scmcp-shared 0.3.7__py3-none-any.whl → 0.5.0__py3-none-any.whl

scmcp_shared/schema/preset/__init__.py

@@ -0,0 +1,15 @@
+from __future__ import annotations
+
+from pydantic import Field, BaseModel, ConfigDict
+
+
+class AdataInfo(BaseModel):
+    """Input schema for the adata tool."""
+
+    sampleid: str | None = Field(default=None, description="adata sampleid")
+    adtype: str = Field(
+        default="exp",
+        description="The input adata.X data type for preprocess/analysis/plotting",
+    )
+
+    model_config = ConfigDict(extra="ignore")

scmcp_shared/schema/preset/io.py

@@ -0,0 +1,103 @@
+from pydantic import Field, field_validator, model_validator, BaseModel
+from typing import Optional, Literal
+
+
+class ReadParam(BaseModel):
+    """Input schema for the read tool."""
+
+    filename: str = Field(..., description="Path to the file to read.")
+
+    backed: Literal["r", "r+"] = Field(
+        default=None,
+        description="If 'r', load AnnData in 'backed' mode instead of fully loading it into memory ('memory' mode). If you want to modify backed attributes of the AnnData object, you need to choose 'r+'.",
+    )
+    sheet: str = Field(
+        default=None, description="Name of sheet/table in hdf5 or Excel file."
+    )
+    delimiter: str = Field(
+        default=None,
+        description="Delimiter that separates data within text file. If None, will split at arbitrary number of white spaces, which is different from enforcing splitting at any single white space.",
+    )
+    first_column_names: bool = Field(
+        default=False,
+        description="Assume the first column stores row names. This is only necessary if these are not strings: strings in the first column are automatically assumed to be row names.",
+    )
+    transpose: bool = Field(
+        default=False, description="If True, the data will be transposed."
+    )
+    backup_url: str = Field(
+        default=None,
+        description="Retrieve the file from an URL if not present on disk.",
+    )
+    cache: bool = Field(
+        default=False,
+        description="If False, read from source, if True, read from fast 'h5ad' cache.",
+    )
+    cache_compression: Literal["gzip", "lzf"] = Field(
+        default=None,
+        description="See the h5py dataset_compression. (Default: settings.cache_compression)",
+    )
+    var_names: str = Field(
+        default="gene_symbols",
+        description="The variables index for 10x mtx format. Either 'gene_symbols' or 'gene_ids'.",
+    )
+    make_unique: bool = Field(
+        default=True,
+        description="Whether to make the variables index unique by appending '-1', '-2' etc. or not. Used for 10x mtx format.",
+    )
+    gex_only: bool = Field(
+        default=True,
+        description="Only keep 'Gene Expression' data and ignore other feature types, e.g. 'Antibody Capture', 'CRISPR Guide Capture', or 'Custom'. Used for 10x formats.",
+    )
+    prefix: str = Field(
+        default=None,
+        description="Any prefix before matrix.mtx, genes.tsv and barcodes.tsv. For instance, if the files are named patientA_matrix.mtx, patientA_genes.tsv and patientA_barcodes.tsv the prefix is patientA_. Used for 10x mtx format.",
+    )
+
+    @field_validator("backed")
+    def validate_backed(cls, v: Optional[str]) -> Optional[str]:
+        if v is not None and v not in ["r", "r+"]:
+            raise ValueError("If backed is provided, it must be either 'r' or 'r+'")
+        return v
+
+    @field_validator("cache_compression")
+    def validate_cache_compression(cls, v: Optional[str]) -> Optional[str]:
+        if v is not None and v not in ["gzip", "lzf"]:
+            raise ValueError("cache_compression must be either 'gzip', 'lzf', or None")
+        return v
+
+    @field_validator("var_names")
+    def validate_var_names(cls, v: Optional[str]) -> Optional[str]:
+        if v is not None and v not in ["gene_symbols", "gene_ids"]:
+            raise ValueError("var_names must be either 'gene_symbols' or 'gene_ids'")
+        return v
+
+
+class WriteParam(BaseModel):
+    """Input schema for the write tool."""
+
+    filename: str = Field(
+        description="Path to save the file. If no extension is provided, the default format will be used."
+    )
+    ext: Literal["h5", "csv", "txt", "npz"] = Field(
+        default=None,
+        description="File extension to infer file format. If None, defaults to scanpy's settings.file_format_data.",
+    )
+    compression: Literal["gzip", "lzf"] = Field(
+        default="gzip", description="Compression format for h5 files."
+    )
+    compression_opts: int = Field(
+        default=None, description="Compression options for h5 files."
+    )
+
+    @field_validator("filename")
+    def validate_filename(cls, v: str) -> str:
+        # Allow any filename since the extension is optional and can be inferred
+        return v
+
+    @model_validator(mode="after")
+    def validate_extension_compression(self) -> "WriteParam":
+        # If ext is provided and not h5, compression should be None
+        if self.ext is not None and self.ext != "h5" and self.compression is not None:
+            raise ValueError("Compression can only be used with h5 files")
+        return self