HCMI / GDC Tool Error

[jjacobson95]

Receiving a new error from the GDC tool. This seems to be consistent (3x in a row, but all attempts within 12hrs of each other) and I'm not positive we can solve on our end. We already have retries built-in, but it's failing every time. Might need to wait for GDC to fix on their end?

Also, no updates have been made to the tool itself, but maybe a change was made to the API (which passes the status_code param to the tool) leading to the tool being outdated.

ERROR: ('Connection aborted.', ConnectionResetError(104, 'Connection reset by peer'))
ERROR: An unexpected error has occurred during normal operation of the client. Please report the following exception to GDC support <support@nci-gdc.datacommons.io>.
ERROR: 'NoneType' object has no attribute 'status_code'
Traceback (most recent call last):
  File "gdc_client/cli.py", line 102, in main
  File "gdc_client/download/parser.py", line 93, in download
  File "gdc_client/download/client.py", line 283, in download_small_groups
  File "gdc_client/download/client.py", line 223, in _download_tarfile
AttributeError: 'NoneType' object has no attribute 'status_code'
ERROR: Exiting

[jjacobson95]

Issue submitted to support@nci-gdc.datacommons.io, waiting on response

[jjacobson95]

After further exploration of the logs, I think that its possible that the GDC API is/was actively being worked on because the errors appear to change across re-attempts.

A downstream issue that was in the same logs.

Polars found a filename. Ensure you pass a path to the file instead of a python file object when possible for best performance.
thread '<unnamed>' panicked at py-polars/src/file.rs:129:18:
Expecting to be able to downcast into bytes from read result.: PyDowncastError { from: '#version gdc-1.0.0\n#annotation.spec gdc-2.0.0-aliquot-merged-masked\n#contigs chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr1
4,chr15,chr16,chr17,chr18,chr19,chr20,chr21,chr22,chrX,chrY,chrM\n#sort.order BarcodesAndCoordinate\n#filedate 20221011\n#normal.aliquot f694511f-4aa2-4258-8765-bbb24bf00092\n#tumor.aliquot 4267c9b2-139a-4abd-ac70-5f5a47ea1e30\nHugo_Symbol\
tEntrez_Gene_Id\tCenter\tNCBI_Build\tChromosome\tStart_Position\tEnd_Position\tStrand\tVariant_Classification\tVariant_Type\tReference_Allele\tTumor_Seq_Allele1\tTumor_Seq_Allele2\tdbSNP_RS\tdbSNP_Val_Status\tTumor_Sample_Barcode\tMatched_N
orm_Sample_Barcode\tMatch_Norm_Seq_Allele1\tMatch_Norm_Seq_Allele2\tTumor_Validation_Allele1\tTumor_Validation_Allele2\tMatch_Norm_Validation_Allele1\tMatch_Norm_Validation_Allele2\tVerification_Status\tValidation_Status\tMutation_Status\tS
equencing_Phase\tSequence_Source\tValidation_Method\tScore\tBAM_File\tSequencer\tTumor_Sample_UUID\tMatched_Norm_Sample_UUID\tHGVSc\tHGVSp\tHGVSp_Short\tTranscript_ID\tExon_Number\tt_depth\tt_ref_count\tt_alt_count\tn_depth\tn_ref_count\tn_
alt_count\tall_effects\tAllele\tGene\tFeature\tFeature_type\tOne_Consequence\tConsequence\t...{hundreds/thousands more lines of this}...', to: "PyBytes" }
note: run with `RUST_BACKTRACE=1` environment variable to display a backtrace