def get_tree(dict_argv):
"""
Check that arguments given for tree step are compatible
"""
# Get arguments from config file and add them (overwrite if needed)
if not "configfile" in dict_argv:
conf_conffile = utils_argparse.Conf_all_parser("", ["tree"])
else:
conf_conffile = utils_argparse.Conf_all_parser(dict_argv['configfile'],
readsec=["tree"])
# Add arguments from commandline
conf_conffile.update(dict_argv, "tree")
# Add default arguments if not found in commandline nor config file
defaults = {
"verbose": 0,
"quiet": False,
"threads": 1,
"soft": "iqtree",
"model": None,
"boot": 0,
"write_boot": False,
"memory": None,
"fast": False
}
conf_conffile.add_default(defaults, "tree")
conf_conffile.set_boolean("tree", "quiet")
conf_conffile.set_boolean("tree", "fast")
conf_conffile.set_boolean("tree", "write_boot")
conf_conffile.set_int("tree", "boot")
conf_conffile.set_int("tree", "verbose")
conf_conffile.set_int("tree", "threads")
tree_dict = conf_conffile.get_section_dict("tree")
return tree_dict
def test_conf_parser_update(capsys):
"""
Test update section
Update current parameters with values given
"""
c1 = autils.Conf_all_parser(CONFFILE, ["sec1", "sec4"])
update = {"param1": "55", "defparam": "default value"}
# Add default parameters to sec1
c1.update(update, "sec1")
assert c1.get_section_dict("sec1") == {"param1": "55", "param2": "10", 'sec1p': "",
"toto": "parameter", "titi": "my value",
"defparam": "default value"}
assert c1.get_section_dict("sec4") == {}
c1["sec1"]["param1"] == "10"
c1["sec1"]["defparam"] == "default value"
c1["sec4"]["param1"] == "3" # sec4 has default parameter found in configfile
# Add default parameters to sec1
c2 = autils.Conf_all_parser(CONFFILE, ["sec1", "sec4"])
c2.update(update, "sec4")
assert c2.get_section_dict("sec1") == {"param1": "10", "param2": "10", 'sec1p': "",
"toto": "parameter", "titi": "my value"}
assert c2.get_section_dict("sec4") == {"param1": "55", "defparam": "default value"}
c2["sec1"]["param1"] == "10"
c2["sec4"]["param1"] == "55" # sec4 has default parameter found in configfile
def test_conf_parser_init_empty(capsys):
"""
test class Conf_all_parser init when no config file or empty config file
"""
# No conf file, no section
c = autils.Conf_all_parser("")
assert c.sec_dicts == {}
# No conf file, empty section list
c = autils.Conf_all_parser("", [])
assert c.sec_dicts == {}
# No conf file, sections
c = autils.Conf_all_parser("", ["sec1", "sec2"])
assert c.sec_dicts == {"sec1": {}, "sec2": {}}
confdir = os.path.join("test", "data", "generated_by_utils")
os.makedirs(confdir)
conffile = os.path.join(confdir, "conf.ini")
open(conffile, "w").close()
# Empty conffile, no section
c = autils.Conf_all_parser(conffile)
assert c.sec_dicts == {}
# Empty conffile, sections
c = autils.Conf_all_parser(conffile, ["sec1", "sec2"])
assert c.sec_dicts == {"sec1": {}, "sec2": {}}
shutil.rmtree(confdir)
def get_corepers(dict_argv):
"""
Check that arguments given for corepers step are compatible
"""
# Get arguments from config file and add them (overwrite if needed)
if not "configfile" in dict_argv:
conf_conffile = utils_argparse.Conf_all_parser("", ["corepers"])
else:
conf_conffile = utils_argparse.Conf_all_parser(dict_argv['configfile'],
readsec=["corepers"])
# Add arguments from commandline
conf_conffile.update(dict_argv, "corepers")
# Add default arguments if not found in commandline nor config file
defaults = {
"verbose": 0,
"quiet": False,
"tol": 1,
"mixed": False,
"multi": False,
"floor": False,
"threads": 1
}
conf_conffile.add_default(defaults, "corepers")
conf_conffile.set_boolean("corepers", "quiet")
conf_conffile.set_boolean("corepers", "floor")
conf_conffile.set_boolean("corepers", "mixed")
conf_conffile.set_boolean("corepers", "multi")
conf_conffile.set_int("corepers", "verbose")
conf_conffile.set_float("corepers", "tol")
conf_conffile.set_int("corepers", "threads")
corepers_dict = conf_conffile.get_section_dict("corepers")
return corepers_dict
def get_pangenome(dict_argv):
"""
Check that arguments given for pangenome step are compatible
"""
# Get arguments from config file and add them (overwrite if needed)
if not "configfile" in dict_argv:
conf_conffile = utils_argparse.Conf_all_parser("", ["pangenome"])
else:
conf_conffile = utils_argparse.Conf_all_parser(dict_argv['configfile'],
readsec=["pangenome"])
# Add arguments from commandline
conf_conffile.update(dict_argv, "pangenome")
# Add default arguments if not found in commandline nor config file
defaults = {
"verbose": 0,
"threads": 1,
"min_id": 0.8,
"quiet": False,
"clust_mode": 1,
"outfile": "",
"spedir": ""
}
conf_conffile.add_default(defaults, "pangenome")
conf_conffile.set_boolean("pangenome", "quiet")
conf_conffile.set_int("pangenome", "verbose")
conf_conffile.set_int("pangenome", "threads")
conf_conffile.set_float("pangenome", "min_id")
pan_dict = conf_conffile.get_section_dict("pangenome")
return pan_dict
def test_conf_parser_setbool(capsys):
"""
try to convert a given parameter to a boolean
"""
c1 = autils.Conf_all_parser(CONFFILE, ["sec_bool"])
# 0/1 to False/True
c1.set_boolean("sec_bool", "bool num_false")
assert c1["sec_bool"]["bool num_false"] == "0"
assert c1.sec_dicts["sec_bool"]["bool num_false"] == False
c1.set_boolean("sec_bool", "bool_num_true")
assert c1["sec_bool"]["bool_num_true"] == "1"
assert c1.sec_dicts["sec_bool"]["bool_num_true"] == True
# off/on to False/True
c1.set_boolean("sec_bool", "bool_f")
assert c1["sec_bool"]["bool_f"] == "off"
assert c1.sec_dicts["sec_bool"]["bool_f"] == False
c1.set_boolean("sec_bool", "bool_t")
assert c1["sec_bool"]["bool_t"] == "ON"
assert c1.sec_dicts["sec_bool"]["bool_t"] == True
# no/yes to False/True
c1.set_boolean("sec_bool", "bool_n")
assert c1["sec_bool"]["bool_n"] == "no"
assert c1.sec_dicts["sec_bool"]["bool_n"] == False
c1.set_boolean("sec_bool", "bool_y")
assert c1["sec_bool"]["bool_y"] == "YES"
assert c1.sec_dicts["sec_bool"]["bool_y"] == True
# false/true to False/True
c1.set_boolean("sec_bool", "bool_false")
assert c1["sec_bool"]["bool_false"] == "FalSe"
assert c1.sec_dicts["sec_bool"]["bool_false"] == False
c1.set_boolean("sec_bool", "bool_true")
assert c1["sec_bool"]["bool_true"] == "tRUE"
assert c1.sec_dicts["sec_bool"]["bool_true"] == True
# With a boolean called with "", not cleaned
cfg_file = os.path.join("test", "data", "utils", "configfile-str.ini")
c_str = autils.Conf_all_parser(cfg_file, ["sec_bool"], clean_str=False)
with pytest.raises(SystemExit):
c_str.set_boolean("sec_bool", "bool_f")
out, err = capsys.readouterr()
assert ('ERROR: bool_f must be a boolean. Wrong value: "off".') in out
# With a boolean called with "" but cleaned
cfg_file = os.path.join("test", "data", "utils", "configfile-str.ini")
c_str = autils.Conf_all_parser(cfg_file, ["sec_bool"])
c_str.set_boolean("sec_bool", "bool_f")
assert c1["sec_bool"]["bool_f"] == 'off'
assert c1.sec_dicts["sec_bool"]["bool_f"] == False
# error
with pytest.raises(SystemExit):
c1.set_boolean('sec1', "param1")
out, err = capsys.readouterr()
assert ('ERROR: param1 must be a boolean. Wrong value: 10.') in out
def get_prepare(dict_argv):
"""
Check that arguments given for prepare step are compatible
"""
# Get arguments from config file and add them (overwrite if needed)
if not "configfile" in dict_argv:
conf_conffile = utils_argparse.Conf_all_parser("", ["prepare"])
else:
conf_conffile = utils_argparse.Conf_all_parser(dict_argv['configfile'],
readsec=["prepare"])
# Add arguments from commandline
conf_conffile.update(dict_argv, "prepare")
# Add default arguments if not found in cmd line nor config file
defaults = {
"verbose": 0,
"threads": 1,
"cutn": 5,
"l90": 100,
"nbcont": 999,
"levels": "all",
"quiet": False,
"ncbi_species_name": "",
"ncbi_species_taxid": "",
"ncbi_taxid": "",
"strains": "",
"tmp_dir": "",
"db_dir": "",
"info_file": "",
"min_dist": 1e-4,
"max_dist": 0.06,
"norefseq": False,
"only_mash": False,
"ncbi_section": "refseq"
}
conf_conffile.add_default(defaults, "prepare")
# Change to expected types (boolean, int, float)
conf_conffile.set_boolean("prepare", "quiet")
conf_conffile.set_boolean("prepare", "only_mash")
conf_conffile.set_boolean("prepare", "norefseq")
conf_conffile.set_int("prepare", "threads")
conf_conffile.set_int("prepare", "verbose")
conf_conffile.set_int("prepare", "cutn")
conf_conffile.set_int("prepare", "l90")
conf_conffile.set_int("prepare", "nbcont")
conf_conffile.set_float("prepare", "min_dist")
conf_conffile.set_float("prepare", "max_dist")
prep_dict = conf_conffile.get_section_dict("prepare")
return prep_dict
def test_conf_parser_add_default(capsys):
"""
Test add default parameters to config parser.
If parameter given already exists, do nothing. If does not exist, add it with given value
"""
c = autils.Conf_all_parser(CONFFILE, ["sec1", "sec4"])
defaults = {"param1": "55", "defparam": "default value"}
# Add default parameters to sec1
c.add_default(defaults, "sec1")
assert c.get_section_dict("sec1") == {"param1": "10", "param2": "10", 'sec1p': "",
"toto": "parameter", "titi": "my value",
"defparam": "default value"}
assert c.get_section_dict("sec4") == {}
c["sec1"]["param1"] == "10"
c["sec1"]["defparam"] == "default value"
c["sec4"]["param1"] == "3" # sec4 has default parameter found in configfile
# Add default parameters to sec4 (sec1 already have them)
c.add_default(defaults, "sec4")
assert c.get_section_dict("sec1") == {"param1": "10", "param2": "10", 'sec1p': "",
"toto": "parameter", "titi": "my value",
"defparam": "default value"}
assert c.get_section_dict("sec4") == {"param1": "55", "defparam": "default value"}
c["sec1"]["param1"] == "10"
c["sec1"]["defparam"] == "default value"
c["sec4"]["param1"] == "55"
def test_conf_parser_init_notexisting(capsys):
"""
test class Conf_all_parser init when given configfile does not exist
"""
with pytest.raises(SystemExit):
autils.Conf_all_parser("not_existing_conffile.ini")
out, err = capsys.readouterr()
assert "Error: config file not_existing_conffile.ini not found." in out
def get_align(dict_argv):
"""
Check that arguments given for align step are compatible
"""
# Get arguments from config file and add them (overwrite if needed)
if not "configfile" in dict_argv:
conf_conffile = utils_argparse.Conf_all_parser("", ["align"])
else:
conf_conffile = utils_argparse.Conf_all_parser(dict_argv['configfile'],
readsec=["align"])
# Add arguments from commandline
conf_conffile.update(dict_argv, "align")
# Add default arguments if not found in commandline nor config file
defaults = {"prot_ali": False}
conf_conffile.add_default(defaults, "align")
conf_conffile.set_boolean("align", "prot_ali")
ali_dict = conf_conffile.get_section_dict("align")
return ali_dict
def test_conf_parser_init_duplicate(capsys):
"""
test class Conf_all_parser configfile contains a duplicated parameter
-> raises error
"""
conffile = os.path.join("test", "data", "utils", "configfile-dup.ini")
with pytest.raises(SystemExit):
autils.Conf_all_parser(conffile)
out, err = capsys.readouterr()
assert "option 'bool_y' in section 'sec_bool' already exists" in out
def get_annotate(dict_argv):
"""
Check that arguments given for annotate step are compatible
"""
# Get arguments from config file and add them (overwrite if needed)
if not "configfile" in dict_argv:
conf_conffile = utils_argparse.Conf_all_parser("", ["annotate"])
else:
conf_conffile = utils_argparse.Conf_all_parser(dict_argv['configfile'],
readsec=["annotate"])
# Add arguments from commandline
not_allowed = ["l90", "nbcont", "cutn"]
for param in not_allowed:
if param in conf_conffile.get_section_dict("annotate").keys():
print(f"{param} not allowed in annotate section.")
sys.exit(1)
conf_conffile.update(dict_argv, "annotate")
if "date" not in dict(conf_conffile["annotate"]):
import time
date = time.strftime("%m%y")
conf_conffile.update({"date": date}, "annotate")
# Add default arguments if not found in commandline nor config file
defaults = {
"verbose": 0,
"threads": 1,
"quiet": False,
"prodigal_only": False,
"small": False,
"qc_only": False,
"list_file": "list_file",
"db_path": "db_path",
"from_info": False
}
conf_conffile.add_default(defaults, "annotate")
conf_conffile.set_boolean("annotate", "quiet")
conf_conffile.set_boolean("annotate", "prodigal_only")
conf_conffile.set_boolean("annotate", "small")
conf_conffile.set_boolean("annotate", "qc_only")
conf_conffile.set_int("annotate", "verbose")
conf_conffile.set_int("annotate", "threads")
annot_dict = conf_conffile.get_section_dict("annotate")
return annot_dict
def test_conf_parser_setint(capsys):
"""
try to convert a given parameter to an int
"""
c1 = autils.Conf_all_parser(CONFFILE, ["sec1"])
c1.set_int("sec1", "param1")
assert c1["sec1"]["param1"] == "10"
assert c1.sec_dicts["sec1"]["param1"] == 10
# With an int called with "" but cleaned
cfg_file = os.path.join("test", "data", "utils", "configfile-str.ini")
c_str = autils.Conf_all_parser(cfg_file, ["sec2"])
assert c_str.sec_dicts["sec2"]["paramint"] == "2"
c_str.set_int("sec2", "paramint")
assert c_str["sec2"]["paramint"] == "2"
assert c_str.sec_dicts["sec2"]["paramint"] == 2
with pytest.raises(SystemExit):
c1.set_int("sec1", "toto")
out, err = capsys.readouterr()
assert ('ERROR: toto must be an int. Wrong value: parameter.') in out
def test_conf_parser_init():
"""
Test config parser with a given config file. Check value of defaults etc.
"""
# configfile but no section
c = autils.Conf_all_parser(CONFFILE)
assert c["sec1"]["toto"] == "parameter"
assert c["sec1"]["param1"] == "10"
assert c["sec2"]["param1"] == "3"
assert c["sec3"]["param1"] == "3"
assert c["sec1"]["param2"] == "10"
assert c["sec2"]["param2"] == ''
assert c["sec3"]["param2"] == "10"
assert c.sec_dicts == {}
# configfile and 2 sections among 3 existing in configfile
c = autils.Conf_all_parser(CONFFILE, ["sec1", "sec3"])
assert c["sec1"]["toto"] == "parameter"
assert c["sec1"]["param1"] == "10"
assert c["sec2"]["param1"] == "3"
assert c["sec2"]["myval"] == "parameter"
assert c["sec3"]["param1"] == "3"
assert c["sec1"]["param2"] == "10"
assert c["sec2"]["param2"] == ''
assert c["sec3"]["param2"] == "10"
assert c.sec_dicts == {"sec1": {"param1": "10", "param2": "10", 'sec1p': "",
"toto": "parameter", "titi": "my value"},
"sec3": {"param1": "3", "param2": "10"}}
# configfile 2 sections, 1 not in configfile
c = autils.Conf_all_parser(CONFFILE, ["sec1", "sec4"])
assert c["sec1"]["toto"] == "parameter"
assert c["sec1"]["param1"] == "10"
assert c["sec2"]["param1"] == "3"
assert c["sec4"]["param1"] == "3" # created sec4 with default parameters
assert c["sec4"]["param2"] == "10" # created sec4 with default parameters
assert not "toto" in c["sec4"] # created sec4 with default parameters
assert c.sec_dicts == {"sec1": {"param1": "10", "param2": "10", 'sec1p': "",
"toto": "parameter", "titi": "my value"},
"sec4": {}} # But sec4 dict is empty (no param given in configfile)
def test_conf_parser_clean_str(capsys):
"""
Check that surounding "" are removed
"""
cfg_file = os.path.join("test", "data", "utils", "configfile-str.ini")
c = autils.Conf_all_parser(cfg_file, ["sec2", "sec_bool"])
assert c.get_section_dict("sec2") == {"param2": "", "myval": "parameter",
'param3': "myparameter",
"param1": "3", "paramint": "2"}
assert c.get_section_dict("sec_bool") == {"bool num_false": "0", "bool_num_true": "1",
"bool_f": "off", "bool_t": "ON", "bool_n": "no",
"bool_y": "YES",
"bool_false": "FalSe", "bool_true": "tRUE",
"param1": "3", "param2": "10"}
def test_conf_parser_get_section(capsys):
"""
Test get dict of values for a given section
"""
c = autils.Conf_all_parser(CONFFILE, ["sec1", "sec4"])
# Get sec1 dict
assert c.get_section_dict("sec1") == {"param1": "10", "param2": "10", 'sec1p': "",
"toto": "parameter", "titi": "my value"}
assert c.get_section_dict("sec4") == {}
# Try to get sec2 dict, but does not exist
with pytest.raises(SystemExit):
c.get_section_dict("sec2")
out, err = capsys.readouterr()
assert ('No section sec2 in test/data/utils/configfile.ini') in out
def test_conf_parser_setfloat(capsys):
"""
try to convert a given parameter to a float
"""
c1 = autils.Conf_all_parser(CONFFILE, ["sec_float"])
# float with decimal
c1.set_float("sec_float", "float_param")
assert c1["sec_float"]["float_param"] == "0.12"
assert c1.sec_dicts["sec_float"]["float_param"] == 0.12
# exp format
c1.set_float("sec_float", "float_param2")
assert c1["sec_float"]["float_param2"] == "1e5"
assert c1.sec_dicts["sec_float"]["float_param2"] == 100000
with pytest.raises(SystemExit):
c1.set_float("sec1", "toto")
out, err = capsys.readouterr()
assert ('ERROR: toto must be a float. Wrong value: parameter.') in out
# With a fload called with "" but cleaned
cfg_file = os.path.join("test", "data", "utils", "configfile-str.ini")
c_str = autils.Conf_all_parser(cfg_file, ["sec_float"])
assert c_str.sec_dicts["sec_float"]["float_param"] == "0.12"
c_str.set_float("sec_float", "float_param")
assert c_str["sec_float"]["float_param"] == "0.12"
assert c_str.sec_dicts["sec_float"]["float_param"] == 0.12
# With a fload called with "" not cleaned
cfg_file = os.path.join("test", "data", "utils", "configfile-str.ini")
c_str = autils.Conf_all_parser(cfg_file, ["sec_float"], clean_str=False)
assert c_str.sec_dicts["sec_float"]["float_param"] == '"0.12"'
with pytest.raises(SystemExit):
c_str.set_float("sec_float", "float_param")
out, err = capsys.readouterr()
assert ('ERROR: float_param must be a float. Wrong value: "0.12".') in out
def test_conf_parser_init_noCleanStr():
"""
Test config parser with a given config file. Do not clean str (keep surounding "")
"""
# configfile but no section
cfg_file = os.path.join("test", "data", "utils", "configfile-str.ini")
c = autils.Conf_all_parser(cfg_file, clean_str=False)
assert c["sec2"]["param1"] == "3"
assert c["sec2"]["param2"] == ''
assert c["sec2"]["myval"] == '"parameter"'
assert c["sec2"]["param3"] == 'myparameter'
assert c["sec3"]["param1"] == "3"
assert c["sec3"]["param2"] == "10"
assert c["sec_bool"]["bool num_false"] == "0"
assert c["sec_bool"]["bool_t"] == "ON"
assert c["sec_bool"]["bool_f"] == '"off"'
assert c.sec_dicts == {}
