ga4gh / ga4gh/cloud-interop-testing

Anvil PFB export from GTEx fails on BigQuery import

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Dominant language
Python
Stars
9
Forks
8
PR merge metrics
No merged PRs in 30d

Description

Exported a PFB file for the GTEX project from Anvil Gen3.
Uploaded the avro file to a Google bucket.
Use Create table in BigQuery from the Avro file

The import job results in the following error:
"Error while reading data, error message: The Apache Avro library failed to parse the header with the following error: Invalid name: Text describing innheritance model"

Note: Posting here as this the work is part of using Search with DRS. The problem seems to be with the PFB exported from Gen3 Anvil. No issue tracker on PFB is available currently.

Contributor guide

No contributing guide indexed for this repository

Research direction

Start by reproducing the failure with the GTEx PFB exported from Anvil Gen3: upload the Avro file to a Google bucket and use BigQuery's Create table flow. Compare the import error with the PFB metadata, including the text describing the inheritance model. Done means identifying whether the defect is in the exported PFB and documenting or validating a compatible import path for Search with DRS.

Written by the indexing model from the issue text.

Assessment

Tech stack
google-cloud
Domain
cloud, databases
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
25/100

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