def testValidity():
if len(sys.argv) == 3:
try:
directory = sys.argv[1]
numberOfBestMatch = int(sys.argv[2])
except:
print(__doc__)
sys.exit(1)
elif len(sys.argv) == 4:
try:
directory = sys.argv[1]
pathToContigsIdFile = sys.argv[3]
tempFile = open(pathToContigsIdFile, 'r')
tempFile.close()
numberOfBestMatch = int(sys.argv[2])
except:
print(__doc__)
sys.exit(1)
else:
print(__doc__)
sys.exit(1)
try:
tempFile = open(directory+"/_DeNovoAssembly/Contigs.tsv", 'r')
tempFile.close()
except:
Error.error("Unable to open: "+directory+"/_DeNovoAssembly/Contigs.tsv")
sys.exit(1)
def close(text):
if 'word' in text:
return os.system('taskkill/f /im WINWORD.EXE')
elif 'ppt' in text or 'powerpoint' in text:
return os.system('taskkill/f /im POWERPNT.EXE')
elif 'excel' in text:
return os.system('taskkill/f /im EXCEL.EXE')
elif 'pub' in text or 'publisher' in text:
return os.system('taskkill/f /im MSPUB.EXE')
elif 'outlook' in text:
return os.system('taskkill/f /im OUTLOOK.EXE')
elif 'onenote' in text:
return os.system('taskkill/f /im ONENOTE.EXE')
elif 'access' in text:
return os.system('taskkill/f /im MSACCESS.EXE')
elif 'browser' in text:
return os.system('taskkill/f /im chrome.exe')
elif 'notepad' in text:
return os.system('taskkill/f /im notepad.exe')
elif 'discord' in text:
return os.system('taskkill/f /im Discord.exe')
elif 'groove' in text:
return os.system('taskkill/f /im Music.UI.exe')
elif 'adobe' in text:
return os.system('taskkill/f /im AcroRd32.exe')
elif 'explorer' in text or 'windows explorer' in text:
return os.system('taskkill/f /im explorer.exe & start explorer')
else:
if len(text) > 0:
return Error.printline(f"[ERROR]: {text} is not available.")
else:
return Error.printline(f"[ERROR]: No input found.")
def AlterTableFK(nodo, tablaSimbolos):
global useActual
global consola
base = tablaSimbolos.get(useActual)
tabla = base.getTabla(nodo.idtabla)
for i in range(len(nodo.idlocal)):
idlocal = nodo.idlocal[i].valor
idfk = nodo.idfk[i].valor
columnafk = tablaSimbolos.getColumna(useActual, nodo.idtablafk, idfk)
columnalocal = tabla.getColumna(idlocal)
if columnafk != None and columnalocal != None:
if columnafk.tipo.tipo == columnalocal.tipo.tipo:
tabla.modificarFk(idlocal, nodo.idtablafk, idfk)
listaFK.append(
TS.llaveForanea(useActual, nodo.idtabla, nodo.idtablafk,
idlocal, idfk))
consola += "Se agrego la llave foranea a " + idlocal + " exitosamente \n"
else:
listaSemanticos.append(
Error.ErrorS(
"Error Semantico",
"La columna %s y la columna %s no tienen el mismo tipo"
% (idlocal, idfk)))
else:
listaSemanticos.append(
Error.ErrorS("Error Semantico", "No se encontró la columna"))
def inBetween(x, y):
if x > y:
temp = x
x = y
y = temp
linex = getLineOfHole(x)
liney = getLineOfHole(y)
# first condition: if on same line, then
# must be exactly two away for valid jump
if liney == linex:
if y - x == 2:
return y - 1
else:
raise e.InvalidJumpError()
# second condition: if on different lines, those
# lines must be two apart, leaving room for a piece
# to be jumped but not too far of a jump
elif liney - linex != 2:
raise e.InvalidJumpError()
# lastly, if on lines 2 apart must follow the rule:
# going up 2 lines to the left, as would be required for a
# legal jump, requires a difference of (2*line_no) + 1
# going up 2 lines to the right, as would be required for a
# legal jump in that direction, requires difference of
# (2*line_no) - 1, where line_no is the greater of the line
# numbers of the two holes
else:
if x == y - (2*liney + 1):
# going up left
return y - (liney + 1)
elif x == y - (2*liney - 1):
# going up right
return y - liney
else:
raise e.InvalidJumpError()
def Nome_Funcao(tokens, i, first, SemanticTable):
linha = tokens[i][2]
if (tokens[i][0] == 'function'):
i += 1
else:
Error.SyntaticError(tokens[i])
global escopo
escopo = tokens[i][1]
classificador = tokens[i][1]
i = Identificador(tokens, i, first, SemanticTable)
if (tokens[i][0] == 'Abreparêntese'):
i += 1
else:
Error.SyntaticError(tokens[i])
global flagparametro
global numParametro
flagparametro = True
numParametro = 0
i = Variaveis(tokens, i, first, SemanticTable)
flagparametro = False
if (tokens[i][0] == 'Fechaparêntese'):
i += 1
else:
Error.SyntaticError(tokens[i])
if (tokens[i][0] == 'DoisPontos'):
i += 1
else:
Error.SyntaticError(tokens[i])
i = Tipo_Dado(tokens, i, first, SemanticTable)
SemanticTable.append(
[classificador, linha, 'global', tipo, 'function', numParametro])
return i
def unique_family_spouse_marriage_date(parsed_file, errors):
"""
US24:No more than one family with the same spouses by name and the same marriage date should appear in a GEDCOM file
"""
family_info = {} # fid:{spouse:[], marriage_date: str}
for k in parsed_file['family'].keys():
family = parsed_file['family'][k]
spouse1, spouse2 = family['Spouse 1 Name'], family['Spouse 2 Name']
marriage_date = family['Married']
for key, value in family_info.items():
if operator.eq(sorted([spouse1, spouse2]),
sorted(value['spouses'])):
us24Err = Error.Error(Error.ErrorEnum.US24)
us24Err.alterErrMsg(key, k)
errors.add(us24Err)
continue
if marriage_date == value['marriage_date']:
us24Err = Error.Error(Error.ErrorEnum.US24)
us24Err.alterErrMsg(key, k)
errors.add(us24Err)
else:
family_info[k] = {
'spouses': [spouse1, spouse2],
'marriage_date': marriage_date
}
return errors
def __init__(self, ctl, ccver, platform, config, logfile, verbose):
self.clsname = self.__class__.__name__
self.version = 1.0
#
self.ctl = ctl
self.ccver = ccver
self.platform = platform
self.config = config
self.logfile = logfile
self.verbose = verbose
#
# このファイルは ".../core/test/bin" に置くこと
script_dir = os.path.abspath(__file__).split(os.sep)[:-1]
script_dir = os.sep.join(script_dir)
setup_file = script_dir + '../../../src/setup.conf'
setup_file = os.path.abspath(setup_file)
self.setup_file_exists = False
if os.path.exists(setup_file):
print(' setup file exists')
self.setup_file_exists = True
self.sf = SetupFile(setup_file)
self.sf.setenv()
#
self.generator = self.__find_generator(ccver)
self.error = Error(self.clsname)
def make_makefile(module, fname, interfs, inchdrs, srchdrs):
target = '%s/EP%s.cpp' % (embpythondir, module)
dependencies = []
dependencies.extend(interfs)
dependencies.extend(inchdrs)
dependencies.extend(srchdrs)
if verbose:
print(' target: [%s]' % target)
print(' dependencies: [%s]' % dependencies)
lines = []
lines.append('# Do not edit. RunSwig_EmbPython will update this file.')
lines.append('# File: %s' % fname)
lines.append('')
lines.append('all:\t%s' % target)
lines.append('%s:\t%s' % (target, ' '.join(dependencies)))
lines.append('\t@python %s %s' % (swig, module))
lines.append('')
for f in dependencies:
lines.append('%s:' % f)
fio = TextFio(fname, 'w')
if fio.open() != 0:
msg = '%s: can not open file (write)' % fname
Error(prog).abort(msg)
rc = fio.writelines(lines)
fio.close()
if rc != 0:
msg = '%s: write failed' % fname
Error(prog).abort(msg)
def findLCA(self, node1, node2):
if self.nodeExist(node1) and self.nodeExist(node2):
pass
else:
if not(self.nodeExist(node1)):
sys.stderr.write("Node does not exist: "+str(node1))
if not(self.nodeExist(node2)):
sys.stderr.write("Node does not exist: "+str(node2))
Error.error("Logic error, asked to find LCA for a node that does not exists"+str(node1) +str(node2)+"\n")
parentsOfNode1 = []
parentsOfNode1.append(node1)
parentsOfNode2 = []
parentsOfNode2.append(node2)
lca = -1
#i = -1
while self.getNodes(node1).hasParent():
parentToAdd = self.getNodes(node1).getParents()
parentsOfNode1.append(parentToAdd)
node1 = parentToAdd
while self.getNodes(node2).hasParent():
parentToAdd = self.getNodes(node2).getParents()
parentsOfNode2.append(parentToAdd)
node2 = parentToAdd
for i in parentsOfNode1:
if i in parentsOfNode2:
lca = i
break
if lca == -1:
Error.warning("Have not found the LCA for nodes:" +str(node1)+" and "+str(node2))
return lca
def __init__(self,
root=None,
url_info=None,
folder_name=None,
protected=False,
name=None):
"""
A valid addon requires at least the root folder and url_info tuple (repo_type, url) or
a root folder and an addon folder.
@param root: the folder containing the addon folder(absolute path)
@type root: str
@param url_info: a (repo_type, url) tuple, which contains the url and
the corresponding repository type (currently supporting: git, svn, hg)
@type url_info: tuple
@param folder_name: the addon folder name
@type folder_name: str
@param protected: a protected addon can't be modified
@type protected: bool
@param name: the addon's name (just for recognition)
@type name: str
#raise: Error.AddonRootError , Error.AddonInitError
"""
#note difference between self._root and self.url_info assignments
#in the second case the property function _set_url_info is called
try:
if not root:
raise Error.AddonRootError()
if (url_info) or (folder_name):
#TODO check if its an absolute path, does the url start with a '/' ?
self._root = os.path.expanduser(root)
self.name = name
self.url_info = url_info
#valid folder required for cloning
if folder_name == None:
self.folder_name = "TmpFolder_" + str(
self.__class__.num_addons)
else:
self.folder_name = folder_name
#protected addons cannot be changed, deleted, updated, cleaned, etc.
self.protected = protected
#config file (usually .pkgmeta file)
#currently only changed by the parse_pkgmeta_file() function
self._config_info = {}
self._config_file_parsed = False
#increment counter
self.__class__.num_addons += 1
else:
raise Error.AddonInitError()
except (Error.AddonRootError, Error.AddonInitError) as e:
print(e)
def AlterAddColumn(nodo, tablaSimbolos):
global consola
global useActual
base = tablaSimbolos.get(useActual)
tabla = base.getTabla(nodo.idtabla)
for col in nodo.listaColumnas:
auxcol = TS.SimboloColumna(col.idcolumna, col.tipo, False, None, None,
None, True, None)
if tabla.crearColumna(col.idcolumna, auxcol):
b = jBase.alterAddColumn(useActual, nodo.idtabla, col.idcolumna)
if b == 0:
consola += "La columna " + col.idcolumna + " se agregó a la tabla " + nodo.idtabla + " \n"
elif b == 1:
listaSemanticos.append(
Error.ErrorS("Error Semantico", "Error en la operacion."))
elif b == 2:
listaSemanticos.append(
Error.ErrorS("Error Semantico",
"Error la base " + useActual + "no existe"))
elif b == 3:
listaSemanticos.append(
Error.ErrorS(
"Error Semantico",
"Error la tabla " + nodo.idtabla + "no existe"))
else:
consola += "Error al crear la columna " + col.idcolumna + " \n"
def output(fname, lines):
fobj = TextFio(fname, 'w', encoding='utf8')
if fobj.open() < 0:
Error(prog).error(fobj.error())
if fobj.writelines(lines, '\n') < 0:
Error(prog).error(fobj.error())
fobj.close()
def __init__(self, name, time_stamp, header=None):
self._platform = Platform.Platform()
self._os = OS.OS()
self._name = name
self._ERR_FILE_EXIST = "ERROR: Log file '%s' already exists" % name
self._ERR_FILE_OPEN = "ERROR: Unable to open log file '%s'" % name
if self._os.is_file(name):
raise Error.Error(msg=self._ERR_FILE_EXIST)
else:
try:
f = open(name, 'w')
except IOError:
raise Error.Error(msg=self._ERR_FILE_OPEN)
if header != None:
f.write("%s\n" % header)
line = "Generated %s" % time_stamp.as_string()
f.write(line+"\n\n")
line = "System: %s" % self._platform.system()
f.write(line+"\n")
line = "Python version: %s" % self._platform.python_version()
f.write(line+"\n")
line = ("Python implementation: %s"
% self._platform.python_implementation())
f.write(line+"\n\n")
f.close()
def execute(self, data, tbname, cons, idconst='ALTER'):
#validate if listaid1 exists
colindex = 0
found = False
for colu in data.tablaSimbolos[
data.databaseSeleccionada]['tablas'][tbname]['columns']:
if colu.name == self.id.upper():
found = True
if not colu.pk == None or not colu.unique == None:
error = Error(
'Semántico',
'Error(???): La primary key o unique no puede modificarse.',
0, 0)
return error
break
colindex += 1
if not found:
error = Error(
'Semántico',
'Error(???): No existe la columna ' + self.id.upper(), 0, 0)
return error
data.tablaSimbolos[data.databaseSeleccionada]['tablas'][tbname][
'columns'][colindex].null = self.option
print('Cambio Not null / null exitoso')
return 'Cambio Not null / null exitoso'
def __mediasetSearch(self, html):
mediasetchannel = re.findall('s.eVar3="(.*)"', html)[0]
programa = re.findall('s.eVar7="(.*)"', html)[0]
temporada = re.findall('s.eVar8=".* ([0-9].*)"', html)[0]
capitulo = re.findall('s.eVar9=".* ([0-9].*)"', html)[0]
if int(temporada) < 10: temporada = "0%s" % (temporada)
if int(capitulo) < 10: capitulo = "0%s" % (capitulo)
abuscar = urllib2.quote("%s T%sxC%s" % (programa, temporada, capitulo))
search = "http://www.%s.es/buscador/?text=%s" % (mediasetchannel,
abuscar)
self.debug(u"Programa: %s" % programa)
self.debug(u"Temporada: %s" % temporada)
self.debug(u"Capitulo: %s" % capitulo)
self.debug(u"Search... %s" % search)
results = Descargar.get(search)
self.debug(search)
try:
r = results.split('<h2 class="headline')[1].split(
'href="')[1].split('"')[0]
except IndexError:
raise Error.GeneralPyspainTVsError(
"mitele.es: RTMP no soportado para el canal por ahora.")
mediasetLink = "http://www.%s.es%s" % (mediasetchannel, r)
if mediasetchannel == "telecinco":
from telecinco import Telecinco as newChannel
elif mediasetchannel == "cuatro":
from cuatro import Cuatro as newChannel
else:
raise Error.GeneralPyspainTVsError(
"mitele.es: RTMP no soportado para el canal por ahora.")
channel = newChannel(mediasetLink)
return channel.getInfo()
def testValidity():
if len(sys.argv) == 3:
try:
directory = sys.argv[1]
numberOfBestMatch = int(sys.argv[2])
except:
print(__doc__)
sys.exit(1)
elif len(sys.argv) == 4:
try:
directory = sys.argv[1]
pathToContigsIdFile = sys.argv[3]
tempFile = open(pathToContigsIdFile, 'r')
tempFile.close()
numberOfBestMatch = int(sys.argv[2])
except:
print(__doc__)
sys.exit(1)
else:
print(__doc__)
sys.exit(1)
try:
tempFile = open(directory + "/_DeNovoAssembly/Contigs.tsv", 'r')
tempFile.close()
except:
Error.error("Unable to open: " + directory +
"/_DeNovoAssembly/Contigs.tsv")
sys.exit(1)
def findLCA(self, node1, node2):
if self.nodeExist(node1) and self.nodeExist(node2):
pass
else:
if not (self.nodeExist(node1)):
sys.stderr.write("Node does not exist: " + str(node1))
if not (self.nodeExist(node2)):
sys.stderr.write("Node does not exist: " + str(node2))
Error.error(
"Logic error, asked to find LCA for a node that does not exists"
+ str(node1) + str(node2) + "\n")
parentsOfNode1 = []
parentsOfNode1.append(node1)
parentsOfNode2 = []
parentsOfNode2.append(node2)
lca = -1
#i = -1
while self.getNodes(node1).hasParent():
parentToAdd = self.getNodes(node1).getParents()
parentsOfNode1.append(parentToAdd)
node1 = parentToAdd
while self.getNodes(node2).hasParent():
parentToAdd = self.getNodes(node2).getParents()
parentsOfNode2.append(parentToAdd)
node2 = parentToAdd
for i in parentsOfNode1:
if i in parentsOfNode2:
lca = i
break
if lca == -1:
Error.warning("Have not found the LCA for nodes:" + str(node1) +
" and " + str(node2))
return lca
def __cp(self, src, dst, follow_symlinks=True):
if self.verbose:
print('__cp: %s -> %s' % (src, dst))
#
rc = 0
try:
if self.verbose:
print(' cwd: %s' % Util.upath(os.getcwd()))
print(' src: %s' % Util.upath(src))
print(' dst: %s' % Util.upath(dst))
if os.path.isdir(src):
if os.path.exists(dst):
prog = '%s: cp' % self.clsname
msg = '"%s" exists' % dst
Error(prog).error(msg)
return 1
if self.verbose:
print(' shutil.copytree()')
shutil.copytree(src, dst, follow_symlinks)
else:
if self.verbose:
print(' shutil.copy2()')
shutil.copy2(src, dst)
except OSError as why:
prog = '%s: cp' % self.clsname
Error(prog).error(str(why))
rc = 1
return rc
def AlterRenameColumn(nodo, tablaSimbolos):
base = tablaSimbolos.get(useActual)
tabla = base.getTabla(nodo.idtabla)
global consola
op = tabla.renameColumna(nodo.idcolumna, nodo.idnuevo)
if op == 0:
for fk in listaFK:
if fk.idcfk == nodo.idcolumna:
fk.idcfk = nodo.idnuevo
tablaRF = base.getTabla(fk.idtlocal)
columnaRF = tablaRF.getColumna(fk.idclocal)
columnaRF.foreign_key["columna"] = nodo.idnuevo
elif fk.idclocal == nodo.idcolumna:
fk.idclocal = nodo.idnuevo
for cons in listaConstraint:
if cons.idcol == nodo.idcolumna:
cons.idcol = nodo.idnuevo
consola += "Se cambio el nombre de la columna " + nodo.idcolumna + " a " + nodo.idnuevo + " con exito \n"
elif op == 1:
listaSemanticos.append(
Error.ErrorS(
"Error Semantico",
"La columna con nombre " + nodo.idnuevo + " ya existe"))
elif op == 2:
listaSemanticos.append(
Error.ErrorS(
"Error Semantico",
"La columna con nombre " + nodo.idactual + " no existe"))
def delete():
body_data = request.json
print(body_data)
try:
pizza_type = body_data['pizza']
print(pizza)
if pizza_type == "" or pizza_type is None:
return err.ReturnValueError()
conn = connect.ConnectMySql()
print(f'Connection status : {conn.is_connected()}')
if (conn is False):
return err.ReturnConnectionError()
else:
cur1 = conn.cursor()
print(f'Cursor object : {cur1}')
query = (f'DELETE from orderPizza where pizza_type="{pizza}"')
cur1.execute(query)
cur2 = conn.cursor()
selectquery = SelectQuery()
cur2.execute(selectquery)
msg = "Data deleted succesfully"
result = res.generateResponse(cur2, msg)
conn.close()
return result
except KeyError as e:
return err.ReturnKeyError()
except Exception as e:
print(e)
return e
def _remove_tree(self, file):
"""
A little support function to delete directories/files/links.
Deleting files is only possible within the addon root folder.
returns True, if everything worked. None otherwise
@param file: file or folder (absolute path) to be removed recursively
@type file: str
OSError is handled
"""
try:
try:
#is it a subfolder/subfile in the addon root ?
if file.startswith(self.root):
if os.path.isfile(file):
os.remove(file)
else:
shutil.rmtree(file)
else:
raise Error.CommonRemoveTreeError(self.root, file)
return True
except OSError as e:
raise Error.CommonOSError(e)
except Error.CommonRemoveTreeError as e:
print(e)
except Error.CommonOSError as e:
print(e)
def fetch():
body_data = request.json
print(body_data)
try:
status = body_data['status']
print(status)
if status == "" or status is None:
return err.ReturnValueError()
conn = connect.ConnectMySql()
print(f'Connection status : {conn.is_connected()}')
if (conn is False):
return ReturnConnectionError()
else:
cur = conn.cursor()
print(f'Cursor object : {cur}')
query = (f'SELECT * from orderPizza where status="{status}"')
cur.execute(query)
msg = "Fetched data succesfully"
result = res.generateResponse(cur, msg)
conn.close()
return result
except KeyError as e:
return err.ReturnKeyError()
except Exception as e:
print(e)
return err.ReturnFetchError()
def range(*args):
"""
Wrapper for range usage, returning an iterator regardless of if
python 2 or python 3 is used
"""
if len(args) < 1 or len(args) > 3:
err_msg = "ERROR: Anguilla range function takes 1, 2, or 3 arguments"
raise Error.Error(msg=err_msg)
start = 0
stop = 1
step = 1
if len(args) == 1:
stop = args[0]
if len(args) == 2:
start = args[0]
stop = args[1]
if len(args) == 3:
start = args[0]
stop = args[1]
step = args[2]
if platform.is_python2():
return builtins.xrange(start, stop, step)
elif platform.is_python3():
return builtins.range(start, stop, step)
else:
err_msg = "ERROR: Unknown python platform"
raise Error.Error(msg=err_msg)
def parseRequest(self,request):
try:
lines=request.splitlines()
index=lines.index("") if "" in lines else len(lines)
headers=lines[1:index]
body=lines[index+1:]
method,path,version = lines[0].split()
if not method in self.methods or version.upper()!='HTTP/1.1':
raise Error('400')
dic={
'method':method,
'path':path,
'version':version,
'headers':{},
'body':body[0] if len(body)>0 else ''
}
for i in range(0,len(headers)):
title,content=headers[i].split(':',1)
dic['headers'][title]=content.strip(' ')
return dic
except :
raise Error('400')
def AlterDatabase(nodo, tablaSimbolos):
global consola
if nodo.rename:
b = jBase.alterDatabase(nodo.id.valor, nodo.idnuevo)
if b == 0:
base = tablaSimbolos.renameBase(nodo.id.valor, nodo.idnuevo)
if base:
for fk in listaFK:
if fk.idbase == nodo.id.valor:
fk.idbase = nodo.idnuevo
for cons in listaConstraint:
if cons.idbase == nodo.id.valor:
cons.idbase = nodo.idnuevo
consola += "La base se renombró con éxito " + nodo.idnuevo + " \n"
else:
consola += "Error no se pudo renombrar la base " + nodo.id.valor + " en la tabla de simbolos \n"
elif b == 2:
listaSemanticos.append(
Error.ErrorS(
"Error Semantico",
"La base de datos " + nodo.id.valor + " no existe"))
elif b == 3:
listaSemanticos.append(
Error.ErrorS("Error Semantico",
"La base de datos ya existe " + nodo.idnuevo))
elif b == 1:
listaSemanticos.append(
Error.ErrorS("Error Semantico", "Error en la operacion."))
def __read_usage(self, path): if not os.path.exists(path): msg = 'no such file: "%s"' % path Error(self.clsname).abort(msg) # read the file f = TextFio(path) if f.open() < 0: Error(self.clsname).abort(f.error()) lines = f.read() f.close() # find pattern usage = None patt = '#(define|undef)\s+USE_CLOSED_SRC' for line in lines: m = re.match(patt, line) if m: matched = m.group(1) if matched == 'define': usage = CSU.USE if matched == 'undef': usage = CSU.UNUSE break if usage is None: msg = 'bad closed-src-header' Error(self.clsname).abort(msg) return usage
def execute(self):
left = self.leftOperator.execute()
if isinstance(left, Error):
return left
right = self.rightOperator.execute()
if isinstance(right, Error):
return right
if self.sign == '>':
if (left.type == 'integer' and right.type == 'integer') or (
left.type == 'float' and right.type == 'float') or (
left.type == 'float' and right.type == 'integer') or (
left.type == 'integer' and right.type == 'float'):
comp = int(left.val) > int(right.val)
return Primitive('boolean', comp)
else:
error = Error(
'Semántico',
'Error de tipos en MAYOR QUE, no se puede operar ' +
left.type + ' con ' + right.type, 0, 0)
return error
else:
if (left.type == 'integer' and right.type == 'integer') or (
left.type == 'float' and right.type == 'float') or (
left.type == 'float' and right.type == 'integer') or (
left.type == 'integer' and right.type == 'float'):
comp = int(left.val) < int(right.val)
return Primitive('boolean', comp)
else:
error = Error(
'Semántico',
'Error de tipos en MENOR QUE, no se puede operar ' +
left.type + ' con ' + right.type, 0, 0)
return error
def translate_using_sequence(self, contig):
"""
Translate the SNPs at this position and give the proportion.
:param contig: A Contig object with associated Gene(s)
:return:A line to stdout
"""
if type(contig).__name__ != "Contig":
Error.error("Genomic_environment: translate_using_sequence: The object passed is not of type Contig")
#For each gene in Contig... we search for the one that contain the position
gene = Gene.__init__()
for orf in contig.genes:
if orf.start <= self.position <= orf.end:
gene = orf
if gene.sequence == "":
Error.error("Genomic_environment: translate_using_sequence: There is no sequence in the selected gene")
orf_seq = Seq(gene.sequence, IUPAC.unambiguous_dna)
amino_acid_sequence = str(orf_seq.translate(table=11))
orf_seq = orf_seq.tomutable()
nucleotides_sequences = self.group_environment()
total = len(self.reads)
header = "Contig\tSNP position(contig)\tFrame\tAmino acid\tProportion\n"
#We put - in the frame number column.
print(header),
for entry in nucleotides_sequences:
mutation = entry[2]
mutated_seq = copy.copy(orf_seq)
mutated_seq[self.position-gene.start] = mutation
mutated_prot_seq = str(mutated_seq.translate(table=11))
changed_amino_acid_position = math.ceil(float(self.position-gene.start+1)/3)
changed_amino_acid = mutated_prot_seq[changed_amino_acid_position-1] #-1 cuz its a python string.
line = (self.contig+"\t"+self.position+"\t-\t"+changed_amino_acid+"\t" +
str(float(nucleotides_sequences[entry])/total))
print(line)
def execute(self, data, tbname = 'NADA'):
if self.type == 'foreign':
if self.tableExists(data):
#validando que ambas listas tengan el mismo tamaño
if len(self.list) != len(self.extra) :
error = Error('Semántico', 'Error(FK): El númmero de FK especificadas no coincide con el de columnas de referencia.', 0, 0)
return error
#validando si las colunas de la lista extra existen
tabla = self.id.upper()
for col in self.extra :
found = False
for column in data.tablaSimbolos[data.databaseSeleccionada]['tablas'][tabla]['columns'] :
if col.column.lower() == column.name.lower() :
found = True
if not found :
error = Error('Semántico', 'Error(FK): La columna: ' + col.column.upper() +' no existe.', 0, 0)
return error
#validando que las columnas de la lista list existan
colindex = []
for col in self.list :
found = False
i = 0
for column in data.tablaSimbolos[data.databaseSeleccionada]['tablas'][tbname.upper()]['columns'] :
if col.column.lower() == column.name.lower() :
found = True
colindex.append(i)
i += 1
if not found :
error = Error('Semántico', 'Error(FK): La columna: ' + col.column.upper() +' no existe.', 0, 0)
return error
#agregando a tabla de simbolos
referenceslist = []
for id in self.extra :
referenceslist.append(Identificador(self.id.upper(), id.column.upper()))
print(referenceslist)
i = 0
for index in colindex :
idconst = 'FK_'+tbname+'_'+data.tablaSimbolos[data.databaseSeleccionada]['tablas'][tbname]['columns'][index].name
checkData = ConstraintData(idconst, referenceslist[i], 'fk')
data.tablaSimbolos[data.databaseSeleccionada]['tablas'][tbname]['columns'][index].fk.append(checkData)
i += 1
print(self)
else:
error = Error('Semántico', 'Error(FK): La tabla: ' + self.id +' no existe.', 0, 0)
return error
elif self.type == 'references' :
print(self)
return self
def __init__(self, *args, **kwargs):
if kwargs.get('window_dimension') is None:
raise Error.InputError('Window dimension',
'is a required parameter')
self.window_dimension = kwargs.get('window_dimension')
if self.__class__ is MovingWindow:
raise Error.Error('MovingWindow is an abstract base class')
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 find(self, key):
if self.head is None:
raise Error.EmptyLinkedList("No data found")
curr = self.head
while curr.next:
if curr.data == key:
return curr
curr = curr.next
raise Error.KeyNotFound("Key %s not found", str(key))
def register(toolname, protgen):
global tools
for t in tools:
if t.name == toolname:
registerToolGen(t, protgen)
return
protgen.tool = None
Error.showWarningOnce("Could not find tool %s" % toolname)
def checkIfLvalueValid(self, token):
if token.data[0].id == '&':
raise SyntaxError(Error.generateErrorMessageWithNoArguement('Invalid lvalue type of assignment', token))
elif token.data[0].id in ('(identifier)', '(literal)'):
return
elif token.data[0].arity == 3 and token.data[0].id != '[':
Error.generateErrorMessageWithNoArguement('Invalid lvalue type of assignment', token)
else:
self.checkIfLvalueValid(token.data[0])
def loadConverter(self, file_name):
sys.stderr.write("Loading converter from file\n")
if Utility.isValid(file_name):
f = open(file_name, "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 countLines(file_name):
lines = 0
try:
for i in open(file):
lines += 1
except:
lines = 0
if lines == 0:
Error.error("File "+str(file)+" is empty")
return lines
def addTaxonName(self, file_name):
sys.stderr.write("Adding taxon name to tree\n")
Utility.isValid(file_name)
for line in open(file_name):
id = int(line.split('\t')[0])
name = line.split('\t')[1]
rank = line.split('\t')[2]
if self.nodeExist(id):
self.getNodes()[id].getTaxonName().setAll(name, rank)
else:
Error.warning("A taxon is missing")
def add_alignement_position(self, sample, gen_position):
try:
if gen_position.position <= 0:
Error.error("Aligned_contig:add_alignement: The gen_position was not set")
else:
self.comparable_sample[sample].append(gen_position)
self.comparable_sample[sample].sort(key=lambda x: x.position) #We keep the list in order for ordered output.
#TODO: execute sort only when output is aksed?
except:
Error.error("Aligned_contig:set_alignement: Object is not good")
def parseDatabaseHeader(self) :
databaseHeader = DatabaseHeader(self.inputPath)
databaseHeader.parseDabaseHeader()
if databaseHeader.getSignature() != -1985229329 : #\xef\xcd\xab\x89
Error.printError(0)
self.status = databaseHeader.getStatus()
self.pageSize = databaseHeader.getPageSize()
self.version = databaseHeader.getVersion()
self.revision = databaseHeader.getRevision()
self.pageHeaderSize = databaseHeader.getPageHeaderSize()
databaseHeader = None
def readPathsFile(pathToContigsIdFile):
#TODO: verifier que si les fichiers ont ou non le ContigIdentifications.tsv a la fin.
contigIdentificationsFiles = []
try:
tempfile = open(pathToContigsIdFile, 'r')
tempfile.close()
except:
Error.error("Unable to open: "+pathToContigsIdFile)
sys.exit(1)
for lines in open(pathToContigsIdFile, 'r'):
contigIdentificationsFiles.append(lines[0:len(lines)-1])
return contigIdentificationsFiles
def StartClient(self):
connected = False
i = 0
while not connected and i != 5:
try:
self.local_socket.connect(("10.92.5.20", COM_PORT))
connected = True
except: i += 1
if i >= 5:
Error.error_msg()
""" look for the ip again, gil sent a func that gets an ip (the servers ip) by the mac address """
def _postRequestRenderer(*args):
global _doingDeferred
_doingDeferred = 1
try:
for name, argDict, auxArgs, compType, srcModTime, cached in _postRequestRenderList:
try:
DEBUG(COMPONENT, "deferredly rendering %s" % name)
_renderComponentAndCache(name, argDict, auxArgs, compType, srcModTime, cached)
except:
Error.logException()
_postRequestRenderList[:] = []
finally:
_doingDeferred = 0
def _renderComponentAndCache(name, argDict, auxArgs, compType, srcModTime, cached):
DEBUG(COMPONENT, "_renderComponentAndCache")
try:
mashed = argDict.copy()
(out, cache_exp_time) = _realRenderComponent(name, argDict, auxArgs, compType, srcModTime)
mashed.update(auxArgs)
Cache.putCachedComponent(name, mashed, out, cache_exp_time)
except:
if cfg.Configuration.fallbackToCache and cached:
DEBUG(COMPONENT, "execution explosion and fallback active")
Error.logException()
DEBUG(COMPONENT, "After logexc")
return cached.out
raise
return out
def nud(self):
self.arity = thisContext.PREFIX_UNARY
thisContext.contextManager.parser.lexer.advance()
returnedToken = thisContext.contextManager.parser.parse(120)
idenToken = thisContext.getIdentifier(returnedToken)
if idenToken is None:
raise SyntaxError(Error.generateErrorMessageWithNoArguement('(literal) do not have address', returnedToken))
self.data.append(returnedToken)
return self
def readItemBig(self, itemOffset, size):
value = None
parsingOffset = itemOffset + self.standdardOffset
if size < 0 :
Error.printError(1)
elif size == 0 :
value = 0
elif size == 1 :
value = self.hexReader.readByte(parsingOffset)
elif size == 2 :
value = self.hexReader.readUnsignedShortBig(parsingOffset)
elif size == 4 :
value = self.hexReader.readUnsignedIntegerBig(parsingOffset)
elif size == 8 :
value = self.hexReader.readUnsignedLongBig(parsingOffset)
else :
value = self.hexReader.readUnsignedNumberBig(parsingOffset, size)
return value
def readItem(self, itemOffset, size):
value = None
parsingOffset = itemOffset + self.standdardOffset
if size < 0 :
Error.printError(1)
elif size == 0 :
value = 0
elif size == 1 :
value = self.hexReader.readByte(parsingOffset)
elif size == 2 :
value = self.hexReader.readShort(parsingOffset)
elif size == 4 :
value = self.hexReader.readInteger(parsingOffset)
elif size == 8 :
value = self.hexReader.readLong(parsingOffset)
else :
value = self.hexReader.readHexDump(parsingOffset, size)
return value
def readContigIdentificationFiles(files, biologicalAbundanceContigs):
for line in open(files, 'r'):
if line == "":
break
if line[0] == '#':
continue
else:
try:
contigName = line.split()[0]
sequenceName = line.split('\t')[6]
sequenceLength = int(line.split('\t')[7])
matches = int(line.split('\t')[8])
biologicalAbundanceContigs[contigName].addNewContigIdentification(sequenceName, sequenceLength, matches)
except:
message = ("File: " + files +
" can not be read or do not correspond to the usual patern. It has been discarded")
Error.warning(message)
def checkTree(self):
numOfNode = len(self.getNodes())
sys.stderr.write(str(numOfNode)+ " to be checked\n")
checked = 0
root = []
for i in self.Nodes:
#print(self.Nodes[i].getId()==1);
#if not(self.Nodes[i].getId()):
# print("my parents")
# print(self.Nodes[i].getParents());
# print("my kids")
# print(self.Nodes[i].getKids());
if self.Nodes[i].getParents():
if self.nodeExist(self.Nodes[i].getParents()):
pass
#print("One parent checked")
else:
Error.error("Logic error: tree is not valid because this parent does not exist:"+str(self.Nodes[i].getParents()));
else:
sys.stderr.write("Found a root\n")
root.append(self.Nodes[i])
for k in self.Nodes[i].getKids():
if self.nodeExist(k):
pass
#print("One kid checked");
else:
Error.error("Logic error: tree is not valid because this kid does not exist:"+str(k));
checked += 1
if checked % 50000 == 0:
sys.stderr.write(str(checked)+" nodes checked\n")
if len(root) > 1:
Error.warning("There is more than one root\n")
sys.stderr.write("Taxonomic tree is considered valid\n")
def start(self):
i = 0
while i < MAX_CONNECTIONS:
try:
self.socket.connect((SERVER_ADDRESS, SERVER_PORT))
print "connected"
break
except:
i += 1
if i == MAX_CONNECTIONS or i > MAX_CONNECTIONS:
Error.server_error_msg()
return
self.socket.send('Hello\r\n')
data = self.socket.recv(LEN_UNIT_BUF).split(END_LINE)[0]
if not self.verify_hello(data):
self.socket.close()
return
if Crypto().key_exchange(self.key, self.socket):
print "finished key exchange"
try:
subprocess.Popen("ClientEngine.py 1", shell=True)
except:
Error.error_msg()
return
socket_obj = LocalPythonCommunication()
socket_obj.StartServer()
i = 0
while True:
i += 1
request = socket_obj.Recv()
while request == "":
request = socket_obj.Recv()
self.send(request)
print "from client " + request + " request %d" % i
answer = self.recv()
socket_obj.Send(answer)
print "from client " + answer + " answer %d" % i
def main():
batch=None
username=raw_input("Username >>>")
pwd=getpass.getpass("Password >>>")
with open('TeacherRecords.txt') as readTeacherFile:
jsonData1=json.load(readTeacherFile)
for i in range(len(jsonData1)):
if jsonData1[i]['username']==username and jsonData1[i]['password']==pwd :
batch=jsonData1[i]['batch']
print "\n",jsonData1[i]['name']," -Batch ",batch,"\n","Access Granted"
if jsonData1[i]['is_Marks_Updated']=="False":
print "Reminder to upload the latest test marks"
break
if batch==None:
print "Access Denied"
print "Username or password or both are incorrect!!!Please try again"
return
while True:
print "\n1. See the list of students in ur batch"
print "2. Upload marks of the Latest Test"
print "3. Modify marks of individual student"
print "0. Quit"
choice=input(">>>")
obj=TeacherInterface()
if choice==1:
obj.showListOfStudents(batch)
elif choice==2:
obj.uploadMarks(batch)
elif choice==3:
obj.modifyMarks(batch)
elif choice==0:
break
else:
Error.showError()
def sendToFlash(message):
try:
flashConnection.send(message.encode('utf-8'))
except socket.error:
Error.flashClientFail(flashSock, iTunesSock)
flashSock.bind(('127.0.0.1', PORT))
flashSock.listen(1)
# 60 second connection to flash timeout so aethyrHelper doesn't live forever
flashSock.settimeout(60)
# launch flash frontend
if hasattr(sys, 'frozen'):
os.startfile(os.path.abspath("AethyrBin.exe"))
# wait for flash to connect
try:
flashConnection, address = flashSock.accept()
except socket.error, e:
print('Exception while connecting to Flash: ' + str(e))
Error.flashClientFail(flashSock, iTunesSock)
# remove timeout
flashSock.setblocking(1)
flashConnection.setblocking(1)
# must be non-blocking to utilize threads properly
iTunesSock.setblocking(0)
if (Helper.isNeedUpdate()):
sendToFlash('needToUpdateClient' + DELIMITER)
##########
global tracks
global currentLibrary
def __init__(self, path) : self.path = path if not os.path.isfile(self.path) : Error.printError(0) self.f = open(self.path,"rb")
datadict={'name':jsonDataSorted[i]['name'],'marks':jsonDataSorted[i]['marks'],"batch":jsonDataSorted[i]['batch']}
listObj.append(datadict)
json.dump(listObj,open('MarkSheet.txt','w'))
jsonDataSorted=json.load(open('MarkSheet.txt'))
open('MarkSheet.txt','w').write(json.dumps(jsonDataSorted,indent=4))
os.system('MarkSheet.txt')
def AdmInterface(choice):
AdmObj=Administrator()
if choice==2:
AdmObj.startNewTest() #upload marks for all the students
elif choice==3:
AdmObj.reMapping() #Shuffle students and allot them batches
while(True):
print "\nPress 1 to Access the Coaching Students Database"
print "Press 2 to start a new test(give reminders to teachers)"
print "Press 3 for Batch Allotment"
print "Press 0 to exit"
choicefour=input(">>>")
if choicefour==1:
coachingtemp.accessStuData()
elif choicefour==2 or choicefour==3:
AdmInterface(choicefour)
elif choicefour==0:
break
else:
Error.showError()
def __init__(self, contig):
if type(contig).__name__ != "Contig":
Error.error("Aligned_contig: __init__: The object passed is not of type Contig")
self.contig = contig
self.comparable_samples = {} #a list of Genomic_position for each comparable sample
self.bam_file_lists = {} #Sample name, list of bam_file. The sample names are the same than in comparable_samples
def translate_all_frames(self):
"""
Will translate every possible amino acid that are in the environment.
:return: A tsv table to stdout
"""
nucleotides_sequences = self.group_environment()
total = 0
for entry in nucleotides_sequences:
total += nucleotides_sequences[entry]
if total != len(self.reads):
Error.LogicError("Genomic_environment: translate_all_frames: Total is different" +
" than depth")
frames = []
for i in range(0, 6):
new_frame = {}
frames.append(new_frame)
for entry in nucleotides_sequences:
#Kinda fuzzy... we must find the amino acid in all frames.
#We will have a list of frame where each fram is a dict stored with aa.
if len(entry) != 5:
Error.error("Length of sequence: %s is not 5" % entry)
#I dont see a way to avoid hardcoding :(
#Frame 1
print(entry)
print(entry[0:3])
#print(len(entry[0:3]))
codon = Seq(entry[0:3], IUPAC.unambiguous_dna)
aa = str(codon.translate(table=11))
if not aa in frames[0]:
frames[0][aa] = 0
frames[0][aa] += nucleotides_sequences[entry]
#frame 2
print(entry[1:4])
codon = Seq(entry[1:4], IUPAC.unambiguous_dna)
aa = str(codon.translate(table=11))
if not aa in frames[1]:
frames[1][aa] = 0
frames[1][aa] += nucleotides_sequences[entry]
#Frame 3
print(entry[2:5])
codon = Seq(entry[2:5], IUPAC.unambiguous_dna)
aa = str(codon.translate(table=11))
if not aa in frames[2]:
frames[2][aa] = 0
frames[2][aa] += nucleotides_sequences[entry]
reverse_entry = entry[::-1]
#Frame 4 (reverse starting from right)
print(reverse_entry[0:3])
codon = Seq(reverse_entry[0:3], IUPAC.unambiguous_dna)
aa = str(codon.translate(table=11))
if not aa in frames[3]:
frames[3][aa] = 0
frames[3][aa] += nucleotides_sequences[entry]
#Frame 5
print(reverse_entry[1:4])
codon = Seq(reverse_entry[1:4], IUPAC.unambiguous_dna)
aa = str(codon.translate(table=11))
if not aa in frames[4]:
frames[4][aa] = 0
frames[4][aa] += nucleotides_sequences[entry]
#Frame 6
print(reverse_entry[2:5])
codon = Seq(reverse_entry[2:5], IUPAC.unambiguous_dna)
aa = str(codon.translate(table=11))
if not aa in frames[5]:
frames[5][aa] = 0
frames[5][aa] += nucleotides_sequences[entry]
##We output this in a cute way
header = "Contig\tSNP position(contig)\tFrame\tAmino acid\tProportion\n"
print(header),
for frame in range(0, 6):
frame_number = str(frame+1)
for amino_acid in frames[frame]:
line = ""
line = self.contig+"\t"+str(self.position)+'\t'+frame_number+"\t"+amino_acid+"\t"+str(float(frames[frame][amino_acid]/total))
print(line)
def checkFiles(listOfFile):
for i in listOfFile:
if not(isValid(i)):
Error.error("File"+str(i)+"can't be opened")
def getNode(self, nodeId):
if self.nodeExist(nodeId):
return self.Nodes[nodeId]
else:
Error.error("Logic error: required node does not exist")
def addNode(self, node):
if self.nodeExist(node.getId()):
Error.error("Logic error: node already exist. Node number:"+str(node.getId()))
self.Nodes[node.getId()] = node
def nud(self):
raise SyntaxError(Error.generateErrorMessageWithNoArguement('Expect (identifier) before {}', self, self.id))
