handle / in citekeys

pubs/apis.py

@@ -15,7 +15,7 @@ class ReferenceNotFoundError(Exception):
     pass
 
 
-def get_bibentry_from_api(id_str, id_type, try_doi=True, ui=None):
+def get_bibentry_from_api(id_str, id_type, try_doi=True, ui=None, raw=False):
     """Return a bibtex string from various ID methods.
 
     This is a wrapper around functions that will return a bibtex string given
@@ -50,6 +50,9 @@ def get_bibentry_from_api(id_str, id_type, try_doi=True, ui=None):
         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)
+    if raw:
+        return bibentry_raw
+
     bibentry = endecoder.EnDecoder().decode_bibdata(bibentry_raw)
     if bibentry is None:
         raise ReferenceNotFoundError(

pubs/bibstruct.py

@@ -51,7 +51,7 @@ def author_last(author_str):
     return author_str.split(',')[0]
 
 
-def generate_citekey(bibdata):
+def generate_citekey(bibdata, generate=True):
     """ Generate a citekey from bib_data.
 
         :param generate:  if False, return the citekey defined in the file,

pubs/commands/__init__.py

@@ -18,3 +18,4 @@ from . import import_cmd
 # bonus
 from . import websearch_cmd
 from . import url_cmd
+#from . import bibtex_cmd

pubs/commands/add_cmd.py

@@ -72,6 +72,22 @@ def bibentry_from_editor(conf, ui):
     return bibentry
 
 
+def bibentry_from_api(args, ui, raw=False):
+    try:
+        if args.doi is not None:
+            return apis.get_bibentry_from_api(args.doi, 'doi', ui=ui, raw=raw)
+        elif args.isbn is not None:
+            return apis.get_bibentry_from_api(args.isbn, 'isbn', ui=ui, raw=raw)
+            # TODO distinguish between cases, offer to open the error page in a webbrowser.
+            # TODO offer to confirm/change citekey
+        elif args.arxiv is not None:
+            return apis.get_bibentry_from_api(args.arxiv, 'arxiv', ui=ui, raw=raw)
+    except apis.ReferenceNotFoundError as e:
+        ui.error(str(e))
+        ui.exit(1)
+
+
+
 def command(conf, args):
     """
     :param bibfile: bibtex file (in .bib, .bibml or .yaml format.
@@ -92,19 +108,7 @@ def command(conf, args):
         if args.doi is None and args.isbn is None and args.arxiv is None:
             bibentry = bibentry_from_editor(conf, ui)
         else:
-            bibentry = None
-            try:
-                if args.doi is not None:
-                    bibentry = apis.get_bibentry_from_api(args.doi, 'doi', ui=ui)
-                elif args.isbn is not None:
-                    bibentry = apis.get_bibentry_from_api(args.isbn, 'isbn', ui=ui)
-                    # TODO distinguish between cases, offer to open the error page in a webbrowser.
-                    # 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.ReferenceNotFoundError as e:
-                ui.error(str(e))
-                ui.exit(1)
+            bibentry = bibentry_from_api(args, ui)
     else:
         bibentry_raw = content.get_content(bibfile, ui=ui)
         bibentry = decoder.decode_bibdata(bibentry_raw)
@@ -116,7 +120,7 @@ def command(conf, args):
     citekey = args.citekey
     if citekey is None:
         base_key = bibstruct.extract_citekey(bibentry)
-        citekey = rp.unique_citekey(base_key)
+        citekey = rp.unique_citekey(base_key, bibentry)
     elif citekey in rp:
         ui.error('citekey already exist {}.'.format(citekey))
         ui.exit(1)

pubs/commands/import_cmd.py

@@ -14,26 +14,28 @@ from ..content import system_path, read_text_file
 from ..command_utils import add_doc_copy_arguments
 
 
-_ABORT_USE_IGNORE_MSG = "Aborting import. Use --ignore-malformed to ignore."
+_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')
+        help='import paper(s) to the repository.')
     parser.add_argument(
         'bibpath',
-        help='path to bibtex, bibtexml or bibyaml file (or directory)')
+        help=("path to bibtex, bibtexml or bibyaml file, or a directory "
+              "containing such files; will not recurse into subdirectories."))
     parser.add_argument(
         'keys', nargs='*',
-        help="one or several keys to import from the file")
+        help=("one or several keys to import from the file; if not provided,"
+              " all entries will be imported."))
     parser.add_argument(
         '-O', '--overwrite', action='store_true', default=False,
-        help="Overwrite keys already in the database")
+        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")
+        help="ignore malformed and unreadable files and entries.")
     add_doc_copy_arguments(parser, copy=False)
     return parser
 

pubs/p3.py

@@ -87,10 +87,14 @@ else:
             super(StdIO, self).__init__(*args, **kwargs)
 
         def write(self, s):
+            super(StdIO, self).write(s)
             if self.additional_out is not None:
+                try:
+                    s = s.decode()
+                except AttributeError:
+                    pass
                 self.additional_out.write(s)
 
-            super(StdIO, self).write(s)
 
     # Only for tests to capture std{out,err}
     def _fake_stdio(additional_out=False):

pubs/pubs_cmd.py

@@ -32,6 +32,7 @@ CORE_CMDS = collections.OrderedDict([
 
     ('websearch', commands.websearch_cmd),
     ('url', commands.url_cmd),
+    #('bibtex', commands.bibtex_cmd),
 ])
 
 

pubs/repo.py

@@ -192,8 +192,16 @@ class Repository(object):
         p.docpath = docfile
         self.push_paper(p, overwrite=True, event=False)
 
-    def unique_citekey(self, base_key):
-        """Create a unique citekey for a given basekey."""
+    def unique_citekey(self, base_key, bibentry):
+        """Create a unique citekey for a given base key.
+
+        :param base_key:  the base key in question.
+        :param bibentry:  the bib entry to possibly generate the citekey.
+        """
+        # can't have `/` in citekeys
+        # FIXME: a bit crude, but efficient for now (and allows unicode citekeys)
+        if '/' in base_key:
+            base_key = bibstruct.generate_citekey(bibentry)
         for n in itertools.count():
             if not base_key + _base27(n) in self.citekeys:
                 return base_key + _base27(n)

readme.md

@@ -86,7 +86,7 @@ and then add `\cite{Loeb_2012}` in your manuscript. After exporting the bibliogr
 
 You can attach a document to a reference:
   ```
-  pubs add Loeb2012_downloaded.pdf Loeb_2012
+  pubs doc add Loeb2012_downloaded.pdf Loeb_2012
   ```
 
 And open your documents automatically from the command line:

tests/data/collection.bib

@@ -0,0 +1,41 @@
+@article{Einstein_1935,
+	doi = {10.1103/physrev.47.777},
+	url = {https://doi.org/10.1103%2Fphysrev.47.777},
+	year = 1935,
+	month = {may},
+	publisher = {American Physical Society ({APS})},
+	volume = {47},
+	number = {10},
+	pages = {777--780},
+	author = {A. Einstein and B. Podolsky and N. Rosen},
+	title = {Can Quantum-Mechanical Description of Physical Reality Be Considered Complete?},
+	journal = {Physical Review}
+}
+
+@article{Schrodinger_1935,
+	doi = {10.1017/s0305004100013554},
+	url = {https://doi.org/10.1017%2Fs0305004100013554},
+	year = 1935,
+	month = {oct},
+	publisher = {Cambridge University Press ({CUP})},
+	volume = {31},
+	number = {04},
+	pages = {555},
+	author = {E. Schrödinger and M. Born},
+	title = {Discussion of Probability Relations between Separated Systems},
+	journal = {Mathematical Proceedings of the Cambridge Philosophical Society}
+}
+
+@article{Bell_1964,
+	doi = {10.1103/physicsphysiquefizika.1.195},
+	url = {https://doi.org/10.1103%2Fphysicsphysiquefizika.1.195},
+	year = 1964,
+	month = {nov},
+	publisher = {American Physical Society ({APS})},
+	volume = {1},
+	number = {3},
+	pages = {195--200},
+	author = {J. S. Bell},
+	title = {On the Einstein Podolsky Rosen paradox},
+	journal = {Physics Physique {\cyrchar\cyrf}{\cyrchar\cyri}{\cyrchar\cyrz}{\cyrchar\cyri}{\cyrchar\cyrk}{\cyrchar\cyra}}
+}

tests/readme.md

@@ -1,7 +1,11 @@
 1. Install the dependencies using:
-> pip install -r requirements.txt
+```
+pip install -r ../dev_requirements.txt
+```
 
 2. Run the tests using:
-> python -m unittest discover
+```
+python setup.py test
+```
 
 If you use nosetest, it will complain about addExpectedFailure, which you can safely disregard.

tests/test_apis.py

@@ -16,8 +16,12 @@ import mock_requests
 
 
 class APITests(unittest.TestCase):
-    pass
 
+    @mock.patch('pubs.apis.requests.get', side_effect=mock_requests.mock_requests_get)
+    def test_readme(self, reqget):
+        apis.doi2bibtex('10.1007/s00422-012-0514-6')
+        apis.isbn2bibtex('978-0822324669')
+        apis.arxiv2bibtex('math/9501234')
 
 class TestDOI2Bibtex(APITests):
 

tests/test_repo.py

@@ -29,10 +29,12 @@ class TestCitekeyGeneration(TestRepo):
 
     def test_generated_key_is_unique(self):
         self.repo.push_paper(Paper.from_bibentry(fixtures.doe_bibentry))
-        c = self.repo.unique_citekey('Doe2013')
+        c = self.repo.unique_citekey('Doe2013', fixtures.doe_bibentry)
         self.repo.push_paper(Paper.from_bibentry(fixtures.doe_bibentry,
                                                  citekey='Doe2013a'))
-        c = self.repo.unique_citekey('Doe2013')
+        c = self.repo.unique_citekey('Doe2013', fixtures.doe_bibentry)
+        self.assertEqual(c, 'Doe2013b')
+        c = self.repo.unique_citekey('bla/bla', fixtures.doe_bibentry)
         self.assertEqual(c, 'Doe2013b')
 
 

tests/test_usecase.py

@@ -10,10 +10,13 @@ import mock
 
 import six
 import ddt
+import certifi
+import mock
 from pyfakefs.fake_filesystem import FakeFileOpen
 
 import dotdot
 import fake_env
+import mock_requests
 
 from pubs import pubs_cmd, color, content, uis, p3, endecoder
 from pubs.config import conf
@@ -153,9 +156,10 @@ class DataCommandTestCase(CommandTestCase):
         super(DataCommandTestCase, self).setUp(nsec_stat=nsec_stat)
         self.fs.add_real_directory(os.path.join(self.rootpath, 'data'), read_only=False)
         self.fs.add_real_directory(os.path.join(self.rootpath, 'bibexamples'), read_only=False)
+        # add certificate for web querries
+        self.fs.add_real_file(certifi.where(), read_only=True)
+        self.fs.add_real_file(mock_requests._data_filepath, read_only=False)
 
-        # fake_env.copy_dir(self.fs, os.path.join(os.path.dirname(__file__), 'data'), 'data')
-        # fake_env.copy_dir(self.fs, os.path.join(os.path.dirname(__file__), 'bibexamples'), 'bibexamples')
 
     def assertFileContentEqual(self, path, expected_content):
         self.assertTrue(os.path.isfile(path))
@@ -849,7 +853,7 @@ class TestUsecase(DataCommandTestCase):
                ]
 
         outs = self.execute_cmds(cmds)
-        self.assertEqual(4 + 1, len(outs[-1].split('\n')))
+        self.assertEqual(8, len(outs[-1].split('\n')))
 
     def test_import_one(self):
         cmds = ['pubs init',
@@ -1002,10 +1006,10 @@ class TestUsecase(DataCommandTestCase):
         self.assertEqual(lines[2], 'Total tags: 3, 2 (50%) of papers have at least one tag')
 
     def test_add_no_extension(self):
-        # This tests checks that a paper which document has no
-        # extension does not raise issues when listing. This test might
-        # be removed if decided to prevent such documents. It would then need
-        # to be replaced by a check that this is prevented.
+        """This tests checks that a paper which document has no extension does
+        not raise issues when listing. This test might be removed if decided to
+        prevent such documents. It would then need to be replaced by a check
+        that this is prevented."""
         self.fs.add_real_file(os.path.join(self.rootpath, 'data', 'pagerank.pdf'),
                               target_path=os.path.join('data', 'no-ext'))
         correct = ['Initializing pubs in /pubs\n',
@@ -1019,6 +1023,26 @@ class TestUsecase(DataCommandTestCase):
                ]
         self.assertEqual(correct, self.execute_cmds(cmds, capture_output=True))
 
+    @mock.patch('pubs.apis.requests.get', side_effect=mock_requests.mock_requests_get)
+    def test_readme(self, reqget):
+        """Test that the readme example work."""
+        self.fs.add_real_file(os.path.join(self.rootpath, 'data/pagerank.pdf'), target_path='data/Loeb_2012.pdf')
+        self.fs.add_real_file(os.path.join(self.rootpath, 'data/pagerank.pdf'), target_path='data/oyama2000the.pdf')
+        self.fs.add_real_file(os.path.join(self.rootpath, 'data/pagerank.pdf'), target_path='data/Knuth1995.pdf')
+
+        cmds = ['pubs init',
+                'pubs import data/collection.bib',
+                'pubs add data/pagerank.bib -d data/pagerank.pdf',
+                #'pubs add -D 10.1007/s00422-012-0514-6 -d data/pagerank.pdf',
+                'pubs add -I 978-0822324669 -d data/oyama2000the.pdf',
+                'pubs add -X math/9501234 -d data/Knuth1995.pdf',
+                'pubs add -D 10.1007/s00422-012-0514-6',
+                'pubs doc add data/Loeb_2012.pdf Loeb_2012',
+               ]
+        self.execute_cmds(cmds, capture_output=True)
+#        self.assertEqual(correct, self.execute_cmds(cmds, capture_output=True))
+
+
 
 @ddt.ddt
 class TestCache(DataCommandTestCase):