fountain-life-service-clients 3.30.0__py3-none-any.whl → 3.32.0__py3-none-any.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- fountain_life_service_clients/genomics_service.py +201 -0
- {fountain_life_service_clients-3.30.0.dist-info → fountain_life_service_clients-3.32.0.dist-info}/METADATA +1 -1
- {fountain_life_service_clients-3.30.0.dist-info → fountain_life_service_clients-3.32.0.dist-info}/RECORD +4 -3
- {fountain_life_service_clients-3.30.0.dist-info → fountain_life_service_clients-3.32.0.dist-info}/WHEEL +0 -0
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# This file was generated automatically. Do not edit it directly.
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from typing import (
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List,
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Literal,
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NotRequired,
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Optional,
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TypedDict,
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Union,
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Unpack,
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cast,
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)
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from fountain_life_service_clients._base_client import (
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AlphaConfig,
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AlphaResponse,
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BaseClient,
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)
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SearchVariantsRequest = TypedDict(
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"SearchVariantsRequest",
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{
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"variantSetIds": str,
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"include": NotRequired[str],
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"variantId": NotRequired[Union[str, List[str]]],
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"sequenceType": NotRequired[Union[Literal["somatic"], Literal["germline"]]],
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"gene": NotRequired[Union[str, List[str]]],
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"aminoAcidChange": NotRequired[Union[str, List[str]]],
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"drugAssociations": NotRequired[bool],
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"hasJaxKnowledge": NotRequired[bool],
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"transcript_in_jaxckb": NotRequired[bool],
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"cosmic_sample_count": NotRequired[float],
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"class": NotRequired[Union[str, List[str]]],
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"group": NotRequired[Union[str, List[str]]],
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"impact": NotRequired[Union[str, List[str]]],
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"biotype": NotRequired[Union[str, List[str]]],
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"rs_id": NotRequired[Union[str, List[str]]],
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"chromosome": NotRequired[Union[str, List[str]]],
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"clinvar_allele_id": NotRequired[Union[str, List[str]]],
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"clinvar_disease": NotRequired[Union[str, List[str]]],
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"clinvar_review": NotRequired[Union[str, List[str]]],
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"clinvar_significance": NotRequired[Union[str, List[str]]],
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"clinvar_submission": NotRequired[Union[str, List[str]]],
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"transcript_gene": NotRequired[Union[str, List[str]]],
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"transcript_gene_id": NotRequired[Union[str, List[str]]],
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"transcript_classification": NotRequired[Union[str, List[str]]],
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"transcript_group": NotRequired[Union[str, List[str]]],
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"transcript_impact": NotRequired[Union[str, List[str]]],
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"transcript_id": NotRequired[Union[str, List[str]]],
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"transcript_biotype": NotRequired[Union[str, List[str]]],
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"transcript_exon_intron_rank": NotRequired[Union[str, List[str]]],
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"transcript_hgvs_amino_acid_change": NotRequired[Union[str, List[str]]],
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"transcript_nucleotide_change": NotRequired[Union[str, List[str]]],
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"transcript_jax_protein_effect": NotRequired[Union[str, List[str]]],
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"transcript_jax_knowledge": NotRequired[Union[str, List[str]]],
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"cosmic_id": NotRequired[Union[str, List[str]]],
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"cosmic_mutation_status": NotRequired[Union[str, List[str]]],
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"cosmic_histology": NotRequired[Union[str, List[str]]],
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"cosmic_tumor_site": NotRequired[Union[str, List[str]]],
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"dbnsfp_fathmm_pred": NotRequired[Union[str, List[str]]],
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"dbnsfp_mutationtaster_pred": NotRequired[Union[str, List[str]]],
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"dbnsfp_sift_pred": NotRequired[Union[str, List[str]]],
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"sample_zygosity": NotRequired[Union[str, List[str]]],
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"sample_genotype": NotRequired[Union[str, List[str]]],
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"sample_filter": NotRequired[Union[str, List[str]]],
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"sample_vendsig": NotRequired[Union[str, List[str]]],
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"sequence_type": NotRequired[Union[str, List[str]]],
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"position": NotRequired[Union[str, List[str]]],
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"clinvar_near_variant": NotRequired[Union[str, List[str]]],
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"cosmic_near_variant": NotRequired[Union[str, List[str]]],
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"minimum_allele_frequency": NotRequired[Union[str, List[str]]],
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"maximum_allele_frequency": NotRequired[Union[str, List[str]]],
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"population_allele_frequency": NotRequired[Union[str, List[str]]],
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"exac_allele_frequency": NotRequired[Union[str, List[str]]],
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"exac_homozygous": NotRequired[Union[str, List[str]]],
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"dbnsfp_damaging_count": NotRequired[Union[str, List[str]]],
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"dbnsfp_damaging_predictor": NotRequired[Union[str, List[str]]],
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"dbnsfp_damaging_vote": NotRequired[Union[str, List[str]]],
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"dbnsfp_fathmm_rankscore": NotRequired[Union[str, List[str]]],
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"dbnsfp_mean_rankscore": NotRequired[Union[str, List[str]]],
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"dbnsfp_mean_rankscore_predictor": NotRequired[Union[str, List[str]]],
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"dbnsfp_mutationtaster_rankscore": NotRequired[Union[str, List[str]]],
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"dbnsfp_sift_rankscore": NotRequired[Union[str, List[str]]],
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"sample_allele_frequency": NotRequired[Union[str, List[str]]],
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"sample_quality": NotRequired[Union[str, List[str]]],
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"sample_read_depth": NotRequired[Union[str, List[str]]],
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"sample_alternate_read_depth": NotRequired[Union[str, List[str]]],
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"sample_reference_read_depth": NotRequired[Union[str, List[str]]],
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"nextPageToken": NotRequired[str],
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"pageSize": NotRequired[float],
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},
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)
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class Clinvar(TypedDict):
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nearVariant: float
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class Cosmic(TypedDict):
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sampleCount: float
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nearVariant: float
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tumorSite: NotRequired[str]
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histology: NotRequired[str]
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cosmicId: NotRequired[str]
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status: NotRequired[str]
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EnsemblCanonItem = TypedDict(
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"EnsemblCanonItem",
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{
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"class": NotRequired[str],
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"impact": NotRequired[str],
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"gene": NotRequired[str],
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"geneId": NotRequired[str],
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"transcriptId": NotRequired[str],
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"biotype": NotRequired[str],
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"exonIntronRank": NotRequired[str],
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"nucleotideChange": NotRequired[str],
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"aminoAcidChange": NotRequired[str],
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"hgvsAminoAcidChange": NotRequired[str],
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},
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)
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class Dbnsfp(TypedDict):
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siftPred: List[Optional[str]]
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mutationTasterPred: List[Optional[str]]
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fathmmPred: List[Optional[str]]
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EnsemblItem = TypedDict(
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"EnsemblItem",
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{
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"class": NotRequired[str],
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"impact": NotRequired[str],
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"gene": NotRequired[str],
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"geneId": NotRequired[str],
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"transcriptId": NotRequired[str],
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"biotype": NotRequired[str],
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"exonIntronRank": NotRequired[str],
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"nucleotideChange": NotRequired[str],
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"aminoAcidChange": NotRequired[str],
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"hgvsAminoAcidChange": NotRequired[str],
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},
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)
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class Vcf(TypedDict):
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quality: float
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filter: str
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variantAllelicFrequency: float
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coverage: str
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class Item(TypedDict):
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id: str
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chromosome: str
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reference: str
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alternate: str
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position: float
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minimumAlleleFrequency: float
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maximumAlleleFrequency: float
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gnomadAlleleFrequency: float
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gnomadHomozygous: float
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rsid: str
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zygosity: str
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clinvar: Clinvar
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cosmic: Cosmic
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ensemblCanon: List[EnsemblCanonItem]
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dbnsfp: Dbnsfp
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ensembl: NotRequired[List[EnsemblItem]]
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vcf: NotRequired[Vcf]
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class Links(TypedDict):
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self: str
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next: NotRequired[str]
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class Invalid(TypedDict):
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variantSetIds: List[str]
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class SearchVariantsResponse(TypedDict):
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items: NotRequired[List[Item]]
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links: Links
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sorted: NotRequired[bool]
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count: NotRequired[float]
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invalid: NotRequired[Invalid]
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class GenomicsServiceClient(BaseClient):
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def __init__(self, **cfg: Unpack[AlphaConfig]):
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kwargs = {"target": "lambda://genomics-service:deployed", **(cfg or {})}
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super().__init__(**kwargs)
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async def search_variants(self, body: SearchVariantsRequest):
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"""Search for variants"""
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res = await self.client.request(
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path="/v1/genomics/variants/_search", method="POST", body=cast(dict, body)
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)
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return cast(AlphaResponse[SearchVariantsResponse], res)
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@@ -13,6 +13,7 @@ fountain_life_service_clients/email_service_sms.py,sha256=6W9Ba0Qj8oRtPMOrMx2HPk
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fountain_life_service_clients/fhir_post_processor_service.py,sha256=4IsyyRoCIzSNIBMvJFi1QyFuekikmtoY7ahQCh8Oncw,1355
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fountain_life_service_clients/fhir_search_service.py,sha256=O_y8YrOjvKj_Tfs5Pj4MM4X6RvV1E2s762lRH5U8ji8,6014
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fountain_life_service_clients/file_service.py,sha256=CY36fpvCAi17npAKAWkFDDaNhwbvTC5hx-sGZmPfyBM,4046
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fountain_life_service_clients/genomics_service.py,sha256=Am6cAg_hQKhY9W6bHjKyW4LQw_S2W0IiKNagkD8sQis,7425
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fountain_life_service_clients/invitation_service.py,sha256=tKWgb-bGIwT4x3MWSLiVChQRaZURj43S6Uyrg3Lt7HA,2596
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fountain_life_service_clients/medical_results_service_results.py,sha256=L0clTifU4LWWKgBsIzEfelmkaICxG1_q8sHyrdA5es4,4876
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fountain_life_service_clients/member_notification_service.py,sha256=wRkgmUqAV59BV81c3Iwz7JxSTuOLagHrcJcXvMbdBco,1814
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@@ -24,6 +25,6 @@ fountain_life_service_clients/rules_service.py,sha256=VxPYboYQmw--6Kn78RKu6_9as1
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fountain_life_service_clients/scheduler_service.py,sha256=IkwRns_QHh6fx1IZWEXZ35DeRiW7OHaROM5wjWubZm4,4440
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fountain_life_service_clients/survey_service.py,sha256=hxOl3gBDxEdjrsKcMCoPl9RxumQzRT-e4zTbEAA0Iq4,13343
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fountain_life_service_clients/user_service.py,sha256=rM9xcF-VzdLp9aDOhg1UbecX2VPPMxH9PlgpNpGdC18,4253
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fountain_life_service_clients-3.
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fountain_life_service_clients-3.
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fountain_life_service_clients-3.
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fountain_life_service_clients-3.32.0.dist-info/METADATA,sha256=y0-VaE64BYAoWHg6EIy9coMQYZ_T2RZfCVpT7l8s8B0,1405
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fountain_life_service_clients-3.32.0.dist-info/WHEEL,sha256=M5asmiAlL6HEcOq52Yi5mmk9KmTVjY2RDPtO4p9DMrc,88
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fountain_life_service_clients-3.32.0.dist-info/RECORD,,
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File without changes
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