Source code for qiime2.core.cite

# ----------------------------------------------------------------------------
# Copyright (c) 2016-2023, QIIME 2 development team.
# Distributed under the terms of the Modified BSD License.
# The full license is in the file LICENSE, distributed with this software.
# ----------------------------------------------------------------------------

import os
import pkg_resources
import collections

import bibtexparser as bp

CitationRecord = collections.namedtuple('CitationRecord', ['type', 'fields'])

[docs] class Citations(collections.OrderedDict): @classmethod def load(cls, path, package=None): if package is not None: root = pkg_resources.resource_filename(package, '.') root = os.path.abspath(root) path = os.path.join(root, path) parser = bp.bparser.BibTexParser() # Downstream tooling is much easier with unicode. For actual latex # users, use the modern biber backend instead of bibtex parser.customization = bp.customization.convert_to_unicode with open(path) as fh: try: db = bp.load(fh, parser=parser) except Exception as e: raise ValueError("There was a problem loading the BiBTex file:" "%r" % path) from e entries = collections.OrderedDict() for entry in db.entries: id_ = entry.pop('ID') type_ = entry.pop('ENTRYTYPE') if id_ in entries: raise ValueError("Duplicate entry-key found in BibTex file: %r" % id_) entries[id_] = CitationRecord(type_, entry) return cls(entries) def __iter__(self): return iter(self.values()) def save(self, f): entries = [] for key, citation in self.items(): entry = citation.fields.copy() entry['ID'] = key entry['ENTRYTYPE'] = citation.type entries.append(entry) db = bp.bibdatabase.BibDatabase() db.entries = entries writer = bp.bwriter.BibTexWriter() writer.order_entries_by = tuple(self.keys()) owned = False if type(f) is str: f = open(f, 'w') owned = True try: bp.dump(db, f, writer=writer) finally: if owned: f.close()