Update Model with accession GFE->Accession

nmdp-bioinformatics / gfe-db

Graph database representing IPD-IMGT/HLA sequence data as GFE

https://gfe-db.readthedocs.io

GNU General Public License v3.0

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Update Model with accession GFE->Accession #71

Closed pbashyal-nmdp closed 1 year ago

pbashyal-nmdp commented 1 year ago

Update Model with GFE->Accession instead of IPD_Allele->Accession
Upgrade py-ard to support 3130
Fix for IMGT DB versions with 3 digits
Add Sequence to Feature node

chrisammon3000 commented 1 year ago

Tested this in my environment by loading the full dataset for 3490 with no problems.

Node summaries:	Label	Count
`["GFE"]`	33446
`["Submitter"]`	1
`["Sequence"]`	33446
`["Feature"]`	28687
`["IPD_Allele"]`	33446
`["IPD_Accession"]`	33446

Relationship summaries:	Relationship	Count
"HAS_FEATURE"	577924
"HAS_SEQUENCE"	66892
"SUBMITTED"	66892
"HAS_IPD_ACCESSION"	66892
"HAS_IPD_ALLELE"	66892

chrisammon3000 commented 1 year ago

Had to make a small change to docker build to get it to work, but I will update this in a separate pull request with other changes, just leaving it here because it's good to know.

# gfe-db/pipeline/jobs/Makefile
docker build \
    -t "$${BUILD_REPOSITORY}" \
    --platform "linux/amd64" \ # specifying the deployment platform prevents errors if you're using Apple silicon M1/M2 (these use linux/arm) 
    build/ && \

pbashyal-nmdp commented 1 year ago

Awesome. Thanks for the tip!