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
maniarathi
023ae10822
Update unit tests for CXG conversion to check for actual content rather than file names alone which have changed with the recent 0.9 release of tiledb's python package. ( #2249 )
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* Update unit tests for CXG conversion to check for actual content rather than file names alone which have changed with the recent 0.9 release of tiledb's python package.
* Some cleanup
* Undo a bad line
2021-06-19 09:37:05 -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
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
Timmy Huang
8d932fb47d
thuang-126-CZIF-policy-updates ( #2111 ) ( #2112 )
2021-03-17 16:07:42 -07:00
Madison Dunitz
920d71e6b7
pin numba req ( #2110 )
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* pin numba req
* make req more flexible
2021-03-16 11:45:27 -05:00
Bruce Martin
31e0326ded
gene sets summary route ( #2099 )
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* gene sets summary route
* lint
* clarify return type
* style
2021-03-10 16:02:05 -08:00
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
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
maniarathi
b3aadf6632
Release version 0.16.7 ( #2081 )
2021-02-27 22:10:53 -08:00
Bruce Martin
f3a3820ffa
genesets route for local server ( #2079 )
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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
2021-02-26 17:53:07 -08:00
09466a5c32
fix: server/requirements-dev.txt to reduce vulnerabilities ( #2055 )
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The following vulnerabilities are fixed by pinning transitive dependencies:
- https://snyk.io/vuln/SNYK-PYTHON-RSA-1038401
Co-authored-by: snyk-bot <snyk-bot@snyk.io >
Co-authored-by: Madison Dunitz <madison.dunitz@chanzuckerberg.com >
2021-02-25 12:24:06 -08:00
Bruce Martin
de571ce0b3
fix local_server unit-test target ( #2078 )
2021-02-23 16:49:43 -08:00
Marcus Kinsella
fb61bd6e9c
Split out the local backend ( #2052 )
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This splits the backend into two parts: the local backend for desktop cellxgene and the AWS backend for hosted cellxgene. The local backend is in local_server while the hosted remains in server. The general idea is to copy everything from server to local_server, pull unneeded stuff out of local_server, and keep server as-is for this PR. Not touching server means all the infra and deployment code will continue working just as it did before so we can make those changes incrementally.
2021-02-18 12:58:22 -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
e6281baa39
improve error message for OBO parse failure ( #2053 )
2021-02-05 12:19:40 -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
Severiano Badajoz