ebi-ait / hca-ebi-wrangler-central

This repo is for tracking work related to wrangling datasets for the HCA, associated tasks and for maintaining related documentation.
https://ebi-ait.github.io/hca-ebi-wrangler-central/
Apache License 2.0
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EGAS00001004653 - PancreasTopographiesTosti10x #1296

Closed arschat closed 1 month ago

arschat commented 2 months ago

Project short name:

SPAN PancreasTopographiesTosti10x

Primary Wrangler:

Arsenios

Secondary Wrangler:

Associated files

Published study links

Key Events

arschat commented 2 months ago

Dataset has been partially wrangled, but it contains invalid metadata. Should be revised and resubmitted as is part of Pancreas bionetwork list.

arschat commented 1 month ago

Seems that project was partially wrangled by Ami, but abandoned because no sequence or analysis files were available at that time #827 Now analysis files are available at http://singlecell.charite.de/pancreas, I've downloaded them and start wrangling dataset again.

arschat commented 1 month ago

Removing previous submission since it had not being published before. Spreadsheet saved here.

arschat commented 1 month ago

hca-util area 39d07165-5711-4c82-870a-7496214fde73

I added the schema tab in the spreadsheeet to specify the version of the files that allows the validation (until EDAM update is completed).

arschat commented 1 month ago

Graph valid and ready for sec review!

idazucchi commented 1 month ago

Hi! Nice job on this dataset, I have only a couple of small comments

Donor / Specimen

Collection protocol

Cell suspension

Analysis file

arschat commented 1 month ago

Nice catch on the wrong CS for the chronic_* files! Thank you for the review. I applied all changes to the submission, and is now exported!

arschat commented 1 month ago

Noticed a flip of diseases for donors TUM_25_donor and TUM_C1_donor. Replaced that in staging area's metadata jsons.

  1. Copied contents of the json files
    gsutil cat gs://broad-dsp-monster-hca-prod-ebi-storage/prod/b3938158-4e8d-4fdb-9e13-9e94270dde16/metadata/donor_organism/2fbd1774-f11b-46f7-983a-54544fd04824_2024-09-12T13:36:24.874000Z.json
    gsutil cat gs://broad-dsp-monster-hca-prod-ebi-storage/prod/b3938158-4e8d-4fdb-9e13-9e94270dde16/metadata/donor_organism/0887b590-a8ab-4dee-a2be-9b0bb589709d_2024-09-16T10:00:02.351000Z.json
  2. Created locally the files and flipped the diseases field with text editor
  3. Uploaded edited files to staging area
    gsutil cp 2fbd1774-f11b-46f7-983a-54544fd04824_2024-09-12T13:36:24.874000Z.json gs://broad-dsp-monster-hca-prod-ebi-storage/prod/b3938158-4e8d-4fdb-9e13-9e94270dde16/metadata/donor_organism/2fbd1774-f11b-46f7-983a-54544fd04824_2024-09-12T13:36:24.874000Z.json
    gsutil cp 0887b590-a8ab-4dee-a2be-9b0bb589709d_2024-09-16T10:00:02.351000Z.json gs://broad-dsp-monster-hca-prod-ebi-storage/prod/b3938158-4e8d-4fdb-9e13-9e94270dde16/metadata/donor_organism/0887b590-a8ab-4dee-a2be-9b0bb589709d_2024-09-16T10:00:02.351000Z.json
  4. I updated both biomaterials in ingest as well TUM_25_donor, and TUM_C1_donor
  5. change status to exported
image.png
arschat commented 5 days ago

verified in browser