Cleanup Paper class and adds test.

papers/files.py

@@ -1,12 +1,7 @@
-import sys, os
+import os
 import subprocess
 import tempfile
 
-try:
-    import ConfigParser as configparser
-except ImportError:
-    import configparser
-    
 import yaml
 
 import color
@@ -24,87 +19,116 @@ try:
     import pybtex.database.output.bibyaml
 
 except ImportError:
-    print '{}error{}: you need to install Pybtex; try running \'pip install pybtex\' or \'easy_install pybtex\''.format(color.red, color.end)
+    print '{}error{}: you need to install Pybtex; try running \'pip install'
+    'pybtex\' or \'easy_install pybtex\''.format(color.red, color.end)
 
 
 _papersdir = None
 
+try:
+    EDITOR = os.environ['EDITOR']
+except KeyError:
+    EDITOR = 'nano'
+
+
 def find_papersdir():
     """Find .papers directory in this directory and the parent directories"""
     global _papersdir
     if _papersdir is None:
         curdir = os.path.abspath(os.getcwd())
         while curdir != '':
-            if os.path.exists(curdir + '/.papers') and os.path.isdir(curdir + '/.papers'):
+            if (os.path.exists(curdir + '/.papers')
+                    and os.path.isdir(curdir + '/.papers')):
                 _papersdir = curdir + '/.papers'
                 curdir = ''
             if curdir == '/':
                 curdir = ''
             else:
                 curdir = os.path.split(curdir)[0]
-
         if _papersdir is None:
-            print '{}error{} : no papers repo found in this directory or in any parent directory.{}'.format(
-                   color.red, color.grey, color.end)
+            print '{}error{} : no papers repo found in this directory or in'
+            'any parent directory.{}'.format(color.red, color.grey, color.end)
             exit(-1)
-
     return _papersdir
 
-def name_from_path(fullpdfpath, verbose = False):
+
+def name_from_path(fullpdfpath, verbose=False):
     name, ext = os.path.splitext(os.path.split(fullpdfpath)[1])
     if verbose:
         if ext != '.pdf' and ext != '.ps':
             print('{}warning{}: extension {}{}{} not recognized{}'.format(
-                   color.yellow, color.grey, color.cyan, ext, color.grey, color.end))
+                   color.yellow, color.grey, color.cyan, ext, color.grey,
+                   color.end))
     return name, ext
 
+
 def check_file(filepath):
     if not os.path.exists(filepath):
         print '{}error{}: {}{}{} does not exists{}'.format(
-               color.red, color.grey, color.cyan, filepath, color.grey, color.end)
+               color.red, color.grey, color.cyan, filepath, color.grey,
+               color.end)
         exit(-1)
     if not os.path.isfile(filepath):
         print '{}error{}: {}{}{} is not a file{}'.format(
-               color.red, color.grey, color.cyan, filepath, color.grey, color.end)
+               color.red, color.grey, color.cyan, filepath, color.grey,
+               color.end)
         exit(-1)
 
+
 # yaml I/O
 
 def write_yamlfile(filepath, datamap):
     try:
         with open(filepath, 'w') as f:
             yaml.dump(datamap, f)
-    except IOError as e:
+    except IOError:
         print '{}error{} : impossible to read file {}{:s}{}'.format(
                color.red, color.grey, color.cyan, filepath, color.end)
         exit(-1)
 
+
 def read_yamlfile(filepath):
     check_file(filepath)
     try:
         with open(filepath, 'r') as f:
             return yaml.load(f)
-    except IOError as e:
+    except IOError:
         print '{}error{} : impossible to read file {}{:s}{}'.format(
-               color.red, color.grey, color.cyan, paperdir, color.end)
+               color.red, color.grey, color.cyan, filepath, color.end)
         exit(-1)
 
+
 def save_papers(datamap):
     paperyaml = find_papersdir() + os.sep + 'papers.yaml'
     write_yamlfile(paperyaml, datamap)
 
+
 def load_papers():
-    paperyaml = find_papersdir() + os.sep + 'papers.yaml'
+    paperyaml = os.path.join(find_papersdir(), 'papers.yaml')
     return read_yamlfile(paperyaml)
 
-def save_meta(meta_data, filename):
-    filepath = os.path.join(find_papersdir(), 'meta', filename + '.meta')
+
+def path_to_paper_file(name, file_, path_to_repo=None):
+    if path_to_repo is None:
+        path_to_repo = find_papersdir()
+    if file_ == 'bib':
+        return os.path.join(path_to_repo, 'bibdata', name + '.bibyaml')
+    elif file_ == 'meta':
+        return os.path.join(path_to_repo, 'meta', name + '.meta')
+    else:
+        raise(ValueError, "%s is not a valid paper file." % file_)
+
+
+def save_meta(meta_data, filename, path=None):
+    filepath = path_to_paper_file(filename, 'meta', path_to_repo=path)
     write_yamlfile(filepath, meta_data)
 
-def load_meta(filename):
-    filepath = os.path.join(find_papersdir(), 'meta', filename + '.meta')
+
+def load_meta(filename, path=None):
+    filepath = path_to_paper_file(filename, 'meta', path_to_repo=path)
     return read_yamlfile(filepath)
 
+
 # specific to bibliography data
 
 def load_externalbibfile(fullbibpath):
@@ -127,24 +151,22 @@ def load_externalbibfile(fullbibpath):
 
     return bib_data
 
-def load_bibdata(filename):
-    fullbibpath = os.path.join(find_papersdir(), 'bibdata', filename + '.bibyaml')
-    return load_externalbibfile(fullbibpath)
 
-def save_bibdata(bib_data, filename):
-    filepath = os.path.join(find_papersdir(), 'bibdata', filename + '.bibyaml')
+def load_bibdata(filename, path=None):
+    filepath = path_to_paper_file(filename, 'bib', path_to_repo=path)
+    return load_externalbibfile(filepath)
+
+
+def save_bibdata(bib_data, filename, path=None):
+    filepath = path_to_paper_file(filename, 'bib', path_to_repo=path)
     with open(filepath, 'w') as f:
         parser = pybtex.database.output.bibyaml.Writer()
         parser.write_stream(bib_data, f)
 
-# vim input
 
-try:
-    EDITOR = os.environ['EDITOR']
-except KeyError:
-    EDITOR = 'nano'
+# vim input
 
-def vim_input(initial = ""):
+def vim_input(initial=""):
     """Use an editor to get input"""
 
     with tempfile.NamedTemporaryFile(suffix=".tmp", delete=False) as temp_file:

papers/paper.py

@@ -2,11 +2,15 @@ import os
 import unicodedata
 import re
 
+from pybtex.database import Entry, BibliographyData
+
 import files
 import color
 import pretty
 
 
+DEFAULT_TYPE = 'article'
+
 CONTROL_CHARS = ''.join(map(unichr, range(0, 32) + range(127, 160)))
 CITEKEY_FORBIDDEN_CHARS = '@\'\\,#}{~%/'  # '/' is OK for bibtex but forbidden
 # here since we transform citekeys into filenames
@@ -15,7 +19,10 @@ CITEKEY_EXCLUDE_RE = re.compile('[%s]'
 
 
 def str2citekey(s):
-    return CITEKEY_EXCLUDE_RE.sub('', s)
+    key = unicodedata.normalize('NFKD', unicode(s)).encode('ascii', 'ignore')
+    key = CITEKEY_EXCLUDE_RE.sub('', key)
+    # Normalize chars and remove non-ascii
+    return key
 
 
 class NoDocumentFile(Exception):
@@ -23,31 +30,54 @@ class NoDocumentFile(Exception):
 
 
 class Paper(object):
-    """Paper class. The object is responsible for the integrity of its own data,
-    and for loading and writing it to disc.
+    """Paper class. The object is responsible for the integrity of its own
+    data, and for loading and writing it to disc.
+
+    The object uses a pybtex.database.BibliographyData object to store
+    biblography data and an additional dictionary to store meta data.
     """
 
     @classmethod
-    def from_disc(cls, name, citekey = None):
-        bib_data = files.load_bibdata(name)
-        metadata = files.load_meta(name)
-        p = Paper(name, bib_data = bib_data, metadata = metadata,
-                        citekey = citekey)
+    def load(cls, bibpath, metapath):
+        bib_data = files.load_externalbibfile(bibpath)
+        metadata = files.read_yamlfile(metapath)
+        # Extract first entry (supposed to be the only one)
+        first_key = bib_data.entries.keys()[0]
+        first_entry = bib_data.entries[first_key]
+        p = Paper(bibentry=first_entry, metadata=metadata, citekey=first_key)
         return p
 
-    @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)
+#    @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)
+        self.bibentry = bibentry
+        if not metadata:
+            metadata = Paper.create_meta()
+        self.metadata = metadata
+        self.citekey = citekey
 
-        return p
+    def __eq__(self, other):
+        return (type(other) is Paper
+            and self.bibentry == other.bibentry
+            and self.metadata == other.metadata
+            and self.citekey == other.citekey)
 
-    def __init__(self, bib_data = None, metadata = None,
-                       citekey = None):
-        self.citekey  = citekey
-        self.bib_data = bib_data
-        self.metadata = metadata
+    def __repr__(self):
+        return 'Paper(%s, %s, %s)' % (
+                self.citekey, self.bibentry, self.metadata)
+
+    def __str__(self):
+        return self.__repr__()
+
+    # TODO add mechanism to verify keys (15/12/2012)
 
     def has_file(self):
         """Whether there exist a document file for this entry.
@@ -70,68 +100,53 @@ class Paper(object):
             KeyError if no author nor editor is defined.
         """
         author_key = 'author'
-        if not 'author' in self.bib_data.persons:
+        if not 'author' in self.bibentry.persons:
             author_key = 'editor'
         try:
-            first_author = self.bib_data.persons[author_key][0]
+            first_author = self.bibentry.persons[author_key][0]
         except KeyError:
             raise(ValueError,
                     'No author or editor defined: cannot generate a citekey.')
         try:
-            year = entry.fields['year']
+            year = self.bibentry.fields['year']
         except KeyError:
             year = ''
-        prefix = u'{}{}'.format(first_author.last()[0][:6], year)
-        prefix = str2citekey(prefix)
-        # Normalize chars and remove non-ascii
-        prefix = unicodedata.normalize('NFKD', prefix
-                ).encode('ascii', 'ignore')
-        letter = 0
-        citekey = prefix
-        while citekey in self.citekeys and citekey not in allowed:
-            citekey = prefix + ALPHABET[letter]
-            letter += 1
-        return citekey
-
-
-    def save_to_disc(self):
-        files.save_bibdata(self.bib_data, self.citekey)
-        files.save_meta(self.metadata, self.citekey)
+        citekey = u'{}{}'.format(u''.join(first_author.last()), year)
+        return str2citekey(citekey)
+
+    def save_to_disc(self, path):
+        """Creates a BibliographyData object containing a single entry and
+        saves it to disc.
+        """
+        if self.citekey is None:
+            raise(ValueError,
+                'No valid citekey initialized. Cannot save paper')
+        bibdata = BibliographyData(entries={self.citekey: self.bibentry})
+        files.save_bibdata(bibdata, self.citekey, path=path)
+        files.save_meta(self.metadata, self.citekey, path=path)
         # TODO move to repo
 
     @classmethod
     def import_bibdata(cls, bibfile):
         """Import bibligraphic data from a .bibyaml, .bib or .bibtex file"""
         fullbibpath = os.path.abspath(bibfile)
-
         bib_data = files.load_externalbibfile(fullbibpath)
         print('{}bibliographic data present in {}{}{}'.format(
                color.grey, color.cyan, bibfile, color.end))
         print(pretty.bib_desc(bib_data))
-
         return bib_data
 
     @classmethod
-    def create_meta(cls, bib_data, pdfpath=None):
-
+    def create_meta(cls, pdfpath=None):
         if pdfpath is None:
-            citekey = bib_data.entries.keys()[0]
-            # TODO this introduces a bug and a security issue since the name
-            # is used to generate a file name that is written. It should be
-            # escaped here. (22/10/2012)
-            fullpdfpath, ext = None, None
+            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['name'] = name
+        meta['filename'] = name  # TODO remove ?
         meta['extension'] = ext
         meta['path'] = fullpdfpath
-
         meta['notes'] = []
-
-        return name, meta
+        return meta

papers/repo.py

@@ -34,7 +34,7 @@ class Repository(object):
     def paper_from_citekey(self, citekey, fatal=True):
         """Load a paper by its citekey from disk, if necessary."""
         try:
-            return Paper.from_disc(citekey)
+            return Paper.load(citekey)
         except KeyError:
             if fatal:
                 print('{}error{}: no paper with citekey {}{}{}'.format(
@@ -70,6 +70,7 @@ class Repository(object):
         self.citekeys.append(p.citekey)
 
         # writing all to disk
+        # TODO Update by giving filename (17/12/2012)
         p.save_to_disc()
         files.save_papers(self.papers_config)
         print "Added: %s" % p.citekey
@@ -80,7 +81,8 @@ class Repository(object):
         for k in bib_data.entries:
             sub_bib = type(bib_data)(preamble=bib_data._preamble)
             sub_bib.add_entry(k, bib_data.entries[k])
-            name, meta = Paper.create_meta(sub_bib, pdfpath=None)
+            meta = Paper.create_meta(pdfpath=None)
+            name = meta['filename']
             p = Paper(name, bib_data = sub_bib, metadata = meta)
             self.add_paper(p)
 

tests/test_paper.py

@@ -0,0 +1,113 @@
+# -*- coding: utf-8 -*-
+import os
+import unittest
+import tempfile
+import shutil
+
+import yaml
+from pybtex.database import Person
+
+from papers.paper import Paper
+from papers import files
+
+
+BIB = """
+entries:
+    Turing1950:
+        author:
+        -   first: 'Alan'
+            last: 'Turing'
+        title: 'Computing machinery and intelligence.'
+        type: article
+        year: '1950'
+"""
+META = """
+filename: null
+extension: null
+notes: []
+path: null
+"""
+
+
+class TestCreateCitekey(unittest.TestCase):
+
+    def test_fails_on_empty_paper(self):
+        paper = Paper()
+        with self.assertRaises(ValueError):
+            paper.generate_citekey()
+
+    def test_escapes_chars(self):
+        paper = Paper()
+        paper.bibentry.persons['author'] = [
+                Person(last=u'Z ôu\\@/', first='Zde'),
+                Person(string='John Doe')]
+        key = paper.generate_citekey()
+        self.assertEqual(key, 'Zou')
+
+    def test_simple(self):
+        paper = Paper()
+        paper.bibentry.persons['author'] = [Person(string='John Doe')]
+        paper.bibentry.fields['year'] = '2001'
+        key = paper.generate_citekey()
+        self.assertEqual(key, 'Doe2001')
+
+
+class TestSaveLoad(unittest.TestCase):
+
+    def setUp(self):
+        self.tmpdir = tempfile.mkdtemp()
+        os.makedirs(os.path.join(self.tmpdir, 'bibdata'))
+        os.makedirs(os.path.join(self.tmpdir, 'meta'))
+        self.bibfile = os.path.join(self.tmpdir, 'bib.bibyaml')
+        with open(self.bibfile, 'w') as f:
+            f.write(BIB)
+        self.metafile = os.path.join(self.tmpdir, 'meta.meta')
+        with open(self.metafile, 'w') as f:
+            f.write(META)
+        self.turing1950 = Paper()
+        self.turing1950.bibentry.fields['title'] = u'Computing machinery and intelligence.'
+        self.turing1950.bibentry.fields['year'] = u'1950'
+        self.turing1950.bibentry.persons['author'] = [Person(u'Alan Turing')]
+        self.turing1950.citekey = self.turing1950.generate_citekey()
+
+    def test_load_valid(self):
+        p = Paper.load(self.bibfile, self.metafile)
+        self.assertEqual(self.turing1950, p)
+
+    def test_save_fails_with_no_citekey(self):
+        p = Paper()
+        with self.assertRaises(ValueError):
+            p.save_to_disc(self.tmpdir)
+
+    def test_save_creates_bib(self):
+        self.turing1950.save_to_disc(self.tmpdir)
+        bibfile = files.path_to_paper_file('Turing1950', 'bib',
+                path_to_repo=self.tmpdir)
+        self.assertTrue(os.path.exists(bibfile))
+
+    def test_save_creates_meta(self):
+        self.turing1950.save_to_disc(self.tmpdir)
+        metafile = files.path_to_paper_file('Turing1950', 'meta',
+                path_to_repo=self.tmpdir)
+        self.assertTrue(os.path.exists(metafile))
+
+    def test_save_right_bib(self):
+        self.turing1950.save_to_disc(self.tmpdir)
+        bibfile = files.path_to_paper_file('Turing1950', 'bib',
+                path_to_repo=self.tmpdir)
+        with open(bibfile, 'r') as f:
+            written = yaml.load(f)
+            ok = yaml.load(BIB)
+            self.assertEqual(written, ok)
+
+    def test_save_right_meta(self):
+        self.turing1950.save_to_disc(self.tmpdir)
+        metafile = files.path_to_paper_file('Turing1950', 'meta',
+                path_to_repo=self.tmpdir)
+        with open(metafile, 'r') as f:
+            written = yaml.load(f)
+            ok = yaml.load(META)
+            self.assertEqual(written, ok)
+
+    def teardown(self):
+        shutil.rmtree(self.tmpdir)