Seve Badajoz
e49ad7a433
type camera
2021-08-12 16:35:27 -07:00
Severiano Badajoz
925b785b1f
fix: disable FE auth testing on compatibility tests ( #2377 )
2021-08-12 18:34:04 +00:00
Bruce Martin
660dff256c
add array type foundations ( #2376 )
2021-08-12 07:17:05 -07:00
Timmy Huang
59c475b821
chore: extract schema types ( #2375 )
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* chore: extract schema types
* address comments
2021-08-12 03:12:21 +00:00
Timmy Huang
fc60b2acef
fix: thuang-fix-tsconfig-path ( #2372 )
...
Thanks so much for the quick review, Bruce!!
2021-08-11 01:38:33 +00:00
Timmy Huang
26de334274
chore: add schema types ( #2369 )
2021-08-04 13:16:18 -07:00
Timmy Huang
95ce39f2e9
chore: Add global type file ( #2363 )
2021-08-03 21:52:10 +00:00
Bruce Martin
03bb904f24
remove unused packages from client ( #2359 )
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* remove unused packages from client
* add missing peer dep
2021-07-30 20:00:00 -07:00
Colin Megill
01d34580b9
genesets e2e tests, undo/redo ( #2327 )
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* undo redo create
* edit undo redo
* all tests pass, add, edit
* description
* remove RER1
* remove rer1
* remove from hosted
2021-07-30 16:52:49 -07:00
Timmy Huang and bkmartinjr
5ab96ed360
disable formatting rules for eslint and add prettier in lint-staged ( #2355 )
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* disable formatting rules for eslint and add prettier in lint-staged
* update npm modules
* set plugin-proposal-private-methods to loose
* update snapshots due to popover package update
* add missing quotes
Co-authored-by: bkmartinjr <bruce@chanzuckerberg.com >
2021-07-30 12:27:47 -07:00
Bruce Martin
97fb98b4eb
API update for tests ( #2354 )
2021-07-29 20:27:29 -07:00
Bruce Martin
0e7daea737
temp fixes for TS lint ( #2352 )
2021-07-29 18:31:38 -07:00
Bruce Martin
8136387127
Clean up max-category front-end limit ( #2347 )
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* remove topN category truncation from component rendering layer
* clean up category item limit implementation
* name change for clarity
* fix snapshot
* comments
2021-07-29 16:05:10 -07:00
Mim Hastie and Timmy Huang
27575b8d86
Added @typescript-eslint/recommended config with suppressions ( #2345 )
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* Disabled @blueprintjs/classes-constants. #2288 .
* thuang-eslint-bp-off (#2344 )
* Disabled @blueprintjs/classes-constants on webpack dev and shared. #2288 .
* Added TS recommended, suppress lint errors codemod.
* Added per-error/warning ignore for tests.
* Added per-error/warning ignore for configuration.
* Added per-error/warning ignore for src. Removed suppress package.
* Minor linting.
Co-authored-by: Timmy Huang <tihuan@users.noreply.github.com >
2021-07-28 16:06:34 -07:00
Bruce Martin
32f60a1547
clean up type inferencing ( #2332 )
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* unit tests for 64 bit conversion
* clean up type handling
* type inference tests
* more type inference fixes
* use schema to determine user intent for data typing
* stop using deprecated API
* fbs type encoding test
* add missing test
* add more tests
* correctly infer X type for CXG adaptor
* lint
* fix typo
* ts migration
* cleanup from PR review
* lint
* PR review changes
2021-07-28 15:10:12 -07:00
934cc5c69b
TS migration. #2288 . ( #2328 )
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* Added TS. Updated build and linting config. Added types.
* [ts-migrate][.] Rename files from JS/JSX to TS/TSX
Co-authored-by: ts-migrate <>
* [ts-migrate][.] Run TS Migrate
Co-authored-by: ts-migrate <>
* Corrected files mangled by ts-migrate.
* Updated lint config, minor linting.
* Re-enabled Husky.
* Updated tests and config.
* Reverted webpack devtool config.
* Removed obsolete snapshots.
* Added annotations snap.
* Updated tsconfig includes wrt linting.
* Removed ts-migrate.
Co-authored-by: Timmy Huang <tihuan@users.noreply.github.com >
2021-07-26 20:18:17 +00:00
Bruce Martin
3d7490e0a9
gene expression perf work ( #2305 )
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* gene expression perf work
* lint
2021-07-16 12:56:42 -07:00
Bruce Martin
0667ad0274
remove experimental reembedding support ( #2301 )
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* remove experimental reembedding support
* lint
* lint
* add prepare requirements to requirements-dev
* oops, revert accidental deletion of import
* more test modifications
* remove obsolete unit tests
2021-07-15 13:55:26 -07:00
Bruce Martin
e334fbe96e
remove experimental ontology support ( #2300 )
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* remove experimental ontology support
* lint
* remove ontologies from unit tests
* additional test changes
2021-07-14 07:23:38 -07:00
Severiano Badajoz
07816c2f93
docs: release 0.17.0 ( #2278 )
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* Bump version: 0.16.7 → 0.17.0-rc.0
* Bump version: 0.17.0-rc.0 → 0.17.0
2021-07-07 15:07:37 -07:00
signechambers1 and Seve Badajoz
56fcbae672
Remove safari from supported browsers ( #2272 )
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* Update README.md
* Update package.json
* Update obsoleteHTMLTemplate.html
* remove unneeded polyfills
* explicit deny safari
* remove from webpack and update lock
Co-authored-by: Seve Badajoz <sbadajoz@chanzuckerberg.com >
2021-07-06 10:09:51 -10:00
face1b3033
genesets e2e tests ( #2241 )
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* __test: create geneset
* example dataset test geneset
* delete geneset test
* edit __test
* gene crud
* Update client/Makefile
Co-authored-by: Severiano Badajoz <sbadajoz@chanzuckerberg.com >
* copy gene sets separately
* make fix
* ignore test files locally
* csv update
* updated csvs
* fix unit tests for gene set load routes
* add missing fix to czi_hosted unit test
* pin tiledb version, for czi_hosted backend, to <0.9
* Revert tiledb pin to be less than 0.9. Broken tests have been updated in main branch.
* newline, gitignore
* color by and subset
* diffexp sets equal
* add diff exp test class
* fix data class
* diffexp snapshot
* snapshot
* snap3
* snapshot parentInnerhtml
* remove snap
* updated anno snaps
* add test class to gene list div
* new snapshots
* kick off
* Revert "kick off"
This reverts commit 743f551d55sbadajoz@chanzuckerberg.com >
Co-authored-by: bkmartinjr <bruce@chanzuckerberg.com >
Co-authored-by: Arathi Mani <arathi.mani@chanzuckerberg.com >
Co-authored-by: maniarathi <mani.arathi@gmail.com >
2021-07-01 21:29:06 -04:00
Severiano Badajoz
b714c18e75
feat: frontend geneset validation ( #2258 )
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* add geneset name validation
* validate genes before addition
* display error messages
2021-07-01 22:09:50 +00:00
Severiano Badajoz
b8b1d0dd9e
fix: reset gene set colorScale on gene set deletion ( #2264 )
2021-06-30 16:46:44 -07:00
Severiano Badajoz
82de4178d9
feat: add quick gene lookup functionality ( #2250 )
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* add/remove gene functionality back with geneset style gene
* styling and expansion
* memo gene list to prevent re render
2021-06-23 13:59:10 -04:00
28b526b3fc
feat: diffexp returns two genesets ( #2230 )
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* feat: return two lists for diffexp (#2221 )
* sp
* split out derive sort order, tests passing
* sp
* return diff exp results in two lists
* update
* copy implementation over to desktop
* add tests for two lists
* small fixes to complete backend implementation
* accept new diffexp response
* map diff exp response to genesets
* delete )
* name diffexp genesets with population names
* take constants out of state and allow width prop to override
* shorten mini-histo properly truncate and resize depending on expansion
* prepend new genesets
* rename data within diffexp action
* backend
* move diffexp ttest to common code module, update tests
* update for unit tests
* reference actual var
Co-authored-by: Madison Dunitz <madison.dunitz@chanzuckerberg.com >
Co-authored-by: Madison Dunitz <dunitzm@gmail.com >
2021-06-08 21:02:19 +00:00
Severiano Badajoz
7ed53c0f5b
fix: add placeholder test so suite doesn't fail ( #2233 )
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* comment out test suite
* actually just put in placeholdertest
2021-05-26 12:41:16 -07:00
Severiano Badajoz
a4050f10e1
feat(geneset): save diff exp result as geneset ( #2216 )
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* update package lock
* allow falsey vals
* remove old diff exp handling
* save diff exp results as geneset
* delete test
* check for undefined or null
* use global geneset description for diffexp
* remove diffexp special code, no longer showing adjpval + logfoldchange
* remove differential map to state
* remove clear from FSM, since we no longer support those actions
* restore controlHelpers test with todo
2021-05-25 10:51:31 -07:00
Severiano Badajoz
265ccf3682
fix: use env specific secret ( #2204 )
2021-05-13 14:28:16 -07:00
Colin Megill and bkmartinjr
d04dba225f
Filename dialogue includes gene sets ( #2185 )
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* 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 and bkmartinjr
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 and Timmy Huang
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
Severiano Badajoz
f36d889455
fix: explicitly depend on favicons ( #2143 )
2021-04-08 15:55:00 -07:00
Severiano Badajoz
4510c8c8a4
Fetch passwords from secretsmanager ( #2138 )
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* add aws secretsmanagerclient
* create custom globalsetup
* consume secret password and enable tests
* update npm
2021-04-05 14:16:10 -07:00
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
Madison Dunitz
78c9d24ed4
Refactor czi_hosted and server into backend directory, pull common code into backend/common, refactor tests ( #2102 )
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* move local_server -> backend/server server-> backend/czi_hosted, pull common code into backend/common update imports, tests and make commands
2021-03-26 00:27:07 -05:00
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
Severiano Badajoz
1d3d9237e7
temp disable auth testing ( #2092 )
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* disable auth testing
* revert some deletion
2021-03-04 13:56:48 -08:00
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
Seve Badajoz