| | |
| |
|
| | """Convert plain-text standoff ChemDNER text and annotation files into BioC XML.""" |
| |
|
| | import os |
| | import sys |
| |
|
| | from datetime import date |
| | from xml.sax.saxutils import escape |
| |
|
| | __author__ = "Florian Leitner" |
| | __version__ = "1.0" |
| |
|
| |
|
| | def main(abstracts_path, annotations_path, keyfile): |
| | source = os.path.splitext(os.path.basename(abstracts_path))[0] |
| | today = str(date.today()).replace('-', '') |
| | print('<?xml version="1.0" encoding="%s"?>' % sys.getdefaultencoding()) |
| | print('<!DOCTYPE collection SYSTEM "BioC.dtd">') |
| | print('<collection>\n <source>%s</source>\n <date>%s</date>\n <key>%s</key>' % ( |
| | source, today, os.path.basename(keyfile) |
| | )) |
| |
|
| | with open(annotations_path) as annotations_stream: |
| | annotations = dict(annotations_iter(annotations_stream)) |
| |
|
| | with open(abstracts_path) as abstracts_stream: |
| | for pmid, title, abstract in abstract_iter(abstracts_stream): |
| | title_anns, abstract_anns = annotations[pmid] if pmid in annotations else ([], []) |
| | print(' <document><id>%s</id>' % pmid) |
| | passage("title", title, title_anns) |
| | passage("abstract", abstract, abstract_anns) |
| | print(' </document>') |
| |
|
| | print('</collection>') |
| |
|
| |
|
| | def abstract_iter(stream): |
| | for line in stream: |
| | yield line.strip().split('\t') |
| |
|
| |
|
| | def annotations_iter(stream): |
| | current_pmid, title_anns, abstract_anns = None, None, None |
| | lno = 0 |
| |
|
| | try: |
| | for lno, line in enumerate(stream, 1): |
| | pmid, section, start, end, text, infon = line.strip().split('\t') |
| | ann = (infon, int(start), int(end), text) |
| |
|
| | if pmid != current_pmid: |
| | if current_pmid is not None: |
| | yield current_pmid, (title_anns, abstract_anns) |
| |
|
| | current_pmid, title_anns, abstract_anns = pmid, [], [] |
| |
|
| | if section == 'A': |
| | abstract_anns.append(ann) |
| | elif section == 'T': |
| | title_anns.append(ann) |
| | else: |
| | raise RuntimeError('unknown annotation section "%s"' % section) |
| | except UnicodeDecodeError as e: |
| | raise RuntimeError('encoding error in %s at line %d: %s' % (stream.name, lno, str(e))) |
| |
|
| |
|
| | def passage(name, text, annotations): |
| | passage = ' <passage>\n <infon key="type">%s</infon>\n <offset>0</offset>' |
| | print(passage % name) |
| | print(' <text>%s</text>' % escape(text)) |
| |
|
| | for data in annotations: |
| | annotation(*data) |
| |
|
| | print(' </passage>') |
| |
|
| |
|
| | def annotation(infon, start, end, text): |
| | print(' <annotation>') |
| | print(' <infon key="class">%s</infon>' % infon) |
| | print(' <location offset="%d" length="%d" />' % (start, end - start)) |
| | print(' <text>%s</text>' % escape(text)) |
| | print(' </annotation>') |
| |
|
| |
|
| | if __name__ == '__main__': |
| | name = os.path.basename(sys.argv[0]) |
| |
|
| | if '-h' in sys.argv or '--help' in sys.argv: |
| | print('usage: %s [-h|--help] ABSTRACTS.tsv ANNOTATIONS.tsv INFONS.key\n' % name) |
| | print(__doc__) |
| | sys.exit(0) |
| |
|
| | if len(sys.argv) != 4: |
| | print('wrong number of arguments\n', file=sys.stderr) |
| | print('usage: %s [-h|--help] ABSTRACTS.tsv ANNOTATIONS.tsv INFONS.key' % name, |
| | file=sys.stderr) |
| | sys.exit(2) |
| |
|
| | try: |
| | main(*sys.argv[1:]) |
| | sys.exit(0) |
| | except Exception as e: |
| | print(e, file=sys.stderr) |
| | sys.exit(1) |
| |
|
