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Add spatial #1003

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merged 84 commits into from
Dec 6, 2024
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12659b1
add Spatial panel to Data Exploration
alexvpickering Sep 30, 2024
8171063
hardcode omeTiffUrl for demo
alexvpickering Oct 4, 2024
9bc1b40
revert to LTS node
alexvpickering Oct 4, 2024
5249acd
update lockfile version
alexvpickering Oct 4, 2024
f00a415
update vitessce; add viv
alexvpickering Oct 4, 2024
421d558
fix visibility of embedding for new vitessce
alexvpickering Oct 5, 2024
0d10e08
spatial component worksgit add .
alexvpickering Oct 6, 2024
06955ff
document vitessce code lifts
alexvpickering Oct 6, 2024
a07335d
mock spatial feature plot
alexvpickering Oct 15, 2024
92cd1f9
spatial feature plot loads from ome zarr url
alexvpickering Oct 15, 2024
ed58645
use hexagon markers
alexvpickering Oct 15, 2024
5a011b9
add seurat_spatial_object to upload techs
alexvpickering Oct 16, 2024
be1816b
closer with dual images
alexvpickering Oct 25, 2024
ae061d6
side by side works
alexvpickering Oct 25, 2024
40b884d
grid works!
alexvpickering Oct 28, 2024
44e604e
simplify
alexvpickering Oct 28, 2024
c1cda0a
works for incomplete grid
alexvpickering Oct 28, 2024
687aa15
improve logic and cleanup
alexvpickering Oct 29, 2024
bf0759a
zip file store works
alexvpickering Oct 30, 2024
33aa6c5
get sample ids associated with zarrs
alexvpickering Nov 7, 2024
c22ff95
init offset of spot coords
alexvpickering Nov 8, 2024
bad8d82
hidden converted to white diamonds
alexvpickering Nov 8, 2024
141c86e
centroids disapear on hide
alexvpickering Nov 8, 2024
8a3d774
lasso works
alexvpickering Nov 8, 2024
664046a
cell tooltip works
alexvpickering Nov 8, 2024
33eacf2
add sample to tooltip
alexvpickering Nov 10, 2024
53d3529
fix colon space
alexvpickering Nov 10, 2024
56dd9ed
line up vitessce controls
alexvpickering Nov 10, 2024
a5d09df
faster hidden cells heatmap
alexvpickering Nov 10, 2024
c5254be
go jump when hide cell set
alexvpickering Nov 10, 2024
1ceb48f
reduce space for warning
alexvpickering Nov 11, 2024
24a3bff
add opacity slider
alexvpickering Nov 11, 2024
389d004
opacity works
alexvpickering Nov 11, 2024
99a3d42
keep heatmap settings open on click
alexvpickering Nov 12, 2024
c15fa7e
fix warning
alexvpickering Nov 12, 2024
3d8fc33
init spatial settings
alexvpickering Nov 12, 2024
108a568
fix initial load
alexvpickering Nov 12, 2024
f8996b6
init group images setting
alexvpickering Nov 13, 2024
6474d59
spatial feature plot renders with embedding
alexvpickering Nov 13, 2024
5a2abfc
zoom works for image and points
alexvpickering Nov 14, 2024
ed9f664
fix point visibility
alexvpickering Nov 14, 2024
0929b0e
fix point hiding with custom range
alexvpickering Nov 14, 2024
eaa80bb
init toggle axes; revert mouse zoom
alexvpickering Nov 15, 2024
28f06ac
init toggle outline
alexvpickering Nov 15, 2024
2e4a34f
adjust control styling
alexvpickering Nov 15, 2024
a93db40
fix legend position
alexvpickering Nov 15, 2024
7212d95
add colons
alexvpickering Nov 15, 2024
0d5881c
add spatial feature image
alexvpickering Nov 15, 2024
b4d6f6e
init spatial categorical
alexvpickering Nov 16, 2024
9c65ba1
restore accordion
alexvpickering Nov 18, 2024
49779d4
add option groups to technology selector
alexvpickering Nov 18, 2024
a89fc1a
adjust modal text for spatial
alexvpickering Nov 18, 2024
d9939a3
adapt multiview for spatial clusters
alexvpickering Nov 19, 2024
912df3a
improve image position
alexvpickering Nov 19, 2024
d3fff5d
add preview for spatial categorical
alexvpickering Nov 19, 2024
f77b2e5
avoid overlapping labels
alexvpickering Nov 19, 2024
c027cd4
fix label transform
alexvpickering Nov 19, 2024
909269b
labels work for spatial categorical
alexvpickering Nov 19, 2024
0c1f3fc
use median for label calc
alexvpickering Nov 19, 2024
6690a39
adjust base ranges
alexvpickering Nov 19, 2024
e6bdd22
update layout based on sample type
alexvpickering Nov 20, 2024
0cce082
plots reactive to spatial experiment
alexvpickering Nov 20, 2024
b22eb99
fix eslint
alexvpickering Nov 21, 2024
5bc38c1
fixing tests
alexvpickering Nov 25, 2024
cc6940b
Merge branch 'master' into add-spatial
alexvpickering Dec 2, 2024
568f742
await all promises
alexvpickering Dec 2, 2024
56a1b9e
factor out getImageUrls
alexvpickering Dec 2, 2024
76f182e
cleanup
alexvpickering Dec 2, 2024
3598f1b
tests pass
alexvpickering Dec 3, 2024
761c599
revert dynamic changes
alexvpickering Dec 3, 2024
b4dba2c
bump actions to node 20.18
alexvpickering Dec 3, 2024
8ed1e65
Merge branch 'master' into add-spatial
alexvpickering Dec 3, 2024
8e8d649
revert fname
alexvpickering Dec 3, 2024
f3e435d
Merge branch 'master' into add-spatial
alexvpickering Dec 3, 2024
67506b0
fix docker ci
alexvpickering Dec 3, 2024
57edd10
rename file
alexvpickering Dec 4, 2024
a989b1e
init tests for SpatialViewer
alexvpickering Dec 4, 2024
d21b196
fix init tests
alexvpickering Dec 4, 2024
9d287fc
adapt ZipFileStore to use GET only
alexvpickering Dec 5, 2024
6d1d317
fix visible layers toggle
alexvpickering Dec 5, 2024
ef7bfca
cleanup
alexvpickering Dec 6, 2024
74ae4f6
revert
alexvpickering Dec 6, 2024
dc811a6
remove unused module
alexvpickering Dec 6, 2024
12a34f7
cleanup
alexvpickering Dec 6, 2024
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4 changes: 2 additions & 2 deletions Dockerfile
Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
# pull official base image
FROM node:22.9.0-alpine AS builder
FROM node:20.18.0-alpine AS builder

# set working directory
WORKDIR /app
Expand All @@ -12,7 +12,7 @@ COPY package.json package-lock.json /app/

# install dependencies
RUN apk add --no-cache git
RUN git config --global url."https://".insteadOf ssh:// && npm ci --only=production
RUN git config --global url."https://".insteadOf ssh:// && npm ci --only=production --legacy-peer-deps

# copy rest of app
COPY . .
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3 changes: 3 additions & 0 deletions __mocks__/@hms-dbmi/viv.js
Original file line number Diff line number Diff line change
@@ -0,0 +1,3 @@
module.exports = {
ZarrPixelSource: jest.fn(),
};
3 changes: 3 additions & 0 deletions __mocks__/zarrita.js
Original file line number Diff line number Diff line change
@@ -0,0 +1,3 @@
module.exports = {
root: jest.fn(() => 'zarrRoot'),
};
4 changes: 4 additions & 0 deletions jest.config.js
Original file line number Diff line number Diff line change
Expand Up @@ -46,6 +46,10 @@ module.exports = {
'^react-native$': 'react-native-web',
'^.+\\.module\\.(css|sass|scss)$': 'identity-obj-proxy',
uuid: require.resolve('uuid'), // https://stackoverflow.com/a/73203803

// couldn't get these to work in tests so mocking
'^zarrita$': '<rootDir>/__mocks__/zarrita.js',
'^@hms-dbmi/viv$': '<rootDir>/__mocks__/@hms-dbmi/viv.js',
},
moduleFileExtensions: [
'web.js',
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