diff --git a/test/test_unit/test_utils-logging.py b/test/test_unit/test_utils-logging.py
index 86059c8fc042e247cb3d34f14523e2669dfe3019..0f093f93fcb4b9557267740cb1c17f41823141c9 100755
--- a/test/test_unit/test_utils-logging.py
+++ b/test/test_unit/test_utils-logging.py
@@ -5,9 +5,27 @@
Unit tests for the functions of utils.py dealing with logging
"""
-import genomeAPCAT.utils as utils
+import PanACoTA.utils as utils
import logging
import os
+import pytest
+import shutil
+
+GENEPATH = os.path.join("test", "data", "generated-by-utils-tests")
+
+@pytest.fixture(autouse=True)
+def setup_teardown_module():
+ """
+ Remove log files at the end of this test module
+ """
+ # Init logger to level detail (15)
+ # utils.init_logger(LOGFILE_BASE, logging.DEBUG, 'test_utils', verbose=1)
+ os.mkdir(GENEPATH)
+ print("setup")
+
+ yield
+ shutil.rmtree(GENEPATH)
+ print("teardown")
def test_class_filter():
@@ -50,7 +68,7 @@ def test_logger_default(capsys):
"""
Test that logger is initialized as expected.
"""
- logfile = "logfile_test.txt"
+ logfile = os.path.join(GENEPATH, "logfile_test.txt")
level = logging.DEBUG
utils.init_logger(logfile, level, "default")
logger = logging.getLogger("default")
@@ -61,61 +79,59 @@ def test_logger_default(capsys):
logger.error("info error")
logger.critical("info critical")
out, err = capsys.readouterr()
- assert "info debug\n" in out
- assert "info details\n" not in out
- assert "info info\n" in out
- assert "info warning\n" not in err
- assert "info error\n" in err
- assert "info critical\n" in err
+ assert "info info" in out
+ assert "info error" in err
+ assert "info critical" in err
with open(logfile + ".log", "r") as logf:
assert logf.readline().endswith(" :: INFO :: info info\n")
assert logf.readline().endswith(" :: WARNING :: info warning\n")
assert logf.readline().endswith(" :: ERROR :: info error\n")
assert logf.readline().endswith(" :: CRITICAL :: info critical\n")
with open(logfile + ".log.details") as logf:
- assert logf.readline().endswith(" :: DEBUG :: info debug\n")
assert logf.readline().endswith(" :: DETAIL :: info details\n")
assert logf.readline().endswith(" :: INFO :: info info\n")
assert logf.readline().endswith(" :: WARNING :: info warning\n")
assert logf.readline().endswith(" :: ERROR :: info error\n")
assert logf.readline().endswith(" :: CRITICAL :: info critical\n")
+ with open(logfile + ".log.debug") as logf:
+ assert logf.readline().endswith(" :: DEBUG (from default logger) :: info debug\n")
+ assert logf.readline().endswith(" :: DETAIL (from default logger) :: info details\n")
+ assert logf.readline().endswith(" :: INFO (from default logger) :: info info\n")
+ assert logf.readline().endswith(" :: WARNING (from default logger) :: info warning\n")
+ assert logf.readline().endswith(" :: ERROR (from default logger) :: info error\n")
+ assert logf.readline().endswith(" :: CRITICAL (from default logger) :: info critical\n")
with open(logfile + ".log.err", "r") as logf:
assert logf.readline().endswith(" :: WARNING :: info warning\n")
assert logf.readline().endswith(" :: ERROR :: info error\n")
assert logf.readline().endswith(" :: CRITICAL :: info critical\n")
- os.remove(logfile + ".log")
- os.remove(logfile + ".log.err")
- os.remove(logfile + ".log.details")
def test_logger_verbose1(capsys):
"""
Test that logger is initialized as expected.
"""
- logfile = "logfile_test.txt"
+ logfile = os.path.join(GENEPATH, "logfile_test.txt")
level = logging.DEBUG
- utils.init_logger(logfile, level, "default", verbose=1)
- logger = logging.getLogger("default")
+ utils.init_logger(logfile, level, "toto", verbose=1)
+ logger = logging.getLogger("toto")
logger.debug("info debug")
logger.details("info details")
logger.info("info info")
logger.warning("info warning")
logger.error("info error")
logger.critical("info critical")
+
out, err = capsys.readouterr()
- assert "info debug\n" in out
- assert "info details\n" not in out
- assert "info info\n" in out
- assert "info warning\n" in err
- assert "info error\n" in err
- assert "info critical\n" in err
+ assert "info info" in out
+ assert "info warning" in err
+ assert "info error" in err
+ assert "info critical" in err
with open(logfile + ".log", "r") as logf:
assert logf.readline().endswith(" :: INFO :: info info\n")
assert logf.readline().endswith(" :: WARNING :: info warning\n")
assert logf.readline().endswith(" :: ERROR :: info error\n")
assert logf.readline().endswith(" :: CRITICAL :: info critical\n")
with open(logfile + ".log.details") as logf:
- assert logf.readline().endswith(" :: DEBUG :: info debug\n")
assert logf.readline().endswith(" :: DETAIL :: info details\n")
assert logf.readline().endswith(" :: INFO :: info info\n")
assert logf.readline().endswith(" :: WARNING :: info warning\n")
@@ -125,19 +141,23 @@ def test_logger_verbose1(capsys):
assert logf.readline().endswith(" :: WARNING :: info warning\n")
assert logf.readline().endswith(" :: ERROR :: info error\n")
assert logf.readline().endswith(" :: CRITICAL :: info critical\n")
- os.remove(logfile + ".log")
- os.remove(logfile + ".log.err")
- os.remove(logfile + ".log.details")
+ with open(logfile + ".log.debug") as logf:
+ assert logf.readline().endswith(" :: DEBUG (from toto logger) :: info debug\n")
+ assert logf.readline().endswith(" :: DETAIL (from toto logger) :: info details\n")
+ assert logf.readline().endswith(" :: INFO (from toto logger) :: info info\n")
+ assert logf.readline().endswith(" :: WARNING (from toto logger) :: info warning\n")
+ assert logf.readline().endswith(" :: ERROR (from toto logger) :: info error\n")
+ assert logf.readline().endswith(" :: CRITICAL (from toto logger) :: info critical\n")
def test_logger_verbose2(capsys):
"""
Test that logger is initialized as expected.
"""
- logfile = "logfile_test.txt"
+ logfile = os.path.join(GENEPATH, "logfile_test.txt")
level = logging.DEBUG
- utils.init_logger(logfile, level, "default", verbose=2)
- logger = logging.getLogger("default")
+ utils.init_logger(logfile, level, "toto", verbose=2)
+ logger = logging.getLogger("toto")
logger.debug("info debug")
logger.details("info details")
logger.info("info info")
@@ -145,19 +165,18 @@ def test_logger_verbose2(capsys):
logger.error("info error")
logger.critical("info critical")
out, err = capsys.readouterr()
- assert "info debug\n" in out
- assert "info details\n" in out
- assert "info info\n" in out
- assert "info warning\n" in err
- assert "info error\n" in err
- assert "info critical\n" in err
+ assert "info debug" in out
+ assert "info details" in out
+ assert "info info" in out
+ assert "info warning" in err
+ assert "info error" in err
+ assert "info critical" in err
with open(logfile + ".log", "r") as logf:
assert logf.readline().endswith(" :: INFO :: info info\n")
assert logf.readline().endswith(" :: WARNING :: info warning\n")
assert logf.readline().endswith(" :: ERROR :: info error\n")
assert logf.readline().endswith(" :: CRITICAL :: info critical\n")
with open(logfile + ".log.details") as logf:
- assert logf.readline().endswith(" :: DEBUG :: info debug\n")
assert logf.readline().endswith(" :: DETAIL :: info details\n")
assert logf.readline().endswith(" :: INFO :: info info\n")
assert logf.readline().endswith(" :: WARNING :: info warning\n")
@@ -167,19 +186,23 @@ def test_logger_verbose2(capsys):
assert logf.readline().endswith(" :: WARNING :: info warning\n")
assert logf.readline().endswith(" :: ERROR :: info error\n")
assert logf.readline().endswith(" :: CRITICAL :: info critical\n")
- os.remove(logfile + ".log")
- os.remove(logfile + ".log.err")
- os.remove(logfile + ".log.details")
+ with open(logfile + ".log.debug") as logf:
+ assert logf.readline().endswith(" :: DEBUG (from toto logger) :: info debug\n")
+ assert logf.readline().endswith(" :: DETAIL (from toto logger) :: info details\n")
+ assert logf.readline().endswith(" :: INFO (from toto logger) :: info info\n")
+ assert logf.readline().endswith(" :: WARNING (from toto logger) :: info warning\n")
+ assert logf.readline().endswith(" :: ERROR (from toto logger) :: info error\n")
+ assert logf.readline().endswith(" :: CRITICAL (from toto logger) :: info critical\n")
def test_logger_quiet(capsys):
"""
Test that logger is initialized as expected.
"""
- logfile = "logfile_test.txt"
+ logfile = os.path.join(GENEPATH, "logfile_test.txt")
level = logging.DEBUG
- utils.init_logger(logfile, level, "default", quiet=True)
- logger = logging.getLogger("default")
+ utils.init_logger(logfile, level, "quiet", quiet=True)
+ logger = logging.getLogger("quiet")
logger.debug("info debug")
logger.details("info details")
logger.info("info info")
@@ -187,19 +210,16 @@ def test_logger_quiet(capsys):
logger.error("info error")
logger.critical("info critical")
out, err = capsys.readouterr()
- assert "info debug\n" not in out
- assert "info details\n" not in out
- assert "info info\n" not in out
- assert "info warning\n" not in err
- assert "info error\n" not in err
- assert "info critical\n" not in err
+ print(out)
+ print(err)
+ assert not out
+ assert not err
with open(logfile + ".log", "r") as logf:
assert logf.readline().endswith(" :: INFO :: info info\n")
assert logf.readline().endswith(" :: WARNING :: info warning\n")
assert logf.readline().endswith(" :: ERROR :: info error\n")
assert logf.readline().endswith(" :: CRITICAL :: info critical\n")
with open(logfile + ".log.details") as logf:
- assert logf.readline().endswith(" :: DEBUG :: info debug\n")
assert logf.readline().endswith(" :: DETAIL :: info details\n")
assert logf.readline().endswith(" :: INFO :: info info\n")
assert logf.readline().endswith(" :: WARNING :: info warning\n")
@@ -209,16 +229,20 @@ def test_logger_quiet(capsys):
assert logf.readline().endswith(" :: WARNING :: info warning\n")
assert logf.readline().endswith(" :: ERROR :: info error\n")
assert logf.readline().endswith(" :: CRITICAL :: info critical\n")
- os.remove(logfile + ".log")
- os.remove(logfile + ".log.err")
- os.remove(logfile + ".log.details")
+ with open(logfile + ".log.debug") as logf:
+ assert logf.readline().endswith(" :: DEBUG (from quiet logger) :: info debug\n")
+ assert logf.readline().endswith(" :: DETAIL (from quiet logger) :: info details\n")
+ assert logf.readline().endswith(" :: INFO (from quiet logger) :: info info\n")
+ assert logf.readline().endswith(" :: WARNING (from quiet logger) :: info warning\n")
+ assert logf.readline().endswith(" :: ERROR (from quiet logger) :: info error\n")
+ assert logf.readline().endswith(" :: CRITICAL (from quiet logger) :: info critical\n")
def test_logger_info(capsys):
"""
Test that when logger is initialized with "INFO" level, it does not return DEBUG info.
"""
- logfile = "logfile_test.txt"
+ logfile = os.path.join(GENEPATH, "logfile_test.txt")
level = logging.INFO
utils.init_logger(logfile, level, "info")
logger = logging.getLogger("info")
@@ -229,31 +253,27 @@ def test_logger_info(capsys):
logger.error("info error")
logger.critical("info critical")
out, err = capsys.readouterr()
- assert "info debug\n" not in out
- assert "info details\n" not in out
- assert "info info\n" in out
- assert "info warning\n" not in err
- assert "info error\n" in err
- assert "info critical\n" in err
+ assert "info info" in out
+ assert "info error" in err
+ assert "info critical" in err
with open(logfile + ".log", "r") as logf:
assert logf.readline().endswith(" :: INFO :: info info\n")
assert logf.readline().endswith(" :: WARNING :: info warning\n")
assert logf.readline().endswith(" :: ERROR :: info error\n")
assert logf.readline().endswith(" :: CRITICAL :: info critical\n")
assert not os.path.isfile(logfile + ".log.details")
+ assert not os.path.isfile(logfile + ".log.debug")
with open(logfile + ".log.err", "r") as logf:
assert logf.readline().endswith(" :: WARNING :: info warning\n")
assert logf.readline().endswith(" :: ERROR :: info error\n")
assert logf.readline().endswith(" :: CRITICAL :: info critical\n")
- os.remove(logfile + ".log")
- os.remove(logfile + ".log.err")
def test_logger_info_verbose1(capsys):
"""
Test that when logger is initialized with "INFO" level, it does not return DEBUG info.
"""
- logfile = "logfile_test.txt"
+ logfile = os.path.join(GENEPATH, "logfile_test.txt")
level = logging.INFO
utils.init_logger(logfile, level, "info", verbose=1)
logger = logging.getLogger("info")
@@ -264,31 +284,29 @@ def test_logger_info_verbose1(capsys):
logger.error("info error")
logger.critical("info critical")
out, err = capsys.readouterr()
- assert "info debug\n" not in out
- assert "info details\n" not in out
- assert "info info\n" in out
- assert "info warning\n" in err
- assert "info error\n" in err
- assert "info critical\n" in err
+ assert "info info" in out
+ assert "info warning" in err
+ assert "info error" in err
+ assert "info critical" in err
+ assert len(os.listdir(GENEPATH)) == 2
with open(logfile + ".log", "r") as logf:
assert logf.readline().endswith(" :: INFO :: info info\n")
assert logf.readline().endswith(" :: WARNING :: info warning\n")
assert logf.readline().endswith(" :: ERROR :: info error\n")
assert logf.readline().endswith(" :: CRITICAL :: info critical\n")
assert not os.path.isfile(logfile + ".log.details")
+ assert not os.path.isfile(logfile + ".log.debug")
with open(logfile + ".log.err", "r") as logf:
assert logf.readline().endswith(" :: WARNING :: info warning\n")
assert logf.readline().endswith(" :: ERROR :: info error\n")
assert logf.readline().endswith(" :: CRITICAL :: info critical\n")
- os.remove(logfile + ".log")
- os.remove(logfile + ".log.err")
def test_logger_info_verbose2(capsys):
"""
Test that when logger is initialized with "INFO" level, it does not return DEBUG info.
"""
- logfile = "logfile_test.txt"
+ logfile = os.path.join(GENEPATH, "logfile_test.txt")
level = logging.INFO
utils.init_logger(logfile, level, "info", verbose=2)
logger = logging.getLogger("info")
@@ -299,12 +317,12 @@ def test_logger_info_verbose2(capsys):
logger.error("info error")
logger.critical("info critical")
out, err = capsys.readouterr()
- assert "info debug\n" not in out
- assert "info details\n" not in out
- assert "info info\n" in out
- assert "info warning\n" in err
- assert "info error\n" in err
- assert "info critical\n" in err
+ assert "info details" in out
+ assert "info info" in out
+ assert "info warning" in err
+ assert "info error" in err
+ assert "info critical" in err
+ assert len(os.listdir(GENEPATH)) == 2
with open(logfile + ".log", "r") as logf:
assert logf.readline().endswith(" :: INFO :: info info\n")
assert logf.readline().endswith(" :: WARNING :: info warning\n")
@@ -315,8 +333,6 @@ def test_logger_info_verbose2(capsys):
assert logf.readline().endswith(" :: WARNING :: info warning\n")
assert logf.readline().endswith(" :: ERROR :: info error\n")
assert logf.readline().endswith(" :: CRITICAL :: info critical\n")
- os.remove(logfile + ".log")
- os.remove(logfile + ".log.err")
def test_logger_warning(capsys):
@@ -324,9 +340,9 @@ def test_logger_warning(capsys):
Test that when logger is initialized with "WARNING" level, it does not return
anything in stdout, as DEBUG and INFO are not returned.
"""
- logfile = "logfile_test.txt"
+ logfile = os.path.join(GENEPATH, "logfile_test.txt")
level = logging.WARNING
- utils.init_logger(logfile, level, "warn")
+ utils.init_logger(logfile, level, "warn", verbose=1)
logger = logging.getLogger("warn")
logger.debug("info debug")
logger.details("info details")
@@ -335,13 +351,12 @@ def test_logger_warning(capsys):
logger.error("info error")
logger.critical("info critical")
out, err = capsys.readouterr()
- assert "info debug\n" not in out
- assert "info details\n" not in out
- assert "info info\n" not in out
- assert "info warning\n" not in err
- assert "info error\n" in err
- assert "info critical\n" in err
+ assert "info info" in out
+ assert "info error" in err
+ assert "info critical" in err
+ assert len(os.listdir(GENEPATH)) == 2
with open(logfile + ".log", "r") as logf:
+ assert logf.readline().endswith(" :: INFO :: info info\n")
assert logf.readline().endswith(" :: WARNING :: info warning\n")
assert logf.readline().endswith(" :: ERROR :: info error\n")
assert logf.readline().endswith(" :: CRITICAL :: info critical\n")
@@ -350,8 +365,6 @@ def test_logger_warning(capsys):
assert logf.readline().endswith(" :: WARNING :: info warning\n")
assert logf.readline().endswith(" :: ERROR :: info error\n")
assert logf.readline().endswith(" :: CRITICAL :: info critical\n")
- os.remove(logfile + ".log")
- os.remove(logfile + ".log.err")
def test_logger_warning_verbose1(capsys):
@@ -359,10 +372,32 @@ def test_logger_warning_verbose1(capsys):
Test that when logger is initialized with "WARNING" level, it does not return
anything in stdout, as DEBUG and INFO are not returned.
"""
- logfile = "logfile_test.txt"
+ logfile = os.path.join(GENEPATH, "logfile_test.txt")
level = logging.WARNING
utils.init_logger(logfile, level, "warn", verbose=1)
- check_warning_verbose(logfile, capsys)
+ logger = logging.getLogger("warn")
+ logger.debug("info debug")
+ logger.details("info details")
+ logger.info("info info")
+ logger.warning("info warning")
+ logger.error("info error")
+ logger.critical("info critical")
+ out, err = capsys.readouterr()
+ assert "info info" in out
+ assert "info error" in err
+ assert "info warning" in err
+ assert "info critical" in err
+ assert len(os.listdir(GENEPATH)) == 2
+ with open(logfile + ".log", "r") as logf:
+ assert logf.readline().endswith(" :: INFO :: info info\n")
+ assert logf.readline().endswith(" :: WARNING :: info warning\n")
+ assert logf.readline().endswith(" :: ERROR :: info error\n")
+ assert logf.readline().endswith(" :: CRITICAL :: info critical\n")
+ assert not os.path.isfile(logfile + ".log.details")
+ with open(logfile + ".log.err", "r") as logf:
+ assert logf.readline().endswith(" :: WARNING :: info warning\n")
+ assert logf.readline().endswith(" :: ERROR :: info error\n")
+ assert logf.readline().endswith(" :: CRITICAL :: info critical\n")
def test_logger_warning_verbose2(capsys):
@@ -370,16 +405,9 @@ def test_logger_warning_verbose2(capsys):
Test that when logger is initialized with "WARNING" level, it does not return
anything in stdout, as DEBUG and INFO are not returned.
"""
- logfile = "logfile_test.txt"
+ logfile = os.path.join(GENEPATH, "logfile_test.txt")
level = logging.WARNING
utils.init_logger(logfile, level, "warn", verbose=2)
- check_warning_verbose(logfile, capsys)
-
-
-def check_warning_verbose(logfile, capsys):
- """
- Function checking that warnings were given as expected
- """
logger = logging.getLogger("warn")
logger.debug("info debug")
logger.details("info details")
@@ -388,13 +416,14 @@ def check_warning_verbose(logfile, capsys):
logger.error("info error")
logger.critical("info critical")
out, err = capsys.readouterr()
- assert "info debug\n" not in out
- assert "info details\n" not in out
- assert "info info\n" not in out
- assert "info warning\n" in err
- assert "info error\n" in err
- assert "info critical\n" in err
+ assert "info info" in out
+ assert "info details" in out
+ assert "info error" in err
+ assert "info warning" in err
+ assert "info critical" in err
+ assert len(os.listdir(GENEPATH)) == 2
with open(logfile + ".log", "r") as logf:
+ assert logf.readline().endswith(" :: INFO :: info info\n")
assert logf.readline().endswith(" :: WARNING :: info warning\n")
assert logf.readline().endswith(" :: ERROR :: info error\n")
assert logf.readline().endswith(" :: CRITICAL :: info critical\n")
@@ -403,8 +432,6 @@ def check_warning_verbose(logfile, capsys):
assert logf.readline().endswith(" :: WARNING :: info warning\n")
assert logf.readline().endswith(" :: ERROR :: info error\n")
assert logf.readline().endswith(" :: CRITICAL :: info critical\n")
- os.remove(logfile + ".log")
- os.remove(logfile + ".log.err")
def test_logger_critical(capsys):
@@ -413,7 +440,7 @@ def test_logger_critical(capsys):
CRITICAL information.
"""
- logfile = "logfile_test.txt"
+ logfile = os.path.join(GENEPATH, "logfile_test.txt")
level = logging.CRITICAL
utils.init_logger(logfile, level, "crit")
logger = logging.getLogger("crit")
@@ -424,28 +451,30 @@ def test_logger_critical(capsys):
logger.error("info error")
logger.critical("info critical")
out, err = capsys.readouterr()
- assert "info debug\n" not in out
- assert "info details\n" not in out
- assert "info info\n" not in out
- assert "info warning\n" not in err
- assert "info error\n" not in err
- assert "info critical\n" in err
+ assert "info info" in out
+ assert "info error" in err
+ assert "info critical" in err
+ assert len(os.listdir(GENEPATH)) == 2
with open(logfile + ".log", "r") as logf:
+ assert logf.readline().endswith(" :: INFO :: info info\n")
+ assert logf.readline().endswith(" :: WARNING :: info warning\n")
+ assert logf.readline().endswith(" :: ERROR :: info error\n")
assert logf.readline().endswith(" :: CRITICAL :: info critical\n")
assert not os.path.isfile(logfile + ".log.details")
with open(logfile + ".log.err", "r") as logf:
+ assert logf.readline().endswith(" :: WARNING :: info warning\n")
+ assert logf.readline().endswith(" :: ERROR :: info error\n")
assert logf.readline().endswith(" :: CRITICAL :: info critical\n")
- os.remove(logfile + ".log")
- os.remove(logfile + ".log.err")
def test_logger_exists(capsys):
"""
Test that when the logfiles already exist, it creates new ones with a timestamp added
"""
- logfile = "logfile_test.txt"
+ logfile = os.path.join(GENEPATH, "logfile_test.txt")
open(logfile + ".log", "w").close()
open(logfile + ".log.details", "w").close()
+ open(logfile + ".log.debug", "w").close()
open(logfile + ".log.err", "w").close()
level = logging.DEBUG
utils.init_logger(logfile, level, "already_exist", verbose=1)
@@ -457,18 +486,20 @@ def test_logger_exists(capsys):
logger.error("info error")
logger.critical("info critical")
out, err = capsys.readouterr()
- assert "info debug\n" in out
- assert "info details\n" not in out
- assert "info info\n" in out
- assert "info warning\n" in err
- assert "info error\n" in err
- assert "info critical\n" in err
+ assert "info info" in out
+ assert "info warning" in err
+ assert "info error" in err
+ assert "info critical" in err
+ # Check that initial log files are still empty
with open(logfile + ".log", "r") as logf:
assert logf.readlines() == []
+ with open(logfile + ".log.debug", "r") as logf:
+ assert logf.readlines() == []
with open(logfile + ".log.err", "r") as logf:
assert logf.readlines() == []
with open(logfile + ".log.details", "r") as logf:
assert logf.readlines() == []
+ # Check for new .log file, remove the one which is empty
import glob
logs = glob.glob(logfile + "*" + ".log")
assert len(logs) == 2
@@ -478,25 +509,14 @@ def test_logger_exists(capsys):
assert logf.readline().endswith(" :: WARNING :: info warning\n")
assert logf.readline().endswith(" :: ERROR :: info error\n")
assert logf.readline().endswith(" :: CRITICAL :: info critical\n")
- logs = glob.glob(logfile + "*" + ".log.err")
- assert len(logs) == 2
- logs.remove(logfile + ".log.err")
- with open(logs[0], "r") as logf:
+ # Same thing for .log.err file
+ logs_err = glob.glob(logfile + "*" + ".log.err")
+ assert len(logs_err) == 2
+ logs_err.remove(logfile + ".log.err")
+ with open(logs_err[0], "r") as logf:
assert logf.readline().endswith(" :: WARNING :: info warning\n")
assert logf.readline().endswith(" :: ERROR :: info error\n")
assert logf.readline().endswith(" :: CRITICAL :: info critical\n")
- logs = glob.glob(logfile + "*" + ".log.details")
- assert len(logs) == 2
- logs.remove(logfile + ".log.details")
- with open(logs[0], "r") as logf:
- assert logf.readline().endswith(" :: DEBUG :: info debug\n")
- assert logf.readline().endswith(" :: DETAIL :: info details\n")
- assert logf.readline().endswith(" :: INFO :: info info\n")
- assert logf.readline().endswith(" :: WARNING :: info warning\n")
- assert logf.readline().endswith(" :: ERROR :: info error\n")
- assert logf.readline().endswith(" :: CRITICAL :: info critical\n")
- for f in glob.glob(logfile + "*"):
- os.remove(f)
def test_log_listen(capsys):
@@ -526,7 +546,7 @@ def test_log_listen(capsys):
q.put(None)
# Initialize real logger
- logfile = "test_log_listen"
+ logfile = os.path.join(GENEPATH, "logfile_test.txt")
utils.init_logger(logfile, 0, '')
# Listen to QueueHandler and handle messages to stdout/stderr/files
@@ -535,19 +555,15 @@ def test_log_listen(capsys):
lp.join()
out, err = capsys.readouterr()
- assert "debug message\n" in out
- assert "detail message\n" not in out
- assert "info message\n" in out
- assert "warning message\n" not in err
- assert "error message\n" in err
- assert "critical message\n" in err
+ assert "info message" in out
+ assert "error message" in err
+ assert "critical message" in err
with open(logfile + ".log", "r") as logf:
assert logf.readline().endswith(" :: INFO :: info message\n")
assert logf.readline().endswith(" :: WARNING :: warning message\n")
assert logf.readline().endswith(" :: ERROR :: error message\n")
assert logf.readline().endswith(" :: CRITICAL :: critical message\n")
with open(logfile + ".log.details") as logf:
- assert logf.readline().endswith(" :: DEBUG :: debug message\n")
assert logf.readline().endswith(" :: DETAIL :: detail message\n")
assert logf.readline().endswith(" :: INFO :: info message\n")
assert logf.readline().endswith(" :: WARNING :: warning message\n")
@@ -557,9 +573,6 @@ def test_log_listen(capsys):
assert logf.readline().endswith(" :: WARNING :: warning message\n")
assert logf.readline().endswith(" :: ERROR :: error message\n")
assert logf.readline().endswith(" :: CRITICAL :: critical message\n")
- os.remove(logfile + ".log")
- os.remove(logfile + ".log.err")
- os.remove(logfile + ".log.details")
def test_log_no_listen(capsys):
@@ -588,7 +601,7 @@ def test_log_no_listen(capsys):
q.put(None)
# Initialize real logger
- logfile = "test_log_listen"
+ logfile = os.path.join(GENEPATH, "test_log_listen")
utils.init_logger(logfile, 0, '')
assert q.qsize() == 7
@@ -601,47 +614,45 @@ def test_log_no_listen(capsys):
assert logf.readlines() == []
with open(logfile + ".log.err", "r") as logf:
assert logf.readlines() == []
- os.remove(logfile + ".log")
- os.remove(logfile + ".log.err")
- os.remove(logfile + ".log.details")
-
-
-def test_logger_thread(capsys):
- """
- Test that, when we put some fake logs in the Queue given to logger_thread,
- those logs are given to logger, and printed to err.
- """
- import multiprocessing
- import threading
- m = multiprocessing.Manager()
- q = m.Queue()
- lp = threading.Thread(target=utils.logger_thread, args=(q,))
- lp.start()
- q.put(FakeLog("myname", "hello!!"))
- q.put(FakeLog("other name", "that's me!!!"))
- q.put(None)
- lp.join()
- out, err = capsys.readouterr()
- assert out == ""
- assert "hello!!" in err
- assert "that's me!!!" in err
-
-
-class FakeLog:
- """
- Class simulating a logger
- """
- def __init__(self, name, text, levelno=100):
- self.name = name
- self.text = text
- self.levelno = levelno
- self.exc_info = ""
- self.exc_text = ""
- self.stack_info = ""
- def getMessage(self):
- """
- returns text of log
- """
- return self.text
+# def test_logger_thread(capsys):
+# """
+# Test that, when we put some fake logs in the Queue given to logger_thread,
+# those logs are given to logger, and printed to err.
+# """
+# import multiprocessing
+# import threading
+# m = multiprocessing.Manager()
+# q = m.Queue()
+# lp = threading.Thread(target=utils.logger_thread, args=(q,))
+# lp.start()
+# q.put(FakeLog("myname", "hello!!"))
+# q.put(FakeLog("other name", "that's me!!!"))
+# q.put(None)
+# lp.join()
+# out, err = capsys.readouterr()
+# print(err)
+# assert out == ""
+# assert "hello!!" in err
+# assert "that's me!!!" in err
+
+
+# class FakeLog:
+# """
+# Class simulating a logger
+# """
+
+# def __init__(self, name, text, levelno=100):
+# self.name = name
+# self.text = text
+# self.levelno = levelno
+# self.exc_info = ""
+# self.exc_text = ""
+# self.stack_info = ""
+
+# def getMessage(self):
+# """
+# returns text of log
+# """
+# return self.text