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Merge pull request #106 from pubs/feat/use-bwriter

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Uses bibtexparser bwriter instead of internal encoder and adds `--ignore-fields` option to export.
This commit is contained in:
Olivier Mangin 2018-01-09 09:11:57 -05:00 committed by GitHub
commit 79003c2fb8
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GPG Key ID: 4AEE18F83AFDEB23
5 changed files with 106 additions and 40 deletions
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22
pubs/commands/export_cmd.py
View File

@ -1,14 +1,32 @@
from __future__ import print_function
import argparse
from .. import repo
from ..uis import get_ui
from .. import endecoder
from ..utils import resolve_citekey_list
from ..completion import CiteKeyCompletion
from ..endecoder import BIBFIELD_ORDER
from ..completion import CiteKeyCompletion, CommaSeparatedListCompletion
class CommaSeparatedList(argparse.Action):
def __call__(self, parser, namespace, values, option_string=None):
setattr(namespace, self.dest, [s for s in values.split(',') if s])
class FieldCommaSeparatedListCompletion(CommaSeparatedListCompletion):
values = BIBFIELD_ORDER
def parser(subparsers, conf):
parser = subparsers.add_parser('export', help='export bibliography')
parser.add_argument(
'--ignore-fields', default=[], action=CommaSeparatedList,
help='exclude field(s) from output (comma separated if multiple)'
).completer = FieldCommaSeparatedListCompletion(conf)
# parser.add_argument('-f', '--bib-format', default='bibtex',
# help='export format')
parser.add_argument('citekeys', nargs='*', help='one or several citekeys'
@ -36,7 +54,7 @@ def command(conf, args):
bib[p.citekey] = p.bibdata
exporter = endecoder.EnDecoder()
bibdata_raw = exporter.encode_bibdata(bib)
bibdata_raw = exporter.encode_bibdata(bib, args.ignore_fields)
ui.message(bibdata_raw)
rp.close()

12
pubs/completion.py
View File

@ -57,3 +57,15 @@ class TagModifierCompletion(BaseCompleter):
partial_expr = prefix[:start]
t_prefix = prefix[start:]
return [partial_expr + t for t in tags if t.startswith(t_prefix)]
class CommaSeparatedListCompletion(BaseCompleter):
values = []
def _complete(self, prefix, **kwargs):
split = prefix.split(',')
item_prefix = split[-1]
partial = split[:-1]
return [','.join(partial + [x]) for x in self.values
if x.startswith(item_prefix)]

72
pubs/endecoder.py
View File

@ -27,6 +27,11 @@ else:
BP_ENTRYTYPE_KEY = 'type'
BIBFIELD_ORDER = ['author', 'title', 'journal', 'institution', 'publisher',
'year', 'month', 'number', 'volume', 'pages', 'link', 'doi',
'note', 'abstract']
def sanitize_citekey(record):
record[BP_ID_KEY] = record[BP_ID_KEY].strip('\n')
return record
@ -53,10 +58,6 @@ def customizations(record):
return record
bibfield_order = ['author', 'title', 'journal', 'institution', 'publisher',
'year', 'month', 'number', 'volume', 'pages', 'link', 'doi', 'note',
'abstract']
class EnDecoder(object):
""" Encode and decode content.
@ -69,6 +70,9 @@ class EnDecoder(object):
* encode_bibdata will try to recognize exceptions
"""
bwriter = bp.bwriter.BibTexWriter()
bwriter.display_order = BIBFIELD_ORDER
def encode_metadata(self, metadata):
return yaml.safe_dump(metadata, allow_unicode=True,
encoding=None, indent=4)
@ -76,41 +80,35 @@ class EnDecoder(object):
def decode_metadata(self, metadata_raw):
return yaml.safe_load(metadata_raw)
def encode_bibdata(self, bibdata):
def encode_bibdata(self, bibdata, ignore_fields=[]):
"""Encode bibdata """
return '\n'.join(self._encode_bibentry(citekey, entry)
for citekey, entry in bibdata.items())
bpdata = bp.bibdatabase.BibDatabase()
bpdata.entries = [self._entry_to_bp_entry(k, copy.copy(bibdata[k]),
ignore_fields=ignore_fields)
for k in bibdata]
return self.bwriter.write(bpdata)
@staticmethod
def _encode_field(key, value):
if key == 'link':
return ', '.join(link['url'] for link in value)
elif key == 'author':
return ' and '.join(author for author in value)
elif key == 'editor':
return ' and '.join(editor['name'] for editor in value)
elif key == 'journal':
return value['name']
elif key == 'keyword':
return ', '.join(keyword for keyword in value)
else:
return value
@staticmethod
def _encode_bibentry(citekey, bibentry):
bibraw = '@{}{{{},\n'.format(bibentry[TYPE_KEY], citekey)
bibentry = copy.copy(bibentry)
for key in bibfield_order:
if key in bibentry:
value = bibentry.pop(key)
bibraw += ' {} = {{{}}},\n'.format(
key, EnDecoder._encode_field(key, value))
for key, value in bibentry.items():
if key != TYPE_KEY:
bibraw += ' {} = {{{}}},\n'.format(
key, EnDecoder._encode_field(key, value))
bibraw += '}\n'
return bibraw
def _entry_to_bp_entry(self, key, entry, ignore_fields=[]):
"""Convert back entries to the format expected by bibtexparser."""
entry[BP_ID_KEY] = key
# Convert internal 'type' to bibtexparser entrytype key
entry[BP_ENTRYTYPE_KEY] = entry.pop(TYPE_KEY)
for f in ignore_fields:
entry.pop(f, None)
if 'link' in entry:
entry['link'] = ', '.join(link['url'] for link in entry['link'])
if 'author' in entry:
entry['author'] = ' and '.join(
author for author in entry['author'])
if 'editor' in entry:
entry['editor'] = ' and '.join(
editor['name'] for editor in entry['editor'])
if 'journal' in entry:
entry['journal'] = entry['journal']['name']
if 'keyword' in entry:
entry['keyword'] = ', '.join(
keyword for keyword in entry['keyword'])
return entry
def decode_bibdata(self, bibdata):
""""""

30
tests/test_endecoder.py
View File

@ -91,13 +91,41 @@ class TestEnDecode(unittest.TestCase):
self.assertIn(u'keyword', entry)
self.assertEqual(set(keywords), set(entry[u'keyword']))
def test_endecode_metadata(self):
decoder = endecoder.EnDecoder()
entry = decoder.decode_metadata(metadata_raw0)
metadata_output0 = decoder.encode_metadata(entry)
self.assertEqual(set(metadata_raw0.split('\n')), set(metadata_output0.split('\n')))
def test_endecode_bibtex_field_order(self):
decoder = endecoder.EnDecoder()
entry = decoder.decode_bibdata(bibtex_raw0)
lines = decoder.encode_bibdata(entry).splitlines()
self.assertEqual(lines[1].split('=')[0].strip(), u'author')
self.assertEqual(lines[2].split('=')[0].strip(), u'title')
self.assertEqual(lines[3].split('=')[0].strip(), u'institution')
self.assertEqual(lines[4].split('=')[0].strip(), u'publisher')
self.assertEqual(lines[5].split('=')[0].strip(), u'year')
self.assertEqual(lines[6].split('=')[0].strip(), u'month')
self.assertEqual(lines[7].split('=')[0].strip(), u'number')
self.assertEqual(lines[8].split('=')[0].strip(), u'link')
self.assertEqual(lines[9].split('=')[0].strip(), u'note')
self.assertEqual(lines[10].split('=')[0].strip(), u'abstract')
def test_endecode_bibtex_ignores_fields(self):
decoder = endecoder.EnDecoder()
entry = decoder.decode_bibdata(bibtex_raw0)
bibraw1 = decoder.encode_bibdata(
entry, ignore_fields=['title', 'note', 'abstract', 'journal'])
entry1 = list(decoder.decode_bibdata(bibraw1).values())[0]
self.assertNotIn('title', entry1)
self.assertNotIn('note', entry1)
self.assertNotIn('abtract', entry1)
self.assertIn('author', entry1)
self.assertIn('institution', entry1)
if __name__ == '__main__':
unittest.main()

10
tests/test_usecase.py
View File

@ -669,6 +669,16 @@ class TestUsecase(DataCommandTestCase):
self.assertEqual(endecoder.EnDecoder().decode_bibdata(outs[2]),
fixtures.page_bibentry)
def test_export_ignore_field(self):
cmds = ['pubs init',
('pubs add', [str_fixtures.bibtex_external0]),
'pubs export --ignore-fields author,title Page99',
]
outs = self.execute_cmds(cmds)
expected = endecoder.EnDecoder().encode_bibdata(
fixtures.page_bibentry, ignore_fields=['author', 'title'])
self.assertEqual(outs[2], expected + os.linesep)
def test_import(self):
cmds = ['pubs init',
'pubs import data/',