from __future__ import annotations
from collections.abc import Mapping
from typing import Any, TypeVar, TYPE_CHECKING
from attrs import define as _attrs_define
from attrs import field as _attrs_field
from ..types import UNSET, Unset
from ..models.genome_type import GenomeType
from dateutil.parser import isoparse
from typing import cast
import datetime
if TYPE_CHECKING:
from ..models.biome import Biome
from ..models.genome_catalogue_base import GenomeCatalogueBase
from ..models.m_gnify_genome_download_file import MGnifyGenomeDownloadFile
T = TypeVar("T", bound="GenomeDetail")
[docs]
@_attrs_define
class GenomeDetail:
"""
Attributes:
accession (str):
ena_genome_accession (None | str):
ena_sample_accession (None | str):
ena_study_accession (None | str):
ncbi_genome_accession (None | str):
ncbi_study_accession (None | str):
img_genome_accession (None | str):
patric_genome_accession (None | str):
length (int):
num_contigs (int):
n_50 (int):
gc_content (float):
type_ (GenomeType):
completeness (float):
contamination (float):
catalogue_id (str):
taxon_lineage (str):
updated_at (datetime.datetime):
geographic_origin (None | str):
downloads (list[MGnifyGenomeDownloadFile]):
num_genomes_total (int | None | Unset):
geographic_range (list[str] | None | Unset):
biome (Biome | None | Unset):
rna_5s (float | None | Unset):
rna_5_8s (float | None | Unset):
rna_16s (float | None | Unset):
rna_18s (float | None | Unset):
rna_23s (float | None | Unset):
rna_28s (float | None | Unset):
trnas (float | None | Unset):
nc_rnas (float | None | Unset):
eggnog_coverage (float | None | Unset):
ipr_coverage (float | None | Unset):
num_proteins (int | None | Unset):
catalogue (GenomeCatalogueBase | None | Unset):
"""
accession: str
ena_genome_accession: None | str
ena_sample_accession: None | str
ena_study_accession: None | str
ncbi_genome_accession: None | str
ncbi_study_accession: None | str
img_genome_accession: None | str
patric_genome_accession: None | str
length: int
num_contigs: int
n_50: int
gc_content: float
type_: GenomeType
completeness: float
contamination: float
catalogue_id: str
taxon_lineage: str
updated_at: datetime.datetime
geographic_origin: None | str
downloads: list[MGnifyGenomeDownloadFile]
num_genomes_total: int | None | Unset = UNSET
geographic_range: list[str] | None | Unset = UNSET
biome: Biome | None | Unset = UNSET
rna_5s: float | None | Unset = UNSET
rna_5_8s: float | None | Unset = UNSET
rna_16s: float | None | Unset = UNSET
rna_18s: float | None | Unset = UNSET
rna_23s: float | None | Unset = UNSET
rna_28s: float | None | Unset = UNSET
trnas: float | None | Unset = UNSET
nc_rnas: float | None | Unset = UNSET
eggnog_coverage: float | None | Unset = UNSET
ipr_coverage: float | None | Unset = UNSET
num_proteins: int | None | Unset = UNSET
catalogue: GenomeCatalogueBase | None | Unset = UNSET
additional_properties: dict[str, Any] = _attrs_field(init=False, factory=dict)
[docs]
def to_dict(self) -> dict[str, Any]:
from ..models.biome import Biome
from ..models.genome_catalogue_base import GenomeCatalogueBase
accession = self.accession
ena_genome_accession: None | str
ena_genome_accession = self.ena_genome_accession
ena_sample_accession: None | str
ena_sample_accession = self.ena_sample_accession
ena_study_accession: None | str
ena_study_accession = self.ena_study_accession
ncbi_genome_accession: None | str
ncbi_genome_accession = self.ncbi_genome_accession
ncbi_study_accession: None | str
ncbi_study_accession = self.ncbi_study_accession
img_genome_accession: None | str
img_genome_accession = self.img_genome_accession
patric_genome_accession: None | str
patric_genome_accession = self.patric_genome_accession
length = self.length
num_contigs = self.num_contigs
n_50 = self.n_50
gc_content = self.gc_content
type_ = self.type_.value
completeness = self.completeness
contamination = self.contamination
catalogue_id = self.catalogue_id
taxon_lineage = self.taxon_lineage
updated_at = self.updated_at.isoformat()
geographic_origin: None | str
geographic_origin = self.geographic_origin
downloads = []
for downloads_item_data in self.downloads:
downloads_item = downloads_item_data.to_dict()
downloads.append(downloads_item)
num_genomes_total: int | None | Unset
if isinstance(self.num_genomes_total, Unset):
num_genomes_total = UNSET
else:
num_genomes_total = self.num_genomes_total
geographic_range: list[str] | None | Unset
if isinstance(self.geographic_range, Unset):
geographic_range = UNSET
elif isinstance(self.geographic_range, list):
geographic_range = self.geographic_range
else:
geographic_range = self.geographic_range
biome: dict[str, Any] | None | Unset
if isinstance(self.biome, Unset):
biome = UNSET
elif isinstance(self.biome, Biome):
biome = self.biome.to_dict()
else:
biome = self.biome
rna_5s: float | None | Unset
if isinstance(self.rna_5s, Unset):
rna_5s = UNSET
else:
rna_5s = self.rna_5s
rna_5_8s: float | None | Unset
if isinstance(self.rna_5_8s, Unset):
rna_5_8s = UNSET
else:
rna_5_8s = self.rna_5_8s
rna_16s: float | None | Unset
if isinstance(self.rna_16s, Unset):
rna_16s = UNSET
else:
rna_16s = self.rna_16s
rna_18s: float | None | Unset
if isinstance(self.rna_18s, Unset):
rna_18s = UNSET
else:
rna_18s = self.rna_18s
rna_23s: float | None | Unset
if isinstance(self.rna_23s, Unset):
rna_23s = UNSET
else:
rna_23s = self.rna_23s
rna_28s: float | None | Unset
if isinstance(self.rna_28s, Unset):
rna_28s = UNSET
else:
rna_28s = self.rna_28s
trnas: float | None | Unset
if isinstance(self.trnas, Unset):
trnas = UNSET
else:
trnas = self.trnas
nc_rnas: float | None | Unset
if isinstance(self.nc_rnas, Unset):
nc_rnas = UNSET
else:
nc_rnas = self.nc_rnas
eggnog_coverage: float | None | Unset
if isinstance(self.eggnog_coverage, Unset):
eggnog_coverage = UNSET
else:
eggnog_coverage = self.eggnog_coverage
ipr_coverage: float | None | Unset
if isinstance(self.ipr_coverage, Unset):
ipr_coverage = UNSET
else:
ipr_coverage = self.ipr_coverage
num_proteins: int | None | Unset
if isinstance(self.num_proteins, Unset):
num_proteins = UNSET
else:
num_proteins = self.num_proteins
catalogue: dict[str, Any] | None | Unset
if isinstance(self.catalogue, Unset):
catalogue = UNSET
elif isinstance(self.catalogue, GenomeCatalogueBase):
catalogue = self.catalogue.to_dict()
else:
catalogue = self.catalogue
field_dict: dict[str, Any] = {}
field_dict.update(self.additional_properties)
field_dict.update(
{
"accession": accession,
"ena_genome_accession": ena_genome_accession,
"ena_sample_accession": ena_sample_accession,
"ena_study_accession": ena_study_accession,
"ncbi_genome_accession": ncbi_genome_accession,
"ncbi_study_accession": ncbi_study_accession,
"img_genome_accession": img_genome_accession,
"patric_genome_accession": patric_genome_accession,
"length": length,
"num_contigs": num_contigs,
"n_50": n_50,
"gc_content": gc_content,
"type": type_,
"completeness": completeness,
"contamination": contamination,
"catalogue_id": catalogue_id,
"taxon_lineage": taxon_lineage,
"updated_at": updated_at,
"geographic_origin": geographic_origin,
"downloads": downloads,
}
)
if num_genomes_total is not UNSET:
field_dict["num_genomes_total"] = num_genomes_total
if geographic_range is not UNSET:
field_dict["geographic_range"] = geographic_range
if biome is not UNSET:
field_dict["biome"] = biome
if rna_5s is not UNSET:
field_dict["rna_5s"] = rna_5s
if rna_5_8s is not UNSET:
field_dict["rna_5_8s"] = rna_5_8s
if rna_16s is not UNSET:
field_dict["rna_16s"] = rna_16s
if rna_18s is not UNSET:
field_dict["rna_18s"] = rna_18s
if rna_23s is not UNSET:
field_dict["rna_23s"] = rna_23s
if rna_28s is not UNSET:
field_dict["rna_28s"] = rna_28s
if trnas is not UNSET:
field_dict["trnas"] = trnas
if nc_rnas is not UNSET:
field_dict["nc_rnas"] = nc_rnas
if eggnog_coverage is not UNSET:
field_dict["eggnog_coverage"] = eggnog_coverage
if ipr_coverage is not UNSET:
field_dict["ipr_coverage"] = ipr_coverage
if num_proteins is not UNSET:
field_dict["num_proteins"] = num_proteins
if catalogue is not UNSET:
field_dict["catalogue"] = catalogue
return field_dict
[docs]
@classmethod
def from_dict(cls: type[T], src_dict: Mapping[str, Any]) -> T:
from ..models.biome import Biome
from ..models.genome_catalogue_base import GenomeCatalogueBase
from ..models.m_gnify_genome_download_file import MGnifyGenomeDownloadFile
d = dict(src_dict)
accession = d.pop("accession")
def _parse_ena_genome_accession(data: object) -> None | str:
if data is None:
return data
return cast(None | str, data)
ena_genome_accession = _parse_ena_genome_accession(
d.pop("ena_genome_accession")
)
def _parse_ena_sample_accession(data: object) -> None | str:
if data is None:
return data
return cast(None | str, data)
ena_sample_accession = _parse_ena_sample_accession(
d.pop("ena_sample_accession")
)
def _parse_ena_study_accession(data: object) -> None | str:
if data is None:
return data
return cast(None | str, data)
ena_study_accession = _parse_ena_study_accession(d.pop("ena_study_accession"))
def _parse_ncbi_genome_accession(data: object) -> None | str:
if data is None:
return data
return cast(None | str, data)
ncbi_genome_accession = _parse_ncbi_genome_accession(
d.pop("ncbi_genome_accession")
)
def _parse_ncbi_study_accession(data: object) -> None | str:
if data is None:
return data
return cast(None | str, data)
ncbi_study_accession = _parse_ncbi_study_accession(
d.pop("ncbi_study_accession")
)
def _parse_img_genome_accession(data: object) -> None | str:
if data is None:
return data
return cast(None | str, data)
img_genome_accession = _parse_img_genome_accession(
d.pop("img_genome_accession")
)
def _parse_patric_genome_accession(data: object) -> None | str:
if data is None:
return data
return cast(None | str, data)
patric_genome_accession = _parse_patric_genome_accession(
d.pop("patric_genome_accession")
)
length = d.pop("length")
num_contigs = d.pop("num_contigs")
n_50 = d.pop("n_50")
gc_content = d.pop("gc_content")
type_ = GenomeType(d.pop("type"))
completeness = d.pop("completeness")
contamination = d.pop("contamination")
catalogue_id = d.pop("catalogue_id")
taxon_lineage = d.pop("taxon_lineage")
updated_at = isoparse(d.pop("updated_at"))
def _parse_geographic_origin(data: object) -> None | str:
if data is None:
return data
return cast(None | str, data)
geographic_origin = _parse_geographic_origin(d.pop("geographic_origin"))
downloads = []
_downloads = d.pop("downloads")
for downloads_item_data in _downloads:
downloads_item = MGnifyGenomeDownloadFile.from_dict(downloads_item_data)
downloads.append(downloads_item)
def _parse_num_genomes_total(data: object) -> int | None | Unset:
if data is None:
return data
if isinstance(data, Unset):
return data
return cast(int | None | Unset, data)
num_genomes_total = _parse_num_genomes_total(d.pop("num_genomes_total", UNSET))
def _parse_geographic_range(data: object) -> list[str] | None | Unset:
if data is None:
return data
if isinstance(data, Unset):
return data
try:
if not isinstance(data, list):
raise TypeError()
geographic_range_type_0 = cast(list[str], data)
return geographic_range_type_0
except (TypeError, ValueError, AttributeError, KeyError):
pass
return cast(list[str] | None | Unset, data)
geographic_range = _parse_geographic_range(d.pop("geographic_range", UNSET))
def _parse_biome(data: object) -> Biome | None | Unset:
if data is None:
return data
if isinstance(data, Unset):
return data
try:
if not isinstance(data, dict):
raise TypeError()
biome_type_0 = Biome.from_dict(data)
return biome_type_0
except (TypeError, ValueError, AttributeError, KeyError):
pass
return cast(Biome | None | Unset, data)
biome = _parse_biome(d.pop("biome", UNSET))
def _parse_rna_5s(data: object) -> float | None | Unset:
if data is None:
return data
if isinstance(data, Unset):
return data
return cast(float | None | Unset, data)
rna_5s = _parse_rna_5s(d.pop("rna_5s", UNSET))
def _parse_rna_5_8s(data: object) -> float | None | Unset:
if data is None:
return data
if isinstance(data, Unset):
return data
return cast(float | None | Unset, data)
rna_5_8s = _parse_rna_5_8s(d.pop("rna_5_8s", UNSET))
def _parse_rna_16s(data: object) -> float | None | Unset:
if data is None:
return data
if isinstance(data, Unset):
return data
return cast(float | None | Unset, data)
rna_16s = _parse_rna_16s(d.pop("rna_16s", UNSET))
def _parse_rna_18s(data: object) -> float | None | Unset:
if data is None:
return data
if isinstance(data, Unset):
return data
return cast(float | None | Unset, data)
rna_18s = _parse_rna_18s(d.pop("rna_18s", UNSET))
def _parse_rna_23s(data: object) -> float | None | Unset:
if data is None:
return data
if isinstance(data, Unset):
return data
return cast(float | None | Unset, data)
rna_23s = _parse_rna_23s(d.pop("rna_23s", UNSET))
def _parse_rna_28s(data: object) -> float | None | Unset:
if data is None:
return data
if isinstance(data, Unset):
return data
return cast(float | None | Unset, data)
rna_28s = _parse_rna_28s(d.pop("rna_28s", UNSET))
def _parse_trnas(data: object) -> float | None | Unset:
if data is None:
return data
if isinstance(data, Unset):
return data
return cast(float | None | Unset, data)
trnas = _parse_trnas(d.pop("trnas", UNSET))
def _parse_nc_rnas(data: object) -> float | None | Unset:
if data is None:
return data
if isinstance(data, Unset):
return data
return cast(float | None | Unset, data)
nc_rnas = _parse_nc_rnas(d.pop("nc_rnas", UNSET))
def _parse_eggnog_coverage(data: object) -> float | None | Unset:
if data is None:
return data
if isinstance(data, Unset):
return data
return cast(float | None | Unset, data)
eggnog_coverage = _parse_eggnog_coverage(d.pop("eggnog_coverage", UNSET))
def _parse_ipr_coverage(data: object) -> float | None | Unset:
if data is None:
return data
if isinstance(data, Unset):
return data
return cast(float | None | Unset, data)
ipr_coverage = _parse_ipr_coverage(d.pop("ipr_coverage", UNSET))
def _parse_num_proteins(data: object) -> int | None | Unset:
if data is None:
return data
if isinstance(data, Unset):
return data
return cast(int | None | Unset, data)
num_proteins = _parse_num_proteins(d.pop("num_proteins", UNSET))
def _parse_catalogue(data: object) -> GenomeCatalogueBase | None | Unset:
if data is None:
return data
if isinstance(data, Unset):
return data
try:
if not isinstance(data, dict):
raise TypeError()
catalogue_type_0 = GenomeCatalogueBase.from_dict(data)
return catalogue_type_0
except (TypeError, ValueError, AttributeError, KeyError):
pass
return cast(GenomeCatalogueBase | None | Unset, data)
catalogue = _parse_catalogue(d.pop("catalogue", UNSET))
genome_detail = cls(
accession=accession,
ena_genome_accession=ena_genome_accession,
ena_sample_accession=ena_sample_accession,
ena_study_accession=ena_study_accession,
ncbi_genome_accession=ncbi_genome_accession,
ncbi_study_accession=ncbi_study_accession,
img_genome_accession=img_genome_accession,
patric_genome_accession=patric_genome_accession,
length=length,
num_contigs=num_contigs,
n_50=n_50,
gc_content=gc_content,
type_=type_,
completeness=completeness,
contamination=contamination,
catalogue_id=catalogue_id,
taxon_lineage=taxon_lineage,
updated_at=updated_at,
geographic_origin=geographic_origin,
downloads=downloads,
num_genomes_total=num_genomes_total,
geographic_range=geographic_range,
biome=biome,
rna_5s=rna_5s,
rna_5_8s=rna_5_8s,
rna_16s=rna_16s,
rna_18s=rna_18s,
rna_23s=rna_23s,
rna_28s=rna_28s,
trnas=trnas,
nc_rnas=nc_rnas,
eggnog_coverage=eggnog_coverage,
ipr_coverage=ipr_coverage,
num_proteins=num_proteins,
catalogue=catalogue,
)
genome_detail.additional_properties = d
return genome_detail
@property
def additional_keys(self) -> list[str]:
return list(self.additional_properties.keys())
def __getitem__(self, key: str) -> Any:
return self.additional_properties[key]
def __setitem__(self, key: str, value: Any) -> None:
self.additional_properties[key] = value
def __delitem__(self, key: str) -> None:
del self.additional_properties[key]
def __contains__(self, key: str) -> bool:
return key in self.additional_properties
