def testWrappers(self):
image = ImageI()
info = image._field_info
assert info.name.wrapper == rstring
assert info.acquisitionDate.wrapper == rtime
assert not info.name.nullable
assert not info.acquisitionDate.nullable
image.setAcquisitionDate("1", wrap=True)
assert type(image.acquisitionDate) == type(rtime(0))
# The following causes pytest to fail!
# image.setAcquisitionDate("", wrap=True)
# Note: collections still don't work well
if False:
image.addPixels(PixelsI())
image.setPixels(0, "Pixels:1", wrap=True)
assert type(image.pixels) == omero.model.PixelsI
image.setPixels(0, "Pixels", wrap=True)
image.setPixels(0, "Unknown", wrap=True)
link = DatasetImageLinkI()
link.setParent("Dataset:1")
link.setChild("Image:1")
def testWrappers(self):
image = ImageI()
info = image._field_info
assert info.name.wrapper == rstring
assert info.acquisitionDate.wrapper == rtime
assert not info.name.nullable
assert info.acquisitionDate.nullable
image.setAcquisitionDate("1", wrap=True)
assert type(image.acquisitionDate) == type(rtime(0))
# The following causes pytest to fail!
# image.setAcquisitionDate("", wrap=True)
# Note: collections still don't work well
if False:
image.addPixels(PixelsI())
image.setPixels(0, "Pixels:1", wrap=True)
assert type(image.pixels) == omero.model.PixelsI
image.setPixels(0, "Pixels", wrap=True)
image.setPixels(0, "Unknown", wrap=True)
link = DatasetImageLinkI()
link.setParent("Dataset:1")
link.setChild("Image:1")
def testLinkingAndUnlinking(self):
d = DatasetI()
i = ImageI()
d.linkImage(i)
assert d.sizeOfImageLinks() == 1
d.unlinkImage(i)
assert d.sizeOfImageLinks() == 0
d = DatasetI()
i = ImageI()
d.linkImage(i)
assert i.sizeOfDatasetLinks() == 1
i.unlinkDataset(d)
assert d.sizeOfImageLinks() == 0
d = DatasetI()
i = ImageI()
dil = DatasetImageLinkI()
dil.link(d, i)
d.addDatasetImageLink(dil, False)
assert d.sizeOfImageLinks() == 1
assert i.sizeOfDatasetLinks() == 0
def testLinkingAndUnlinking(self):
d = DatasetI()
i = ImageI()
d.linkImage(i)
self.assert_(d.sizeOfImageLinks() == 1)
d.unlinkImage(i)
self.assert_(d.sizeOfImageLinks() == 0)
d = DatasetI()
i = ImageI()
d.linkImage(i)
self.assert_(i.sizeOfDatasetLinks() == 1)
i.unlinkDataset(d)
self.assert_(d.sizeOfImageLinks() == 0)
d = DatasetI()
i = ImageI()
dil = DatasetImageLinkI()
dil.link(d, i)
d.addDatasetImageLink(dil, False)
self.assert_(d.sizeOfImageLinks() == 1)
self.assert_(i.sizeOfDatasetLinks() == 0)
def testLinkingAndUnlinking(self):
d = DatasetI()
i = ImageI()
d.linkImage(i)
assert d.sizeOfImageLinks() == 1
d.unlinkImage(i)
assert d.sizeOfImageLinks() == 0
d = DatasetI()
i = ImageI()
d.linkImage(i)
assert i.sizeOfDatasetLinks() == 1
i.unlinkDataset(d)
assert d.sizeOfImageLinks() == 0
d = DatasetI()
i = ImageI()
dil = DatasetImageLinkI()
dil.link(d, i)
d.addDatasetImageLink(dil, False)
assert d.sizeOfImageLinks() == 1
assert i.sizeOfDatasetLinks() == 0
def testLinkingAndUnlinking(self):
d = DatasetI()
i = ImageI()
d.linkImage(i)
self.assert_( d.sizeOfImageLinks() == 1 )
d.unlinkImage(i)
self.assert_( d.sizeOfImageLinks() == 0 )
d = DatasetI()
i = ImageI()
d.linkImage(i)
self.assert_( i.sizeOfDatasetLinks() == 1 )
i.unlinkDataset(d)
self.assert_( d.sizeOfImageLinks() == 0 )
d = DatasetI()
i = ImageI()
dil = DatasetImageLinkI()
dil.link(d,i)
d.addDatasetImageLink(dil, False)
self.assert_( d.sizeOfImageLinks() == 1 )
self.assert_( i.sizeOfDatasetLinks() == 0 )
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)
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 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())
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 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)