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chore: Also fix the NCBI URL in the tests
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Signed-off-by: Kai Blin <kblin@biosustain.dtu.dk>
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@kblin
kblin committed Jul 3, 2024
1 parent a57c5b2 commit a5d8caf
Showing 1 changed file with 19 additions and 19 deletions.
38 changes: 19 additions & 19 deletions tests/test_core.py
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Original file line number Diff line number Diff line change
Expand Up @@ -107,7 +107,7 @@ def test_download_connection_err(monkeypatch, mocker):

def test_download(monkeypatch, mocker, req):
summary_contents = open(_get_file('partial_summary.txt'), 'r').read()
req.get('https://ftp.ncbi.nih.gov/genomes/refseq/bacteria/assembly_summary.txt',
req.get('https://ftp.ncbi.nlm.nih.gov/genomes/refseq/bacteria/assembly_summary.txt',
text=summary_contents)
mocker.spy(core, 'get_summary')
mocker.spy(core, 'parse_summary')
Expand All @@ -122,7 +122,7 @@ def test_download_metadata(monkeypatch, mocker, req, tmpdir):
"""Test creating the metadata file works."""
metadata_file = tmpdir.join('metadata.tsv')
summary_contents = open(_get_file('partial_summary.txt'), 'r').read()
req.get('https://ftp.ncbi.nih.gov/genomes/refseq/bacteria/assembly_summary.txt',
req.get('https://ftp.ncbi.nlm.nih.gov/genomes/refseq/bacteria/assembly_summary.txt',
text=summary_contents)
mocker.spy(core, 'get_summary')
mocker.spy(core, 'parse_summary')
Expand Down Expand Up @@ -166,7 +166,7 @@ def test_metadata_fill_multi(req, tmpdir):

def test_download_complete(monkeypatch, mocker, req):
summary_contents = open(_get_file('assembly_status.txt'), 'r').read()
req.get('https://ftp.ncbi.nih.gov/genomes/refseq/bacteria/assembly_summary.txt',
req.get('https://ftp.ncbi.nlm.nih.gov/genomes/refseq/bacteria/assembly_summary.txt',
text=summary_contents)
mocker.spy(core, 'get_summary')
mocker.spy(core, 'parse_summary')
Expand All @@ -181,7 +181,7 @@ def test_download_complete(monkeypatch, mocker, req):

def test_download_chromosome(monkeypatch, mocker, req):
summary_contents = open(_get_file('assembly_status.txt'), 'r').read()
req.get('https://ftp.ncbi.nih.gov/genomes/refseq/bacteria/assembly_summary.txt',
req.get('https://ftp.ncbi.nlm.nih.gov/genomes/refseq/bacteria/assembly_summary.txt',
text=summary_contents)
mocker.spy(core, 'get_summary')
mocker.spy(core, 'parse_summary')
Expand All @@ -196,7 +196,7 @@ def test_download_chromosome(monkeypatch, mocker, req):

def test_download_scaffold(monkeypatch, mocker, req):
summary_contents = open(_get_file('assembly_status.txt'), 'r').read()
req.get('https://ftp.ncbi.nih.gov/genomes/refseq/bacteria/assembly_summary.txt',
req.get('https://ftp.ncbi.nlm.nih.gov/genomes/refseq/bacteria/assembly_summary.txt',
text=summary_contents)
mocker.spy(core, 'get_summary')
mocker.spy(core, 'parse_summary')
Expand All @@ -211,7 +211,7 @@ def test_download_scaffold(monkeypatch, mocker, req):

def test_download_contig(monkeypatch, mocker, req):
summary_contents = open(_get_file('assembly_status.txt'), 'r').read()
req.get('https://ftp.ncbi.nih.gov/genomes/refseq/bacteria/assembly_summary.txt',
req.get('https://ftp.ncbi.nlm.nih.gov/genomes/refseq/bacteria/assembly_summary.txt',
text=summary_contents)
mocker.spy(core, 'get_summary')
mocker.spy(core, 'parse_summary')
Expand All @@ -226,7 +226,7 @@ def test_download_contig(monkeypatch, mocker, req):

def test_download_genus(monkeypatch, mocker, req):
summary_contents = open(_get_file('partial_summary.txt'), 'r').read()
req.get('https://ftp.ncbi.nih.gov/genomes/refseq/bacteria/assembly_summary.txt',
req.get('https://ftp.ncbi.nlm.nih.gov/genomes/refseq/bacteria/assembly_summary.txt',
text=summary_contents)
mocker.spy(core, 'get_summary')
mocker.spy(core, 'parse_summary')
Expand All @@ -242,7 +242,7 @@ def test_download_genus(monkeypatch, mocker, req):

def test_download_genus_lowercase(monkeypatch, mocker, req):
summary_contents = open(_get_file('partial_summary.txt'), 'r').read()
req.get('https://ftp.ncbi.nih.gov/genomes/refseq/bacteria/assembly_summary.txt',
req.get('https://ftp.ncbi.nlm.nih.gov/genomes/refseq/bacteria/assembly_summary.txt',
text=summary_contents)
mocker.spy(core, 'get_summary')
mocker.spy(core, 'parse_summary')
Expand All @@ -258,7 +258,7 @@ def test_download_genus_lowercase(monkeypatch, mocker, req):

def test_download_genus_fuzzy(monkeypatch, mocker, req):
summary_contents = open(_get_file('partial_summary.txt'), 'r').read()
req.get('https://ftp.ncbi.nih.gov/genomes/refseq/bacteria/assembly_summary.txt',
req.get('https://ftp.ncbi.nlm.nih.gov/genomes/refseq/bacteria/assembly_summary.txt',
text=summary_contents)
mocker.spy(core, 'get_summary')
mocker.spy(core, 'parse_summary')
Expand All @@ -274,7 +274,7 @@ def test_download_genus_fuzzy(monkeypatch, mocker, req):

def test_download_taxid(monkeypatch, mocker, req):
summary_contents = open(_get_file('partial_summary.txt'), 'r').read()
req.get('https://ftp.ncbi.nih.gov/genomes/refseq/bacteria/assembly_summary.txt',
req.get('https://ftp.ncbi.nlm.nih.gov/genomes/refseq/bacteria/assembly_summary.txt',
text=summary_contents)
mocker.spy(core, 'get_summary')
mocker.spy(core, 'parse_summary')
Expand All @@ -290,7 +290,7 @@ def test_download_taxid(monkeypatch, mocker, req):

def test_download_species_taxid(monkeypatch, mocker, req):
summary_contents = open(_get_file('partial_summary.txt'), 'r').read()
req.get('https://ftp.ncbi.nih.gov/genomes/refseq/bacteria/assembly_summary.txt',
req.get('https://ftp.ncbi.nlm.nih.gov/genomes/refseq/bacteria/assembly_summary.txt',
text=summary_contents)
mocker.spy(core, 'get_summary')
mocker.spy(core, 'parse_summary')
Expand All @@ -306,7 +306,7 @@ def test_download_species_taxid(monkeypatch, mocker, req):

def test_download_refseq_category(monkeypatch, mocker, req):
summary_contents = open(_get_file('assembly_status.txt'), 'r').read()
req.get('https://ftp.ncbi.nih.gov/genomes/refseq/bacteria/assembly_summary.txt',
req.get('https://ftp.ncbi.nlm.nih.gov/genomes/refseq/bacteria/assembly_summary.txt',
text=summary_contents)
mocker.spy(core, 'get_summary')
mocker.spy(core, 'parse_summary')
Expand All @@ -322,7 +322,7 @@ def test_download_refseq_category(monkeypatch, mocker, req):

def test_download_type_material(monkeypatch, mocker, req):
summary_contents = open(_get_file('type_material.txt'), 'r').read()
req.get('https://ftp.ncbi.nih.gov/genomes/refseq/bacteria/assembly_summary.txt',
req.get('https://ftp.ncbi.nlm.nih.gov/genomes/refseq/bacteria/assembly_summary.txt',
text=summary_contents)
print(summary_contents)
mocker.spy(core, 'get_summary')
Expand All @@ -339,7 +339,7 @@ def test_download_type_material(monkeypatch, mocker, req):

def test_download_type_material_no_match(monkeypatch, mocker, req):
summary_contents = open(_get_file('type_material.txt'), 'r').read()
req.get('https://ftp.ncbi.nih.gov/genomes/refseq/bacteria/assembly_summary.txt',
req.get('https://ftp.ncbi.nlm.nih.gov/genomes/refseq/bacteria/assembly_summary.txt',
text=summary_contents)
print(summary_contents)
mocker.spy(core, 'get_summary')
Expand All @@ -356,7 +356,7 @@ def test_get_summary(monkeypatch, req, tmpdir):
cache_dir = tmpdir.mkdir('cache')
monkeypatch.setattr(core, 'CACHE_DIR', str(cache_dir))
cache_file = cache_dir.join('refseq_bacteria_assembly_summary.txt')
req.get('https://ftp.ncbi.nih.gov/genomes/refseq/bacteria/assembly_summary.txt', text='test')
req.get('https://ftp.ncbi.nlm.nih.gov/genomes/refseq/bacteria/assembly_summary.txt', text='test')

ret = core.get_summary('refseq', 'bacteria', NgdConfig.get_default('uri'), False)
assert ret.read() == 'test'
Expand All @@ -366,7 +366,7 @@ def test_get_summary(monkeypatch, req, tmpdir):
assert ret.read() == 'test'
assert cache_file.check()

req.get('https://ftp.ncbi.nih.gov/genomes/refseq/bacteria/assembly_summary.txt', text='never read')
req.get('https://ftp.ncbi.nlm.nih.gov/genomes/refseq/bacteria/assembly_summary.txt', text='never read')
ret = core.get_summary('refseq', 'bacteria', NgdConfig.get_default('uri'), True)
assert ret.read() == 'test'

Expand All @@ -375,7 +375,7 @@ def test_get_summary_error_handling(monkeypatch, mocker, req, tmpdir):
"""Test get_summary error handling."""
cache_dir = tmpdir.join('cache')
monkeypatch.setattr(core, 'CACHE_DIR', str(cache_dir))
req.get('https://ftp.ncbi.nih.gov/genomes/refseq/bacteria/assembly_summary.txt', text='test')
req.get('https://ftp.ncbi.nlm.nih.gov/genomes/refseq/bacteria/assembly_summary.txt', text='test')

fake_makedirs = mocker.MagicMock(side_effect=OSError(13, "Permission denied"))
monkeypatch.setattr(os, 'makedirs', fake_makedirs)
Expand Down Expand Up @@ -588,8 +588,8 @@ def test_create_readable_dir_virus(tmpdir):


def test_grab_checksums_file(req):
req.get('https://ftp.ncbi.nih.gov/genomes/all/FAKE0.1/md5checksums.txt', text='test')
entry = {'ftp_path': 'ftp://ftp.ncbi.nih.gov/genomes/all/FAKE0.1'}
req.get('https://ftp.ncbi.nlm.nih.gov/genomes/all/FAKE0.1/md5checksums.txt', text='test')
entry = {'ftp_path': 'ftp://ftp.ncbi.nlm.nih.gov/genomes/all/FAKE0.1'}
ret = core.grab_checksums_file(entry)
assert ret == 'test'

Expand Down

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