def sets(self, args):
"""List filesets by various criteria
Filesets are bundles of original data imported into OMERO 5 and above
which represent 1 *or more* images.
Examples:
bin/omero fs sets --order=newest # Default
bin/omero fs sets --order=oldest
bin/omero fs sets --order=largest
bin/omero fs sets --without-images # Corrupt filesets
bin/omero fs sets --with-transfer=ln_s # Symlinked filesets
bin/omero fs sets --check # Proof the checksums
"""
from omero.constants.namespaces import NSFILETRANSFER
from omero_sys_ParametersI import ParametersI
from omero.rtypes import unwrap
client = self.ctx.conn(args)
service = client.sf.getQueryService()
admin = client.sf.getAdminService()
if args.check and not admin.getEventContext().isAdmin:
self.error_admin_only(fatal=True)
annselect = (
"(select ann.textValue from Fileset f4 "
"join f4.annotationLinks fal join fal.child ann "
"where f4.id = fs.id and ann.ns =:ns) ")
select = (
"select fs.id, fs.templatePrefix, "
"(select size(f2.images) from Fileset f2 "
"where f2.id = fs.id),"
"(select size(f3.usedFiles) from Fileset f3 "
"where f3.id = fs.id),") \
+ annselect
query1 = (
"from Fileset fs "
"where 1 = 1 ")
query2 = (
"group by fs.id, fs.templatePrefix ")
if args.order:
if args.order == "newest":
query2 += "order by fs.id desc"
elif args.order == "oldest":
query2 += "order by fs.id asc"
elif args.order == "prefix":
query2 += "order by fs.templatePrefix"
if args.without_images:
query = "%s and fs.images is empty %s" % (query1, query2)
else:
query = "%s %s" % (query1, query2)
params = ParametersI()
params.addString("ns", NSFILETRANSFER)
count = service.projection("select count(fs) " + query1,
params, {"omero.group": "-1"})
params.page(args.offset, args.limit)
objs = service.projection(select + query,
params, {"omero.group": "-1"})
objs = unwrap(objs)
count = unwrap(count)[0][0]
cols = ["Id", "Prefix", "Images", "Files", "Transfer"]
if args.check:
cols.append("Check")
tb = self._table(args)
tb.cols(cols)
tb.page(args.offset, args.limit, count)
# Map any requested transfers as well
if args.with_transfer:
restricted = [TRANSFERS.get(x, x) for x in args.with_transfer[0]]
else:
restricted = None
for idx, obj in enumerate(objs):
# Map the transfer name to the CLI symbols
ns = obj[-1]
if ns is None:
ns = ""
elif ns in TRANSFERS:
ns = TRANSFERS[ns]
obj[-1] = ns
# Filter based on the ns symbols
if restricted and ns not in restricted:
continue
# Now perform check if required
if args.check:
from omero.grid import RawAccessRequest
desc, prx = self.get_managed_repo(client)
ctx = client.getContext(group=-1)
check_params = ParametersI()
check_params.addId(obj[0])
rows = service.projection((
"select h.value, f.hash, "
"f.path || '/' || f.name "
"from Fileset fs join fs.usedFiles uf "
"join uf.originalFile f join f.hasher h "
"where fs.id = :id"
), check_params, ctx)
if not rows:
obj.append("Empty")
err = None
for row in rows:
row = unwrap(row)
raw = RawAccessRequest()
raw.repoUuid = desc.hash.val
raw.command = "checksum"
raw.args = map(str, row)
try:
cb = client.submit(raw)
cb.close(True)
except CmdError, ce:
err = ce.err
self.ctx.dbg(err)
if err:
obj.append("ERROR!")
elif rows:
obj.append("OK")
tb.row(idx, *tuple(obj))
try:
mrepo = client.getManagedRepository()
root = mrepo.root()
prefix = prep_directory(client, mrepo)
self.ctx.err("Renaming Fileset:%s to %s" % (fid, prefix))
tomove = rename_fileset(client, mrepo, fileset, prefix)
finally:
if new_client is not None:
new_client.__del__()
if not tomove:
self.ctx.die(113, "No files moved!")
elif not args.no_move:
from omero.grid import RawAccessRequest
for from_path, to_path in tomove:
raw = RawAccessRequest()
raw.repoUuid = root.hash.val
raw.command = "mv"
raw.args = [from_path, to_path]
self.ctx.err("Moving %s to %s" % (from_path, to_path))
try:
self.ctx.get_client().submit(raw)
except CmdError, ce:
self.ctx.die(114, ce.err)
else:
self.ctx.err(
"Done. You will now need to move these files manually:")
self.ctx.err(
"-----------------------------------------------------")
b = "".join([root.path.val, root.name.val])
for from_path, to_path in tomove:
def sets(self, args):
"""List filesets by various criteria
Filesets are bundles of original data imported into OMERO 5 and above
which represent 1 *or more* images.
Examples:
bin/omero fs sets --order=newest # Default
bin/omero fs sets --order=oldest
bin/omero fs sets --order=largest
bin/omero fs sets --without-images # Corrupt filesets
bin/omero fs sets --with-transfer=ln_s # Symlinked filesets
bin/omero fs sets --check # Proof the checksums
"""
from omero.constants.namespaces import NSFILETRANSFER
from omero_sys_ParametersI import ParametersI
from omero.rtypes import unwrap
client = self.ctx.conn(args)
service = client.sf.getQueryService()
admin = client.sf.getAdminService()
if args.check and not admin.getEventContext().isAdmin:
self.error_admin_only(fatal=True)
annselect = (
"(select ann.textValue from Fileset f4 "
"join f4.annotationLinks fal join fal.child ann "
"where f4.id = fs.id and ann.ns =:ns) "
)
select = (
"select fs.id, fs.templatePrefix, "
"(select size(f2.images) from Fileset f2 "
"where f2.id = fs.id),"
"(select size(f3.usedFiles) from Fileset f3 "
"where f3.id = fs.id),"
) + annselect
query1 = "from Fileset fs " "where 1 = 1 "
query2 = "group by fs.id, fs.templatePrefix "
if args.order:
if args.order == "newest":
query2 += "order by fs.id desc"
elif args.order == "oldest":
query2 += "order by fs.id asc"
elif args.order == "prefix":
query2 += "order by fs.templatePrefix"
if args.without_images:
query = "%s and fs.images is empty %s" % (query1, query2)
else:
query = "%s %s" % (query1, query2)
params = ParametersI()
params.addString("ns", NSFILETRANSFER)
count = service.projection("select count(fs) " + query1, params, {"omero.group": "-1"})
params.page(args.offset, args.limit)
objs = service.projection(select + query, params, {"omero.group": "-1"})
objs = unwrap(objs)
count = unwrap(count)[0][0]
cols = ["Id", "Prefix", "Images", "Files", "Transfer"]
if args.check:
cols.append("Check")
tb = self._table(args)
tb.cols(cols)
tb.page(args.offset, args.limit, count)
# Map any requested transfers as well
if args.with_transfer:
restricted = [TRANSFERS.get(x, x) for x in args.with_transfer[0]]
else:
restricted = None
for idx, obj in enumerate(objs):
# Map the transfer name to the CLI symbols
ns = obj[-1]
if ns is None:
ns = ""
elif ns in TRANSFERS:
ns = TRANSFERS[ns]
obj[-1] = ns
# Filter based on the ns symbols
if restricted and ns not in restricted:
continue
# Now perform check if required
if args.check:
from omero.grid import RawAccessRequest
desc, prx = self.get_managed_repo(client)
ctx = client.getContext(group=-1)
check_params = ParametersI()
check_params.addId(obj[0])
rows = service.projection(
(
"select h.value, f.hash, "
"f.path || '/' || f.name "
"from Fileset fs join fs.usedFiles uf "
"join uf.originalFile f join f.hasher h "
"where fs.id = :id"
),
check_params,
ctx,
)
if not rows:
obj.append("Empty")
err = None
for row in rows:
row = unwrap(row)
raw = RawAccessRequest()
raw.repoUuid = desc.hash.val
raw.command = "checksum"
raw.args = map(str, row)
try:
cb = client.submit(raw)
cb.close(True)
except CmdError, ce:
err = ce.err
self.ctx.dbg(err)
if err:
obj.append("ERROR!")
elif rows:
obj.append("OK")
tb.row(idx, *tuple(obj))
def sets(self, args):
"""List filesets by various criteria
Filesets are bundles of original data imported into OMERO 5 and above
which represent 1 *or more* images.
Examples:
bin/omero fs sets --order=newest # Default
bin/omero fs sets --order=oldest
bin/omero fs sets --order=largest
bin/omero fs sets --without-images # Corrupt filesets
bin/omero fs sets --with-transfer=ln_s # Symlinked filesets
bin/omero fs sets --check # Proof the checksums
"""
from omero.constants.namespaces import NSFILETRANSFER
from omero_sys_ParametersI import ParametersI
from omero.rtypes import unwrap
from omero.cmd import OK
client = self.ctx.conn(args)
service = client.sf.getQueryService()
select = (
"select fs.id, fs.templatePrefix, "
"(select size(f2.images) from Fileset f2 where f2.id = fs.id),"
"(select size(f3.usedFiles) from Fileset f3 where f3.id = fs.id),"
"ann.textValue ")
query1 = (
"from Fileset fs "
"left outer join fs.annotationLinks fal "
"left outer join fal.child ann "
"where (ann is null or ann.ns = :ns) ")
query2 = (
"group by fs.id, fs.templatePrefix, ann.textValue ")
if args.order:
if args.order == "newest":
query2 += "order by fs.id desc"
elif args.order == "oldest":
query2 += "order by fs.id asc"
elif args.order == "prefix":
query2 += "order by fs.templatePrefix"
if args.without_images:
query = "%s and fs.images is empty %s" % (query1, query2)
else:
query = "%s %s" % (query1, query2)
params = ParametersI()
params.addString("ns", NSFILETRANSFER)
count = service.projection("select count(fs) " + query1,
params, {"omero.group": "-1"})
params.page(args.offset, args.limit)
objs = service.projection(select + query,
params, {"omero.group": "-1"})
objs = unwrap(objs)
count = unwrap(count)[0][0]
cols = ["Id", "Prefix", "Images", "Files", "Transfer"]
if args.check:
cols.append("Check")
tb = self._table(args)
tb.cols(cols)
tb.page(args.offset, args.limit, count)
for idx, obj in enumerate(objs):
# Map the transfer name to the CLI symbols
ns = obj[-1]
if ns is None:
ns = ""
elif ns in TRANSFERS:
ns = TRANSFERS[ns]
obj[-1] = ns
# Map any requested transfers as well
allowed = args.with_transfer is not None \
and args.with_transfer or []
for idx, x in enumerate(allowed):
x = x[0] # Strip argparse wrapper
x = TRANSFERS.get(x, x) # map
allowed[idx] = x
# Filter based on the ns symbols
if allowed:
if ns not in allowed:
continue
# Now perform check if required
if args.check:
from omero.grid import RawAccessRequest
desc, prx = self.get_managed_repo(client)
ctx = client.getContext(group=-1)
check_params = ParametersI()
check_params.addId(obj[0])
rows = service.projection((
"select h.value, f.hash, "
"f.path || '/' || f.name "
"from Fileset fs join fs.usedFiles uf "
"join uf.originalFile f join f.hasher h "
"where fs.id = :id"
), check_params, ctx)
if not rows:
obj.append("Empty")
err = None
for row in rows:
row = unwrap(row)
raw = RawAccessRequest()
raw.repoUuid = desc.hash.val
raw.command = "checksum"
raw.args = map(str, row)
cb = client.submit(raw)
try:
rsp = cb.getResponse()
if not isinstance(rsp, OK):
err = rsp
break
finally:
cb.close(True)
if err:
obj.append("ERROR!")
elif rows:
obj.append("OK")
tb.row(idx, *tuple(obj))
self.ctx.out(str(tb.build()))
mrepo = client.getManagedRepository()
root = mrepo.root()
prefix = prep_directory(client, mrepo)
self.ctx.err("Renaming Fileset:%s to %s" % (fid, prefix))
tomove = rename_fileset(client, mrepo, fileset, prefix)
finally:
if new_client is not None:
new_client.__del__()
if not tomove:
self.ctx.die(113, "No files moved!")
elif not args.no_move:
from omero.grid import RawAccessRequest
for from_path, to_path in tomove:
raw = RawAccessRequest()
raw.repoUuid = root.hash.val
raw.command = "mv"
raw.args = [from_path, to_path]
self.ctx.err("Moving %s to %s" % (from_path, to_path))
try:
self.ctx.get_client().submit(raw)
except CmdError, ce:
self.ctx.die(114, ce.err)
else:
self.ctx.err("Done. You will now need to move these files manually:")
self.ctx.err("-----------------------------------------------------")
b = "".join([root.path.val, root.name.val])
for from_path, to_path in tomove:
t = "/".join([b, to_path])
f = "/".join([b, from_path])