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)
