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Source code for galaxy.webapps.galaxy.api.genomes

from typing import (
    Any,
    List,
)

from fastapi import (
    Path,
    Query,
)
from fastapi.responses import Response

from galaxy.managers.context import ProvidesUserContext
from galaxy.managers.genomes import GenomesManager
from . import (
    depends,
    DependsOnTrans,
    Router,
)

router = Router(tags=["genomes"])

IdPathParam: str = Path(..., title="Genome ID", description="Genome ID")

ChromInfoQueryParam: bool = Query(
    None, title="ChromInfo", description="If true, return genome keys with chromosome lengths"
)

NumQueryParam: int = Query(
    None,
    title="Number",
    description="Limits size of returned data",
)

ChromQueryParam: Any = Query(
    None,
    title="Chrom",
    description="Limits size of returned data",
)

LowQueryParam: int = Query(
    None,
    title="Low",
    description="Limits size of returned data",
)

HighQueryParam: int = Query(
    None,
    title="High",
    description="Limits size of returned data",
)

FormatQueryParam: str = Query(None, title="Format", description="Format")

ReferenceQueryParam: bool = Query(None, title="Reference", description="If true, return reference data")

IndexTypeQueryParam: str = Query(
    "fasta_indexes", title="Index type", description="Index type"  # currently this is the only supported index type
)


[docs]def get_id(base, format): if format: return f"{base}.{format}" return base
[docs]@router.cbv class FastAPIGenomes: manager: GenomesManager = depends(GenomesManager)
[docs] @router.get("/api/genomes", summary="Return a list of installed genomes", response_description="Installed genomes") def index( self, trans: ProvidesUserContext = DependsOnTrans, chrom_info: bool = ChromInfoQueryParam ) -> List[List[str]]: return self.manager.get_dbkeys(trans.user, chrom_info)
[docs] @router.get( "/api/genomes/{id}", summary="Return information about build <id>", response_description="Information about genome build <id>", ) def show( self, trans: ProvidesUserContext = DependsOnTrans, id: str = IdPathParam, reference: bool = ReferenceQueryParam, num: int = NumQueryParam, chrom: str = ChromQueryParam, low: int = LowQueryParam, high: int = HighQueryParam, format: str = FormatQueryParam, ) -> Any: id = get_id(id, format) return self.manager.get_genome(trans, id, num, chrom, low, high, reference)
[docs] @router.get( "/api/genomes/{id}/indexes", summary="Return all available indexes for a genome id for provided type", response_description="Indexes for a genome id for provided type", ) def indexes( self, id: str = IdPathParam, type: str = IndexTypeQueryParam, format: str = FormatQueryParam, ) -> Any: id = get_id(id, format) rval = self.manager.get_indexes(id, type) return Response(rval)
[docs] @router.get( "/api/genomes/{id}/sequences", summary="Return raw sequence data", response_description="Raw sequence data" ) def sequences( self, trans: ProvidesUserContext = DependsOnTrans, id: str = IdPathParam, reference: bool = ReferenceQueryParam, chrom: str = ChromQueryParam, low: int = LowQueryParam, high: int = HighQueryParam, format: str = FormatQueryParam, ) -> Any: id = get_id(id, format) rval = self.manager.get_sequence(trans, id, chrom, low, high) return Response(rval)