def project_datasets(self, user1):
"""Return Project with Datasets and an orphaned Dataset."""
# Create and name all the objects
project = ProjectI()
project.name = rstring('Project')
# Create 5 Datasets, each with 0-4 images.
for d in range(5):
dataset1 = DatasetI()
dataset1.name = rstring('Dataset%s' % d)
for i in range(d):
image = self.create_test_image(size_x=5,
size_y=5,
session=user1[0].getSession(),
name="Image%s" % i)
image = ImageI(image.id.val, False)
dataset1.linkImage(image)
project.linkDataset(dataset1)
# Create single orphaned Dataset
dataset = DatasetI()
dataset.name = rstring('Dataset')
project = get_update_service(user1).saveAndReturnObject(project)
dataset = get_update_service(user1).saveAndReturnObject(dataset)
return project, dataset
def testListOrphans(self, orphaned, load_pixels, gatewaywrapper):
# We login as 'User', since they have no other orphaned images
gatewaywrapper.loginAsUser()
conn = gatewaywrapper.gateway
eid = conn.getUserId()
# Create 5 orphaned images
iids = []
for i in range(0, 5):
img = gatewaywrapper.createTestImage(imageName=str(uuid.uuid1()))
iids.append(img.id)
# Create image in Dataset, to check this isn't found
dataset = DatasetI()
dataset.name = wrap('testListOrphans')
image = ImageI()
image.name = wrap('testListOrphans')
dataset.linkImage(image)
dataset = conn.getUpdateService().saveAndReturnObject(dataset)
try:
# Only test listOrphans() if orphaned
if orphaned:
# Pagination
params = omero.sys.ParametersI()
params.page(1, 3)
findImagesInPage = list(
conn.listOrphans("Image", eid=eid, params=params))
assert len(findImagesInPage) == 3
# No pagination (all orphans)
findImages = list(
conn.listOrphans("Image", loadPixels=load_pixels))
assert len(findImages) == 5
for p in findImages:
assert p._obj.pixelsLoaded == load_pixels
# Test getObjects() with 'orphaned' option
opts = {'orphaned': orphaned, 'load_pixels': load_pixels}
getImages = list(conn.getObjects("Image", opts=opts))
assert orphaned == (len(getImages) == 5)
for p in getImages:
assert p._obj.pixelsLoaded == load_pixels
# Simply check this doesn't fail See https://github.com/
# openmicroscopy/openmicroscopy/pull/4950#issuecomment-264142956
dsIds = [d.id for d in conn.listOrphans("Dataset")]
assert dataset.id.val in dsIds
finally:
# Cleanup - Delete what we created
conn.deleteObjects('Image', iids, deleteAnns=True, wait=True)
conn.deleteObjects('Dataset', [dataset.id.val],
deleteChildren=True,
wait=True)
def project_dataset_image(self):
"""
Returns a new OMERO Project, linked Dataset and linked Image populated
by an L{test.integration.library.ITest} instance with required fields
set.
"""
project = ProjectI()
project.name = rstring(self.uuid())
dataset = DatasetI()
dataset.name = rstring(self.uuid())
image = self.new_image(name=self.uuid())
dataset.linkImage(image)
project.linkDataset(dataset)
return self.update.saveAndReturnObject(project)
def project_dataset_image(request, itest, update_service):
"""
Returns a new OMERO Project, linked Dataset and linked Image populated
by an L{test.integration.library.ITest} instance with required fields
set.
"""
project = ProjectI()
project.name = rstring(itest.uuid())
dataset = DatasetI()
dataset.name = rstring(itest.uuid())
image = itest.new_image(name=itest.uuid())
dataset.linkImage(image)
project.linkDataset(dataset)
return update_service.saveAndReturnObject(project)
def project_hierarchy_user1_group1(self, user1):
"""
Returns OMERO Projects with Dataset Children with Image Children
Note: This returns a list of mixed objects in a specified order
"""
# Create and name all the objects
project1 = ProjectI()
project1.name = rstring('Project1')
project2 = ProjectI()
project2.name = rstring('Project2')
dataset1 = DatasetI()
dataset1.name = rstring('Dataset1')
dataset2 = DatasetI()
dataset2.name = rstring('Dataset2')
image1 = self.new_image(name='Image1')
image2 = self.new_image(name='Image2')
# Link them together like so:
# project1
# dataset1
# image1
# image2
# dataset2
# image2
# project2
# dataset2
# image2
project1.linkDataset(dataset1)
project1.linkDataset(dataset2)
project2.linkDataset(dataset2)
dataset1.linkImage(image1)
dataset1.linkImage(image2)
dataset2.linkImage(image2)
to_save = [project1, project2]
projects = get_update_service(user1).saveAndReturnArray(to_save)
projects.sort(key=lambda x: lower_or_none(unwrap(x.name)))
datasets = projects[0].linkedDatasetList()
datasets.sort(key=lambda x: lower_or_none(unwrap(x.name)))
images = datasets[0].linkedImageList()
images.sort(key=lambda x: lower_or_none(unwrap(x.name)))
return projects + datasets + images
def dataset_images(self, user1):
"""Return Dataset with Images and an orphaned Image."""
dataset = DatasetI()
dataset.name = rstring('Dataset')
# Create 5 Images in Dataset
for i in range(5):
img = self.create_test_image(size_x=125, size_y=125,
session=user1[0].getSession(),
name="Image%s" % i)
img = ImageI(img.id.val, False)
dataset.linkImage(img)
# Create a single orphaned Image
image = self.create_test_image(size_x=125, size_y=125,
session=user1[0].getSession())
dataset = get_update_service(user1).saveAndReturnObject(dataset)
return dataset, image
def projects_dataset_image_tag(self):
"""
Returns 2 new OMERO Projects, linked Dataset and linked Image populated
by an L{test.integration.library.ITest} instance with required fields
set. Also a Tag linked to both Projects.
"""
project1 = ProjectI()
project1.name = rstring(f'P1_{self.uuid()}')
project2 = ProjectI()
project2.name = rstring(f'P2_{self.uuid()}')
dataset = DatasetI()
dataset.name = rstring(f'D{self.uuid()}')
image = self.new_image(f'I{self.uuid()}')
dataset.linkImage(image)
project1.linkDataset(dataset)
project2.linkDataset(dataset)
tag = TagAnnotationI()
tag.textValue = rstring("ChgrpTag")
project1.linkAnnotation(tag)
project2.linkAnnotation(tag)
return self.update.saveAndReturnArray([project1, project2])
def create_project(with_datasets=False, with_images=False):
project = ProjectI()
project.id = rlong(1L)
project.name = rstring("the_name")
project.description = rstring("the_description")
dataset_count = 2
if not with_datasets:
return project
for dataset_id in range(0, dataset_count):
dataset = DatasetI()
dataset.id = rlong(dataset_id + 1)
dataset.name = rstring("dataset_name_%d" % (dataset_id + 1))
dataset.description = rstring("dataset_description_%d" % (dataset_id + 1))
project.linkDataset(dataset)
if not with_images:
continue
for image_id in range(1, 3):
image_id = (dataset_id * dataset_count) + image_id
dataset.linkImage(create_image(image_id))
return project
def projects_dataset_image_tag(self):
"""
Returns 2 new OMERO Projects, linked Dataset and linked Image populated
by an L{test.integration.library.ITest} instance with required fields
set. Also a Tag linked to both Projects.
"""
project1 = ProjectI()
project1.name = rstring(self.uuid())
project2 = ProjectI()
project2.name = rstring(self.uuid())
dataset = DatasetI()
dataset.name = rstring(self.uuid())
image = self.new_image(name=self.uuid())
dataset.linkImage(image)
project1.linkDataset(dataset)
project2.linkDataset(dataset)
tag = TagAnnotationI()
tag.textValue = rstring("ChgrpTag")
project1.linkAnnotation(tag)
project2.linkAnnotation(tag)
return self.update.saveAndReturnArray([project1, project2])
def create_project(with_datasets=False, with_images=False):
project = ProjectI()
project.id = rlong(1)
project.name = rstring('the_name')
project.description = rstring('the_description')
dataset_count = 2
if not with_datasets:
return project
for dataset_id in range(0, dataset_count):
dataset = DatasetI()
dataset.id = rlong(dataset_id + 1)
dataset.name = rstring('dataset_name_%d' % (dataset_id + 1))
dataset.description = rstring('dataset_description_%d' %
(dataset_id + 1))
project.linkDataset(dataset)
if not with_images:
continue
for image_id in range(1, 3):
image_id = (dataset_id * dataset_count) + image_id
dataset.linkImage(create_image(image_id))
return project
