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Merge pull request #57 from philip-schrodt/master
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Bug fixes
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@johnb30
johnb30 committed Sep 2, 2014
2 parents 1f9d61d + b2e1099 commit 185f33e
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82 changes: 53 additions & 29 deletions docs/source/petrarch.rst
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Original file line number Diff line number Diff line change
Expand Up @@ -14,40 +14,29 @@ individual sentence. As can be seen in the section below, the data *is*
organized within the program at the story level, but both the StanfordNLP and
event coding process occurs stricly at the sentence level.

Command Line Interface
----------------------

Internal Data Structures
------------------------
The following options can be used in the command line

The main data format within PETRARCH is a Python dictionary that is structured
around unique story IDs as the keys for the dictionary and another dictionary
as the value. The value dictionary contains the relevant information for the
sentences within the story, and the meta information about the story such as
the date and source. The broad format of this internal dictionary is:

::
-i, --inputs File, or directory of files, to parse.

{story_id: {'sents': {0: {'content': 'String of content', 'parsed': 'StanfordNLP parse tree',
'coref': 'Optional list of corefs', 'events': 'List of coded events',
'issues': 'Optional list of issues'},
1: {'content': 'String of content', 'parsed': 'StanfordNLP parse tree',
'coref': 'Optional list of corefs', 'events': 'List of coded events',
'issues': 'Optional list of issues'}
}
'meta': {'date': 'YYYYMMDD', 'other': "This is the holding dict for misc info."}
},
story_id: {'sents': {0: {'content': 'String of content', 'parsed': 'StanfordNLP parse tree',
'coref': 'Optional list of corefs', 'events': 'List of coded events',
'issues': 'Optional list of issues'},
1: {'content': 'String of content', 'parsed': 'StanfordNLP parse tree',
'coref': 'Optional list of corefs', 'events': 'List of coded events',
'issues': 'Optional list of issues'}
}
'meta': {'date': 'YYYYMMDD', 'other': "This is the holding dict for misc info."}
},
}
-o, --output Output file for parsed events

-P, --parsed Input has already been parsed: all input records contain StanfordNLP-parsed <Parse>...</Parse> block. Defaults to ``False``.

-c, --config Filepath for the PETRARCH configuration file. Defaults to ``PETR_config.ini``.


**Other options**

``parse``
Run the PETRARCH parser

``validate``
Command to run the PETRARCH validation suite. If combined with ``-i``, validation records are read from that file (which needs to be in the validation file format, not the standard format) ; otherwise the input file is PETR.UnitTest.records.txt

This consistent internal format allows for the easy extension of the program
through external hooks.

Configuration File
------------------
Expand Down Expand Up @@ -136,3 +125,38 @@ PETRARCH.
[StanfordNLP]
stanford_dir = ~/stanford-corenlp/


Internal Data Structures
------------------------

The main data format within PETRARCH is a Python dictionary that is structured
around unique story IDs as the keys for the dictionary and another dictionary
as the value. The value dictionary contains the relevant information for the
sentences within the story, and the meta information about the story such as
the date and source. The broad format of this internal dictionary is:

::

{story_id: {'sents': {0: {'content': 'String of content', 'parsed': 'StanfordNLP parse tree',
'coref': 'Optional list of corefs', 'events': 'List of coded events',
'issues': 'Optional list of issues'},
1: {'content': 'String of content', 'parsed': 'StanfordNLP parse tree',
'coref': 'Optional list of corefs', 'events': 'List of coded events',
'issues': 'Optional list of issues'}
}
'meta': {'date': 'YYYYMMDD', 'other': "This is the holding dict for misc info."}
},
story_id: {'sents': {0: {'content': 'String of content', 'parsed': 'StanfordNLP parse tree',
'coref': 'Optional list of corefs', 'events': 'List of coded events',
'issues': 'Optional list of issues'},
1: {'content': 'String of content', 'parsed': 'StanfordNLP parse tree',
'coref': 'Optional list of corefs', 'events': 'List of coded events',
'issues': 'Optional list of issues'}
}
'meta': {'date': 'YYYYMMDD', 'other': "This is the holding dict for misc info."}
},
}

This consistent internal format allows for the easy extension of the program
through external hooks.

111 changes: 78 additions & 33 deletions petrarch/petrarch.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -186,14 +186,35 @@ def check_balance():
nclose = 0
ka = 0
while ka < len(ParseList):
if ParseList[ka] == '(':
if ParseList[ka][0] == '(':
nopen += 1
elif ParseList[ka] == '~':
elif ParseList[ka][0] == '~':
nclose += 1
ka += 1
if nopen != nclose:
raise UnbalancedTree

def check_exceptions():
"""
This checks for some known idiosyncratic ParseList patterns that indicate problems in
the input text. Logs the specific issue but does not raise an error yet.
Currently tracking:
-- Dateline
"""
ntag = 0
taglist = []
ka = 0
while ka < len(ParseList):
if ParseList[ka][0] == '(':
taglist.append(ParseList[ka])
ntag += 1
if ntag > 2: break # this is all we need for dateline
ka += 1
# print('ce1:',taglist)
if taglist[:3] == ['(ROOT','(NE','(NEC']:
logger = logging.getLogger('petr_log')
logger.warning('Dateline pattern found in ParseList; record skipped: {}'.format(SentenceID))

# ========================== VALIDATION FUNCTIONS ========================== #


Expand Down Expand Up @@ -674,7 +695,7 @@ def mark_compounds():
# convert CC to CCP, though <14.05.12> we don't actually do
# anything with this yet: (NEC is the trigger for additional
# processing of compounds
treestr = treestr[:ka + 4] + 'P' + treestr[ka + 4:]
treestr = treestr[:ka + 3] + 'P' + treestr[ka + 3:]
if ShowMarkCompd:
print('\nMC2:', treestr[kb:])
# nested compounds: don't go there...
Expand Down Expand Up @@ -1010,6 +1031,16 @@ def process_preposition(ka):

ParseStart = 2 # skip (ROOT (S

try:
check_exceptions()
except:
try:
# this can re-raise UnbalancedTree
raise_parsing_error('end of read_TreeBank()')
except UnbalancedTree:
logger.warning('\tUnbalanced tree. Passing.')
#raise SkipRecord

try:
check_balance()
except:
Expand Down Expand Up @@ -1080,7 +1111,7 @@ def add_code(neloc, isupperseq):
codelist.append(accode)

codelist = []
# print 'GLC0',thisloc
# print ('GLC0',thisloc)
# print ' USeq:',UpperSeq
# print ' LSeq:',LowerSeq
if thisloc[1]:
Expand All @@ -1091,7 +1122,7 @@ def add_code(neloc, isupperseq):
# necessarily unbalanced
raise_parsing_error('get_loccodes()-1')

# print 'GLC1',neitem
# print ('GLC1',neitem)
# extract the compound codes from the (NEC ... ~NEC sequence
if '(NEC' in neitem:
ka = thisloc[0] - 1 # UpperSeq is stored in reverse order
Expand All @@ -1116,11 +1147,11 @@ def add_code(neloc, isupperseq):
# at this point some sort of markup we can't handle, not
# necessarily unbalanced
raise_parsing_error('get_loccodes()-3')
# print 'GLC3',neitem
# print ('GLC3',neitem)
StoryEventList.append([SentenceID])
for event in CodedEvents:
StoryEventList.append(event)
# print SentenceID + '\t' + event[0] + '\t' + event[1] + '\t' + event[2]
print(SentenceID + '\t' + event[0] + '\t' + event[1] + '\t' + event[2])
if '(NEC' in neitem: # extract the compound codes
ka = thisloc[0] + 1
while '~NEC' not in LowerSeq[ka]:
Expand All @@ -1138,6 +1169,8 @@ def add_code(neloc, isupperseq):
else:
add_code(thisloc[0], False) # simple code
# print 'GLC5',codelist
if len(codelist) == 0: # this can occur if all codes in an (NEC are null
codelist = ['---']
return codelist


Expand Down Expand Up @@ -1361,8 +1394,8 @@ def find_ne(kseq):
# return the location of the (NE element in aseq starting from kseq, which
# is inside an NE
ka = kseq
# print "fn-1/VPM:" , ka, aseq[ka] # debug
# print "fn-2/VPM:" , aseq, isupperseq # debug
# print("fn-1/VPM:" , ka, aseq[ka]) # debug
# print("fn-2/VPM:" , aseq, isupperseq) # debug
while '(NE' not in aseq[ka]:
if isupperseq:
ka += 1
Expand All @@ -1371,9 +1404,10 @@ def find_ne(kseq):
if ka < 0 or ka >= len(aseq):
# at this point some sort of markup we can't handle, not
# necessarily unbalanced
# print('Bombed here, yessiree bob!...')
raise_parsing_error('find_ne(kseq) in verb_pattern_match()')

# print "VPM/FN-1: Found NE:" , ka, aseq[ka] # debug
# print("fn-3/VPM: Found NE:" , ka, aseq[ka]) # debug
return ka

def syn_match(isupperseq):
Expand Down Expand Up @@ -1413,11 +1447,11 @@ def syn_match(isupperseq):
if ka == len(wordlist):
# last_seq() will also increment
kseq += len(wordlist) - 1
# print words,"matches", kseq
# print(words,"matches", kseq)
return True
return False
else:
# print "&Match:",aseq[kseq]
# print( "&Match:",aseq[kseq])
return True
else:
# throw an error here, but actually should trap these in
Expand All @@ -1428,6 +1462,7 @@ def last_seqword():
global kseq
kseq += 1
if kseq >= len(aseq):
# print('Return on seqword')
return True # hit end of sequence before full pattern matched
else:
return False
Expand All @@ -1436,6 +1471,7 @@ def last_patword():
global kpatword
kpatword += 2 # skip connector
if kpatword >= len(patlist):
# print('Return on patword')
return True
else:
return False
Expand Down Expand Up @@ -1471,38 +1507,48 @@ def no_skip():
continue

if ('~NE' in aseq[kseq]) or ('(NE' in aseq[kseq]):
# print "NE flip", kseq, aseq[kseq], insideNE,
"""
print("NE flip", kseq, aseq[kseq], insideNE,)
if isupperseq: # this doesn't always signal an error but tends to be associated with them
if '~NE' in aseq[kseq] and insideNE:
print(" ==> insideNE error on ~NE")
if '(NE' in aseq[kseq] and not insideNE:
print(" ==> insideNE error on (NE")
else:
if '~NE' in aseq[kseq] and not insideNE:
print(" ==> insideNE error on ~NE")
if '(NE' in aseq[kseq] and insideNE:
print(" ==> insideNE error on (NE") """
if last_seqword():
return False # hit end of sequence before full pattern matched
insideNE = not insideNE
# print "NE result", insideNE
# print("NE result", insideNE) # almost impossible for this to be the error

elif len(patlist[kpatword]) == 1: # deal with token assignments here
if insideNE:
if patlist[kpatword] == '$':
# print('vpm-mk1')
SourceLoc = [find_ne(kseq), isupperseq]
elif patlist[kpatword] == '+':
# print('vpm-mk2')
TargetLoc = [find_ne(kseq), isupperseq]

elif patlist[kpatword] == '^': # skip to the end of the (NE
# print "Skipping",kseq, aseq[kseq:kseq+8], insideNE
# print("Skipping-mk1:",kseq, aseq[kseq:kseq+8], insideNE)
while '~NE' not in aseq[kseq]:
if isupperseq:
kseq -= 1
else:
kseq += 1
if kseq < 0 or kseq >= len(aseq):
# print "skip/VPM:", kseq, aseq,'\n', aseq[kseq-8:kseq-1] # debug
# print("skip/VPM error:", kseq, aseq,'\n', aseq[kseq-8:kseq-1]) # debug
# at this point some sort of markup we can't
# handle, not necessarily unbalanced
raise_parsing_error("""find_ne(kseq) in skip
assessment,
verb_pattern_match()""")
raise_parsing_error("find_ne(kseq) in skip assessment, verb_pattern_match()")
if ShowVPM:
print("VPM/FN-1: Found NE:", kseq, aseq[kseq]) # debug
insideNE = False
# print "VPM-2:" , kseq, aseq[kseq] # debug
# print "VPM-3:" , aseq, isupperseq # debug
print("VPM/FN-1: Found NE:", kseq, aseq[kseq]) # debug
insideNE = isupperseq
# print("VPM-2:" , aseq, isupperseq) # debug

elif patlist[kpatword] == '%': # deal with compound
ka = kseq
Expand All @@ -1515,14 +1561,15 @@ def no_skip():
TargetLoc = [ka,isupperseq]

if ShowVPM:
# debug
# debug
print('vpm-mk3')
print("VPM-4: Token assignment ", patlist[kpatword], aseq[find_ne(kseq)])
if last_patword():
return True
if last_seqword():
return False
# print "VPM-4:" , kseq, aseq[kseq], insideNE # debug
# print "VPM-5:" , aseq, isupperseq # debug
# print("VPM-4:" , kseq, aseq[kseq], insideNE) # debug
# print("VPM-5:" , aseq, isupperseq) # debug
elif patlist[kpatword - 1] == ' ':
if last_seqword():
return False
Expand Down Expand Up @@ -1660,6 +1707,7 @@ def check_passive(kitem):
if ShowPattMatch: print("CV-2 patlist", patternlist)
while kpat < len(patternlist):
SourceLoc = [-1,True] ; TargetLoc = [-1,True]
if ShowPattMatch: print("CV-2: Checking",targ, patternlist[kpat])
if verb_pattern_match(patternlist[kpat][0], UpperSeq, True):
if ShowPattMatch: print("Found upper pattern match") # debug
if verb_pattern_match(patternlist[kpat][1], LowerSeq, False):
Expand Down Expand Up @@ -2063,7 +2111,7 @@ def expand_compound_element(kstart):

try:
kend = ParseList.index('~NE', kstart)
print('exCel1:', ParseList[kstart:kend])
# print('exCel1:', ParseList[kstart:kend])
ncstart = ParseList.index('(NEC', kstart, kend)
ncend = ParseList.index('~NEC', ncstart, kend)
except ValueError:
Expand Down Expand Up @@ -2250,7 +2298,7 @@ def expand_compound_codes(codelist):
kb -= 1

logger = logging.getLogger('petr_log')
# print 'MES1: ',SourceLoc, TargetLoc
# print('MES1: ',SourceLoc, TargetLoc)
srccodes = get_loccodes(SourceLoc)
expand_compound_codes(srccodes)
tarcodes = get_loccodes(TargetLoc)
Expand All @@ -2259,11 +2307,8 @@ def expand_compound_codes(codelist):
#TODO: This needs to be fixed
SentenceLoc = ''

# print 'MES2: ',srccodes, tarcodes, EventCode
# print('MES2: ',srccodes, tarcodes, EventCode)
if len(srccodes) == 0 or len(tarcodes) == 0:
# <14.02.27> This is here temporarily (ha!) to just get this thing to
# handle timing tests (and in the presence of some known bugs): this
# should not be a persistent issue. Really
logger.warning('Empty codes in make_event_strings(): {}'.format(SentenceID))
return

Expand Down Expand Up @@ -2821,7 +2866,7 @@ def main():
elif os.path.isfile(cli_args.inputs):
paths = [cli_args.inputs]
else:
print('Please enter a valid directory or file of source texts.')
print('\nFatal runtime error:\n"'+cli_args.inputs+'" could not be located\nPlease enter a valid directory or file of source texts.')
sys.exit()

print('\n\n')
Expand Down

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