def update(self, row):
'''
update the expander
:param row: the row to get thevalues from
'''
syn_box = self.widgets.sp_synonyms_box
# remove old labels
syn_box.foreach(syn_box.remove)
logger.debug(row.synonyms)
from sqlalchemy.orm.session import object_session
self.session = object_session(row)
syn = self.session.query(SpeciesSynonym).filter(
SpeciesSynonym.synonym_id == row.id).first()
accepted = syn and syn.species
logger.debug("species %s is synonym of %s and has synonyms %s" %
(row, accepted, row.synonyms))
self.set_label(_("Synonyms")) # reset default value
on_label_clicked = lambda l, e, syn: select_in_search_results(syn)
if accepted is not None:
self.set_label(_("Accepted name"))
# create clickable label that will select the synonym
# in the search results
box = gtk.EventBox()
label = gtk.Label()
label.set_alignment(0, .5)
label.set_markup(Species.str(accepted, 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)
self.show_all()
self.set_sensitive(True)
self.set_expanded(True)
elif len(row.synonyms) == 0:
self.set_sensitive(False)
self.set_expanded(False)
else:
# remove all the children
syn_box.foreach(syn_box.remove)
for syn in row.synonyms:
# create clickable label that will select the synonym
# in the search results
box = gtk.EventBox()
label = gtk.Label()
label.set_alignment(0, .5)
label.set_markup(Species.str(syn, 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)
self.show_all()
self.set_sensitive(True)
# TODO: get expanded state from prefs
self.set_expanded(True)
def update(self, row):
'''
update the expander
:param row: the row to get thevalues from
'''
syn_box = self.widgets.sp_synonyms_box
# remove old labels
syn_box.foreach(syn_box.remove)
logger.debug(row.synonyms)
from sqlalchemy.orm.session import object_session
self.session = object_session(row)
syn = self.session.query(SpeciesSynonym).filter(
SpeciesSynonym.synonym_id == row.id).first()
accepted = syn and syn.species
logger.debug("species %s is synonym of %s and has synonyms %s" %
(row, accepted, row.synonyms))
self.set_label(_("Synonyms")) # reset default value
on_label_clicked = lambda l, e, syn: select_in_search_results(syn)
if accepted is not None:
self.set_label(_("Accepted name"))
# create clickable label that will select the synonym
# in the search results
box = gtk.EventBox()
label = gtk.Label()
label.set_alignment(0, .5)
label.set_markup(Species.str(accepted, 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)
self.show_all()
self.set_sensitive(True)
self.set_expanded(True)
elif len(row.synonyms) == 0:
self.set_sensitive(False)
self.set_expanded(False)
else:
# remove all the children
syn_box.foreach(syn_box.remove)
for syn in row.synonyms:
# create clickable label that will select the synonym
# in the search results
box = gtk.EventBox()
label = gtk.Label()
label.set_alignment(0, .5)
label.set_markup(Species.str(syn, 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)
self.show_all()
self.set_sensitive(True)
# TODO: get expanded state from prefs
self.set_expanded(True)
def test_between_evaluate(self):
'use BETWEEN value and value'
Family = self.Family
Genus = self.Genus
from bauble.plugins.plants.species_model import Species
from bauble.plugins.garden.accession import Accession
#from bauble.plugins.garden.location import Location
#from bauble.plugins.garden.plant import Plant
family2 = Family(epithet=u'family2')
g2 = Genus(family=family2, epithet=u'genus2')
f3 = Family(epithet=u'fam3', aggregate=u'agg.')
g3 = Genus(family=f3, epithet=u'Ixora')
sp = Species(epithet=u"coccinea", genus=g3)
ac = Accession(species=sp, code=u'1979.0001')
self.session.add_all([family2, g2, f3, g3, sp, ac])
self.session.commit()
mapper_search = search.get_strategy('MapperSearch')
self.assertTrue(isinstance(mapper_search, search.MapperSearch))
s = 'accession where code between "1978" and "1980"'
results = mapper_search.search(s, self.session)
self.assertEqual(results, set([ac]))
s = 'accession where code between "1980" and "1980"'
results = mapper_search.search(s, self.session)
self.assertEqual(results, set())
def test_search_by_query22_underscore(self):
"""can use fields starting with an underscore"""
import datetime
Family = self.Family
Genus = self.Genus
from bauble.plugins.plants.species_model import Species
from bauble.plugins.garden.accession import Accession
from bauble.plugins.garden.location import Location
from bauble.plugins.garden.plant import Plant
family2 = Family(epithet=u'family2')
g2 = Genus(family=family2, epithet=u'genus2')
f3 = Family(epithet=u'fam3', aggregate=u'agg.')
g3 = Genus(family=f3, epithet=u'Ixora')
sp = Species(epithet=u"coccinea", genus=g3)
ac = Accession(species=sp, code=u'1979.0001')
lc = Location(name=u'loc1', code=u'loc1')
pp = Plant(accession=ac, code=u'01', location=lc, quantity=1)
pp._last_updated = datetime.datetime(2009, 2, 13)
self.session.add_all([family2, g2, f3, g3, sp, ac, lc, pp])
self.session.commit()
mapper_search = search.get_strategy('MapperSearch')
self.assertTrue(isinstance(mapper_search, search.MapperSearch))
s = 'plant where _last_updated < |datetime|2000,1,1|'
results = mapper_search.search(s, self.session)
self.assertEqual(results, set())
s = 'plant where _last_updated > |datetime|2000,1,1|'
results = mapper_search.search(s, self.session)
self.assertEqual(results, set([pp]))
def __init__(self, model=None, parent=None):
'''
:param model: a species instance or None
:param parent: the parent window or None
'''
if model is None:
model = Species()
super(SpeciesEditorMenuItem, self).__init__(model, parent)
if not parent and bauble.gui:
parent = bauble.gui.window
self.parent = parent
self._committed = []
view = SpeciesEditorView(parent=self.parent)
self.presenter = SpeciesEditorPresenter(self.model, view)
## I do not follow this: we have a MVP model, but also an extra
## 'Editor' thing and is it stealing functionality from either the
## view or the presenter?
self.view = view
# add quick response keys
self.attach_response(view.get_window(), gtk.RESPONSE_OK, 'Return',
gtk.gdk.CONTROL_MASK)
self.attach_response(view.get_window(), self.RESPONSE_OK_AND_ADD, 'k',
gtk.gdk.CONTROL_MASK)
self.attach_response(view.get_window(), self.RESPONSE_NEXT, 'n',
gtk.gdk.CONTROL_MASK)
# set default focus
if self.model.genus is None:
view.widgets.sp_genus_entry.grab_focus()
else:
view.widgets.sp_species_entry.grab_focus()
def add_species_callback(genera):
session = db.Session()
genus = session.merge(genera[0])
from bauble.plugins.plants.species_editor import edit_species
result = edit_species(model=Species(genus=genus)) is not None
session.close()
return result
def refresh_fullname_label(self, widget=None):
'''
set the value of sp_fullname_label to either '--' if there
is a problem or to the name of the string returned by Species.str
'''
logger.debug("SpeciesEditorPresenter:refresh_fullname_label %s"
% widget)
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)
self.view.set_label('sp_fullname_label', sp_str)
if self.model.genus is not None:
genus = self.model.genus
epithet = self.view.widget_get_value('sp_species_entry')
omonym = self.session.query(
Species).filter(
Species.genus == genus,
Species.sp == epithet
).first()
logger.debug("looking for %s %s, found %s"
% (genus, epithet, omonym))
if omonym in [None, self.model]:
## should not warn, so check warning and remove
if self.omonym_box is not None:
self.view.remove_box(self.omonym_box)
self.omonym_box = None
elif self.omonym_box is None: # should warn, but not twice
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)
def on_response(button, response):
self.view.remove_box(self.omonym_box)
self.omonym_box = None
if response:
logger.warning('yes')
else:
self.view.widget_set_value('sp_species_entry', '')
box = self.omonym_box = (
self.view.add_message_box(utils.MESSAGE_BOX_YESNO))
box.message = msg
box.on_response = on_response
box.show()
self.view.add_box(box)
def setUp(self):
super(BinomialSearchTests, self).setUp()
db.engine.execute('delete from genus')
db.engine.execute('delete from family')
from bauble.plugins.plants.family import Family
from bauble.plugins.plants.genus import Genus
from bauble.plugins.plants.species import Species
f1 = Family(epithet=u'family1', aggregate=u'agg.')
g1 = Genus(family=f1, epithet=u'genus1')
f2 = Family(epithet=u'family2')
g2 = Genus(family=f2, epithet=u'genus2')
f3 = Family(epithet=u'fam3', aggregate=u'agg.')
g3 = Genus(family=f3, epithet=u'Ixora')
sp = Species(epithet=u"coccinea", genus=g3)
sp2 = Species(epithet=u"peruviana", genus=g3)
sp3 = Species(epithet=u"chinensis", genus=g3)
g4 = Genus(family=f3, epithet=u'Pachystachys')
sp4 = Species(epithet=u'coccinea', genus=g4)
self.session.add_all([f1, f2, g1, g2, f3, g3, sp, sp2, sp3, g4, sp4])
self.session.commit()
self.ixora, self.ic, self.pc = g3, sp, sp4
def setUp(self):
super(AggregatingFunctions, self).setUp()
db.engine.execute('delete from genus')
db.engine.execute('delete from family')
db.engine.execute('delete from species')
db.engine.execute('delete from accession')
from bauble.plugins.plants import Family, Genus, Species
f1 = Family(epithet=u'Rutaceae', aggregate=u'')
g1 = Genus(family=f1, epithet=u'Citrus')
sp1 = Species(epithet=u"medica", genus=g1)
sp2 = Species(epithet=u"maxima", genus=g1)
sp3 = Species(epithet=u"aurantium", genus=g1)
f2 = Family(epithet=u'Sapotaceae')
g2 = Genus(family=f2, epithet=u'Manilkara')
sp4 = Species(epithet=u'zapota', genus=g2)
sp5 = Species(epithet=u'zapotilla', genus=g2)
g3 = Genus(family=f2, epithet=u'Pouteria')
sp6 = Species(epithet=u'stipitata', genus=g3)
f3 = Family(epithet=u'Musaceae')
g4 = Genus(family=f3, epithet=u'Musa')
self.session.add_all(
[f1, f2, f3, g1, g2, g3, g4, sp1, sp2, sp3, sp4, sp5, sp6])
self.session.commit()
def test_cultivar_also_matched(self):
mapper_search = search.get_strategy('MapperSearch')
self.assertTrue(isinstance(mapper_search, search.MapperSearch))
from bauble.plugins.plants.species import Species
from bauble.plugins.plants.genus import Genus
g3 = self.session.query(Genus).filter(Genus.epithet == u'Ixora').one()
sp5 = Species(epithet=u"coccinea",
genus=g3,
infrasp1_rank=u'cv.',
infrasp1=u'Nora Grant')
self.session.add_all([sp5])
self.session.commit()
s = 'Ixora coccinea' # matches I.coccinea and Nora Grant
results = mapper_search.search(s, self.session)
self.assertEqual(results, set([self.ic, sp5]))
def on_remove_button_clicked(self, button, data=None):
"""
removes the currently selected synonym from the list of synonyms for
this species
"""
# TODO: maybe we should only ask 'are you sure' if the selected value
# is an instance, this means it will be deleted from the database
tree = self.view.widgets.sp_syn_treeview
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)
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)
)
if not utils.yes_no_dialog(msg, parent=self.view.get_window()):
return
tree_model.remove(tree_model.get_iter(path))
self.model.synonyms.remove(value.synonym)
utils.delete_or_expunge(value)
# TODO: ** important ** this doesn't respect any unique
# contraints on the species for synonyms and allow a
# species to have another species as a synonym multiple
# times...see below
# TODO: using session.flush here with an argument is
# deprecated in SA 0.5 and will probably removed in SA
# 0.6...but how do we only flush the one value..unless we
# create a new session, merge it, commit that session,
# close it and then refresh the same object in
# self.session
# make the change in synonym immediately available so that if
# we try to add the same species again we don't break the
# SpeciesSynonym UniqueConstraint
# tmp_session = db.Session()
# tmp_value = tmp.session.merge(value)
# tmp.session.commit()
# tmp.session.close()
# self.session.refresh(value)
# self.session.flush([value])
self._dirty = True
self.parent_ref().refresh_sensitivity()
def on_remove_button_clicked(self, button, data=None):
'''
removes the currently selected synonym from the list of synonyms for
this species
'''
# TODO: maybe we should only ask 'are you sure' if the selected value
# is an instance, this means it will be deleted from the database
tree = self.view.widgets.sp_syn_treeview
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)
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)
if not utils.yes_no_dialog(msg, parent=self.view.get_window()):
return
tree_model.remove(tree_model.get_iter(path))
self.model.synonyms.remove(value.synonym)
utils.delete_or_expunge(value)
# TODO: ** important ** this doesn't respect any unique
# contraints on the species for synonyms and allow a
# species to have another species as a synonym multiple
# times...see below
# TODO: using session.flush here with an argument is
# deprecated in SA 0.5 and will probably removed in SA
# 0.6...but how do we only flush the one value..unless we
# create a new session, merge it, commit that session,
# close it and then refresh the same object in
# self.session
# make the change in synonym immediately available so that if
# we try to add the same species again we don't break the
# SpeciesSynonym UniqueConstraint
# tmp_session = db.Session()
# tmp_value = tmp.session.merge(value)
# tmp.session.commit()
# tmp.session.close()
# self.session.refresh(value)
#self.session.flush([value])
self._dirty = True
self.parent_ref().refresh_sensitivity()
def test_search_by_query_binomial(self):
"""can use genus_species binomial identification"""
raise SkipTest("related to issue 192")
Family = self.Family
Genus = self.Genus
from bauble.plugins.plants.species_model import Species
family2 = Family(family=u'family2')
g2 = Genus(family=family2, genus=u'genus2')
f3 = Family(family=u'fam3', qualifier=u's. lat.')
g3 = Genus(family=f3, genus=u'Ixora')
sp = Species(sp=u"coccinea", genus=g3)
self.session.add_all([family2, g2, f3, g3, sp])
self.session.commit()
mapper_search = search.get_strategy('MapperSearch')
self.assertTrue(isinstance(mapper_search, search.MapperSearch))
s = '"Ixora coccinea"'
results = mapper_search.search(s, self.session)
self.assertEqual(results, set([sp]))
def test_search_by_query_vernacural(self):
"""can find species by vernacular name"""
Family = self.Family
Genus = self.Genus
from bauble.plugins.plants.species_model import Species
from bauble.plugins.plants.species_model import VernacularName
family2 = Family(epithet=u'family2')
g2 = Genus(family=family2, epithet=u'genus2')
f3 = Family(epithet=u'fam3', aggregate=u'agg.')
g3 = Genus(family=f3, epithet=u'Ixora')
sp = Species(epithet=u"coccinea", genus=g3)
vn = VernacularName(name=u"coral rojo", language=u"es", species=sp)
self.session.add_all([family2, g2, f3, g3, sp, vn])
self.session.commit()
mapper_search = search.get_strategy('MapperSearch')
self.assertTrue(isinstance(mapper_search, search.MapperSearch))
s = "rojo"
results = mapper_search.search(s, self.session)
self.assertEqual(results, set([sp]))
utils.message_details_dialog(msg, traceback.format_exc(),
gtk.MESSAGE_ERROR)
return False
elif self.presenter.is_dirty() and utils.yes_no_dialog(not_ok_msg) \
or not self.presenter.is_dirty():
self.session.rollback()
self.view.close_boxes()
return True
else:
return False
more_committed = None
if response == self.RESPONSE_NEXT:
self.presenter.cleanup()
e = SpeciesEditorMenuItem(
Species(genus=self.model.genus), self.parent)
more_committed = e.start()
elif response == self.RESPONSE_OK_AND_ADD:
from bauble.plugins.garden.accession import (
AccessionEditor, Accession)
e = AccessionEditor(Accession(species=self.model),
parent=self.parent)
more_committed = e.start()
if more_committed is not None:
if isinstance(more_committed, list):
self._committed.extend(more_committed)
else:
self._committed.append(more_committed)
self.view.close_boxes()
logger.debug(traceback.format_exc())
utils.message_details_dialog(msg, traceback.format_exc(),
gtk.MESSAGE_ERROR)
return False
elif self.presenter.is_dirty() and utils.yes_no_dialog(not_ok_msg) \
or not self.presenter.is_dirty():
self.session.rollback()
self.view.close_boxes()
return True
else:
return False
more_committed = None
if response == self.RESPONSE_NEXT:
self.presenter.cleanup()
e = SpeciesEditorMenuItem(Species(genus=self.model.genus),
self.parent)
more_committed = e.start()
elif response == self.RESPONSE_OK_AND_ADD:
from bauble.plugins.garden.accession import (AccessionEditor,
Accession)
e = AccessionEditor(Accession(species=self.model),
parent=self.parent)
more_committed = e.start()
if more_committed is not None:
if isinstance(more_committed, list):
self._committed.extend(more_committed)
else:
self._committed.append(more_committed)
return True
else:
# we should never really even get here since we would have
# to hit something besides "OK" and the above elif should
# handle all the possible cases
return False
# respond to responses
more_committed = None
if response == self.RESPONSE_NEXT:
self.presenter.cleanup()
model = Genus(family=self.model.family)
e = GenusEditor(model=model, parent=self.parent)
more_committed = e.start()
elif response == self.RESPONSE_OK_AND_ADD:
sp = Species(genus=self.model)
more_committed = edit_species(model=sp, parent=self.parent)
if more_committed is not None:
if isinstance(more_committed, list):
self._committed.extend(more_committed)
else:
self._committed.append(more_committed)
return True
def start(self):
if self.session.query(Family).count() == 0:
msg = _('You must first add or import at least one Family into '
'the database before you can add plants.')
utils.message_dialog(msg)
