Merge branch 'master' into jma/arxiv

changelog.md

@@ -0,0 +1,72 @@
+# Changelog
+
+
+## Current master
+
+[Full Changelog](https://github.com/pubs/pubs/compare/v0.7.0...master)
+
+
+### Implemented enhancements
+
+- Better dialog after editing paper [(#142)](https://github.com/pubs/pubs/issues/142)
+
+- Add a command to open urls ([#139](https://github.com/pubs/pubs/issues/139) by [ksunden](https://github.com/ksunden))
+
+- More robust cache on version change [(#138)](https://github.com/pubs/pubs/issues/138)
+
+- Allow utf8 citekeys [(#133)](https://github.com/pubs/pubs/issues/133)
+
+- Adds tag list completion in `pubs add -t ` [(#130)](https://github.com/pubs/pubs/issues/130)
+
+- Wider Travis coverage ([#107](https://github.com/pubs/pubs/issues/107) and [#108](https://github.com/pubs/pubs/issues/108))
+
+- Uses bibtexparser bwriter instead of internal encoder and adds `--ignore-fields` option to export. [(#106)](https://github.com/pubs/pubs/issues/106)
+
+- Configurable alias descriptions ([#104](https://github.com/pubs/pubs/issues/104) by [wflynny](https://github.com/wflynny))
+
+- Support year ranges in query [(#102)](https://github.com/pubs/pubs/issues/102)
+
+
+### Fixed bugs
+
+- [[#149]](https://github.com/pubs/pubs/issues/149) More robust handling of parsing and citekey errors [(#87)](https://github.com/pubs/pubs/pull/87)
+
+- [[#148]](https://github.com/pubs/pubs/issues/148) Fix compatibility with Pyfakefs 3.7 [(#151)](https://github.com/pubs/pubs/pull/151)
+
+- [[#95]](https://github.com/pubs/pubs/issues/95) Error message when editor is missing [(#141)](https://github.com/pubs/pubs/issues/141)
+
+- Fixes tests for printing help on `--help` and without argument. [(#137)](https://github.com/pubs/pubs/issues/137)
+
+- [[#126]](https://github.com/pubs/pubs/issues/126) Removes journal customization [(#127)](https://github.com/pubs/pubs/issues/127)
+
+- Fixes Travis failure on installing python3 for OSX [(#125)](https://github.com/pubs/pubs/issues/125)
+
+- [[#119]](https://github.com/pubs/pubs/issues/119) Removes link and DOI customization. [(#124)](https://github.com/pubs/pubs/issues/124)
+
+- [[#122]](https://github.com/pubs/pubs/issues/122) Fixes common strings [(#123)](https://github.com/pubs/pubs/issues/123)
+
+- [[#28]](https://github.com/pubs/pubs/issues/28) allow utf8 in citekeys [(#120)](https://github.com/pubs/pubs/issues/120)
+
+- Fixes field orders to use 'url' and fixes broken test. [(#118)](https://github.com/pubs/pubs/issues/118)
+
+- [[#25]](https://github.com/pubs/pubs/issues/25) Fix bibtex testcase [(#117)](https://github.com/pubs/pubs/issues/117)
+
+- [[#103]](https://github.com/pubs/pubs/issues/103) Fixes unicode comparison [(#116)](https://github.com/pubs/pubs/issues/116)
+
+- [[#95]](https://github.com/pubs/pubs/issues/95) robust handling of DOIs ([#105](https://github.com/pubs/pubs/issues/105) by [wflynny](https://github.com/wflynny))
+
+- [[#99]](https://github.com/pubs/pubs/issues/99) Print help when no subcommand is provided ([#100](https://github.com/pubs/pubs/issues/100) by [wflynny](https://github.com/wflynny))
+
+- Fix defaults not used in config. [(#97)](https://github.com/pubs/pubs/issues/97)
+
+- Fixes content not read from urls because of call to `os.abspath` [(#96)](https://github.com/pubs/pubs/issues/96)
+
+- [[#93]](https://github.com/pubs/pubs/issues/93) actually save the modifications on `edit -m`. [(#94)](https://github.com/pubs/pubs/issues/94)
+
+- [[#88]](https://github.com/pubs/pubs/issues/88) Adds proper escaping for
+arguments in alias plugin. [(#91)](https://github.com/pubs/pubs/issues/91)
+
+
+## [v0.7.0](https://github.com/pubs/pubs/compare/v0.6.0...v0.7.0) (2017-08-06)
+
+[Full Changelog](https://github.com/pubs/pubs/compare/v0.6.0...v0.7.0)

pubs/commands/add_cmd.py

@@ -11,6 +11,7 @@ from .. import templates
 from .. import apis
 from .. import pretty
 from .. import utils
+from .. import endecoder
 from ..completion import CommaSeparatedTagsCompletion
 
 
@@ -58,12 +59,13 @@ def bibentry_from_editor(conf, ui, rp):
                 bibstruct.verify_bibdata(bibentry)
                 # REFACTOR Generate citykey
                 again = False
-        except ValueError:
+
+        except endecoder.EnDecoder.BibDecodingError:
             again = ui.input_yn(
-                question='Invalid bibfile. Edit again ?',
+                question='Invalid bibfile. Edit again?',
                 default='y')
             if not again:
-                ui.exit(0)
+                ui.exit()
 
     return bibentry
 

pubs/commands/edit_cmd.py

@@ -54,12 +54,24 @@ def command(conf, args):
                 new_paper = Paper(paper.citekey, paper.bibdata,
                                   metadata=content)
                 rp.push_paper(new_paper, overwrite=True, event=False)
+                ui.info(('The metadata of paper `{}`  was successfully '
+                         'edited.'.format(citekey)))
             else:
                 new_paper = Paper.from_bibentry(content,
                                                 metadata=paper.metadata)
-                rp.rename_paper(new_paper, old_citekey=paper.citekey)
+                if rp.rename_paper(new_paper, old_citekey=paper.citekey):
+                    ui.info(('Paper `{}` was successfully edited and renamed '
+                             'as `{}`.'.format(citekey, new_paper.citekey)))
+                else:
+                    ui.info(('Paper `{}` was successfully edited.'.format(
+                        citekey)))
             break
 
+        except coder.BibDecodingError:
+            if not ui.input_yn(question="Error parsing bibdata. Edit again?"):
+                ui.error("Aborting, paper not updated.")
+                ui.exit()
+
         except repo.CiteKeyCollision:
             options = ['overwrite', 'edit again', 'abort']
             choice = options[ui.input_choice(
@@ -71,6 +83,7 @@ def command(conf, args):
                 break
             elif choice == 'overwrite':
                 paper = rp.push_paper(paper, overwrite=True)
+                ui.info(('Paper `{}` was overwritten.'.format(citekey)))
                 break
             # else edit again
         # Also handle malformed bibtex and metadata

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 it."
+
+
 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(bibpath):
+def many_from_path(ui, bibpath, ignore=False):
     """Extract list of papers found in bibliographic files in path.
 
     The behavior is to:
@@ -49,16 +55,31 @@ def many_from_path(bibpath):
 
     biblist = []
     for filepath in all_files:
-        biblist.append(coder.decode_bibdata(read_text_file(filepath)))
+        try:
+            biblist.append(coder.decode_bibdata(read_text_file(filepath)))
+        except coder.BibDecodingError:
+            error = "Could not parse bibtex at {}.".format(filepath)
+            if ignore:
+                ui.warning(error + _IGNORING_MSG)
+            else:
+                ui.error(error + _ABORT_USE_IGNORE_MSG)
+                ui.exit()
 
     papers = {}
     for b in biblist:
         for k, b in b.items():
+            if k in papers:
+                ui.warning('Duplicated citekey {}. Keeping the last one.'.format(k))
             try:
                 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
 
 
@@ -75,20 +96,17 @@ def command(conf, args):
 
     rp = repo.Repository(conf)
     # Extract papers from bib
-    papers = many_from_path(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()

pubs/databroker.py

@@ -45,7 +45,11 @@ class DataBroker(object):
 
     def pull_bibentry(self, citekey):
         bibdata_raw = self.filebroker.pull_bibfile(citekey)
-        return self.endecoder.decode_bibdata(bibdata_raw)
+        try:
+            return self.endecoder.decode_bibdata(bibdata_raw)
+        except self.endecoder.BibDecodingError as e:
+            e.message = "Unable to decode bibtex for paper {}.".format(citekey)
+            raise e
 
     def push_metadata(self, citekey, metadata):
         metadata_raw = self.endecoder.encode_metadata(metadata)

pubs/endecoder.py

@@ -66,6 +66,16 @@ class EnDecoder(object):
         * encode_bibdata will try to recognize exceptions
     """
 
+    class BibDecodingError(Exception):
+
+        message = "Could not parse provided bibdata:\n---\n{}\n---"
+
+        def __init__(self, bibdata):
+            self.data = bibdata
+
+        def __str__(self):
+            return self.message.format(self.data)
+
     bwriter = bp.bwriter.BibTexWriter()
     bwriter.display_order = BIBFIELD_ORDER
 
@@ -103,7 +113,10 @@ class EnDecoder(object):
         return entry
 
     def decode_bibdata(self, bibdata):
-        """"""
+        """Decodes bibdata from string.
+
+        If the decoding fails, returns a BibParseError.
+        """
         try:
             entries = bp.bparser.BibTexParser(
                 bibdata, common_strings=True,
@@ -121,4 +134,5 @@ class EnDecoder(object):
         except Exception:
             import traceback
             traceback.print_exc()
-        raise ValueError('could not parse provided bibdata:\n{}'.format(bibdata))
+        raise self.BibDecodingError(bibdata)
+        # TODO: filter exceptions from pyparsing and pass reason upstream

pubs/repo.py

@@ -141,6 +141,13 @@ class Repository(object):
             pass
 
     def rename_paper(self, paper, new_citekey=None, old_citekey=None):
+        """Move a paper from a citekey to another one.
+
+        Even if the new and old citekey are the same, the paper instance is
+        pushed to disk.
+
+        :return:  True if a rename happened, False if not.
+        """
         if old_citekey is None:
             old_citekey = paper.citekey
         if new_citekey is None:
@@ -149,6 +156,7 @@ class Repository(object):
         # check if new_citekey is not the same as paper.citekey
         if old_citekey == new_citekey:
             self.push_paper(paper, overwrite=True, event=False)
+            return False
         else:
             # check if new_citekey does not exists
             if new_citekey in self:
@@ -171,6 +179,7 @@ class Repository(object):
             self.remove_paper(old_citekey, event=False)
             # send event
             events.RenameEvent(paper, old_citekey).send()
+            return True
 
     def push_doc(self, citekey, docfile, copy=None):
         p = self.pull_paper(citekey)

pubs/uis.py

@@ -11,11 +11,11 @@ import subprocess
 from . import color
 from . import config
 from .p3 import _get_raw_stdout, _get_raw_stderr, input, ustr
-from .content import check_file, read_text_file, write_file, system_path
+from .content import check_file, read_text_file, write_file
 
 
 DEBUG = False  # unhandled exceptions traces are printed
-DEBUG_ALL_TRACES = False # handled exceptions traces are printed
+DEBUG_ALL_TRACES = False  # handled exceptions traces are printed
 # package-shared ui that can be accessed using :
 # from uis import get_ui
 # ui = get_ui()
@@ -38,40 +38,14 @@ def _get_encoding(conf):
 def _get_local_editor():
     """Get the editor from environment variables.
 
-    Use nano as a default.
+    Use vi as a default.
     """
-    return os.environ.get('EDITOR', 'nano')
+    return os.environ.get('EDITOR', 'vi')
-
-
-def _editor_input(editor, initial='', suffix='.tmp'):
-    """Use an editor to get input"""
-    str_initial = initial.encode('utf-8')  # TODO: make it a configuration item
-    with tempfile.NamedTemporaryFile(suffix=suffix, delete=False) as temp_file:
-        tfile_name = temp_file.name
-        temp_file.write(str_initial)
-    cmd = shlex.split(editor)  # this enable editor command with option, e.g. gvim -f
-    cmd.append(tfile_name)
-    subprocess.call(cmd)
-    content = read_text_file(tfile_name)
-    os.remove(tfile_name)
-    return content
-
-
-def _edit_file(editor, path_to_file, temporary=True):
-    if temporary:
-        check_file(path_to_file, fail=True)
-        content = read_text_file(path_to_file)
-        content = _editor_input(editor, content)
-        write_file(path_to_file, content)
-    else:
-        cmd = editor.split()  # this enable editor command with option, e.g. gvim -f
-        cmd.append(system_path(path_to_file))
-        subprocess.call(cmd)
 
 
 def get_ui():
     if _ui is None:
-        return PrintUI(config.load_default_conf()) # no editor support. (#FIXME?)
+        return PrintUI(config.load_default_conf())  # no editor support. (#FIXME?)
     return _ui
 
 
@@ -111,7 +85,7 @@ class PrintUI(object):
         kwargs['file'] = self._stderr
         print('{}: {}'.format(color.dye_err('error', 'error'), message), **kwargs)
 
-        if DEBUG_ALL_TRACES: # if an exception has been raised, print the trace.
+        if DEBUG_ALL_TRACES:  # if an exception has been raised, print the trace.
             if sys.exc_info()[0] is not None:
                 traceback.print_exception(*sys.exc_info)
 
@@ -130,6 +104,7 @@ class PrintUI(object):
             self.exit()
         return True # never happens
 
+
 class InputUI(PrintUI):
     """UI class. Stores configuration parameters and system information.
     """
@@ -144,7 +119,7 @@ class InputUI(PrintUI):
         except EOFError:
             self.error('Standard input ended while waiting for answer.')
             self.exit(1)
-        return ustr(data) #.decode('utf-8')
+        return ustr(data)  #.decode('utf-8')
 
     def input_choice_ng(self, options, option_chars=None, default=None, question=''):
         """Ask the user to chose between a set of options. The user is asked
@@ -184,7 +159,6 @@ class InputUI(PrintUI):
                         pass
             self.message('Incorrect option.', option_str)
 
-
     def input_choice(self, options, option_chars, default=None, question=''):
         """Ask the user to chose between a set of options. The user is asked
         to input a char corresponding to the option he chooses.
@@ -223,7 +197,41 @@ class InputUI(PrintUI):
         return [True, False][answer]
 
     def editor_input(self, initial="", suffix='.tmp'):
-        return _editor_input(self.editor, initial=initial, suffix=suffix)
+        """Use an editor to get input"""
+        str_initial = initial.encode('utf-8')  # TODO: make it a configuration item
+        with tempfile.NamedTemporaryFile(suffix=suffix, delete=False) as temp_file:
+            tfile_name = temp_file.name
+            temp_file.write(str_initial)
+        self._call_editor(tfile_name)
+        content = read_text_file(tfile_name)
+        os.remove(tfile_name)
+        return content
 
     def edit_file(self, path, temporary):
-        _edit_file(self.editor, path, temporary=temporary)
+        if temporary:
+            check_file(path, fail=True)
+            content = read_text_file(path)
+            content = self.editor_input(content)
+            write_file(path, content)
+        else:
+            self._call_editor(path)
+
+    def _call_editor(self, path):
+        """Call the editor, and checks that no error were raised by the OS"""
+        cmd = shlex.split(self.editor)  # this enable editor command with option, e.g. gvim -f
+        cmd.append(path)
+        try:
+            subprocess.call(cmd)
+        except OSError as e:
+            if e.errno == os.errno.ENOENT:
+                self.error(("Error while calling editor '{}'. The editor may "
+                            "not be present. You can change the text editor "
+                            "that pubs uses by setting the $EDITOR environment "
+                            "variable, or by running `pubs conf` and setting "
+                            "the `edit_cmd` field."
+                            ).format(self.editor))
+                # handle file not found error.
+                self.exit()
+            else:
+                # Something else went wrong while trying to run `wget`
+                self.handle_exception(e)

readme.md

@@ -125,3 +125,4 @@ You can access the self-documented configuration by using `pubs conf`, and all t
 - [Tyler Earnest](https://github.com/tmearnest)
 - [Dennis Wilson](https://github.com/d9w)
 - [Bill Flynn](https://github.com/wflynny)
+- [ksunden](https://github.com/ksunden)

tests/fake_env.py

@@ -74,12 +74,21 @@ class FakeInput():
     def as_global(self):
         for md in self.module_list:
             md.input = self
-            md._editor_input = self
+            if md.__name__ == 'pubs.uis':
-            md._edit_file = self.input_to_file
+                md.InputUI.editor_input = self
-            # if mdname.endswith('files'):
+                md.InputUI.edit_file = self.input_to_file
-            #     md.editor_input = self
+                # Do not catch UnexpectedInput
+                original_handler = md.InputUI.handle_exception
 
-    def input_to_file(self, _, path_to_file, temporary=True):
+                def handler(ui, exc):
+                    if isinstance(exc, self.UnexpectedInput):
+                        raise
+                    else:
+                        original_handler(ui, exc)
+
+                md.InputUI.handle_exception = handler
+
+    def input_to_file(self, path_to_file, temporary=True):
         content.write_file(path_to_file, self())
 
     def add_input(self, inp):
@@ -98,11 +107,16 @@ class TestFakeFs(fake_filesystem_unittest.TestCase):
 
     def setUp(self):
         self.rootpath = os.path.abspath(os.path.dirname(__file__))
+        self.homepath = os.path.expanduser('~')
         self.setUpPyfakefs()
-        self.fs.CreateDirectory(os.path.expanduser('~'))
+        self.reset_fs()
-        self.fs.CreateDirectory(self.rootpath)
-        os.chdir(self.rootpath)
 
     def reset_fs(self):
-        self._stubber.tearDown()  # renew the filesystem
+        """Reset the fake filesystem"""
-        self.setUp()
+        for dir_name in self.fs.listdir('/'):
+            if dir_name not in ['var', 'tmp']:
+                self.fs.remove_object(os.path.join('/', dir_name))
+
+        self.fs.create_dir(os.path.expanduser('~'))
+        self.fs.create_dir(self.rootpath)
+        os.chdir(self.rootpath)

tests/requirements.txt

@@ -1,5 +1,5 @@
 # those are the additional packages required to run the tests
 six
-pyfakefs==3.3
+pyfakefs
 ddt
 mock

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_apis.py

@@ -32,7 +32,7 @@ class TestDOI2Bibtex(unittest.TestCase):
 
     def test_parse_fails_on_incorrect_DOI(self):
         bib = doi2bibtex('999999')
-        with self.assertRaises(ValueError):
+        with self.assertRaises(EnDecoder.BibDecodingError):
             self.endecoder.decode_bibdata(bib)
 
 
@@ -56,7 +56,7 @@ class TestISBN2Bibtex(unittest.TestCase):
 
     def test_parse_fails_on_incorrect_ISBN(self):
         bib = doi2bibtex('9' * 13)
-        with self.assertRaises(ValueError):
+        with self.assertRaises(EnDecoder.BibDecodingError):
             self.endecoder.decode_bibdata(bib)
 
 

tests/test_bibstruct.py

@@ -1,7 +1,6 @@
 # -*- coding: utf-8 -*-
 from __future__ import unicode_literals
 
-import os
 import unittest
 import copy
 

tests/test_config.py

@@ -2,7 +2,7 @@
 import unittest
 
 import dotdot
-from pubs.config import conf
+# from pubs.config import conf
 
 # class TestConfig(unittest.TestCase):
 #

tests/test_databroker.py

@@ -5,8 +5,7 @@ import os
 import dotdot
 import fake_env
 
-from pubs import content, filebroker, databroker, datacache
+from pubs import content, databroker, datacache
-from pubs.config import conf
 
 import str_fixtures
 from pubs import endecoder
@@ -35,7 +34,7 @@ class TestDataBroker(fake_env.TestFakeFs):
 
             self.assertEqual(db.pull_metadata('citekey1'), page99_metadata)
             pulled = db.pull_bibentry('citekey1')['Page99']
-            for key, value in pulled.items():
+            for key in pulled.keys():
                 self.assertEqual(pulled[key], page99_bibentry['Page99'][key])
             self.assertEqual(db.pull_bibentry('citekey1'), page99_bibentry)
 
@@ -91,4 +90,4 @@ class TestDataBroker(fake_env.TestFakeFs):
 
 
 if __name__ == '__main__':
-    unittest.main()
+    unittest.main(verbosity=2)

tests/test_datacache.py

@@ -3,7 +3,6 @@ import unittest
 import time
 
 import dotdot
-import fake_env
 
 from pubs.datacache import CacheEntrySet
 

tests/test_endecoder.py

@@ -52,7 +52,7 @@ class TestEnDecode(unittest.TestCase):
 
         self.assertEqual(bibraw1, bibraw2)
 
-    def test_endecode_bibtex(self):
+    def test_endecode_bibtex_converts_month_string(self):
         """Test if `month=dec` is correctly recognized and transformed into
         `month={December}`"""
         decoder = endecoder.EnDecoder()
@@ -147,6 +147,11 @@ class TestEnDecode(unittest.TestCase):
         self.assertIn('author', entry1)
         self.assertIn('institution', entry1)
 
+    def test_endecodes_raises_exception(self):
+        decoder = endecoder.EnDecoder()
+        with self.assertRaises(decoder.BibDecodingError):
+            decoder.decode_bibdata("@misc{I am not a correct bibtex{{}")
+
 
 if __name__ == '__main__':
     unittest.main()

tests/test_pretty.py

@@ -1,10 +1,8 @@
 from __future__ import unicode_literals
 
 import unittest
-import os
 
 import dotdot
-import fake_env
 
 from pubs import endecoder, pretty, color, config
 

tests/test_usecase.py

@@ -15,14 +15,12 @@ from pyfakefs.fake_filesystem import FakeFileOpen
 import dotdot
 import fake_env
 
-from pubs import pubs_cmd, update, color, content, filebroker, uis, p3, endecoder
+from pubs import pubs_cmd, color, content, uis, p3, endecoder
 from pubs.config import conf
-import configobj
 
 import str_fixtures
 import fixtures
 
-from pubs.commands import init_cmd, import_cmd
 
 # makes the tests very noisy
 PRINT_OUTPUT   = False
@@ -45,9 +43,8 @@ class FakeSystemExit(Exception):
             "Exited with code: {}.".format(self.code), *args)
 
 
-# code for fake fs
+class TestInput(unittest.TestCase):
-
+    """Test that the fake input mechanisms work correctly in the tests"""
-class TestFakeInput(unittest.TestCase):
 
     def test_input(self):
         input = fake_env.FakeInput(['yes', 'no'])
@@ -65,13 +62,16 @@ class TestFakeInput(unittest.TestCase):
             color.input()
 
     def test_editor_input(self):
+        sample_conf = conf.load_default_conf()
+        ui = uis.InputUI(sample_conf)
+
         other_input = fake_env.FakeInput(['yes', 'no'],
-                                         module_list=[uis, color])
+                                         module_list=[uis])
         other_input.as_global()
-        self.assertEqual(uis._editor_input(), 'yes')
+        self.assertEqual(ui.editor_input('fake_editor'), 'yes')
-        self.assertEqual(uis._editor_input(), 'no')
+        self.assertEqual(ui.editor_input('fake_editor'), 'no')
         with self.assertRaises(fake_env.FakeInput.UnexpectedInput):
-            color.input()
+            ui.editor_input()
 
 
 class CommandTestCase(fake_env.TestFakeFs):
@@ -82,7 +82,6 @@ class CommandTestCase(fake_env.TestFakeFs):
     def setUp(self, nsec_stat=True):
         super(CommandTestCase, self).setUp()
         os.stat_float_times(nsec_stat)
-        # self.fs = fake_env.create_fake_fs([content, filebroker, conf, init_cmd, import_cmd, configobj, update], nsec_stat=nsec_stat)
         self.default_pubs_dir = os.path.expanduser('~/.pubs')
         self.default_conf_path = os.path.expanduser('~/.pubsrc')
 
@@ -129,7 +128,7 @@ class CommandTestCase(fake_env.TestFakeFs):
                         outs.append(color.undye(actual_out))
                     else:
                         pubs_cmd.execute(actual_cmd.split())
-                except fake_env.FakeInput.UnexpectedInput as e:
+                except fake_env.FakeInput.UnexpectedInput:
                     self.fail('Unexpected input asked by command: {}.'.format(
                         actual_cmd))
             return outs
@@ -178,7 +177,7 @@ class URLContentTestCase(DataCommandTestCase):
         return p3.urlparse(url).path
 
     def url_exists(self, url):
-        return self.fs.Exists(self._url_to_path(url))
+        return self.fs.exists(self._url_to_path(url))
 
     def url_to_byte_content(self, url, ui=None):
         path = self._url_to_path(url)
@@ -198,7 +197,7 @@ class TestAlone(CommandTestCase):
     def test_alone_misses_command(self):
         with self.assertRaises(FakeSystemExit) as cm:
             self.execute_cmds(['pubs'])
-            self.assertEqual(cm.exception.code, 2)
+        self.assertEqual(cm.exception.code, 2)
 
     def test_alone_prints_help(self):
         # capturing the output of `pubs --help` is difficult because argparse
@@ -335,11 +334,20 @@ class TestAdd(URLContentTestCase):
     def test_add_no_citekey_fails(self):
         # See #113
         cmds = ['pubs init',
-                ('pubs add', [str_fixtures.bibtex_no_citekey]),
+                ('pubs add', [str_fixtures.bibtex_no_citekey, 'n']),
                 ]
         with self.assertRaises(FakeSystemExit):
             self.execute_cmds(cmds)
 
+    def test_add_edit_fails(self):
+        cmds = ['pubs init',
+                ('pubs add',
+                    ['@misc{I am not a correct bibtex{{}', 'n']),
+                ]
+        with self.assertRaises(FakeSystemExit) as cm:
+            self.execute_cmds(cmds)
+        self.assertEqual(cm.exception.code, 1)
+
 
 class TestList(DataCommandTestCase):
 
@@ -355,8 +363,8 @@ class TestList(DataCommandTestCase):
 
     def test_list_several_no_date(self):
         self.execute_cmds(['pubs init -p testrepo'])
-        os.chdir('/') # weird fix for shutil.rmtree invocation.
+        os.chdir('/')  # weird fix for shutil.rmtree invocation.
-        shutil.rmtree(self.rootpath + '/testrepo')
+        shutil.rmtree(os.path.join(self.rootpath, 'testrepo'))
         os.chdir(self.rootpath)
         self.fs.add_real_directory(os.path.join(self.rootpath, 'testrepo'), read_only=False)
 
@@ -680,16 +688,40 @@ class TestUsecase(DataCommandTestCase):
         self.assertFileContentEqual(os.path.expanduser('~/.pubsrc'),
                                     str_fixtures.sample_conf)
 
-    def test_editor_abort(self):
+    def test_editor_aborts(self):
         with self.assertRaises(FakeSystemExit):
             cmds = ['pubs init',
-                    ('pubs add', ['abc', 'n']),
-                    ('pubs add', ['abc', 'y', 'abc', 'n']),
                     'pubs add data/pagerank.bib',
-                    ('pubs edit Page99', ['', 'a']),
+                    ('pubs edit Page99', ['', 'n']),
+                   ]
+            self.execute_cmds(cmds)
+
+    def test_editor_succeeds_on_second_edit(self):
+        cmds = ['pubs init',
+                'pubs add data/pagerank.bib',
+                ('pubs edit Page99', [
+                    '@misc{Page99, title="TTT" author="X. YY"}', 'y',
+                    '@misc{Page99, title="TTT", author="X. YY"}', '']),
+                ('pubs list', [], '[Page99] YY, X. "TTT" \n')
+                ]
+        self.execute_cmds(cmds)
+
+    def test_add_aborts(self):
+        with self.assertRaises(FakeSystemExit):
+            cmds = ['pubs init',
+                    ('pubs add New', ['']),
                    ]
             self.execute_cmds(cmds)
 
+    def test_add_succeeds_on_second_edit(self):
+        cmds = ['pubs init',
+                ('pubs add', [
+                    '', 'y',
+                    '@misc{New, title="TTT", author="X. YY"}', '']),
+                ('pubs list', [], '[New] YY, X. "TTT" \n')
+                ]
+        self.execute_cmds(cmds)
+
     def test_editor_success(self):
         cmds = ['pubs init',
                 ('pubs add', [str_fixtures.bibtex_external0]),
@@ -791,6 +823,25 @@ 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',
@@ -920,4 +971,4 @@ class TestCache(DataCommandTestCase):
 
 
 if __name__ == '__main__':
-    unittest.main()
+    unittest.main(verbosity=2)