def test_init_defaults_duplicates(self):
ma = MapAnnotationI(1)
ma.setMapValue([NamedValue('a', '1'), NamedValue('a', '1')])
with pytest.raises(ValueError) as excinfo:
CanonicalMapAnnotation(ma)
assert str(excinfo.value).startswith('Duplicate ')
def test_init_missing_primary_key(self):
ma = MapAnnotationI(1)
ma.setMapValue([NamedValue('b', '2')])
with pytest.raises(MapAnnotationPrimaryKeyException) as excinfo:
CanonicalMapAnnotation(ma, primary_keys=['a', 'b'])
assert str(excinfo.value).startswith('Missing ')
def test_map_annotation(self):
"""Tests MapAnnotationWrapper.getValue() returns unicode"""
values = [(u'one', u'₹₹'), (u'two', u'¥¥')]
obj = MapAnnotationI()
data = [NamedValue(d[0], d[1]) for d in values]
obj.setMapValue(data)
map_ann = MockConnection(obj).getObject("Annotation", 1)
assert map_ann.getValue() == values
def test_init_defaults_empty(self, ns):
ma = MapAnnotationI(1)
if ns is not None:
ma.setNs(rstring(ns))
cma = CanonicalMapAnnotation(ma)
assert cma.ma is ma
expectedns = ns if ns else ''
assert cma.ns == expectedns
assert cma.kvpairs == []
assert cma.primary is None
assert cma.parents == set()
def test_get_mapann(self):
ma = MapAnnotationI(1)
ma.setMapValue([NamedValue('a', '1')])
cma = CanonicalMapAnnotation(ma, primary_keys=['a'])
cma.add_parent('Parent', 1)
cma.kvpairs.append(('b', '2'))
newma = cma.get_mapann()
assert newma is ma
mv = newma.getMapValue()
assert len(mv) == 2
assert_equal_name_value(mv[0], NamedValue('a', '1'))
assert_equal_name_value(mv[1], NamedValue('b', '2'))
def test_update_existing_mapann(self):
ns1, ns3, mids = self.create_mas()
pks = ['a']
mgr = MapAnnotationManager()
mgr.add_from_namespace_query(self.sf, ns1, pks)
ma4 = MapAnnotationI()
ma4 = MapAnnotationI()
ma4.setNs(wrap(ns1))
ma4.setMapValue([NamedValue('a', '2'), NamedValue('b', '3'), ])
cma = CanonicalMapAnnotation(ma4, pks)
# This should modify ma2
r = mgr.add(cma)
assert r is cma
cmas = mgr.get_map_annotations()
assert len(cmas) == 2
rs = self.update.saveAndReturnArray([c.get_mapann() for c in cmas])
rs = sorted(rs, key=lambda x: unwrap(x.getId()))
assert_equal_map_value(rs[0].getMapValue(), [NamedValue('a', '1')])
assert unwrap(rs[0].getNs()) == ns1
assert_equal_map_value(rs[1].getMapValue(), [
NamedValue('a', '2'), NamedValue('b', '3')])
assert unwrap(rs[1].getNs()) == ns1
def create_map_annotation(
targets, rowkvs, ns=omero.constants.namespaces.NSBULKANNOTATIONS):
ma = MapAnnotationI()
ma.setNs(rstring(ns))
mv = []
for k, vs in rowkvs:
if not isinstance(vs, (tuple, list)):
vs = [vs]
mv.extend(NamedValue(k, str(v)) for v in vs)
ma.setMapValue(mv)
links = []
for target in targets:
otype = target.ice_staticId().split('::')[-1]
link = getattr(omero.model, '%sAnnotationLinkI' % otype)()
link.setParent(target)
link.setChild(ma)
links.append(link)
return links
def create_cmas(self, pk2):
ma1 = MapAnnotationI(1)
ma1.setMapValue([NamedValue('a', '1')])
cma1 = CanonicalMapAnnotation(ma1, primary_keys=['a'])
cma1.add_parent('Parent', 1)
ma2 = MapAnnotationI(2)
ma2.setMapValue([NamedValue('b', '2'), NamedValue('a', '1')])
cma2 = CanonicalMapAnnotation(ma2, primary_keys=[pk2])
cma2.add_parent('Parent', 1)
cma2.add_parent('Parent', 2)
return cma1, cma2
def test_add_parent(self):
ma = MapAnnotationI(1)
cma = CanonicalMapAnnotation(ma)
assert cma.parents == set()
cma.add_parent('A', 1)
assert cma.parents == set([('A', 1)])
cma.add_parent('B', 2)
assert cma.parents == set([('A', 1), ('B', 2)])
with pytest.raises(ValueError) as excinfo:
cma.add_parent('C', '3')
assert str(excinfo.value).startswith('Expected parent')
def test_init_defaults_kvpairs(self, ns):
ma = MapAnnotationI(1)
ma.setMapValue([NamedValue('b', '2'), NamedValue('a', '1')])
if ns is not None:
ma.setNs(rstring(ns))
cma = CanonicalMapAnnotation(ma)
assert cma.ma is ma
expectedns = ns if ns else ''
assert cma.ns == expectedns
assert cma.kvpairs == [('b', '2'), ('a', '1')]
assert cma.primary is None
assert cma.parents == set()
def test_merge(self, reverse):
ma1 = MapAnnotationI(1)
ma1.setMapValue([NamedValue('a', '1')])
cma1 = CanonicalMapAnnotation(ma1, primary_keys=['a'])
cma1.add_parent('Parent', 1)
ma2 = MapAnnotationI(2)
ma2.setMapValue([NamedValue('b', '2'), NamedValue('a', '1')])
cma2 = CanonicalMapAnnotation(ma2, primary_keys=['b'])
cma2.add_parent('Parent', 1)
cma2.add_parent('Parent', 2)
if reverse:
cma2.merge(cma1)
assert cma2.kvpairs == [('b', '2'), ('a', '1')]
assert cma2.parents == set([('Parent', 1), ('Parent', 2)])
assert cma2.primary == ('', frozenset([('b', '2')]))
else:
cma1.merge(cma2)
assert cma1.kvpairs == [('a', '1'), ('b', '2')]
assert cma1.parents == set([('Parent', 1), ('Parent', 2)])
assert cma1.primary == ('', frozenset([('a', '1')]))
def test_init_primary_keys(self, ns, primary_keys):
ma = MapAnnotationI(1)
ma.setNs(rstring(ns))
ma.setMapValue([NamedValue('b', '2'), NamedValue('a', '1')])
cma = CanonicalMapAnnotation(ma, primary_keys=primary_keys)
assert cma.ma is ma
expectedns = ns if ns else ''
assert cma.ns == expectedns
assert cma.kvpairs == [('b', '2'), ('a', '1')]
expectedpks = [('a', '1'), ('b', '2')][:len(primary_keys)]
if primary_keys:
expectedpri = (expectedns, frozenset(expectedpks))
else:
expectedpri = None
assert cma.primary == expectedpri
assert cma.parents == set()
def create_map_annotation(targets,
rowkvs,
ns=omero.constants.namespaces.NSBULKANNOTATIONS):
ma = MapAnnotationI()
ma.setNs(rstring(ns))
mv = []
for k, vs in rowkvs:
if not isinstance(vs, (tuple, list)):
vs = [vs]
mv.extend(NamedValue(k, str(v)) for v in vs)
ma.setMapValue(mv)
links = []
for target in targets:
otype = target.ice_staticId().split('::')[-1]
link = getattr(omero.model, '%sAnnotationLinkI' % otype)()
link.setParent(target)
link.setChild(ma)
links.append(link)
return links
def create_mas(self):
ns1 = self.uuid()
ns3 = self.uuid()
ma1 = MapAnnotationI()
ma1.setNs(wrap(ns1))
ma1.setMapValue([NamedValue('a', '1')])
ma2 = MapAnnotationI()
ma2.setNs(wrap(ns1))
ma2.setMapValue([NamedValue('a', '2')])
ma3 = MapAnnotationI()
ma3.setNs(wrap(ns3))
ma3.setMapValue([NamedValue('a', '1')])
mids = self.update.saveAndReturnIds([ma1, ma2, ma3])
print ns1, ns3, mids
return ns1, ns3, mids
def screen_metadata(client, file, object):
query = client.sf.getQueryService()
update = client.sf.getUpdateService()
name, oid = object.split(":")
do_update = False
query = (
"select x from %s x join fetch x.annotationLinks xal "
"join fetch xal.child where x.id = %d"
)
obj = query.findByQuery(query % (name, long(oid)), None)
ann = None
for link in obj.copyAnnotationLinks():
if isinstance(link.child, MapAnnotationI):
if ann is not None:
raise Exception("2 maps!")
ann = link.child
print "Found map:", ann.id.val
if ann is None:
ann = MapAnnotationI()
ann.setNs(rstring("openmicroscopy.org/omero/client/mapAnnotation"))
ann.setMapValue(list())
obj.linkAnnotation(ann)
do_update = True
print "Creating new map"
old = unwrap(obj.description)
desc = ""
values = dict()
for line in input([file]):
parts = line.strip().split("\t")
key = parts[0]
if len(parts) > 1:
val = parts[1]
else:
val = None
if key == "Study " + P_T:
desc += P_T
desc += "\n"
desc += val
desc += "\n\n"
elif key == E_D:
desc += E_D
desc += "\n"
desc += val
elif key == P_M[0]:
x, y = P_M
values[y] = "%s http://www.ncbi.nlm.nih.gov/pubmed/%s" % (val, val)
elif key == P_D[0]:
x, y = P_D
doi = val.split("dx.doi.org")[-1][1:]
values[y] = "%s %s" % (doi, val)
else:
for x, y in (S_T, I_T, P_A):
if key == x:
values[y] = val.strip('"')
old_values = dict()
for x in ann.getMapValue():
old_values[x.name] = x
for x, y in (S_T, I_T, P_A, P_M, P_D):
if y not in old_values:
ann.getMapValue().append(NamedValue(y, values[y]))
do_update = True
print "found new named value"
elif old_values[y].value != values[y]:
old_values[y].value = values[y]
do_update = True
print "changed named value"
if old != desc:
do_update = True
obj.description = rstring(desc)
else:
print "descriptions match"
if do_update:
print "updating"
update.saveObject(obj)
print values
def add_annotations(o):
'''
Annotation
BasicAnnotation
BooleanAnnotation
BooleanAnnotationI
NumericAnnotation
DoubleAnnotation
DoubleAnnotationI
LongAnnotation
LongAnnotationI
TermAnnotation
TermAnnotationI
TimestampAnnotation
TimestampAnnotationI
ListAnnotation
ListAnnotationI
MapAnnotation
MapAnnotationI
TextAnnotation
CommentAnnotation
CommentAnnotationI
TagAnnotation
TagAnnotationI
XmlAnnotation
XmlAnnotationI
TypeAnnotation
FileAnnotation
FileAnnotationI
'''
annotation = BooleanAnnotationI()
annotation.description = rstring('the_description')
annotation.ns = rstring('boolean_annotation')
annotation.boolValue = rbool(True)
o.linkAnnotation(annotation)
annotation = CommentAnnotationI()
annotation.description = rstring('the_description')
annotation.ns = rstring('comment_annotation')
annotation.textValue = rstring('text_value')
o.linkAnnotation(annotation)
annotation = DoubleAnnotationI()
annotation.description = rstring('the_description')
annotation.ns = rstring('double_annotation')
annotation.doubleValue = rdouble(1.0)
o.linkAnnotation(annotation)
annotation = LongAnnotationI()
annotation.description = rstring('the_description')
annotation.ns = rstring('long_annotation')
annotation.longValue = rlong(1L)
o.linkAnnotation(annotation)
annotation = MapAnnotationI()
annotation.description = rstring('the_description')
annotation.ns = rstring('map_annotation')
annotation.setMapValue([NamedValue('a', '1'), NamedValue('b', '2')])
o.linkAnnotation(annotation)
annotation = TagAnnotationI()
annotation.description = rstring('the_description')
annotation.ns = rstring('tag_annotation')
annotation.textValue = rstring('tag_value')
o.linkAnnotation(annotation)
annotation = TermAnnotationI()
annotation.description = rstring('the_description')
annotation.ns = rstring('term_annotation')
annotation.termValue = rstring('term_value')
o.linkAnnotation(annotation)
annotation = TimestampAnnotationI()
annotation.description = rstring('the_description')
annotation.ns = rstring('timestamp_annotation')
annotation.timeValue = rtime(1)
o.linkAnnotation(annotation)
annotation = XmlAnnotationI()
annotation.description = rstring('the_description')
annotation.ns = rstring('xml_annotation')
annotation.textValue = rstring('<xml_value></xml_value>')
o.linkAnnotation(annotation)
def screen_metadata(client, file, object):
query = client.sf.getQueryService()
update = client.sf.getUpdateService()
name, oid = object.split(":")
do_update = False
query = ("select x from %s x join fetch x.annotationLinks xal "
"join fetch xal.child where x.id = %d")
obj = query.findByQuery(query % (name, long(oid)), None)
ann = None
for link in obj.copyAnnotationLinks():
if isinstance(link.child, MapAnnotationI):
if ann is not None:
raise Exception("2 maps!")
ann = link.child
print "Found map:", ann.id.val
if ann is None:
ann = MapAnnotationI()
ann.setNs(rstring("openmicroscopy.org/omero/client/mapAnnotation"))
ann.setMapValue(list())
obj.linkAnnotation(ann)
do_update = True
print "Creating new map"
old = unwrap(obj.description)
desc = ""
values = dict()
for line in input([file]):
parts = line.strip().split("\t")
key = parts[0]
if len(parts) > 1:
val = parts[1]
else:
val = None
if key == "Study " + P_T:
desc += P_T
desc += "\n"
desc += val
desc += "\n\n"
elif key == E_D:
desc += E_D
desc += "\n"
desc += val
elif key == P_M[0]:
x, y = P_M
values[y] = "%s http://www.ncbi.nlm.nih.gov/pubmed/%s" % (val, val)
elif key == P_D[0]:
x, y = P_D
doi = val.split("dx.doi.org")[-1][1:]
values[y] = "%s %s" % (doi, val)
else:
for x, y in (S_T, I_T, P_A):
if key == x:
values[y] = val.strip('"')
old_values = dict()
for x in ann.getMapValue():
old_values[x.name] = x
for x, y in (S_T, I_T, P_A, P_M, P_D):
if y not in old_values:
ann.getMapValue().append(NamedValue(y, values[y]))
do_update = True
print "found new named value"
elif old_values[y].value != values[y]:
old_values[y].value = values[y]
do_update = True
print "changed named value"
if old != desc:
do_update = True
obj.description = rstring(desc)
else:
print "descriptions match"
if do_update:
print "updating"
update.saveObject(obj)
print values