def test_binomial_no_match(self):
mapper_search = search.get_strategy('MapperSearch')
self.assertTrue(isinstance(mapper_search, search.MapperSearch))
s = 'Cosito inesistente' # matches nothing
results = mapper_search.search(s, self.session)
self.assertEqual(results, set())
def test_in_singleton(self):
mapper_search = search.get_strategy('MapperSearch')
self.assertTrue(isinstance(mapper_search, search.MapperSearch))
s = 'genus where id in 1'
results = mapper_search.search(s, self.session)
self.assertEqual(results, set([self.g1]))
def test_almost_binomial(self):
mapper_search = search.get_strategy('MapperSearch')
self.assertTrue(isinstance(mapper_search, search.MapperSearch))
s = 'ixora coccinea' # matches Ixora, I.coccinea, P.coccinea
results = mapper_search.search(s, self.session)
self.assertEqual(results, set([self.ixora, self.ic, self.pc]))
def test_search_by_query21(self):
"query with MapperSearch, joined tables, one predicate"
# test does not depend on plugin functionality
Family = self.Family
Genus = self.Genus
family2 = Family(epithet=u'family2')
genus2 = Genus(family=family2, epithet=u'genus2')
self.session.add_all([family2, genus2])
self.session.commit()
mapper_search = search.get_strategy('MapperSearch')
self.assertTrue(isinstance(mapper_search, search.MapperSearch))
# search cls.parent.column
results = mapper_search.search('genus where family.epithet=family1',
self.session)
self.assertEquals(len(results), 1)
g0 = list(results)[0]
self.assertTrue(isinstance(g0, Genus))
self.assertEquals(g0.id, self.genus.id)
# search cls.children.column
results = mapper_search.search('family where genera.epithet=genus1',
self.session)
self.assertEquals(len(results), 1)
f = list(results)[0]
self.assertEqual(len(results), 1)
self.assertTrue(isinstance(f, Family))
self.assertEqual(f.id, self.family.id)
def test_search_by_query22like(self):
"query with MapperSearch, joined tables, LIKE"
# test does not depend on plugin functionality
Family = self.Family
Genus = self.Genus
family2 = Family(family=u'family2')
family3 = Family(family=u'afamily3')
genus21 = Genus(family=family2, genus=u'genus21')
genus31 = Genus(family=family3, genus=u'genus31')
genus32 = Genus(family=family3, genus=u'genus32')
genus33 = Genus(family=family3, genus=u'genus33')
f3 = Family(family=u'fam3')
g3 = Genus(family=f3, genus=u'genus31')
self.session.add_all([family3, family2, genus21, genus31, genus32,
genus33, f3, g3])
self.session.commit()
mapper_search = search.get_strategy('MapperSearch')
self.assertTrue(isinstance(mapper_search, search.MapperSearch))
# test partial string matches on a query
s = 'genus where family.family like family%'
results = mapper_search.search(s, self.session)
self.assertEquals(set(results), set([self.genus, genus21]))
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(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)
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 test_canfindspeciesfromgenus(self):
'can find species from genus'
mapper_search = search.get_strategy('MapperSearch')
results = mapper_search.search('species where species.genus=genus1')
print dir(results)
self.assertEqual(str(results.statement), "SELECT * FROM species WHERE (species.genus = 'genus1')")
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 search(self, text, session):
from genus import Genus, GenusSynonym
super(SynonymSearch, self).search(text, session)
if not prefs[self.return_synonyms_pref]:
return
mapper_search = search.get_strategy('MapperSearch')
r1 = mapper_search.search(text, session)
if not r1:
return []
results = []
for result in r1:
# iterate through the results and see if we can find some
# synonyms for the returned values
if isinstance(result, Species):
q = session.query(SpeciesSynonym).\
filter_by(synonym_id=result.id)
results.extend([syn.species for syn in q])
elif isinstance(result, Genus):
q = session.query(GenusSynonym).\
filter_by(synonym_id=result.id)
results.extend([syn.genus for syn in q])
elif isinstance(results, VernacularName):
q = session.query(SpeciesSynonym).\
filter_by(synonym_id=result.species.id)
results.extend([syn.species for syn in q])
return results
def search(self, text, session):
from genus import Genus, GenusSynonym
super(SynonymSearch, self).search(text, session)
if not prefs[self.return_synonyms_pref]:
return []
mapper_search = search.get_strategy('MapperSearch')
r1 = mapper_search.search(text, session)
if not r1:
return []
results = []
for result in r1:
# iterate through the results and for all objects considered
# synonym of something else, include that something else. that
# is, the accepted name.
if isinstance(result, Species):
q = session.query(SpeciesSynonym).\
filter_by(synonym_id=result.id)
results.extend([syn.species for syn in q])
elif isinstance(result, Genus):
q = session.query(GenusSynonym).\
filter_by(synonym_id=result.id)
results.extend([syn.genus for syn in q])
elif isinstance(results, VernacularName):
q = session.query(SpeciesSynonym).\
filter_by(synonym_id=result.species.id)
results.extend([syn.species for syn in q])
return results
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_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(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)
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_binomial_incomplete(self):
mapper_search = search.get_strategy('MapperSearch')
self.assertTrue(isinstance(mapper_search, search.MapperSearch))
s = 'Ix cocc' # matches Ixora coccinea
results = mapper_search.search(s, self.session)
self.assertEqual(results, set([self.ic]))
def test_in_list_no_result(self):
mapper_search = search.get_strategy('MapperSearch')
self.assertTrue(isinstance(mapper_search, search.MapperSearch))
s = 'genus where id in 5,6'
results = mapper_search.search(s, self.session)
self.assertEqual(results, set())
def test_in_list_no_result(self):
mapper_search = search.get_strategy('MapperSearch')
self.assertTrue(isinstance(mapper_search, search.MapperSearch))
s = 'genus where id in 5,6'
results = mapper_search.search(s, self.session)
self.assertEqual(results, set())
def test_in_composite_expression_excluding(self):
mapper_search = search.get_strategy('MapperSearch')
self.assertTrue(isinstance(mapper_search, search.MapperSearch))
s = 'genus where id in 1,2,4 and id<3'
results = mapper_search.search(s, self.session)
self.assertEqual(results, set([self.g1, self.g2]))
def test_search_by_query13(self):
"query with MapperSearch, single table, p1 AND p2"
# test does not depend on plugin functionality
Family = self.Family
Genus = self.Genus
family2 = Family(family=u'family2')
genus2 = Genus(family=family2, genus=u'genus2')
f3 = Family(family=u'fam3')
g3 = Genus(family=f3, genus=u'genus2')
g4 = Genus(family=f3, genus=u'genus4')
self.session.add_all([family2, genus2, f3, g3, g4])
self.session.commit()
mapper_search = search.get_strategy('MapperSearch')
self.assertTrue(isinstance(mapper_search, search.MapperSearch))
s = 'genus where id>1 AND id<3'
results = mapper_search.search(s, self.session)
self.assertEqual(len(results), 1)
result = results.pop()
self.assertEqual(result.id, 2)
s = 'genus where id>0 AND id<3'
results = list(mapper_search.search(s, self.session))
self.assertEqual(len(results), 2)
self.assertEqual(set(i.id for i in results), set([1, 2]))
def test_in_singleton(self):
mapper_search = search.get_strategy('MapperSearch')
self.assertTrue(isinstance(mapper_search, search.MapperSearch))
s = 'genus where id in 1'
results = mapper_search.search(s, self.session)
self.assertEqual(results, set([self.g1]))
def test_search_by_query21(self):
"query with MapperSearch, joined tables, one predicate"
# test does not depend on plugin functionality
Family = self.Family
Genus = self.Genus
family2 = Family(family=u'family2')
genus2 = Genus(family=family2, genus=u'genus2')
self.session.add_all([family2, genus2])
self.session.commit()
mapper_search = search.get_strategy('MapperSearch')
self.assertTrue(isinstance(mapper_search, search.MapperSearch))
# search cls.parent.column
results = mapper_search.search('genus where family.family=family1',
self.session)
self.assertEquals(len(results), 1)
g0 = list(results)[0]
self.assertTrue(isinstance(g0, Genus))
self.assertEquals(g0.id, self.genus.id)
# search cls.children.column
results = mapper_search.search('family where genera.genus=genus1',
self.session)
self.assertEquals(len(results), 1)
f = list(results)[0]
self.assertEqual(len(results), 1)
self.assertTrue(isinstance(f, Family))
self.assertEqual(f.id, self.family.id)
def test_search_by_query22Symbolic(self):
"query with &&, ||, !"
# test does not depend on plugin functionality
Family = self.Family
Genus = self.Genus
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'genus3')
self.session.add_all([family2, g2, f3, g3])
self.session.commit()
mapper_search = search.get_strategy('MapperSearch')
self.assertTrue(isinstance(mapper_search, search.MapperSearch))
s = 'genus where genus=genus2 && family.family=fam3'
results = mapper_search.search(s, self.session)
self.assertEqual(len(results), 0)
s = 'family where family=family1 || family=fam3'
results = mapper_search.search(s, self.session)
self.assertEqual(len(results), 2)
s = 'family where ! family=family1'
results = mapper_search.search(s, self.session)
self.assertEqual(len(results), 2)
def search(self, text, session):
from genus import Genus, GenusSynonym
super(SynonymSearch, self).search(text, session)
if not prefs[self.return_synonyms_pref]:
return
mapper_search = search.get_strategy('MapperSearch')
r1 = mapper_search.search(text, session)
if not r1:
return []
results = []
for result in r1:
# iterate through the results and see if we can find some
# synonyms for the returned values
if isinstance(result, Species):
q = session.query(SpeciesSynonym).\
filter_by(synonym_id=result.id)
results.extend([syn.species for syn in q])
elif isinstance(result, Genus):
q = session.query(GenusSynonym).\
filter_by(synonym_id=result.id)
results.extend([syn.genus for syn in q])
elif isinstance(results, VernacularName):
q = session.query(SpeciesSynonym).\
filter_by(synonym_id=result.species.id)
results.extend([syn.species for syn in q])
return results
def search(self, text, session):
from genus import Genus, GenusSynonym
super(SynonymSearch, self).search(text, session)
if not prefs[self.return_synonyms_pref]:
return []
mapper_search = search.get_strategy('MapperSearch')
r1 = mapper_search.search(text, session)
if not r1:
return []
results = []
for result in r1:
# iterate through the results and for all objects considered
# synonym of something else, include that something else. that
# is, the accepted name.
if isinstance(result, Species):
q = session.query(SpeciesSynonym).\
filter_by(synonym_id=result.id)
results.extend([syn.species for syn in q])
elif isinstance(result, Genus):
q = session.query(GenusSynonym).\
filter_by(synonym_id=result.id)
results.extend([syn.genus for syn in q])
elif isinstance(results, VernacularName):
q = session.query(SpeciesSynonym).\
filter_by(synonym_id=result.species.id)
results.extend([syn.species for syn in q])
return results
def test_search_by_expression_genus_eq_nomatch(self):
mapper_search = search.get_strategy('MapperSearch')
self.assertTrue(isinstance(mapper_search, search.MapperSearch))
# search for genus by domain
results = mapper_search.search('genus=g', self.session)
self.assertEquals(len(results), 0)
def test_search_by_expression_genus_like_contains_eq(self):
mapper_search = search.get_strategy('MapperSearch')
self.assertTrue(isinstance(mapper_search, search.MapperSearch))
Family = self.Family
f2 = Family(family=u'family2')
f3 = Family(family=u'afamily3')
f4 = Family(family=u'fam4')
self.session.add_all([f3, f2, f4])
self.session.commit()
# search for family by domain
results = mapper_search.search('family contains fam', self.session)
self.assertEquals(len(results), 4) # all do
results = mapper_search.search('family like f%', self.session)
self.assertEquals(len(results), 3) # three start by f
results = mapper_search.search('family like af%', self.session)
self.assertEquals(len(results), 1) # one starts by af
results = mapper_search.search('family like fam', self.session)
self.assertEquals(len(results), 0)
results = mapper_search.search('family = fam', self.session)
self.assertEquals(len(results), 0)
results = mapper_search.search('family = fam4', self.session)
self.assertEquals(len(results), 1) # exact name match
results = mapper_search.search('family = Fam4', self.session)
self.assertEquals(len(results), 0) # = is case sensitive
results = mapper_search.search('family like Fam4', self.session)
self.assertEquals(len(results), 1) # like is case insensitive
results = mapper_search.search('family contains FAM', self.session)
self.assertEquals(len(results), 4) # they case insensitively do
def test_search_by_query22like(self):
"query with MapperSearch, joined tables, LIKE"
# test does not depend on plugin functionality
Family = self.Family
Genus = self.Genus
family2 = Family(epithet=u'family2')
family3 = Family(epithet=u'afamily3')
genus21 = Genus(family=family2, epithet=u'genus21')
genus31 = Genus(family=family3, epithet=u'genus31')
genus32 = Genus(family=family3, epithet=u'genus32')
genus33 = Genus(family=family3, epithet=u'genus33')
f3 = Family(epithet=u'fam3')
g3 = Genus(family=f3, epithet=u'genus31')
self.session.add_all(
[family3, family2, genus21, genus31, genus32, genus33, f3, g3])
self.session.commit()
mapper_search = search.get_strategy('MapperSearch')
self.assertTrue(isinstance(mapper_search, search.MapperSearch))
# test partial string matches on a query
s = 'genus where family.epithet like family%'
results = mapper_search.search(s, self.session)
self.assertEquals(set(results), set([self.genus, genus21]))
def test_in_composite_expression_excluding(self):
mapper_search = search.get_strategy('MapperSearch')
self.assertTrue(isinstance(mapper_search, search.MapperSearch))
s = 'genus where id in 1,2,4 and id<3'
results = mapper_search.search(s, self.session)
self.assertEqual(results, set([self.g1, self.g2]))
def test_search_by_query22Symbolic(self):
"query with &&, ||, !"
# test does not depend on plugin functionality
Family = self.Family
Genus = self.Genus
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'genus3')
self.session.add_all([family2, g2, f3, g3])
self.session.commit()
mapper_search = search.get_strategy('MapperSearch')
self.assertTrue(isinstance(mapper_search, search.MapperSearch))
s = 'genus where epithet=genus2 && family.epithet=fam3'
results = mapper_search.search(s, self.session)
self.assertEqual(len(results), 0)
s = 'family where epithet=family1 || epithet=fam3'
results = mapper_search.search(s, self.session)
self.assertEqual(len(results), 2)
s = 'family where ! epithet=family1'
results = mapper_search.search(s, self.session)
self.assertEqual(len(results), 2)
def test_search_by_query13(self):
"query with MapperSearch, single table, p1 AND p2"
# test does not depend on plugin functionality
Family = self.Family
Genus = self.Genus
family2 = Family(epithet=u'family2')
genus2 = Genus(family=family2, epithet=u'genus2')
f3 = Family(epithet=u'fam3')
g3 = Genus(family=f3, epithet=u'genus2')
g4 = Genus(family=f3, epithet=u'genus4')
self.session.add_all([family2, genus2, f3, g3, g4])
self.session.commit()
mapper_search = search.get_strategy('MapperSearch')
self.assertTrue(isinstance(mapper_search, search.MapperSearch))
s = 'genus where id>1 AND id<3'
results = mapper_search.search(s, self.session)
self.assertEqual(len(results), 1)
result = results.pop()
self.assertEqual(result.id, 2)
s = 'genus where id>0 AND id<3'
results = list(mapper_search.search(s, self.session))
self.assertEqual(len(results), 2)
self.assertEqual(set(i.id for i in results), set([1, 2]))
def test_binomial_incomplete(self):
mapper_search = search.get_strategy('MapperSearch')
self.assertTrue(isinstance(mapper_search, search.MapperSearch))
s = 'Ix cocc' # matches Ixora coccinea
results = mapper_search.search(s, self.session)
self.assertEqual(results, set([self.ic]))
def test_search_by_expression_genus_like_contains_eq(self):
mapper_search = search.get_strategy('MapperSearch')
self.assertTrue(isinstance(mapper_search, search.MapperSearch))
Family = self.Family
f2 = Family(epithet=u'family2')
f3 = Family(epithet=u'afamily3')
f4 = Family(epithet=u'fam4')
self.session.add_all([f3, f2, f4])
self.session.commit()
# search for family by domain
results = mapper_search.search('family contains fam', self.session)
self.assertEquals(len(results), 4) # all do
results = mapper_search.search('family like f%', self.session)
self.assertEquals(len(results), 3) # three start by f
results = mapper_search.search('family like af%', self.session)
self.assertEquals(len(results), 1) # one starts by af
results = mapper_search.search('family like fam', self.session)
self.assertEquals(len(results), 0)
results = mapper_search.search('family = fam', self.session)
self.assertEquals(len(results), 0)
results = mapper_search.search('family = fam4', self.session)
self.assertEquals(len(results), 1) # exact name match
results = mapper_search.search('family = Fam4', self.session)
self.assertEquals(len(results), 0) # = is case sensitive
results = mapper_search.search('family like Fam4', self.session)
self.assertEquals(len(results), 1) # like is case insensitive
results = mapper_search.search('family contains FAM', self.session)
self.assertEquals(len(results), 4) # they case insensitively do
def test_search_by_expression_genus_eq_nomatch(self):
mapper_search = search.get_strategy('MapperSearch')
self.assertTrue(isinstance(mapper_search, search.MapperSearch))
# search for genus by domain
results = mapper_search.search('genus=g', self.session)
self.assertEquals(len(results), 0)
def test_binomial_no_match(self):
mapper_search = search.get_strategy('MapperSearch')
self.assertTrue(isinstance(mapper_search, search.MapperSearch))
s = 'Cosito inesistente' # matches nothing
results = mapper_search.search(s, self.session)
self.assertEqual(results, set())
def test_almost_binomial(self):
mapper_search = search.get_strategy('MapperSearch')
self.assertTrue(isinstance(mapper_search, search.MapperSearch))
s = 'ixora coccinea' # matches Ixora, I.coccinea, P.coccinea
results = mapper_search.search(s, self.session)
self.assertEqual(results, set([self.ixora, self.ic, self.pc]))
def init(cls):
from bauble.view import SearchView
mapper_search = search.get_strategy('MapperSearch')
mapper_search.add_meta(('tag', 'tags'), Tag, ['tag'])
SearchView.view_meta[Tag].set(children=natsort_kids('objects'),
context_menu=tag_context_menu)
if bauble.gui is not None:
_reset_tags_menu()
def init(cls):
from bauble.view import SearchView
mapper_search = search.get_strategy('MapperSearch')
mapper_search.add_meta(('tag', 'tags'), Tag, ['tag'])
SearchView.view_meta[Tag].set(children=natsort_kids('objects'),
context_menu=tag_context_menu)
if bauble.gui is not None:
_reset_tags_menu()
def test_canfindfamilyfromgenus(self):
'can find family from genus'
mapper_search = search.get_strategy('MapperSearch')
results = mapper_search.search('family where family.genus=genus1')
self.assertEqual(
str(results.statement),
"SELECT * FROM family WHERE (family.genus = 'genus1')")
def test_canfindplantbyaccession(self):
'can find plant from the accession id'
mapper_search = search.get_strategy('MapperSearch')
results = mapper_search.search('plant where accession.species.id=113')
self.assertEqual(
str(results.statement),
'SELECT * FROM plant WHERE (accession.species.id = 113)')
def test_canfindspeciesfromgenus(self):
'can find species from genus'
mapper_search = search.get_strategy('MapperSearch')
results = mapper_search.search('species where species.genus=genus1')
print dir(results)
self.assertEqual(
str(results.statement),
"SELECT * FROM species WHERE (species.genus = 'genus1')")
def test_search_by_expression_genus_eq_1match(self):
mapper_search = search.get_strategy('MapperSearch')
self.assertTrue(isinstance(mapper_search, search.MapperSearch))
# search for genus by domain
results = mapper_search.search('gen=genus1', self.session)
self.assertEquals(len(results), 1)
g = list(results)[0]
self.assertTrue(isinstance(g, self.Genus))
self.assertEqual(g.id, self.genus.id)
def test_search_by_expression_family_eq(self):
mapper_search = search.get_strategy('MapperSearch')
self.assertTrue(isinstance(mapper_search, search.MapperSearch))
# search for family by domain
results = mapper_search.search('fam=family1', self.session)
self.assertEquals(len(results), 1)
f = list(results)[0]
self.assertTrue(isinstance(f, self.Family))
self.assertEquals(f.id, self.family.id)
def test_search_by_expression_family_eq(self):
mapper_search = search.get_strategy('MapperSearch')
self.assertTrue(isinstance(mapper_search, search.MapperSearch))
# search for family by domain
results = mapper_search.search('fam=family1', self.session)
self.assertEquals(len(results), 1)
f = list(results)[0]
self.assertTrue(isinstance(f, self.Family))
self.assertEquals(f.id, self.family.id)
def test_search_by_expression_genus_eq_1match(self):
mapper_search = search.get_strategy('MapperSearch')
self.assertTrue(isinstance(mapper_search, search.MapperSearch))
# search for genus by domain
results = mapper_search.search('gen=genus1', self.session)
self.assertEquals(len(results), 1)
g = list(results)[0]
self.assertTrue(isinstance(g, self.Genus))
self.assertEqual(g.id, self.genus.id)
def test_canfindgenusfromfamily(self):
'can find genus from family'
mapper_search = search.get_strategy('MapperSearch')
results = mapper_search.search('genus where genus.family=family2')
print dir(plants)
print 1, results, type(results)
print 2, results.statement
print 3, results.statement.query.filter.express(self.session)
self.assertEqual(str(results.statement), "SELECT * FROM genus WHERE (genus.family = 'family2')")
def test_canuselogicaloperators(self):
'can use logical operators'
mapper_search = search.get_strategy('MapperSearch')
results = mapper_search.search(
'species where species.genus=genus1 or species.sp=name and species.genus.family.family=name'
)
self.assertEqual(
str(results.statement),
"SELECT * FROM species WHERE ((species.genus = 'genus1') OR ((species.sp = 'name') AND (species.genus.family.family = 'name')))"
)
def test_canfindgenusfromfamily(self):
'can find genus from family'
mapper_search = search.get_strategy('MapperSearch')
results = mapper_search.search('genus where genus.family=family2')
print dir(plants)
print 1, results, type(results)
print 2, results.statement
print 3, results.statement.query.filter.express(self.session)
self.assertEqual(
str(results.statement),
"SELECT * FROM genus WHERE (genus.family = 'family2')")
def test_search_by_query22(self):
"query with MapperSearch, joined tables, multiple predicates"
# test does not depend on plugin functionality
Family = self.Family
Genus = self.Genus
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"genus3")
self.session.add_all([family2, g2, f3, g3])
self.session.commit()
mapper_search = search.get_strategy("MapperSearch")
self.assertTrue(isinstance(mapper_search, search.MapperSearch))
s = "genus where genus=genus2 AND family.family=fam3"
results = mapper_search.search(s, self.session)
self.assertEqual(len(results), 0)
s = "genus where genus=genus3 AND family.family=fam3"
results = mapper_search.search(s, self.session)
self.assertEqual(len(results), 1)
g0 = list(results)[0]
self.assertTrue(isinstance(g0, Genus))
self.assertEqual(g0.id, g3.id)
s = 'genus where family.family="Orchidaceae" AND family.qualifier=""'
results = mapper_search.search(s, self.session)
r = list(results)
self.assertEqual(r, [])
s = 'genus where family.family=fam3 AND family.qualifier=""'
results = mapper_search.search(s, self.session)
self.assertEqual(results, set([]))
# sqlite3 stores None as the empty string.
s = 'genus where family.qualifier=""'
results = mapper_search.search(s, self.session)
self.assertEqual(results, set([g2]))
# test where the column is ambiguous so make sure we choose
# the right one, in this case we want to make sure we get the
# qualifier on the family and not the genus
s = (
'plant where accession.species.genus.family.family="Orchidaceae" '
'AND accession.species.genus.family.qualifier=""'
)
results = mapper_search.search(s, self.session)
self.assertEqual(results, set([]))
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 init(cls):
if 'GardenPlugin' in pluginmgr.plugins:
species_context_menu.insert(1, add_accession_action)
vernname_context_menu.insert(1, add_accession_action)
mapper_search = search.get_strategy('MapperSearch')
mapper_search.add_meta(('family', 'fam'), Family, ['family'])
SearchView.row_meta[Family].set(children="genera",
infobox=FamilyInfoBox,
context_menu=family_context_menu)
mapper_search.add_meta(('genus', 'gen'), Genus, ['genus'])
SearchView.row_meta[Genus].set(children="species",
infobox=GenusInfoBox,
context_menu=genus_context_menu)
from functools import partial
search.add_strategy(SynonymSearch)
mapper_search.add_meta(('species', 'sp'), Species,
['sp', 'sp2', 'infrasp1', 'infrasp2',
'infrasp3', 'infrasp4'])
SearchView.row_meta[Species].set(
children=partial(db.natsort, 'accessions'),
infobox=SpeciesInfoBox,
context_menu=species_context_menu)
mapper_search.add_meta(('vernacular', 'vern', 'common'),
VernacularName, ['name'])
SearchView.row_meta[VernacularName].set(
children=partial(db.natsort, 'species.accessions'),
infobox=VernacularNameInfoBox,
context_menu=vernname_context_menu)
mapper_search.add_meta(('geography', 'geo'), Geography, ['name'])
SearchView.row_meta[Geography].set(children=get_species_in_geography)
## now it's the turn of the DefaultView
logger.debug('PlantsPlugin::init, registering splash info box')
DefaultView.infoboxclass = SplashInfoBox
if bauble.gui is not None:
bauble.gui.add_to_insert_menu(FamilyEditor, _('Family'))
bauble.gui.add_to_insert_menu(GenusEditor, _('Genus'))
bauble.gui.add_to_insert_menu(SpeciesEditorMenuItem, _('Species'))
if sys.platform == 'win32':
# TODO: for some reason using the cross as the hybrid
# character doesn't work on windows
Species.hybrid_char = 'x'
def init(cls):
if 'GardenPlugin' in pluginmgr.plugins:
species_context_menu.insert(1, add_accession_action)
vernname_context_menu.insert(1, add_accession_action)
mapper_search = search.get_strategy('MapperSearch')
mapper_search.add_meta(('family', 'fam'), Family, ['family'])
SearchView.row_meta[Family].set(children="genera",
infobox=FamilyInfoBox,
context_menu=family_context_menu)
mapper_search.add_meta(('genus', 'gen'), Genus, ['genus'])
SearchView.row_meta[Genus].set(children="species",
infobox=GenusInfoBox,
context_menu=genus_context_menu)
from functools import partial
search.add_strategy(SynonymSearch)
mapper_search.add_meta(
('species', 'sp'), Species,
['sp', 'sp2', 'infrasp1', 'infrasp2', 'infrasp3', 'infrasp4'])
SearchView.row_meta[Species].set(children=partial(
db.natsort, 'accessions'),
infobox=SpeciesInfoBox,
context_menu=species_context_menu)
mapper_search.add_meta(('vernacular', 'vern', 'common'),
VernacularName, ['name'])
SearchView.row_meta[VernacularName].set(
children=partial(db.natsort, 'species.accessions'),
infobox=VernacularNameInfoBox,
context_menu=vernname_context_menu)
mapper_search.add_meta(('geography', 'geo'), Geography, ['name'])
SearchView.row_meta[Geography].set(children=get_species_in_geography)
## now it's the turn of the DefaultView
logger.debug('PlantsPlugin::init, registering splash info box')
DefaultView.infoboxclass = SplashInfoBox
if bauble.gui is not None:
bauble.gui.add_to_insert_menu(FamilyEditor, _('Family'))
bauble.gui.add_to_insert_menu(GenusEditor, _('Genus'))
bauble.gui.add_to_insert_menu(SpeciesEditorMenuItem, _('Species'))
if sys.platform == 'win32':
# TODO: for some reason using the cross as the hybrid
# character doesn't work on windows
Species.hybrid_char = 'x'
def test_search_by_query22(self):
"query with MapperSearch, joined tables, multiple predicates"
# test does not depend on plugin functionality
Family = self.Family
Genus = self.Genus
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'genus3')
self.session.add_all([family2, g2, f3, g3])
self.session.commit()
mapper_search = search.get_strategy('MapperSearch')
self.assertTrue(isinstance(mapper_search, search.MapperSearch))
s = 'genus where epithet=genus2 AND family.epithet=fam3'
results = mapper_search.search(s, self.session)
self.assertEqual(len(results), 0)
s = 'genus where epithet=genus3 AND family.epithet=fam3'
results = mapper_search.search(s, self.session)
self.assertEqual(len(results), 1)
g0 = list(results)[0]
self.assertTrue(isinstance(g0, Genus))
self.assertEqual(g0.id, g3.id)
s = 'genus where family.epithet="Orchidaceae" AND family.aggregate=""'
results = mapper_search.search(s, self.session)
r = list(results)
self.assertEqual(r, [])
s = 'genus where family.epithet=fam3 AND family.aggregate=""'
results = mapper_search.search(s, self.session)
self.assertEqual(results, set([]))
# sqlite3 stores None as the empty string.
s = 'genus where family.aggregate=""'
results = mapper_search.search(s, self.session)
self.assertEqual(results, set([g2]))
# test where the column is ambiguous so make sure we choose
# the right one, in this case we want to make sure we get the
# aggregate on the family and not the genus
s = 'plant where accession.species.genus.family.epithet="Orchidaceae" '\
'AND accession.species.genus.family.aggregate=""'
results = mapper_search.search(s, self.session)
self.assertEqual(results, set([]))
def init(cls):
if 'GardenPlugin' in pluginmgr.plugins:
species_context_menu.insert(1, add_accession_action)
vernname_context_menu.insert(1, add_accession_action)
mapper_search = search.get_strategy('MapperSearch')
mapper_search.add_meta(('family', 'fam'), Family, ['family'])
SearchView.view_meta[Family].set(children="genera",
infobox=FamilyInfoBox,
context_menu=family_context_menu,
markup_func=family_markup_func)
mapper_search.add_meta(('genus', 'gen'), Genus, ['genus'])
SearchView.view_meta[Genus].set(children="species",
infobox=GenusInfoBox,
context_menu=genus_context_menu,
markup_func=genus_markup_func)
search.add_strategy(SynonymSearch)
mapper_search.add_meta(
('species', 'sp'), Species,
['sp', 'sp2', 'infrasp1', 'infrasp2', 'infrasp3', 'infrasp4'])
SearchView.view_meta[Species].set(children=species_get_kids,
infobox=SpeciesInfoBox,
context_menu=species_context_menu,
markup_func=species_markup_func)
mapper_search.add_meta(('vernacular', 'vern', 'common'),
VernacularName, ['name'])
SearchView.view_meta[VernacularName].set(
children=vernname_get_kids,
infobox=VernacularNameInfoBox,
context_menu=vernname_context_menu,
markup_func=vernname_markup_func)
mapper_search.add_meta(('geography', 'geo'), Geography, ['name'])
SearchView.view_meta[Geography].set(children=get_species_in_geography)
if bauble.gui is not None:
bauble.gui.add_to_insert_menu(FamilyEditor, _('Family'))
bauble.gui.add_to_insert_menu(GenusEditor, _('Genus'))
bauble.gui.add_to_insert_menu(SpeciesEditorMenuItem, _('Species'))
if sys.platform == 'win32':
# TODO: for some reason using the cross as the hybrid
# character doesn't work on windows
Species.hybrid_char = 'x'
def init(cls):
if 'GardenPlugin' in pluginmgr.plugins:
species_context_menu.insert(1, add_accession_action)
vernname_context_menu.insert(1, add_accession_action)
mapper_search = search.get_strategy('MapperSearch')
mapper_search.add_meta(('family', 'fam'), Family, ['family'])
SearchView.view_meta[Family].set(children="genera",
infobox=FamilyInfoBox,
context_menu=family_context_menu,
markup_func=family_markup_func)
mapper_search.add_meta(('genus', 'gen'), Genus, ['genus'])
SearchView.view_meta[Genus].set(children="species",
infobox=GenusInfoBox,
context_menu=genus_context_menu,
markup_func=genus_markup_func)
search.add_strategy(SynonymSearch)
mapper_search.add_meta(('species', 'sp'), Species,
['sp', 'sp2', 'infrasp1', 'infrasp2',
'infrasp3', 'infrasp4'])
SearchView.view_meta[Species].set(children=species_get_kids,
infobox=SpeciesInfoBox,
context_menu=species_context_menu,
markup_func=species_markup_func)
mapper_search.add_meta(('vernacular', 'vern', 'common'),
VernacularName, ['name'])
SearchView.view_meta[VernacularName].set(
children=vernname_get_kids,
infobox=VernacularNameInfoBox,
context_menu=vernname_context_menu,
markup_func=vernname_markup_func)
mapper_search.add_meta(('geography', 'geo'), Geography, ['name'])
SearchView.view_meta[Geography].set(children=get_species_in_geography)
if bauble.gui is not None:
bauble.gui.add_to_insert_menu(FamilyEditor, _('Family'))
bauble.gui.add_to_insert_menu(GenusEditor, _('Genus'))
bauble.gui.add_to_insert_menu(SpeciesEditorMenuItem, _('Species'))
if sys.platform == 'win32':
# TODO: for some reason using the cross as the hybrid
# character doesn't work on windows
Species.hybrid_char = 'x'
def test_search_by_values(self):
"search by values"
mapper_search = search.get_strategy('MapperSearch')
self.assertTrue(isinstance(mapper_search, search.MapperSearch))
# search for family by family name
results = mapper_search.search('family1', self.session)
self.assertEquals(len(results), 1)
f = list(results)[0]
self.assertEqual(f.id, self.family.id)
# search for genus by genus name
results = mapper_search.search('genus1', self.session)
self.assertEquals(len(results), 1)
g = list(results)[0]
self.assertEqual(g.id, self.genus.id)
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 test_search_by_values(self):
"search by values"
mapper_search = search.get_strategy('MapperSearch')
self.assertTrue(isinstance(mapper_search, search.MapperSearch))
# search for family by family name
results = mapper_search.search('family1', self.session)
self.assertEquals(len(results), 1)
f = list(results)[0]
self.assertEqual(f.id, self.family.id)
# search for genus by genus name
results = mapper_search.search('genus1', self.session)
self.assertEquals(len(results), 1)
g = list(results)[0]
self.assertEqual(g.id, self.genus.id)
def init(cls):
from bauble.view import SearchView
from functools import partial
mapper_search = search.get_strategy('MapperSearch')
mapper_search.add_meta(('tag', 'tags'), Tag, ['tag'])
SearchView.row_meta[Tag].set(children=partial(db.natsort, 'objects'),
context_menu=tag_context_menu)
SearchView.bottom_info[Tag] = {
'page_widget': 'taginfo_scrolledwindow',
'fields_used': ['tag', 'description'],
'glade_name': os.path.join(paths.lib_dir(),
'plugins/tag/tag.glade'),
'name': _('Tags'),
}
if bauble.gui is not None:
_reset_tags_menu()
else:
pass
def init(cls):
from bauble.view import SearchView
from functools import partial
mapper_search = search.get_strategy('MapperSearch')
mapper_search.add_meta(('tag', 'tags'), Tag, ['tag'])
SearchView.row_meta[Tag].set(children=partial(db.natsort, 'objects'),
context_menu=tag_context_menu)
SearchView.bottom_info[Tag] = {
'page_widget': 'taginfo_scrolledwindow',
'fields_used': ['tag', 'description'],
'glade_name': os.path.join(paths.lib_dir(),
'plugins/tag/tag.glade'),
'name': _('Tags'),
}
if bauble.gui is not None:
_reset_tags_menu()
else:
pass
def test_search_by_query_synonyms(self):
"""SynonymSearch strategy gives all synonyms of given taxon."""
Family = self.Family
Genus = self.Genus
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')
g4 = Genus(family=f3, genus=u'Schetti')
self.session.add_all([family2, g2, f3, g3, g4])
g4.accepted = g3
self.session.commit()
mapper_search = search.get_strategy('SynonymSearch')
s = 'Schetti'
results = mapper_search.search(s, self.session)
self.assertEqual(results, [g3])
def test_search_by_query_synonyms_disabled(self):
"""SynonymSearch strategy gives all synonyms of given taxon."""
Family = self.Family
Genus = self.Genus
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')
g4 = Genus(family=f3, epithet=u'Schetti')
self.session.add_all([family2, g2, f3, g3, g4])
g4.accepted = g3
self.session.commit()
prefs.prefs['bauble.search.return_synonyms'] = False
mapper_search = search.get_strategy('SynonymSearch')
s = 'Schetti'
results = mapper_search.search(s, self.session)
self.assertEqual(results, [])
def test_count(self):
mapper_search = search.get_strategy('MapperSearch')
self.assertTrue(isinstance(mapper_search, search.MapperSearch))
s = 'genus where count(species.id) > 3'
results = mapper_search.search(s, self.session)
self.assertEqual(len(results), 0)
s = 'genus where count(species.id) > 2'
results = mapper_search.search(s, self.session)
self.assertEqual(len(results), 1)
result = results.pop()
self.assertEqual(result.id, 1)
s = 'genus where count(species.id) == 2'
results = mapper_search.search(s, self.session)
self.assertEqual(len(results), 1)
result = results.pop()
self.assertEqual(result.id, 2)