GSE176201 - Covid19LungSequelae

[ofanobilbao]

Project short name:

Covid19LungSequelae

Primary Wrangler:

Ida

Secondary Wrangler:

Arsenios

Link to Ingest

https://contribute.data.humancellatlas.org/projects/detail?uuid=fae72d89-4ac4-4aab-9b93-574775e168d4&tab=project

Associated files

• Google Drive: folder

Published study links

• Paper: Immune signatures underlying post-acute COVID-19 lung sequelae

• Accessioned data: GSE176201

Key Events

• [x] Convert published metadata to HCA spreadsheet
• [x] Manually curate dataset to meet HCA metadata standard
• [x] Collect any matrix and cell-type annotation files
• [ ] Are the analysis files suitable for CellxGene? If something is missing get in touch with the authors to request it
• [x] Upload sheet to validate metadata
• [x] Transfer raw files to ingest to validate data files
• [x] Check linking using ingest graph validator
• [x] Ask the Secondary Wrangler for an end-to-end review of the project. Ask the Expertise Wrangler to review specific tabs if needed
• [x] Submit dataset to Production
• [x] Complete the Export SOP
• [ ] Convert project data to SCEA format following the SCEA conversion SOP if appropriate

[idazucchi]

ready for secondary review!

[arschat]

Great submission, only two minor comments.

• Could add the hca_bionetworks.name and hca_bionetworks.atlas_project fields in Project.
• Could add insdc_experiment_accession in Donor organism & Cell suspension tab.

[idazucchi]

I've added the hca_bionetworks info by uploading a spreasheet to the existing submission the incovenient thing is I did it twice so this bit of metadata is repeated twice since the hca_bionetworks is loaded as an array - I think I can fix it with the api

[ofanobilbao]

@idazucchi will attempt with Enrique's guide. @arschat can help if needed as he did this a short while ago

[ESapenaVentura]

I have a feeling programmatic updates with POST requests delete the submissionDate - Please refrain from making them, use PATCH instead :)

This dataset is missing the project submissionDate as the other R28 error, so the actions are similar:

• [x] Update staging area with submission date (Take from submission entity) for both project and supplementary file metadata
• [ ] Update ingest with that same information for project

[ESapenaVentura]

Operational fixes for staging area

# Project metadata
gsutil cat gs://broad-dsp-monster-hca-prod-ebi-storage/prod/fae72d89-4ac4-4aab-9b93-574775e168d4/metadata/project/fae72d89-4ac4-4aab-9b93-574775e168d4_2023-05-18T14:16:29.973000Z.json | jq -jc '.provenance.submission_date = "2023-03-31T06:06:350Z"' > fae72d89-4ac4-4aab-9b93-574775e168d4_2023-05-18T14:16:29.973000Z.json
gsutil cp fae72d89-4ac4-4aab-9b93-574775e168d4_2023-05-18T14:16:29.973000Z.json gs://broad-dsp-monster-hca-prod-ebi-storage/prod/fae72d89-4ac4-4aab-9b93-574775e168d4/metadata/project/fae72d89-4ac4-4aab-9b93-574775e168d4_2023-05-18T14:16:29.973000Z.json

# Supplementary file metadata
gsutil cat gs://broad-dsp-monster-hca-prod-ebi-storage/prod/fae72d89-4ac4-4aab-9b93-574775e168d4/metadata/supplementary_file/25f32c01-fffb-5b75-a0fc-621313b0ba92_2023-05-18T16:53:24.450000Z.json | jq -jc '.provenance.submission_date = "2023-03-31T06:06:350Z"' > 25f32c01-fffb-5b75-a0fc-621313b0ba92_2023-05-18T16:53:24.450000Z.json
gsutil cp 25f32c01-fffb-5b75-a0fc-621313b0ba92_2023-05-18T16:53:24.450000Z.json gs://broad-dsp-monster-hca-prod-ebi-storage/prod/fae72d89-4ac4-4aab-9b93-574775e168d4/metadata/supplementary_file/25f32c01-fffb-5b75-a0fc-621313b0ba92_2023-05-18T16:53:24.450000Z.json

[ofanobilbao]

@ESapenaVentura to confirm if we still need to do the updates in Ingest. We submitted already the changes to DCP right?

[ofanobilbao]

If changes are done in ingest we would be able to close this ticket right?

[ofanobilbao]

@ESapenaVentura was this done as part of the Release 28 import errors that Amnon resolved last week? Or is this still pending and we need to flag it with Amnon?

[idazucchi]

missing submissionDate was add back to ingest by Amnon - this ticket can be closed!