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(self):
"""
Test the HistoryMapperExtension
"""
from bauble.plugins.plants import Family
f = Family(epithet=u'Family')
self.session.add(f)
self.session.commit()
q = self.session.query(db.History).\
order_by(db.History.timestamp.desc())
history = q.first()
base_count = q.count()
self.assertEquals(history.table_name, 'family')
self.assertEquals(history.operation, 'insert')
f.author = u'L.'
self.session.commit()
q = self.session.query(db.History).\
order_by(db.History.timestamp.desc())
history = q.first()
self.assertEquals(q.count(), base_count + 1)
self.assertEquals(history.table_name, 'family')
self.assertEquals(history.operation, 'update')
f.author = u'Rch.'
self.session.commit()
q = self.session.query(db.History).\
order_by(db.History.timestamp.desc())
history = q.first()
self.assertEquals(q.count(), base_count + 2)
self.assertEquals(history.table_name, 'family')
self.assertEquals(history.operation, 'update')
f.epithet = u'CanWeRename'
self.session.commit()
q = self.session.query(db.History).\
order_by(db.History.timestamp.desc())
history = q.first()
self.assertEquals(q.count(), base_count + 3)
self.assertEquals(history.table_name, 'family')
self.assertEquals(history.operation, 'update')
self.session.delete(f)
self.session.commit()
q = self.session.query(db.History).\
order_by(db.History.timestamp.desc())
history = q.first()
self.assertEquals(q.count(), base_count + 4)
self.assertEquals(history.table_name, 'family')
self.assertEquals(history.operation, 'delete')
def test_get_tag_ids(self):
family2 = Family(family=u'family2')
self.session.add(family2)
self.session.commit()
tag_plugin.tag_objects('test', [self.family, family2])
tag_plugin.tag_objects('test2', [self.family])
# test we only return the ids the objects have in common
#sel = select([tag_table.c.id], tag_table.c.tag==u'test')
results = self.session.query(Tag.id).filter_by(tag=u'test')
test_id = [r[0] for r in results]
# should only return id for "test"
ids = tag_plugin.get_tag_ids([self.family, family2])
self.assert_(ids == test_id, '%s==%s' % (ids, test_id))
# test that we return multiple tag ids if the objs share tags
tag_plugin.tag_objects('test2', [family2])
#sel = select([tag_table.c.id], or_(tag_table.c.tag==u'test',
# tag_table.c.tag==u'test2'))
results = self.session.query(Tag.id).filter(
or_(Tag.tag == u'test', Tag.tag == u'test2'))
test_id = sorted([r[0] for r in results])
# should return ids for both test and test2
ids = sorted(tag_plugin.get_tag_ids([self.family, family2]))
self.assert_(ids == test_id, '%s == %s' % (ids, test_id))
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_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_tag_objects(self):
family2 = Family(epithet=u'family2')
self.session.add(family2)
self.session.commit()
family1_id = self.family.id
family2_id = family2.id
tag_plugin.tag_objects('test', [self.family, family2])
# we do not offer gettin object by string
# get object by tag
tag = self.session.query(Tag).filter_by(tag=u'test').one()
tagged_objs = tag.objects
sorted_pairs = sorted([(type(o), o.id) for o in tagged_objs])
self.assertEquals(sorted([(Family, family1_id),
(Family, family2_id)]),
sorted_pairs)
tag_plugin.tag_objects('test', [self.family, family2])
self.assertEquals(tag.objects, [self.family, family2])
#
# now untag everything
#
tag_plugin.untag_objects('test', [self.family, family2])
# get object by tag
tag = self.session.query(Tag).filter_by(tag=u'test').one()
tagged_objs = tag.objects
self.assertEquals(tagged_objs, [])
def setUp(self):
super(AttachedToTests, self).setUp()
obj1 = Tag(tag=u'medicinal')
obj2 = Tag(tag=u'maderable')
obj3 = Tag(tag=u'frutal')
fam = Family(family=u'Solanaceae')
self.session.add_all([obj1, obj2, obj3, fam])
self.session.commit()
def test(self):
"""
Test the HistoryMapperExtension
"""
from bauble.plugins.plants import Family
f = Family(family=u"Family")
self.session.add(f)
self.session.commit()
history = self.session.query(db.History).order_by(db.History.timestamp.desc()).first()
assert history.table_name == "family" and history.operation == "insert"
f.family = u"Family2"
self.session.commit()
history = self.session.query(db.History).order_by(db.History.timestamp.desc()).first()
assert history.table_name == "family" and history.operation == "update"
self.session.delete(f)
self.session.commit()
history = self.session.query(db.History).order_by(db.History.timestamp.desc()).first()
assert history.table_name == "family" and history.operation == "delete"
def test(self):
"""
Test the HistoryMapperExtension
"""
from bauble.plugins.plants import Family
f = Family(family=u'Family')
self.session.add(f)
self.session.commit()
history = self.session.query(db.History).\
order_by(db.History.timestamp.desc()).first()
assert history.table_name == 'family' and history.operation == 'insert'
f.family = u'Family2'
self.session.commit()
history = self.session.query(db.History).\
order_by(db.History.timestamp.desc()).first()
assert history.table_name == 'family' and history.operation == 'update'
self.session.delete(f)
self.session.commit()
history = self.session.query(db.History).\
order_by(db.History.timestamp.desc()).first()
assert history.table_name == 'family' and history.operation == 'delete'
def test(self):
"""
Test the HistoryMapperExtension
"""
from bauble.plugins.plants import Family
f = Family(family=u'Family')
self.session.add(f)
self.session.commit()
history = self.session.query(db.History).\
order_by(db.History.timestamp.desc()).first()
assert history.table_name == 'family' and history.operation == 'insert'
f.family = u'Family2'
self.session.commit()
history = self.session.query(db.History).\
order_by(db.History.timestamp.desc()).first()
assert history.table_name == 'family' and history.operation == 'update'
self.session.delete(f)
self.session.commit()
history = self.session.query(db.History).\
order_by(db.History.timestamp.desc()).first()
assert history.table_name == 'family' and history.operation == 'delete'
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 test_tag_objects(self):
family2 = Family(family=u'family2')
self.session.add(family2)
self.session.commit()
family1_id = self.family.id
family2_id = family2.id
tag_plugin.tag_objects('test', [self.family, family2])
# get object by string
tagged_objs = tag_plugin.get_tagged_objects('test')
sorted_pairs = sorted([(type(o), o.id) for o in tagged_objs],
cmp=lambda x, y: cmp(x[0], y[0]))
self.assert_(
sorted_pairs == [(Family, family1_id), (Family, family2_id)],
sorted_pairs)
# get object by tag
tag = self.session.query(Tag).filter_by(tag=u'test').one()
tagged_objs = tag_plugin.get_tagged_objects(tag)
sorted_pairs = sorted([(type(o), o.id) for o in tagged_objs],
cmp=lambda x, y: cmp(x[0], y[0]))
self.assert_(
sorted_pairs == [(Family, family1_id), (Family, family2_id)],
sorted_pairs)
tag_plugin.tag_objects('test', [self.family, family2])
#
# now untag everything
#
tag_plugin.untag_objects('test', [self.family, family2])
# get object by string
tagged_objs = tag_plugin.get_tagged_objects('test')
pairs = [(type(o), o.id) for o in tagged_objs]
self.assert_(pairs == [], pairs)
# get object by tag
tag = self.session.query(Tag).filter_by(tag=u'test').one()
tagged_objs = tag_plugin.get_tagged_objects(tag)
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()
def setUp(self):
super(TagTests, self).setUp()
self.family = Family(family=u'family')
self.session.add(self.family)
self.session.commit()
