Submit ToL data to EMBL-EBI ENA & BioSamples
Notes:
INITIAL SETUP:
Copy all of the COPO development branch into the COPO folder. https://github.com/collaborative-open-plant-omics/COPO
python3 -m venv venv
source venv/bin/activate
pip install -r requirements.txt
Copy DToL classes into ToL classes, just to keep our hacking different
cp submissions/COPO/web/apps/web_copo/utils/dtol/*.py .
mv Dtol_Helpers.py Tol_Helpers.py
mv Dtol_Spreadsheet.py Tol_Spreadsheet.py
mv Dtol_Submission.py Tol_Submission.py
Change COPO relative paths in the python classes. Example
from:
import web.apps.web_copo.schemas.utils.data_utils as d_utils
from api.utils import map_to_dict
To:
import COPO.web.apps.web_copo.schemas.utils.data_utils as d_utils
from COPO.api.utils import map_to_dict
CLARIFICATION:
Q: Ken Haug. I am puzzled by the order of ENA vs BioSamples, but the code is making this more clear. Yes, I will map this against a spreadsheet or database. Do I need separate ENA (Webin) and BioSamples accounts, I assume not.
A: alice minotto. We only submit to ENA, they return both their accession and the biosample accession (so the biosample is created automatically by submitting to ENA), plus a "submission accession", which is a single accession code for the whole submission so if you are submitting 200 samples all together, you would only get one submission accession
WEBIN account:
Your new submission account has been created. The submission account id is Webin-58409. Email: [email protected]
For submission guidelines please see: https://urldefense.proofpoint.com/v2/url?u=http-3A__ena-2Ddocs.readthedocs.io_en_latest_index.html&d=DwICAg&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=niIFX4ijhZ7nQFbTJqwQSb5VItoTCmHYLVHPara9N14&m=dI4cdozOXMtg-MjiEeV7rpS3AGuQevHXdw8JGzbbbts&s=V36t4ufpn5OtbKnCRtoAcSpGtO7gE6VqsjIOiaQgrFY&e=
ToDo list:
- Change from mongo db to database orm/spreadsheet
- Change project from DTOL/ASG to TOL
- Test that we can submit to the ENA DTOL profile