fountain-life-service-clients 3.34.2__py3-none-any.whl → 3.35.1__py3-none-any.whl

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Files changed (5) hide show
  1. fountain_life_service_clients/ga4gh_service.py +34 -0
  2. fountain_life_service_clients/genomics_service.py +4 -73
  3. {fountain_life_service_clients-3.34.2.dist-info → fountain_life_service_clients-3.35.1.dist-info}/METADATA +1 -1
  4. {fountain_life_service_clients-3.34.2.dist-info → fountain_life_service_clients-3.35.1.dist-info}/RECORD +5 -4
  5. {fountain_life_service_clients-3.34.2.dist-info → fountain_life_service_clients-3.35.1.dist-info}/WHEEL +0 -0
fountain_life_service_clients/ga4gh_service.py ADDED
@@ -0,0 +1,34 @@
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+ # This file was generated automatically. Do not edit it directly.
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+ from typing import List, NotRequired, TypedDict, Unpack, cast
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+ from urllib.parse import quote
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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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+
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+
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+ class Sample(TypedDict):
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+ sampleId: str
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+ patientId: NotRequired[str]
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+
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+
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+ class GetVariantSetResponse(TypedDict):
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+ id: str
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+ datasetId: str
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+ patientId: NotRequired[str]
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+ samples: NotRequired[List[Sample]]
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+
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+
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+ class Ga4ghServiceClient(BaseClient):
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+ def __init__(self, **cfg: Unpack[AlphaConfig]):
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+ kwargs = {"target": "lambda://ga4gh-service:deployed", **(cfg or {})}
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+ super().__init__(**kwargs)
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+
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+ async def get_variant_set(self, account: str, id: str):
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+ """Get a variant set by id"""
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+ res = await self.client.request(
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+ path=f"/{quote(account)}/v1/variantsets/{quote(id)}", method="GET"
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+ )
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+ return cast(AlphaResponse[GetVariantSetResponse], res)
fountain_life_service_clients/genomics_service.py CHANGED
@@ -9,7 +9,6 @@ from typing import (
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  Unpack,
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  cast,
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  )
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- from urllib.parse import quote
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  from fountain_life_service_clients._base_client import (
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  AlphaConfig,
@@ -17,19 +16,6 @@ from fountain_life_service_clients._base_client import (
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  BaseClient,
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  )
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-
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- class Sample(TypedDict):
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- sampleId: str
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- patientId: NotRequired[str]
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-
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-
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- class GetVariantSetResponse(TypedDict):
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- id: str
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- datasetId: str
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- patientId: NotRequired[str]
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- samples: NotRequired[List[Sample]]
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-
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-
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  SearchVariantsRequest = TypedDict(
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  "SearchVariantsRequest",
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  {
@@ -41,66 +27,18 @@ SearchVariantsRequest = TypedDict(
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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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+ "rsid": 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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+ "popAlleleFrequency": NotRequired[str],
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+ "genesPair": NotRequired[str],
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+ "clinvarSignificance": NotRequired[Union[str, List[str]]],
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  },
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  )
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@@ -212,13 +150,6 @@ class GenomicsServiceClient(BaseClient):
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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 get_variant_set(self, id: str):
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- """Get a variant set by id"""
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- res = await self.client.request(
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- path=f"/v1/genomics/variantsets/{quote(id)}", method="GET"
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- )
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- return cast(AlphaResponse[GetVariantSetResponse], res)
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-
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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(
{fountain_life_service_clients-3.34.2.dist-info → fountain_life_service_clients-3.35.1.dist-info}/METADATA RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: fountain-life-service-clients
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- Version: 3.34.2
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+ Version: 3.35.1
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  Summary:
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  License: UNLICENSED
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  Author: Fountain Life
{fountain_life_service_clients-3.34.2.dist-info → fountain_life_service_clients-3.35.1.dist-info}/RECORD RENAMED
@@ -13,7 +13,8 @@ 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=folZvWiDFZltWqcle_4Ch-b_cg53Sw36oSjeeXZSkdY,8041
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+ fountain_life_service_clients/ga4gh_service.py,sha256=SSFdYM_oW2ZATUOaZT_xjp3jlEJt7rR_ai2US6HolgI,989
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+ fountain_life_service_clients/genomics_service.py,sha256=Xx5rhgzjEJfdNA_g0Je4xDo26NKZQiIuNC88cUI-v-s,4225
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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
@@ -25,6 +26,6 @@ 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-3.34.2.dist-info/METADATA,sha256=oaAiqWtnGu8Wh0Fl24HXsssry0-e7DThMvSWevjpqH0,1405
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- fountain_life_service_clients-3.34.2.dist-info/WHEEL,sha256=M5asmiAlL6HEcOq52Yi5mmk9KmTVjY2RDPtO4p9DMrc,88
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- fountain_life_service_clients-3.34.2.dist-info/RECORD,,
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+ fountain_life_service_clients-3.35.1.dist-info/METADATA,sha256=2yt9wrkl01wmOW2ukRa-35SRQNETez_y4VZ8H9y5KkI,1405
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+ fountain_life_service_clients-3.35.1.dist-info/WHEEL,sha256=M5asmiAlL6HEcOq52Yi5mmk9KmTVjY2RDPtO4p9DMrc,88
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+ fountain_life_service_clients-3.35.1.dist-info/RECORD,,