def __listDirectory__(directory, files=False, exclude_pattern_starts_with=None):
"""
Devuelve las carpetas contenidas en el directorio indicado. Si se quieren listar los
ficheros se deberá indicar el argumento files=True. En el caso de querer excluir ficheros o carpetas
se indicará en el argumento exclude_pattern_starts_with con el comienzo de los mism__os.
"""
mypath = __join(__this_dir__, directory)
data = ''
if files:
data = [f for f in __listdir(mypath) if __isfile(__join(mypath, f))]
else:
data = [f for f in __listdir(mypath) if not __isfile(__join(mypath, f))]
if __blacklist_extensions__:
new_data = []
for d in data:
has_extension = False
for black_ext in __blacklist_extensions__:
if black_ext in d:
has_extension = True
if not has_extension:
new_data.append(d)
data = new_data
if exclude_pattern_starts_with:
new_data = []
for d in data:
if not d.startswith(exclude_pattern_starts_with):
new_data.append(d)
data = new_data
if __blacklist_directories__:
new_data = []
for d in data:
for direc in __blacklist_directories__:
if not direc in d:
new_data.append(d)
data = new_data
if __ignore_folders__:
new_data = []
for d in data:
exists = False
for direc in __ignore_folders__:
if direc in d:
exists = True
if not exists:
new_data.append(d)
data = new_data
if files and __ignore_files__:
new_data = []
for d in data:
for file_ign in __ignore_files__:
if not file_ign in d:
new_data.append(d)
data = new_data
return data
def __cleanOutputModules__():
for mod in getModulesNames():
cat = getModuleCategory(mod)
output_dir = __join(__os.path.dirname(__file__), 'modules', cat, mod.replace('ht_', ''), 'output')
if __os.path.isdir(output_dir):
for temp_file in __listdir(output_dir):
__os.remove(__join(output_dir, temp_file))
def get_deck(deck_name: str):
"""Reads a deck file and returns the
ids of the cards in it"""
deck_path = __join(deck_folder_path, f"{deck_name}.ydk")
deck_exists = __exists(deck_path)
if not deck_exists:
return None
deck = open(deck_path, mode="r", encoding="utf8")
cards = __filter_card_id([l.strip() for l in deck.readlines()])
return cards
def which(program):
"""returns path to an executable if it is found in the path"""
fpath, fname = __split(program)
if fpath:
if __isfile(program) and __os.access(program, __os.X_OK):
return program
else:
paths_to_search = __os.environ["PATH"].split(__os.pathsep)
paths_to_search.extend((omelib_directory, ome_directory))
for path in paths_to_search:
exe_file = __join(path, program)
if __isfile(exe_file) and __os.access(exe_file, __os.X_OK):
return exe_file
if __os.name == "nt" and not program.endswith(".exe"):
return which(program + ".exe")
return None
def which(program):
"""returns path to an executable if it is found in the path"""
fpath, fname = __split(program)
if fpath:
if __isfile(program) and __os.access(program, __os.X_OK):
return program
else:
paths_to_search = __os.environ["PATH"].split(__os.pathsep)
paths_to_search.extend((trnlib_directory, trn_directory))
for path in paths_to_search:
exe_file = __join(path, program)
if __isfile(exe_file) and __os.access(exe_file, __os.X_OK):
return exe_file
if __os.name == "nt" and not program.endswith(".exe"):
return which(program + ".exe")
return None
def download_image(card_id: int, is_artwork: bool = False):
"""Downloads the card image or artwork and
puts in the specified folder"""
img_url = "https://storage.googleapis.com/ygoprodeck.com/pics"
if not is_artwork:
img_url += f"/{card_id}.jpg"
store_at = "./pics/"
else:
img_url += f"_artgame/{card_id}.jpg"
store_at = "./pics/field/"
file_path = __join(store_at, f"{card_id}.jpg")
try:
__request.urlretrieve(img_url, file_path)
return True
except Exception as e:
print(e)
return False
def __removeModule__(moduleName, category):
modulePath = __join(__this_dir__, 'modules', category, moduleName.replace('ht_', ''))
try:
__os.chmod(modulePath, 777)
except:
pass
try:
if __os.path.isdir(modulePath):
__shutil.rmtree(modulePath, ignore_errors=True)
except:
pass
try:
if __os.path.isdir(modulePath):
__os.rmdir(modulePath)
except:
pass
try:
if __os.path.isdir(modulePath):
__os.removedirs(modulePath)
except:
pass
from __future__ import with_statement, absolute_import
import sys
from os import name as __name
available_tests = ['unit_tests', 'solvers', 'flux_analysis', 'io_tests']
del __name
from os.path import abspath as __abspath
from os.path import join as __join
from os.path import split as __split
from os.path import sep as __sep
cobra_directory = __abspath(__join(__split(__abspath(__file__))[0], ".."))
cobra_location = __abspath(__join(cobra_directory, ".."))
data_directory = __join(__split(__abspath(__file__))[0], "data")
if not data_directory.endswith(__sep):
data_directory += __sep
salmonella_sbml = __join(data_directory, "salmonella.xml")
salmonella_fbc_sbml = __join(data_directory, "salmonella_fbc.xml")
salmonella_pickle = __join(data_directory, "salmonella.pickle")
salmonella_reaction_p_values_pickle = __join(data_directory, "salmonella_reaction_p_values.pickle")
ecoli_sbml = __join(data_directory, "iJO1366.xml")
ecoli_pickle = __join(data_directory, "iJO1366.pickle")
ecoli_mat = __join(data_directory, "iJO1366.mat")
ecoli_json = __join(data_directory, "iJO1366.json")
yersinia_sbml = __join(data_directory, 'Yersinia_pestis_CO92_iPC815.xml')
yersinia_pickle = __join(data_directory, 'Yersinia_pestis_CO92_iPC815.pickle')
__test_pickles = {'Salmonella_enterica': salmonella_pickle,
'Escherichia_coli': ecoli_pickle,
def load_settings_from_file(filepath="settings.ini", in_trnlib=True):
"""reload settings from a different settings file
filepath: The path to the settings file to use
in_trnlib: Whether or not the path given is a relative path from the trnlib
directory"""
if in_trnlib:
filepath = __join(trnlib_directory, filepath)
config.read(filepath)
# attempt to intellegently determine more difficult settings
if not config.has_option("DATABASE", "user"):
if "USERNAME" in __os.environ: # windows
user = __os.environ["USERNAME"]
elif "USER" in __os.environ: # unix
user = __os.environ["USER"]
config.set("DATABASE", "user", user)
if not config.has_option("EXECUTABLES", "psql"):
psql = which("psql91")
if psql is None:
psql = which("psql")
if psql is None:
psql = "SET_PATH_TO_PSQL"
config.set("EXECUTABLES", "psql", psql)
if not config.has_option("EXECUTABLES", "R"):
R = which("R")
if R is None:
R = "SET_PATH_TO_R"
config.set("EXECUTABLES", "R", R)
if not config.has_option("EXECUTABLES", "Rscript"):
Rscript = which("Rscript")
if Rscript is None:
Rscript = "SET_PATH_TO_Rscript"
config.set("EXECUTABLES", "Rscript", Rscript)
if not config.has_option("EXECUTABLES", "primer3"):
primer3 = which("primer3_core")
if primer3 is None:
primer3 = "./primer3_core"
config.set("EXECUTABLES", "primer3", primer3)
# write the options back to the file
with open(filepath, "w") as outfile:
config.write(outfile)
# save options as variables
self.user = config.get("DATABASE", "user")
self.password = config.get("DATABASE", "password")
if len(self.password) > 0:
__os.environ["PGPASSWORD"] = self.password
self.host = config.get("DATABASE", "host")
self.database = config.get("DATABASE", "database")
self.schema = config.get("DATABASE", "schema")
self.psql = _escape_space(config.get("EXECUTABLES", "psql"))
self.R = _escape_space(config.get("EXECUTABLES", "R"))
self.Rscript = _escape_space(config.get("EXECUTABLES", "Rscript"))
self.primer3 = _escape_space(config.get("EXECUTABLES", "primer3"))
# make a psql string with the database options included
self.hostname, self.port = host.split(":")
self.psql_full = "%s --host=%s --username=%s --port=%s %s" % \
(self.psql, self.hostname, self.user, self.port, self.database)
self.entrez_email = config.get("MISC", "entrez_email")
if self.entrez_email == "SET_ENTREZ_EMAIL": self.entrez_email = None
#set home directory
self.home_directory = config.get("MISC", "home_directory")
self.dropbox_directory = config.get("MISC", "dropbox_directory")
self.data_directory = config.get("MISC", "data_directory")
self.dropbox_trn_directory = self.data_directory # TODO depracate
"""retrive local user settings"""
from ConfigParser import SafeConfigParser
import os as __os
from os.path import split as __split, join as __join, abspath as __abspath, \
isfile as __isfile
from sys import modules
self = modules[__name__]
# define various filepaths
omelib_directory = __join(__split(__abspath(__file__))[0], "")
ome_directory = __join(__abspath(__join(omelib_directory, "..")), "")
def which(program):
"""returns path to an executable if it is found in the path"""
fpath, fname = __split(program)
if fpath:
if __isfile(program) and __os.access(program, __os.X_OK):
return program
else:
paths_to_search = __os.environ["PATH"].split(__os.pathsep)
paths_to_search.extend((omelib_directory, ome_directory))
for path in paths_to_search:
exe_file = __join(path, program)
if __isfile(exe_file) and __os.access(exe_file, __os.X_OK):
return exe_file
if __os.name == "nt" and not program.endswith(".exe"):
return which(program + ".exe")
return None
"""retrive local user settings"""
from configparser import SafeConfigParser
import os as __os
from os.path import split as __split, join as __join, abspath as __abspath, \
isfile as __isfile
from sys import modules
self = modules[__name__]
# define various filepaths
trnlib_directory = __join(__split(__abspath(__file__))[0], "")
trn_directory = __join(__abspath(__join(trnlib_directory, "..")), "")
def which(program):
"""returns path to an executable if it is found in the path"""
fpath, fname = __split(program)
if fpath:
if __isfile(program) and __os.access(program, __os.X_OK):
return program
else:
paths_to_search = __os.environ["PATH"].split(__os.pathsep)
paths_to_search.extend((trnlib_directory, trn_directory))
for path in paths_to_search:
exe_file = __join(path, program)
if __isfile(exe_file) and __os.access(exe_file, __os.X_OK):
return exe_file
if __os.name == "nt" and not program.endswith(".exe"):
return which(program + ".exe")
return None
from __future__ import with_statement, absolute_import
import sys
from os import name as __name
available_tests = ['unit_tests']
del __name
from os.path import abspath as __abspath
from os.path import join as __join
from os.path import split as __split
from os.path import sep as __sep
from cobra.manipulation import initialize_growth_medium
gim3e_directory = __abspath(__join(__split(__abspath(__file__))[0], ".."))
gim3e_location = __abspath(__join(gim3e_directory, ".."))
data_directory = gim3e_directory + "/data/"
gim3e_directory += '/core/'
salmonella_pickle = __join(data_directory, "salmonella_gem.pickle")
ecoli_sbml = __join(data_directory, "E_coli_core_M9.xml")
del __abspath, __join, __split, __sep
def create_test_model(test_pickle=salmonella_pickle):
"""Returns a cobra model for testing. The default model is the
version of the Salmonella enterica Typhimurium LT2 model published in
Thiele et al. 2011 BMC Sys Bio 5:8, which has some updated metabolite
KEGG id data for Schmidt et al. 2013 Bioinformatics
test_pickle: The complete file name of a pickled cobra.Model or SBML XML
file to be read. We currently provide Salmonella enterica Typhimurium
from __future__ import with_statement, absolute_import
import sys
from os import name as __name
available_tests = ['unit_tests']
del __name
from os.path import abspath as __abspath
from os.path import join as __join
from os.path import split as __split
from os.path import sep as __sep
nampy_directory = __abspath(__join(__split(__abspath(__file__))[0], ".."))
nampy_location = __abspath(__join(nampy_directory, ".."))
data_directory = nampy_directory + "/data/"
nampy_directory += '/core/'
humannet_filename = __join(data_directory, "HumanNet_v1_join_networkonly.txt")
recon_1_filename = __join(data_directory, "recon_1_nampy_v01")
del __abspath, __join, __split, __sep
def create_test_model(test_network_file = humannet_filename):
"""Returns a nampy model for testing.
test_network_file: a two-column network file to be read
"""
# from os import name as __name
from nampy.networkio import networkio
def load_settings_from_file(filepath="settings.ini", in_omelib=True):
"""reload settings from a different settings file
filepath: The path to the settings file to use
in_omelib: Whether or not the path given is a relative path from the omelib
directory"""
if in_omelib:
filepath = __join(omelib_directory, filepath)
config.read(filepath)
# attempt to intellegently determine more difficult settings
if not config.has_option("DATABASE", "user"):
if "USERNAME" in __os.environ: # windows
user = __os.environ["USERNAME"]
elif "USER" in __os.environ: # unix
user = __os.environ["USER"]
config.set("DATABASE", "user", user)
if not config.has_option("EXECUTABLES", "psql"):
psql = which("psql91")
if psql is None:
psql = which("psql")
if psql is None:
psql = "SET_PATH_TO_PSQL"
config.set("EXECUTABLES", "psql", psql)
if not config.has_option("EXECUTABLES", "R"):
R = which("R")
if R is None:
R = "SET_PATH_TO_R"
config.set("EXECUTABLES", "R", R)
if not config.has_option("EXECUTABLES", "Rscript"):
Rscript = which("Rscript")
if Rscript is None:
Rscript = "SET_PATH_TO_Rscript"
config.set("EXECUTABLES", "Rscript", Rscript)
if not config.has_option("EXECUTABLES", "primer3"):
primer3 = which("primer3_core")
if primer3 is None:
primer3 = "./primer3_core"
config.set("EXECUTABLES", "primer3", primer3)
if not config.has_option("EXECUTABLES", "cufflinks"):
cufflinks = which("cufflinks")
if cufflinks is None:
cufflinks = "./cufflinks"
config.set("EXECUTABLES", "cufflinks", cufflinks)
# write the options back to the file
with open(filepath, "w") as outfile:
config.write(outfile)
# save options as variables
self.postgres_user = config.get("DATABASE", "postgres_user")
self.postgres_password = config.get("DATABASE", "postgres_password")
if len(self.postgres_password) > 0:
__os.environ["PGPASSWORD"] = self.postgres_password
self.postgres_database = config.get("DATABASE", "postgres_database")
self.postgres_host = config.get("DATABASE", "postgres_host")
self.psql = _escape_space(config.get("EXECUTABLES", "psql"))
self.R = _escape_space(config.get("EXECUTABLES", "R"))
self.Rscript = _escape_space(config.get("EXECUTABLES", "Rscript"))
self.primer3 = _escape_space(config.get("EXECUTABLES", "primer3"))
self.cufflinks = config.get("EXECUTABLES", "cufflinks")
# make a psql string with the database options included
self.hostname, self.port = postgres_host.split(":")
self.psql_full = "%s --host=%s --username=%s --port=%s " % \
(self.psql, self.hostname, self.postgres_user, self.port)
self.entrez_email = config.get("MISC", "entrez_email")
if self.entrez_email == "SET_ENTREZ_EMAIL": self.entrez_email = None
#set home directory
self.home_directory = config.get("MISC", "home_directory")
self.data_directory = config.get("MISC", "data_directory")
"""retrive local user settings"""
from ConfigParser import SafeConfigParser
import os as __os
from os.path import split as __split, join as __join, abspath as __abspath, \
isfile as __isfile
from sys import modules
self = modules[__name__]
# define various filepaths
omelib_directory = __join(__split(__abspath(__file__))[0], "")
ome_directory = __join(__abspath(__join(omelib_directory, "..")), "")
def which(program):
"""returns path to an executable if it is found in the path"""
fpath, fname = __split(program)
if fpath:
if __isfile(program) and __os.access(program, __os.X_OK):
return program
else:
paths_to_search = __os.environ["PATH"].split(__os.pathsep)
paths_to_search.extend((omelib_directory, ome_directory))
for path in paths_to_search:
exe_file = __join(path, program)
if __isfile(exe_file) and __os.access(exe_file, __os.X_OK):
return exe_file
if __os.name == "nt" and not program.endswith(".exe"):
return which(program + ".exe")
return None
"""retrive local user settings"""
from configparser import SafeConfigParser
import os as __os
from os.path import split as __split, join as __join, abspath as __abspath, \
isfile as __isfile
from sys import modules
self = modules[__name__]
# define various filepaths
trnlib_directory = __join(__split(__abspath(__file__))[0], "")
trn_directory = __join(__abspath(__join(trnlib_directory, "..")), "")
def which(program):
"""returns path to an executable if it is found in the path"""
fpath, fname = __split(program)
if fpath:
if __isfile(program) and __os.access(program, __os.X_OK):
return program
else:
paths_to_search = __os.environ["PATH"].split(__os.pathsep)
paths_to_search.extend((trnlib_directory, trn_directory))
for path in paths_to_search:
exe_file = __join(path, program)
if __isfile(exe_file) and __os.access(exe_file, __os.X_OK):
return exe_file
if __os.name == "nt" and not program.endswith(".exe"):
return which(program + ".exe")
return None
from __future__ import with_statement, absolute_import
import sys
from os import name as __name
available_tests = ['unit_tests', 'solvers', 'flux_analysis', 'io_tests']
del __name
from os.path import abspath as __abspath
from os.path import join as __join
from os.path import split as __split
from os.path import sep as __sep
cobra_directory = __abspath(__join(__split(__abspath(__file__))[0], ".."))
cobra_location = __abspath(__join(cobra_directory, ".."))
data_directory = __join(__split(__abspath(__file__))[0], "data")
if not data_directory.endswith(__sep):
data_directory += __sep
salmonella_sbml = __join(data_directory, "salmonella.xml")
salmonella_fbc_sbml = __join(data_directory, "salmonella_fbc.xml")
salmonella_pickle = __join(data_directory, "salmonella.pickle")
salmonella_reaction_p_values_pickle = __join(
data_directory, "salmonella_reaction_p_values.pickle")
ecoli_sbml = __join(data_directory, "iJO1366.xml")
ecoli_pickle = __join(data_directory, "iJO1366.pickle")
ecoli_mat = __join(data_directory, "iJO1366.mat")
ecoli_json = __join(data_directory, "iJO1366.json")
yersinia_sbml = __join(data_directory, 'Yersinia_pestis_CO92_iPC815.xml')
yersinia_pickle = __join(data_directory, 'Yersinia_pestis_CO92_iPC815.pickle')
__test_pickles = {
from __future__ import with_statement, absolute_import
import sys
from os import name as __name
available_tests = ['unit_tests']
del __name
from os.path import abspath as __abspath
from os.path import join as __join
from os.path import split as __split
from os.path import sep as __sep
from cobra.manipulation import initialize_growth_medium
gim3e_directory = __abspath(__join(__split(__abspath(__file__))[0], ".."))
gim3e_location = __abspath(__join(gim3e_directory, ".."))
data_directory = gim3e_directory + "/data/"
gim3e_directory += '/core/'
salmonella_pickle = __join(data_directory, "salmonella_gem.pickle")
ecoli_sbml = __join(data_directory, "E_coli_core_M9.xml")
del __abspath, __join, __split, __sep
def create_test_model(test_pickle=salmonella_pickle):
"""Returns a cobra model for testing. The default model is the
version of the Salmonella enterica Typhimurium LT2 model published in
Thiele et al. 2011 BMC Sys Bio 5:8, which has some updated metabolite
KEGG id data for Schmidt et al. 2013 Bioinformatics
test_pickle: The complete file name of a pickled cobra.Model or SBML XML
file to be read. We currently provide Salmonella enterica Typhimurium
and Escherichia coli core models whose paths are stored in cobra.test.salmonella_pickle
from __future__ import with_statement, absolute_import
import sys
from os import name as __name
available_tests = ['unit_tests', 'solvers', 'flux_analysis']
#if not using jython then add the tests that don't currently run through jython
## if __name != 'java':
## available_tests += ['flux_analysis']
del __name
from os.path import abspath as __abspath
from os.path import join as __join
from os.path import split as __split
from os.path import sep as __sep
cobra_directory = __abspath(__join(__split(__abspath(__file__))[0], ".."))
cobra_location = __abspath(__join(cobra_directory, ".."))
data_directory = __join(__split(__abspath(__file__))[0], "data")
if not data_directory.endswith(__sep):
data_directory += __sep
salmonella_sbml = __join(data_directory, "salmonella.xml")
salmonella_pickle = __join(data_directory, "salmonella.pickle")
salmonella_reaction_p_values_pickle = __join(data_directory, "salmonella_reaction_p_values.pickle")
ecoli_sbml = __join(data_directory, "iJO1366.xml")
ecoli_pickle = __join(data_directory, "iJO1366.pickle")
ecoli_mat = __join(data_directory, "iJO1366.mat")
__test_pickles = {'Salmonella_enterica': salmonella_pickle,
'Escherichia_coli': ecoli_pickle}
__test_xml = {'Salmonella_enterica': salmonella_sbml,
'Escherichia_coli': ecoli_sbml}
