def __init__(self, decorated=None):
"""Initialize the DebuggingConsumer."""
self.linenum = 0
if decorated is None:
decorated = ParserSupport.AbstractConsumer()
self.decorated = decorated
self._prev_attr = None
def test_blast_output(outfile):
# Try to auto-detect the format
if 1:
print("No parser specified. I'll try to choose one for you based")
print("on the format of the output file.")
print("")
parser_class = choose_parser(outfile)
print("It looks like you have given output that should be parsed")
print("with %s.%s. If I'm wrong, you can select the correct parser" %\
(parser_class.__module__, parser_class.__name__))
print("on the command line of this script (NOT IMPLEMENTED YET).")
else:
raise NotImplementedError
parser_class = NCBIWWW.BlastParser
print("Using %s to parse the file." % parser_class.__name__)
print("")
scanner_class = parser_class()._scanner.__class__
consumer_class = parser_class()._consumer.__class__
#parser_class()._scanner.feed(
# open(outfile), ParserSupport.TaggingConsumer())
print(
"I'm going to run the data through the parser to see what happens...")
parser = parser_class()
try:
rec = parser.parse_file(outfile)
except (KeyboardInterrupt, SystemExit):
raise
except Exception as x:
exception_info = str(x)
print("Dang, the parsing failed.")
else:
print("Parsing succeeded, no problems detected.")
print("However, you should check to make sure the following scanner")
print("trace looks reasonable.")
print("")
parser_class()._scanner.feed(open(outfile),
ParserSupport.TaggingConsumer())
return 0
print("")
print("Alright. Let me try and figure out where in the parser the")
print("problem occurred...")
etype, value, tb = sys.exc_info()
ftb = traceback.extract_tb(tb)
ftb.reverse()
class_found = None
for err_file, err_line, err_function, err_text in ftb:
if hasattr(consumer_class, err_function):
class_found = consumer_class
break
elif hasattr(scanner_class, err_function):
class_found = scanner_class
break
if class_found is None:
print("Sorry, I could not pinpoint the error to the parser.")
print("There's nothing more I can tell you.")
print("Here's the traceback:")
traceback.print_exception(etype, value, tb)
return 1
else:
print("I found the problem in %s.%s.%s, line %d:" % \
(class_found.__module__, class_found.__name__,
err_function, err_line))
print(" %s" % err_text)
print("This output caused an %s to be raised with the" % etype)
print("information %r." % exception_info)
print("")
print("Let me find the line in the file that triggers the problem...")
parser = parser_class()
scanner, consumer = parser._scanner, parser._consumer
consumer = DebuggingConsumer(consumer)
try:
scanner.feed(open(outfile), consumer)
except etype as x:
pass
else:
print("Odd, the exception disappeared! What happened?")
return 3
print("It's caused by line %d:" % consumer.linenum)
lines = open(outfile).readlines()
start, end = consumer.linenum - CONTEXT, consumer.linenum + CONTEXT + 1
if start < 0:
start = 0
if end > len(lines):
end = len(lines)
ndigits = len(str(end))
for linenum in range(start, end):
line = chomp(lines[linenum])
if linenum == consumer.linenum:
prefix = '*'
else:
prefix = ' '
s = "%s%*d %s" % (prefix, ndigits, linenum, line)
s = s[:80]
print(s)
print("")
if class_found == scanner_class:
print("Problems in %s are most likely caused by changed formats." % \
class_found.__name__)
print("You can start to fix this by going to line %d in module %s." % \
(err_line, class_found.__module__))
print("Perhaps the scanner needs to be made more lenient by accepting")
print("the changed format?")
print("")
if VERBOSITY <= 0:
print("For more help, you can run this script in verbose mode")
print("to see detailed information about how the scanner")
print("identifies each line.")
else:
print("OK, let's see what the scanner's doing!")
print("")
print("*" * 20 + " BEGIN SCANNER TRACE " + "*" * 20)
try:
parser_class()._scanner.feed(open(outfile),
ParserSupport.TaggingConsumer())
except etype as x:
pass
print("*" * 20 + " END SCANNER TRACE " + "*" * 20)
print("")
elif class_found == consumer_class:
print("Problems in %s can be caused by two things:" % \
class_found.__name__)
print(" - The format of the line parsed by '%s' changed." % \
err_function)
print(" - The scanner misidentified the line.")
print("Check to make sure '%s' should parse the line:" % \
err_function)
s = " %s" % chomp(lines[consumer.linenum])
s = s[:80]
print(s)
print("If so, debug %s.%s. Otherwise, debug %s." % \
(class_found.__name__, err_function, scanner_class.__name__))
def __init__(self, decorated=None):
self.linenum = 0
if decorated is None:
decorated = ParserSupport.AbstractConsumer()
self.decorated = decorated
self._prev_attr = None
filter= "F > /etc/passwd'")
assert False, "Attempted output redirection not caught!"
except ValueError, e:
assert str(e) == "Rejecting suspicious argument for filter"
#Good
### _Scanner
print "Running tests on _Scanner"
scanner = NCBIStandalone._Scanner()
for test in all_tests:
print "*" * 50, "TESTING %s" % test
datafile = os.path.join("Blast", test)
scanner.feed(open(datafile), ParserSupport.AbstractConsumer())
for test in detailed_tests:
print "*" * 50, "TESTING %s" % test
datafile = os.path.join("Blast", test)
scanner.feed(open(datafile), ParserSupport.TaggingConsumer())
### BlastParser
print "Running tests on BlastParser"
parser = NCBIStandalone.BlastParser()
pb_parser = NCBIStandalone.PSIBlastParser()
for test in all_tests:
print "*" * 50, "TESTING %s" % test
datafile = os.path.join("Blast", test)
print "I'm going to run the data through the parser to see what happens..."
parser = parser_class()
try:
rec = parser.parse_file(outfile)
except KeyboardInterrupt, SystemExit:
raise
except Exception, x:
exception_info = str(x)
print "Dang, the parsing failed."
else:
print "Parsing succeeded, no problems detected."
print "However, you should check to make sure the following scanner"
print "trace looks reasonable."
print
parser_class()._scanner.feed(open(outfile),
ParserSupport.TaggingConsumer())
return 0
print
print "Alright. Let me try and figure out where in the parser the"
print "problem occurred..."
etype, value, tb = sys.exc_info()
ftb = traceback.extract_tb(tb)
ftb.reverse()
class_found = None
for err_file, err_line, err_function, err_text in ftb:
if hasattr(consumer_class, err_function):
class_found = consumer_class
break
elif hasattr(scanner_class, err_function):
class_found = scanner_class
from Bio.File import UndoHandle
meme_tests = [
"meme.dna.oops.txt", "meme.protein.oops.txt", "meme.protein.tcm.txt"
]
mast_tests = [
"mast.dna.oops.txt", "mast.protein.oops.txt", "mast.protein.tcm.txt"
]
print "Testing MEME Scanner"
datafile = os.path.join("MEME", meme_tests[0])
uhandle = UndoHandle(open(datafile))
scanner = Parser._MEMEScanner()
consumer = ParserSupport.TaggingConsumer()
scanner.feed(uhandle, consumer)
print "Running tests on MEME parser"
meme_parser = Parser.MEMEParser()
for test in meme_tests:
print "*" * 50, "TESTING %s" % test
datafile = os.path.join("MEME", test)
rec = meme_parser.parse(open(datafile))
print "Testing MEME Scanner"
datafile = os.path.join("MEME", mast_tests[0])
uhandle = UndoHandle(open(datafile))
def pb(b):
if b:
return 1
return 0
# TaggingConsumer
print("Running tests on TaggingConsumer")
class TestHandle(object):
def write(self, s):
print(s)
h = TestHandle()
tc = ParserSupport.TaggingConsumer(handle=h, colwidth=5)
tc.start_section() # '***** start_section\n'
tc.test1('myline') # 'test1: myline\n'
tc.end_section() # '***** end_section\n'
# is_blank_line
print("Running tests on is_blank_line")
is_blank_line = lambda *args, **keywds: \
pb(ParserSupport.is_blank_line(*args, **keywds))
print(is_blank_line('\n')) # 1
print(is_blank_line('\r\n')) # 1
print(is_blank_line('\r')) # 1
def write(self, s):
print s
h = TestHandle()
tc = ParserSupport.TaggingConsumer(handle=h, colwidth=5)
tc.start_section() # '***** start_section\n'
tc.test1("myline") # 'test1: myline\n'
tc.end_section() # '***** end_section\n'
### is_blank_line
print "Running tests on is_blank_line"
is_blank_line = lambda *args, **keywds: pb(ParserSupport.is_blank_line(*args, **keywds))
print is_blank_line("\n") # 1
print is_blank_line("\r\n") # 1
print is_blank_line("\r") # 1
print is_blank_line("") # 1
print is_blank_line("", allow_spaces=1) # 1
print is_blank_line("", allow_spaces=0) # 1
print is_blank_line(string.whitespace, allow_spaces=1) # 1
print is_blank_line("hello") # 0
print is_blank_line("hello", allow_spaces=1) # 0
print is_blank_line("hello", allow_spaces=0) # 0
print is_blank_line(string.whitespace, allow_spaces=0) # 0
### safe_readline
print "I'm going to run the data through the parser to see what happens..."
parser = parser_class()
try:
rec = parser.parse_file(outfile)
except KeyboardInterrupt, SystemExit:
raise
except Exception, x:
exception_info = str(x)
print "Dang, the parsing failed."
else:
print "Parsing succeeded, no problems detected."
print "However, you should check to make sure the following scanner"
print "trace looks reasonable."
print
parser_class()._scanner.feed(
open(outfile), ParserSupport.TaggingConsumer())
return 0
print
print "Alright. Let me try and figure out where in the parser the"
print "problem occurred..."
etype, value, tb = sys.exc_info()
ftb = traceback.extract_tb(tb)
ftb.reverse()
class_found = None
for err_file, err_line, err_function, err_text in ftb:
if hasattr(consumer_class, err_function):
class_found = consumer_class
break
elif hasattr(scanner_class, err_function):
class_found = scanner_class