regarding #264. trying to respect literature without breaking too muc…

…h of what Bauble has always been doing.

bauble/plugins/garden/accession.py

@@ -609,15 +609,16 @@ def validate_stripping(self, key, value):
                                    translations=recvd_type_values),
                         default=None)
 
-    # "id_qual" new in 0.7
+    # ITF2 - C24 - Rank Qualified Flag - Transfer code: rkql
+    ## B: Below Family; F: Family; G: Genus; S: Species; I: first
+    ## Infraspecific Epithet; J: second Infraspecific Epithet; C: Cultivar;
+    id_qual_rank = Column(Unicode(10))
+
+    # ITF2 - C25 - Identification Qualifier - Transfer code: idql
     id_qual = Column(types.Enum(values=['aff.', 'cf.', 'incorrect',
                                         'forsan', 'near', '?', None]),
                      default=None)
 
-    # new in 0.9, this column should contain the name of the column in
-    # the species table that the id_qual refers to, e.g. genus, sp, etc.
-    id_qual_rank = Column(Unicode(10))
-
     # "private" new in 0.8b2
     private = Column(Boolean, default=False)
     species_id = Column(Integer, ForeignKey('species.id'), nullable=False)
@@ -725,27 +726,11 @@ def species_str(self, authors=False, markup=False):
             self.__warned_about_id_qual = True
 
         if self.id_qual:
-            # copy the species so we don't affect the original
-            session = db.Session()
-            species = session.merge(self.species)  # , dont_load=True)
-
-            # generate the string
-            if self.id_qual in ('aff.', 'cf.'):
-                if self.id_qual_rank == 'infrasp':
-                    species.sp = '%s %s' % (species.sp, self.id_qual)
-                elif self.id_qual_rank:
-                    setattr(species, self.id_qual_rank,
-                            '%s %s' % (self.id_qual,
-                                       getattr(species, self.id_qual_rank)))
-                sp_str = Species.str(species, authors, markup)
-            elif self.id_qual:
-                sp_str = '%s(%s)' % (Species.str(species, authors, markup),
-                                     self.id_qual)
-            # clean up and return the string
-            del species
-            session.close()
+            sp_str = self.species.str(
+                authors, markup, remove_zws=True,
+                qualification=(self.id_qual_rank, self.id_qual))
         else:
-            sp_str = Species.str(self.species, authors, markup)
+            sp_str = self.species.str(authors, markup, remove_zws=True)
 
         self.__cached_species_str[(markup, authors)] = sp_str
         return sp_str
@@ -971,7 +956,7 @@ def species_cell_data_func(column, renderer, model, treeiter, data=None):
         """
         v = model[treeiter][0]
         renderer.set_property(
-            'text', '%s (%s)' % (Species.str(v, authors=True), v.genus.family))
+            'text', '%s (%s)' % (v.str(authors=True), v.genus.family))
 
 
 class VoucherPresenter(editor.GenericEditorPresenter):
@@ -1198,7 +1183,7 @@ def sp_get_completions(text):
             def sp_cell_data_func(col, cell, model, treeiter, data=None):
                 v = model[treeiter][0]
                 cell.set_property('text', '%s (%s)' %
-                                  (Species.str(v, authors=True),
+                                  (v.str(authors=True),
                                    v.genus.family))
 
             ver_prev_taxon_entry = self.widgets.ver_prev_taxon_entry

bauble/plugins/garden/plant.py

@@ -765,13 +765,13 @@ def on_select(value):
             # new accession, fixes bug #103946
             self.view.widgets.acc_species_label.set_markup('')
             if value is not None:
-                sp_str = Species.str(self.model.accession.species, markup=True)
+                sp_str = self.model.accession.species.str(markup=True)
                 self.view.widgets.acc_species_label.set_markup(sp_str)
                 self.view.widgets.plant_code_entry.emit('changed')
         self.assign_completions_handler('plant_acc_entry', acc_get_completions,
                                         on_select=on_select)
         if self.model.accession:
-            sp_str = Species.str(self.model.accession.species, markup=True)
+            sp_str = self.model.accession.species.str(markup=True)
         else:
             sp_str = ''
         self.view.widgets.acc_species_label.set_markup(sp_str)

bauble/plugins/garden/test.py

@@ -877,79 +877,179 @@ def test_details_editor(self):
         e.start()
 
 
-class AccessionTests(GardenTestCase):
+class AccessionQualifiedTaxon(GardenTestCase):
 
     def __init__(self, *args):
-        super(AccessionTests, self).__init__(*args)
+        super(AccessionQualifiedTaxon, self).__init__(*args)
 
     def setUp(self):
-        super(AccessionTests, self).setUp()
+        super(AccessionQualifiedTaxon, self).setUp()
+        self.sp3 = Species(genus=self.genus, sp=u'grusonii',
+                           infrasp1_rank=u'var.', infrasp1=u'albispinus')
+        self.session.add(self.sp3)
+        self.session.commit()
+        self.ac1 = self.create(Accession, species=self.species, code=u'1')
+        self.ac2 = self.create(Accession, species=self.sp3, code=u'2')
 
     def tearDown(self):
-        super(AccessionTests, self).tearDown()
+        super(AccessionQualifiedTaxon, self).tearDown()
 
-    def test_species_str(self):
-        """
-        Test Accession.species_str()
-        """
-        acc = self.create(Accession, species=self.species, code=u'1')
+    def test_species_str_plain(self):
+        s = u'Echinocactus grusonii'
+        sp_str = self.ac1.species_str()
+        self.assertEquals(remove_zws(sp_str), s)
+
+        s = u'<i>Echinocactus</i> <i>grusonii</i> var. <i>albispinus</i>'
+        sp_str = self.ac2.species_str(markup=True)
+        self.assertEquals(remove_zws(sp_str), s)
+
+    def test_species_str_without_zws(self):
+        s = u'Echinocactus grusonii'
+        sp_str = self.species.str(remove_zws=True)
+        self.assertEquals(sp_str, s)
+        s = u'Echinocactus grusonii var. albispinus'
+        sp_str = self.sp3.str(remove_zws=True)
+        self.assertEquals(sp_str, s)
+        s = u'<i>Echinocactus</i> <i>grusonii</i> var. <i>albispinus</i>'
+        sp_str = self.sp3.str(remove_zws=True, markup=True)
+        self.assertEquals(sp_str, s)
+
+    def test_species_str_with_qualification_too_deep(self):
+        self.ac1.id_qual = u'?'
+        self.ac1.id_qual_rank = u'infrasp'
+        s = u'<i>Echinocactus</i> <i>grusonii</i>'
+        sp_str = self.ac1.species_str(markup=True)
+        self.assertEquals(remove_zws(sp_str), s)
         s = u'Echinocactus grusonii'
-        sp_str = acc.species_str()
+        sp_str = self.ac1.species_str()
+        self.assertEquals(sp_str, s)
+
+        self.ac1.id_qual = 'cf.'
+        self.ac1.id_qual_rank = 'infrasp'
+        s = u'Echinocactus grusonii'
+        sp_str = self.ac1.species_str()
+        self.assertEquals(remove_zws(sp_str), s)
+
+    def test_species_str_with_qualification_correct(self):
+        self.ac1.id_qual = u'?'
+        self.ac1.id_qual_rank = u'sp'
+        s = u'<i>Echinocactus</i> ? <i>grusonii</i>'
+        sp_str = self.ac1.species_str(markup=True)
+        self.assertEquals(remove_zws(sp_str), s)
+
+        # aff. before qualified epithet
+        self.ac1.id_qual = 'aff.'
+        self.ac1.id_qual_rank = u'genus'
+        s = u'aff. <i>Echinocactus</i> <i>grusonii</i>'
+        sp_str = self.ac1.species_str(markup=True)
         self.assertEquals(remove_zws(sp_str), s)
 
-        acc.id_qual = '?'
-        s = u'Echinocactus grusonii(?)'
-        sp_str = acc.species_str()
+        self.ac1.id_qual_rank = u'sp'
+        s = u'<i>Echinocactus</i> aff. <i>grusonii</i>'
+        sp_str = self.ac1.species_str(markup=True)
         self.assertEquals(remove_zws(sp_str), s)
 
-        acc.id_qual = 'aff.'
-        acc.id_qual_rank = u'sp'
+        self.ac2.id_qual = 'aff.'
+        self.ac2.id_qual_rank = u'infrasp'
+        s = u'<i>Echinocactus</i> <i>grusonii</i> aff. var. <i>albispinus</i>'
+        sp_str = self.ac2.species_str(markup=True)
+        self.assertEquals(remove_zws(sp_str), s)
+
+        self.ac1.id_qual = 'cf.'
+        self.ac1.id_qual_rank = u'sp'
+        s = u'<i>Echinocactus</i> cf. <i>grusonii</i>'
+        sp_str = self.ac1.species_str(markup=True)
+        self.assertEquals(remove_zws(sp_str), s)
+
+        self.ac1.id_qual = 'aff.'
+        self.ac1.id_qual_rank = u'sp'
         s = u'Echinocactus aff. grusonii'
-        sp_str = acc.species_str()
+        sp_str = self.ac1.species_str()
+        self.assertEquals(remove_zws(sp_str), s)
+
+        self.ac1.id_qual = 'forsan'
+        self.ac1.id_qual_rank = u'sp'
+        s = u'Echinocactus forsan grusonii'
+        sp_str = self.ac1.species_str()
+        self.assertEquals(remove_zws(sp_str), s)
+
+        ## add cultivar to species and refer to it as cf.
+        self.ac1.species.set_infrasp(1, u'cv.', u'Cultivar')
+        self.ac1.id_qual = u'cf.'
+        self.ac1.id_qual_rank = u'infrasp'
+        s = u"Echinocactus grusonii cf. 'Cultivar'"
+        sp_str = self.ac1.species_str()
         self.assertEquals(remove_zws(sp_str), s)
 
-        # here species.infrasp is None but we still allow the string
-        acc.id_qual = 'cf.'
-        acc.id_qual_rank = 'infrasp'
-        s = u'Echinocactus grusonii cf.'  # ' None'
-        sp_str = acc.species_str()
+    def test_species_str_qualification_appended(self):
+        # previously, if the id_qual is set but the id_qual_rank isn't then
+        # we would get an error. now we just log a warning and append it
+        #
+        # self.ac1.id_qual = 'aff.'
+        # self.ac1.id_qual_rank = None
+        # self.assertRaises(CheckConditionError, self.ac1.species_str)
+
+        self.ac1.id_qual = None
+        self.ac1.id_qual = '?'
+        s = u'Echinocactus grusonii (?)'
+        sp_str = self.ac1.species_str()
         self.assertEquals(remove_zws(sp_str), s)
 
         # species.infrasp is still none but these just get pasted on
         # the end so it doesn't matter
-        acc.id_qual = 'incorrect'
-        acc.id_qual_rank = 'infrasp'
-        s = u'Echinocactus grusonii(incorrect)'
-        sp_str = acc.species_str()
+        self.ac1.id_qual = 'incorrect'
+        self.ac1.id_qual_rank = 'infrasp'
+        s = u'Echinocactus grusonii (incorrect)'
+        sp_str = self.ac1.species_str()
         self.assertEquals(remove_zws(sp_str), s)
 
-        acc.id_qual = 'forsan'
-        acc.id_qual_rank = u'sp'
-        s = u'Echinocactus grusonii(forsan)'
-        sp_str = acc.species_str()
+        self.ac1.id_qual = 'incorrect'
+        self.ac1.id_qual_rank = 'sp'
+        s = u'<i>Echinocactus</i> <i>grusonii</i> (incorrect)'
+        sp_str = self.ac1.species_str(markup=True)
         self.assertEquals(remove_zws(sp_str), s)
 
-        acc.species.set_infrasp(1, u'cv.', u'Cultivar')
-        acc.id_qual = u'cf.'
-        acc.id_qual_rank = u'infrasp'
+    def test_species_str_is_cached(self):
+        self.ac1.species.set_infrasp(1, u'cv.', u'Cultivar')
+        self.ac1.id_qual = u'cf.'
+        self.ac1.id_qual_rank = u'infrasp'
         s = u"Echinocactus grusonii cf. 'Cultivar'"
-        sp_str = acc.species_str()
+        sp_str = self.ac1.species_str()
         self.assertEquals(remove_zws(sp_str), s)
 
-        # test that the cached string is returned
-
         # have to commit because the cached string won't be returned
         # on dirty species
         self.session.commit()
-        s2 = acc.species_str()
+        s2 = self.ac1.species_str()
         self.assertEquals(id(sp_str), id(s2))
 
-        # this used to test that if the id_qual was set but the
-        # id_qual_rank wasn't then we would get an error. now we just
-        # show an warning and put the id_qual on the end of the string
-#         acc.id_qual = 'aff.'
-#         acc.id_qual_rank = None
-#         self.assertRaises(CheckConditionError, acc.species_str)
+    def test_species_str_be_specific_in_infraspecific(self):
+        'be specific qualifying infraspecific identification - still unused'
+        ## add  to species with variety and refer to it as cf.
+        self.sp3.set_infrasp(2, u'cv.', u'Cultivar')
+        self.ac2.id_qual = u'cf.'
+        self.ac2.id_qual_rank = u'cv.'
+        s = u"Echinocactus grusonii var. albispinus cf. 'Cultivar'"
+        sp_str = self.ac2.species_str()
+        self.assertEquals(remove_zws(sp_str), s)
+
+        self.ac2.id_qual = u'cf.'
+        self.ac2.id_qual_rank = u'var.'
+        s = u"Echinocactus grusonii var. cf. albispinus 'Cultivar'"
+        sp_str = self.ac2.species_str()
+        self.assertEquals(remove_zws(sp_str), s)
+
+
+class AccessionTests(GardenTestCase):
+
+    def __init__(self, *args):
+        super(AccessionTests, self).__init__(*args)
+
+    def setUp(self):
+        super(AccessionTests, self).setUp()
+
+    def tearDown(self):
+        super(AccessionTests, self).tearDown()
 
     def test_delete(self):
         """

bauble/plugins/plants/species.py

@@ -242,7 +242,7 @@ def update(self, row):
             box = gtk.EventBox()
             label = gtk.Label()
             label.set_alignment(0, .5)
-            label.set_markup(Species.str(accepted, markup=True, authors=True))
+            label.set_markup(accepted.str(markup=True, authors=True))
             box.add(label)
             utils.make_label_clickable(label, on_label_clicked, accepted)
             syn_box.pack_start(box, expand=False, fill=False)
@@ -261,7 +261,7 @@ def update(self, row):
                 box = gtk.EventBox()
                 label = gtk.Label()
                 label.set_alignment(0, .5)
-                label.set_markup(Species.str(syn, markup=True, authors=True))
+                label.set_markup(syn.str(markup=True, authors=True))
                 box.add(label)
                 utils.make_label_clickable(label, on_label_clicked, syn)
                 syn_box.pack_start(box, expand=False, fill=False)

bauble/plugins/plants/species_editor.py

@@ -429,7 +429,7 @@ def refresh_fullname_label(self, widget=None):
         if len(self.problems) > 0 or self.model.genus is None:
             self.view.set_label('sp_fullname_label', '--')
             return
-        sp_str = Species.str(self.model, markup=True, authors=True)
+        sp_str = self.model.str(markup=True, authors=True)
         self.view.set_label('sp_fullname_label', sp_str)
         if self.model.genus is not None:
             genus = self.model.genus
@@ -450,7 +450,7 @@ def refresh_fullname_label(self, widget=None):
                 msg = _("This binomial name is already in your collection"
                         ", as %s.\n\n"
                         "Are you sure you want to insert it again?") % \
-                    Species.str(omonym, authors=True, markup=True)
+                    omonym.str(authors=True, markup=True)
 
                 def on_response(button, response):
                     self.view.remove_box(self.omonym_box)
@@ -1015,7 +1015,7 @@ def on_remove_button_clicked(self, button, data=None):
         path, col = tree.get_cursor()
         tree_model = tree.get_model()
         value = tree_model[tree_model.get_iter(path)][0]
-        s = Species.str(value.synonym, markup=True)
+        s = value.synonym.str(markup=True)
         msg = 'Are you sure you want to remove %s as a synonym to the ' \
               'current species?\n\n<i>Note: This will not remove the species '\
               '%s from the database.</i>' % (s, s)