Broadinstitute catch - elegant way to disable tests requiring online access?
Hello,
This package is one of the closest that we have on our radar to suit
virologists, to I went for CATCH from the broad institute at
https://github.com/broadinstitute/catch . Conda has it already, does not
surface on bio.tools, though.
Testing takes quite a while (~15mins) and the few that fail seem to
depend on viral sequence data that cannot be downloaded. So, I consider
the package functional, but don't really know what to do with the test
that fail because they have to fail.
Are there suggestions from your sides what to do about them?
On another note, when I just wanted to inject it all to salsa, it failed
to create the pristine-tar:
steffen@wurzel:~/Med/catch/broad-catch$ gbp import-orig --pristine-tar
../broad-catch_1.4.0.orig.tar.gz
What will be the source package name? [broad-catch]
What is the upstream version? [1.4.0]
gbp:info: Importing '../broad-catch_1.4.0.orig.tar.gz' to branch
'upstream'...
gbp:info: Source package is broad-catch
gbp:info: Upstream version is 1.4.0
gbp:error: Import of ../broad-catch_1.4.0.orig.tar.gz failed: Error
running git add: git-lfs filter-process: 1: git-lfs: not found
fatal: the remote end hung up unexpectedly
gbp:error: Error detected, Will roll back changes.
gbp:info: Rolling back branch 'upstream' by deleting it
gbp:error: Rolled back changes after import error.
And with git-lsf installed this does not look too different as
gbp:info: Importing '../broad-catch_1.4.0.orig.tar.gz' to branch
'upstream'...
gbp:info: Source package is broad-catch
gbp:info: Upstream version is 1.4.0
gbp:error: Import of ../broad-catch_1.4.0.orig.tar.gz failed: Error
running git reset: Downloading
catch/datasets/data/achimota_rubulavirus_1.fasta.gz (5.2 KB)
Error downloading object:
catch/datasets/data/achimota_rubulavirus_1.fasta.gz (895bdf9): Smudge
error: Error downloading
catch/datasets/data/achimota_rubulavirus_1.fasta.gz
(895bdf954b08626bc420f660693aa13fce85523743f67bbcdfbca65821f8b912):
batch request: missing protocol: ""
Errors logged to
/home/steffen/Med/catch/broad-catch/.git/lfs/logs/20210727T172624.851291063.log
Use `git lfs logs last` to view the log.
error: external filter 'git-lfs filter-process' failed
fatal: catch/datasets/data/achimota_rubulavirus_1.fasta.gz: smudge
filter lfs failed
gbp:error: Error detected, Will roll back changes.
gbp:info: Rolling back branch 'upstream' by deleting it
gbp:info: Rolling back branch 'pristine-tar' by deleting it
gbp:info: Rolling back tag 'upstream/1.4.0' by deleting it
gbp:info: Rolling back branch 'master' by deleting it
gbp:error: Automatic rollback failed [('master', 'branch', 'delete',
None, GitRepositoryError("Can't delete the branch you're on"))]
gbp:error: Clean up manually and please report a bug: [('master',
'branch', 'delete', None, GitRepositoryError("Can't delete the branch
you're on"))]
That file is small
$ du -sh catch/datasets/data/achimota_rubulavirus_1.fasta.gz
8.5K catch/datasets/data/achimota_rubulavirus_1.fasta.gz
so there is no need for git-lsf in the first place, right?
Any idea?
Thanks,
Steffen
======================================================================
ERROR: test_n_string
(catch.filter.tests.test_candidate_probes.TestCandidateProbesOnEbolaZaire)
Test that no probes have a string of two or more 'N's.
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/home/steffen/Med/catch/catch-1.4.0/.pybuild/cpython3_3.9_catch/build/catch/filter/tests/test_candidate_probes.py",
line 144, in setUp
for gnm in seq_io.read_dataset_genomes(zaire_ebolavirus)]
File
"/home/steffen/Med/catch/catch-1.4.0/.pybuild/cpython3_3.9_catch/build/catch/utils/seq_io.py",
line 71, in read_dataset_genomes
seqs = list(read_fasta(fn).values())
File
"/home/steffen/Med/catch/catch-1.4.0/.pybuild/cpython3_3.9_catch/build/catch/utils/seq_io.py",
line 152, in read_fasta
with gzip.open(fn, 'rt') as f:
File "/usr/lib/python3.9/gzip.py", line 58, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/usr/lib/python3.9/gzip.py", line 173, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory:
'/home/steffen/Med/catch/catch-1.4.0/.pybuild/cpython3_3.9_catch/build/catch/datasets/data/zaire_ebolavirus.fasta.gz'
======================================================================
ERROR: test_probe_count
(catch.filter.tests.test_candidate_probes.TestCandidateProbesOnEbolaZaire)
Test that probe counts are in roughly a correct ratio.
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/home/steffen/Med/catch/catch-1.4.0/.pybuild/cpython3_3.9_catch/build/catch/filter/tests/test_candidate_probes.py",
line 144, in setUp
for gnm in seq_io.read_dataset_genomes(zaire_ebolavirus)]
File
"/home/steffen/Med/catch/catch-1.4.0/.pybuild/cpython3_3.9_catch/build/catch/utils/seq_io.py",
line 71, in read_dataset_genomes
seqs = list(read_fasta(fn).values())
File
"/home/steffen/Med/catch/catch-1.4.0/.pybuild/cpython3_3.9_catch/build/catch/utils/seq_io.py",
line 152, in read_fasta
with gzip.open(fn, 'rt') as f:
File "/usr/lib/python3.9/gzip.py", line 58, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/usr/lib/python3.9/gzip.py", line 173, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory:
'/home/steffen/Med/catch/catch-1.4.0/.pybuild/cpython3_3.9_catch/build/catch/datasets/data/zaire_ebolavirus.fasta.gz'
======================================================================
ERROR: test_probe_length
(catch.filter.tests.test_candidate_probes.TestCandidateProbesOnEbolaZaire)
Test that all probes are the correct length.
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/home/steffen/Med/catch/catch-1.4.0/.pybuild/cpython3_3.9_catch/build/catch/filter/tests/test_candidate_probes.py",
line 144, in setUp
for gnm in seq_io.read_dataset_genomes(zaire_ebolavirus)]
File
"/home/steffen/Med/catch/catch-1.4.0/.pybuild/cpython3_3.9_catch/build/catch/utils/seq_io.py",
line 71, in read_dataset_genomes
seqs = list(read_fasta(fn).values())
File
"/home/steffen/Med/catch/catch-1.4.0/.pybuild/cpython3_3.9_catch/build/catch/utils/seq_io.py",
line 152, in read_fasta
with gzip.open(fn, 'rt') as f:
File "/usr/lib/python3.9/gzip.py", line 58, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/usr/lib/python3.9/gzip.py", line 173, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory:
'/home/steffen/Med/catch/catch-1.4.0/.pybuild/cpython3_3.9_catch/build/catch/datasets/data/zaire_ebolavirus.fasta.gz'
======================================================================
ERROR: test_custom_cover_range_fn
(catch.filter.tests.test_set_cover_filter.TestSetCoverFilter)
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/home/steffen/Med/catch/catch-1.4.0/.pybuild/cpython3_3.9_catch/build/catch/filter/tests/test_set_cover_filter.py",
line 560, in test_custom_cover_range_fn
f = scf.SetCoverFilter(0, 0,
File
"/home/steffen/Med/catch/catch-1.4.0/.pybuild/cpython3_3.9_catch/build/catch/filter/set_cover_filter.py",
line 175, in __init__
self.cover_range_fn = dynamic_load.load_function_from_path(
File
"/home/steffen/Med/catch/catch-1.4.0/.pybuild/cpython3_3.9_catch/build/catch/utils/dynamic_load.py",
line 49, in load_function_from_path
module = load_module_from_path(path)
File
"/home/steffen/Med/catch/catch-1.4.0/.pybuild/cpython3_3.9_catch/build/catch/utils/dynamic_load.py",
line 30, in load_module_from_path
spec.loader.exec_module(module)
File "<frozen importlib._bootstrap_external>", line 786, in exec_module
File "<frozen importlib._bootstrap_external>", line 922, in get_code
File "<frozen importlib._bootstrap_external>", line 979, in get_data
FileNotFoundError: [Errno 2] No such file or directory:
'/home/steffen/Med/catch/catch-1.4.0/.pybuild/cpython3_3.9_catch/build/catch/filter/tests/input/custom_cover_range_fn.py'
======================================================================
ERROR: test_higher_dimensional_search_vwafr_too_small_counts
(catch.pool.tests.test_param_search.TestSearchFunctions)
Integration test with the V-WAfr probe set data.
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/home/steffen/Med/catch/catch-1.4.0/.pybuild/cpython3_3.9_catch/build/catch/pool/tests/test_param_search.py",
line 95, in setUp
table_vall = pool_probes_io.read_table_of_probe_counts(fn_vall)
File
"/home/steffen/Med/catch/catch-1.4.0/.pybuild/cpython3_3.9_catch/build/catch/utils/pool_probes_io.py",
line 32, in read_table_of_probe_counts
with open(fn) as f:
FileNotFoundError: [Errno 2] No such file or directory:
'/home/steffen/Med/catch/catch-1.4.0/.pybuild/cpython3_3.9_catch/build/catch/pool/tests/input/num-probes.V-All.201606.tsv'
======================================================================
ERROR: test_higher_dimensional_search_vwafr_typical_counts
(catch.pool.tests.test_param_search.TestSearchFunctions)
Integration test with the V-WAfr probe set data.
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/home/steffen/Med/catch/catch-1.4.0/.pybuild/cpython3_3.9_catch/build/catch/pool/tests/test_param_search.py",
line 95, in setUp
table_vall = pool_probes_io.read_table_of_probe_counts(fn_vall)
File
"/home/steffen/Med/catch/catch-1.4.0/.pybuild/cpython3_3.9_catch/build/catch/utils/pool_probes_io.py",
line 32, in read_table_of_probe_counts
with open(fn) as f:
FileNotFoundError: [Errno 2] No such file or directory:
'/home/steffen/Med/catch/catch-1.4.0/.pybuild/cpython3_3.9_catch/build/catch/pool/tests/input/num-probes.V-All.201606.tsv'
======================================================================
ERROR: test_higher_dimensional_search_vwafr_with_third_param
(catch.pool.tests.test_param_search.TestSearchFunctions)
Integration test with the V-WAfr probe set data.
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/home/steffen/Med/catch/catch-1.4.0/.pybuild/cpython3_3.9_catch/build/catch/pool/tests/test_param_search.py",
line 95, in setUp
table_vall = pool_probes_io.read_table_of_probe_counts(fn_vall)
File
"/home/steffen/Med/catch/catch-1.4.0/.pybuild/cpython3_3.9_catch/build/catch/utils/pool_probes_io.py",
line 32, in read_table_of_probe_counts
with open(fn) as f:
FileNotFoundError: [Errno 2] No such file or directory:
'/home/steffen/Med/catch/catch-1.4.0/.pybuild/cpython3_3.9_catch/build/catch/pool/tests/input/num-probes.V-All.201606.tsv'
======================================================================
ERROR: test_standard_search_vwafr_high_count
(catch.pool.tests.test_param_search.TestSearchFunctions)
Integration test with the V-WAfr probe set data.
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/home/steffen/Med/catch/catch-1.4.0/.pybuild/cpython3_3.9_catch/build/catch/pool/tests/test_param_search.py",
line 95, in setUp
table_vall = pool_probes_io.read_table_of_probe_counts(fn_vall)
File
"/home/steffen/Med/catch/catch-1.4.0/.pybuild/cpython3_3.9_catch/build/catch/utils/pool_probes_io.py",
line 32, in read_table_of_probe_counts
with open(fn) as f:
FileNotFoundError: [Errno 2] No such file or directory:
'/home/steffen/Med/catch/catch-1.4.0/.pybuild/cpython3_3.9_catch/build/catch/pool/tests/input/num-probes.V-All.201606.tsv'
======================================================================
ERROR: test_standard_search_vwafr_too_small_counts
(catch.pool.tests.test_param_search.TestSearchFunctions)
Integration test with the V-WAfr probe set data.
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/home/steffen/Med/catch/catch-1.4.0/.pybuild/cpython3_3.9_catch/build/catch/pool/tests/test_param_search.py",
line 95, in setUp
table_vall = pool_probes_io.read_table_of_probe_counts(fn_vall)
File
"/home/steffen/Med/catch/catch-1.4.0/.pybuild/cpython3_3.9_catch/build/catch/utils/pool_probes_io.py",
line 32, in read_table_of_probe_counts
with open(fn) as f:
FileNotFoundError: [Errno 2] No such file or directory:
'/home/steffen/Med/catch/catch-1.4.0/.pybuild/cpython3_3.9_catch/build/catch/pool/tests/input/num-probes.V-All.201606.tsv'
======================================================================
ERROR: test_standard_search_vwafr_typical_counts
(catch.pool.tests.test_param_search.TestSearchFunctions)
Integration test with the V-WAfr probe set data.
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/home/steffen/Med/catch/catch-1.4.0/.pybuild/cpython3_3.9_catch/build/catch/pool/tests/test_param_search.py",
line 95, in setUp
table_vall = pool_probes_io.read_table_of_probe_counts(fn_vall)
File
"/home/steffen/Med/catch/catch-1.4.0/.pybuild/cpython3_3.9_catch/build/catch/utils/pool_probes_io.py",
line 32, in read_table_of_probe_counts
with open(fn) as f:
FileNotFoundError: [Errno 2] No such file or directory:
'/home/steffen/Med/catch/catch-1.4.0/.pybuild/cpython3_3.9_catch/build/catch/pool/tests/input/num-probes.V-All.201606.tsv'
======================================================================
ERROR: test_standard_search_vwafr_with_coefficients
(catch.pool.tests.test_param_search.TestSearchFunctions)
Integration test with the V-WAfr probe set data.
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/home/steffen/Med/catch/catch-1.4.0/.pybuild/cpython3_3.9_catch/build/catch/pool/tests/test_param_search.py",
line 95, in setUp
table_vall = pool_probes_io.read_table_of_probe_counts(fn_vall)
File
"/home/steffen/Med/catch/catch-1.4.0/.pybuild/cpython3_3.9_catch/build/catch/utils/pool_probes_io.py",
line 32, in read_table_of_probe_counts
with open(fn) as f:
FileNotFoundError: [Errno 2] No such file or directory:
'/home/steffen/Med/catch/catch-1.4.0/.pybuild/cpython3_3.9_catch/build/catch/pool/tests/input/num-probes.V-All.201606.tsv'
======================================================================
ERROR: test_standard_search_vwafr_with_dataset_weights
(catch.pool.tests.test_param_search.TestSearchFunctions)
Integration test with the V-Wafr probe set data.
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/home/steffen/Med/catch/catch-1.4.0/.pybuild/cpython3_3.9_catch/build/catch/pool/tests/test_param_search.py",
line 95, in setUp
table_vall = pool_probes_io.read_table_of_probe_counts(fn_vall)
File
"/home/steffen/Med/catch/catch-1.4.0/.pybuild/cpython3_3.9_catch/build/catch/utils/pool_probes_io.py",
line 32, in read_table_of_probe_counts
with open(fn) as f:
FileNotFoundError: [Errno 2] No such file or directory:
'/home/steffen/Med/catch/catch-1.4.0/.pybuild/cpython3_3.9_catch/build/catch/pool/tests/input/num-probes.V-All.201606.tsv'
======================================================================
ERROR: test_load_function
(catch.utils.tests.test_dynamic_load.TestLoadFunction)
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/home/steffen/Med/catch/catch-1.4.0/.pybuild/cpython3_3.9_catch/build/catch/utils/tests/test_dynamic_load.py",
line 46, in test_load_function
sum_fn = dynamic_load.load_function_from_path(self.module_path, 'sum')
File
"/home/steffen/Med/catch/catch-1.4.0/.pybuild/cpython3_3.9_catch/build/catch/utils/dynamic_load.py",
line 49, in load_function_from_path
module = load_module_from_path(path)
File
"/home/steffen/Med/catch/catch-1.4.0/.pybuild/cpython3_3.9_catch/build/catch/utils/dynamic_load.py",
line 30, in load_module_from_path
spec.loader.exec_module(module)
File "<frozen importlib._bootstrap_external>", line 786, in exec_module
File "<frozen importlib._bootstrap_external>", line 922, in get_code
File "<frozen importlib._bootstrap_external>", line 979, in get_data
FileNotFoundError: [Errno 2] No such file or directory:
'/home/steffen/Med/catch/catch-1.4.0/.pybuild/cpython3_3.9_catch/build/catch/utils/tests/input/test_module.py'
======================================================================
ERROR: test_load_module (catch.utils.tests.test_dynamic_load.TestLoadModule)
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/home/steffen/Med/catch/catch-1.4.0/.pybuild/cpython3_3.9_catch/build/catch/utils/tests/test_dynamic_load.py",
line 24, in test_load_module
module = dynamic_load.load_module_from_path(self.module_path)
File
"/home/steffen/Med/catch/catch-1.4.0/.pybuild/cpython3_3.9_catch/build/catch/utils/dynamic_load.py",
line 30, in load_module_from_path
spec.loader.exec_module(module)
File "<frozen importlib._bootstrap_external>", line 786, in exec_module
File "<frozen importlib._bootstrap_external>", line 922, in get_code
File "<frozen importlib._bootstrap_external>", line 979, in get_data
FileNotFoundError: [Errno 2] No such file or directory:
'/home/steffen/Med/catch/catch-1.4.0/.pybuild/cpython3_3.9_catch/build/catch/utils/tests/input/test_module.py'
======================================================================
ERROR: test_construct_fasta_for_taxid
(catch.utils.tests.test_ncbi_neighbors.TestConstructFastaFromTaxIDIntegration)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/lib/python3.9/urllib/request.py", line 1346, in do_open
h.request(req.get_method(), req.selector, req.data, headers,
File "/usr/lib/python3.9/http/client.py", line 1255, in request
self._send_request(method, url, body, headers, encode_chunked)
File "/usr/lib/python3.9/http/client.py", line 1301, in _send_request
self.endheaders(body, encode_chunked=encode_chunked)
File "/usr/lib/python3.9/http/client.py", line 1250, in endheaders
self._send_output(message_body, encode_chunked=encode_chunked)
File "/usr/lib/python3.9/http/client.py", line 1010, in _send_output
self.send(msg)
File "/usr/lib/python3.9/http/client.py", line 950, in send
self.connect()
File "/usr/lib/python3.9/http/client.py", line 1417, in connect
super().connect()
File "/usr/lib/python3.9/http/client.py", line 921, in connect
self.sock = self._create_connection(
File "/usr/lib/python3.9/socket.py", line 843, in create_connection
raise err
File "/usr/lib/python3.9/socket.py", line 831, in create_connection
sock.connect(sa)
ConnectionRefusedError: [Errno 111] Connection refused
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/home/steffen/Med/catch/catch-1.4.0/.pybuild/cpython3_3.9_catch/build/catch/utils/tests/test_ncbi_neighbors.py",
line 241, in test_construct_fasta_for_taxid
fasta_tf = nn.construct_fasta_for_taxid(TAXIDS['ZIKV'])
File
"/home/steffen/Med/catch/catch-1.4.0/.pybuild/cpython3_3.9_catch/build/catch/utils/ncbi_neighbors.py",
line 442, in construct_fasta_for_taxid
neighbors = construct_neighbors(taxid)
File
"/home/steffen/Med/catch/catch-1.4.0/.pybuild/cpython3_3.9_catch/build/catch/utils/ncbi_neighbors.py",
line 270, in construct_neighbors
for line in fetch_neighbors_table(taxid):
File
"/home/steffen/Med/catch/catch-1.4.0/.pybuild/cpython3_3.9_catch/build/catch/utils/ncbi_neighbors.py",
line 108, in fetch_neighbors_table
r = urlopen_with_tries(url)
File
"/home/steffen/Med/catch/catch-1.4.0/.pybuild/cpython3_3.9_catch/build/catch/utils/ncbi_neighbors.py",
line 53, in urlopen_with_tries
r = urllib.request.urlopen(url)
File "/usr/lib/python3.9/urllib/request.py", line 214, in urlopen
return opener.open(url, data, timeout)
File "/usr/lib/python3.9/urllib/request.py", line 517, in open
response = self._open(req, data)
File "/usr/lib/python3.9/urllib/request.py", line 534, in _open
result = self._call_chain(self.handle_open, protocol, protocol +
File "/usr/lib/python3.9/urllib/request.py", line 494, in _call_chain
result = func(*args)
File "/usr/lib/python3.9/urllib/request.py", line 1389, in https_open
return self.do_open(http.client.HTTPSConnection, req,
File "/usr/lib/python3.9/urllib/request.py", line 1349, in do_open
raise URLError(err)
urllib.error.URLError: <urlopen error [Errno 111] Connection refused>
======================================================================
ERROR: test_construct_neighbors_for_influenza
(catch.utils.tests.test_ncbi_neighbors.TestConstructNeighborsIntegration)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/lib/python3.9/urllib/request.py", line 1563, in ftp_open
fw = self.connect_ftp(user, passwd, host, port, dirs, req.timeout)
File "/usr/lib/python3.9/urllib/request.py", line 1584, in connect_ftp
return ftpwrapper(user, passwd, host, port, dirs, timeout,
File "/usr/lib/python3.9/urllib/request.py", line 2405, in __init__
self.init()
File "/usr/lib/python3.9/urllib/request.py", line 2414, in init
self.ftp.connect(self.host, self.port, self.timeout)
File "/usr/lib/python3.9/ftplib.py", line 156, in connect
self.sock = socket.create_connection((self.host, self.port),
self.timeout,
File "/usr/lib/python3.9/socket.py", line 843, in create_connection
raise err
File "/usr/lib/python3.9/socket.py", line 831, in create_connection
sock.connect(sa)
TimeoutError: [Errno 110] Connection timed out
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/home/steffen/Med/catch/catch-1.4.0/.pybuild/cpython3_3.9_catch/build/catch/utils/tests/test_ncbi_neighbors.py",
line 172, in test_construct_neighbors_for_influenza
neighbors = nn.construct_influenza_genome_neighbors(TAXIDS['IAV'])
File
"/home/steffen/Med/catch/catch-1.4.0/.pybuild/cpython3_3.9_catch/build/catch/utils/ncbi_neighbors.py",
line 371, in construct_influenza_genome_neighbors
for line in fetch_influenza_genomes_table(species_name, database):
File
"/home/steffen/Med/catch/catch-1.4.0/.pybuild/cpython3_3.9_catch/build/catch/utils/ncbi_neighbors.py",
line 148, in fetch_influenza_genomes_table
r = urlopen_with_tries(url)
File
"/home/steffen/Med/catch/catch-1.4.0/.pybuild/cpython3_3.9_catch/build/catch/utils/ncbi_neighbors.py",
line 53, in urlopen_with_tries
r = urllib.request.urlopen(url)
File "/usr/lib/python3.9/urllib/request.py", line 214, in urlopen
return opener.open(url, data, timeout)
File "/usr/lib/python3.9/urllib/request.py", line 517, in open
response = self._open(req, data)
File "/usr/lib/python3.9/urllib/request.py", line 534, in _open
result = self._call_chain(self.handle_open, protocol, protocol +
File "/usr/lib/python3.9/urllib/request.py", line 494, in _call_chain
result = func(*args)
File "/usr/lib/python3.9/urllib/request.py", line 1581, in ftp_open
raise exc.with_traceback(sys.exc_info()[2])
File "/usr/lib/python3.9/urllib/request.py", line 1563, in ftp_open
fw = self.connect_ftp(user, passwd, host, port, dirs, req.timeout)
File "/usr/lib/python3.9/urllib/request.py", line 1584, in connect_ftp
return ftpwrapper(user, passwd, host, port, dirs, timeout,
File "/usr/lib/python3.9/urllib/request.py", line 2405, in __init__
self.init()
File "/usr/lib/python3.9/urllib/request.py", line 2414, in init
self.ftp.connect(self.host, self.port, self.timeout)
File "/usr/lib/python3.9/ftplib.py", line 156, in connect
self.sock = socket.create_connection((self.host, self.port),
self.timeout,
File "/usr/lib/python3.9/socket.py", line 843, in create_connection
raise err
File "/usr/lib/python3.9/socket.py", line 831, in create_connection
sock.connect(sa)
urllib.error.URLError: <urlopen error ftp error: TimeoutError(110,
'Connection timed out')>
======================================================================
ERROR: test_construct_neighbors_for_zika
(catch.utils.tests.test_ncbi_neighbors.TestConstructNeighborsIntegration)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/lib/python3.9/urllib/request.py", line 1346, in do_open
h.request(req.get_method(), req.selector, req.data, headers,
File "/usr/lib/python3.9/http/client.py", line 1255, in request
self._send_request(method, url, body, headers, encode_chunked)
File "/usr/lib/python3.9/http/client.py", line 1301, in _send_request
self.endheaders(body, encode_chunked=encode_chunked)
File "/usr/lib/python3.9/http/client.py", line 1250, in endheaders
self._send_output(message_body, encode_chunked=encode_chunked)
File "/usr/lib/python3.9/http/client.py", line 1010, in _send_output
self.send(msg)
File "/usr/lib/python3.9/http/client.py", line 950, in send
self.connect()
File "/usr/lib/python3.9/http/client.py", line 1417, in connect
super().connect()
File "/usr/lib/python3.9/http/client.py", line 921, in connect
self.sock = self._create_connection(
File "/usr/lib/python3.9/socket.py", line 843, in create_connection
raise err
File "/usr/lib/python3.9/socket.py", line 831, in create_connection
sock.connect(sa)
ConnectionRefusedError: [Errno 111] Connection refused
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/home/steffen/Med/catch/catch-1.4.0/.pybuild/cpython3_3.9_catch/build/catch/utils/tests/test_ncbi_neighbors.py",
line 150, in test_construct_neighbors_for_zika
neighbors = nn.construct_neighbors(TAXIDS['ZIKV'])
File
"/home/steffen/Med/catch/catch-1.4.0/.pybuild/cpython3_3.9_catch/build/catch/utils/ncbi_neighbors.py",
line 270, in construct_neighbors
for line in fetch_neighbors_table(taxid):
File
"/home/steffen/Med/catch/catch-1.4.0/.pybuild/cpython3_3.9_catch/build/catch/utils/ncbi_neighbors.py",
line 108, in fetch_neighbors_table
r = urlopen_with_tries(url)
File
"/home/steffen/Med/catch/catch-1.4.0/.pybuild/cpython3_3.9_catch/build/catch/utils/ncbi_neighbors.py",
line 53, in urlopen_with_tries
r = urllib.request.urlopen(url)
File "/usr/lib/python3.9/urllib/request.py", line 214, in urlopen
return opener.open(url, data, timeout)
File "/usr/lib/python3.9/urllib/request.py", line 517, in open
response = self._open(req, data)
File "/usr/lib/python3.9/urllib/request.py", line 534, in _open
result = self._call_chain(self.handle_open, protocol, protocol +
File "/usr/lib/python3.9/urllib/request.py", line 494, in _call_chain
result = func(*args)
File "/usr/lib/python3.9/urllib/request.py", line 1389, in https_open
return self.do_open(http.client.HTTPSConnection, req,
File "/usr/lib/python3.9/urllib/request.py", line 1349, in do_open
raise URLError(err)
urllib.error.URLError: <urlopen error [Errno 111] Connection refused>
======================================================================
ERROR: test_fetch_fastas
(catch.utils.tests.test_ncbi_neighbors.TestFetchFastasFromAccessionsIntegration)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/lib/python3.9/urllib/request.py", line 1346, in do_open
h.request(req.get_method(), req.selector, req.data, headers,
File "/usr/lib/python3.9/http/client.py", line 1255, in request
self._send_request(method, url, body, headers, encode_chunked)
File "/usr/lib/python3.9/http/client.py", line 1301, in _send_request
self.endheaders(body, encode_chunked=encode_chunked)
File "/usr/lib/python3.9/http/client.py", line 1250, in endheaders
self._send_output(message_body, encode_chunked=encode_chunked)
File "/usr/lib/python3.9/http/client.py", line 1010, in _send_output
self.send(msg)
File "/usr/lib/python3.9/http/client.py", line 950, in send
self.connect()
File "/usr/lib/python3.9/http/client.py", line 1417, in connect
super().connect()
File "/usr/lib/python3.9/http/client.py", line 921, in connect
self.sock = self._create_connection(
File "/usr/lib/python3.9/socket.py", line 843, in create_connection
raise err
File "/usr/lib/python3.9/socket.py", line 831, in create_connection
sock.connect(sa)
ConnectionRefusedError: [Errno 111] Connection refused
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/home/steffen/Med/catch/catch-1.4.0/.pybuild/cpython3_3.9_catch/build/catch/utils/tests/test_ncbi_neighbors.py",
line 205, in test_fetch_fastas
fasta_tf = nn.fetch_fastas(ZIKV_ACCS)
File
"/home/steffen/Med/catch/catch-1.4.0/.pybuild/cpython3_3.9_catch/build/catch/utils/ncbi_neighbors.py",
line 206, in fetch_fastas
r = urlopen_with_tries(url)
File
"/home/steffen/Med/catch/catch-1.4.0/.pybuild/cpython3_3.9_catch/build/catch/utils/ncbi_neighbors.py",
line 53, in urlopen_with_tries
r = urllib.request.urlopen(url)
File "/usr/lib/python3.9/urllib/request.py", line 214, in urlopen
return opener.open(url, data, timeout)
File "/usr/lib/python3.9/urllib/request.py", line 517, in open
response = self._open(req, data)
File "/usr/lib/python3.9/urllib/request.py", line 534, in _open
result = self._call_chain(self.handle_open, protocol, protocol +
File "/usr/lib/python3.9/urllib/request.py", line 494, in _call_chain
result = func(*args)
File "/usr/lib/python3.9/urllib/request.py", line 1389, in https_open
return self.do_open(http.client.HTTPSConnection, req,
File "/usr/lib/python3.9/urllib/request.py", line 1349, in do_open
raise URLError(err)
urllib.error.URLError: <urlopen error [Errno 111] Connection refused>
======================================================================
ERROR: test_multi_chr_dataset
(catch.utils.tests.test_seq_io.TestDatasetGenomeRead)
Tests that the lassa_mammarenavirus dataset can be read.
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/home/steffen/Med/catch/catch-1.4.0/.pybuild/cpython3_3.9_catch/build/catch/utils/tests/test_seq_io.py",
line 98, in test_multi_chr_dataset
genomes = seq_io.read_dataset_genomes(lassa_mammarenavirus)
File
"/home/steffen/Med/catch/catch-1.4.0/.pybuild/cpython3_3.9_catch/build/catch/utils/seq_io.py",
line 54, in read_dataset_genomes
seq_map = read_fasta(fn)
File
"/home/steffen/Med/catch/catch-1.4.0/.pybuild/cpython3_3.9_catch/build/catch/utils/seq_io.py",
line 152, in read_fasta
with gzip.open(fn, 'rt') as f:
File "/usr/lib/python3.9/gzip.py", line 58, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/usr/lib/python3.9/gzip.py", line 173, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory:
'/home/steffen/Med/catch/catch-1.4.0/.pybuild/cpython3_3.9_catch/build/catch/datasets/data/lassa_mammarenavirus.fasta.gz'
======================================================================
ERROR: test_single_chr_dataset
(catch.utils.tests.test_seq_io.TestDatasetGenomeRead)
Tests that the genomes obtained from reading the
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/home/steffen/Med/catch/catch-1.4.0/.pybuild/cpython3_3.9_catch/build/catch/utils/tests/test_seq_io.py",
line 83, in test_single_chr_dataset
genomes = seq_io.read_dataset_genomes(zaire_ebolavirus)
File
"/home/steffen/Med/catch/catch-1.4.0/.pybuild/cpython3_3.9_catch/build/catch/utils/seq_io.py",
line 71, in read_dataset_genomes
seqs = list(read_fasta(fn).values())
File
"/home/steffen/Med/catch/catch-1.4.0/.pybuild/cpython3_3.9_catch/build/catch/utils/seq_io.py",
line 152, in read_fasta
with gzip.open(fn, 'rt') as f:
File "/usr/lib/python3.9/gzip.py", line 58, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/usr/lib/python3.9/gzip.py", line 173, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory:
'/home/steffen/Med/catch/catch-1.4.0/.pybuild/cpython3_3.9_catch/build/catch/datasets/data/zaire_ebolavirus.fasta.gz'
======================================================================
ERROR: test_generator
(catch.utils.tests.test_seq_io.TestEbolaZaireFASTARead)
Test that the generator works correctly.
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/home/steffen/Med/catch/catch-1.4.0/.pybuild/cpython3_3.9_catch/build/catch/utils/tests/test_seq_io.py",
line 26, in setUp
self.seqs_map = seq_io.read_fasta(zaire_ebolavirus.fasta_paths[0])
File
"/home/steffen/Med/catch/catch-1.4.0/.pybuild/cpython3_3.9_catch/build/catch/utils/seq_io.py",
line 152, in read_fasta
with gzip.open(fn, 'rt') as f:
File "/usr/lib/python3.9/gzip.py", line 58, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/usr/lib/python3.9/gzip.py", line 173, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory:
'/home/steffen/Med/catch/catch-1.4.0/.pybuild/cpython3_3.9_catch/build/catch/datasets/data/zaire_ebolavirus.fasta.gz'
======================================================================
ERROR: test_num_seqs (catch.utils.tests.test_seq_io.TestEbolaZaireFASTARead)
Test that there are 1525 sequences.
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/home/steffen/Med/catch/catch-1.4.0/.pybuild/cpython3_3.9_catch/build/catch/utils/tests/test_seq_io.py",
line 26, in setUp
self.seqs_map = seq_io.read_fasta(zaire_ebolavirus.fasta_paths[0])
File
"/home/steffen/Med/catch/catch-1.4.0/.pybuild/cpython3_3.9_catch/build/catch/utils/seq_io.py",
line 152, in read_fasta
with gzip.open(fn, 'rt') as f:
File "/usr/lib/python3.9/gzip.py", line 58, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/usr/lib/python3.9/gzip.py", line 173, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory:
'/home/steffen/Med/catch/catch-1.4.0/.pybuild/cpython3_3.9_catch/build/catch/datasets/data/zaire_ebolavirus.fasta.gz'
======================================================================
ERROR: test_seq_content
(catch.utils.tests.test_seq_io.TestEbolaZaireFASTARead)
Test that all sequences contain valid characters.
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/home/steffen/Med/catch/catch-1.4.0/.pybuild/cpython3_3.9_catch/build/catch/utils/tests/test_seq_io.py",
line 26, in setUp
self.seqs_map = seq_io.read_fasta(zaire_ebolavirus.fasta_paths[0])
File
"/home/steffen/Med/catch/catch-1.4.0/.pybuild/cpython3_3.9_catch/build/catch/utils/seq_io.py",
line 152, in read_fasta
with gzip.open(fn, 'rt') as f:
File "/usr/lib/python3.9/gzip.py", line 58, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/usr/lib/python3.9/gzip.py", line 173, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory:
'/home/steffen/Med/catch/catch-1.4.0/.pybuild/cpython3_3.9_catch/build/catch/datasets/data/zaire_ebolavirus.fasta.gz'
======================================================================
ERROR: test_seq_length
(catch.utils.tests.test_seq_io.TestEbolaZaireFASTARead)
Test that all sequences are of length 17-20 kbp.
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/home/steffen/Med/catch/catch-1.4.0/.pybuild/cpython3_3.9_catch/build/catch/utils/tests/test_seq_io.py",
line 26, in setUp
self.seqs_map = seq_io.read_fasta(zaire_ebolavirus.fasta_paths[0])
File
"/home/steffen/Med/catch/catch-1.4.0/.pybuild/cpython3_3.9_catch/build/catch/utils/seq_io.py",
line 152, in read_fasta
with gzip.open(fn, 'rt') as f:
File "/usr/lib/python3.9/gzip.py", line 58, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/usr/lib/python3.9/gzip.py", line 173, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory:
'/home/steffen/Med/catch/catch-1.4.0/.pybuild/cpython3_3.9_catch/build/catch/datasets/data/zaire_ebolavirus.fasta.gz'
----------------------------------------------------------------------
Ran 297 tests in 822.901s
FAILED (errors=24)
E: pybuild pybuild:353: test: plugin distutils failed with: exit code=1:
cd
/home/steffen/Med/catch/catch-1.4.0/.pybuild/cpython3_3.9_catch/build;
python3.9 -m unittest discover -v
dh_auto_test: error: pybuild --test -i python{version} -p 3.9 returned
exit code 13
make: *** [debian/rules:9: binary] Error 255
dpkg-buildpackage: error: debian/rules binary subprocess returned exit
status 2
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