def testUnloadCheckPtr(self):
img = ImageI()
self.assert_(img.isLoaded())
self.assert_(img.getDetails()) # details are auto instantiated
self.assert_(not img.getName()) # no other single-valued field is
img.unload()
self.assert_(not img.isLoaded())
self.assertRaises(omero.UnloadedEntityException, img.getDetails)
def testUnloadCheckPtr(self):
img = ImageI()
assert img.isLoaded()
assert img.getDetails() # details are auto instantiated
assert not img.getName() # no other single-valued field is
img.unload()
assert not img.isLoaded()
pytest.raises(omero.UnloadedEntityException, img.getDetails)
def testSequences(self):
img = ImageI()
self.assert_( img.sizeOfAnnotationLinks() >= 0 )
img.linkAnnotation(None)
img.unload()
try:
self.assert_( not img.sizeOfAnnotationLinks() >= 0 )
self.assert_( len(img.copyAnnotationLinks()) == 0 )
self.fail("can't reach here")
except:
# These are true, but can't be tested
pass
def testSequences(self):
img = ImageI()
self.assert_(img.sizeOfAnnotationLinks() >= 0)
img.linkAnnotation(None)
img.unload()
try:
self.assert_(not img.sizeOfAnnotationLinks() >= 0)
self.assert_(len(img.copyAnnotationLinks()) == 0)
self.fail("can't reach here")
except:
# These are true, but can't be tested
pass
def testSequences(self):
img = ImageI()
assert img.sizeOfAnnotationLinks() >= 0
img.linkAnnotation(None)
img.unload()
try:
assert not img.sizeOfAnnotationLinks() >= 0
assert len(img.copyAnnotationLinks()) == 0
assert False, "can't reach here"
except:
# These are true, but can't be tested
pass
def testSequences(self):
img = ImageI()
assert img.sizeOfAnnotationLinks() >= 0
img.linkAnnotation(None)
img.unload()
try:
assert not img.sizeOfAnnotationLinks() >= 0
assert len(img.copyAnnotationLinks()) == 0
assert False, "can't reach here"
except:
# These are true, but can't be tested
pass
def test2327(self):
### create two users in two groups
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('test2327'))
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.assert_(len(share1.getContents(sid)) == 1)
# add comment by the owner
share1.addComment(sid, 'test comment by the owner %s' % user1.id.val)
## login as user2
share2 = client_share2.sf.getShareService()
query2 = client_share2.sf.getQueryService()
l = share2.getMemberShares(False)
self.assertEquals(1, len(l))
# add comment by the member
share2.addComment(sid,
'test comment by the member %s' % (user2.id.val))
# Don't have to activate share2
#get comments
# by user1
c1 = len(share1.getComments(sid))
self.assertEquals(2, c1)
# by user2
c2 = len(share2.getComments(sid))
self.assertEquals(2, c2)
def test1157(self):
uuid = self.root.sf.getAdminService().getEventContext().sessionUuid
share = self.root.sf.getShareService()
### 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.assert_(len(share1.getContents(sid)) == 1)
# add comment by the owner
share.addComment(sid, 'test comment by the owner %s' % (uuid))
## login as user2
share2 = client_share2.sf.getShareService()
query2 = client_share2.sf.getQueryService()
# add comment by the member
share2.addComment(sid, 'test comment by the member %s' % (uuid))
# Don't have to activate share2
#get comments
# by user1
c1 = len(share.getComments(sid))
self.assertEquals(2, c1)
# by user2
c2 = len(share2.getComments(sid))
self.assertEquals(2, c2)
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 test2327(self):
### create two users in two groups
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('test2327'))
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.assert_(len(share1.getContents(sid)) == 1)
# add comment by the owner
share1.addComment(sid, 'test comment by the owner %s' % user1.id.val)
## login as user2
share2 = client_share2.sf.getShareService()
query2 = client_share2.sf.getQueryService()
l = share2.getMemberShares(False)
self.assertEquals(1, len(l))
# add comment by the member
share2.addComment(sid, 'test comment by the member %s' % (user2.id.val))
# Don't have to activate share2
#get comments
# by user1
c1 = len(share1.getComments(sid))
self.assertEquals(2, c1)
# by user2
c2 = len(share2.getComments(sid))
self.assertEquals(2, c2)
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 test1157(self):
uuid = self.root.sf.getAdminService().getEventContext().sessionUuid
share = self.root.sf.getShareService()
### 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.assert_(len(share1.getContents(sid)) == 1)
# add comment by the owner
share.addComment(sid, 'test comment by the owner %s' % (uuid))
## login as user2
share2 = client_share2.sf.getShareService()
query2 = client_share2.sf.getQueryService()
# add comment by the member
share2.addComment(sid, 'test comment by the member %s' % (uuid))
# Don't have to activate share2
#get comments
# by user1
c1 = len(share.getComments(sid))
self.assertEquals(2,c1)
# by user2
c2 = len(share2.getComments(sid))
self.assertEquals(2,c2)
def test2327(self):
# create two users in two groups
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("test2327"))
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)
assert len(share1.getContents(sid)) == 1
# add comment by the owner
share1.addComment(sid, "test comment by the owner %s" % user1.id.val)
# login as user2
share2 = client_share2.sf.getShareService()
l = share2.getMemberShares(False)
assert 1 == len(l)
# add comment by the member
share2.addComment(sid, "test comment by the member %s" % user2.id.val)
# get comments
# by user1
c1 = len(share1.getComments(sid))
assert 2 == c1
# by user2
c2 = len(share2.getComments(sid))
assert 2 == c2
def testAccessors(self):
name = rstring("name")
img = ImageI()
assert not img.getName()
img.setName(name)
assert img.getName()
name = img.getName()
assert name.val == "name"
assert name == name
img.setName(rstring("name2"))
assert img.getName().val == "name2"
assert img.getName()
img.unload()
try:
assert not img.getName()
assert False, "should fail"
except:
# Is true, but cannot test
pass
def testAccessors(self):
name = rstring("name")
img = ImageI()
self.assert_( not img.getName() )
img.setName( name )
self.assert_( img.getName() )
name = img.getName()
self.assert_( name.val == "name" )
self.assert_( name == name )
img.setName(rstring("name2"))
self.assert_( img.getName().val == "name2" )
self.assert_( img.getName() )
img.unload()
try:
self.assert_( not img.getName() )
self.fail("should fail")
except:
# Is true, but cannot test
pass
def testAccessors(self):
name = rstring("name")
img = ImageI()
assert not img.getName()
img.setName(name)
assert img.getName()
name = img.getName()
assert name.val == "name"
assert name == name
img.setName(rstring("name2"))
assert img.getName().val == "name2"
assert img.getName()
img.unload()
try:
assert not img.getName()
assert False, "should fail"
except:
# Is true, but cannot test
pass
def testAccessors(self):
name = rstring("name")
img = ImageI()
self.assert_(not img.getName())
img.setName(name)
self.assert_(img.getName())
name = img.getName()
self.assert_(name.val == "name")
self.assert_(name == name)
img.setName(rstring("name2"))
self.assert_(img.getName().val == "name2")
self.assert_(img.getName())
img.unload()
try:
self.assert_(not img.getName())
self.fail("should fail")
except:
# Is true, but cannot test
pass
def test1163(self):
uuid = self.uuid()
new_gr1 = self.new_group(perms="rw----")
client_share1, new_exp_obj = self.new_client_and_user(new_gr1)
update1 = client_share1.sf.getUpdateService()
search1 = client_share1.sf.createSearchService()
# create image and index
img = ImageI()
img.setName(rstring('test1154-img-%s' % (uuid)))
img.setAcquisitionDate(rtime(0))
img = update1.saveAndReturnObject(img)
img.unload()
self.index(img)
# search
search1.onlyType('Image')
search1.addOrderByAsc("name")
search1.byFullText("test*")
self.assertTrue(search1.hasNext())
res = search1.results()
self.assertEquals(1, len(res))
def test1163(self):
uuid = self.uuid()
new_gr1 = self.new_group(perms="rw----")
client_share1, new_exp_obj = self.new_client_and_user(new_gr1)
update1 = client_share1.sf.getUpdateService()
search1 = client_share1.sf.createSearchService()
# create image and index
img = ImageI()
img.setName(rstring('test1154-img-%s' % (uuid)))
img.setAcquisitionDate(rtime(0))
img = update1.saveAndReturnObject(img)
img.unload()
self.index(img)
# search
search1.onlyType('Image')
search1.addOrderByAsc("name")
search1.byFullText("test*")
assert search1.hasNext()
res = search1.results()
assert 1 == len(res)
def test8118(self):
uuid = self.root.sf.getAdminService().getEventContext().sessionUuid
share_serv = self.root.sf.getShareService()
update_serv = self.root.sf.getUpdateService()
# create user
user1 = self.new_user()
# create image
img = ImageI()
img.setName(rstring('test8118-img-%s' % (uuid)))
img.setAcquisitionDate(rtime(0))
img = update_serv.saveAndReturnObject(img)
img.unload()
# create share
description = "my description"
timeout = None
objects = [img]
experimenters = [user1]
guests = []
enabled = True
sid = share_serv.createShare(description, timeout, objects,
experimenters, guests, enabled)
suuid = share_serv.getShare(sid).uuid
self.assertEquals(1, len(share_serv.getContents(sid)))
# join share
user1_client = omero.client()
try:
user1_client.createSession(suuid, suuid)
user1_share = user1_client.sf.getShareService()
user1_share.activate(sid)
self.assertEquals(1, len(user1_share.getContents(sid)))
finally:
user1_client.__del__()
def test8118(self):
uuid = self.root.sf.getAdminService().getEventContext().sessionUuid
share_serv = self.root.sf.getShareService()
update_serv = self.root.sf.getUpdateService()
# create user
user1 = self.new_user()
# create image
img = ImageI()
img.setName(rstring('test8118-img-%s' % (uuid)))
img.setAcquisitionDate(rtime(0))
img = update_serv.saveAndReturnObject(img)
img.unload()
# create share
description = "my description"
timeout = None
objects = [img]
experimenters = [user1]
guests = []
enabled = True
sid = share_serv.createShare(description, timeout, objects,experimenters, guests, enabled)
suuid = share_serv.getShare(sid).uuid
self.assertEquals(1,len(share_serv.getContents(sid)))
# join share
user1_client = omero.client()
try:
user1_client.createSession(suuid,suuid)
user1_share = user1_client.sf.getShareService()
user1_share.activate(sid)
self.assertEquals(1, len(user1_share.getContents(sid)))
finally:
user1_client.__del__()
def test1071_1(self):
admin = self.root.sf.getAdminService()
common_group = self.new_group(perms="rwrw--")
c1 = self.new_client(common_group)
c2 = self.new_client(common_group)
c1_pojos = c1.sf.getContainerService()
c1_query = c1.sf.getQueryService()
c1_update = c1.sf.getUpdateService()
c1_uuid = c1.sf.getAdminService().getEventContext().sessionUuid
c2_pojos = c2.sf.getContainerService()
c2_query = c2.sf.getQueryService()
c2_update = c2.sf.getUpdateService()
c2_uuid = c2.sf.getAdminService().getEventContext().sessionUuid
#projects
pr1 = ProjectI()
pr1.setName(rstring('test1071-pr1-%s' % (c1_uuid)))
pr1 = c1_update.saveAndReturnObject(pr1)
pr1.unload()
pr2 = ProjectI()
pr2.setName(rstring('test1071-pr2-%s' % (c2_uuid)))
pr2 = c2_update.saveAndReturnObject(pr2)
pr2.unload()
#datasets
ds1 = DatasetI()
ds1.setName(rstring('test1071-ds1-%s' % (c1_uuid)))
ds1 = c1_update.saveAndReturnObject(ds1)
ds1.unload()
ds2 = DatasetI()
ds2.setName(rstring('test1071-ds2-%s' % (c2_uuid)))
ds2 = c2_update.saveAndReturnObject(ds2)
ds2.unload()
#images
im2 = ImageI()
im2.setName(rstring('test1071-im2-%s' % (c2_uuid)))
im2.acquisitionDate = rtime(0)
im2 = c2_update.saveAndReturnObject(im2)
im2.unload()
#links
# im2 owned by u2
#
# im2 -> ds2 --> pr2 (owned by u2)
# |
# \-> ds1 --> pr1 (owned by u1)
#
pdl1 = ProjectDatasetLinkI()
pdl1.setParent(pr1)
pdl1.setChild(ds1)
c1_update.saveObject(pdl1)
pdl2 = ProjectDatasetLinkI()
pdl2.setParent(pr2)
pdl2.setChild(ds2)
c2_update.saveObject(pdl2)
dil2 = DatasetImageLinkI()
dil2.setParent(ds2)
dil2.setChild(im2)
c2_update.saveObject(dil2)
dil1 = DatasetImageLinkI()
dil1.setParent(ds1)
dil1.setChild(im2)
c1_update.saveObject(dil1)
#test:
hier = c2_pojos.findContainerHierarchies("Project", [long(im2.id.val)], None)
assert 2 == len(hier), "size of hier != 2: %s" % [type(x) for x in hier]
for c in hier:
if c.id.val == pr1.id.val and isinstance(c, ProjectI):
assert 1 == c.sizeOfDatasetLinks()
for pdl in c.copyDatasetLinks():
assert 1 == pdl.child.sizeOfImageLinks()
for dil in pdl.child.copyImageLinks():
assert dil.child.id.val == im2.id.val
elif c.id.val == pr2.id.val and isinstance(c, ProjectI):
assert 1 == c.sizeOfDatasetLinks()
elif c.id.val == ds3.id.val and isinstance(c, DatasetI):
assert 1 == c.sizeOfImageLinks()
def testVirtual(self):
img = ImageI()
imgI = ImageI()
img.unload()
imgI.unload()
def testFindAndCountAnnotationsForSharedData(self):
uuid = self.root.sf.getAdminService().getEventContext().sessionUuid
query = self.root.sf.getQueryService()
update = self.root.sf.getUpdateService()
admin = self.root.sf.getAdminService()
ipojo = self.root.sf.getContainerService()
### create new users
#group1
new_gr1 = ExperimenterGroupI()
new_gr1.name = rstring("group1_%s" % uuid)
gid = admin.createGroup(new_gr1)
#new user1
new_exp = ExperimenterI()
new_exp.omeName = rstring("user1_%s" % uuid)
new_exp.firstName = rstring("New")
new_exp.lastName = rstring("Test")
defaultGroup = admin.getGroup(gid)
listOfGroups = list()
listOfGroups.append(admin.lookupGroup("user"))
eid = admin.createExperimenterWithPassword(new_exp, rstring("ome"),
defaultGroup, listOfGroups)
#new user2
new_exp2 = ExperimenterI()
new_exp2.omeName = rstring("user2_%s" % uuid)
new_exp2.firstName = rstring("New2")
new_exp2.lastName = rstring("Test2")
defaultGroup = admin.getGroup(gid)
listOfGroups = list()
listOfGroups.append(admin.lookupGroup("user"))
eid2 = admin.createExperimenterWithPassword(new_exp2, rstring("ome"),
defaultGroup, listOfGroups)
## get users
user1 = admin.getExperimenter(eid)
user2 = admin.getExperimenter(eid2)
## login as user1
cl1 = self.new_client(user=user1, password="******")
update1 = cl1.sf.getUpdateService()
ipojo1 = cl1.sf.getContainerService()
# create image
img = ImageI()
img.setName(rstring('test1154-img-%s' % (uuid)))
img.setAcquisitionDate(rtime(0))
# default permission 'rw----':
img = update1.saveAndReturnObject(img)
img.unload()
ann1 = CommentAnnotationI()
ann1.textValue = rstring("user comment - %s" % uuid)
l_ann1 = ImageAnnotationLinkI()
l_ann1.setParent(img)
l_ann1.setChild(ann1)
update1.saveObject(l_ann1)
#user retrives the annotations for image
coll_count = ipojo1.getCollectionCount(
"Image", "ome.model.containers.Image_annotationLinks",
[img.id.val], None)
self.assertEquals(1, coll_count.get(img.id.val, []))
#self.assertEquals(1, len(ipojo1.findAnnotations("Image", [img.id.val], None, None).get(img.id.val, [])))
## login as user2
cl2 = self.new_client(user=user2, password="******")
update2 = cl1.sf.getUpdateService()
ann = CommentAnnotationI()
ann.textValue = rstring("user2 comment - %s" % uuid)
l_ann = ImageAnnotationLinkI()
l_ann.setParent(img)
l_ann.setChild(ann)
update2.saveObject(l_ann)
#do they see the same vals?
#print ipojo1.getCollectionCount("Image", "ome.model.containers.Image_annotationLinks", [img.id.val], None)
#print ipojo.getCollectionCount("Image", "ome.model.containers.Image_annotationLinks", [img.id.val], None)
#print len(ipojo1.findAnnotations("Image", [img.id.val], None, None).get(img.id.val, []))
#print len(ipojo.findAnnotations("Image", [img.id.val], None, None).get(img.id.val, []))
coll_count = ipojo1.getCollectionCount(
"Image", "ome.model.containers.Image_annotationLinks",
[img.id.val], None)
self.assertEquals(2, coll_count.get(img.id.val, []))
#anns = ipojo1.findAnnotations("Image", [img.id.val], None, None).get(img.id.val, [])
#self.assertEquals(2, len(anns))
#self.assert_(anns[0].details.permissions == 'rw----')
#self.assert_(anns[1].details.permissions == 'rw----')
cl1.sf.closeOnDestroy()
cl2.sf.closeOnDestroy()
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 test1071(self):
uuid = self.root.sf.getAdminService().getEventContext().sessionUuid
pojos = self.root.sf.getContainerService()
query = self.root.sf.getQueryService()
update = self.root.sf.getUpdateService()
#projects
pr1 = ProjectI()
pr1.setName(rstring('test1071-pr1-%s' % (uuid)))
pr1 = update.saveAndReturnObject(pr1)
pr1.unload()
pr2 = ProjectI()
pr2.setName(rstring('test1071-pr2-%s' % (uuid)))
pr2 = update.saveAndReturnObject(pr2)
pr2.unload()
#datasets
ds1 = DatasetI()
ds1.setName(rstring('test1071-ds1-%s' % (uuid)))
ds1 = update.saveAndReturnObject(ds1)
ds1.unload()
ds2 = DatasetI()
ds2.setName(rstring('test1071-ds2-%s' % (uuid)))
ds2 = update.saveAndReturnObject(ds2)
ds2.unload()
ds3 = DatasetI()
ds3.setName(rstring('test1071-ds3-%s' % (uuid)))
ds3 = update.saveAndReturnObject(ds3)
ds3.unload()
#images
im2 = ImageI()
im2.setName(rstring('test1071-im2-%s' % (uuid)))
im2.acquisitionDate = rtime(0)
im2 = update.saveAndReturnObject(im2)
im2.unload()
#links
#
# im2 -> ds3
# +-> ds2 --> pr2
# | \
# \-> ds1 --> pr1
#
pdl1 = ProjectDatasetLinkI()
pdl1.setParent(pr1)
pdl1.setChild(ds1)
update.saveObject(pdl1)
pdl2 = ProjectDatasetLinkI()
pdl2.setParent(pr1)
pdl2.setChild(ds2)
update.saveObject(pdl2)
pdl3 = ProjectDatasetLinkI()
pdl3.setParent(pr2)
pdl3.setChild(ds2)
update.saveObject(pdl3)
dil4 = DatasetImageLinkI()
dil4.setParent(ds1)
dil4.setChild(im2)
update.saveObject(dil4)
dil5 = DatasetImageLinkI()
dil5.setParent(ds2)
dil5.setChild(im2)
update.saveObject(dil5)
dil6 = DatasetImageLinkI()
dil6.setParent(ds3)
dil6.setChild(im2)
update.saveObject(dil6)
#test:
hier = pojos.findContainerHierarchies("Project", [long(im2.id.val)],
None)
self.assertEquals(3, len(hier),
"len of hier != 3: %s" % [type(x) for x in hier])
for c in hier:
if c.id.val == pr1.id.val and isinstance(c, ProjectI):
self.assert_(c.sizeOfDatasetLinks() == 2,
"length 2 != " + str(c.sizeOfDatasetLinks()))
for pdl in c.copyDatasetLinks():
self.assert_(pdl.child.sizeOfImageLinks() == 1)
for dil in pdl.child.copyImageLinks():
self.assert_(dil.child.id.val == im2.id.val)
elif c.id.val == pr2.id.val and isinstance(c, ProjectI):
self.assert_(c.sizeOfDatasetLinks() == 1)
elif c.id.val == ds3.id.val and isinstance(c, DatasetI):
self.assert_(c.sizeOfImageLinks() == 1)
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 testVirtual(self):
img = ImageI()
imgI = ImageI()
img.unload()
imgI.unload()
def testFindAndCountAnnotationsForSharedData(self):
uuid = self.root.sf.getAdminService().getEventContext().sessionUuid
query = self.root.sf.getQueryService()
update = self.root.sf.getUpdateService()
admin = self.root.sf.getAdminService()
ipojo = self.root.sf.getContainerService()
### create new users
#group1
new_gr1 = ExperimenterGroupI()
new_gr1.name = rstring("group1_%s" % uuid)
gid = admin.createGroup(new_gr1)
#new user1
new_exp = ExperimenterI()
new_exp.omeName = rstring("user1_%s" % uuid)
new_exp.firstName = rstring("New")
new_exp.lastName = rstring("Test")
defaultGroup = admin.getGroup(gid)
listOfGroups = list()
listOfGroups.append(admin.lookupGroup("user"))
eid = admin.createExperimenterWithPassword(new_exp, rstring("ome"), defaultGroup, listOfGroups)
#new user2
new_exp2 = ExperimenterI()
new_exp2.omeName = rstring("user2_%s" % uuid)
new_exp2.firstName = rstring("New2")
new_exp2.lastName = rstring("Test2")
defaultGroup = admin.getGroup(gid)
listOfGroups = list()
listOfGroups.append(admin.lookupGroup("user"))
eid2 = admin.createExperimenterWithPassword(new_exp2, rstring("ome"), defaultGroup, listOfGroups)
## get users
user1 = admin.getExperimenter(eid)
user2 = admin.getExperimenter(eid2)
## login as user1
cl1 = self.new_client(user=user1, password="******")
update1 = cl1.sf.getUpdateService()
ipojo1 = cl1.sf.getContainerService()
# create image
img = ImageI()
img.setName(rstring('test1154-img-%s' % (uuid)))
img.setAcquisitionDate(rtime(0))
# default permission 'rw----':
img = update1.saveAndReturnObject(img)
img.unload()
ann1 = CommentAnnotationI()
ann1.textValue = rstring("user comment - %s" % uuid)
l_ann1 = ImageAnnotationLinkI()
l_ann1.setParent(img)
l_ann1.setChild(ann1)
update1.saveObject(l_ann1)
#user retrives the annotations for image
coll_count = ipojo1.getCollectionCount("Image", "ome.model.containers.Image_annotationLinks", [img.id.val], None)
self.assertEquals(1, coll_count.get(img.id.val, []))
#self.assertEquals(1, len(ipojo1.findAnnotations("Image", [img.id.val], None, None).get(img.id.val, [])))
## login as user2
cl2 = self.new_client(user=user2, password="******")
update2 = cl1.sf.getUpdateService()
ann = CommentAnnotationI()
ann.textValue = rstring("user2 comment - %s" % uuid)
l_ann = ImageAnnotationLinkI()
l_ann.setParent(img)
l_ann.setChild(ann)
update2.saveObject(l_ann)
#do they see the same vals?
#print ipojo1.getCollectionCount("Image", "ome.model.containers.Image_annotationLinks", [img.id.val], None)
#print ipojo.getCollectionCount("Image", "ome.model.containers.Image_annotationLinks", [img.id.val], None)
#print len(ipojo1.findAnnotations("Image", [img.id.val], None, None).get(img.id.val, []))
#print len(ipojo.findAnnotations("Image", [img.id.val], None, None).get(img.id.val, []))
coll_count = ipojo1.getCollectionCount("Image", "ome.model.containers.Image_annotationLinks", [img.id.val], None)
self.assertEquals(2, coll_count.get(img.id.val, []))
#anns = ipojo1.findAnnotations("Image", [img.id.val], None, None).get(img.id.val, [])
#self.assertEquals(2, len(anns))
#self.assert_(anns[0].details.permissions == 'rw----')
#self.assert_(anns[1].details.permissions == 'rw----')
cl1.sf.closeOnDestroy()
cl2.sf.closeOnDestroy()
def test1071(self):
uuid = self.root.sf.getAdminService().getEventContext().sessionUuid
pojos = self.root.sf.getContainerService()
query = self.root.sf.getQueryService()
update = self.root.sf.getUpdateService()
#projects
pr1 = ProjectI()
pr1.setName(rstring('test1071-pr1-%s' % (uuid)))
pr1 = update.saveAndReturnObject(pr1)
pr1.unload()
pr2 = ProjectI()
pr2.setName(rstring('test1071-pr2-%s' % (uuid)))
pr2 = update.saveAndReturnObject(pr2)
pr2.unload()
#datasets
ds1 = DatasetI()
ds1.setName(rstring('test1071-ds1-%s' % (uuid)))
ds1 = update.saveAndReturnObject(ds1)
ds1.unload()
ds2 = DatasetI()
ds2.setName(rstring('test1071-ds2-%s' % (uuid)))
ds2 = update.saveAndReturnObject(ds2)
ds2.unload()
ds3 = DatasetI()
ds3.setName(rstring('test1071-ds3-%s' % (uuid)))
ds3 = update.saveAndReturnObject(ds3)
ds3.unload()
#images
im2 = ImageI()
im2.setName(rstring('test1071-im2-%s' % (uuid)))
im2.acquisitionDate = rtime(0)
im2 = update.saveAndReturnObject(im2)
im2.unload()
#links
#
# im2 -> ds3
# +-> ds2 --> pr2
# | \
# \-> ds1 --> pr1
#
pdl1 = ProjectDatasetLinkI()
pdl1.setParent(pr1)
pdl1.setChild(ds1)
update.saveObject(pdl1)
pdl2 = ProjectDatasetLinkI()
pdl2.setParent(pr1)
pdl2.setChild(ds2)
update.saveObject(pdl2)
pdl3 = ProjectDatasetLinkI()
pdl3.setParent(pr2)
pdl3.setChild(ds2)
update.saveObject(pdl3)
dil4 = DatasetImageLinkI()
dil4.setParent(ds1)
dil4.setChild(im2)
update.saveObject(dil4)
dil5 = DatasetImageLinkI()
dil5.setParent(ds2)
dil5.setChild(im2)
update.saveObject(dil5)
dil6 = DatasetImageLinkI()
dil6.setParent(ds3)
dil6.setChild(im2)
update.saveObject(dil6)
#test:
hier = pojos.findContainerHierarchies("Project", [long(im2.id.val)], None)
assert 3 == len(hier), "len of hier != 3: %s" % [type(x) for x in hier]
for c in hier:
if c.id.val == pr1.id.val and isinstance(c, ProjectI):
assert c.sizeOfDatasetLinks() == 2, "length 2 != " + str(c.sizeOfDatasetLinks())
for pdl in c.copyDatasetLinks():
assert pdl.child.sizeOfImageLinks() == 1
for dil in pdl.child.copyImageLinks():
assert dil.child.id.val == im2.id.val
elif c.id.val == pr2.id.val and isinstance(c, ProjectI):
assert c.sizeOfDatasetLinks() == 1
elif c.id.val == ds3.id.val and isinstance(c, DatasetI):
assert c.sizeOfImageLinks() == 1
def test1071_1(self):
admin = self.root.sf.getAdminService()
common_group = self.new_group(perms="rwrw--")
c1 = self.new_client(common_group)
c2 = self.new_client(common_group)
c1_pojos = c1.sf.getContainerService()
c1_query = c1.sf.getQueryService()
c1_update = c1.sf.getUpdateService()
c1_uuid = c1.sf.getAdminService().getEventContext().sessionUuid
c2_pojos = c2.sf.getContainerService()
c2_query = c2.sf.getQueryService()
c2_update = c2.sf.getUpdateService()
c2_uuid = c2.sf.getAdminService().getEventContext().sessionUuid
#projects
pr1 = ProjectI()
pr1.setName(rstring('test1071-pr1-%s' % (c1_uuid)))
pr1 = c1_update.saveAndReturnObject(pr1)
pr1.unload()
pr2 = ProjectI()
pr2.setName(rstring('test1071-pr2-%s' % (c2_uuid)))
pr2 = c2_update.saveAndReturnObject(pr2)
pr2.unload()
#datasets
ds1 = DatasetI()
ds1.setName(rstring('test1071-ds1-%s' % (c1_uuid)))
ds1 = c1_update.saveAndReturnObject(ds1)
ds1.unload()
ds2 = DatasetI()
ds2.setName(rstring('test1071-ds2-%s' % (c2_uuid)))
ds2 = c2_update.saveAndReturnObject(ds2)
ds2.unload()
#images
im2 = ImageI()
im2.setName(rstring('test1071-im2-%s' % (c2_uuid)))
im2.acquisitionDate = rtime(0)
im2 = c2_update.saveAndReturnObject(im2)
im2.unload()
#links
# im2 owned by u2
#
# im2 -> ds2 --> pr2 (owned by u2)
# |
# \-> ds1 --> pr1 (owned by u1)
#
pdl1 = ProjectDatasetLinkI()
pdl1.setParent(pr1)
pdl1.setChild(ds1)
c1_update.saveObject(pdl1)
pdl2 = ProjectDatasetLinkI()
pdl2.setParent(pr2)
pdl2.setChild(ds2)
c2_update.saveObject(pdl2)
dil2 = DatasetImageLinkI()
dil2.setParent(ds2)
dil2.setChild(im2)
c2_update.saveObject(dil2)
dil1 = DatasetImageLinkI()
dil1.setParent(ds1)
dil1.setChild(im2)
c1_update.saveObject(dil1)
#test:
hier = c2_pojos.findContainerHierarchies("Project", [long(im2.id.val)],
None)
self.assertEquals(2, len(hier),
"size of hier != 2: %s" % [type(x) for x in hier])
for c in hier:
if c.id.val == pr1.id.val and isinstance(c, ProjectI):
self.assertEquals(1, c.sizeOfDatasetLinks())
for pdl in c.copyDatasetLinks():
self.assertEquals(1, pdl.child.sizeOfImageLinks())
for dil in pdl.child.copyImageLinks():
self.assert_(dil.child.id.val == im2.id.val)
elif c.id.val == pr2.id.val and isinstance(c, ProjectI):
self.assertEquals(1, c.sizeOfDatasetLinks())
elif c.id.val == ds3.id.val and isinstance(c, DatasetI):
self.assertEquals(1, c.sizeOfImageLinks())
