def listMostRecentAnnotations (conn, limit, eid=None):
"""
Retrieve most recent annotations available
@return: Generator yielding BlitzObjectWrapper
@rtype: L{BlitzObjectWrapper} generator
"""
tm = conn.getTimelineService()
p = omero.sys.Parameters()
p.map = {}
f = omero.sys.Filter()
if eid:
f.ownerId = rlong(eid)
else:
f.groupId = rlong(conn.getEventContext().groupId)
f.limit = rint(limit)
p.theFilter = f
anns = []
# get ALL parent-types, child-types, namespaces:
annTypes = ['LongAnnotation', 'TagAnnotation', 'CommentAnnotation'] # etc. Only query 1 at at time!
for at in annTypes:
for a in tm.getMostRecentAnnotationLinks(None, [at], None, p):
# TODO: maybe load parent for each link here
wrapper = AnnotationWrapper._wrap(conn, a.child, a)
anns.append(wrapper)
return anns
def testUpdateSessions(self, who):
who, idlediff, livediff = who
if who.startswith("root"):
client = self.root
else:
client = self.client
uuid = client.getSessionId()
service = client.sf.getSessionService()
obj_before = service.getSession(uuid)
live = unwrap(obj_before.timeToLive)
idle = unwrap(obj_before.timeToIdle)
req = UpdateSessionTimeoutRequest()
req.session = uuid
if livediff is not None:
req.timeToLive = rlong(live+livediff)
if idlediff is not None:
req.timeToIdle = rlong(idle+idlediff)
try:
cb = client.submit(req)
cb.getResponse()
cb.close(True)
assert not who.startswith("bad") # must throw
except omero.CmdError, ce:
if who.startswith("bad"):
assert ce.err.name == "non-admin-increase"
return
else:
print ce.err.parameters.get("stacktrace")
raise Exception(ce.err.category,
ce.err.name)
def _upload(self, client, filename, name, format):
if not format:
return
filename = str(filename) # Might be path.path
sz = os.path.getsize(filename)
if not sz:
self.status("No %s" % name)
return
try:
ofile = client.upload(filename, name=name, type=format)
jobid = long(client.getProperty("omero.job"))
link = omero.model.JobOriginalFileLinkI()
if self.params is None:
link.parent = omero.model.ParseJobI(rlong(jobid), False)
else:
link.parent = omero.model.ScriptJobI(rlong(jobid), False)
link.child = ofile.proxy()
client.getSession().getUpdateService().saveObject(link)
self.status(
"Uploaded %s bytes of %s to %s" %
(sz, filename, ofile.id.val))
except:
self.logger.error(
"Error on upload of %s for pid=%s (%s)",
filename, self.pid, self.uuid, exc_info=True)
def get_image_ids(conn, datasetId=None, groupId=-1, ownerId=None):
"""
Retrieves a list of all image IDs in a Dataset or Orphaned
(with owner specified by ownerId). The groupId can be specified
as needed, particuarly when querying orphaned images.
"""
qs = conn.getQueryService()
p = omero.sys.ParametersI()
so = deepcopy(conn.SERVICE_OPTS)
so.setOmeroGroup(groupId)
if datasetId is not None:
p.add('did', rlong(datasetId))
q = """select image.id from Image image
join image.datasetLinks dlink where dlink.parent.id = :did
order by lower(image.name), image.id"""
else:
p.add('ownerId', rlong(ownerId))
q = """select image.id from Image image where
image.details.owner.id = :ownerId and
not exists (
select dilink from DatasetImageLink as dilink
where dilink.child = image.id
) and
not exists (
select ws from WellSample ws
where ws.image.id = image.id
)
order by lower(image.name), image.id"""
iids = [i[0].val for i in qs.projection(q, p, so)]
return iids
def testGeneral(self):
uuid = self.ctx.sessionUuid
timeline = self.sf.getTimelineService()
im_ids = dict()
for i in range(0, 10):
# create image
acquired = long(time.time() * 1000)
img = self.make_image(name='test-img-%s' % uuid, date=acquired)
im_ids[i] = [img.id.val, acquired]
# Here we assume that this test is not run within the last 1 second
start = acquired - 86400
end = acquired + 1
p = omero.sys.Parameters()
p.map = {}
f = omero.sys.Filter()
f.ownerId = rlong(self.ctx.userId)
f.groupId = rlong(self.ctx.groupId)
p.theFilter = f
M = timeline.countByPeriod
A = rtime(long(start))
B = rtime(long(end))
counter = M(['Image'], A, B, p)
assert counter['Image'] == 10
# And with #9609
counter = M(['Image'], A, B, p, {"omero.group": "-1"})
assert counter['Image'] == 10
p2 = omero.sys.Parameters()
p2.map = {}
f2 = omero.sys.Filter()
f2.ownerId = rlong(self.ctx.userId)
f2.groupId = rlong(self.ctx.groupId)
f2.limit = rint(5)
p2.theFilter = f2
# p.map["start"] = rtime(long(start))
# p.map["end"] = rtime(long(end))
M = timeline.getMostRecentObjects
res = M(['Image'], p2, False)["Image"]
assert 5 == len(res)
# And with #9609
res = M(['Image'], p2, False, {"omero.group": "-1"})["Image"]
assert 5 == len(res)
# 1st element should be the 9th from the im_ids
assert im_ids[9][0] == res[0].id.val
# 2nd element should be the 8th from the im_ids
assert im_ids[8][0] == res[1].id.val
# 3rd element should be the 7th from the im_ids
assert im_ids[7][0] == res[2].id.val
# 4th element should be the 6th from the im_ids
assert im_ids[6][0] == res[3].id.val
# 5th element should be the 5th from the im_ids
assert im_ids[5][0] == res[4].id.val
def test_marshal_plate_acquisition_name_no_start_no_end(self, mock_conn, owner_permissions):
row = [rlong(1L), rstring("name"), rlong(1L), owner_permissions, None, None]
expected = {
"id": 1L,
"ownerId": 1L,
"name": "name",
"permsCss": "canEdit canAnnotate canLink canDelete isOwned canChgrp",
}
def test_marshal_plate_acquisition_no_name_start_end(self, mock_conn, owner_permissions, start_time, end_time):
row = [rlong(1L), None, rlong(1L), owner_permissions, start_time, end_time]
expected = {
"id": 1L,
"ownerId": 1L,
"name": "2014-05-08 10:37:02 - 2014-05-08 10:38:30",
"permsCss": "canEdit canAnnotate canLink canDelete isOwned canChgrp",
}
def testResuingClass(self):
myLong = rlong(5)
myLongFromString = rlong("5")
assert myLong.val == myLongFromString.val
ctor1 = myLong.__class__(5)
ctor2 = myLongFromString.__class__("5")
assert ctor1.val == ctor2.val
def testOwnerId(self):
p = ParametersI()
self.assertNull(p.theFilter)
p.exp(rlong(1))
self.assertNotNull(p.theFilter)
self.assertNotNull(p.theFilter.ownerId)
assert rlong(1) == p.getExperimenter()
self.assertNull(p.allExps().getExperimenter())
self.assertNotNull(p.theFilter)
def test_marshal_dataset(self, mock_conn, owner_permissions):
row = [rlong(1L), rstring("name"), rlong(1L), owner_permissions, rlong(1L)]
expected = {
"id": 1L,
"ownerId": 1L,
"name": "name",
"permsCss": "canEdit canAnnotate canLink canDelete isOwned canChgrp",
"childCount": 1,
}
def test_marshal_plate_not_owner(self, mock_conn, owner_permissions):
row = [rlong(1L), rstring("name"), rlong(2L), owner_permissions, 2]
expected = {
"id": 1L,
"ownerId": 2L,
"name": "name",
"permsCss": "canEdit canAnnotate canLink canDelete",
"childCount": 2,
}
def testGroupId(self):
p = ParametersI()
self.assertNull(p.theFilter)
p.grp(rlong(1))
self.assertNotNull(p.theFilter)
self.assertNotNull(p.theFilter.groupId)
assert rlong(1) == p.getGroup()
self.assertNull(p.allGrps().getGroup())
self.assertNotNull(p.theFilter)
def list_tagsets(self, args, tag):
"""
Returns a TagCollection of just the tagsets.
If tag is provided, will return the tagsets with those tags.
"""
params = omero.sys.ParametersI()
params.addString('ns', omero.constants.metadata.NSINSIGHTTAGSET)
ice_map = dict()
if args.admin:
ice_map["omero.group"] = "-1"
client = self.ctx.conn(args)
session = client.getSession()
q = session.getQueryService()
tc = TagCollection()
if tag:
sql = """
select a.id, a.description, a.textValue,
a.details.owner.id, a.details.owner.firstName,
a.details.owner.lastName
from AnnotationAnnotationLink b
inner join b.parent a
where a.ns=:ns
"""
sql += " and b.child.id = :tid"
params.map['tid'] = rlong(long(tag))
else:
sql = """
select a.id, a.description, a.textValue,
a.details.owner.id, a.details.owner.firstName,
a.details.owner.lastName
from TagAnnotation a
where a.ns=:ns
"""
if args.uid:
params.map["eid"] = rlong(long(args.uid))
sql += " and a.details.owner.id = :eid"
for element in q.projection(sql, params, ice_map):
tag_id, description, text, owner, first, last = map(unwrap,
element)
tc.tags[tag_id] = Tag(
tag_id=tag_id,
name=text,
description=description,
owner=owner
)
tc.owners[owner] = "%s %s" % (first, last)
return tc
def screen_with_plates(screen):
for plate_id in range(5, 7):
o = PlateI()
o.id = rlong(plate_id)
o.name = rstring('plate_name_%d' % plate_id)
o.description = rstring('plate_description_%d' % plate_id)
o.columnNamingConvention = rstring('number')
o.rowNamingConvention = rstring('letter')
o.columns = rint(12)
o.rows = rint(8)
o.defaultSample = rint(0)
o.externalIdentifier = rstring('external_identifier_%d' % plate_id)
o.status = rstring('status_%d' % plate_id)
o.wellOriginX = LengthI(0.1, UnitsLength.REFERENCEFRAME)
o.wellOriginY = LengthI(1.1, UnitsLength.REFERENCEFRAME)
screen.linkPlate(o)
for well_id in range(7, 9):
well = WellI()
well.id = rlong(well_id)
well.column = rint(2)
well.row = rint(1)
well.externalDescription = \
rstring('external_description_%d' % well_id)
well.externalIdentifier = \
rstring('external_identifier_%d' % well_id)
well.type = rstring('the_type')
well.alpha = rint(0)
well.red = rint(255)
well.green = rint(0)
well.blue = rint(0)
well.status = rstring('the_status')
o.addWell(well)
plateacquisition = PlateAcquisitionI()
plateacquisition.id = rlong(well_id)
plateacquisition.name = rstring(
'plateacquisition_name_%d' % well_id)
plateacquisition.description = rstring(
'plateacquisition_description_%d' % well_id)
plateacquisition.maximumFieldCount = rint(1)
plateacquisition.startTime = rtime(1L)
plateacquisition.endTime = rtime(2L)
for wellsample_id in range(9, 11):
wellsample = WellSampleI()
wellsample.setPlateAcquisition(plateacquisition)
wellsample.id = rlong(wellsample_id)
wellsample.posX = LengthI(1.0, UnitsLength.REFERENCEFRAME)
wellsample.posY = LengthI(2.0, UnitsLength.REFERENCEFRAME)
wellsample.timepoint = rtime(1L)
wellsample.image = create_image(1L)
well.addWellSample(wellsample)
return screen
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)
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)
assert 24 == len(res)
end = time.time()
elapsed = end - start
assert elapsed < 3.0,\
"Expected the test to complete in < 3 seconds, took: %f" % elapsed
def testCollaborativeTimeline(self):
"""
Create some images as one user - test if another user
can see these events in timeline.
"""
client2, user2 = self.new_client_and_user(group=self.group)
# log in as first user & create images
timeline2 = client2.sf.getTimelineService()
im_ids = dict()
for i in range(0, 10):
# create image
acquired = long(time.time() * 1000)
img = self.make_image(name='test-img-%s' % client2.sf,
date=acquired, client=client2)
im_ids[i] = [img.id.val, acquired]
# Here we assume that this test is not run within the last 1 second
start = acquired - 86400
end = acquired + 1
ownerId = rlong(user2.id.val)
groupId = rlong(self.group.id.val)
def assert_timeline(timeline, start, end, ownerId=None, groupId=None):
p = omero.sys.Parameters()
p.map = {}
f = omero.sys.Filter()
if ownerId is not None:
f.ownerId = ownerId
if groupId is not None:
f.groupId = groupId
p.theFilter = f
counter = timeline.countByPeriod(
['Image'], rtime(long(start)), rtime(long(end)), p)
assert 10 == counter['Image']
data = timeline.getByPeriod(
['Image'], rtime(long(start)), rtime(long(end)), p, False)
assert 10 == len(data['Image'])
assert_timeline(timeline2, start, end, ownerId, groupId)
# now log in as another user (default group is same as user-created
# images above)
assert_timeline(
self.sf.getTimelineService(), start, end, ownerId, groupId)
def testGetAttrWorks(self):
rbool(True).val
rdouble(0.0).val
rfloat(0.0).val
rint(0).val
rlong(0).val
rtime(0).val
rinternal(None).val
robject(None).val
rstring("").val
rclass("").val
rarray().val
rlist().val
rset().val
rmap().val
def testExperimenter(self):
p = ParametersI()
p.exp(rlong(1))
assert p.isExperimenter()
assert p.getExperimenter().getValue() == 1L
p.allExps()
assert not p.isExperimenter()
def externalInfo():
o = ExternalInfoI()
o.entityId = rlong(123)
o.entityType = rstring('test')
o.lsid = rstring('ABCDEF')
o.uuid = rstring('f90a1fd5-275c-4d14-82b3-87b5ef0f07de')
return o
def test1173(self):
uuid = self.root.sf.getAdminService().getEventContext().sessionUuid
timeline = self.root.sf.getTimelineService()
# create image
ds = self.make_dataset(name='test1173-ds-%s' % uuid, client=self.root)
ds.unload()
# Here we assume that this test is not run within the last 1 second
start = long(time.time() * 1000 - 86400)
end = long(time.time() * 1000 + 86400)
p = omero.sys.Parameters()
p.map = {}
f = omero.sys.Filter()
f.ownerId = rlong(self.new_user().id.val)
p.theFilter = f
M = timeline.getEventLogsByPeriod
A = rtime(long(start))
B = rtime(long(end))
rv = M(A, B, p)
assert rv > 0
# And now for #9609
rv = M(A, B, p, {"omero.group": "-1"})
assert rv > 0
def test1088(self):
admin = self.root.sf.getAdminService()
q = self.root.sf.getQueryService()
cx = admin.getEventContext()
p = omero.sys.Parameters()
p.map = {}
p.map["uid"] = rlong(cx.userId)
p.map['start'] = start = rtime(1218529874000)
p.map['end'] = end = rtime(1221121874000)
sql1 = "select el from EventLog el left outer join fetch el.event ev " \
"where el.entityType in ('ome.model.core.Pixels', 'ome.model.core.Image', " \
"'ome.model.containers.Dataset', 'ome.model.containers.Project') " \
"and ev.id in (select id from Event where experimenter.id=:uid and time > :start and time < :end)"
sql2 = "select el from EventLog el left outer join fetch el.event ev " \
"where el.entityType in ('ome.model.core.Pixels', 'ome.model.core.Image', " \
"'ome.model.containers.Dataset', 'ome.model.containers.Project') " \
"and ev.experimenter.id=:uid and ev.time > :start and ev.time < :end"
import time
sql1_start = time.time()
l = q.findAllByQuery(sql1, p)
sql1_stop = time.time()
# print "\nSQL1: %s objects in %s seconds" % (str(len(l)), str(sql1_stop - sql1_start))
sql2_start = time.time()
l = q.findAllByQuery(sql2, p)
sql2_stop = time.time()
def test1175(self):
uuid = self.root.sf.getAdminService().getEventContext().sessionUuid
update = self.root.sf.getUpdateService()
timeline = self.root.sf.getTimelineService()
# create dataset
ds = self.make_dataset(name='test1154-ds-%s' % (uuid),
client=self.root)
ds.unload()
# create tag
ann = omero.model.TagAnnotationI()
ann.textValue = rstring('tag-%s' % (uuid))
ann.setDescription(rstring('tag-%s' % (uuid)))
t_ann = omero.model.DatasetAnnotationLinkI()
t_ann.setParent(ds)
t_ann.setChild(ann)
update.saveObject(t_ann)
p = omero.sys.Parameters()
p.map = {}
f = omero.sys.Filter()
f.ownerId = rlong(0)
f.limit = rint(10)
p.theFilter = f
M = timeline.getMostRecentAnnotationLinks
res = M(None, ['TagAnnotation'], None, p)
assert len(res) > 0
# And now for #9609
res = M(None, ['TagAnnotation'], None, p, {"omero.group": "-1"})
assert len(res) > 0
def test1173(self):
client2, user2 = self.new_client_and_user(group=self.group)
timeline = client2.sf.getTimelineService()
uuid = client2.sf.getAdminService().getEventContext().sessionUuid
# create dataset
ds = self.make_dataset(name='test1173-ds-%s' % uuid, client=client2)
ds.unload()
# Here we assume that this test is not run within the last 1 second
start = int(time.time() * 1000 - 86400)
end = int(time.time() * 1000 + 86400)
p = omero.sys.Parameters()
p.map = {}
f = omero.sys.Filter()
f.ownerId = rlong(user2.id.val)
p.theFilter = f
M = timeline.getEventLogsByPeriod
A = rtime(start)
B = rtime(end)
rv = M(A, B, p)
assert len(rv) > 0
# And now for #9609
rv = M(A, B, p, {"omero.group": "-1"})
assert len(rv) > 0
def testBasicUsage(self):
gateway = self.client.sf.createGateway()
gateway.getProjects([0], False)
try:
# query below does not find image if created with
# self.createTestImage() even though it uses 'identical' code to
# createTestImage(self.client.sf), which uses script_utils
# iid = self.createTestImage().getId().getValue()
iid = createTestImage(self.client.sf)
print iid, type(iid)
query = self.client.sf.getQueryService()
params = omero.sys.Parameters()
params.map = {}
params.map["oid"] = rlong(iid)
params.theFilter = omero.sys.Filter()
params.theFilter.offset = rint(0)
params.theFilter.limit = rint(1)
pixel = query.findByQuery(
"select p from Pixels as p left outer join\
fetch p.image as i where i.id=:oid", params)
print pixel
imgid = pixel.image.id.val
print imgid
gateway.getRenderedImage(pixel.id.val, 0, 0)
except omero.ValidationException:
print "testBasicUsage - createTestImage has failed.\
This fixture method needs to be fixed."
gateway.close()
def getTimes(conn, image, theC=0):
"""
Get a dict of tIndex:time (seconds) for the first plane (Z = 0) at
each time-point for the defined image and Channel.
@param conn: BlitzGateway connection
@param image: ImageWrapper
@return: A map of tIndex: timeInSecs
"""
queryService = conn.getQueryService()
pixelsId = image.getPixelsId()
params = omero.sys.ParametersI()
params.add("theC", rint(theC))
params.add("theZ", rint(0))
params.add("pixelsId", rlong(pixelsId))
query = "from PlaneInfo as Info where Info.theZ=:theZ and" \
" Info.theC=:theC and pixels.id=:pixelsId"
infoList = queryService.findAllByQuery(query, params, conn.SERVICE_OPTS)
timeMap = {}
for info in infoList:
tIndex = info.theT.getValue()
time = info.deltaT.getValue()
timeMap[tIndex] = time
return timeMap
def get_managed_groups(conn):
"""
List of groups that the user can administer
All groups for admins
For other users, only groups of which they are the owner
"""
service_opts = deepcopy(conn.SERVICE_OPTS)
service_opts.setOmeroGroup(-1)
params = omero.sys.ParametersI()
qs = conn.getQueryService()
q = """
SELECT grp.id,
grp.name,
grp.details.permissions
FROM ExperimenterGroup grp
"""
if conn.isAdmin() is not True:
user = conn.getUser()
params.add('mid', rlong(user.getId()))
q += """
JOIN grp.groupExperimenterMap grexp
WHERE grp.name != 'user'
AND grexp.child.id = :mid
AND grexp.owner = true
ORDER BY lower(grp.name)
"""
groups = []
for e in qs.projection(q, params, service_opts):
groups.append(_marshal_group(conn, e[0:3]))
return groups
def api_thumbnails(request, conn=None, **kwargs):
"""
Return data like
{ project-1: {thumbnail: base64data, image: {id:1}} }
"""
project_ids = request.GET.getlist('project')
screen_ids = request.GET.getlist('screen')
image_ids = {}
for obj_type, ids in zip(['project', 'screen'], [project_ids, screen_ids]):
for obj_id in ids:
images = _get_study_images(conn, obj_type, obj_id)
if len(images) > 0:
image_ids[images[0].id.val] = "%s-%s" % (obj_type, obj_id)
thumbnails = conn.getThumbnailSet([rlong(i) for i in image_ids.keys()], 96)
rv = {}
for i, obj_id in image_ids.items():
rv[obj_id] = {"image": {'id': i}}
try:
t = thumbnails[i]
if len(t) > 0:
# replace thumbnail urls by base64 encoded image
rv[obj_id]["thumbnail"] = ("data:image/jpeg;base64,%s" %
base64.b64encode(t).decode("utf-8"))
except KeyError:
logger.error("Thumbnail not available. (img id: %d)" % i)
return rv
def createset(self, args):
"""
Create a tag set command.
"""
tags = []
if args.tag:
if type(args.tag) is list:
tags = args.tag
else:
tags = [args.tag]
else:
# Should not happen
self.ctx.err("Missing tag parameter")
sys.exit(1)
tag = self.create_tag(args.name, args.desc, text="tag set")
tag.ns = rstring(omero.constants.metadata.NSINSIGHTTAGSET)
links = []
for t in tags:
link = AnnotationAnnotationLinkI()
link.parent = tag
link.child = TagAnnotationI(rlong(int(t)), False)
links.append(link)
client = self.ctx.conn(args)
session = client.getSession()
update_service = session.getUpdateService()
try:
links = update_service.saveAndReturnArray(links)
self.ctx.out("TagAnnotation:%s" % links[0].parent.id.val)
except omero.ValidationException as e:
self.ctx.err(e.message)
self.ctx.err("Check that tag '%s' exists." % t)
sys.exit(1)
def getDatasetMap(self):
"""
Convert unique list of dataset names to a map
(dataset_name, dataset_object).
"""
dataset_map = {}
params = omero.sys.ParametersI()
params.add("pid", rlong(self.target_project_id))
for name in self.target_dataset_names:
params.add("dname", rstring(name))
dataset = self.query_service.findByQuery(self.dataset_query,
params)
if dataset is None:
print("Creating new datset")
dataset = omero.model.DatasetI()
dataset.setName(rstring(name))
dataset = \
self.update_service.saveAndReturnObject(dataset)
datasetId = dataset.getId().getValue()
print(("\tNew dataset ID:", datasetId))
link = omero.model.ProjectDatasetLinkI()
print(("\tLinking dataset to:", self.target_project_id))
link.parent = omero.model.ProjectI(self.target_project_id,
False)
link.child = omero.model.DatasetI(datasetId, False)
self.update_service.saveObject(link)
dataset = self.query_service.findByQuery(
self.dataset_query, params)
dataset_map[name] = dataset
return dataset_map
def timeout(self, args):
client = self.ctx.conn(args)
svc = client.sf.getSessionService()
uuid = args.session
if uuid is None:
uuid = self.ctx.get_event_context().sessionUuid
try:
obj = svc.getSession(uuid)
except:
self.ctx.dbg(traceback.format_exc())
self.ctx.die(557, "cannot get session: %s" % uuid)
if args.seconds is None:
# Query only
secs = unwrap(obj.timeToIdle) / 1000.0
self.ctx.out(secs)
return secs
req = omero.cmd.UpdateSessionTimeoutRequest()
req.session = uuid
req.timeToIdle = rlong(args.seconds * 1000)
try:
cb = client.submit(req) # Response is "OK"
cb.close(True)
except omero.CmdError, ce:
self.ctx.dbg(str(ce.err))
self.ctx.die(558, "CmdError: %s" % ce.err.name)
def runAsScript():
"""
The main entry point of the script, as called by the client via the
scripting service, passing the required parameters.
"""
printDuration(False) # start timer
dataTypes = [rstring('Dataset'), rstring('Image')]
client = scripts.client(
'Images_From_ROIs.py',
"""Create new Images from the regions defined by Rectangle ROIs on \
other Images.
Designed to work with single-plane images (Z=1 T=1) with multiple ROIs per \
image.
If you choose to make an image stack from all the ROIs, this script \
assumes that all the ROIs on each Image are the same size.""",
scripts.String(
"Data_Type", optional=False, grouping="1",
description="Choose Images via their 'Dataset' or directly by "
" 'Image' IDs.", values=dataTypes, default="Image"),
scripts.List(
"IDs", optional=False, grouping="2",
description="List of Dataset IDs or Image IDs to "
" process.").ofType(rlong(0)),
scripts.String(
"Container_Name", grouping="3",
description="Option: put Images in new Dataset with this name"
" OR use this name for new Image stacks, if 'Make_Image_Stack')",
default="From_ROIs"),
scripts.Bool(
"Make_Image_Stack", grouping="4", default=False,
description="If true, make a single Image (stack) from all the"
" ROIs of each parent Image"),
version="4.2.0",
authors=["William Moore", "OME Team"],
institutions=["University of Dundee"],
contact="*****@*****.**",
)
try:
parameterMap = client.getInputs(unwrap=True)
print parameterMap
# create a wrapper so we can use the Blitz Gateway.
conn = BlitzGateway(client_obj=client)
robj, message = makeImagesFromRois(conn, parameterMap)
client.setOutput("Message", rstring(message))
if robj is not None:
client.setOutput("Result", robject(robj))
finally:
client.closeSession()
printDuration()
def get_managed_groups(conn):
"""
List of groups that the user can administer
All groups for admins
For other users, only groups of which they are the owner
"""
service_opts = deepcopy(conn.SERVICE_OPTS)
service_opts.setOmeroGroup(-1)
params = omero.sys.ParametersI()
qs = conn.getQueryService()
q = """
SELECT grp.id,
grp.name,
grp.details.permissions
FROM ExperimenterGroup grp
"""
if conn.isAdmin() is not True:
user = conn.getUser()
params.add('mid', rlong(user.getId()))
q += """
JOIN grp.groupExperimenterMap grexp
WHERE grp.name != 'user'
AND grexp.child.id = :mid
AND grexp.owner = true
ORDER BY lower(grp.name)
"""
groups = []
for e in qs.projection(q, params, service_opts):
groups.append(_marshal_group(conn, e[0:3]))
return groups
def createAnnotationsLinks(self, atype, tids, oids):
"""
Links existing annotations to 1 or more objects
@param atype: Annotation type E.g. "tag", "file"
@param tids: Annotation IDs
@param oids: Dict of Objects and IDs. E.g. {"Image": [1,2,3],
"Dataset", [6]}
"""
atype = str(atype).lower()
if not atype.lower() in ("tag", "comment", "file"):
raise AttributeError("Object type must be: tag, comment, file.")
new_links = list()
annotations = list(self.conn.getObjects("Annotation", tids))
parent_objs = []
for k in oids:
if len(oids[k]) > 0:
if k.lower() == 'acquisition':
parent_type = 'PlateAcquisition'
else:
parent_type = k.lower().title()
parent_ids = [o.id for o in oids[k]]
# check for existing links belonging to Current user
params = omero.sys.Parameters()
params.theFilter = omero.sys.Filter()
params.theFilter.ownerId = rlong(self.conn.getUserId())
links = self.conn.getAnnotationLinks(parent_type,
parent_ids=parent_ids,
ann_ids=tids,
params=params)
pcLinks = [(link.parent.id.val, link.child.id.val)
for link in links]
# Create link between each object and annotation
for obj in self.conn.getObjects(parent_type, parent_ids):
parent_objs.append(obj)
for a in annotations:
if (obj.id, a.id) in pcLinks:
continue # link already exists
l_ann = getattr(omero.model,
parent_type + "AnnotationLinkI")()
l_ann.setParent(obj._obj)
l_ann.setChild(a._obj)
new_links.append(l_ann)
failed = 0
saved_links = []
try:
# will fail if any of the links already exist
saved_links = self.conn.getUpdateService().saveAndReturnArray(
new_links, self.conn.SERVICE_OPTS)
except omero.ValidationException:
for link in new_links:
try:
saved_links.append(
self.conn.getUpdateService().saveAndReturnObject(
link, self.conn.SERVICE_OPTS))
except Exception:
failed += 1
return tids
def well():
"""Basic Well for testing Color. Full test of Well below."""
well = WellI()
well.id = rlong(1)
well.column = rint(0)
well.row = rint(0)
return well
def testOddMessage(self):
store = self.client.sf.createRawFileStore()
images = list()
for i in range(0, 10):
img = self.make_image()
iid = img.getId().getValue()
oFile = omero.model.OriginalFileI()
oFile.setName(rstring('companion_file.txt'))
oFile.setPath(rstring('/my/path/to/the/file/'))
oFile.setSize(rlong(7471))
oFile.setHash(rstring("pending"))
oFile.setMimetype(rstring('Companion/Deltavision'))
ofid = self.update.saveAndReturnObject(oFile).id.val
store.setFileId(ofid)
binary = 'aaa\naaaa\naaaaa'
store.write(binary, 0, 0)
of = store.save()
fa = omero.model.FileAnnotationI()
fa.setNs(rstring(omero.constants.namespaces.NSCOMPANIONFILE))
fa.setFile(of)
self.link(img, fa)
images.append(iid)
command = Delete2(targetObjects={"Image": images})
handle = self.client.sf.submit(command)
callback = self.wait_on_cmd(self.client, handle)
callback.close(True)
def opt_unit_label(identity_transform):
o = LabelI()
populate_shape(o, identity_transform, False)
o.x = rdouble(1.0)
o.y = rdouble(2.0)
o.id = rlong(7)
return o
def test_marshal_plate_not_owner(self, mock_conn, owner_permissions):
row = [
rlong(1L),
rstring('name'),
rlong(2L),
owner_permissions,
]
expected = {
'id': 1L,
'name': 'name',
'permsCss': 'canEdit canAnnotate canLink canDelete',
'plateAcquisitions': list()
}
marshaled = marshal_plate(mock_conn, row)
assert marshaled == expected
def runAsScript():
"""
The main entry point of the script, as called by the client via the
scripting service, passing the required parameters.
"""
printDuration(False) # start timer
dataTypes = [rstring('Dataset'), rstring('Image')]
client = scripts.client(
'Images_From_ROIs.py',
"""Create new Images from the regions defined by Rectangle ROIs on \
other Images.
Designed to work with single-plane images (Z=1 T=1) with multiple ROIs per \
image.
If you choose to make an image stack from all the ROIs, this script \
assumes that all the ROIs on each Image are the same size.""",
scripts.String(
"Data_Type", optional=False, grouping="1",
description="Choose Images via their 'Dataset' or directly by "
" 'Image' IDs.", values=dataTypes, default="Image"),
scripts.List(
"IDs", optional=False, grouping="2",
description="List of Dataset IDs or Image IDs to "
" process.").ofType(rlong(0)),
scripts.String(
"Container_Name", grouping="3",
description="Option: put Images in new Dataset with this name"
" OR use this name for new Image stacks, if 'Make_Image_Stack')",
default="From_ROIs"),
scripts.Bool(
"Make_Image_Stack", grouping="4", default=False,
description="If true, make a single Image (stack) from all the"
" ROIs of each parent Image"),
version="4.2.0",
authors=["William Moore", "OME Team"],
institutions=["University of Dundee"],
contact="*****@*****.**",
)
try:
parameterMap = client.getInputs(unwrap=True)
print parameterMap
# create a wrapper so we can use the Blitz Gateway.
conn = BlitzGateway(client_obj=client)
robj, message = makeImagesFromRois(conn, parameterMap)
client.setOutput("Message", rstring(message))
if robj is not None:
client.setOutput("Result", robject(robj))
finally:
client.closeSession()
printDuration()
def getTimes(conn, image, theC=0):
"""
Get a dict of tIndex:time (seconds) for the first plane (Z = 0) at
each time-point for the defined image and Channel.
@param conn: BlitzGateway connection
@param image: ImageWrapper
@return: A map of tIndex: timeInSecs
"""
queryService = conn.getQueryService()
pixelsId = image.getPixelsId()
params = omero.sys.ParametersI()
params.add("theC", rint(theC))
params.add("theZ", rint(0))
params.add("pixelsId", rlong(pixelsId))
query = "from PlaneInfo as Info where Info.theZ=:theZ and Info.theC=:theC and pixels.id=:pixelsId"
infoList = queryService.findAllByQuery(query, params, conn.SERVICE_OPTS)
timeMap = {}
for info in infoList:
tIndex = info.theT.getValue()
time = info.deltaT.getValue()
timeMap[tIndex] = time
return timeMap
def testGroup(self):
p = ParametersI()
p.grp(rlong(1))
assert p.isGroup()
assert p.getGroup().getValue() == 1L
p.allGrps()
assert not p.isGroup()
def label():
o = LabelI()
populate_shape(o)
o.x = rdouble(1.0)
o.y = rdouble(2.0)
o.id = rlong(7L)
return o
def opt_unit_label():
o = LabelI()
populate_shape(o, False)
o.x = rdouble(1.0)
o.y = rdouble(2.0)
o.id = rlong(7L)
return o
def point():
o = PointI()
populate_shape(o)
o.cx = rdouble(1.0)
o.cy = rdouble(2.0)
o.id = rlong(3L)
return o
def externalInfo():
o = ExternalInfoI()
o.entityId = rlong(123L)
o.entityType = rstring("test")
o.lsid = rstring("ABCDEF")
o.uuid = rstring("f90a1fd5-275c-4d14-82b3-87b5ef0f07de")
return o
def testExperimenter(self):
p = ParametersI()
p.exp(rlong(1))
assert p.isExperimenter()
assert p.getExperimenter().getValue() == 1L
p.allExps()
assert not p.isExperimenter()
def test1088(self):
admin = self.root.sf.getAdminService()
q = self.root.sf.getQueryService()
cx = admin.getEventContext()
p = omero.sys.Parameters()
p.map = {}
p.map["uid"] = rlong(cx.userId)
p.map['start'] = start = rtime(1218529874000)
p.map['end'] = end = rtime(1221121874000)
sql1 = "select el from EventLog el left outer join fetch el.event ev " \
"where el.entityType in ('ome.model.core.Pixels', 'ome.model.core.Image', " \
"'ome.model.containers.Dataset', 'ome.model.containers.Project') " \
"and ev.id in (select id from Event where experimenter.id=:uid and time > :start and time < :end)"
sql2 = "select el from EventLog el left outer join fetch el.event ev " \
"where el.entityType in ('ome.model.core.Pixels', 'ome.model.core.Image', " \
"'ome.model.containers.Dataset', 'ome.model.containers.Project') " \
"and ev.experimenter.id=:uid and ev.time > :start and ev.time < :end"
import time
sql1_start = time.time()
l = q.findAllByQuery(sql1, p)
sql1_stop = time.time()
# print "\nSQL1: %s objects in %s seconds" % (str(len(l)), str(sql1_stop - sql1_start))
sql2_start = time.time()
l = q.findAllByQuery(sql2, p)
sql2_stop = time.time()
def testGroup(self):
p = ParametersI()
p.grp(rlong(1))
assert p.isGroup()
assert p.getGroup().getValue() == 1L
p.allGrps()
assert not p.isGroup()
def createset(self, args):
"""
Create a tag set command.
"""
tags = []
if args.tag:
if type(args.tag) is list:
tags = args.tag
else:
tags = [args.tag]
else:
# Should not happen
self.ctx.err("Missing tag parameter")
sys.exit(1)
tag = self.create_tag(args.name, args.desc, text="tag set")
tag.ns = rstring(omero.constants.metadata.NSINSIGHTTAGSET)
links = []
for t in tags:
link = AnnotationAnnotationLinkI()
link.parent = tag
link.child = TagAnnotationI(rlong(long(t)), False)
links.append(link)
client = self.ctx.conn(args)
session = client.getSession()
update_service = session.getUpdateService()
try:
links = update_service.saveAndReturnArray(links)
self.ctx.out("TagAnnotation:%s" % links[0].parent.id.val)
except omero.ValidationException as e:
self.ctx.err(e.message)
self.ctx.err("Check that tag '%s' exists." % t)
sys.exit(1)
def timeout(self, args):
client = self.ctx.conn(args)
svc = client.sf.getSessionService()
uuid = args.session
if uuid is None:
uuid = self.ctx.get_event_context().sessionUuid
try:
obj = svc.getSession(uuid)
except:
self.ctx.dbg(traceback.format_exc())
self.ctx.die(557, "cannot get session: %s" % uuid)
if args.seconds is None:
# Query only
secs = unwrap(obj.timeToIdle)/1000.0
self.ctx.out(secs)
return secs
req = omero.cmd.UpdateSessionTimeoutRequest()
req.session = uuid
req.timeToIdle = rlong(args.seconds * 1000)
try:
cb = client.submit(req) # Response is "OK"
cb.close(True)
except omero.CmdError, ce:
self.ctx.dbg(str(ce.err))
self.ctx.die(558, "CmdError: %s" % ce.err.name)
def _getProcessor(self):
scripts = self.root.getSession().getScriptService()
id = scripts.uploadOfficialScript("/tests/cli/%s.py" % self.uuid(),
SCRIPT)
j = omero.model.ScriptJobI()
j.linkOriginalFile(omero.model.OriginalFileI(rlong(id), False))
p = self.client.sf.sharedResources().acquireProcessor(j, 100)
return p
def testPingViaISCript(self):
p = self._getProcessor()
input = rmap({})
input.val["a"] = rlong(2)
input.val["b"] = rstring("d")
process = p.execute(input)
output = self.assertSuccess(p, process)
assert output.val["a"].val == 2
def testInsightPolygonMarshal(self):
shape = omero.model.PolygonI()
shape.id = rlong(self.DEFAULT_ID)
shape.points = rstring('points[1,2 2,3 4,5] points1[1,2 2,3 4,5] points2[1,2 2,3 4,5] mask[0,0,0]')
marshaled = shapeMarshal(shape)
self.assertEqual('Polygon', marshaled['type'])
self.assertEqual(self.DEFAULT_ID, marshaled['id'])
self.assertEquals('M 1 2 L 2 3 L 4 5 z' , marshaled['points'])
def test_marshal_plate_acquisition_name_no_start_no_end(
self, mock_conn, owner_permissions):
row = [
rlong(1),
rstring("name"),
rlong(1), owner_permissions, None, None
]
expected = {
"id": 1,
"ownerId": 1,
"name": "name",
"permsCss":
"canEdit canAnnotate canLink canDelete canChgrp isOwned",
}
marshaled = _marshal_plate_acquisition(mock_conn, row)
assert marshaled == expected
def test_marshal_dataset_not_owner(self, mock_conn, owner_permissions):
row = [
rlong(1),
rstring("name"),
rlong(2), owner_permissions,
rlong(1)
]
expected = {
"id": 1,
"ownerId": 2,
"name": "name",
"permsCss": "canEdit canAnnotate canLink canDelete canChgrp",
"childCount": 1,
}
marshaled = _marshal_dataset(mock_conn, row)
assert marshaled == expected
def test_marshal_plate_acquisition_name_no_start_no_end(
self, mock_conn, owner_permissions):
row = [
rlong(1),
rstring('name'),
rlong(1), owner_permissions, None, None
]
expected = {
'id': 1,
'ownerId': 1,
'name': 'name',
'permsCss':
'canEdit canAnnotate canLink canDelete canChgrp isOwned'
}
marshaled = _marshal_plate_acquisition(mock_conn, row)
assert marshaled == expected
def project_with_datasets(project):
for dataset_id in range(1, 3):
o = DatasetI()
o.id = rlong(dataset_id)
o.name = rstring('dataset_name_%d' % dataset_id)
o.description = rstring('dataset_description_%d' % dataset_id)
project.linkDataset(o)
return project
def basic_polyline(request, default_id):
points = request.param
shape = omero.model.PolylineI()
shape.id = rlong(default_id)
shape.points = rstring(points)
# r=17,g=34,b=51,a=0
shape.strokeColor = rint(ctypes.c_int(0x11223300).value)
return shape
def testOmeXmlPolygonMarshal(self):
shape = omero.model.PolygonI()
shape.id = rlong(self.DEFAULT_ID)
shape.points = rstring('1,2 2,3 4,5')
marshaled = shapeMarshal(shape)
self.assertEqual('Polygon', marshaled['type'])
self.assertEqual(self.DEFAULT_ID, marshaled['id'])
self.assertEquals('M 1 2 L 2 3 L 4 5 z' , marshaled['points'])
def test_marshal_dataset_not_owner(self, mock_conn, owner_permissions):
row = [
rlong(1),
rstring('name'),
rlong(2), owner_permissions,
rlong(1)
]
expected = {
'id': 1,
'ownerId': 2,
'name': 'name',
'permsCss': 'canEdit canAnnotate canLink canDelete canChgrp',
'childCount': 1
}
marshaled = _marshal_dataset(mock_conn, row)
assert marshaled == expected
def testInsightPolyLineFloatMarshal(self):
shape = omero.model.PolylineI()
shape.id = rlong(self.DEFAULT_ID)
shape.points = rstring('points[1.5,2.5 2,3 4.1,5.1] points1[1.5,2.5 2,3 4.1,5.1] points2[1.5,2.5 2,3 4.1,5.1] mask[0,0,0]')
marshaled = shapeMarshal(shape)
self.assertEqual('PolyLine', marshaled['type'])
self.assertEqual(self.DEFAULT_ID, marshaled['id'])
self.assertEquals('M 1.5 2.5 L 2 3 L 4.1 5.1' , marshaled['points'])
