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_fileset(files):
"""Create a new Fileset from local files."""
fileset = omero.model.FilesetI()
for f in files:
entry = omero.model.FilesetEntryI()
entry.setClientPath(rstring(f))
fileset.addFilesetEntry(entry)
# Fill version info
system, node, release, version, machine, processor = platform.uname()
client_version_info = [
NamedValue('omero.version', omero_version),
NamedValue('os.name', system),
NamedValue('os.version', release),
NamedValue('os.architecture', machine)
]
try:
client_version_info.append(
NamedValue('locale',
locale.getdefaultlocale()[0]))
except:
pass
upload = omero.model.UploadJobI()
upload.setVersionInfo(client_version_info)
fileset.linkJob(upload)
return fileset
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_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_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 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 create_map_annotation(ctx, annotation, target_id, target_type="Project"):
"""Creates a map annotation, uploads it to Omero, and links it to target object"""
# populate new MapAnnotationData object with dictionary
result = ArrayList()
for item in annotation:
# add key:value pairs; both need to be strings
result.add(NamedValue(str(item), str(annotation[item])))
data = MapAnnotationData()
data.setContent(result)
data.setDescription("Demo Example")
#Use the following namespace if you want the annotation to be editable in the webclient and insight
data.setNameSpace(MapAnnotationData.NS_CLIENT_CREATED)
dm = gateway.getFacility(DataManagerFacility)
target_obj = None
# use the appropriate target DataObject and attach the MapAnnotationData object to it
if target_type == "Project":
target_obj = ProjectData(ProjectI(target_id, False))
elif target_type == "Dataset":
target_obj = DatasetData(DatasetI(target_id, False))
elif target_type == "Image":
target_obj = ImageData(ImageI(target_id, False))
result = dm.attachAnnotation(ctx, data, target_obj)
return result
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 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 decode(self, data):
v = super(MapAnnotationDecoder, self).decode(data)
map_value = data.get('Value', list())
map_value = [
NamedValue(key, value) for key, value in map_value
]
v.setMapValue(map_value)
return v
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 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 get_mapann(self):
"""
Update and return an omero.model.MapAnnotation with merged/combined
fields
"""
mv = [NamedValue(*kv) for kv in self.kvpairs]
self.ma.setMapValue(mv)
self.ma.setNs(rstring(self.ns))
return self.ma
def _dict_to_map_annotation(dictionary, description=None):
result = []
for element in dictionary:
result.append(NamedValue(element, dictionary[element]))
map_data = MapAnnotationData()
map_data.setContent(result)
if description:
map_data.setDescription(description)
map_data.setNameSpace(MapAnnotationData.NS_CLIENT_CREATED)
return map_data
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_add_from_namespace_query(self):
ns1, ns3, mids = self.create_mas()
pks = ['a']
mgr = MapAnnotationManager()
mgr.add_from_namespace_query(self.sf, ns1, pks)
assert len(mgr.mapanns) == 2
pk1 = (ns1, frozenset([('a', '1')]))
pk2 = (ns1, frozenset([('a', '2')]))
assert len(mgr.mapanns) == 2
assert pk1 in mgr.mapanns
assert pk2 in mgr.mapanns
cma1 = mgr.mapanns[pk1]
assert cma1.kvpairs == [('a', '1')]
assert cma1.parents == set()
mv1 = cma1.get_mapann().getMapValue()
assert_equal_map_value(mv1, [NamedValue('a', '1')])
cma2 = mgr.mapanns[pk2]
assert cma2.kvpairs == [('a', '2')]
assert cma2.parents == set()
mv2 = cma2.get_mapann().getMapValue()
assert_equal_map_value(mv2, [NamedValue('a', '2')])
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 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
