A particular sample always crashes for me #117
Description
Hi folks, sorry to leave another bug, but I seem to be having trouble fetching some samples. Many thousands of others I have downloaded over the past couple of weeks were fine, but specifically human oral (or Animal secretion) samples with ids matching '\.raw' fail. Perhaps not all of them, but excluding all 172 of them seems to make the other ~17k (~24k for Animal secretion) samples download without problems. This was the first example I found:
$ redbiom --version
redbiom, version 0.3.8
$ echo $context
Deblur_2021.09-Illumina-16S-V4-150nt-ac8c0b
$ redbiom fetch samples --context $context --output samples.biom 11896.A2.raw
Traceback (most recent call last):
File "/home/ben/miniconda3/envs/qiime2-2022.2/bin/redbiom", line 10, in <module>
sys.exit(cli())
File "/home/ben/miniconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/click/core.py", line 829, in __call__
return self.main(*args, **kwargs)
File "/home/ben/miniconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/click/core.py", line 782, in main
rv = self.invoke(ctx)
File "/home/ben/miniconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/click/core.py", line 1259, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/home/ben/miniconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/click/core.py", line 1259, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/home/ben/miniconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/click/core.py", line 1066, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/home/ben/miniconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/click/core.py", line 610, in invoke
return callback(*args, **kwargs)
File "/home/ben/miniconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/redbiom/commands/fetch.py", line 203, in fetch_samples_from_samples
table, ambig = redbiom.fetch.data_from_samples(context, iterable,
File "/home/ben/miniconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/redbiom/fetch.py", line 306, in data_from_samples
return _biom_from_samples(context, samples, skip_taxonomy=skip_taxonomy)
File "/home/ben/miniconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/redbiom/fetch.py", line 367, in _biom_from_samples
data = se(fetch_sample, 0, context, id_)
File "/home/ben/miniconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/redbiom/_requests.py", line 110, in f
return json.loads(_parse_validate_request(s.get(url), 'EVALSHA'))
File "/home/ben/miniconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/redbiom/_requests.py", line 6, in _parse_validate_request
return req.json()[command]
File "/home/ben/miniconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/requests/models.py", line 899, in json
return complexjson.loads(
File "/home/ben/miniconda3/envs/qiime2-2022.2/lib/python3.8/json/__init__.py", line 357, in loads
return _default_decoder.decode(s)
File "/home/ben/miniconda3/envs/qiime2-2022.2/lib/python3.8/json/decoder.py", line 337, in decode
obj, end = self.raw_decode(s, idx=_w(s, 0).end())
File "/home/ben/miniconda3/envs/qiime2-2022.2/lib/python3.8/json/decoder.py", line 355, in raw_decode
raise JSONDecodeError("Expecting value", s, err.value) from None
json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0)Thanks very much for looking at this!