def gene_mapping(cls, idx, idx_type, test_mode=False):
''' Load the mapping for the gene index. '''
props = MappingProperties(idx_type)
props.add_property("symbol", "string", analyzer="full_name") \
.add_property("synonyms", "string", analyzer="full_name") \
.add_property("chromosome", "string") \
.add_property("source", "string") \
.add_property("start", "long") \
.add_property("stop", "long") \
.add_property("strand", "string") \
.add_property("description", "string") \
.add_property("biotype", "string") \
.add_property("pmids", "string") \
.add_property("suggest", "completion", analyzer="full_name")
dbxref_props = cls._get_nested_prop("dbxrefs", "ensembl")
ortholog_props = MappingProperties("orthologs")
ortholog_props.add_properties(cls._get_nested_prop("mmusculus", "ensembl"))
ortholog_props.add_properties(cls._get_nested_prop("rnorvegicus", "ensembl"))
dbxref_props.add_properties(ortholog_props)
props.add_properties(dbxref_props)
tags = MappingProperties("tags")
tags.add_property("weight", "integer", index="not_analyzed")
props.add_properties(tags)
''' create index and add mapping '''
load = Loader()
options = {"indexName": idx, "shards": 5}
if not test_mode:
load.mapping(props, idx_type, analyzer=Loader.KEYWORD_ANALYZER, **options)
return props
def mapping(cls, idx, idx_type):
''' Create the mapping for disease indexing '''
props = MappingProperties("disease")
props.add_property("name", "string") \
.add_property("code", "string") \
.add_property("description", "string", index="not_analyzed") \
.add_property("colour", "string", index="not_analyzed") \
.add_property("tier", "integer", index="not_analyzed") \
.add_property("suggest", "completion", analyzer="full_name")
tags = MappingProperties("tags")
tags.add_property("weight", "integer", index="not_analyzed")
props.add_properties(tags)
load = Loader()
options = {"indexName": idx, "shards": 1}
load.mapping(props, 'disease', analyzer=Loader.KEYWORD_ANALYZER, **options)
def _create_mapping(self, **options):
''' Create the mapping for gene names indexing '''
props = MappingProperties("gene")
props.add_property("gene_symbol", "string", analyzer="full_name") \
.add_property("biotype", "string") \
.add_property("synonyms", "string", analyzer="full_name") \
.add_property("hgnc", "string") \
.add_property("dbxrefs", "object") \
.add_property("organism", "string")
featureloc_props = MappingProperties("featureloc")
featureloc_props.add_property("start", "integer") \
.add_property("end", "integer") \
.add_property("seqid", "string") \
.add_property("build", "string")
props.add_properties(featureloc_props)
''' create index and add mapping '''
self.mapping(props, 'gene', analyzer=self.KEYWORD_ANALYZER, **options)
def create_criteria_mapping(cls, idx, idx_type, test_mode=False):
''' function to create mapping for criteria indexes
@type idx: string
@param idx: name of the index
@type idx_type: string
@param idx_type: name of the idx type, each criteria is an index type
@type test_mode: string
@param test_mode: flag to create or not create the mapping
'''
logger.warning('Idx ' + idx)
logger.warning('Idx_type ' + idx_type)
''' Create the mapping for alias indexing '''
props = MappingProperties(idx_type)
props.add_property("score", "integer")
props.add_property("disease_tags", "string", index="not_analyzed")
props.add_property("qid", "string", index="not_analyzed")
(main_codes, other_codes) = CriteriaManager().get_available_diseases()
for disease in main_codes + other_codes:
criteria_tags = MappingProperties(disease)
criteria_tags.add_property("fid", "string", index="not_analyzed")
criteria_tags.add_property("fname", "string", index="not_analyzed")
fnotes = MappingProperties('fnotes')
fnotes.add_property('linkid', "string", index="not_analyzed")
fnotes.add_property('linkname', "string", index="not_analyzed")
fnotes.add_property('linkdata', "string", index="not_analyzed")
fnotes.add_property('linkvalue', "string", index="not_analyzed")
criteria_tags.add_properties(fnotes)
props.add_properties(criteria_tags)
''' create index and add mapping '''
load = Loader()
options = {"indexName": idx, "shards": 5}
'''add meta info'''
config = CriteriaManager.get_criteria_config()
idx_type_cfg = config[idx_type]
desc = idx_type_cfg['desc']
meta = {"desc": desc}
if not test_mode:
load.mapping(props, idx_type, meta=meta, analyzer=Loader.KEYWORD_ANALYZER, **options)
return props
def _create_snp_mapping(self, idx_type, **options):
''' Create the mapping for snp index '''
props = MappingProperties(idx_type)
props.add_property("seqid", "string", index="not_analyzed") \
.add_property("start", "integer", index="not_analyzed") \
.add_property("id", "string", analyzer="full_name") \
.add_property("ref", "string", index="no") \
.add_property("alt", "string", index="no") \
.add_property("qual", "string", index="no") \
.add_property("filter", "string", index="no") \
.add_property("info", "string", index="no") \
.add_property("suggest", "completion", analyzer="full_name")
tags = MappingProperties("tags")
tags.add_property("weight", "integer", index="not_analyzed")
props.add_properties(tags)
self.mapping(props,
idx_type,
analyzer=Loader.KEYWORD_ANALYZER,
**options)
return props
