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Task #12906 (new)

Opened 4 years ago

Last modified 4 years ago

RFE: Export of metadata within file names

Reported by: pwalczysko Owned by:
Priority: critical Milestone: Metadata
Component: Services Version: 5.1.1
Keywords: n.a. Cc: ux@…, spli
Resources: n.a. Referenced By: n.a.
References: n.a. Remaining Time: n.a.
Sprint: n.a.

Description

During an outreach, a question from EMBL came up about the possibility of writing metadata into the names of original files (HCS data, names of single wells should contain metadata describing the experiment). There is an export step in their workflow -> the ORIGINAL exported files must have changed names.

Also, a script in OMERO is needed for the automatic renaming of the files (if not renamed on export stage).

See second paragraph in https://docs.google.com/document/d/1VytVDpdwG8FJlzn7xba9MRClNZsOMi7GVX0naya8bu0/edit and https://trello.com/c/dzgjhH1d/57-elmi-19-22-05-2015

Change History (9)

comment:1 Changed 4 years ago by spli

Couldn't this still be scripted? It's up to the script to name the original file when it's saved locally. Or do you mean modifying the metadata inside the original file?

comment:2 Changed 4 years ago by pwalczysko

@spli I think it could be scripted. The condition is thoiugh that every well will have a separate name with the metadata in the name. I do not think that they modify the metadata of the original file. A file would have to be created for every well.

comment:3 Changed 4 years ago by spli

Presumably the original data is in the form of one file per well? Otherwise we're not exporting original data and this discussion is about something else.

comment:4 Changed 4 years ago by pwalczysko

Yes, it must be so. The user mentioned that the data are "converted to .tiffs". But this would have to be clarified with the user.

comment:5 Changed 4 years ago by spli

Maybe the Batch image download script could be modified to:

  • Download original files
  • Have a template parameter for file/directory names

comment:6 Changed 4 years ago by pwalczysko

From the answer of the user who asked the original question:

...
We ourselves are not looking for any renaming solution, sine we have a
high-throughput pipeline including a database solution.
Having the treatment information inside the image file name might be a
solution for many other scientist (HTS) not having access to any database in
their institute.
...

comment:7 Changed 4 years ago by jamoore

  • Milestone changed from 5.1.4 to OMERO-5.1.4

Splitting 5.1.4 due to milestone decoupling

comment:8 Changed 4 years ago by sbesson

  • Milestone changed from OMERO-5.1.4 to 5.x

As per discussion earlier today, pushing to 5.x

comment:9 Changed 4 years ago by jamoore

  • Milestone changed from 5.x to Metadata
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