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 testUnloadSet(self):
img = ImageI()
self.assert_(img.sizeOfPixels() >= 0)
img.addPixels(PixelsI())
self.assert_(1 == img.sizeOfPixels())
img.unloadPixels()
self.assert_(img.sizeOfPixels() < 0)
def testUnloadSet(self):
img = ImageI()
assert img.sizeOfPixels() >= 0
img.addPixels(PixelsI())
assert 1 == img.sizeOfPixels()
img.unloadPixels()
assert img.sizeOfPixels() < 0
def testClearSet(self):
img = ImageI()
self.assert_(img.sizeOfPixels() >= 0)
img.addPixels(PixelsI())
self.assert_(1 == img.sizeOfPixels())
img.clearPixels()
self.assert_(img.sizeOfPixels() >= 0)
self.assert_(0 == img.sizeOfPixels())
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 testClearSet(self):
img = ImageI()
assert img.sizeOfPixels() >= 0
img.addPixels(PixelsI())
assert 1 == img.sizeOfPixels()
img.clearPixels()
assert img.sizeOfPixels() >= 0
assert 0 == img.sizeOfPixels()
def testCreateAfterBlitzPort(self):
ipojo = self.client.sf.getContainerService()
i = ImageI()
i.setName(rstring("name"))
i.setAcquisitionDate(rtime(0))
i = ipojo.createDataObject(i, None)
o = i.getDetails().owner
self.assertEquals(-1, o.sizeOfGroupExperimenterMap())
def testIterators(self):
d = DatasetI()
image = ImageI()
image.linkDataset(d)
it = image.iterateDatasetLinks()
count = 0
for i in it:
count += 1
self.assert_(count == 1)
def testUnloadedCtor(self):
img = ImageI(rlong(1), False)
self.assert_(not img.isLoaded())
try:
self.assert_(img.sizeOfDatasetLinks() < 0)
self.fail("Should throw")
except:
# Is true, but can't test it.
pass
def testUnloadedCtor(self):
img = ImageI(rlong(1), False)
assert not img.isLoaded()
try:
assert img.sizeOfDatasetLinks() < 0
assert False, "Should throw"
except:
# Is true, but can't test it.
pass
def testRemoveFromSet(self):
pix = PixelsI()
img = ImageI()
assert img.sizeOfPixels() >= 0
img.addPixels(pix)
assert 1 == img.sizeOfPixels()
img.removePixels(pix)
assert 0 == img.sizeOfPixels()
def testRemoveFromSet(self):
pix = PixelsI()
img = ImageI()
self.assert_(img.sizeOfPixels() >= 0)
img.addPixels(pix)
self.assert_(1 == img.sizeOfPixels())
img.removePixels(pix)
self.assert_(0 == img.sizeOfPixels())
def testGetAttrGood(self):
i = ImageI()
self.assert_(i.loaded)
self.assert_(i.isLoaded())
self.assert_(not i.name)
i.name = rstring("name")
self.assert_(i.name)
i.setName(None)
self.assert_(not i.getName())
i.copyAnnotationLinks()
i.linkAnnotation(omero.model.BooleanAnnotationI())
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()
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 test1184(self):
uuid = self.uuid()
client = self.new_client(perms="rw----")
share = client.sf.getShareService()
query = client.sf.getQueryService()
update = client.sf.getUpdateService()
admin = client.sf.getAdminService()
cont = client.sf.getContainerService()
ds = DatasetI()
ds.setName(rstring('test1184-ds-%s' % (uuid)))
for i in range(1, 2001):
img = ImageI()
img.setName(rstring('img1184-%s' % (uuid)))
img.setAcquisitionDate(rtime(time.time()))
# Saving in one go
#dil = DatasetImageLinkI()
#dil.setParent(ds)
#dil.setChild(img)
#update.saveObject(dil)
ds.linkImage(img)
ds = update.saveAndReturnObject(ds)
c = cont.getCollectionCount(ds.__class__.__name__, ("imageLinks"),
[ds.id.val], None)
self.assert_(c[ds.id.val] == 2000)
page = 1
p = omero.sys.Parameters()
p.map = {}
p.map["eid"] = rlong(admin.getEventContext().userId)
p.map["oid"] = rlong(ds.id.val)
if page is not None:
f = omero.sys.Filter()
f.limit = rint(24)
f.offset = rint((int(page) - 1) * 24)
p.theFilter = f
sql = "select im from Image im join fetch im.details.owner join fetch im.details.group " \
"left outer join fetch im.datasetLinks dil left outer join fetch dil.parent d " \
"where d.id = :oid and im.details.owner.id=:eid order by im.id asc"
start = time.time()
res = query.findAllByQuery(sql, p)
self.assertEquals(24, len(res))
end = time.time()
elapsed = end - start
self.assertTrue(
elapsed < 3.0,
"Expected the test to complete in < 3 seconds, took: %f" % elapsed)
def testGetAttrBad(self):
i = ImageI()
def assign_loaded():
i.loaded = False
self.assertRaises( AttributeError, assign_loaded )
self.assertRaises( AttributeError, lambda: i.foo )
def assign_foo():
i.foo = 1
self.assertRaises( AttributeError, assign_foo )
self.assertRaises( AttributeError, lambda: i.annotationLinks )
self.assertRaises( AttributeError, lambda: i.getAnnotationLinks() )
def assign_links():
i.annotationLinks = []
self.assertRaises( AttributeError, assign_links)
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 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 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 testGetAttrBad(self):
i = ImageI()
def assign_loaded():
i.loaded = False
pytest.raises(AttributeError, assign_loaded)
pytest.raises(AttributeError, lambda: i.foo)
def assign_foo():
i.foo = 1
pytest.raises(AttributeError, assign_foo)
pytest.raises(AttributeError, lambda: i.annotationLinks)
pytest.raises(AttributeError, lambda: i.getAnnotationLinks())
def assign_links():
i.annotationLinks = []
pytest.raises(AttributeError, assign_links)
def test_none_pixel_size(self):
"""
Tests display of core metatada still works even when image
doesn't have pixels data
"""
img = ImageI()
img.setName(rstring("no_pixels"))
img.setDescription(rstring("empty image without pixels data"))
conn = omero.gateway.BlitzGateway(client_obj=self.client)
img = conn.getUpdateService().saveAndReturnObject(img)
request_url = reverse('load_metadata_details',
args=['image', img.id.val])
# Just check that the metadata panel is loaded
rsp = get(self.django_client, request_url, status_code=200)
assert "no_pixels" in rsp.content.decode("utf-8")
def testBasicUsage(self):
usr = self.client.sf.getAdminService().getEventContext().userId
img = ImageI()
img.name = rstring("name")
img.acquisitionDate = rtime(0)
tag = TagAnnotationI()
img.linkAnnotation(tag)
img = self.client.sf.getUpdateService().saveAndReturnObject(img)
img = self.client.sf.getQueryService().findByQuery(
"""
select img from Image img
join fetch img.annotationLinksCountPerOwner
where img.id = %s
""" % (img.id.val), None)
self.assert_(img)
self.assert_(img.getAnnotationLinksCountPerOwner()[usr] > 0)
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 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 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)
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())
