def citation_to_citeproc(citation, prune=True):
"""
Return a dictionary with citation metadata
"""
citation == standardize_citation(citation, warn_if_changed=True)
source, identifier = citation.split(':', 1)
if source in citeproc_retrievers:
citeproc_retriever = import_function(citeproc_retrievers[source])
csl_item = citeproc_retriever(identifier)
else:
msg = f'Unsupported citation source {source} in {citation}'
raise ValueError(msg)
from manubot import __version__ as manubot_version
from manubot.cite.citeproc import (
citeproc_passthrough,
append_to_csl_item_note,
)
note_text = f'This CSL JSON Item was automatically generated by Manubot v{manubot_version} using citation-by-identifier.'
note_dict = {
'standard_id': citation,
}
append_to_csl_item_note(csl_item, note_text, note_dict)
short_id = get_citation_short_id(citation)
csl_item = citeproc_passthrough(csl_item, set_id=short_id, prune=prune)
return csl_item
def citekey_to_csl_item(citekey, prune=True):
"""
Generate a CSL Item (Python dictionary) for the input citekey.
"""
from manubot.cite.csl_item import CSL_Item
from manubot import __version__ as manubot_version
citekey == standardize_citekey(citekey, warn_if_changed=True)
source, identifier = citekey.split(':', 1)
if source not in citeproc_retrievers:
msg = f'Unsupported citation source {source!r} in {citekey!r}'
raise ValueError(msg)
citeproc_retriever = import_function(citeproc_retrievers[source])
csl_item = citeproc_retriever(identifier)
csl_item = CSL_Item(csl_item)
note_text = f'This CSL JSON Item was automatically generated by Manubot v{manubot_version} using citation-by-identifier.'
note_dict = {
'standard_id': citekey,
}
csl_item.note_append_text(note_text)
csl_item.note_append_dict(note_dict)
short_citekey = shorten_citekey(citekey)
csl_item.set_id(short_citekey)
csl_item.clean(prune=prune)
return csl_item
def citekey_to_csl_item(citekey, prune=True):
"""
Generate a CSL Item (Python dictionary) for the input citekey.
"""
citekey == standardize_citekey(citekey, warn_if_changed=True)
source, identifier = citekey.split(':', 1)
if source in citeproc_retrievers:
citeproc_retriever = import_function(citeproc_retrievers[source])
csl_item = citeproc_retriever(identifier)
else:
msg = f'Unsupported citation source {source!r} in {citekey!r}'
raise ValueError(msg)
from manubot import __version__ as manubot_version
from manubot.cite.citeproc import (
csl_item_passthrough,
append_to_csl_item_note,
)
note_text = f'This CSL JSON Item was automatically generated by Manubot v{manubot_version} using citation-by-identifier.'
note_dict = {
'standard_id': citekey,
}
append_to_csl_item_note(csl_item, note_text, note_dict)
short_citekey = shorten_citekey(citekey)
csl_item = csl_item_passthrough(csl_item,
set_id=short_citekey,
prune=prune)
return csl_item
def main():
"""
Called as a console_scripts entry point in setup.py. This function defines
the manubot command line script.
"""
# Track if message gets logged with severity of error or greater
# See https://stackoverflow.com/a/45446664/4651668
import errorhandler
error_handler = errorhandler.ErrorHandler()
# Log DeprecationWarnings
warnings.simplefilter('always', DeprecationWarning)
logging.captureWarnings(True)
# Log to stderr
logger = logging.getLogger()
stream_handler = logging.StreamHandler(stream=sys.stderr)
stream_handler.setFormatter(
logging.Formatter('## {levelname}\n{message}', style='{'))
logger.addHandler(stream_handler)
args = parse_arguments()
logger.setLevel(getattr(logging, args.log_level))
function = import_function(args.function)
function(args)
if error_handler.fired:
logging.critical('Failure: exiting with code 1 due to logged errors')
raise SystemExit(1)
def get_handler(prefix_lower):
if not isinstance(prefix_lower, str):
raise TypeError(
f"prefix_lower should be a str, instead received {prefix_lower.__class__.__name__}"
)
assert prefix_lower == prefix_lower.lower()
handler = prefix_to_handler[prefix_lower]
handler = import_function(handler)(prefix_lower)
return handler
def main():
"""
Called as a console_scripts entry point in setup.cfg. This function defines
the manubot command line script.
"""
diagnostics = setup_logging_and_errors()
args = parse_arguments()
diagnostics["logger"].setLevel(getattr(logging, args.log_level))
function = import_function(args.function)
function(args)
exit_if_error_handler_fired(diagnostics["error_handler"])
def citation_to_citeproc(citation, prune=True):
"""
Return a dictionary with citation metadata
"""
assert citation == standardize_citation(citation)
source, identifier = citation.split(':', 1)
if source in citeproc_retrievers:
citeproc_retriever = import_function(citeproc_retrievers[source])
citeproc = citeproc_retriever(identifier)
else:
msg = f'Unsupported citation source {source} in {citation}'
raise ValueError(msg)
citation_id = get_citation_id(citation)
from manubot.cite.citeproc import citeproc_passthrough
citeproc = citeproc_passthrough(citeproc, set_id=citation_id, prune=prune)
return citeproc
def _generate_prefix_to_handler() -> typing.Dict[str, str]:
"""
Generate complete dictionary for prefix_to_handler.
"""
import inspect
from .curie import get_curie_handlers
curie_handlers = get_curie_handlers()
pth = {}
for handler in curie_handlers + _local_handlers:
if isinstance(handler, str):
handler = import_function(handler)("dummy_prefix_lower")
for prefix in handler.prefixes:
pth[
prefix
] = f"{inspect.getmodule(handler).__name__}.{handler.__class__.__name__}"
pth = dict(sorted(pth.items())) # sort for clean diffs of serialized dict
return pth