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will-moore avatar will-moore commented on September 12, 2024

When looking into the usage of Pixels path/name in IDR, I think I checked a bunch of Filesets in IDR to see if the first File matched the path/name in Pixels and found that there were differences in many cases. Unfortunately I can't remember where I documented that...
Also I don't know if Bio-Formats would have behaved differently if the different path/name was used in setId().

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will-moore avatar will-moore commented on September 12, 2024

Ah - I found it: IDR/idr-metadata#660 (comment)
So, testing 1 image from each study in IDR (to get a good mix of formats etc) it looks like there were 22 studies where the Pixels path/name didn't match the first OriginalFile from the Fileset.

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sbesson avatar sbesson commented on September 12, 2024

Thanks @will-moore looking at your list of mismatches, all of these examples are multi-file & multi-folder file formats, primarily HCS but not only. Also from a quick search using the IDR UI, it seems that the first FilesetEntry.clientPath is matches Pixels.path and Pixels.name. Both of these observations are consistent with my expectations based on preliminary investigation.

Also I don't know if Bio-Formats would have behaved differently if the different path/name was used in setId().

Unfortunately, the answer here is "it depends". In the worst case scenario, Bio-Formats would throw an UnknownFormatException on setId.

As a next step here my plan is to write a pre-check SQL script that iterates through all the Fileset in a database and tries to match the first FilesetEntry with any of the OriginalFile using fileset.clientPath and originalfile.{path,name}. We should be able to run this script against the IDR database and other OMERO databases to give us a feeling on whether we can fix these links in an authoritative manner.

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