Consequences #3073
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Consequences #3073
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…visible to all (but disabled for no kf-investigator)
adipaul1981
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Apr 12, 2021
francisl
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Apr 12, 2021
evans-g-crsj
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Apr 13, 2021
* Studies data refresh (#2990) * studies * fix filters and refactoring * add studies search filters * add cohort buider * fix Cohort builder * fix bug remove last filter * add missing filters * feat: #2337 Styling for filter/table * fix: #2337 refactor studies * feat(studies): #2934 filters with Sqon * rebase * rebase * fix: #2337 removed any type in results * feat: #2934 cleanup and fix filters with sqon * fix: #2337 fix relative font issue * fix: #2337 Push apollo before routing * fix mapping types * fix: #2337 fix font size in cohort builder and file repo Co-authored-by: Francis Lavoie <flavoie@ferlab.bio> * fix: #2991 studi page flash when loading new data * fix: #2993 new project (#2994) * fix: #2995 remove style leaking, update specific styling * fix: #2998 Sidebar Style update * fix: #3006 fix table with new columns (#3007) * build(deps): bump elliptic from 6.5.2 to 6.5.4 Bumps [elliptic](https://github.com/indutny/elliptic) from 6.5.2 to 6.5.4. - [Release notes](https://github.com/indutny/elliptic/releases) - [Commits](indutny/elliptic@v6.5.2...v6.5.4) Signed-off-by: dependabot[bot] <support@github.com> * fix: #2999 Fix Querybuilder and button default theme * fix * feat (variant page): minimal UI (#2982) * feat (variant page): minimal UI * incorporate code review * add basic layout and style for table * WIP: suggestions * WIP: incorporate code review * plug data to table * fix merge + display consequences according to specs * incorporate code review * code review * make sure test passes * fix warnings * use enum instead of string * fix: #3010 Update querybuilder color, icons * fix: #3019 facet tag count proper color * fix linter * Add filters to cb and file repo (#3022) * add filter to FR and CB * feat: #3004 participant table replace study name by study code * fix: #3024 fix checkbox colors and tag aligment * WIP: connect to cluster component (#3021) * WIP: connect to cluster component * avoid abusing await (from code review) * add link to cohortbuilder on p_ids * WIP: connect to cluster component * avoid abusing await (from code review) * add link to cohortbuilder on p_ids * eslint * fix: variant overflow * Progress bar variants page (#3028) * 1) make sure that you can connect to a cluster only if allowed 2) progress bar 3) keep search text when navigating 4) fix display algorithm for consequences. * remove css. * fix: #3030 study table column width (#3031) * fix: #2997 fix boolean filter (#3029) * Feat/study page link cb (#3033) * feat: #3032 link to cb * feat: #3032 fix add on empty query * feat: #3032 fix css * feat: #3032 review comments * fix: #3034 fix variant page link to CB (#3035) * fix: #3034 fix variant page link to CB * fix: #3034 review comments * Variant entity page (#3036) * feat: #3020 variant Entity page * feat: #3020 fix varaint page container * feat: #3020 fix css container * wip variant page * review comments * fix * fix * fix colors * make base for entity page * make base for entity page * remove unused * use correct func. * better naming. * phenotype table * incorporate review Co-authored-by: Adrian Paul <adipaul1981@yahoo.ca> Co-authored-by: evans-g-crsj <eg.crsj@gmail.com> * data for clinical tab (#3037) * data for clinical tab * frequencies tab * fix: #3039 remove search in studies * fix pr comments * fix: #3015 Functional pagination * fix pr comments * fix: #3042 variant page fix header * fix comment * fix: #3046 fix background and table border variant * fix: #3045 add dbgap to studies column, fix pagination, add filter studies name (#3048) * WIP: summary tab tables (data only). Note: all rules are not clear so… (#3050) * WIP: summary tab tables (data only). Note: all rules are not clear so I left identity functions as placeholder for coming work. * fix eslint error. * incorporate code review comments * fix variant mapping (#3051) * fix: #3054 update variant menu link * fix: #3052 variable table container * fix * fix: #3056 variant update table title and menu * fix variant stats (#3059) * fix variant stats * fix css * fix icons colors * fix comments * add expendable columns + expendable tables + some UI teaks (#3061) * add expendable columns + expendable tables + some UI teaks * add 'hide transcripts' * incorporate code review comments * fix: #3058 remove old workbench code * fix: #3064 variant update design summary header * add link to variant entity and fix various issues (#3063) * add link to variant entity and fx various issues * comments * multiple fixes (#3066) * multiple fixes * better naming for func (more generic) * add sort + encore suggestion (#3068) * fix pagination (#3069) * fix: #3071 fix table layout (#3072) * fix: #3071 fix table layout * fix * fix types * fix types Co-authored-by: Francis Lavoie <flavoie@ferlab.bio> * Consequences (#3073) * sort consequences correctly + show pagination count + make workbench visible to all (but disabled for no kf-investigator) * sort consequences + move file * make sure func name is not misleading (filterThanSort.. vs sort) * make sure alternate allele points on correct property + remove S in conservation + hide value if no data in impact column (summary tab) + fix warning in expand cell. (#3074) * fix: #3075 summary search result table style update * add link to CB from variant frequencies (#3077) * add link to CB from variant frequencies * review comments * review comments fix * review comments fix * fix: #3078 studies pagination * Add static links (#3081) * add external link in summary * add external links * remove ) * incorporate code review comment * format num * fix table header right aligment * fix: #3085 fix button on hover (#3086) Co-authored-by: Francis Lavoie <flavoie@ferlab.bio> * add gene consequeces title * fix: #3089 table alignment accros tables * Tweaks clininal tab and search (#3088) * remove sorter in variant table + better display in clinical associations tab. FIXME: use object vs array for Condition Type * remove biotype from title in summary tab * Feat/3084 variant search page link to cb for studies (#3090) * add studies link to CB from variant search page * change variant stats date * fix participant total link Co-authored-by: Evans Girard <54366437+evans-g-crsj@users.noreply.github.com> * fix: #3092 variant tag match default theme color * fixme: test + display items as list (#3094) * clinvar link + remove mim on hpo (#3095) * fix ex Co-authored-by: adipaul1981 <adipaul1981@yahoo.ca> Co-authored-by: Francis Lavoie <flavoie@ferlab.bio> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Francis Lavoie <flavoie.crsj+github@gmail.com>
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