def build_id_query(self, vid, scopes=None):
_default_scopes = '_id'
scopes = scopes or _default_scopes
if is_str(scopes):
_query = {
"match": {
scopes: {
"query": "{}".format(vid),
"operator": "and"
}
}
}
elif is_seq(scopes):
_query = {
"multi_match": {
"query": "{}".format(vid),
"fields": scopes,
"operator": "and"
}
}
else:
raise ValueError('"scopes" cannot be "%s" type'.format(
type(scopes)))
_q = {"query": _query}
self._query_options.pop(
"query",
None) # avoid "query" be overwritten by self.query_options
_q.update(self._query_options)
return _q
def build_id_query(self, vid, scopes=None):
# _default_scopes = [
# '_id',
# 'rsid', "dbnsfp.rsid", "dbsnp.rsid", "evs.rsid", "mutdb.rsid" # for rsid
# "dbsnp.gene.symbol", 'evs.gene.symbol', 'clinvar.gene.symbol',
# 'dbnsfp.genename', "cadd.gene.genename", "docm.genename", # for gene symbols
# ]
_default_scopes = '_id'
scopes = scopes or _default_scopes
if is_str(scopes):
_query = {
"match": {
scopes: {
"query": "{}".format(vid),
"operator": "and"
}
}
}
elif is_seq(scopes):
_query = {
"multi_match": {
"query": "{}".format(vid),
"fields": scopes,
"operator": "and"
}
}
else:
raise ValueError('"scopes" cannot be "%s" type'.format(type(scopes)))
_q = {"query": _query}
self._query_options.pop("query", None) # avoid "query" be overwritten by self.query_options
_q.update(self._query_options)
return _q
def build_id_query(self, vid, scopes=None):
_default_scopes = '_id'
scopes = scopes or _default_scopes
if is_str(scopes):
_query = {
"match": {
scopes: {
"query": "{}".format(vid),
"operator": "and"
}
}
}
elif is_seq(scopes):
_query = {
"multi_match": {
"query": "{}".format(vid),
"fields": scopes,
"operator": "and"
}
}
else:
raise ValueError('"scopes" cannot be "%s" type'.format(type(scopes)))
_q = {"query": _query}
self._query_options.pop("query", None) # avoid "query" be overwritten by self.query_options
_q.update(self._query_options)
return _q
def build_id_query(self, vid, scopes=None):
# _default_scopes = [
# '_id',
# 'rsid', "dbnsfp.rsid", "dbsnp.rsid", "evs.rsid", "mutdb.rsid" # for rsid
# "dbsnp.gene.symbol", 'evs.gene.symbol', 'clinvar.gene.symbol',
# 'dbnsfp.genename', "cadd.gene.genename", "docm.genename", # for gene symbols
# ]
_default_scopes = '_id'
scopes = scopes or _default_scopes
if is_str(scopes):
_query = {
"match": {
scopes: {
"query": "{}".format(vid),
"operator": "and"
}
}
}
elif is_seq(scopes):
_query = {
"multi_match": {
"query": "{}".format(vid),
"fields": scopes,
"operator": "and"
}
}
else:
raise ValueError('"scopes" cannot be "%s" type'.format(
type(scopes)))
_q = {"query": _query}
self._query_options.pop(
"query",
None) # avoid "query" be overwritten by self.query_options
_q.update(self._query_options)
return _q
def _cleaned_scopes(self, scopes):
'''return a cleaned scopes parameter.
should be either a string or a list of scope fields.
'''
if scopes:
if is_str(scopes):
scopes = [x.strip() for x in scopes.split(',')]
if is_seq(scopes):
scopes = [x for x in scopes if x]
if len(scopes) == 1:
scopes = scopes[0]
else:
scopes = None
else:
scopes = None
return scopes
def _cleaned_scopes(self, scopes):
'''return a cleaned scopes parameter.
should be either a string or a list of scope fields.
'''
if scopes:
if is_str(scopes):
scopes = [x.strip() for x in scopes.split(',')]
if is_seq(scopes):
scopes = [x for x in scopes if x]
if len(scopes) == 1:
scopes = scopes[0]
else:
scopes = None
else:
scopes = None
return scopes
