def test_import_species_to_new_genus_and_family(self):
"species referring to non existing genus (family is specified)"
## precondition: the species is not there
sp = self.session.query(Species).filter(
Species.sp == u'lawrenceae').join(Genus).filter(
Genus.genus == u'Aerides').all()
self.assertEquals(sp, [])
json_string = '[{"rank": "Species", "epithet": "lawrenceae", '\
'"ht-rank": "Genus", "ht-epithet": "Aerides", '\
'"familia": "Orchidaceae", "author" : "Rchb. f."}]'
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()
## postcondition: the species is there
sp = self.session.query(Species).filter(
Species.sp == u'lawrenceae').join(Genus).filter(
Genus.genus == u'Aerides').all()
self.assertEquals(len(sp), 1)
sp = sp[0]
genus = self.session.query(Genus).filter(
Genus.genus == u'Aerides').first()
family = self.session.query(Family).filter(
Family.family == u'Orchidaceae').first()
self.assertEquals(sp.genus, genus)
self.assertEquals(genus.family, family)
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_import_new_inserts_lowercase(self):
"importing new taxon adds it to database, rank name can be\
all lower case."
json_string = '[{"rank": "genus", "epithet": "Neogyna", "ht-rank"'\
': "familia", "ht-epithet": "Orchidaceae", "author": "Rchb. f."}]'
with open(self.temp_path, "w") as f:
f.write(json_string)
self.assertEquals(len(self.session.query(Genus).filter(
Genus.genus == u"Neogyna").all()), 0)
importer = JSONImporter(MockImportView())
importer.filename = self.temp_path
importer.on_btnok_clicked(None)
self.assertEquals(len(self.session.query(Genus).filter(
Genus.genus == u"Neogyna").all()), 1)
def test_import_species_to_new_genus_fails(self):
"importing new species referring to non existing genus logs a warning."
json_string = '[{"rank": "Species", "epithet": "lawrenceae", '\
'"ht-rank": "Genus", "ht-epithet": "Aerides", "author": '\
'"Rchb. f."}]'
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)
## should check the logs
## check the species is still not there
sp = self.session.query(Species).filter(
Species.sp == u'lawrenceae').join(Genus).filter(
Genus.genus == u'Aerides').all()
self.assertEquals(sp, [])
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_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_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 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 test_on_btnbrowse_clicked(self):
view = MockView()
exporter = JSONImporter(view)
view.reply_file_chooser_dialog = ['/tmp/test.json']
exporter.on_btnbrowse_clicked('button')
exporter.on_text_entry_changed('input_filename')
self.assertEquals(exporter.filename, '/tmp/test.json')
self.assertEquals(JSONImporter.last_folder, '/tmp')
