-
Notifications
You must be signed in to change notification settings - Fork 0
/
text_extraction.py
1053 lines (993 loc) · 49.7 KB
/
text_extraction.py
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
import sys
import logging as log
import os
import json
from csv import DictReader
from lxml import etree as ET
import re
#############################################
## Minor helper functions to help simplify
## the apparent logic of extracting out
## annotations
#############################################
def create_annotation_entry( begin_pos = -1 , begin_pos_mapped = None ,
end_pos = -1 , end_pos_mapped = None ,
raw_text = None ,
pivot_attr = None , pivot_value = None ,
parity = None ,
tag_name = None ):
new_entry = dict( begin_pos = begin_pos ,
end_pos = end_pos ,
raw_text = raw_text ,
type = tag_name
)
##
if( begin_pos_mapped != None ):
new_entry[ 'begin_pos_mapped' ] = begin_pos_mapped
##
if( end_pos_mapped != None ):
new_entry[ 'end_pos_mapped' ] = end_pos_mapped
##
if( pivot_attr != None ):
new_entry[ 'pivot_attr' ] = pivot_attr
if( pivot_value != None ):
new_entry[ 'pivot_value' ] = pivot_value
if( parity != None ):
new_entry[ 'parity' ] = parity
return new_entry
def map_position( offset_mapping , position , direction ):
"""Convert a character position to the closest non-skipped position.
Use the offset mapping dictionary to convert a position to the
closest valid character position. We include a direction for the
mapping because it is important to consider the closest position
to the right or left of a position when mapping the start or
end position, respectively.
:param offset_mapping: a dictionary mapping character positions to
``None`` if the character is in the skip
list or to an int, otherwise
:param position: current character position
:param direction: 1, if moving right; -1 if moving left
:returns: character position if all skipped characters were removed
from the document and positions re-assigned or
``None``, on KeyError
"""
if( not bool( offset_mapping ) ):
return None
else:
try:
while( offset_mapping[ position ] == None ):
position = str( int( position ) + direction )
return offset_mapping[ position ]
except KeyError:
if( direction < 0 ):
return 'EOF'
elif( direction > 0 ):
return 'SOF'
else:
return None
#############################################
##
#############################################
def extract_annotations_xml( ingest_file ,
offset_mapping ,
annotation_path ,
tag_name ,
namespaces = {} ,
begin_attribute = None ,
end_attribute = None ,
text_attribute = None ,
optional_attributes = [] ,
normalization_engines = [] ):
log.debug( "Entering '{}'".format( sys._getframe().f_code.co_name ) )
found_annots = {}
strict_starts = {}
##
tree = ET.parse( ingest_file )
root = tree.getroot()
##
try:
found_annots = root.findall( annotation_path , namespaces )
except SyntaxError as e:
log.warning( 'I had a problem parsing the XML file. Are you sure your XPath is correct and matches your namespace?\n\tSkipping file ({}) and XPath ({})\n\tReported Error: {}'.format( ingest_file , annotation_path , e ) )
log.debug( "-- Leaving '{}'".format( sys._getframe().f_code.co_name ) )
return strict_starts
##
log.debug( 'Found {} annotation(s) matching the pattern \'{}\''.format(
len( found_annots ) , annotation_path ) )
for annot in found_annots:
if( begin_attribute != None ):
try:
begin_pos = annot.get( begin_attribute )
begin_pos_mapped = map_position( offset_mapping , begin_pos , 1 )
except NameError as e:
log.error( 'NameError: {}'.format( e ) )
if( end_attribute != None ):
## TODO - add flag to distinguish between conditions
## when the end_pos marks the last character
## vs. when the end_pos is the position after
## the last character
try:
end_pos = annot.get( end_attribute )
end_pos_mapped = map_position( offset_mapping , end_pos , -1 )
except NameError as e:
log.error( 'NameError: {}'.format( e ) )
if( text_attribute == None ):
raw_text = annot.text
else:
raw_text = annot.get( text_attribute )
new_entry = create_annotation_entry( begin_pos = begin_pos ,
begin_pos_mapped = begin_pos_mapped ,
end_pos = end_pos ,
end_pos_mapped = end_pos_mapped ,
raw_text = raw_text ,
tag_name = tag_name )
## TODO - do we need to sheild this in case an optional attribute
## doesn't exist in the annotation or does Python (and
## later etude engine code) handle a null correctly/safely?
for optional_attr in optional_attributes:
new_entry[ optional_attr ] = annot.get( optional_attr )
## TODO - do we need to sheild this in case a normalization engine
## doesn't exist in the annotation or does Python (and
## later etude engine code) handle a null correctly/safely?
for normalization_engine in normalization_engines:
if( normalization_engine in annot.attrib ):
new_entry[ normalization_engine ] = annot.get( normalization_engine )
##
if( begin_pos in strict_starts ):
strict_starts[ begin_pos ].append( new_entry )
else:
strict_starts[ begin_pos ] = [ new_entry ]
##
return strict_starts
def extract_annotations_xml_spanless( ingest_file ,
annotation_path ,
tag_name ,
pivot_attribute ,
parity ,
namespaces = {} ,
text_attribute = None ,
optional_attributes = [] ):
log.debug( "Entering '{}'".format( sys._getframe().f_code.co_name ) )
found_annots = {}
strict_starts = {}
##
tree = ET.parse( ingest_file )
root = tree.getroot()
##
try:
found_annots = root.findall( annotation_path , namespaces )
except SyntaxError as e:
log.warning( 'I had a problem parsing the XML file. Are you sure your XPath is correct and matches your namespace?\n\tSkipping file ({}) and XPath ({})\n\tReported Error: {}'.format( ingest_file , annotation_path , e ) )
log.debug( "-- Leaving '{}'".format( sys._getframe().f_code.co_name ) )
return strict_starts
##
log.debug( 'Found {} annotation(s) matching the pattern \'{}\''.format(
len( found_annots ) , annotation_path ) )
for annot in found_annots:
pivot_value = annot.get( pivot_attribute )
new_entry = create_annotation_entry( pivot_attr = pivot_attribute ,
pivot_value = pivot_value ,
parity = parity ,
tag_name = tag_name )
##
for optional_attr in optional_attributes:
new_entry[ optional_attr ] = annot.get( optional_attr )
##
if( -1 in strict_starts ):
for old_entry in strict_starts[ -1 ]:
## TODO - current logic allows multiple instances of the same type
## if they differ on their pivot_value. This is good for topic
## tagging or similar annotations but is bad for most instances
## of publication date or author tagging.
if( new_entry[ 'pivot_value' ] != old_entry[ 'pivot_value' ] ):
strict_starts[ -1 ].append( new_entry )
break
else:
strict_starts[ -1 ] = [ new_entry ]
##
return strict_starts
#############################################
##
#############################################
def extract_annotations_json( ingest_file ,
raw_content ,
offset_mapping ,
annotation_path ,
tag_name ,
begin_attribute = None ,
end_attribute = None ,
optional_attributes = [] ,
normalization_engines = [] ):
log.debug( "Entering '{}'".format( sys._getframe().f_code.co_name ) )
found_annots = {}
strict_starts = {}
##
with open( ingest_file , 'r' ) as fp:
raw_json = json.load( fp )
## TODO - we're assuming four levels to the annotation path
## because that's what our first sample dataset has. This needs to
## be made generic (preferably through integration with a JSONPath
## library).
levels = annotation_path.split( '/' )
type_key , type_value = levels[ 2 ].split( '=' )
if( levels[ 0 ] in raw_json ):
for aset in raw_json[ levels[ 0 ] ]:
if( type_key in aset and
aset[ type_key ] == type_value ):
## TODO - this branching tree in the JSON is currently
## hard-coded but should not be. We need to integrate
## this path into the config file as well
for annot in aset[ 'annots' ]:
begin_pos = annot[ 0 ]
begin_pos_mapped = map_position( offset_mapping , begin_pos , 1 )
end_pos = annot[ 1 ]
end_pos_mapped = map_position( offset_mapping , end_pos , -1 )
raw_text = raw_content[ begin_pos:end_pos ]
new_entry = create_annotation_entry( begin_pos = begin_pos ,
begin_pos_mapped = begin_pos_mapped ,
end_pos = end_pos ,
end_pos_mapped = end_pos_mapped ,
raw_text = raw_text ,
tag_name = tag_name )
##
if( begin_pos in strict_starts ):
strict_starts[ begin_pos ].append( new_entry )
else:
strict_starts[ begin_pos ] = [ new_entry ]
##
return strict_starts
def extract_brat_text_bound_annotation( ingest_file ,
annot_line ,
offset_mapping ,
tag_name ,
line_type,
optional_attributes = [] ):
## Continuous:
## T1 Organization 0 43 International Business Machines Corporation
## Discontinuous (0..23):
## T1 Location 0 5;16 23 North America
## T1 Location 0 5;8 12;16 23 North America
## TODO - add flag to accommodate different scoring styles for
## discontinuous spans. Current approach treats these
## spans as equivalent to the maximal span of all sub-spans.
matches = re.match( r'^(T[0-9]+)\s+([\w\-]+)\s+([0-9]+)\s+([0-9]+;[0-9]+\s+)*([0-9]+)\s+(.*)' ,
annot_line )
if( matches ):
found_tag = matches.group( 2 )
if( found_tag != tag_name and found_tag != line_type):
return None
match_index = matches.group( 1 )
begin_pos = matches.group( 3 )
begin_pos_mapped = map_position( offset_mapping , begin_pos , 1 )
end_pos = matches.group( 5 )
end_pos_mapped = map_position( offset_mapping , end_pos , -1 )
raw_text = matches.group( 6 )
new_entry = create_annotation_entry( begin_pos = begin_pos ,
begin_pos_mapped = begin_pos_mapped ,
end_pos = end_pos ,
end_pos_mapped = end_pos_mapped ,
raw_text = raw_text ,
tag_name = tag_name )
new_entry[ 'match_index' ] = match_index
for optional_attr in optional_attributes:
new_entry[ optional_attr ] = 'false'
return new_entry
else:
log.warning( 'I had a problem parsing a brat text-bound annotation line ({}):{}'.format( ingest_file ,
annot_line ) )
return None
def extract_brat_relation( ingest_file ,
annot_line ,
tag_name ,
optional_attributes = [] ):
## T3 Organization 33 41 Ericsson
## T4 Country 75 81 Sweden
## R1 Origin Arg1:T3 Arg2:T4
return None
def extract_brat_equivalence( ingest_file ,
annot_line ,
optional_attributes = [] ):
## T1 Organization 0 43 International Business Machines Corporation
## T2 Organization 45 48 IBM
## T3 Organization 52 60 Big Blue
## * Equiv T1 T2 T3
return None
def extract_brat_event( ingest_file ,
annot_line ,
tag_name ,
optional_attributes = [] ):
## T1 Organization 0 4 Sony
## T2 MERGE-ORG 14 27 joint venture
## T3 Organization 33 41 Ericsson
## E1 MERGE-ORG:T2 Org1:T1 Org2:T3
return None
def extract_brat_attribute( ingest_file ,
annot_line ,
optional_attributes = [] ):
## A1 Negated T34
## TODO - support multi-valued attributes
## A2 Confidence E2 L1
matches = re.match( r'^([AM][0-9]+)\s+(\w+)\s+([TREAMN\*][0-9]+)$' ,
annot_line )
match_index = None
attribute = None
key = None
attribute_value = 'true'
if( matches ):
attribute = matches.group( 2 )
match_index = matches.group( 3 )
if( attribute in optional_attributes ):
key = attribute
return( [ match_index , attribute , key , attribute_value ] )
else:
log.warning( 'I had a problem parsing a brat attribute line ({}):{}'.format( ingest_file ,
annot_line ) )
return None
def extract_brat_normalization( ingest_file ,
annot_line ,
normalization_engines = [] ):
## N1 Reference T1 Wikipedia:534366 Barack Obama
matches = re.match( r'^(N[0-9]+)\s+Reference\s+([TREAMN\*][0-9]+)\s+([^:]+):([^\s]+)\s+(.+)$' ,
annot_line )
match_index = None
normalization_engine = None
normalization_id = None
normalized_value = None
if( matches ):
match_index = matches.group( 2 )
normalization_engine = matches.group( 3 )
normalization_id = matches.group( 4 )
normalized_value = matches.group( 5 )
if( normalization_engine in normalization_engines ):
return( [ match_index ,
normalization_engine , normalization_id ,
normalized_value ] )
else:
return( None )
else:
log.warning( 'I had a problem parsing a brat normalization line ({}):{}'.format( ingest_file ,
annot_line ) )
return None
def extract_annotations_brat_standoff( ingest_file ,
offset_mapping ,
type_prefix ,
tag_name ,
line_type ,
optional_attributes = [] ,
normalization_engines = [] ):
log.debug( "Entering '{}'".format( sys._getframe().f_code.co_name ) )
annots_by_index = dict()
##
try:
with open( ingest_file , 'r' ) as fp:
for line in fp:
line = line.rstrip()
brat_annotation_type = line[ 0 ]
if( brat_annotation_type == 'T' ):
## T1 Organization 0 43 International Business Machines Corporation
new_entry = extract_brat_text_bound_annotation( ingest_file ,
line ,
offset_mapping ,
tag_name ,
line_type,
optional_attributes )
## A non-None entry means we were able to parse the line
if( new_entry != None ):
annots_by_index[ new_entry[ 'match_index' ] ] = new_entry
## TODO - support discontinous spans:
## T1 Location 0 5;16 23 North America
## T2 Location 10 23
elif( brat_annotation_type == 'A' or
brat_annotation_type == 'M' ):
## A1 Negated T34
new_attribute_value = extract_brat_attribute( ingest_file ,
line ,
optional_attributes )
if( new_attribute_value[ 0 ] != None and
new_attribute_value[ 0 ] in annots_by_index and
new_attribute_value[ 2 ] != None ):
annots_by_index[ new_attribute_value[ 0 ] ][ new_attribute_value[ 2 ] ] = new_attribute_value[ 3 ]
elif( brat_annotation_type == 'R' ):
## R1 Origin Arg1:T3 Arg2:T4
new_entry = extract_brat_relation( ingest_file ,
line ,
tag_name ,
optional_attributes )
elif( brat_annotation_type == '*' ):
## * Equiv T1 T2 T3
new_entry = extract_brat_relation( ingest_file ,
line ,
optional_attributes )
elif( brat_annotation_type == 'E' ):
## E1 MERGE-ORG:T2 Org1:T1 Org2:T3
new_entry = extract_brat_relation( ingest_file ,
line ,
tag_name ,
optional_attributes )
elif( brat_annotation_type == 'N' ):
## N1 Reference T1 Wikipedia:534366 Barack Obama
new_normalization = extract_brat_normalization( ingest_file ,
line ,
normalization_engines )
if( new_normalization is not None and
new_normalization[ 0 ] is not None and
new_normalization[ 0 ] in annots_by_index and
new_normalization[ 1 ] is not None and
new_normalization[ 2 ] is not None ):
annots_by_index[ new_normalization[ 0 ] ][ new_normalization[ 1 ] ] = new_normalization[ 2 ]
##elif( brat_annotation_type == '#' ):
## ## Do nothing. We don't support comments.
##
except IOError as e:
log.warning( 'I had a problem reading the standoff notation file ({}).\n\tReported Error: {}'.format( ingest_file ,
e ) )
log.debug( "-- Leaving '{}'".format( sys._getframe().f_code.co_name ) )
strict_starts = {}
for match_index in annots_by_index:
new_entry = annots_by_index[ match_index ]
begin_pos = new_entry[ 'begin_pos' ]
if( begin_pos in strict_starts ):
strict_starts[ begin_pos ].append( new_entry )
else:
strict_starts[ begin_pos ] = [ new_entry ]
return strict_starts
def extract_annotations_semeval_pipes( ingest_file ,
offset_mapping ,
tag_name ,
optional_attributes = [] ):
log.debug( "Entering '{}'".format( sys._getframe().f_code.co_name ) )
strict_starts = {}
##
try:
with open( ingest_file , 'r' ) as fp:
for line in fp:
line = line.rstrip()
cols = line.split( '|' )
## TODO - we treat all discontinous spans as the maximal span
spans = cols[ 1 ].split( '-' )
begin_pos = spans[ 0 ]
begin_pos_mapped = map_position( offset_mapping , begin_pos , 1 )
end_pos = spans[ -1 ]
end_pos_mapped = map_position( offset_mapping , end_pos , -1 )
raw_text = ''
cui = cols[ 2 ]
new_entry = create_annotation_entry( begin_pos = begin_pos ,
begin_pos_mapped = begin_pos_mapped ,
end_pos = end_pos ,
end_pos_mapped = end_pos_mapped ,
raw_text = raw_text ,
tag_name = tag_name )
new_entry[ 'CUI' ] = cui
## TODO - parse optional attributes, attribute ordering
#for optional_attr in optional_attributes:
# new_entry[ optional_attr ] = 'false'
if( begin_pos in strict_starts ):
strict_starts[ begin_pos ].append( new_entry )
else:
strict_starts[ begin_pos ] = [ new_entry ]
except IOError as e:
log.warning( 'I had a problem reading the pipe-delimited notation file ({}).\n\tReported Error: {}'.format( ingest_file ,
e ) )
log.debug( "-- Leaving '{}'".format( sys._getframe().f_code.co_name ) )
return strict_starts
#############################################
##
#############################################
def extract_annotations_csv( csv_file ,
delimiter ,
tag_name ,
begin_column = None ,
end_column = None ,
text_column = None ,
optional_attributes = [] ):
log.debug( "Entering '{}'".format( sys._getframe().f_code.co_name ) )
found_annots = {}
strict_starts = {}
##
with open( csv_file , 'r' ) as fp:
csv_dict_reader = DictReader( fp )
for cols in csv_dict_reader:
## TODO - the begin column and end column are
## hard-coded. These should be extracted from the
## configurable values of: pattern_entry[ 'begin_attr' ],
## pattern_entry[ 'end_attr' ]
begin_pos = cols[ 'START' ]
begin_pos_mapped = begin_pos
end_pos = cols[ 'END' ]
end_pos_mapped = end_pos
raw_text = cols[ 'SPAN' ]
new_entry = create_annotation_entry( begin_pos = begin_pos ,
begin_pos_mapped = begin_pos_mapped ,
end_pos = end_pos ,
end_pos_mapped = end_pos_mapped ,
raw_text = raw_text ,
tag_name = tag_name )
## TODO - do we need to sheild this in case an optional attribute
## doesn't exist in the annotation or does Python (and
## later etude engine code) handle a null correctly/safely?
for optional_attr in optional_attributes:
## Empty negation columns appear to also mean 'affirmed'
if( optional_attr == 'affirmed' and
cols[ 'NEGATION' ] == '' ):
new_entry[ optional_attr ] = "true"
elif( cols[ 'NEGATION' ] == optional_attr ):
new_entry[ optional_attr ] = "true"
else:
new_entry[ optional_attr ] = "false"
##
if( begin_pos in strict_starts ):
strict_starts[ begin_pos ].append( new_entry )
else:
strict_starts[ begin_pos ] = [ new_entry ]
##
return strict_starts
def extract_annotations_tsv( tsv_file ,
raw_content ,
offset_mapping ,
tag_name ,
optional_attributes = [] ):
log.debug( "Entering '{}'".format( sys._getframe().f_code.co_name ) )
found_annots = {}
strict_starts = {}
## TODO - I re-used this bit from
## extract_annotations_plaintext(). Is there a reason to do this
## rather than direct string positional extraction? I'm concerned
## that there may be a mutli-char bug lurking in either this
## choice of the other choice. Hmmm.
list_of_chars = list( raw_content )
##
with open( tsv_file , 'r' ) as fp:
tsv_dict_reader = DictReader( fp ,
delimiter = '\t' ,
fieldnames = [ 'index' ,
'start' ,
'end' ] )
for cols in tsv_dict_reader:
if( cols[ 'end' ] is None ):
continue
begin_pos = cols[ 'start' ]
begin_pos_mapped = map_position( offset_mapping , begin_pos , 1 )
end_pos = cols[ 'end' ]
end_pos_mapped = map_position( offset_mapping , end_pos , -1 )
raw_text = ''.join( list_of_chars[ int( begin_pos ):int( end_pos ) ] )
new_entry = create_annotation_entry( begin_pos = begin_pos ,
begin_pos_mapped = begin_pos_mapped ,
end_pos = end_pos ,
end_pos_mapped = end_pos_mapped ,
raw_text = raw_text ,
tag_name = tag_name )
##
if( begin_pos in strict_starts ):
strict_starts[ begin_pos ].append( new_entry )
else:
strict_starts[ begin_pos ] = [ new_entry ]
##
return strict_starts
def extract_annotations_plaintext( offset_mapping ,
raw_content ,
delimiter ,
tag_name ):
strict_starts = {}
init_offset = 0
last_offset = 0
##
list_of_chars = list( raw_content )
##
for char in list_of_chars:
if( re.search( delimiter , char ) ):
## Skip when we see multiple of the same delimiter in a row
if( init_offset == last_offset ):
init_offset += 1
last_offset = init_offset
continue
begin_pos = str( last_offset )
begin_pos_mapped = map_position( offset_mapping , begin_pos , 1 )
## TODO - add flag to distinguish between conditions
## when the end_pos marks the last character
## vs. when the end_pos is the position after
## the last character
last_offset = init_offset + 1
end_pos = str( init_offset )
end_pos_mapped = map_position( offset_mapping , end_pos , -1 )
raw_text = ''.join( list_of_chars[ int( begin_pos ):int( end_pos ) ] )
new_entry = create_annotation_entry( begin_pos = begin_pos ,
begin_pos_mapped = \
begin_pos_mapped ,
end_pos = end_pos ,
end_pos_mapped = end_pos_mapped ,
raw_text = raw_text ,
tag_name = tag_name )
##
if( begin_pos in strict_starts ):
strict_starts[ begin_pos ].append( new_entry )
else:
strict_starts[ begin_pos ] = [ new_entry ]
init_offset += 1
##
if( last_offset < init_offset ):
begin_pos = str( last_offset )
begin_pos_mapped = map_position( offset_mapping , begin_pos , 1 )
## TODO - add flag to distinguish between conditions
## when the end_pos marks the last character
## vs. when the end_pos is the position after
## the last character
last_offset = init_offset + 1
end_pos = str( init_offset )
end_pos_mapped = map_position( offset_mapping , end_pos , -1 )
raw_text = ''.join( list_of_chars[ int( begin_pos ):int( end_pos ) ] )
new_entry = create_annotation_entry( begin_pos = begin_pos ,
begin_pos_mapped = begin_pos_mapped ,
end_pos = end_pos ,
end_pos_mapped = end_pos_mapped ,
raw_text = raw_text ,
tag_name = tag_name )
##
if( begin_pos in strict_starts ):
strict_starts[ begin_pos ].append( new_entry )
else:
strict_starts[ begin_pos ] = [ new_entry ]
##
log.debug( "-- Leaving '{}'".format( sys._getframe().f_code.co_name ) )
##
return strict_starts
def write_annotations_to_disk( annotations , out_file ):
log.debug( "Entering '{}'".format( sys._getframe().f_code.co_name ) )
if( out_file == None ):
log.debug( "-- Leaving '{}'".format( sys._getframe().f_code.co_name ) )
return
##
## TODO - add directory existence check
with open( out_file , 'w' ) as output:
json.dump( annotations , output ,
sort_keys = True , indent = 4 )
log.debug( "-- Leaving '{}'".format( sys._getframe().f_code.co_name ) )
def split_content( raw_text , offset_mapping , skip_chars ):
log.debug( "Entering '{}'".format( sys._getframe().f_code.co_name ) )
list_of_chars = list( raw_text )
init_offset = 0
mapped_offset = 0
for char in list_of_chars:
if( re.match( skip_chars , char ) ):
offset_mapping[ '{}'.format( init_offset ) ] = None
else:
offset_mapping[ '{}'.format( init_offset ) ] = '{}'.format( mapped_offset )
mapped_offset += 1
init_offset += 1
log.debug( "-- Leaving '{}'".format( sys._getframe().f_code.co_name ) )
return offset_mapping
def extract_chars( ingest_file ,
namespaces ,
document_data ,
skip_chars = None ):
log.debug( "Entering '{}'".format( sys._getframe().f_code.co_name ) )
offset_mapping = {}
##
cdata_flag = False
attribute_flag = False
if( 'cdata_xpath' in document_data ):
cdata_flag = True
content_path = document_data[ 'cdata_xpath' ]
elif( 'content_attribute' in document_data ):
attribute_flag = True
content_path = document_data[ 'tag_xpath' ]
attribute_name = document_data[ 'content_attribute' ]
else:
log.debug( "Leaving '{}'".format( sys._getframe().f_code.co_name ) )
return None , offset_mapping
##
tree = ET.parse( ingest_file )
root = tree.getroot()
##
try:
found_annots = root.findall( content_path , namespaces )
except SyntaxError as e:
log.warning( 'I had a problem parsing the XML file. Are you sure your XPath is correct and matches your namespace?\n\tSkipping file ({}) and XPath ({})\n\tReported Error: {}'.format( ingest_file , content_path , e ) )
log.debug( "-- Leaving '{}'".format( sys._getframe().f_code.co_name ) )
return None , offset_mapping
##
raw_text = None
log.debug( 'Found {} match(es) for the pattern \'{}\''.format( len( found_annots ) ,
content_path ) )
if( len( found_annots ) > 1 ):
log.warning( 'Expected to only find a single pattern matching content XPath (\'{}\') but found {}. Using first match.'.format( content_path , len( found_annots ) ) )
elif( len( found_annots ) == 0 ):
log.warning( 'Expected to find exactly one match for content XPath (\'{}\') but found {}. Returning empty document content.'.format( content_path , len( found_annots ) ) )
log.debug( "-- Leaving '{}'".format( sys._getframe().f_code.co_name ) )
return None , offset_mapping
for annot in found_annots:
if( cdata_flag ):
raw_text = annot.text
break
elif( attribute_flag ):
try:
raw_text = annot.attrib[ attribute_name ]
break
except KeyError as e:
log.warning( 'KeyError: could not find attribute_name {} in the matched path \'{}\''.format( e , content_path ) )
raw_text = None
##
if( raw_text != None and skip_chars != None ):
offset_mapping = split_content( raw_text ,
offset_mapping ,
skip_chars )
log.debug( "-- Leaving '{}'".format( sys._getframe().f_code.co_name ) )
return raw_text , offset_mapping
def extract_json_chars( ingest_file ,
document_data ,
skip_chars = None ):
log.debug( "Entering '{}'".format( sys._getframe().f_code.co_name ) )
offset_mapping = {}
##
raw_text = None
with open( ingest_file , 'r' ) as fp:
raw_json = json.load( fp )
if( document_data[ 'content_jsonpath' ] not in raw_json ):
log.debug( 'JSON name pair not found for content JSONPath (\'{}\')'.format( document_data[ 'content_jsonpath' ] ) )
else:
raw_text = raw_json[ document_data[ 'content_jsonpath' ] ]
##
if( raw_text != None and skip_chars != None ):
offset_mapping = split_content( raw_text ,
offset_mapping ,
skip_chars )
log.debug( "-- Leaving '{}'".format( sys._getframe().f_code.co_name ) )
return raw_text , offset_mapping
def extract_plaintext( ingest_file , skip_chars ):
offset_mapping = {}
##
with open( ingest_file , 'r' ) as fp:
raw_text = fp.read()
if( raw_text != None and skip_chars != None ):
offset_mapping = split_content( raw_text ,
offset_mapping ,
skip_chars )
return raw_text , offset_mapping
def extract_piped_text( ingest_file , skip_chars ):
offset_mapping = {}
##
with open( ingest_file , 'r' ) as fp:
raw_text = fp.read()
if( raw_text != None and skip_chars != None ):
text_body = raw_text.split( '\t||||\t' )[ -1 ]
offset_mapping = split_content( text_body ,
offset_mapping ,
skip_chars )
return raw_text , offset_mapping
def align_tokens_on_whitespace( dictionary ,
out_file ):
if( out_file != None and
os.path.exists( out_file ) ):
os.remove( out_file )
mapping = dictionary[ 'offset_mapping' ]
keys = list( mapping )
content = dictionary[ 'raw_content' ]
keys.sort( key = int )
token_start = None
for this_token in keys:
##print( '{}\t{}\t{}'.format( token_start ,
## this_token ,
## mapping[ this_token ] ) )
if( mapping[ this_token ] != None and
token_start == None ):
token_start = this_token
elif( mapping[ this_token ] == None and
token_start != None ):
if( out_file != None ):
with open( out_file , 'a' ) as fp:
fp.write( '{}\n'.format( ##token_start , previous_token ,
content[ int( token_start ):int( this_token ) ] ) )
token_start = None
#print( '{} vs. {}'.format( len( dictionary[ 'raw_content' ] ) ,
# len( dictionary[ 'raw_content' ] ) ) )
#############################################
##
#############################################
def extract_annotations( ingest_file ,
namespaces ,
document_data ,
patterns ,
skip_chars = None ,
out_file = None ):
log.debug( "Entering '{}'".format( sys._getframe().f_code.co_name ) )
raw_content = None
annotations = {}
offset_mapping = {}
file_dictionary = {}
if( bool( document_data ) ):
if( 'format' in document_data and
document_data[ 'format' ] == 'txt' ):
try:
raw_content , offset_mapping = extract_plaintext( ingest_file ,
skip_chars )
except:
e = sys.exc_info()[0]
log.error( 'Uncaught exception in extract_plaintext: {}'.format( e ) )
elif( 'format' in document_data and
( document_data[ 'format' ] == '.ann .txt' or
document_data[ 'format' ] == '.phi .text' ) ):
annot_suffix , txt_suffix = document_data[ 'format' ].split( ' ' )
plaintext_alternate_file = re.sub( '{}$'.format( annot_suffix ) ,
txt_suffix ,
ingest_file )
try:
raw_content , offset_mapping = extract_plaintext( plaintext_alternate_file ,
skip_chars )
except:
e = sys.exc_info()[0]
log.error( 'Uncaught exception in extract_plaintext: {}'.format( e ) )
elif( 'format' in document_data and
document_data[ 'format' ] == 'csv' ):
1 ## no-op for now. TODO - make this function more flexible
elif( 'format' in document_data and
document_data[ 'format' ] == '.pipe .text' ):
## TODO use format to change filename according to pattern
## document_data[ 'format' ]
piped_text_alternate_file = re.sub( '.pipe$' ,
'.text' ,
ingest_file )
try:
raw_content , offset_mapping = extract_piped_text( piped_text_alternate_file ,
skip_chars )
except NameError as e:
log.error( 'NameError in extract_piped_text: {}'.format( e ) )
except:
e = sys.exc_info()[0]
log.error( 'Uncaught exception in extract_piped_text: {}'.format( e ) )
elif( 'format' in document_data and
document_data[ 'format' ] == 'JSON' ):
raw_content , offset_mapping = extract_json_chars( ingest_file ,
document_data ,
skip_chars )
else:
try:
raw_content , offset_mapping = extract_chars( ingest_file ,
namespaces ,
document_data ,
skip_chars )
except ET.ParseError as e:
log.warning( 'ParseError in file ({}): {}'.format( ingest_file , e ) )
log.debug( "-- Leaving '{}'".format( sys._getframe().f_code.co_name ) )
return offset_mapping , annotations
except UnicodeEncodeError as e:
print(( '{}'.format( e ) ))
except:
e = sys.exc_info()[0]
log.error( 'Uncaught exception in extract_chars: {}'.format( e ) )
if( skip_chars and raw_content == None ):
log.error( 'I could not find the raw content for this document but was asked to ignore its whitespace. Add document data to the config file for extracting raw content or use the --heed-whitespace flag.' )
log.debug( "-- Leaving '{}'".format( sys._getframe().f_code.co_name ) )
return offset_mapping , annotations
## Normalization engines are global for the config file
## rather than pattern-specific
norm_eng = []
if( 'normalization_engines' in document_data ):
norm_eng = document_data[ 'normalization_engines' ]
for pattern in patterns:
new_annots = None
if( 'delimiter' in pattern ):
if( pattern[ 'delimiter' ] == ',' ):
new_annots = \
extract_annotations_csv( csv_file = ingest_file ,
delimiter = \
pattern[ 'delimiter' ] ,
tag_name = pattern[ 'type' ] ,
optional_attributes = \
pattern[ 'optional_attributes' ] )
elif( pattern[ 'delimiter' ] == '\\t' ):
new_annots = \
extract_annotations_tsv( tsv_file = ingest_file ,
raw_content = raw_content ,
offset_mapping = offset_mapping ,
tag_name = pattern[ 'type' ] ,
optional_attributes = \
pattern[ 'optional_attributes' ] )
else:
new_annots = \
extract_annotations_plaintext( offset_mapping = offset_mapping ,
raw_content = raw_content ,
delimiter = \
pattern[ 'delimiter' ] ,
tag_name = pattern[ 'type' ] )
elif( 'format' in document_data and
document_data[ 'format' ] == '.pipe .text' ):
new_annots = \
extract_annotations_semeval_pipes( ingest_file ,
offset_mapping = offset_mapping ,
tag_name = pattern[ 'type' ] ,
optional_attributes = \
pattern[ 'optional_attributes' ] )
elif( 'type_prefix' in pattern ):
norm_eng = []
if( 'normalization_engines' in document_data ):
norm_eng = document_data[ 'normalization_engines' ]
opt_attr = []
if( 'optional_attributes' in pattern ):
opt_attr = pattern[ 'optional_attributes' ]
new_annots = \
extract_annotations_brat_standoff( ingest_file ,
offset_mapping = offset_mapping ,
type_prefix = \
pattern[ 'type_prefix' ] ,
tag_name = pattern[ 'type' ] ,
line_type = pattern [ 'short_name' ] ,
optional_attributes = opt_attr ,
normalization_engines = norm_eng )
elif( 'xpath' in pattern and
'begin_attr' in pattern and
'end_attr' in pattern ):
new_annots = \
extract_annotations_xml( ingest_file ,
offset_mapping = offset_mapping ,
namespaces = namespaces ,
annotation_path = pattern[ 'xpath' ] ,
tag_name = pattern[ 'type' ] ,
begin_attribute = \
pattern[ 'begin_attr' ] ,
end_attribute = \
pattern[ 'end_attr' ] ,
optional_attributes = \
pattern[ 'optional_attributes' ] ,
normalization_engines = norm_eng )
elif( 'jsonpath' in pattern ):
new_annots = \
extract_annotations_json( ingest_file ,
raw_content = raw_content ,
offset_mapping = offset_mapping ,
annotation_path = pattern[ 'jsonpath' ] ,
tag_name = pattern[ 'type' ] ,
begin_attribute = \
pattern[ 'begin_attr' ] ,
end_attribute = \
pattern[ 'end_attr' ] ,