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 )
...
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
Björn Grüning
d821f0eac9
More cellxgene Galaxy information for the extensions ( #2024 )
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This PR adds some more text and direct links to the cellxgene Galaxy section.
Thanks!
#### Reviewers
**Functional:**
**Readability:**
---
## Changes
- add
- remove
- modify
2021-02-03 14:38:54 -08:00
Marcus Kinsella
3c0b1d45db
Fix deprecated np.unicode type ( #2035 )
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Until numpy version 1.20.0, numpy.unicode was an alias for str in python3. In 1.20.0, it's fully deprecated and is an int. This is bad and breaks things. This commit drops the np.unicode alias and just uses str, as is advised here:
https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
2021-02-03 09:22:27 -08:00
bmccandless
90a4ff7526
allow cellxgene datasets urls to have a trailing slash or not. ( #2028 )
...
#550
2021-01-20 15:19:13 -08:00
bmccandless
d5ad823895
simple solution to the locust test problem ( #2026 )
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In this solution, all the server requirements are installed.
This is a slightly overkill, but it avoid having to restructure
any of the server or test code to avoid unnecessary imports.
#2019
2021-01-20 08:56:54 -08:00
bmccandless
0e48b335be
update umap version ( #2021 )
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There is an interface change in 0.5.0 which is not compatible with our
version of scanpy.
2021-01-13 13:01:46 -08:00
Ambrose J Carr
e264724597
Add extension showcase to documentation ( #1878 )
2021-01-12 08:55:14 -05:00
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
maniarathi