Source code for vermouth.citation_parser

# Copyright 2018 University of Groningen
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# See the License for the specific language governing permissions and
# limitations under the License.
import re

[docs]class BibTexDirector(): """ Lightweight parser for BibTex files. BibTex files in general have an assorment of entries that describe the corresponding sort of publication to refer to and then a number required and optional fields for the different types of entries. A field for example would be Title giving the title of a publication. The syntax in general looks as follows: @<entry>{<some custom ID>, field = {<content>}, field = {<content>}} Alternatively the {} can be replaced by quotation marks. This parser only parses the version with {} as used by google scholar. In addition we do not check for missing fields or invalid fields. All fields are accepted and no fields are required. """ def __init__(self, force_field): self.force_field = force_field self.known_entries = ["article", "book", "booklet", "conference", "inbook", "incollection", "inproceedings", "manual", "mastersthesis", "misc", "phdthesis", "proceedings", "techreport", "unpublished" ]
[docs] @staticmethod def prepare_file(lines): """ Bibtex is not sensitive to line spacing so we join the line as one string. Comment characters are not allowed. """ return " ".join(line.strip() for line in lines)
[docs] @staticmethod def find_entries(citation_string): """ Look in a string where `@` indicates the beginning of a new entry and return the indices. Parameters ----------- citation_string: str Yields -------- int position of '@' in citation_string """ for idx, token in enumerate(citation_string): if token == "@": yield idx
[docs] def pop_entry_type(self, entry_string): """ Given a string describing a single entry strip that entry from the string and return it. Note the string MUST contain the @. Parameters ------------ entry_string: str Returns --------- str The entry type str The shortened string """ assert entry_string[0] == "@" entry_type = entry_string[1:entry_string.find('{')] assert entry_type in self.known_entries entry_string = entry_string[len(entry_type)+1:] return entry_type, entry_string
[docs] @staticmethod def pop_key(entry_string): """ Given a string of a single entry from which the entry_type has already been removed (see pop_entry_type) get the custom ID, strip it and return the entry_string without that ID. Parameters ----------- entry_string: str Returns -------- str, str the key and the string without key """ key_idx = entry_string.find(',') return entry_string[:key_idx].strip("{").strip(" "), entry_string[key_idx:]
[docs] @staticmethod def extract_fields(entry_string): """ Given an entry string without entry type and identified (i.e. ,<field_type> = {<content>}, etc.) split all the contents and field-types using a regular expression. Parameters ----------- entry_string: str Yields ------- str, str the field type, the field content """ for field, value in re.findall("(.*?)=(.*?)\}", entry_string): yield field.strip(",").strip(" "), value.strip("{").strip("}")
[docs] def parse_entry(self, entry_string): """ Given a string describing a single entry, parse it and then update the force_field citations dict with a field dict. """ entry_type, entry_string = self.pop_entry_type(entry_string) cite_key, entry_string = self.pop_key(entry_string) field_dict = dict(self.extract_fields(entry_string)) field_dict["type"] = entry_type self.force_field.citations[cite_key] = field_dict
[docs] def parse(self, lines): """ Given lines from a bibtex file parse them and update the force-field citation instance variable. """ # convert file to string deleting end of line charcters citations_string = self.prepare_file(lines) # extract the entries from the string entries = list(self.find_entries(citations_string)) entries.append(len(citations_string)) # parse each entry to generate a citation for idx, jdx in zip(entries[:-1], entries[1:]): self.parse_entry(citations_string[idx:jdx]) return self.force_field.citations
[docs]def read_bib(lines, force_field): director = BibTexDirector(force_field=force_field) return director.parse(iter(lines))
[docs]def citation_formatter(citation, title=False): """ Very basic and minimal formatter for citations. It is adopted from basic ACS style formatting. Fields within [] are optional. <authors> [journal] <year>; [doi] Note that the formatter cannot fromat latex like syntax (e.g. a{\"} for ae) """ # first we split the author-list citation_string = "" # the spaces around the and are required! for match in citation["author"].split(" and "): last_name, first_names = match.split(",", 1) citation_string += last_name.strip() + "," for name in first_names.strip().split(' '): citation_string += " " + name.strip()[0] citation_string += "; " if "journal" in citation: citation_string += " " + citation["journal"] citation_string += " " + citation["year"] if "doi" in citation: citation_string += "; " + citation["doi"] return citation_string