it's->its (but misses translations now); some minor documentation edits.

bauble/connmgr.py

@@ -292,11 +292,11 @@ def remove_connection(self, name):
     def on_remove_button_clicked(self, button, data=None):
         """
         remove the connection from connection list, this does not affect
-        the database or it's data
+        the database or its data
         """
         msg = (_('Are you sure you want to remove "%s"?\n\n'
                  '<i>Note: This only removes the connection to the database '
-                 'and does not affect the database or it\'s data</i>')
+                 'and does not affect the database or its data</i>')
                % self.current_name)
 
         if not utils.yes_no_dialog(msg):

bauble/editor.py

@@ -826,7 +826,7 @@ class GenericModelViewPresenterEditor(object):
     GenericModelViewPresenterEditor assume that model is an instance
     of object mapped to a SQLAlchemy table
 
-    The editor creates it's own session and merges the model into
+    The editor creates its own session and merges the model into
     it.  If the model is already in another session that original
     session will not be effected.
 

bauble/pluginmgr.py

@@ -430,8 +430,8 @@ class View(gtk.VBox):
 
     def __init__(self, *args, **kwargs):
         """
-        If a class extends this View and provides it's own __init__ it *must*
-        call it's parent (this) __init__
+        If a class extends this View and provides its own __init__ it *must*
+        call its parent (this) __init__
         """
         super(View, self).__init__(*args, **kwargs)
 

bauble/plugins/garden/location.py

@@ -105,6 +105,11 @@ def __str__(self):
         else:
             return str(self.code)
 
+    def has_accessions(self):
+        '''true if location is linked to at least one accession
+        '''
+
+        return False
 
 
 class LocationEditorView(GenericEditorView):
@@ -115,7 +120,7 @@ class LocationEditorView(GenericEditorView):
                                 'later to refer to this location.'),
         'loc_desc_textview': _('Any information that might be relevant to '\
                                'the location such as where it is or what\'s '\
-                               'it\'s purpose')
+                               'its purpose')
         }
 
     def __init__(self, parent=None):

bauble/plugins/plants/family.py

@@ -164,6 +164,12 @@ def str(family, qualifier=False):
             return ' '.join([s for s in [
                 family.family, family.qualifier] if s not in (None, '')])
 
+    def has_accessions(self):
+        '''true if family is linked to at least one accession
+        '''
+
+        return False
+
 
 class FamilyNote(db.Base):
     """

bauble/plugins/plants/genus.py

@@ -188,6 +188,12 @@ def str(genus, author=False):
                              xml.sax.saxutils.escape(genus.author)]
                  if s not in ('', None)])
 
+    def has_accessions(self):
+        '''true if genus is linked to at least one accession
+        '''
+
+        return False
+
 
 class GenusNote(db.Base):
     """
@@ -765,35 +771,30 @@ def __init__(self, widgets):
 
         def on_family_clicked(*args):
             select_in_search_results(self.current_obj.family)
-
-        utils.make_label_clickable(self.widgets.gen_fam_data,
-                                   on_family_clicked)
+        utils.make_label_clickable(self.widgets.gen_fam_data, on_family_clicked)
 
         def on_nsp_clicked(*args):
             g = self.current_obj
             cmd = 'species where genus.genus="%s" and genus.qualifier="%s"' \
                 % (g.genus, g.qualifier)
             bauble.gui.send_command(cmd)
-        utils.make_label_clickable(self.widgets.gen_nsp_data,
-                                   on_nsp_clicked)
+        utils.make_label_clickable(self.widgets.gen_nsp_data, on_nsp_clicked)
 
         def on_nacc_clicked(*args):
             g = self.current_obj
             cmd = 'acc where species.genus.genus="%s" ' \
                 'and species.genus.qualifier="%s"' \
                 % (g.genus, g.qualifier)
             bauble.gui.send_command(cmd)
-        utils.make_label_clickable(self.widgets.gen_nacc_data,
-                                   on_nacc_clicked)
+        utils.make_label_clickable(self.widgets.gen_nacc_data, on_nacc_clicked)
 
         def on_nplants_clicked(*args):
             g = self.current_obj
             cmd = 'plant where accession.species.genus.genus="%s" and ' \
                 'accession.species.genus.qualifier="%s"' \
                 % (g.genus, g.qualifier)
             bauble.gui.send_command(cmd)
-        utils.make_label_clickable(self.widgets.gen_nplants_data,
-                                   on_nplants_clicked)
+        utils.make_label_clickable(self.widgets.gen_nplants_data, on_nplants_clicked)
 
     def update(self, row):
         '''

bauble/plugins/plants/species_model.py

@@ -1,6 +1,22 @@
+# -*- coding: utf-8 -*-
 #
-# species_model.py
+# Copyright 2008-2010 Brett Adams
+# Copyright 2012-2015 Mario Frasca <mario@anche.no>.
 #
+# This file is part of bauble.classic.
+#
+# bauble.classic is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# bauble.classic is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with bauble.classic. If not, see <http://www.gnu.org/licenses/>.
 
 import traceback
 import xml.sax.saxutils as sax
@@ -197,19 +213,18 @@ class Species(db.Base):
     def __init__(self, *args, **kwargs):
         super(Species, self).__init__(*args, **kwargs)
 
-
     def __str__(self):
         '''
         returns a string representation of this species,
         calls Species.str(self)
         '''
         return Species.str(self)
 
-
     def _get_default_vernacular_name(self):
         if self._default_vernacular_name is None:
             return None
         return self._default_vernacular_name.vernacular_name
+
     def _set_default_vernacular_name(self, vn):
         if vn is None:
             del self.default_vernacular_name
@@ -233,7 +248,6 @@ def distribution_str(self):
             dist = ['%s' % d for d in self.distribution]
             return unicode(', ').join(sorted(dist))
 
-
     def markup(self, authors=False):
         '''
         returns this object as a string with markup
@@ -243,7 +257,6 @@ def markup(self, authors=False):
         '''
         return Species.str(self, authors, True)
 
-
     # in PlantPlugins.init() we set this to 'x' for win32
     hybrid_char = utils.utf8(u'\u2a09') # U+2A09
 
@@ -331,6 +344,11 @@ def str(species, authors=False, markup=False):
         s = utils.utf8(' '.join(filter(lambda x: x not in ('', None), parts)))
         return s
 
+    def has_accessions(self):
+        '''true if species is linked to at least one accession
+        '''
+
+        return False
 
     infrasp_attr = {1: {'rank': 'infrasp1_rank',
                         'epithet': 'infrasp1',
@@ -345,7 +363,6 @@ def str(species, authors=False, markup=False):
                         'epithet': 'infrasp4',
                         'author': 'infrasp4_author'}}
 
-
     def get_infrasp(self, level):
         """
         level should be 1-4
@@ -354,7 +371,6 @@ def get_infrasp(self, level):
             getattr(self, self.infrasp_attr[level]['epithet']), \
             getattr(self, self.infrasp_attr[level]['author'])
 
-
     def set_infrasp(self, level, rank, epithet, author=None):
         """
         level should be 1-4
@@ -364,7 +380,6 @@ def set_infrasp(self, level, rank, epithet, author=None):
         setattr(self, self.infrasp_attr[level]['author'], author)
 
 
-
 class SpeciesNote(db.Base):
     """
     Notes for the species table

bauble/search.py

@@ -1,7 +1,7 @@
-# encoding: utf-8
+# -*- coding: utf-8 -*-
 #
 # Copyright 2008, 2009, 2010 Brett Adams
-# Copyright 2014 Mario Frasca <mario@anche.no>.
+# Copyright 2014-2015 Mario Frasca <mario@anche.no>.
 #
 # This file is part of bauble.classic.
 #
@@ -259,6 +259,14 @@ def __repr__(self):
 
 
 class DomainExpressionAction(object):
+    """created when the parser hits a domain_expression token.
+
+    Searching using domain expressions is a little more magical than an
+    explicit query. you give a domain, a binary_operator and a value,
+    the domain expression will return all object with at least one
+    property (as passed to add_meta) matching (according to the binop)
+    the value.
+    """
 
     def __init__(self, t):
         self.domain = t[0]
@@ -269,16 +277,6 @@ def __repr__(self):
         return "%s %s %s" % (self.domain, self.cond, self.values)
 
     def invoke(self, search_strategy):
-        """
-        Called when the parser hits a domain_expression token.
-
-        Searching using domain expressions is a little more magical
-        and queries mapper properties that were passed to add_meta()
-
-        To do a case sensitive search for a specific string use the
-        double equals, '=='
-        """
-
         try:
             if self.domain in search_strategy._shorthand:
                 self.domain = search_strategy._shorthand[self.domain]
@@ -288,6 +286,10 @@ def invoke(self, search_strategy):
 
         query = search_strategy._session.query(cls)
 
+        ## here is the place where to optionally filter out unrepresented
+        ## domain values. each domain class should define its own 'I have
+        ## accessions' filter. see issue #42
+
         result = set()
 
         # select all objects from the domain

bauble/utils/__init__.py

@@ -785,13 +785,14 @@ def reset_sequence(column):
 
 def make_label_clickable(label, on_clicked, *args):
     """
-    :param label: a gtk.Label that has a gtk.EventBox as it's parent
+    :param label: a gtk.Label that has a gtk.EventBox as its parent
     :param on_clicked: callback to be called when the label is clicked
       on_clicked(label, event, data)
     """
     eventbox = label.parent
+
     check(eventbox != None and isinstance(eventbox, gtk.EventBox),
-          'label must have an gtk.EventBox as it\'s parent')
+          'label must have an gtk.EventBox as its parent')
     label.__pressed = False
     def on_enter_notify(*args):
         label.modify_fg(gtk.STATE_NORMAL, gtk.gdk.color_parse("blue"))

doc/report.rst

@@ -5,7 +5,7 @@ Using the Mako Report Formatter
 -------------------------------
 
 The Mako report formatter uses the Mako template language for
-generating reports. More information about Mako and it's language can
+generating reports. More information about Mako and its language can
 be found at `makotemplates.org <http://www.makotemplates.org>`_.
 
 The Mako templating system should already be installed on your

doc/searching.rst

@@ -87,7 +87,8 @@ max% then it search for all value that start with max. If you search
 for %max it searches for all values that end in max. The string %max%a
 would search for all value that contain max and end in a.
 
-For more information about the different search domain see…..TODO
+For more information about the different search domain and their short-hand
+aliases, see search-domains_ .
 
 If expression are invalid they are usually used as search by value
 searchs. For example the search string ``gen=`` will execute a search by
@@ -111,6 +112,14 @@ are located in Block 10.
 Searching with queries usually requires some knowledge of the Bauble
 internals and database table layouts.  
 
+A couple of useful examples:
+
+Which locations are in use:
+``location where plants.id!=0``
+
+Which genera are associated to at least one accession:
+``genus where species.accession.id!=0``
+
 .. _search-domains:
 
 Domains 
@@ -122,16 +131,16 @@ expression. The queries do not use the default columns.
 
 
 :Domains:
-    fam, family: Search :class:`bauble.plugins.plants.Family`
+    family, fam: Search :class:`bauble.plugins.plants.Family`
 
-    gen, genus: Search :class:`bauble.plugins.plants.Genus`
+    genus, gen: Search :class:`bauble.plugins.plants.Genus`
 
-    sp: Search :class:`bauble.plugins.plants.Species`
+    species, sp: Search :class:`bauble.plugins.plants.Species`
 
     geography: Search :class:`bauble.plugins.plants.Geography`
 
     acc: Search :class:`bauble.plugins.garden.Accession`
 
     plant: Search :class:`bauble.plugins.garden.Plant`
 
-    loc, location: Search :class:`bauble.plugins.garden.Location`
+    location, loc: Search :class:`bauble.plugins.garden.Location`