Adds update funciton for paper and required API and test updates.

- Adds update function that handle changes in citekey.
- Adds copy functions to paper classes.
- Adds tests.
- FIX a few bugs.

papers/paper.py

@@ -3,9 +3,8 @@ import os
 import unicodedata
 import re
 from cStringIO import StringIO
-import glob
 
-from pybtex.database import Entry, BibliographyData
+from pybtex.database import Entry, BibliographyData, FieldDict, Person
 
 import files
 
@@ -49,6 +48,21 @@ def get_bibentry_from_string(content):
     return first_key, first_entry
 
 
+def copy_person(p):
+    return Person(first=p.get_part_as_text('first'),
+                  middle=p.get_part_as_text('middle'),
+                  prelast=p.get_part_as_text('prelast'),
+                  last=p.get_part_as_text('last'),
+                  lineage=p.get_part_as_text('lineage'))
+
+
+def copy_bibentry(entry):
+    fd = FieldDict(entry.fields.parent, entry.fields)
+    persons = dict([(k, [copy_person(p) for p in v])
+                    for k, v in entry.persons.items()])
+    return Entry(entry.type, fields=fd, persons=persons)
+
+
 def get_safe_metadata(metapath):
     if metapath is None:
         return None
@@ -81,7 +95,7 @@ class Paper(object):
         self.citekey = citekey
 
     def __eq__(self, other):
-        return (type(other) is Paper
+        return (isinstance(self, Paper) and type(other) is type(self)
             and self.bibentry == other.bibentry
             and self.metadata == other.metadata
             and self.citekey == other.citekey)
@@ -168,6 +182,11 @@ class Paper(object):
         except (KeyError, IndexError):
             raise(NoDocumentFile('No file found in bib data.'))
 
+    def copy(self):
+        return Paper(bibentry=copy_bibentry(self.bibentry),
+                     metadata=self.metadata.copy(),
+                     citekey=self.citekey)
+
     @classmethod
     def load(cls, bibpath, metapath=None):
         key, entry = get_bibentry_from_file(bibpath)
@@ -211,12 +230,7 @@ class PaperInRepo(Paper):
         self.repo = repo
 
     def get_document_path_in_repo(self):
-        doc_dir = files.clean_path(self.repo.get_document_directory())
+        return self.repo.find_document(self.citekey)
-        found = glob.glob(doc_dir + "/%s.*" % self.citekey)
-        if found:
-            return found[0]
-        else:
-            raise NoDocumentFile
 
     def get_document_path(self):
         try:
@@ -224,6 +238,14 @@ class PaperInRepo(Paper):
         except NoDocumentFile:
             return self.get_external_document_path()
 
+    def copy(self):
+        return PaperInRepo.from_paper(self.as_paper().copy(), self.repo)
+
+    def as_paper(self):
+        return Paper(bibentry=self.bibentry,
+                     metadata=self.metadata,
+                     citekey=self.citekey)
+
     @classmethod
     def load(cls, repo, bibpath, metapath=None):
         key, entry = get_bibentry_from_file(bibpath)
@@ -231,3 +253,10 @@ class PaperInRepo(Paper):
         p = PaperInRepo(repo, bibentry=entry, metadata=metadata,
                                  citekey=key)
         return p
+
+    @classmethod
+    def from_paper(cls, paper, repo):
+        return PaperInRepo(repo,
+                           bibentry=paper.bibentry,
+                           metadata=paper.metadata,
+                           citekey=paper.citekey)

papers/repo.py

@@ -1,8 +1,9 @@
 import os
 import shutil
+import glob
 
 import files
-from paper import Paper, PaperInRepo
+from paper import Paper, PaperInRepo, NoDocumentFile
 from color import colored
 import configs
 
@@ -23,7 +24,8 @@ class Repository(object):
             config = configs.CONFIG
         self.config = config
 
-    # loading existing papers
+    def has_paper(self, citekey):
+        return citekey in self.citekeys
 
     def paper_from_citekey(self, citekey):
         """Load a paper by its citekey from disk, if necessary."""
@@ -64,7 +66,7 @@ class Repository(object):
     def add_paper(self, p):
         if p.citekey is None:  # TODO also test if citekey is valid
             raise(ValueError("Invalid citekey: %s." % p.citekey))
-        elif p.citekey in self.citekeys:
+        elif self.has_paper(p.citekey):
             raise(ValueError("Citekey already exists in repository: %s"
                     % p.citekey))
         self.citekeys.append(p.citekey)
@@ -76,22 +78,57 @@ class Repository(object):
         print "Added: %s" % p.citekey
 
     def add_or_update(self, paper):
-        if not paper.citekey in self.citekeys:
+        if not self.has_paper(paper.citekey):
             self.add_paper(paper)
         else:
             self.save_paper(paper)
 
+    def update(self, paper, old_citekey=None, overwrite=False):
+        """Updates a paper, eventually changing its citekey.
+        The paper should be in repository. If the citekey changes,
+        the new citekey should be free excpet if the overwrite argumnent
+        is set to True.
+        """
+        if old_citekey is None:
+            old_citekey = paper.citekey
+        if old_citekey not in self.citekeys:
+            raise(ValueError, 'Paper not in repository. Add first')
+        else:
+            if paper.citekey == old_citekey:
+                self.save_paper(paper)
+            else:
+                if self.has_paper(paper.citekey):
+                    if not overwrite:
+                        raise(ValueError,
+                            "There is already a paper with citekey: %s."
+                                % paper.citekey)
+                    else:
+                        self.save_paper(paper)
+                else:
+                    self.add_paper(paper)
+                # Eventually move document file
+                paper = PaperInRepo.from_paper(paper, self)
+                try:
+                    path = self.find_document(old_citekey)
+                    self.import_document(paper.citekey, path)
+                except NoDocumentFile:
+                    pass
+                self.remove(old_citekey)
+
     def remove(self, citekey):
-        self.citetekeys.remove(citekey)
+        self.citekeys.remove(citekey)
         paper = self.paper_from_citekey(citekey)
         for f in ('bib', 'meta'):
-            shutil.rmtree(self.path_to_paper_file(citekey, f))
+            os.remove(self.path_to_paper_file(citekey, f))
-        # TODO change
+        # Eventually remove associated document
-        if paper.metadata['in-repo']:
+        try:
-            shutil.rmtree(self.path_to_paper_file(citekey, f))
+            path = paper.get_document_path_in_repo()
+            os.remove(path)
+        except NoDocumentFile:
+            pass
 
     def save_paper(self, paper):
-        if not paper.citekey in self.citekeys:
+        if not self.has_paper(paper.citekey):
             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'))
@@ -124,6 +161,7 @@ class Repository(object):
         self.papersdir = papersdir
         os.makedirs(os.path.join(self.papersdir, BIB_DIR))
         os.makedirs(os.path.join(self.papersdir, META_DIR))
+        os.makedirs(self.get_document_directory())
         self.save()
 
     def path_to_paper_file(self, citekey, file_):
@@ -140,6 +178,14 @@ class Repository(object):
         else:
             return os.path.join(self.papersdir, DOC_DIR)
 
+    def find_document(self, citekey):
+        doc_dir = files.clean_path(self.get_document_directory())
+        found = glob.glob(doc_dir + "/%s.*" % citekey)
+        if found:
+            return found[0]
+        else:
+            raise NoDocumentFile
+
     def all_papers(self):
         for key in self.citekeys:
             yield self.paper_from_citekey(key)

tests/test_paper.py

@@ -22,10 +22,8 @@ entries:
         year: '1950'
 """
 META = """
-filename: null
+external-document: null
-extension: null
 notes: []
-path: null
 """
 
 
@@ -100,3 +98,22 @@ class TestSaveLoad(unittest.TestCase):
 
     def tearDown(self):
         shutil.rmtree(self.tmpdir)
+
+
+class TestCopy(unittest.TestCase):
+
+    def setUp(self):
+        self.orig = Paper()
+        self.orig.bibentry.fields['title'] = u'Nice title.'
+        self.orig.bibentry.fields['year'] = u'2013'
+        self.orig.bibentry.persons['author'] = [Person(u'John Doe')]
+        self.orig.citekey = self.orig.generate_citekey()
+
+    def test_copy_equal(self):
+        copy = self.orig.copy()
+        self.assertEqual(copy, self.orig)
+
+    def test_copy_can_be_changed(self):
+        copy = self.orig.copy()
+        copy.bibentry.fields['year'] = 2014
+        self.assertEqual(self.orig.bibentry.fields['year'], u'2013')

tests/test_repo.py

@@ -5,6 +5,7 @@ import os
 
 import fixtures
 from papers.repo import Repository, _str_incr, _to_suffix, BIB_DIR, META_DIR
+from papers.paper import PaperInRepo
 
 
 class TestCitekeyGeneration(unittest.TestCase):
@@ -29,7 +30,7 @@ class TestCitekeyGeneration(unittest.TestCase):
         self.assertEqual(c, 'Turing1950b')
 
 
-class TestAddPaper(unittest.TestCase):
+class TestRepo(unittest.TestCase):
 
     def setUp(self):
         self.tmpdir = tempfile.mkdtemp()
@@ -37,6 +38,12 @@ class TestAddPaper(unittest.TestCase):
         self.repo.init(self.tmpdir)
         self.repo.add_paper(fixtures.turing1950)
 
+    def tearDown(self):
+        shutil.rmtree(self.tmpdir)
+
+
+class TestAddPaper(TestRepo):
+
     def test_raises_value_error_on_existing_key(self):
         with self.assertRaises(ValueError):
             self.repo.add_paper(fixtures.turing1950)
@@ -49,5 +56,48 @@ class TestAddPaper(unittest.TestCase):
         self.assertTrue(os.path.exists(os.path.join(self.tmpdir, META_DIR,
             'Turing1950.meta')))
 
-    def tearDown(self):
+
-        shutil.rmtree(self.tmpdir)
+class TestUpdatePaper(TestRepo):
+
+    def test_raises_value_error_on_unknown_paper(self):
+        with self.assertRaises(ValueError):
+            self.repo.update(fixtures.doe2013)
+        with self.assertRaises(ValueError):
+            self.repo.update(fixtures.doe2013, old_citekey='zou')
+
+    def test_raises_value_error_on_existing_destination(self):
+        self.repo.add_paper(fixtures.doe2013)
+        with self.assertRaises(ValueError):
+            self.repo.update(fixtures.turing1950, old_citekey='Doe2013')
+
+    def test_updates_same_key(self):
+        new = self.repo.paper_from_citekey('Turing1950')
+        new.bibentry.fields['journal'] = u'Mind'
+        self.repo.update(new)
+        self.assertEqual(new, self.repo.paper_from_citekey('Turing1950'))
+
+    def test_updates_same_key_with_old_arg(self):
+        new = self.repo.paper_from_citekey('Turing1950')
+        new.bibentry.fields['journal'] = u'Mind'
+        self.repo.update(new, old_citekey='Turing1950')
+        self.assertEqual(new, self.repo.paper_from_citekey('Turing1950'))
+
+    def test_update_new_key_removes_old(self):
+        self.repo.update(fixtures.doe2013, old_citekey='Turing1950')
+        self.assertFalse(self.repo.has_paper('Turing1950'))
+
+    def test_update_new_key_updates(self):
+        self.repo.update(fixtures.doe2013, old_citekey='Turing1950')
+        self.assertTrue(self.repo.has_paper('Doe2013'))
+        self.assertEqual(self.repo.paper_from_citekey('Doe2013'),
+                         PaperInRepo.from_paper(fixtures.doe2013, self.repo))
+
+    def test_update_new_key_moves_doc(self):
+        self.repo.import_document('Turing1950',
+                                  os.path.join(os.path.dirname(__file__),
+                                               'data/pagerank.pdf'))
+        self.repo.update(fixtures.doe2013, old_citekey='Turing1950')
+        self.assertFalse(os.path.exists(os.path.join(
+            self.repo.get_document_directory(), 'Turing1950.pdf')))
+        self.assertTrue(os.path.exists(os.path.join(
+            self.repo.get_document_directory(), 'Doe2013.pdf')))