def testChgrpImage(self):
"""
Tests chgrp for a dummny image object (no Pixels)
"""
# One user in two groups
client, exp = self.new_client_and_user()
grp = self.new_group([exp])
gid = grp.id.val
client.sf.getAdminService().getEventContext() # Reset session
update = client.sf.getUpdateService()
query = client.sf.getQueryService()
admin = client.sf.getAdminService()
first_gid = admin.getEventContext().groupId
# Create a dataset in the 'first group'
ds = self.make_dataset(name="testChgrpImage_target", client=client)
ds_id = ds.id.val
# Change our context to new group and create image
admin.setDefaultGroup(exp, ExperimenterGroupI(gid, False))
self.set_context(client, gid)
update = client.sf.getUpdateService() # do we need to get this again?
img = self.new_image()
img = update.saveAndReturnObject(img)
# Move image to new group
chgrp = Chgrp2(
targetObjects={'Image': [img.id.val]}, groupId=first_gid)
# Link to Save
link = DatasetImageLinkI()
link.child = ImageI(img.id.val, False)
link.parent = DatasetI(ds_id, False)
save = Save()
save.obj = link
requests = [chgrp, save] # we're going to chgrp THEN save DIlink
# Change our context to original group...
admin.setDefaultGroup(exp, ExperimenterGroupI(first_gid, False))
self.set_context(client, first_gid)
# We have to be in destination group for link Save to work
self.doSubmit(requests, client)
# ...check image
img = client.sf.getQueryService().get("Image", img.id.val)
assert img.details.group.id.val == first_gid
# check Dataset
query = "select link from DatasetImageLink link\
where link.child.id=%s" % img.id.val
l = client.sf.getQueryService().findByQuery(query, None)
assert l is not None, "New DatasetImageLink on image not found"
assert l.details.group.id.val == first_gid,\
"Link Created in same group as Image target"
def testChgrpImage(self):
"""
Tests chgrp for a dummny image object (no Pixels)
"""
# One user in two groups
client, exp = self.new_client_and_user()
grp = self.new_group([exp])
gid = grp.id.val
client.sf.getAdminService().getEventContext() # Reset session
update = client.sf.getUpdateService()
query = client.sf.getQueryService()
admin = client.sf.getAdminService()
first_gid = admin.getEventContext().groupId
# Create a dataset in the 'first group'
ds = self.make_dataset(name="testChgrpImage_target", client=client)
ds_id = ds.id.val
# Change our context to new group and create image
admin.setDefaultGroup(exp, ExperimenterGroupI(gid, False))
self.set_context(client, gid)
update = client.sf.getUpdateService() # do we need to get this again?
img = self.new_image()
img = update.saveAndReturnObject(img)
# Move image to new group
chgrp = Chgrp2(targetObjects={'Image': [img.id.val]},
groupId=first_gid)
# Link to Save
link = DatasetImageLinkI()
link.child = ImageI(img.id.val, False)
link.parent = DatasetI(ds_id, False)
save = Save()
save.obj = link
requests = [chgrp, save] # we're going to chgrp THEN save DIlink
# Change our context to original group...
admin.setDefaultGroup(exp, ExperimenterGroupI(first_gid, False))
self.set_context(client, first_gid)
# We have to be in destination group for link Save to work
self.doSubmit(requests, client)
# ...check image
img = client.sf.getQueryService().get("Image", img.id.val)
assert img.details.group.id.val == first_gid
# check Dataset
query = "select link from DatasetImageLink link\
where link.child.id=%s" % img.id.val
l = client.sf.getQueryService().findByQuery(query, None)
assert l is not None, "New DatasetImageLink on image not found"
assert l.details.group.id.val == first_gid,\
"Link Created in same group as Image target"
def images_to_dataset(conn, params):
figure_ids = params["Figure_IDs"]
dataset_id = params["IDs"][0]
dataset = conn.getObject("Dataset", dataset_id)
if dataset is None:
return "Dataset %s not found" % dataset_id, dataset
gid = dataset.getDetails().group.id.val
print("Dataset: %s, Group: %s" % (dataset.name, gid))
update = conn.getUpdateService()
conn.SERVICE_OPTS.setOmeroGroup(-1)
if len(figure_ids) == 0:
return "Enter Figure IDs separated with a comma: '1,2'", dataset
image_ids = []
for figure_id in figure_ids:
file_ann = conn.getObject("FileAnnotation", figure_id)
if file_ann is None:
print("Figure File-Annotation %s not found" % figure_id)
figure_json = b"".join(list(file_ann.getFileInChunks()))
figure_json = figure_json.decode('utf8')
json_data = json.loads(figure_json)
image_ids.extend([p["imageId"] for p in json_data.get("panels")])
image_ids = list(set(image_ids))
if len(image_ids) == 0:
return "No Images found. Check Info log", dataset
print("Image IDs: %s" % image_ids)
conn.SERVICE_OPTS.setOmeroGroup(gid)
added_count = 0
for image_id in image_ids:
link = DatasetImageLinkI()
link.parent = DatasetI(dataset_id, False)
link.child = ImageI(image_id, False)
try:
update.saveObject(link, conn.SERVICE_OPTS)
added_count += 1
except Exception:
print("Image %s not linked to Dataset. "
"Link exists or permissions failed" % image_id)
return "Added %s images to Dataset" % added_count, dataset
def chgrpImagesToTargetDataset(self, imgCount):
"""
Helper method to test chgrp of image(s) to target Dataset
"""
# One user in two groups
client, user = self.new_client_and_user(perms=PRIVATE)
admin = client.sf.getAdminService()
target_grp = self.new_group([user], perms=PRIVATE)
target_gid = target_grp.id.val
images = self.importMIF(imgCount, client=client)
ds = self.createDSInGroup(target_gid, client=client)
# each chgrp includes a 'save' link to target dataset
saves = []
ids = []
for i in images:
ids.append(i.id.val)
link = DatasetImageLinkI()
link.child = ImageI(i.id.val, False)
link.parent = DatasetI(ds.id.val, False)
save = Save()
save.obj = link
saves.append(save)
chgrp = Chgrp2(
targetObjects={"Image": ids}, groupId=target_gid)
requests = [chgrp]
requests.extend(saves)
self.doSubmit(requests, client, omero_group=target_gid)
# Check Images moved to correct group
queryService = client.sf.getQueryService()
ctx = {'omero.group': '-1'} # query across groups
for i in images:
image = queryService.get('Image', i.id.val, ctx)
img_gid = image.details.group.id.val
assert target_gid == img_gid,\
"Image should be in group: %s, NOT %s" % (target_gid, img_gid)
# Check Dataset has images linked
dsImgs = client.sf.getContainerService().getImages(
'Dataset', [ds.id.val], None, ctx)
assert len(dsImgs) == len(images),\
"All Images should be in target Dataset"
previous_gid = admin.getEventContext().groupId
return (ds, images, client, user, previous_gid, target_gid)
def chgrpImagesToTargetDataset(self, imgCount):
"""
Helper method to test chgrp of image(s) to target Dataset
"""
# One user in two groups
client, user = self.new_client_and_user(perms=PRIVATE)
admin = client.sf.getAdminService()
target_grp = self.new_group([user], perms=PRIVATE)
target_gid = target_grp.id.val
images = self.importMIF(imgCount, client=client)
ds = self.createDSInGroup(target_gid, client=client)
# each chgrp includes a 'save' link to target dataset
saves = []
ids = []
for i in images:
ids.append(i.id.val)
link = DatasetImageLinkI()
link.child = ImageI(i.id.val, False)
link.parent = DatasetI(ds.id.val, False)
save = Save()
save.obj = link
saves.append(save)
chgrp = Chgrp2(targetObjects={"Image": ids}, groupId=target_gid)
requests = [chgrp]
requests.extend(saves)
self.doSubmit(requests, client, omero_group=target_gid)
# Check Images moved to correct group
queryService = client.sf.getQueryService()
ctx = {'omero.group': '-1'} # query across groups
for i in images:
image = queryService.get('Image', i.id.val, ctx)
img_gid = image.details.group.id.val
assert target_gid == img_gid,\
"Image should be in group: %s, NOT %s" % (target_gid, img_gid)
# Check Dataset has images linked
dsImgs = client.sf.getContainerService().getImages(
'Dataset', [ds.id.val], None, ctx)
assert len(dsImgs) == len(images),\
"All Images should be in target Dataset"
previous_gid = admin.getEventContext().groupId
return (ds, images, client, user, previous_gid, target_gid)
def testChgrpImageToTargetDatasetAndBackDS(self):
"""
Chgrp a single Image to target Dataset and then back
see ticket:11118
"""
new_ds, images, client, user, old_gid, new_gid =\
self.chgrpImagesToTargetDataset(1)
# create Dataset in original group
old_ds = self.createDSInGroup(old_gid, client=client)
link = DatasetImageLinkI()
link.parent = old_ds.proxy()
link.child = images[0].proxy()
chgrp = Chgrp2(
targetObjects={"Image": [images[0].id.val]}, groupId=old_gid)
save = Save(link)
self.doSubmit([chgrp, save], client, omero_group=old_gid)
dils = client.sf.getQueryService().findAllByQuery(
"select dil from DatasetImageLink dil where dil.child.id = :id",
omero.sys.ParametersI().addId(images[0].id.val),
{"omero.group": "-1"})
assert 1 == len(dils)
def testChgrpImageToTargetDatasetAndBackDS(self):
"""
Chgrp a single Image to target Dataset and then back
see ticket:11118
"""
new_ds, images, client, user, old_gid, new_gid =\
self.chgrpImagesToTargetDataset(1)
# create Dataset in original group
old_ds = self.createDSInGroup(old_gid, client=client)
link = DatasetImageLinkI()
link.parent = old_ds.proxy()
link.child = images[0].proxy()
chgrp = Chgrp2(targetObjects={"Image": [images[0].id.val]},
groupId=old_gid)
save = Save(link)
self.doSubmit([chgrp, save], client, omero_group=old_gid)
dils = client.sf.getQueryService().findAllByQuery(
"select dil from DatasetImageLink dil where dil.child.id = :id",
omero.sys.ParametersI().addId(images[0].id.val),
{"omero.group": "-1"})
assert 1 == len(dils)
def link(self, obj1, obj2, client=None):
"""
Links two linkable model entities together by creating an instance of
the correct link entity (e.g. ProjectDatasetLinkI) and persisting it
in the DB. Accepts client instance to allow calls to happen in correct
user contexts. Currently support links are:
* project/dataset
* dataset/image
* image/annotation
:param obj1: parent object
:param obj2: child object
:param client: The client to use to create the link
"""
if client is None:
client = self.client
if isinstance(obj1, ProjectI):
if isinstance(obj2, DatasetI):
link = ProjectDatasetLinkI()
elif isinstance(obj1, DatasetI):
if isinstance(obj2, ImageI):
link = DatasetImageLinkI()
elif isinstance(obj1, ImageI):
if isinstance(obj2, Annotation):
link = ImageAnnotationLinkI()
else:
assert False, "Object type not supported."
"""check if object exist or not"""
if obj1.id is None:
link.setParent(obj1)
else:
link.setParent(obj1.proxy())
if obj2.id is None:
link.setChild(obj2)
else:
link.setChild(obj2.proxy())
return client.sf.getUpdateService().saveAndReturnObject(link)
