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Update civic mapping.
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@everaldorodrigo
everaldorodrigo committed Nov 22, 2024
1 parent 7aae4b1 commit 0e2d495
Showing 1 changed file with 0 additions and 366 deletions.
366 changes: 0 additions & 366 deletions src/hub/dataload/sources/civic/civic_upload.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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": {
Expand Down Expand Up @@ -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"
}
}
}
}

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