search command fails with KeyError: 'submitter'
Closed this issue · 3 comments
papanikos commented
On a fresh conda/mamba installation with:
$ mamba create -n genomepy genomepy
- version
(genomepy)$ genomepy --version
genomepy, version 0.16.0
- Test search command
(genomepy)$ genomepy search e coli
12:46:31 | INFO | Downloading assembly summaries from GENCODE
12:46:37 | INFO | Downloading assembly summaries from UCSC
12:46:42 | INFO | Downloading assembly summaries from Ensembl
12:46:51 | INFO | Downloading assembly summaries from NCBI, this will take a while...
genbank_historical: 43.3k genomes [00:01, 36.7k genomes/s]
refseq_historical: 69.7k genomes [00:01, 41.8k genomes/s]
genbank: 1.69M genomes [00:25, 66.6k genomes/s]
refseq: 307k genomes [00:04, 61.7k genomes/s]
Traceback (most recent call last):
File "/home/nikos/miniconda3/envs/genomepy/bin/genomepy", line 10, in <module>
sys.exit(cli())
^^^^^
File "/home/nikos/miniconda3/envs/genomepy/lib/python3.11/site-packages/click/core.py", line 1130, in __call__
return self.main(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/nikos/miniconda3/envs/genomepy/lib/python3.11/site-packages/click/core.py", line 1055, in main
rv = self.invoke(ctx)
^^^^^^^^^^^^^^^^
File "/home/nikos/miniconda3/envs/genomepy/lib/python3.11/site-packages/click/core.py", line 1657, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/nikos/miniconda3/envs/genomepy/lib/python3.11/site-packages/click/core.py", line 1404, in invoke
return ctx.invoke(self.callback, **ctx.params)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/nikos/miniconda3/envs/genomepy/lib/python3.11/site-packages/click/core.py", line 760, in invoke
return __callback(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/nikos/miniconda3/envs/genomepy/lib/python3.11/site-packages/genomepy/cli.py", line 412, in search
for row in genomepy.search(term, provider, exact, size):
File "/home/nikos/miniconda3/envs/genomepy/lib/python3.11/site-packages/genomepy/providers/__init__.py", line 136, in search
for row in p.search(term, exact, size):
File "/home/nikos/miniconda3/envs/genomepy/lib/python3.11/site-packages/genomepy/providers/base.py", line 394, in search
for name in search_function(term, exact):
File "/home/nikos/miniconda3/envs/genomepy/lib/python3.11/site-packages/genomepy/providers/base.py", line 334, in _search_text
texts = [name] + [str(metadata[f]) for f in self.description_fields]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/nikos/miniconda3/envs/genomepy/lib/python3.11/site-packages/genomepy/providers/base.py", line 334, in <listcomp>
texts = [name] + [str(metadata[f]) for f in self.description_fields]
~~~~~~~~^^^
KeyError: 'submitter'
- Test example search command with xenopus tropicalis
(genomepy)$ genomepy search xenopus tro
name provider accession tax_id annotation species other_info
n r e k <- UCSC options (see help)
UCB_Xtro_10.0 Ensembl GCA_000004195.4 8364 ✓ Xenopus tropicalis 2020-09-Ensembl/2021-02
xenTro1 UCSC na 8364 ✗ ✗ ✗ ✗ Xenopus tropicalis Oct. 2004 (JGI 3.0/xenTro1)
xenTro10 UCSC GCF_000004195.4 8364 ✓ ✓ ✗ ✗ Xenopus tropicalis Nov. 2019 (UCB_Xtro_10.0/xenTro10)
xenTro2 UCSC na 8364 ✗ ✓ ✓ ✗ Xenopus tropicalis Aug. 2005 (JGI 4.1/xenTro2)
xenTro3 UCSC GCA_000004195.1 8364 ✗ ✓ ✓ ✗ Xenopus tropicalis Nov. 2009 (JGI 4.2/xenTro3)
xenTro7 UCSC GCA_000004195.2 8364 ✓ ✓ ✗ ✗ Xenopus tropicalis Sep. 2012 (JGI 7.0/xenTro7)
xenTro9 UCSC GCA_000004195.3 8364 ✓ ✓ ✓ ✗ Xenopus tropicalis Jul. 2016 (Xenopus_tropicalis_v9.1/xenTro9)
Traceback (most recent call last):
File "/home/nikos/miniconda3/envs/genomepy/bin/genomepy", line 10, in <module>
sys.exit(cli())
^^^^^
File "/home/nikos/miniconda3/envs/genomepy/lib/python3.11/site-packages/click/core.py", line 1130, in __call__
return self.main(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/nikos/miniconda3/envs/genomepy/lib/python3.11/site-packages/click/core.py", line 1055, in main
rv = self.invoke(ctx)
^^^^^^^^^^^^^^^^
File "/home/nikos/miniconda3/envs/genomepy/lib/python3.11/site-packages/click/core.py", line 1657, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/nikos/miniconda3/envs/genomepy/lib/python3.11/site-packages/click/core.py", line 1404, in invoke
return ctx.invoke(self.callback, **ctx.params)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/nikos/miniconda3/envs/genomepy/lib/python3.11/site-packages/click/core.py", line 760, in invoke
return __callback(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/nikos/miniconda3/envs/genomepy/lib/python3.11/site-packages/genomepy/cli.py", line 412, in search
for row in genomepy.search(term, provider, exact, size):
File "/home/nikos/miniconda3/envs/genomepy/lib/python3.11/site-packages/genomepy/providers/__init__.py", line 136, in search
for row in p.search(term, exact, size):
File "/home/nikos/miniconda3/envs/genomepy/lib/python3.11/site-packages/genomepy/providers/base.py", line 394, in search
for name in search_function(term, exact):
File "/home/nikos/miniconda3/envs/genomepy/lib/python3.11/site-packages/genomepy/providers/base.py", line 334, in _search_text
texts = [name] + [str(metadata[f]) for f in self.description_fields]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/nikos/miniconda3/envs/genomepy/lib/python3.11/site-packages/genomepy/providers/base.py", line 334, in <listcomp>
texts = [name] + [str(metadata[f]) for f in self.description_fields]
~~~~~~~~^^^
KeyError: 'submitter'
papanikos commented
This only happens with NCBI as the provider.
With a quick check on the assembly_summary_refseq_historical.txt from https://ftp.ncbi.nlm.nih.gov/genomes/ASSEMBLY_REPORTS/ there is not a submitter field but an asm_submitter. Maybe something relevant for this line in the NcbiProvider.
siebrenf commented
It is, thank you for the warning! I'll try to get a hotfix out
siebrenf commented
Hotfix 0.16.1 is out and should be available on Conda in an hour or so.
Closing the issue. Feel free to reopen this is the error was not fixed.