def get_vessel(self, label):
"""
Return the Vessel object labeled 'label' or None if nothing
matches 'label'. A label 'foo:A1' is interpreted as well 'A1' of
plate 'foo'.
"""
import re
if re.match(r'^.*::+.*$', label):
# Labels like SAMPLE::PROTOCOL must be considered as a single label
parts = [label]
else:
parts = label.split(':')
if len(parts) == 1:
query = 'select t from Tube t where t.label = :label'
pars = self.kb.ome_query_params({'label': wp.ome_wrap(label, wp.STRING)})
result = self.kb.ome_operation("getQueryService", "findByQuery",
query, pars)
return None if result is None else self.kb.factory.wrap(result)
elif len(parts) == 2:
query = """select pw from PlateWell pw join fetch pw.container as ct
where pw.label = :wlabel and ct.label = :clabel
"""
pars = self.kb.ome_query_params({
'clabel': wp.ome_wrap(parts[0], wp.STRING),
'wlabel': wp.ome_wrap(parts[1], wp.STRING),
})
result = self.kb.ome_operation("getQueryService", "findByQuery",
query, pars)
return None if result is None else self.kb.factory.wrap(result)
else:
raise ValueError('Bad label %s value' % label)
def find_all_by_query(self, query, params, factory):
if params:
xpars = {}
for k,v in params.iteritems():
xpars[k] = ome_wrap(*v) if type(v) == tuple else ome_wrap(v)
pars = self.ome_query_params(xpars)
else:
pars = None
result = self.ome_operation("getQueryService", "findAllByQuery",
query, pars)
return [] if result is None else [factory.wrap(r) for r in result]
def get_enrollment(self, study, ind_label):
query = """select e
from Enrollment e join fetch e.study as s
where e.studyCode = :ilabel and s.id = :sid
"""
pars = self.kb.ome_query_params({
'ilabel': wp.ome_wrap(ind_label),
'sid': wp.ome_wrap(study.omero_id),
})
result = self.kb.ome_operation("getQueryService", "findByQuery",
query, pars)
return None if result is None else self.kb.factory.wrap(result)
def get_vessels_collection(self, label):
"""
Return the VesselsCollection object labeled 'label' or None if
nothing matches 'label'.
"""
query = 'select vc from VesselsCollection vc where vc.label = :label'
pars = self.kb.ome_query_params({'label' : wp.ome_wrap(label, wp.STRING)})
result = self.kb.ome_operation('getQueryService', 'findByQuery',
query, pars)
return None if result is None else self.kb.factory.wrap(result)
def get_data_collection(self, label):
"""
Return the DataCollection object labeled 'label' or
None if nothing matches 'label'.
"""
query = 'select dc from DataCollection dc where dc.label = :label'
pars = self.kb.ome_query_params({'label': wp.ome_wrap(label, wp.STRING)})
result = self.kb.ome_operation("getQueryService", "findByQuery",
query, pars)
return None if result is None else self.kb.factory.wrap(result)
def get_study(self, label):
"""
Return the Study object labeled 'label' or None if nothing
matches 'label'.
"""
query = 'select st from Study st where st.label = :label'
pars = self.kb.ome_query_params({'label': wp.ome_wrap(label, wp.STRING)})
result = self.kb.ome_operation("getQueryService", "findByQuery",
query, pars)
return None if result is None else self.kb.factory.wrap(result)
def get_container(self, label):
assert isinstance(label, str)
query = """select c
from Container c
where c.label = :label
"""
pars = self.kb.ome_query_params({'label': wp.ome_wrap(label)})
result = self.kb.ome_operation("getQueryService", "findByQuery",
query, pars)
return None if result is None else self.kb.factory.wrap(result)
def get_data_objects(self, sample):
query = """select do
from DataObject do
join fetch do.sample as s
where s.id = :sid
"""
pars = self.kb.ome_query_params({
'sid': wp.ome_wrap(sample.omero_id, wp.LONG),
})
result = self.kb.ome_operation("getQueryService", "findAllByQuery",
query, pars)
return [self.kb.factory.wrap(i) for i in result]
def get_vessels_collection_items(self, vc):
query = """select i
from VesselsCollectionItem i
join fetch i.vessel as v
join fetch i.vesselsCollection as vc
where vc.id = :vcid
"""
pars = self.kb.ome_query_params({
'vcid' : wp.ome_wrap(vc.omero_id, wp.LONG),
})
result = self.kb.ome_operation('getQueryService', 'findAllByQuery',
query, pars)
return [self.kb.factory.wrap(i) for i in result]
def get_data_collection_items(self, dc):
query = """select i
from DataCollectionItem i
join fetch i.dataSample as s
join fetch i.dataCollection as dc
where dc.id = :dcid
"""
pars = self.kb.ome_query_params({
'dcid': wp.ome_wrap(dc.omero_id, wp.LONG),
})
result = self.kb.ome_operation("getQueryService", "findAllByQuery",
query, pars)
return [self.kb.factory.wrap(i) for i in result]
def get_enrolled(self, study):
query = """select e
from Enrollment e
join fetch e.study as s
join fetch e.individual as i
where s.label = :slabel
"""
pars = self.kb.ome_query_params({
'slabel': wp.ome_wrap(study.label, wp.STRING),
})
result = self.kb.ome_operation("getQueryService", "findAllByQuery",
query, pars)
return [self.kb.factory.wrap(e) for e in result]
def get_snp_markers_set(self, label, maker, model, release):
if label:
query = """select ms
from SNPMarkersSet ms
where ms.label = :label
"""
pars = self.kb.ome_query_params({'label': wp.ome_wrap(label)})
else:
if not (maker and model and release):
raise ValueError('maker model and release should be all provided')
query = """select ms
from SNPMarkersSet ms
where ms.maker = :maker
and ms.model = :model
and ms.release = :release
"""
pars = self.kb.ome_query_params({
'maker': wp.ome_wrap(maker),
'model': wp.ome_wrap(model),
'release': wp.ome_wrap(release),
})
result = self.kb.ome_operation("getQueryService", "findByQuery",
query, pars)
return None if result is None else self.kb.factory.wrap(result)
def get_vessels(self, klass, content):
if not issubclass(klass, self.kb.Vessel):
raise ValueError('klass should be a subclass of Vessel')
if not content:
query = "select v from %s v" % klass.get_ome_table()
pars = None
elif isinstance(content, self.kb.VesselContent):
value = content.ome_obj.value._val
query = """select v from %s v join fetch v.content as c
where c.value = :cvalue
""" % klass.get_ome_table()
pars = self.kb.ome_query_params({'cvalue': wp.ome_wrap(value)})
else:
raise ValueError('content should be an instance of VesselContent')
results = self.kb.ome_operation('getQueryService', 'findAllByQuery',
query, pars)
return [self.kb.factory.wrap(v) for v in results]