From 2992d17c1d79818d98427c65ed1956763e241f2f Mon Sep 17 00:00:00 2001 From: Bruce Martin Date: Tue, 19 May 2020 14:24:27 -0700 Subject: [PATCH 01/20] add more detasets to hosted site (#1481) * add more detasets to hosted site * fix build --- docs/_site/index.html | 6 +-- docs/_site/posts/annotations.html | 6 +-- docs/_site/posts/contact.html | 6 +-- docs/_site/posts/contribute.html | 6 +-- docs/_site/posts/demo-data.html | 6 +-- docs/_site/posts/gallery.html | 6 +-- docs/_site/posts/hosted.html | 6 +-- docs/_site/posts/install.html | 6 +-- docs/_site/posts/launch.html | 6 +-- docs/_site/posts/methods.html | 6 +-- docs/_site/posts/prepare.html | 6 +-- docs/_site/posts/roadmap.html | 6 +-- docs/_site/posts/troubleshooting.html | 6 +-- docs/posts/cellxgene_cziscience_com.md | 64 ++++++++++++++++++++++++-- 14 files changed, 100 insertions(+), 42 deletions(-) diff --git a/docs/_site/index.html b/docs/_site/index.html index ce1a61e9..51bd2b56 100644 --- a/docs/_site/index.html +++ b/docs/_site/index.html @@ -5,7 +5,7 @@ - + Index | cellxgene @@ -16,10 +16,10 @@ +{"description":"An interactive explorer for single-cell transcriptomics data","publisher":{"@type":"Organization","logo":{"@type":"ImageObject","url":"https://chanzuckerberg.github.io/cellxgene/cellxgene-logo.png"}},"@type":"WebSite","headline":"Index","url":"https://chanzuckerberg.github.io/cellxgene/","name":"cellxgene","@context":"http://schema.org"} - + diff --git a/docs/_site/posts/annotations.html b/docs/_site/posts/annotations.html index af27f5f8..aff4fa54 100644 --- a/docs/_site/posts/annotations.html +++ b/docs/_site/posts/annotations.html @@ -5,7 +5,7 @@ - + annotations | cellxgene @@ -16,10 +16,10 @@ +{"description":"Creating annotations","publisher":{"@type":"Organization","logo":{"@type":"ImageObject","url":"https://chanzuckerberg.github.io/cellxgene/cellxgene-logo.png"}},"@type":"WebPage","headline":"annotations","url":"https://chanzuckerberg.github.io/cellxgene/posts/annotations.html","@context":"http://schema.org"} - + diff --git a/docs/_site/posts/contact.html b/docs/_site/posts/contact.html index 18d25b9b..dd696127 100644 --- a/docs/_site/posts/contact.html +++ b/docs/_site/posts/contact.html @@ -5,7 +5,7 @@ - + Contact | cellxgene @@ -16,10 +16,10 @@ +{"description":"Contact","publisher":{"@type":"Organization","logo":{"@type":"ImageObject","url":"https://chanzuckerberg.github.io/cellxgene/cellxgene-logo.png"}},"@type":"WebPage","headline":"Contact","url":"https://chanzuckerberg.github.io/cellxgene/posts/contact.html","@context":"http://schema.org"} - + diff --git a/docs/_site/posts/contribute.html b/docs/_site/posts/contribute.html index 19cb1827..587af5cb 100644 --- a/docs/_site/posts/contribute.html +++ b/docs/_site/posts/contribute.html @@ -5,7 +5,7 @@ - + Code of conduct | cellxgene @@ -16,10 +16,10 @@ +{"description":"An interactive explorer for single-cell transcriptomics data","publisher":{"@type":"Organization","logo":{"@type":"ImageObject","url":"https://chanzuckerberg.github.io/cellxgene/cellxgene-logo.png"}},"@type":"WebPage","headline":"Code of conduct","url":"https://chanzuckerberg.github.io/cellxgene/posts/contribute.html","@context":"http://schema.org"} - + diff --git a/docs/_site/posts/demo-data.html b/docs/_site/posts/demo-data.html index 8334380c..967fbf9e 100644 --- a/docs/_site/posts/demo-data.html +++ b/docs/_site/posts/demo-data.html @@ -5,7 +5,7 @@ - + demo-data | cellxgene @@ -16,10 +16,10 @@ +{"description":"Demo datasets","publisher":{"@type":"Organization","logo":{"@type":"ImageObject","url":"https://chanzuckerberg.github.io/cellxgene/cellxgene-logo.png"}},"@type":"WebPage","headline":"demo-data","url":"https://chanzuckerberg.github.io/cellxgene/posts/demo-data.html","@context":"http://schema.org"} - + diff --git a/docs/_site/posts/gallery.html b/docs/_site/posts/gallery.html index 21271f02..87e458be 100644 --- a/docs/_site/posts/gallery.html +++ b/docs/_site/posts/gallery.html @@ -5,7 +5,7 @@ - + Gallery | cellxgene @@ -16,10 +16,10 @@ +{"description":"An interactive explorer for single-cell transcriptomics data","publisher":{"@type":"Organization","logo":{"@type":"ImageObject","url":"https://chanzuckerberg.github.io/cellxgene/cellxgene-logo.png"}},"@type":"WebPage","headline":"Gallery","url":"https://chanzuckerberg.github.io/cellxgene/posts/gallery.html","@context":"http://schema.org"} - + diff --git a/docs/_site/posts/hosted.html b/docs/_site/posts/hosted.html index 0a2a56c9..fa8a8e0f 100644 --- a/docs/_site/posts/hosted.html +++ b/docs/_site/posts/hosted.html @@ -5,7 +5,7 @@ - + Hosting cellxgene on the web | cellxgene @@ -16,10 +16,10 @@ +{"description":"An interactive explorer for single-cell transcriptomics data","publisher":{"@type":"Organization","logo":{"@type":"ImageObject","url":"https://chanzuckerberg.github.io/cellxgene/cellxgene-logo.png"}},"@type":"WebPage","headline":"Hosting cellxgene on the web","url":"https://chanzuckerberg.github.io/cellxgene/posts/hosted.html","@context":"http://schema.org"} - + diff --git a/docs/_site/posts/install.html b/docs/_site/posts/install.html index f86de462..147a82af 100644 --- a/docs/_site/posts/install.html +++ b/docs/_site/posts/install.html @@ -5,7 +5,7 @@ - + Install | cellxgene @@ -16,10 +16,10 @@ +{"description":"An interactive explorer for single-cell transcriptomics data","publisher":{"@type":"Organization","logo":{"@type":"ImageObject","url":"https://chanzuckerberg.github.io/cellxgene/cellxgene-logo.png"}},"@type":"WebPage","headline":"Install","url":"https://chanzuckerberg.github.io/cellxgene/posts/install.html","@context":"http://schema.org"} - + diff --git a/docs/_site/posts/launch.html b/docs/_site/posts/launch.html index 55d57112..63b5d415 100644 --- a/docs/_site/posts/launch.html +++ b/docs/_site/posts/launch.html @@ -5,7 +5,7 @@ - + demo-data | cellxgene @@ -16,10 +16,10 @@ +{"description":"Demo datasets","publisher":{"@type":"Organization","logo":{"@type":"ImageObject","url":"https://chanzuckerberg.github.io/cellxgene/cellxgene-logo.png"}},"@type":"WebPage","headline":"demo-data","url":"https://chanzuckerberg.github.io/cellxgene/posts/launch.html","@context":"http://schema.org"} - + diff --git a/docs/_site/posts/methods.html b/docs/_site/posts/methods.html index 57a2b355..a69bdeec 100644 --- a/docs/_site/posts/methods.html +++ b/docs/_site/posts/methods.html @@ -5,7 +5,7 @@ - + Methods | cellxgene @@ -16,10 +16,10 @@ +{"description":"An interactive explorer for single-cell transcriptomics data","publisher":{"@type":"Organization","logo":{"@type":"ImageObject","url":"https://chanzuckerberg.github.io/cellxgene/cellxgene-logo.png"}},"@type":"WebPage","headline":"Methods","url":"https://chanzuckerberg.github.io/cellxgene/posts/methods.html","@context":"http://schema.org"} - + diff --git a/docs/_site/posts/prepare.html b/docs/_site/posts/prepare.html index 114c812c..05f88230 100644 --- a/docs/_site/posts/prepare.html +++ b/docs/_site/posts/prepare.html @@ -5,7 +5,7 @@ - + prepare | cellxgene @@ -16,10 +16,10 @@ +{"description":"Preparing your data","publisher":{"@type":"Organization","logo":{"@type":"ImageObject","url":"https://chanzuckerberg.github.io/cellxgene/cellxgene-logo.png"}},"@type":"WebPage","headline":"prepare","url":"https://chanzuckerberg.github.io/cellxgene/posts/prepare.html","@context":"http://schema.org"} - + diff --git a/docs/_site/posts/roadmap.html b/docs/_site/posts/roadmap.html index 14e96e5b..1d053152 100644 --- a/docs/_site/posts/roadmap.html +++ b/docs/_site/posts/roadmap.html @@ -5,7 +5,7 @@ - + roadmap | cellxgene @@ -16,10 +16,10 @@ +{"description":"Roadmap","publisher":{"@type":"Organization","logo":{"@type":"ImageObject","url":"https://chanzuckerberg.github.io/cellxgene/cellxgene-logo.png"}},"@type":"WebPage","headline":"roadmap","url":"https://chanzuckerberg.github.io/cellxgene/posts/roadmap.html","@context":"http://schema.org"} - + diff --git a/docs/_site/posts/troubleshooting.html b/docs/_site/posts/troubleshooting.html index 0430afc8..f0586b56 100644 --- a/docs/_site/posts/troubleshooting.html +++ b/docs/_site/posts/troubleshooting.html @@ -5,7 +5,7 @@ - + Troubleshooting | cellxgene @@ -16,10 +16,10 @@ +{"description":"Troubleshooting","publisher":{"@type":"Organization","logo":{"@type":"ImageObject","url":"https://chanzuckerberg.github.io/cellxgene/cellxgene-logo.png"}},"@type":"WebPage","headline":"Troubleshooting","url":"https://chanzuckerberg.github.io/cellxgene/posts/troubleshooting.html","@context":"http://schema.org"} - + diff --git a/docs/posts/cellxgene_cziscience_com.md b/docs/posts/cellxgene_cziscience_com.md index 0a1bc9f7..51fa3c25 100644 --- a/docs/posts/cellxgene_cziscience_com.md +++ b/docs/posts/cellxgene_cziscience_com.md @@ -125,13 +125,71 @@ with a link to embed on your own site, please drop us a note at - A single-cell atlas of the peripheral immune response to severe COVID-19 - + A single-cell atlas of the peripheral immune response to severe COVID-19 Blish Lab, medRxiv preprint - + + Atlas of Healthy and SHIV-Infected Non-Human Primate Lung and Ileum ACE2+ Cells - Ileum + + Single Cell Portal + + + + Atlas of Healthy and SHIV-Infected Non-Human Primate Lung and Ileum ACE2+ Cells - Lung + + Single Cell Portal + + + + Allergic inflammatory memory in human respiratory epithelial progenitor cells - epithelial cells + + Single Cell Portal + + + + Allergic inflammatory memory in human respiratory epithelial progenitor cells - nasal scrapings + + Single Cell Portal + + + + Allergic inflammatory memory in human respiratory epithelial progenitor cells - surgical + + Single Cell Portal + + + + Allergic inflammatory memory in human respiratory epithelial progenitor cells - nasal SSS + + Single Cell Portal + + + + ACE2 and TMPRSS2 expression in human non-inflamed terminal ileum - epithelial cells + + Single Cell Portal + + + + ACE2 and TMPRSS2 expression in human non-inflamed terminal ileum + + Single Cell Portal + + + + Human Lung HIV-TB Co-infection ACE2+ Cells + + Single Cell Portal + + + + Epithelial Cells in NHP mTB Granuloma and Uninvolved Lung + + Single Cell Portal + + From ce819383afc275a85a7e7c656460b29d718761ea Mon Sep 17 00:00:00 2001 From: Severiano Badajoz Date: Tue, 19 May 2020 15:46:04 -0700 Subject: [PATCH 02/20] re-enable front-end lint test (#1483) * change lint to only src * reenable lint all --- .github/workflows/push_tests.yml | 10 +++++----- client/Makefile | 2 +- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/.github/workflows/push_tests.yml b/.github/workflows/push_tests.yml index 8ed6803f..913e3899 100644 --- a/.github/workflows/push_tests.yml +++ b/.github/workflows/push_tests.yml @@ -35,11 +35,11 @@ jobs: - name: Lint with flake8 run: | make lint-server - # - name: Lint all with eslint - # working-directory: ./client - # if: github.event_name != 'pull_request' - # run: | - # make lint + - name: Lint src with eslint + working-directory: ./client + if: github.event_name != 'pull_request' + run: | + make lint # - name: Lint diff with eslint # working-directory: ./client # if: github.event_name == 'pull_request' diff --git a/client/Makefile b/client/Makefile index ff8eb1b5..86ecbe90 100644 --- a/client/Makefile +++ b/client/Makefile @@ -25,7 +25,7 @@ build: .PHONY: lint lint: - npx eslint . + npx eslint ./src/ .PHONY: lint-diff lint-diff: From bc5b01da0f802503d6b5c8eb1a646af8e8982040 Mon Sep 17 00:00:00 2001 From: Colin Megill Date: Wed, 20 May 2020 16:22:29 -0400 Subject: [PATCH 03/20] Break out anno plus button (#1473) * break out plus button * remove menu item * padding, remove icon * icon padding --- .../categorical/category/annoMenuCategory.js | 95 +++++++++++-------- .../components/categorical/category/index.js | 3 - .../src/components/categorical/value/index.js | 7 +- 3 files changed, 59 insertions(+), 46 deletions(-) diff --git a/client/src/components/categorical/category/annoMenuCategory.js b/client/src/components/categorical/category/annoMenuCategory.js index 4df30db2..b1190f67 100644 --- a/client/src/components/categorical/category/annoMenuCategory.js +++ b/client/src/components/categorical/category/annoMenuCategory.js @@ -6,9 +6,13 @@ import { MenuItem, Popover, Position, + Tooltip, + Icon, PopoverInteractionKind, } from "@blueprintjs/core"; +import * as globals from "../../../globals"; + @connect((state) => ({ annotations: state.annotations, })) @@ -56,46 +60,57 @@ class AnnoMenuCategory extends React.PureComponent { return ( <> {isUserAnno ? ( - - - - - - } - > -