Colin Megill
d04dba225f
Filename dialogue includes gene sets ( #2185 )
...
* change filenames
* gene-sets to anno dialogue
* logging, lambda
* celllabels
* cell dash labels
* space
* fix 2182 - annotation file name change on the backend
Co-authored-by: bkmartinjr <bruce@chanzuckerberg.com >
2021-05-07 17:32:11 -04:00
Colin Megill
096d8ff1d2
Geneset remove toggle ( #2184 )
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* no toggle, histo at top
* set mean expression, truncation
* gene set
2021-05-05 19:51:05 -04:00
Colin Megill
25b308c532
conditional colon ( #2181 )
2021-05-04 13:43:02 -04:00
Bruce Martin
f2e9aecebe
hosted gene sets routes, plus a few bug fixes ( #2155 )
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* first cut at hosted gs routes
* lint
* update tests to match csv parser changes
* update tests to new API
* update gene set name validation rules to match requirements
* add path mapping from dataset to geneset
* add test cases for geneset GET route
* fix test assertion
* remove debugging code
* update gene set uri mapping function
* fix error message
* allow extra user-specified headers in gene set csv file
* clarify comment
2021-04-27 13:58:58 -07:00
Colin Megill
fd2a7a53ab
Color by gene set mean expression ( #2157 )
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* colorby histo
* color graph by mean expression
* move var index after returns
* add genesets as an argument
* varindex
* undo redo for mean expression
* destructure
* ternary
* Revert "destructure"
This reverts commit 2d9432c1c7
2021-04-22 13:58:30 -04:00
Colin Megill
876ceb4d8b
Create / edit geneset description ( #2139 )
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* geneset description add
* edit geneset description
* default state for desc
* remove log
* naming, todo
* check for both dup name and desc
* fixes
* do not store gene set modal state in history stack
* Update createGenesetDialogue.js
* Update editGenesetNameDialogue.js
Co-authored-by: bkmartinjr <bruce@chanzuckerberg.com >
2021-04-21 19:50:29 -04:00
Bruce Martin
99a795a688
Updating front-end dependencies ( #2167 )
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* update to webpack 5
* update babel
* update eslint
* update cheerio
* update npm min to v7
* revert engine change
* generate package lock with npm v6 (lockfileVersion 1)
* add region to test setup
* update blueprint popover2
* tabindex changes due to blueprint popover2 revision
* update snapshots
* update lodash and pako
* fix typo
* fix lodash refactoring
* more lodash refactoring
* update babel and blueprintjs
* update jest support packages
* update puppeteer
* update regl
* update react-icons and react-helmet
* update react and react-dom
2021-04-21 07:23:31 -07:00
maniarathi
e2ce9a90ca
Remove updates coming from cookie banner since updates have already been executed. ( #2161 )
...
Co-authored-by: Timmy Huang <tihuan@users.noreply.github.com >
2021-04-19 08:42:34 -07:00
Colin Megill
c23b25d4e8
geneset description ( #2141 )
2021-04-12 16:31:21 -04:00
Colin Megill
b446bf7144
Handle empty gene set ( #2128 )
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* handle empty gene set case
* merge error, remove conflict markers
* paren
2021-04-01 13:45:47 -04:00
Colin Megill
20bfa4cc97
prepopulate input ( #2129 )
2021-04-01 06:21:59 -04:00
Bruce Martin
2fa19c756c
propagate diffexp state through component tree ( #2135 )
2021-03-31 12:23:38 -07:00
Bruce Martin
ae30b66123
gene set summary progress ( #2127 )
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* revert removal of cache control headers
* checkpoint work on revising summary route
* add summary query support to annoMatrix
* summarize route cleanup
* add mising file
* clean up summarize route
* add summary histogram
* update deps
* lint
* more lint
* lint
* manage crossfiler during gene set state changes
* remove obsolete debugging code
* correctly perform async watch in histogram
* better error handling
2021-03-30 14:43:53 -07:00
Bruce Martin
bfb9e1edcc
increase default diffexp gene count to 50 ( #2130 )
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* increase default diffexp gene count
* try tiledb version fix
2021-03-30 13:10:09 -07:00
Colin Megill
e6e358ddc8
Gene sets UI, right sidebar refactor ( #2097 )
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* prototyping
* render histos on open gene set
* prototyping
* render histos on open gene set
* factor out add genes to own component
* remove unused import
* mock reducer
* color by geneset stub
* menus and buttons
* geneset dialogue stub
* remove heatmap mock
* componetize histogram
* reenable add genes
* re-add isuserdefined
* test data
* remove have fetched
* add isExpanded state to gene, and pass to histogram
* expand button
* toggleable
* mini
* bump number of genes to 50
* don't clear diffexp on subset
* move create category to top
* render diffexp as geneset
* geneset show mean expression
* gene set reducer
* add geneset UI reducer
* wire e2e gene set loading prototype
* fix sniffing bug
* fix typo
* add gene modals
* client/src/actions/
* add autosave
* rename data-dir cli param
* add geneset, add gene, delete set
* prototype: remove csv upload placeholder
* handle delete gene from set
* prepopulate geneset with genes from modal
* add geneset: rename action
* icons, language consistency
* chevron after
* handle empty string case on genes for create geneset
* edit geneset
* fix language on create
* copy correction
* add popper2
upgrade react popper
upgrade react popper
adding popover2 package
* truncate uses tooltip2
* gene set button text typo
* remove logging
* moving server over
* remove test imports
* don't try to destructure map, use array.from
* fix add gene map datastructure error
* Revert "fix add gene map datastructure error"
This reverts commit b0eed45952sbadajoz@chanzuckerberg.com >
* remove unused geneset validation code
* tmp format pending geneset description
* move magic number into variable
* reorganize genesetsUI reducer pending tests
* rewire edit given new action name
* add basic validation and feedback for geneset name uniqueness
* mv annoDialog
* mv label, repair paths
* Update client/src/components/brushableHistogram/header.js
Co-authored-by: Severiano Badajoz <sbadajoz@chanzuckerberg.com >
* add imports for icon in histo
* update jest snapshots given blueprint/tooltip2 usage of index -1
* ensure no empty paragraph
* intent from blueprint
* remove remainder of jshint references
* do not push undo when autosave fires
* fix autosave bugs
* remove todos
* clamp to util
* scient to util
* revert clearing diffexp
* rename value to be more specific stacked bar
* clean up logging and commetns
* remove gene entry tests pending rewrite
* tab index -1
* update jest snapshot, blueprint tooltip 2
* caret margin
* snapshot update
* ensure histogram is centered
* add geneset actions to config
* comment maybeScientific
* comment clamp
* comment ui reducer
* remove prototype code
* remove error log
* remove references to bl.ocks
* componetize parseBulkGeneString
* catch case where geneset rename same name
* genesetui reducer tests
* add geneset ui to index reducer config
Co-authored-by: bkmartinjr <bruce@chanzuckerberg.com >
Co-authored-by: Severiano Badajoz <sbadajoz@chanzuckerberg.com >
2021-03-24 16:33:26 -04:00
Timmy Huang
8d932fb47d
thuang-126-CZIF-policy-updates ( #2111 ) ( #2112 )
2021-03-17 16:07:42 -07:00
Bruce Martin
c037f4eaa6
rename "geneset" to "gene set" in CLI ( #2088 )
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* remove dead code
* rename geneset to gene_set
2021-03-02 15:36:01 -08:00
Bruce Martin
b00496198d
wire up geneset reducer ( #2082 )
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* first cut at GET /genesets route
* update existing tests to match code changes
* more GET /genesets and initial tests
* add missing test fixture
* geneset validation accepts OTA format
* genesets route: better error handling, more tests
* lint
* genesets reducer and initial load
* fix lint
* add autosave support for genesets
* remove debug logging
* fix typo
* fix another typo
* update smoke test config for genesets
* smoke test fixes
* more fiddling with smoke tests
2021-03-02 12:12:58 -08:00
Bruce Martin
036b5f8c0f
Fix indexing bug in user-specified colors ( #2051 )
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* repaint category value when color changes
* bug fix incorrect indexing of user colors
* add test for bug 2007
* lint
2021-02-08 18:00:03 -08:00
Bruce Martin
3aef21f76c
alpha blending fix in scatterplots ( #2033 )
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* explicitly specify alpha blending; rename NaN flag to accurately describe function
* fix incorret dest alpha blending function
2021-02-05 09:34:37 -08:00
bmccandless
c7eb319817
P value and Log fold change not showing up for all DE results ( #2016 )
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The HistogramFooter needs to distinguish between an undefined
value and a value of 0. If the pvalAdj was 0, then the logFolChange
was previously not showing up.
#1888
2021-01-08 09:44:17 -08:00
Marcus Kinsella
46d02b1987
Handle schema v1.1.0 ( #2002 )
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Correctly display datasets that follow schema version 1.1.0
2020-12-14 15:20:29 -08:00
Severiano Badajoz
0b91371ea8
check if viewport has changed and render accordingly ( #1996 )
2020-12-03 15:14:57 -08:00
bmccandless
2cc02a84cb
Convert float annotations if possible. ( #1987 )
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* Convert float annotations if possible.
The client converts all arrays to floats.
If a category contains integer labels, and that category is copied, it will contains floats (e.g 1.0 instead of 1).
When that category is put back to the server, it fails in the tiledb code, which does not accept floats.
The solution is to convert a float category to integer, if possible.
#1984
* updates
2020-11-20 17:01:53 -06:00
Timmy Huang
2cf55ab819
thuang-compress-annotation ( #1980 )
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* thuang-compress-annotation
* compress test
* use zlib.decompress directly
2020-11-17 14:05:07 -08:00
Bruce Martin
06b88cda20
do not update GPU buffers if data has not changed ( #1967 )
...
Co-authored-by: maniarathi <mani.arathi@gmail.com >
Co-authored-by: Severiano Badajoz <sbadajoz@chanzuckerberg.com >
2020-11-09 10:41:39 -08:00
Bruce Martin
b5856ff9bc
fix accidental state error ( #1966 )
2020-11-04 18:46:04 -08:00
Severiano Badajoz
d87551ce5e
fix version check ( #1968 )
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Inverted the schema version check so that we check that it IS 1.0.0.
2020-11-04 17:43:41 -08:00
Severiano Badajoz
a5c9ae2432
Data drawer final round of prod QA fixes ( #1955 )
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* add long title
* add organism to Dataset Metadata and create headers
* begin HTMLTable for metadata
* switch out truncating for scrolling
* add optional chaining to redux state mapping
Co-authored-by: maniarathi <mani.arathi@gmail.com >
2020-11-04 09:43:43 -08:00
Severiano Badajoz
727af83152
remove conditional rendering cases from color legend ( #1952 )
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* Revert "Remove Continuous vars with 1 value from histogram, add to info drawer (#1927 )"
This reverts commit 242546371bmadison.dunitz@chanzuckerberg.com >
2020-10-28 15:35:28 -07:00
Severiano Badajoz
924b518492
Revert "Remove Continuous vars with 1 value from histogram, add to info drawer ( #1927 )" ( #1953 )
...
This reverts commit 242546371b
2020-10-27 17:12:13 -07:00
maniarathi
9793398737
Add in missing previous crossfilter which was causing the re-embedding feature to fail. ( #1936 )
2020-10-21 09:16:13 -07:00
Severiano Badajoz
c9f9549118
Adopt JS standards once userinfo data is in frontend ( #1930 )
2020-10-16 11:59:28 -07:00
Madison Dunitz
242546371b
Remove Continuous vars with 1 value from histogram, add to info drawer ( #1927 )
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* remove single val continous metadata from histogram, add to info drawer
* refactor to save singleContinuous values in state
* fix edge case, single continuous values reappeard in rsb when clipped
2020-10-14 12:46:24 -05:00
maniarathi
798976e4c1
Fix custom color handling ( #1929 )
2020-10-13 15:47:56 -07:00
maniarathi
5325495123
Speed up dataset drawer rendering ( #1926 )
2020-10-12 11:20:58 -07:00
maniarathi
86ff48ae36
Revert "Allow columns encoded in float64 to be rendered as part of continuous value histograms. ( #1905 )" ( #1925 )
...
This reverts commit b048fd8d9a
2020-10-09 10:09:32 -07:00
Timmy Huang
c01a2c72b6
thuang-1840-authn-prompt ( #1911 )
2020-10-08 16:57:53 -07:00
Severiano Badajoz
6677d0de56
disable profile picture ( #1923 )
2020-10-08 12:16:02 -06:00
Severiano Badajoz
c4c48b9a57
create e2e test for auth buttons ( #1907 )
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This PR adds a few helpful additions regarding authentication.
Changes:
* e2e tests are now run on test_oauth via a passed config.yaml
* node dev server correctly handles `/login` and `/logout` endpoints to make developing for auth easier
* Introduced auth e2e tests to check that buttons display and work
2020-10-08 10:02:40 -07:00
Severiano Badajoz
1c4c501c43
Auth UI tweaks ( #1915 )
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* remove auth buttons and dataset info from info menu
* add auth buttons to menubar
* remove auth from top left
* new auth buttons
* move infomenu to lsb dir
* styling fixes
* feedback
* more feedback
Co-authored-by: Timmy Huang <thuang@chanzuckerberg.com >
2020-10-07 15:02:55 -07:00
maniarathi
b048fd8d9a
Allow columns encoded in float64 to be rendered as part of continuous value histograms. ( #1905 )
2020-10-06 12:59:07 -07:00
Timmy Huang
99152dd5aa
add-menu-test-id ( #1895 )
2020-09-30 12:53:51 -07:00
Colin Megill
04a3c3c6b6
Partial fix for 1830 ( #1863 )
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* Remove door icon from log in button
* Move log in and info buttons from the top bar to in line with the cellxgene icon and dataset name
* Hover over on login button should say "Log in to cellxgene"
* Show email
closes #1830
2020-09-30 11:45:10 -07:00
maniarathi
4aabb8e092
Make sure there are more than 1 values in a category before rendering it ( #1871 )
2020-09-29 15:32:21 -07:00
Severiano Badajoz
7bee09cd16
Add blueprint eslint plugin ( #1892 )
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* add bp3 eslint plugin
* first eslint runthrough + manual changes
* small fixes
* update snapshots
* update h1 to h4
Co-authored-by: czimergebot <35308261+czimergebot@users.noreply.github.com >
2020-09-29 15:00:56 -07:00
Severiano Badajoz
21dfdb91a9
skip user annos when building dataset metadata ( #1881 )
2020-09-28 13:17:14 -07:00
Severiano Badajoz
374bb11279
Handle case where new drag starts while existing lasso is not finished ( #1864 )
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* handle case where new drag starts while existing lasso is not finished
* flip variable
2020-09-28 10:34:47 -07:00
Severiano Badajoz
210042814f
Info Drawer format adjustments ( #1853 )
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This PR tweaks the look and feel of the info drawer in response to QA from @signechambers1
2020-09-18 13:16:28 -07:00
Severiano Badajoz
3e9cb0265e
Fix InfoFormat parameter checking ( #1831 )
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Went through and ensured that undefined/null values were caught and handled correctly in render functions. Also documented some of the more complicated functions.
---
Closes #1825
2020-09-15 12:03:59 -07:00
