diff --git a/src/hub/dataload/sources/civic/civic_upload.py b/src/hub/dataload/sources/civic/civic_upload.py index 2ffb238d..ff26996f 100644 --- a/src/hub/dataload/sources/civic/civic_upload.py +++ b/src/hub/dataload/sources/civic/civic_upload.py @@ -28,333 +28,6 @@ def load_data(self, data_folder): @classmethod def get_mapping(klass): mapping = { - "clinvar": { - "properties": { - "allele_id": { - "type": "integer" - }, - "chrom": { - "normalizer": "keyword_lowercase_normalizer", - "type": "keyword" - }, - "hg19": { - "properties": { - "start": { - "type": "integer" - }, - "end": { - "type": "integer" - } - } - }, - "hg38": { - "properties": { - "start": { - "type": "integer" - }, - "end": { - "type": "integer" - } - } - }, - "type": { - "type": "text" - }, - "gene": { - "properties": { - "id": { - "normalizer": "keyword_lowercase_normalizer", - "type": "keyword" - }, - "symbol": { - "normalizer": "keyword_lowercase_normalizer", - "type": "keyword" - } - } - }, - "rcv": { - "properties": { - "accession": { - "normalizer": "keyword_lowercase_normalizer", - "type": "keyword" - }, - "number_submitters": { - "type": "integer" - }, - "last_evaluated": { - "normalizer": "keyword_lowercase_normalizer", - "type": "keyword" - }, - "conditions": { - "properties": { - "synonyms": { - "type": "text" - }, - "identifiers": { - "properties": { - "mondo": { - "normalizer": "keyword_lowercase_normalizer", - "type": "keyword" - }, - "medgen": { - "normalizer": "keyword_lowercase_normalizer", - "type": "keyword" - }, - "orphanet": { - "normalizer": "keyword_lowercase_normalizer", - "type": "keyword" - }, - "omim": { - "normalizer": "keyword_lowercase_normalizer", - "type": "keyword" - }, - "mesh": { - "normalizer": "keyword_lowercase_normalizer", - "type": "keyword" - }, - "human_phenotype_ontology": { - "normalizer": "keyword_lowercase_normalizer", - "type": "keyword" - }, - "gene": { - "normalizer": "keyword_lowercase_normalizer", - "type": "keyword" - }, - "efo": { - "normalizer": "keyword_lowercase_normalizer", - "type": "keyword" - } - } - }, - "name": { - "type": "text" - } - } - }, - "origin": { - "type": "text" - }, - "preferred_name": { - "type": "text" - }, - "clinical_significance": { - "type": "text" - }, - "review_status": { - "type": "text" - } - } - }, - "rsid": { - "normalizer": "keyword_lowercase_normalizer", - "type": "keyword" - }, - "cytogenic": { - "normalizer": "keyword_lowercase_normalizer", - "type": "keyword" - }, - "hgvs": { - "properties": { - "genomic": { - "normalizer": "keyword_lowercase_normalizer", - "type": "text" - }, - "coding": { - "normalizer": "keyword_lowercase_normalizer", - "type": "text" - }, - "protein": { - "normalizer": "keyword_lowercase_normalizer", - "type": "text" - }, - "non-coding": { - "normalizer": "keyword_lowercase_normalizer", - "type": "keyword" - } - } - }, - "ref": { - "normalizer": "keyword_lowercase_normalizer", - "type": "keyword" - }, - "alt": { - "normalizer": "keyword_lowercase_normalizer", - "type": "keyword" - }, - "variant_id": { - "type": "integer" - }, - "omim": { - "normalizer": "keyword_lowercase_normalizer", - "type": "keyword" - }, - "uniprot": { - "normalizer": "keyword_lowercase_normalizer", - "type": "keyword" - }, - "genotypeset": { - "properties": { - "type": { - "normalizer": "keyword_lowercase_normalizer", - "type": "keyword" - }, - "genotype": { - "normalizer": "keyword_lowercase_normalizer", - "type": "keyword" - } - } - }, - "dbvar": { - "normalizer": "keyword_lowercase_normalizer", - "type": "keyword" - }, - "cosmic": { - "normalizer": "keyword_lowercase_normalizer", - "type": "keyword" - }, - "coding_hgvs_only": { - "type": "boolean" - } - } - }, - "observed": { - "type": "boolean" - }, - "chrom": { - "normalizer": "keyword_lowercase_normalizer", - "type": "keyword" - }, - "geno2mp": { - "properties": { - "hpo_count": { - "type": "integer" - } - } - }, - "emv": { - "properties": { - "gene": { - "normalizer": "keyword_lowercase_normalizer", - "type": "keyword" - }, - "variant_id": { - "type": "integer" - }, - "exon": { - "normalizer": "keyword_lowercase_normalizer", - "type": "keyword" - }, - "egl_variant": { - "normalizer": "keyword_lowercase_normalizer", - "type": "keyword" - }, - "egl_classification_date": { - "normalizer": "keyword_lowercase_normalizer", - "type": "keyword" - }, - "hgvs": { - "normalizer": "keyword_lowercase_normalizer", - "type": "text" - }, - "egl_classification": { - "type": "text" - }, - "egl_protein": { - "type": "text" - } - } - }, - "_seqhashed": { - "properties": { - "5a21cf84e3a3e4af232feff295ee633a": { - "normalizer": "keyword_lowercase_normalizer", - "type": "keyword" - }, - "_flag": { - "type": "boolean" - }, - "78b0b513aa8eb34923b286a3f0ca701d": { - "normalizer": "keyword_lowercase_normalizer", - "type": "keyword" - }, - "405a1d903d4f3a36f5539f25f8683249": { - "normalizer": "keyword_lowercase_normalizer", - "type": "keyword" - }, - "3f519fe63c5b559640b1c4f6bfb0a679": { - "normalizer": "keyword_lowercase_normalizer", - "type": "keyword" - }, - "b90e716ad05b07dc447b5518b3eb0477": { - "normalizer": "keyword_lowercase_normalizer", - "type": "keyword" - }, - "3e2c783bc2e14e7de924b6c883bdd306": { - "normalizer": "keyword_lowercase_normalizer", - "type": "keyword" - }, - "1313e0def30bc4edbd118bec7d203fb8": { - "normalizer": "keyword_lowercase_normalizer", - "type": "keyword" - }, - "747ec6db2b9ebf18f0b97a391d9d5dd0": { - "normalizer": "keyword_lowercase_normalizer", - "type": "keyword" - }, - "284427e1eca1d0e83a020aafa68876d5": { - "normalizer": "keyword_lowercase_normalizer", - "type": "keyword" - }, - "c58354303f41353943eb8a8810e1aa11": { - "normalizer": "keyword_lowercase_normalizer", - "type": "keyword" - }, - "adf7574e78e79c17459be352a7393328": { - "normalizer": "keyword_lowercase_normalizer", - "type": "keyword" - }, - "fb5db2f0237a002afbcace53db5d3432": { - "normalizer": "keyword_lowercase_normalizer", - "type": "keyword" - }, - "0f6f8c2f73969dbb7db1817184d9d9e4": { - "normalizer": "keyword_lowercase_normalizer", - "type": "keyword" - }, - "02ce1b5fcf372de6bd92bd39cf445422": { - "normalizer": "keyword_lowercase_normalizer", - "type": "keyword" - }, - "442c06338cdfb26311fe627eaa680e6b": { - "normalizer": "keyword_lowercase_normalizer", - "type": "keyword" - }, - "825a02344ce11a0dd0eb1722aa6b6e0e": { - "normalizer": "keyword_lowercase_normalizer", - "type": "keyword" - }, - "a23c64fa372ecc697b8ce37adae16faf": { - "normalizer": "keyword_lowercase_normalizer", - "type": "keyword" - }, - "ec307c5205ae6883b4fe0e1b36a1e964": { - "normalizer": "keyword_lowercase_normalizer", - "type": "keyword" - }, - "b982aea1997ac85b0cd440bbf522df1d": { - "normalizer": "keyword_lowercase_normalizer", - "type": "keyword" - }, - "c12e792ab0a1707d0c16122e05de2c12": { - "normalizer": "keyword_lowercase_normalizer", - "type": "keyword" - }, - "d5197641182c8e4316d4bd40d1827ff1": { - "normalizer": "keyword_lowercase_normalizer", - "type": "keyword" - } - } - }, "civic": { "properties": { "contributors": { @@ -1181,45 +854,6 @@ def get_mapping(klass): } } } - }, - "cgi": { - "properties": { - "region": { - "normalizer": "keyword_lowercase_normalizer", - "type": "keyword" - }, - "cdna": { - "normalizer": "keyword_lowercase_normalizer", - "type": "keyword" - }, - "transcript": { - "normalizer": "keyword_lowercase_normalizer", - "type": "keyword" - }, - "gene": { - "normalizer": "keyword_lowercase_normalizer", - "type": "keyword" - }, - "protein_change": { - "normalizer": "keyword_lowercase_normalizer", - "type": "keyword" - }, - "association": { - "type": "text" - }, - "source": { - "type": "text" - }, - "evidence_level": { - "type": "text" - }, - "primary_tumor_type": { - "type": "text" - }, - "drug": { - "type": "text" - } - } } }