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"""
Contains possible interactions with the Galaxy Histories
"""
from typing import (
Any,
Dict,
Optional,
TYPE_CHECKING,
)
from typing_extensions import Literal
from bioblend.galaxy.client import Client
if TYPE_CHECKING:
from bioblend.galaxy import GalaxyInstance
class GenomeClient(Client):
module = "genomes"
def __init__(self, galaxy_instance: "GalaxyInstance") -> None:
super().__init__(galaxy_instance)
def get_genomes(self) -> list:
"""
Returns a list of installed genomes
:rtype: list
:return: List of installed genomes
"""
genomes = self._get()
return genomes
def show_genome(
self,
id: str,
num: Optional[str] = None,
chrom: Optional[str] = None,
low: Optional[str] = None,
high: Optional[str] = None,
) -> Dict[str, Any]:
"""
Returns information about build <id>
:type id: str
:param id: Genome build ID to use
:type num: str
:param num: num
:type chrom: str
:param chrom: chrom
:type low: str
:param low: low
:type high: str
:param high: high
:rtype: dict
:return: Information about the genome build
"""
params: Dict[str, str] = {}
if num:
params["num"] = num
if chrom:
params["chrom"] = chrom
if low:
params["low"] = low
if high:
params["high"] = high
return self._get(id=id, params=params)
def install_genome(
self,
func: Literal["download", "index"] = "download",
source: Optional[str] = None,
dbkey: Optional[str] = None,
ncbi_name: Optional[str] = None,
ensembl_dbkey: Optional[str] = None,
url_dbkey: Optional[str] = None,
indexers: Optional[list] = None,
) -> Dict[str, Any]:
"""
Download and/or index a genome.
:type func: str
:param func: Allowed values: 'download', Download and index; 'index', Index only
:type source: str
:param source: Data source for this build. Can be: UCSC, Ensembl, NCBI, URL
:type dbkey: str
:param dbkey: DB key of the build to download, ignored unless 'UCSC' is specified as the source
:type ncbi_name: str
:param ncbi_name: NCBI's genome identifier, ignored unless NCBI is specified as the source
:type ensembl_dbkey: str
:param ensembl_dbkey: Ensembl's genome identifier, ignored unless Ensembl is specified as the source
:type url_dbkey: str
:param url_dbkey: DB key to use for this build, ignored unless URL is specified as the source
:type indexers: list
:param indexers: POST array of indexers to run after downloading (indexers[] = first, indexers[] = second, ...)
:rtype: dict
:return: dict( status: 'ok', job: <job ID> )
If error:
dict( status: 'error', error: <error message> )
"""
payload: Dict[str, Any] = {}
if source:
payload["source"] = source
if func:
payload["func"] = func
if dbkey:
payload["dbkey"] = dbkey
if ncbi_name:
payload["ncbi_name"] = ncbi_name
if ensembl_dbkey:
payload["ensembl_dbkey"] = ensembl_dbkey
if url_dbkey:
payload["url_dbkey"] = url_dbkey
if indexers:
payload["indexers"] = indexers
return self._post(payload)
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