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Fiji links do not point to container roots #118

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bogovicj opened this issue Mar 6, 2024 · 2 comments
Open

Fiji links do not point to container roots #118

bogovicj opened this issue Mar 6, 2024 · 2 comments

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@bogovicj
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bogovicj commented Mar 6, 2024

My recollection is that the "Copy Fiji Link" buttons used to point to the root of the n5 (or soon, zarr) containers, and that seems not to be the case anymore.

For example, the button on this page
https://openorganelle.janelia.org/datasets/jrc_hela-2
should copy this url: s3://janelia-cosem-datasets/jrc_hela-2/jrc_hela-2.n5

but it currently copies this one: s3://janelia-cosem-datasets/jrc_hela-2 which can cause problems (1)

This behavior seems consistent across the site, here's the next three I tried:

  • jrc_macrophage-2 produces s3://janelia-cosem-datasets/jrc_macrophage-2/
  • jrc_cos7-11 produces s3://janelia-cosem-datasets/jrc_cos7-11/
  • jrc_ctl-id8-3 produces s3://janelia-cosem-datasets/jrc_ctl-id8-3/

(1) Fiji will have to guess what the storage format it will be, and the extension is a strong hint that the urls currently being copied don't have.

@d-v-b
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d-v-b commented Mar 7, 2024

this is fixed via #119 . the current solution is a hack -- it checks whether there are more n5-formatted images than zarr-formatted images, and associates the url behind the "fiji link" button with the majority. I think most datasets today are essentially 99% or more n5, or 99% or more zarr, so this hack will work.

But the long-term solution is to associate a fiji link with an individual image, not an entire dataset. this will require some more changes to the site that are planned but not in motion yet (see #115 )

@bogovicj
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bogovicj commented Mar 7, 2024

Looks good now, thanks @d-v-b , feel free to close this issue if you'd like, or leave it open until your preferred solution is ready - up to you.

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