def test_pformat__atomiccmd__simple_with_stdout_pipe():
cmd = AtomicCmd(("echo", "!"), OUT_STDOUT=AtomicCmd.PIPE)
assert_equal(pformat(cmd),
("Command = echo '!'\n"
"STDOUT = <PIPE>\n"
"STDERR* = '${TEMP_DIR}/pipe_echo_%i.stderr'")
% (id(cmd),))
def test_pformat__atomiccmd__simple_with_temp_stdin__set_cwd():
cmd = AtomicCmd("gzip", TEMP_IN_STDIN="stabstabstab", set_cwd=True)
assert pformat(cmd) == ("Command = gzip\n"
"STDIN* = 'stabstabstab'\n"
"STDOUT* = 'pipe_gzip_%i.stdout'\n"
"STDERR* = 'pipe_gzip_%i.stderr'\n"
"CWD = '${TEMP_DIR}'") % (id(cmd), id(cmd))
def test_pformat__atomiccmd__simple_with_stdin__cmd():
cmd_1 = AtomicCmd("gzip", OUT_STDOUT=AtomicCmd.PIPE)
cmd_2 = AtomicCmd("gzip", IN_STDIN=cmd_1)
assert_equal(pformat(cmd_2), ("<Command = ['gzip']\n"
" STDIN = <PIPE>\n"
" STDOUT* = '${TEMP_DIR}/pipe_gzip_%i.stdout'\n"
" STDERR* = '${TEMP_DIR}/pipe_gzip_%i.stderr'>") % (id(cmd_2), id(cmd_2)))
def test_pformat__atomiccmd__simple_with_temp_stdin__set_cwd():
cmd = AtomicCmd("gzip", TEMP_IN_STDIN="stabstabstab", set_cwd=True)
assert_equal(pformat(cmd), ("<Command = ['gzip']\n"
" STDIN* = 'stabstabstab'\n"
" STDOUT* = 'pipe_gzip_%i.stdout'\n"
" STDERR* = 'pipe_gzip_%i.stderr'\n"
" CWD = '${TEMP_DIR}'>") % (id(cmd), id(cmd)))
def test_pformat__atomiccmd__simple_with_temp_infile():
cmd = AtomicCmd(("cat", "%(TEMP_IN_FILE)s"), TEMP_IN_FILE="infile.txt")
assert pformat(cmd) == ("Command = cat '${TEMP_DIR}/infile.txt'\n"
"STDOUT* = '${TEMP_DIR}/pipe_cat_%i.stdout'\n"
"STDERR* = '${TEMP_DIR}/pipe_cat_%i.stderr'") % (
id(cmd), id(cmd))
def test_pformat__atomiccmd__simple_with_stdin():
cmd = AtomicCmd("gzip", IN_STDIN="/etc/fstab")
assert pformat(cmd) == ("Command = gzip\n"
"STDIN = '/etc/fstab'\n"
"STDOUT* = '${TEMP_DIR}/pipe_gzip_%i.stdout'\n"
"STDERR* = '${TEMP_DIR}/pipe_gzip_%i.stderr'") % (
id(cmd), id(cmd))
def test_pformat__atomiccmd__simple_with_stdout():
cmd = AtomicCmd(("echo", "Water. Water."), OUT_STDOUT="/dev/ls")
assert_equal(pformat(cmd),
("Command = echo 'Water. Water.'\n"
"STDOUT = '${TEMP_DIR}/ls'\n"
"STDERR* = '${TEMP_DIR}/pipe_echo_%i.stderr'")
% (id(cmd),))
def test_pformat__atomiccmd__simple_with_temp_stdout():
cmd = AtomicCmd(("echo", "Oil. Oil."), TEMP_OUT_STDOUT="dm")
assert_equal(pformat(cmd),
("Command = echo 'Oil. Oil.'\n"
"STDOUT* = '${TEMP_DIR}/dm'\n"
"STDERR* = '${TEMP_DIR}/pipe_echo_%i.stderr'")
% (id(cmd),))
def test_pformat__sets__nested():
cmd_1 = AtomicCmd(("echo", "foo"), OUT_STDOUT=AtomicCmd.PIPE)
cmd_2 = AtomicCmd("gzip", IN_STDIN=cmd_1)
cmd_3 = AtomicCmd("sha1sum")
set_1 = ParallelCmds((cmd_1, cmd_2))
set_2 = SequentialCmds((set_1, cmd_3))
assert pformat(set_2) == (
"Sequential processes:\n"
" Parallel processes:\n"
" Process 1:\n"
" Command = echo foo\n"
" STDOUT = Piped to process 2\n"
" STDERR* = '${{TEMP_DIR}}/pipe_echo_{cmd_1}.stderr'\n"
"\n"
" Process 2:\n"
" Command = gzip\n"
" STDIN = Piped from process 1\n"
" STDOUT* = '${{TEMP_DIR}}/pipe_gzip_{cmd_2}.stdout'\n"
" STDERR* = '${{TEMP_DIR}}/pipe_gzip_{cmd_2}.stderr'\n"
"\n"
" Process 3:\n"
" Command = sha1sum\n"
" STDOUT* = '${{TEMP_DIR}}/pipe_sha1sum_{cmd_3}.stdout'\n"
" STDERR* = '${{TEMP_DIR}}/pipe_sha1sum_{cmd_3}.stderr'").format(
cmd_1=id(cmd_1), cmd_2=id(cmd_2), cmd_3=id(cmd_3))
def test_pformat__atomiccmd__simple_with_infile():
cmd = AtomicCmd(("cat", "%(IN_SOMETHING)s"), IN_SOMETHING="/etc/fstab")
assert_equal(pformat(cmd),
("Command = cat /etc/fstab\n"
"STDOUT* = '${TEMP_DIR}/pipe_cat_%i.stdout'\n"
"STDERR* = '${TEMP_DIR}/pipe_cat_%i.stderr'")
% (id(cmd), id(cmd)))
def test_pformat__simple():
cmd = AtomicCmd(("touch", "something"))
assert_equal(pformat(cmd),
("Command = touch something\n"
"STDOUT* = '${TEMP_DIR}/pipe_touch_%i.stdout'\n"
"STDERR* = '${TEMP_DIR}/pipe_touch_%i.stderr'") %
(id(cmd), id(cmd)))
def test_pformat__atomiccmd__simple_with_outfile():
cmd = AtomicCmd(("touch", "%(OUT_RC)s"), OUT_RC="/etc/bashrc")
assert_equal(pformat(cmd),
("Command = touch '${TEMP_DIR}/bashrc'\n"
"STDOUT* = '${TEMP_DIR}/pipe_touch_%i.stdout'\n"
"STDERR* = '${TEMP_DIR}/pipe_touch_%i.stderr'")
% (id(cmd), id(cmd)))
def test_pformat__atomiccmd__simple_with_temp_outfile():
cmd = AtomicCmd(("touch", "%(TEMP_OUT_RC)s"), TEMP_OUT_RC="bashrc")
assert pformat(cmd) == ("Command = touch '${TEMP_DIR}/bashrc'\n"
"STDOUT* = '${TEMP_DIR}/pipe_touch_%i.stdout'\n"
"STDERR* = '${TEMP_DIR}/pipe_touch_%i.stderr'") % (
id(cmd), id(cmd))
def test_pformat__simple():
cmd = AtomicCmd(("touch", "something"))
assert_equal(pformat(cmd),
("Command = touch something\n"
"STDOUT* = '${TEMP_DIR}/pipe_touch_%i.stdout'\n"
"STDERR* = '${TEMP_DIR}/pipe_touch_%i.stderr'")
% (id(cmd), id(cmd)))
def test_pformat__sets__nested():
cmd_1 = AtomicCmd(("echo", "foo"), OUT_STDOUT=AtomicCmd.PIPE)
cmd_2 = AtomicCmd("gzip", IN_STDIN=cmd_1)
cmd_3 = AtomicCmd("sha1sum")
set_1 = ParallelCmds((cmd_1, cmd_2))
set_2 = SequentialCmds((set_1, cmd_3))
assert_equal(pformat(set_2),
("Sequential processes:\n"
" Parallel processes:\n"
" Process 1:\n"
" Command = echo foo\n"
" STDOUT = Piped to process 2\n"
" STDERR* = '${{TEMP_DIR}}/pipe_echo_{cmd_1}.stderr'\n"
"\n"
" Process 2:\n"
" Command = gzip\n"
" STDIN = Piped from process 1\n"
" STDOUT* = '${{TEMP_DIR}}/pipe_gzip_{cmd_2}.stdout'\n"
" STDERR* = '${{TEMP_DIR}}/pipe_gzip_{cmd_2}.stderr'\n"
"\n"
" Process 3:\n"
" Command = sha1sum\n"
" STDOUT* = '${{TEMP_DIR}}/pipe_sha1sum_{cmd_3}.stdout'\n"
" STDERR* = '${{TEMP_DIR}}/pipe_sha1sum_{cmd_3}.stderr'")
.format(cmd_1=id(cmd_1),
cmd_2=id(cmd_2),
cmd_3=id(cmd_3)))
def test_pformat__atomiccmd__simple_with_infile__set_cwd():
cmd = AtomicCmd(("cat", "%(IN_SOMETHING)s"),
IN_SOMETHING="/etc/fstab",
set_cwd=True)
assert_equal(pformat(cmd), ("<Command = ['cat', '/etc/fstab']\n"
" STDOUT* = 'pipe_cat_%i.stdout'\n"
" STDERR* = 'pipe_cat_%i.stderr'\n"
" CWD = '${TEMP_DIR}'>") % (id(cmd), id(cmd)))
def test_pformat__atomiccmd__simple_with_temp_stdin():
cmd = AtomicCmd("gzip", TEMP_IN_STDIN="stabstabstab")
assert_equal(pformat(cmd),
("Command = gzip\n"
"STDIN* = '${TEMP_DIR}/stabstabstab'\n"
"STDOUT* = '${TEMP_DIR}/pipe_gzip_%i.stdout'\n"
"STDERR* = '${TEMP_DIR}/pipe_gzip_%i.stderr'")
% (id(cmd), id(cmd)))
def test_pformat__atomiccmd__simple_with_temp_infile__set_cwd():
cmd = AtomicCmd(("zcat", "%(TEMP_IN_FILE)s"),
TEMP_IN_FILE="infile.gz",
set_cwd=True)
assert_equal(pformat(cmd), ("<Command = ['zcat', 'infile.gz']\n"
" STDOUT* = 'pipe_zcat_%i.stdout'\n"
" STDERR* = 'pipe_zcat_%i.stderr'\n"
" CWD = '${TEMP_DIR}'>") % (id(cmd), id(cmd)))
def _test_pformat__sets__simple(cls, description):
cmd_1 = AtomicCmd(("echo", "foo"), OUT_STDOUT=AtomicCmd.PIPE)
cmd_2 = AtomicCmd("gzip", IN_STDIN=cmd_1)
cmd = cls((cmd_1, cmd_2))
assert_equal(pformat(cmd),
template.format(description=description,
cmd_1_id=id(cmd_1),
cmd_2_id=id(cmd_2)))
def test_pformat__atomiccmd__simple_with_temp_stdout__set_cwd():
cmd = AtomicCmd(("echo", "Room service. Room service."),
TEMP_OUT_STDOUT="pv",
set_cwd=True)
assert_equal(pformat(cmd), ("<Command = ['echo', 'Room service. Room service.']\n"
" STDOUT* = 'pv'\n"
" STDERR* = 'pipe_echo_%i.stderr'\n"
" CWD = '${TEMP_DIR}'>") % (id(cmd),))
def test_pformat__atomiccmd__simple_with_infile__set_cwd():
cmd = AtomicCmd(("cat", "%(IN_SOMETHING)s"),
IN_SOMETHING="/etc/fstab",
set_cwd=True)
assert pformat(cmd) == ("Command = cat /etc/fstab\n"
"STDOUT* = 'pipe_cat_%i.stdout'\n"
"STDERR* = 'pipe_cat_%i.stderr'\n"
"CWD = '${TEMP_DIR}'") % (id(cmd), id(cmd))
def test_pformat__atomiccmd__simple_with_stdin__set_cwd():
cmd = AtomicCmd("gzip", IN_STDIN="/etc/fstab", set_cwd=True)
assert_equal(pformat(cmd),
("Command = gzip\n"
"STDIN = '/etc/fstab'\n"
"STDOUT* = 'pipe_gzip_%i.stdout'\n"
"STDERR* = 'pipe_gzip_%i.stderr'\n"
"CWD = '${TEMP_DIR}'") % (id(cmd), id(cmd)))
def test_pformat__atomiccmd__simple_with_temp_stdin():
cmd = AtomicCmd("gzip", TEMP_IN_STDIN="stabstabstab")
assert_equal(pformat(cmd),
("Command = gzip\n"
"STDIN* = '${TEMP_DIR}/stabstabstab'\n"
"STDOUT* = '${TEMP_DIR}/pipe_gzip_%i.stdout'\n"
"STDERR* = '${TEMP_DIR}/pipe_gzip_%i.stderr'") %
(id(cmd), id(cmd)))
def test_pformat__atomiccmd__simple_with_stdout__set_cwd():
cmd = AtomicCmd(("echo", "*pant*. *pant*."),
OUT_STDOUT="/dev/barf", set_cwd=True)
assert_equal(pformat(cmd),
("Command = echo '*pant*. *pant*.'\n"
"STDOUT = 'barf'\n"
"STDERR* = 'pipe_echo_%i.stderr'\n"
"CWD = '${TEMP_DIR}'") % (id(cmd),))
def test_pformat__atomiccmd__simple_with_temp_stdout__set_cwd():
cmd = AtomicCmd(("echo", "Room service. Room service."),
TEMP_OUT_STDOUT="pv",
set_cwd=True)
assert pformat(cmd) == ("Command = echo 'Room service. Room service.'\n"
"STDOUT* = 'pv'\n"
"STDERR* = 'pipe_echo_%i.stderr'\n"
"CWD = '${TEMP_DIR}'") % (id(cmd), )
def test_pformat__atomiccmd__simple_with_stdin__cmd():
cmd_1 = AtomicCmd("gzip", OUT_STDOUT=AtomicCmd.PIPE)
cmd_2 = AtomicCmd("gzip", IN_STDIN=cmd_1)
assert pformat(cmd_2) == (
"Command = gzip\n"
"STDIN = <PIPE>\n"
"STDOUT* = '${TEMP_DIR}/pipe_gzip_%i.stdout'\n"
"STDERR* = '${TEMP_DIR}/pipe_gzip_%i.stderr'") % (id(cmd_2), id(cmd_2))
def test_pformat__atomiccmd__simple_with_stdout__set_cwd():
cmd = AtomicCmd(("echo", "*pant*. *pant*."),
OUT_STDOUT="/dev/barf",
set_cwd=True)
assert pformat(cmd) == ("Command = echo '*pant*. *pant*.'\n"
"STDOUT = 'barf'\n"
"STDERR* = 'pipe_echo_%i.stderr'\n"
"CWD = '${TEMP_DIR}'") % (id(cmd), )
def _test_pformat__sets__simple(cls, description):
cmd_1 = AtomicCmd(("echo", "foo"), OUT_STDOUT=AtomicCmd.PIPE)
cmd_2 = AtomicCmd("gzip", IN_STDIN=cmd_1)
cmd = cls((cmd_1, cmd_2))
assert_equal(
pformat(cmd),
template.format(description=description,
cmd_1_id=id(cmd_1),
cmd_2_id=id(cmd_2)))
def test_pformat__atomiccmd__simple_with_temp_infile():
cmd = AtomicCmd(("cat", "%(TEMP_IN_FILE)s"),
TEMP_IN_FILE="infile.txt")
assert_equal(pformat(cmd),
("Command = cat '${TEMP_DIR}/infile.txt'\n"
"STDOUT* = '${TEMP_DIR}/pipe_cat_%i.stdout'\n"
"STDERR* = '${TEMP_DIR}/pipe_cat_%i.stderr'")
% (id(cmd), id(cmd)))
def test_pformat__atomiccmd__simple_with_stdin__set_cwd():
cmd = AtomicCmd("gzip", IN_STDIN="/etc/fstab", set_cwd=True)
assert_equal(pformat(cmd),
("Command = gzip\n"
"STDIN = '/etc/fstab'\n"
"STDOUT* = 'pipe_gzip_%i.stdout'\n"
"STDERR* = 'pipe_gzip_%i.stderr'\n"
"CWD = '${TEMP_DIR}'")
% (id(cmd), id(cmd)))
def test_pformat__atomiccmd__simple_with_temp_infile__set_cwd():
cmd = AtomicCmd(("zcat", "%(TEMP_IN_FILE)s"),
TEMP_IN_FILE="infile.gz",
set_cwd=True)
assert pformat(cmd) == ("Command = zcat infile.gz\n"
"STDOUT* = 'pipe_zcat_%i.stdout'\n"
"STDERR* = 'pipe_zcat_%i.stderr'\n"
"CWD = '${TEMP_DIR}'") % (id(cmd), id(cmd))
def test_pformat__atomiccmd__simple_with_temp_outfile__set_cwd():
cmd = AtomicCmd(("touch", "%(TEMP_OUT_RC)s"),
TEMP_OUT_RC="bashrc",
set_cwd=True)
assert pformat(cmd) == ("Command = touch bashrc\n"
"STDOUT* = 'pipe_touch_%i.stdout'\n"
"STDERR* = 'pipe_touch_%i.stderr'\n"
"CWD = '${TEMP_DIR}'") % (id(cmd), id(cmd))
def test_pformat__simple__done__set_cwd(temp_folder):
cmd = AtomicCmd("true", set_cwd=True)
cmd.run(temp_folder)
assert_equal(cmd.join(), [0])
assert_equal(pformat(cmd), ("<Command = ['true']\n"
" Status = Exited with return-code 0\n"
" STDOUT* = 'pipe_true_{id}.stdout'\n"
" STDERR* = 'pipe_true_{id}.stderr'\n"
" CWD = '{temp_dir}'>").format(id=id(cmd),
temp_dir=temp_folder))
def test_pformat__simple__done__set_cwd(tmp_path):
cmd = AtomicCmd("true", set_cwd=True)
cmd.run(tmp_path)
assert cmd.join() == [0]
assert pformat(cmd) == ("Command = true\n"
"Status = Exited with return-code 0\n"
"STDOUT* = 'pipe_true_{id}.stdout'\n"
"STDERR* = 'pipe_true_{id}.stderr'\n"
"CWD = '{temp_dir}'").format(id=id(cmd),
temp_dir=tmp_path)
def test_pformat__simple__running__set_cwd(temp_folder):
cmd = AtomicCmd(("sleep", "10"), set_cwd=True)
cmd.run(temp_folder)
assert_equal(pformat(cmd), ("<Command = ['sleep', '10']\n"
" Status = Running ...\n"
" STDOUT* = 'pipe_sleep_{id}.stdout'\n"
" STDERR* = 'pipe_sleep_{id}.stderr'\n"
" CWD = '{temp_dir}'>").format(id=id(cmd),
temp_dir=temp_folder))
cmd.terminate()
cmd.join()
def test_pformat__simple__running__set_cwd(tmp_path):
cmd = AtomicCmd(("sleep", "10"), set_cwd=True)
cmd.run(tmp_path)
assert pformat(cmd) == ("Command = sleep 10\n"
"Status = Running\n"
"STDOUT* = 'pipe_sleep_{id}.stdout'\n"
"STDERR* = 'pipe_sleep_{id}.stderr'\n"
"CWD = '{temp_dir}'").format(id=id(cmd),
temp_dir=tmp_path)
cmd.terminate()
cmd.join()
def test_pformat__simple__temp_root_in_arguments(tmp_path):
cmd = AtomicCmd(("echo", "${TEMP_DIR}"))
cmd.run(tmp_path)
assert cmd.join() == [0]
assert pformat(cmd) == ("Command = echo '{temp_dir}'\n"
"Status = Exited with return-code 0\n"
"STDOUT* = '{temp_dir}/pipe_echo_{id}.stdout'\n"
"STDERR* = '{temp_dir}/pipe_echo_{id}.stderr'\n"
"CWD = '{cwd}'").format(id=id(cmd),
temp_dir=tmp_path,
cwd=os.getcwd())
def test_pformat__atomiccmd__simple_with_temp_outfile__set_cwd():
cmd = AtomicCmd(("touch", "%(TEMP_OUT_RC)s"),
TEMP_OUT_RC="bashrc",
set_cwd=True)
assert_equal(pformat(cmd),
("Command = touch bashrc\n"
"STDOUT* = 'pipe_touch_%i.stdout'\n"
"STDERR* = 'pipe_touch_%i.stderr'\n"
"CWD = '${TEMP_DIR}'")
% (id(cmd), id(cmd)))
def test_pformat__simple__done__before_join(tmp_path):
cmd = AtomicCmd("true")
cmd.run(tmp_path)
cmd._proc.wait()
assert pformat(cmd) == ("Command = true\n"
"Status = Exited with return-code 0\n"
"STDOUT* = '{temp_dir}/pipe_true_{id}.stdout'\n"
"STDERR* = '{temp_dir}/pipe_true_{id}.stderr'\n"
"CWD = '{cwd}'").format(id=id(cmd),
cwd=os.getcwd(),
temp_dir=tmp_path)
assert cmd.join() == [0]
def test_pformat__simple__done(temp_folder):
cmd = AtomicCmd("true")
cmd.run(temp_folder)
assert_equal(cmd.join(), [0])
assert_equal(pformat(cmd),
("Command = true\n"
"Status = Exited with return-code 0\n"
"STDOUT* = '{temp_dir}/pipe_true_{id}.stdout'\n"
"STDERR* = '{temp_dir}/pipe_true_{id}.stderr'\n"
"CWD = '{cwd}'").format(id=id(cmd),
cwd=os.getcwd(),
temp_dir=temp_folder))
def test_pformat__simple__killed(temp_folder):
cmd = AtomicCmd(("sleep", "10"))
cmd.run(temp_folder)
cmd.terminate()
assert_equal(cmd.join(), ["SIGTERM"])
assert_equal(pformat(cmd), ("<Command = ['sleep', '10']\n"
" Status = Terminated with signal SIGTERM\n"
" STDOUT* = '{temp_dir}/pipe_sleep_{id}.stdout'\n"
" STDERR* = '{temp_dir}/pipe_sleep_{id}.stderr'\n"
" CWD = '{cwd}'>").format(id=id(cmd),
temp_dir=temp_folder,
cwd=os.getcwd()))
def test_pformat__simple__killed_by_signal(tmp_path):
cmd = AtomicCmd(("sleep", "10"))
cmd.run(tmp_path)
os.killpg(cmd._proc.pid, signal.SIGTERM)
assert cmd.join() == ["SIGTERM"]
assert pformat(cmd) == ("Command = sleep 10\n"
"Status = Terminated with signal SIGTERM\n"
"STDOUT* = '{temp_dir}/pipe_sleep_{id}.stdout'\n"
"STDERR* = '{temp_dir}/pipe_sleep_{id}.stderr'\n"
"CWD = '{cwd}'").format(id=id(cmd),
temp_dir=tmp_path,
cwd=os.getcwd())
def test_pformat__simple__done(temp_folder):
cmd = AtomicCmd("true")
cmd.run(temp_folder)
assert_equal(cmd.join(), [0])
assert_equal(pformat(cmd),
("Command = true\n"
"Status = Exited with return-code 0\n"
"STDOUT* = '{temp_dir}/pipe_true_{id}.stdout'\n"
"STDERR* = '{temp_dir}/pipe_true_{id}.stderr'\n"
"CWD = '{cwd}'").format(id=id(cmd),
cwd=os.getcwd(),
temp_dir=temp_folder))
def test_pformat__simple__terminated_by_pipeline(tmp_path):
cmd = AtomicCmd(("sleep", "10"))
cmd.run(tmp_path)
cmd.terminate()
assert cmd.join() == ["SIGTERM"]
assert pformat(cmd) == ("Command = sleep 10\n"
"Status = Automatically terminated by PALEOMIX\n"
"STDOUT* = '{temp_dir}/pipe_sleep_{id}.stdout'\n"
"STDERR* = '{temp_dir}/pipe_sleep_{id}.stderr'\n"
"CWD = '{cwd}'").format(id=id(cmd),
temp_dir=tmp_path,
cwd=os.getcwd())
def test_pformat__simple__running(temp_folder):
cmd = AtomicCmd(("sleep", "10"))
cmd.run(temp_folder)
assert_equal(pformat(cmd),
("Command = sleep 10\n"
"Status = Running ...\n"
"STDOUT* = '{temp_dir}/pipe_sleep_{id}.stdout'\n"
"STDERR* = '{temp_dir}/pipe_sleep_{id}.stderr'\n"
"CWD = '{cwd}'").format(id=id(cmd),
cwd=os.getcwd(),
temp_dir=temp_folder))
cmd.terminate()
cmd.join()
def test_pformat__simple__terminated_by_pipeline(temp_folder):
cmd = AtomicCmd(("sleep", "10"))
cmd.run(temp_folder)
cmd.terminate()
assert_equal(cmd.join(), ["SIGTERM"])
assert_equal(pformat(cmd),
("Command = sleep 10\n"
"Status = Automatically terminated by PALEOMIX\n"
"STDOUT* = '{temp_dir}/pipe_sleep_{id}.stdout'\n"
"STDERR* = '{temp_dir}/pipe_sleep_{id}.stderr'\n"
"CWD = '{cwd}'").format(id=id(cmd),
temp_dir=temp_folder,
cwd=os.getcwd()))
def test_pformat__simple__running(temp_folder):
cmd = AtomicCmd(("sleep", "10"))
cmd.run(temp_folder)
assert_equal(pformat(cmd),
("Command = sleep 10\n"
"Status = Running ...\n"
"STDOUT* = '{temp_dir}/pipe_sleep_{id}.stdout'\n"
"STDERR* = '{temp_dir}/pipe_sleep_{id}.stderr'\n"
"CWD = '{cwd}'").format(id=id(cmd),
cwd=os.getcwd(),
temp_dir=temp_folder))
cmd.terminate()
cmd.join()
def test_pformat__simple__temp_root_in_arguments(temp_folder):
cmd = AtomicCmd(("echo", "${TEMP_DIR}"))
cmd.run(temp_folder)
assert_equal(cmd.join(), [0])
assert_equal(pformat(cmd),
("Command = echo '{temp_dir}'\n"
"Status = Exited with return-code 0\n"
"STDOUT* = '{temp_dir}/pipe_echo_{id}.stdout'\n"
"STDERR* = '{temp_dir}/pipe_echo_{id}.stderr'\n"
"CWD = '{cwd}'")
.format(id=id(cmd),
temp_dir=temp_folder,
cwd=os.getcwd()))
def test_pformat__simple__done__before_join(temp_folder):
cmd = AtomicCmd("true")
cmd.run(temp_folder)
# pylint: disable=protected-access
cmd._proc.wait()
assert_equal(pformat(cmd),
("Command = true\n"
"Status = Exited with return-code 0\n"
"STDOUT* = '{temp_dir}/pipe_true_{id}.stdout'\n"
"STDERR* = '{temp_dir}/pipe_true_{id}.stderr'\n"
"CWD = '{cwd}'").format(id=id(cmd),
cwd=os.getcwd(),
temp_dir=temp_folder))
assert_equal(cmd.join(), [0])
def test_pformat__simple__killed_by_signal(temp_folder):
cmd = AtomicCmd(("sleep", "10"))
cmd.run(temp_folder)
# pylint: disable=protected-access
os.killpg(cmd._proc.pid, signal.SIGTERM)
assert_equal(cmd.join(), ["SIGTERM"])
assert_equal(pformat(cmd),
("Command = sleep 10\n"
"Status = Terminated with signal SIGTERM\n"
"STDOUT* = '{temp_dir}/pipe_sleep_{id}.stdout'\n"
"STDERR* = '{temp_dir}/pipe_sleep_{id}.stderr'\n"
"CWD = '{cwd}'").format(id=id(cmd),
temp_dir=temp_folder,
cwd=os.getcwd()))
def test_pformat__simple__killed_by_signal(temp_folder):
cmd = AtomicCmd(("sleep", "10"))
cmd.run(temp_folder)
# pylint: disable=protected-access
os.killpg(cmd._proc.pid, signal.SIGTERM)
assert_equal(cmd.join(), ["SIGTERM"])
assert_equal(pformat(cmd),
("Command = sleep 10\n"
"Status = Terminated with signal SIGTERM\n"
"STDOUT* = '{temp_dir}/pipe_sleep_{id}.stdout'\n"
"STDERR* = '{temp_dir}/pipe_sleep_{id}.stderr'\n"
"CWD = '{cwd}'").format(id=id(cmd),
temp_dir=temp_folder,
cwd=os.getcwd()))
def test_pformat__simple__done__before_join(temp_folder):
cmd = AtomicCmd("true")
cmd.run(temp_folder)
# pylint: disable=protected-access
cmd._proc.wait()
assert_equal(pformat(cmd),
("Command = true\n"
"Status = Exited with return-code 0\n"
"STDOUT* = '{temp_dir}/pipe_true_{id}.stdout'\n"
"STDERR* = '{temp_dir}/pipe_true_{id}.stderr'\n"
"CWD = '{cwd}'").format(id=id(cmd),
cwd=os.getcwd(),
temp_dir=temp_folder))
assert_equal(cmd.join(), [0])
def _do_test_pformat__sets__simple(cls, description):
cmd_1 = AtomicCmd(("echo", "foo"), OUT_STDOUT=AtomicCmd.PIPE)
cmd_2 = AtomicCmd("gzip", IN_STDIN=cmd_1)
cmd = cls((cmd_1, cmd_2))
assert_equal(pformat(cmd),
("<{description}:\n"
" - <00> Command = ['echo', 'foo']\n"
" STDOUT = <01>\n"
" STDERR* = '${{TEMP_DIR}}/pipe_echo_{cmd_1_id}.stderr'\n"
" - <01> Command = ['gzip']\n"
" STDIN = <00>\n"
" STDOUT* = '${{TEMP_DIR}}/pipe_gzip_{cmd_2_id}.stdout'\n"
" STDERR* = '${{TEMP_DIR}}/pipe_gzip_{cmd_2_id}.stderr'>")
.format(description=description,
cmd_1_id=id(cmd_1),
cmd_2_id=id(cmd_2)))
def test_pformat__sets__simple(cls, description):
template = ("{description}:\n"
" Process 1:\n"
" Command = echo foo\n"
" STDOUT = Piped to process 2\n"
" STDERR* = '${{TEMP_DIR}}/pipe_echo_{cmd_1_id}.stderr'\n"
"\n"
" Process 2:\n"
" Command = gzip\n"
" STDIN = Piped from process 1\n"
" STDOUT* = '${{TEMP_DIR}}/pipe_gzip_{cmd_2_id}.stdout'\n"
" STDERR* = '${{TEMP_DIR}}/pipe_gzip_{cmd_2_id}.stderr'")
cmd_1 = AtomicCmd(("echo", "foo"), OUT_STDOUT=AtomicCmd.PIPE)
cmd_2 = AtomicCmd("gzip", IN_STDIN=cmd_1)
cmd = cls((cmd_1, cmd_2))
assert pformat(cmd) == template.format(description=description,
cmd_1_id=id(cmd_1),
cmd_2_id=id(cmd_2))
def test_pformat__sets__nested():
cmd_1 = AtomicCmd(("echo", "foo"), OUT_STDOUT=AtomicCmd.PIPE)
cmd_2 = AtomicCmd("gzip", IN_STDIN=cmd_1)
cmd_3 = AtomicCmd("sha1sum")
set_1 = ParallelCmds((cmd_1, cmd_2))
set_2 = SequentialCmds((set_1, cmd_3))
assert_equal(pformat(set_2),
("<Sequential commands:\n"
" - Parallel commands:\n"
" - <00> Command = ['echo', 'foo']\n"
" STDOUT = <01>\n"
" STDERR* = '${{TEMP_DIR}}/pipe_echo_{cmd_1_id}.stderr'\n"
" - <01> Command = ['gzip']\n"
" STDIN = <00>\n"
" STDOUT* = '${{TEMP_DIR}}/pipe_gzip_{cmd_2_id}.stdout'\n"
" STDERR* = '${{TEMP_DIR}}/pipe_gzip_{cmd_2_id}.stderr'\n"
" - <02> Command = ['sha1sum']\n"
" STDOUT* = '${{TEMP_DIR}}/pipe_sha1sum_{cmd_3_id}.stdout'\n"
" STDERR* = '${{TEMP_DIR}}/pipe_sha1sum_{cmd_3_id}.stderr'>")
.format(cmd_1_id=id(cmd_1),
cmd_2_id=id(cmd_2),
cmd_3_id=id(cmd_3)))
def test_pformat__bad_input(value):
with pytest.raises(TypeError):
pformat(value)
def __str__(self):
return atomicpp.pformat(self)
def test_pformat__atomiccmd__simple_with_stdout_pipe():
cmd = AtomicCmd(("echo", "!"), OUT_STDOUT=AtomicCmd.PIPE)
assert pformat(
cmd) == ("Command = echo '!'\n"
"STDOUT = <PIPE>\n"
"STDERR* = '${TEMP_DIR}/pipe_echo_%i.stderr'") % (id(cmd), )
def __str__(self):
return atomicpp.pformat(self)
def test_pformat__atomiccmd__simple_with_temp_stdout():
cmd = AtomicCmd(("echo", "Oil. Oil."), TEMP_OUT_STDOUT="dm")
assert pformat(
cmd) == ("Command = echo 'Oil. Oil.'\n"
"STDOUT* = '${TEMP_DIR}/dm'\n"
"STDERR* = '${TEMP_DIR}/pipe_echo_%i.stderr'") % (id(cmd), )
