def create_snp_markers_set(self, label, maker, model, release,
N, stream, action):
"""
Given a stream of (marker_vid, marker_indx, allele_flip) tuples,
build and save a new marker set.
"""
assert type(N) == int and N > 0
set_vid = vlu.make_vid()
conf = {
'label': label,
'maker': maker,
'model': model,
'release': release,
'markersSetVID': set_vid,
'action': action,
}
mset = self.factory.create(self.SNPMarkersSet, conf)
mset.save()
def gen(stream):
for t in stream:
yield {'marker_vid': t[0], 'marker_indx': t[1], 'allele_flip': t[2]}
# TODO: add better exception handling to the following code
try:
self.gadpt.create_snp_markers_set_tables(mset.id, N)
counted = self.gadpt.define_snp_markers_set(set_vid, gen(stream),
action.id)
if counted != N:
raise ValueError('there are %d records in stream (expected %d)' %
(counted, N))
except:
self.gadpt.delete_snp_markers_set_tables(mset.id)
self.delete(mset)
raise
return mset
def configurator(self, ome_obj, conf):
base.__config__(self, ome_obj, conf)
conf = self.__preprocess_conf__(conf)
for k, t in fields.iteritems():
if k is 'vid':
setattr(ome_obj, k, self.to_omero(STRING, vlu.make_vid()))
elif k in conf:
setattr(ome_obj, k, self.to_omero(t[0], conf[k]))
elif t[1] is REQUIRED:
raise ValueError('missing value for required field %s' % k)
def configurator(self, ome_obj, conf):
base.__config__(self, ome_obj, conf)
conf = self.__preprocess_conf__(conf)
for k, t in fields.iteritems():
if k is "vid":
setattr(ome_obj, k, self.to_omero(STRING, vlu.make_vid()))
elif k in conf:
setattr(ome_obj, k, self.to_omero(t[0], conf[k]))
elif t[1] is REQUIRED:
raise ValueError("missing value for required field %s" % k)
def add_ehr_record(self, action, timestamp, archetype, rec):
"""
multi-field records will be expanded to groups of records all
with the same (assumed to be unique within a KB) group id.
:param action: action that generated this record
:type action: ActionOnIndividual
:param timestamp: when this record was collected, in millisecond
since the Epoch
:type timestamp: long
:param archetype: a legal archetype id, e.g.,
``openEHR-EHR-EVALUATION.problem-diagnosis.v1``
:type archetype: str
:param rec: keys and values for this specific archetype instance,
e.g., ``{'at0002.1':
'terminology://apps.who.int/classifications/apps/gE10.htm#E10'}``
:type rec: dict
"""
self.__check_type('action', self.ActionOnIndividual, action)
self.__check_type('rec', dict, rec)
action.reload()
a_id = action.id
target = action.target
target.reload()
i_id = target.id
# TODO add archetype consistency checks
g_id = vlu.make_vid()
for k in rec:
row = {
'timestamp': timestamp,
'i_vid': i_id,
'a_vid': a_id,
'valid': True,
'g_vid': g_id,
'archetype': archetype,
'field': k,
'value': rec[k],
}
self.eadpt.add_eav_record_row(row)
def add_ehr_record(self, action, timestamp, archetype, rec):
"""
multi-field records will be expanded to groups of records all
with the same (assumed to be unique within a KB) group id.
:param action: action that generated this record
:type action: ActionOnIndividual
:param timestamp: when this record was collected, in millisecond
since the Epoch
:type timestamp: long
:param archetype: a legal archetype id, e.g.,
``openEHR-EHR-EVALUATION.problem-diagnosis.v1``
:type archetype: str
:param rec: keys and values for this specific archetype instance,
e.g., ``{'at0002.1':
'terminology://apps.who.int/classifications/apps/gE10.htm#E10'}``
:type rec: dict
"""
self.__check_type('action', self.ActionOnIndividual, action)
self.__check_type('rec', dict, rec)
action.reload()
a_id = action.id
target = action.target
target.reload()
i_id = target.id
# TODO add archetype consistency checks
g_id = vlu.make_vid()
for k in rec:
row = {
'timestamp': timestamp,
'i_vid': i_id,
'a_vid': a_id,
'valid': True,
'g_vid': g_id,
'archetype': archetype,
'field': k,
'value': rec[k],
}
self.eadpt.add_eav_record_row(row)
def create_snp_markers_set(self, label, maker, model, release, N, stream,
action):
"""
Given a stream of (marker_vid, marker_indx, allele_flip) tuples,
build and save a new marker set.
"""
assert type(N) == int and N > 0
set_vid = vlu.make_vid()
conf = {
'label': label,
'maker': maker,
'model': model,
'release': release,
'markersSetVID': set_vid,
'action': action,
}
mset = self.factory.create(self.SNPMarkersSet, conf)
mset.save()
def gen(stream):
for t in stream:
yield {
'marker_vid': t[0],
'marker_indx': t[1],
'allele_flip': t[2]
}
# TODO: add better exception handling to the following code
try:
self.gadpt.create_snp_markers_set_tables(mset.id, N)
counted = self.gadpt.define_snp_markers_set(
set_vid, gen(stream), action.id)
if counted != N:
raise ValueError(
'there are %d records in stream (expected %d)' %
(counted, N))
except:
self.gadpt.delete_snp_markers_set_tables(mset.id)
self.delete(mset)
raise
return mset
def assign_vid(conf):
conf.setdefault('vid', vu.make_vid())
return conf
def assign_vid(conf):
conf.setdefault('vid', vu.make_vid())
return conf
