better error message when parsing of bibtex fails
Plus, slight refactoring: remove `databroker.verify()` method
This commit is contained in:
Fabien C. Y. Benureau
parent
69f760cac6
commit
be80e75cbb
@ -8,6 +8,10 @@
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### Implemented enhancements
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- Support for downloading arXiv reference from their ID ([#146](https://github.com/pubs/pubs/issues/146) by [joe-antognini](https://github.com/joe-antognini))
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- Better feedback when an error is encountered while adding a reference from a DOI, ISBN or arXiv ID [#155](https://github.com/pubs/pubs/issues/155)
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- Better dialog after editing paper [(#142)](https://github.com/pubs/pubs/issues/142)
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- Add a command to open urls ([#139](https://github.com/pubs/pubs/issues/139) by [ksunden](https://github.com/ksunden))
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@ -26,6 +30,7 @@
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- Support year ranges in query [(#102)](https://github.com/pubs/pubs/issues/102)
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- Tests can now be run with `python setup.py test` [#155](https://github.com/pubs/pubs/issues/155)
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### Fixed bugs
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@ -13,7 +13,7 @@ class ReferenceNotFoundError(Exception):
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pass
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def get_bibentry_from_api(id_str, id_type, rp, ui=None):
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def get_bibentry_from_api(id_str, id_type, try_doi=True, ui=None):
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"""Return a bibtex string from various ID methods.
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This is a wrapper around functions that will return a bibtex string given
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@ -46,8 +46,8 @@ def get_bibentry_from_api(id_str, id_type, rp, ui=None):
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if id_type not in id_fns.keys():
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raise ValueError('id_type must be one of `doi`, `isbn`, or `arxiv`.')
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bibentry_raw = id_fns[id_type](id_str)
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bibentry = rp.databroker.verify(bibentry_raw)
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bibentry_raw = id_fns[id_type](id_str, try_doi=try_doi, ui=ui)
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endecoder.EnDecoder().decode_bibdata(bibentry_raw)
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if bibentry is None:
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raise ReferenceNotFoundException(
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'invalid {} {} or unable to retrieve bibfile from it.'.format(id_type, id_str))
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@ -43,22 +43,25 @@ def parser(subparsers, conf):
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return parser
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def bibentry_from_editor(conf, ui, rp):
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def bibentry_from_editor(conf, ui):
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again = True
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bibstr = templates.add_bib
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bibentry_raw = templates.add_bib
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decoder = endecoder.EnDecoder()
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while again:
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try:
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bibstr = ui.editor_input(initial=bibstr, suffix='.bib')
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if bibstr == templates.add_bib:
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bibentry_raw = ui.editor_input(initial=bibentry_raw, suffix='.bib')
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if bibentry_raw == templates.add_bib:
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again = ui.input_yn(
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question='Bibfile not edited. Edit again ?',
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default='y')
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if not again:
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ui.exit(0)
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else:
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bibentry = rp.databroker.verify(bibstr)
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bibentry = decoder.decode_bibdata(bibentry_raw)
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bibstruct.verify_bibdata(bibentry)
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# REFACTOR Generate citykey
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# REFACTOR Generate citekey
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again = False
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except endecoder.EnDecoder.BibDecodingError:
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@ -84,28 +87,29 @@ def command(conf, args):
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citekey = args.citekey
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rp = repo.Repository(conf)
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decoder = endecoder.EnDecoder()
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# get bibtex entry
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if bibfile is None:
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if args.doi is None and args.isbn is None and args.arxiv is None:
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bibentry = bibentry_from_editor(conf, ui, rp)
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bibentry = bibentry_from_editor(conf, ui)
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else:
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bibentry = None
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try:
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if args.doi is not None:
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bibentry = apis.get_bibentry_from_api(args.doi, 'doi', rp)
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bibentry = apis.get_bibentry_from_api(args.doi, 'doi', ui=ui)
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elif args.isbn is not None:
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bibentry = apis.get_bibentry_from_api(args.isbn, 'isbn', rp)
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bibentry = apis.get_bibentry_from_api(args.isbn, 'isbn', ui=ui)
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# TODO distinguish between cases, offer to open the error page in a webbrowser.
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# TODO offer to confirm/change citekey
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elif args.arxiv is not None:
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bibentry = apis.get_bibentry_from_api(args.arxiv, 'arxiv', rp)
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bibentry = apis.get_bibentry_from_api(args.arxiv, 'arxiv', ui=ui)
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except apis.ReferenceNotFoundException as e:
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ui.error(e.message)
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ui.exit(1)
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else:
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bibentry_raw = content.get_content(bibfile, ui=ui)
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bibentry = rp.databroker.verify(bibentry_raw)
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bibentry = decoder.decode_bibdata(bibentry_raw)
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if bibentry is None:
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ui.error('invalid bibfile {}.'.format(bibfile))
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@ -79,16 +79,6 @@ class DataBroker(object):
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def listing(self, filestats=True):
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return self.filebroker.listing(filestats=filestats)
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def verify(self, bibdata_raw):
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"""Will return None if bibdata_raw can't be decoded"""
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try:
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if bibdata_raw.startswith('\ufeff'):
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# remove BOM, because bibtexparser does not support it.
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bibdata_raw = bibdata_raw[1:]
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return self.endecoder.decode_bibdata(bibdata_raw)
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except ValueError as e:
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return None
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# docbroker
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def in_docsdir(self, docpath):
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@ -163,9 +163,6 @@ class DataCache(object):
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def listing(self, filestats=True):
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return self.databroker.listing(filestats=filestats)
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def verify(self, bibdata_raw):
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return self.databroker.verify(bibdata_raw)
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# docbroker
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def in_docsdir(self, docpath):
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@ -1,9 +1,16 @@
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from __future__ import absolute_import, unicode_literals
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import copy
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import logging
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# both needed to intercept exceptions.
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import pyparsing
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import bibtexparser
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try:
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import bibtexparser as bp
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# don't let bibtexparser display stuff
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# bp.bparser.logger.setLevel(level=logging.CRITICAL)
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except ImportError:
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print("error: you need to install bibterxparser; try running 'pip install "
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"bibtexparser'.")
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@ -68,14 +75,16 @@ class EnDecoder(object):
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class BibDecodingError(Exception):
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message = "Could not parse provided bibdata:\n---\n{}\n---"
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# message = "Could not parse provided bibdata:\n---\n{}\n---"
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def __init__(self, bibdata):
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def __init__(self, error_msg, bibdata):
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"""
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:param error_msg: specific message about what went wrong
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:param bibdata: the data that was unsuccessfully decoded.
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"""
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super(Exception, self).__init__(error_msg) # make `str(self)` work.
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self.data = bibdata
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def __str__(self):
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return self.message.format(self.data)
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bwriter = bp.bwriter.BibTexWriter()
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bwriter.display_order = BIBFIELD_ORDER
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@ -117,10 +126,12 @@ class EnDecoder(object):
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If the decoding fails, returns a BibParseError.
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"""
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if len(bibdata) == 0:
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error_msg = 'parsing error: the provided string has length zero.'
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raise self.BibDecodingError(error_msg, bibdata)
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try:
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entries = bp.bparser.BibTexParser(
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bibdata, common_strings=True,
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customization=customizations,
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bibdata, common_strings=True, customization=customizations,
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homogenize_fields=True).get_entry_dict()
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# Remove id from bibtexparser attribute which is stored as citekey
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@ -131,8 +142,18 @@ class EnDecoder(object):
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entries[e][TYPE_KEY] = t
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if len(entries) > 0:
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return entries
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except Exception:
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import traceback
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traceback.print_exc()
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raise self.BibDecodingError(bibdata)
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# TODO: filter exceptions from pyparsing and pass reason upstream
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except (pyparsing.ParseException, pyparsing.ParseSyntaxException) as e:
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error_msg = self._format_parsing_error(e)
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raise self.BibDecodingError(error_msg, bibdata)
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except bibtexparser.bibdatabase.UndefinedString as e:
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error_msg = 'parsing error: undefined string in provided data: {}'.format(e)
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raise self.BibDecodingError(error_msg, bibdata)
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@classmethod
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def _format_parsing_error(cls, e):
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"""Transform a pyparsing exception into an error message
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Does a best effort to be useful, but might need to be improved.
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"""
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return '{}\n{}^\n{}'.format(e.line, (e.column - 1) * ' ', e)
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@ -2,6 +2,7 @@
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from __future__ import unicode_literals
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import unittest
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import socket
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import dotdot
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@ -20,9 +21,11 @@ def _is_connected():
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try:
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host = socket.gethostbyname('www.google.com')
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s = socket.create_connection((host, 80), 2)
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s.close()
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return True
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except:
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return False
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except socket.error:
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pass
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return False
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class APITests(unittest.TestCase):
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@ -78,6 +81,14 @@ class TestISBN2Bibtex(APITests):
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class TestArxiv2Bibtex(APITests):
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def test_new_style(self):
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bib = arxiv2bibtex('astro-ph/9812133')
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b = self.endecoder.decode_bibdata(bib)
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self.assertEqual(len(b), 1)
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entry = b[list(b)[0]]
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self.assertEqual(entry['author'][0], 'Perlmutter, S.')
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self.assertEqual(entry['year'], '1999')
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def test_parses_to_bibtex_with_doi(self):
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bib = arxiv2bibtex('astro-ph/9812133')
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b = self.endecoder.decode_bibdata(bib)
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@ -23,6 +23,11 @@ def compare_yaml_str(s1, s2):
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class TestEnDecode(unittest.TestCase):
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def test_decode_emptystring(self):
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decoder = endecoder.EnDecoder()
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with self.assertRaises(decoder.BibDecodingError):
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entry = decoder.decode_bibdata('')
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def test_encode_bibtex_is_unicode(self):
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decoder = endecoder.EnDecoder()
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entry = decoder.decode_bibdata(bibtex_raw0)
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@ -52,6 +57,18 @@ class TestEnDecode(unittest.TestCase):
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self.assertEqual(bibraw1, bibraw2)
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def test_endecode_bibtex_BOM(self):
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"""Test that bibtexparser if fine with BOM-prefixed data"""
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decoder = endecoder.EnDecoder()
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bom_str = '\ufeff'
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entry_1 = decoder.decode_bibdata(bibtex_raw0)
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bibraw_1 = decoder.encode_bibdata(entry_1)
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entry_2 = decoder.decode_bibdata(bom_str + bibraw_1)
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bibraw_2 = decoder.encode_bibdata(entry_2)
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self.assertEqual(bibraw_1, bibraw_2)
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def test_endecode_bibtex_converts_month_string(self):
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"""Test if `month=dec` is correctly recognized and transformed into
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`month={December}`"""
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