonTableColumn.tsx
- 42ca507
<42ca507>
Fixed faulty conversion to boolean causing all credsets to have good_cs to
true
- 30ca999
<30ca999>
Merge pull request #388 from FINNGEN/fix_good_cs_mk
- da10404
<da10404>
Merge pull request #389 from FINNGEN/fix_risteys_link_mk
- 640eac8
<640eac8>
example metaresults
- 69909ca
<69909ca>
Added standard error to download tables in variant, gene (association
results) and pheno (credible set tab) pages.
- a9482b6
<a9482b6>
Merge pull request #397 from
FINNGEN/391-add-standard-errors-to-all-download-tables
- d85e867
<d85e867>
Type alias gene-phenotype detail to the definition in the index
File Changes
(300 files <https://github.com/statgen/pheweb/pull/210/files>)
- *A* .dockerignore
<https://github.com/statgen/pheweb/pull/210/files#diff-2f754321d62f08ba8392b9b168b83e24ea2852bb5d815d63e767f6c3d23c6ac5>
(16)
- *A* .gitattributes
<https://github.com/statgen/pheweb/pull/210/files#diff-618cd5b83d62060ba3d027e314a21ceaf75d36067ff820db126642944145393e>
(1)
- *M* .gitignore
<https://github.com/statgen/pheweb/pull/210/files#diff-bc37d034bad564583790a46f19d807abfe519c5671395fd494d8cce506c42947>
(79)
- *A*
<https://github.com/statgen/pheweb/pull/210/files#diff-63a9c44a44acf85fea213a857769990937107cf072831e1a26808cfde9d096b9>
|
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