def test_import_create_no_update(self):
'existing remains untouched, not existing is created'
## T_0
ataceae = Family(family=u'Anacampserotaceae') # Eggli & Nyffeler
linnaeus = Genus(family=ataceae, genus=u'Anacampseros') # L.
self.session.add_all([ataceae, linnaeus])
self.session.commit()
## offer two objects for import
importer = JSONImporter(MockImportView())
json_string = '[{"author": "L.", "epithet": "Anacampseros", '\
'"ht-epithet": "Anacampserotaceae", "ht-rank": "familia", '\
'"object": "taxon", "rank": "genus"}, {"author": "L.", '\
'"epithet": "Sedum", "ht-epithet": "Crassulaceae", '\
'"ht-rank": "familia", "object": "taxon", '\
'"rank": "genus"}]'
with open(self.temp_path, "w") as f:
f.write(json_string)
importer.filename = self.temp_path
importer.create = True
importer.update = False
importer.on_btnok_clicked(None)
self.session.commit()
## T_1
sedum = Genus.retrieve_or_create(
self.session, {'epithet': u"Sedum"}, create=False)
self.assertEquals(sedum.__class__, Genus)
self.assertEquals(sedum.author, u'L.')
anacampseros = Genus.retrieve_or_create(
self.session, {'epithet': u"Anacampseros"}, create=False)
self.assertEquals(anacampseros.__class__, Genus)
self.assertEquals(anacampseros.author, u'')
def test_partial_taxonomic_with_synonymy(self):
"exporting one genus which is not an accepted name."
f = self.session.query(
Family).filter(
Family.family == u'Orchidaceae').one()
bu = Genus(family=f, genus=u'Bulbophyllum') # accepted
zy = Genus(family=f, genus=u'Zygoglossum') # synonym
bu.synonyms.append(zy)
self.session.add_all([f, bu, zy])
self.session.commit()
selection = self.session.query(Genus).filter(
Genus.genus == u'Zygoglossum').all()
exporter = JSONExporter(MockView())
exporter.view.selection = selection
exporter.selection_based_on == 'sbo_selection'
exporter.include_private = True
exporter.filename = self.temp_path
exporter.run()
result = json.load(open(self.temp_path))
self.assertEquals(len(result), 1)
self.assertEquals(result[0]['rank'], 'genus')
self.assertEquals(result[0]['epithet'], 'Zygoglossum')
self.assertEquals(result[0]['ht-rank'], 'familia')
self.assertEquals(result[0]['ht-epithet'], 'Orchidaceae')
accepted = result[0].get('accepted')
self.assertTrue(isinstance(accepted, dict))
self.assertEquals(accepted['rank'], 'genus')
self.assertEquals(accepted['epithet'], 'Bulbophyllum')
self.assertEquals(accepted['ht-rank'], 'familia')
self.assertEquals(accepted['ht-epithet'], 'Orchidaceae')
def test_use_author_to_break_ties(self):
"importing homonym taxon is possible if authorship breaks ties"
# Anacampseros was used twice, by Linnaeus, and by Miller
ataceae = Family(family=u'Anacampserotaceae') # Eggli & Nyffeler
linnaeus = Genus(family=ataceae, genus=u'Anacampseros', author=u'L.')
claceae = Family(family=u'Crassulaceae') # J. St.-Hil.
miller = Genus(family=claceae, genus=u'Anacampseros', author=u'Mill.')
self.session.add_all([claceae, ataceae, linnaeus, miller])
self.session.commit()
## T_0
accepted = Genus.retrieve_or_create(
self.session, {'epithet': u"Sedum"}, create=False)
self.assertEquals(accepted, None)
self.assertEquals(miller.accepted, None)
## what if we update Anacampseros Mill., with `accepted` information?
json_string = ' {"author": "Mill.", "epithet": "Anacampseros", '\
'"ht-epithet": "Crassulaceae", "ht-rank": "familia", '\
'"object": "taxon", "rank": "genus", "accepted": {'\
'"author": "L.", "epithet": "Sedum", "ht-epithet": '\
'"Crassulaceae", "ht-rank": "familia", "object": "taxon", '\
'"rank": "genus"}}'
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()
## T_1
accepted = Genus.retrieve_or_create(
self.session, {'epithet': u"Sedum"}, create=False)
self.assertEquals(accepted.__class__, Genus)
self.assertEquals(miller.accepted, accepted)
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_new(self):
"importing taxon disregards id value if present (new taxon)."
previously = Genus.retrieve_or_create(
self.session, {'epithet': u"Neogyna"})
self.assertEquals(previously, None)
json_string = '[{"rank": "Genus", "epithet": "Neogyna", '\
'"ht-rank": "Familia", "ht-epithet": "Orchidaceae", '\
'"author": "Rchb. f.", "id": 1}]'
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()
real_id = Genus.retrieve_or_create(self.session,
{'epithet': u"Neogyna"}).id
self.assertTrue(real_id != 1)
def test_import_with_synonym(self):
"importing taxon with `accepted` field imports both taxa"
json_string = '[{"rank": "Genus", "epithet": "Zygoglossum", '\
'"ht-rank": "Familia", "ht-epithet": "Orchidaceae", '\
'"author": "Reinw.", "accepted": {"rank": "Genus", '\
'"epithet": "Bulbophyllum", "ht-rank": "Familia", '\
'"ht-epithet": "Orchidaceae", "author": "Thouars"}}]'
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()
synonym = Genus.retrieve_or_create(
self.session, {'epithet': u"Zygoglossum"})
self.assertEquals(synonym.accepted.__class__, Genus)
accepted = Genus.retrieve_or_create(
self.session, {'epithet': u"Bulbophyllum"})
self.assertEquals(synonym.accepted, accepted)
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 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()
