Updates commands. Many bug fix.

papers/commands/add_cmd.py

@@ -12,5 +12,5 @@ def command(config, pdffile, bibfile):
     :param pdffilepath  path (no url yet) to a pdf or ps file
     :param bibtex       bibtex file (in .bib, .bibml or .yaml format.
     """
-    rp = repo.Repository()
+    rp = repo.Repository.from_directory()
     rp.add_paper_from_paths(pdffile, bibfile)

papers/commands/add_library_cmd.py

@@ -11,5 +11,5 @@ def command(config, bibfile):
     """
     :param bibtex       bibtex file (in .bib, .bibml or .yaml format.
     """
-    rp = repo.Repository()
+    rp = repo.Repository.from_directory()
     rp.add_papers(bibfile)

papers/commands/init_cmd.py

@@ -1,17 +1,14 @@
 # init command
 
 import os
-try:
-    import ConfigParser as configparser
-except ImportError:
-    import configparser
 
 from ..repo import Repository
 from .. import color
 
 
 def parser(subparsers, config):
-    parser = subparsers.add_parser('init', help="initialize the .papers directory")
+    parser = subparsers.add_parser('init',
+            help="initialize the .papers directory")
     return parser
 
 

papers/commands/list_cmd.py

@@ -5,18 +5,19 @@ from .. import pretty
 from .. import color
 from .. import repo
 
+
 def parser(subparsers, config):
     parser = subparsers.add_parser('list', help="list all papers")
     return parser
 
+
 def command(config):
-    rp = repo.Repository()
+    rp = repo.Repository.from_directory()
-    
     articles = []
     for n in range(rp.size()):
         paper = rp.paper_from_number(n, fatal=True)
-        bibdesc = pretty.bib_oneliner(paper.bib_data)
+        bibdesc = pretty.bib_oneliner(paper.bibentry)
-        articles.append((u'{:3d} {}{}{}{}   {}'.format(int(paper.number), color.purple, paper.citekey, color.end, (10 - len(paper.citekey))*' ', bibdesc)).encode('utf-8'))
+        articles.append((u'{:3d} {}{}{}{}   {}'.format(int(n), color.purple, rp.citekeys[n], color.end, (10 - len(paper.citekey))*' ', bibdesc)).encode('utf-8'))
 
     with tempfile.NamedTemporaryFile(suffix=".tmp", delete=True) as tmpf:
         tmpf.write('\n'.join(articles))

papers/commands/open_cmd.py

@@ -10,17 +10,17 @@ def parser(subparsers, config):
     return parser
 
 def command(config, citekey):
-    rp = repo.Repository()
+    rp = repo.Repository.from_directory()
-    paper = rp.paper_from_any(citekey, fatal = True)
+    paper = rp.paper_from_any(citekey, fatal=True)
     try:
         if paper.check_file():
             filepath = paper.get_file_path()
-
+            subprocess.Popen(['open', filepath])
-            p = subprocess.Popen(['open', filepath])
             print('{}{}{} opened.{}'.format(
                 color.filepath, filepath, color.normal, color.end))
+        else:
+            raise NoDocumentFile
     except NoDocumentFile:
         print('{}error{}: No document associated to this entry {}{}{}'.format(
             color.error, color.normal, color.citekey, citekey, color.end))
         exit(-1)
-

papers/commands/websearch_cmd.py

@@ -1,11 +1,13 @@
 import webbrowser
 import urllib
 
+
 def parser(subparsers, config):
     parser = subparsers.add_parser('websearch', help="launch a search on Google Scholar")
     parser.add_argument("search_string", help="the search query (anything googly is possible)")
     return parser
 
+
 def command(config, search_string):
     url = 'https://scholar.google.fr/scholar?q={}&lr='.format(urllib.quote_plus(search_string))
-    webbrowser.open(url)
+    webbrowser.open(url)

papers/paper.py

@@ -5,8 +5,6 @@ import re
 from pybtex.database import Entry, BibliographyData
 
 import files
-import color
-import pretty
 
 
 DEFAULT_TYPE = 'article'
@@ -17,6 +15,13 @@ CITEKEY_FORBIDDEN_CHARS = '@\'\\,#}{~%/'  # '/' is OK for bibtex but forbidden
 CITEKEY_EXCLUDE_RE = re.compile('[%s]'
         % re.escape(CONTROL_CHARS + CITEKEY_FORBIDDEN_CHARS))
 
+BASE_META = {
+    'filename': None,
+    'extension': None,
+    'path': None,
+    'notes': []
+    }
+
 
 def str2citekey(s):
     key = unicodedata.normalize('NFKD', unicode(s)).encode('ascii', 'ignore')
@@ -37,14 +42,6 @@ class Paper(object):
     biblography data and an additional dictionary to store meta data.
     """
 
-#    @classmethod
-#    def from_bibpdffiles(cls, pdfpath, bibpath):
-#        bib_data = cls.import_bibdata(bibpath)
-#        name, meta = cls.create_meta(bib_data, pdfpath=pdfpath)
-#        p = Paper(name, bib_data = bib_data, metadata = meta)
-#
-#        return p
-
     def __init__(self, bibentry=None, metadata=None, citekey=None):
         if not bibentry:
             bibentry = Entry(DEFAULT_TYPE)
@@ -54,7 +51,7 @@ class Paper(object):
         self.metadata = metadata
         # TODO This is not the right way to test that (17/12/2012)
         if unicode(citekey) != str2citekey(citekey):
-            raise(ValueError, "Wrong citekey: %s" % citekey)
+            raise(ValueError("Invalid citekey: %s" % citekey))
         self.citekey = citekey
 
     def __eq__(self, other):
@@ -84,7 +81,8 @@ class Paper(object):
             raise NoDocumentFile
 
     def check_file(self):
-        return files.check_file(self.get_file_path())
+        path = self.get_file_path()
+        return os.path.exists(path) and os.path.isfile(path)
 
     def generate_citekey(self):
         """Generate a citekey from bib_data.
@@ -98,8 +96,8 @@ class Paper(object):
         try:
             first_author = self.bibentry.persons[author_key][0]
         except KeyError:
-            raise(ValueError,
+            raise(ValueError(
-                    'No author or editor defined: cannot generate a citekey.')
+                    'No author or editor defined: cannot generate a citekey.'))
         try:
             year = self.bibentry.fields['year']
         except KeyError:
@@ -107,48 +105,44 @@ class Paper(object):
         citekey = u'{}{}'.format(u''.join(first_author.last()), year)
         return str2citekey(citekey)
 
+    def set_pdf(self, pdfpath):
+        fullpdfpath = os.path.abspath(pdfpath)
+        files.check_file(fullpdfpath)
+        name, ext = files.name_from_path(pdfpath)
+        self.metadata['filename'] = name
+        self.metadata['extension'] = ext
+        self.metadata['path'] = fullpdfpath
+
     def save_to_disc(self, bib_filepath, meta_filepath):
         """Creates a BibliographyData object containing a single entry and
         saves it to disc.
         """
         if self.citekey is None:
-            raise(ValueError,
+            raise(ValueError(
-                'No valid citekey initialized. Cannot save paper')
+                'No valid citekey initialized. Cannot save paper'))
         bibdata = BibliographyData(entries={self.citekey: self.bibentry})
         files.save_bibdata(bibdata, bib_filepath)
         files.save_meta(self.metadata, meta_filepath)
 
     @classmethod
-    def load(cls, bibpath, metapath):
+    def load(cls, bibpath, metapath=None):
-        bib_data = files.load_externalbibfile(bibpath)
+        key, entry = cls.get_bibentry(bibpath)
-        metadata = files.read_yamlfile(metapath)
+        if metapath is None:
-        # Extract first entry (supposed to be the only one)
+            metadata = None
-        first_key = bib_data.entries.keys()[0]
+        else:
-        first_entry = bib_data.entries[first_key]
+            metadata = files.read_yamlfile(metapath)
-        p = Paper(bibentry=first_entry, metadata=metadata, citekey=first_key)
+        p = Paper(bibentry=entry, metadata=metadata, citekey=key)
         return p
 
     @classmethod
-    def import_bibdata(cls, bibfile):
+    def get_bibentry(cls, bibfile):
-        """Import bibligraphic data from a .bibyaml, .bib or .bibtex file"""
+        """Extract first entry (supposed to be the only one) from given file.
-        fullbibpath = os.path.abspath(bibfile)
+        """
-        bib_data = files.load_externalbibfile(fullbibpath)
+        bib_data = files.load_externalbibfile(bibfile)
-        print('{}bibliographic data present in {}{}{}'.format(
+        first_key = bib_data.entries.keys()[0]
-               color.grey, color.cyan, bibfile, color.end))
+        first_entry = bib_data.entries[first_key]
-        print(pretty.bib_desc(bib_data))
+        return first_key, first_entry
-        return bib_data
 
     @classmethod
-    def create_meta(cls, pdfpath=None):
+    def create_meta(cls):
-        if pdfpath is None:
+        return BASE_META.copy()
-            name, fullpdfpath, ext = None, None, None
-        else:
-            fullpdfpath = os.path.abspath(pdfpath)
-            files.check_file(fullpdfpath)
-            name, ext = files.name_from_path(pdfpath)
-        meta = {}
-        meta['filename'] = name  # TODO remove ?
-        meta['extension'] = ext
-        meta['path'] = fullpdfpath
-        meta['notes'] = []
-        return meta

papers/pretty.py

@@ -9,16 +9,15 @@ def person_repr(p):
                                  ' '.join(p.last(abbr = False)),
                                  ' '.join(p.lineage(abbr = True))] if s)
 
-def bib_oneliner(bib_data):
+def bib_oneliner(bibentry):
-    article = bib_data.entries[list(bib_data.entries.keys())[0]]
+    authors = ', '.join(person_repr(p) for p in bibentry.persons['author'])
-    authors = ', '.join(person_repr(p) for p in article.persons['author'])
+    title = bibentry.fields['title']
-    title = article.fields['title']
+    year = bibentry.fields.get('year', '')
-    year = article.fields.get('year', '')
     journal = ''
     field = 'journal'
-    if article.type == 'inproceedings':
+    if bibentry.type == 'inproceedings':
         field = 'booktitle'
-    journal = article.fields.get(field, '')
+    journal = bibentry.fields.get(field, '')
     return u'{}{}{} \"{}{}{}\" {}{}{} {}({}{}{}){}'.format(
             color.green, authors, color.grey, color.bcyan, title, color.grey,
             color.yellow, journal, color.end, color.grey, color.end, year,

papers/repo.py

@@ -33,20 +33,20 @@ class Repository(object):
                     color.error, color.normal, color.citekey, citekey,
                     color.end))
                 exit(-1)
-            raise(IOError, 'file not found')
+            raise(IOError('file not found'))
 
     def paper_from_citekey(self, citekey, fatal=True):
         """Load a paper by its citekey from disk, if necessary."""
         if citekey in self.citekeys:
             return Paper.load(self.path_to_paper_file(citekey, 'bib'),
-                self.path_to_paper_file(citekey, 'meta'))
+                metapath=self.path_to_paper_file(citekey, 'meta'))
         else:
             if fatal:
                 print('{}error{}: no paper with citekey {}{}{}'.format(
                        color.error, color.normal, color.citekey, citekey,
                        color.end))
                 exit(-1)
-            raise(IOError, 'file not found')
+            raise(IOError('file not found'))
 
     def paper_from_any(self, key, fatal=True):
         try:
@@ -59,20 +59,21 @@ class Repository(object):
                     print('{}error{}: paper with citekey or number {}{}{} not found{}'.format(
                         color.error, color.normal, color.citekey, key, color.normal, color.end))
                     exit(-1)
-                raise(IOError, 'file not found')
+                raise(IOError('file not found'))
 
     # creating new papers
 
     def add_paper_from_paths(self, pdfpath, bibpath):
-        p = Paper.from_bibpdffiles(pdfpath, bibpath)
+        p = Paper.load(bibpath)
+        p.set_pdf(pdfpath)
         self.add_paper(p)
 
     def add_paper(self, p):
         if p.citekey is None:  # TODO also test if citekey is valid
-            raise(ValueError, "Invalid citekey: %s." % p.citekey)
+            raise(ValueError("Invalid citekey: %s." % p.citekey))
         elif p.citekey in self.citekeys:
-            raise(ValueError, "Citekey already exists in repository: %s"
+            raise(ValueError("Citekey already exists in repository: %s"
-                    % p.citekey)
+                    % p.citekey))
         self.citekeys.append(p.citekey)
         # write paper files
         self.save_paper(p)
@@ -89,14 +90,14 @@ class Repository(object):
 
     def save_paper(self, paper):
         if not paper.citekey in self.citekeys:
-            raise(ValueError, 'Paper not in repository, first add it.')
+            raise(ValueError('Paper not in repository, first add it.'))
         paper.save_to_disc(self.path_to_paper_file(paper.citekey, 'bib'),
                 self.path_to_paper_file(paper.citekey, 'meta'))
 
     def add_papers(self, bibpath):
-        bib_data = Paper.import_bibdata(bibpath)
+        bib_data = files.load_externalbibfile(bibpath)
         for k in bib_data.entries:
-            sub_bib = type(bib_data)(preamble=bib_data._preamble)
+            sub_bib = bib_data.entries[k]
             p = Paper(bibentry=sub_bib, citekey=k)
             self.add_paper(p)
 
@@ -135,11 +136,11 @@ class Repository(object):
         elif file_ == 'meta':
             return os.path.join(self.papersdir, META_DIR, citekey + '.meta')
         else:
-            raise(ValueError, "%s is not a valid paper file." % file_)
+            raise(ValueError("%s is not a valid paper file." % file_))
 
     @classmethod
     def from_directory(cls, papersdir=None):
-        repo = cls.__init__(papersdir=papersdir)
+        repo = cls(papersdir=papersdir)
         repo.load()
         return repo
 

tests/test_paper.py

@@ -68,7 +68,7 @@ class TestSaveLoad(unittest.TestCase):
         self.dest_metafile = os.path.join(self.tmpdir, 'written_meta.yaml')
 
     def test_load_valid(self):
-        p = Paper.load(self.bibfile, self.metafile)
+        p = Paper.load(self.bibfile, metapath=self.metafile)
         self.assertEqual(fixtures.turing1950, p)
 
     def test_save_fails_with_no_citekey(self):