def testAllParametersChecked(self):
params = omero.grid.JobParams()
param = omero.grid.Param()
param.prototype = rlist(rstring(""))
params.inputs = {"a": param}
input = rlist(rstring("foo"), rint(1))
inputs = {"a": input}
assert not "" == validate_inputs(params, inputs)
def testRListRList(self):
params = omero.grid.JobParams()
param = omero.grid.Param()
param.prototype = rlist(rlist())
params.inputs = {"a": param}
input = rlist(rlist(rint(1), rstring("a")))
inputs = {"a": input}
assert "" == validate_inputs(params, inputs)
def testRListRList(self):
params = omero.grid.JobParams()
param = omero.grid.Param()
param.prototype = rlist(rlist())
params.inputs = {"a": param}
input = rlist(rlist(rint(1), rstring("a")))
inputs = {"a": input}
assert "" == validate_inputs(params, inputs)
def testAllParametersChecked(self):
params = omero.grid.JobParams()
param = omero.grid.Param()
param.prototype = rlist(rstring(""))
params.inputs = {"a": param}
input = rlist(rstring("foo"), rint(1))
inputs = {"a": input}
assert not "" == validate_inputs(params, inputs)
def testRListRListRString(self):
params = omero.grid.JobParams()
param = omero.grid.Param()
param.prototype = rlist(rlist(rstring("")))
params.inputs = {"a": param}
input = rlist(rlist(rstring("a")))
inputs = {"a": input}
assert "" == validate_inputs(params, inputs)
input.val[0].val.insert(0, rint(1))
assert not "" == validate_inputs(params, inputs)
def testRListRListRString(self):
params = omero.grid.JobParams()
param = omero.grid.Param()
param.prototype = rlist(rlist(rstring("")))
params.inputs = {"a": param}
input = rlist(rlist(rstring("a")))
inputs = {"a": input}
assert "" == validate_inputs(params, inputs)
input.val[0].val.insert(0, rint(1))
assert not "" == validate_inputs(params, inputs)
def testGetAttrWorks(self):
rbool(True).val
rdouble(0.0).val
rfloat(0.0).val
rint(0).val
rlong(0).val
rtime(0).val
rinternal(None).val
robject(None).val
rstring("").val
rclass("").val
rarray().val
rlist().val
rset().val
rmap().val
def testGetAttrWorks(self):
rbool(True).val
rdouble(0.0).val
rfloat(0.0).val
rint(0).val
rlong(0).val
rtime(0).val
rinternal(None).val
robject(None).val
rstring("").val
rclass("").val
rarray().val
rlist().val
rset().val
rmap().val
def testListCreationEqualsHash(self):
list_notnull1 = rlist(ids)
list_notnull2 = rlist(ids)
# Equals based on content
assert list_notnull1 == list_notnull2
# But content is copied!
assert not list_notnull1.getValue() is list_notnull2.getValue()
list_null1 = rlist()
list_null2 = rlist(None)
list_null3 = rlist(*[])
# All different since the contents are mutable.
assert list_null1 is not list_notnull1
assert list_null1 is not list_null2
assert list_null1 is not list_null3
def testListCreationEqualsHash(self):
list_notnull1 = rlist(ids)
list_notnull2 = rlist(ids)
# Equals based on content
assert list_notnull1 == list_notnull2
# But content is copied!
assert not list_notnull1.getValue() is list_notnull2.getValue()
list_null1 = rlist()
list_null2 = rlist(None)
list_null3 = rlist(*[])
# All different since the contents are mutable.
assert list_null1 is not list_notnull1
assert list_null1 is not list_null2
assert list_null1 is not list_null3
def populate_test_data(client, cli, remote_conn):
image_ids = []
query_service = client.getSession().getQueryService()
params = om_sys.Parameters()
params.map = {}
for dataset_name in DATASET_NAMES:
dataset_id = create_dataset(cli, dataset_name, 'Test dataset')
print(dataset_id)
# get created dataset object
dataset_ids = map(
rtypes.rlong,
[dataset_id
]) # wrap dataset ID in list since it's only one ID to map
params.map = {'dids': rtypes.rlist(dataset_ids)}
datasets = query_service.findAllByQuery(DATASETS_BY_ID_QUERY, params)
for i in range(0, 4):
tag_label = random.choice(TAG_LABELS)
tag_desc = random.choice(TAG_DESCRIPTIONS)
tag_id = create_tag(cli, tag_label, tag_desc)
update_object_tag(client, datasets, rtypes.rlong(tag_id))
try:
image_ids = import_image(IMAGE_PATH, remote_conn, dataset_id,
client.getSessionId())
# get created image object
image_ids = map(
rtypes.rlong, image_ids
) # wrap image ID in list since it's only one ID to map
params.map = {'iids': rtypes.rlist(image_ids)}
images = query_service.findAllByQuery(IMAGES_BY_ID_QUERY, params)
for image in images:
for i in range(0, 4):
tag_label = random.choice(TAG_LABELS)
tag_desc = random.choice(TAG_DESCRIPTIONS)
tag_id = create_tag(cli, tag_label, tag_desc)
update_object_tag(client, [image], rtypes.rlong(tag_id))
except Exception as e:
print(IMAGE_PATH)
print(image_ids)
def getAnnotationsForObjects(obj_type, oids):
# Get the images that match
hql = "select distinct link.child.id from %sAnnotationLink link " \
"where link.parent.id in (:oids)" % obj_type
params = Parameters()
params.map = {}
params.map["oids"] = rlist([rlong(o) for o in oids])
qs = conn.getQueryService()
return [result[0].val for result in qs.projection(hql,params, service_opts)]
def _set_parameters(mapann_ns=[],
mapann_names=[],
mapann_query=None,
mapann_value=None,
params=None,
experimenter_id=-1,
page=1,
limit=settings.PAGE):
if params is None:
params = omero.sys.ParametersI()
# Paging
if page is not None and page > 0:
params.page((page - 1) * limit, limit)
where_clause = []
if mapann_names is not None and len(mapann_names) > 0:
manlist = [rstring(str(n)) for n in mapann_names]
params.add("filter", rlist(manlist))
where_clause.append('mv.name in (:filter)')
if mapann_ns is not None and len(mapann_ns) > 0:
mnslist = [rstring(str(n)) for n in mapann_ns]
params.add("ns", rlist(mnslist))
where_clause.append('a.ns in (:ns)')
if experimenter_id is not None and experimenter_id != -1:
params.addId(experimenter_id)
where_clause.append('a.details.owner.id = :id')
if mapann_query:
# query starts from search terms
params.addString("query", rstring("%s%%" % str(mapann_query).lower()))
where_clause.append('lower(mv.value) like :query')
if mapann_value:
params.addString("value", mapann_value)
where_clause.append('mv.value = :value')
return params, where_clause
def getObjectsWithAllAnnotations(obj_type, annids):
# Get the images that match
hql = "select link.parent.id from %sAnnotationLink link " \
"where link.child.id in (:oids) " \
"group by link.parent.id " \
"having count (distinct link.child) = %s" % (obj_type, len(annids))
params = Parameters()
params.map = {}
params.map["oids"] = rlist([rlong(o) for o in set(annids)])
qs = conn.getQueryService()
return [x[0].getValue() for x in qs.projection(hql,params,service_opts)]
def test_batch_image_export(self):
sid = super(TestExportScripts, self).get_script(batch_image_export)
assert sid > 0
client, user = self.new_client_and_user()
# x,y,z,c,t
image = self.create_test_image(100, 100, 1, 1, 1, client.getSession())
image_ids = []
image_ids.append(rlong(image.id.val))
args = {"Data_Type": rstring("Image"), "IDs": rlist(image_ids)}
ann = run_script(client, sid, args, "File_Annotation")
c = self.new_client(user=user)
check_file_annotation(c, ann)
def getAnnotationsForObjects(obj_type, oids):
# Get the images that match
hql = "select distinct link.child.id from %sAnnotationLink link " \
"where link.parent.id in (:oids)" % obj_type
params = Parameters()
params.map = {}
params.map["oids"] = rlist([rlong(o) for o in oids])
qs = conn.getQueryService()
return [
result[0].val
for result in qs.projection(hql, params, service_opts)
]
def test1154(self):
uuid = self.root.sf.getAdminService().getEventContext().sessionUuid
### create two users in one group
client_share1, user1 = self.new_client_and_user()
client_share2, user2 = self.new_client_and_user()
## login as user1
share1 = client_share1.sf.getShareService()
update1 = client_share1.sf.getUpdateService()
# create image
img = ImageI()
img.setName(rstring('test1154-img-%s' % (uuid)))
img.setAcquisitionDate(rtime(0))
img = update1.saveAndReturnObject(img)
img.unload()
# create share
description = "my description"
timeout = None
objects = [img]
experimenters = [user2]
guests = []
enabled = True
sid = share1.createShare(description, timeout, objects,experimenters, guests, enabled)
self.assertEquals(1,len(share1.getContents(sid)))
## login as user2
share2 = client_share2.sf.getShareService()
query2 = client_share2.sf.getQueryService()
content = share2.getContents(sid)
self.assertEquals(1,len(share2.getContents(sid)))
# get shared image when share is activated
share2.activate(sid)
p = omero.sys.Parameters()
p.map = {}
p.map["ids"] = rlist([rlong(img.id.val)])
sql = "select im from Image im where im.id in (:ids) order by im.name"
res = query2.findAllByQuery(sql, p)
self.assertEquals(1,len(res))
for e in res:
self.assert_(e.id.val == img.id.val)
def test1154(self):
uuid = self.root.sf.getAdminService().getEventContext().sessionUuid
### create two users in one group
client_share1, user1 = self.new_client_and_user()
client_share2, user2 = self.new_client_and_user()
## login as user1
share1 = client_share1.sf.getShareService()
update1 = client_share1.sf.getUpdateService()
# create image
img = ImageI()
img.setName(rstring('test1154-img-%s' % (uuid)))
img.setAcquisitionDate(rtime(0))
img = update1.saveAndReturnObject(img)
img.unload()
# create share
description = "my description"
timeout = None
objects = [img]
experimenters = [user2]
guests = []
enabled = True
sid = share1.createShare(description, timeout, objects, experimenters,
guests, enabled)
self.assertEquals(1, len(share1.getContents(sid)))
## login as user2
share2 = client_share2.sf.getShareService()
query2 = client_share2.sf.getQueryService()
content = share2.getContents(sid)
self.assertEquals(1, len(share2.getContents(sid)))
# get shared image when share is activated
share2.activate(sid)
p = omero.sys.Parameters()
p.map = {}
p.map["ids"] = rlist([rlong(img.id.val)])
sql = "select im from Image im where im.id in (:ids) order by im.name"
res = query2.findAllByQuery(sql, p)
self.assertEquals(1, len(res))
for e in res:
self.assert_(e.id.val == img.id.val)
def getObjectsWithAllAnnotations(obj_type, annids):
# Get the images that match
hql = "select link.parent.id from %sAnnotationLink link " \
"where link.child.id in (:oids) " \
"group by link.parent.id " \
"having count (distinct link.child) = %s" % (obj_type,
len(annids))
params = Parameters()
params.map = {}
params.map["oids"] = rlist([rlong(o) for o in set(annids)])
qs = conn.getQueryService()
return [
x[0].getValue()
for x in qs.projection(hql, params, service_opts)
]
def get_tag_annos_for_labels(self, tag_labels=None):
anno_list = []
if tag_labels is not None:
c, cli, remote_conn = self.connect_to_remote(
self.USERNAME, self.PASSWORD)
params = om_sys.Parameters()
for tag_label in tag_labels:
tag_rstr_label = rtypes.rstring(tag_label)
params.map = {'anno_text': rtypes.rlist(tag_rstr_label)}
anno_list.extend(
self.find_objects_by_query(c,
TAG_ANNOS_BY_TEXT_VALUES_QUERY,
params))
self.session_exit_condition = True
self.close_remote_connection(c, cli, remote_conn)
return anno_list
def testCanAnnotate(self):
# Users in Private and Read-annotate groups
private_g = self.new_group(perms="rw----")
readann_g = self.new_group(perms="rwra--")
# User 1 is only in private group
client1, user1 = self.new_client_and_user(group=private_g)
# User2 is in read-ann group (default) AND private group
user2 = self.new_user(group=readann_g)
self.add_groups(user2, [private_g])
client2 = self.new_client(user=user2)
# User 1 creates image in Private group...
img = self.make_image(name='ishare_testCanAnnotate', client=client1)
assert not img.details.permissions.isGroupRead()
assert not img.details.permissions.isGroupAnnotate()
# ...Adds it to share
description = "my description"
timeout = None
objects = [img]
experimenters = [user2]
guests = []
enabled = True
share1 = client1.sf.getShareService()
sid = share1.createShare(description, timeout, objects,
experimenters, guests, enabled)
# User 2 logs in, gets image from share
query2 = client2.sf.getQueryService()
p = omero.sys.Parameters()
p.map = {"ids": rlist([rlong(img.id.val)])}
sql = "select im from Image im where im.id in (:ids) order by im.name"
res = query2.findAllByQuery(sql, p, {'omero.share': str(sid)})
assert 1 == len(res)
# User should not be able to annotate private image.
for e in res:
canAnn = e.getDetails().getPermissions().canAnnotate()
assert not canAnn
assert e.id.val == img.id.val
def testCanAnnotate(self):
# Users in Private and Read-annotate groups
private_g = self.new_group(perms="rw----")
readann_g = self.new_group(perms="rwra--")
# User 1 is only in private group
client1, user1 = self.new_client_and_user(group=private_g)
# User2 is in read-ann group (default) AND private group
user2 = self.new_user(group=readann_g)
self.add_groups(user2, [private_g])
client2 = self.new_client(user=user2)
# User 1 creates image in Private group...
img = self.make_image(name='ishare_testCanAnnotate', client=client1)
assert not img.details.permissions.isGroupRead()
assert not img.details.permissions.isGroupAnnotate()
# ...Adds it to share
description = "my description"
timeout = None
objects = [img]
experimenters = [user2]
guests = []
enabled = True
share1 = client1.sf.getShareService()
sid = share1.createShare(description, timeout, objects, experimenters,
guests, enabled)
# User 2 logs in, gets image from share
query2 = client2.sf.getQueryService()
p = omero.sys.Parameters()
p.map = {"ids": rlist([rlong(img.id.val)])}
sql = "select im from Image im where im.id in (:ids) order by im.name"
res = query2.findAllByQuery(sql, p, {'omero.share': str(sid)})
assert 1 == len(res)
# User should not be able to annotate private image.
for e in res:
canAnn = e.getDetails().getPermissions().canAnnotate()
assert not canAnn
assert e.id.val == img.id.val
def test1154(self):
uuid = self.root.sf.getAdminService().getEventContext().sessionUuid
# create two users in one group
client_share1, user1 = self.new_client_and_user()
client_share2, user2 = self.new_client_and_user()
# login as user1
share1 = client_share1.sf.getShareService()
# create image
img = self.make_image(name='test1154-img-%s' % uuid)
# create share
description = "my description"
timeout = None
objects = [img]
experimenters = [user2]
guests = []
enabled = True
sid = share1.createShare(description, timeout, objects,
experimenters, guests, enabled)
assert 1 == len(share1.getContents(sid))
# login as user2
share2 = client_share2.sf.getShareService()
query2 = client_share2.sf.getQueryService()
share2.getContents(sid)
assert 1 == len(share2.getContents(sid))
# get shared image when share is activated
share2.activate(sid)
p = omero.sys.Parameters()
p.map = {"ids": rlist([rlong(img.id.val)])}
sql = "select im from Image im where im.id in (:ids) order by im.name"
res = query2.findAllByQuery(sql, p)
assert 1 == len(res)
for e in res:
assert e.id.val == img.id.val
def test1154(self):
uuid = self.root.sf.getAdminService().getEventContext().sessionUuid
# create two users in one group
client_share1, user1 = self.new_client_and_user()
client_share2, user2 = self.new_client_and_user()
# login as user1
share1 = client_share1.sf.getShareService()
# create image
img = self.make_image(name='test1154-img-%s' % uuid)
# create share
description = "my description"
timeout = None
objects = [img]
experimenters = [user2]
guests = []
enabled = True
sid = share1.createShare(description, timeout, objects, experimenters,
guests, enabled)
assert 1 == len(share1.getContents(sid))
# login as user2
share2 = client_share2.sf.getShareService()
query2 = client_share2.sf.getQueryService()
share2.getContents(sid)
assert 1 == len(share2.getContents(sid))
# get shared image when share is activated
share2.activate(sid)
p = omero.sys.Parameters()
p.map = {"ids": rlist([rlong(img.id.val)])}
sql = "select im from Image im where im.id in (:ids) order by im.name"
res = query2.findAllByQuery(sql, p)
assert 1 == len(res)
for e in res:
assert e.id.val == img.id.val
def update_tag_links(self,
duplicate_tag_ids,
client,
query,
replacement_tag_id,
dry_run=False):
params = om_sys.Parameters()
params.map = {}
anno_ids = map(rtypes.rlong, duplicate_tag_ids)
params.map = {'aids': rtypes.rlist(anno_ids)}
objects_list = self.find_objects_by_query(client, query, params)
object_ids = [i.getId().getValue() for i in objects_list]
logging.info("updating these objects: {}".format(object_ids))
self.update_object_tag(client,
objects_list,
replacement_tag_id,
dry_run=dry_run)
def attributes_by_attributes(conn,
name="Gene Symbol",
value="ASH2L",
ns="openmicroscopy.org/mapr/gene",
ns2="openmicroscopy.org/mapr/phenotype",
name2=None,
sId=None
):
"""
Return a list of neighbours attributes
for given case insensitive attribute value. (Uses the python blitz gateway)
"""
from omero.rtypes import rstring, rlist, unwrap
from omero.sys import ParametersI
params = ParametersI()
params.addString("value", value.lower())
q = (
"select distinct new map( mv.value as value) "
"from Annotation as a "
"join a.mapValue as mv "
"where lower(mv.value) = :value {where_claus}"
)
where_claus = []
if name:
params.addString("name", name)
where_claus.append("and mv.name = :name")
q = q.format(**{'where_claus':" ".join(where_claus)})
values = [v[0]['value'] for v in unwrap(
conn.getQueryService().projection(q, params))]
params = ParametersI()
valuelist = [rstring(unicode(v)) for v in values]
params.add('values', rlist(valuelist))
params.addString("ns", ns)
params.addString("ns2", ns2)
q = (
"select distinct new map("
"mv.name as name, "
"mv.value as value, "
"mv2.name as name2, "
"mv2.value as value2) "
"from Image as i "
"join i.annotationLinks as ial "
"join i.annotationLinks as ial2 "
"join ial.child as a "
"join a.mapValue as mv "
"join ial2.child as a2 "
"join a2.mapValue as mv2 "
"where a.ns = :ns and a2.ns = :ns2 "
"and mv.value in (:values) {where_claus} "
)
where_claus = []
if name:
params.addString("name", name)
where_claus.append("and mv.name = :name")
if name2:
params.addString("name2", name2)
where_claus.append("and mv2.name = :name2")
q = q.format(**{'where_claus':" ".join(where_claus)})
if sId != None:
q = q + ("and i in (select image from WellSample "
"where well.plate in "
"(select child from ScreenPlateLink where parent.id = {sId}))")
screenidList = []
screenidList.append(str(sId))
q = q.format(**{'sId':" ".join(screenidList)})
res = {}
for r in unwrap(conn.getQueryService().projection(q, params)):
r = r[0]
try:
res[(r['name'], r['value'])].append((r['name2'], r['value2']))
except KeyError:
res[(r['name'], r['value'])] = [(r['name2'], r['value2'])]
return res
def __init__(self,
name,
optional=True,
out=False,
description=None,
default=None,
**kwargs):
# Non-Param attributes
omero.grid.Param.__init__(self)
# Non-Param attributes
self._name = name
self._in = True
self._out = out
# Other values will be filled in by the kwargs
# Mostly leaving these for backwards compatibility
self.description = description
self.optional = optional
# Assign all the kwargs
for k, v in list(kwargs.items()):
if not hasattr(self, k):
TYPE_LOG.warn("Unknown property: %s", k)
setattr(self, k, v)
_DEF = self.__get(self.PROTOTYPE_DEFAULT, False)
_FUN = self.__get(self.PROTOTYPE_FUNCTION)
_MAX = self.__get(self.PROTOTYPE_MAX)
_MIN = self.__get(self.PROTOTYPE_MIN)
_VAL = self.__get(self.PROTOTYPE_VALUES)
# Someone specifically set the prototype, then
# we assume that useDefault should be True
# For whatever reason, inheritance isn't working.
if default is not None:
newfunc = _FUN
newdefault = default
if isinstance(self, List):
if isinstance(default, (list, tuple)):
newdefault = wrap(default).val
elif isinstance(default, omero.RCollection):
newfunc = lambda x: x
elif isinstance(default, omero.RType):
default = [default]
else:
newfunc = lambda x: x
newdefault = rlist([rtype(default)])
self.useDefault = True
self.prototype = newfunc(newdefault)
else:
if not callable(_FUN):
raise ValueError("Bad prototype function: %s" % _FUN)
# To prevent weirdness, if the class default is
# callable, we'll assume its a constructor and
# create a new one to prevent modification.
try:
_def = _DEF()
except TypeError:
_def = _DEF
self.prototype = _FUN(_def)
# The following use wrap to guarantee that an rtype is present
if self.min is not None:
if _MIN is None:
self.min = _FUN(self.min)
else:
self.min = _MIN(self.min)
if self.max is not None:
if _MAX is None:
self.max = _FUN(self.max)
else:
self.max = _MAX(self.max)
if self.values is not None:
if _VAL is None:
self.values = wrap(self.values)
else:
self.values = _VAL(self.values)
# Now if useDefault has been set, either manually, or
# via setting default="..." we check that the default
# value matches a value if present
if self.values is not None and self.values and self.useDefault:
if isinstance(self.prototype, omero.RCollection):
test = unwrap(self.prototype.val[0])
else:
test = unwrap(self.prototype)
values = unwrap(self.values)
if test not in values:
raise ValueError("%s is not in %s" % (test, values))
def test1172(self):
uuid = self.root.sf.getAdminService().getEventContext().sessionUuid
share = self.root.sf.getShareService()
query = self.root.sf.getQueryService()
update = self.root.sf.getUpdateService()
### create user
client_share1, user1 = self.new_client_and_user()
#create dataset with image
#dataset with image
ds = omero.model.DatasetI()
ds.setName(rstring("dataset-%s" % (uuid)))
ds = update.saveAndReturnObject(ds)
ds.unload()
# create image
img = ImageI()
img.setName(rstring('test-img in dataset-%s' % (uuid)))
img.setAcquisitionDate(rtime(0))
img = update.saveAndReturnObject(img)
img.unload()
dil = DatasetImageLinkI()
dil.setParent(ds)
dil.setChild(img)
dil = update.saveAndReturnObject(dil)
dil.unload()
# create share by root
items = list()
ms = list()
p = omero.sys.Parameters()
p.map = {}
p.map["oid"] = ds.id
sql = "select ds from Dataset ds join fetch ds.details.owner join fetch ds.details.group " \
"left outer join fetch ds.imageLinks dil left outer join fetch dil.child i " \
"where ds.id=:oid"
items.extend(query.findAllByQuery(sql, p))
self.assertEquals(1, len(items))
#members
p.map["eid"] = rlong(user1.id.val)
sql = "select e from Experimenter e where e.id =:eid order by e.omeName"
ms = query.findAllByQuery(sql, p)
sid = share.createShare(("test-share-%s" % uuid),
rtime(long(time.time() * 1000 + 86400)), items,
ms, [], True)
# USER RETRIEVAL
## login as user1
share1 = client_share1.sf.getShareService()
query1 = client_share1.sf.getQueryService()
cntar1 = client_share1.sf.getContainerService()
content = share1.getContents(sid)
# Content now contains just the dataset with nothing loaded
self.assertEquals(1, len(content))
# get shared dataset and image when share is activated
share1.activate(sid)
#retrieve dataset
p = omero.sys.Parameters()
p.map = {}
p.map["ids"] = rlist([ds.id])
sql = "select ds from Dataset ds join fetch ds.details.owner join fetch ds.details.group " \
"left outer join fetch ds.imageLinks dil left outer join fetch dil.child i " \
"where ds.id in (:ids) order by ds.name"
try:
res1 = query1.findAllByQuery(sql, p)
self.fail("This should throw an exception")
except:
pass
#
# Now we add all the other elements to the share to prevent
# the security violation
#
# Not working imgs = cntar.getImages("Dataset",[ds.id.val], None)
img = query.findByQuery(
"select i from Image i join fetch i.datasetLinks dil join dil.parent d where d.id = %s "
% ds.id.val, None)
self.assert_(img)
share.addObject(sid, img)
share.addObjects(sid, img.copyDatasetLinks())
self.assertEquals(3, len(share.getContents(sid)))
#
# And try again to load them
#
share1.activate(sid)
res1 = query1.findAllByQuery(sql, p)
self.assert_(len(res1) == 1)
for e in res1:
self.assert_(e.id.val == ds.id.val)
# retrieve only image
p = omero.sys.Parameters()
p.map = {}
p.map["oid"] = rlong(img.id)
sql = "select im from Image im " \
"where im.id=:oid order by im.name"
res2 = query1.findByQuery(sql, p)
self.assert_(res2.id.val == img.id.val)
def test1172(self):
uuid = self.root.sf.getAdminService().getEventContext().sessionUuid
share = self.root.sf.getShareService()
query = self.root.sf.getQueryService()
# create user
client_share1, user1 = self.new_client_and_user()
# create dataset with image
ds = self.make_dataset(name="dataset-%s" % uuid, client=self.root)
img = self.new_image(name='test-img in dataset-%s' % uuid)
self.link(ds, img, client=self.root)
items = list()
p = omero.sys.Parameters()
p.map = {"oid": ds.id}
sql = (
"select ds from Dataset ds "
"join fetch ds.details.owner "
"join fetch ds.details.group "
"left outer join fetch ds.imageLinks dil "
"left outer join fetch dil.child i "
"where ds.id=:oid")
items.extend(query.findAllByQuery(sql, p))
assert 1 == len(items)
# members
p.map["eid"] = rlong(user1.id.val)
sql = ("select e from Experimenter e "
"where e.id =:eid order by e.omeName")
ms = query.findAllByQuery(sql, p)
sid = share.createShare(("test-share-%s" % uuid),
rtime(long(time.time() * 1000 + 86400)),
items, ms, [], True)
# USER RETRIEVAL
# login as user1
share1 = client_share1.sf.getShareService()
query1 = client_share1.sf.getQueryService()
content = share1.getContents(sid)
# Content now contains just the dataset with nothing loaded
assert 1 == len(content)
# get shared dataset and image when share is activated
share1.activate(sid)
# retrieve dataset
p = omero.sys.Parameters()
p.map = {"ids": rlist([ds.id])}
sql = (
"select ds from Dataset ds "
"join fetch ds.details.owner "
"join fetch ds.details.group "
"left outer join fetch ds.imageLinks dil "
"left outer join fetch dil.child i "
"where ds.id in (:ids) order by ds.name")
try:
res1 = query1.findAllByQuery(sql, p)
assert False, "This should throw an exception"
except:
pass
# Now we add all the other elements to the share to prevent
# the security violation
#
# Not working imgs = cntar.getImages("Dataset",[ds.id.val], None)
img = query.findByQuery(
"select i from Image i join fetch i.datasetLinks dil "
"join dil.parent d where d.id = %s " % ds.id.val, None)
assert img
share.addObject(sid, img)
share.addObjects(sid, img.copyDatasetLinks())
assert 3 == len(share.getContents(sid))
# And try again to load them
share1.activate(sid)
res1 = query1.findAllByQuery(sql, p)
assert len(res1) == 1
for e in res1:
assert e.id.val == ds.id.val
# retrieve only image
p = omero.sys.Parameters()
p.map = {"oid": rlong(img.id)}
sql = "select im from Image im " \
"where im.id=:oid order by im.name"
res2 = query1.findByQuery(sql, p)
assert res2.id.val == img.id.val
def addLongs(self, name, longs):
rlongs = rlist([])
for l in longs:
rlongs.val.append(rlong(l))
self.add(name, rlongs)
return self
def __init__(self, name, optional=True, out=False, description=None, default=None, **kwargs):
# Non-Param attributes
omero.grid.Param.__init__(self)
# Non-Param attributes
self._name = name
self._in = True
self._out = out
# Other values will be filled in by the kwargs
# Mostly leaving these for backwards compatibility
self.description = description
self.optional = optional
# Assign all the kwargs
for k, v in kwargs.items():
if not hasattr(self, k):
TYPE_LOG.warn("Unknown property: %s", k)
setattr(self, k, v)
_DEF = self.__get(self.PROTOTYPE_DEFAULT, False)
_FUN = self.__get(self.PROTOTYPE_FUNCTION)
_MAX = self.__get(self.PROTOTYPE_MAX)
_MIN = self.__get(self.PROTOTYPE_MIN)
_VAL = self.__get(self.PROTOTYPE_VALUES)
# Someone specifically set the prototype, then
# we assume that useDefault should be True
# For whatever reason, inheritance isn't working.
if default is not None:
newfunc = _FUN
newdefault = default
if isinstance(self, List):
if isinstance(default, (list, tuple)):
newdefault = wrap(default).val
elif isinstance(default, omero.RCollection):
newfunc = lambda x: x
elif isinstance(default, omero.RType):
default = [default]
else:
newfunc = lambda x: x
newdefault = rlist([rtype(default)])
self.useDefault = True
self.prototype = newfunc(newdefault)
else:
if not callable(_FUN):
raise ValueError("Bad prototype function: %s" % _FUN)
# To prevent weirdness, if the class default is
# callable, we'll assume its a constructor and
# create a new one to prevent modification.
try:
_def = _DEF()
except TypeError:
_def = _DEF
self.prototype = _FUN(_def)
# The following use wrap to guarantee that an rtype is present
if self.min is not None:
if _MIN is None:
self.min = _FUN(self.min)
else:
self.min = _MIN(self.min)
if self.max is not None:
if _MAX is None:
self.max = _FUN(self.max)
else:
self.max = _MAX(self.max)
if self.values is not None:
if _VAL is None:
self.values = wrap(self.values)
else:
self.values = _VAL(self.values)
# Now if useDefault has been set, either manually, or
# via setting default="..." we check that the default
# value matches a value if present
if self.values is not None and self.values and self.useDefault:
if isinstance(self.prototype, omero.RCollection):
test = unwrap(self.prototype.val[0])
else:
test = unwrap(self.prototype)
values = unwrap(self.values)
if test not in values:
raise ValueError("%s is not in %s" % (test, values))
def test3639(self):
uuid = self.client.sf.getAdminService().getEventContext().sessionUuid
group = self.client.sf.getAdminService().getGroup(
self.client.sf.getAdminService().getEventContext().groupId)
update = self.client.sf.getUpdateService()
images = list()
for i in range(0, 5):
img = self.new_image()
img = update.saveAndReturnObject(img)
images.append(img.id.val)
p = omero.sys.Parameters()
p.map = {}
p.map["oids"] = rlist([rlong(s) for s in images])
# create dataset
dataset = omero.model.DatasetI()
dataset.name = rstring('DS-test-2936-%s' % (uuid))
dataset = update.saveAndReturnObject(dataset)
# put image in dataset
for iid in images:
dlink = omero.model.DatasetImageLinkI()
dlink.parent = omero.model.DatasetI(dataset.id.val, False)
dlink.child = omero.model.ImageI(iid, False)
update.saveAndReturnObject(dlink)
# log in as group owner:
client_o, owner = self.new_client_and_user(group=group, admin=True)
query_o = client_o.sf.getQueryService()
handlers = list()
op = dict()
op["/Image"] = "KEEP"
dc = omero.cmd.Delete('/Dataset', long(dataset.id.val), op)
handlers.append(str(client_o.sf.submit(dc)))
imageToDelete = images[2]
images.remove(imageToDelete)
dc2 = omero.cmd.Delete('/Image', long(imageToDelete), {})
handlers.append(str(client_o.sf.submit(dc2)))
def _formatReport(delete_handle):
"""
Added as workaround to the changes made in #3006.
"""
delete_report = delete_handle.getResponse()
rv = []
if isinstance(delete_report, omero.cmd.ERR):
rv.append(str(delete_report))
else:
if delete_report.warning:
rv.append(delete_report.warning)
if len(rv) > 0:
return "; ".join(rv)
return None
failure = list()
in_progress = 0
r = None
while(len(handlers) > 0):
for cbString in handlers:
try:
with pytest.raises(Ice.ObjectNotExistException):
handle = omero.cmd.HandlePrx.checkedCast(
client_o.ic.stringToProxy(cbString))
cb = omero.callbacks.CmdCallbackI(client_o, handle)
if not cb.block(500): # ms.
# No errors possible if in progress(
# (since no response)
print "in progress", _formatReport(handle)
in_progress += 1
else:
rsp = cb.getResponse()
if isinstance(rsp, omero.cmd.ERR):
r = _formatReport(handle)
if r is not None:
failure.append(r)
else:
failure.append("No report!!!")
else:
r = _formatReport(handle)
if r is not None:
failure.append(r)
cb.close(True) # Close handle
handlers.remove(cbString)
except Exception:
if r is not None:
failure.append(traceback.format_exc())
if len(failure) > 0:
assert False, ";".join(failure)
assert not query_o.find('Dataset', dataset.id.val)
def testPassThroughNoneAndRTypes(self):
"""
To prevent having to check for isintance(int,...) or
isintance(RInt,...) all over the place, the static methods
automatically check for acceptable
types and simply pass them through. Similarly, the primitive types all
check for None and return a null RType if necessary.
"""
# Bool
assert None == rbool(None)
assert rbool(True) == rbool(rbool(True))
assert rbool(True) == rbool(1)
assert rbool(False) == rbool(0)
# Double
assert None == rdouble(None)
assert rdouble(0.0) == rdouble(rdouble(0.0))
assert rdouble(0.0) == rdouble(rdouble(0))
assert rdouble(0.0) == rdouble(rdouble("0.0"))
pytest.raises(ValueError, lambda: rdouble("string"))
# Float
assert None == rfloat(None)
assert rfloat(0.0) == rfloat(rfloat(0.0))
assert rfloat(0.0) == rfloat(rfloat(0))
assert rfloat(0.0) == rfloat(rfloat("0.0"))
pytest.raises(ValueError, lambda: rfloat("string"))
# Long
assert None == rlong(None)
assert rlong(0) == rlong(rlong(0))
assert rlong(0) == rlong(rlong(0.0))
assert rlong(0) == rlong(rlong("0"))
pytest.raises(ValueError, lambda: rlong("string"))
# Time
assert None == rtime(None)
assert rtime(0) == rtime(rtime(0))
assert rtime(0) == rtime(rtime(0.0))
assert rtime(0) == rtime(rtime("0"))
pytest.raises(ValueError, lambda: rtime("string"))
# Int
assert None == rint(None)
assert rint(0) == rint(rint(0))
assert rint(0) == rint(rint(0.0))
assert rint(0) == rint(rint("0"))
pytest.raises(ValueError, lambda: rint("string"))
#
# Starting here handling of null is different.
#
# String
assert rstring("") == rstring(None)
assert rstring("a") == rstring(rstring("a"))
assert rstring("0") == rstring(0)
# Class
assert rclass("") == rclass(None)
assert rclass("c") == rclass(rclass("c"))
pytest.raises(ValueError, lambda: rclass(0))
# Internal
internal = omero.Internal()
assert rinternal(None) == rinternal(None)
assert rinternal(internal) == rinternal(rinternal(internal))
pytest.raises(ValueError, lambda: rinternal("string"))
# Object
obj = omero.model.ImageI()
assert robject(None) == robject(None)
assert robject(obj) == robject(robject(obj))
pytest.raises(ValueError, lambda: robject("string"))
#
# Same does not hold for collections
#
# Array
assert rarray([]) == rarray(None)
# assert rarray(obj) == rarray(rarray(obj))
# pytest.raises(ValueError, lambda : rarray("string"))
# List
assert rlist([]) == rlist(None)
# assert rlist(obj) == rlist(rlist(obj))
# pytest.raises(ValueError, lambda : rlist("string"))
# Set
assert rset([]) == rset(None)
# assert rset(obj) == rset(rset(obj))
# pytest.raises(ValueError, lambda : rset("string"))
# Map
assert rmap({}) == rmap(None)
def testUnwrap(self):
# NUMS plain
assert 0 == unwrap(0)
assert 1 == unwrap(1)
assert 0.0 == unwrap(0.0)
assert 1.0 == unwrap(1.0)
# NUMS rtyped
assert 0 == unwrap(rint(0))
assert 0 == unwrap(rlong(0))
assert 1 == unwrap(rint(1))
assert 1 == unwrap(rlong(1))
assert 0.0 == unwrap(rfloat(0.0))
assert 0.0 == unwrap(rdouble(0.0))
assert 1.0 == unwrap(rfloat(1.0))
assert 1.0 == unwrap(rdouble(1.0))
# STRINGS
assert "" == unwrap("")
assert "str" == unwrap("str")
# BOOL
assert True == unwrap(True)
assert False == unwrap(False)
assert True == unwrap(rbool(True))
assert False == unwrap(rbool(False))
# TIME
# Bit odd, do we want the long for time, or transformed?
assert 0 == unwrap(rtime(0))
assert 1 == unwrap(rtime(1))
# CLASS
# same for class, should we map it?
assert "k" == unwrap(rclass("k"))
# INTERNAL
color = omero.Color()
assert color == unwrap(rinternal(color))
# OBJECT
image = omero.model.ImageI()
assert image == unwrap(robject(image))
# COLLECTIONS
# empty
assert [] == unwrap([])
assert {} == unwrap({})
assert set() == unwrap(set())
# plain in collection
assert [1] == unwrap([1])
# rtype in collection
assert [1] == unwrap([rint(1)])
assert {"a": 1} == unwrap({"a": 1})
# plain in rcollection ILLEGAL
# assert [1] == unwrap(rlist([1]))
# assert {"a":1} == unwrap(rmap({"a":1}))
# rtype in rcollection
assert [1] == unwrap(rlist([rint(1)]))
assert {"a": 1} == unwrap(rmap({"a": rint(1)}))
# rtype keys ILLEGAL
# assert {"a":1} == unwrap(rmap({rstring("a"):rint(1)}))
# recursion, ticket:1977
m1 = rmap({"a": rint(1)})
m1.val["m1"] = m1
m2 = {"a": 1}
m2["m1"] = m2
unwrap(m1)
assert m2["a"] == unwrap(m1)["a"]
# Can't compare directly "maximum recursion depth exceeded in cmp"
assert type(m2["m1"]) == type(unwrap(m1)["m1"])
def _set_parameters(mapann_ns=[], mapann_names=[],
mapann_value=None, query=False, case_sensitive=True,
params=None, experimenter_id=-1,
page=None, limit=settings.PAGE):
''' Helper to map ParametersI
@param mapann_ns The Map annotation namespace to filter by.
@type mapann_ns L{string}
@param mapann_names The Map annotation names to filter by.
@type mapann_names L{string}
@param mapann_value The Map annotation value to filter by.
@type mapann_value L{string}
@param query Flag allowing to search for value patters.
@type query L{boolean}
@param params Instance of ParametersI
@type params L{omero.sys.ParametersI}
@param experimenter_id The Experimenter (user) ID to filter by
or -1 for all experimenters
@type experimenter_id L{long}
@param page Page number of results to get. `None` or 0 for no paging
defaults to None
@type page L{long}
@param limit The limit of results per page to get
defaults to the value set in settings.PAGE
@type page L{long}
'''
if params is None:
params = omero.sys.ParametersI()
# Paging
if page is not None and page > 0:
params.page((page-1) * limit, limit)
where_clause = []
if mapann_names is not None and len(mapann_names) > 0:
manlist = [rstring(unicode(n)) for n in mapann_names]
params.add('filter', rlist(manlist))
where_clause.append("mv.name in (:filter)")
if mapann_ns is not None and len(mapann_ns) > 0:
mnslist = [rstring(unicode(n)) for n in mapann_ns]
params.add("ns", rlist(mnslist))
where_clause.append("a.ns in (:ns)")
if experimenter_id is not None and experimenter_id != -1:
params.addId(experimenter_id)
where_clause.append("a.details.owner.id = :id")
if mapann_value:
mapann_value = mapann_value if case_sensitive else mapann_value.lower()
_cwc = 'mv.value' if case_sensitive else 'lower(mv.value)'
if query:
params.addString(
"query",
rstring("%%%s%%" % _escape_chars_like(mapann_value)))
where_clause.append("%s like :query" % _cwc)
else:
params.addString('value', mapann_value)
where_clause.append("%s = :value" % _cwc)
else:
where_clause.append("mv.value != '' ")
return params, where_clause
def discover(self, args):
import omero
ldap = self.__import_ldap__()
c = self.ctx.conn(args)
iconfig = c.sf.getConfigService()
iadmin = c.sf.getAdminService()
iquery = c.sf.getQueryService()
LDAP_PROPERTIES = """
omero.ldap.urls
omero.ldap.username
omero.ldap.password
omero.ldap.base
omero.ldap.user_filter
omero.ldap.user_mapping
omero.ldap.group_filter
omero.ldap.group_mapping
omero.ldap.new_user_group
""".split()
cfg = dict()
for key in LDAP_PROPERTIES:
cfg[key.split(".")[-1]] = iconfig.getConfigValue(key)
urls = args.urls and args.urls or cfg["urls"]
basedn = args.base and args.base or cfg["base"]
for url in urls.split(","):
self.ctx.err("Connecting to %s..." % url)
ld = ldap.initialize(url)
ld.simple_bind_s(cfg['username'], cfg['password'])
user_filter = cfg["user_filter"]
user_mapping = cfg["user_mapping"]
user_mapping = user_mapping.split(",")
omeName_mapping = None
for um in user_mapping:
parts = um.split("=")
if parts[0] == "omeName":
omeName_mapping = parts[1]
from ldap.controls import SimplePagedResultsControl
cookie = ''
# This is the limit for Active Directory, 1000. However
# the LDAP connection has a sizeLimit that overrides
# this value if the page_size exceeds it so it is safe
# to enter pretty much anything here when using paged results.
page_size = 1000
results = []
first = True
page_control = SimplePagedResultsControl(False, page_size, cookie)
while first or page_control.cookie:
first = False
try:
msgid = ld.search_ext(
basedn, ldap.SCOPE_SUBTREE,
user_filter, serverctrls=[page_control]
)
except:
self.ctx.die(1, "Failed to execute LDAP search")
result_type, results, msgid, serverctrls = ld.result3(msgid)
if serverctrls:
page_control.cookie = serverctrls[0].cookie
user_names = set()
user_dns = {}
for dn, entry in results:
omeName = entry[omeName_mapping]
if isinstance(omeName, (list, tuple)):
if len(omeName) == 1:
omeName = omeName[0]
user_names.add(omeName)
user_dns[omeName] = dn
else:
self.ctx.err("Failed to unwrap omeName: %s" %
omeName)
continue
if not user_names:
continue # Early exit!
from omero.rtypes import rlist
from omero.rtypes import rstring
from omero.rtypes import unwrap
params = omero.sys.ParametersI()
params.add("names", rlist([rstring(x) for x in user_names]))
id_names = unwrap(iquery.projection(
"select id, omeName from Experimenter "
"where omeName in (:names)", params))
for eid, omeName in id_names:
try:
olddn = iadmin.lookupLdapAuthExperimenter(eid)
dn = user_dns[omeName]
except omero.ApiUsageException:
continue # Unknown user
if olddn:
if olddn.lower() != dn.lower():
self.ctx.err("Found different DN for %s: %s"
% (omeName, olddn))
else:
self.ctx.dbg("DN already set for %s: %s"
% (omeName, olddn))
else:
if args.commands:
self.ctx.out("%s ldap setdn %s %s"
% (sys.argv[0], omeName, dn))
else:
self.ctx.out("Experimenter:%s\tomeName=%s\t%s"
% (eid, omeName, dn))
def test1172(self):
uuid = self.root.sf.getAdminService().getEventContext().sessionUuid
share = self.root.sf.getShareService()
query = self.root.sf.getQueryService()
# create user
client_share1, user1 = self.new_client_and_user()
# create dataset with image
ds = self.make_dataset(name="dataset-%s" % uuid, client=self.root)
img = self.new_image(name='test-img in dataset-%s' % uuid)
self.link(ds, img, client=self.root)
items = list()
p = omero.sys.Parameters()
p.map = {"oid": ds.id}
sql = ("select ds from Dataset ds "
"join fetch ds.details.owner "
"join fetch ds.details.group "
"left outer join fetch ds.imageLinks dil "
"left outer join fetch dil.child i "
"where ds.id=:oid")
items.extend(query.findAllByQuery(sql, p))
assert 1 == len(items)
# members
p.map["eid"] = rlong(user1.id.val)
sql = ("select e from Experimenter e "
"where e.id =:eid order by e.omeName")
ms = query.findAllByQuery(sql, p)
sid = share.createShare(("test-share-%s" % uuid),
rtime(long(time.time() * 1000 + 86400)), items,
ms, [], True)
# USER RETRIEVAL
# login as user1
share1 = client_share1.sf.getShareService()
query1 = client_share1.sf.getQueryService()
content = share1.getContents(sid)
# Content now contains just the dataset with nothing loaded
assert 1 == len(content)
# get shared dataset and image when share is activated
share1.activate(sid)
# retrieve dataset
p = omero.sys.Parameters()
p.map = {"ids": rlist([ds.id])}
sql = ("select ds from Dataset ds "
"join fetch ds.details.owner "
"join fetch ds.details.group "
"left outer join fetch ds.imageLinks dil "
"left outer join fetch dil.child i "
"where ds.id in (:ids) order by ds.name")
try:
res1 = query1.findAllByQuery(sql, p)
assert False, "This should throw an exception"
except:
pass
# Now we add all the other elements to the share to prevent
# the security violation
#
# Not working imgs = cntar.getImages("Dataset",[ds.id.val], None)
img = query.findByQuery(
"select i from Image i join fetch i.datasetLinks dil "
"join dil.parent d where d.id = %s " % ds.id.val, None)
assert img
share.addObject(sid, img)
share.addObjects(sid, img.copyDatasetLinks())
assert 3 == len(share.getContents(sid))
# And try again to load them
share1.activate(sid)
res1 = query1.findAllByQuery(sql, p)
assert len(res1) == 1
for e in res1:
assert e.id.val == ds.id.val
# retrieve only image
p = omero.sys.Parameters()
p.map = {"oid": rlong(img.id)}
sql = "select im from Image im " \
"where im.id=:oid order by im.name"
res2 = query1.findByQuery(sql, p)
assert res2.id.val == img.id.val
def discover(self, args):
import omero
ldap = self.__import_ldap__()
c = self.ctx.conn(args)
iconfig = c.sf.getConfigService()
iadmin = c.sf.getAdminService()
iquery = c.sf.getQueryService()
LDAP_PROPERTIES = """
omero.ldap.urls
omero.ldap.username
omero.ldap.password
omero.ldap.base
omero.ldap.user_filter
omero.ldap.user_mapping
omero.ldap.group_filter
omero.ldap.group_mapping
omero.ldap.new_user_group
""".split()
cfg = dict()
for key in LDAP_PROPERTIES:
cfg[key.split(".")[-1]] = iconfig.getConfigValue(key)
urls = args.urls and args.urls or cfg["urls"]
basedn = args.base and args.base or cfg["base"]
for url in urls.split(","):
self.ctx.err("Connecting to %s..." % url)
ld = ldap.initialize(url)
ld.simple_bind_s(cfg['username'], cfg['password'])
user_filter = cfg["user_filter"]
user_mapping = cfg["user_mapping"]
user_mapping = user_mapping.split(",")
omeName_mapping = None
for um in user_mapping:
parts = um.split("=")
if parts[0] == "omeName":
omeName_mapping = parts[1]
from ldap.controls import SimplePagedResultsControl
cookie = ''
# This is the limit for Active Directory, 1000. However
# the LDAP connection has a sizeLimit that overrides
# this value if the page_size exceeds it so it is safe
# to enter pretty much anything here when using paged results.
page_size = 1000
results = []
first = True
page_control = SimplePagedResultsControl(False, page_size, cookie)
while first or page_control.cookie:
first = False
try:
msgid = ld.search_ext(basedn,
ldap.SCOPE_SUBTREE,
user_filter,
serverctrls=[page_control])
except:
self.ctx.die(1, "Failed to execute LDAP search")
result_type, results, msgid, serverctrls = ld.result3(msgid)
if serverctrls:
page_control.cookie = serverctrls[0].cookie
user_names = set()
user_dns = {}
for dn, entry in results:
omeName = entry[omeName_mapping]
if isinstance(omeName, (list, tuple)):
if len(omeName) == 1:
omeName = omeName[0]
user_names.add(omeName)
user_dns[omeName] = dn
else:
self.ctx.err("Failed to unwrap omeName: %s" %
omeName)
continue
if not user_names:
continue # Early exit!
from omero.rtypes import rlist
from omero.rtypes import rstring
from omero.rtypes import unwrap
params = omero.sys.ParametersI()
params.add("names", rlist([rstring(x) for x in user_names]))
id_names = unwrap(
iquery.projection(
"select id, omeName from Experimenter "
"where omeName in (:names)", params))
for eid, omeName in id_names:
try:
olddn = iadmin.lookupLdapAuthExperimenter(eid)
dn = user_dns[omeName]
except omero.ApiUsageException:
continue # Unknown user
if olddn:
if olddn.lower() != dn.lower():
self.ctx.err("Found different DN for %s: %s" %
(omeName, olddn))
else:
self.ctx.dbg("DN already set for %s: %s" %
(omeName, olddn))
else:
if args.commands:
self.ctx.out("%s ldap setdn %s %s" %
(sys.argv[0], omeName, dn))
else:
self.ctx.out("Experimenter:%s\tomeName=%s\t%s" %
(eid, omeName, dn))
def test1172(self):
uuid = self.root.sf.getAdminService().getEventContext().sessionUuid
share = self.root.sf.getShareService()
query = self.root.sf.getQueryService()
update = self.root.sf.getUpdateService()
### create user
client_share1, user1 = self.new_client_and_user()
#create dataset with image
#dataset with image
ds = omero.model.DatasetI()
ds.setName(rstring("dataset-%s" % (uuid)))
ds = update.saveAndReturnObject(ds)
ds.unload()
# create image
img = ImageI()
img.setName(rstring('test-img in dataset-%s' % (uuid)))
img.setAcquisitionDate(rtime(0))
img = update.saveAndReturnObject(img)
img.unload()
dil = DatasetImageLinkI()
dil.setParent(ds)
dil.setChild(img)
dil = update.saveAndReturnObject(dil)
dil.unload()
# create share by root
items = list()
ms = list()
p = omero.sys.Parameters()
p.map = {}
p.map["oid"] = ds.id
sql = "select ds from Dataset ds join fetch ds.details.owner join fetch ds.details.group " \
"left outer join fetch ds.imageLinks dil left outer join fetch dil.child i " \
"where ds.id=:oid"
items.extend(query.findAllByQuery(sql, p))
self.assertEquals(1, len(items))
#members
p.map["eid"] = rlong(user1.id.val)
sql = "select e from Experimenter e where e.id =:eid order by e.omeName"
ms = query.findAllByQuery(sql, p)
sid = share.createShare(("test-share-%s" % uuid), rtime(long(time.time()*1000 + 86400)) , items, ms, [], True)
# USER RETRIEVAL
## login as user1
share1 = client_share1.sf.getShareService()
query1 = client_share1.sf.getQueryService()
cntar1 = client_share1.sf.getContainerService()
content = share1.getContents(sid)
# Content now contains just the dataset with nothing loaded
self.assertEquals(1, len(content))
# get shared dataset and image when share is activated
share1.activate(sid)
#retrieve dataset
p = omero.sys.Parameters()
p.map = {}
p.map["ids"] = rlist([ds.id])
sql = "select ds from Dataset ds join fetch ds.details.owner join fetch ds.details.group " \
"left outer join fetch ds.imageLinks dil left outer join fetch dil.child i " \
"where ds.id in (:ids) order by ds.name"
try:
res1 = query1.findAllByQuery(sql, p)
self.fail("This should throw an exception")
except:
pass
#
# Now we add all the other elements to the share to prevent
# the security violation
#
# Not working imgs = cntar.getImages("Dataset",[ds.id.val], None)
img = query.findByQuery("select i from Image i join fetch i.datasetLinks dil join dil.parent d where d.id = %s " % ds.id.val, None)
self.assert_(img)
share.addObject(sid, img)
share.addObjects(sid, img.copyDatasetLinks())
self.assertEquals(3, len(share.getContents(sid)))
#
# And try again to load them
#
share1.activate(sid)
res1 = query1.findAllByQuery(sql, p)
self.assert_(len(res1) == 1)
for e in res1:
self.assert_(e.id.val == ds.id.val)
# retrieve only image
p = omero.sys.Parameters()
p.map = {}
p.map["oid"] = rlong(img.id)
sql = "select im from Image im " \
"where im.id=:oid order by im.name"
res2 = query1.findByQuery(sql, p)
self.assert_(res2.id.val == img.id.val)
def test_batch_roi_export(self, all_planes):
sid = super(TestExportScripts, self).get_script(batch_roi_export)
assert sid > 0
client, user = self.new_client_and_user()
session = client.getSession()
# x,y,z,c,t
size_c = 2
size_z = 3
size_t = 4
image_name = "ROI_image"
label_text = "Shape_Text"
image = self.create_test_image(100,
100,
size_z,
size_c,
size_t,
session,
name=image_name)
# Add 2 Shapes... A Rectangle and Polygon covering same area
polygon = omero.model.PolygonI()
polygon.points = rstring("10,10, 91,10, 91,91, 10,91")
polygon.textValue = rstring(label_text)
rect = omero.model.RectangleI()
rect.x = rdouble(10)
rect.y = rdouble(10)
rect.width = rdouble(81)
rect.height = rdouble(81)
rect.theZ = rint(1)
rect.theT = rint(1)
# ...to an ROI
roi = omero.model.RoiI()
roi.setImage(image)
roi.addShape(polygon)
roi.addShape(rect)
roi = session.getUpdateService().saveAndReturnObject(roi)
shapes = roi.copyShapes()
polygon = shapes[0]
image_ids = []
file_name = "test_batch_roi_export"
image_ids.append(rlong(image.id.val))
channels = [rint(c) for c in range(4)]
args = {
"Data_Type": rstring("Image"),
"IDs": rlist(image_ids),
# Should ignore Channels out of range. 1-based index
"Channels": rlist(channels),
"Export_All_Planes": rbool(all_planes),
"File_Name": rstring(file_name)
}
ann = run_script(client, sid, args, "File_Annotation")
c = self.new_client(user=user)
check_file_annotation(c, ann, file_name="%s.csv" % file_name)
file_id = ann.getValue().getFile().id.val
csv_text = get_file_contents(self.new_client(user=user), file_id)
# Check we have expected number of rows
polygon_planes = size_c
if all_planes:
polygon_planes = size_c * size_z * size_t
# Rows: Header + rect with Z/T set + polygon without Z/T
row_count = 1 + size_c + polygon_planes
assert len(csv_text.split("\n")) == row_count
# Check first 2 rows of csv (except Std dev)
zt = ","
points_min_max_sum_mean = ",,,,"
area = "6561.0"
if all_planes:
zt = "1,1"
points_min_max_sum_mean = "6561,10.0,90.0,328050.0,50.0"
expected = ("image_id,image_name,roi_id,shape_id,type,text,"
"z,t,channel,area (pixels),length (pixels),"
"points,min,max,sum,mean,std_dev,"
"X,Y,Width,Height,RadiusX,RadiusY,X1,Y1,X2,Y2,Points\n"
"%s,\"%s\",%s,%s,polygon,\"%s\",%s,0,%s,,%s,") % (
image.id.val, image_name, roi.id.val, polygon.id.val,
label_text, zt, area, points_min_max_sum_mean)
assert csv_text.startswith(expected)
def testPassThroughNoneAndRTypes(self):
"""
To prevent having to check for isintance(int,...) or
isintance(RInt,...) all over the place, the static methods
automatically check for acceptable
types and simply pass them through. Similarly, the primitive types all
check for None and return a null RType if necessary.
"""
# Bool
assert None == rbool(None)
assert rbool(True) == rbool(rbool(True))
assert rbool(True) == rbool(1)
assert rbool(False) == rbool(0)
# Double
assert None == rdouble(None)
assert rdouble(0.0) == rdouble(rdouble(0.0))
assert rdouble(0.0) == rdouble(rdouble(0))
assert rdouble(0.0) == rdouble(rdouble("0.0"))
pytest.raises(ValueError, lambda: rdouble("string"))
# Float
assert None == rfloat(None)
assert rfloat(0.0) == rfloat(rfloat(0.0))
assert rfloat(0.0) == rfloat(rfloat(0))
assert rfloat(0.0) == rfloat(rfloat("0.0"))
pytest.raises(ValueError, lambda: rfloat("string"))
# Long
assert None == rlong(None)
assert rlong(0) == rlong(rlong(0))
assert rlong(0) == rlong(rlong(0.0))
assert rlong(0) == rlong(rlong("0"))
pytest.raises(ValueError, lambda: rlong("string"))
# Time
assert None == rtime(None)
assert rtime(0) == rtime(rtime(0))
assert rtime(0) == rtime(rtime(0.0))
assert rtime(0) == rtime(rtime("0"))
pytest.raises(ValueError, lambda: rtime("string"))
# Int
assert None == rint(None)
assert rint(0) == rint(rint(0))
assert rint(0) == rint(rint(0.0))
assert rint(0) == rint(rint("0"))
pytest.raises(ValueError, lambda: rint("string"))
#
# Starting here handling of null is different.
#
# String
assert rstring("") == rstring(None)
assert rstring("a") == rstring(rstring("a"))
assert rstring("0") == rstring(0)
# Class
assert rclass("") == rclass(None)
assert rclass("c") == rclass(rclass("c"))
pytest.raises(ValueError, lambda: rclass(0))
# Internal
internal = omero.Internal()
assert rinternal(None) == rinternal(None)
assert rinternal(internal) == rinternal(rinternal(internal))
pytest.raises(ValueError, lambda: rinternal("string"))
# Object
obj = omero.model.ImageI()
assert robject(None) == robject(None)
assert robject(obj) == robject(robject(obj))
pytest.raises(ValueError, lambda: robject("string"))
#
# Same does not hold for collections
#
# Array
assert rarray([]) == rarray(None)
# assert rarray(obj) == rarray(rarray(obj))
# pytest.raises(ValueError, lambda : rarray("string"))
# List
assert rlist([]) == rlist(None)
# assert rlist(obj) == rlist(rlist(obj))
# pytest.raises(ValueError, lambda : rlist("string"))
# Set
assert rset([]) == rset(None)
# assert rset(obj) == rset(rset(obj))
# pytest.raises(ValueError, lambda : rset("string"))
# Map
assert rmap({}) == rmap(None)
def addLongs(self, name, longs):
rlongs = rlist([])
for l in longs:
rlongs.val.append(rlong(l))
self.add(name, rlongs)
return self
def testUnwrap(self):
# NUMS plain
assert 0 == unwrap(0)
assert 1 == unwrap(1)
assert 0.0 == unwrap(0.0)
assert 1.0 == unwrap(1.0)
# NUMS rtyped
assert 0 == unwrap(rint(0))
assert 0 == unwrap(rlong(0))
assert 1 == unwrap(rint(1))
assert 1 == unwrap(rlong(1))
assert 0.0 == unwrap(rfloat(0.0))
assert 0.0 == unwrap(rdouble(0.0))
assert 1.0 == unwrap(rfloat(1.0))
assert 1.0 == unwrap(rdouble(1.0))
# STRINGS
assert "" == unwrap("")
assert "str" == unwrap("str")
# BOOL
assert True == unwrap(True)
assert False == unwrap(False)
assert True == unwrap(rbool(True))
assert False == unwrap(rbool(False))
# TIME
# Bit odd, do we want the long for time, or transformed?
assert 0 == unwrap(rtime(0))
assert 1 == unwrap(rtime(1))
# CLASS
# same for class, should we map it?
assert "k" == unwrap(rclass("k"))
# INTERNAL
color = omero.Color()
assert color == unwrap(rinternal(color))
# OBJECT
image = omero.model.ImageI()
assert image == unwrap(robject(image))
# COLLECTIONS
# empty
assert [] == unwrap([])
assert {} == unwrap({})
assert set() == unwrap(set())
# plain in collection
assert [1] == unwrap([1])
# rtype in collection
assert [1] == unwrap([rint(1)])
assert {"a": 1} == unwrap({"a": 1})
# plain in rcollection ILLEGAL
# assert [1] == unwrap(rlist([1]))
# assert {"a":1} == unwrap(rmap({"a":1}))
# rtype in rcollection
assert [1] == unwrap(rlist([rint(1)]))
assert {"a": 1} == unwrap(rmap({"a": rint(1)}))
# rtype keys ILLEGAL
# assert {"a":1} == unwrap(rmap({rstring("a"):rint(1)}))
# recursion, ticket:1977
m1 = rmap({"a": rint(1)})
m1.val["m1"] = m1
m2 = {"a": 1}
m2["m1"] = m2
unwrap(m1)
assert m2["a"] == unwrap(m1)["a"]
# Can't compare directly "maximum recursion depth exceeded in cmp"
assert type(m2["m1"]) == type(unwrap(m1)["m1"])
def manage_duplicate_tags(self,
client,
target_tag_id=None,
merge_tag_ids=None,
dry_run=False):
params = om_sys.Parameters()
params.map = {}
query_filter = om_sys.Filter()
#query_filter.limit = rtypes.rint(10) # should limit and enhance performance of query, but does not seem to
params.theFilter = query_filter
anno_list = []
if merge_tag_ids == None or len(merge_tag_ids) == 0:
anno_list = self.find_objects_by_query(client,
DUPLICATE_TAGS_S1_QUERY,
params)
anno_list.extend(
self.find_objects_by_query(client, DUPLICATE_TAGS_S2_QUERY,
params))
anno_list.extend(
self.find_objects_by_query(client, DUPLICATE_TAGS_S3_QUERY,
params))
anno_list.extend(
self.find_objects_by_query(client, DUPLICATE_TAGS_S4_QUERY,
params))
anno_list.extend(
self.find_objects_by_query(client, DUPLICATE_TAGS_S5_QUERY,
params))
anno_list.extend(
self.find_objects_by_query(client, DUPLICATE_TAGS_S6_QUERY,
params))
else:
if len(merge_tag_ids) > 0:
all_tag_ids = merge_tag_ids
all_tag_ids.append(target_tag_id)
anno_ids = map(rtypes.rlong, all_tag_ids)
params.map = {'aids': rtypes.rlist(anno_ids)}
anno_list = self.find_objects_by_query(client,
ANNOS_BY_IDS_QUERY,
params)
cur_tag_name, cur_tag_id = None, None
duplicate_tag_ids = []
merge_tag_id = None
if merge_tag_ids == None or len(merge_tag_ids) == 0:
for anno in anno_list:
if isinstance(anno, model.TagAnnotationI):
tag_name = anno.getTextValue().getValue()
tag_id = anno.getId().getValue()
if tag_name != cur_tag_name and tag_id != cur_tag_id:
# it's a fresh tag; find all datasets for tag and update them
# params.map = {'aid': rtypes.rlong(cur_tag_id)}
if len(duplicate_tag_ids) > 0:
if target_tag_id is None:
merge_tag_id = cur_tag_id
else:
merge_tag_id = target_tag_id
self.do_tag_merge(client,
merge_tag_id,
duplicate_tag_ids,
dry_run=dry_run)
# reset the parameters
cur_tag_name = tag_name
cur_tag_id = tag_id
duplicate_tag_ids = []
merge_tag_id = None
elif tag_name == cur_tag_name and tag_id != cur_tag_id:
# it's a duplicate tag;
if tag_id not in duplicate_tag_ids:
duplicate_tag_ids.append(tag_id)
else:
duplicate_tag_ids = merge_tag_ids
# catch the final iteration
if len(duplicate_tag_ids) > 0:
if target_tag_id is None:
merge_tag_id = cur_tag_id
else:
merge_tag_id = target_tag_id
self.do_tag_merge(client,
merge_tag_id,
duplicate_tag_ids,
dry_run=dry_run)
def _set_parameters(mapann_ns=[],
mapann_names=[],
mapann_value=None,
query=False,
case_sensitive=True,
params=None,
experimenter_id=-1,
page=None,
limit=settings.PAGE):
''' Helper to map ParametersI
@param mapann_ns The Map annotation namespace to filter by.
@type mapann_ns L{string}
@param mapann_names The Map annotation names to filter by.
@type mapann_names L{string}
@param mapann_value The Map annotation value to filter by.
@type mapann_value L{string}
@param query Flag allowing to search for value patters.
@type query L{boolean}
@param params Instance of ParametersI
@type params L{omero.sys.ParametersI}
@param experimenter_id The Experimenter (user) ID to filter by
or -1 for all experimenters
@type experimenter_id L{long}
@param page Page number of results to get. `None` or 0 for no paging
defaults to None
@type page L{long}
@param limit The limit of results per page to get
defaults to the value set in settings.PAGE
@type page L{long}
'''
if params is None:
params = omero.sys.ParametersI()
# Paging
if page is not None and page > 0:
params.page((page - 1) * limit, limit)
where_clause = []
if mapann_names is not None and len(mapann_names) > 0:
manlist = [rstring(n) for n in mapann_names]
params.add('filter', rlist(manlist))
where_clause.append("mv.name in (:filter)")
if mapann_ns is not None and len(mapann_ns) > 0:
mnslist = [rstring(n) for n in mapann_ns]
params.add("ns", rlist(mnslist))
where_clause.append("a.ns in (:ns)")
if experimenter_id is not None and experimenter_id != -1:
params.addId(experimenter_id)
where_clause.append("a.details.owner.id = :id")
if mapann_value:
mapann_value = mapann_value if case_sensitive else mapann_value.lower()
_cwc = 'mv.value' if case_sensitive else 'lower(mv.value)'
if query:
params.addString(
"query", rstring("%%%s%%" % _escape_chars_like(mapann_value)))
where_clause.append("%s like :query" % _cwc)
else:
params.addString('value', mapann_value)
where_clause.append("%s = :value" % _cwc)
else:
where_clause.append("mv.value != '' ")
return params, where_clause
#!/usr/bin/env python
# -*- coding: utf-8 -*-
from omero.rtypes import rstring, rint, rset, rlist
# Sets and Lists may be interpreted differently on the server
list = rlist(rstring("a"), rstring("b"))
set = rset(rint(1), rint(2))
def test3639(self):
uuid = self.ctx.sessionUuid
images = list()
for i in range(0, 5):
images.append(self.make_image())
p = omero.sys.Parameters()
p.map = {}
p.map["oids"] = rlist([rlong(s.id.val) for s in images])
# create dataset
dataset = self.make_dataset('DS-test-2936-%s' % uuid)
# put image in dataset
for image in images:
self.link(dataset, image)
# log in as group owner:
client_o, owner = self.new_client_and_user(group=self.group,
owner=True)
query_o = client_o.sf.getQueryService()
handlers = list()
keep = ChildOption(excludeType=["Image"])
dc = Delete2(targetObjects={'Dataset': [dataset.id.val]},
childOptions=[keep])
handlers.append(str(client_o.sf.submit(dc)))
imageToDelete = images[2].id.val
dc2 = Delete2(targetObjects={'Image': [imageToDelete]})
handlers.append(str(client_o.sf.submit(dc2)))
def _formatReport(delete_handle):
"""
Added as workaround to the changes made in #3006.
"""
delete_report = delete_handle.getResponse()
rv = []
if isinstance(delete_report, omero.cmd.ERR):
rv.append(str(delete_report))
if len(rv) > 0:
return "; ".join(rv)
return None
failure = list()
in_progress = 0
r = None
while (len(handlers) > 0):
for cbString in handlers:
try:
with pytest.raises(Ice.ObjectNotExistException):
handle = omero.cmd.HandlePrx.checkedCast(
client_o.ic.stringToProxy(cbString))
cb = omero.callbacks.CmdCallbackI(client_o, handle)
if not cb.block(500): # ms.
# No errors possible if in progress(
# (since no response)
print "in progress", _formatReport(handle)
in_progress += 1
else:
rsp = cb.getResponse()
if isinstance(rsp, omero.cmd.ERR):
r = _formatReport(handle)
if r is not None:
failure.append(r)
else:
failure.append("No report!!!")
else:
r = _formatReport(handle)
if r is not None:
failure.append(r)
cb.close(True) # Close handle
handlers.remove(cbString)
except Exception:
if r is not None:
failure.append(traceback.format_exc())
if len(failure) > 0:
assert False, ";".join(failure)
assert not query_o.find('Dataset', dataset.id.val)
def test3639(self):
uuid = self.client.sf.getAdminService().getEventContext().sessionUuid
group = self.client.sf.getAdminService().getGroup(
self.client.sf.getAdminService().getEventContext().groupId)
update = self.client.sf.getUpdateService()
images = list()
for i in range(0, 5):
img = self.new_image()
img = update.saveAndReturnObject(img)
images.append(img.id.val)
p = omero.sys.Parameters()
p.map = {}
p.map["oids"] = rlist([rlong(s) for s in images])
# create dataset
dataset = omero.model.DatasetI()
dataset.name = rstring('DS-test-2936-%s' % (uuid))
dataset = update.saveAndReturnObject(dataset)
# put image in dataset
for iid in images:
dlink = omero.model.DatasetImageLinkI()
dlink.parent = omero.model.DatasetI(dataset.id.val, False)
dlink.child = omero.model.ImageI(iid, False)
update.saveAndReturnObject(dlink)
# log in as group owner:
client_o, owner = self.new_client_and_user(group=group, admin=True)
query_o = client_o.sf.getQueryService()
handlers = list()
op = dict()
op["/Image"] = "KEEP"
dc = omero.cmd.Delete('/Dataset', long(dataset.id.val), op)
handlers.append(str(client_o.sf.submit(dc)))
imageToDelete = images[2]
images.remove(imageToDelete)
dc2 = omero.cmd.Delete('/Image', long(imageToDelete), {})
handlers.append(str(client_o.sf.submit(dc2)))
def _formatReport(delete_handle):
"""
Added as workaround to the changes made in #3006.
"""
delete_report = delete_handle.getResponse()
rv = []
if isinstance(delete_report, omero.cmd.ERR):
rv.append(str(delete_report))
else:
if delete_report.warning:
rv.append(delete_report.warning)
if len(rv) > 0:
return "; ".join(rv)
return None
failure = list()
in_progress = 0
r = None
while(len(handlers) > 0):
for cbString in handlers:
try:
with pytest.raises(Ice.ObjectNotExistException):
handle = omero.cmd.HandlePrx.checkedCast(
client_o.ic.stringToProxy(cbString))
cb = omero.callbacks.CmdCallbackI(client_o, handle)
if not cb.block(500): # ms.
# No errors possible if in progress(
# (since no response)
print "in progress", _formatReport(handle)
in_progress += 1
else:
rsp = cb.getResponse()
if isinstance(rsp, omero.cmd.ERR):
r = _formatReport(handle)
if r is not None:
failure.append(r)
else:
failure.append("No report!!!")
else:
r = _formatReport(handle)
if r is not None:
failure.append(r)
cb.close(True) # Close handle
handlers.remove(cbString)
except Exception:
if r is not None:
failure.append(traceback.format_exc())
if len(failure) > 0:
assert False, ";".join(failure)
assert not query_o.find('Dataset', dataset.id.val)