def update(self, row):
"""
Update the Picasa info page.
:param: a Species instance
"""
self._current_row = row
token_meta = meta.get_default(utils.utf8(PICASA_TOKEN_KEY))
if not token_meta:
msg = _('Could not login to PicasaWeb account.')
self.on_error(msg, species=row)
return
token = token_meta.value
self.gd_client.SetClientLoginToken(token)
tag = Species.str(row, markup=False, authors=False)
self.set_busy()
worker = populate_iconview(self.gd_client, self.iconview, tag)
def on_done(*args):
if not _exc_queue.empty():
exc = _exc_queue.get()
msg = 'Could not retrieve the photos.\n\n'
if isinstance(exc, gdata.photos.service.GooglePhotosException):
msg += exc.message
else:
msg += str(exc)
gobject.idle_add(self.on_error, msg, row)
return
self.set_busy(False)
model = self.iconview.get_model()
if len(model) == 0:
gobject.idle_add(self.status_box.set_text, _('No images'))
gobject.idle_add(self.show_status_box)
else:
gobject.idle_add(self.hide_status_box)
worker.connect('done', on_done, False)
def test_export_with_vernacular(self):
"exporting one genus which is not an accepted name."
## precondition
sola = Family(family='Solanaceae')
brug = Genus(family=sola, genus=u'Brugmansia')
arbo = Species(genus=brug, sp=u'arborea')
vern = VernacularName(species=arbo,
language=u"es", name=u"Floripondio")
self.session.add_all([sola, brug, arbo, vern])
self.session.commit()
## action
exporter = JSONExporter(MockView())
exporter.view.selection = None
exporter.selection_based_on = 'sbo_taxa'
exporter.include_private = False
exporter.filename = self.temp_path
exporter.run()
## check
result = json.load(open(self.temp_path))
vern_from_json = [i for i in result
if i['object'] == 'vernacular_name']
self.assertEquals(len(vern_from_json), 1)
self.assertEquals(vern_from_json[0]['language'], 'es')
def test_import_ignores_id_updating(self):
"importing taxon disregards id value if present (updating taxon)."
previously = Species.retrieve_or_create(self.session,
{'ht-epithet': u"Calopogon",
'epithet': u"tuberosus"}).id
json_string = '[{"rank": "Species", "epithet": "tuberosus", '\
'"ht-rank": "Genus", "ht-epithet": "Calopogon", "hybrid": false, '\
'"id": 8}]'
with open(self.temp_path, "w") as f:
f.write(json_string)
importer = JSONImporter(MockImportView())
importer.filename = self.temp_path
importer.on_btnok_clicked(None)
self.session.commit()
afterwards = Species.retrieve_or_create(self.session,
{'ht-epithet': u"Calopogon",
'epithet': u"tuberosus"}).id
self.assertEquals(previously, afterwards)
def test_import_existing_updates(self):
"importing existing taxon updates it"
json_string = '[{"rank": "Species", "epithet": "tuberosus", "ht-rank"'\
': "Genus", "ht-epithet": "Calopogon", "hybrid": false, "author"'\
': "Britton et al."}]'
with open(self.temp_path, "w") as f:
f.write(json_string)
previously = Species.retrieve_or_create(
self.session, {'ht-epithet': u"Calopogon",
'epithet': u"tuberosus"})
self.assertEquals(previously.sp_author, None)
importer = JSONImporter(MockImportView())
importer.filename = self.temp_path
importer.on_btnok_clicked(None)
self.session.commit()
afterwards = Species.retrieve_or_create(
self.session, {'ht-epithet': u"Calopogon",
'epithet': u"tuberosus"})
self.assertEquals(afterwards.sp_author, u"Britton et al.")
def species_to_fix(ssn, binomial, author, create=False):
if binomial.find(' ') == -1:
return None
binomial = utils.to_unicode(binomial)
author = utils.to_unicode(author)
gen_epithet, sp_epithet = binomial.split(' ', 1)
return Species.retrieve_or_create(
ssn, {'object': 'taxon',
'rank': 'species',
'ht-epithet': gen_epithet,
'epithet': sp_epithet,
'ht-rank': 'genus',
'author': author},
create=create)
def test_export_none_is_empty(self):
"""
Test exporting a None column exports a ''
"""
species = Species(genus_id=1, sp='sp')
self.assertTrue(species is not None)
from tempfile import mkdtemp
temp_path = mkdtemp()
exporter = CSVExporter()
exporter.start(temp_path)
f = open(os.path.join(temp_path, 'species.txt'))
reader = csv.DictReader(f, dialect=csv.excel)
row = reader.next()
self.assert_(row['cv_group'] == '')
def species_to_fix(ssn, binomial, author, create=False):
if binomial.find(' ') == -1:
return None
binomial = utils.to_unicode(binomial)
author = utils.to_unicode(author)
gen_epithet, sp_epithet = binomial.split(' ', 1)
return Species.retrieve_or_create(
ssn, {'object': 'taxon',
'rank': 'species',
'ht-epithet': gen_epithet,
'epithet': sp_epithet,
'ht-rank': 'genus',
'author': author},
create=create)
def species_to_fix(ssn, binomial, author, create=False):
if binomial.find(" ") == -1:
return None
binomial = utils.to_unicode(binomial)
author = utils.to_unicode(author)
gen_epithet, sp_epithet = binomial.split(" ", 1)
return Species.retrieve_or_create(
ssn,
{
"object": "taxon",
"rank": "species",
"ht-epithet": gen_epithet,
"epithet": sp_epithet,
"ht-rank": "genus",
"author": author,
},
create=create,
)
def setUp(self, *args):
super(MakoFormatterTests, self).setUp()
fctr = gctr = sctr = actr = pctr = 0
for f in xrange(2):
fctr += 1
family = Family(id=fctr, epithet=u'fam%s' % fctr)
self.session.add(family)
for g in range(2):
gctr += 1
genus = Genus(id=gctr, family=family, epithet=u'gen%s' % gctr)
self.session.add(genus)
for s in range(2):
sctr += 1
sp = Species(id=sctr, genus=genus, epithet=u'sp%s' % sctr)
# TODO: why doesn't this geography, species
# distribution stuff seem to work
geo = Geography(id=sctr, name=u'Mexico%s' % sctr)
dist = SpeciesDistribution(geography_id=sctr)
sp.distribution.append(dist)
vn = VernacularName(id=sctr,
species=sp,
name=u'name%s' % sctr)
self.session.add_all([sp, geo, dist, vn])
for a in range(2):
actr += 1
acc = Accession(id=actr, species=sp, code=u'%s' % actr)
self.session.add(acc)
for p in range(2):
pctr += 1
loc = Location(id=pctr,
code=u'%s' % pctr,
name=u'site%s' % pctr)
plant = Plant(id=pctr,
accession=acc,
location=loc,
code=u'%s' % pctr,
quantity=1)
#debug('fctr: %s, gctr: %s, actr: %s, pctr: %s' \
# % (fctr, gctr, actr, pctr))
self.session.add_all([loc, plant])
self.session.commit()
def test_infopage(self):
raise SkipTest('Not Implemented')
from bauble.plugins.plants import Family, Genus, Species
email = ''
passwd = ''
album = 'Plants'
if email:
token = picasa.get_auth_token(email, passwd)
picasa.update_meta(email=email, album=album, token=token)
f = Family(family=u'Orchidaceae')
g = Genus(family=f, genus=u'Maxillaria')
sp = Species(genus=g, sp=u'elatior')
self.session.add_all([f, g, sp])
self.session.commit()
self.dialog = gtk.Dialog()
self.dialog.set_size_request(250, 700)
page = picasa.PicasaInfoPage()
page.update(sp)
self.dialog.vbox.pack_start(page)
self.dialog.show_all()
self.dialog.run()
def update(self, row):
"""
Update the Picasa info page.
:param: a Species instance
"""
self._current_row = row
token_meta = meta.get_default(utils.utf8(PICASA_TOKEN_KEY))
if not token_meta:
msg = _('Could not login to PicasaWeb account.')
self.on_error(msg, species=row)
return
token = token_meta.value
self.gd_client.SetClientLoginToken(token)
tag = Species.str(row, markup=False, authors=False)
self.set_busy()
worker = populate_iconview(self.gd_client, self.iconview, tag)
def on_done(*args):
if not _exc_queue.empty():
exc = _exc_queue.get()
msg = 'Could not retrieve the photos.\n\n'
if isinstance(exc, gdata.photos.service.GooglePhotosException):
msg += exc.message
else:
msg += str(exc)
gobject.idle_add(self.on_error, msg, row)
return
self.set_busy(False)
model = self.iconview.get_model()
if len(model) == 0:
gobject.idle_add(self.status_box.set_text, _('No images'))
gobject.idle_add(self.show_status_box)
else:
gobject.idle_add(self.hide_status_box)
worker.connect('done', on_done, False)
def setUp(self):
super(ReportTests, self).setUp()
fctr = gctr = sctr = actr = pctr = 0
for f in xrange(2):
fctr += 1
family = Family(id=fctr, epithet=u'fam%s' % fctr)
self.session.add(family)
for g in range(2):
gctr += 1
genus = Genus(id=gctr, family=family, epithet=u'gen%s' % gctr)
self.session.add(genus)
for s in range(2):
sctr += 1
sp = Species(id=sctr, genus=genus, epithet=u'sp%s' % sctr)
vn = VernacularName(id=sctr,
species=sp,
name=u'name%s' % sctr)
self.session.add_all([sp, vn])
for a in range(2):
actr += 1
acc = Accession(id=actr, species=sp, code=u'%s' % actr)
self.session.add(acc)
for p in range(2):
pctr += 1
loc = Location(id=pctr,
code=u'%s' % pctr,
name=u'site%s' % pctr)
plant = Plant(id=pctr,
accession=acc,
location=loc,
code=u'%s' % pctr,
quantity=1)
#debug('fctr: %s, gctr: %s, actr: %s, pctr: %s' \
# % (fctr, gctr, actr, pctr))
self.session.add_all([loc, plant])
self.session.commit()
