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Merge pull request #167 from pubs/fix/doi_stats

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Fix/doi stats
This commit is contained in:
Fabien C. Y. Benureau 2018-08-28 10:20:13 +09:00 committed by GitHub
commit 047e11f1f8
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12 changed files with 84 additions and 74 deletions
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20
pubs/apis.py
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@ -8,6 +8,8 @@ from bibtexparser.bibdatabase import BibDatabase
import feedparser
from bs4 import BeautifulSoup
from . import endecoder
class ReferenceNotFoundError(Exception):
pass
@ -34,7 +36,7 @@ def get_bibentry_from_api(id_str, id_type, try_doi=True, ui=None):
Raises:
ValueError: if `id_type` is not one of `doi`, `isbn`, or `arxiv`.
apis.ReferenceNotFoundException: if no valid reference could be found.
apis.ReferenceNotFoundError: if no valid reference could be found.
"""
id_fns = {
@ -43,13 +45,14 @@ def get_bibentry_from_api(id_str, id_type, try_doi=True, ui=None):
'arxiv': arxiv2bibtex,
}
id_type = id_type.lower()
if id_type not in id_fns.keys():
raise ValueError('id_type must be one of `doi`, `isbn`, or `arxiv`.')
bibentry_raw = id_fns[id_type](id_str, try_doi=try_doi, ui=ui)
endecoder.EnDecoder().decode_bibdata(bibentry_raw)
bibentry = endecoder.EnDecoder().decode_bibdata(bibentry_raw)
if bibentry is None:
raise ReferenceNotFoundException(
raise ReferenceNotFoundError(
'invalid {} {} or unable to retrieve bibfile from it.'.format(id_type, id_str))
return bibentry
@ -72,7 +75,7 @@ def _get_request(url, headers=None):
## DOI support
def doi2bibtex(doi, **kwargs):
"""Return a bibtex string of metadata from a DOI"""
"""Return a bibtex string from a DOI"""
url = 'https://dx.doi.org/{}'.format(doi)
headers = {'accept': 'application/x-bibtex'}
@ -87,13 +90,16 @@ def doi2bibtex(doi, **kwargs):
def isbn2bibtex(isbn, **kwargs):
"""Return a bibtex string of metadata from an ISBN"""
"""Return a bibtex string from an ISBN"""
url = 'https://www.ottobib.com/isbn/{}/bibtex'.format(isbn)
r = _get_request(url)
soup = BeautifulSoup(r.text, "html.parser")
citation = soup.find("textarea").text
if len(citation) == 0:
raise ReferenceNotFoundError("No information could be retrieved about ISBN '{}'. ISBN databases are notoriously incomplete. If the ISBN is correct, you may have to enter information manually by invoking 'pubs add' without the '-I' argument.".format(isbn))
return citation
# Note: apparently ottobib.com uses caracter modifiers for accents instead
@ -106,7 +112,7 @@ _months = ['jan', 'feb', 'mar', 'apr', 'may', 'jun',
'jul', 'aug', 'sep', 'oct', 'nov', 'dec']
def _is_arxiv_oldstyle(arxiv_id):
return re.match(r"(arXiv\:)?[a-z\-]+\/[0-9]+(v[0-9]+)?", arxiv_id) is not None
return re.match(r"(arxiv\:)?[a-z\-]+\/[0-9]+(v[0-9]+)?", arxiv_id.lower()) is not None
def _extract_arxiv_id(entry):
pattern = r"http[s]?://arxiv.org/abs/(?P<entry_id>.+)"
@ -114,7 +120,7 @@ def _extract_arxiv_id(entry):
def arxiv2bibtex(arxiv_id, try_doi=True, ui=None):
"""Return a bibtex string of metadata from an arXiv ID
"""Return a bibtex string from an arXiv ID
:param arxiv_id: arXiv id, with or without the `arXiv:` prefix and version
suffix (e.g. `v1`). Old an new style are accepted. Here are

4
pubs/commands/add_cmd.py
View File

@ -102,8 +102,8 @@ def command(conf, args):
# TODO offer to confirm/change citekey
elif args.arxiv is not None:
bibentry = apis.get_bibentry_from_api(args.arxiv, 'arxiv', ui=ui)
except apis.ReferenceNotFoundException as e:
ui.error(e.message)
except apis.ReferenceNotFoundError as e:
ui.error(str(e))
ui.exit(1)
else:
bibentry_raw = content.get_content(bibfile, ui=ui)

2
pubs/commands/conf_cmd.py
View File

@ -25,7 +25,7 @@ def command(conf, args):
ui.message('The configuration file was updated.')
break
except AssertionError as e: # TODO better error message
ui.error('Error reading the modified configuration file [' + e.message + '].')
ui.error('Error reading the modified configuration file [' + str(e) + '].')
options = ['edit_again', 'abort']
choice = options[ui.input_choice(
options, ['e', 'a'],

32
pubs/commands/statistics_cmd.py
View File

@ -16,18 +16,22 @@ def command(conf, args):
papers = list(rp.all_papers())
paper_count = len(papers)
doc_count = sum([0 if p.docpath is None else 1 for p in papers])
tag_count = len(list(rp.get_tags()))
papers_with_tags = sum([0 if p.tags else 1 for p in papers])
if paper_count == 0:
ui.message('Your pubs repository is empty.')
ui.message(color.dye_out('Repository statistics:', 'bold'))
ui.message('Total papers: {}, {} ({}) have a document attached'.format(
color.dye_out('{:d}'.format(paper_count), 'bgreen'),
color.dye_out('{:d}'.format(doc_count), 'bold'),
'{:.0f}%'.format(100. * doc_count / paper_count),
))
ui.message('Total tags: {}, {} ({}) of papers have at least one tag'.format(
color.dye_out('{:d}'.format(tag_count), 'bgreen'),
color.dye_out('{:d}'.format(papers_with_tags), 'bold'),
'{:.0f}%'.format(100. * papers_with_tags / paper_count),
))
else:
doc_count = sum([0 if p.docpath is None else 1 for p in papers])
tag_count = len(list(rp.get_tags()))
papers_with_tags = sum([0 if p.tags else 1 for p in papers])
ui.message(color.dye_out('Repository statistics:', 'bold'))
ui.message('Total papers: {}, {} ({}) have a document attached'.format(
color.dye_out('{:d}'.format(paper_count), 'bgreen'),
color.dye_out('{:d}'.format(doc_count), 'bold'),
'{:.0f}%'.format(100. * doc_count / paper_count),
))
ui.message('Total tags: {}, {} ({}) of papers have at least one tag'.format(
color.dye_out('{:d}'.format(tag_count), 'bgreen'),
color.dye_out('{:d}'.format(papers_with_tags), 'bold'),
'{:.0f}%'.format(100. * papers_with_tags / paper_count),
))

3
pubs/databroker.py
View File

@ -48,7 +48,8 @@ class DataBroker(object):
try:
return self.endecoder.decode_bibdata(bibdata_raw)
except self.endecoder.BibDecodingError as e:
e.message = "Unable to decode bibtex for paper {}.".format(citekey)
# QUESTION: do we really want to obscure a more precise error message here?
e.args = "Unable to decode bibtex for paper {}.".format(citekey)
raise e
def push_metadata(self, citekey, metadata):

2
pubs/endecoder.py
View File

@ -80,7 +80,7 @@ class EnDecoder(object):
:param error_msg: specific message about what went wrong
:param bibdata: the data that was unsuccessfully decoded.
"""
super(Exception, self).__init__(error_msg) # make `str(self)` work.
super(Exception, self).__init__(error_msg) # make `str(self)` work.
self.data = bibdata
bwriter = bp.bwriter.BibTexWriter()

6
pubs/pubs_cmd.py
View File

@ -69,10 +69,11 @@ def execute(raw_args=sys.argv):
uis.init_ui(conf, force_colors=top_args.force_colors)
ui = uis.get_ui()
parser = p3.ArgumentParser(description="research papers repository",
desc = 'Pubs: your bibliography on the command line.\nVisit https://github.com/pubs/pubs for more information.'
parser = p3.ArgumentParser(description=desc,
prog="pubs", add_help=True)
parser.add_argument('--version', action='version', version=__version__)
subparsers = parser.add_subparsers(title="valid commands", dest="command")
subparsers = parser.add_subparsers(title="commands", dest="command")
# Populate the parser with core commands
for cmd_name, cmd_mod in CORE_CMDS.items():
@ -91,7 +92,6 @@ def execute(raw_args=sys.argv):
# if no command, print help and exit peacefully (as '--help' does)
args = parser.parse_args(remaining_args)
if not args.command:
ui.error("Too few arguments!\n")
parser.print_help(file=sys.stderr)
sys.exit(2)

3
pubs/uis.py
View File

@ -6,6 +6,7 @@ import shlex
import locale
import codecs
import tempfile
import traceback
import subprocess
from . import color
@ -87,7 +88,7 @@ class PrintUI(object):
if DEBUG_ALL_TRACES: # if an exception has been raised, print the trace.
if sys.exc_info()[0] is not None:
traceback.print_exception(*sys.exc_info)
traceback.print_exception(*sys.exc_info())
def exit(self, error_code=1):
sys.exit(error_code)

2
pubs/utils.py
View File

@ -82,7 +82,7 @@ def standardize_doi(doi):
match = doi_pattern.search(doi)
if not match:
raise ValueError("Not a valid doi: %s", doi)
raise ValueError("Not a valid doi: {}".format(doi))
new_doi = match.group(0)
return new_doi

8
setup.py
View File

@ -1,4 +1,5 @@
#!/usr/bin/env python
import os
import unittest
from setuptools import setup
@ -6,6 +7,10 @@ from setuptools import setup
with open('pubs/version.py') as f:
exec(f.read()) # defines __version__
here = os.path.abspath(os.path.dirname(__file__))
with open(os.path.join(here, 'readme.md'), 'r') as fd:
long_description = fd.read()
def pubs_test_suite():
test_loader = unittest.TestLoader()
test_suite = test_loader.discover('tests', pattern='test_*.py')
@ -20,6 +25,9 @@ setup(
url='https://github.com/pubs/pubs',
description='command-line scientific bibliography manager',
long_description=long_description,
long_description_content_type='text/markdown',
packages=['pubs',
'pubs.config',
'pubs.commands',

73
tests/test_apis.py
View File

@ -9,34 +9,29 @@ import mock
import dotdot
from pubs.p3 import ustr
from pubs.endecoder import EnDecoder
from pubs.apis import ReferenceNotFoundError, arxiv2bibtex, doi2bibtex, isbn2bibtex, _is_arxiv_oldstyle, _extract_arxiv_id
from pubs import apis
from pubs.apis import _is_arxiv_oldstyle, _extract_arxiv_id
import mock_requests
class APITests(unittest.TestCase):
def setUp(self):
self.endecoder = EnDecoder()
pass
class TestDOI2Bibtex(APITests):
@mock.patch('pubs.apis.requests.get', side_effect=mock_requests.mock_requests_get)
def test_unicode(self, reqget):
bib = doi2bibtex('10.1007/BF01700692')
bib = apis.doi2bibtex('10.1007/BF01700692')
self.assertIsInstance(bib, ustr)
self.assertIn('Kurt Gödel', bib)
@mock.patch('pubs.apis.requests.get', side_effect=mock_requests.mock_requests_get)
def test_parses_to_bibtex(self, reqget):
bib = doi2bibtex('10.1007/BF01700692')
b = self.endecoder.decode_bibdata(bib)
self.assertEqual(len(b), 1)
entry = b[list(b)[0]]
bib = apis.get_bibentry_from_api('10.1007/BF01700692', 'DOI')
self.assertEqual(len(bib), 1)
entry = bib[list(bib)[0]]
self.assertEqual(entry['author'][0], 'Gödel, Kurt')
self.assertEqual(entry['title'],
'Über formal unentscheidbare Sätze der Principia '
@ -45,59 +40,54 @@ class TestDOI2Bibtex(APITests):
@mock.patch('pubs.apis.requests.get', side_effect=mock_requests.mock_requests_get)
def test_retrieve_fails_on_incorrect_DOI(self, reqget):
with self.assertRaises(apis.ReferenceNotFoundError):
doi2bibtex('999999')
apis.get_bibentry_from_api('999999', 'doi')
class TestISBN2Bibtex(APITests):
@mock.patch('pubs.apis.requests.get', side_effect=mock_requests.mock_requests_get)
def test_unicode(self, reqget):
bib = isbn2bibtex('9782081336742')
bib = apis.isbn2bibtex('9782081336742')
self.assertIsInstance(bib, ustr)
self.assertIn('Poincaré, Henri', bib)
@mock.patch('pubs.apis.requests.get', side_effect=mock_requests.mock_requests_get)
def test_parses_to_bibtex(self, reqget):
bib = isbn2bibtex('9782081336742')
b = self.endecoder.decode_bibdata(bib)
self.assertEqual(len(b), 1)
entry = b[list(b)[0]]
bib = apis.get_bibentry_from_api('9782081336742', 'ISBN')
self.assertEqual(len(bib), 1)
entry = bib[list(bib)[0]]
self.assertEqual(entry['author'][0], 'Poincaré, Henri')
self.assertEqual(entry['title'], 'La science et l\'hypothèse')
@mock.patch('pubs.apis.requests.get', side_effect=mock_requests.mock_requests_get)
def test_retrieve_fails_on_incorrect_ISBN(self, reqget):
bib = isbn2bibtex('9' * 13)
with self.assertRaises(EnDecoder.BibDecodingError):
self.endecoder.decode_bibdata(bib)
with self.assertRaises(apis.ReferenceNotFoundError):
apis.get_bibentry_from_api('9' * 13, 'isbn')
class TestArxiv2Bibtex(APITests):
@mock.patch('pubs.apis.requests.get', side_effect=mock_requests.mock_requests_get)
def test_new_style(self, reqget):
bib = arxiv2bibtex('astro-ph/9812133')
b = self.endecoder.decode_bibdata(bib)
self.assertEqual(len(b), 1)
entry = b[list(b)[0]]
bib = apis.get_bibentry_from_api('astro-ph/9812133', 'arXiv')
self.assertEqual(len(bib), 1)
entry = bib[list(bib)[0]]
self.assertEqual(entry['author'][0], 'Perlmutter, S.')
self.assertEqual(entry['year'], '1999')
@mock.patch('pubs.apis.requests.get', side_effect=mock_requests.mock_requests_get)
def test_parses_to_bibtex_with_doi(self, reqget):
bib = arxiv2bibtex('astro-ph/9812133')
b = self.endecoder.decode_bibdata(bib)
self.assertEqual(len(b), 1)
entry = b[list(b)[0]]
bib = apis.get_bibentry_from_api('astro-ph/9812133', 'arxiv')
self.assertEqual(len(bib), 1)
entry = bib[list(bib)[0]]
self.assertEqual(entry['author'][0], 'Perlmutter, S.')
self.assertEqual(entry['year'], '1999')
@mock.patch('pubs.apis.requests.get', side_effect=mock_requests.mock_requests_get)
def test_parses_to_bibtex_without_doi(self, reqget):
bib = arxiv2bibtex('math/0211159')
b = self.endecoder.decode_bibdata(bib)
self.assertEqual(len(b), 1)
entry = b[list(b)[0]]
bib = apis.get_bibentry_from_api('math/0211159', 'ARXIV')
self.assertEqual(len(bib), 1)
entry = bib[list(bib)[0]]
self.assertEqual(entry['author'][0], 'Perelman, Grisha')
self.assertEqual(entry['year'], '2002')
self.assertEqual(
@ -106,31 +96,28 @@ class TestArxiv2Bibtex(APITests):
@mock.patch('pubs.apis.requests.get', side_effect=mock_requests.mock_requests_get)
def test_arxiv_wrong_id(self, reqget):
with self.assertRaises(ReferenceNotFoundError):
bib = arxiv2bibtex('INVALIDID')
with self.assertRaises(apis.ReferenceNotFoundError):
bib = apis.get_bibentry_from_api('INVALIDID', 'arxiv')
@mock.patch('pubs.apis.requests.get', side_effect=mock_requests.mock_requests_get)
def test_arxiv_wrong_doi(self, reqget):
bib = arxiv2bibtex('1312.2021')
b = self.endecoder.decode_bibdata(bib)
entry = b[list(b)[0]]
bib = apis.get_bibentry_from_api('1312.2021', 'arXiv')
entry = bib[list(bib)[0]]
self.assertEqual(entry['arxiv_doi'], '10.1103/INVALIDDOI.89.084044')
@mock.patch('pubs.apis.requests.get', side_effect=mock_requests.mock_requests_get)
def test_arxiv_good_doi(self, reqget):
"""Get the DOI bibtex instead of the arXiv one if possible"""
bib = arxiv2bibtex('1710.08557')
b = self.endecoder.decode_bibdata(bib)
entry = b[list(b)[0]]
bib = apis.get_bibentry_from_api('1710.08557', 'arXiv')
entry = bib[list(bib)[0]]
self.assertTrue(not 'arxiv_doi' in entry)
self.assertEqual(entry['doi'], '10.1186/s12984-017-0305-3')
self.assertEqual(entry['title'].lower(), 'on neuromechanical approaches for the study of biological and robotic grasp and manipulation')
@mock.patch('pubs.apis.requests.get', side_effect=mock_requests.mock_requests_get)
def test_arxiv_good_doi_force_arxiv(self, reqget):
bib = arxiv2bibtex('1710.08557', try_doi=False)
b = self.endecoder.decode_bibdata(bib)
entry = b[list(b)[0]]
bib = apis.get_bibentry_from_api('1710.08557', 'arXiv', try_doi=False)
entry = bib[list(bib)[0]]
self.assertEqual(entry['arxiv_doi'], '10.1186/s12984-017-0305-3')
self.assertEqual(entry['title'].lower(), 'on neuromechanical approaches for the study of biological grasp and\nmanipulation')

3
tests/test_usecase.py
View File

@ -984,6 +984,7 @@ class TestUsecase(DataCommandTestCase):
def test_statistics(self):
cmds = ['pubs init',
'pubs statistics',
'pubs add data/pagerank.bib',
'pubs add -d data/turing-mind-1950.pdf data/turing1950.bib',
'pubs add data/martius.bib',
@ -993,6 +994,8 @@ class TestUsecase(DataCommandTestCase):
'pubs statistics',
]
out = self.execute_cmds(cmds)
lines = out[1].splitlines()
self.assertEqual(lines[0], 'Your pubs repository is empty.')
lines = out[-1].splitlines()
self.assertEqual(lines[0], 'Repository statistics:')
self.assertEqual(lines[1], 'Total papers: 4, 1 (25%) have a document attached')