From 7f6e642fa667ff65d3aab690e0f355060abe63e5 Mon Sep 17 00:00:00 2001
From: Amandine PERRIN <amandine.perrin@pasteur.fr>
Date: Sat, 17 Oct 2020 11:55:42 +0200
Subject: [PATCH] finish functional tests for prepare module
---
.gitlab-ci.yml | 1 -
PanACoTA/subcommands/prepare.py | 2 +-
PanACoTA/utils.py | 2 +-
PanACoTA/utils_argparse.py | 2 +-
test/test_functional/test_annote.py | 4 +-
test/test_functional/test_corepers.py | 3 +-
test/test_functional/test_prepare-parser.py | 8 +-
test/test_functional/test_prepare.py | 84 +++++++++++++++++++++
test/test_unit/test_utils-argparse.py | 36 +++++++++
test/test_unit/test_utils-logging.py | 33 ++++++--
test/test_unit/test_utils.py | 4 +-
11 files changed, 158 insertions(+), 21 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index fe551a83..88daf349 100755
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -113,7 +113,6 @@ func-test-ubuntu:
# - py.test test/test_functional/test_align* -vx
- py.test test/test_functional/test_align-parser.py -vx
- py.test test/test_functional/test_tree* -vx
- - py.test test/test_functional/test_tree-parser.py -vx
- py.test test/test_functional/test_annote-parser.py -vx
- py.test test/test_functional/test_annote.py -xv
- mv .coverage .coverage-functional
diff --git a/PanACoTA/subcommands/prepare.py b/PanACoTA/subcommands/prepare.py
index 135628d5..ebe85ea6 100644
--- a/PanACoTA/subcommands/prepare.py
+++ b/PanACoTA/subcommands/prepare.py
@@ -245,7 +245,7 @@ def main(cmd, NCBI_species, NCBI_taxid, levels, outdir, tmp_dir, threads, no_ref
else:
logger.warning('You asked to run only mash steps.')
if not os.path.exists(info_file): # info-file missing -> error and exit
- logger.error(f"Your info file {info_file} does not exist. Please Provide the "
+ logger.error(f"Your info file {info_file} does not exist. Please provide the "
"right name/path, or remove the '--mash-only option to rerun "
"quality control.")
sys.exit(1)
diff --git a/PanACoTA/utils.py b/PanACoTA/utils.py
index 09043506..9828d464 100755
--- a/PanACoTA/utils.py
+++ b/PanACoTA/utils.py
@@ -824,7 +824,7 @@ def read_genomes_info(list_file, name, date=None, logger=None):
if len(genomes) > 0:
logger.info(("Found {} genomes in total").format(len(genomes)))
else:
- logger.error(f"no genome listed in {list_file} were found.")
+ logger.error(f"No genome listed in {list_file} was found.")
sys.exit(1)
return genomes
diff --git a/PanACoTA/utils_argparse.py b/PanACoTA/utils_argparse.py
index 9f4d1e4b..f553a571 100644
--- a/PanACoTA/utils_argparse.py
+++ b/PanACoTA/utils_argparse.py
@@ -120,6 +120,6 @@ def mash_dist(param):
msg = f"error: mash distance: invalid float value: '{param}'"
raise argparse.ArgumentTypeError(msg)
if param < 0 or param > 1:
- msg = f"error: mash_distance must be between 0 and 1: invalid value: '{param}'"
+ msg = f"error: mash distance must be between 0 and 1: invalid value: '{param}'"
raise argparse.ArgumentTypeError(msg)
return param
diff --git a/test/test_functional/test_annote.py b/test/test_functional/test_annote.py
index 950a6179..e4c3ca1c 100755
--- a/test/test_functional/test_annote.py
+++ b/test/test_functional/test_annote.py
@@ -582,8 +582,8 @@ def test_main_novalid_genome_frominfo(capsys):
prodigal_only=True, small=True)
out, err = capsys.readouterr()
# Check logs
- assert ("no genome listed in test/data/annotate/test_files/lstinfo-no-genome.lst "
- "were found.") in err
+ assert ("No genome listed in test/data/annotate/test_files/lstinfo-no-genome.lst "
+ "was found.") in err
# Check output folders not created
protdir = os.path.join(GENEPATH, "Proteins")
diff --git a/test/test_functional/test_corepers.py b/test/test_functional/test_corepers.py
index d4e778ca..9d07b799 100755
--- a/test/test_functional/test_corepers.py
+++ b/test/test_functional/test_corepers.py
@@ -34,7 +34,8 @@ def setup_teardown_module():
- remove all log files
- remove directory with generated results
"""
- os.mkdir(GENEPATH)
+ if not os.path.isdir(GENEPATH):
+ os.mkdir(GENEPATH)
shutil.copyfile(OPAN, UPAN)
print("setup")
diff --git a/test/test_functional/test_prepare-parser.py b/test/test_functional/test_prepare-parser.py
index 30d7a4fb..b0571710 100644
--- a/test/test_functional/test_prepare-parser.py
+++ b/test/test_functional/test_prepare-parser.py
@@ -164,12 +164,12 @@ def test_max_mash_dist(capsys):
with pytest.raises(SystemExit):
prepare.parse(parser, "--max_dist 1.5".split())
_, err = capsys.readouterr()
- assert "error: mash_distance must be between 0 and 1: invalid value: '1.5'" in err
+ assert "error: mash distance must be between 0 and 1: invalid value: '1.5'" in err
# < 0
with pytest.raises(SystemExit):
prepare.parse(parser, "--max_dist -0.5".split())
_, err = capsys.readouterr()
- assert "error: mash_distance must be between 0 and 1: invalid value: '-0.5'" in err
+ assert "error: mash distance must be between 0 and 1: invalid value: '-0.5'" in err
def test_min_mash_dist(capsys):
@@ -191,12 +191,12 @@ def test_min_mash_dist(capsys):
with pytest.raises(SystemExit):
prepare.parse(parser, "--min_dist 1.5".split())
_, err = capsys.readouterr()
- assert "error: mash_distance must be between 0 and 1: invalid value: '1.5'" in err
+ assert "error: mash distance must be between 0 and 1: invalid value: '1.5'" in err
# < 0
with pytest.raises(SystemExit):
prepare.parse(parser, "--min_dist -0.5".split())
_, err = capsys.readouterr()
- assert "error: mash_distance must be between 0 and 1: invalid value: '-0.5'" in err
+ assert "error: mash distance must be between 0 and 1: invalid value: '-0.5'" in err
def test_min_sup_max(capsys):
diff --git a/test/test_functional/test_prepare.py b/test/test_functional/test_prepare.py
index f60f3d72..4a84da72 100644
--- a/test/test_functional/test_prepare.py
+++ b/test/test_functional/test_prepare.py
@@ -485,3 +485,87 @@ def test_only_mash(capsys):
assert tutil.compare_order_content(out_lst, exp_lst)
+def test_only_mash_empty_lstinfo(capsys):
+ """
+ Running only mash step giving an empty lstinfo file -> error, no genome found
+ """
+ NCBI_species = ""
+ NCBI_taxid = ""
+ levels = ""
+ outdir = GENEPATH
+ tmp_dir = ""
+ threads = 1
+ no_refseq = False
+ db_dir = ""
+ only_mash = True
+ # Create empty lstinfo file
+ info_file = os.path.join(GENEPATH, "LSTINFO-empty.lst")
+ open(info_file, "w").close()
+ l90 = 100
+ nbcont = 999
+ cutn = 5
+ min_dist = 1e-4
+ max_dist = 0.06
+ verbose = 1
+ quiet = False
+ with pytest.raises(SystemExit):
+ prepare.main("cmd", NCBI_species, NCBI_taxid, levels, outdir, tmp_dir, threads, no_refseq,
+ db_dir, only_mash, info_file, l90, nbcont, cutn, min_dist, max_dist,
+ verbose, quiet)
+ out, err = capsys.readouterr()
+ assert ("You asked to run only mash steps") in err
+ assert ("You want to run only mash steps. Getting information from "
+ "test/data/prepare/generated_by_func-tests/LSTINFO-empty.lst") in out
+ assert ("No genome listed in test/data/prepare/generated_by_func-tests/LSTINFO-empty.lst "
+ "was found.") in err
+
+ # Check output files
+ assert len(os.listdir(os.path.join(outdir, "tmp_files"))) == 0
+ # Check logfiles are here
+ log_files = glob.glob(os.path.join(outdir, "*log*"))
+ assert len(log_files) == 3
+ # Check lstinfo file is still here and still empty
+ assert os.stat(info_file).st_size == 0
+
+
+def test_only_mash_no_lstinfo(capsys):
+ """
+ Running only mash step giving an info file which does not exist -> error missing infofile
+ """
+ NCBI_species = ""
+ NCBI_taxid = ""
+ levels = ""
+ outdir = GENEPATH
+ tmp_dir = ""
+ threads = 1
+ no_refseq = False
+ db_dir = ""
+ only_mash = True
+ # Create empty lstinfo file
+ info_file = "info_file.lst"
+ l90 = 100
+ nbcont = 999
+ cutn = 5
+ min_dist = 1e-4
+ max_dist = 0.06
+ verbose = 1
+ quiet = False
+ with pytest.raises(SystemExit):
+ prepare.main("cmd", NCBI_species, NCBI_taxid, levels, outdir, tmp_dir, threads, no_refseq,
+ db_dir, only_mash, info_file, l90, nbcont, cutn, min_dist, max_dist,
+ verbose, quiet)
+ out, err = capsys.readouterr()
+ assert ("You asked to run only mash steps") in err
+ assert ("Your info file info_file.lst does not exist. Please provide the "
+ "right name/path, or remove the '--mash-only option to rerun "
+ "quality control.") in err
+
+ # Check output files
+ assert len(os.listdir(os.path.join(outdir, "tmp_files"))) == 0
+ # Check logfiles are here
+ log_files = glob.glob(os.path.join(outdir, "*log*"))
+ assert len(log_files) == 3
+ # Check that outdir contains only 4 elements: 3 logs + tmp_files repo
+ files = os.listdir(outdir)
+ files = [f for f in files if "fuse" not in f]
+ assert len(files) == 4
diff --git a/test/test_unit/test_utils-argparse.py b/test/test_unit/test_utils-argparse.py
index 61d3efde..fb2a35cc 100644
--- a/test/test_unit/test_utils-argparse.py
+++ b/test/test_unit/test_utils-argparse.py
@@ -97,3 +97,39 @@ def test_thread_num():
assert ("Please provide a positive number of threads (or 0 for all threads): "
"Invalid value: -1") in str(err.value)
assert autils.thread_num(0) == nb_cpu
+
+
+def test_positive_int():
+ """
+ Test checking that given argument is a positive integer
+ """
+ assert autils.positive_int("1") == 1
+ with pytest.raises(argparse.ArgumentTypeError) as err:
+ a = autils.positive_int("1.1")
+ assert ("argument --cutn: invalid int value: '1.1'") in str(err.value)
+ with pytest.raises(argparse.ArgumentTypeError) as err:
+ a = autils.positive_int("-1")
+ assert ("error: argument --cutn must be a positive integer: "
+ "invalid int value: '-1'") in str(err.value)
+
+
+def test_mash_dist():
+ """
+ Test checking that given value is ok for a mash distance
+ """
+ assert autils.mash_dist("0.05") == 0.05
+ assert autils.mash_dist("1e-4") == 0.0001
+ with pytest.raises(argparse.ArgumentTypeError) as err:
+ a = autils.mash_dist("1.1.1")
+ assert ("error: mash distance: invalid float value: '1.1.1'") in str(err.value)
+ with pytest.raises(argparse.ArgumentTypeError) as err:
+ a = autils.mash_dist("one")
+ assert ("error: mash distance: invalid float value: 'one'") in str(err.value)
+ with pytest.raises(argparse.ArgumentTypeError) as err:
+ a = autils.mash_dist("1.000001")
+ assert ("error: mash distance must be between 0 and 1: "
+ "invalid value: '1.000001'") in str(err.value)
+ with pytest.raises(argparse.ArgumentTypeError) as err:
+ a = autils.mash_dist("-1e-4")
+ assert ("error: mash distance must be between 0 and 1: "
+ "invalid value: '-0.0001'") in str(err.value)
diff --git a/test/test_unit/test_utils-logging.py b/test/test_unit/test_utils-logging.py
index 0f093f93..8c59c708 100755
--- a/test/test_unit/test_utils-logging.py
+++ b/test/test_unit/test_utils-logging.py
@@ -20,11 +20,16 @@ def setup_teardown_module():
"""
# Init logger to level detail (15)
# utils.init_logger(LOGFILE_BASE, logging.DEBUG, 'test_utils', verbose=1)
- os.mkdir(GENEPATH)
+ if os.path.isdir(GENEPATH):
+ content = os.listdir(GENEPATH)
+ for f in content:
+ assert f.startswith(".fuse")
+ else:
+ os.mkdir(GENEPATH)
print("setup")
yield
- shutil.rmtree(GENEPATH)
+ shutil.rmtree(GENEPATH, ignore_errors=True)
print("teardown")
@@ -288,7 +293,9 @@ def test_logger_info_verbose1(capsys):
assert "info warning" in err
assert "info error" in err
assert "info critical" in err
- assert len(os.listdir(GENEPATH)) == 2
+ files = os.listdir(GENEPATH)
+ files = [f for f in files if "fuse" not in f]
+ assert len(files) == 2
with open(logfile + ".log", "r") as logf:
assert logf.readline().endswith(" :: INFO :: info info\n")
assert logf.readline().endswith(" :: WARNING :: info warning\n")
@@ -322,7 +329,9 @@ def test_logger_info_verbose2(capsys):
assert "info warning" in err
assert "info error" in err
assert "info critical" in err
- assert len(os.listdir(GENEPATH)) == 2
+ files = os.listdir(GENEPATH)
+ files = [f for f in files if "fuse" not in f]
+ assert len(files) == 2
with open(logfile + ".log", "r") as logf:
assert logf.readline().endswith(" :: INFO :: info info\n")
assert logf.readline().endswith(" :: WARNING :: info warning\n")
@@ -354,7 +363,9 @@ def test_logger_warning(capsys):
assert "info info" in out
assert "info error" in err
assert "info critical" in err
- assert len(os.listdir(GENEPATH)) == 2
+ files = os.listdir(GENEPATH)
+ files = [f for f in files if "fuse" not in f]
+ assert len(files) == 2
with open(logfile + ".log", "r") as logf:
assert logf.readline().endswith(" :: INFO :: info info\n")
assert logf.readline().endswith(" :: WARNING :: info warning\n")
@@ -387,7 +398,9 @@ def test_logger_warning_verbose1(capsys):
assert "info error" in err
assert "info warning" in err
assert "info critical" in err
- assert len(os.listdir(GENEPATH)) == 2
+ files = os.listdir(GENEPATH)
+ files = [f for f in files if "fuse" not in f]
+ assert len(files) == 2
with open(logfile + ".log", "r") as logf:
assert logf.readline().endswith(" :: INFO :: info info\n")
assert logf.readline().endswith(" :: WARNING :: info warning\n")
@@ -421,7 +434,9 @@ def test_logger_warning_verbose2(capsys):
assert "info error" in err
assert "info warning" in err
assert "info critical" in err
- assert len(os.listdir(GENEPATH)) == 2
+ files = os.listdir(GENEPATH)
+ files = [f for f in files if "fuse" not in f]
+ assert len(files) == 2
with open(logfile + ".log", "r") as logf:
assert logf.readline().endswith(" :: INFO :: info info\n")
assert logf.readline().endswith(" :: WARNING :: info warning\n")
@@ -454,7 +469,9 @@ def test_logger_critical(capsys):
assert "info info" in out
assert "info error" in err
assert "info critical" in err
- assert len(os.listdir(GENEPATH)) == 2
+ files = os.listdir(GENEPATH)
+ files = [f for f in files if "fuse" not in f]
+ assert len(files) == 2
with open(logfile + ".log", "r") as logf:
assert logf.readline().endswith(" :: INFO :: info info\n")
assert logf.readline().endswith(" :: WARNING :: info warning\n")
diff --git a/test/test_unit/test_utils.py b/test/test_unit/test_utils.py
index 83917d1a..cd653d4e 100755
--- a/test/test_unit/test_utils.py
+++ b/test/test_unit/test_utils.py
@@ -660,8 +660,8 @@ def test_read_genomes_info_no_genomes(caplog):
utils.read_genomes_info(lstinfo_file, name)
assert ("Reading given information on your genomes in "
"test/data/annotate/test_files/lstinfo-no-genome.lst") in caplog.text
- assert ("no genome listed in test/data/annotate/test_files/lstinfo-no-genome.lst "
- "were found.") in caplog.text
+ assert ("No genome listed in test/data/annotate/test_files/lstinfo-no-genome.lst "
+ "was found.") in caplog.text
def test_read_genomes_info_ok(caplog):
--
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