Merge pull request #167 from pubs/fix/doi_stats

Fix/doi stats

pubs/apis.py

@@ -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

pubs/commands/add_cmd.py

@@ -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:
+            except apis.ReferenceNotFoundError as e:
-                ui.error(e.message)
+                ui.error(str(e))
                 ui.exit(1)
     else:
         bibentry_raw = content.get_content(bibfile, ui=ui)

pubs/commands/conf_cmd.py

@@ -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'],

pubs/commands/statistics_cmd.py

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

pubs/databroker.py

@@ -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):

pubs/endecoder.py

@@ -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()

pubs/pubs_cmd.py

@@ -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)
 

pubs/uis.py

@@ -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)

pubs/utils.py

@@ -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

setup.py

@@ -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',

tests/test_apis.py

@@ -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):
-
+    pass
-    def setUp(self):
-        self.endecoder = EnDecoder()
 
 
 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')
+        bib = apis.get_bibentry_from_api('10.1007/BF01700692', 'DOI')
-        b = self.endecoder.decode_bibdata(bib)
+        self.assertEqual(len(bib), 1)
-        self.assertEqual(len(b), 1)
+        entry = bib[list(bib)[0]]
-        entry = b[list(b)[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')
+        bib = apis.get_bibentry_from_api('9782081336742', 'ISBN')
-        b = self.endecoder.decode_bibdata(bib)
+        self.assertEqual(len(bib), 1)
-        self.assertEqual(len(b), 1)
+        entry = bib[list(bib)[0]]
-        entry = b[list(b)[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(apis.ReferenceNotFoundError):
-        with self.assertRaises(EnDecoder.BibDecodingError):
+            apis.get_bibentry_from_api('9' * 13, 'isbn')
-            self.endecoder.decode_bibdata(bib)
 
 
 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')
+        bib = apis.get_bibentry_from_api('astro-ph/9812133', 'arXiv')
-        b = self.endecoder.decode_bibdata(bib)
+        self.assertEqual(len(bib), 1)
-        self.assertEqual(len(b), 1)
+        entry = bib[list(bib)[0]]
-        entry = b[list(b)[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')
+        bib = apis.get_bibentry_from_api('astro-ph/9812133', 'arxiv')
-        b = self.endecoder.decode_bibdata(bib)
+        self.assertEqual(len(bib), 1)
-        self.assertEqual(len(b), 1)
+        entry = bib[list(bib)[0]]
-        entry = b[list(b)[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')
+        bib = apis.get_bibentry_from_api('math/0211159', 'ARXIV')
-        b = self.endecoder.decode_bibdata(bib)
+        self.assertEqual(len(bib), 1)
-        self.assertEqual(len(b), 1)
+        entry = bib[list(bib)[0]]
-        entry = b[list(b)[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):
+        with self.assertRaises(apis.ReferenceNotFoundError):
-            bib = arxiv2bibtex('INVALIDID')
+            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')
+        bib = apis.get_bibentry_from_api('1312.2021', 'arXiv')
-        b = self.endecoder.decode_bibdata(bib)
+        entry = bib[list(bib)[0]]
-        entry = b[list(b)[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')
+        bib = apis.get_bibentry_from_api('1710.08557', 'arXiv')
-        b = self.endecoder.decode_bibdata(bib)
+        entry = bib[list(bib)[0]]
-        entry = b[list(b)[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)
+        bib = apis.get_bibentry_from_api('1710.08557', 'arXiv', try_doi=False)
-        b = self.endecoder.decode_bibdata(bib)
+        entry = bib[list(bib)[0]]
-        entry = b[list(b)[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')
 

tests/test_usecase.py

@@ -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')