Adds option to ignore malformed bibtex files or entry during import.

pubs/commands/import_cmd.py

@@ -13,6 +13,10 @@ from ..uis import get_ui
 from ..content import system_path, read_text_file
 
 
+_ABORT_USE_IGNORE_MSG = "Aborting import. Use --ignore-malformed to ignore."
+_IGNORING_MSG = " Ignoring."
+
+
 def parser(subparsers, conf):
     parser = subparsers.add_parser('import',
             help='import paper(s) to the repository')
@@ -24,10 +28,12 @@ def parser(subparsers, conf):
             help="one or several keys to import from the file")
     parser.add_argument('-O', '--overwrite', action='store_true', default=False,
             help="Overwrite keys already in the database")
+    parser.add_argument('-i', '--ignore-malformed', action='store_true', default=False,
+            help="Ignore malformed and unreadable files and entries")
     return parser
 
 
-def many_from_path(ui, bibpath):
+def many_from_path(ui, bibpath, ignore=False):
     """Extract list of papers found in bibliographic files in path.
 
     The behavior is to:
@@ -52,8 +58,12 @@ def many_from_path(ui, bibpath):
         try:
             biblist.append(coder.decode_bibdata(read_text_file(filepath)))
         except coder.BibDecodingError:
-            ui.error("Could not parse bibtex at {}. Aborting import.".format(filepath))
+            error = "Could not parse bibtex at {}.".format(filepath)
-            ui.exit()
+            if ignore:
+                ui.warning(error + _IGNORING_MSG)
+            else:
+                ui.error(error + _ABORT_USE_IGNORE_MSG)
+                ui.exit()
 
     papers = {}
     for b in biblist:
@@ -64,7 +74,12 @@ def many_from_path(ui, bibpath):
                 papers[k] = Paper(k, b)
                 papers[k].added = datetime.datetime.now()
             except ValueError as e:
-                papers[k] = e
+                error = 'Could not load entry for citekey {} ({}).'.format(k, e)
+                if ignore:
+                    ui.warning(error + _IGNORING_MSG)
+                else:
+                    ui.error(error + _ABORT_USE_IGNORE_MSG)
+                    ui.exit()
     return papers
 
 
@@ -81,20 +96,17 @@ def command(conf, args):
 
     rp = repo.Repository(conf)
     # Extract papers from bib
-    papers = many_from_path(ui, bibpath)
+    papers = many_from_path(ui, bibpath, ignore=args.ignore_malformed)
     keys = args.keys or papers.keys()
     for k in keys:
         p = papers[k]
-        if isinstance(p, Exception):
+        rp.push_paper(p, overwrite=args.overwrite)
-            ui.error('Could not load entry for citekey {}.'.format(k))
+        ui.info('{} imported.'.format(color.dye_out(p.citekey, 'citekey')))
+        docfile = bibstruct.extract_docfile(p.bibdata)
+        if docfile is None:
+            ui.warning("No file for {}.".format(p.citekey))
         else:
-            rp.push_paper(p, overwrite=args.overwrite)
+            rp.push_doc(p.citekey, docfile, copy=copy)
-            ui.info('{} imported.'.format(color.dye_out(p.citekey, 'citekey')))
+            # FIXME should move the file if configured to do so.
-            docfile = bibstruct.extract_docfile(p.bibdata)
-            if docfile is None:
-                ui.warning("No file for {}.".format(p.citekey))
-            else:
-                rp.push_doc(p.citekey, docfile, copy=copy)
-                #FIXME should move the file if configured to do so.
 
     rp.close()

tests/str_fixtures.py

@@ -69,7 +69,7 @@ bibtex_no_citekey = """@Manual{,
 }
 """
 
-bibtex_month= """@inproceedings{Goyal2017,
+bibtex_month = """@inproceedings{Goyal2017,
  author = {Goyal, Anirudh and Sordoni, Alessandro and C{\^{o}}t{\'{e}}, Marc-Alexandre and Ke, Nan Rosemary and Bengio, Yoshua},
  title = {Z-Forcing: Training Stochastic Recurrent Networks},
  year = {2017},
@@ -78,6 +78,12 @@ bibtex_month= """@inproceedings{Goyal2017,
 }
 """
 
+not_bibtex = """@misc{this looks,
+  like = a = bibtex file but
+    , is not a real one!
+
+"""
+
 sample_conf = """
 [main]
 

tests/test_usecase.py

@@ -826,6 +826,25 @@ class TestUsecase(DataCommandTestCase):
         outs = self.execute_cmds(cmds)
         self.assertEqual(1 + 1, len(outs[-1].split('\n')))
 
+    def test_import_fails_without_ignore(self):
+        with FakeFileOpen(self.fs)('data/fake.bib', 'w') as f:
+            f.write(str_fixtures.not_bibtex)
+        cmds = ['pubs init',
+                'pubs import data/ Page99',
+                ]
+        with self.assertRaises(FakeSystemExit):
+            self.execute_cmds(cmds)
+
+    def test_import_ignores(self):
+        with FakeFileOpen(self.fs)('data/fake.bib', 'w') as f:
+            f.write(str_fixtures.not_bibtex)
+        cmds = ['pubs init',
+                'pubs import --ignore-malformed data/ Page99',
+                'pubs list'
+                ]
+        outs = self.execute_cmds(cmds)
+        self.assertEqual(1 + 1, len(outs[-1].split('\n')))
+
     def test_update(self):
         cmds = ['pubs init',
                 'pubs add data/pagerank.bib',