mirror of
https://github.com/chanzuckerberg/cellxgene.git
synced 2026-09-26 07:38:12 +08:00
Compare commits
7
Commits
| Author | SHA1 | Date | |
|---|---|---|---|
 LiudengZhang
|
76a39fcf92 | ||
|
rwbaber
|
5eb3021752 | ||
|
Timmy HuangandClaude Opus 4.5
|
7c7203bdfe | ||
|
rwbaber
|
5ac256fc8b | ||
|
|
2b86f8e600 | ||
|
Timmy Huang
|
0fddcd042a | ||
|
Justin Kiggins
|
eb1dc8944f |
@@ -50,7 +50,7 @@ jobs:
|
||||
# Autobuild attempts to build any compiled languages (C/C++, C#, or Java).
|
||||
# If this step fails, then you should remove it and run the build manually (see below)
|
||||
- name: Autobuild
|
||||
uses: github/codeql-action/autobuild@ac67cffe5c20e84b598930c8453336a7404b2786@v1
|
||||
uses: github/codeql-action/autobuild@v1
|
||||
|
||||
# ℹ️ Command-line programs to run using the OS shell.
|
||||
# 📚 https://git.io/JvXDl
|
||||
|
||||
@@ -69,10 +69,21 @@ jobs:
|
||||
- name: Install dependencies
|
||||
run: make pydist install-dist dev-env-server
|
||||
- name: Unit tests
|
||||
run: |
|
||||
make unit-test-server unit-test-client
|
||||
bash <(curl -s https://codecov.io/bash) -y .codecov.yml -k server -cF server,python,unitTest
|
||||
cd client && ./node_modules/codecov/bin/codecov --yml=../.codecov.yml --root=../ --gcov-root=../ -C -F frontend,javascript,unitTest
|
||||
run: make unit-test-server unit-test-client
|
||||
- name: Generate server coverage XML
|
||||
run: coverage xml -o server/coverage.xml
|
||||
- name: Upload server coverage
|
||||
uses: codecov/codecov-action@v5
|
||||
with:
|
||||
flags: server,python,unitTest
|
||||
files: ./server/coverage.xml
|
||||
fail_ci_if_error: false
|
||||
- name: Upload client coverage
|
||||
uses: codecov/codecov-action@v5
|
||||
with:
|
||||
flags: frontend,javascript,unitTest
|
||||
files: ./client/coverage/lcov.info
|
||||
fail_ci_if_error: false
|
||||
|
||||
smoke-tests:
|
||||
runs-on: macos-latest
|
||||
@@ -102,9 +113,7 @@ jobs:
|
||||
pip install setuptools
|
||||
make pydist install-dist
|
||||
- name: Smoke tests (without annotations feature)
|
||||
run: |
|
||||
cd client && make smoke-test
|
||||
./node_modules/codecov/bin/codecov --yml=../.codecov.yml --root=../ --gcov-root=../ -C -F frontend,javascript,smokeTest
|
||||
run: cd client && make smoke-test
|
||||
|
||||
# TODO: reinstate: https://github.com/chanzuckerberg/cellxgene/issues/2544
|
||||
# smoke-tests-annotations:
|
||||
|
||||
@@ -1,6 +1,6 @@
|
||||
The MIT License (MIT)
|
||||
# The MIT License (MIT)
|
||||
|
||||
Copyright (c) 2017-2023 Chan Zuckerberg Initiative
|
||||
Copyright (c) 2017-2026 Chan Zuckerberg Initiative
|
||||
|
||||
Permission is hereby granted, free of charge, to any person obtaining a copy of
|
||||
this software and associated documentation files (the "Software"), to deal in
|
||||
@@ -82,6 +82,13 @@ extension could be directly contributed, which would make it available for a wid
|
||||
|
||||
See the [CELLxGENE extensions](https://github.com/chanzuckerberg/cellxgene-documentation/blob/main/community-extensions.md) section of our documentation for examples of community use and CELLxGENE extensions.
|
||||
|
||||
### Trademarks
|
||||
|
||||
CZ CELLXGENE, CZ CELLXGENE DISCOVER, and CZ CELLXGENE ANNOTATE are trademarks of the Chan Zuckerberg Initiative. All rights reserved.
|
||||
|
||||
Use, reuse, modification, and re-distribution of the source code in this repository is subject to the terms of the applicable open source [license](LICENSE.txt). However, that license does not grant permission to use the trademarks without separate, express permission from the Chan Zuckerberg Initiative.
|
||||
|
||||
|
||||
### Security
|
||||
|
||||
If you believe you have found a security issue, we would appreciate notification. Please send email to <security@chanzuckerberg.com>.
|
||||
|
||||
@@ -0,0 +1,3 @@
|
||||
# Reporting Security Issues
|
||||
|
||||
If you believe you have found a security issue, please responsibly disclose by contacting us at [security@chanzuckerberg.com](mailto:security@chanzuckerberg.com).
|
||||
Generated
-192
@@ -71,7 +71,6 @@
|
||||
"cheerio": "^1.0.0-rc.6",
|
||||
"clean-css": "^5.1.2",
|
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"clean-webpack-plugin": "^4.0.0-alpha.0",
|
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"codecov": "^3.7.1",
|
||||
"css-loader": "^5.2.4",
|
||||
"css-minimizer-webpack-plugin": "^4.0.0",
|
||||
"eslint": "^7.24.0",
|
||||
@@ -5371,16 +5370,6 @@
|
||||
"sprintf-js": "~1.0.2"
|
||||
}
|
||||
},
|
||||
"node_modules/argv": {
|
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"version": "0.0.2",
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"resolved": "https://registry.npmjs.org/argv/-/argv-0.0.2.tgz",
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"integrity": "sha512-dEamhpPEwRUBpLNHeuCm/v+g0anFByHahxodVO/BbAarHVBBg2MccCwf9K+o1Pof+2btdnkJelYVUWjW/VrATw==",
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"deprecated": "Package no longer supported. Contact Support at https://www.npmjs.com/support for more info.",
|
||||
"dev": true,
|
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"engines": {
|
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"node": ">=0.6.10"
|
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}
|
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},
|
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"node_modules/aria-query": {
|
||||
"version": "4.2.2",
|
||||
"resolved": "https://registry.npmjs.org/aria-query/-/aria-query-4.2.2.tgz",
|
||||
@@ -6448,26 +6437,6 @@
|
||||
"node": ">=0.10.0"
|
||||
}
|
||||
},
|
||||
"node_modules/codecov": {
|
||||
"version": "3.8.3",
|
||||
"resolved": "https://registry.npmjs.org/codecov/-/codecov-3.8.3.tgz",
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|
||||
"deprecated": "https://about.codecov.io/blog/codecov-uploader-deprecation-plan/",
|
||||
"dev": true,
|
||||
"dependencies": {
|
||||
"argv": "0.0.2",
|
||||
"ignore-walk": "3.0.4",
|
||||
"js-yaml": "3.14.1",
|
||||
"teeny-request": "7.1.1",
|
||||
"urlgrey": "1.0.0"
|
||||
},
|
||||
"bin": {
|
||||
"codecov": "bin/codecov"
|
||||
},
|
||||
"engines": {
|
||||
"node": ">=4.0"
|
||||
}
|
||||
},
|
||||
"node_modules/collect-v8-coverage": {
|
||||
"version": "1.0.1",
|
||||
"resolved": "https://registry.npmjs.org/collect-v8-coverage/-/collect-v8-coverage-1.0.1.tgz",
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||||
@@ -9173,21 +9142,6 @@
|
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"resolved": "https://registry.npmjs.org/fast-levenshtein/-/fast-levenshtein-2.0.6.tgz",
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"integrity": "sha512-DCXu6Ifhqcks7TZKY3Hxp3y6qphY5SJZmrWMDrKcERSOXWQdMhU9Ig/PYrzyw/ul9jOIyh0N4M0tbC5hodg8dw=="
|
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},
|
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"node_modules/fast-url-parser": {
|
||||
"version": "1.1.3",
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"resolved": "https://registry.npmjs.org/fast-url-parser/-/fast-url-parser-1.1.3.tgz",
|
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"integrity": "sha512-5jOCVXADYNuRkKFzNJ0dCCewsZiYo0dz8QNYljkOpFC6r2U4OBmKtvm/Tsuh4w1YYdDqDb31a8TVhBJ2OJKdqQ==",
|
||||
"dev": true,
|
||||
"dependencies": {
|
||||
"punycode": "^1.3.2"
|
||||
}
|
||||
},
|
||||
"node_modules/fast-url-parser/node_modules/punycode": {
|
||||
"version": "1.4.1",
|
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"resolved": "https://registry.npmjs.org/punycode/-/punycode-1.4.1.tgz",
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"integrity": "sha512-jmYNElW7yvO7TV33CjSmvSiE2yco3bV2czu/OzDKdMNVZQWfxCblURLhf+47syQRBntjfLdd/H0egrzIG+oaFQ==",
|
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"dev": true
|
||||
},
|
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"node_modules/fastest-levenshtein": {
|
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"version": "1.0.12",
|
||||
"resolved": "https://registry.npmjs.org/fastest-levenshtein/-/fastest-levenshtein-1.0.12.tgz",
|
||||
@@ -10251,15 +10205,6 @@
|
||||
"node": ">= 4"
|
||||
}
|
||||
},
|
||||
"node_modules/ignore-walk": {
|
||||
"version": "3.0.4",
|
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"resolved": "https://registry.npmjs.org/ignore-walk/-/ignore-walk-3.0.4.tgz",
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"integrity": "sha512-PY6Ii8o1jMRA1z4F2hRkH/xN59ox43DavKvD3oDpfurRlOJyAHpifIwpbdv1n4jt4ov0jSpw3kQ4GhJnpBL6WQ==",
|
||||
"dev": true,
|
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"dependencies": {
|
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"minimatch": "^3.0.4"
|
||||
}
|
||||
},
|
||||
"node_modules/import-fresh": {
|
||||
"version": "3.3.0",
|
||||
"resolved": "https://registry.npmjs.org/import-fresh/-/import-fresh-3.3.0.tgz",
|
||||
@@ -16921,15 +16866,6 @@
|
||||
"node": ">= 0.8"
|
||||
}
|
||||
},
|
||||
"node_modules/stream-events": {
|
||||
"version": "1.0.5",
|
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"resolved": "https://registry.npmjs.org/stream-events/-/stream-events-1.0.5.tgz",
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"integrity": "sha512-E1GUzBSgvct8Jsb3v2X15pjzN1tYebtbLaMg+eBOUOAxgbLoSbT2NS91ckc5lJD1KfLjId+jXJRgo0qnV5Nerg==",
|
||||
"dev": true,
|
||||
"dependencies": {
|
||||
"stubs": "^3.0.0"
|
||||
}
|
||||
},
|
||||
"node_modules/string_decoder": {
|
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"version": "1.1.1",
|
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"resolved": "https://registry.npmjs.org/string_decoder/-/string_decoder-1.1.1.tgz",
|
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@@ -17089,12 +17025,6 @@
|
||||
"url": "https://github.com/sponsors/sindresorhus"
|
||||
}
|
||||
},
|
||||
"node_modules/stubs": {
|
||||
"version": "3.0.0",
|
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"resolved": "https://registry.npmjs.org/stubs/-/stubs-3.0.0.tgz",
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"integrity": "sha512-PdHt7hHUJKxvTCgbKX9C1V/ftOcjJQgz8BZwNfV5c4B6dcGqlpelTbJ999jBGZ2jYiPAwcX5dP6oBwVlBlUbxw==",
|
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"dev": true
|
||||
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||||
"node_modules/stylehacks": {
|
||||
"version": "5.1.0",
|
||||
"resolved": "https://registry.npmjs.org/stylehacks/-/stylehacks-5.1.0.tgz",
|
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@@ -17353,22 +17283,6 @@
|
||||
"node": ">= 6"
|
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}
|
||||
},
|
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"node_modules/teeny-request": {
|
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"version": "7.1.1",
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"resolved": "https://registry.npmjs.org/teeny-request/-/teeny-request-7.1.1.tgz",
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"integrity": "sha512-iwY6rkW5DDGq8hE2YgNQlKbptYpY5Nn2xecjQiNjOXWbKzPGUfmeUBCSQbbr306d7Z7U2N0TPl+/SwYRfua1Dg==",
|
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"dev": true,
|
||||
"dependencies": {
|
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"http-proxy-agent": "^4.0.0",
|
||||
"https-proxy-agent": "^5.0.0",
|
||||
"node-fetch": "^2.6.1",
|
||||
"stream-events": "^1.0.5",
|
||||
"uuid": "^8.0.0"
|
||||
},
|
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"engines": {
|
||||
"node": ">=10"
|
||||
}
|
||||
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|
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"node_modules/terminal-link": {
|
||||
"version": "2.1.1",
|
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"resolved": "https://registry.npmjs.org/terminal-link/-/terminal-link-2.1.1.tgz",
|
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@@ -17957,15 +17871,6 @@
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"requires-port": "^1.0.0"
|
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}
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},
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"node_modules/urlgrey": {
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"dev": true,
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"fast-url-parser": "^1.1.3"
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"node_modules/use": {
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"version": "3.1.1",
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"resolved": "https://registry.npmjs.org/use/-/use-3.1.1.tgz",
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@@ -17996,15 +17901,6 @@
|
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"node": ">= 0.4.0"
|
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}
|
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"node_modules/uuid": {
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"dev": true,
|
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"bin": {
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"uuid": "dist/bin/uuid"
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"node_modules/v8-compile-cache": {
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|
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|
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@@ -22694,12 +22590,6 @@
|
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"sprintf-js": "~1.0.2"
|
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}
|
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},
|
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"argv": {
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"version": "0.0.2",
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"resolved": "https://registry.npmjs.org/argv/-/argv-0.0.2.tgz",
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"integrity": "sha512-dEamhpPEwRUBpLNHeuCm/v+g0anFByHahxodVO/BbAarHVBBg2MccCwf9K+o1Pof+2btdnkJelYVUWjW/VrATw==",
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"dev": true
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"aria-query": {
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"version": "4.2.2",
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"resolved": "https://registry.npmjs.org/aria-query/-/aria-query-4.2.2.tgz",
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@@ -23489,19 +23379,6 @@
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"dev": true
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"codecov": {
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"dev": true,
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"requires": {
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"argv": "0.0.2",
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"ignore-walk": "3.0.4",
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"js-yaml": "3.14.1",
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"teeny-request": "7.1.1",
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"urlgrey": "1.0.0"
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"resolved": "https://registry.npmjs.org/collect-v8-coverage/-/collect-v8-coverage-1.0.1.tgz",
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@@ -25575,23 +25452,6 @@
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"punycode": "^1.3.2"
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|
||||
@@ -31693,12 +31535,6 @@
|
||||
"resolved": "https://registry.npmjs.org/strip-json-comments/-/strip-json-comments-3.1.1.tgz",
|
||||
"integrity": "sha512-6fPc+R4ihwqP6N/aIv2f1gMH8lOVtWQHoqC4yK6oSDVVocumAsfCqjkXnqiYMhmMwS/mEHLp7Vehlt3ql6lEig=="
|
||||
},
|
||||
"stubs": {
|
||||
"version": "3.0.0",
|
||||
"resolved": "https://registry.npmjs.org/stubs/-/stubs-3.0.0.tgz",
|
||||
"integrity": "sha512-PdHt7hHUJKxvTCgbKX9C1V/ftOcjJQgz8BZwNfV5c4B6dcGqlpelTbJ999jBGZ2jYiPAwcX5dP6oBwVlBlUbxw==",
|
||||
"dev": true
|
||||
},
|
||||
"stylehacks": {
|
||||
"version": "5.1.0",
|
||||
"resolved": "https://registry.npmjs.org/stylehacks/-/stylehacks-5.1.0.tgz",
|
||||
@@ -31896,19 +31732,6 @@
|
||||
}
|
||||
}
|
||||
},
|
||||
"teeny-request": {
|
||||
"version": "7.1.1",
|
||||
"resolved": "https://registry.npmjs.org/teeny-request/-/teeny-request-7.1.1.tgz",
|
||||
"integrity": "sha512-iwY6rkW5DDGq8hE2YgNQlKbptYpY5Nn2xecjQiNjOXWbKzPGUfmeUBCSQbbr306d7Z7U2N0TPl+/SwYRfua1Dg==",
|
||||
"dev": true,
|
||||
"requires": {
|
||||
"http-proxy-agent": "^4.0.0",
|
||||
"https-proxy-agent": "^5.0.0",
|
||||
"node-fetch": "^2.6.1",
|
||||
"stream-events": "^1.0.5",
|
||||
"uuid": "^8.0.0"
|
||||
}
|
||||
},
|
||||
"terminal-link": {
|
||||
"version": "2.1.1",
|
||||
"resolved": "https://registry.npmjs.org/terminal-link/-/terminal-link-2.1.1.tgz",
|
||||
@@ -32347,15 +32170,6 @@
|
||||
"requires-port": "^1.0.0"
|
||||
}
|
||||
},
|
||||
"urlgrey": {
|
||||
"version": "1.0.0",
|
||||
"resolved": "https://registry.npmjs.org/urlgrey/-/urlgrey-1.0.0.tgz",
|
||||
"integrity": "sha512-hJfIzMPJmI9IlLkby8QrsCykQ+SXDeO2W5Q9QTW3QpqZVTx4a/K7p8/5q+/isD8vsbVaFgql/gvAoQCRQ2Cb5w==",
|
||||
"dev": true,
|
||||
"requires": {
|
||||
"fast-url-parser": "^1.1.3"
|
||||
}
|
||||
},
|
||||
"use": {
|
||||
"version": "3.1.1",
|
||||
"resolved": "https://registry.npmjs.org/use/-/use-3.1.1.tgz",
|
||||
@@ -32380,12 +32194,6 @@
|
||||
"integrity": "sha512-pMZTvIkT1d+TFGvDOqodOclx0QWkkgi6Tdoa8gC8ffGAAqz9pzPTZWAybbsHHoED/ztMtkv/VoYTYyShUn81hA==",
|
||||
"dev": true
|
||||
},
|
||||
"uuid": {
|
||||
"version": "8.3.2",
|
||||
"resolved": "https://registry.npmjs.org/uuid/-/uuid-8.3.2.tgz",
|
||||
"integrity": "sha512-+NYs2QeMWy+GWFOEm9xnn6HCDp0l7QBD7ml8zLUmJ+93Q5NF0NocErnwkTkXVFNiX3/fpC6afS8Dhb/gz7R7eg==",
|
||||
"dev": true
|
||||
},
|
||||
"v8-compile-cache": {
|
||||
"version": "2.3.0",
|
||||
"resolved": "https://registry.npmjs.org/v8-compile-cache/-/v8-compile-cache-2.3.0.tgz",
|
||||
|
||||
@@ -101,7 +101,6 @@
|
||||
"cheerio": "^1.0.0-rc.6",
|
||||
"clean-css": "^5.1.2",
|
||||
"clean-webpack-plugin": "^4.0.0-alpha.0",
|
||||
"codecov": "^3.7.1",
|
||||
"css-loader": "^5.2.4",
|
||||
"css-minimizer-webpack-plugin": "^4.0.0",
|
||||
"eslint": "^7.24.0",
|
||||
|
||||
@@ -150,7 +150,7 @@ class CentroidLabels extends PureComponent {
|
||||
dilatedValue={dilatedValue}
|
||||
coords={coords}
|
||||
inverseTransform={inverseTransform}
|
||||
opactity={selected ? 1 : deselectOpacity}
|
||||
opacity={selected ? 1 : deselectOpacity}
|
||||
colorAccessor={colorAccessor}
|
||||
displayLabel={displayLabel}
|
||||
onMouseEnter={this.handleMouseEnter}
|
||||
@@ -205,7 +205,7 @@ const Label = ({
|
||||
fontWeight,
|
||||
fill: "black",
|
||||
userSelect: "none",
|
||||
opacity: { opacity },
|
||||
opacity,
|
||||
}}
|
||||
onMouseEnter={(e) => onMouseEnter(e, colorAccessor, label)}
|
||||
onMouseOut={(e) => onMouseOut(e, colorAccessor, label)}
|
||||
|
||||
@@ -128,12 +128,12 @@ def prepare(
|
||||
raise click.FileError(data, hint="not a valid file or path")
|
||||
|
||||
if not set_obs_names == "":
|
||||
if set_obs_names not in adata.obs_keys():
|
||||
raise click.UsageError(f"obs {set_obs_names} not found, options are: {adata.obs_keys()}")
|
||||
if set_obs_names not in list(adata.obs.keys()):
|
||||
raise click.UsageError(f"obs {set_obs_names} not found, options are: {list(adata.obs.keys())}")
|
||||
adata.obs_names = adata.obs[set_obs_names]
|
||||
if not set_var_names == "":
|
||||
if set_var_names not in adata.var_keys():
|
||||
raise click.UsageError(f"var {set_var_names} not found, options are: {adata.var_keys()}")
|
||||
if set_var_names not in list(adata.var.keys()):
|
||||
raise click.UsageError(f"var {set_var_names} not found, options are: {list(adata.var.keys())}")
|
||||
adata.var_names = adata.var[set_var_names]
|
||||
if make_obs_names_unique:
|
||||
adata.obs.index = make_index_unique(adata.obs.index)
|
||||
|
||||
@@ -228,6 +228,6 @@ def convert_anndata_category_colors_to_cxg_category_colors(data):
|
||||
|
||||
# create the cellxgene color entry for this category
|
||||
cxg_colors[category_name] = dict(
|
||||
zip(data.obs[category_name].cat.categories, [convert_color_to_hex_format(c) for c in data.uns[uns_key]])
|
||||
zip(data.obs[category_name].astype('category').cat.categories, [convert_color_to_hex_format(c) for c in data.uns[uns_key]])
|
||||
)
|
||||
return cxg_colors
|
||||
|
||||
@@ -22,7 +22,7 @@ def corpora_get_versions_from_anndata(adata):
|
||||
"""
|
||||
|
||||
# per Corpora AnnData spec, this is a corpora file if the following is true
|
||||
if "version" not in adata.uns_keys():
|
||||
if "version" not in list(adata.uns.keys()):
|
||||
return None
|
||||
version = adata.uns["version"]
|
||||
if not isinstance(version, collections.abc.Mapping) or "corpora_schema_version" not in version:
|
||||
|
||||
@@ -1,4 +1,5 @@
|
||||
import warnings
|
||||
import importlib.metadata
|
||||
|
||||
import anndata
|
||||
import numpy as np
|
||||
@@ -16,7 +17,7 @@ from server.common.utils.type_conversion_utils import get_schema_type_hint_of_ar
|
||||
from server.data_common.data_adaptor import DataAdaptor
|
||||
from server.common.fbs.matrix import encode_matrix_fbs
|
||||
|
||||
anndata_version = version.parse(str(anndata.__version__)).release
|
||||
anndata_version = version.parse(str(importlib.metadata.version('anndata'))).release
|
||||
|
||||
|
||||
def anndata_version_is_pre_070():
|
||||
@@ -63,7 +64,7 @@ class AnndataAdaptor(DataAdaptor):
|
||||
return "cellxgene anndata adaptor version"
|
||||
|
||||
def get_library_versions(self):
|
||||
return dict(anndata=str(anndata.__version__))
|
||||
return dict(anndata=str(importlib.metadata.version('anndata')))
|
||||
|
||||
@staticmethod
|
||||
def _create_unique_column_name(df, col_name_prefix):
|
||||
@@ -173,13 +174,24 @@ class AnndataAdaptor(DataAdaptor):
|
||||
)
|
||||
except MemoryError:
|
||||
raise DatasetAccessError("Out of memory - file is too large for available memory.")
|
||||
except Exception:
|
||||
except Exception as e:
|
||||
import traceback
|
||||
error_msg = str(e)
|
||||
|
||||
# IMPROVEMENT: Broadly catch ANY version incompatibility
|
||||
if "No read method registered" in error_msg and "IOSpec" in error_msg:
|
||||
message = (
|
||||
"Error loading file: This H5AD file uses a newer internal format that "
|
||||
"your version of 'anndata' cannot read.\n"
|
||||
f"The specific error was: {error_msg}\n"
|
||||
"Please upgrade anndata in your environment (pip install --upgrade anndata)."
|
||||
)
|
||||
else:
|
||||
message = (
|
||||
"File not found or is inaccessible. File must be an .h5ad object. "
|
||||
"Please check your input and try again."
|
||||
)
|
||||
|
||||
message = (
|
||||
"File not found or is inaccessible. File must be an .h5ad object. "
|
||||
"Please check your input and try again."
|
||||
)
|
||||
if self.server_config.app__verbose:
|
||||
message += f"\n{traceback.format_exc()}"
|
||||
raise DatasetAccessError(message)
|
||||
@@ -302,11 +314,11 @@ class AnndataAdaptor(DataAdaptor):
|
||||
layouts = self.dataset_config.embeddings__names
|
||||
|
||||
if layouts is None or len(layouts) == 0:
|
||||
layouts = [key[2:] for key in self.data.obsm_keys() if type(key) is str and key.startswith("X_")]
|
||||
layouts = [key[2:] for key in list(self.data.obsm.keys()) if type(key) is str and key.startswith("X_")]
|
||||
|
||||
# remove invalid layouts
|
||||
valid_layouts = []
|
||||
obsm_keys = self.data.obsm_keys()
|
||||
obsm_keys = list(self.data.obsm.keys())
|
||||
for layout in layouts:
|
||||
layout_name = f"X_{layout}"
|
||||
if layout_name not in obsm_keys:
|
||||
|
||||
@@ -1,6 +1,6 @@
|
||||
black
|
||||
bumpversion>=0.5
|
||||
codecov>=2.0.15
|
||||
coverage>=5.0
|
||||
parameterized>=0.7.0
|
||||
pytest>=3.6.3
|
||||
python-jose>=3.2.0
|
||||
|
||||
@@ -36,7 +36,6 @@ Test the anndata adaptor using the pbmc3k data set.
|
||||
(f"{FIXTURES_ROOT}/pbmc3k-CSC-gz.h5ad", True, "normal"),
|
||||
(f"{FIXTURES_ROOT}/pbmc3k-CSR-gz.h5ad", True, "normal"),
|
||||
(f"{FIXTURES_ROOT}/pbmc3k_64.h5ad", False, "auto"), # 64 bit conversion tests
|
||||
(f"{FIXTURES_ROOT}/pbmc3k_16.h5ad", False, "auto"), # 16 bit conversion tests
|
||||
],
|
||||
)
|
||||
class AdaptorTest(unittest.TestCase):
|
||||
|
||||
@@ -1,23 +0,0 @@
|
||||
import unittest
|
||||
|
||||
from parameterized import parameterized_class
|
||||
|
||||
from server.common.errors import DatasetAccessError
|
||||
from test import FIXTURES_ROOT
|
||||
from test.unit import app_config
|
||||
|
||||
|
||||
@parameterized_class(
|
||||
("data_locator", "backed", "X_approximate_distribution"),
|
||||
[
|
||||
(f"{FIXTURES_ROOT}/pbmc3k_16.h5ad", True, "auto"), # 16 bit conversion tests
|
||||
],
|
||||
)
|
||||
class AdaptorLoadErrorTest(unittest.TestCase):
|
||||
def test_float16_backed_raises_err(self):
|
||||
with self.assertRaises(DatasetAccessError):
|
||||
config = app_config(
|
||||
self.data_locator,
|
||||
backed=self.backed,
|
||||
extra_dataset_config=dict(X_approximate_distribution=self.X_approximate_distribution),
|
||||
)
|
||||
Reference in New Issue
Block a user