def fetch_core(file_dir, url, access_token):
# Initialize the needed modules
CHandler = urllib2.HTTPCookieProcessor(cookielib.CookieJar())
browser = urllib2.build_opener(CHandler)
browser.addheaders = [('User-agent', 'InFB - [email protected] - http://ruel.me')]
urllib2.install_opener(browser)
# print 'Using access token: %s' % access_token + '\n'
url = 'https://graph.facebook.com/'+url+ ('?limit=100&access_token=%s' % access_token)
print url
res = browser.open(url)
fres = res.read()
jdata = json.loads(fres)
fres = json.dumps(jdata, ensure_ascii=False)
i=1
FileUtility.write(file_dir+"/data"+str(i)+".json",fres)
while len(jdata['data'])>0:
data = jdata['data']
for sub_data in data:
pid = sub_data['id']
FetchPostsDetail.fetch_core(pid,access_token, browser)
url = jdata['paging']['next']
print url
res = browser.open(url)
fres = res.read()
jdata = json.loads(fres)
fres = json.dumps(jdata, ensure_ascii=False)
i=i+1
FileUtility.write(file_dir+"/data"+str(i)+".json", fres)
def testSaveIfEmptyDirectory(self, mocked_pd_csv, mocked_pl_join,
mocked_pl_mkdir, mocked_pl_isdir):
'''
Test that metric is saved correctly with an empty directory path given
'''
# assert mocks
self.assertIs(pd.Series.to_csv, mocked_pd_csv)
self.assertIs(Path.mkdir, mocked_pl_mkdir)
self.assertIs(Path.joinpath, mocked_pl_join)
self.assertIs(Path.is_dir, mocked_pl_isdir)
# create mock values
mocked_metric = pd.Series([.1, .2, .3],
name='metric-mock',
dtype=float)
mocked_pl_isdir.return_value = False # create default directory
mocked_pl_join.return_value = Path('default/directory/file')
# call function to test
fut.save_metric_to_file(mocked_metric) # save to default directory
# assert calls
mocked_pl_isdir.assert_called() # called twice
mocked_pl_mkdir.assert_called_once()
mocked_pl_join.assert_called() # called twice
mocked_pd_csv.assert_called_once()
def index(self):
# Every yield line adds one part to the total result body.
home_page = public.INDEX_PAGE
if not FileUtility.fileExists(home_page):
yield "您所访问的页面不存在！"
if FileUtility.fileSize(home_page) <= 1024:
content = FileUtility.fileRead( home_page )
if content == None:
content = "您所访问的页面不存在！"
yield content
else:
try:
fp = None
fp = open(home_page, "rb")
max_size = FileUtility.fileSize(home_page)
pos = 0
size = 1024
while pos < max_size:
if pos + size >= max_size:
size = max_size - pos
content = fp.read(size)
yield content
pos += size
except Exception, e:
pass
finally:
def fetch_core(uid, access_token):
uid = str(uid)
# Initialize the needed modules
CHandler = urllib2.HTTPCookieProcessor(cookielib.CookieJar())
browser = urllib2.build_opener(CHandler)
browser.addheaders = [('User-agent', 'InFB - [email protected] - http://ruel.me')]
urllib2.install_opener(browser)
# print 'Using access token: %s' % access_token + '\n'
url = 'https://graph.facebook.com/%s?access_token=%s' % (uid, access_token)
print url
res = browser.open(url)
fres = res.read()
jdata = json.loads(fres)
fres = json.dumps(jdata, ensure_ascii=False)
FileUtility.write('data/profile/%s.json' % uid,fres)
# fetch profile picture
if os.path.isfile('data/profile/%s_picture_large.png'%uid) == False:
f = open('data/profile/%s_picture_large.png'%uid,"wb")
f.write(urllib.urlopen('https://graph.facebook.com/%s/picture?type=large'%uid ).read())
f.close()
if os.path.isfile('data/profile/%s_picture.png'%uid) == False:
f = open('data/profile/%s_picture.png'%uid,"wb")
f.write(urllib.urlopen('https://graph.facebook.com/%s/picture'%uid ).read())
f.close()
def load_sgf(self, fn):
content = ""
if fn :
path = os.path.join(self.dbhome, fn)
if FileUtility.fileExists(path):
content = FileUtility.fileRead(path)
return content
def __save(self, df, alpha_date, month, discard_days):
df['code'] = df['code'] + '-CN'
FileUtility.create_dir('{2}/PMOM{0}{1}'.format(month, discard_days, self.output_path))
df = df[['code', 'adj_return']]
df.columns = ['S_INFO_WINDCODE', 'PMOM%s%s_raw' % (month, discard_days)]
df = df.to_csv(
'{3}/PMOM{1}{2}/PMOM{1}{2}_raw_CN_{0}.csv'.format(alpha_date.strftime('%Y%m%d'), month,
discard_days, self.output_path), index=False)
def edit_double_attr(new_attr, rng):
rng = [int(n) for n in rng.split("-")]
remainder = new_attr % 256
multiplier = new_attr // 256
new_attr = remainder + (256 * multiplier)
new_attr = hex(new_attr).encode().split(b'x')
new_attr = new_attr[1].zfill(4)
new_attr = [(new_attr[i:i + 2]) for i in range(0, len(new_attr), 2)]
FileUtility.change_value(new_attr, rng)
def __init__(self, dbfile=None):
if dbfile != None:
self.dbfile = dbfile
else:
self.dbfile = public.DB_FILE
if not FileUtility.fileExists(self.dbfile):
FileUtility.createFile(self.dbfile)
self.conn = None
self.cursor = None
self.conn_failed = False
def prepareConverter(self, fileIn):
FileUtility.isValid(fileIn)
sys.stderr.write("counting lines to prepare converter\n")
numOfLines = FileUtility.countLines(fileIn)
sys.stderr.write(str(numOfLines)+" to read\n")
readed = 0
for line in open(fileIn):
genome = int(line.split()[0])
taxon = int(line.split()[1])
self.Converter[genome] = taxon
readed += 1
if readed%100000 == 0:
sys.stderr.write(str(readed)+" lines readed out of "+str(numOfLines)+"\n")
def prepareConverter(self, fileIn):
FileUtility.isValid(fileIn)
sys.stderr.write("counting lines to prepare converter\n")
numOfLines = FileUtility.countLines(fileIn)
sys.stderr.write(str(numOfLines) + " to read\n")
readed = 0
for line in open(fileIn):
genome = int(line.split()[0])
taxon = int(line.split()[1])
self.Converter[genome] = taxon
readed += 1
if readed % 100000 == 0:
sys.stderr.write(
str(readed) + " lines readed out of " + str(numOfLines) +
"\n")
def __init__(self, callback):
LoadUtility.__init__(self, callback)
phasesToScan = ["phase_3/models"]
self.models = FileUtility.findAllModelFilesInVFS(phasesToScan)
self.version_lbl = None
self.clouds = None
self.barShadow = None
def testValidFilePath(self):
'''
Test that the last element is returned if a valid path is given
'''
valid_path = 'valid/path/to/filename.py'
returned_name = fut.extract_filename(valid_path)
self.assertEqual(returned_name, 'filename.py')
def testEmptyFilePath(self):
'''
Test that an empty filename is returned although an empty
filepath is given
'''
returned_name = fut.extract_filename('')
self.assertEqual(returned_name, '')
def __init__(self, callback):
LoadUtility.__init__(self, callback)
phasesToScan = ['models', 'phase_3/models']
self.models = FileUtility.findAllModelFilesInVFS(phasesToScan)
self.version_lbl = None
self.clouds = None
return
def testEmptyDirectory(self):
'''
Test that a valid list is returned, although
an empty directory is provided
'''
returned_type = fut.get_all_code_files('', ['.h'])
self.assertIsInstance(returned_type, list)
self.assertEqual(returned_type, [])
def testEmptyExtensionsList(self):
'''
Test that a valid list is returned, although
an empty extensions-list is provided
'''
returned_type = fut.get_all_code_files('../', [])
self.assertIsInstance(returned_type, list)
self.assertEqual(returned_type, [])
def is_sgf_file(self, fn):
ext = FileUtility.fileExt(fn)
if ext == 'sgf':
ret = 0
elif ext == 'sgf_':
ret = 1
else:
ret = None
return ret
def loadConverter(self, file):
sys.stderr.write("Loading converter from file\n")
if FileUtility.isValid(file):
f = open(file, "rb")
self.Converter = pickle.load(f)
f.close()
sys.stderr.write("Converted loaded\n")
else:
Error.error("Converter.bin can not be opened. You should produce or reproduce it using prepare.py")
def initDB(self):
"""
初始化每个习题集的数据库，不要sqlite的原因如下：
1）sqlite在cubieboard等板子中速度较慢。
2）sqlite不支持多线程。
每个习题集用一个json数据库文件, 文件名用md5归一化，加载前
先初始化。该数据库文件格式如下：
{
sum: xx,
finish_sum: xx,
current_num: xx,
files:{
<fn1>: { s : 0 | 1, ## status：0：未完成，1：已完成
t1: xxx, ## start time 开始答题时间，以秒为单位
t2: xxx, ## end time 结束答题时间
c : 0 | 1, ## crypt 0：未加密，1：已加密
n : yyy, ## file index number 题目编号
st : xx, ## 行棋的步骤
tr : xx, ## 尝试的步骤
d : 0 | 1 ## 是否看了答案
},
<fn2>: { s : 0 | 1, ## status
t1: xxx, ## start time
t2: xxx, ## end time
c : 0 | 1, ## crypt
n : yyy, ## file index number
st : xx, ## 行棋的步骤
tr : xx, ## 尝试的步骤
d : 0 | 1 ## 是否看了答案
},
....
}
}
"""
if FileUtility.fileExists(self.dbfile): return True
db = {}
files = {}
count = 0
finish = 0
current= 0
for fn in self.sgf_db.list_dir():
crypt = self.is_sgf_file(fn)
if None == crypt: continue
files[fn] = {}
files[fn]['c'] = crypt ## crypt
files[fn]['s'] = 0 ## status
files[fn]['t1']= 0 ## start time
files[fn]['t2']= 0 ## end time
files[fn]['n'] = count ## fn index
count += 1
db['sum'] = count
db['finish_sum'] = finish
db['current_num']= current
db['files'] = files
self.saveDB(self.dbfile, db)
del db
def validate_choice(choice, bound, save=False):
try:
choice = int(choice)
if choice not in range(0, bound + 1): raise ValueError
except ValueError:
if isinstance(choice, str) and choice.upper() == 'S' and bound <= 11:
FileUtility.write_file()
save = True
print("File Saved")
elif isinstance(choice, str) and bound > 50:
print("Non-numeric value entered")
raise ValueError
elif isinstance(choice, int) and choice > bound:
print("Value entered is out of bounds")
raise ValueError
else:
print("Unknown command")
return -1, save
return choice, save
def loadConverter(self, file):
sys.stderr.write("Loading converter from file\n")
if FileUtility.isValid(file):
f = open(file, "rb")
self.Converter = pickle.load(f)
f.close()
sys.stderr.write("Converted loaded\n")
else:
Error.error(
"Converter.bin can not be opened. You should produce or reproduce it using prepare.py"
)
def create_db(self, dest_file, src_path, suffix = ["sgf", "sgf_"]):
try:
tar = None
tar = tarfile.open(dest_file,"w:") ##
path = os.path.normpath(src_path.strip())
for root, dir, files in os.walk(path):
for fn in files:
if FileUtility.fileExt(fn) not in suffix: continue
fullpath = os.path.join(root, fn)
tar.add(fullpath)
except Exception, e:
print e
def read(self, filename, isAbs=False):
if not isAbs:
filename = FileUtility.getAbsFilePath(filename)
file = open(filename)
content = ""
try:
content = file.read()
except:
file.close()
return ErrorCode.Status.READ_FILE_ERROR, content
file.close()
return ErrorCode.Status.SUCC, content
def fetch_core(post_id, access_token, browser):
if os.path.isdir("data/posts/"+post_id) == False:
os.mkdir("data/posts/"+post_id)
else:
print 'File has aleary existed, skip!!'
return
print 'In FetchPostsDetail.py parse' + post_id
url = 'https://graph.facebook.com/'+post_id+ ('&access_token=%s' % access_token)
res = try_brower(browser, url)
fres = res.read()
jdata = json.loads(fres)
fres = json.dumps(jdata, ensure_ascii=False)
FileUtility.write("data/posts/"+post_id+"/content.json",fres)
url = 'https://graph.facebook.com/'+post_id+'/likes'+ ('&access_token=%s' % access_token)
res = try_brower(browser, url)
fres = res.read()
jdata = json.loads(fres)
fres = json.dumps(jdata, ensure_ascii=False)
FileUtility.write("data/posts/"+post_id+"/likes.json",fres)
url = 'https://graph.facebook.com/'+post_id+'/comments'+ ('&access_token=%s' % access_token)
res = try_brower(browser, url)
fres = res.read()
jdata = json.loads(fres)
fres = json.dumps(jdata, ensure_ascii=False)
FileUtility.write("data/posts/"+post_id+"/comments.json",fres)
def write(self, filename, content, isAbs=False):
processingFilename = self.__get_tmp_filename(filename)
if not isAbs:
processingFilename = FileUtility.getAbsFilePath(processingFilename)
file = open(processingFilename, 'w')
try:
file.write(content)
except:
file.close()
return ErrorCode.Status.SAVE_FILE_ERROR
file.close()
shutil.move(processingFilename, filename)
return ErrorCode.Status.SUCC
def read_tree_of_life(self, file_in):
FileUtility.isValid(file_in)
to_read = FileUtility.countLines(file_in)
sys.stderr.write(str(to_read)+" lines to read to construct tree\n")
num_line = 0
for line in open(file_in):
parent = int(line.split()[0])
kid = int(line.split()[1])
if kid == parent:
sys.stderr.write("Warning: I can't create a link from %s to %s (line %s)\n" % (parent, kid, num_line))
continue
if self.node_exist(parent):
if self.node_exist(kid):
self.get_node(parent).add_kid(kid)
self.get_node(kid).set_parent(parent)
else:
new_node = Taxon(kid)
self.create_node(new_node)
self.get_node(parent).add_kid(kid)
self.get_node(kid).set_parent(parent)
else:
if self.node_exist(kid):
new_node = Taxon(parent)
self.create_node(new_node)
self.get_node(kid).set_parent(parent)
self.get_node(parent).add_kid(kid)
else:
new_kid = Taxon(kid)
new_parent = Taxon(parent)
new_kid.set_parent(parent)
new_parent.add_kid(kid)
self.create_node(new_kid)
self.create_node(new_parent)
num_line += 1
if num_line % 100000 == 0:
sys.stderr.write(str(num_line)+" lines read\n")
sys.stderr.write("Tree base constructed\n")
def testNoneListType(self):
'''
Test that an empty list is returned, although
an invalid type is provided, and a warning is thrown
'''
with warnings.catch_warnings(record=True) as w:
# Cause all warnings to always be triggered.
warnings.simplefilter("always")
returned_type = fut.get_all_code_files('../', None)
self.assertIsInstance(returned_type, list)
self.assertEqual(returned_type, [])
self.assertEqual(len(w), 1)
self.assertTrue('Returning empty list..' in str(w[-1].message))
def testSaveIfExistingDirectory(self, mocked_pd_csv, mocked_pl_join,
mocked_pl_isdir):
'''
Test that metric is saved correctly given an existing directory path
'''
# assert mocks
self.assertIs(pd.Series.to_csv, mocked_pd_csv)
self.assertIs(Path.joinpath, mocked_pl_join)
self.assertIs(Path.is_dir, mocked_pl_isdir)
# create mock values
mocked_metric = pd.Series([.1, .2, .3],
name='metric-mock',
dtype=float)
mocked_pl_isdir.return_value = True # given directory given
mocked_pl_join.return_value = Path('default/directory/file')
# call function to test
fut.save_metric_to_file(mocked_metric, 'dummy/directory')
# assert calls
mocked_pl_isdir.assert_called_once()
mocked_pl_join.assert_called_once()
mocked_pd_csv.assert_called_once()
def append(self, filename, content, isAbs=False):
processingFilename = self.__get_tmp_filename(filename)
if os.path.exists(filename):
shutil.copy(filename, processingFilename)
if not isAbs:
processingFilename = FileUtility.getAbsFilePath(processingFilename)
file = open(processingFilename, 'a')
try:
# 移动到文件尾
file.seek(0, 2)
file.write(content)
except:
file.close()
return ErrorCode.Status.SAVE_FILE_ERROR
file.close()
shutil.move(processingFilename, filename)
return ErrorCode.Status.SUCC
def load_conf(self):
try:
conf = FileUtility.readFile(self.conf).replace("\r", "")
exec conf
gl = locals()
for var in self.conf_vars.keys():
if gl.has_key(var):
self.conf_vars[var] = gl[var]
## patch xiti_home, because run as daemon, which need full path
if 'xiti_home' in self.conf_vars:
xiti_home = self.conf_vars['xiti_home']
conf_path, pf = os.path.split(self.conf)
if not os.path.isabs(xiti_home):
xiti_home = os.path.normpath(os.path.join(conf_path, xiti_home))
self.conf_vars['xiti_home'] = xiti_home
self.xiti_conf = [ ["" , self.conf_vars['xiti_conf'] ] ]
del self.conf_vars['xiti_conf']
except Exception, e:
print e
def create_db(self, src_path, suffix = ["sgf", "sgf_"]):
logdb_file = self.dbfile
if os.path.exists(logdb_file):
import FileUtility as fu
dirname = os.path.dirname(logdb_file)
if not fu.pathExists(dirname):
fu.createPath(dirname)
self.createTable()
for p in FileUtility.listAll(src_path, just_directory = True, contain_file = True):
norm_p = p.replace("\\", "/")
if not norm_p.startswith("/"): norm_p = "/" + norm_p
norm_p = UnicodeUtil.get_unicode_str(norm_p)
xiti_set_saved = False
fp = os.path.join(src_path, p.lstrip(os.path.sep))
fp = UnicodeUtil.get_unicode_str(fp)
for fn in FileUtility.listfiles(fp):
#print fn
if FileUtility.fileExt(fn) not in suffix: continue
if xiti_set_saved == False:
fid = file_id(norm_p)
self.add_xiti_set(norm_p, fid)
xiti_set_saved = True
fn = os.path.join(fp, fn)
self.add_xiti(fid, fn)
def populate(self, file_name1, taxon_name):
# Create table...
curs = self.cursor
curs.execute("create table GENOME_TO_TAXON (GENOMES integer, TAXON integer, PRIMARY KEY (GENOMES))")
self.converter.commit()
# Check is file is ok
FileUtility.isValid(file_name1)
sys.stderr.write("counting lines to prepare converter\n")
n_lines = FileUtility.countLines(file_name1)
sys.stderr.write(str(n_lines)+" to read\n")
readed = 0
# populate the DB
for line in open(file_name1):
genome = int(line.split()[0])
taxon = int(line.split()[1])
curs.execute('insert into GENOME_TO_TAXON (GENOMES, TAXON) values (?, ?)', (genome, taxon))
readed += 1
if readed % 10000 == 0:
self.converter.commit()
sys.stderr.write(str(readed)+" lines readed out of "+str(n_lines)+"\n")
FileUtility.isValid(taxon_name)
sys.stderr.write("counting lines to prepare converter\n")
n_lines = FileUtility.countLines(taxon_name)
sys.stderr.write(str(n_lines)+" to read\n")
readed = 0
curs.execute("create table TAXON_NAMES (TAXON integer, NAME VARCHAR(100), RANK VARCHAR(30), "
"PRIMARY KEY (TAXON))")
for line in open(taxon_name):
taxon = int(line.split("\t")[0])
name = str(line.split("\t")[1])
rank = str(line.split("\t")[2]).rstrip("\n")
curs.execute('insert into TAXON_NAMES (TAXON, NAME, RANK) values (?, ?, ?)', (taxon, name, rank))
readed += 1
if readed % 10000 == 0:
self.converter.commit()
sys.stderr.write(str(readed)+" lines readed out of "+str(n_lines)+"\n")
res = try_brower(browser, url)
fres = res.read()
jdata = json.loads(fres)
fres = json.dumps(jdata, ensure_ascii=False)
FileUtility.write("data/posts/"+post_id+"/likes.json",fres)
url = 'https://graph.facebook.com/'+post_id+'/comments'+ ('&access_token=%s' % access_token)
res = try_brower(browser, url)
fres = res.read()
jdata = json.loads(fres)
fres = json.dumps(jdata, ensure_ascii=False)
FileUtility.write("data/posts/"+post_id+"/comments.json",fres)
if __name__ == '__main__':
# Initialize the needed modules
CHandler = urllib2.HTTPCookieProcessor(cookielib.CookieJar())
browser = urllib2.build_opener(CHandler)
browser.addheaders = [('User-agent', 'InFB - [email protected] - http://ruel.me')]
urllib2.install_opener(browser)
FileUtility.user = '******'
FileUtility.make_data_path()
user = '******'
passw = 'plumggmtutu'
token = Token.get(user, passw)
fetch_core('100000154563058_407470182627805', token, browser)
'''
This module contains all character related functions
and also items, reagents, armaments, spells, & equipment
'''
import binascii
import OffsetDict
import FileUtility
# Read the contents of the "SAVED.GAM" file
file = FileUtility.read_file()
SEPARATOR = "________________________________"
# A function that validates the character name
def name_check(name):
if name.isalpha() and len(name) <= 9: return True
else: return False
# A function that reads the character name
def read_name(rng):
rng = [int(n) for n in rng.split("-")]
name = file[rng[0]:rng[1]]
name = b''.join(name)
name = binascii.unhexlify(name).decode()
return name
# A function that edits the character name
print " -c clade file with [o1g1,o1g2....][o2g1,o2g2...]. For"
print " verify_match, this is the coord file"
print " -D directory with sequence files"
print " -gap Gap file generated by ParseBlast.parse_gap"
print " -wdir working dir, default ./"
print " -infile tfasty output"
print " -top return top match only, default 1 (true)"
print ""
sys.exit(0)
if __name__ == '__main__':
util = blast_util()
fm = FastaManager.fasta_manager()
fu = FileUtility.file_util()
pb = ParseBlast.parser()
f = fasta = p = o = g = fasta2 = s1 = s2 = b = dat = c = gap = \
D = wdir = infile = pm = db = fdir = outname = ""
d = 0
m = 9
w = 5000
W = 3
s = w
e = "1"
n = 1
r = 0
F = 0
DEBUG = 0
by = 1
bdir = "/usr/bin/blast"
def list_dir(self):
return FileUtility.listDir(self.dbhome, False, True)
def __init__(self, callback):
LoadUtility.__init__(self, callback)
phasesToScan = ['phase_3.5/models']
self.models = FileUtility.findAllModelFilesInVFS(phasesToScan)
required=False, default=0.00001)
self.parser_plot.add_argument("-t", type=str, help="File type: db or taxonomy. Dafault = taxonomy",
required=False, default="taxonomy")
self.parser_plot.add_argument("-value", type=bool, help="Show values for each bar", required=False,
default=False)
self.parser_plot.add_argument("-multi", type=bool, help="If true, the -f file contains a list of biological"+
"abundance file to plot in the same figure",
required=False, default=False)
self.parser_plot.add_argument("-stacked", type=bool, help="Create a stacked bar graph instead of the"+
"normal graph", required=False, default=False)
self.parser_plot.add_argument("-o", type=str, help="Name of the output file. Will not open a new window",
required=False, default=None)
#parse the args...
self.Arguments = vars(self.parser.parse_args(args))
#Needed to get the args
def getArguments(self):
return self.Arguments
def getParser(self):
return self.parser
if __name__=="__main__":
parser = OptionParser(sys.argv[1:])
arg = parser.getArguments()
print(arg)
print(arg['f'])
print(FileUtility.isValid(arg['f']))
def edit_single_attr(new_attr, rng):
rng = int(rng)
new_attr = hex(int(new_attr)).split('x')
new_attr = new_attr[1].encode().zfill(2)
FileUtility.change_value(new_attr, rng)
def __init__(self, callback):
LoadUtility.__init__(self, callback)
phasesToScan = ['models', 'phase_3/models']
self.models = FileUtility.findAllModelFilesInVFS(phasesToScan)
self.version_lbl = None
return
CONF_DIR = "conf"
LOG_DIR = "log"
WEBUI_DIR = "webui"
XITI_DIR = "sgf"
XITIDB_DIR= "db"
WEBUI_HOME= os.path.abspath(os.path.join("..", WEBUI_DIR))
XITI_HOME = os.path.abspath(os.path.join("..", XITI_DIR))
CONF_FILE = "websrv.conf"
CONF_HOME = os.path.abspath(os.path.join(HOME, CONF_DIR))
LOG_HOME = os.path.abspath(os.path.join(HOME, LOG_DIR))
XITI_DB_HOME= os.path.abspath(os.path.join(CONF_HOME, XITIDB_DIR))
if not os.path.exists(XITI_DB_HOME):
import FileUtility as fu
fu.createDir(XITI_DB_HOME)
SRV_CONF = os.path.join(CONF_HOME, CONF_FILE)
DB_FILE = os.path.abspath(os.path.join(LOG_HOME, "mbdb.dat"))
LOG_FILE = os.path.abspath(os.path.join(LOG_HOME, "log.txt"))
INDEX_PAGE= os.path.abspath(os.path.join(WEBUI_HOME, "weiqi.htm"))
XITI_CONF = os.path.abspath(os.path.join(CONF_HOME, "xiti.conf"))
SGF_DB = os.path.abspath(os.path.join(XITI_HOME, "sgf.db")) ## sgf tar
SGF_DB_FILE = 0
SGF_DB_TAR = 1
SGF_DB_SQL = 2
bool_tbl = {'True': True, 'False': False}
def get_websrv_conf():
def feed(access_token):
dir_path = FileUtility.get_feed_data_path()
print 'now fetching = feed\n'
fetch_core(dir_path, "me/feed", access_token)
def __init__(self, filePath): self.filePath = filePath readData = FileUtility.readFile(filePath) self.height = MerkleTree.getHeightOfMerkleTree(self.filePath, MerkleTree.DEFAULT_CHUNK_SIZE) print "filePath: " + self.filePath + " Length: " + str(len(readData)) + " Height: " + str(self.height) self.buildTree(readData)
def __init__(self, callback):
LoadUtility.__init__(self, callback)
phasesToScan = ['phase_3.5/models']
self.models = FileUtility.findAllModelFilesInVFS(phasesToScan)
def posts(access_token):
dir_path = FileUtility.get_posts_data_path()
print 'now fetching = posts\n'
fetch_core(dir_path, "me/posts", access_token)
def get_file_base64_content(self, fn):
content = FileUtility.fileRead(fn)
if content:
return base64.b64encode(content)
else:
return None
print (" -c clade file with [o1g1,o1g2....][o2g1,o2g2...]. For")
print (" verify_match, this is the coord file")
print (" -D directory with sequence files")
print (" -gap Gap file generated by ParseBlast.parse_gap")
print (" -wdir working dir, default ./")
print (" -infile tfasty output")
print (" -top return top match only, default 1 (true)")
print ("")
sys.exit(0)
if __name__ == '__main__':
util = blast_util()
fm = FastaManager.fasta_manager()
fu = FileUtility.file_util()
pb = ParseBlast.parser()
f = fasta = p = o = g = fasta2 = s1 = s2 = b = dat = c = gap = \
D = wdir = infile = pm = db = fdir = outname = ""
d = 0
m = 9
w = 5000
W = 3
s = w
e = "1"
n = 1
r = 0
F = 0
DEBUG = 0
by = 1
bdir = "/usr/bin/blast"
def open_book(self, book_name):
self._book_handler = FileUtility.bookOperations(book_name)
self._book_handler.open_book()
self._cache = self._book_handler.fill_cache()
def edit_name(new_name, rng):
rng = [int(n) for n in rng.split("-")]
new_name = binascii.hexlify(new_name.encode())
new_name = new_name.ljust(20, b'0')
new_name = [(new_name[i:i + 2]) for i in range(0, len(new_name), 2)]
FileUtility.change_value(new_name, rng, value_flag=1)
