def get_image_ids(conn, plate_id, field_id=0):
"""Get image IDs for images in Plate"""
conn.SERVICE_OPTS.setOmeroGroup('-1')
query_service = conn.getQueryService()
params = ParametersI()
params.addId(plate_id)
params.add('wsidx', rint(field_id))
query = "select img.id "\
"from Well well "\
"join well.wellSamples ws "\
"join ws.image img "\
"where well.plate.id = :id "\
"and index(ws) = :wsidx"
p = query_service.projection(query, params, conn.SERVICE_OPTS)
img_ids = [i[0].val for i in p]
return img_ids
def get_child_counts(conn, link_class, parent_ids):
"""
Count child links for the specified parent_ids.
@param conn: BlitzGateway
@param link_class: Type of link, e.g. 'ProjectDatasetLink'
@param parent_ids: List of Parent IDs
@return A dict of parent_id: child_count
"""
ctx = deepcopy(conn.SERVICE_OPTS)
ctx.setOmeroGroup(-1)
params = ParametersI()
params.add('ids', wrap([rlong(id) for id in parent_ids]))
query = ("select chl.parent.id, count(chl.id) from %s chl"
" where chl.parent.id in (:ids) group by chl.parent.id"
% link_class)
result = conn.getQueryService().projection(query, params, ctx)
counts = {}
for d in result:
counts[d[0].val] = unwrap(d[1])
return counts
def get_wellsample_indices(conn, plate_id=None, plateacquisition_id=None):
"""
Return min and max WellSample index for a Plate OR PlateAcquisition
@param conn: BlitzGateway
@param plate_id: Plate ID
@param plateacquisition_id: PlateAcquisition ID
@return A dict of parent_id: child_count
"""
ctx = deepcopy(conn.SERVICE_OPTS)
ctx.setOmeroGroup(-1)
params = ParametersI()
query = "select minIndex(ws), maxIndex(ws) from Well well " \
"join well.wellSamples ws"
if plate_id is not None:
query += " where well.plate.id=:plate_id "
params.add('plate_id', rlong(plate_id))
elif plateacquisition_id is not None:
query += " where ws.plateAcquisition.id=:plateacquisition_id"
params.add('plateacquisition_id', rlong(plateacquisition_id))
result = conn.getQueryService().projection(query, params, ctx)
result = [r for r in unwrap(result)[0] if r is not None]
return result
def attributes_by_attributes(conn,
name="Gene Symbol",
value="ASH2L",
ns="openmicroscopy.org/mapr/gene",
ns2="openmicroscopy.org/mapr/phenotype",
name2=None,
sId=None
):
"""
Return a list of neighbours attributes
for given case insensitive attribute value. (Uses the python blitz gateway)
"""
from omero.rtypes import rstring, rlist, unwrap
from omero.sys import ParametersI
params = ParametersI()
params.addString("value", value.lower())
q = (
"select distinct new map( mv.value as value) "
"from Annotation as a "
"join a.mapValue as mv "
"where lower(mv.value) = :value {where_claus}"
)
where_claus = []
if name:
params.addString("name", name)
where_claus.append("and mv.name = :name")
q = q.format(**{'where_claus':" ".join(where_claus)})
values = [v[0]['value'] for v in unwrap(
conn.getQueryService().projection(q, params))]
params = ParametersI()
valuelist = [rstring(unicode(v)) for v in values]
params.add('values', rlist(valuelist))
params.addString("ns", ns)
params.addString("ns2", ns2)
q = (
"select distinct new map("
"mv.name as name, "
"mv.value as value, "
"mv2.name as name2, "
"mv2.value as value2) "
"from Image as i "
"join i.annotationLinks as ial "
"join i.annotationLinks as ial2 "
"join ial.child as a "
"join a.mapValue as mv "
"join ial2.child as a2 "
"join a2.mapValue as mv2 "
"where a.ns = :ns and a2.ns = :ns2 "
"and mv.value in (:values) {where_claus} "
)
where_claus = []
if name:
params.addString("name", name)
where_claus.append("and mv.name = :name")
if name2:
params.addString("name2", name2)
where_claus.append("and mv2.name = :name2")
q = q.format(**{'where_claus':" ".join(where_claus)})
if sId != None:
q = q + ("and i in (select image from WellSample "
"where well.plate in "
"(select child from ScreenPlateLink where parent.id = {sId}))")
screenidList = []
screenidList.append(str(sId))
q = q.format(**{'sId':" ".join(screenidList)})
res = {}
for r in unwrap(conn.getQueryService().projection(q, params)):
r = r[0]
try:
res[(r['name'], r['value'])].append((r['name2'], r['value2']))
except KeyError:
res[(r['name'], r['value'])] = [(r['name2'], r['value2'])]
return res
def testQueryTaggedUnique(self):
# get group we're working on...
ctx = self.client.sf.getAdminService().getEventContext()
groupId = ctx.groupId
print 'groupId', groupId
# Admin sets permissions to read-ann
admin = self.root.sf.getAdminService()
rootUpdate = self.root.sf.getUpdateService()
gr = admin.getGroup(groupId)
p = PermissionsI()
p.setUserRead(True)
p.setUserWrite(True)
p.setGroupRead(True)
p.setGroupAnnotate(True)
p.setGroupWrite(False)
p.setWorldRead(False)
p.setWorldAnnotate(False)
p.setWorldWrite(False)
gr.details.permissions = p
admin.updateGroup(gr)
# Update context for user
ctx = self.client.sf.getAdminService().getEventContext()
update = self.client.sf.getUpdateService()
queryService = self.client.sf.getQueryService()
tagCount = 5
# User creates tag linked to images
tag = TagAnnotationI()
tag.textValue = wrap("test_iQuerySpeed")
links = []
for i in range(tagCount):
iid = createImageWithPixels(self.client, self.uuid())
link = ImageAnnotationLinkI()
link.parent = ImageI(iid, False)
link.child = tag
links.append(link)
links = update.saveAndReturnArray(links)
tag = links[0].child
# check permissions
p = tag.getDetails().getPermissions()
assert p.isGroupRead()
assert p.isGroupAnnotate()
# Root also links user's tag to images
rootLinks = []
for l in links:
link = ImageAnnotationLinkI()
link.parent = ImageI(l.parent.id, False)
link.child = TagAnnotationI(l.child.id, False)
rootLinks.append(link)
rootUpdate.saveAndReturnArray(rootLinks, {'omero.group': str(groupId)})
q = """select distinct new map(obj.id as id,
obj.name as name,
obj.details.owner.id as ownerId,
obj as image_details_permissions,
obj.fileset.id as filesetId,
lower(obj.name) as n
,
pix.sizeX as sizeX,
pix.sizeY as sizeY,
pix.sizeZ as sizeZ
)
from Image obj left outer join obj.pixels pix
join obj.annotationLinks alink
where %s
order by lower(obj.name), obj.id """
params = ParametersI()
params.add('tid', tag.id)
# We can get all the tagged images like this.
# We use an additional select statement to give 'unique' results
uniqueClause = """alink.id = (select max(alink.id)
from ImageAnnotationLink alink
where alink.child.id=:tid and alink.parent.id=obj.id)"""
query = q % uniqueClause
result1 = queryService.projection(query, params,
{'omero.group': str(groupId)})
assert len(result1) == tagCount
# Without the select statement, we get the same image returned
# multiple times if there is no 'distinct'
clause = "alink.child.id=:tid"
query = q % clause
result2 = queryService.projection(query, params,
{'omero.group': str(groupId)})
assert len(result2) == tagCount
for idx in range(len(result1)-1):
# Omit final since == isn't defined for Ice objects.
assert result1[idx] == result2[idx]
host=os.environ.get('IDR_HOST', 'localhost'))
conn.connect()
conn.setGroupForSession(3) # Public
query_service = conn.getQueryService()
# Find the plates of idr0004.
query = """
SELECT child.id
FROM ScreenPlateLink
WHERE parent.name LIKE :name
"""
params = ParametersI()
params.add('name', wrap('idr0004-%'))
rows = query_service.projection(query, params)
plate_ids = [row[0].val for row in rows]
assert plate_ids
# Loop through each field of those plates.
query = """
SELECT id, image.name, image.fileset.id, well.row, well.column, well.plate.name
FROM WellSample
WHERE well.plate.id IN (:ids)
"""
def testQueryTaggedUnique(self):
# get group we're working on...
ctx = self.client.sf.getAdminService().getEventContext()
groupId = ctx.groupId
print 'groupId', groupId
# Admin sets permissions to read-ann
admin = self.root.sf.getAdminService()
rootUpdate = self.root.sf.getUpdateService()
gr = admin.getGroup(groupId)
p = PermissionsI()
p.setUserRead(True)
p.setUserWrite(True)
p.setGroupRead(True)
p.setGroupAnnotate(True)
p.setGroupWrite(False)
p.setWorldRead(False)
p.setWorldAnnotate(False)
p.setWorldWrite(False)
gr.details.permissions = p
admin.updateGroup(gr)
# Update context for user
ctx = self.client.sf.getAdminService().getEventContext()
update = self.client.sf.getUpdateService()
queryService = self.client.sf.getQueryService()
tagCount = 5
# User creates tag linked to images
tag = TagAnnotationI()
tag.textValue = wrap("test_iQuerySpeed")
links = []
for i in range(tagCount):
iid = createImageWithPixels(self.client, self.uuid())
link = ImageAnnotationLinkI()
link.parent = ImageI(iid, False)
link.child = tag
links.append(link)
links = update.saveAndReturnArray(links)
tag = links[0].child
# check permissions
p = tag.getDetails().getPermissions()
assert p.isGroupRead()
assert p.isGroupAnnotate()
# Root also links user's tag to images
rootLinks = []
for l in links:
link = ImageAnnotationLinkI()
link.parent = ImageI(l.parent.id, False)
link.child = TagAnnotationI(l.child.id, False)
rootLinks.append(link)
rootUpdate.saveAndReturnArray(rootLinks, {'omero.group': str(groupId)})
q = """select distinct new map(obj.id as id,
obj.name as name,
obj.details.owner.id as ownerId,
obj as image_details_permissions,
obj.fileset.id as filesetId,
lower(obj.name) as n
,
pix.sizeX as sizeX,
pix.sizeY as sizeY,
pix.sizeZ as sizeZ
)
from Image obj left outer join obj.pixels pix
join obj.annotationLinks alink
where %s
order by lower(obj.name), obj.id """
params = ParametersI()
params.add('tid', tag.id)
# We can get all the tagged images like this.
# We use an additional select statement to give 'unique' results
uniqueClause = """alink.id = (select max(alink.id)
from ImageAnnotationLink alink
where alink.child.id=:tid and alink.parent.id=obj.id)"""
query = q % uniqueClause
result1 = queryService.projection(query, params,
{'omero.group': str(groupId)})
assert len(result1) == tagCount
# Without the select statement, we get the same image returned
# multiple times if there is no 'distinct'
clause = "alink.child.id=:tid"
query = q % clause
result2 = queryService.projection(query, params,
{'omero.group': str(groupId)})
assert len(result2) == tagCount
for idx in range(len(result1)-1):
# Omit final since == isn't defined for Ice objects.
assert result1[idx] == result2[idx]
host=os.environ.get('IDR_HOST', 'localhost'))
conn.connect()
conn.setGroupForSession(3) # Public
query_service = conn.getQueryService()
# Find the plates of idr0004.
query = """
SELECT child.id
FROM ScreenPlateLink
WHERE parent.name LIKE :name
"""
params = ParametersI()
params.add('name', wrap('idr0004-%'))
rows = query_service.projection(query, params)
plate_ids = [row[0].val for row in rows]
assert plate_ids
# Loop through each field of those plates.
query = """
SELECT id, image.name, image.fileset.id, well.row, well.column, well.plate.name
FROM WellSample
WHERE well.plate.id IN (:ids)
"""
