def to_element(self, e = None):
if e is None:
e = DataElement()
e["name"] = self.name
e["conf"] = self.conf
self.root_node.update_tasks_count_by_state()
self.root_node.update_modules_count_by_state()
self.root_node.to_element(e.create_element("root"))
return e
def _task_config_to_element(task):
e = DataElement(key_sep = "/")
e["id"] = task.id
e["name"] = task.name
e["index"] = task.index
e["module"] = task.parent.id
e["instance"] = task.instance.name
e["conf"] = task.conf
#TODO depends on module definition
iter = e.create_element("iteration")
iter["strategy"] = "dot"
iter["size"] = 0
ports = e.create_element("ports")
in_ports = ports.create_list("in")
for i, port_node in enumerate(task.parent.in_ports):
pe = DataElement(key_sep = "/")
# pe["name"] = port_node.name
# pe["serializer"] = port_node.serializer
# pe["partition"] = pdata.partition
# pe["start"] = pdata.start
# pe["size"] = pdata.size
#task.in_port_data[i].fill_element(pe.create_element("data"))
task.in_port_data[i].fill_element(pe)
in_ports.append(pe)
out_ports = ports.create_list("out")
for i, port_node in enumerate(task.parent.out_ports):
pe = DataElement(key_sep = "/")
# pe["name"] = port_node.name
# pe["serializer"] = port_node.serializer
# pe["partition"] = pdata.partition
#task.out_port_data[i].fill_element(pe.create_element("data"))
task.out_port_data[i].fill_element(pe)
out_ports.append(pe)
return e
def main():
# Initialization
task.check_conf(["entities"])
conf = task.conf
log = task.logger()
oncodrive_port, combination_port = \
task.ports("oncodrive_ids", "combinations")
es = EntityServer(conf["entities"])
em = es.manager()
log.info("Indexing available {} results ...".format(types.CNV_COMBINATION))
comb_results_index = em.group_ids(
["icdo_topography", "icdo_morphology", "id_type"],
types.CNV_COMBINATION, unique = True)
ENSEMBL_GENE = "ensembl:gene"
classif = {}
log.info("Classifying oncodrive results ...")
for oid in oncodrive_port:
o = em.find(oid, types.CNV_ONCODRIVE_GENES)
if o is None:
log.error("{} not found: {}".format(types.CNV_ONCODRIVE_GENES, oid))
continue
okey = (o["study_id"], o["platform_id"], o["icdo_topography"], o["icdo_morphology"])
key = (o["icdo_topography"], o["icdo_morphology"], ENSEMBL_GENE)
log.debug("Oncodrive results ({}) [{}] classified into ({}) ...".format(", ".join(okey), oid, ", ".join(key)))
if key in classif:
classif[key] += [o]
else:
classif[key] = [o]
log.info("Preparing combinations ...")
for key in sorted(classif):
if key in comb_results_index:
cid = comb_results_index[key][0]
c = em.find(cid, types.CNV_COMBINATION)
if c is None:
log.error("{} not found: {}".format(types.CNV_COMBINATION, cid))
return
else:
c = DataElement(key_sep = "/")
c["id"] = cid = str(uuid.uuid4())
c["icdo_topography"] = key[0]
c["icdo_morphology"] = key[1]
c["id_type"] = ENSEMBL_GENE
olist = classif[key]
log.info("({}) [{}] --> {} results".format(", ".join(key), cid, len(olist)))
ids = c.create_list()
flist = c.create_list()
for o in olist:
ids += [o["id"]]
flist += [o["results_file"]]
c["source"] = src = c.create_element()
src["type"] = types.CNV_ONCODRIVE_GENES
src["ids"] = ids
c["files"] = flist
combination_port.write(c.to_native())
em.close()
es.close()
def main():
# Initialization
task.check_conf(["entities"])
conf = task.conf
log = task.logger()
enrichment_port, combination_port = \
task.ports("enrichment_ids", "combinations")
es = EntityServer(conf["entities"])
em = es.manager()
log.info("Indexing available {} results ...".format(types.CNV_COMBINATION))
comb_results_index = em.group_ids(
["icdo_topography", "icdo_morphology", "id_type"],
types.CNV_COMBINATION, unique = True)
classif = {}
log.info("Classifying enrichment results ...")
for eid in enrichment_port:
e = em.find(eid, types.CNV_ENRICHMENT)
if e is None:
log.error("{} not found: {}".format(types.CNV_ENRICHMENT, eid))
continue
ekey = (e["study_id"], e["platform_id"], e["icdo_topography"], e["icdo_morphology"], e["id_type"])
key = (e["icdo_topography"], e["icdo_morphology"], e["id_type"])
log.debug("Enrichment results ({}) [{}] classified into ({}) ...".format(", ".join(ekey), eid, ", ".join(key)))
if key in classif:
classif[key] += [e]
else:
classif[key] = [e]
log.info("Preparing combinations ...")
for key in sorted(classif):
if key in comb_results_index:
cid = comb_results_index[key][0]
c = em.find(cid, types.CNV_COMBINATION)
if c is None:
log.error("{} not found: {}".format(types.CNV_COMBINATION, cid))
return
else:
c = DataElement(key_sep = "/")
c["id"] = cid = str(uuid.uuid4())
c["icdo_topography"] = key[0]
c["icdo_morphology"] = key[1]
c["id_type"] = key[2]
elist = classif[key]
log.info("({}) [{}] --> {} results".format(", ".join(key), cid, len(elist)))
ids = c.create_list()
flist = c.create_list()
for e in elist:
ids += [e["id"]]
flist += [e["results_file"]]
c["source"] = src = c.create_element()
src["type"] = types.CNV_ENRICHMENT
src["ids"] = ids
c["files"] = flist
combination_port.write(c.to_native())
em.close()
es.close()