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Merge pull request #159 from pubs/fix/doc_add

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Fixes #144: behavior of add_copy mode during add.

- correctly handles `add_copy` mode and configuration,
- adds option top force 'copy' mode in `add` command,
- reverts default to `copy` instead of move for the `add` command,
- fixes assumption in tests about the default,
- do not try to delete the source when it is an URL,
- set default to `copy` during `import` commands and provides option for `move` or `link` alternatives.
This commit is contained in:
Olivier Mangin 2018-08-20 14:02:34 +02:00 committed by GitHub
commit 4f57aecfa4
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6 changed files with 116 additions and 39 deletions
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4
changelog.md
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@ -8,6 +8,8 @@
### Implemented enhancements
- Adds `move`, and `link` options for handling of documents during `import` (copy being the default). Makes `copy` the default for document handling during `add`. [(#159)](https://github.com/pubs/pubs/pull/159)
- Support for downloading arXiv reference from their ID ([#146](https://github.com/pubs/pubs/issues/146) by [joe-antognini](https://github.com/joe-antognini))
- Better feedback when an error is encountered while adding a reference from a DOI, ISBN or arXiv ID [#155](https://github.com/pubs/pubs/issues/155)
@ -34,6 +36,8 @@
### Fixed bugs
- [[#144]](https://github.com/pubs/pubs/issues/144) More robust handling of the `doc_add` options [(#159)](https://github.com/pubs/pubs/pull/159)
- [[#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)

18
pubs/command_utils.py Normal file
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@ -0,0 +1,18 @@
"""Contains code that is reused over commands, like argument definition
or help messages.
"""
def add_doc_copy_arguments(parser, copy=True):
doc_add_group = parser.add_mutually_exclusive_group()
doc_add_group.add_argument(
'-L', '--link', action='store_const', dest='doc_copy', const='link',
default=None,
help="don't copy document files, just create a link.")
if copy:
doc_add_group.add_argument(
'-C', '--copy', action='store_const', dest='doc_copy', const='copy',
help="copy document (keep source).")
doc_add_group.add_argument(
'-M', '--move', action='store_const', dest='doc_copy', const='move',
help="move document (copy and remove source).")

29
pubs/commands/add_cmd.py
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@ -12,6 +12,7 @@ from .. import apis
from .. import pretty
from .. import utils
from .. import endecoder
from ..command_utils import add_doc_copy_arguments
from ..completion import CommaSeparatedTagsCompletion
@ -36,10 +37,7 @@ def parser(subparsers, conf):
).completer = CommaSeparatedTagsCompletion(conf)
parser.add_argument('-k', '--citekey', help='citekey associated with the paper;\nif not provided, one will be generated automatically.',
default=None, type=p3.u_maybe)
parser.add_argument('-L', '--link', action='store_false', dest='copy', default=True,
help="don't copy document files, just create a link.")
parser.add_argument('-M', '--move', action='store_true', dest='move', default=False,
help="move document instead of of copying (ignored if --link).")
add_doc_copy_arguments(parser)
return parser
@ -140,25 +138,20 @@ def command(conf, args):
'{}, using {} instead.').format(bib_docfile, docfile))
# create the paper
copy = args.copy
if copy is None:
copy = conf['main']['doc_add'] in ('copy', 'move')
move = args.move
if move is None:
move = conf['main']['doc_add'] == 'move'
doc_add = args.doc_copy
if doc_add is None:
doc_add = conf['main']['doc_add']
rp.push_paper(p)
ui.message('added to pubs:\n{}'.format(pretty.paper_oneliner(p)))
if docfile is not None:
rp.push_doc(p.citekey, docfile, copy=copy or args.move)
if copy:
if move:
content.remove_file(docfile)
rp.push_doc(p.citekey, docfile, copy=(doc_add in ('copy', 'move')))
if doc_add == 'move' and content.content_type(docfile) != 'url':
content.remove_file(docfile)
if copy:
if move:
ui.message('{} was moved to the pubs repository.'.format(docfile))
else:
if doc_add == 'move':
ui.message('{} was moved to the pubs repository.'.format(docfile))
elif doc_add == 'copy':
ui.message('{} was copied to the pubs repository.'.format(docfile))
rp.close()

41
pubs/commands/import_cmd.py
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@ -7,10 +7,11 @@ from .. import repo
from .. import endecoder
from .. import bibstruct
from .. import color
from .. import content
from ..paper import Paper
from ..uis import get_ui
from ..content import system_path, read_text_file
from ..command_utils import add_doc_copy_arguments
_ABORT_USE_IGNORE_MSG = "Aborting import. Use --ignore-malformed to ignore."
@ -18,18 +19,22 @@ _IGNORING_MSG = " Ignoring it."
def parser(subparsers, conf):
parser = subparsers.add_parser('import',
help='import paper(s) to the repository')
parser.add_argument('bibpath',
help='path to bibtex, bibtexml or bibyaml file (or directory)')
parser.add_argument('-L', '--link', action='store_false', dest='copy', default=True,
help="don't copy document files, just create a link.")
parser.add_argument('keys', nargs='*',
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")
parser = subparsers.add_parser(
'import',
help='import paper(s) to the repository')
parser.add_argument(
'bibpath',
help='path to bibtex, bibtexml or bibyaml file (or directory)')
parser.add_argument(
'keys', nargs='*',
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")
add_doc_copy_arguments(parser, copy=False)
return parser
@ -90,9 +95,7 @@ def command(conf, args):
ui = get_ui()
bibpath = args.bibpath
copy = args.copy
if copy is None:
copy = conf['main']['doc_add'] in ('copy', 'move')
doc_import = args.doc_copy or 'copy'
rp = repo.Repository(conf)
# Extract papers from bib
@ -106,7 +109,9 @@ def command(conf, args):
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.push_doc(p.citekey, docfile,
copy=(doc_import in ('copy', 'move')))
if doc_import == 'move' and content.content_type(docfile) != 'url':
content.remove_file(docfile)
rp.close()

2
pubs/config/spec.py
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@ -11,7 +11,7 @@ docsdir = string(default="docsdir://")
# Specify if a document should be copied or moved in the docdir, or only
# linked when adding a publication.
doc_add = option('copy', 'move', 'link', default='move')
doc_add = option('copy', 'move', 'link', default='copy')
# the command to use when opening document files
open_cmd = string(default=None)

61
tests/test_usecase.py
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@ -292,9 +292,66 @@ class TestAdd(URLContentTestCase):
'pubs add data/pagerank.bib --link -d data/pagerank.pdf',
]
self.execute_cmds(cmds)
self.assertEqual(os.listdir(
os.path.join(self.default_pubs_dir, 'doc')),
self.assertEqual(
os.listdir(os.path.join(self.default_pubs_dir, 'doc')),
[])
self.assertTrue(os.path.exists('data/pagerank.pdf'))
def test_add_doc_nocopy_from_config_does_not_copy(self):
self.execute_cmds(['pubs init'])
config = conf.load_conf()
config['main']['doc_add'] = 'link'
conf.save_conf(config)
cmds = ['pubs add data/pagerank.bib -d data/pagerank.pdf']
self.execute_cmds(cmds)
self.assertEqual(
os.listdir(os.path.join(self.default_pubs_dir, 'doc')),
[])
self.assertTrue(os.path.exists('data/pagerank.pdf'))
def test_add_doc_copy(self):
cmds = ['pubs init',
'pubs add data/pagerank.bib --copy -d data/pagerank.pdf',
]
self.execute_cmds(cmds)
self.assertEqual(
os.listdir(os.path.join(self.default_pubs_dir, 'doc')),
['Page99.pdf'])
self.assertTrue(os.path.exists('data/pagerank.pdf'))
def test_add_doc_copy_from_config(self):
self.execute_cmds(['pubs init'])
config = conf.load_conf()
config['main']['doc_add'] = 'copy'
conf.save_conf(config)
cmds = ['pubs add data/pagerank.bib -d data/pagerank.pdf']
self.execute_cmds(cmds)
self.assertEqual(
os.listdir(os.path.join(self.default_pubs_dir, 'doc')),
['Page99.pdf'])
self.assertTrue(os.path.exists('data/pagerank.pdf'))
def test_add_doc_move(self):
cmds = ['pubs init',
'pubs add data/pagerank.bib --move -d data/pagerank.pdf',
]
self.execute_cmds(cmds)
self.assertEqual(
os.listdir(os.path.join(self.default_pubs_dir, 'doc')),
['Page99.pdf'])
self.assertFalse(os.path.exists('data/pagerank.pdf'))
def test_add_doc_move_from_config(self):
self.execute_cmds(['pubs init'])
config = conf.load_conf()
config['main']['doc_add'] = 'move'
conf.save_conf(config)
cmds = ['pubs add data/pagerank.bib -d data/pagerank.pdf']
self.execute_cmds(cmds)
self.assertEqual(
os.listdir(os.path.join(self.default_pubs_dir, 'doc')),
['Page99.pdf'])
self.assertFalse(os.path.exists('data/pagerank.pdf'))
def test_add_move_removes_doc(self):
cmds = ['pubs init',