Fix tests and terminology.

First this brings a change to the paper API: the terminology of bibdata
and bibentry is clarified: now bibentry is a dictionary of the form
{citekey: bibdata} where bibdata corresponds to the actual dictionary of
bibliographic fields and values {author: ..., year: ...}.
Now bibentry is an attribute of the paper object that is generated from
citekey and bibdata.

This commit fixes all tests in particular an issue with citekey in
bibentry not updated.

Also removes prints in tests and deprecated assertEquals.

Usecase tests now fail if the command ask for unexpected inputs.

Removes queries for user input in attach and add commands (for deletion
of a copied document file). The input was not coherent with tests and is
annoying.

pubs/bibstruct.py

@@ -5,12 +5,12 @@ import re
 
 from .p3 import ustr, uchr
 
-    # citekey stuff
+# Citekey stuff
 
 TYPE_KEY = 'type'
 
 CONTROL_CHARS = ''.join(map(uchr, list(range(0, 32)) + list(range(127, 160))))
-CITEKEY_FORBIDDEN_CHARS = '@\'\\,#}{~%/'  # '/' is OK for bibtex but forbidden
+CITEKEY_FORBIDDEN_CHARS = '@\'\\,#}{~%/ '  # '/' is OK for bibtex but forbidden
 # here since we transform citekeys into filenames
 CITEKEY_EXCLUDE_RE = re.compile('[%s]'
         % re.escape(CONTROL_CHARS + CITEKEY_FORBIDDEN_CHARS))
@@ -75,24 +75,22 @@ def extract_docfile(bibdata, remove=False):
 
         :param remove: remove field after extracting information (default: False)
     """
-    citekey, entry = get_entry(bibdata)
-
     try:
-        if 'file' in entry:
+        if 'file' in bibdata:
-            field = entry['file']
+            field = bibdata['file']
             # Check if this is mendeley specific
             for f in field.split(':'):
                 if len(f) > 0:
                     break
             if remove:
-                entry.pop('file')
+                bibdata.pop('file')
             # This is a hck for Mendeley. Make clean
             if f[0] != '/':
                 f = '/' + f
             return f
-        if 'attachments' in entry:
+        if 'attachments' in bibdata:
-            return entry['attachments']
+            return bibdata['attachments']
-        if 'pdf' in entry:
+        if 'pdf' in bibdata:
-            return entry['pdf']
+            return bibdata['pdf']
     except (KeyError, IndexError):
         return None

pubs/commands/add_cmd.py

@@ -12,7 +12,7 @@ from .. import pretty
 
 def parser(subparsers):
     parser = subparsers.add_parser('add', help='add a paper to the repository')
-    parser.add_argument('bibfile', nargs='?', default = None,
+    parser.add_argument('bibfile', nargs='?', default=None,
                         help='bibtex file')
     parser.add_argument('-D', '--doi', help='doi number to retrieve the bibtex entry, if it is not provided', default=None)
     parser.add_argument('-I', '--isbn', help='isbn number to retrieve the bibtex entry, if it is not provided', default=None)
@@ -26,7 +26,7 @@ def parser(subparsers):
     return parser
 
 
-def bibdata_from_editor(ui, rp):
+def bibentry_from_editor(ui, rp):
     again = True
     bibstr = templates.add_bib
     while again:
@@ -41,8 +41,8 @@ def bibdata_from_editor(ui, rp):
                 if not again:
                     ui.exit(0)
             else:
-                bibdata = rp.databroker.verify(bibstr)
+                bibentry = rp.databroker.verify(bibstr)
-                bibstruct.verify_bibdata(bibdata)
+                bibstruct.verify_bibdata(bibentry)
                 # REFACTOR Generate citykey
                 again = False
         except ValueError:
@@ -52,7 +52,8 @@ def bibdata_from_editor(ui, rp):
             if not again:
                 ui.exit(0)
 
-    return bibdata
+    return bibentry
+
 
 def command(args):
     """
@@ -64,47 +65,47 @@ def command(args):
     bibfile = args.bibfile
     docfile = args.docfile
     tags = args.tags
-    citekey = args.copy
+    citekey = args.citekey
 
     rp = repo.Repository(config())
 
     # get bibtex entry
     if bibfile is None:
         if args.doi is None and args.isbn is None:
-            bibdata = bibdata_from_editor(ui, rp)
+            bibentry = bibentry_from_editor(ui, rp)
         else:
             if args.doi is not None:
-                bibdata_raw = apis.doi2bibtex(args.doi)
+                bibentry_raw = apis.doi2bibtex(args.doi)
-                bibdata = rp.databroker.verify(bibdata_raw)
+                bibentry = rp.databroker.verify(bibentry_raw)
-                if bibdata is None:
+                if bibentry is None:
                     ui.error('invalid doi {} or unable to retrieve bibfile from it.'.format(args.doi))
                     if args.isbn is None:
                         ui.exit(1)
             if args.isbn is not None:
-                bibdata_raw = apis.isbn2bibtex(args.isbn)
+                bibentry_raw = apis.isbn2bibtex(args.isbn)
-                bibdata = rp.databroker.verify(bibdata_raw)
+                bibentry = rp.databroker.verify(bibentry_raw)
-                if bibdata is None:
+                if bibentry is None:
                     ui.error('invalid isbn {} or unable to retrieve bibfile from it.'.format(args.isbn))
                     ui.exit(1)
                 # TODO distinguish between cases, offer to open the error page in a webbrowser.
                 # TODO offer to confirm/change citekey
     else:
-        bibdata_raw = content.get_content(bibfile, ui=ui)
+        bibentry_raw = content.get_content(bibfile, ui=ui)
-        bibdata = rp.databroker.verify(bibdata_raw)
+        bibentry = rp.databroker.verify(bibentry_raw)
-        if bibdata is None:
+        if bibentry is None:
             ui.error('invalid bibfile {}.'.format(bibfile))
 
     # citekey
 
     citekey = args.citekey
     if citekey is None:
-        base_key = bibstruct.extract_citekey(bibdata)
+        base_key = bibstruct.extract_citekey(bibentry)
         citekey = rp.unique_citekey(base_key)
     elif citekey in rp:
         ui.error('citekey already exist {}.'.format(citekey))
         ui.exit(1)
 
-    p = paper.Paper(bibdata, citekey=citekey)
+    p = paper.Paper.from_bibentry(bibentry, citekey=citekey)
 
     # tags
 
@@ -113,7 +114,7 @@ def command(args):
 
     # document file
 
-    bib_docfile = bibstruct.extract_docfile(bibdata)
+    bib_docfile = bibstruct.extract_docfile(bibentry)
     if docfile is None:
         docfile = bib_docfile
     elif bib_docfile is not None:
@@ -126,9 +127,6 @@ def command(args):
         rp.push_paper(p)
         if docfile is not None:
             rp.push_doc(p.citekey, docfile, copy=args.copy)
-            if args.copy:
-                if ui.input_yn('{} has been copied into pubs; should the original be removed?'.format(color.dye(docfile, color.bold))):
-                    content.remove_file(docfile)
         ui.print_('{}\nwas added to pubs.'.format(pretty.paper_oneliner(p)))
     except ValueError as v:
         ui.error(v.message)

pubs/commands/attach_cmd.py

@@ -32,9 +32,6 @@ def command(args):
     try:
         document = args.document
         rp.push_doc(paper.citekey, document, copy=args.copy)
-        if args.copy:
-            if ui.input_yn('{} has been copied into pubs; should the original be removed?'.format(color.dye(document, color.bold))):
-                content.remove_file(document)
         ui.print_('{} attached to {}'.format(color.dye(document, color.bold), color.dye(paper.citekey, color.citekey)))
 
     except ValueError as v:

pubs/commands/edit_cmd.py

@@ -5,6 +5,7 @@ from ..uis import get_ui
 from ..endecoder import EnDecoder
 from ..utils import resolve_citekey
 
+
 def parser(subparsers):
     parser = subparsers.add_parser('edit',
             help='open the paper bibliographic file in an editor')
@@ -34,7 +35,7 @@ def command(args):
         encode = coder.encode_bibdata
         decode = coder.decode_bibdata
         suffix = '.bib'
-        raw_content = encode(paper.bibdata)
+        raw_content = encode(paper.bibentry)
 
     while True:
         # Get new content from user
@@ -44,10 +45,11 @@ def command(args):
             content = decode(raw_content)
 
             if meta:
-                new_paper = Paper(paper.bibdata, citekey=paper.citekey,
+                new_paper = Paper(paper.citekey, paper.bibdata,
                                   metadata=content)
             else:
-                new_paper = Paper(content, metadata=paper.metadata)
+                new_paper = Paper.from_bibentry(content,
+                                                metadata=paper.metadata)
                 rp.rename_paper(new_paper, old_citekey=paper.citekey)
             break
 

pubs/commands/export_cmd.py

@@ -33,7 +33,7 @@ def command(args):
         papers = rp.all_papers()
     bib = {}
     for p in papers:
-        bib[p.citekey] = p.bibentry
+        bib[p.citekey] = p.bibdata
     exporter = endecoder.EnDecoder()
     bibdata_raw = exporter.encode_bibdata(bib)
     ui.print_(bibdata_raw)

pubs/commands/import_cmd.py

@@ -49,12 +49,9 @@ def many_from_path(bibpath):
 
     papers = {}
     for b in biblist:
-        for k in b.keys():
+        for k, b in b.items():
             try:
-                bibdata = {}
+                papers[k] = Paper(k, b)
-                bibdata[k] = b[k]
-
-                papers[k] = Paper(bibdata, citekey=k)
                 papers[k].added = datetime.datetime.now()
             except ValueError as e:
                 papers[k] = e

pubs/commands/list_cmd.py

@@ -73,10 +73,10 @@ def _lower(s, lower=True):
 
 def _check_author_match(paper, query, case_sensitive=False):
     """Only checks within last names."""
-    if not 'author' in paper.bibentry:
+    if not 'author' in paper.bibdata:
         return False
     return any([query in _lower(bibstruct.author_last(p), lower=(not case_sensitive))
-                for p in paper.bibentry['author']])
+                for p in paper.bibdata['author']])
 
 
 
@@ -86,8 +86,8 @@ def _check_tag_match(paper, query, case_sensitive=False):
 
 
 def _check_field_match(paper, field, query, case_sensitive=False):
-    return query in _lower(paper.bibentry[field],
+    return query in _lower(paper.bibdata[field],
-                       lower=(not case_sensitive))
+                           lower=(not case_sensitive))
 
 
 def _check_query_block(paper, query_block, case_sensitive=None):
@@ -100,7 +100,7 @@ def _check_query_block(paper, query_block, case_sensitive=None):
         return _check_tag_match(paper, value, case_sensitive=case_sensitive)
     elif field == 'author':
         return _check_author_match(paper, value, case_sensitive=case_sensitive)
-    elif field in paper.bibentry:
+    elif field in paper.bibdata:
         return _check_field_match(paper, field, value,
                                   case_sensitive=case_sensitive)
     else:

pubs/configs.py

@@ -66,12 +66,12 @@ class Config(object):
         if not check_file(path, fail=False):
             raise IOError(("The configuration file {} does not exist."
                            " Did you run 'pubs init' ?").format(path))
-        with _open(path, 'rb+') as f:
+        with _open(path, 'r+') as f:
             _read_config(self._cfg, f)
         return self
 
     def save(self, path=DFT_CONFIG_PATH):
-        with _open(path, 'wb+') as f:
+        with _open(path, 'w+') as f:
             self._cfg.write(f)
 
     def __setattr__(self, name, value):

pubs/databroker.py

@@ -21,7 +21,7 @@ class DataBroker(object):
         metadata_raw = self.filebroker.pull_metafile(citekey)
         return self.endecoder.decode_metadata(metadata_raw)
 
-    def pull_bibdata(self, citekey):
+    def pull_bibentry(self, citekey):
         bibdata_raw = self.filebroker.pull_bibfile(citekey)
         return self.endecoder.decode_bibdata(bibdata_raw)
 
@@ -29,7 +29,7 @@ class DataBroker(object):
         metadata_raw = self.endecoder.encode_metadata(metadata)
         self.filebroker.push_metafile(citekey, metadata_raw)
 
-    def push_bibdata(self, citekey, bibdata):
+    def push_bibentry(self, citekey, bibdata):
         bibdata_raw = self.endecoder.encode_bibdata(bibdata)
         self.filebroker.push_bibfile(citekey, bibdata_raw)
 

pubs/datacache.py

@@ -31,14 +31,14 @@ class DataCache(object):
     def pull_metadata(self, citekey):
         return self.databroker.pull_metadata(citekey)
 
-    def pull_bibdata(self, citekey):
+    def pull_bibentry(self, citekey):
-        return self.databroker.pull_bibdata(citekey)
+        return self.databroker.pull_bibentry(citekey)
 
     def push_metadata(self, citekey, metadata):
         self.databroker.push_metadata(citekey, metadata)
 
-    def push_bibdata(self, citekey, bibdata):
+    def push_bibentry(self, citekey, bibdata):
-        self.databroker.push_bibdata(citekey, bibdata)
+        self.databroker.push_bibentry(citekey, bibdata)
 
     def push(self, citekey, metadata, bibdata):
         self.databroker.push(citekey, metadata, bibdata)

pubs/paper.py

@@ -28,19 +28,11 @@ class Paper(object):
         in a pythonic manner.
     """
 
-    def __init__(self, bibdata, citekey=None, metadata=None):
+    def __init__(self, citekey, bibdata, metadata=None):
         self.citekey = citekey
         self.metadata = _clean_metadata(metadata)
         self.bibdata = bibdata
-
+        bibstruct.check_citekey(self.citekey)
-        _, self.bibentry = bibstruct.get_entry(self.bibdata)
-
-        if self.citekey is None:
-            self.citekey = bibstruct.extract_citekey(self.bibdata)
-            bibstruct.check_citekey(self.citekey)
-        else:
-            def_citekey = bibstruct.extract_citekey(self.bibdata)
-            self.bibdata = {citekey: self.bibdata[def_citekey]}
 
     def __eq__(self, other):
         return (isinstance(self, Paper) and type(other) is type(self)
@@ -50,15 +42,15 @@ class Paper(object):
 
     def __repr__(self):
         return 'Paper(%s, %s, %s)' % (
-                self.citekey, self.bibentry, self.metadata)
+                self.citekey, self.bibdata, self.metadata)
 
     def __deepcopy__(self, memo):
-        return Paper(citekey =self.citekey,
+        return Paper(citekey=self.citekey,
                      metadata=copy.deepcopy(self.metadata, memo),
                      bibdata=copy.deepcopy(self.bibdata, memo))
 
     def __copy__(self):
-        return Paper(citekey =self.citekey,
+        return Paper(citekey=self.citekey,
                      metadata=self.metadata,
                      bibdata=self.bibdata)
 
@@ -67,6 +59,10 @@ class Paper(object):
 
         # docpath
 
+    @property
+    def bibentry(self):
+        return {self.citekey: self.bibdata}
+
     @property
     def docpath(self):
         return self.metadata.get('docfile', '')
@@ -105,3 +101,10 @@ class Paper(object):
     @added.setter
     def added(self, value):
         self.metadata['added'] = value
+
+    @staticmethod
+    def from_bibentry(bibentry, citekey=None, metadata=None):
+        bibentry_key, bibdata = bibstruct.get_entry(bibentry)
+        if citekey is None:
+            citekey = bibentry_key
+        return Paper(citekey, bibdata, metadata=metadata)

pubs/pretty.py

@@ -1,6 +1,7 @@
 # display formatting
 
 from . import color
+from .bibstruct import TYPE_KEY
 
 
 # should be adaptated to bibtexparser dicts
@@ -12,9 +13,9 @@ def person_repr(p):
         ' '.join(p.lineage(abbr=True))] if s)
 
 
-def short_authors(bibentry):
+def short_authors(bibdata):
     try:
-        authors = [p for p in bibentry['author']]
+        authors = [p for p in bibdata['author']]
         if len(authors) < 3:
             return ' and '.join(authors)
         else:
@@ -23,19 +24,19 @@ def short_authors(bibentry):
         return ''
 
 
-def bib_oneliner(bibentry):
+def bib_oneliner(bibdata):
-    authors = short_authors(bibentry)
+    authors = short_authors(bibdata)
     journal = ''
-    if 'journal' in bibentry:
+    if 'journal' in bibdata:
-        journal = ' ' + bibentry['journal']['name']
+        journal = ' ' + bibdata['journal']['name']
-    elif bibentry['type'] == 'inproceedings':
+    elif bibdata[TYPE_KEY] == 'inproceedings':
-        journal = ' ' + bibentry.get('booktitle', '')
+        journal = ' ' + bibdata.get('booktitle', '')
 
     return u'{authors} \"{title}\"{journal}{year}'.format(
             authors=color.dye(authors, color.grey, bold=True),
-            title=bibentry.get('title', ''),
+            title=bibdata.get('title', ''),
             journal=color.dye(journal, color.yellow),
-            year=' ({})'.format(bibentry['year']) if 'year' in bibentry else '',
+            year=' ({})'.format(bibdata['year']) if 'year' in bibdata else '',
             )
 
 
@@ -48,11 +49,11 @@ def bib_desc(bib_data):
     return s
 
 
-def paper_oneliner(p, citekey_only = False):
+def paper_oneliner(p, citekey_only=False):
     if citekey_only:
         return p.citekey
     else:
-        bibdesc = bib_oneliner(p.bibentry)
+        bibdesc = bib_oneliner(p.bibdata)
         tags = '' if len(p.tags) == 0 else '| {}'.format(
             ','.join(color.dye(t, color.tag) for t in sorted(p.tags)))
         return u'[{citekey}] {descr} {tags}'.format(

pubs/repo.py

@@ -58,9 +58,10 @@ class Repository(object):
     def pull_paper(self, citekey):
         """Load a paper by its citekey from disk, if necessary."""
         if citekey in self:
-            return Paper(self.databroker.pull_bibdata(citekey),
+            return Paper.from_bibentry(
-                         citekey=citekey,
+                self.databroker.pull_bibentry(citekey),
-                         metadata=self.databroker.pull_metadata(citekey))
+                citekey=citekey,
+                metadata=self.databroker.pull_metadata(citekey))
         else:
             raise InvalidReference('{} citekey not found'.format(citekey))
 
@@ -75,7 +76,7 @@ class Repository(object):
             raise CiteKeyCollision('citekey {} already in use'.format(paper.citekey))
         if not paper.added:
             paper.added = datetime.now()
-        self.databroker.push_bibdata(paper.citekey, paper.bibdata)
+        self.databroker.push_bibentry(paper.citekey, paper.bibentry)
         self.databroker.push_metadata(paper.citekey, paper.metadata)
         self.citekeys.add(paper.citekey)
         if event:

tests/fake_env.py

@@ -202,6 +202,9 @@ class FakeInput():
         input() raises IndexError
      """
 
+    class UnexpectedInput(Exception):
+        pass
+
     def __init__(self, inputs, module_list=tuple()):
         self.inputs = list(inputs) or []
         self.module_list = module_list
@@ -218,9 +221,12 @@ class FakeInput():
         self.inputs.append(inp)
 
     def __call__(self, *args, **kwargs):
-        inp = self.inputs[self._cursor]
+        try:
-        self._cursor += 1
+            inp = self.inputs[self._cursor]
-        return inp
+            self._cursor += 1
+            return inp
+        except IndexError:
+            raise self.UnexpectedInput('Unexpected user input in test.')
 
 
 class TestFakeFs(unittest.TestCase):

tests/fixtures.py

@@ -23,18 +23,18 @@ doe_bib = """
 
 dummy_metadata = {'docfile': 'docsdir://hop.la', 'tags': set(['a', 'b'])}
 
-franny_bibdata  = coder.decode_bibdata(franny_bib)
+franny_bibentry = coder.decode_bibdata(franny_bib)
-franny_bibentry = franny_bibdata['Franny1961']
+franny_bibdata  = franny_bibentry['Franny1961']
 
-doe_bibdata     = coder.decode_bibdata(doe_bib)
+doe_bibentry    = coder.decode_bibdata(doe_bib)
-doe_bibentry    = doe_bibdata['Doe2013']
+doe_bibdata     = doe_bibentry['Doe2013']
 
-turing_bibdata  = coder.decode_bibdata(str_fixtures.turing_bib)
+turing_bibentry = coder.decode_bibdata(str_fixtures.turing_bib)
-turing_bibentry = turing_bibdata['turing1950computing']
+turing_bibdata  = turing_bibentry['turing1950computing']
 turing_metadata = coder.decode_metadata(str_fixtures.turing_meta)
 
-page_bibdata    = coder.decode_bibdata(str_fixtures.bibtex_raw0)
+page_bibentry   = coder.decode_bibdata(str_fixtures.bibtex_raw0)
-page_bibentry   = page_bibdata['Page99']
+page_bibdata    = page_bibentry['Page99']
 page_metadata   = coder.decode_metadata(str_fixtures.metadata_raw0)
 
 page_metadata   = coder.decode_metadata(str_fixtures.metadata_raw0)

tests/test_bibstruct.py

@@ -16,18 +16,19 @@ class TestGenerateCitekey(unittest.TestCase):
             bibstruct.generate_citekey(None)
 
     def test_escapes_chars(self):
-        doe_bibdata = copy.deepcopy(fixtures.doe_bibdata)
+        doe_bibentry = copy.deepcopy(fixtures.doe_bibentry)
-        citekey, entry = bibstruct.get_entry(doe_bibdata)
+        citekey, bibdata = bibstruct.get_entry(doe_bibentry)
-        entry['author'] = [u'Zôu\\@/ , John']
+        bibdata['author'] = [u'Zôu\\@/ , John']
-        key = bibstruct.generate_citekey(doe_bibdata)
+        key = bibstruct.generate_citekey(doe_bibentry)
+        self.assertEqual(key, 'Zou2013')
 
     def test_simple(self):
-        bibdata = copy.deepcopy(fixtures.doe_bibdata)
+        bibentry = copy.deepcopy(fixtures.doe_bibentry)
-        key = bibstruct.generate_citekey(bibdata)
+        key = bibstruct.generate_citekey(bibentry)
         self.assertEqual(key, 'Doe2013')
 
-        bibdata = copy.deepcopy(fixtures.franny_bibdata)
+        bibentry = copy.deepcopy(fixtures.franny_bibentry)
-        key = bibstruct.generate_citekey(bibdata)
+        key = bibstruct.generate_citekey(bibentry)
         self.assertEqual(key, 'Salinger1961')
 
 

tests/test_databroker.py

@@ -17,7 +17,7 @@ class TestDataBroker(unittest.TestCase):
 
         ende = endecoder.EnDecoder()
         page99_metadata = ende.decode_metadata(str_fixtures.metadata_raw0)
-        page99_bibdata  = ende.decode_bibdata(str_fixtures.bibtex_raw0)
+        page99_bibentry = ende.decode_bibdata(str_fixtures.bibtex_raw0)
 
         for db_class in [databroker.DataBroker, datacache.DataCache]:
             self.fs = fake_env.create_fake_fs([content, filebroker, configs])
@@ -28,22 +28,22 @@ class TestDataBroker(unittest.TestCase):
             self.assertFalse(db.exists('citekey1', meta_check=True))
             self.assertFalse(db.exists('citekey1', meta_check=False))
 
-            db.push_bibdata('citekey1', page99_bibdata)
+            db.push_bibentry('citekey1', page99_bibentry)
             self.assertTrue(db.exists('citekey1', meta_check=False))
             self.assertTrue(db.exists('citekey1', meta_check=True))
 
             self.assertEqual(db.pull_metadata('citekey1'), page99_metadata)
-            pulled = db.pull_bibdata('citekey1')['Page99']
+            pulled = db.pull_bibentry('citekey1')['Page99']
             for key, value in pulled.items():
-                self.assertEqual(pulled[key], page99_bibdata['Page99'][key])
+                self.assertEqual(pulled[key], page99_bibentry['Page99'][key])
-            self.assertEqual(db.pull_bibdata('citekey1'), page99_bibdata)
+            self.assertEqual(db.pull_bibentry('citekey1'), page99_bibentry)
 
             fake_env.unset_fake_fs([content, filebroker])
 
     def test_existing_data(self):
 
         ende = endecoder.EnDecoder()
-        page99_bibdata  = ende.decode_bibdata(str_fixtures.bibtex_raw0)
+        page99_bibentry = ende.decode_bibdata(str_fixtures.bibtex_raw0)
 
         for db_class in [databroker.DataBroker, datacache.DataCache]:
             self.fs = fake_env.create_fake_fs([content, filebroker])
@@ -51,16 +51,16 @@ class TestDataBroker(unittest.TestCase):
 
             db = db_class('repo', create=False)
 
-            self.assertEqual(db.pull_bibdata('Page99'), page99_bibdata)
+            self.assertEqual(db.pull_bibentry('Page99'), page99_bibentry)
 
             for citekey in ['10.1371_journal.pone.0038236',
                             '10.1371journal.pone.0063400',
                             'journal0063400']:
-                db.pull_bibdata(citekey)
+                db.pull_bibentry(citekey)
                 db.pull_metadata(citekey)
 
             with self.assertRaises(IOError):
-                db.pull_bibdata('citekey')
+                db.pull_bibentry('citekey')
             with self.assertRaises(IOError):
                 db.pull_metadata('citekey')
 

tests/test_endecoder.py

@@ -86,9 +86,7 @@ class TestEnDecode(unittest.TestCase):
         biblines = turing_bib.splitlines()
         biblines.insert(-3, keyword_str)
         bibsrc = '\n'.join(biblines)
-        print(bibsrc)
         entry = decoder.decode_bibdata(bibsrc)['turing1950computing']
-        print(entry)
         self.assertNotIn(u'keywords', entry)
         self.assertIn(u'keyword', entry)
         self.assertEqual(set(keywords), set(entry[u'keyword']))

tests/test_events.py

@@ -75,19 +75,19 @@ class TestEvents(unittest.TestCase):
         correct = ['abcdefghijklmnopqrstuvwxyz 12 15',
                    'Helloword',
                    'one']
-        self.assertEquals(_output, correct)
+        self.assertEqual(_output, correct)
 
     def test_listen_AddEvent(self):
         addevent = AddEvent()
         addevent.send()
         correct = [42]
-        self.assertEquals(_output, correct)
+        self.assertEqual(_output, correct)
 
     def test_listen_Info(self):
         Info('info').send()
         SpecificInfo('info', 'specific').send()
         correct = ['info', 'info', 'specific']
-        self.assertEquals(_output, correct)
+        self.assertEqual(_output, correct)
 
 
 if __name__ == '__main__':

tests/test_paper.py

@@ -1,5 +1,5 @@
 # -*- coding: utf-8 -*-
-import os
+
 import unittest
 
 import dotdot
@@ -9,38 +9,38 @@ from pubs.paper import Paper
 
 class TestAttributes(unittest.TestCase):
 
+    def setUp(self):
+        self.p = Paper.from_bibentry(
+            fixtures.page_bibentry,
+            metadata=fixtures.page_metadata).deepcopy()
+
     def test_tags(self):
-        p = Paper(fixtures.page_bibdata, metadata=fixtures.page_metadata).deepcopy()
+        self.assertEqual(self.p.tags, set(['search', 'network']))
-        self.assertEqual(p.tags, set(['search', 'network']))
 
     def test_add_tag(self):
-        p = Paper(fixtures.page_bibdata, metadata=fixtures.page_metadata).deepcopy()
+        self.p.add_tag('algorithm')
-        p.add_tag('algorithm')
+        self.assertEqual(self.p.tags, set(['search', 'network', 'algorithm']))
-        self.assertEqual(p.tags, set(['search', 'network', 'algorithm']))
+        self.p.add_tag('algorithm')
-        p.add_tag('algorithm')
+        self.assertEqual(self.p.tags, set(['search', 'network', 'algorithm']))
-        self.assertEqual(p.tags, set(['search', 'network', 'algorithm']))
 
     def test_set_tags(self):
-        p = Paper(fixtures.page_bibdata, metadata=fixtures.page_metadata).deepcopy()
+        self.p.tags = ['algorithm']
-        p.tags = ['algorithm']
+        self.assertEqual(self.p.tags, set(['algorithm']))
-        self.assertEqual(p.tags, set(['algorithm']))
 
     def test_remove_tags(self):
-        p = Paper(fixtures.page_bibdata, metadata=fixtures.page_metadata).deepcopy()
+        self.p.remove_tag('network')
-        p.remove_tag('network')
+        self.assertEqual(self.p.tags, set(['search']))
-        self.assertEqual(p.tags, set(['search']))
 
     def test_mixed_tags(self):
-        p = Paper(fixtures.page_bibdata, metadata=fixtures.page_metadata).deepcopy()
+        self.p.add_tag('algorithm')
-        p.add_tag('algorithm')
+        self.assertEqual(self.p.tags, set(['search', 'network', 'algorithm']))
-        self.assertEqual(p.tags, set(['search', 'network', 'algorithm']))
+        self.p.remove_tag('network')
-        p.remove_tag('network')
+        self.assertEqual(self.p.tags, set(['search', 'algorithm']))
-        self.assertEqual(p.tags, set(['search', 'algorithm']))
+        self.p.tags = ['ranking']
-        p.tags = ['ranking']
+        self.assertEqual(self.p.tags, set(['ranking']))
-        self.assertEqual(p.tags, set(['ranking']))
+        self.p.remove_tag('ranking')
-        p.remove_tag('ranking')
+        self.assertEqual(self.p.tags, set())
-        self.assertEqual(p.tags, set())
+        self.p.remove_tag('ranking')
-        p.remove_tag('ranking')
 
 
 if __name__ == '__main__':

tests/test_queries.py

@@ -2,18 +2,19 @@ import unittest
 
 import dotdot
 from pubs.commands.list_cmd import (_check_author_match,
-                                      _check_field_match,
+                                    _check_field_match,
-                                      _check_query_block,
+                                    _check_query_block,
-                                      filter_paper,
+                                    filter_paper,
-                                      InvalidQuery)
+                                    InvalidQuery)
 
 from pubs.paper import Paper
 
 import fixtures
 
-doe_paper    = Paper(fixtures.doe_bibdata)
+doe_paper    = Paper.from_bibentry(fixtures.doe_bibentry)
-page_paper   = Paper(fixtures.page_bibdata)
+page_paper   = Paper.from_bibentry(fixtures.page_bibentry)
-turing_paper = Paper(fixtures.turing_bibdata, metadata=fixtures.turing_metadata)
+turing_paper = Paper.from_bibentry(fixtures.turing_bibentry,
+                                   metadata=fixtures.turing_metadata)
 
 class TestAuthorFilter(unittest.TestCase):
 

tests/test_repo.py

@@ -15,7 +15,7 @@ class TestRepo(fake_env.TestFakeFs):
     def setUp(self):
         super(TestRepo, self).setUp()
         self.repo = Repository(configs.Config(), create=True)
-        self.repo.push_paper(Paper(fixtures.turing_bibdata))
+        self.repo.push_paper(Paper.from_bibentry(fixtures.turing_bibentry))
 
 
 class TestCitekeyGeneration(TestRepo):
@@ -27,9 +27,10 @@ class TestCitekeyGeneration(TestRepo):
             self.assertEqual(_base27(26 + i + 1), 'a' + chr(97 + i))
 
     def test_generated_key_is_unique(self):
-        self.repo.push_paper(Paper(fixtures.doe_bibdata))
+        self.repo.push_paper(Paper.from_bibentry(fixtures.doe_bibentry))
         c = self.repo.unique_citekey('Doe2013')
-        self.repo.push_paper(Paper(fixtures.doe_bibdata, citekey='Doe2013a'))
+        self.repo.push_paper(Paper.from_bibentry(fixtures.doe_bibentry,
+                                                 citekey='Doe2013a'))
         c = self.repo.unique_citekey('Doe2013')
         self.assertEqual(c, 'Doe2013b')
 
@@ -38,25 +39,27 @@ class TestPushPaper(TestRepo):
 
     def test_raises_value_error_on_existing_key(self):
         with self.assertRaises(CiteKeyCollision):
-            self.repo.push_paper(Paper(fixtures.turing_bibdata))
+            self.repo.push_paper(Paper.from_bibentry(fixtures.turing_bibentry))
 
     def test_pushes_paper_bibdata(self):
-        orig = fixtures.doe_bibdata
+        orig = fixtures.doe_bibentry
-        self.repo.push_paper(Paper(orig))
+        self.repo.push_paper(Paper.from_bibentry(orig))
-        retrieved = self.repo.databroker.pull_bibdata('Doe2013')
+        retrieved = self.repo.databroker.pull_bibentry('Doe2013')
-        self.assertEquals(orig, retrieved)
+        self.assertEqual(orig, retrieved)
 
     def test_pushes_paper_metadata(self):
         orig = {'docfile': 'dummy', 'tags': set(['tag', 'another']),
                 'added': datetime(2012, 12, 12, 12, 12, 12, 12)}
-        self.repo.push_paper(Paper(fixtures.doe_bibdata, metadata=orig))
+        self.repo.push_paper(Paper.from_bibentry(fixtures.doe_bibentry,
+                                                 metadata=orig))
         retrieved = self.repo.databroker.pull_metadata('Doe2013')
-        self.assertEquals(orig, retrieved)
+        self.assertEqual(orig, retrieved)
 
     def test_pushes_paper_metadata_set_added(self):
         orig = {'docfile': 'dummy', 'tags': set(['tag', 'another'])}
         now = datetime.now()
-        self.repo.push_paper(Paper(fixtures.doe_bibdata, metadata=orig))
+        self.repo.push_paper(Paper.from_bibentry(fixtures.doe_bibentry,
+                                                 metadata=orig))
         retrieved = self.repo.databroker.pull_metadata('Doe2013')
         self.assertIn('added', retrieved)
         self.assertTrue(now < retrieved['added'])

tests/test_usecase.py

@@ -29,7 +29,7 @@ class TestFakeInput(unittest.TestCase):
         input = fake_env.FakeInput(['yes', 'no'])
         self.assertEqual(input(), 'yes')
         self.assertEqual(input(), 'no')
-        with self.assertRaises(IndexError):
+        with self.assertRaises(fake_env.FakeInput.UnexpectedInput):
             input()
 
     def test_input2(self):
@@ -37,7 +37,7 @@ class TestFakeInput(unittest.TestCase):
         other_input.as_global()
         self.assertEqual(color.input(), 'yes')
         self.assertEqual(color.input(), 'no')
-        with self.assertRaises(IndexError):
+        with self.assertRaises(fake_env.FakeInput.UnexpectedInput):
             color.input()
 
     def test_editor_input(self):
@@ -46,7 +46,7 @@ class TestFakeInput(unittest.TestCase):
         other_input.as_global()
         self.assertEqual(content.editor_input(), 'yes')
         self.assertEqual(content.editor_input(), 'no')
-        with self.assertRaises(IndexError):
+        with self.assertRaises(fake_env.FakeInput.UnexpectedInput):
             color.input()
 
 
@@ -66,35 +66,41 @@ class CommandTestCase(unittest.TestCase):
         In the latter case, the command is :
         1. a string reprensenting the command to execute
         2. the user inputs to feed to the command during execution
-        3. the output expected, verified with assertEqual
+        3. the output expected, verified with assertEqual. Always captures
+        output in this case.
 
         """
         outs = []
         for cmd in cmds:
+            inputs = []
+            output = None
+            actual_cmd = cmd
+            current_capture_output = capture_output
             if not isinstance(cmd, p3.ustr):
-                if len(cmd) == 2:
+                actual_cmd = cmd[0]
-                    input = fake_env.FakeInput(cmd[1], [content, uis, p3])
+                if len(cmd) == 2:  # Inputs provided
-                    input.as_global()
+                    inputs = cmd[1]
-
+                if len(cmd) == 3:  # Expected output provided
-                if capture_output:
+                    current_capture_output = True
-                    _, stdout, stderr = fake_env.redirect(pubs_cmd.execute)(cmd[0].split())
+                    output = cmd[2]
-                    if len(cmd) == 3 and capture_output:
+            # Always set fake input: test should not ask unexpected user input
-                        actual_out  = color.undye(stdout)
+            input = fake_env.FakeInput(inputs, [content, uis, p3])
-                        correct_out = color.undye(cmd[2])
+            input.as_global()
+            try:
+                if current_capture_output:
+                    _, stdout, stderr = fake_env.redirect(pubs_cmd.execute)(
+                        actual_cmd.split())
+                    self.assertEqual(stderr, '')
+                    actual_out = color.undye(stdout)
+                    if output is not None:
+                        correct_out = color.undye(output)
                         self.assertEqual(actual_out, correct_out)
+                    outs.append(color.undye(actual_out))
                 else:
                     pubs_cmd.execute(cmd.split())
-
+            except fake_env.FakeInput.UnexpectedInput:
-            else:
+                self.fail('Unexpected input asked by command: {}.'.format(
-                if capture_output:
+                    actual_cmd))
-                    assert p3.isbasestr(cmd)
-                    _, stdout, stderr = fake_env.redirect(pubs_cmd.execute)(cmd.split())
-                else:
-                    pubs_cmd.execute(cmd.split())
-
-            if capture_output:
-                assert(stderr == '')
-                outs.append(color.undye(stdout))
         if PRINT_OUTPUT:
             print(outs)
         return outs
@@ -161,7 +167,7 @@ class TestAdd(DataCommandTestCase):
 
     def test_add_doc_nocopy_does_not_copy(self):
         cmds = ['pubs init',
-                'pubs add /data/pagerank.bib -C -d /data/pagerank.pdf',
+                'pubs add /data/pagerank.bib --link -d /data/pagerank.pdf',
                 ]
         self.execute_cmds(cmds)
         self.assertEqual(self.fs['os'].listdir(
@@ -186,10 +192,8 @@ class TestList(DataCommandTestCase):
                 'pubs list',
                 ]
         outs = self.execute_cmds(cmds)
-        print(outs[1].splitlines())
+        self.assertEqual(0, len(outs[1].splitlines()))
-        self.assertEquals(0, len(outs[1].splitlines()))
+        self.assertEqual(1, len(outs[3].splitlines()))
-        print(outs[3].splitlines())
-        self.assertEquals(1, len(outs[3].splitlines()))
 
     def test_list_several_no_date(self):
         self.execute_cmds(['pubs init -p /testrepo'])
@@ -203,14 +207,11 @@ class TestList(DataCommandTestCase):
                 'pubs list',
                 ]
         outs = self.execute_cmds(cmds)
-        print(outs[0].splitlines())
+        self.assertEqual(4, len(outs[0].splitlines()))
-        self.assertEquals(4, len(outs[0].splitlines()))
+        self.assertEqual(3, len(outs[2].splitlines()))
-        print(outs[2].splitlines())
+        self.assertEqual(4, len(outs[4].splitlines()))
-        self.assertEquals(3, len(outs[2].splitlines()))
-        print(outs[4].splitlines())
-        self.assertEquals(4, len(outs[4].splitlines()))
         # Last added should be last
-        self.assertEquals('[Page99]', outs[4].splitlines()[-1][:8])
+        self.assertEqual('[Page99]', outs[4].splitlines()[-1][:8])
 
     def test_list_smart_case(self):
         cmds = ['pubs init',
@@ -219,8 +220,7 @@ class TestList(DataCommandTestCase):
                 'pubs list title:language author:Saunders',
                 ]
         outs = self.execute_cmds(cmds)
-        print(outs[-1])
+        self.assertEqual(1, len(outs[-1].splitlines()))
-        self.assertEquals(1, len(outs[-1].splitlines()))
 
     def test_list_ignore_case(self):
         cmds = ['pubs init',
@@ -229,8 +229,7 @@ class TestList(DataCommandTestCase):
                 'pubs list --ignore-case title:lAnguAge author:saunders',
                 ]
         outs = self.execute_cmds(cmds)
-        print(outs[-1])
+        self.assertEqual(1, len(outs[-1].splitlines()))
-        self.assertEquals(1, len(outs[-1].splitlines()))
 
     def test_list_force_case(self):
         cmds = ['pubs init',
@@ -239,7 +238,7 @@ class TestList(DataCommandTestCase):
                 'pubs list --force-case title:Language author:saunders',
                 ]
         outs = self.execute_cmds(cmds)
-        self.assertEquals(0 + 1, len(outs[-1].split('\n')))
+        self.assertEqual(0 + 1, len(outs[-1].split('\n')))
 
 
 
@@ -247,12 +246,12 @@ class TestUsecase(DataCommandTestCase):
 
     def test_first(self):
         correct = ['Initializing pubs in /paper_first\n',
-                   '',
+                   '[Page99] Page, Lawrence et al. "The PageRank Citation Ranking: Bringing Order to the Web." (1999) \nwas added to pubs.\n',
                    '[Page99] Page, Lawrence et al. "The PageRank Citation Ranking: Bringing Order to the Web." (1999) \n',
                    '\n',
                    '',
                    'network search\n',
-                   '[Page99] Page, Lawrence et al. "The PageRank Citation Ranking: Bringing Order to the Web." (1999) network search\n'
+                   '[Page99] Page, Lawrence et al. "The PageRank Citation Ranking: Bringing Order to the Web." (1999) | network,search\n',
                   ]
 
         cmds = ['pubs init -p paper_first/',
@@ -264,7 +263,7 @@ class TestUsecase(DataCommandTestCase):
                 'pubs tag search',
                ]
 
-        self.assertEqual(correct, self.execute_cmds(cmds))
+        self.assertEqual(correct, self.execute_cmds(cmds, capture_output=True))
 
     def test_second(self):
         cmds = ['pubs init -p paper_second/',
@@ -290,7 +289,6 @@ class TestUsecase(DataCommandTestCase):
                ]
         self.execute_cmds(cmds)
         docdir = self.fs['os'].path.expanduser('~/.pubs/doc/')
-        print(self.fs['os'].listdir(docdir))
         self.assertNotIn('turing-mind-1950.pdf', self.fs['os'].listdir(docdir))
 
 
@@ -364,7 +362,7 @@ class TestUsecase(DataCommandTestCase):
                ]
         outs = self.execute_cmds(cmds)
         self.assertEqual(endecoder.EnDecoder().decode_bibdata(outs[2]),
-                         fixtures.page_bibdata)
+                         fixtures.page_bibentry)
 
     def test_import(self):
         cmds = ['pubs init',