Arathi Mani
4a9e53aa97
Revert tiledb pin to be less than 0.9. Broken tests have been updated in main branch.
2021-06-20 21:08:31 -07:00
bkmartinjr
d82b69d0ac
pin tiledb version, for czi_hosted backend, to <0.9
2021-06-17 09:13:04 -07:00
bkmartinjr
40291b9bba
add missing fix to czi_hosted unit test
2021-06-17 08:34:29 -07:00
bkmartinjr
2261d5e82c
fix unit tests for gene set load routes
2021-06-17 08:06:42 -07:00
Colin Megill
acc7436106
updated csvs
2021-06-16 20:48:24 -07:00
Colin Megill
4449b8cff2
csv update
2021-06-15 14:05:06 -07:00
Colin Megill
f5bbe8a669
ignore test files locally
2021-06-14 16:21:32 -07:00
Colin Megill
fd28c176db
make fix
2021-06-14 13:39:06 -07:00
Colin Megill
f320f7fd31
copy gene sets separately
2021-06-10 17:28:51 -07:00
Colin Megill and Severiano Badajoz
e075c487e2
Update client/Makefile
...
Co-authored-by: Severiano Badajoz <sbadajoz@chanzuckerberg.com >
2021-06-09 17:43:40 -07:00
Colin Megill
0716cb1d3f
Merge branch 'main' into colinmegill/#2042-geneset-tests
2021-06-08 17:05:27 -07:00
Colin Megill
c78c367c34
gene crud
2021-06-08 17:03:40 -07:00
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
Colin Megill
022ffc22e6
edit __test
2021-06-08 13:15:15 -07:00
Colin Megill
8b9a7b4283
delete geneset test
2021-06-07 15:41:55 -07:00
Colin Megill
10506059d3
example dataset test geneset
2021-06-07 10:27:08 -07:00
Colin Megill
68a5b632d1
__test: create geneset
2021-06-04 02:10:36 -07:00
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
Madison Dunitz
6f6634a4d9
add action to deploy on on push to canary branch ( #2196 )
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* add action to deploy on on push to canary branch
2021-05-17 16:15:48 -07:00
Severiano Badajoz
265ccf3682
fix: use env specific secret ( #2204 )
2021-05-13 14:28:16 -07:00
maniarathi
59ec3afbb9
Pin versions of flatbuffer and Flask to be less than 2.0 ( #2199 )
2021-05-12 15:13:10 -07:00
Madison Dunitz
4666f1f044
add rule for static assest without dataset id ( #2194 )
2021-05-07 21:17:31 -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
maniarathi
ebeb1c8818
Fix command to EB to use the artifact.zip file during deployment instead of the source code in the directory. ( #2174 )
2021-04-23 11:07:57 -07:00
maniarathi
b60d20eb2f
Fix phony ( #2173 )
2021-04-22 18:00:00 -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
Bruce Martin
860547ced1
update requirements for server ( #2172 )
2021-04-21 17:12:16 -07:00
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
Madison Dunitz
63cf82c60e
Dunitz/scale test update ( #2159 )
2021-04-18 13:33:04 -05:00
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 and Ambrose J Carr
6ecdfa4940
Create design_principles.md ( #1903 )
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* Create design_principles.md
* Update design_principles.md
* Update design_principles.md
* Update design_principles.md
* Update design_principles.md
* Update design_principles.md
* Update dev_docs/design_principles.md
Co-authored-by: Ambrose J Carr <ambrosejcarr@users.noreply.github.com >
* Update dev_docs/design_principles.md
Co-authored-by: Ambrose J Carr <ambrosejcarr@users.noreply.github.com >
Co-authored-by: Ambrose J Carr <ambrosejcarr@users.noreply.github.com >
2021-04-01 16:50:09 -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
Madison Dunitz
ae23c9e5b9
white space change to run tests ( #2132 )
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* update tiledb reqs
2021-03-30 14:34:39 -05:00
Bruce Martin
b494dd31f4
revert removal of cache control headers ( #2118 )
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* revert removal of cache control headers
* always generate cache header for health route
2021-03-26 08:49:44 -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
5335c39184
Prod ( #2123 )
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* thuang-126-CZIF-policy-updates (#2111 )
* thuang-130-CZIF-policy-change-for-real (#2119 )
2021-03-24 10:34:36 -07:00
Bruce Martin
a89362c1ad
update gene set name validation to match latest requirements ( #2117 )
2021-03-22 14:54:12 -07:00
Arathi Mani