Samples viewer

[will-moore]

Work in progress; Exploring options for showing summary of sample data.

Deployed at e.g. https://samples-viewer--ome2024-ngff-challenge.netlify.app/?csv=https://raw.githubusercontent.com/will-moore/ome2024-ngff-challenge/samples_viewer/samples/idr0157_samples.csv

You can update the query string to point at any other csv, which simply expects a URL on each row.

There is a web page that loads the "master" csv via query string ?csv=https://raw.githubusercontent.com/will-moore/ome2024-ngff-challenge/samples_viewer/samples/ngff_samples.csv and recursively follows links to any other csvs.

Web page is a Svelte.js app - probably a bit of an overkill just now, but makes it easier to grow.

Currently, we display data like this (screenshot below) - Some of the earlier samples here don't have written bytes info as that came later.

Questions etc: We need to make a bunch of http requests for each sample row in the table, and we are currently ONLY loading the highest resolution array - bytes written to other resolutions are ignored:

• for each plate row: 3 requests: plate, multiscales (field 0 from first well), array
• for each bioformats2raw layout: 3 requests: bf2raw, multiscales (0 only), array
• multiscales rows: 2 requests: multiscales and array
• ro-crate-metadata.json is loaded on request (button).

Not yet loading:

• actually showing images e.g. as we do at https://ome.github.io/ome-zarr-catalog/?csv=https://raw.githubusercontent.com/ome/ome-zarr-catalog/main/public/zarr_samples.csv

This approach gives a nice summary for a reasonable number of samples, but in it's current form it won't scale very nicely for all the data we're planning to show. E.g, it will take a long time to get summary data for all the samples.

We could probably load the URLs for all samples (load ALL the CSVs) and say "10k samples" and then load the samples themselves incrementally, e.g. as you scroll through the list, or random slide-show etc.

NB: I have got netlify to deploy from this branch. Need to get OME's netlify to deploy from main once merged.

See screenshots below for latest changes...

[joshmoore]

@will-moore: what's the best way to review? Is there a URL somewhere?

[will-moore]

We need to activate netlify to build it, same as for ngff-validator... You have an OME account for netlify?

[will-moore]

@joshmoore Need to somehow point netlify at the ome2024-ngff-challenge directory below the parent repo.

[joshmoore]

Command: npm run build

5:03:40 PM: Failed during stage 'Reading and parsing configuration files': 
When resolving config:
Base directory does not exist: /opt/build/repo/ome2024-ngff-challenge

: exit status 1

[will-moore]

I think it's maybe trying to build the main branch, which doesn't yet contain the app?
I'm just trying to get netlify to build my branch directly. The build completed but the app isn't loading for some reason..
Let me look at it for a bit....

[netlify]

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[will-moore]

OK, I got it to deploy at https://66e06a54f9201459706a0106--ome2024-ngff-challenge.netlify.app/?csv=https://raw.githubusercontent.com/will-moore/ome2024-ngff-challenge/samples_viewer/samples/ngff_samples.csv

Some of the key settings (apart from specifying to just use build this branch from my repo):

Base directory: ome2024-ngff-challenge
Build command: npm run build
Publish directory: ome2024-ngff-challenge/dist

[will-moore]

@joshmoore That doesn't look quite right. I think it's the same problem I had initially - serving src etc instead of from /dist. E.g. https://deploy-preview-50--euphonious-mochi-664405.netlify.app/src/App.svelte is available.
Do you have the Publish directory: ome2024-ngff-challenge/dist ?

[will-moore]

Also, you can give the netlify app a name instead of the random one it generates. I think I might have claimed ome2024-ngff-challenge in my testing, but you can pick something similar?

[joshmoore]

@sbesson suggested during the call adding a "provider" or "source" column to the default view.

Thinking of the implementation of that, @will-moore, Can we have:

• top-level .csv: 2 columns, source & path/link to .csv
• nested .csv: path/link to .zarr

i.e., no mixing at the top-level?

[will-moore]

After that commit: loading ro-crate-metadata.json (on user request, so as not to make too many requests initially).
Also showing a summary of counts:
https://samples-viewer--ome2024-ngff-challenge.netlify.app/?csv=https://raw.githubusercontent.com/will-moore/ome2024-ngff-challenge/samples_viewer/samples/idr0157_samples.csv

[imagesc-bot]

This pull request has been mentioned on Image.sc Forum. There might be relevant details there:

https://forum.image.sc/t/ome2024-ngff-challenge/97363/38