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Samples viewer #50

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b6bfb2a
Add a svelte.js app for loading a CSV of zarr samples
will-moore Sep 4, 2024
322d434
Add ngff_samples.csv
will-moore Sep 4, 2024
ab25468
Move idr0090 samples to new csv
will-moore Sep 4, 2024
9d35f98
Add idr0090_samples.csv to ngff_samples.csv
will-moore Sep 4, 2024
9f19993
Basic recursive loading of csv files and zarr.json
will-moore Sep 4, 2024
ce293f5
Loading array data for images, bf2raw and plates
will-moore Sep 4, 2024
44323b1
Load and display bytes written
will-moore Sep 5, 2024
18ed84f
Add idr0010_samples.csv
will-moore Sep 6, 2024
0c1142e
Add plate data to table, show total written bytes
will-moore Sep 6, 2024
9757ef7
Add idr0012_samples.csv
will-moore Sep 9, 2024
8db4ae3
Typo and css table tweaks
will-moore Sep 10, 2024
2b8a653
Show summary counts and total size
will-moore Sep 10, 2024
2c89d47
Add idr0157_samples.csv
will-moore Sep 11, 2024
b628dd0
Load ro-crate-metadata.json, lookup organism
will-moore Sep 11, 2024
171f7d0
Add idr0013 and idr0015 samples.csv
will-moore Sep 11, 2024
260f324
Lookup fbbi imaging modality
will-moore Sep 12, 2024
fc4d780
Handle csv files with or without header row
will-moore Sep 12, 2024
230f31e
use parent csv row to populate child rows
will-moore Sep 12, 2024
b8f726c
Update ngff_samples.csv with source column and row names
will-moore Sep 12, 2024
362ac11
Load 5 rows at a time from each csv
will-moore Sep 12, 2024
fb59295
Add idr0013, idr0015, idr0157 csvs to ngff_samples.csv
will-moore Sep 16, 2024
e44d093
Add idr0011 to samples.csv
will-moore Sep 16, 2024
c3fb665
Basic table sorting on select columns
will-moore Sep 16, 2024
77f5b83
Add idr0016 and idr0026 samples
will-moore Sep 18, 2024
02ec0c4
Fix urls in idr0011_samples.csv
will-moore Sep 18, 2024
0b3f599
Add idr0033, idr0035, idr0036 samples.csv
will-moore Sep 21, 2024
baab773
Handle 404 errors
will-moore Sep 21, 2024
b56351d
Handle 404s and show progress
will-moore Sep 22, 2024
6ca2d33
Load RO-Crate metadata json in batches
will-moore Sep 23, 2024
66eca9f
Show thumbnail. Only load 1st image of child csvs
will-moore Sep 23, 2024
911f823
Add ThumbGallery at top of page
will-moore Sep 24, 2024
58351ab
Reorgaise samples.csv
will-moore Sep 24, 2024
2f3479c
Only show collections in ThumbGallery
will-moore Sep 24, 2024
9f9a48d
Fix other_samples.csv header
will-moore Sep 24, 2024
3d78367
Handle gallery click to load csv in main table
will-moore Sep 24, 2024
67af583
Show csv name and source on gallery item hover
will-moore Sep 24, 2024
ec1059e
Add idr0044_samples.csv
will-moore Sep 24, 2024
13b7bc8
Fix samples viewer page title
will-moore Sep 25, 2024
1d31e62
Support 'origin' url and fix ro-crate-metadata loading
will-moore Sep 25, 2024
2628ddd
Add 'origin' column to idr0090_samples.csv
will-moore Sep 25, 2024
eab8ca5
Add idr0051_samples and BioImage-Archive ebi-ngff-challenge-samples.csv
will-moore Sep 25, 2024
2742ff6
Only show Plate columns if needed
will-moore Sep 25, 2024
565f0b9
Fix last 2 samples for idr0090_samples.csv
will-moore Sep 25, 2024
1fdd5d9
Default thumbnail uses sizeT/2 for theT index
will-moore Sep 26, 2024
f57adbf
add Webknossos samples
normanrz Sep 26, 2024
d4fb126
Add 'origin' and 'written' columns to sample.csvs
will-moore Sep 27, 2024
33492ff
Add written columns to idr0157_samples.csv
will-moore Sep 29, 2024
2a3610d
Fix idr0090 columns
will-moore Sep 29, 2024
5b90410
Fix idr0010_samples.csv header
will-moore Sep 29, 2024
c92a95c
Update ebi-ngff-challenge-samples.csv with pre-calculated 'written' c…
will-moore Sep 30, 2024
aaa0545
Add written column to other_samples.csv
will-moore Sep 30, 2024
2d7c552
Use pre-calculated 'written' from csv instead of reading from zarr.json
will-moore Sep 30, 2024
6536b6a
Add JAX KOMP_adult_lacZ.csv to ngff_samples.csv
will-moore Sep 30, 2024
60deded
Merge branch 'samples_viewer' into samples_wk
will-moore Sep 30, 2024
244fec7
Merge pull request #1 from normanrz/samples_wk
will-moore Sep 30, 2024
6ef9122
Use 'written' column name in webknossos_samples.csv
will-moore Sep 30, 2024
7c376a7
Remove duplicate row from webknossos_samples.csv
will-moore Sep 30, 2024
a2259b3
Zarr urls don't need '.zarr'. Ensure no duplicate urls
will-moore Sep 30, 2024
669a3a7
Nest all IDR samples under idr_samples.csv
will-moore Sep 30, 2024
285346a
Rename column source -> origin in webknossos_samples.csv
will-moore Sep 30, 2024
908fbfe
Remove incomplete samples.csv from idr_samples.csv for idr0044, idr00…
will-moore Sep 30, 2024
a000130
Handle failure to find/parse array zarr.json
will-moore Sep 30, 2024
1e967f6
Fix button text for dark mode
will-moore Sep 30, 2024
7968cd1
Add load_zarr_stats.py
will-moore Sep 30, 2024
43efdc4
Show 'ALL Samples' link if not showing
will-moore Sep 30, 2024
31b905f
Show Icons for gallery source
will-moore Oct 3, 2024
712131e
Add missing idr.svg
will-moore Oct 3, 2024
df37e12
Add background grid and random pixels
will-moore Oct 3, 2024
3248605
Add Nav bar, css tweaks
will-moore Oct 4, 2024
5cadf33
Update ngff_samples.csv
perlman Oct 4, 2024
78136cc
Allow larger thumbnails for gallery
will-moore Oct 4, 2024
0cd3c6b
Fix column sort buttons, fix dark mode background
will-moore Oct 4, 2024
16a7f95
Add OME logo to nav bar
will-moore Oct 4, 2024
3423248
Fix 'strikethrough' effect by adding background to csv URL
will-moore Oct 4, 2024
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2 changes: 1 addition & 1 deletion .pre-commit-config.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -59,7 +59,7 @@ repos:
rev: "v2.2.6"
hooks:
- id: codespell
args: ["-L crate,Crate"]
args: ["-L crate,Crate,bellow"]

- repo: https://github.com/shellcheck-py/shellcheck-py
rev: "v0.10.0.1"
Expand Down
24 changes: 24 additions & 0 deletions ome2024-ngff-challenge/.gitignore
Original file line number Diff line number Diff line change
@@ -0,0 +1,24 @@
# Logs
logs
*.log
npm-debug.log*
yarn-debug.log*
yarn-error.log*
pnpm-debug.log*
lerna-debug.log*

node_modules
dist
dist-ssr
*.local

# Editor directories and files
.vscode/*
!.vscode/extensions.json
.idea
.DS_Store
*.suo
*.ntvs*
*.njsproj
*.sln
*.sw?
3 changes: 3 additions & 0 deletions ome2024-ngff-challenge/.vscode/extensions.json
Original file line number Diff line number Diff line change
@@ -0,0 +1,3 @@
{
"recommendations": ["svelte.svelte-vscode"]
}
15 changes: 15 additions & 0 deletions ome2024-ngff-challenge/README.md
Original file line number Diff line number Diff line change
@@ -0,0 +1,15 @@
# ome2024-ngff-challenge web page

This is a Svelte.js app for loading CSV file(s) that list NGFF samples and
displaying a summary.

Development: cd into this directory, then...

```
$ npm install
$ npm run dev
```

Go to
http://localhost:5173/?csv=https://raw.githubusercontent.com/will-moore/ome2024-ngff-challenge/samples_viewer/samples/ngff_samples.csv
to open a csv file.
10 changes: 10 additions & 0 deletions ome2024-ngff-challenge/index.html
Original file line number Diff line number Diff line change
@@ -0,0 +1,10 @@
<!doctype html>
<html lang="en">
<head>
<meta charset="UTF-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>ome2024-ngff-challenge</title>
</head>
<body id="app"></body>
<script type="module" src="/src/main.js"></script>
</html>
32 changes: 32 additions & 0 deletions ome2024-ngff-challenge/jsconfig.json
Original file line number Diff line number Diff line change
@@ -0,0 +1,32 @@
{
"compilerOptions": {
"moduleResolution": "bundler",
"target": "ESNext",
"module": "ESNext",
/**
* svelte-preprocess cannot figure out whether you have
* a value or a type, so tell TypeScript to enforce using
* `import type` instead of `import` for Types.
*/
"verbatimModuleSyntax": true,
"isolatedModules": true,
"resolveJsonModule": true,
/**
* To have warnings / errors of the Svelte compiler at the
* correct position, enable source maps by default.
*/
"sourceMap": true,
"esModuleInterop": true,
"skipLibCheck": true,
/**
* Typecheck JS in `.svelte` and `.js` files by default.
* Disable this if you'd like to use dynamic types.
*/
"checkJs": true
},
/**
* Use global.d.ts instead of compilerOptions.types
* to avoid limiting type declarations.
*/
"include": ["src/**/*.d.ts", "src/**/*.js", "src/**/*.svelte"]
}
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