def test_compare_corrupted_md5(delete_config):
chmdfile = "ref_prok_rep_genomes.05.tar.gz.md5"
create_mock_archives()
shutil.rmtree("md5_files")
G.create_directory("md5_files")
os.chdir(tmpdir)
for files in os.listdir(tmpdir):
if (
files.startswith("ref_prok_rep_genomes.05")
and "tar.gz" not in files
):
os.remove(files)
with open(chmdfile, "r") as f:
for line in f:
info = (
line.strip().split(" ")[0][0:-1] + "q67 " +
line.strip().split(" ")[1])
with open(chmdfile, "w") as f:
f.write(info)
getblastdb.download_from_ftp([chmdfile], delete_config)
check_part_five(outcome=True)
remove_tmp_db()
os.chdir("..")
if os.path.isdir(tmpdir):
shutil.rmtree(tmpdir)
def test_skipdownload_nomd5(delete_config):
create_mock_archives()
os.chdir(tmpdir)
chmdfile = "ref_prok_rep_genomes.05.tar.gz.md5"
refmd5 = os.path.join("md5_files", chmdfile)
if os.path.isfile(refmd5):
os.remove(refmd5)
getblastdb.download_from_ftp([chmdfile], delete_config)
check_part_five(outcome=True)
remove_tmp_db()
os.chdir("..")
if os.path.isdir(tmpdir):
shutil.rmtree(tmpdir)
def test_archiveextract(delete_config):
chmdfile = "ref_prok_rep_genomes.05.tar.gz.md5"
create_mock_archives()
os.chdir(tmpdir)
for files in os.listdir(tmpdir):
if (
files.startswith("ref_prok_rep_genomes.05")
and not files.endswith(".md5")
):
os.remove(files)
getblastdb.download_from_ftp([chmdfile], delete_config)
check_part_five(outcome=True)
assert os.path.isfile("ref_prok_rep_genomes.05.tar.gz") is False
remove_tmp_db()
os.chdir("..")
if os.path.isdir(tmpdir):
shutil.rmtree(tmpdir)
def test_skipdownload(delete_config):
create_mock_archives()
os.chdir(tmpdir)
chmdfile = "ref_prok_rep_genomes.05.tar.gz.md5"
with open(chmdfile, "r") as f:
for line in f:
info = (
line.strip().split(" ")[0][0:-1] + "k " +
line.strip().split(" ")[1])
with open(chmdfile, "w") as f:
f.write(info)
getblastdb.download_from_ftp([chmdfile], delete_config)
check_part_five(outcome=True)
remove_tmp_db()
os.chdir("..")
if os.path.isdir(tmpdir):
shutil.rmtree(tmpdir)
def test_compare_md5_files_witharchive(delete_config):
chmdfile = "ref_prok_rep_genomes.05.tar.gz.md5"
create_mock_archives()
os.chdir(tmpdir)
for files in os.listdir(tmpdir):
if (
files.startswith("ref_prok_rep_genomes.05")
and "tar.gz" not in files
):
os.remove(files)
archive = os.path.join(downdir, "ref_prok_rep_genomes.05.tar.gz")
shutil.copy(archive, "ref_prok_rep_genomes.05.tar.gz")
getblastdb.download_from_ftp([chmdfile], delete_config)
check_part_five(outcome=True)
remove_tmp_db()
os.chdir("..")
if os.path.isdir(tmpdir):
shutil.rmtree(tmpdir)
def test_onlymd5(keep_config):
chmdfile = "ref_prok_rep_genomes.05.tar.gz.md5"
refmd5 = os.path.join("md5_files", chmdfile)
create_mock_archives()
os.chdir(tmpdir)
for files in os.listdir(tmpdir):
if (
files.startswith("ref_prok_rep_genomes.05")
and not files.endswith(".md5")
):
os.remove(files)
shutil.copy(chmdfile, refmd5)
getblastdb.download_from_ftp([chmdfile], keep_config)
check_part_five(outcome=True)
assert os.path.isfile("ref_prok_rep_genomes.05.tar.gz") is True
remove_tmp_db()
os.chdir("..")
if os.path.isdir(tmpdir):
shutil.rmtree(tmpdir)
def test_compare_md5_archive_changed(delete_config):
chmdfile = "ref_prok_rep_genomes.05.tar.gz.md5"
archive = chmdfile.split(".md5")[0]
create_mock_archives()
shutil.rmtree("md5_files")
G.create_directory("md5_files")
os.chdir(tmpdir)
with tarfile.open(archive, "w:gz") as tar:
for files in os.listdir(tmpdir):
if files.startswith("ref_prok_rep_genomes.05"):
tar.add(files)
for files in os.listdir(tmpdir):
if (
files.startswith("ref_prok_rep_genomes.05")
and "tar.gz" not in files
):
os.remove(files)
getblastdb.download_from_ftp([chmdfile], delete_config)
check_part_five(outcome=True)
remove_tmp_db()
os.chdir("..")
if os.path.isdir(tmpdir):
shutil.rmtree(tmpdir)
def test_checksum_incorrect(delete_config):
create_mock_archives()
os.chdir(tmpdir)
for files in os.listdir(tmpdir):
if (
files.startswith("ref_prok_rep_genomes.05")
and not files.endswith(".md5")
):
os.remove(files)
chmdfile = "ref_prok_rep_genomes.05.tar.gz.md5"
with open(chmdfile, "r") as f:
for line in f:
info = (
line.strip().split(" ")[0][0:-1] + "q67 " +
line.strip().split(" ")[1])
with open(chmdfile, "w") as f:
f.write(info)
with pytest.raises(Exception):
getblastdb.download_from_ftp([chmdfile], delete_config)
check_part_five(outcome=False)
remove_tmp_db()
os.chdir("..")
if os.path.isdir(tmpdir):
shutil.rmtree(tmpdir)
