Merge pull request #159 from pubs/fix/doc_add

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.

changelog.md

@@ -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)

pubs/command_utils.py

@@ -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).")

pubs/commands/add_cmd.py

@@ -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,
+    add_doc_copy_arguments(parser)
-                        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).")
     return parser
 
 
@@ -140,25 +138,20 @@ def command(conf, args):
                     '{}, using {} instead.').format(bib_docfile, docfile))
 
     # create the paper
-    copy = args.copy
+    doc_add = args.doc_copy
-    if copy is None:
+    if doc_add is None:
-        copy = conf['main']['doc_add'] in ('copy', 'move')
+        doc_add = conf['main']['doc_add']
-    move = args.move
-    if move is None:
-        move = conf['main']['doc_add'] == 'move'
 
     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)
+        rp.push_doc(p.citekey, docfile, copy=(doc_add in ('copy', 'move')))
-        if copy:
+        if doc_add == 'move' and content.content_type(docfile) != 'url':
-            if move:
+            content.remove_file(docfile)
-                content.remove_file(docfile)
+
-
+        if doc_add == 'move':
-        if copy:
+            ui.message('{} was moved to the pubs repository.'.format(docfile))
-            if move:
+        elif doc_add == 'copy':
-                ui.message('{} was moved to the pubs repository.'.format(docfile))
-            else:
                 ui.message('{} was copied to the pubs repository.'.format(docfile))
 
     rp.close()

pubs/commands/import_cmd.py

@@ -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',
+    parser = subparsers.add_parser(
-            help='import paper(s) to the repository')
+        'import',
-    parser.add_argument('bibpath',
+        help='import paper(s) to the repository')
-            help='path to bibtex, bibtexml or bibyaml file (or directory)')
+    parser.add_argument(
-    parser.add_argument('-L', '--link', action='store_false', dest='copy', default=True,
+        'bibpath',
-            help="don't copy document files, just create a link.")
+        help='path to bibtex, bibtexml or bibyaml file (or directory)')
-    parser.add_argument('keys', nargs='*',
+    parser.add_argument(
-            help="one or several keys to import from the file")
+        'keys', nargs='*',
-    parser.add_argument('-O', '--overwrite', action='store_true', default=False,
+        help="one or several keys to import from the file")
-            help="Overwrite keys already in the database")
+    parser.add_argument(
-    parser.add_argument('-i', '--ignore-malformed', action='store_true', default=False,
+        '-O', '--overwrite', action='store_true', default=False,
-            help="Ignore malformed and unreadable files and entries")
+        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
+    doc_import = args.doc_copy or 'copy'
-    if copy is None:
-        copy = conf['main']['doc_add'] in ('copy', 'move')
 
     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)
+            rp.push_doc(p.citekey, docfile,
-            # FIXME should move the file if configured to do so.
+                        copy=(doc_import in ('copy', 'move')))
+            if doc_import == 'move' and content.content_type(docfile) != 'url':
+                content.remove_file(docfile)
 
     rp.close()

pubs/config/spec.py

@@ -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)

tests/test_usecase.py

@@ -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(
+        self.assertEqual(
-                os.path.join(self.default_pubs_dir, 'doc')),
+            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',