SACGF / SACGF/variantgrid

Classification export fails on entrez error

Open
#1,687 4 comments 0 reactions 1 assignee Claimed by @davmlaw View on GitHub
Dominant language
Python
Stars
30
Forks
3
Avg merge
9h 28m
Merged PRs (30d)
42

Description

https://shariant.org.au/classification/export_redirect?share_level=public&build=GRCh38&type=json&exclude_orgs=sa_pathology

Died with:

```
Traceback (most recent call last):
 File "/opt/variantgrid/annotation/models/models_citations.py", line 678, in _load_from_entrez
   records = list(Medline.parse(handle))
 File "/opt/variantgrid/env/lib/python3.11/site-packages/Bio/Medline/__init__.py", line 168, in parse
   for line in handle:
 File "/usr/lib/python3.11/http/client.py", line 678, in read1
   return self._read1_chunked(n)
 File "/usr/lib/python3.11/http/client.py", line 719, in _read1_chunked
   chunk_left = self._get_chunk_left()
 File "/usr/lib/python3.11/http/client.py", line 580, in _get_chunk_left
   raise IncompleteRead(b'')
IncompleteRead: IncompleteRead(0 bytes read)Traceback (most recent call last):
 File "/usr/lib/python3.11/http/client.py", line 578, in _get_chunk_left
   chunk_left = self._read_next_chunk_size()
 File "/usr/lib/python3.11/http/client.py", line 545, in _read_next_chunk_size
   return int(line, 16)
ValueError: invalid literal for int() with base 16: b''
```

I have tried to recreate this, but can't. I suspect because this is cached?

Contributor guide

No contributing guide indexed for this repository

Assessment

This issue has not been assessed yet.

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.