adds a *doc add|remove|export|open* command; depricates commands *open* and *attach*; fixed typos in readme.md and uis;

pubs/commands/__init__.py

@@ -7,8 +7,7 @@ from . import rename_cmd
 from . import remove_cmd
 from . import list_cmd
 # doc
-from . import attach_cmd
+from . import doc_cmd
-from . import open_cmd
 from . import tag_cmd
 from . import note_cmd
 # bulk

pubs/commands/attach_cmd.py

@@ -1,50 +0,0 @@
-from .. import repo
-from .. import color
-from ..uis import get_ui
-from .. import content
-
-def parser(subparsers):
-    parser = subparsers.add_parser('attach',
-            help='attach a document to an existing paper')
-    # parser.add_argument('-c', '--copy', action='store_true', default=True,
-    #         help="copy document files into library directory (default)")
-    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).")
-    parser.add_argument('citekey',
-            help='citekey of the paper')
-    parser.add_argument('document',
-            help='document file')
-    return parser
-
-
-def command(conf, args):
-    """
-    :param bibfile: bibtex file (in .bib, .bibml or .yaml format.
-    :param docfile: path (no url yet) to a pdf or ps file
-    """
-
-    ui = get_ui()
-
-    rp = repo.Repository(conf)
-    paper = rp.pull_paper(args.citekey)
-
-    try:
-        document = args.document
-        rp.push_doc(paper.citekey, document, copy=args.copy)
-        if args.copy:
-            if args.move:
-                content.remove_file(document)
-            # else:
-            #     if ui.input_yn('{} has been copied into pubs; should the original be removed?'.format(color.dye_out(document, 'filepath'))):
-            #         content.remove_file(document)
-
-        ui.message('{} attached to {}'.format(color.dye_out(document, 'filepath'), color.dye_out(paper.citekey, 'citekey')))
-
-    except ValueError as v:
-        ui.error(v.message)
-        ui.exit(1)
-    except IOError as v:
-        ui.error(v.message)
-        ui.exit(1)

pubs/commands/doc_cmd.py

@@ -0,0 +1,160 @@
+import os
+import subprocess
+
+from .. import repo
+from .. import color
+from ..uis import get_ui
+from .. import content
+from ..utils import resolve_citekey, resolve_citekey_list
+
+# doc --+- add $file $key [[-L|--link] | [-M|--move]] [-f|--force]
+#       +- remove $key [$key [...]] [-f|--force]
+#       +- export $key [$path]
+#       +- open $key [-w|--with $cmd]
+# supplements attach, open
+
+def parser(subparsers):
+    doc_parser = subparsers.add_parser('doc', help='manage the document relating to a publication')
+    doc_subparsers = doc_parser.add_subparsers(title='document actions', help='actions to interact with the documents',
+                                               dest='action')
+
+    add_parser = doc_subparsers.add_parser('add', help='add a document to a publication')
+    add_parser.add_argument('-f', '--force', action='store_true', dest='force', default=False,
+                           help='force overwriting an already assigned document')
+    add_parser.add_argument('document', nargs=1, help='document file to assign')
+    add_parser.add_argument('citekey', nargs=1, help='citekey of the publication')
+    add_exclusives = add_parser.add_mutually_exclusive_group()
+    add_exclusives.add_argument('-L', '--link', action='store_false', dest='link', default=False,
+                           help='do not copy document files, just create a link')
+    add_exclusives.add_argument('-M', '--move', action='store_true', dest='move', default=False,
+                           help='move document instead of of copying (ignored if --link)')
+
+    remove_parser = doc_subparsers.add_parser('remove', help='remove assigned documents from publications')
+    remove_parser.add_argument('citekeys', nargs='+', help='citekeys of the publications')
+    remove_parser.add_argument('-f', '--force', action='store_true', dest='force', default=False,
+                              help='force removing assigned documents')
+
+    # favor key+ path  over:  key
+    export_parser = doc_subparsers.add_parser('export', help='export assigned documents to given path')
+    export_parser.add_argument('citekeys', nargs='+', help='citekeys of the documents to export')
+    export_parser.add_argument('path', nargs=1, help='directory to export the files to')
+
+    open_parser = doc_subparsers.add_parser('open', help='open an assigned document')
+    open_parser.add_argument('citekey', nargs=1, help='citekey of the document to open')
+    open_parser.add_argument('-w', '--with', dest='cmd', help='command to open the file with')
+
+    return doc_parser
+
+def command(conf, args):
+
+    ui = get_ui()
+    rp = repo.Repository(conf)
+
+
+    # print(args)
+    # ui.exit()
+
+    if args.action == 'add':
+        citekey = resolve_citekey(rp, args.citekey[0], ui=ui, exit_on_fail=True)
+        paper = rp.pull_paper(citekey)
+
+        if paper.docpath is not None and not args.force:
+            msg = ("The publication {} has already the document {} assigned." + os.linesep +
+               "Overwrite? ").format(color.dye_out(paper.citekey, 'citekey'), color.dye_out(paper.docpath, 'filepath'))
+            if not ui.input_yn(question=msg, default='n'):
+                ui.exit(0)
+            else:
+                try:
+                    rp.remove_doc(paper.citekey)
+                except (ValueError, IOError) as v:
+                    ui.error(v.message)
+                    ui.exit(1)
+
+        try:
+            document = args.document[0]
+            if args.link:
+                rp.push_doc(paper.citekey, document, copy=False)
+            else:
+                rp.push_doc(paper.citekey, document, copy=True)
+            if not args.link and args.move:
+                content.remove_file(document)
+
+            ui.message('{} added to {}'.format(color.dye_out(document, 'filepath'),
+                                                  color.dye_out(paper.citekey, 'citekey')))
+        except (ValueError, IOError) as v:
+            ui.error(v.message)
+            ui.exit(1)
+
+    elif args.action == 'remove':
+
+        for key in resolve_citekey_list(rp, args.citekeys, ui=ui, exit_on_fail=True):
+            paper = rp.pull_paper(key)
+
+            # if there is no document (and the user cares) -> inform + continue
+            if paper.docpath is None and not args.force:
+                ui.message('Publication {} has no assigned document. Not removed.'.format(
+                    color.dye_out(paper.citekey, 'citekey')))
+                continue
+
+            if not args.force:
+                msg = 'Do you really want to remove {} from {} ?'.format(color.dye_out(paper.docpath, 'filepath'),
+                                                                         color.dye_out(paper.citekey, 'citekey'))
+                if not ui.input_yn(question=msg, default='n'):
+                    continue
+
+            try:
+                rp.remove_doc(paper.citekey)
+            except (ValueError, IOError) as v:
+                ui.error(v.message)
+                ui.exit(1)
+
+    elif args.action == 'export':
+
+        if os.path.isdir(args.path[0]):
+            path = args.path[0]
+            if not path.endswith('/'):
+                path += '/'
+        else:
+            ui.error('{} is not a directory.'.format(
+                color.dye_err(args.path[0], 'filepath')))
+            ui.exit(1)
+
+        for key in resolve_citekey_list(rp, args.citekeys, ui=ui, exit_on_fail=True):
+            try:
+                paper = rp.pull_paper(key)
+                doc = paper.docpath
+
+                if doc is None:
+                    ui.message('Publication {} has no document assigned.'.format(
+                        color.dye_out(paper.citekey, 'citekey')))
+                else:
+                    real_doc_path = rp.pull_docpath(key)
+                    dest_path = path + os.path.basename(real_doc_path)
+                    content.copy_content(real_doc_path, dest_path)
+            except (ValueError, IOError) as e:
+                ui.error(e.message)
+
+    elif args.action == 'open':
+        with_command = args.cmd
+        citekey = resolve_citekey(rp, args.citekey[0], ui=ui, exit_on_fail=True)
+        paper = rp.pull_paper(citekey)
+
+        if paper.docpath is None:
+            ui.error('No document associated with the entry {}.'.format(
+                      color.dye_err(citekey, 'citekey')))
+            ui.exit()
+
+        if with_command is None:
+            with_command = conf['main']['open_cmd']
+        if with_command is None: # default in conf have not been changed
+            pass # TODO platform specific
+
+        try:
+            docpath = content.system_path(rp.databroker.real_docpath(paper.docpath))
+            cmd = with_command.split()
+            cmd.append(docpath)
+            subprocess.Popen(cmd)
+            ui.message('{} opened.'.format(color.dye_out(docpath, 'filepath')))
+        except OSError:
+            ui.error("Command does not exist: %s." % with_command)
+            ui.exit(127)

pubs/commands/open_cmd.py

@@ -1,47 +0,0 @@
-import subprocess
-
-from .. import repo
-
-from ..uis import get_ui
-from .. import color
-from ..content import system_path
-from ..utils import resolve_citekey
-
-def parser(subparsers):
-    parser = subparsers.add_parser('open',
-            help='open the paper in a pdf viewer')
-    parser.add_argument('-w', '--with', dest='with_command', default=None,
-            help='command to use to open the document file')
-    parser.add_argument('citekey',
-            help='citekey of the paper')
-    return parser
-
-
-def command(conf, args):
-
-    ui = get_ui()
-    with_command = args.with_command
-
-    rp = repo.Repository(conf)
-    citekey = resolve_citekey(rp, args.citekey, ui=ui, exit_on_fail=True)
-    paper = rp.pull_paper(citekey)
-
-    if with_command is None:
-        with_command = conf['main']['open_cmd']
-    if with_command is None: # default in conf have not been changed
-        pass # TODO platform specific
-
-    if paper.docpath is None:
-        ui.error('No document associated with the entry {}.'.format(
-                 color.dye_err(citekey, 'citekey')))
-        ui.exit()
-
-    try:
-        docpath = system_path(rp.databroker.real_docpath(paper.docpath))
-        cmd = with_command.split()
-        cmd.append(docpath)
-        subprocess.Popen(cmd)
-        ui.message('{} opened.'.format(color.dye_out(docpath, 'filepath')))
-    except OSError:
-        ui.error("Command does not exist: %s." % with_command)
-        ui.exit(127)

pubs/pubs_cmd.py

@@ -18,8 +18,7 @@ CORE_CMDS = collections.OrderedDict([
     ('remove', commands.remove_cmd),
     ('list', commands.list_cmd),
 
-    ('attach', commands.attach_cmd),
+    ('doc', commands.doc_cmd),
-    ('open', commands.open_cmd),
     ('tag', commands.tag_cmd),
     ('note', commands.note_cmd),
 

pubs/repo.py

@@ -84,22 +84,40 @@ class Repository(object):
 
     def remove_paper(self, citekey, remove_doc=True, event=True):
         """ Remove a paper. Is silent if nothing needs to be done."""
-
         if event:
             events.RemoveEvent(citekey).send()
         if remove_doc:
-            try:
+            self.remove_doc(citekey, detach_only=True)
-                metadata = self.databroker.pull_metadata(citekey)
+        try:
-                docpath = metadata.get('docfile')
+            self.databroker.remove_note(citekey, silent=True)
-                self.databroker.remove_doc(docpath, silent=True)
+        except IOError:
-                self.databroker.remove_note(citekey, silent=True)
+            pass # FIXME: if IOError is about being unable to
-            except IOError:
+                 # remove the file, we need to issue an error.I
-                pass # FXME: if IOError is about being unable to
-                     # remove the file, we need to issue an error.I
-
         self.citekeys.remove(citekey)
         self.databroker.remove(citekey)
 
+    def remove_doc(self, citekey, detach_only=False):
+        """ Remove a doc. Is silent if nothing needs to be done."""
+        try:
+            metadata = self.databroker.pull_metadata(citekey)
+            docpath = metadata.get('docfile')
+            self.databroker.remove_doc(docpath, silent=True)
+            if not detach_only:
+                p = self.pull_paper(citekey)
+                p.docpath = None
+                self.push_paper(p, overwrite=True, event=False)
+        except IOError:
+            pass # FIXME: if IOError is about being unable to
+                 # remove the file, we need to issue an error.I
+
+    def pull_docpath(self, citekey):
+        try:
+            p = self.pull_paper(citekey)
+            return self.databroker.real_docpath(p.docpath)
+        except IOError:
+            pass # FIXME: if IOError is about being unable to
+                 # remove the file, we need to issue an error.I
+
     def rename_paper(self, paper, new_citekey=None, old_citekey=None):
         if old_citekey is None:
             old_citekey = paper.citekey

pubs/uis.py

@@ -87,8 +87,8 @@ class InputUI(PrintUI):
         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 iser is asked
+        """Ask the user to chose between a set of options. The user is asked
-        to input a char corresponding to the option he choses.
+        to input a char corresponding to the option he chooses.
 
         :param options: list of strings
             list of options
@@ -126,8 +126,8 @@ class InputUI(PrintUI):
 
 
     def input_choice(self, options, option_chars, default=None, question=''):
-        """Ask the user to chose between a set of options. The iser is asked
+        """Ask the user to chose between a set of options. The user is asked
-        to input a char corresponding to the option he choses.
+        to input a char corresponding to the option he chooses.
 
         :param options: list of strings
             list of options

pubs/utils.py

@@ -9,18 +9,18 @@ def resolve_citekey(repo, citekey, ui=None, exit_on_fail=True):
     citekeys = repo.citekeys_from_prefix(citekey)
     if len(citekeys) == 0:
         if ui is not None:
-            ui.error("no citekey named or beginning with '{}'".format(color.dye_out(citekey, 'citekey')))
+            ui.error("No citekey named or beginning with '{}'".format(color.dye_out(citekey, 'citekey')))
             if exit_on_fail:
                 ui.exit()
     elif len(citekeys) == 1:
         if citekeys[0] != citekey:
             if ui is not None:
-                ui.warning("provided citekey '{}' has been autocompleted into '{}'".format(color.dye_out(citekey, 'citekey'), color.dye_out(citekeys[0], 'citekey')))
+                ui.warning("Provided citekey '{}' has been autocompleted into '{}'".format(color.dye_out(citekey, 'citekey'), color.dye_out(citekeys[0], 'citekey')))
             citekey = citekeys[0]
     elif citekey not in citekeys:
         if ui is not None:
             citekeys = sorted(citekeys)
-            ui.error("be more specific; provided citekey '{}' matches multiples citekeys:".format(
+            ui.error("Be more specific; Provided citekey '{}' matches multiples citekeys:".format(
                      citekey))
             for c in citekeys:
                 p = repo.pull_paper(c)
@@ -28,3 +28,18 @@ def resolve_citekey(repo, citekey, ui=None, exit_on_fail=True):
             if exit_on_fail:
                 ui.exit()
     return citekey
+
+
+def resolve_citekey_list(repo, citekeys, ui=None, exit_on_fail=True):
+    shutdown = False
+    keys = []
+    for key in citekeys:
+        try:
+            keys.append(resolve_citekey(repo, key, ui, exit_on_fail))
+        except SystemExit:
+            shutdown = exit_on_fail
+
+    if shutdown and ui is not None:
+        ui.exit()
+    else:
+        return keys

readme.md

@@ -46,7 +46,7 @@ If you use latex, you can automatize references, by creating a bash script with:
     bibtex manuscript
     latex manuscript.tex
 
-This ensure that your reference file is always up-to-date; you can cite a paper in your manuscript a soon as you add it in pubs. This means that if you have, for instance, a doi on a webpage, you only need to do:
+This ensures that your reference file is always up-to-date; you can cite a paper in your manuscript a soon as you add it in pubs. This means that if you have, for instance, a doi on a webpage, you only need to do:
 
     pubs add -D 10.1007/s00422-012-0514-6
 

tests/test_usecase.py

@@ -352,7 +352,7 @@ class TestUsecase(DataCommandTestCase):
                 'pubs add data/martius.bib',
                 'pubs add data/10.1371%2Fjournal.pone.0038236.bib',
                 'pubs list',
-                'pubs attach Page99 data/pagerank.pdf'
+                'pubs doc add data/pagerank.pdf Page99'
                ]
         self.execute_cmds(cmds)
 
@@ -363,7 +363,7 @@ class TestUsecase(DataCommandTestCase):
                 'pubs add data/martius.bib',
                 'pubs add data/10.1371%2Fjournal.pone.0038236.bib',
                 'pubs list',
-                'pubs attach Page99 data/pagerank.pdf',
+                'pubs doc add data/pagerank.pdf Page99',
                 ('pubs remove Page99', ['y']),
                 'pubs remove -f turing1950computing',
                ]
@@ -461,19 +461,6 @@ class TestUsecase(DataCommandTestCase):
         outs = self.execute_cmds(cmds)
         self.assertEqual(1 + 1, len(outs[-1].split('\n')))
 
-    def test_open(self):
-        cmds = ['pubs init',
-                'pubs add data/pagerank.bib',
-                'pubs open Page99'
-               ]
-
-        with self.assertRaises(SystemExit):
-            self.execute_cmds(cmds)
-
-        with self.assertRaises(SystemExit):
-            cmds[-1] == 'pubs open Page8'
-            self.execute_cmds(cmds)
-
     def test_update(self):
         cmds = ['pubs init',
                 'pubs add data/pagerank.bib',
@@ -491,10 +478,21 @@ class TestUsecase(DataCommandTestCase):
         outs = self.execute_cmds(cmds)
         self.assertEqual(1, len(outs[2].splitlines()))
 
-    def test_attach(self):
+    def test_doc_open(self):
         cmds = ['pubs init',
                 'pubs add data/pagerank.bib',
-                'pubs attach Page99 data/pagerank.pdf'
+                'pubs doc open Page99'
+               ]
+        with self.assertRaises(SystemExit):
+            self.execute_cmds(cmds)
+        with self.assertRaises(SystemExit):
+            cmds[-1] == 'pubs doc open Page8'
+            self.execute_cmds(cmds)
+
+    def test_doc_add(self):
+        cmds = ['pubs init',
+                'pubs add data/pagerank.bib',
+                'pubs doc add data/pagerank.pdf Page99'
                ]
         self.execute_cmds(cmds)
         self.assertTrue(self.fs['os'].path.exists(
@@ -504,15 +502,36 @@ class TestUsecase(DataCommandTestCase):
         # Also test that do not remove original
         self.assertTrue(self.fs['os'].path.exists('/data/pagerank.pdf'))
 
-    def test_attach_with_move(self):
+    def test_doc_add_with_move(self):
         cmds = ['pubs init -p paper_second/',
                 'pubs add data/pagerank.bib',
-                'pubs attach --move Page99 data/pagerank.pdf'
+                'pubs doc add --move data/pagerank.pdf Page99'
                ]
         self.execute_cmds(cmds)
         self.assertTrue(self.fs['os'].path.isfile(self.default_conf_path))
         self.assertFalse(self.fs['os'].path.exists('/data/pagerank.pdf'))
 
+    def test_doc_remove(self):
+        cmds = ['pubs init',
+                'pubs add data/pagerank.bib',
+                'pubs doc add data/pagerank.pdf Page99',
+                ('pubs doc remove Page99', ['y']),
+               ]
+        self.execute_cmds(cmds)
+        docdir = self.fs['os'].path.expanduser('~/.pubs/doc/')
+        self.assertNotIn('turing-mind-1950.pdf', self.fs['os'].listdir(docdir))
+
+    def test_doc_export(self):
+        cmds = ['pubs init',
+                'pubs add data/pagerank.bib',
+                'pubs rename Page99 page100',
+                'pubs doc add data/pagerank.pdf page100',
+                'pubs doc export page100 /'
+                ]
+        self.execute_cmds(cmds)
+        self.assertIn('page100.pdf', self.fs['os'].listdir('/'))
+
+
     def test_alternate_config(self):
         alt_conf = self.fs['os'].path.expanduser('~/.alt_conf')
         cmds = ['pubs -c ' + alt_conf + ' init',