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Ability to fetch annotation extensions in GOlr query. #134

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Ability to fetch annotation extensions in GOlr query. #134

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a109f5c
Ability to fetch annotation extensions in GOlr query.
dustine32 Jan 24, 2018
878e902
Adding 'golr-able' fields evidence_with, evidence_type, and reference
dustine32 Feb 1, 2018
1787cad
Merge branch 'master' of https://github.com/biolink/ontobio
dustine32 Feb 1, 2018
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15 changes: 14 additions & 1 deletion ontobio/golr/golr_query.py
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Original file line number Diff line number Diff line change
Expand Up @@ -100,6 +100,10 @@ class GolrFields:
EVIDENCE_OBJECT_LABEL='evidence_object_label'
_VERSION_='_version_'
SUBJECT_GENE_CLOSURE_LABEL_SEARCHABLE='subject_gene_closure_label_searchable'
ANNOTATION_EXTENSION_JSON="annotation_extension_json"
EVIDENCE_WITH="evidence_with"
REFERENCE="reference"
EVIDENCE_TYPE="evidence_type"

RELATION='relation'
RELATION_LABEL='relation_label'
Expand Down Expand Up @@ -529,7 +533,7 @@ def __init__(self,
# test if client explicitly passes a URL; do not override
self.is_explicit_url = url is not None
self.non_null_fields=non_null_fields

if self.facet_fields is None:
self.facet_fields = [
M.SUBJECT_TAXON_LABEL,
Expand Down Expand Up @@ -1144,6 +1148,15 @@ def translate_doc(self, d, field_mapping=None, map_identifiers=None, **kwargs):
# solr does not allow nested objects, so evidence graph is json-encoded
if M.EVIDENCE_GRAPH in d:
assoc[M.EVIDENCE_GRAPH] = json.loads(d[M.EVIDENCE_GRAPH])

if M.ANNOTATION_EXTENSION_JSON in d:
assoc['annotation_extensions'] = [json.loads(ext) for ext in d[M.ANNOTATION_EXTENSION_JSON]]
if M.EVIDENCE_TYPE in d:
assoc[M.EVIDENCE_TYPE] = d[M.EVIDENCE_TYPE]
if M.EVIDENCE_WITH in d:
assoc[M.EVIDENCE_WITH] = d[M.EVIDENCE_WITH]
if M.REFERENCE in d:
assoc[M.REFERENCE] = d[M.REFERENCE]
return assoc

def translate_docs(self, ds, **kwargs):
Expand Down