Improves document handling.

- configuration is now referenced in repo object,
- introduces new class PaperInRepo,
- simplifies storage of documents in metadata,
- changes a few names.

papers/commands/import_cmd.py

@@ -1,7 +1,3 @@
-import os
-import sys
-import shutil
-
 from .. import repo
 from ..paper import Paper, NoDocumentFile
 from .. import files
@@ -27,30 +23,23 @@ def command(config, ui, bibpath, copy):
     if copy is None:
         copy = config.get('papers', 'import-copy')
     rp = repo.Repository.from_directory()
-    # Get directory for document
-    doc_path = files.clean_path(rp.get_document_directory(config))
-    if not (os.path.exists(doc_path) and os.path.isdir(doc_path)):
-        print "Document directory %s, does not exist." % doc_path
-        sys.exit(1)
     # Extract papers from bib
     papers = Paper.many_from_path(bibpath, fatal=False)
     for p in papers:
         doc_file = None
         try:
             file_path = p.get_document_file_from_bibdata(remove=True)
-            if os.path.exists(file_path):
+            if files.check_file(file_path):
                 doc_file = file_path
             else:
-                print "File does not exist for %s." % p.citekey
+                print("File does not exist for %s (%s)."
+                      % (p.citekey, file_path))
         except NoDocumentFile:
             print "No file for %s." % p.citekey
         rp.add_paper(p)
         if doc_file:
             if copy:
-                ext = os.path.splitext(doc_file)[1]
+                rp.import_document(p.citekey, doc_file)
-                new_doc_file = os.path.join(doc_path, p.citekey + ext)
-                shutil.copy(doc_file, new_doc_file)
             else:
-                new_doc_file = doc_file
+                p.set_external_document(doc_file)
-            p.set_document(new_doc_file)
+                rp.add_or_update(p)
-            rp.add_or_update(p)

papers/commands/open_cmd.py

@@ -17,14 +17,10 @@ def command(config, ui, citekey):
     rp = repo.Repository.from_directory()
     paper = rp.paper_from_ref(citekey, fatal=True)
     try:
-        if paper.check_file():
+        filepath = paper.get_document_path()
-            filepath = paper.get_file_path()
+        subprocess.Popen([config.get('papers', 'open-cmd'), filepath])
-            subprocess.Popen([config.get('papers', 'open-cmd'),
+        print("%s opened." % colored(filepath, 'filepath'))
-                filepath])
-            print('{} opened.'.format(colored(filepath, 'filepath')))
-        else:
-            raise NoDocumentFile
     except NoDocumentFile:
-        print('{}: No document associated to this entry {}{}{}'.format(
+        print("%s: No document associated to this entry %s."
-            colored('error', 'error'), colored('citekey', 'citekey')))
+                % (colored('error', 'error'), colored(citekey, 'citekey')))
         exit(-1)

papers/files.py

@@ -72,17 +72,15 @@ def name_from_path(fullpdfpath, verbose=False):
     return name, ext
 
 
-def check_file(filepath):
+def check_file(path, fail=False):
-    if not os.path.exists(filepath):
+    if fail:
-        print(colored('error', 'error') +
+        if not os.path.exists(path):
-                ': {} does not exists'.format(
+            raise(IOError, "File does not exist: %s." % path)
-               colored(filepath, 'filepath')))
+        if not os.path.isfile(path):
-        exit(-1)
+            raise(IOError, "%s is not a file." % path)
-    if not os.path.isfile(filepath):
+        return True
-        print(colored('error', 'error')
+    else:
-                + ': {} is not a file'.format(
+        return os.path.exists(path) and os.path.isfile(path)
-                    colored(filepath, 'filepath')))
-        exit(-1)
 
 
 # yaml I/O
@@ -99,7 +97,7 @@ def write_yamlfile(filepath, datamap):
 
 
 def read_yamlfile(filepath):
-    check_file(filepath)
+    check_file(filepath, fail=True)
     try:
         with open(filepath, 'r') as f:
             return yaml.load(f)
@@ -131,8 +129,7 @@ def load_meta(filepath):
 # specific to bibliography data
 
 def load_externalbibfile(fullbibpath):
-    check_file(fullbibpath)
+    check_file(fullbibpath, fail=True)
-
     filename, ext = os.path.splitext(os.path.split(fullbibpath)[1])
     if ext[1:] in FORMATS.keys():
         with open(fullbibpath) as f:

papers/paper.py

@@ -1,6 +1,9 @@
 import os
+
 import unicodedata
 import re
+from cStringIO import StringIO
+import glob
 
 from pybtex.database import Entry, BibliographyData
 
@@ -16,9 +19,7 @@ CITEKEY_EXCLUDE_RE = re.compile('[%s]'
         % re.escape(CONTROL_CHARS + CITEKEY_FORBIDDEN_CHARS))
 
 BASE_META = {
-    'filename': None,
+    'external-document': None,
-    'extension': None,
-    'path': None,
     'notes': []
     }
 
@@ -30,6 +31,31 @@ def str2citekey(s):
     return key
 
 
+def get_bibentry_from_file(bibfile):
+    """Extract first entry (supposed to be the only one) from given file.
+    """
+    bib_data = files.load_externalbibfile(bibfile)
+    first_key = bib_data.entries.keys()[0]
+    first_entry = bib_data.entries[first_key]
+    return first_key, first_entry
+
+
+def get_bibentry_from_string(content):
+    """Extract first entry (supposed to be the only one) from given file.
+    """
+    bib_data = files.parse_bibdata(StringIO(content))
+    first_key = bib_data.entries.keys()[0]
+    first_entry = bib_data.entries[first_key]
+    return first_key, first_entry
+
+
+def get_safe_metadata(metapath):
+    if metapath is None:
+        return None
+    else:
+        return files.read_yamlfile(metapath)
+
+
 class NoDocumentFile(Exception):
     pass
 
@@ -69,20 +95,22 @@ class Paper(object):
 
     # TODO add mechanism to verify keys (15/12/2012)
 
-    def has_file(self):
+    def get_external_document_path(self):
-        """Whether there exist a document file for this entry.
+        if self.metadata['external-document'] is not None:
-        """
+            return self.metadata['external-document']
-        return self.metadata['path'] is not None
-
-    def get_file_path(self):
-        if self.has_file():
-            return self.metadata['path']
         else:
             raise NoDocumentFile
 
-    def check_file(self):
+    def get_document_path(self):
-        path = self.get_file_path()
+        return self.get_external_document_path()
-        return os.path.exists(path) and os.path.isfile(path)
+
+    def set_external_document(self, docpath):
+        fullpdfpath = os.path.abspath(docpath)
+        files.check_file(fullpdfpath, fail=True)
+        self.metadata['external-document'] = fullpdfpath
+
+    def check_document_path(self):
+        return files.check_file(self.get_external_document_path())
 
     def generate_citekey(self):
         """Generate a citekey from bib_data.
@@ -105,14 +133,6 @@ class Paper(object):
         citekey = u'{}{}'.format(u''.join(first_author.last()), year)
         return str2citekey(citekey)
 
-    def set_document(self, docpath):
-        fullpdfpath = os.path.abspath(docpath)
-        files.check_file(fullpdfpath)
-        name, ext = files.name_from_path(docpath)
-        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.
@@ -150,23 +170,11 @@ class Paper(object):
 
     @classmethod
     def load(cls, bibpath, metapath=None):
-        key, entry = cls.get_bibentry(bibpath)
+        key, entry = get_bibentry_from_file(bibpath)
-        if metapath is None:
+        metadata = get_safe_metadata(metapath)
-            metadata = None
-        else:
-            metadata = files.read_yamlfile(metapath)
         p = Paper(bibentry=entry, metadata=metadata, citekey=key)
         return p
 
-    @classmethod
-    def get_bibentry(cls, bibfile):
-        """Extract first entry (supposed to be the only one) from given file.
-        """
-        bib_data = files.load_externalbibfile(bibfile)
-        first_key = bib_data.entries.keys()[0]
-        first_entry = bib_data.entries[first_key]
-        return first_key, first_entry
-
     @classmethod
     def create_meta(cls):
         return BASE_META.copy()
@@ -194,3 +202,32 @@ class Paper(object):
                     except ValueError, e:
                         print "Warning, skipping paper (%s)." % e
             return papers
+
+
+class PaperInRepo(Paper):
+
+    def __init__(self, repo, *args, **kwargs):
+        Paper.__init__(self, *args, **kwargs)
+        self.repo = repo
+
+    def get_document_path_in_repo(self):
+        doc_dir = files.clean_path(self.repo.get_document_directory())
+        found = glob.glob(doc_dir + "/%s.*" % self.citekey)
+        if found:
+            return found[0]
+        else:
+            raise NoDocumentFile
+
+    def get_document_path(self):
+        try:
+            return self.get_document_path_in_repo()
+        except NoDocumentFile:
+            return self.get_external_document_path()
+
+    @classmethod
+    def load(cls, repo, bibpath, metapath=None):
+        key, entry = get_bibentry_from_file(bibpath)
+        metadata = get_safe_metadata(metapath)
+        p = PaperInRepo(repo, bibentry=entry, metadata=metadata,
+                                 citekey=key)
+        return p

papers/pretty.py

@@ -14,12 +14,14 @@ def person_repr(p):
 
 
 def short_authors(bibentry):
-    authors = [person_repr(p) for p in bibentry.persons['author']]
+    try:
-    if len(authors) < 3:
+        authors = [person_repr(p) for p in bibentry.persons['author']]
-        return ', '.join(authors)
+        if len(authors) < 3:
-    else:
+            return ', '.join(authors)
-        return authors[0] + (' et al.' if len(authors) > 1 else '')
+        else:
-
+            return authors[0] + (' et al.' if len(authors) > 1 else '')
+    except KeyError:  # When no author is defined
+        return ''
 
 def bib_oneliner(bibentry):
     authors = short_authors(bibentry)

papers/repo.py

@@ -1,8 +1,10 @@
-from .color import colored
 import os
+import shutil
 
 import files
-from paper import Paper
+from paper import Paper, PaperInRepo
+from color import colored
+import configs
 
 
 ALPHABET = 'abcdefghijklmopqrstuvwxyz'
@@ -14,16 +16,20 @@ DOC_DIR = 'doc'
 
 class Repository(object):
 
-    def __init__(self):
+    def __init__(self, config=None):
         self.papersdir = None
         self.citekeys = []
+        if config is None:
+            config = configs.CONFIG
+        self.config = config
 
     # loading existing papers
 
     def paper_from_citekey(self, citekey):
         """Load a paper by its citekey from disk, if necessary."""
-        return Paper.load(self.path_to_paper_file(citekey, 'bib'),
+        return PaperInRepo.load(
-            metapath=self.path_to_paper_file(citekey, 'meta'))
+                self, self.path_to_paper_file(citekey, 'bib'),
+                metapath=self.path_to_paper_file(citekey, 'meta'))
 
     def citekey_from_ref(self, ref, fatal=True):
         """Tries to get citekey from given ref.
@@ -48,9 +54,11 @@ class Repository(object):
 
     # creating new papers
 
+    # Deprecated
+    # TODO merge
     def add_paper_from_paths(self, docpath, bibpath):
         p = Paper.load(bibpath)
-        p.set_document(docpath)
+        p.set_external_document(docpath)
         self.add_paper(p)
 
     def add_paper(self, p):
@@ -73,6 +81,15 @@ class Repository(object):
         else:
             self.save_paper(paper)
 
+    def remove(self, citekey):
+        self.citetekeys.remove(citekey)
+        paper = self.paper_from_citekey(citekey)
+        for f in ('bib', 'meta'):
+            shutil.rmtree(self.path_to_paper_file(citekey, f))
+        # TODO change
+        if paper.metadata['in-repo']:
+            shutil.rmtree(self.path_to_paper_file(citekey, f))
+
     def save_paper(self, paper):
         if not paper.citekey in self.citekeys:
             raise(ValueError('Paper not in repository, first add it.'))
@@ -117,9 +134,9 @@ class Repository(object):
         else:
             raise(ValueError("%s is not a valid paper file." % file_))
 
-    def get_document_directory(self, config):
+    def get_document_directory(self):
-        if config.has_option('papers', 'document-directory'):
+        if self.config.has_option('papers', 'document-directory'):
-            return config.get('papers', 'document-directory')
+            return self.config.get('papers', 'document-directory')
         else:
             return os.path.join(self.papersdir, DOC_DIR)
 
@@ -127,6 +144,18 @@ class Repository(object):
         for key in self.citekeys:
             yield self.paper_from_citekey(key)
 
+    def import_document(self, citekey, doc_file):
+        if citekey not in self.citekeys:
+            raise(ValueError, "Unknown citekey: %s." % citekey)
+        else:
+            doc_path = self.get_document_directory()
+            if not (os.path.exists(doc_path) and os.path.isdir(doc_path)):
+                raise(ValueError,
+                      "Document directory %s, does not exist." % doc_path)
+            ext = os.path.splitext(doc_file)[1]
+            new_doc_file = os.path.join(doc_path, citekey + ext)
+            shutil.copy(doc_file, new_doc_file)
+
     @classmethod
     def from_directory(cls, papersdir=None):
         repo = cls()