def edit(D, text):
L = '\r\n'
K = 'utf-8-sig'
A = text
import tempfile as H
A = A or ''
E = type(A) in [bytes, bytearray]
if not E and A and not A.endswith(_D): A += _D
I, B = H.mkstemp(prefix='editor-', suffix=D.extension)
try:
if not E:
if WIN:
F = K
A = A.replace(_D, L)
else:
F = 'utf-8'
A = A.encode(F)
C = os.fdopen(I, 'wb')
C.write(A)
C.close()
J = os.path.getmtime(B)
D.edit_file(B)
if D.require_save and os.path.getmtime(B) == J: return _A
C = open(B, 'rb')
try:
G = C.read()
finally:
C.close()
if E: return G
else: return G.decode(K).replace(L, _D)
finally:
os.unlink(B)
def testTrollitaireConverter(self):
"""Test that the Trollitaire converter works properly."""
# First test case (no surprises)
tempfile = cStringIO.StringIO()
with open(old_troll_file) as infile:
trollconvert.convert_draft_file(infile, tempfile)
expected = open(converted_troll).read()
tempfile.seek(0)
result = tempfile.read()
self.assertEqual(expected, result)
# Second test case (has an UNDO)
tempfile = cStringIO.StringIO()
with open(old_troll_file2) as infile:
trollconvert.convert_draft_file(infile, tempfile)
expected = open(converted_troll2).read()
tempfile.seek(0)
result = tempfile.read()
self.assertEqual(expected, result)
def _load_db_to_memory(in_db_path):
# Read database to tempfile
conn = sqlite3.connect('file:%s?mode=ro' % in_db_path, uri=True)
tempfile = io.StringIO()
for line in conn.iterdump():
tempfile.write('%s\n' % line)
conn.close()
tempfile.seek(0)
# Create a database in memory and import from tempfile
conn = sqlite3.connect(":memory:")
conn.cursor().executescript(tempfile.read())
return conn
def _copy_temp_to_perm(self):
# This is a really stupid way to do this.
# FIXME: abstract out the duplicated code, lazybones.
if self.gsettings.expert is False:
permfile = open(self.filesinkpath, 'wb')
self.tempfile.close()
self.tempfile = open(self.temppath, 'rb')
permfile.write(self.tempfile.read())
permfile.close()
else:
for i in (1, 2):
permfile = open(self.filesinkpath + '-' + str(i) + '.wav',
'wb')
tf = eval('self.tempfile' + str(i))
tf.close()
tempfile = open(eval('self.temppath' + str(i)), 'rb')
permfile.write(tempfile.read())
permfile.close()
def run(self, args, trust_dir, stdinput=None, username_passwd=None):
"""
Runs the notary client in a subprocess, and returns the output
"""
command = self.client + ["-d", trust_dir] + list(args)
print("$ " + " ".join(command))
# username password require newlines - EOF doesn't seem to do it.
communicate_input = (tuple((x + "\n" for x in self.username_passwd))
if username_passwd is None else username_passwd)
# Input comes before the username/password, and if there is a username
# and password, we need a newline after the input. Otherwise, just use
# EOF (for instance if we're piping text to verify)
if stdinput is not None:
if communicate_input:
communicate_input = (stdinput + "\n", ) + communicate_input
else:
communicate_input = (stdinput, )
_, filename = mkstemp()
with open(filename, 'wb') as tempfile:
process = Popen(command,
env=self.env,
stdout=tempfile,
stdin=PIPE,
universal_newlines=True)
# communicate writes once then closes stdin for the process
process.communicate("".join(communicate_input))
process.wait()
with open(filename) as tempfile:
output = tempfile.read()
retcode = process.poll()
cleanup(filename)
print(output)
if retcode:
raise CalledProcessError(retcode, command, output=output)
return output
def run(self, args, trust_dir, stdinput=None, username_passwd=None):
"""
Runs the notary client in a subprocess, and returns the output
"""
command = self.client + ["-d", trust_dir] + list(args)
print("$ " + " ".join(command))
# username password require newlines - EOF doesn't seem to do it.
communicate_input = (tuple((x + "\n" for x in self.username_passwd))
if username_passwd is None else username_passwd)
# Input comes before the username/password, and if there is a username
# and password, we need a newline after the input. Otherwise, just use
# EOF (for instance if we're piping text to verify)
if stdinput is not None:
if communicate_input:
communicate_input = (stdinput + "\n",) + communicate_input
else:
communicate_input = (stdinput,)
_, filename = mkstemp()
with open(filename, 'wb') as tempfile:
process = Popen(command, env=self.env, stdout=tempfile, stdin=PIPE,
universal_newlines=True)
# communicate writes once then closes stdin for the process
process.communicate("".join(communicate_input))
process.wait()
with open(filename) as tempfile:
output = tempfile.read()
retcode = process.poll()
cleanup(filename)
print(output)
if retcode:
raise CalledProcessError(retcode, command, output=output)
return output
def main(path_to_debug_info=None, gdb_argv=None, no_import=False):
"""
Start the Cython debugger. This tells gdb to import the Cython and Python
extensions (libcython.py and libpython.py) and it enables gdb's pending
breakpoints.
path_to_debug_info is the path to the Cython build directory
gdb_argv is the list of options to gdb
no_import tells cygdb whether it should import debug information
"""
parser = optparse.OptionParser(usage=usage)
parser.add_option("--gdb-executable",
dest="gdb",
default='gdb',
help="gdb executable to use [default: gdb]")
parser.add_option(
"--verbose",
"-v",
dest="verbosity",
action="count",
default=0,
help="Verbose mode. Multiple -v options increase the verbosity")
(options, args) = parser.parse_args()
if path_to_debug_info is None:
if len(args) > 1:
path_to_debug_info = args[0]
else:
path_to_debug_info = os.curdir
if gdb_argv is None:
gdb_argv = args[1:]
if path_to_debug_info == '--':
no_import = True
logging_level = logging.WARN
if options.verbosity == 1:
logging_level = logging.INFO
if options.verbosity >= 2:
logging_level = logging.DEBUG
logging.basicConfig(level=logging_level)
logger.info("verbosity = %r", options.verbosity)
logger.debug("options = %r; args = %r", options, args)
logger.debug(
"Done parsing command-line options. path_to_debug_info = %r, gdb_argv = %r",
path_to_debug_info, gdb_argv)
tempfilename = make_command_file(path_to_debug_info, no_import=no_import)
logger.info("Launching %s with command file: %s and gdb_argv: %s",
options.gdb, tempfilename, gdb_argv)
with open(tempfilename) as tempfile:
logger.debug('Command file (%s) contains: """\n%s"""', tempfilename,
tempfile.read())
logger.info("Spawning %s...", options.gdb)
p = subprocess.Popen([options.gdb, '-command', tempfilename] +
gdb_argv)
logger.info("Spawned %s (pid %d)", options.gdb, p.pid)
while True:
try:
logger.debug("Waiting for gdb (pid %d) to exit...", p.pid)
ret = p.wait()
logger.debug(
"Wait for gdb (pid %d) to exit is done. Returned: %r",
p.pid, ret)
except KeyboardInterrupt:
pass
else:
break
logger.debug("Closing temp command file with fd: %s",
tempfile.fileno())
logger.debug("Removing temp command file: %s", tempfilename)
os.remove(tempfilename)
logger.debug("Removed temp command file: %s", tempfilename)
if trace_user and trace_kernel:
tempfile.write("collect regs->cs\n")
tempfile.write("collect $current_task_pid\n")
tempfile.write("end\n")
tempfile.write("trace smp_apic_timer_interrupt\n")
tempfile.write("condition $bpnum " + pid_str + cond_str + "\n")
tempfile.write("commands\n")
tempfile.write("collect regs->ip\n")
if trace_user and trace_kernel:
tempfile.write("collect regs->cs\n")
tempfile.write("collect $current_task_pid\n")
tempfile.write("end\n")
tempfile.close()
tempfile = open(tempfilename, "r")
print "Tracepoint command:"
print tempfile.read()
tempfile.close()
gdb.execute("source " + tempfilename, True, False)
os.remove(tempfilename)
gdb.execute("set disconnected-tracing on", True, False)
gdb.execute("tstart")
gdb.execute("kill", True, False)
signal.signal(signal.SIGINT, sigint_handler)
signal.siginterrupt(signal.SIGINT, False)
#Connect to pipe
gdb.execute("target tfile /sys/kernel/debug/gtpframe_pipe")
#--------------------------------------------------------------------------------------------------
#cycle
if trace_user and trace_kernel:
tempfile.write("collect regs->cs\n")
tempfile.write("collect $current_task_pid\n")
tempfile.write("end\n")
tempfile.write("trace smp_apic_timer_interrupt\n")
tempfile.write("condition $bpnum "+pid_str+cond_str+"\n")
tempfile.write("commands\n")
tempfile.write("collect regs->ip\n")
if trace_user and trace_kernel:
tempfile.write("collect regs->cs\n")
tempfile.write("collect $current_task_pid\n")
tempfile.write("end\n")
tempfile.close()
tempfile = open(tempfilename, "r")
print "Tracepoint command:"
print tempfile.read()
tempfile.close()
gdb.execute("source "+tempfilename, True, False)
os.remove(tempfilename)
gdb.execute("set disconnected-tracing on", True, False)
gdb.execute("tstart")
gdb.execute("kill", True, False)
signal.signal(signal.SIGINT, sigint_handler);
signal.siginterrupt(signal.SIGINT, False);
#Connect to pipe
gdb.execute("target tfile /sys/kernel/debug/gtpframe_pipe")
#--------------------------------------------------------------------------------------------------
#cycle
#tempfile module import tempfile #create a temp file tempfile = tempfile.TemporaryFile() #write to a temp file tempfile.write(b'Save this special nnumber for me: 01722750669') tempfile.seek(0) #read the temp file print(tempfile.read()) tempfile.close()
def pack(self):
"""
Packs the fasta and sqlite databases to remove redundancy and merge sqlite columns
Returns:
void
"""
# First we handle the fastq file
unique_hash = set()
redundant_file = fasta.file(self.database_fasta_file)
temp = gzip.open(self.database_temp_file,'wb')
for record in redundant_file.read():
if not record['header'] in unique_hash :
unique_hash.add(record['header'])
temp.write('>'+record['header']+os.linesep+record['sequence']+os.linesep)
os.rename(self.database_temp_file , self.database_fasta_file)
# Now the sqlite (http://stackoverflow.com/a/10856450)
from StringIO import StringIO
tempfile = StringIO()
for line in self.sq3_connection.iterdump():
tempfile.write('%s\n' % line)
tempfile.seek(0)
sq3_temp_connection = sql.connect(self.database_temp_file)
sq3_temp_cursor = sq3_temp_connection.cursor()
sq3_temp_cursor.execute("CREATE TABLE IF NOT EXISTS genes ( sequence_hash TEXT, genus TEXT, species TEXT, NCBItaxID TEXT, kegg_ontology TEXT , kegg_reaction TEXT , go_term TEXT, kegg_map TEXT , sequence TEXT)")
sq3_temp_connection.commit()
sq3_memory_connection = sql.connect(":memory:")
sq3_memory_cursor = sq3_memory_connection.cursor()
sq3_memory_cursor.executescript(tempfile.read())
sq3_memory_connection.commit()
sq3_memory_connection.row_factory = sql.Row
for h in unique_hash:
sq3_memory_cursor.execute('SELECT * FROM genes WHERE `sequence_hash` = \'%s\'' % h)
rows = sq3_memory_cursor.fetchall()
rows_selected = len(rows)
columns = tuple ([c[0] for c in sq3_memory_cursor.description])
merge_dict = dict.fromkeys(columns)
for r in rows:
r=[str(x) if x else None for x in r ]
incoming = dict(zip(columns,r))
merge_dict = merge_insert_dicts(merge_dict,incoming)
merge_dict = {i:j for i,j in merge_dict.items() if j != []}
insert = 'INSERT INTO genes({}) VALUES ({})'.format(', '.join(merge_dict.keys()),', '.join('?' * len(merge_dict)))
try:
sq3_temp_cursor.execute(insert,merge_dict.values())
except sql.Error as e:
print merge_dict
logger.warn(e)
raise
sq3_temp_connection.commit()
sq3_temp_connection.close()
def main(path_to_debug_info=None, gdb_argv=None, no_import=False):
"""
Start the Cython debugger. This tells gdb to import the Cython and Python
extensions (libcython.py and libpython.py) and it enables gdb's pending
breakpoints.
path_to_debug_info is the path to the Cython build directory
gdb_argv is the list of options to gdb
no_import tells cygdb whether it should import debug information
"""
parser = optparse.OptionParser(usage=usage)
parser.add_option("--gdb-executable",
dest="gdb", default='gdb',
help="gdb executable to use [default: gdb]")
parser.add_option("--verbose", "-v",
dest="verbosity", action="count", default=0,
help="Verbose mode. Multiple -v options increase the verbosity")
(options, args) = parser.parse_args()
if path_to_debug_info is None:
if len(args) > 1:
path_to_debug_info = args[0]
else:
path_to_debug_info = os.curdir
if gdb_argv is None:
gdb_argv = args[1:]
if path_to_debug_info == '--':
no_import = True
logging_level = logging.WARN
if options.verbosity == 1:
logging_level = logging.INFO
if options.verbosity >= 2:
logging_level = logging.DEBUG
logging.basicConfig(level=logging_level)
logger.info("verbosity = %r", options.verbosity)
logger.debug("options = %r; args = %r", options, args)
logger.debug("Done parsing command-line options. path_to_debug_info = %r, gdb_argv = %r",
path_to_debug_info, gdb_argv)
tempfilename = make_command_file(path_to_debug_info, no_import=no_import)
logger.info("Launching %s with command file: %s and gdb_argv: %s",
options.gdb, tempfilename, gdb_argv)
with open(tempfilename) as tempfile:
logger.debug('Command file (%s) contains: """\n%s"""', tempfilename, tempfile.read())
logger.info("Spawning %s...", options.gdb)
p = subprocess.Popen([options.gdb, '-command', tempfilename] + gdb_argv)
logger.info("Spawned %s (pid %d)", options.gdb, p.pid)
while True:
try:
logger.debug("Waiting for gdb (pid %d) to exit...", p.pid)
ret = p.wait()
logger.debug("Wait for gdb (pid %d) to exit is done. Returned: %r", p.pid, ret)
except KeyboardInterrupt:
pass
else:
break
logger.debug("Closing temp command file with fd: %s", tempfile.fileno())
logger.debug("Removing temp command file: %s", tempfilename)
os.remove(tempfilename)
logger.debug("Removed temp command file: %s", tempfilename)