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3,700 | bkabrda/flask-whooshee | flask_whooshee.py | Whooshee.create_index | def create_index(cls, app, wh):
"""Creates and opens an index for the given whoosheer and app.
If the index already exists, it just opens it, otherwise it creates
it first.
:param app: The application instance.
:param wh: The whoosheer instance for which a index should be created.
"""
# TODO: do we really want/need to use camel casing?
# everywhere else, there is just .lower()
if app.extensions['whooshee']['memory_storage']:
storage = RamStorage()
index = storage.create_index(wh.schema)
assert index
return index
else:
index_path = os.path.join(app.extensions['whooshee']['index_path_root'],
getattr(wh, 'index_subdir', cls.camel_to_snake(wh.__name__)))
if whoosh.index.exists_in(index_path):
index = whoosh.index.open_dir(index_path)
else:
if not os.path.exists(index_path):
os.makedirs(index_path)
index = whoosh.index.create_in(index_path, wh.schema)
return index | python | def create_index(cls, app, wh):
"""Creates and opens an index for the given whoosheer and app.
If the index already exists, it just opens it, otherwise it creates
it first.
:param app: The application instance.
:param wh: The whoosheer instance for which a index should be created.
"""
# TODO: do we really want/need to use camel casing?
# everywhere else, there is just .lower()
if app.extensions['whooshee']['memory_storage']:
storage = RamStorage()
index = storage.create_index(wh.schema)
assert index
return index
else:
index_path = os.path.join(app.extensions['whooshee']['index_path_root'],
getattr(wh, 'index_subdir', cls.camel_to_snake(wh.__name__)))
if whoosh.index.exists_in(index_path):
index = whoosh.index.open_dir(index_path)
else:
if not os.path.exists(index_path):
os.makedirs(index_path)
index = whoosh.index.create_in(index_path, wh.schema)
return index | [
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If the index already exists, it just opens it, otherwise it creates
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:param app: The application instance.
:param wh: The whoosheer instance for which a index should be created. | [
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3,701 | bkabrda/flask-whooshee | flask_whooshee.py | Whooshee.get_or_create_index | def get_or_create_index(cls, app, wh):
"""Gets a previously cached index or creates a new one for the
given app and whoosheer.
:param app: The application instance.
:param wh: The whoosheer instance for which the index should be
retrieved or created.
"""
if wh in app.extensions['whooshee']['whoosheers_indexes']:
return app.extensions['whooshee']['whoosheers_indexes'][wh]
index = cls.create_index(app, wh)
app.extensions['whooshee']['whoosheers_indexes'][wh] = index
return index | python | def get_or_create_index(cls, app, wh):
"""Gets a previously cached index or creates a new one for the
given app and whoosheer.
:param app: The application instance.
:param wh: The whoosheer instance for which the index should be
retrieved or created.
"""
if wh in app.extensions['whooshee']['whoosheers_indexes']:
return app.extensions['whooshee']['whoosheers_indexes'][wh]
index = cls.create_index(app, wh)
app.extensions['whooshee']['whoosheers_indexes'][wh] = index
return index | [
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3,702 | bkabrda/flask-whooshee | flask_whooshee.py | Whooshee.on_commit | def on_commit(self, changes):
"""Method that gets called when a model is changed. This serves
to do the actual index writing.
"""
if _get_config(self)['enable_indexing'] is False:
return None
for wh in self.whoosheers:
if not wh.auto_update:
continue
writer = None
for change in changes:
if change[0].__class__ in wh.models:
method_name = '{0}_{1}'.format(change[1], change[0].__class__.__name__.lower())
method = getattr(wh, method_name, None)
if method:
if not writer:
writer = type(self).get_or_create_index(_get_app(self), wh).\
writer(timeout=_get_config(self)['writer_timeout'])
method(writer, change[0])
if writer:
writer.commit() | python | def on_commit(self, changes):
"""Method that gets called when a model is changed. This serves
to do the actual index writing.
"""
if _get_config(self)['enable_indexing'] is False:
return None
for wh in self.whoosheers:
if not wh.auto_update:
continue
writer = None
for change in changes:
if change[0].__class__ in wh.models:
method_name = '{0}_{1}'.format(change[1], change[0].__class__.__name__.lower())
method = getattr(wh, method_name, None)
if method:
if not writer:
writer = type(self).get_or_create_index(_get_app(self), wh).\
writer(timeout=_get_config(self)['writer_timeout'])
method(writer, change[0])
if writer:
writer.commit() | [
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3,703 | bkabrda/flask-whooshee | flask_whooshee.py | Whooshee.reindex | def reindex(self):
"""Reindex all data
This method retrieves all the data from the registered models and
calls the ``update_<model>()`` function for every instance of such
model.
"""
for wh in self.whoosheers:
index = type(self).get_or_create_index(_get_app(self), wh)
writer = index.writer(timeout=_get_config(self)['writer_timeout'])
for model in wh.models:
method_name = "{0}_{1}".format(UPDATE_KWD, model.__name__.lower())
for item in model.query.all():
getattr(wh, method_name)(writer, item)
writer.commit() | python | def reindex(self):
"""Reindex all data
This method retrieves all the data from the registered models and
calls the ``update_<model>()`` function for every instance of such
model.
"""
for wh in self.whoosheers:
index = type(self).get_or_create_index(_get_app(self), wh)
writer = index.writer(timeout=_get_config(self)['writer_timeout'])
for model in wh.models:
method_name = "{0}_{1}".format(UPDATE_KWD, model.__name__.lower())
for item in model.query.all():
getattr(wh, method_name)(writer, item)
writer.commit() | [
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3,704 | spry-group/python-vultr | examples/basic_list.py | dump_info | def dump_info():
'''Shows various details about the account & servers'''
vultr = Vultr(API_KEY)
try:
logging.info('Listing account info:\n%s', dumps(
vultr.account.info(), indent=2
))
logging.info('Listing apps:\n%s', dumps(
vultr.app.list(), indent=2
))
logging.info('Listing backups:\n%s', dumps(
vultr.backup.list(), indent=2
))
logging.info('Listing DNS:\n%s', dumps(
vultr.dns.list(), indent=2
))
logging.info('Listing ISOs:\n%s', dumps(
vultr.iso.list(), indent=2
))
logging.info('Listing OSs:\n%s', dumps(
vultr.os.list(), indent=2
))
logging.info('Listing plans:\n%s', dumps(
vultr.plans.list(), indent=2
))
logging.info('Listing regions:\n%s', dumps(
vultr.regions.list(), indent=2
))
logging.info('Listing servers:\n%s', dumps(
vultr.server.list(), indent=2
))
logging.info('Listing snapshots:\n%s', dumps(
vultr.snapshot.list(), indent=2
))
logging.info('Listing SSH keys:\n%s', dumps(
vultr.sshkey.list(), indent=2
))
logging.info('Listing startup scripts:\n%s', dumps(
vultr.startupscript.list(), indent=2
))
except VultrError as ex:
logging.error('VultrError: %s', ex) | python | def dump_info():
'''Shows various details about the account & servers'''
vultr = Vultr(API_KEY)
try:
logging.info('Listing account info:\n%s', dumps(
vultr.account.info(), indent=2
))
logging.info('Listing apps:\n%s', dumps(
vultr.app.list(), indent=2
))
logging.info('Listing backups:\n%s', dumps(
vultr.backup.list(), indent=2
))
logging.info('Listing DNS:\n%s', dumps(
vultr.dns.list(), indent=2
))
logging.info('Listing ISOs:\n%s', dumps(
vultr.iso.list(), indent=2
))
logging.info('Listing OSs:\n%s', dumps(
vultr.os.list(), indent=2
))
logging.info('Listing plans:\n%s', dumps(
vultr.plans.list(), indent=2
))
logging.info('Listing regions:\n%s', dumps(
vultr.regions.list(), indent=2
))
logging.info('Listing servers:\n%s', dumps(
vultr.server.list(), indent=2
))
logging.info('Listing snapshots:\n%s', dumps(
vultr.snapshot.list(), indent=2
))
logging.info('Listing SSH keys:\n%s', dumps(
vultr.sshkey.list(), indent=2
))
logging.info('Listing startup scripts:\n%s', dumps(
vultr.startupscript.list(), indent=2
))
except VultrError as ex:
logging.error('VultrError: %s', ex) | [
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3,705 | spry-group/python-vultr | vultr/utils.py | update_params | def update_params(params, updates):
'''Merges updates into params'''
params = params.copy() if isinstance(params, dict) else dict()
params.update(updates)
return params | python | def update_params(params, updates):
'''Merges updates into params'''
params = params.copy() if isinstance(params, dict) else dict()
params.update(updates)
return params | [
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3,706 | spry-group/python-vultr | vultr/utils.py | VultrBase._request_get_helper | def _request_get_helper(self, url, params=None):
'''API GET request helper'''
if not isinstance(params, dict):
params = dict()
if self.api_key:
params['api_key'] = self.api_key
return requests.get(url, params=params, timeout=60) | python | def _request_get_helper(self, url, params=None):
'''API GET request helper'''
if not isinstance(params, dict):
params = dict()
if self.api_key:
params['api_key'] = self.api_key
return requests.get(url, params=params, timeout=60) | [
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3,707 | spry-group/python-vultr | vultr/utils.py | VultrBase._request_post_helper | def _request_post_helper(self, url, params=None):
'''API POST helper'''
if self.api_key:
query = {'api_key': self.api_key}
return requests.post(url, params=query, data=params, timeout=60) | python | def _request_post_helper(self, url, params=None):
'''API POST helper'''
if self.api_key:
query = {'api_key': self.api_key}
return requests.post(url, params=query, data=params, timeout=60) | [
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3,708 | spry-group/python-vultr | vultr/utils.py | VultrBase._request_helper | def _request_helper(self, url, params, method):
'''API request helper method'''
try:
if method == 'POST':
return self._request_post_helper(url, params)
elif method == 'GET':
return self._request_get_helper(url, params)
raise VultrError('Unsupported method %s' % method)
except requests.RequestException as ex:
raise RuntimeError(ex) | python | def _request_helper(self, url, params, method):
'''API request helper method'''
try:
if method == 'POST':
return self._request_post_helper(url, params)
elif method == 'GET':
return self._request_get_helper(url, params)
raise VultrError('Unsupported method %s' % method)
except requests.RequestException as ex:
raise RuntimeError(ex) | [
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3,709 | spry-group/python-vultr | examples/basic_haltRunning.py | halt_running | def halt_running():
'''Halts all running servers'''
vultr = Vultr(API_KEY)
try:
serverList = vultr.server.list()
#logging.info('Listing servers:\n%s', dumps(
#serverList, indent=2
#))
except VultrError as ex:
logging.error('VultrError: %s', ex)
for serverID in serverList:
if serverList[serverID]['power_status'] == 'running':
logging.info(serverList[serverID]['label'] + " will be gracefully shutdown.")
vultr.server.halt(serverID) | python | def halt_running():
'''Halts all running servers'''
vultr = Vultr(API_KEY)
try:
serverList = vultr.server.list()
#logging.info('Listing servers:\n%s', dumps(
#serverList, indent=2
#))
except VultrError as ex:
logging.error('VultrError: %s', ex)
for serverID in serverList:
if serverList[serverID]['power_status'] == 'running':
logging.info(serverList[serverID]['label'] + " will be gracefully shutdown.")
vultr.server.halt(serverID) | [
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3,710 | inspirehep/refextract | refextract/references/tag.py | tag_arxiv | def tag_arxiv(line):
"""Tag arxiv report numbers
We handle arXiv in 2 ways:
* starting with arXiv:1022.1111
* this format exactly 9999.9999
We also format the output to the standard arxiv notation:
* arXiv:2007.12.1111
* arXiv:2007.12.1111v2
"""
def tagger(match):
groups = match.groupdict()
if match.group('suffix'):
groups['suffix'] = ' ' + groups['suffix']
else:
groups['suffix'] = ''
return u'<cds.REPORTNUMBER>arXiv:%(year)s'\
u'%(month)s.%(num)s%(suffix)s' \
u'</cds.REPORTNUMBER>' % groups
line = re_arxiv_5digits.sub(tagger, line)
line = re_arxiv.sub(tagger, line)
line = re_new_arxiv_5digits.sub(tagger, line)
line = re_new_arxiv.sub(tagger, line)
return line | python | def tag_arxiv(line):
"""Tag arxiv report numbers
We handle arXiv in 2 ways:
* starting with arXiv:1022.1111
* this format exactly 9999.9999
We also format the output to the standard arxiv notation:
* arXiv:2007.12.1111
* arXiv:2007.12.1111v2
"""
def tagger(match):
groups = match.groupdict()
if match.group('suffix'):
groups['suffix'] = ' ' + groups['suffix']
else:
groups['suffix'] = ''
return u'<cds.REPORTNUMBER>arXiv:%(year)s'\
u'%(month)s.%(num)s%(suffix)s' \
u'</cds.REPORTNUMBER>' % groups
line = re_arxiv_5digits.sub(tagger, line)
line = re_arxiv.sub(tagger, line)
line = re_new_arxiv_5digits.sub(tagger, line)
line = re_new_arxiv.sub(tagger, line)
return line | [
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* starting with arXiv:1022.1111
* this format exactly 9999.9999
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* arXiv:2007.12.1111
* arXiv:2007.12.1111v2 | [
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3,711 | inspirehep/refextract | refextract/references/tag.py | tag_arxiv_more | def tag_arxiv_more(line):
"""Tag old arxiv report numbers
Either formats:
* hep-th/1234567
* arXiv:1022111 [hep-ph] which transforms to hep-ph/1022111
"""
line = RE_ARXIV_CATCHUP.sub(ur"\g<suffix>/\g<year>\g<month>\g<num>", line)
for report_re, report_repl in RE_OLD_ARXIV:
report_number = report_repl + ur"/\g<num>"
line = report_re.sub(
u'<cds.REPORTNUMBER>' + report_number + u'</cds.REPORTNUMBER>',
line
)
return line | python | def tag_arxiv_more(line):
"""Tag old arxiv report numbers
Either formats:
* hep-th/1234567
* arXiv:1022111 [hep-ph] which transforms to hep-ph/1022111
"""
line = RE_ARXIV_CATCHUP.sub(ur"\g<suffix>/\g<year>\g<month>\g<num>", line)
for report_re, report_repl in RE_OLD_ARXIV:
report_number = report_repl + ur"/\g<num>"
line = report_re.sub(
u'<cds.REPORTNUMBER>' + report_number + u'</cds.REPORTNUMBER>',
line
)
return line | [
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3,712 | inspirehep/refextract | refextract/references/tag.py | tag_pos_volume | def tag_pos_volume(line):
"""Tag POS volume number
POS is journal that has special volume numbers
e.g. PoS LAT2007 (2007) 369
"""
def tagger(match):
groups = match.groupdict()
try:
year = match.group('year')
except IndexError:
# Extract year from volume name
# which should always include the year
g = re.search(re_pos_year_num, match.group(
'volume_num'), re.UNICODE)
year = g.group(0)
if year:
groups[
'year'] = ' <cds.YR>(%s)</cds.YR>' % year.strip().strip('()')
else:
groups['year'] = ''
return '<cds.JOURNAL>PoS</cds.JOURNAL>' \
' <cds.VOL>%(volume_name)s%(volume_num)s</cds.VOL>' \
'%(year)s' \
' <cds.PG>%(page)s</cds.PG>' % groups
for p in re_pos:
line = p.sub(tagger, line)
return line | python | def tag_pos_volume(line):
"""Tag POS volume number
POS is journal that has special volume numbers
e.g. PoS LAT2007 (2007) 369
"""
def tagger(match):
groups = match.groupdict()
try:
year = match.group('year')
except IndexError:
# Extract year from volume name
# which should always include the year
g = re.search(re_pos_year_num, match.group(
'volume_num'), re.UNICODE)
year = g.group(0)
if year:
groups[
'year'] = ' <cds.YR>(%s)</cds.YR>' % year.strip().strip('()')
else:
groups['year'] = ''
return '<cds.JOURNAL>PoS</cds.JOURNAL>' \
' <cds.VOL>%(volume_name)s%(volume_num)s</cds.VOL>' \
'%(year)s' \
' <cds.PG>%(page)s</cds.PG>' % groups
for p in re_pos:
line = p.sub(tagger, line)
return line | [
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3,713 | inspirehep/refextract | refextract/references/tag.py | find_numeration_more | def find_numeration_more(line):
"""Look for other numeration in line."""
# First, attempt to use marked-up titles
patterns = (
re_correct_numeration_2nd_try_ptn1,
re_correct_numeration_2nd_try_ptn2,
re_correct_numeration_2nd_try_ptn3,
re_correct_numeration_2nd_try_ptn4,
)
for pattern in patterns:
match = pattern.search(line)
if match:
info = match.groupdict()
series = extract_series_from_volume(info['vol'])
if not info['vol_num']:
info['vol_num'] = info['vol_num_alt']
if not info['vol_num']:
info['vol_num'] = info['vol_num_alt2']
return {'year': info.get('year', None),
'series': series,
'volume': info['vol_num'],
'page': info['page'] or info['jinst_page'],
'page_end': info['page_end'],
'len': len(info['aftertitle'])}
return None | python | def find_numeration_more(line):
"""Look for other numeration in line."""
# First, attempt to use marked-up titles
patterns = (
re_correct_numeration_2nd_try_ptn1,
re_correct_numeration_2nd_try_ptn2,
re_correct_numeration_2nd_try_ptn3,
re_correct_numeration_2nd_try_ptn4,
)
for pattern in patterns:
match = pattern.search(line)
if match:
info = match.groupdict()
series = extract_series_from_volume(info['vol'])
if not info['vol_num']:
info['vol_num'] = info['vol_num_alt']
if not info['vol_num']:
info['vol_num'] = info['vol_num_alt2']
return {'year': info.get('year', None),
'series': series,
'volume': info['vol_num'],
'page': info['page'] or info['jinst_page'],
'page_end': info['page_end'],
'len': len(info['aftertitle'])}
return None | [
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3,714 | inspirehep/refextract | refextract/references/tag.py | identify_ibids | def identify_ibids(line):
"""Find IBIDs within the line, record their position and length,
and replace them with underscores.
@param line: (string) the working reference line
@return: (tuple) containing 2 dictionaries and a string:
Dictionary: matched IBID text: (Key: position of IBID in
line; Value: matched IBID text)
String: working line with matched IBIDs removed
"""
ibid_match_txt = {}
# Record details of each matched ibid:
for m_ibid in re_ibid.finditer(line):
ibid_match_txt[m_ibid.start()] = m_ibid.group(0)
# Replace matched text in line with underscores:
line = line[0:m_ibid.start()] + \
"_" * len(m_ibid.group(0)) + \
line[m_ibid.end():]
return ibid_match_txt, line | python | def identify_ibids(line):
"""Find IBIDs within the line, record their position and length,
and replace them with underscores.
@param line: (string) the working reference line
@return: (tuple) containing 2 dictionaries and a string:
Dictionary: matched IBID text: (Key: position of IBID in
line; Value: matched IBID text)
String: working line with matched IBIDs removed
"""
ibid_match_txt = {}
# Record details of each matched ibid:
for m_ibid in re_ibid.finditer(line):
ibid_match_txt[m_ibid.start()] = m_ibid.group(0)
# Replace matched text in line with underscores:
line = line[0:m_ibid.start()] + \
"_" * len(m_ibid.group(0)) + \
line[m_ibid.end():]
return ibid_match_txt, line | [
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@return: (tuple) containing 2 dictionaries and a string:
Dictionary: matched IBID text: (Key: position of IBID in
line; Value: matched IBID text)
String: working line with matched IBIDs removed | [
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3,715 | inspirehep/refextract | refextract/references/tag.py | find_numeration | def find_numeration(line):
"""Given a reference line, attempt to locate instances of citation
'numeration' in the line.
@param line: (string) the reference line.
@return: (string) the reference line after numeration has been checked
and possibly recognized/marked-up.
"""
patterns = (
# vol,page,year
re_numeration_vol_page_yr,
re_numeration_vol_nucphys_page_yr,
re_numeration_nucphys_vol_page_yr,
# With sub volume
re_numeration_vol_subvol_nucphys_yr_page,
re_numeration_vol_nucphys_yr_subvol_page,
# vol,year,page
re_numeration_vol_yr_page,
re_numeration_nucphys_vol_yr_page,
re_numeration_vol_nucphys_series_yr_page,
# vol,page,year
re_numeration_vol_series_nucphys_page_yr,
re_numeration_vol_nucphys_series_page_yr,
# year,vol,page
re_numeration_yr_vol_page,
)
for pattern in patterns:
match = pattern.match(line)
if match:
info = match.groupdict()
series = info.get('series', None)
if not series:
series = extract_series_from_volume(info['vol'])
if not info['vol_num']:
info['vol_num'] = info['vol_num_alt']
if not info['vol_num']:
info['vol_num'] = info['vol_num_alt2']
return {'year': info.get('year', None),
'series': series,
'volume': info['vol_num'],
'page': info['page'] or info['jinst_page'],
'page_end': info['page_end'],
'len': match.end()}
return None | python | def find_numeration(line):
"""Given a reference line, attempt to locate instances of citation
'numeration' in the line.
@param line: (string) the reference line.
@return: (string) the reference line after numeration has been checked
and possibly recognized/marked-up.
"""
patterns = (
# vol,page,year
re_numeration_vol_page_yr,
re_numeration_vol_nucphys_page_yr,
re_numeration_nucphys_vol_page_yr,
# With sub volume
re_numeration_vol_subvol_nucphys_yr_page,
re_numeration_vol_nucphys_yr_subvol_page,
# vol,year,page
re_numeration_vol_yr_page,
re_numeration_nucphys_vol_yr_page,
re_numeration_vol_nucphys_series_yr_page,
# vol,page,year
re_numeration_vol_series_nucphys_page_yr,
re_numeration_vol_nucphys_series_page_yr,
# year,vol,page
re_numeration_yr_vol_page,
)
for pattern in patterns:
match = pattern.match(line)
if match:
info = match.groupdict()
series = info.get('series', None)
if not series:
series = extract_series_from_volume(info['vol'])
if not info['vol_num']:
info['vol_num'] = info['vol_num_alt']
if not info['vol_num']:
info['vol_num'] = info['vol_num_alt2']
return {'year': info.get('year', None),
'series': series,
'volume': info['vol_num'],
'page': info['page'] or info['jinst_page'],
'page_end': info['page_end'],
'len': match.end()}
return None | [
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3,716 | inspirehep/refextract | refextract/references/engine.py | remove_reference_line_marker | def remove_reference_line_marker(line):
"""Trim a reference line's 'marker' from the beginning of the line.
@param line: (string) - the reference line.
@return: (tuple) containing two strings:
+ The reference line's marker (or if there was not one,
a 'space' character.
+ The reference line with it's marker removed from the
beginning.
"""
# Get patterns to identify reference-line marker patterns:
marker_patterns = get_reference_line_numeration_marker_patterns()
line = line.lstrip()
marker_match = regex_match_list(line, marker_patterns)
if marker_match is not None:
# found a marker:
marker_val = marker_match.group(u'mark')
# trim the marker from the start of the line:
line = line[marker_match.end():].lstrip()
else:
marker_val = u" "
return (marker_val, line) | python | def remove_reference_line_marker(line):
"""Trim a reference line's 'marker' from the beginning of the line.
@param line: (string) - the reference line.
@return: (tuple) containing two strings:
+ The reference line's marker (or if there was not one,
a 'space' character.
+ The reference line with it's marker removed from the
beginning.
"""
# Get patterns to identify reference-line marker patterns:
marker_patterns = get_reference_line_numeration_marker_patterns()
line = line.lstrip()
marker_match = regex_match_list(line, marker_patterns)
if marker_match is not None:
# found a marker:
marker_val = marker_match.group(u'mark')
# trim the marker from the start of the line:
line = line[marker_match.end():].lstrip()
else:
marker_val = u" "
return (marker_val, line) | [
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3,717 | inspirehep/refextract | refextract/references/engine.py | roman2arabic | def roman2arabic(num):
"""Convert numbers from roman to arabic
This function expects a string like XXII
and outputs an integer
"""
t = 0
p = 0
for r in num:
n = 10 ** (205558 % ord(r) % 7) % 9995
t += n - 2 * p % n
p = n
return t | python | def roman2arabic(num):
"""Convert numbers from roman to arabic
This function expects a string like XXII
and outputs an integer
"""
t = 0
p = 0
for r in num:
n = 10 ** (205558 % ord(r) % 7) % 9995
t += n - 2 * p % n
p = n
return t | [
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3,718 | inspirehep/refextract | refextract/references/engine.py | format_report_number | def format_report_number(citation_elements):
"""Format report numbers that are missing a dash
e.g. CERN-LCHH2003-01 to CERN-LHCC-2003-01
"""
re_report = re.compile(ur'^(?P<name>[A-Z-]+)(?P<nums>[\d-]+)$', re.UNICODE)
for el in citation_elements:
if el['type'] == 'REPORTNUMBER':
m = re_report.match(el['report_num'])
if m:
name = m.group('name')
if not name.endswith('-'):
el['report_num'] = m.group('name') + '-' + m.group('nums')
return citation_elements | python | def format_report_number(citation_elements):
"""Format report numbers that are missing a dash
e.g. CERN-LCHH2003-01 to CERN-LHCC-2003-01
"""
re_report = re.compile(ur'^(?P<name>[A-Z-]+)(?P<nums>[\d-]+)$', re.UNICODE)
for el in citation_elements:
if el['type'] == 'REPORTNUMBER':
m = re_report.match(el['report_num'])
if m:
name = m.group('name')
if not name.endswith('-'):
el['report_num'] = m.group('name') + '-' + m.group('nums')
return citation_elements | [
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3,719 | inspirehep/refextract | refextract/references/engine.py | format_hep | def format_hep(citation_elements):
"""Format hep-th report numbers with a dash
e.g. replaces hep-th-9711200 with hep-th/9711200
"""
prefixes = ('astro-ph-', 'hep-th-', 'hep-ph-', 'hep-ex-', 'hep-lat-',
'math-ph-')
for el in citation_elements:
if el['type'] == 'REPORTNUMBER':
for p in prefixes:
if el['report_num'].startswith(p):
el['report_num'] = el['report_num'][:len(p) - 1] + '/' + \
el['report_num'][len(p):]
return citation_elements | python | def format_hep(citation_elements):
"""Format hep-th report numbers with a dash
e.g. replaces hep-th-9711200 with hep-th/9711200
"""
prefixes = ('astro-ph-', 'hep-th-', 'hep-ph-', 'hep-ex-', 'hep-lat-',
'math-ph-')
for el in citation_elements:
if el['type'] == 'REPORTNUMBER':
for p in prefixes:
if el['report_num'].startswith(p):
el['report_num'] = el['report_num'][:len(p) - 1] + '/' + \
el['report_num'][len(p):]
return citation_elements | [
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3,720 | inspirehep/refextract | refextract/references/engine.py | look_for_books | def look_for_books(citation_elements, kbs):
"""Look for books in our kb
Create book tags by using the authors and the title to find books
in our knowledge base
"""
title = None
for el in citation_elements:
if el['type'] == 'QUOTED':
title = el
break
if title:
normalized_title = title['title'].upper()
if normalized_title in kbs['books']:
line = kbs['books'][normalized_title]
el = {'type': 'BOOK',
'misc_txt': '',
'authors': line[0],
'title': line[1],
'year': line[2].strip(';')}
citation_elements.append(el)
citation_elements.remove(title)
return citation_elements | python | def look_for_books(citation_elements, kbs):
"""Look for books in our kb
Create book tags by using the authors and the title to find books
in our knowledge base
"""
title = None
for el in citation_elements:
if el['type'] == 'QUOTED':
title = el
break
if title:
normalized_title = title['title'].upper()
if normalized_title in kbs['books']:
line = kbs['books'][normalized_title]
el = {'type': 'BOOK',
'misc_txt': '',
'authors': line[0],
'title': line[1],
'year': line[2].strip(';')}
citation_elements.append(el)
citation_elements.remove(title)
return citation_elements | [
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3,721 | inspirehep/refextract | refextract/references/engine.py | split_volume_from_journal | def split_volume_from_journal(citation_elements):
"""Split volume from journal title
We need this because sometimes the volume is attached to the journal title
instead of the volume. In those cases we move it here from the title to the
volume
"""
for el in citation_elements:
if el['type'] == 'JOURNAL' and ';' in el['title']:
el['title'], series = el['title'].rsplit(';', 1)
el['volume'] = series + el['volume']
return citation_elements | python | def split_volume_from_journal(citation_elements):
"""Split volume from journal title
We need this because sometimes the volume is attached to the journal title
instead of the volume. In those cases we move it here from the title to the
volume
"""
for el in citation_elements:
if el['type'] == 'JOURNAL' and ';' in el['title']:
el['title'], series = el['title'].rsplit(';', 1)
el['volume'] = series + el['volume']
return citation_elements | [
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3,722 | inspirehep/refextract | refextract/references/engine.py | remove_b_for_nucl_phys | def remove_b_for_nucl_phys(citation_elements):
"""Removes b from the volume of some journals
Removes the B from the volume for Nucl.Phys.Proc.Suppl. because in INSPIRE
that journal is handled differently.
"""
for el in citation_elements:
if el['type'] == 'JOURNAL' and el['title'] == 'Nucl.Phys.Proc.Suppl.' \
and 'volume' in el \
and (el['volume'].startswith('b') or el['volume'].startswith('B')):
el['volume'] = el['volume'][1:]
return citation_elements | python | def remove_b_for_nucl_phys(citation_elements):
"""Removes b from the volume of some journals
Removes the B from the volume for Nucl.Phys.Proc.Suppl. because in INSPIRE
that journal is handled differently.
"""
for el in citation_elements:
if el['type'] == 'JOURNAL' and el['title'] == 'Nucl.Phys.Proc.Suppl.' \
and 'volume' in el \
and (el['volume'].startswith('b') or el['volume'].startswith('B')):
el['volume'] = el['volume'][1:]
return citation_elements | [
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3,723 | inspirehep/refextract | refextract/references/engine.py | mangle_volume | def mangle_volume(citation_elements):
"""Make sure the volume letter is before the volume number
e.g. transforms 100B to B100
"""
volume_re = re.compile(ur"(\d+)([A-Z])", re.U | re.I)
for el in citation_elements:
if el['type'] == 'JOURNAL':
matches = volume_re.match(el['volume'])
if matches:
el['volume'] = matches.group(2) + matches.group(1)
return citation_elements | python | def mangle_volume(citation_elements):
"""Make sure the volume letter is before the volume number
e.g. transforms 100B to B100
"""
volume_re = re.compile(ur"(\d+)([A-Z])", re.U | re.I)
for el in citation_elements:
if el['type'] == 'JOURNAL':
matches = volume_re.match(el['volume'])
if matches:
el['volume'] = matches.group(2) + matches.group(1)
return citation_elements | [
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3,724 | inspirehep/refextract | refextract/references/engine.py | split_citations | def split_citations(citation_elements):
"""Split a citation line in multiple citations
We handle the case where the author has put 2 citations in the same line
but split with ; or some other method.
"""
splitted_citations = []
new_elements = []
current_recid = None
current_doi = None
def check_ibid(current_elements, trigger_el):
for el in new_elements:
if el['type'] == 'AUTH':
return
# Check for ibid
if trigger_el.get('is_ibid', False):
if splitted_citations:
els = chain(reversed(current_elements),
reversed(splitted_citations[-1]))
else:
els = reversed(current_elements)
for el in els:
if el['type'] == 'AUTH':
new_elements.append(el.copy())
break
def start_new_citation():
"""Start new citation"""
splitted_citations.append(new_elements[:])
del new_elements[:]
for el in citation_elements:
try:
el_recid = el['recid']
except KeyError:
el_recid = None
if current_recid and el_recid and current_recid == el_recid:
# Do not start a new citation
pass
elif current_recid and el_recid and current_recid != el_recid \
or current_doi and el['type'] == 'DOI' and \
current_doi != el['doi_string']:
start_new_citation()
# Some authors may be found in the previous citation
balance_authors(splitted_citations, new_elements)
elif ';' in el['misc_txt']:
misc_txt, el['misc_txt'] = el['misc_txt'].split(';', 1)
if misc_txt:
new_elements.append({'type': 'MISC',
'misc_txt': misc_txt})
start_new_citation()
# In case el['recid'] is None, we want to reset it
# because we are starting a new reference
current_recid = el_recid
while ';' in el['misc_txt']:
misc_txt, el['misc_txt'] = el['misc_txt'].split(';', 1)
if misc_txt:
new_elements.append({'type': 'MISC',
'misc_txt': misc_txt})
start_new_citation()
current_recid = None
if el_recid:
current_recid = el_recid
if el['type'] == 'DOI':
current_doi = el['doi_string']
check_ibid(new_elements, el)
new_elements.append(el)
splitted_citations.append(new_elements)
return [el for el in splitted_citations if not empty_citation(el)] | python | def split_citations(citation_elements):
"""Split a citation line in multiple citations
We handle the case where the author has put 2 citations in the same line
but split with ; or some other method.
"""
splitted_citations = []
new_elements = []
current_recid = None
current_doi = None
def check_ibid(current_elements, trigger_el):
for el in new_elements:
if el['type'] == 'AUTH':
return
# Check for ibid
if trigger_el.get('is_ibid', False):
if splitted_citations:
els = chain(reversed(current_elements),
reversed(splitted_citations[-1]))
else:
els = reversed(current_elements)
for el in els:
if el['type'] == 'AUTH':
new_elements.append(el.copy())
break
def start_new_citation():
"""Start new citation"""
splitted_citations.append(new_elements[:])
del new_elements[:]
for el in citation_elements:
try:
el_recid = el['recid']
except KeyError:
el_recid = None
if current_recid and el_recid and current_recid == el_recid:
# Do not start a new citation
pass
elif current_recid and el_recid and current_recid != el_recid \
or current_doi and el['type'] == 'DOI' and \
current_doi != el['doi_string']:
start_new_citation()
# Some authors may be found in the previous citation
balance_authors(splitted_citations, new_elements)
elif ';' in el['misc_txt']:
misc_txt, el['misc_txt'] = el['misc_txt'].split(';', 1)
if misc_txt:
new_elements.append({'type': 'MISC',
'misc_txt': misc_txt})
start_new_citation()
# In case el['recid'] is None, we want to reset it
# because we are starting a new reference
current_recid = el_recid
while ';' in el['misc_txt']:
misc_txt, el['misc_txt'] = el['misc_txt'].split(';', 1)
if misc_txt:
new_elements.append({'type': 'MISC',
'misc_txt': misc_txt})
start_new_citation()
current_recid = None
if el_recid:
current_recid = el_recid
if el['type'] == 'DOI':
current_doi = el['doi_string']
check_ibid(new_elements, el)
new_elements.append(el)
splitted_citations.append(new_elements)
return [el for el in splitted_citations if not empty_citation(el)] | [
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3,725 | inspirehep/refextract | refextract/references/engine.py | look_for_hdl | def look_for_hdl(citation_elements):
"""Looks for handle identifiers in the misc txt of the citation elements
When finding an hdl, creates a new HDL element.
@param citation_elements: (list) elements to process
"""
for el in list(citation_elements):
matched_hdl = re_hdl.finditer(el['misc_txt'])
for match in reversed(list(matched_hdl)):
hdl_el = {'type': 'HDL',
'hdl_id': match.group('hdl_id'),
'misc_txt': el['misc_txt'][match.end():]}
el['misc_txt'] = el['misc_txt'][0:match.start()]
citation_elements.insert(citation_elements.index(el) + 1, hdl_el) | python | def look_for_hdl(citation_elements):
"""Looks for handle identifiers in the misc txt of the citation elements
When finding an hdl, creates a new HDL element.
@param citation_elements: (list) elements to process
"""
for el in list(citation_elements):
matched_hdl = re_hdl.finditer(el['misc_txt'])
for match in reversed(list(matched_hdl)):
hdl_el = {'type': 'HDL',
'hdl_id': match.group('hdl_id'),
'misc_txt': el['misc_txt'][match.end():]}
el['misc_txt'] = el['misc_txt'][0:match.start()]
citation_elements.insert(citation_elements.index(el) + 1, hdl_el) | [
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3,726 | inspirehep/refextract | refextract/references/engine.py | look_for_hdl_urls | def look_for_hdl_urls(citation_elements):
"""Looks for handle identifiers that have already been identified as urls
When finding an hdl, creates a new HDL element.
@param citation_elements: (list) elements to process
"""
for el in citation_elements:
if el['type'] == 'URL':
match = re_hdl.match(el['url_string'])
if match:
el['type'] = 'HDL'
el['hdl_id'] = match.group('hdl_id')
del el['url_desc']
del el['url_string'] | python | def look_for_hdl_urls(citation_elements):
"""Looks for handle identifiers that have already been identified as urls
When finding an hdl, creates a new HDL element.
@param citation_elements: (list) elements to process
"""
for el in citation_elements:
if el['type'] == 'URL':
match = re_hdl.match(el['url_string'])
if match:
el['type'] = 'HDL'
el['hdl_id'] = match.group('hdl_id')
del el['url_desc']
del el['url_string'] | [
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3,727 | inspirehep/refextract | refextract/references/engine.py | parse_reference_line | def parse_reference_line(ref_line, kbs, bad_titles_count={}, linker_callback=None):
"""Parse one reference line
@input a string representing a single reference bullet
@output parsed references (a list of elements objects)
"""
# Strip the 'marker' (e.g. [1]) from this reference line:
line_marker, ref_line = remove_reference_line_marker(ref_line)
# Find DOI sections in citation
ref_line, identified_dois = identify_and_tag_DOI(ref_line)
# Identify and replace URLs in the line:
ref_line, identified_urls = identify_and_tag_URLs(ref_line)
# Tag <cds.JOURNAL>, etc.
tagged_line, bad_titles_count = tag_reference_line(ref_line,
kbs,
bad_titles_count)
# Debug print tagging (authors, titles, volumes, etc.)
LOGGER.debug("tags %r", tagged_line)
# Using the recorded information, create a MARC XML representation
# of the rebuilt line:
# At the same time, get stats of citations found in the reference line
# (titles, urls, etc):
citation_elements, line_marker, counts = \
parse_tagged_reference_line(line_marker,
tagged_line,
identified_dois,
identified_urls)
# Transformations on elements
split_volume_from_journal(citation_elements)
format_volume(citation_elements)
handle_special_journals(citation_elements, kbs)
format_report_number(citation_elements)
format_author_ed(citation_elements)
look_for_books(citation_elements, kbs)
format_hep(citation_elements)
remove_b_for_nucl_phys(citation_elements)
mangle_volume(citation_elements)
arxiv_urls_to_report_numbers(citation_elements)
look_for_hdl(citation_elements)
look_for_hdl_urls(citation_elements)
# Link references if desired
if linker_callback:
associate_recids(citation_elements, linker_callback)
# Split the reference in multiple ones if needed
splitted_citations = split_citations(citation_elements)
# Look for implied ibids
look_for_implied_ibids(splitted_citations)
# Find year
add_year_elements(splitted_citations)
# Look for books in misc field
look_for_undetected_books(splitted_citations, kbs)
if linker_callback:
# Link references with the newly added ibids/books information
for citations in splitted_citations:
associate_recids(citations, linker_callback)
# FIXME: Needed?
# Remove references with only misc text
# splitted_citations = remove_invalid_references(splitted_citations)
# Merge references with only misc text
# splitted_citations = merge_invalid_references(splitted_citations)
remove_duplicated_authors(splitted_citations)
remove_duplicated_dois(splitted_citations)
remove_duplicated_collaborations(splitted_citations)
add_recid_elements(splitted_citations)
# For debugging purposes
print_citations(splitted_citations, line_marker)
return splitted_citations, line_marker, counts, bad_titles_count | python | def parse_reference_line(ref_line, kbs, bad_titles_count={}, linker_callback=None):
"""Parse one reference line
@input a string representing a single reference bullet
@output parsed references (a list of elements objects)
"""
# Strip the 'marker' (e.g. [1]) from this reference line:
line_marker, ref_line = remove_reference_line_marker(ref_line)
# Find DOI sections in citation
ref_line, identified_dois = identify_and_tag_DOI(ref_line)
# Identify and replace URLs in the line:
ref_line, identified_urls = identify_and_tag_URLs(ref_line)
# Tag <cds.JOURNAL>, etc.
tagged_line, bad_titles_count = tag_reference_line(ref_line,
kbs,
bad_titles_count)
# Debug print tagging (authors, titles, volumes, etc.)
LOGGER.debug("tags %r", tagged_line)
# Using the recorded information, create a MARC XML representation
# of the rebuilt line:
# At the same time, get stats of citations found in the reference line
# (titles, urls, etc):
citation_elements, line_marker, counts = \
parse_tagged_reference_line(line_marker,
tagged_line,
identified_dois,
identified_urls)
# Transformations on elements
split_volume_from_journal(citation_elements)
format_volume(citation_elements)
handle_special_journals(citation_elements, kbs)
format_report_number(citation_elements)
format_author_ed(citation_elements)
look_for_books(citation_elements, kbs)
format_hep(citation_elements)
remove_b_for_nucl_phys(citation_elements)
mangle_volume(citation_elements)
arxiv_urls_to_report_numbers(citation_elements)
look_for_hdl(citation_elements)
look_for_hdl_urls(citation_elements)
# Link references if desired
if linker_callback:
associate_recids(citation_elements, linker_callback)
# Split the reference in multiple ones if needed
splitted_citations = split_citations(citation_elements)
# Look for implied ibids
look_for_implied_ibids(splitted_citations)
# Find year
add_year_elements(splitted_citations)
# Look for books in misc field
look_for_undetected_books(splitted_citations, kbs)
if linker_callback:
# Link references with the newly added ibids/books information
for citations in splitted_citations:
associate_recids(citations, linker_callback)
# FIXME: Needed?
# Remove references with only misc text
# splitted_citations = remove_invalid_references(splitted_citations)
# Merge references with only misc text
# splitted_citations = merge_invalid_references(splitted_citations)
remove_duplicated_authors(splitted_citations)
remove_duplicated_dois(splitted_citations)
remove_duplicated_collaborations(splitted_citations)
add_recid_elements(splitted_citations)
# For debugging purposes
print_citations(splitted_citations, line_marker)
return splitted_citations, line_marker, counts, bad_titles_count | [
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3,728 | inspirehep/refextract | refextract/references/engine.py | search_for_book_in_misc | def search_for_book_in_misc(citation, kbs):
"""Searches for books in the misc_txt field if the citation is not recognized as anything like a journal, book, etc.
"""
citation_year = year_from_citation(citation)
for citation_element in citation:
LOGGER.debug(u"Searching for book title in: %s", citation_element['misc_txt'])
for title in kbs['books']:
startIndex = find_substring_ignore_special_chars(citation_element['misc_txt'], title)
if startIndex != -1:
line = kbs['books'][title.upper()]
book_year = line[2].strip(';')
book_authors = line[0]
book_found = False
if citation_year == book_year:
# For now consider the citation as valid, we are using
# an exact search, we don't need to check the authors
# However, the code below will be useful if we decide
# to introduce fuzzy matching.
book_found = True
for author in get_possible_author_names(citation):
if find_substring_ignore_special_chars(book_authors, author) != -1:
book_found = True
for author in re.findall('[a-zA-Z]{4,}', book_authors):
if find_substring_ignore_special_chars(citation_element['misc_txt'], author) != -1:
book_found = True
if book_found:
LOGGER.debug(u"Book found: %s", title)
book_element = {'type': 'BOOK',
'misc_txt': '',
'authors': book_authors,
'title': line[1],
'year': book_year}
citation.append(book_element)
citation_element['misc_txt'] = cut_substring_with_special_chars(citation_element['misc_txt'], title, startIndex)
# Remove year from misc txt
citation_element['misc_txt'] = remove_year(citation_element['misc_txt'], book_year)
return True
LOGGER.debug("Book not found!")
return False | python | def search_for_book_in_misc(citation, kbs):
"""Searches for books in the misc_txt field if the citation is not recognized as anything like a journal, book, etc.
"""
citation_year = year_from_citation(citation)
for citation_element in citation:
LOGGER.debug(u"Searching for book title in: %s", citation_element['misc_txt'])
for title in kbs['books']:
startIndex = find_substring_ignore_special_chars(citation_element['misc_txt'], title)
if startIndex != -1:
line = kbs['books'][title.upper()]
book_year = line[2].strip(';')
book_authors = line[0]
book_found = False
if citation_year == book_year:
# For now consider the citation as valid, we are using
# an exact search, we don't need to check the authors
# However, the code below will be useful if we decide
# to introduce fuzzy matching.
book_found = True
for author in get_possible_author_names(citation):
if find_substring_ignore_special_chars(book_authors, author) != -1:
book_found = True
for author in re.findall('[a-zA-Z]{4,}', book_authors):
if find_substring_ignore_special_chars(citation_element['misc_txt'], author) != -1:
book_found = True
if book_found:
LOGGER.debug(u"Book found: %s", title)
book_element = {'type': 'BOOK',
'misc_txt': '',
'authors': book_authors,
'title': line[1],
'year': book_year}
citation.append(book_element)
citation_element['misc_txt'] = cut_substring_with_special_chars(citation_element['misc_txt'], title, startIndex)
# Remove year from misc txt
citation_element['misc_txt'] = remove_year(citation_element['misc_txt'], book_year)
return True
LOGGER.debug("Book not found!")
return False | [
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3,729 | inspirehep/refextract | refextract/references/engine.py | map_tag_to_subfield | def map_tag_to_subfield(tag_type, line, cur_misc_txt, dest):
"""Create a new reference element"""
closing_tag = '</cds.%s>' % tag_type
# extract the institutional report-number from the line:
idx_closing_tag = line.find(closing_tag)
# Sanity check - did we find a closing tag?
if idx_closing_tag == -1:
# no closing </cds.TAG> tag found - strip the opening tag and move past this
# recognised reportnumber as it is unreliable:
identified_citation_element = None
line = line[len('<cds.%s>' % tag_type):]
else:
tag_content = line[:idx_closing_tag]
identified_citation_element = {'type': tag_type,
'misc_txt': cur_misc_txt,
dest: tag_content}
ending_tag_pos = idx_closing_tag + len(closing_tag)
line = line[ending_tag_pos:]
cur_misc_txt = u""
return identified_citation_element, line, cur_misc_txt | python | def map_tag_to_subfield(tag_type, line, cur_misc_txt, dest):
"""Create a new reference element"""
closing_tag = '</cds.%s>' % tag_type
# extract the institutional report-number from the line:
idx_closing_tag = line.find(closing_tag)
# Sanity check - did we find a closing tag?
if idx_closing_tag == -1:
# no closing </cds.TAG> tag found - strip the opening tag and move past this
# recognised reportnumber as it is unreliable:
identified_citation_element = None
line = line[len('<cds.%s>' % tag_type):]
else:
tag_content = line[:idx_closing_tag]
identified_citation_element = {'type': tag_type,
'misc_txt': cur_misc_txt,
dest: tag_content}
ending_tag_pos = idx_closing_tag + len(closing_tag)
line = line[ending_tag_pos:]
cur_misc_txt = u""
return identified_citation_element, line, cur_misc_txt | [
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3,730 | inspirehep/refextract | refextract/references/engine.py | remove_leading_garbage_lines_from_reference_section | def remove_leading_garbage_lines_from_reference_section(ref_sectn):
"""Sometimes, the first lines of the extracted references are completely
blank or email addresses. These must be removed as they are not
references.
@param ref_sectn: (list) of strings - the reference section lines
@return: (list) of strings - the reference section without leading
blank lines or email addresses.
"""
p_email = re.compile(ur'^\s*e\-?mail', re.UNICODE)
while ref_sectn and (ref_sectn[0].isspace() or p_email.match(ref_sectn[0])):
ref_sectn.pop(0)
return ref_sectn | python | def remove_leading_garbage_lines_from_reference_section(ref_sectn):
"""Sometimes, the first lines of the extracted references are completely
blank or email addresses. These must be removed as they are not
references.
@param ref_sectn: (list) of strings - the reference section lines
@return: (list) of strings - the reference section without leading
blank lines or email addresses.
"""
p_email = re.compile(ur'^\s*e\-?mail', re.UNICODE)
while ref_sectn and (ref_sectn[0].isspace() or p_email.match(ref_sectn[0])):
ref_sectn.pop(0)
return ref_sectn | [
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3,731 | inspirehep/refextract | refextract/references/engine.py | get_plaintext_document_body | def get_plaintext_document_body(fpath, keep_layout=False):
"""Given a file-path to a full-text, return a list of unicode strings
whereby each string is a line of the fulltext.
In the case of a plain-text document, this simply means reading the
contents in from the file. In the case of a PDF however,
this means converting the document to plaintext.
It raises UnknownDocumentTypeError if the document is not a PDF or
plain text.
@param fpath: (string) - the path to the fulltext file
@return: (list) of strings - each string being a line in the document.
"""
textbody = []
mime_type = magic.from_file(fpath, mime=True)
if mime_type == "text/plain":
with open(fpath, "r") as f:
textbody = [line.decode("utf-8") for line in f.readlines()]
elif mime_type == "application/pdf":
textbody = convert_PDF_to_plaintext(fpath, keep_layout)
else:
raise UnknownDocumentTypeError(mime_type)
return textbody | python | def get_plaintext_document_body(fpath, keep_layout=False):
"""Given a file-path to a full-text, return a list of unicode strings
whereby each string is a line of the fulltext.
In the case of a plain-text document, this simply means reading the
contents in from the file. In the case of a PDF however,
this means converting the document to plaintext.
It raises UnknownDocumentTypeError if the document is not a PDF or
plain text.
@param fpath: (string) - the path to the fulltext file
@return: (list) of strings - each string being a line in the document.
"""
textbody = []
mime_type = magic.from_file(fpath, mime=True)
if mime_type == "text/plain":
with open(fpath, "r") as f:
textbody = [line.decode("utf-8") for line in f.readlines()]
elif mime_type == "application/pdf":
textbody = convert_PDF_to_plaintext(fpath, keep_layout)
else:
raise UnknownDocumentTypeError(mime_type)
return textbody | [
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3,732 | inspirehep/refextract | refextract/references/engine.py | parse_references | def parse_references(reference_lines,
recid=None,
override_kbs_files=None,
reference_format=u"{title} {volume} ({year}) {page}",
linker_callback=None):
"""Parse a list of references
Given a list of raw reference lines (list of strings),
output a list of dictionaries containing the parsed references
"""
# RefExtract knowledge bases
kbs = get_kbs(custom_kbs_files=override_kbs_files)
# Identify journal titles, report numbers, URLs, DOIs, and authors...
processed_references, counts, dummy_bad_titles_count = \
parse_references_elements(reference_lines, kbs, linker_callback)
return (build_references(processed_references, reference_format),
build_stats(counts)) | python | def parse_references(reference_lines,
recid=None,
override_kbs_files=None,
reference_format=u"{title} {volume} ({year}) {page}",
linker_callback=None):
"""Parse a list of references
Given a list of raw reference lines (list of strings),
output a list of dictionaries containing the parsed references
"""
# RefExtract knowledge bases
kbs = get_kbs(custom_kbs_files=override_kbs_files)
# Identify journal titles, report numbers, URLs, DOIs, and authors...
processed_references, counts, dummy_bad_titles_count = \
parse_references_elements(reference_lines, kbs, linker_callback)
return (build_references(processed_references, reference_format),
build_stats(counts)) | [
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3,733 | inspirehep/refextract | refextract/references/engine.py | build_stats | def build_stats(counts):
"""Return stats information from counts structure."""
stats = {
'status': 0,
'reportnum': counts['reportnum'],
'title': counts['title'],
'author': counts['auth_group'],
'url': counts['url'],
'doi': counts['doi'],
'misc': counts['misc'],
}
stats_str = "%(status)s-%(reportnum)s-%(title)s-%(author)s-%(url)s-%(doi)s-%(misc)s" % stats
stats["old_stats_str"] = stats_str
stats["date"] = datetime.now().strftime("%Y-%m-%d %H:%M:%S")
stats["version"] = version
return stats | python | def build_stats(counts):
"""Return stats information from counts structure."""
stats = {
'status': 0,
'reportnum': counts['reportnum'],
'title': counts['title'],
'author': counts['auth_group'],
'url': counts['url'],
'doi': counts['doi'],
'misc': counts['misc'],
}
stats_str = "%(status)s-%(reportnum)s-%(title)s-%(author)s-%(url)s-%(doi)s-%(misc)s" % stats
stats["old_stats_str"] = stats_str
stats["date"] = datetime.now().strftime("%Y-%m-%d %H:%M:%S")
stats["version"] = version
return stats | [
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3,734 | inspirehep/refextract | refextract/documents/pdf.py | replace_undesirable_characters | def replace_undesirable_characters(line):
"""
Replace certain bad characters in a text line.
@param line: (string) the text line in which bad characters are to
be replaced.
@return: (string) the text line after the bad characters have been
replaced.
"""
# These are separate because we want a particular order
for bad_string, replacement in UNDESIRABLE_STRING_REPLACEMENTS:
line = line.replace(bad_string, replacement)
for bad_char, replacement in iteritems(UNDESIRABLE_CHAR_REPLACEMENTS):
line = line.replace(bad_char, replacement)
return line | python | def replace_undesirable_characters(line):
"""
Replace certain bad characters in a text line.
@param line: (string) the text line in which bad characters are to
be replaced.
@return: (string) the text line after the bad characters have been
replaced.
"""
# These are separate because we want a particular order
for bad_string, replacement in UNDESIRABLE_STRING_REPLACEMENTS:
line = line.replace(bad_string, replacement)
for bad_char, replacement in iteritems(UNDESIRABLE_CHAR_REPLACEMENTS):
line = line.replace(bad_char, replacement)
return line | [
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3,735 | inspirehep/refextract | refextract/documents/pdf.py | convert_PDF_to_plaintext | def convert_PDF_to_plaintext(fpath, keep_layout=False):
""" Convert PDF to txt using pdftotext
Take the path to a PDF file and run pdftotext for this file, capturing
the output.
@param fpath: (string) path to the PDF file
@return: (list) of unicode strings (contents of the PDF file translated
into plaintext; each string is a line in the document.)
"""
if not os.path.isfile(CFG_PATH_PDFTOTEXT):
raise IOError('Missing pdftotext executable')
if keep_layout:
layout_option = "-layout"
else:
layout_option = "-raw"
doclines = []
# Pattern to check for lines with a leading page-break character.
# If this pattern is matched, we want to split the page-break into
# its own line because we rely upon this for trying to strip headers
# and footers, and for some other pattern matching.
p_break_in_line = re.compile(ur'^\s*\f(.+)$', re.UNICODE)
# build pdftotext command:
cmd_pdftotext = [CFG_PATH_PDFTOTEXT, layout_option, "-q",
"-enc", "UTF-8", fpath, "-"]
LOGGER.debug(u"%s", ' '.join(cmd_pdftotext))
# open pipe to pdftotext:
pipe_pdftotext = subprocess.Popen(cmd_pdftotext, stdout=subprocess.PIPE)
# read back results:
for docline in pipe_pdftotext.stdout:
unicodeline = docline.decode("utf-8")
# Check for a page-break in this line:
m_break_in_line = p_break_in_line.match(unicodeline)
if m_break_in_line is None:
# There was no page-break in this line. Just add the line:
doclines.append(unicodeline)
else:
# If there was a page-break character in the same line as some
# text, split it out into its own line so that we can later
# try to find headers and footers:
doclines.append(u"\f")
doclines.append(m_break_in_line.group(1))
LOGGER.debug(u"convert_PDF_to_plaintext found: %s lines of text", len(doclines))
return doclines | python | def convert_PDF_to_plaintext(fpath, keep_layout=False):
""" Convert PDF to txt using pdftotext
Take the path to a PDF file and run pdftotext for this file, capturing
the output.
@param fpath: (string) path to the PDF file
@return: (list) of unicode strings (contents of the PDF file translated
into plaintext; each string is a line in the document.)
"""
if not os.path.isfile(CFG_PATH_PDFTOTEXT):
raise IOError('Missing pdftotext executable')
if keep_layout:
layout_option = "-layout"
else:
layout_option = "-raw"
doclines = []
# Pattern to check for lines with a leading page-break character.
# If this pattern is matched, we want to split the page-break into
# its own line because we rely upon this for trying to strip headers
# and footers, and for some other pattern matching.
p_break_in_line = re.compile(ur'^\s*\f(.+)$', re.UNICODE)
# build pdftotext command:
cmd_pdftotext = [CFG_PATH_PDFTOTEXT, layout_option, "-q",
"-enc", "UTF-8", fpath, "-"]
LOGGER.debug(u"%s", ' '.join(cmd_pdftotext))
# open pipe to pdftotext:
pipe_pdftotext = subprocess.Popen(cmd_pdftotext, stdout=subprocess.PIPE)
# read back results:
for docline in pipe_pdftotext.stdout:
unicodeline = docline.decode("utf-8")
# Check for a page-break in this line:
m_break_in_line = p_break_in_line.match(unicodeline)
if m_break_in_line is None:
# There was no page-break in this line. Just add the line:
doclines.append(unicodeline)
else:
# If there was a page-break character in the same line as some
# text, split it out into its own line so that we can later
# try to find headers and footers:
doclines.append(u"\f")
doclines.append(m_break_in_line.group(1))
LOGGER.debug(u"convert_PDF_to_plaintext found: %s lines of text", len(doclines))
return doclines | [
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3,736 | inspirehep/refextract | refextract/authors/regexs.py | get_author_affiliation_numeration_str | def get_author_affiliation_numeration_str(punct=None):
"""The numeration which can be applied to author names. Numeration
is sometimes found next to authors of papers.
@return: (string), which can be compiled into a regex; identifies
numeration next to an author name.
"""
# FIXME cater for start or end numeration (ie two puncs)
# Number to look for, either general or specific
re_number = r'(?:\d\d?)'
re_chained_numbers = r"(?:(?:[,;]\s*%s\.?\s*))*" % re_number
# Punctuation surrounding the number, either general or specific again
if punct is None:
re_punct = r"(?:[\{\(\[]?)"
else:
re_punct = re.escape(punct)
# Generic number finder (MUST NOT INCLUDE NAMED GROUPS!!!)
numeration_str = r"""
(?:\s*(%(punct)s)\s* ## Left numeration punctuation
(%(num)s\s* ## Core numeration item, either specific or generic
%(num_chain)s ## Extra numeration, either generic or empty
)
(?:(%(punct)s)) ## Right numeration punctuation
)""" % {'num': re_number,
'num_chain': re_chained_numbers,
'punct': re_punct}
return numeration_str | python | def get_author_affiliation_numeration_str(punct=None):
"""The numeration which can be applied to author names. Numeration
is sometimes found next to authors of papers.
@return: (string), which can be compiled into a regex; identifies
numeration next to an author name.
"""
# FIXME cater for start or end numeration (ie two puncs)
# Number to look for, either general or specific
re_number = r'(?:\d\d?)'
re_chained_numbers = r"(?:(?:[,;]\s*%s\.?\s*))*" % re_number
# Punctuation surrounding the number, either general or specific again
if punct is None:
re_punct = r"(?:[\{\(\[]?)"
else:
re_punct = re.escape(punct)
# Generic number finder (MUST NOT INCLUDE NAMED GROUPS!!!)
numeration_str = r"""
(?:\s*(%(punct)s)\s* ## Left numeration punctuation
(%(num)s\s* ## Core numeration item, either specific or generic
%(num_chain)s ## Extra numeration, either generic or empty
)
(?:(%(punct)s)) ## Right numeration punctuation
)""" % {'num': re_number,
'num_chain': re_chained_numbers,
'punct': re_punct}
return numeration_str | [
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"return",
"numeration_str"
] | The numeration which can be applied to author names. Numeration
is sometimes found next to authors of papers.
@return: (string), which can be compiled into a regex; identifies
numeration next to an author name. | [
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"numeration",
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] | d70e3787be3c495a3a07d1517b53f81d51c788c7 | https://github.com/inspirehep/refextract/blob/d70e3787be3c495a3a07d1517b53f81d51c788c7/refextract/authors/regexs.py#L36-L64 |
3,737 | inspirehep/refextract | refextract/authors/regexs.py | make_auth_regex_str | def make_auth_regex_str(etal, initial_surname_author=None, surname_initial_author=None):
"""
Returns a regular expression to be used to identify groups of author names in a citation.
This method contains patterns for default authors, so no arguments are needed for the
most reliable form of matching.
The returned author pattern is capable of:
1. Identifying single authors, with at least one initial, of the form:
'Initial. [surname prefix...] Surname'
2. Identifying multiple authors, each with at least one initial, of the form:
'Initial. [surname prefix...] Surname, [and] [Initial. [surname prefix...] Surname ... ]'
***(Note that a full stop, hyphen or apostrophe after each initial is
absolutely vital in identifying authors for both of these above methods.
Initials must also be uppercase.)***
3. Capture 'et al' statements at the end of author groups (allows for authors with et al
to be processed differently from 'standard' authors)
4. Identifying a single author surname name positioned before the phrase 'et al',
with no initials: 'Surname et al'
5. Identifying two author surname name positioned before the phrase 'et al',
with no initials, but separated by 'and' or '&': 'Surname [and|&] Surname et al'
6. Identifying authors of the form:
'Surname Initials, Initials Surname [Initials Surname]...'. Some authors choose
to represent the most important cited author (in a list of authors) by listing first
their surname, and then their initials. Since this form has little distinguishing
characteristics which could be used to create a reliable a pattern, at least one
standard author must be present after it in order to improve the accuracy.
7. Capture editor notation, of which can take many forms e.g.
'eds. editors. edited by. etc.'. Authors captured in this way can be treated as
'editor groups', and hence processed differently if needed from standard authors
@param etal: (string) The regular expression used to identify 'etal' notation
@param author: (string) An optional argument, which replaces the default author
regex used to identify author groups (initials, surnames... etc)
@return: (string) The full author group identification regex, which will:
- detect groups of authors in a range of formats, e.g.:
C. Hayward, V van Edwards, M. J. Woodbridge, and L. Kelloggs et al.,
- detect whether the author group has been marked up as editors of the doc.
(therefore they will NOT be marked up as authors) e.g.:
ed. C Hayward | (ed) V van Edwards | ed by, M. J. Woodbridge and V van Edwards
| L. Kelloggs (editors) | M. Jackson (eds.) | ...
-detect a maximum of two surnames only if the surname(s) is followed by 'et al'
(must be separated by 'and' if there are two), e.g.:
Amaldi et al., | Hayward and Yellow et al.,
"""
if not initial_surname_author:
# Standard author, with a maximum of 6 initials, and a surname.
# The Initials MUST be uppercase, and MUST have at least a dot, hypen
# or apostrophe between them.
initial_surname_author = get_initial_surname_author_pattern()
if not surname_initial_author:
# The author name of the form: 'surname initial(s)'
# This is sometimes the represention of the first author found inside an author group.
# This author pattern is only used to find a maximum of ONE author inside an author group.
# Authors of this form MUST have either a comma after the initials, or an 'and',
# which denotes the presence of other authors in the author group.
surname_initial_author = get_surname_initial_author_pattern()
# Pattern used to locate a GROUP of author names in a reference
# The format of an author can take many forms:
# J. Bloggs, W.-H. Smith, D. De Samuel, G.L. Bayetian, C. Hayward et al.,
# (the use of 'et. al' is a giveaway that the preceeding
# text was indeed an author name)
# This will also match authors which seem to be labeled as editors (with the phrase 'ed.')
# In which case, the author will be thrown away later on.
# The regex returned has around 100 named groups already (max), so any new groups must be
# started using '?:'
return ur"""
(?:^|\s+|\() ## Must be the start of the line, or a space (or an opening bracket in very few cases)
(?P<es> ## Look for editor notation before the author
(?:(?:(?:[Ee][Dd]s?|[Ee]dited|[Ee]ditors?)((?:\.\s?)|(?:\.?\s))) ## 'eds?. ' | 'ed ' | 'ed.'
|(?:(?:[Ee][Dd]s?|[Ee]dited|[Ee]ditions?)(?:(?:\.\s?)|(?:\.?\s))by(?:\s|([:,]\s))) ## 'eds?. by, ' | 'ed. by: ' | 'ed by ' | 'ed. by '| 'ed by: '
|(?:\(\s?([Ee][Dd]s?|[Ee]dited|[Ee]ditors?)(?:(?:\.\s?)|(?:\.?\s))?\))) ## '( eds?. )' | '(ed.)' | '(ed )' | '( ed )' | '(ed)'
)?
## **** (1) , one or two surnames which MUST end with 'et al' (e.g. Amaldi et al.,)
(?P<author_names>
(?:
(?:[A-Z](?:\s*[.'’-]{1,2}\s*[A-Z]){0,4}[.\s]\s*)? ## Initials
[A-Z][^0-9_\.\s]{2,20}(?:(?:[,\.]\s*)|(?:[,\.]?\s+)) ## Surname
(?:[A-Z](?:\s*[.'’-]{1,2}\s*[A-Z]){0,4}[.\s]\s*)? ## Initials
(?P<multi_surs>
(?:(?:[Aa][Nn][Dd]|\&)\s+) ## Maybe 'and' or '&' tied with another name
[A-Z][^0-9_\.\s]{3,20}(?:(?:[,\.]\s*)|(?:[,\.]?\s+)) ## More surnames
(?:[A-Z](?:[ -][A-Z])?\s+)? ## with initials
)?
(?: # Look for editor notation after the author group...
\s*[,\s]?\s* # Eventually a coma/space
%(ed)s
)?
(?P<et2>
%(etal)s ## et al, MUST BE PRESENT however, for this author form
)
(?: # Look for editor notation after the author group...
\s*[,\s]?\s* # Eventually a coma/space
%(ed)s
)?
) |
(?:
## **** (2) , The standard author form.. (e.g. J. Bloggs)
## This author form can either start with a normal 'initial surname' author,
## or it can begin with a single 'surname initial' author
(?: ## The first author in the 'author group'
%(i_s_author)s |
(?P<sur_initial_auth>%(s_i_author)s)
)
(?P<multi_auth>
(?: ## Then 0 or more author names
\s*[,\s]\s*
(?:
%(i_s_author)s | %(s_i_author)s
)
)*
(?: ## Maybe 'and' or '&' tied with another name
(?:
\s*[,\s]\s* ## handle "J. Dan, and H. Pon"
(?:[Aa][Nn][DdsS]|\&)
\s+
)
(?P<mult_auth_sub>
%(i_s_author)s | %(s_i_author)s
)
)?
)
(?P<et> # 'et al' need not be present for either of
\s*[,\s]\s*
%(etal)s # 'initial surname' or 'surname initial' authors
)?
)
)
(?P<ee>
\s*[,\s]\s*
\(?
(?:[Ee][Dd]s|[Ee]ditors)\.?
\)?
[\.\,]{0,2}
)?
# End of all author name patterns
\)? # A possible closing bracket to finish the author group
(?=[\s,.;:]) # Consolidate by checking we are not partially matching
# something else
""" % {'etal': etal,
'i_s_author': initial_surname_author,
's_i_author': surname_initial_author,
'ed': re_ed_notation} | python | def make_auth_regex_str(etal, initial_surname_author=None, surname_initial_author=None):
"""
Returns a regular expression to be used to identify groups of author names in a citation.
This method contains patterns for default authors, so no arguments are needed for the
most reliable form of matching.
The returned author pattern is capable of:
1. Identifying single authors, with at least one initial, of the form:
'Initial. [surname prefix...] Surname'
2. Identifying multiple authors, each with at least one initial, of the form:
'Initial. [surname prefix...] Surname, [and] [Initial. [surname prefix...] Surname ... ]'
***(Note that a full stop, hyphen or apostrophe after each initial is
absolutely vital in identifying authors for both of these above methods.
Initials must also be uppercase.)***
3. Capture 'et al' statements at the end of author groups (allows for authors with et al
to be processed differently from 'standard' authors)
4. Identifying a single author surname name positioned before the phrase 'et al',
with no initials: 'Surname et al'
5. Identifying two author surname name positioned before the phrase 'et al',
with no initials, but separated by 'and' or '&': 'Surname [and|&] Surname et al'
6. Identifying authors of the form:
'Surname Initials, Initials Surname [Initials Surname]...'. Some authors choose
to represent the most important cited author (in a list of authors) by listing first
their surname, and then their initials. Since this form has little distinguishing
characteristics which could be used to create a reliable a pattern, at least one
standard author must be present after it in order to improve the accuracy.
7. Capture editor notation, of which can take many forms e.g.
'eds. editors. edited by. etc.'. Authors captured in this way can be treated as
'editor groups', and hence processed differently if needed from standard authors
@param etal: (string) The regular expression used to identify 'etal' notation
@param author: (string) An optional argument, which replaces the default author
regex used to identify author groups (initials, surnames... etc)
@return: (string) The full author group identification regex, which will:
- detect groups of authors in a range of formats, e.g.:
C. Hayward, V van Edwards, M. J. Woodbridge, and L. Kelloggs et al.,
- detect whether the author group has been marked up as editors of the doc.
(therefore they will NOT be marked up as authors) e.g.:
ed. C Hayward | (ed) V van Edwards | ed by, M. J. Woodbridge and V van Edwards
| L. Kelloggs (editors) | M. Jackson (eds.) | ...
-detect a maximum of two surnames only if the surname(s) is followed by 'et al'
(must be separated by 'and' if there are two), e.g.:
Amaldi et al., | Hayward and Yellow et al.,
"""
if not initial_surname_author:
# Standard author, with a maximum of 6 initials, and a surname.
# The Initials MUST be uppercase, and MUST have at least a dot, hypen
# or apostrophe between them.
initial_surname_author = get_initial_surname_author_pattern()
if not surname_initial_author:
# The author name of the form: 'surname initial(s)'
# This is sometimes the represention of the first author found inside an author group.
# This author pattern is only used to find a maximum of ONE author inside an author group.
# Authors of this form MUST have either a comma after the initials, or an 'and',
# which denotes the presence of other authors in the author group.
surname_initial_author = get_surname_initial_author_pattern()
# Pattern used to locate a GROUP of author names in a reference
# The format of an author can take many forms:
# J. Bloggs, W.-H. Smith, D. De Samuel, G.L. Bayetian, C. Hayward et al.,
# (the use of 'et. al' is a giveaway that the preceeding
# text was indeed an author name)
# This will also match authors which seem to be labeled as editors (with the phrase 'ed.')
# In which case, the author will be thrown away later on.
# The regex returned has around 100 named groups already (max), so any new groups must be
# started using '?:'
return ur"""
(?:^|\s+|\() ## Must be the start of the line, or a space (or an opening bracket in very few cases)
(?P<es> ## Look for editor notation before the author
(?:(?:(?:[Ee][Dd]s?|[Ee]dited|[Ee]ditors?)((?:\.\s?)|(?:\.?\s))) ## 'eds?. ' | 'ed ' | 'ed.'
|(?:(?:[Ee][Dd]s?|[Ee]dited|[Ee]ditions?)(?:(?:\.\s?)|(?:\.?\s))by(?:\s|([:,]\s))) ## 'eds?. by, ' | 'ed. by: ' | 'ed by ' | 'ed. by '| 'ed by: '
|(?:\(\s?([Ee][Dd]s?|[Ee]dited|[Ee]ditors?)(?:(?:\.\s?)|(?:\.?\s))?\))) ## '( eds?. )' | '(ed.)' | '(ed )' | '( ed )' | '(ed)'
)?
## **** (1) , one or two surnames which MUST end with 'et al' (e.g. Amaldi et al.,)
(?P<author_names>
(?:
(?:[A-Z](?:\s*[.'’-]{1,2}\s*[A-Z]){0,4}[.\s]\s*)? ## Initials
[A-Z][^0-9_\.\s]{2,20}(?:(?:[,\.]\s*)|(?:[,\.]?\s+)) ## Surname
(?:[A-Z](?:\s*[.'’-]{1,2}\s*[A-Z]){0,4}[.\s]\s*)? ## Initials
(?P<multi_surs>
(?:(?:[Aa][Nn][Dd]|\&)\s+) ## Maybe 'and' or '&' tied with another name
[A-Z][^0-9_\.\s]{3,20}(?:(?:[,\.]\s*)|(?:[,\.]?\s+)) ## More surnames
(?:[A-Z](?:[ -][A-Z])?\s+)? ## with initials
)?
(?: # Look for editor notation after the author group...
\s*[,\s]?\s* # Eventually a coma/space
%(ed)s
)?
(?P<et2>
%(etal)s ## et al, MUST BE PRESENT however, for this author form
)
(?: # Look for editor notation after the author group...
\s*[,\s]?\s* # Eventually a coma/space
%(ed)s
)?
) |
(?:
## **** (2) , The standard author form.. (e.g. J. Bloggs)
## This author form can either start with a normal 'initial surname' author,
## or it can begin with a single 'surname initial' author
(?: ## The first author in the 'author group'
%(i_s_author)s |
(?P<sur_initial_auth>%(s_i_author)s)
)
(?P<multi_auth>
(?: ## Then 0 or more author names
\s*[,\s]\s*
(?:
%(i_s_author)s | %(s_i_author)s
)
)*
(?: ## Maybe 'and' or '&' tied with another name
(?:
\s*[,\s]\s* ## handle "J. Dan, and H. Pon"
(?:[Aa][Nn][DdsS]|\&)
\s+
)
(?P<mult_auth_sub>
%(i_s_author)s | %(s_i_author)s
)
)?
)
(?P<et> # 'et al' need not be present for either of
\s*[,\s]\s*
%(etal)s # 'initial surname' or 'surname initial' authors
)?
)
)
(?P<ee>
\s*[,\s]\s*
\(?
(?:[Ee][Dd]s|[Ee]ditors)\.?
\)?
[\.\,]{0,2}
)?
# End of all author name patterns
\)? # A possible closing bracket to finish the author group
(?=[\s,.;:]) # Consolidate by checking we are not partially matching
# something else
""" % {'etal': etal,
'i_s_author': initial_surname_author,
's_i_author': surname_initial_author,
'ed': re_ed_notation} | [
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] | Returns a regular expression to be used to identify groups of author names in a citation.
This method contains patterns for default authors, so no arguments are needed for the
most reliable form of matching.
The returned author pattern is capable of:
1. Identifying single authors, with at least one initial, of the form:
'Initial. [surname prefix...] Surname'
2. Identifying multiple authors, each with at least one initial, of the form:
'Initial. [surname prefix...] Surname, [and] [Initial. [surname prefix...] Surname ... ]'
***(Note that a full stop, hyphen or apostrophe after each initial is
absolutely vital in identifying authors for both of these above methods.
Initials must also be uppercase.)***
3. Capture 'et al' statements at the end of author groups (allows for authors with et al
to be processed differently from 'standard' authors)
4. Identifying a single author surname name positioned before the phrase 'et al',
with no initials: 'Surname et al'
5. Identifying two author surname name positioned before the phrase 'et al',
with no initials, but separated by 'and' or '&': 'Surname [and|&] Surname et al'
6. Identifying authors of the form:
'Surname Initials, Initials Surname [Initials Surname]...'. Some authors choose
to represent the most important cited author (in a list of authors) by listing first
their surname, and then their initials. Since this form has little distinguishing
characteristics which could be used to create a reliable a pattern, at least one
standard author must be present after it in order to improve the accuracy.
7. Capture editor notation, of which can take many forms e.g.
'eds. editors. edited by. etc.'. Authors captured in this way can be treated as
'editor groups', and hence processed differently if needed from standard authors
@param etal: (string) The regular expression used to identify 'etal' notation
@param author: (string) An optional argument, which replaces the default author
regex used to identify author groups (initials, surnames... etc)
@return: (string) The full author group identification regex, which will:
- detect groups of authors in a range of formats, e.g.:
C. Hayward, V van Edwards, M. J. Woodbridge, and L. Kelloggs et al.,
- detect whether the author group has been marked up as editors of the doc.
(therefore they will NOT be marked up as authors) e.g.:
ed. C Hayward | (ed) V van Edwards | ed by, M. J. Woodbridge and V van Edwards
| L. Kelloggs (editors) | M. Jackson (eds.) | ...
-detect a maximum of two surnames only if the surname(s) is followed by 'et al'
(must be separated by 'and' if there are two), e.g.:
Amaldi et al., | Hayward and Yellow et al., | [
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] | d70e3787be3c495a3a07d1517b53f81d51c788c7 | https://github.com/inspirehep/refextract/blob/d70e3787be3c495a3a07d1517b53f81d51c788c7/refextract/authors/regexs.py#L192-L350 |
3,738 | inspirehep/refextract | refextract/references/find.py | find_reference_section | def find_reference_section(docbody):
"""Search in document body for its reference section.
More precisely, find
the first line of the reference section. Effectively, the function starts
at the end of a document and works backwards, line-by-line, looking for
the title of a reference section. It stops when (if) it finds something
that it considers to be the first line of a reference section.
@param docbody: (list) of strings - the full document body.
@return: (dictionary) :
{ 'start_line' : (integer) - index in docbody of 1st reference line,
'title_string' : (string) - title of the reference section.
'marker' : (string) - the marker of the first reference line,
'marker_pattern' : (string) - regexp string used to find the marker,
'title_marker_same_line' : (integer) - flag to indicate whether the
reference section title was on the same
line as the first reference line's
marker or not. 1 if it was; 0 if not.
}
Much of this information is used by later functions to rebuild
a reference section.
-- OR --
(None) - when the reference section could not be found.
"""
ref_details = None
title_patterns = get_reference_section_title_patterns()
# Try to find refs section title:
for title_pattern in title_patterns:
# Look for title pattern in docbody
for reversed_index, line in enumerate(reversed(docbody)):
title_match = title_pattern.match(line)
if title_match:
title = title_match.group('title')
index = len(docbody) - 1 - reversed_index
temp_ref_details, found_title = find_numeration(docbody[index:index + 6], title)
if temp_ref_details:
if ref_details and 'title' in ref_details and ref_details['title'] and not temp_ref_details['title']:
continue
if ref_details and 'marker' in ref_details and ref_details['marker'] and not temp_ref_details['marker']:
continue
ref_details = temp_ref_details
ref_details['start_line'] = index
ref_details['title_string'] = title
if found_title:
break
if ref_details:
break
return ref_details | python | def find_reference_section(docbody):
"""Search in document body for its reference section.
More precisely, find
the first line of the reference section. Effectively, the function starts
at the end of a document and works backwards, line-by-line, looking for
the title of a reference section. It stops when (if) it finds something
that it considers to be the first line of a reference section.
@param docbody: (list) of strings - the full document body.
@return: (dictionary) :
{ 'start_line' : (integer) - index in docbody of 1st reference line,
'title_string' : (string) - title of the reference section.
'marker' : (string) - the marker of the first reference line,
'marker_pattern' : (string) - regexp string used to find the marker,
'title_marker_same_line' : (integer) - flag to indicate whether the
reference section title was on the same
line as the first reference line's
marker or not. 1 if it was; 0 if not.
}
Much of this information is used by later functions to rebuild
a reference section.
-- OR --
(None) - when the reference section could not be found.
"""
ref_details = None
title_patterns = get_reference_section_title_patterns()
# Try to find refs section title:
for title_pattern in title_patterns:
# Look for title pattern in docbody
for reversed_index, line in enumerate(reversed(docbody)):
title_match = title_pattern.match(line)
if title_match:
title = title_match.group('title')
index = len(docbody) - 1 - reversed_index
temp_ref_details, found_title = find_numeration(docbody[index:index + 6], title)
if temp_ref_details:
if ref_details and 'title' in ref_details and ref_details['title'] and not temp_ref_details['title']:
continue
if ref_details and 'marker' in ref_details and ref_details['marker'] and not temp_ref_details['marker']:
continue
ref_details = temp_ref_details
ref_details['start_line'] = index
ref_details['title_string'] = title
if found_title:
break
if ref_details:
break
return ref_details | [
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the title of a reference section. It stops when (if) it finds something
that it considers to be the first line of a reference section.
@param docbody: (list) of strings - the full document body.
@return: (dictionary) :
{ 'start_line' : (integer) - index in docbody of 1st reference line,
'title_string' : (string) - title of the reference section.
'marker' : (string) - the marker of the first reference line,
'marker_pattern' : (string) - regexp string used to find the marker,
'title_marker_same_line' : (integer) - flag to indicate whether the
reference section title was on the same
line as the first reference line's
marker or not. 1 if it was; 0 if not.
}
Much of this information is used by later functions to rebuild
a reference section.
-- OR --
(None) - when the reference section could not be found. | [
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3,739 | inspirehep/refextract | refextract/references/find.py | find_numeration | def find_numeration(docbody, title):
"""Find numeration pattern
1st try to find numeration in the title
e.g.
References [4] Riotto...
2nd find the numeration alone in the line after the title
e.g.
References
1
Riotto
3rnd find the numeration in the following line
e.g.
References
[1] Riotto
"""
ref_details, found_title = find_numeration_in_title(docbody, title)
if not ref_details:
ref_details, found_title = find_numeration_in_body(docbody)
return ref_details, found_title | python | def find_numeration(docbody, title):
"""Find numeration pattern
1st try to find numeration in the title
e.g.
References [4] Riotto...
2nd find the numeration alone in the line after the title
e.g.
References
1
Riotto
3rnd find the numeration in the following line
e.g.
References
[1] Riotto
"""
ref_details, found_title = find_numeration_in_title(docbody, title)
if not ref_details:
ref_details, found_title = find_numeration_in_body(docbody)
return ref_details, found_title | [
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References [4] Riotto...
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References
1
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References
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3,740 | inspirehep/refextract | refextract/references/text.py | get_reference_lines | def get_reference_lines(docbody,
ref_sect_start_line,
ref_sect_end_line,
ref_sect_title,
ref_line_marker_ptn,
title_marker_same_line):
"""After the reference section of a document has been identified, and the
first and last lines of the reference section have been recorded, this
function is called to take the reference lines out of the document body.
The document's reference lines are returned in a list of strings whereby
each string is a reference line. Before this can be done however, the
reference section is passed to another function that rebuilds any broken
reference lines.
@param docbody: (list) of strings - the entire document body.
@param ref_sect_start_line: (integer) - the index in docbody of the first
reference line.
@param ref_sect_end_line: (integer) - the index in docbody of the last
reference line.
@param ref_sect_title: (string) - the title of the reference section
(e.g. "References").
@param ref_line_marker_ptn: (string) - the patern used to match the
marker for each reference line (e.g., could be used to match lines
with markers of the form [1], [2], etc.)
@param title_marker_same_line: (integer) - a flag to indicate whether
or not the reference section title was on the same line as the first
reference line's marker.
@return: (list) of strings. Each string is a reference line, extracted
from the document.
"""
start_idx = ref_sect_start_line
if title_marker_same_line:
# Title on same line as 1st ref- take title out!
title_start = docbody[start_idx].find(ref_sect_title)
if title_start != -1:
# Set the first line with no title
docbody[start_idx] = docbody[start_idx][title_start +
len(ref_sect_title):]
elif ref_sect_title is not None:
# Set the start of the reference section to be after the title line
start_idx += 1
if ref_sect_end_line is not None:
ref_lines = docbody[start_idx:ref_sect_end_line + 1]
else:
ref_lines = docbody[start_idx:]
if ref_sect_title:
ref_lines = strip_footer(ref_lines, ref_sect_title)
# Now rebuild reference lines:
# (Go through each raw reference line, and format them into a set
# of properly ordered lines based on markers)
return rebuild_reference_lines(ref_lines, ref_line_marker_ptn) | python | def get_reference_lines(docbody,
ref_sect_start_line,
ref_sect_end_line,
ref_sect_title,
ref_line_marker_ptn,
title_marker_same_line):
"""After the reference section of a document has been identified, and the
first and last lines of the reference section have been recorded, this
function is called to take the reference lines out of the document body.
The document's reference lines are returned in a list of strings whereby
each string is a reference line. Before this can be done however, the
reference section is passed to another function that rebuilds any broken
reference lines.
@param docbody: (list) of strings - the entire document body.
@param ref_sect_start_line: (integer) - the index in docbody of the first
reference line.
@param ref_sect_end_line: (integer) - the index in docbody of the last
reference line.
@param ref_sect_title: (string) - the title of the reference section
(e.g. "References").
@param ref_line_marker_ptn: (string) - the patern used to match the
marker for each reference line (e.g., could be used to match lines
with markers of the form [1], [2], etc.)
@param title_marker_same_line: (integer) - a flag to indicate whether
or not the reference section title was on the same line as the first
reference line's marker.
@return: (list) of strings. Each string is a reference line, extracted
from the document.
"""
start_idx = ref_sect_start_line
if title_marker_same_line:
# Title on same line as 1st ref- take title out!
title_start = docbody[start_idx].find(ref_sect_title)
if title_start != -1:
# Set the first line with no title
docbody[start_idx] = docbody[start_idx][title_start +
len(ref_sect_title):]
elif ref_sect_title is not None:
# Set the start of the reference section to be after the title line
start_idx += 1
if ref_sect_end_line is not None:
ref_lines = docbody[start_idx:ref_sect_end_line + 1]
else:
ref_lines = docbody[start_idx:]
if ref_sect_title:
ref_lines = strip_footer(ref_lines, ref_sect_title)
# Now rebuild reference lines:
# (Go through each raw reference line, and format them into a set
# of properly ordered lines based on markers)
return rebuild_reference_lines(ref_lines, ref_line_marker_ptn) | [
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each string is a reference line. Before this can be done however, the
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@return: (list) of strings. Each string is a reference line, extracted
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3,741 | inspirehep/refextract | refextract/references/text.py | match_pagination | def match_pagination(ref_line):
"""Remove footer pagination from references lines"""
pattern = ur'\(?\[?(\d{1,4})\]?\)?\.?\s*$'
re_footer = re.compile(pattern, re.UNICODE)
match = re_footer.match(ref_line)
if match:
return int(match.group(1))
return None | python | def match_pagination(ref_line):
"""Remove footer pagination from references lines"""
pattern = ur'\(?\[?(\d{1,4})\]?\)?\.?\s*$'
re_footer = re.compile(pattern, re.UNICODE)
match = re_footer.match(ref_line)
if match:
return int(match.group(1))
return None | [
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3,742 | inspirehep/refextract | refextract/references/text.py | strip_footer | def strip_footer(ref_lines, section_title):
"""Remove footer title from references lines"""
pattern = ur'\(?\[?\d{0,4}\]?\)?\.?\s*%s\s*$' % re.escape(section_title)
re_footer = re.compile(pattern, re.UNICODE)
return [l for l in ref_lines if not re_footer.match(l)] | python | def strip_footer(ref_lines, section_title):
"""Remove footer title from references lines"""
pattern = ur'\(?\[?\d{0,4}\]?\)?\.?\s*%s\s*$' % re.escape(section_title)
re_footer = re.compile(pattern, re.UNICODE)
return [l for l in ref_lines if not re_footer.match(l)] | [
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3,743 | inspirehep/refextract | refextract/references/api.py | extract_references_from_url | def extract_references_from_url(url, headers=None, chunk_size=1024, **kwargs):
"""Extract references from the pdf specified in the url.
The first parameter is the URL of the file.
It returns a list of parsed references.
It raises FullTextNotAvailableError if the URL gives a 404,
UnknownDocumentTypeError if it is not a PDF or plain text.
The standard reference format is: {title} {volume} ({year}) {page}.
E.g. you can change that by passing the reference_format:
>>> extract_references_from_url(path, reference_format="{title},{volume},{page}")
If you want to also link each reference to some other resource (like a record),
you can provide a linker_callback function to be executed for every reference
element found.
To override KBs for journal names etc., use ``override_kbs_files``:
>>> extract_references_from_url(path, override_kbs_files={'journals': 'my/path/to.kb'})
"""
# Get temporary filepath to download to
filename, filepath = mkstemp(
suffix=u"_{0}".format(os.path.basename(url)),
)
os.close(filename)
try:
req = requests.get(
url=url,
headers=headers,
stream=True
)
req.raise_for_status()
with open(filepath, 'wb') as f:
for chunk in req.iter_content(chunk_size):
f.write(chunk)
references = extract_references_from_file(filepath, **kwargs)
except requests.exceptions.HTTPError:
raise FullTextNotAvailableError(u"URL not found: '{0}'".format(url)), None, sys.exc_info()[2]
finally:
os.remove(filepath)
return references | python | def extract_references_from_url(url, headers=None, chunk_size=1024, **kwargs):
"""Extract references from the pdf specified in the url.
The first parameter is the URL of the file.
It returns a list of parsed references.
It raises FullTextNotAvailableError if the URL gives a 404,
UnknownDocumentTypeError if it is not a PDF or plain text.
The standard reference format is: {title} {volume} ({year}) {page}.
E.g. you can change that by passing the reference_format:
>>> extract_references_from_url(path, reference_format="{title},{volume},{page}")
If you want to also link each reference to some other resource (like a record),
you can provide a linker_callback function to be executed for every reference
element found.
To override KBs for journal names etc., use ``override_kbs_files``:
>>> extract_references_from_url(path, override_kbs_files={'journals': 'my/path/to.kb'})
"""
# Get temporary filepath to download to
filename, filepath = mkstemp(
suffix=u"_{0}".format(os.path.basename(url)),
)
os.close(filename)
try:
req = requests.get(
url=url,
headers=headers,
stream=True
)
req.raise_for_status()
with open(filepath, 'wb') as f:
for chunk in req.iter_content(chunk_size):
f.write(chunk)
references = extract_references_from_file(filepath, **kwargs)
except requests.exceptions.HTTPError:
raise FullTextNotAvailableError(u"URL not found: '{0}'".format(url)), None, sys.exc_info()[2]
finally:
os.remove(filepath)
return references | [
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The first parameter is the URL of the file.
It returns a list of parsed references.
It raises FullTextNotAvailableError if the URL gives a 404,
UnknownDocumentTypeError if it is not a PDF or plain text.
The standard reference format is: {title} {volume} ({year}) {page}.
E.g. you can change that by passing the reference_format:
>>> extract_references_from_url(path, reference_format="{title},{volume},{page}")
If you want to also link each reference to some other resource (like a record),
you can provide a linker_callback function to be executed for every reference
element found.
To override KBs for journal names etc., use ``override_kbs_files``:
>>> extract_references_from_url(path, override_kbs_files={'journals': 'my/path/to.kb'}) | [
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] | d70e3787be3c495a3a07d1517b53f81d51c788c7 | https://github.com/inspirehep/refextract/blob/d70e3787be3c495a3a07d1517b53f81d51c788c7/refextract/references/api.py#L54-L99 |
3,744 | inspirehep/refextract | refextract/references/api.py | extract_references_from_file | def extract_references_from_file(path,
recid=None,
reference_format=u"{title} {volume} ({year}) {page}",
linker_callback=None,
override_kbs_files=None):
"""Extract references from a local pdf file.
The first parameter is the path to the file.
It returns a list of parsed references.
It raises FullTextNotAvailableError if the file does not exist,
UnknownDocumentTypeError if it is not a PDF or plain text.
The standard reference format is: {title} {volume} ({year}) {page}.
E.g. you can change that by passing the reference_format:
>>> extract_references_from_file(path, reference_format=u"{title},{volume},{page}")
If you want to also link each reference to some other resource (like a record),
you can provide a linker_callback function to be executed for every reference
element found.
To override KBs for journal names etc., use ``override_kbs_files``:
>>> extract_references_from_file(path, override_kbs_files={'journals': 'my/path/to.kb'})
"""
if not os.path.isfile(path):
raise FullTextNotAvailableError(u"File not found: '{0}'".format(path))
docbody = get_plaintext_document_body(path)
reflines, dummy, dummy = extract_references_from_fulltext(docbody)
if not reflines:
docbody = get_plaintext_document_body(path, keep_layout=True)
reflines, dummy, dummy = extract_references_from_fulltext(docbody)
parsed_refs, stats = parse_references(
reflines,
recid=recid,
reference_format=reference_format,
linker_callback=linker_callback,
override_kbs_files=override_kbs_files,
)
if magic.from_file(path, mime=True) == "application/pdf":
texkeys = extract_texkeys_from_pdf(path)
if len(texkeys) == len(parsed_refs):
parsed_refs = [dict(ref, texkey=[key]) for ref, key in izip(parsed_refs, texkeys)]
return parsed_refs | python | def extract_references_from_file(path,
recid=None,
reference_format=u"{title} {volume} ({year}) {page}",
linker_callback=None,
override_kbs_files=None):
"""Extract references from a local pdf file.
The first parameter is the path to the file.
It returns a list of parsed references.
It raises FullTextNotAvailableError if the file does not exist,
UnknownDocumentTypeError if it is not a PDF or plain text.
The standard reference format is: {title} {volume} ({year}) {page}.
E.g. you can change that by passing the reference_format:
>>> extract_references_from_file(path, reference_format=u"{title},{volume},{page}")
If you want to also link each reference to some other resource (like a record),
you can provide a linker_callback function to be executed for every reference
element found.
To override KBs for journal names etc., use ``override_kbs_files``:
>>> extract_references_from_file(path, override_kbs_files={'journals': 'my/path/to.kb'})
"""
if not os.path.isfile(path):
raise FullTextNotAvailableError(u"File not found: '{0}'".format(path))
docbody = get_plaintext_document_body(path)
reflines, dummy, dummy = extract_references_from_fulltext(docbody)
if not reflines:
docbody = get_plaintext_document_body(path, keep_layout=True)
reflines, dummy, dummy = extract_references_from_fulltext(docbody)
parsed_refs, stats = parse_references(
reflines,
recid=recid,
reference_format=reference_format,
linker_callback=linker_callback,
override_kbs_files=override_kbs_files,
)
if magic.from_file(path, mime=True) == "application/pdf":
texkeys = extract_texkeys_from_pdf(path)
if len(texkeys) == len(parsed_refs):
parsed_refs = [dict(ref, texkey=[key]) for ref, key in izip(parsed_refs, texkeys)]
return parsed_refs | [
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The first parameter is the path to the file.
It returns a list of parsed references.
It raises FullTextNotAvailableError if the file does not exist,
UnknownDocumentTypeError if it is not a PDF or plain text.
The standard reference format is: {title} {volume} ({year}) {page}.
E.g. you can change that by passing the reference_format:
>>> extract_references_from_file(path, reference_format=u"{title},{volume},{page}")
If you want to also link each reference to some other resource (like a record),
you can provide a linker_callback function to be executed for every reference
element found.
To override KBs for journal names etc., use ``override_kbs_files``:
>>> extract_references_from_file(path, override_kbs_files={'journals': 'my/path/to.kb'}) | [
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3,745 | inspirehep/refextract | refextract/references/api.py | extract_references_from_string | def extract_references_from_string(source,
is_only_references=True,
recid=None,
reference_format="{title} {volume} ({year}) {page}",
linker_callback=None,
override_kbs_files=None):
"""Extract references from a raw string.
The first parameter is the path to the file.
It returns a tuple (references, stats).
If the string does not only contain references, improve accuracy by
specifing ``is_only_references=False``.
The standard reference format is: {title} {volume} ({year}) {page}.
E.g. you can change that by passing the reference_format:
>>> extract_references_from_string(path, reference_format="{title},{volume},{page}")
If you want to also link each reference to some other resource (like a record),
you can provide a linker_callback function to be executed for every reference
element found.
To override KBs for journal names etc., use ``override_kbs_files``:
>>> extract_references_from_string(path, override_kbs_files={'journals': 'my/path/to.kb'})
"""
docbody = source.split('\n')
if not is_only_references:
reflines, dummy, dummy = extract_references_from_fulltext(docbody)
else:
refs_info = get_reference_section_beginning(docbody)
if not refs_info:
refs_info, dummy = find_numeration_in_body(docbody)
refs_info['start_line'] = 0
refs_info['end_line'] = len(docbody) - 1,
reflines = rebuild_reference_lines(
docbody, refs_info['marker_pattern'])
parsed_refs, stats = parse_references(
reflines,
recid=recid,
reference_format=reference_format,
linker_callback=linker_callback,
override_kbs_files=override_kbs_files,
)
return parsed_refs | python | def extract_references_from_string(source,
is_only_references=True,
recid=None,
reference_format="{title} {volume} ({year}) {page}",
linker_callback=None,
override_kbs_files=None):
"""Extract references from a raw string.
The first parameter is the path to the file.
It returns a tuple (references, stats).
If the string does not only contain references, improve accuracy by
specifing ``is_only_references=False``.
The standard reference format is: {title} {volume} ({year}) {page}.
E.g. you can change that by passing the reference_format:
>>> extract_references_from_string(path, reference_format="{title},{volume},{page}")
If you want to also link each reference to some other resource (like a record),
you can provide a linker_callback function to be executed for every reference
element found.
To override KBs for journal names etc., use ``override_kbs_files``:
>>> extract_references_from_string(path, override_kbs_files={'journals': 'my/path/to.kb'})
"""
docbody = source.split('\n')
if not is_only_references:
reflines, dummy, dummy = extract_references_from_fulltext(docbody)
else:
refs_info = get_reference_section_beginning(docbody)
if not refs_info:
refs_info, dummy = find_numeration_in_body(docbody)
refs_info['start_line'] = 0
refs_info['end_line'] = len(docbody) - 1,
reflines = rebuild_reference_lines(
docbody, refs_info['marker_pattern'])
parsed_refs, stats = parse_references(
reflines,
recid=recid,
reference_format=reference_format,
linker_callback=linker_callback,
override_kbs_files=override_kbs_files,
)
return parsed_refs | [
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It returns a tuple (references, stats).
If the string does not only contain references, improve accuracy by
specifing ``is_only_references=False``.
The standard reference format is: {title} {volume} ({year}) {page}.
E.g. you can change that by passing the reference_format:
>>> extract_references_from_string(path, reference_format="{title},{volume},{page}")
If you want to also link each reference to some other resource (like a record),
you can provide a linker_callback function to be executed for every reference
element found.
To override KBs for journal names etc., use ``override_kbs_files``:
>>> extract_references_from_string(path, override_kbs_files={'journals': 'my/path/to.kb'}) | [
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] | d70e3787be3c495a3a07d1517b53f81d51c788c7 | https://github.com/inspirehep/refextract/blob/d70e3787be3c495a3a07d1517b53f81d51c788c7/refextract/references/api.py#L154-L201 |
3,746 | inspirehep/refextract | refextract/references/api.py | extract_journal_reference | def extract_journal_reference(line, override_kbs_files=None):
"""Extract the journal reference from string.
Extracts the journal reference from string and parses for specific
journal information.
"""
kbs = get_kbs(custom_kbs_files=override_kbs_files)
references, dummy_m, dummy_c, dummy_co = parse_reference_line(line, kbs)
for elements in references:
for el in elements:
if el['type'] == 'JOURNAL':
return el | python | def extract_journal_reference(line, override_kbs_files=None):
"""Extract the journal reference from string.
Extracts the journal reference from string and parses for specific
journal information.
"""
kbs = get_kbs(custom_kbs_files=override_kbs_files)
references, dummy_m, dummy_c, dummy_co = parse_reference_line(line, kbs)
for elements in references:
for el in elements:
if el['type'] == 'JOURNAL':
return el | [
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3,747 | inspirehep/refextract | refextract/references/record.py | build_references | def build_references(citations, reference_format=False):
"""Build list of reference dictionaries from a references list
"""
# Now, run the method which will take as input:
# 1. A list of lists of dictionaries, where each dictionary is a piece
# of citation information corresponding to a tag in the citation.
# 2. The line marker for this entire citation line (mulitple citation
# 'finds' inside a single citation will use the same marker value)
# The resulting xml line will be a properly marked up form of the
# citation. It will take into account authors to try and split up
# references which should be read as two SEPARATE ones.
return [c for citation_elements in citations
for elements in citation_elements['elements']
for c in build_reference_fields(elements,
citation_elements['line_marker'],
citation_elements['raw_ref'],
reference_format)] | python | def build_references(citations, reference_format=False):
"""Build list of reference dictionaries from a references list
"""
# Now, run the method which will take as input:
# 1. A list of lists of dictionaries, where each dictionary is a piece
# of citation information corresponding to a tag in the citation.
# 2. The line marker for this entire citation line (mulitple citation
# 'finds' inside a single citation will use the same marker value)
# The resulting xml line will be a properly marked up form of the
# citation. It will take into account authors to try and split up
# references which should be read as two SEPARATE ones.
return [c for citation_elements in citations
for elements in citation_elements['elements']
for c in build_reference_fields(elements,
citation_elements['line_marker'],
citation_elements['raw_ref'],
reference_format)] | [
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3,748 | inspirehep/refextract | refextract/references/record.py | build_reference_fields | def build_reference_fields(citation_elements, line_marker, raw_ref,
reference_format):
"""Create the final representation of the reference information.
@param citation_elements: (list) an ordered list of dictionary elements,
with each element corresponding to a found
piece of information from a reference line.
@param line_marker: (string) The line marker for this single reference
line (e.g. [19])
@param raw_ref: (string) The raw string of this line
@return reference_fields: (list) A list of one dictionary containing the
reference elements
"""
# Begin the datafield element
current_field = create_reference_field(line_marker)
current_field['raw_ref'] = [raw_ref]
reference_fields = [current_field]
for element in citation_elements:
# Before going onto checking 'what' the next element is,
# handle misc text and semi-colons
# Multiple misc text subfields will be compressed later
# This will also be the only part of the code that deals with MISC
# tag_typed elements
misc_txt = element['misc_txt']
if misc_txt.strip("., [](){}"):
misc_txt = misc_txt.lstrip('])} ,.').rstrip('[({ ,.')
add_subfield(current_field, 'misc', misc_txt)
# Now handle the type dependent actions
# JOURNAL
if element['type'] == "JOURNAL":
add_journal_subfield(current_field, element, reference_format)
# REPORT NUMBER
elif element['type'] == "REPORTNUMBER":
add_subfield(current_field, 'reportnumber', element['report_num'])
# URL
elif element['type'] == "URL":
if element['url_string'] == element['url_desc']:
# Build the datafield for the URL segment of the reference
# line:
add_subfield(current_field, 'url', element['url_string'])
# Else, in the case that the url string and the description differ
# in some way, include them both
else:
add_subfield(current_field, 'url', element['url_string'])
add_subfield(current_field, 'urldesc', element['url_desc'])
# DOI
elif element['type'] == "DOI":
add_subfield(current_field, 'doi', 'doi:' + element['doi_string'])
# HDL
elif element['type'] == "HDL":
add_subfield(current_field, 'hdl', 'hdl:' + element['hdl_id'])
# AUTHOR
elif element['type'] == "AUTH":
value = element['auth_txt']
if element['auth_type'] == 'incl':
value = "(%s)" % value
add_subfield(current_field, 'author', value)
elif element['type'] == "QUOTED":
add_subfield(current_field, 'title', element['title'])
elif element['type'] == "ISBN":
add_subfield(current_field, 'isbn', element['ISBN'])
elif element['type'] == "BOOK":
add_subfield(current_field, 'title', element['title'])
elif element['type'] == "PUBLISHER":
add_subfield(current_field, 'publisher', element['publisher'])
elif element['type'] == "YEAR":
add_subfield(current_field, 'year', element['year'])
elif element['type'] == "COLLABORATION":
add_subfield(current_field,
'collaboration',
element['collaboration'])
elif element['type'] == "RECID":
add_subfield(current_field, 'recid', str(element['recid']))
return reference_fields | python | def build_reference_fields(citation_elements, line_marker, raw_ref,
reference_format):
"""Create the final representation of the reference information.
@param citation_elements: (list) an ordered list of dictionary elements,
with each element corresponding to a found
piece of information from a reference line.
@param line_marker: (string) The line marker for this single reference
line (e.g. [19])
@param raw_ref: (string) The raw string of this line
@return reference_fields: (list) A list of one dictionary containing the
reference elements
"""
# Begin the datafield element
current_field = create_reference_field(line_marker)
current_field['raw_ref'] = [raw_ref]
reference_fields = [current_field]
for element in citation_elements:
# Before going onto checking 'what' the next element is,
# handle misc text and semi-colons
# Multiple misc text subfields will be compressed later
# This will also be the only part of the code that deals with MISC
# tag_typed elements
misc_txt = element['misc_txt']
if misc_txt.strip("., [](){}"):
misc_txt = misc_txt.lstrip('])} ,.').rstrip('[({ ,.')
add_subfield(current_field, 'misc', misc_txt)
# Now handle the type dependent actions
# JOURNAL
if element['type'] == "JOURNAL":
add_journal_subfield(current_field, element, reference_format)
# REPORT NUMBER
elif element['type'] == "REPORTNUMBER":
add_subfield(current_field, 'reportnumber', element['report_num'])
# URL
elif element['type'] == "URL":
if element['url_string'] == element['url_desc']:
# Build the datafield for the URL segment of the reference
# line:
add_subfield(current_field, 'url', element['url_string'])
# Else, in the case that the url string and the description differ
# in some way, include them both
else:
add_subfield(current_field, 'url', element['url_string'])
add_subfield(current_field, 'urldesc', element['url_desc'])
# DOI
elif element['type'] == "DOI":
add_subfield(current_field, 'doi', 'doi:' + element['doi_string'])
# HDL
elif element['type'] == "HDL":
add_subfield(current_field, 'hdl', 'hdl:' + element['hdl_id'])
# AUTHOR
elif element['type'] == "AUTH":
value = element['auth_txt']
if element['auth_type'] == 'incl':
value = "(%s)" % value
add_subfield(current_field, 'author', value)
elif element['type'] == "QUOTED":
add_subfield(current_field, 'title', element['title'])
elif element['type'] == "ISBN":
add_subfield(current_field, 'isbn', element['ISBN'])
elif element['type'] == "BOOK":
add_subfield(current_field, 'title', element['title'])
elif element['type'] == "PUBLISHER":
add_subfield(current_field, 'publisher', element['publisher'])
elif element['type'] == "YEAR":
add_subfield(current_field, 'year', element['year'])
elif element['type'] == "COLLABORATION":
add_subfield(current_field,
'collaboration',
element['collaboration'])
elif element['type'] == "RECID":
add_subfield(current_field, 'recid', str(element['recid']))
return reference_fields | [
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@param citation_elements: (list) an ordered list of dictionary elements,
with each element corresponding to a found
piece of information from a reference line.
@param line_marker: (string) The line marker for this single reference
line (e.g. [19])
@param raw_ref: (string) The raw string of this line
@return reference_fields: (list) A list of one dictionary containing the
reference elements | [
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] | d70e3787be3c495a3a07d1517b53f81d51c788c7 | https://github.com/inspirehep/refextract/blob/d70e3787be3c495a3a07d1517b53f81d51c788c7/refextract/references/record.py#L71-L161 |
3,749 | inspirehep/refextract | refextract/references/pdf.py | extract_texkeys_from_pdf | def extract_texkeys_from_pdf(pdf_file):
"""
Extract the texkeys from the given PDF file
This is done by looking up the named destinations in the PDF
@param pdf_file: path to a PDF
@return: list of all texkeys found in the PDF
"""
with open(pdf_file, 'rb') as pdf_stream:
try:
pdf = PdfFileReader(pdf_stream, strict=False)
destinations = pdf.getNamedDestinations()
except Exception:
LOGGER.debug(u"PDF: Internal PyPDF2 error, no TeXkeys returned.")
return []
# not all named destinations point to references
refs = [dest for dest in destinations.iteritems()
if re_reference_in_dest.match(dest[0])]
try:
if _destinations_in_two_columns(pdf, refs):
LOGGER.debug(u"PDF: Using two-column layout")
def sortfunc(dest_couple):
return _destination_position(pdf, dest_couple[1])
else:
LOGGER.debug(u"PDF: Using single-column layout")
def sortfunc(dest_couple):
(page, _, ypos, xpos) = _destination_position(
pdf, dest_couple[1])
return (page, ypos, xpos)
refs.sort(key=sortfunc)
# extract the TeXkey from the named destination name
return [re_reference_in_dest.match(destname).group(1)
for (destname, _) in refs]
except Exception:
LOGGER.debug(u"PDF: Impossible to determine layout, no TeXkeys returned")
return [] | python | def extract_texkeys_from_pdf(pdf_file):
"""
Extract the texkeys from the given PDF file
This is done by looking up the named destinations in the PDF
@param pdf_file: path to a PDF
@return: list of all texkeys found in the PDF
"""
with open(pdf_file, 'rb') as pdf_stream:
try:
pdf = PdfFileReader(pdf_stream, strict=False)
destinations = pdf.getNamedDestinations()
except Exception:
LOGGER.debug(u"PDF: Internal PyPDF2 error, no TeXkeys returned.")
return []
# not all named destinations point to references
refs = [dest for dest in destinations.iteritems()
if re_reference_in_dest.match(dest[0])]
try:
if _destinations_in_two_columns(pdf, refs):
LOGGER.debug(u"PDF: Using two-column layout")
def sortfunc(dest_couple):
return _destination_position(pdf, dest_couple[1])
else:
LOGGER.debug(u"PDF: Using single-column layout")
def sortfunc(dest_couple):
(page, _, ypos, xpos) = _destination_position(
pdf, dest_couple[1])
return (page, ypos, xpos)
refs.sort(key=sortfunc)
# extract the TeXkey from the named destination name
return [re_reference_in_dest.match(destname).group(1)
for (destname, _) in refs]
except Exception:
LOGGER.debug(u"PDF: Impossible to determine layout, no TeXkeys returned")
return [] | [
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@param pdf_file: path to a PDF
@return: list of all texkeys found in the PDF | [
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3,750 | inspirehep/refextract | refextract/references/regexs.py | get_reference_line_numeration_marker_patterns | def get_reference_line_numeration_marker_patterns(prefix=u''):
"""Return a list of compiled regex patterns used to search for the marker
of a reference line in a full-text document.
@param prefix: (string) the possible prefix to a reference line
@return: (list) of compiled regex patterns.
"""
title = u""
if type(prefix) in (str, unicode):
title = prefix
g_name = u'(?P<mark>'
g_close = u')'
space = ur'\s*'
patterns = [
# [1]
space + title + g_name + ur'\[\s*(?P<marknum>\d+)\s*\]' + g_close,
# [<letters and numbers]
space + title + g_name +
ur'\[\s*[a-zA-Z:-]+\+?\s?(\d{1,4}[A-Za-z:-]?)?\s*\]' + g_close,
# {1}
space + title + g_name + ur'\{\s*(?P<marknum>\d+)\s*\}' + g_close,
# (1)
space + title + g_name + ur'\<\s*(?P<marknum>\d+)\s*\>' + g_close,
space + title + g_name + ur'\(\s*(?P<marknum>\d+)\s*\)' + g_close,
space + title + g_name + ur'(?P<marknum>\d+)\s*\.(?!\d)' + g_close,
space + title + g_name + ur'(?P<marknum>\d+)\s+' + g_close,
space + title + g_name + ur'(?P<marknum>\d+)\s*\]' + g_close,
# 1]
space + title + g_name + ur'(?P<marknum>\d+)\s*\}' + g_close,
# 1}
space + title + g_name + ur'(?P<marknum>\d+)\s*\)' + g_close,
# 1)
space + title + g_name + ur'(?P<marknum>\d+)\s*\>' + g_close,
# [1.1]
space + title + g_name + ur'\[\s*\d+\.\d+\s*\]' + g_close,
# [ ]
space + title + g_name + ur'\[\s*\]' + g_close,
# *
space + title + g_name + ur'\*' + g_close,
]
return [re.compile(p, re.I | re.UNICODE) for p in patterns] | python | def get_reference_line_numeration_marker_patterns(prefix=u''):
"""Return a list of compiled regex patterns used to search for the marker
of a reference line in a full-text document.
@param prefix: (string) the possible prefix to a reference line
@return: (list) of compiled regex patterns.
"""
title = u""
if type(prefix) in (str, unicode):
title = prefix
g_name = u'(?P<mark>'
g_close = u')'
space = ur'\s*'
patterns = [
# [1]
space + title + g_name + ur'\[\s*(?P<marknum>\d+)\s*\]' + g_close,
# [<letters and numbers]
space + title + g_name +
ur'\[\s*[a-zA-Z:-]+\+?\s?(\d{1,4}[A-Za-z:-]?)?\s*\]' + g_close,
# {1}
space + title + g_name + ur'\{\s*(?P<marknum>\d+)\s*\}' + g_close,
# (1)
space + title + g_name + ur'\<\s*(?P<marknum>\d+)\s*\>' + g_close,
space + title + g_name + ur'\(\s*(?P<marknum>\d+)\s*\)' + g_close,
space + title + g_name + ur'(?P<marknum>\d+)\s*\.(?!\d)' + g_close,
space + title + g_name + ur'(?P<marknum>\d+)\s+' + g_close,
space + title + g_name + ur'(?P<marknum>\d+)\s*\]' + g_close,
# 1]
space + title + g_name + ur'(?P<marknum>\d+)\s*\}' + g_close,
# 1}
space + title + g_name + ur'(?P<marknum>\d+)\s*\)' + g_close,
# 1)
space + title + g_name + ur'(?P<marknum>\d+)\s*\>' + g_close,
# [1.1]
space + title + g_name + ur'\[\s*\d+\.\d+\s*\]' + g_close,
# [ ]
space + title + g_name + ur'\[\s*\]' + g_close,
# *
space + title + g_name + ur'\*' + g_close,
]
return [re.compile(p, re.I | re.UNICODE) for p in patterns] | [
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@return: (list) of compiled regex patterns. | [
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3,751 | inspirehep/refextract | refextract/references/regexs.py | get_post_reference_section_title_patterns | def get_post_reference_section_title_patterns():
"""Return a list of compiled regex patterns used to search for the title
of the section after the reference section in a full-text document.
@return: (list) of compiled regex patterns.
"""
compiled_patterns = []
thead = ur'^\s*([\{\(\<\[]?\s*(\w|\d)\s*[\)\}\>\.\-\]]?\s*)?'
ttail = ur'(\s*\:\s*)?'
numatn = ur'(\d+|\w\b|i{1,3}v?|vi{0,3})[\.\,]{0,2}\b'
roman_numbers = ur'[LVIX]'
patterns = [
# Section titles
thead +
_create_regex_pattern_add_optional_spaces_to_word_characters(
u'appendix') + ttail,
thead +
_create_regex_pattern_add_optional_spaces_to_word_characters(
u'appendices') + ttail,
thead + _create_regex_pattern_add_optional_spaces_to_word_characters(
u'acknowledgement') + ur's?' + ttail,
thead + _create_regex_pattern_add_optional_spaces_to_word_characters(
u'acknowledgment') + ur's?' + ttail,
thead + _create_regex_pattern_add_optional_spaces_to_word_characters(
u'table') + ur'\w?s?\d?' + ttail,
thead +
_create_regex_pattern_add_optional_spaces_to_word_characters(
u'figure') + ur's?' + ttail,
thead + _create_regex_pattern_add_optional_spaces_to_word_characters(
u'list of figure') + ur's?' + ttail,
thead +
_create_regex_pattern_add_optional_spaces_to_word_characters(
u'annex') + ur's?' + ttail,
thead + _create_regex_pattern_add_optional_spaces_to_word_characters(
u'discussion') + ur's?' + ttail,
thead +
_create_regex_pattern_add_optional_spaces_to_word_characters(
u'remercie') + ur's?' + ttail,
thead +
_create_regex_pattern_add_optional_spaces_to_word_characters(
u'index') + ur's?' + ttail,
thead +
_create_regex_pattern_add_optional_spaces_to_word_characters(
u'summary') + ur's?' + ttail,
# Figure nums
ur'^\s*' +
_create_regex_pattern_add_optional_spaces_to_word_characters(
u'figure') + numatn,
ur'^\s*' +
_create_regex_pattern_add_optional_spaces_to_word_characters(
u'fig') + ur'\.\s*' + numatn,
ur'^\s*' +
_create_regex_pattern_add_optional_spaces_to_word_characters(
u'fig') + ur'\.?\s*\d\w?\b',
# Tables
ur'^\s*' +
_create_regex_pattern_add_optional_spaces_to_word_characters(
u'table') + numatn,
ur'^\s*' +
_create_regex_pattern_add_optional_spaces_to_word_characters(
u'tab') + ur'\.\s*' + numatn,
ur'^\s*' +
_create_regex_pattern_add_optional_spaces_to_word_characters(
u'tab') + ur'\.?\s*\d\w?\b',
# Other titles formats
ur'^\s*' + roman_numbers + ur'\.?\s*[Cc]onclusion[\w\s]*$',
ur'^\s*Appendix\s[A-Z]\s*\:\s*[a-zA-Z]+\s*',
]
for p in patterns:
compiled_patterns.append(re.compile(p, re.I | re.UNICODE))
return compiled_patterns | python | def get_post_reference_section_title_patterns():
"""Return a list of compiled regex patterns used to search for the title
of the section after the reference section in a full-text document.
@return: (list) of compiled regex patterns.
"""
compiled_patterns = []
thead = ur'^\s*([\{\(\<\[]?\s*(\w|\d)\s*[\)\}\>\.\-\]]?\s*)?'
ttail = ur'(\s*\:\s*)?'
numatn = ur'(\d+|\w\b|i{1,3}v?|vi{0,3})[\.\,]{0,2}\b'
roman_numbers = ur'[LVIX]'
patterns = [
# Section titles
thead +
_create_regex_pattern_add_optional_spaces_to_word_characters(
u'appendix') + ttail,
thead +
_create_regex_pattern_add_optional_spaces_to_word_characters(
u'appendices') + ttail,
thead + _create_regex_pattern_add_optional_spaces_to_word_characters(
u'acknowledgement') + ur's?' + ttail,
thead + _create_regex_pattern_add_optional_spaces_to_word_characters(
u'acknowledgment') + ur's?' + ttail,
thead + _create_regex_pattern_add_optional_spaces_to_word_characters(
u'table') + ur'\w?s?\d?' + ttail,
thead +
_create_regex_pattern_add_optional_spaces_to_word_characters(
u'figure') + ur's?' + ttail,
thead + _create_regex_pattern_add_optional_spaces_to_word_characters(
u'list of figure') + ur's?' + ttail,
thead +
_create_regex_pattern_add_optional_spaces_to_word_characters(
u'annex') + ur's?' + ttail,
thead + _create_regex_pattern_add_optional_spaces_to_word_characters(
u'discussion') + ur's?' + ttail,
thead +
_create_regex_pattern_add_optional_spaces_to_word_characters(
u'remercie') + ur's?' + ttail,
thead +
_create_regex_pattern_add_optional_spaces_to_word_characters(
u'index') + ur's?' + ttail,
thead +
_create_regex_pattern_add_optional_spaces_to_word_characters(
u'summary') + ur's?' + ttail,
# Figure nums
ur'^\s*' +
_create_regex_pattern_add_optional_spaces_to_word_characters(
u'figure') + numatn,
ur'^\s*' +
_create_regex_pattern_add_optional_spaces_to_word_characters(
u'fig') + ur'\.\s*' + numatn,
ur'^\s*' +
_create_regex_pattern_add_optional_spaces_to_word_characters(
u'fig') + ur'\.?\s*\d\w?\b',
# Tables
ur'^\s*' +
_create_regex_pattern_add_optional_spaces_to_word_characters(
u'table') + numatn,
ur'^\s*' +
_create_regex_pattern_add_optional_spaces_to_word_characters(
u'tab') + ur'\.\s*' + numatn,
ur'^\s*' +
_create_regex_pattern_add_optional_spaces_to_word_characters(
u'tab') + ur'\.?\s*\d\w?\b',
# Other titles formats
ur'^\s*' + roman_numbers + ur'\.?\s*[Cc]onclusion[\w\s]*$',
ur'^\s*Appendix\s[A-Z]\s*\:\s*[a-zA-Z]+\s*',
]
for p in patterns:
compiled_patterns.append(re.compile(p, re.I | re.UNICODE))
return compiled_patterns | [
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3,752 | inspirehep/refextract | refextract/references/regexs.py | get_post_reference_section_keyword_patterns | def get_post_reference_section_keyword_patterns():
"""Return a list of compiled regex patterns used to search for various
keywords that can often be found after, and therefore suggest the end of,
a reference section in a full-text document.
@return: (list) of compiled regex patterns.
"""
compiled_patterns = []
patterns = [u'(' + _create_regex_pattern_add_optional_spaces_to_word_characters(u'prepared') +
ur'|' + _create_regex_pattern_add_optional_spaces_to_word_characters(u'created') +
ur').*(AAS\s*)?\sLATEX',
ur'AAS\s+?LATEX\s+?' +
_create_regex_pattern_add_optional_spaces_to_word_characters(
u'macros') + u'v',
ur'^\s*' + _create_regex_pattern_add_optional_spaces_to_word_characters(
u'This paper has been produced using'),
ur'^\s*' +
_create_regex_pattern_add_optional_spaces_to_word_characters(u'This article was processed by the author using Springer-Verlag') +
u' LATEX']
for p in patterns:
compiled_patterns.append(re.compile(p, re.I | re.UNICODE))
return compiled_patterns | python | def get_post_reference_section_keyword_patterns():
"""Return a list of compiled regex patterns used to search for various
keywords that can often be found after, and therefore suggest the end of,
a reference section in a full-text document.
@return: (list) of compiled regex patterns.
"""
compiled_patterns = []
patterns = [u'(' + _create_regex_pattern_add_optional_spaces_to_word_characters(u'prepared') +
ur'|' + _create_regex_pattern_add_optional_spaces_to_word_characters(u'created') +
ur').*(AAS\s*)?\sLATEX',
ur'AAS\s+?LATEX\s+?' +
_create_regex_pattern_add_optional_spaces_to_word_characters(
u'macros') + u'v',
ur'^\s*' + _create_regex_pattern_add_optional_spaces_to_word_characters(
u'This paper has been produced using'),
ur'^\s*' +
_create_regex_pattern_add_optional_spaces_to_word_characters(u'This article was processed by the author using Springer-Verlag') +
u' LATEX']
for p in patterns:
compiled_patterns.append(re.compile(p, re.I | re.UNICODE))
return compiled_patterns | [
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3,753 | inspirehep/refextract | refextract/references/regexs.py | regex_match_list | def regex_match_list(line, patterns):
"""Given a list of COMPILED regex patters, perform the "re.match" operation
on the line for every pattern.
Break from searching at the first match, returning the match object.
In the case that no patterns match, the None type will be returned.
@param line: (unicode string) to be searched in.
@param patterns: (list) of compiled regex patterns to search "line"
with.
@return: (None or an re.match object), depending upon whether one of
the patterns matched within line or not.
"""
m = None
for ptn in patterns:
m = ptn.match(line)
if m is not None:
break
return m | python | def regex_match_list(line, patterns):
"""Given a list of COMPILED regex patters, perform the "re.match" operation
on the line for every pattern.
Break from searching at the first match, returning the match object.
In the case that no patterns match, the None type will be returned.
@param line: (unicode string) to be searched in.
@param patterns: (list) of compiled regex patterns to search "line"
with.
@return: (None or an re.match object), depending upon whether one of
the patterns matched within line or not.
"""
m = None
for ptn in patterns:
m = ptn.match(line)
if m is not None:
break
return m | [
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3,754 | inspirehep/refextract | refextract/documents/text.py | get_url_repair_patterns | def get_url_repair_patterns():
"""Initialise and return a list of precompiled regexp patterns that
are used to try to re-assemble URLs that have been broken during
a document's conversion to plain-text.
@return: (list) of compiled re regexp patterns used for finding
various broken URLs.
"""
file_types_list = [
ur'h\s*t\s*m', # htm
ur'h\s*t\s*m\s*l', # html
ur't\s*x\s*t' # txt
ur'p\s*h\s*p' # php
ur'a\s*s\s*p\s*' # asp
ur'j\s*s\s*p', # jsp
ur'p\s*y', # py (python)
ur'p\s*l', # pl (perl)
ur'x\s*m\s*l', # xml
ur'j\s*p\s*g', # jpg
ur'g\s*i\s*f' # gif
ur'm\s*o\s*v' # mov
ur's\s*w\s*f' # swf
ur'p\s*d\s*f' # pdf
ur'p\s*s' # ps
ur'd\s*o\s*c', # doc
ur't\s*e\s*x', # tex
ur's\s*h\s*t\s*m\s*l', # shtml
]
pattern_list = [
ur'(h\s*t\s*t\s*p\s*\:\s*\/\s*\/)',
ur'(f\s*t\s*p\s*\:\s*\/\s*\/\s*)',
ur'((http|ftp):\/\/\s*[\w\d])',
ur'((http|ftp):\/\/([\w\d\s\._\-])+?\s*\/)',
ur'((http|ftp):\/\/([\w\d\_\.\-])+\/(([\w\d\_\s\.\-])+?\/)+)',
ur'((http|ftp):\/\/([\w\d\_\.\-])+\/(([\w\d\_\s\.\-])+?\/)*([\w\d\_\s\-]+\.\s?[\w\d]+))',
]
pattern_list = [re.compile(p, re.I | re.UNICODE) for p in pattern_list]
# some possible endings for URLs:
p = ur'((http|ftp):\/\/([\w\d\_\.\-])+\/(([\w\d\_\.\-])+?\/)*([\w\d\_\-]+\.%s))'
for extension in file_types_list:
p_url = re.compile(p % extension, re.I | re.UNICODE)
pattern_list.append(p_url)
# if url last thing in line, and only 10 letters max, concat them
p_url = re.compile(
r'((http|ftp):\/\/([\w\d\_\.\-])+\/(([\w\d\_\.\-])+?\/)*\s*?([\w\d\_\.\-]\s?){1,10}\s*)$',
re.I | re.UNICODE)
pattern_list.append(p_url)
return pattern_list | python | def get_url_repair_patterns():
"""Initialise and return a list of precompiled regexp patterns that
are used to try to re-assemble URLs that have been broken during
a document's conversion to plain-text.
@return: (list) of compiled re regexp patterns used for finding
various broken URLs.
"""
file_types_list = [
ur'h\s*t\s*m', # htm
ur'h\s*t\s*m\s*l', # html
ur't\s*x\s*t' # txt
ur'p\s*h\s*p' # php
ur'a\s*s\s*p\s*' # asp
ur'j\s*s\s*p', # jsp
ur'p\s*y', # py (python)
ur'p\s*l', # pl (perl)
ur'x\s*m\s*l', # xml
ur'j\s*p\s*g', # jpg
ur'g\s*i\s*f' # gif
ur'm\s*o\s*v' # mov
ur's\s*w\s*f' # swf
ur'p\s*d\s*f' # pdf
ur'p\s*s' # ps
ur'd\s*o\s*c', # doc
ur't\s*e\s*x', # tex
ur's\s*h\s*t\s*m\s*l', # shtml
]
pattern_list = [
ur'(h\s*t\s*t\s*p\s*\:\s*\/\s*\/)',
ur'(f\s*t\s*p\s*\:\s*\/\s*\/\s*)',
ur'((http|ftp):\/\/\s*[\w\d])',
ur'((http|ftp):\/\/([\w\d\s\._\-])+?\s*\/)',
ur'((http|ftp):\/\/([\w\d\_\.\-])+\/(([\w\d\_\s\.\-])+?\/)+)',
ur'((http|ftp):\/\/([\w\d\_\.\-])+\/(([\w\d\_\s\.\-])+?\/)*([\w\d\_\s\-]+\.\s?[\w\d]+))',
]
pattern_list = [re.compile(p, re.I | re.UNICODE) for p in pattern_list]
# some possible endings for URLs:
p = ur'((http|ftp):\/\/([\w\d\_\.\-])+\/(([\w\d\_\.\-])+?\/)*([\w\d\_\-]+\.%s))'
for extension in file_types_list:
p_url = re.compile(p % extension, re.I | re.UNICODE)
pattern_list.append(p_url)
# if url last thing in line, and only 10 letters max, concat them
p_url = re.compile(
r'((http|ftp):\/\/([\w\d\_\.\-])+\/(([\w\d\_\.\-])+?\/)*\s*?([\w\d\_\.\-]\s?){1,10}\s*)$',
re.I | re.UNICODE)
pattern_list.append(p_url)
return pattern_list | [
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3,755 | inspirehep/refextract | refextract/documents/text.py | join_lines | def join_lines(line1, line2):
"""Join 2 lines of text
>>> join_lines('abc', 'de')
'abcde'
>>> join_lines('a-', 'b')
'ab'
"""
if line1 == u"":
pass
elif line1[-1] == u'-':
# hyphenated word at the end of the
# line - don't add in a space and remove hyphen
line1 = line1[:-1]
elif line1[-1] != u' ':
# no space at the end of this
# line, add in a space
line1 = line1 + u' '
return line1 + line2 | python | def join_lines(line1, line2):
"""Join 2 lines of text
>>> join_lines('abc', 'de')
'abcde'
>>> join_lines('a-', 'b')
'ab'
"""
if line1 == u"":
pass
elif line1[-1] == u'-':
# hyphenated word at the end of the
# line - don't add in a space and remove hyphen
line1 = line1[:-1]
elif line1[-1] != u' ':
# no space at the end of this
# line, add in a space
line1 = line1 + u' '
return line1 + line2 | [
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3,756 | inspirehep/refextract | refextract/documents/text.py | repair_broken_urls | def repair_broken_urls(line):
"""Attempt to repair broken URLs in a line of text.
E.g.: remove spaces from the middle of a URL; something like that.
@param line: (string) the line in which to check for broken URLs.
@return: (string) the line after any broken URLs have been repaired.
"""
def _chop_spaces_in_url_match(m):
"""Suppresses spaces in a matched URL."""
return m.group(1).replace(" ", "")
for ptn in re_list_url_repair_patterns:
line = ptn.sub(_chop_spaces_in_url_match, line)
return line | python | def repair_broken_urls(line):
"""Attempt to repair broken URLs in a line of text.
E.g.: remove spaces from the middle of a URL; something like that.
@param line: (string) the line in which to check for broken URLs.
@return: (string) the line after any broken URLs have been repaired.
"""
def _chop_spaces_in_url_match(m):
"""Suppresses spaces in a matched URL."""
return m.group(1).replace(" ", "")
for ptn in re_list_url_repair_patterns:
line = ptn.sub(_chop_spaces_in_url_match, line)
return line | [
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3,757 | inspirehep/refextract | refextract/documents/text.py | remove_and_record_multiple_spaces_in_line | def remove_and_record_multiple_spaces_in_line(line):
"""For a given string, locate all ocurrences of multiple spaces
together in the line, record the number of spaces found at each
position, and replace them with a single space.
@param line: (string) the text line to be processed for multiple
spaces.
@return: (tuple) countaining a dictionary and a string. The
dictionary contains information about the number of spaces removed
at given positions in the line. For example, if 3 spaces were
removed from the line at index '22', the dictionary would be set
as follows: { 22 : 3 }
The string that is also returned in this tuple is the line after
multiple-space ocurrences have replaced with single spaces.
"""
removed_spaces = {}
# get a collection of match objects for all instances of
# multiple-spaces found in the line:
multispace_matches = re_group_captured_multiple_space.finditer(line)
# record the number of spaces found at each match position:
for multispace in multispace_matches:
removed_spaces[multispace.start()] = \
(multispace.end() - multispace.start() - 1)
# now remove the multiple-spaces from the line, replacing with a
# single space at each position:
line = re_group_captured_multiple_space.sub(u' ', line)
return (removed_spaces, line) | python | def remove_and_record_multiple_spaces_in_line(line):
"""For a given string, locate all ocurrences of multiple spaces
together in the line, record the number of spaces found at each
position, and replace them with a single space.
@param line: (string) the text line to be processed for multiple
spaces.
@return: (tuple) countaining a dictionary and a string. The
dictionary contains information about the number of spaces removed
at given positions in the line. For example, if 3 spaces were
removed from the line at index '22', the dictionary would be set
as follows: { 22 : 3 }
The string that is also returned in this tuple is the line after
multiple-space ocurrences have replaced with single spaces.
"""
removed_spaces = {}
# get a collection of match objects for all instances of
# multiple-spaces found in the line:
multispace_matches = re_group_captured_multiple_space.finditer(line)
# record the number of spaces found at each match position:
for multispace in multispace_matches:
removed_spaces[multispace.start()] = \
(multispace.end() - multispace.start() - 1)
# now remove the multiple-spaces from the line, replacing with a
# single space at each position:
line = re_group_captured_multiple_space.sub(u' ', line)
return (removed_spaces, line) | [
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3,758 | inspirehep/refextract | refextract/documents/text.py | remove_page_boundary_lines | def remove_page_boundary_lines(docbody):
"""Try to locate page breaks, headers and footers within a document body,
and remove the array cells at which they are found.
@param docbody: (list) of strings, each string being a line in the
document's body.
@return: (list) of strings. The document body, hopefully with page-
breaks, headers and footers removed. Each string in the list once more
represents a line in the document.
"""
number_head_lines = number_foot_lines = 0
# Make sure document not just full of whitespace:
if not document_contains_text(docbody):
# document contains only whitespace - cannot safely
# strip headers/footers
return docbody
# Get list of index posns of pagebreaks in document:
page_break_posns = get_page_break_positions(docbody)
# Get num lines making up each header if poss:
number_head_lines = get_number_header_lines(docbody, page_break_posns)
# Get num lines making up each footer if poss:
number_foot_lines = get_number_footer_lines(docbody, page_break_posns)
# Remove pagebreaks,headers,footers:
docbody = strip_headers_footers_pagebreaks(docbody,
page_break_posns,
number_head_lines,
number_foot_lines)
return docbody | python | def remove_page_boundary_lines(docbody):
"""Try to locate page breaks, headers and footers within a document body,
and remove the array cells at which they are found.
@param docbody: (list) of strings, each string being a line in the
document's body.
@return: (list) of strings. The document body, hopefully with page-
breaks, headers and footers removed. Each string in the list once more
represents a line in the document.
"""
number_head_lines = number_foot_lines = 0
# Make sure document not just full of whitespace:
if not document_contains_text(docbody):
# document contains only whitespace - cannot safely
# strip headers/footers
return docbody
# Get list of index posns of pagebreaks in document:
page_break_posns = get_page_break_positions(docbody)
# Get num lines making up each header if poss:
number_head_lines = get_number_header_lines(docbody, page_break_posns)
# Get num lines making up each footer if poss:
number_foot_lines = get_number_footer_lines(docbody, page_break_posns)
# Remove pagebreaks,headers,footers:
docbody = strip_headers_footers_pagebreaks(docbody,
page_break_posns,
number_head_lines,
number_foot_lines)
return docbody | [
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3,759 | inspirehep/refextract | refextract/documents/text.py | get_page_break_positions | def get_page_break_positions(docbody):
"""Locate page breaks in the list of document lines and create a list
positions in the document body list.
@param docbody: (list) of strings - each string is a line in the
document.
@return: (list) of integer positions, whereby each integer represents the
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page_break_posns = []
p_break = re.compile(ur'^\s*\f\s*$', re.UNICODE)
num_document_lines = len(docbody)
for i in xrange(num_document_lines):
if p_break.match(docbody[i]) is not None:
page_break_posns.append(i)
return page_break_posns | python | def get_page_break_positions(docbody):
"""Locate page breaks in the list of document lines and create a list
positions in the document body list.
@param docbody: (list) of strings - each string is a line in the
document.
@return: (list) of integer positions, whereby each integer represents the
position (in the document body) of a page-break.
"""
page_break_posns = []
p_break = re.compile(ur'^\s*\f\s*$', re.UNICODE)
num_document_lines = len(docbody)
for i in xrange(num_document_lines):
if p_break.match(docbody[i]) is not None:
page_break_posns.append(i)
return page_break_posns | [
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3,760 | inspirehep/refextract | refextract/documents/text.py | get_number_header_lines | def get_number_header_lines(docbody, page_break_posns):
"""Try to guess the number of header lines each page of a document has.
The positions of the page breaks in the document are used to try to guess
the number of header lines.
@param docbody: (list) of strings - each string being a line in the
document
@param page_break_posns: (list) of integers - each integer is the
position of a page break in the document.
@return: (int) the number of lines that make up the header of each page.
"""
remaining_breaks = len(page_break_posns) - 1
num_header_lines = empty_line = 0
# pattern to search for a word in a line:
p_wordSearch = re.compile(ur'([A-Za-z0-9-]+)', re.UNICODE)
if remaining_breaks > 2:
if remaining_breaks > 3:
# Only check odd page headers
next_head = 2
else:
# Check headers on each page
next_head = 1
keep_checking = 1
while keep_checking:
cur_break = 1
if docbody[(page_break_posns[cur_break] +
num_header_lines + 1)].isspace():
# this is a blank line
empty_line = 1
if (page_break_posns[cur_break] + num_header_lines + 1) \
== (page_break_posns[(cur_break + 1)]):
# Have reached next page-break: document has no
# body - only head/footers!
keep_checking = 0
grps_headLineWords = \
p_wordSearch.findall(docbody[(page_break_posns[cur_break] +
num_header_lines + 1)])
cur_break = cur_break + next_head
while (cur_break < remaining_breaks) and keep_checking:
lineno = page_break_posns[cur_break] + num_header_lines + 1
if lineno >= len(docbody):
keep_checking = 0
break
grps_thisLineWords = \
p_wordSearch.findall(docbody[lineno])
if empty_line:
if len(grps_thisLineWords) != 0:
# This line should be empty, but isn't
keep_checking = 0
else:
if (len(grps_thisLineWords) == 0) or \
(len(grps_headLineWords) != len(grps_thisLineWords)):
# Not same num 'words' as equivilent line
# in 1st header:
keep_checking = 0
else:
keep_checking = \
check_boundary_lines_similar(grps_headLineWords,
grps_thisLineWords)
# Update cur_break for nxt line to check
cur_break = cur_break + next_head
if keep_checking:
# Line is a header line: check next
num_header_lines = num_header_lines + 1
empty_line = 0
return num_header_lines | python | def get_number_header_lines(docbody, page_break_posns):
"""Try to guess the number of header lines each page of a document has.
The positions of the page breaks in the document are used to try to guess
the number of header lines.
@param docbody: (list) of strings - each string being a line in the
document
@param page_break_posns: (list) of integers - each integer is the
position of a page break in the document.
@return: (int) the number of lines that make up the header of each page.
"""
remaining_breaks = len(page_break_posns) - 1
num_header_lines = empty_line = 0
# pattern to search for a word in a line:
p_wordSearch = re.compile(ur'([A-Za-z0-9-]+)', re.UNICODE)
if remaining_breaks > 2:
if remaining_breaks > 3:
# Only check odd page headers
next_head = 2
else:
# Check headers on each page
next_head = 1
keep_checking = 1
while keep_checking:
cur_break = 1
if docbody[(page_break_posns[cur_break] +
num_header_lines + 1)].isspace():
# this is a blank line
empty_line = 1
if (page_break_posns[cur_break] + num_header_lines + 1) \
== (page_break_posns[(cur_break + 1)]):
# Have reached next page-break: document has no
# body - only head/footers!
keep_checking = 0
grps_headLineWords = \
p_wordSearch.findall(docbody[(page_break_posns[cur_break] +
num_header_lines + 1)])
cur_break = cur_break + next_head
while (cur_break < remaining_breaks) and keep_checking:
lineno = page_break_posns[cur_break] + num_header_lines + 1
if lineno >= len(docbody):
keep_checking = 0
break
grps_thisLineWords = \
p_wordSearch.findall(docbody[lineno])
if empty_line:
if len(grps_thisLineWords) != 0:
# This line should be empty, but isn't
keep_checking = 0
else:
if (len(grps_thisLineWords) == 0) or \
(len(grps_headLineWords) != len(grps_thisLineWords)):
# Not same num 'words' as equivilent line
# in 1st header:
keep_checking = 0
else:
keep_checking = \
check_boundary_lines_similar(grps_headLineWords,
grps_thisLineWords)
# Update cur_break for nxt line to check
cur_break = cur_break + next_head
if keep_checking:
# Line is a header line: check next
num_header_lines = num_header_lines + 1
empty_line = 0
return num_header_lines | [
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@param docbody: (list) of strings - each string being a line in the
document
@param page_break_posns: (list) of integers - each integer is the
position of a page break in the document.
@return: (int) the number of lines that make up the header of each page. | [
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3,761 | inspirehep/refextract | refextract/documents/text.py | get_number_footer_lines | def get_number_footer_lines(docbody, page_break_posns):
"""Try to guess the number of footer lines each page of a document has.
The positions of the page breaks in the document are used to try to guess
the number of footer lines.
@param docbody: (list) of strings - each string being a line in the
document
@param page_break_posns: (list) of integers - each integer is the
position of a page break in the document.
@return: (int) the number of lines that make up the footer of each page.
"""
num_breaks = len(page_break_posns)
num_footer_lines = 0
empty_line = 0
keep_checking = 1
p_wordSearch = re.compile(unicode(r'([A-Za-z0-9-]+)'), re.UNICODE)
if num_breaks > 2:
while keep_checking:
cur_break = 1
if page_break_posns[cur_break] - num_footer_lines - 1 < 0 or \
page_break_posns[cur_break] - num_footer_lines - 1 > \
len(docbody) - 1:
# Be sure that the docbody list boundary wasn't overstepped:
break
if docbody[(page_break_posns[cur_break] -
num_footer_lines - 1)].isspace():
empty_line = 1
grps_headLineWords = \
p_wordSearch.findall(docbody[(page_break_posns[cur_break] -
num_footer_lines - 1)])
cur_break = cur_break + 1
while (cur_break < num_breaks) and keep_checking:
grps_thisLineWords = \
p_wordSearch.findall(docbody[(page_break_posns[cur_break] -
num_footer_lines - 1)])
if empty_line:
if len(grps_thisLineWords) != 0:
# this line should be empty, but isn't
keep_checking = 0
else:
if (len(grps_thisLineWords) == 0) or \
(len(grps_headLineWords) != len(grps_thisLineWords)):
# Not same num 'words' as equivilent line
# in 1st footer:
keep_checking = 0
else:
keep_checking = \
check_boundary_lines_similar(grps_headLineWords,
grps_thisLineWords)
# Update cur_break for nxt line to check
cur_break = cur_break + 1
if keep_checking:
# Line is a footer line: check next
num_footer_lines = num_footer_lines + 1
empty_line = 0
return num_footer_lines | python | def get_number_footer_lines(docbody, page_break_posns):
"""Try to guess the number of footer lines each page of a document has.
The positions of the page breaks in the document are used to try to guess
the number of footer lines.
@param docbody: (list) of strings - each string being a line in the
document
@param page_break_posns: (list) of integers - each integer is the
position of a page break in the document.
@return: (int) the number of lines that make up the footer of each page.
"""
num_breaks = len(page_break_posns)
num_footer_lines = 0
empty_line = 0
keep_checking = 1
p_wordSearch = re.compile(unicode(r'([A-Za-z0-9-]+)'), re.UNICODE)
if num_breaks > 2:
while keep_checking:
cur_break = 1
if page_break_posns[cur_break] - num_footer_lines - 1 < 0 or \
page_break_posns[cur_break] - num_footer_lines - 1 > \
len(docbody) - 1:
# Be sure that the docbody list boundary wasn't overstepped:
break
if docbody[(page_break_posns[cur_break] -
num_footer_lines - 1)].isspace():
empty_line = 1
grps_headLineWords = \
p_wordSearch.findall(docbody[(page_break_posns[cur_break] -
num_footer_lines - 1)])
cur_break = cur_break + 1
while (cur_break < num_breaks) and keep_checking:
grps_thisLineWords = \
p_wordSearch.findall(docbody[(page_break_posns[cur_break] -
num_footer_lines - 1)])
if empty_line:
if len(grps_thisLineWords) != 0:
# this line should be empty, but isn't
keep_checking = 0
else:
if (len(grps_thisLineWords) == 0) or \
(len(grps_headLineWords) != len(grps_thisLineWords)):
# Not same num 'words' as equivilent line
# in 1st footer:
keep_checking = 0
else:
keep_checking = \
check_boundary_lines_similar(grps_headLineWords,
grps_thisLineWords)
# Update cur_break for nxt line to check
cur_break = cur_break + 1
if keep_checking:
# Line is a footer line: check next
num_footer_lines = num_footer_lines + 1
empty_line = 0
return num_footer_lines | [
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@param docbody: (list) of strings - each string being a line in the
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@param page_break_posns: (list) of integers - each integer is the
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@return: (int) the number of lines that make up the footer of each page. | [
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3,762 | inspirehep/refextract | refextract/documents/text.py | strip_headers_footers_pagebreaks | def strip_headers_footers_pagebreaks(docbody,
page_break_posns,
num_head_lines,
num_foot_lines):
"""Remove page-break lines, header lines, and footer lines from the
document.
@param docbody: (list) of strings, whereby each string in the list is a
line in the document.
@param page_break_posns: (list) of integers, whereby each integer
represents the index in docbody at which a page-break is found.
@param num_head_lines: (int) the number of header lines each page in the
document has.
@param num_foot_lines: (int) the number of footer lines each page in the
document has.
@return: (list) of strings - the document body after the headers,
footers, and page-break lines have been stripped from the list.
"""
num_breaks = len(page_break_posns)
page_lens = []
for x in xrange(0, num_breaks):
if x < num_breaks - 1:
page_lens.append(page_break_posns[x + 1] - page_break_posns[x])
page_lens.sort()
if (len(page_lens) > 0) and \
(num_head_lines + num_foot_lines + 1 < page_lens[0]):
# Safe to chop hdrs & ftrs
page_break_posns.reverse()
first = 1
for i in xrange(0, len(page_break_posns)):
# Unless this is the last page break, chop headers
if not first:
for dummy in xrange(1, num_head_lines + 1):
docbody[page_break_posns[i] +
1:page_break_posns[i] + 2] = []
else:
first = 0
# Chop page break itself
docbody[page_break_posns[i]:page_break_posns[i] + 1] = []
# Chop footers (unless this is the first page break)
if i != len(page_break_posns) - 1:
for dummy in xrange(1, num_foot_lines + 1):
docbody[page_break_posns[i] -
num_foot_lines:page_break_posns[i] -
num_foot_lines + 1] = []
return docbody | python | def strip_headers_footers_pagebreaks(docbody,
page_break_posns,
num_head_lines,
num_foot_lines):
"""Remove page-break lines, header lines, and footer lines from the
document.
@param docbody: (list) of strings, whereby each string in the list is a
line in the document.
@param page_break_posns: (list) of integers, whereby each integer
represents the index in docbody at which a page-break is found.
@param num_head_lines: (int) the number of header lines each page in the
document has.
@param num_foot_lines: (int) the number of footer lines each page in the
document has.
@return: (list) of strings - the document body after the headers,
footers, and page-break lines have been stripped from the list.
"""
num_breaks = len(page_break_posns)
page_lens = []
for x in xrange(0, num_breaks):
if x < num_breaks - 1:
page_lens.append(page_break_posns[x + 1] - page_break_posns[x])
page_lens.sort()
if (len(page_lens) > 0) and \
(num_head_lines + num_foot_lines + 1 < page_lens[0]):
# Safe to chop hdrs & ftrs
page_break_posns.reverse()
first = 1
for i in xrange(0, len(page_break_posns)):
# Unless this is the last page break, chop headers
if not first:
for dummy in xrange(1, num_head_lines + 1):
docbody[page_break_posns[i] +
1:page_break_posns[i] + 2] = []
else:
first = 0
# Chop page break itself
docbody[page_break_posns[i]:page_break_posns[i] + 1] = []
# Chop footers (unless this is the first page break)
if i != len(page_break_posns) - 1:
for dummy in xrange(1, num_foot_lines + 1):
docbody[page_break_posns[i] -
num_foot_lines:page_break_posns[i] -
num_foot_lines + 1] = []
return docbody | [
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@param num_foot_lines: (int) the number of footer lines each page in the
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3,763 | inspirehep/refextract | refextract/documents/text.py | check_boundary_lines_similar | def check_boundary_lines_similar(l_1, l_2):
"""Compare two lists to see if their elements are roughly the same.
@param l_1: (list) of strings.
@param l_2: (list) of strings.
@return: (int) 1/0.
"""
num_matches = 0
if (type(l_1) != list) or (type(l_2) != list) or (len(l_1) != len(l_2)):
# these 'boundaries' are not similar
return 0
num_elements = len(l_1)
for i in xrange(0, num_elements):
if l_1[i].isdigit() and l_2[i].isdigit():
# both lines are integers
num_matches += 1
else:
l1_str = l_1[i].lower()
l2_str = l_2[i].lower()
if (l1_str[0] == l2_str[0]) and \
(l1_str[len(l1_str) - 1] == l2_str[len(l2_str) - 1]):
num_matches = num_matches + 1
if (len(l_1) == 0) or (float(num_matches) / float(len(l_1)) < 0.9):
return 0
else:
return 1 | python | def check_boundary_lines_similar(l_1, l_2):
"""Compare two lists to see if their elements are roughly the same.
@param l_1: (list) of strings.
@param l_2: (list) of strings.
@return: (int) 1/0.
"""
num_matches = 0
if (type(l_1) != list) or (type(l_2) != list) or (len(l_1) != len(l_2)):
# these 'boundaries' are not similar
return 0
num_elements = len(l_1)
for i in xrange(0, num_elements):
if l_1[i].isdigit() and l_2[i].isdigit():
# both lines are integers
num_matches += 1
else:
l1_str = l_1[i].lower()
l2_str = l_2[i].lower()
if (l1_str[0] == l2_str[0]) and \
(l1_str[len(l1_str) - 1] == l2_str[len(l2_str) - 1]):
num_matches = num_matches + 1
if (len(l_1) == 0) or (float(num_matches) / float(len(l_1)) < 0.9):
return 0
else:
return 1 | [
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3,764 | inspirehep/refextract | refextract/references/kbs.py | make_cache_key | def make_cache_key(custom_kbs_files=None):
"""Create cache key for kbs caches instances
This function generates a unique key for a given set of arguments.
The files dictionary is transformed like this:
{'journal': '/var/journal.kb', 'books': '/var/books.kb'}
to
"journal=/var/journal.kb;books=/var/books.kb"
Then _inspire is appended if we are an INSPIRE site.
"""
if custom_kbs_files:
serialized_args = ('%s=%s' % v for v in iteritems(custom_kbs_files))
serialized_args = ';'.join(serialized_args)
else:
serialized_args = "default"
cache_key = md5(serialized_args).digest()
return cache_key | python | def make_cache_key(custom_kbs_files=None):
"""Create cache key for kbs caches instances
This function generates a unique key for a given set of arguments.
The files dictionary is transformed like this:
{'journal': '/var/journal.kb', 'books': '/var/books.kb'}
to
"journal=/var/journal.kb;books=/var/books.kb"
Then _inspire is appended if we are an INSPIRE site.
"""
if custom_kbs_files:
serialized_args = ('%s=%s' % v for v in iteritems(custom_kbs_files))
serialized_args = ';'.join(serialized_args)
else:
serialized_args = "default"
cache_key = md5(serialized_args).digest()
return cache_key | [
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3,765 | inspirehep/refextract | refextract/references/kbs.py | create_institute_numeration_group_regexp_pattern | def create_institute_numeration_group_regexp_pattern(patterns):
"""Using a list of regexp patterns for recognising numeration patterns
for institute preprint references, ordered by length - longest to
shortest - create a grouped 'OR' or of these patterns, ready to be
used in a bigger regexp.
@param patterns: (list) of strings. All of the numeration regexp
patterns for recognising an institute's preprint reference styles.
@return: (string) a grouped 'OR' regexp pattern of the numeration
patterns. E.g.:
(?P<num>[12]\d{3} \d\d\d|\d\d \d\d\d|[A-Za-z] \d\d\d)
"""
patterns_list = [institute_num_pattern_to_regex(p[1]) for p in patterns]
grouped_numeration_pattern = u"(?P<numn>%s)" % u'|'.join(patterns_list)
return grouped_numeration_pattern | python | def create_institute_numeration_group_regexp_pattern(patterns):
"""Using a list of regexp patterns for recognising numeration patterns
for institute preprint references, ordered by length - longest to
shortest - create a grouped 'OR' or of these patterns, ready to be
used in a bigger regexp.
@param patterns: (list) of strings. All of the numeration regexp
patterns for recognising an institute's preprint reference styles.
@return: (string) a grouped 'OR' regexp pattern of the numeration
patterns. E.g.:
(?P<num>[12]\d{3} \d\d\d|\d\d \d\d\d|[A-Za-z] \d\d\d)
"""
patterns_list = [institute_num_pattern_to_regex(p[1]) for p in patterns]
grouped_numeration_pattern = u"(?P<numn>%s)" % u'|'.join(patterns_list)
return grouped_numeration_pattern | [
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3,766 | inspirehep/refextract | refextract/references/kbs.py | build_reportnum_kb | def build_reportnum_kb(fpath):
"""Given the path to a knowledge base file containing the details
of institutes and the patterns that their preprint report
numbering schemes take, create a dictionary of regexp search
patterns to recognise these preprint references in reference
lines, and a dictionary of replacements for non-standard preprint
categories in these references.
The knowledge base file should consist only of lines that take one
of the following 3 formats:
#####Institute Name####
(the name of the institute to which the preprint reference patterns
belong, e.g. '#####LANL#####', surrounded by 5 # on either side.)
<pattern>
(numeration patterns for an institute's preprints, surrounded by
< and >.)
seek-term --- replace-term
(i.e. a seek phrase on the left hand side, a replace phrase on the
right hand side, with the two phrases being separated by 3 hyphens.)
E.g.:
ASTRO PH ---astro-ph
The left-hand side term is a non-standard version of the preprint
reference category; the right-hand side term is the standard version.
If the KB file cannot be read from, or an unexpected line is
encountered in the KB, an error message is output to standard error
and execution is halted with an error-code 0.
@param fpath: (string) the path to the knowledge base file.
@return: (tuple) containing 2 dictionaries. The first contains regexp
search patterns used to identify preprint references in a line. This
dictionary is keyed by a tuple containing the line number of the
pattern in the KB and the non-standard category string.
E.g.: (3, 'ASTRO PH').
The second dictionary contains the standardised category string,
and is keyed by the non-standard category string. E.g.: 'astro-ph'.
"""
def _add_institute_preprint_patterns(preprint_classifications,
preprint_numeration_ptns,
preprint_reference_search_regexp_patterns,
standardised_preprint_reference_categories,
kb_line_num):
"""For a list of preprint category strings and preprint numeration
patterns for a given institute, create the regexp patterns for
each of the preprint types. Add the regexp patterns to the
dictionary of search patterns
(preprint_reference_search_regexp_patterns), keyed by the line
number of the institute in the KB, and the preprint category
search string. Also add the standardised preprint category string
to another dictionary, keyed by the line number of its position
in the KB and its non-standardised version.
@param preprint_classifications: (list) of tuples whereby each tuple
contains a preprint category search string and the line number of
the name of institute to which it belongs in the KB.
E.g.: (45, 'ASTRO PH').
@param preprint_numeration_ptns: (list) of preprint reference
numeration search patterns (strings)
@param preprint_reference_search_regexp_patterns: (dictionary) of
regexp patterns used to search in document lines.
@param standardised_preprint_reference_categories: (dictionary)
containing the standardised strings for preprint reference
categories. (E.g. 'astro-ph'.)
@param kb_line_num: (integer) - the line number int the KB at
which a given institute name was found.
@return: None
"""
if preprint_classifications and preprint_numeration_ptns:
# the previous institute had both numeration styles and categories
# for preprint references.
# build regexps and add them for this institute:
# First, order the numeration styles by line-length, and build a
# grouped regexp for recognising numeration:
ordered_patterns = \
order_reportnum_patterns_bylen(preprint_numeration_ptns)
# create a grouped regexp for numeration part of
# preprint reference:
numeration_regexp = \
create_institute_numeration_group_regexp_pattern(
ordered_patterns)
# for each "classification" part of preprint references, create a
# complete regex:
# will be in the style "(categ)-(numatn1|numatn2|numatn3|...)"
for classification in preprint_classifications:
search_pattern_str = ur'(?:^|[^a-zA-Z0-9\/\.\-])([\[\(]?(?P<categ>' \
+ classification[0].strip() + u')' \
+ numeration_regexp + ur'[\]\)]?)'
re_search_pattern = re.compile(search_pattern_str,
re.UNICODE)
preprint_reference_search_regexp_patterns[(kb_line_num,
classification[0])] =\
re_search_pattern
standardised_preprint_reference_categories[(kb_line_num,
classification[0])] =\
classification[1]
preprint_reference_search_regexp_patterns = {} # a dictionary of patterns
# used to recognise
# categories of preprints
# as used by various
# institutes
standardised_preprint_reference_categories = {} # dictionary of
# standardised category
# strings for preprint cats
current_institute_preprint_classifications = [] # list of tuples containing
# preprint categories in
# their raw & standardised
# forms, as read from KB
current_institute_numerations = [] # list of preprint
# numeration patterns, as
# read from the KB
# pattern to recognise an institute name line in the KB
re_institute_name = re.compile(ur'^\*{5}\s*(.+)\s*\*{5}$', re.UNICODE)
# pattern to recognise an institute preprint categ line in the KB
re_preprint_classification = \
re.compile(ur'^\s*(\w.*)\s*---\s*(\w.*)\s*$', re.UNICODE)
# pattern to recognise a preprint numeration-style line in KB
re_numeration_pattern = re.compile(ur'^\<(.+)\>$', re.UNICODE)
kb_line_num = 0 # when making the dictionary of patterns, which is
# keyed by the category search string, this counter
# will ensure that patterns in the dictionary are not
# overwritten if 2 institutes have the same category
# styles.
with file_resolving(fpath) as fh:
for rawline in fh:
if rawline.startswith('#'):
continue
kb_line_num += 1
m_institute_name = re_institute_name.search(rawline)
if m_institute_name:
# This KB line is the name of an institute
# append the last institute's pattern list to the list of
# institutes:
_add_institute_preprint_patterns(current_institute_preprint_classifications,
current_institute_numerations,
preprint_reference_search_regexp_patterns,
standardised_preprint_reference_categories,
kb_line_num)
# Now start a new dictionary to contain the search patterns
# for this institute:
current_institute_preprint_classifications = []
current_institute_numerations = []
# move on to the next line
continue
m_preprint_classification = \
re_preprint_classification.search(rawline)
if m_preprint_classification:
# This KB line contains a preprint classification for
# the current institute
try:
current_institute_preprint_classifications.append((m_preprint_classification.group(1),
m_preprint_classification.group(2)))
except (AttributeError, NameError):
# didn't match this line correctly - skip it
pass
# move on to the next line
continue
m_numeration_pattern = re_numeration_pattern.search(rawline)
if m_numeration_pattern:
# This KB line contains a preprint item numeration pattern
# for the current institute
try:
current_institute_numerations.append(
m_numeration_pattern.group(1))
except (AttributeError, NameError):
# didn't match the numeration pattern correctly - skip it
pass
continue
_add_institute_preprint_patterns(current_institute_preprint_classifications,
current_institute_numerations,
preprint_reference_search_regexp_patterns,
standardised_preprint_reference_categories,
kb_line_num)
# return the preprint reference patterns and the replacement strings
# for non-standard categ-strings:
return (preprint_reference_search_regexp_patterns,
standardised_preprint_reference_categories) | python | def build_reportnum_kb(fpath):
"""Given the path to a knowledge base file containing the details
of institutes and the patterns that their preprint report
numbering schemes take, create a dictionary of regexp search
patterns to recognise these preprint references in reference
lines, and a dictionary of replacements for non-standard preprint
categories in these references.
The knowledge base file should consist only of lines that take one
of the following 3 formats:
#####Institute Name####
(the name of the institute to which the preprint reference patterns
belong, e.g. '#####LANL#####', surrounded by 5 # on either side.)
<pattern>
(numeration patterns for an institute's preprints, surrounded by
< and >.)
seek-term --- replace-term
(i.e. a seek phrase on the left hand side, a replace phrase on the
right hand side, with the two phrases being separated by 3 hyphens.)
E.g.:
ASTRO PH ---astro-ph
The left-hand side term is a non-standard version of the preprint
reference category; the right-hand side term is the standard version.
If the KB file cannot be read from, or an unexpected line is
encountered in the KB, an error message is output to standard error
and execution is halted with an error-code 0.
@param fpath: (string) the path to the knowledge base file.
@return: (tuple) containing 2 dictionaries. The first contains regexp
search patterns used to identify preprint references in a line. This
dictionary is keyed by a tuple containing the line number of the
pattern in the KB and the non-standard category string.
E.g.: (3, 'ASTRO PH').
The second dictionary contains the standardised category string,
and is keyed by the non-standard category string. E.g.: 'astro-ph'.
"""
def _add_institute_preprint_patterns(preprint_classifications,
preprint_numeration_ptns,
preprint_reference_search_regexp_patterns,
standardised_preprint_reference_categories,
kb_line_num):
"""For a list of preprint category strings and preprint numeration
patterns for a given institute, create the regexp patterns for
each of the preprint types. Add the regexp patterns to the
dictionary of search patterns
(preprint_reference_search_regexp_patterns), keyed by the line
number of the institute in the KB, and the preprint category
search string. Also add the standardised preprint category string
to another dictionary, keyed by the line number of its position
in the KB and its non-standardised version.
@param preprint_classifications: (list) of tuples whereby each tuple
contains a preprint category search string and the line number of
the name of institute to which it belongs in the KB.
E.g.: (45, 'ASTRO PH').
@param preprint_numeration_ptns: (list) of preprint reference
numeration search patterns (strings)
@param preprint_reference_search_regexp_patterns: (dictionary) of
regexp patterns used to search in document lines.
@param standardised_preprint_reference_categories: (dictionary)
containing the standardised strings for preprint reference
categories. (E.g. 'astro-ph'.)
@param kb_line_num: (integer) - the line number int the KB at
which a given institute name was found.
@return: None
"""
if preprint_classifications and preprint_numeration_ptns:
# the previous institute had both numeration styles and categories
# for preprint references.
# build regexps and add them for this institute:
# First, order the numeration styles by line-length, and build a
# grouped regexp for recognising numeration:
ordered_patterns = \
order_reportnum_patterns_bylen(preprint_numeration_ptns)
# create a grouped regexp for numeration part of
# preprint reference:
numeration_regexp = \
create_institute_numeration_group_regexp_pattern(
ordered_patterns)
# for each "classification" part of preprint references, create a
# complete regex:
# will be in the style "(categ)-(numatn1|numatn2|numatn3|...)"
for classification in preprint_classifications:
search_pattern_str = ur'(?:^|[^a-zA-Z0-9\/\.\-])([\[\(]?(?P<categ>' \
+ classification[0].strip() + u')' \
+ numeration_regexp + ur'[\]\)]?)'
re_search_pattern = re.compile(search_pattern_str,
re.UNICODE)
preprint_reference_search_regexp_patterns[(kb_line_num,
classification[0])] =\
re_search_pattern
standardised_preprint_reference_categories[(kb_line_num,
classification[0])] =\
classification[1]
preprint_reference_search_regexp_patterns = {} # a dictionary of patterns
# used to recognise
# categories of preprints
# as used by various
# institutes
standardised_preprint_reference_categories = {} # dictionary of
# standardised category
# strings for preprint cats
current_institute_preprint_classifications = [] # list of tuples containing
# preprint categories in
# their raw & standardised
# forms, as read from KB
current_institute_numerations = [] # list of preprint
# numeration patterns, as
# read from the KB
# pattern to recognise an institute name line in the KB
re_institute_name = re.compile(ur'^\*{5}\s*(.+)\s*\*{5}$', re.UNICODE)
# pattern to recognise an institute preprint categ line in the KB
re_preprint_classification = \
re.compile(ur'^\s*(\w.*)\s*---\s*(\w.*)\s*$', re.UNICODE)
# pattern to recognise a preprint numeration-style line in KB
re_numeration_pattern = re.compile(ur'^\<(.+)\>$', re.UNICODE)
kb_line_num = 0 # when making the dictionary of patterns, which is
# keyed by the category search string, this counter
# will ensure that patterns in the dictionary are not
# overwritten if 2 institutes have the same category
# styles.
with file_resolving(fpath) as fh:
for rawline in fh:
if rawline.startswith('#'):
continue
kb_line_num += 1
m_institute_name = re_institute_name.search(rawline)
if m_institute_name:
# This KB line is the name of an institute
# append the last institute's pattern list to the list of
# institutes:
_add_institute_preprint_patterns(current_institute_preprint_classifications,
current_institute_numerations,
preprint_reference_search_regexp_patterns,
standardised_preprint_reference_categories,
kb_line_num)
# Now start a new dictionary to contain the search patterns
# for this institute:
current_institute_preprint_classifications = []
current_institute_numerations = []
# move on to the next line
continue
m_preprint_classification = \
re_preprint_classification.search(rawline)
if m_preprint_classification:
# This KB line contains a preprint classification for
# the current institute
try:
current_institute_preprint_classifications.append((m_preprint_classification.group(1),
m_preprint_classification.group(2)))
except (AttributeError, NameError):
# didn't match this line correctly - skip it
pass
# move on to the next line
continue
m_numeration_pattern = re_numeration_pattern.search(rawline)
if m_numeration_pattern:
# This KB line contains a preprint item numeration pattern
# for the current institute
try:
current_institute_numerations.append(
m_numeration_pattern.group(1))
except (AttributeError, NameError):
# didn't match the numeration pattern correctly - skip it
pass
continue
_add_institute_preprint_patterns(current_institute_preprint_classifications,
current_institute_numerations,
preprint_reference_search_regexp_patterns,
standardised_preprint_reference_categories,
kb_line_num)
# return the preprint reference patterns and the replacement strings
# for non-standard categ-strings:
return (preprint_reference_search_regexp_patterns,
standardised_preprint_reference_categories) | [
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] | Given the path to a knowledge base file containing the details
of institutes and the patterns that their preprint report
numbering schemes take, create a dictionary of regexp search
patterns to recognise these preprint references in reference
lines, and a dictionary of replacements for non-standard preprint
categories in these references.
The knowledge base file should consist only of lines that take one
of the following 3 formats:
#####Institute Name####
(the name of the institute to which the preprint reference patterns
belong, e.g. '#####LANL#####', surrounded by 5 # on either side.)
<pattern>
(numeration patterns for an institute's preprints, surrounded by
< and >.)
seek-term --- replace-term
(i.e. a seek phrase on the left hand side, a replace phrase on the
right hand side, with the two phrases being separated by 3 hyphens.)
E.g.:
ASTRO PH ---astro-ph
The left-hand side term is a non-standard version of the preprint
reference category; the right-hand side term is the standard version.
If the KB file cannot be read from, or an unexpected line is
encountered in the KB, an error message is output to standard error
and execution is halted with an error-code 0.
@param fpath: (string) the path to the knowledge base file.
@return: (tuple) containing 2 dictionaries. The first contains regexp
search patterns used to identify preprint references in a line. This
dictionary is keyed by a tuple containing the line number of the
pattern in the KB and the non-standard category string.
E.g.: (3, 'ASTRO PH').
The second dictionary contains the standardised category string,
and is keyed by the non-standard category string. E.g.: 'astro-ph'. | [
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3,767 | inspirehep/refextract | refextract/references/kbs.py | _cmp_bystrlen_reverse | def _cmp_bystrlen_reverse(a, b):
"""A private "cmp" function to be used by the "sort" function of a
list when ordering the titles found in a knowledge base by string-
length - LONGEST -> SHORTEST.
@param a: (string)
@param b: (string)
@return: (integer) - 0 if len(a) == len(b); 1 if len(a) < len(b);
-1 if len(a) > len(b);
"""
if len(a) > len(b):
return -1
elif len(a) < len(b):
return 1
else:
return 0 | python | def _cmp_bystrlen_reverse(a, b):
"""A private "cmp" function to be used by the "sort" function of a
list when ordering the titles found in a knowledge base by string-
length - LONGEST -> SHORTEST.
@param a: (string)
@param b: (string)
@return: (integer) - 0 if len(a) == len(b); 1 if len(a) < len(b);
-1 if len(a) > len(b);
"""
if len(a) > len(b):
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else:
return 0 | [
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3,768 | inspirehep/refextract | refextract/references/kbs.py | build_special_journals_kb | def build_special_journals_kb(fpath):
"""Load special journals database from file
Special journals are journals that have a volume which is not unique
among different years. To keep the volume unique we are adding the year
before the volume.
"""
journals = set()
with file_resolving(fpath) as fh:
for line in fh:
# Skip commented lines
if line.startswith('#'):
continue
# Skip empty line
if not line.strip():
continue
journals.add(line.strip())
return journals | python | def build_special_journals_kb(fpath):
"""Load special journals database from file
Special journals are journals that have a volume which is not unique
among different years. To keep the volume unique we are adding the year
before the volume.
"""
journals = set()
with file_resolving(fpath) as fh:
for line in fh:
# Skip commented lines
if line.startswith('#'):
continue
# Skip empty line
if not line.strip():
continue
journals.add(line.strip())
return journals | [
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3,769 | inspirehep/refextract | refextract/references/kbs.py | build_journals_re_kb | def build_journals_re_kb(fpath):
"""Load journals regexps knowledge base
@see build_journals_kb
"""
def make_tuple(match):
regexp = match.group('seek')
repl = match.group('repl')
return regexp, repl
kb = []
with file_resolving(fpath) as fh:
for rawline in fh:
if rawline.startswith('#'):
continue
# Extract the seek->replace terms from this KB line:
m_kb_line = re_kb_line.search(rawline)
kb.append(make_tuple(m_kb_line))
return kb | python | def build_journals_re_kb(fpath):
"""Load journals regexps knowledge base
@see build_journals_kb
"""
def make_tuple(match):
regexp = match.group('seek')
repl = match.group('repl')
return regexp, repl
kb = []
with file_resolving(fpath) as fh:
for rawline in fh:
if rawline.startswith('#'):
continue
# Extract the seek->replace terms from this KB line:
m_kb_line = re_kb_line.search(rawline)
kb.append(make_tuple(m_kb_line))
return kb | [
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3,770 | brettcannon/gidgethub | gidgethub/sansio.py | _parse_content_type | def _parse_content_type(content_type: Optional[str]) -> Tuple[Optional[str], str]:
"""Tease out the content-type and character encoding.
A default character encoding of UTF-8 is used, so the content-type
must be used to determine if any decoding is necessary to begin
with.
"""
if not content_type:
return None, "utf-8"
else:
type_, parameters = cgi.parse_header(content_type)
encoding = parameters.get("charset", "utf-8")
return type_, encoding | python | def _parse_content_type(content_type: Optional[str]) -> Tuple[Optional[str], str]:
"""Tease out the content-type and character encoding.
A default character encoding of UTF-8 is used, so the content-type
must be used to determine if any decoding is necessary to begin
with.
"""
if not content_type:
return None, "utf-8"
else:
type_, parameters = cgi.parse_header(content_type)
encoding = parameters.get("charset", "utf-8")
return type_, encoding | [
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3,771 | brettcannon/gidgethub | gidgethub/sansio.py | _decode_body | def _decode_body(content_type: Optional[str], body: bytes,
*, strict: bool = False) -> Any:
"""Decode an HTTP body based on the specified content type.
If 'strict' is true, then raise ValueError if the content type
is not recognized. Otherwise simply returned the body as a decoded
string.
"""
type_, encoding = _parse_content_type(content_type)
if not len(body) or not content_type:
return None
decoded_body = body.decode(encoding)
if type_ == "application/json":
return json.loads(decoded_body)
elif type_ == "application/x-www-form-urlencoded":
return json.loads(urllib.parse.parse_qs(decoded_body)["payload"][0])
elif strict:
raise ValueError(f"unrecognized content type: {type_!r}")
return decoded_body | python | def _decode_body(content_type: Optional[str], body: bytes,
*, strict: bool = False) -> Any:
"""Decode an HTTP body based on the specified content type.
If 'strict' is true, then raise ValueError if the content type
is not recognized. Otherwise simply returned the body as a decoded
string.
"""
type_, encoding = _parse_content_type(content_type)
if not len(body) or not content_type:
return None
decoded_body = body.decode(encoding)
if type_ == "application/json":
return json.loads(decoded_body)
elif type_ == "application/x-www-form-urlencoded":
return json.loads(urllib.parse.parse_qs(decoded_body)["payload"][0])
elif strict:
raise ValueError(f"unrecognized content type: {type_!r}")
return decoded_body | [
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3,772 | brettcannon/gidgethub | gidgethub/sansio.py | validate_event | def validate_event(payload: bytes, *, signature: str, secret: str) -> None:
"""Validate the signature of a webhook event."""
# https://developer.github.com/webhooks/securing/#validating-payloads-from-github
signature_prefix = "sha1="
if not signature.startswith(signature_prefix):
raise ValidationFailure("signature does not start with "
f"{repr(signature_prefix)}")
hmac_ = hmac.new(secret.encode("UTF-8"), msg=payload, digestmod="sha1")
calculated_sig = signature_prefix + hmac_.hexdigest()
if not hmac.compare_digest(signature, calculated_sig):
raise ValidationFailure("payload's signature does not align "
"with the secret") | python | def validate_event(payload: bytes, *, signature: str, secret: str) -> None:
"""Validate the signature of a webhook event."""
# https://developer.github.com/webhooks/securing/#validating-payloads-from-github
signature_prefix = "sha1="
if not signature.startswith(signature_prefix):
raise ValidationFailure("signature does not start with "
f"{repr(signature_prefix)}")
hmac_ = hmac.new(secret.encode("UTF-8"), msg=payload, digestmod="sha1")
calculated_sig = signature_prefix + hmac_.hexdigest()
if not hmac.compare_digest(signature, calculated_sig):
raise ValidationFailure("payload's signature does not align "
"with the secret") | [
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3,773 | brettcannon/gidgethub | gidgethub/sansio.py | accept_format | def accept_format(*, version: str = "v3", media: Optional[str] = None,
json: bool = True) -> str:
"""Construct the specification of the format that a request should return.
The version argument defaults to v3 of the GitHub API and is applicable to
all requests. The media argument along with 'json' specifies what format
the request should return, e.g. requesting the rendered HTML of a comment.
Do note that not all of GitHub's API supports alternative formats.
The default arguments of this function will always return the latest stable
version of the GitHub API in the default format that this library is
designed to support.
"""
# https://developer.github.com/v3/media/
# https://developer.github.com/v3/#current-version
accept = f"application/vnd.github.{version}"
if media is not None:
accept += f".{media}"
if json:
accept += "+json"
return accept | python | def accept_format(*, version: str = "v3", media: Optional[str] = None,
json: bool = True) -> str:
"""Construct the specification of the format that a request should return.
The version argument defaults to v3 of the GitHub API and is applicable to
all requests. The media argument along with 'json' specifies what format
the request should return, e.g. requesting the rendered HTML of a comment.
Do note that not all of GitHub's API supports alternative formats.
The default arguments of this function will always return the latest stable
version of the GitHub API in the default format that this library is
designed to support.
"""
# https://developer.github.com/v3/media/
# https://developer.github.com/v3/#current-version
accept = f"application/vnd.github.{version}"
if media is not None:
accept += f".{media}"
if json:
accept += "+json"
return accept | [
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3,774 | brettcannon/gidgethub | gidgethub/sansio.py | create_headers | def create_headers(requester: str, *, accept: str = accept_format(),
oauth_token: Optional[str] = None,
jwt: Optional[str] = None) -> Dict[str, str]:
"""Create a dict representing GitHub-specific header fields.
The user agent is set according to who the requester is. GitHub asks it be
either a username or project name.
The 'accept' argument corresponds to the 'accept' field and defaults to the
default result of accept_format(). You should only need to change this value
if you are using a different version of the API -- e.g. one that is under
development -- or if you are looking for a different format return type,
e.g. wanting the rendered HTML of a Markdown file.
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token. This can be important if you need the expanded rate limit provided
by an authenticated request.
The 'jwt' allows authenticating as a GitHub App by passing in the
bearer token.
You can only supply only one of oauth_token or jwt, not both.
For consistency, all keys in the returned dict will be lowercased.
"""
# user-agent: https://developer.github.com/v3/#user-agent-required
# accept: https://developer.github.com/v3/#current-version
# https://developer.github.com/v3/media/
# authorization: https://developer.github.com/v3/#authentication
# authenticating as a GitHub App: https://developer.github.com/apps/building-github-apps/authenticating-with-github-apps/#authenticating-as-a-github-app
if oauth_token is not None and jwt is not None:
raise ValueError("Cannot pass both oauth_token and jwt.")
headers = {"user-agent": requester, "accept": accept}
if oauth_token is not None:
headers["authorization"] = f"token {oauth_token}"
elif jwt is not None:
headers["authorization"] = f"bearer {jwt}"
return headers | python | def create_headers(requester: str, *, accept: str = accept_format(),
oauth_token: Optional[str] = None,
jwt: Optional[str] = None) -> Dict[str, str]:
"""Create a dict representing GitHub-specific header fields.
The user agent is set according to who the requester is. GitHub asks it be
either a username or project name.
The 'accept' argument corresponds to the 'accept' field and defaults to the
default result of accept_format(). You should only need to change this value
if you are using a different version of the API -- e.g. one that is under
development -- or if you are looking for a different format return type,
e.g. wanting the rendered HTML of a Markdown file.
The 'oauth_token' allows making an authenticated request using a personal access
token. This can be important if you need the expanded rate limit provided
by an authenticated request.
The 'jwt' allows authenticating as a GitHub App by passing in the
bearer token.
You can only supply only one of oauth_token or jwt, not both.
For consistency, all keys in the returned dict will be lowercased.
"""
# user-agent: https://developer.github.com/v3/#user-agent-required
# accept: https://developer.github.com/v3/#current-version
# https://developer.github.com/v3/media/
# authorization: https://developer.github.com/v3/#authentication
# authenticating as a GitHub App: https://developer.github.com/apps/building-github-apps/authenticating-with-github-apps/#authenticating-as-a-github-app
if oauth_token is not None and jwt is not None:
raise ValueError("Cannot pass both oauth_token and jwt.")
headers = {"user-agent": requester, "accept": accept}
if oauth_token is not None:
headers["authorization"] = f"token {oauth_token}"
elif jwt is not None:
headers["authorization"] = f"bearer {jwt}"
return headers | [
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3,775 | brettcannon/gidgethub | gidgethub/sansio.py | decipher_response | def decipher_response(status_code: int, headers: Mapping[str, str],
body: bytes) -> Tuple[Any, Optional[RateLimit], Optional[str]]:
"""Decipher an HTTP response for a GitHub API request.
The mapping providing the headers is expected to support lowercase keys.
The parameters of this function correspond to the three main parts
of an HTTP response: the status code, headers, and body. Assuming
no errors which lead to an exception being raised, a 3-item tuple
is returned. The first item is the decoded body (typically a JSON
object, but possibly None or a string depending on the content
type of the body). The second item is an instance of RateLimit
based on what the response specified.
The last item of the tuple is the URL where to request the next
part of results. If there are no more results then None is
returned. Do be aware that the URL can be a URI template and so
may need to be expanded.
If the status code is anything other than 200, 201, or 204, then
an HTTPException is raised.
"""
data = _decode_body(headers.get("content-type"), body)
if status_code in {200, 201, 204}:
return data, RateLimit.from_http(headers), _next_link(headers.get("link"))
else:
try:
message = data["message"]
except (TypeError, KeyError):
message = None
exc_type: Type[HTTPException]
if status_code >= 500:
exc_type = GitHubBroken
elif status_code >= 400:
exc_type = BadRequest
if status_code == 403:
rate_limit = RateLimit.from_http(headers)
if rate_limit and not rate_limit.remaining:
raise RateLimitExceeded(rate_limit, message)
elif status_code == 422:
errors = data.get("errors", None)
if errors:
fields = ", ".join(repr(e["field"]) for e in errors)
message = f"{message} for {fields}"
else:
message = data["message"]
raise InvalidField(errors, message)
elif status_code >= 300:
exc_type = RedirectionException
else:
exc_type = HTTPException
status_code_enum = http.HTTPStatus(status_code)
args: Union[Tuple[http.HTTPStatus, str], Tuple[http.HTTPStatus]]
if message:
args = status_code_enum, message
else:
args = status_code_enum,
raise exc_type(*args) | python | def decipher_response(status_code: int, headers: Mapping[str, str],
body: bytes) -> Tuple[Any, Optional[RateLimit], Optional[str]]:
"""Decipher an HTTP response for a GitHub API request.
The mapping providing the headers is expected to support lowercase keys.
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If the status code is anything other than 200, 201, or 204, then
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"""
data = _decode_body(headers.get("content-type"), body)
if status_code in {200, 201, 204}:
return data, RateLimit.from_http(headers), _next_link(headers.get("link"))
else:
try:
message = data["message"]
except (TypeError, KeyError):
message = None
exc_type: Type[HTTPException]
if status_code >= 500:
exc_type = GitHubBroken
elif status_code >= 400:
exc_type = BadRequest
if status_code == 403:
rate_limit = RateLimit.from_http(headers)
if rate_limit and not rate_limit.remaining:
raise RateLimitExceeded(rate_limit, message)
elif status_code == 422:
errors = data.get("errors", None)
if errors:
fields = ", ".join(repr(e["field"]) for e in errors)
message = f"{message} for {fields}"
else:
message = data["message"]
raise InvalidField(errors, message)
elif status_code >= 300:
exc_type = RedirectionException
else:
exc_type = HTTPException
status_code_enum = http.HTTPStatus(status_code)
args: Union[Tuple[http.HTTPStatus, str], Tuple[http.HTTPStatus]]
if message:
args = status_code_enum, message
else:
args = status_code_enum,
raise exc_type(*args) | [
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no errors which lead to an exception being raised, a 3-item tuple
is returned. The first item is the decoded body (typically a JSON
object, but possibly None or a string depending on the content
type of the body). The second item is an instance of RateLimit
based on what the response specified.
The last item of the tuple is the URL where to request the next
part of results. If there are no more results then None is
returned. Do be aware that the URL can be a URI template and so
may need to be expanded.
If the status code is anything other than 200, 201, or 204, then
an HTTPException is raised. | [
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3,776 | brettcannon/gidgethub | gidgethub/sansio.py | format_url | def format_url(url: str, url_vars: Mapping[str, Any]) -> str:
"""Construct a URL for the GitHub API.
The URL may be absolute or relative. In the latter case the appropriate
domain will be added. This is to help when copying the relative URL directly
from the GitHub developer documentation.
The dict provided in url_vars is used in URI template formatting.
"""
url = urllib.parse.urljoin(DOMAIN, url) # Works even if 'url' is fully-qualified.
expanded_url: str = uritemplate.expand(url, var_dict=url_vars)
return expanded_url | python | def format_url(url: str, url_vars: Mapping[str, Any]) -> str:
"""Construct a URL for the GitHub API.
The URL may be absolute or relative. In the latter case the appropriate
domain will be added. This is to help when copying the relative URL directly
from the GitHub developer documentation.
The dict provided in url_vars is used in URI template formatting.
"""
url = urllib.parse.urljoin(DOMAIN, url) # Works even if 'url' is fully-qualified.
expanded_url: str = uritemplate.expand(url, var_dict=url_vars)
return expanded_url | [
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3,777 | brettcannon/gidgethub | gidgethub/sansio.py | Event.from_http | def from_http(cls, headers: Mapping[str, str], body: bytes,
*, secret: Optional[str] = None) -> "Event":
"""Construct an event from HTTP headers and JSON body data.
The mapping providing the headers is expected to support lowercase keys.
Since this method assumes the body of the HTTP request is JSON, a check
is performed for a content-type of "application/json" (GitHub does
support other content-types). If the content-type does not match,
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If the appropriate headers are provided for event validation, then it
will be performed unconditionally. Any failure in validation
(including not providing a secret) will lead to ValidationFailure being
raised.
"""
if "x-hub-signature" in headers:
if secret is None:
raise ValidationFailure("secret not provided")
validate_event(body, signature=headers["x-hub-signature"],
secret=secret)
elif secret is not None:
raise ValidationFailure("signature is missing")
try:
data = _decode_body(headers["content-type"], body, strict=True)
except (KeyError, ValueError) as exc:
raise BadRequest(http.HTTPStatus(415),
"expected a content-type of "
"'application/json' or "
"'application/x-www-form-urlencoded'") from exc
return cls(data, event=headers["x-github-event"],
delivery_id=headers["x-github-delivery"]) | python | def from_http(cls, headers: Mapping[str, str], body: bytes,
*, secret: Optional[str] = None) -> "Event":
"""Construct an event from HTTP headers and JSON body data.
The mapping providing the headers is expected to support lowercase keys.
Since this method assumes the body of the HTTP request is JSON, a check
is performed for a content-type of "application/json" (GitHub does
support other content-types). If the content-type does not match,
BadRequest is raised.
If the appropriate headers are provided for event validation, then it
will be performed unconditionally. Any failure in validation
(including not providing a secret) will lead to ValidationFailure being
raised.
"""
if "x-hub-signature" in headers:
if secret is None:
raise ValidationFailure("secret not provided")
validate_event(body, signature=headers["x-hub-signature"],
secret=secret)
elif secret is not None:
raise ValidationFailure("signature is missing")
try:
data = _decode_body(headers["content-type"], body, strict=True)
except (KeyError, ValueError) as exc:
raise BadRequest(http.HTTPStatus(415),
"expected a content-type of "
"'application/json' or "
"'application/x-www-form-urlencoded'") from exc
return cls(data, event=headers["x-github-event"],
delivery_id=headers["x-github-delivery"]) | [
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3,778 | brettcannon/gidgethub | gidgethub/sansio.py | RateLimit.from_http | def from_http(cls, headers: Mapping[str, str]) -> Optional["RateLimit"]:
"""Gather rate limit information from HTTP headers.
The mapping providing the headers is expected to support lowercase
keys. Returns ``None`` if ratelimit info is not found in the headers.
"""
try:
limit = int(headers["x-ratelimit-limit"])
remaining = int(headers["x-ratelimit-remaining"])
reset_epoch = float(headers["x-ratelimit-reset"])
except KeyError:
return None
else:
return cls(limit=limit, remaining=remaining, reset_epoch=reset_epoch) | python | def from_http(cls, headers: Mapping[str, str]) -> Optional["RateLimit"]:
"""Gather rate limit information from HTTP headers.
The mapping providing the headers is expected to support lowercase
keys. Returns ``None`` if ratelimit info is not found in the headers.
"""
try:
limit = int(headers["x-ratelimit-limit"])
remaining = int(headers["x-ratelimit-remaining"])
reset_epoch = float(headers["x-ratelimit-reset"])
except KeyError:
return None
else:
return cls(limit=limit, remaining=remaining, reset_epoch=reset_epoch) | [
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3,779 | brettcannon/gidgethub | gidgethub/routing.py | Router.add | def add(self, func: AsyncCallback, event_type: str, **data_detail: Any) -> None:
"""Add a new route.
After registering 'func' for the specified event_type, an
optional data_detail may be provided. By providing an extra
keyword argument, dispatching can occur based on a top-level
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"""
if len(data_detail) > 1:
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elif not data_detail:
callbacks = self._shallow_routes.setdefault(event_type, [])
callbacks.append(func)
else:
data_key, data_value = data_detail.popitem()
data_details = self._deep_routes.setdefault(event_type, {})
specific_detail = data_details.setdefault(data_key, {})
callbacks = specific_detail.setdefault(data_value, [])
callbacks.append(func) | python | def add(self, func: AsyncCallback, event_type: str, **data_detail: Any) -> None:
"""Add a new route.
After registering 'func' for the specified event_type, an
optional data_detail may be provided. By providing an extra
keyword argument, dispatching can occur based on a top-level
key of the data in the event being dispatched.
"""
if len(data_detail) > 1:
msg = ()
raise TypeError("dispatching based on data details is only "
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f"{len(data_detail)} levels specified")
elif not data_detail:
callbacks = self._shallow_routes.setdefault(event_type, [])
callbacks.append(func)
else:
data_key, data_value = data_detail.popitem()
data_details = self._deep_routes.setdefault(event_type, {})
specific_detail = data_details.setdefault(data_key, {})
callbacks = specific_detail.setdefault(data_value, [])
callbacks.append(func) | [
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3,780 | brettcannon/gidgethub | gidgethub/abc.py | GitHubAPI._make_request | async def _make_request(self, method: str, url: str, url_vars: Dict[str, str],
data: Any, accept: str,
jwt: Opt[str] = None,
oauth_token: Opt[str] = None,
) -> Tuple[bytes, Opt[str]]:
"""Construct and make an HTTP request."""
if oauth_token is not None and jwt is not None:
raise ValueError("Cannot pass both oauth_token and jwt.")
filled_url = sansio.format_url(url, url_vars)
if jwt is not None:
request_headers = sansio.create_headers(
self.requester, accept=accept,
jwt=jwt)
elif oauth_token is not None:
request_headers = sansio.create_headers(
self.requester, accept=accept,
oauth_token=oauth_token)
else:
# fallback to using oauth_token
request_headers = sansio.create_headers(
self.requester, accept=accept,
oauth_token=self.oauth_token)
cached = cacheable = False
# Can't use None as a "no body" sentinel as it's a legitimate JSON type.
if data == b"":
body = b""
request_headers["content-length"] = "0"
if method == "GET" and self._cache is not None:
cacheable = True
try:
etag, last_modified, data, more = self._cache[filled_url]
cached = True
except KeyError:
pass
else:
if etag is not None:
request_headers["if-none-match"] = etag
if last_modified is not None:
request_headers["if-modified-since"] = last_modified
else:
charset = "utf-8"
body = json.dumps(data).encode(charset)
request_headers['content-type'] = f"application/json; charset={charset}"
request_headers['content-length'] = str(len(body))
if self.rate_limit is not None:
self.rate_limit.remaining -= 1
response = await self._request(method, filled_url, request_headers, body)
if not (response[0] == 304 and cached):
data, self.rate_limit, more = sansio.decipher_response(*response)
has_cache_details = ("etag" in response[1]
or "last-modified" in response[1])
if self._cache is not None and cacheable and has_cache_details:
etag = response[1].get("etag")
last_modified = response[1].get("last-modified")
self._cache[filled_url] = etag, last_modified, data, more
return data, more | python | async def _make_request(self, method: str, url: str, url_vars: Dict[str, str],
data: Any, accept: str,
jwt: Opt[str] = None,
oauth_token: Opt[str] = None,
) -> Tuple[bytes, Opt[str]]:
"""Construct and make an HTTP request."""
if oauth_token is not None and jwt is not None:
raise ValueError("Cannot pass both oauth_token and jwt.")
filled_url = sansio.format_url(url, url_vars)
if jwt is not None:
request_headers = sansio.create_headers(
self.requester, accept=accept,
jwt=jwt)
elif oauth_token is not None:
request_headers = sansio.create_headers(
self.requester, accept=accept,
oauth_token=oauth_token)
else:
# fallback to using oauth_token
request_headers = sansio.create_headers(
self.requester, accept=accept,
oauth_token=self.oauth_token)
cached = cacheable = False
# Can't use None as a "no body" sentinel as it's a legitimate JSON type.
if data == b"":
body = b""
request_headers["content-length"] = "0"
if method == "GET" and self._cache is not None:
cacheable = True
try:
etag, last_modified, data, more = self._cache[filled_url]
cached = True
except KeyError:
pass
else:
if etag is not None:
request_headers["if-none-match"] = etag
if last_modified is not None:
request_headers["if-modified-since"] = last_modified
else:
charset = "utf-8"
body = json.dumps(data).encode(charset)
request_headers['content-type'] = f"application/json; charset={charset}"
request_headers['content-length'] = str(len(body))
if self.rate_limit is not None:
self.rate_limit.remaining -= 1
response = await self._request(method, filled_url, request_headers, body)
if not (response[0] == 304 and cached):
data, self.rate_limit, more = sansio.decipher_response(*response)
has_cache_details = ("etag" in response[1]
or "last-modified" in response[1])
if self._cache is not None and cacheable and has_cache_details:
etag = response[1].get("etag")
last_modified = response[1].get("last-modified")
self._cache[filled_url] = etag, last_modified, data, more
return data, more | [
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3,781 | brettcannon/gidgethub | gidgethub/abc.py | GitHubAPI.getitem | async def getitem(self, url: str, url_vars: Dict[str, str] = {},
*, accept: str = sansio.accept_format(),
jwt: Opt[str] = None,
oauth_token: Opt[str] = None
) -> Any:
"""Send a GET request for a single item to the specified endpoint."""
data, _ = await self._make_request("GET", url, url_vars, b"", accept,
jwt=jwt, oauth_token=oauth_token)
return data | python | async def getitem(self, url: str, url_vars: Dict[str, str] = {},
*, accept: str = sansio.accept_format(),
jwt: Opt[str] = None,
oauth_token: Opt[str] = None
) -> Any:
"""Send a GET request for a single item to the specified endpoint."""
data, _ = await self._make_request("GET", url, url_vars, b"", accept,
jwt=jwt, oauth_token=oauth_token)
return data | [
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3,782 | brettcannon/gidgethub | gidgethub/abc.py | GitHubAPI.getiter | async def getiter(self, url: str, url_vars: Dict[str, str] = {},
*, accept: str = sansio.accept_format(),
jwt: Opt[str] = None,
oauth_token: Opt[str] = None
) -> AsyncGenerator[Any, None]:
"""Return an async iterable for all the items at a specified endpoint."""
data, more = await self._make_request("GET", url, url_vars, b"", accept,
jwt=jwt, oauth_token=oauth_token)
if isinstance(data, dict) and "items" in data:
data = data["items"]
for item in data:
yield item
if more:
# `yield from` is not supported in coroutines.
async for item in self.getiter(more, url_vars, accept=accept,
jwt=jwt, oauth_token=oauth_token):
yield item | python | async def getiter(self, url: str, url_vars: Dict[str, str] = {},
*, accept: str = sansio.accept_format(),
jwt: Opt[str] = None,
oauth_token: Opt[str] = None
) -> AsyncGenerator[Any, None]:
"""Return an async iterable for all the items at a specified endpoint."""
data, more = await self._make_request("GET", url, url_vars, b"", accept,
jwt=jwt, oauth_token=oauth_token)
if isinstance(data, dict) and "items" in data:
data = data["items"]
for item in data:
yield item
if more:
# `yield from` is not supported in coroutines.
async for item in self.getiter(more, url_vars, accept=accept,
jwt=jwt, oauth_token=oauth_token):
yield item | [
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3,783 | rkargon/pixelsorter | pixelsorter/images2gif.py | NeuQuant.quantize | def quantize(self, image):
""" Use a kdtree to quickly find the closest palette colors for the pixels """
if get_cKDTree():
return self.quantize_with_scipy(image)
else:
print('Scipy not available, falling back to slower version.')
return self.quantize_without_scipy(image) | python | def quantize(self, image):
""" Use a kdtree to quickly find the closest palette colors for the pixels """
if get_cKDTree():
return self.quantize_with_scipy(image)
else:
print('Scipy not available, falling back to slower version.')
return self.quantize_without_scipy(image) | [
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3,784 | rkargon/pixelsorter | pixelsorter/images2gif.py | NeuQuant.inxsearch | def inxsearch(self, r, g, b):
"""Search for BGR values 0..255 and return colour index"""
dists = (self.colormap[:, :3] - np.array([r, g, b]))
a = np.argmin((dists * dists).sum(1))
return a | python | def inxsearch(self, r, g, b):
"""Search for BGR values 0..255 and return colour index"""
dists = (self.colormap[:, :3] - np.array([r, g, b]))
a = np.argmin((dists * dists).sum(1))
return a | [
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3,785 | European-XFEL/karabo-bridge-py | karabo_bridge/cli/glimpse.py | gen_filename | def gen_filename(endpoint):
"""Generate a filename from endpoint with timestamp.
return: str
hostname_port_YearMonthDay_HourMinSecFrac.h5
"""
now = datetime.now().strftime('%Y%m%d_%H%M%S%f')[:-4]
base = endpoint.split('://', 1)[1]
if base.startswith('localhost:'):
base = gethostname().split('.')[0] + base[9:]
base = base.replace(':', '_').replace('/', '_')
return '{}_{}.h5'.format(base, now) | python | def gen_filename(endpoint):
"""Generate a filename from endpoint with timestamp.
return: str
hostname_port_YearMonthDay_HourMinSecFrac.h5
"""
now = datetime.now().strftime('%Y%m%d_%H%M%S%f')[:-4]
base = endpoint.split('://', 1)[1]
if base.startswith('localhost:'):
base = gethostname().split('.')[0] + base[9:]
base = base.replace(':', '_').replace('/', '_')
return '{}_{}.h5'.format(base, now) | [
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3,786 | European-XFEL/karabo-bridge-py | karabo_bridge/cli/glimpse.py | dict_to_hdf5 | def dict_to_hdf5(dic, endpoint):
"""Dump a dict to an HDF5 file.
"""
filename = gen_filename(endpoint)
with h5py.File(filename, 'w') as handler:
walk_dict_to_hdf5(dic, handler)
print('dumped to', filename) | python | def dict_to_hdf5(dic, endpoint):
"""Dump a dict to an HDF5 file.
"""
filename = gen_filename(endpoint)
with h5py.File(filename, 'w') as handler:
walk_dict_to_hdf5(dic, handler)
print('dumped to', filename) | [
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3,787 | European-XFEL/karabo-bridge-py | karabo_bridge/cli/glimpse.py | hdf5_to_dict | def hdf5_to_dict(filepath, group='/'):
"""load the content of an hdf5 file to a dict.
# TODO: how to split domain_type_dev : parameter : value ?
"""
if not h5py.is_hdf5(filepath):
raise RuntimeError(filepath, 'is not a valid HDF5 file.')
with h5py.File(filepath, 'r') as handler:
dic = walk_hdf5_to_dict(handler[group])
return dic | python | def hdf5_to_dict(filepath, group='/'):
"""load the content of an hdf5 file to a dict.
# TODO: how to split domain_type_dev : parameter : value ?
"""
if not h5py.is_hdf5(filepath):
raise RuntimeError(filepath, 'is not a valid HDF5 file.')
with h5py.File(filepath, 'r') as handler:
dic = walk_hdf5_to_dict(handler[group])
return dic | [
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3,788 | European-XFEL/karabo-bridge-py | karabo_bridge/cli/glimpse.py | print_one_train | def print_one_train(client, verbosity=0):
"""Retrieve data for one train and print it.
Returns the (data, metadata) dicts from the client.
This is used by the -glimpse and -monitor command line tools.
"""
ts_before = time()
data, meta = client.next()
ts_after = time()
if not data:
print("Empty data")
return
train_id = list(meta.values())[0].get('timestamp.tid', 0)
print("Train ID:", train_id, "--------------------------")
delta = ts_after - ts_before
print('Data from {} sources, REQ-REP took {:.2f} ms'
.format(len(data), delta))
print()
for i, (source, src_data) in enumerate(sorted(data.items()), start=1):
src_metadata = meta.get(source, {})
tid = src_metadata.get('timestamp.tid', 0)
print("Source {}: {!r} @ {}".format(i, source, tid))
try:
ts = src_metadata['timestamp']
except KeyError:
print("No timestamp")
else:
dt = strftime('%Y-%m-%d %H:%M:%S', localtime(ts))
delay = (ts_after - ts) * 1000
print('timestamp: {} ({}) | delay: {:.2f} ms'
.format(dt, ts, delay))
if verbosity < 1:
print("- data:", sorted(src_data))
print("- metadata:", sorted(src_metadata))
else:
print('data:')
pretty_print(src_data, verbosity=verbosity - 1)
if src_metadata:
print('metadata:')
pretty_print(src_metadata)
print()
return data, meta | python | def print_one_train(client, verbosity=0):
"""Retrieve data for one train and print it.
Returns the (data, metadata) dicts from the client.
This is used by the -glimpse and -monitor command line tools.
"""
ts_before = time()
data, meta = client.next()
ts_after = time()
if not data:
print("Empty data")
return
train_id = list(meta.values())[0].get('timestamp.tid', 0)
print("Train ID:", train_id, "--------------------------")
delta = ts_after - ts_before
print('Data from {} sources, REQ-REP took {:.2f} ms'
.format(len(data), delta))
print()
for i, (source, src_data) in enumerate(sorted(data.items()), start=1):
src_metadata = meta.get(source, {})
tid = src_metadata.get('timestamp.tid', 0)
print("Source {}: {!r} @ {}".format(i, source, tid))
try:
ts = src_metadata['timestamp']
except KeyError:
print("No timestamp")
else:
dt = strftime('%Y-%m-%d %H:%M:%S', localtime(ts))
delay = (ts_after - ts) * 1000
print('timestamp: {} ({}) | delay: {:.2f} ms'
.format(dt, ts, delay))
if verbosity < 1:
print("- data:", sorted(src_data))
print("- metadata:", sorted(src_metadata))
else:
print('data:')
pretty_print(src_data, verbosity=verbosity - 1)
if src_metadata:
print('metadata:')
pretty_print(src_metadata)
print()
return data, meta | [
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Returns the (data, metadata) dicts from the client.
This is used by the -glimpse and -monitor command line tools. | [
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3,789 | European-XFEL/karabo-bridge-py | karabo_bridge/cli/glimpse.py | pretty_print | def pretty_print(d, ind='', verbosity=0):
"""Pretty print a data dictionary from the bridge client
"""
assert isinstance(d, dict)
for k, v in sorted(d.items()):
str_base = '{} - [{}] {}'.format(ind, type(v).__name__, k)
if isinstance(v, dict):
print(str_base.replace('-', '+', 1))
pretty_print(v, ind=ind+' ', verbosity=verbosity)
continue
elif isinstance(v, np.ndarray):
node = '{}, {}, {}'.format(str_base, v.dtype, v.shape)
if verbosity >= 2:
node += '\n{}'.format(v)
elif isinstance(v, Sequence):
if v and isinstance(v, (list, tuple)):
itemtype = ' of ' + type(v[0]).__name__
pos = str_base.find(']')
str_base = str_base[:pos] + itemtype + str_base[pos:]
node = '{}, {}'.format(str_base, v)
if verbosity < 1 and len(node) > 80:
node = node[:77] + '...'
else:
node = '{}, {}'.format(str_base, v)
print(node) | python | def pretty_print(d, ind='', verbosity=0):
"""Pretty print a data dictionary from the bridge client
"""
assert isinstance(d, dict)
for k, v in sorted(d.items()):
str_base = '{} - [{}] {}'.format(ind, type(v).__name__, k)
if isinstance(v, dict):
print(str_base.replace('-', '+', 1))
pretty_print(v, ind=ind+' ', verbosity=verbosity)
continue
elif isinstance(v, np.ndarray):
node = '{}, {}, {}'.format(str_base, v.dtype, v.shape)
if verbosity >= 2:
node += '\n{}'.format(v)
elif isinstance(v, Sequence):
if v and isinstance(v, (list, tuple)):
itemtype = ' of ' + type(v[0]).__name__
pos = str_base.find(']')
str_base = str_base[:pos] + itemtype + str_base[pos:]
node = '{}, {}'.format(str_base, v)
if verbosity < 1 and len(node) > 80:
node = node[:77] + '...'
else:
node = '{}, {}'.format(str_base, v)
print(node) | [
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3,790 | European-XFEL/karabo-bridge-py | karabo_bridge/simulation.py | start_gen | def start_gen(port, ser='msgpack', version='2.2', detector='AGIPD',
raw=False, nsources=1, datagen='random', *,
debug=True):
""""Karabo bridge server simulation.
Simulate a Karabo Bridge server and send random data from a detector,
either AGIPD or LPD.
Parameters
----------
port: str
The port to on which the server is bound.
ser: str, optional
The serialization algorithm, default is msgpack.
version: str, optional
The container version of the serialized data.
detector: str, optional
The data format to send, default is AGIPD detector.
raw: bool, optional
Generate raw data output if True, else CORRECTED. Default is False.
nsources: int, optional
Number of sources.
datagen: string, optional
Generator function used to generate detector data. Default is random.
"""
context = zmq.Context()
socket = context.socket(zmq.REP)
socket.setsockopt(zmq.LINGER, 0)
socket.bind('tcp://*:{}'.format(port))
if ser != 'msgpack':
raise ValueError("Unknown serialisation format %s" % ser)
serialize = partial(msgpack.dumps, use_bin_type=True)
det = Detector.getDetector(detector, raw=raw, gen=datagen)
generator = generate(det, nsources)
print('Simulated Karabo-bridge server started on:\ntcp://{}:{}'.format(
uname().nodename, port))
t_prev = time()
n = 0
try:
while True:
msg = socket.recv()
if msg == b'next':
train = next(generator)
msg = containize(train, ser, serialize, version)
socket.send_multipart(msg, copy=False)
if debug:
print('Server : emitted train:',
train[1][list(train[1].keys())[0]]['timestamp.tid'])
n += 1
if n % TIMING_INTERVAL == 0:
t_now = time()
print('Sent {} trains in {:.2f} seconds ({:.2f} Hz)'
''.format(TIMING_INTERVAL, t_now - t_prev,
TIMING_INTERVAL / (t_now - t_prev)))
t_prev = t_now
else:
print('wrong request')
break
except KeyboardInterrupt:
print('\nStopped.')
finally:
socket.close()
context.destroy() | python | def start_gen(port, ser='msgpack', version='2.2', detector='AGIPD',
raw=False, nsources=1, datagen='random', *,
debug=True):
""""Karabo bridge server simulation.
Simulate a Karabo Bridge server and send random data from a detector,
either AGIPD or LPD.
Parameters
----------
port: str
The port to on which the server is bound.
ser: str, optional
The serialization algorithm, default is msgpack.
version: str, optional
The container version of the serialized data.
detector: str, optional
The data format to send, default is AGIPD detector.
raw: bool, optional
Generate raw data output if True, else CORRECTED. Default is False.
nsources: int, optional
Number of sources.
datagen: string, optional
Generator function used to generate detector data. Default is random.
"""
context = zmq.Context()
socket = context.socket(zmq.REP)
socket.setsockopt(zmq.LINGER, 0)
socket.bind('tcp://*:{}'.format(port))
if ser != 'msgpack':
raise ValueError("Unknown serialisation format %s" % ser)
serialize = partial(msgpack.dumps, use_bin_type=True)
det = Detector.getDetector(detector, raw=raw, gen=datagen)
generator = generate(det, nsources)
print('Simulated Karabo-bridge server started on:\ntcp://{}:{}'.format(
uname().nodename, port))
t_prev = time()
n = 0
try:
while True:
msg = socket.recv()
if msg == b'next':
train = next(generator)
msg = containize(train, ser, serialize, version)
socket.send_multipart(msg, copy=False)
if debug:
print('Server : emitted train:',
train[1][list(train[1].keys())[0]]['timestamp.tid'])
n += 1
if n % TIMING_INTERVAL == 0:
t_now = time()
print('Sent {} trains in {:.2f} seconds ({:.2f} Hz)'
''.format(TIMING_INTERVAL, t_now - t_prev,
TIMING_INTERVAL / (t_now - t_prev)))
t_prev = t_now
else:
print('wrong request')
break
except KeyboardInterrupt:
print('\nStopped.')
finally:
socket.close()
context.destroy() | [
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Simulate a Karabo Bridge server and send random data from a detector,
either AGIPD or LPD.
Parameters
----------
port: str
The port to on which the server is bound.
ser: str, optional
The serialization algorithm, default is msgpack.
version: str, optional
The container version of the serialized data.
detector: str, optional
The data format to send, default is AGIPD detector.
raw: bool, optional
Generate raw data output if True, else CORRECTED. Default is False.
nsources: int, optional
Number of sources.
datagen: string, optional
Generator function used to generate detector data. Default is random. | [
"Karabo",
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] | ca20d72b8beb0039649d10cb01d027db42efd91c | https://github.com/European-XFEL/karabo-bridge-py/blob/ca20d72b8beb0039649d10cb01d027db42efd91c/karabo_bridge/simulation.py#L262-L328 |
3,791 | European-XFEL/karabo-bridge-py | karabo_bridge/client.py | Client.next | def next(self):
"""Request next data container.
This function call is blocking.
Returns
-------
data : dict
The data for this train, keyed by source name.
meta : dict
The metadata for this train, keyed by source name.
This dictionary is populated for protocol version 1.0 and 2.2.
For other protocol versions, metadata information is available in
`data` dict.
Raises
------
TimeoutError
If timeout is reached before receiving data.
"""
if self._pattern == zmq.REQ and not self._recv_ready:
self._socket.send(b'next')
self._recv_ready = True
try:
msg = self._socket.recv_multipart(copy=False)
except zmq.error.Again:
raise TimeoutError(
'No data received from {} in the last {} ms'.format(
self._socket.getsockopt_string(zmq.LAST_ENDPOINT),
self._socket.getsockopt(zmq.RCVTIMEO)))
self._recv_ready = False
return self._deserialize(msg) | python | def next(self):
"""Request next data container.
This function call is blocking.
Returns
-------
data : dict
The data for this train, keyed by source name.
meta : dict
The metadata for this train, keyed by source name.
This dictionary is populated for protocol version 1.0 and 2.2.
For other protocol versions, metadata information is available in
`data` dict.
Raises
------
TimeoutError
If timeout is reached before receiving data.
"""
if self._pattern == zmq.REQ and not self._recv_ready:
self._socket.send(b'next')
self._recv_ready = True
try:
msg = self._socket.recv_multipart(copy=False)
except zmq.error.Again:
raise TimeoutError(
'No data received from {} in the last {} ms'.format(
self._socket.getsockopt_string(zmq.LAST_ENDPOINT),
self._socket.getsockopt(zmq.RCVTIMEO)))
self._recv_ready = False
return self._deserialize(msg) | [
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This function call is blocking.
Returns
-------
data : dict
The data for this train, keyed by source name.
meta : dict
The metadata for this train, keyed by source name.
This dictionary is populated for protocol version 1.0 and 2.2.
For other protocol versions, metadata information is available in
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Raises
------
TimeoutError
If timeout is reached before receiving data. | [
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] | ca20d72b8beb0039649d10cb01d027db42efd91c | https://github.com/European-XFEL/karabo-bridge-py/blob/ca20d72b8beb0039649d10cb01d027db42efd91c/karabo_bridge/client.py#L90-L122 |
3,792 | materialsvirtuallab/monty | monty/io.py | zopen | def zopen(filename, *args, **kwargs):
"""
This function wraps around the bz2, gzip and standard python's open
function to deal intelligently with bzipped, gzipped or standard text
files.
Args:
filename (str/Path): filename or pathlib.Path.
\*args: Standard args for python open(..). E.g., 'r' for read, 'w' for
write.
\*\*kwargs: Standard kwargs for python open(..).
Returns:
File-like object. Supports with context.
"""
if Path is not None and isinstance(filename, Path):
filename = str(filename)
name, ext = os.path.splitext(filename)
ext = ext.upper()
if ext == ".BZ2":
if PY_VERSION[0] >= 3:
return bz2.open(filename, *args, **kwargs)
else:
args = list(args)
if len(args) > 0:
args[0] = "".join([c for c in args[0] if c != "t"])
if "mode" in kwargs:
kwargs["mode"] = "".join([c for c in kwargs["mode"]
if c != "t"])
return bz2.BZ2File(filename, *args, **kwargs)
elif ext in (".GZ", ".Z"):
return gzip.open(filename, *args, **kwargs)
else:
return io.open(filename, *args, **kwargs) | python | def zopen(filename, *args, **kwargs):
"""
This function wraps around the bz2, gzip and standard python's open
function to deal intelligently with bzipped, gzipped or standard text
files.
Args:
filename (str/Path): filename or pathlib.Path.
\*args: Standard args for python open(..). E.g., 'r' for read, 'w' for
write.
\*\*kwargs: Standard kwargs for python open(..).
Returns:
File-like object. Supports with context.
"""
if Path is not None and isinstance(filename, Path):
filename = str(filename)
name, ext = os.path.splitext(filename)
ext = ext.upper()
if ext == ".BZ2":
if PY_VERSION[0] >= 3:
return bz2.open(filename, *args, **kwargs)
else:
args = list(args)
if len(args) > 0:
args[0] = "".join([c for c in args[0] if c != "t"])
if "mode" in kwargs:
kwargs["mode"] = "".join([c for c in kwargs["mode"]
if c != "t"])
return bz2.BZ2File(filename, *args, **kwargs)
elif ext in (".GZ", ".Z"):
return gzip.open(filename, *args, **kwargs)
else:
return io.open(filename, *args, **kwargs) | [
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3,793 | materialsvirtuallab/monty | monty/io.py | reverse_readline | def reverse_readline(m_file, blk_size=4096, max_mem=4000000):
"""
Generator method to read a file line-by-line, but backwards. This allows
one to efficiently get data at the end of a file.
Based on code by Peter Astrand <[email protected]>, using modifications by
Raymond Hettinger and Kevin German.
http://code.activestate.com/recipes/439045-read-a-text-file-backwards
-yet-another-implementat/
Reads file forwards and reverses in memory for files smaller than the
max_mem parameter, or for gzip files where reverse seeks are not supported.
Files larger than max_mem are dynamically read backwards.
Args:
m_file (File): File stream to read (backwards)
blk_size (int): The buffer size. Defaults to 4096.
max_mem (int): The maximum amount of memory to involve in this
operation. This is used to determine when to reverse a file
in-memory versus seeking portions of a file. For bz2 files,
this sets the maximum block size.
Returns:
Generator that returns lines from the file. Similar behavior to the
file.readline() method, except the lines are returned from the back
of the file.
"""
# Check if the file stream is a bit stream or not
is_text = isinstance(m_file, io.TextIOWrapper)
try:
file_size = os.path.getsize(m_file.name)
except AttributeError:
# Bz2 files do not have name attribute. Just set file_size to above
# max_mem for now.
file_size = max_mem + 1
# If the file size is within our desired RAM use, just reverse it in memory
# GZip files must use this method because there is no way to negative seek
if file_size < max_mem or isinstance(m_file, gzip.GzipFile):
for line in reversed(m_file.readlines()):
yield line.rstrip()
else:
if isinstance(m_file, bz2.BZ2File):
# for bz2 files, seeks are expensive. It is therefore in our best
# interest to maximize the blk_size within limits of desired RAM
# use.
blk_size = min(max_mem, file_size)
buf = ""
m_file.seek(0, 2)
if is_text:
lastchar = m_file.read(1)
else:
lastchar = m_file.read(1).decode("utf-8")
trailing_newline = (lastchar == "\n")
while 1:
newline_pos = buf.rfind("\n")
pos = m_file.tell()
if newline_pos != -1:
# Found a newline
line = buf[newline_pos + 1:]
buf = buf[:newline_pos]
if pos or newline_pos or trailing_newline:
line += "\n"
yield line
elif pos:
# Need to fill buffer
toread = min(blk_size, pos)
m_file.seek(pos - toread, 0)
if is_text:
buf = m_file.read(toread) + buf
else:
buf = m_file.read(toread).decode("utf-8") + buf
m_file.seek(pos - toread, 0)
if pos == toread:
buf = "\n" + buf
else:
# Start-of-file
return | python | def reverse_readline(m_file, blk_size=4096, max_mem=4000000):
"""
Generator method to read a file line-by-line, but backwards. This allows
one to efficiently get data at the end of a file.
Based on code by Peter Astrand <[email protected]>, using modifications by
Raymond Hettinger and Kevin German.
http://code.activestate.com/recipes/439045-read-a-text-file-backwards
-yet-another-implementat/
Reads file forwards and reverses in memory for files smaller than the
max_mem parameter, or for gzip files where reverse seeks are not supported.
Files larger than max_mem are dynamically read backwards.
Args:
m_file (File): File stream to read (backwards)
blk_size (int): The buffer size. Defaults to 4096.
max_mem (int): The maximum amount of memory to involve in this
operation. This is used to determine when to reverse a file
in-memory versus seeking portions of a file. For bz2 files,
this sets the maximum block size.
Returns:
Generator that returns lines from the file. Similar behavior to the
file.readline() method, except the lines are returned from the back
of the file.
"""
# Check if the file stream is a bit stream or not
is_text = isinstance(m_file, io.TextIOWrapper)
try:
file_size = os.path.getsize(m_file.name)
except AttributeError:
# Bz2 files do not have name attribute. Just set file_size to above
# max_mem for now.
file_size = max_mem + 1
# If the file size is within our desired RAM use, just reverse it in memory
# GZip files must use this method because there is no way to negative seek
if file_size < max_mem or isinstance(m_file, gzip.GzipFile):
for line in reversed(m_file.readlines()):
yield line.rstrip()
else:
if isinstance(m_file, bz2.BZ2File):
# for bz2 files, seeks are expensive. It is therefore in our best
# interest to maximize the blk_size within limits of desired RAM
# use.
blk_size = min(max_mem, file_size)
buf = ""
m_file.seek(0, 2)
if is_text:
lastchar = m_file.read(1)
else:
lastchar = m_file.read(1).decode("utf-8")
trailing_newline = (lastchar == "\n")
while 1:
newline_pos = buf.rfind("\n")
pos = m_file.tell()
if newline_pos != -1:
# Found a newline
line = buf[newline_pos + 1:]
buf = buf[:newline_pos]
if pos or newline_pos or trailing_newline:
line += "\n"
yield line
elif pos:
# Need to fill buffer
toread = min(blk_size, pos)
m_file.seek(pos - toread, 0)
if is_text:
buf = m_file.read(toread) + buf
else:
buf = m_file.read(toread).decode("utf-8") + buf
m_file.seek(pos - toread, 0)
if pos == toread:
buf = "\n" + buf
else:
# Start-of-file
return | [
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http://code.activestate.com/recipes/439045-read-a-text-file-backwards
-yet-another-implementat/
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3,794 | materialsvirtuallab/monty | monty/io.py | get_open_fds | def get_open_fds():
"""
Return the number of open file descriptors for current process
.. warning: will only work on UNIX-like OS-es.
"""
pid = os.getpid()
procs = subprocess.check_output(["lsof", '-w', '-Ff', "-p", str(pid)])
procs = procs.decode("utf-8")
return len([s for s in procs.split('\n')
if s and s[0] == 'f' and s[1:].isdigit()]) | python | def get_open_fds():
"""
Return the number of open file descriptors for current process
.. warning: will only work on UNIX-like OS-es.
"""
pid = os.getpid()
procs = subprocess.check_output(["lsof", '-w', '-Ff', "-p", str(pid)])
procs = procs.decode("utf-8")
return len([s for s in procs.split('\n')
if s and s[0] == 'f' and s[1:].isdigit()]) | [
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3,795 | materialsvirtuallab/monty | monty/io.py | FileLock.acquire | def acquire(self):
"""
Acquire the lock, if possible. If the lock is in use, it check again
every `delay` seconds. It does this until it either gets the lock or
exceeds `timeout` number of seconds, in which case it throws
an exception.
"""
start_time = time.time()
while True:
try:
self.fd = os.open(self.lockfile,
os.O_CREAT | os.O_EXCL | os.O_RDWR)
break
except (OSError,) as e:
if e.errno != errno.EEXIST:
raise
if (time.time() - start_time) >= self.timeout:
raise FileLockException("%s: Timeout occured." %
self.lockfile)
time.sleep(self.delay)
self.is_locked = True | python | def acquire(self):
"""
Acquire the lock, if possible. If the lock is in use, it check again
every `delay` seconds. It does this until it either gets the lock or
exceeds `timeout` number of seconds, in which case it throws
an exception.
"""
start_time = time.time()
while True:
try:
self.fd = os.open(self.lockfile,
os.O_CREAT | os.O_EXCL | os.O_RDWR)
break
except (OSError,) as e:
if e.errno != errno.EEXIST:
raise
if (time.time() - start_time) >= self.timeout:
raise FileLockException("%s: Timeout occured." %
self.lockfile)
time.sleep(self.delay)
self.is_locked = True | [
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3,796 | materialsvirtuallab/monty | monty/io.py | FileLock.release | def release(self):
""" Get rid of the lock by deleting the lockfile.
When working in a `with` statement, this gets automatically
called at the end.
"""
if self.is_locked:
os.close(self.fd)
os.unlink(self.lockfile)
self.is_locked = False | python | def release(self):
""" Get rid of the lock by deleting the lockfile.
When working in a `with` statement, this gets automatically
called at the end.
"""
if self.is_locked:
os.close(self.fd)
os.unlink(self.lockfile)
self.is_locked = False | [
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3,797 | materialsvirtuallab/monty | monty/fnmatch.py | WildCard.filter | def filter(self, names):
"""
Returns a list with the names matching the pattern.
"""
names = list_strings(names)
fnames = []
for f in names:
for pat in self.pats:
if fnmatch.fnmatch(f, pat):
fnames.append(f)
return fnames | python | def filter(self, names):
"""
Returns a list with the names matching the pattern.
"""
names = list_strings(names)
fnames = []
for f in names:
for pat in self.pats:
if fnmatch.fnmatch(f, pat):
fnames.append(f)
return fnames | [
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3,798 | materialsvirtuallab/monty | monty/fnmatch.py | WildCard.match | def match(self, name):
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Returns True if name matches one of the patterns.
"""
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return False | python | def match(self, name):
"""
Returns True if name matches one of the patterns.
"""
for pat in self.pats:
if fnmatch.fnmatch(name, pat):
return True
return False | [
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3,799 | materialsvirtuallab/monty | monty/dev.py | deprecated | def deprecated(replacement=None, message=None):
"""
Decorator to mark classes or functions as deprecated,
with a possible replacement.
Args:
replacement (callable): A replacement class or method.
message (str): A warning message to be displayed.
Returns:
Original function, but with a warning to use the updated class.
"""
def wrap(old):
def wrapped(*args, **kwargs):
msg = "%s is deprecated" % old.__name__
if replacement is not None:
if isinstance(replacement, property):
r = replacement.fget
elif isinstance(replacement, (classmethod, staticmethod)):
r = replacement.__func__
else:
r = replacement
msg += "; use %s in %s instead." % (r.__name__, r.__module__)
if message is not None:
msg += "\n" + message
warnings.simplefilter('default')
warnings.warn(msg, DeprecationWarning, stacklevel=2)
return old(*args, **kwargs)
return wrapped
return wrap | python | def deprecated(replacement=None, message=None):
"""
Decorator to mark classes or functions as deprecated,
with a possible replacement.
Args:
replacement (callable): A replacement class or method.
message (str): A warning message to be displayed.
Returns:
Original function, but with a warning to use the updated class.
"""
def wrap(old):
def wrapped(*args, **kwargs):
msg = "%s is deprecated" % old.__name__
if replacement is not None:
if isinstance(replacement, property):
r = replacement.fget
elif isinstance(replacement, (classmethod, staticmethod)):
r = replacement.__func__
else:
r = replacement
msg += "; use %s in %s instead." % (r.__name__, r.__module__)
if message is not None:
msg += "\n" + message
warnings.simplefilter('default')
warnings.warn(msg, DeprecationWarning, stacklevel=2)
return old(*args, **kwargs)
return wrapped
return wrap | [
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with a possible replacement.
Args:
replacement (callable): A replacement class or method.
message (str): A warning message to be displayed.
Returns:
Original function, but with a warning to use the updated class. | [
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Subsets and Splits