def list(self, args):
c = self.ctx.conn(args)
iadmin = c.sf.getAdminService()
from omero.rtypes import unwrap
from omero.util.text import TableBuilder
list_of_dn_user_maps = unwrap(iadmin.lookupLdapAuthExperimenters())
if list_of_dn_user_maps is None:
return
count = 0
tb = TableBuilder("#")
if args.style:
tb.set_style(args.style)
tb.cols(["Id", "OmeName", "DN"])
for map in list_of_dn_user_maps:
for dn, id in map.items():
try:
exp = iadmin.getExperimenter(id)
except:
self.ctx.err("Bad experimenter: %s" % id)
tb.row(count, *(id, exp.omeName.val, dn))
count += 1
self.ctx.out(str(tb.build()))
def list(self, args):
c = self.ctx.conn(args)
iadmin = c.sf.getAdminService()
import omero
from omero.rtypes import unwrap
from omero.util.text import TableBuilder
try:
list_of_dn_user_maps = unwrap(iadmin.lookupLdapAuthExperimenters())
if list_of_dn_user_maps is None:
return
count = 0
tb = TableBuilder("#")
tb.cols(["Id", "OmeName", "DN"])
for map in list_of_dn_user_maps:
for dn, id in map.items():
try:
exp = iadmin.getExperimenter(id)
except:
self.ctx.err("Bad experimenter: %s" % id)
tb.row(count, *(id, exp.omeName.val, dn))
count += 1
self.ctx.out(str(tb.build()))
except omero.SecurityViolation, sv:
self.ctx.die(131,
"SecurityViolation: Must be an admin to lists DNs")
def list(self, args):
c = self.ctx.conn(args)
iadmin = c.sf.getAdminService()
from omero.rtypes import unwrap
from omero.util.text import TableBuilder
list_of_dn_user_maps = unwrap(iadmin.lookupLdapAuthExperimenters())
if list_of_dn_user_maps is None:
return
count = 0
tb = TableBuilder("#")
if args.style:
tb.set_style(args.style)
tb.cols(["Id", "OmeName", "DN"])
for map in list_of_dn_user_maps:
for dn, id in list(map.items()):
try:
exp = iadmin.getExperimenter(id)
except:
self.ctx.err("Bad experimenter: %s" % id)
tb.row(count, *(id, exp.omeName.val, dn))
count += 1
self.ctx.out(str(tb.build()))
def list(self, args):
c = self.ctx.conn(args)
iadmin = c.sf.getAdminService()
import omero
from omero.rtypes import unwrap
from omero.util.text import TableBuilder
try:
list_of_dn_user_maps = unwrap(iadmin.lookupLdapAuthExperimenters())
if list_of_dn_user_maps is None:
return
count = 0
tb = TableBuilder("#")
tb.cols(["Id", "OmeName", "DN"])
for map in list_of_dn_user_maps:
for dn, id in map.items():
try:
exp = iadmin.getExperimenter(id)
except:
self.ctx.err("Bad experimenter: %s" % id)
tb.row(count, *(id, exp.omeName.val, dn))
count += 1
self.ctx.out(str(tb.build()))
except omero.SecurityViolation:
self.ctx.die(131,
"SecurityViolation: Must be an admin to lists DNs")
def stat_screens(query):
tb = TableBuilder("Screen")
tb.cols(["ID", "Plates", "Wells", "Images", "Planes", "Bytes"])
plate_count = 0
well_count = 0
image_count = 0
plane_count = 0
byte_count = 0
for study, screens in sorted(studies().items()):
for screen, plates_expected in screens.items():
params = ParametersI()
params.addString("screen", screen)
rv = unwrap(query.projection((
"select s.id, count(distinct p.id), "
" count(distinct w.id), count(distinct i.id),"
" sum(cast(pix.sizeZ as long) * pix.sizeT * pix.sizeC), "
" sum(cast(pix.sizeZ as long) * pix.sizeT * pix.sizeC * "
" pix.sizeX * pix.sizeY * 2) "
"from Screen s "
"left outer join s.plateLinks spl "
"left outer join spl.child as p "
"left outer join p.wells as w "
"left outer join w.wellSamples as ws "
"left outer join ws.image as i "
"left outer join i.pixels as pix "
"where s.name = :screen "
"group by s.id"), params))
if not rv:
tb.row(screen, "MISSING", "", "", "", "", "")
else:
for x in rv:
plate_id, plates, wells, images, planes, bytes = x
plate_count += plates
well_count += wells
image_count += images
if planes:
plane_count += planes
if bytes:
byte_count += bytes
else:
bytes = 0
if plates != len(plates_expected):
plates = "%s of %s" % (plates, len(plates_expected))
tb.row(screen, plate_id, plates, wells, images, planes,
filesizeformat(bytes))
tb.row("Total", "", plate_count, well_count, image_count, plane_count,
filesizeformat(byte_count))
print str(tb.build())
def stat_screens(query):
tb = TableBuilder("Container")
tb.cols(["ID", "Set", "Wells", "Images", "Planes", "Bytes"])
plate_count = 0
well_count = 0
image_count = 0
plane_count = 0
byte_count = 0
for study, containers in sorted(studies().items()):
for container, set_expected in sorted(containers.items()):
params = ParametersI()
params.addString("container", container)
if "Plate" in set_expected:
expected = set_expected["Plate"]
rv = unwrap(query.projection(SPW_QUERY, params))
elif "Dataset" in set_expected:
expected = set_expected["Dataset"]
rv = unwrap(query.projection(PDI_QUERY, params))
else:
raise Exception("unknown: %s" % set_expected.keys())
if not rv:
tb.row(container, "MISSING", "", "", "", "", "")
else:
for x in rv:
plate_id, plates, wells, images, planes, bytes = x
plate_count += plates
well_count += wells
image_count += images
if planes:
plane_count += planes
if bytes:
byte_count += bytes
else:
bytes = 0
if plates != len(expected):
plates = "%s of %s" % (plates, len(expected))
tb.row(container, plate_id, plates, wells, images, planes,
filesizeformat(bytes))
tb.row("Total", "", plate_count, well_count, image_count, plane_count,
filesizeformat(byte_count))
print str(tb.build())
def stat_screens(query):
tb = TableBuilder("Container")
tb.cols(["ID", "Set", "Wells", "Images", "Planes", "Bytes"])
plate_count = 0
well_count = 0
image_count = 0
plane_count = 0
byte_count = 0
for study, containers in sorted(studies().items()):
for container, set_expected in sorted(containers.items()):
params = ParametersI()
params.addString("container", container)
if "Plate" in set_expected:
expected = set_expected["Plate"]
rv = unwrap(query.projection(SPW_QUERY, params))
elif "Dataset" in set_expected:
expected = set_expected["Dataset"]
rv = unwrap(query.projection(PDI_QUERY, params))
else:
raise Exception("unknown: %s" % set_expected.keys())
if not rv:
tb.row(container, "MISSING", "", "", "", "", "")
else:
for x in rv:
plate_id, plates, wells, images, planes, bytes = x
plate_count += plates
well_count += wells
image_count += images
if planes:
plane_count += planes
if bytes:
byte_count += bytes
else:
bytes = 0
if plates != len(expected):
plates = "%s of %s" % (plates, len(expected))
tb.row(container, plate_id, plates, wells, images, planes,
filesizeformat(bytes))
tb.row("Total", "", plate_count, well_count, image_count, plane_count,
filesizeformat(byte_count))
print str(tb.build())
def display(self, rv, cols=None, style=None, idsonly=False):
import omero.all
import omero.rtypes
from omero.util.text import TableBuilder
has_details = []
tb = TableBuilder("#")
if style:
tb.set_style(style)
for idx, object_list in enumerate(rv):
klass = "Null"
id = ""
values = {}
# Handling for simple lookup
if not idsonly and len(object_list) == 1 and \
isinstance(object_list[0], omero.rtypes.RObjectI):
has_details.append(idx)
o = object_list[0].val
if o:
tb.cols(["Class", "Id"])
klass = o.__class__.__name__
id = o.id.val
for k, v in list(o.__dict__.items()):
values[k] = self.unwrap(v)
values = self.filter(values)
tb.cols(list(values.keys()))
tb.row(idx, klass, id, **values)
# Handling for true projections
else:
indices = list(range(1, len(object_list) + 1))
if cols is not None:
tb.cols(cols)
else:
tb.cols(["Col%s" % x for x in indices])
values = tuple([self.unwrap(x) for x in object_list])
tb.row(idx, *values)
self.ctx.out(str(tb.build()))
return has_details
def display(self, rv, cols=None, style=None, idsonly=False):
import omero.all
import omero.rtypes
from omero.util.text import TableBuilder
has_details = []
tb = TableBuilder("#")
if style:
tb.set_style(style)
for idx, object_list in enumerate(rv):
klass = "Null"
id = ""
values = {}
# Handling for simple lookup
if not idsonly and len(object_list) == 1 and \
isinstance(object_list[0], omero.rtypes.RObjectI):
has_details.append(idx)
o = object_list[0].val
if o:
tb.cols(["Class", "Id"])
klass = o.__class__.__name__
id = o.id.val
for k, v in o.__dict__.items():
values[k] = self.unwrap(v)
values = self.filter(values)
tb.cols(values.keys())
tb.row(idx, klass, id, **values)
# Handling for true projections
else:
indices = range(1, len(object_list) + 1)
if cols is not None:
tb.cols(cols)
else:
tb.cols(["Col%s" % x for x in indices])
values = tuple([self.unwrap(x) for x in object_list])
tb.row(idx, *values)
self.ctx.out(str(tb.build()))
return has_details
def stat_plates(query, screen, images=False):
params = ParametersI()
params.addString("screen", screen)
obj = query.findByQuery((
"select s from Screen s "
"where s.name = :screen"), params)
if not obj:
raise Exception("unknown screen: %s" % screen)
if images:
q = ("select %s from Image i "
"join i.wellSamples ws join ws.well w "
"join w.plate p join p.screenLinks sl "
"join sl.parent s where s.name = :screen")
limit = 1000
found = 0
count = unwrap(query.projection(
q % "count(distinct i.id)", params
))[0][0]
print >>stderr, count
params.page(0, limit)
q = q % "distinct i.id"
q = "%s order by i.id" % q
while count > 0:
rv = unwrap(query.projection(q, params))
count -= len(rv)
found += len(rv)
params.page(found, limit)
for x in rv:
yield x[0]
return
plates = glob(join(screen, "plates", "*"))
plates = map(basename, plates)
tb = TableBuilder("Plate")
tb.cols(["PID", "Wells", "Images"])
well_count = 0
image_count = 0
for plate in plates:
params.addString("plate", plate)
rv = unwrap(query.projection((
"select p.id, count(distinct w.id), count(distinct i.id)"
" from Screen s "
"left outer join s.plateLinks spl join spl.child as p "
"left outer join p.wells as w "
"left outer join w.wellSamples as ws "
"left outer join ws.image as i "
"where s.name = :screen and p.name = :plate "
"group by p.id"), params))
if not rv:
tb.row(plate, "MISSING", "", "")
else:
for x in rv:
plate_id, wells, images = x
well_count += wells
image_count += images
tb.row(plate, plate_id, wells, images)
tb.row("Total", "", well_count, image_count)
print str(tb.build())
def stat_plates(query, screen, images=False):
params = ParametersI()
params.addString("screen", screen)
obj = query.findByQuery(("select s from Screen s "
"where s.name = :screen"), params)
if not obj:
raise Exception("unknown screen: %s" % screen)
if images:
q = ("select %s from Image i "
"join i.wellSamples ws join ws.well w "
"join w.plate p join p.screenLinks sl "
"join sl.parent s where s.name = :screen")
limit = 1000
found = 0
count = unwrap(query.projection(q % "count(distinct i.id)",
params))[0][0]
print >> stderr, count
params.page(0, limit)
q = q % "distinct i.id"
q = "%s order by i.id" % q
while count > 0:
rv = unwrap(query.projection(q, params))
count -= len(rv)
found += len(rv)
params.page(found, limit)
for x in rv:
yield x[0]
return
plates = glob(join(screen, "plates", "*"))
plates = map(basename, plates)
tb = TableBuilder("Plate")
tb.cols(["PID", "Wells", "Images"])
well_count = 0
image_count = 0
for plate in plates:
params.addString("plate", plate)
rv = unwrap(
query.projection(
("select p.id, count(distinct w.id), count(distinct i.id)"
" from Screen s "
"left outer join s.plateLinks spl join spl.child as p "
"left outer join p.wells as w "
"left outer join w.wellSamples as ws "
"left outer join ws.image as i "
"where s.name = :screen and p.name = :plate "
"group by p.id"), params))
if not rv:
tb.row(plate, "MISSING", "", "")
else:
for x in rv:
plate_id, wells, images = x
well_count += wells
image_count += images
tb.row(plate, plate_id, wells, images)
tb.row("Total", "", well_count, image_count)
print str(tb.build())
