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Merge pull request #149 from pubs/fix87

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Fix #87 (more robust error handling and list command)
This commit is contained in:
Olivier Mangin 2018-08-01 15:38:02 +02:00 committed by GitHub
commit c6edacf3ec
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12 changed files with 151 additions and 33 deletions
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2
changelog.md
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@ -29,6 +29,8 @@
### Fixed bugs
- [[#149]](https://github.com/pubs/pubs/issues/149) More robust handling of parsing and citekey errors [(#87)](https://github.com/pubs/pubs/pull/87)
- [[#148]](https://github.com/pubs/pubs/issues/148) Fix compatibility with Pyfakefs 3.7 [(#151)](https://github.com/pubs/pubs/pull/151)
- [[#95]](https://github.com/pubs/pubs/issues/95) Error message when editor is missing [(#141)](https://github.com/pubs/pubs/issues/141)

8
pubs/commands/add_cmd.py
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@ -11,6 +11,7 @@ from .. import templates
from .. import apis
from .. import pretty
from .. import utils
from .. import endecoder
from ..completion import CommaSeparatedTagsCompletion
@ -57,12 +58,13 @@ def bibentry_from_editor(conf, ui, rp):
bibstruct.verify_bibdata(bibentry)
# REFACTOR Generate citykey
again = False
except ValueError:
except endecoder.EnDecoder.BibDecodingError:
again = ui.input_yn(
question='Invalid bibfile. Edit again ?',
question='Invalid bibfile. Edit again?',
default='y')
if not again:
ui.exit(0)
ui.exit()
return bibentry

7
pubs/commands/edit_cmd.py
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@ -64,9 +64,14 @@ def command(conf, args):
'as `{}`.'.format(citekey, new_paper.citekey)))
else:
ui.info(('Paper `{}` was successfully edited.'.format(
citekey)))
citekey)))
break
except coder.BibDecodingError:
if not ui.input_yn(question="Error parsing bibdata. Edit again?"):
ui.error("Aborting, paper not updated.")
ui.exit()
except repo.CiteKeyCollision:
options = ['overwrite', 'edit again', 'abort']
choice = options[ui.input_choice(

46
pubs/commands/import_cmd.py
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@ -13,6 +13,10 @@ from ..uis import get_ui
from ..content import system_path, read_text_file
_ABORT_USE_IGNORE_MSG = "Aborting import. Use --ignore-malformed to ignore."
_IGNORING_MSG = " Ignoring it."
def parser(subparsers, conf):
parser = subparsers.add_parser('import',
help='import paper(s) to the repository')
@ -24,10 +28,12 @@ def parser(subparsers, conf):
help="one or several keys to import from the file")
parser.add_argument('-O', '--overwrite', action='store_true', default=False,
help="Overwrite keys already in the database")
parser.add_argument('-i', '--ignore-malformed', action='store_true', default=False,
help="Ignore malformed and unreadable files and entries")
return parser
def many_from_path(bibpath):
def many_from_path(ui, bibpath, ignore=False):
"""Extract list of papers found in bibliographic files in path.
The behavior is to:
@ -49,16 +55,31 @@ def many_from_path(bibpath):
biblist = []
for filepath in all_files:
biblist.append(coder.decode_bibdata(read_text_file(filepath)))
try:
biblist.append(coder.decode_bibdata(read_text_file(filepath)))
except coder.BibDecodingError:
error = "Could not parse bibtex at {}.".format(filepath)
if ignore:
ui.warning(error + _IGNORING_MSG)
else:
ui.error(error + _ABORT_USE_IGNORE_MSG)
ui.exit()
papers = {}
for b in biblist:
for k, b in b.items():
if k in papers:
ui.warning('Duplicated citekey {}. Keeping the last one.'.format(k))
try:
papers[k] = Paper(k, b)
papers[k].added = datetime.datetime.now()
except ValueError as e:
papers[k] = e
error = 'Could not load entry for citekey {} ({}).'.format(k, e)
if ignore:
ui.warning(error + _IGNORING_MSG)
else:
ui.error(error + _ABORT_USE_IGNORE_MSG)
ui.exit()
return papers
@ -75,20 +96,17 @@ def command(conf, args):
rp = repo.Repository(conf)
# Extract papers from bib
papers = many_from_path(bibpath)
papers = many_from_path(ui, bibpath, ignore=args.ignore_malformed)
keys = args.keys or papers.keys()
for k in keys:
p = papers[k]
if isinstance(p, Exception):
ui.error('Could not load entry for citekey {}.'.format(k))
rp.push_paper(p, overwrite=args.overwrite)
ui.info('{} imported.'.format(color.dye_out(p.citekey, 'citekey')))
docfile = bibstruct.extract_docfile(p.bibdata)
if docfile is None:
ui.warning("No file for {}.".format(p.citekey))
else:
rp.push_paper(p, overwrite=args.overwrite)
ui.info('{} imported.'.format(color.dye_out(p.citekey, 'citekey')))
docfile = bibstruct.extract_docfile(p.bibdata)
if docfile is None:
ui.warning("No file for {}.".format(p.citekey))
else:
rp.push_doc(p.citekey, docfile, copy=copy)
#FIXME should move the file if configured to do so.
rp.push_doc(p.citekey, docfile, copy=copy)
# FIXME should move the file if configured to do so.
rp.close()

6
pubs/databroker.py
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@ -45,7 +45,11 @@ class DataBroker(object):
def pull_bibentry(self, citekey):
bibdata_raw = self.filebroker.pull_bibfile(citekey)
return self.endecoder.decode_bibdata(bibdata_raw)
try:
return self.endecoder.decode_bibdata(bibdata_raw)
except self.endecoder.BibDecodingError as e:
e.message = "Unable to decode bibtex for paper {}.".format(citekey)
raise e
def push_metadata(self, citekey, metadata):
metadata_raw = self.endecoder.encode_metadata(metadata)

18
pubs/endecoder.py
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@ -66,6 +66,16 @@ class EnDecoder(object):
* encode_bibdata will try to recognize exceptions
"""
class BibDecodingError(Exception):
message = "Could not parse provided bibdata:\n---\n{}\n---"
def __init__(self, bibdata):
self.data = bibdata
def __str__(self):
return self.message.format(self.data)
bwriter = bp.bwriter.BibTexWriter()
bwriter.display_order = BIBFIELD_ORDER
@ -103,7 +113,10 @@ class EnDecoder(object):
return entry
def decode_bibdata(self, bibdata):
""""""
"""Decodes bibdata from string.
If the decoding fails, returns a BibParseError.
"""
try:
entries = bp.bparser.BibTexParser(
bibdata, common_strings=True,
@ -121,4 +134,5 @@ class EnDecoder(object):
except Exception:
import traceback
traceback.print_exc()
raise ValueError('could not parse provided bibdata:\n{}'.format(bibdata))
raise self.BibDecodingError(bibdata)
# TODO: filter exceptions from pyparsing and pass reason upstream

2
pubs/uis.py
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@ -119,7 +119,7 @@ class InputUI(PrintUI):
except EOFError:
self.error('Standard input ended while waiting for answer.')
self.exit(1)
return ustr(data) #.decode('utf-8')
return ustr(data) #.decode('utf-8')
def input_choice_ng(self, options, option_chars=None, default=None, question=''):
"""Ask the user to chose between a set of options. The user is asked

10
tests/fake_env.py
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@ -77,6 +77,16 @@ class FakeInput():
if md.__name__ == 'pubs.uis':
md.InputUI.editor_input = self
md.InputUI.edit_file = self.input_to_file
# Do not catch UnexpectedInput
original_handler = md.InputUI.handle_exception
def handler(ui, exc):
if isinstance(exc, self.UnexpectedInput):
raise
else:
original_handler(ui, exc)
md.InputUI.handle_exception = handler
def input_to_file(self, path_to_file, temporary=True):
content.write_file(path_to_file, self())

8
tests/str_fixtures.py
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@ -69,7 +69,7 @@ bibtex_no_citekey = """@Manual{,
}
"""
bibtex_month= """@inproceedings{Goyal2017,
bibtex_month = """@inproceedings{Goyal2017,
author = {Goyal, Anirudh and Sordoni, Alessandro and C{\^{o}}t{\'{e}}, Marc-Alexandre and Ke, Nan Rosemary and Bengio, Yoshua},
title = {Z-Forcing: Training Stochastic Recurrent Networks},
year = {2017},
@ -78,6 +78,12 @@ bibtex_month= """@inproceedings{Goyal2017,
}
"""
not_bibtex = """@misc{this looks,
like = a = bibtex file but
, is not a real one!
"""
sample_conf = """
[main]

4
tests/test_apis.py
View File

@ -32,7 +32,7 @@ class TestDOI2Bibtex(unittest.TestCase):
def test_parse_fails_on_incorrect_DOI(self):
bib = doi2bibtex('999999')
with self.assertRaises(ValueError):
with self.assertRaises(EnDecoder.BibDecodingError):
self.endecoder.decode_bibdata(bib)
@ -56,7 +56,7 @@ class TestISBN2Bibtex(unittest.TestCase):
def test_parse_fails_on_incorrect_ISBN(self):
bib = doi2bibtex('9' * 13)
with self.assertRaises(ValueError):
with self.assertRaises(EnDecoder.BibDecodingError):
self.endecoder.decode_bibdata(bib)

7
tests/test_endecoder.py
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@ -52,7 +52,7 @@ class TestEnDecode(unittest.TestCase):
self.assertEqual(bibraw1, bibraw2)
def test_endecode_bibtex(self):
def test_endecode_bibtex_converts_month_string(self):
"""Test if `month=dec` is correctly recognized and transformed into
`month={December}`"""
decoder = endecoder.EnDecoder()
@ -147,6 +147,11 @@ class TestEnDecode(unittest.TestCase):
self.assertIn('author', entry1)
self.assertIn('institution', entry1)
def test_endecodes_raises_exception(self):
decoder = endecoder.EnDecoder()
with self.assertRaises(decoder.BibDecodingError):
decoder.decode_bibdata("@misc{I am not a correct bibtex{{}")
if __name__ == '__main__':
unittest.main()

66
tests/test_usecase.py
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@ -128,7 +128,7 @@ class CommandTestCase(fake_env.TestFakeFs):
outs.append(color.undye(actual_out))
else:
pubs_cmd.execute(actual_cmd.split())
except fake_env.FakeInput.UnexpectedInput as e:
except fake_env.FakeInput.UnexpectedInput:
self.fail('Unexpected input asked by command: {}.'.format(
actual_cmd))
return outs
@ -197,7 +197,7 @@ class TestAlone(CommandTestCase):
def test_alone_misses_command(self):
with self.assertRaises(FakeSystemExit) as cm:
self.execute_cmds(['pubs'])
self.assertEqual(cm.exception.code, 2)
self.assertEqual(cm.exception.code, 2)
def test_alone_prints_help(self):
# capturing the output of `pubs --help` is difficult because argparse
@ -334,11 +334,20 @@ class TestAdd(URLContentTestCase):
def test_add_no_citekey_fails(self):
# See #113
cmds = ['pubs init',
('pubs add', [str_fixtures.bibtex_no_citekey]),
('pubs add', [str_fixtures.bibtex_no_citekey, 'n']),
]
with self.assertRaises(FakeSystemExit):
self.execute_cmds(cmds)
def test_add_edit_fails(self):
cmds = ['pubs init',
('pubs add',
['@misc{I am not a correct bibtex{{}', 'n']),
]
with self.assertRaises(FakeSystemExit) as cm:
self.execute_cmds(cmds)
self.assertEqual(cm.exception.code, 1)
class TestList(DataCommandTestCase):
@ -679,16 +688,40 @@ class TestUsecase(DataCommandTestCase):
self.assertFileContentEqual(os.path.expanduser('~/.pubsrc'),
str_fixtures.sample_conf)
def test_editor_abort(self):
def test_editor_aborts(self):
with self.assertRaises(FakeSystemExit):
cmds = ['pubs init',
('pubs add', ['abc', 'n']),
('pubs add', ['abc', 'y', 'abc', 'n']),
'pubs add data/pagerank.bib',
('pubs edit Page99', ['', 'a']),
('pubs edit Page99', ['', 'n']),
]
self.execute_cmds(cmds)
def test_editor_succeeds_on_second_edit(self):
cmds = ['pubs init',
'pubs add data/pagerank.bib',
('pubs edit Page99', [
'@misc{Page99, title="TTT" author="X. YY"}', 'y',
'@misc{Page99, title="TTT", author="X. YY"}', '']),
('pubs list', [], '[Page99] YY, X. "TTT" \n')
]
self.execute_cmds(cmds)
def test_add_aborts(self):
with self.assertRaises(FakeSystemExit):
cmds = ['pubs init',
('pubs add New', ['']),
]
self.execute_cmds(cmds)
def test_add_succeeds_on_second_edit(self):
cmds = ['pubs init',
('pubs add', [
'', 'y',
'@misc{New, title="TTT", author="X. YY"}', '']),
('pubs list', [], '[New] YY, X. "TTT" \n')
]
self.execute_cmds(cmds)
def test_editor_success(self):
cmds = ['pubs init',
('pubs add', [str_fixtures.bibtex_external0]),
@ -790,6 +823,25 @@ class TestUsecase(DataCommandTestCase):
outs = self.execute_cmds(cmds)
self.assertEqual(1 + 1, len(outs[-1].split('\n')))
def test_import_fails_without_ignore(self):
with FakeFileOpen(self.fs)('data/fake.bib', 'w') as f:
f.write(str_fixtures.not_bibtex)
cmds = ['pubs init',
'pubs import data/ Page99',
]
with self.assertRaises(FakeSystemExit):
self.execute_cmds(cmds)
def test_import_ignores(self):
with FakeFileOpen(self.fs)('data/fake.bib', 'w') as f:
f.write(str_fixtures.not_bibtex)
cmds = ['pubs init',
'pubs import --ignore-malformed data/ Page99',
'pubs list'
]
outs = self.execute_cmds(cmds)
self.assertEqual(1 + 1, len(outs[-1].split('\n')))
def test_update(self):
cmds = ['pubs init',
'pubs add data/pagerank.bib',