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COPO submissions (DToL, ERGA)

Download old filelist if a submission exists. Create new filelist (either just the new files or all files; can use the one produced by ST download filelist button or simple ls command). Use python scripts/filelist_to_filelist_nojson.py <old_filelist> <new_filelist> > new_submission_filelist.tsv

This script checks the files in the new_filelist, if they're new it gets relevant metadata from BioSamples and creates a submission filelist including the files and metadata in the old_filelist.

Darwin Tree of Life sample images

This repository contains code and notes related to hosting sample-associated images for the Darwin Tree of Life, and wider biodiversity projects.

Process

  1. Populate individual GAL collections (?). NHM at least.
  2. Extract from these images, so that these are named by biosamples ID.
  3. Use this to construct a new submission.

After 2., we have a directory like this:

SAMEA111458765_1.jpg
SAMEA111458765_2.jpg
SAMEA111458765_3.jpg
SAMEA111458765_4.jpg
SAMEA111458769_1.jpg
SAMEA111458769_2.jpg

Code

TODO

Fix ordering of multiple samples for a single thing.

Notes

https://www.ebi.ac.uk/biostudies/files/S-BIAD588/C9K02TWY%20-%20Imported%20to%20EMu/NHMUK%20013696854%20(1).JPG

https://www.ebi.ac.uk/biosamples/samples/SAMEA111458349

Fields:

BioSamples ID GAL_sample_id collecting institution geographic location (country and/or sea) geographic location (latitude) geographic location (longitude) geographic location (region and locality) organism organism part sample collection device or method

Warning: Not all BioSamples records have all of these fields (e.g. see SAMEA14448162)

Principles

Pull everything from Biosamples record?

Comments/queries

What about:

cp C9K02U9Z and C9X0CNI7 - Imported to EMu/014425714 (2).JPG NHMUK014425714_1.jpg cp C9K02U9Z and C9X0CNI7 - Imported to EMu/014425714 (3).JPG NHMUK014425714_2.jpg cp C9K02U9Z and C9X0CNI7 - Imported to EMu/014425714.JPG NHMUK014425714_3.jpg cp C9K02U9Z and C9X0CNI7 - Imported to EMu/014425714_dorsal.JPG NHMUK014425714_4.jpg cp C9K02U9Z and C9X0CNI7 - Imported to EMu/014425714_lateral.JPG NHMUK014425714_5.jpg cp C9K02U9Z and C9X0CNI7 - Imported to EMu/014425714_ventral.JPG NHMUK014425714_6.jpg cp C9K02U9Z and C9X0CNI7 - Imported to EMu/014425714_ventral_2.JPG NHMUK014425714_7.jpg