def files_rank_correlation(fileA, fileB):
# read in the file data lines
A_lines = utils.file_read(fileA)
B_lines = utils.file_read(fileB)
assert len(A_lines) == len(B_lines)
correlations = []
# for each line calculate the correlation between the two files
for i in range(len(A_lines)):
# assign an order rank to the values in the line
A_dict_rank = {val: j for j, val in enumerate(A_lines[i].split())}
B_dict_rank = {val: j for j, val in enumerate(B_lines[i].split())}
A_rank = []
B_rank = []
# for each value in line A get the rank order in list A and B
keys = list(A_dict_rank.keys())
max_rank = len(keys)
for key in keys:
A_rank.append(A_dict_rank[key])
B_rank.append(B_dict_rank.get(key, max_rank))
# calculate the spearman's correlation coefficient between the two rankings
corr, _ = stats.spearmanr(A_rank, B_rank)
# print(A_rank)
# print(B_rank)
correlations.append(corr)
return correlations
def generate(self, path):
"""generate an overlay permissions file"""
perm_file = path + '.permissions'
overlay_contents = []
for root, dirs, files in os.walk(path):
for sub_dir in dirs:
overlay_contents.append(os.path.join(root, sub_dir))
for file_name in files:
if not file_name == '.gitignore':
overlay_contents.append(os.path.join(root, file_name))
perm_list = {}
for entry in overlay_contents:
stat = os.stat(entry)
mode = int(oct(stat.st_mode)[3:])
entry = entry.split(path, 1)[1]
if entry == '/root':
perm_list[entry] = ('0700', 0, 0)
elif entry.endswith('.ssh'):
perm_list[entry] = ('0700', 0, 0)
elif entry.endswith('authorized_keys'):
perm_list[entry] = ('0700', 0, 0)
elif entry.startswith('/usr/local/bin'):
perm_list[entry] = ('0755', 0, 0)
elif entry == '/etc/rc.local':
perm_list[entry] = ('0755', 0, 0)
else:
perm_list[entry] = ('%04d' % mode, 0, 0)
if os.path.isfile(perm_file):
data = utils.file_read(perm_file).split('\n')
defined_list = {}
for line in data:
try:
mode, uid, gid, real_path = line.split('\t')
except ValueError:
pass
else:
defined_list[real_path] = (mode, uid, gid)
for real_path in perm_list:
if real_path in defined_list:
perm_list[real_path] = defined_list[real_path]
data = []
header_file = os.path.join(self.cfg['paths']['templates'],
self.cfg['templates']['permission_script'])
header = utils.file_read(header_file)
data.append(header.strip())
for key, value in perm_list.items():
data.append('%s\t%s\t%s\t%s' % (value[0], value[1], value[2], key))
utils.file_write(perm_file, '\n'.join(data) + '\n')
def generate(self, path):
"""generate an overlay permissions file"""
perm_file = path + '.permissions'
overlay_contents = []
for root, dirs, files in os.walk(path):
for sub_dir in dirs:
overlay_contents.append(os.path.join(root, sub_dir))
for file_name in files:
if not file_name == '.gitignore':
overlay_contents.append(os.path.join(root, file_name))
perm_list = {}
for entry in overlay_contents:
stat = os.stat(entry)
mode = int(oct(stat.st_mode)[3:])
entry = entry.split(path, 1)[1]
if entry == '/root':
perm_list[entry] = ('0700', 0, 0)
elif entry.endswith('.ssh'):
perm_list[entry] = ('0700', 0, 0)
elif entry.endswith('authorized_keys'):
perm_list[entry] = ('0700', 0, 0)
elif entry.startswith('/usr/local/bin'):
perm_list[entry] = ('0755', 0, 0)
elif entry == '/etc/rc.local':
perm_list[entry] = ('0755', 0, 0)
else:
perm_list[entry] = ('%04d' % mode, 0, 0)
if os.path.isfile(perm_file):
data = utils.file_read(perm_file).split('\n')
defined_list = {}
for line in data:
try:
mode, uid, gid, real_path = line.split('\t')
except ValueError:
pass
else:
defined_list[real_path] = (mode, uid, gid)
for real_path in perm_list:
if real_path in defined_list:
perm_list[real_path] = defined_list[real_path]
data = []
header_file = os.path.join(self.cfg['paths']['templates'],
self.cfg['templates']['permission_script'])
header = utils.file_read(header_file)
data.append(header.strip())
for key, value in perm_list.items():
data.append('%s\t%s\t%s\t%s' % (value[0], value[1], value[2], key))
utils.file_write(perm_file, '\n'.join(data) + '\n')
def recorrerCarpeta(self, archivo): # print(archivo) if os.path.isdir(archivo): for ruta in os.listdir(archivo): self.recorrerCarpeta(archivo+"/"+ruta) elif os.path.basename(archivo)==self.nombreArchivo and os.path.basename(os.path.dirname(archivo))==self.nombreCarpeta: utils.file_write(archivo, utils.file_read(self.filepath))
def pxe_variables(cfg, address):
"""try to read the pxe variables from the pxelinux.cfg file"""
file_name = os.path.join(cfg['paths']['tftpboot'], 'pxelinux.cfg', address)
if not os.path.isfile(file_name):
raise Exception('"%s" does not exist' % file_name)
data = utils.file_read(file_name)
data = re.search(
r'# \*\*\* start - seedBank pxe variables \*\*\*$(.*?)\*\*\*', data,
re.M | re.S)
data = data.group(1).strip()
data = re.sub('(?m)^#', '', data)
data = [line.strip() for line in data.split('\n') if line]
data = [line.split(' =', 1) for line in data]
data = [(line[0].strip(), line[1].strip()) for line in data]
lines = []
values = ['None', 'False', 'True']
for line in data:
if line[1].startswith('[') or line[1] in values:
lines.append((line[0], ast.literal_eval(line[1])))
else:
lines.append(line)
result = dict(lines)
return result
def puppet(manifest):
"""return the generated seedbank bootstrap init file"""
file_name = os.path.join(cfg['paths']['templates'],
cfg['templates']['puppet_manifest'])
result = utils.file_read(file_name)
result = utils.apply_template(result, {'manifest': manifest}, file_name)
return result
def pxe_variables(cfg, address):
"""try to read the pxe variables from the pxelinux.cfg file"""
file_name = os.path.join(cfg['paths']['tftpboot'], 'pxelinux.cfg', address)
if not os.path.isfile(file_name):
raise Exception('"%s" does not exist' % file_name)
data = utils.file_read(file_name)
data = re.search(
r'# \*\*\* start - seedBank pxe variables \*\*\*$(.*?)\*\*\*',
data, re.M|re.S)
data = data.group(1).strip()
data = re.sub('(?m)^#', '', data)
data = [line.strip() for line in data.split('\n') if line]
data = [line.split(' =', 1) for line in data]
data = [(line[0].strip(), line[1].strip()) for line in data]
lines = []
values = ['None', 'False', 'True']
for line in data:
if line[1].startswith('[') or line[1] in values:
lines.append((line[0], ast.literal_eval(line[1])))
else:
lines.append(line)
result = dict(lines)
return result
def fuzz_check(input_file, n_tests, to_randomize):
"""
Check user inputs and process them as required by fuzz
"""
input_seed = utils.file_read(input_file)
l = len(input_seed)
print('\nInput size is', l, 'bytes')
try:
n_tests = int(n_tests)
if n_tests < 1:
usage('N_TESTS should be > 0')
except ValueError:
usage('"' + str(n_tests) + '" is not a valid integer')
print('Running test', n_tests, 'times')
try:
n_bytes = round(l * float(to_randomize))
if n_bytes < 0 or n_bytes > l:
usage('PART_TO_RANDOMIZE should be between 0 and 1')
except ValueError:
usage('"' + to_randomize + '" is not a valid float')
print('Randomizing', n_bytes, 'bytes\n')
return input_seed, n_tests, n_bytes
def script(self, dst, overlay, prefix):
"""generate the permissions script which will be applied before the end
of an installation"""
path = os.path.join(self.cfg['paths']['overlays'], overlay)
perm_file = path + '.permissions'
perm_script = os.path.join(dst, 'fix_perms.sh')
if os.path.isfile(perm_file):
data = utils.file_read(perm_file).strip()
lines = data.split('\n')
lines = [line for line in lines if not line.startswith('#')]
script = []
for line in lines:
try:
mode, uid, gid, real_path = line.split('\t')
except ValueError:
err = '%s is corrupt, delete or regenerate it with '\
'the "seedbank manage --overlay" command, or fix the '\
'file manually, line "%s" contains errors' % \
(perm_file, line)
raise utils.FatalException(err)
else:
if prefix:
real_path = os.path.join(prefix, real_path[1:])
if real_path.endswith('.sb_template'):
real_path = os.path.splitext(real_path)[0]
script.append('chown %s:%s %s' % (uid, gid, real_path))
script.append('chmod %s %s' % (mode, real_path))
utils.file_write(perm_script, '\n'.join(script))
else:
logging.warning('overlay "%s" has been selected but permission '
'file "%s" does not exist, so all files will be owned by root '
'and will keep the current permissons which could lead to '
'problems', overlay, perm_file)
utils.file_write(perm_script, '')
def puppet(manifest):
"""return the generated seedbank bootstrap init file"""
file_name = os.path.join(cfg['paths']['templates'],
cfg['templates']['puppet_manifest'])
result = utils.file_read(file_name)
result = utils.apply_template(result, {'manifest': manifest}, file_name)
return result
def aplicarSonar(ruta):
text=utils.file_read(ruta)
text=quitCurlyAlones(text)
utils.file_write(ruta, text)
def script(self, dst, overlay, prefix):
"""generate the permissions script which will be applied before the end
of an installation"""
path = os.path.join(self.cfg['paths']['overlays'], overlay)
perm_file = path + '.permissions'
perm_script = os.path.join(dst, 'fix_perms.sh')
if os.path.isfile(perm_file):
data = utils.file_read(perm_file).strip()
lines = data.split('\n')
lines = [line for line in lines if not line.startswith('#')]
script = []
for line in lines:
try:
mode, uid, gid, real_path = line.split('\t')
except ValueError:
err = '%s is corrupt, delete or regenerate it with '\
'the "seedbank manage --overlay" command, or fix the '\
'file manually, line "%s" contains errors' % \
(perm_file, line)
raise utils.FatalException(err)
else:
if prefix:
real_path = os.path.join(prefix, real_path[1:])
if real_path.endswith('.sb_template'):
real_path = os.path.splitext(real_path)[0]
script.append('chown %s:%s %s' % (uid, gid, real_path))
script.append('chmod %s %s' % (mode, real_path))
utils.file_write(perm_script, '\n'.join(script))
else:
logging.warning(
'overlay "%s" has been selected but permission '
'file "%s" does not exist, so all files will be owned by root '
'and will keep the current permissons which could lead to '
'problems', overlay, perm_file)
utils.file_write(perm_script, '')
def run(self, edit):
paquete_snippets=sublime.packages_path()+os.sep+"snippets"
lista=[]
comandos=[]
for archivo in utils.get_files({"folder":paquete_snippets, "ext":"json"}):
snip=utils.load_json(archivo)
lista=lista + list(snip.keys())
lista=list(set(lista))
for snippet in lista:
snippet=snippet.lower().replace("-", "_").replace("(", "").replace(")", "").replace(" ", "").replace("?", "").replace(":", "")
utils.file_write(RUTA_COMANDOS+"code_"+snippet+".bat", "echo code_"+snippet+" > d:/sublime3/comando.txt")
comandos.append("code_"+snippet)
archivos_plantillas=utils.get_files({"folder":RUTA_PLANTILLAS})
for plantilla in archivos_plantillas:
plantilla=os.path.basename(plantilla)
if plantilla.rfind(".")!=-1:plantilla=plantilla[:plantilla.rfind(".")]
plantilla=plantilla.replace(" ", "_").lower()
utils.file_write(RUTA_COMANDOS+"make_"+plantilla+".bat", "echo make_"+plantilla+" > d:/sublime3/comando.txt")
comandos.append("make_"+plantilla)
archivos_python=utils.get_files({"folder":sublime.packages_path(), "ext":".py"})
for programa in archivos_python:
rutaPrograma=programa
try:programa=utils.file_read(programa)
except:
print("saco error al leer : "+rutaPrograma)
continue
comandosPython=re.findall("class ([\w]+)\(sublime_plugin.TextCommand\)",programa, re.IGNORECASE)
for comandoPython in comandosPython:
comandoPython=comandoPython[0].lower()+comandoPython[1:]
cp=""
for c in comandoPython:
if c.isupper():cp+="_"
cp+=c.lower()
if cp.endswith("_command"):cp=cp.replace("_command", "")
comandos.append(cp)
comandosInternos=utils.file_read("D:/sublime3/Data/Packages/User/Default (Windows).sublime-keymap")
comandosInternos=re.findall('"command": *"(\w+)" *\}', comandosInternos, re.IGNORECASE)
for comandoInterno in comandosInternos:comandos.append(comandoInterno)
comandos=sorted(list(set(comandos)))
strComandos=""
for comando in comandos:strComandos+=comando+"\n"
window=sublime.active_window()
view=window.active_view()
utils.file_write("d:/sublime3/comandos.txt", strComandos)
view.run_command("ejecutar_comando", {"comando":"taskkill /f /im CustomizeableJarvis.exe\njarvis\nexit"})
def rclocal(address):
"""return the rc.local file"""
pxe_vars = settings.pxe_variables(cfg, address)
file_name = os.path.join(cfg['paths']['templates'],
cfg['templates']['rc_local'])
result = utils.file_read(file_name)
result = utils.apply_template(result, pxe_vars, file_name)
return result
def rclocal(address):
"""return the rc.local file"""
pxe_vars = settings.pxe_variables(cfg, address)
file_name = os.path.join(cfg['paths']['templates'],
cfg['templates']['rc_local'])
result = utils.file_read(file_name)
result = utils.apply_template(result, pxe_vars, file_name)
return result
def original_count_comment(directory_seq, date, basedir, seconddir='comments'):
targetpath = target_path(directory_seq, date, basedir,seconddir)
filenames = glob.glob('%s/*.json' % targetpath)
cnt_comments = 0
for i, filename in enumerate(filenames):
items = file_read(filename)
cnt_comments = cnt_comments + len(items['comments'])
return cnt_comments
def count_blog_by_directory(directory_seq, date, basedir, seconddir='texts'):
#basedir: /var/data/naver-blog/
targetpath = target_path(directory_seq, date, basedir,seconddir)
filenames = glob.glob('%s/*.json' % targetpath)
cnt_image = 0
for i, filename in enumerate(filenames):
items = file_read(filename)
cnt_image = cnt_image + len(items['images'])
return (len(filenames), cnt_image)
def return_information(directory_seq,
basedir,
date,
crawler_version,
seconddir="lists",
thirddir="texts",
debug=False):
if debug:
print "Start blog text crawling..."
directory_seq = int(directory_seq)
try:
targetpath = '%s/%s/%02d/%s/%02d/%02d'\
% (basedir, seconddir, directory_seq,\
int(date[0:4]), int(date[5:7]), int(date[8:10]))
except TypeError as e:
print e
raise Exception('Please check input values (ex: the date)')
itr1 = 0
filenames = glob.glob('%s/*.json' % targetpath)
for filename in filenames:
print filename
items = file_read(filename)
itr2 = 0
for i, blog in enumerate(items):
try:
check_targetpath = '%s/%s/%02d/%s/%02d/%02d'\
% (basedir, thirddir, directory_seq,\
int(date[0:4]), int(date[5:7]), int(date[8:10]))
check_filename = '%s.json' % (items[i]['logNo'])
if not os.path.isfile('%s/%s' %
(check_targetpath, check_filename)):
web_crawl(items[i]['blogId'],
items[i]['logNo'],
items[i]['crawledTime'],
crawler_version,
items[i]['title'],
items[i]['writtenTime'],
items[i]['url'],
items[i]['tags'],
date,
directory_seq,
basedir,
debug=debug)
except Exception as e:
print e
itr2 += 1
if itr2 == len(items):
print "%s items read completed successfully." % len(items)
else:
print "Not all items read."
itr1 += 1
if len(filenames) == itr1:
print "%s files read completed successfully." % len(filenames)
if len(filenames) == 0:
print "You probably have to crawl lists first."
else:
print "Not all files read."
def original_count_blog_by_directory(directory_seq, date, basedir, seconddir='lists'):
targetpath = target_path(directory_seq, date, basedir,seconddir)
filenames = glob.glob('%s/*.json' % targetpath)
cnt_lists_blog = 0
for i, filename in enumerate(filenames):
items = file_read(filename)
cnt_lists_blog = cnt_lists_blog + len(items)
return cnt_lists_blog
def on_post_save(self, view):
if utils.get_language()!="jsf":return
window=sublime.active_window()
folders=window.folders()
if not folders:return
folderProyecto=folders[0]
if not os.path.exists(os.path.join(folderProyecto, "pom.xml")):return
server=utils.get_preference("server")
folderDeploy=server_folder_deploy[server]
self.folderDeploy=folderDeploy
filepath=utils.get_filepath()
self.filepath=filepath
if server=="weblogic":
threading.Thread(target=self.reemplazarTodos).start()
return
if server!="jboss":
folderDeploy=folderDeploy+os.sep+os.listdir(folderDeploy)[0]
self.folderDeploy=folderDeploy
folderDeploy=os.path.normpath(folderDeploy)
print("the folder deploy is : "+folderDeploy)
nombreProyecto=filepath.replace(folderProyecto+os.sep, "")
#print("el nombre del proyceto es : "+nombreProyecto)
nombreProyecto=nombreProyecto[:nombreProyecto.find(os.sep)]
#print("el nuevo nombre del proyecto es: "+nombreProyecto)
#print("el filepath es : "+filepath)
#print("el folderDeploy es : "+folderDeploy)
fileLocation=filepath[filepath.find("webapp"+os.sep)+7:]
#print("el fileLocation is: "+fileLocation)
print(server)
print("el nombre del proyecto es : "+nombreProyecto)
folders=os.listdir(folderDeploy)
folders=[os.path.join(folderDeploy, x) for x in folders]
def comparador(x):return os.path.getmtime(x)
folders=sorted(folders, key=comparador, reverse=True)
print(folders)
for folderS in folders:
for folder in os.listdir(folderS):
print(folder)
if folder.find(nombreProyecto)!=-1:
fileLocation=folderS+os.sep+folder+os.sep+fileLocation
print("la nueva localizacion del archivo es : "+fileLocation)
utils.file_write(fileLocation, utils.file_read(filepath))
#print("escrito con exito")
return
else:print("no")
def plot_group(inputdir, outputdir, recall_pct):
filecount = 0
group = os.path.basename(inputdir)
filepattern = os.path.join(inputdir, filebase + r'*')
res = StructDict()
for resultfile in glob.iglob(filepattern):
# read in the results files per query size
# get the query size from the end part of the file name
qsize = os.path.basename(resultfile).split('.')[-1]
qsize = int(qsize)
lines = file_read(resultfile)
# 1st line is min/max
# 2nd line is 1st, 2nd, 3rd quartile
minmax = [float(x) for x in lines[0].split()]
quartiles = [float(x) for x in lines[1].split()]
vals = StructDict(
{'min': minmax[0],
'max': minmax[1],
'quart1': quartiles[0],
'quart2': quartiles[1],
'quart3': quartiles[2]}
)
res[qsize] = vals
filecount += 1
# create an array of result values per query size
qsizes = list(res.keys())
qsizes.sort()
print(qsizes)
quartile_1 = [res[qsize]['quart1'] for qsize in qsizes]
quartile_2 = [res[qsize]['quart2'] for qsize in qsizes]
quartile_3 = [res[qsize]['quart3'] for qsize in qsizes]
print(res)
print(quartile_1)
print(quartile_2)
print(quartile_3)
print("Dir {} processed {} files".format(group, filecount))
# plot the array
plt.plot(qsizes, quartile_1, color="gray")
plt.plot(qsizes, quartile_2, color="black")
plt.plot(qsizes, quartile_3, color="gray")
plt.ylim(ymin=0)
plt.grid(which='major', linewidth='0.5', color='darkgray')
plt.grid(which='minor', linewidth='0.5', color='lightgray')
plt.fill_between(qsizes, quartile_1, quartile_3, color="gray")
plt.title('Processes {} genes'.format(group))
plt.xlabel('Query size')
plt.ylabel('Fold precision at {}% over random'.format(recall_pct))
# plt.draw()
# plt.pause(1)
filename = "{}r{}.pdf".format(group, recall_pct)
outputfile = os.path.join(outputdir, filename)
plt.savefig(outputfile)
resfile = os.path.join(outputdir, filename.replace('pdf', 'csv'))
save_vals(res, resfile)
def plot_curve(inputdir, outputdir):
filecount = 0
res = StructDict()
filepattern = os.path.join(inputdir, filebase + r'*')
for resultfile in glob.iglob(filepattern):
# read in the results files per query size
# get the query size from the end part of the file name
recall_pct = os.path.basename(resultfile).split('.')[-1]
recall_pct = int(recall_pct)
lines = file_read(resultfile)
# 1st line is min/max
# 2nd line is 1st, 2nd, 3rd quartile
minmax = [float(x) for x in lines[0].split()]
quartiles = [float(x) for x in lines[1].split()]
vals = StructDict({
'min': minmax[0],
'max': minmax[1],
'quart1': quartiles[0],
'quart2': quartiles[1],
'quart3': quartiles[2]
})
res[recall_pct] = vals
filecount += 1
# create an array of result values per query size
recall_depths = list(res.keys())
recall_depths.sort()
print(recall_depths)
quartile_1 = [res[depth]['quart1'] for depth in recall_depths]
quartile_2 = [res[depth]['quart2'] for depth in recall_depths]
quartile_3 = [res[depth]['quart3'] for depth in recall_depths]
print(res)
print(quartile_1)
print(quartile_2)
print(quartile_3)
print("Processed {} files".format(filecount))
# plot the array
plt.plot(recall_depths, quartile_1, color="gray")
plt.plot(recall_depths, quartile_2, color="black")
plt.plot(recall_depths, quartile_3, color="gray")
plt.ylim(ymin=0)
plt.xscale('log')
plt.grid(which='major', linewidth='0.5', color='darkgray')
plt.grid(which='minor', linewidth='0.5', color='lightgray')
plt.fill_between(recall_depths, quartile_1, quartile_3, color="gray")
plt.title('Seek Search Performance')
plt.xlabel('Recall Percent')
plt.ylabel('Fold precision over random')
# plt.draw()
# plt.pause(1)
filename = "precision_vs_depth.pdf"
outputfile = os.path.join(outputdir, filename)
plt.savefig(outputfile)
resfile = os.path.join(outputdir, filename.replace('pdf', 'csv'))
save_vals(res, resfile)
def _merge_seeds(self, seeds, values):
"""merge the main seed file with the recipe(s) and additional seeds
return it as a string"""
result = ''
for seed in seeds:
file_name = os.path.join(self.cfg['paths']['seeds'], seed + '.seed')
logging.info('applying template values to "%s"', file_name)
data = utils.file_read(file_name)
result += utils.apply_template(data, values, file_name)
return result
def run(self, edit):
archivos=utils.get_files({"folder":sublime.packages_path(), "ext":"py"})
comandos=[]
for archivo in archivos:
texto=utils.file_read(archivo)
comandos+=re.findall("class\s+([\w]+)\(sublime_plugin.TextCommand\):", texto, flags=re.IGNORECASE)
comandos=list(set(comandos))
# print(comandos)
for comando in comandos:
self.generar_comando(comando)
def makePlot1aFilelists(golddir, resultdir, outputdir, genefile):
golddir = utils.makeAbsolutePath(golddir)
resultdir = utils.makeAbsolutePath(resultdir)
outputdir = utils.makeAbsolutePath(outputdir)
genefile = utils.makeAbsolutePath(genefile)
# Note: query and gold standard files will be from the known good results dir
# in this case the 'golddir'
# gscore files will be from the 'resultdir'
filecount = 0
filepattern = os.path.join(golddir, r'[0-9]*.query')
for queryfile in glob.iglob(filepattern):
filecount += 1
# print(queryfile)
# read file to find query size
lines = utils.file_read(queryfile)
assert len(lines) == 1
num_genes = len(lines[0].split())
outbasename = os.path.join(outputdir, 'filelist_q{}'.format(num_genes))
# append the files to the appropriate file lists
# query file list
queryfilelist = outbasename + '.query'
utils.file_appendline(queryfilelist, queryfile)
# gold standard file list
# - gold standard file is the genes that should be correlated with the query genes
goldfilelist = outbasename + '.gold'
utils.file_appendline(goldfilelist, re.sub('query$', 'gold',
queryfile))
# query results 'gscore' file list
# - gscore are the resulting gene correlation scores from the SeekMiner query result
gscorefilelist = outbasename + '.gscore'
qbasename = os.path.basename(queryfile)
gscorefile = os.path.join(resultdir,
qbasename.replace('query', 'gscore'))
utils.file_appendline(gscorefilelist, gscorefile)
# include file list - genes to include in the results
includefile = outbasename + '.include'
utils.file_appendline(includefile, genefile)
# excluse file list
# exclude all genes in the query file
excludefile = outbasename + '.exclude'
utils.file_appendline(excludefile, queryfile)
if filecount == 0:
print("No matching files found")
exit(-1)
print("Num files processed: {}".format(filecount))
def _merge_seeds(self, seeds, values):
"""merge the main seed file with the recipe(s) and additional seeds
return it as a string"""
result = ''
for seed in seeds:
file_name = os.path.join(self.cfg['paths']['seeds'],
seed + '.seed')
logging.info('applying template values to "%s"', file_name)
data = utils.file_read(file_name)
result += utils.apply_template(data, values, file_name)
return result
def crearArchivo(self):
archivo=self.opcion.split(":")
print(archivo)
self.lang=archivo[0].strip()
lang=self.lang
archivo=lang+"/"+archivo[1].strip()+"."+self.extension
archivo=TEMPLATES_PATH+archivo
print("la ubicacion del archivo es : "+archivo)
self.text=utils.file_read(archivo)
print(self.text)
window=sublime.active_window()
window.show_input_panel("File Name", "", self.pedirNombre, None, None)
def generate(self):
"""generate the pxe boot file"""
self.pxe_variables.update({
'config': self.config,
'seeds': self.seeds,
'seed_host': cfg['settings']['seed_host'],
'seed_port': cfg['settings']['bottle_port'],
'address': self.address,
'overlay': self.overlay,
'puppet_manifests': self.puppet,
'host_name': self.host_name,
'dns_domain': self.dns_domain,
'fqdn': self.fqdn,
'query': urllib.urlencode([('address', self.address)]),
'date_generated': utils.date_time(),
'date_disabled': '',
'kernel': '%s/%s/%s' % ('seedbank', self.release, 'linux'),
'initrd': '%s/%s/%s' % ('seedbank', self.release, 'initrd.gz')
})
if self.config:
yaml_file = os.path.join(cfg['paths']['configs'], self.config)
yaml_file = yaml_file + '.yaml'
overrides = utils.yaml_read(yaml_file)
if 'pxe' in overrides:
cfg['pxe'].update(overrides['pxe'])
values = cfg['pxe']
self.pxe_variables.update(values)
distribution = self.release.split('-')[0]
file_name = cfg[distribution]['template_pxe']
file_name = os.path.join(cfg['paths']['templates'], file_name)
if not os.path.isfile(file_name):
err = 'file "%s" does not exist (hint: check the templates '\
'section in your settings)' % file_name
raise utils.FatalException(err)
pxe_variables_custom = []
for variable in self.variables:
key, value = variable
pxe_variables_custom.append('# %s = %s' % (key, value))
self.pxe_variables[key] = value
pxe_variables_custom = '\n'.join(pxe_variables_custom)
data = utils.file_read(file_name)
data = utils.apply_template(data, self.pxe_variables, file_name)
if pxe_variables_custom:
data = re.sub(
'(#\n# \*\*\* end - seedBank pxe variables \*\*\*)',
pxe_variables_custom + '\n\\1', data)
return data
def return_information(directory_seq, basedir, date, crawler_version, seconddir ="lists", thirddir="texts", debug=False):
if debug:
print "Start blog text crawling..."
directory_seq = int(directory_seq)
try:
targetpath = '%s/%s/%02d/%s/%02d/%02d'\
% (basedir, seconddir, directory_seq,\
int(date[0:4]), int(date[5:7]), int(date[8:10]))
except TypeError as e:
print e
raise Exception('Please check input values (ex: the date)')
itr1 = 0
filenames = glob.glob('%s/*.json' % targetpath)
for filename in filenames:
print filename
items = file_read(filename)
itr2 = 0
for i, blog in enumerate(items):
try:
check_targetpath = '%s/%s/%02d/%s/%02d/%02d'\
% (basedir, thirddir, directory_seq,\
int(date[0:4]), int(date[5:7]), int(date[8:10]))
check_filename = '%s.json' % (items[i]['logNo'])
if not os.path.isfile('%s/%s' % (check_targetpath, check_filename)):
web_crawl(items[i]['blogId'],
items[i]['logNo'],
items[i]['crawledTime'],
crawler_version,
items[i]['title'],
items[i]['writtenTime'],
items[i]['url'],
items[i]['tags'],
date,
directory_seq,
basedir, debug=debug)
except Exception as e:
print e
itr2 += 1
if itr2 == len(items):
print "%s items read completed successfully." % len(items)
else:
print "Not all items read."
itr1 += 1
if len(filenames) == itr1:
print "%s files read completed successfully." % len(filenames)
if len(filenames)==0:
print "You probably have to crawl lists first."
else:
print "Not all files read."
def run(self, edit, **args):
if not args.get("nombre"):return
nombre=args.get("nombre")
for c in os.listdir(TEMPLATES_PATH):
# print(c)
if nombre.lower()==c.lower()[:c.rfind(".")]:
texto=utils.file_read(TEMPLATES_PATH+"/"+c)
self.texto=texto
if not utils.get_text().strip():
self.insertar()
else:
# print("no tiene texto")
self.texto=texto
window=sublime.active_window()
window.show_input_panel("", c[c.rfind("."):], self.crear_archivo, None, None)
def run(self, edit):
d={}
modulos=utils.file_read(GO_API_FILE)
lineas=modulos.splitlines()
for linea in lineas:
if linea:
ocurrencias=re.findall(REGEX_FUNCION, linea, re.IGNORECASE)
if ocurrencias:
paquete=ocurrencias[0][0]
if paquete.find("/")!=-1:paquete=paquete[paquete.find("/")+1:]
funcion=ocurrencias[0][1]
if not d.get(paquete):d[paquete]=[]
d[paquete].append(funcion)
utils.save_json(GO_MAIN_MODULE, d)
for key in d.keys():
utils.save_json(GO_MODULES+key+".json", d[key])
def original_count_blog_by_time(directory_seq, date, basedir, seconddir='lists'):
time_cnt = {}
for d in range(0, 2):
tmp_date = datetime.strptime(date, '%Y-%m-%d') + timedelta(days=d)
tmp_date = tmp_date.isoformat()
targetpath = target_path(directory_seq, tmp_date, basedir,seconddir)
filenames = glob.glob('%s/*.json' % targetpath)
for i, filename in enumerate(filenames):
items = file_read(filename)
for j, item in enumerate(items):
written_time = item['writtenTime']
if int(written_time[8:10]) == int(date[8:10]):
key = int(written_time[11:13])
if key in time_cnt.keys():
time_cnt[key] += 1
else:
time_cnt[key] = 0
return [time_cnt]
def return_information(directory_seq, basedir, date, crawler_version,\
seconddir ="lists", thirddir="comments", debug=False):
directory_seq = int(directory_seq)
try:
targetpath = '%s/%s/%02d/%s/%02d/%02d'\
% (basedir, seconddir, directory_seq,\
int(date[0:4]), int(date[5:7]), int(date[8:10]))
except TypeError:
raise Exception('Please check input values (ex: the date)')
itr1 = 0
filenames = glob.glob('%s/*.json' % targetpath)
for filename in filenames:
print filename
items = file_read(filename)
itr2 = 0
for i, blog in enumerate(items):
check_targetpath = '%s/%s/%02d/%s/%02d/%02d'\
% (basedir, thirddir, directory_seq,\
int(date[0:4]), int(date[5:7]), int(date[8:10]))
check_filename = '%s.json' % (items[i]['logNo'])
if not os.path.isfile('%s/%s' %
(check_targetpath, check_filename)):
comment_crawl(items[i]['blogId'],
items[i]['logNo'],
items[i]['writtenTime'],
date,
directory_seq,
basedir,
crawler_version,
debug=debug)
time.sleep(0.1)
itr2 += 1
if itr2 == len(items):
print "%s items read completed successfully." % len(items)
else:
print "Not all items read."
itr1 += 1
if len(filenames) == itr1:
print "%s files read completed successfully." % len(filenames)
else:
print "Not all files read."
def return_information(directory_seq, basedir, date, crawler_version,\
seconddir ="lists", thirddir="comments", debug=False):
directory_seq = int(directory_seq)
try:
targetpath = '%s/%s/%02d/%s/%02d/%02d'\
% (basedir, seconddir, directory_seq,\
int(date[0:4]), int(date[5:7]), int(date[8:10]))
except TypeError:
raise Exception('Please check input values (ex: the date)')
itr1 = 0
filenames = glob.glob('%s/*.json' % targetpath)
for filename in filenames:
print filename
items = file_read(filename)
itr2 = 0
for i, blog in enumerate(items):
check_targetpath = '%s/%s/%02d/%s/%02d/%02d'\
% (basedir, thirddir, directory_seq,\
int(date[0:4]), int(date[5:7]), int(date[8:10]))
check_filename = '%s.json' % (items[i]['logNo'])
if not os.path.isfile('%s/%s' % (check_targetpath, check_filename)):
comment_crawl(items[i]['blogId'],
items[i]['logNo'],
items[i]['writtenTime'],
date, directory_seq, basedir, crawler_version, debug=debug)
time.sleep(0.1)
itr2 += 1
if itr2 == len(items):
print "%s items read completed successfully." % len(items)
else:
print "Not all items read."
itr1 += 1
if len(filenames) == itr1:
print "%s files read completed successfully." % len(filenames)
else:
print "Not all files read."
type=str,
required=True,
help='input file with list of correlated genes')
argParser.add_argument('--group-list',
'-l',
type=str,
required=True,
help='list of GO groups to pull out')
argParser.add_argument('--output-file',
'-o',
type=str,
required=True,
help='output file of matching groups')
args = argParser.parse_args()
glist = file_read(args.group_list)
gmt = parse_gmt(args.gmt_file, 0, sys.maxsize)
gmt_dict = {}
for group in gmt:
desc = group['desc']
desc = desc.lower()
desc = re.sub('__', '_', desc)
gmt_dict[desc] = group
with open(args.output_file, 'w') as fp:
count = 0
for desc in glist:
desc = desc.rstrip()
desc = desc.lower()
def main(argv):
if len(argv) == 0:
print ("""\nUsage: python3 -m adapter config-file.ini ( stop | daemon )
""" + adapter_app +""", version """ + adapter_version +"""
config-file Configuration file, see mcfeedadapter_example.conf for examples.
action Optional, one of the following:
stop Stop running adapter
daemon Start adapter as daemon
""")
return 0
print (adapter_app + """, version """ + adapter_version + "\n")
print ("")
args=readconf.parse_argv(argv)
if cfg.action is not None:
if cfg.action == 'daemon':
utils.become_daemon();
if not readconf.read_conf(args):
return 1;
if not initialize_outputs():
close_outputs()
return 1;
current_pid=utils.file_read(cfg.pid_file)
if cfg.action is not None:
if (cfg.action == 'stop') or (cfg.action == 'status'):
if current_pid is None:
print("Adapter is not running\n")
return 0
process_id=int(current_pid)
print("Adapter found, PID " + str(process_id))
if cfg.action == 'stop':
utils.remove_file(cfg.pid_file)
while utils.is_process_running(process_id):
time.sleep(0.05)
print("Adapter stopped\n")
return 0
if current_pid is not None:
utils.print_error("Adapter for this feed is already running")
return 1
utils.file_write(cfg.pid_file,utils.get_pid())
signal.signal(signal.SIGINT,term_signal_handler)
signal.signal(signal.SIGTERM,term_signal_handler)
current_pid=utils.file_read(cfg.pid_file)
utils.log_write("Adapter started, PID: " + str(current_pid))
while current_pid is not None:
iteration_result=adapter_iteration()
if cfg.action is not None:
if cfg.action == 'term':
utils.remove_file(cfg.pid_file)
current_pid = None
if current_pid is not None:
if not iteration_result[0]:
utils.print_error("Adapter encountered error when processing feed records and will be stopped")
utils.remove_file(cfg.pid_file)
return 1
if not iteration_result[1]:
time.sleep(0.1)
current_pid=utils.file_read(cfg.pid_file)
close_outputs()
utils.log_write("Adapter stopped")
def generate(self):
"""generate the pxe boot file"""
self.pxe_variables.update({
'config':
self.config,
'seeds':
self.seeds,
'seed_host':
cfg['settings']['seed_host'],
'seed_port':
cfg['settings']['bottle_port'],
'address':
self.address,
'overlay':
self.overlay,
'puppet_manifests':
self.puppet,
'host_name':
self.host_name,
'dns_domain':
self.dns_domain,
'fqdn':
self.fqdn,
'query':
urllib.urlencode([('address', self.address)]),
'date_generated':
utils.date_time(),
'date_disabled':
'',
'kernel':
'%s/%s/%s' % ('seedbank', self.release, 'linux'),
'initrd':
'%s/%s/%s' % ('seedbank', self.release, 'initrd.gz')
})
if self.config:
yaml_file = os.path.join(cfg['paths']['configs'], self.config)
yaml_file = yaml_file + '.yaml'
overrides = utils.yaml_read(yaml_file)
if 'pxe' in overrides:
cfg['pxe'].update(overrides['pxe'])
values = cfg['pxe']
self.pxe_variables.update(values)
distribution = self.release.split('-')[0]
file_name = cfg[distribution]['template_pxe']
file_name = os.path.join(cfg['paths']['templates'], file_name)
if not os.path.isfile(file_name):
err = 'file "%s" does not exist (hint: check the templates '\
'section in your settings)' % file_name
raise utils.FatalException(err)
pxe_variables_custom = []
for variable in self.variables:
key, value = variable
pxe_variables_custom.append('# %s = %s' % (key, value))
self.pxe_variables[key] = value
pxe_variables_custom = '\n'.join(pxe_variables_custom)
data = utils.file_read(file_name)
data = utils.apply_template(data, self.pxe_variables, file_name)
if pxe_variables_custom:
data = re.sub('(#\n# \*\*\* end - seedBank pxe variables \*\*\*)',
pxe_variables_custom + '\n\\1', data)
return data
# -*-coding:utf-8-*-
import json
import os
import glob
import csv
from datetime import datetime, timedelta
from utils import checkdir, file_read, get_today, get_version
if __name__ == "__main__":
num_directory_seq = 31
basedir = "/home/web/public_html/data/naver-blog"
seconddir = "statistics"
targetpath = "%s/%s" % (basedir, seconddir)
filenames = glob.glob("%s/*.json" % targetpath)
cnt_files = len(filenames)
table = [[0 for i in range(cnt_files)] for j in range(num_directory_seq + 2)]
for i, filename in enumerate(filenames):
items = file_read(filename)
print filename
table[0][i] = filename.rsplit("statistics/", 1)[1].rsplit(".", 1)[0]
for directory_seq in range(len(items)):
table[directory_seq + 1][i] = items[directory_seq]["countTextsBlog"]
table[num_directory_seq + 1][i] = table[num_directory_seq + 1][i] + table[directory_seq + 1][i]
savefilename = "/home/web/public_html/data/naver-blog/test_file.csv"
csvfile = open(savefilename, "w")
wr = csv.writer(csvfile, dialect="excel")
[wr.writerow(r) for r in table]
def main() -> None:
prefix = "cache/"
now = datetime.datetime.today()
time_ym = now.strftime("%Y-%m")
time_dmy = now.strftime("%d. %b %Y")
semester = utils.json_read(prefix + "current_semester.json", None)
semester = semester[0] +" "+ semester[1]
folder = "gh-pages/"
pflicht: List[Tuple[str, str]] = []
fields: Dict[str, Dict[str, Tuple[str, str]]] = {}
pflicht = utils.json_read(prefix + "pre-tucan-pflicht.json", pflicht)
fields = utils.json_read(prefix + "pre-inferno.json", fields)
#nebenfach = utils.json_read("nebenfach.json")
# back = utils.groupby(((course, major +" · "+ category)
# for major,v in nebenfach.items()
# for category,v in v.items()
# for module in v
# for course in module), key=lambda x:x[0])
# back = {k:["Y Nebenfach · " + " &<br> ".join(i[1] for i in v),""] for k,v in back}
# fields = [back] + list(fields.values())
# print(json.dumps(fields, indent=2))
# dist/main.js with npm; code.orig.js without npm
if os.path.exists("dist/main.js"):
CODE_FILE = "dist/main.js"
else:
CODE_FILE = "code.orig.js"
page_tmpl = utils.file_read("page.html")
index_tmpl = utils.file_read("index.html")
code_tmpl = utils.file_read(CODE_FILE)
style_tmpl = utils.file_read("style.css")
def filename(reg: str) -> str:
return "".join(c for c in reg if c.isalnum())
regulations = [
(k,
k.replace("B.Sc.", "Bachelor")
.replace("M.Sc.", "Master")
.replace(" (2015)", ""),
filename(k) + ".html")
for k in fields.keys()
if k.endswith(" (2015)")
] + [
# other FBs?
("BauUmwelt", "FB 13 Bau, Umwelt", "BauUmwelt.html")
]
listy = [
{'href': href, 'title': semester +" "+ display_regulation}
for regulation, display_regulation, href in regulations
if display_regulation.endswith(" Informatik")
if not display_regulation.startswith("FB ")
]
experimentallist = [
{'href': href, 'title': semester +" "+ display_regulation}
for regulation, display_regulation, href in regulations
if not display_regulation.endswith(" Informatik")
if not display_regulation.startswith("FB ")
]
speciallist = [
{'href': href, 'title': semester +" "+ display_regulation}
for regulation, display_regulation, href in regulations
if display_regulation.startswith("FB ")
]
index_data = {
"list": listy,
"experimentallist": experimentallist,
"speciallist": speciallist,
}
utils.file_write(folder + "/index.html", stache(index_tmpl, index_data))
utils.file_write(folder + "/main.js", code_tmpl)
utils.file_write(folder + "/style.css", style_tmpl)
print(regulations)
for regulation, display_regulation, href in regulations:
print(prefix + "-" + filename(regulation) + ".json")
modules: Dict[str, Module] = {}
modules = utils.json_read(prefix + "-" + filename(regulation) + ".json", modules)
if modules == []: continue # if file exists
data = [clean(module_id, module, fields, regulation)
for module_id, module in modules.items()]
data.sort(key=lambda x: (x['category'], x['id'])) # -int(x['credits'])
js_data = json.dumps(data, indent=1)
page_data = {
"today": time_dmy,
"semester": semester,
"regulation": display_regulation,
"js_data": js_data,
"content": generate_page(data)
}
utils.file_write(folder + "/" + href, stache(page_tmpl, page_data))
print("finished")
import csv
from datetime import datetime, timedelta
from utils import checkdir, file_read, get_today, get_version
if __name__ == '__main__':
num_directory_seq = 31
basedir = '/home/web/public_html/data/naver-blog'
seconddir = 'statistics'
targetpath = '%s/%s' % (basedir, seconddir)
filenames = glob.glob('%s/*.json' % targetpath)
cnt_files = len(filenames)
table = [[0 for i in range(cnt_files)]
for j in range(num_directory_seq + 2)]
for i, filename in enumerate(filenames):
items = file_read(filename)
print filename
table[0][i] = filename.rsplit("statistics/", 1)[1].rsplit(".", 1)[0]
for directory_seq in range(len(items)):
table[directory_seq +
1][i] = items[directory_seq]['countTextsBlog']
table[num_directory_seq +
1][i] = table[num_directory_seq +
1][i] + table[directory_seq + 1][i]
savefilename = '/home/web/public_html/data/naver-blog/test_file.csv'
csvfile = open(savefilename, 'w')
wr = csv.writer(csvfile, dialect='excel')
[wr.writerow(r) for r in table]