File size: 4,044 Bytes
0161e74 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 | import json
from dataclasses import dataclass, field, asdict
from pathlib import Path
from typing import List, Optional, Union
from typing_extensions import Self, Literal
from datasets import Dataset
@dataclass
class DataTable:
"""
The data structure for a single-cell data table.
"""
name: str
data: Optional[Dataset] = None
@property
def is_loaded(self) -> bool:
return self.data is not None and isinstance(self.data, Dataset)
def save(
self,
path: Union[Path, str],
format: Literal["json", "parquet"] = "json",
) -> None:
if not self.is_loaded:
raise ValueError("DataTable is not loaded.")
if isinstance(path, str):
path = Path(path)
if format == "json":
self.data.to_json(path)
elif format == "parquet":
self.data.to_parquet(path)
else:
raise ValueError(f"Unknown format: {format}")
@dataclass
class MetaInfo:
"""
The data structure for meta info of a scBank data directory.
"""
on_disk_path: Union[Path, str, None] = None
on_disk_format: Literal["json", "parquet"] = "json"
main_table_key: Optional[str] = None
# TODO: use md5 to check the vocab file name on disk
gene_vocab_md5: Optional[str] = None
study_ids: Optional[List[int]] = field(
default=None,
metadata={"help": "List of study IDs"},
)
cell_ids: Optional[List[int]] = field(
default=None,
metadata={"help": "List of cell IDs"},
)
# md5: Optional[str] = field(
# default=None,
# metadata={"help": "MD5 hash of the gene vocabulary"},
# )
def __post_init__(self):
if self.on_disk_path is not None:
self.on_disk_path: Path = Path(self.on_disk_path)
def save(self, path: Union[Path, str, None] = None) -> None:
"""
Save meta info to path. If path is None, will save to the same path at
:attr:`on_disk_path`.
"""
if path is None:
path = self.on_disk_path
if isinstance(path, str):
path = Path(path)
manifests = {
"on_disk_format": self.on_disk_format,
"main_data": self.main_table_key,
"gene_vocab_md5": self.gene_vocab_md5,
}
with open(path / "manifest.json", "w") as f:
json.dump(manifests, f, indent=2)
# TODO: currently only save study table, add saving other tables
with open(path / "studytable.json", "w") as f:
json.dump({"study_ids": self.study_ids}, f, indent=2)
def load(self, path: Union[Path, str, None] = None) -> None:
"""
Load meta info from path. If path is None, will load from the same path
at :attr:`on_disk_path`.
"""
if path is None:
path = self.on_disk_path
if isinstance(path, str):
path = Path(path)
with open(path / "manifest.json") as f:
manifests = json.load(f)
self.on_disk_format = manifests["on_disk_format"]
self.main_table_key = manifests["main_data"]
self.gene_vocab_md5 = manifests["gene_vocab_md5"]
if (path / "studytable.json").exists():
with open(path / "studytable.json") as f:
study_ids = json.load(f)
self.study_ids = study_ids["study_ids"]
@classmethod
def from_path(cls, path: Union[Path, str]) -> Self:
"""
Create a MetaInfo object from a path.
"""
if isinstance(path, str):
path = Path(path)
if not path.exists():
raise ValueError(f"Path {path} does not exist.")
if not path.is_dir():
raise ValueError(f"Path {path} is not a directory.")
if not (path / "manifest.json").exists():
raise ValueError(f"Path {path} does not contain manifest.json.")
meta_info = cls()
meta_info.on_disk_path = path
meta_info.load(path)
return meta_info
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