scmcp-shared 0.4.0__py3-none-any.whl → 0.6.0__py3-none-any.whl

scmcp_shared/schema/io.py

@@ -1,113 +1,155 @@
-from pydantic import (
-    Field,
-    field_validator,
-    model_validator, BaseModel
-)
+from pydantic import Field, field_validator, model_validator, BaseModel
 from typing import Optional, Literal
 
 
-
-class ReadParams(BaseModel):
+class ReadParam(BaseModel):
     """Input schema for the read tool."""
+
+    adata: str = Field(
+        ..., description="The AnnData object variable name will be stored in."
+    )
     filename: str = Field(
         ...,
-        description="Path to the file to read."
+        description="Path to the file to read. If the filename has no file extension, it is interpreted as a key for generating a filename via sc.settings.writedir / (filename + sc.settings.file_format_data).",
     )
 
-    backed: Literal['r', 'r+'] = Field(
+    backed: Optional[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+'."
+        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(
+
+    sheet: Optional[str] = Field(
+        default=None, description="Name of sheet/table in hdf5 or Excel file."
+    )
+
+    ext: Optional[str] = Field(
         default=None,
-        description="Name of sheet/table in hdf5 or Excel file."
+        description="Extension that indicates the file type. If None, uses extension of filename.",
     )
-    delimiter: str = Field(
+
+    delimiter: Optional[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."
+        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."
+        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.",
     )
-    backup_url: str = Field(
+
+    backup_url: Optional[str] = Field(
         default=None,
-        description="Retrieve the file from an URL if not present on disk."
+        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."
+        description="If False, read from source, if True, read from fast 'h5ad' cache.",
     )
-    cache_compression: Literal['gzip', 'lzf'] = Field(
+
+    cache_compression: Optional[Literal["gzip", "lzf"]] = Field(
         default=None,
-        description="See the h5py dataset_compression. (Default: settings.cache_compression)"
+        description="See the h5py Filter pipeline. (Default: settings.cache_compression)",
+    )
+
+    @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
+
+
+class Read10xMtxParam(BaseModel):
+    """Input schema for the read_10x_mtx tool."""
+
+    path: str = Field(
+        ...,
+        description="Path to directory for .mtx and .tsv files, e.g. './filtered_gene_bc_matrices/hg19/'.",
     )
-    var_names: str = Field(
-        default="gene_symbols",
-        description="The variables index for 10x mtx format. Either 'gene_symbols' or 'gene_ids'."
+
+    var_names: Literal["gene_symbols", "gene_ids"] = Field(
+        default="gene_symbols", description="The variables index."
     )
+
     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."
+        description="Whether to make the variables index unique by appending '-1', '-2' etc. or not.",
+    )
+
+    cache: bool = Field(
+        default=False,
+        description="If False, read from source, if True, read from fast 'h5ad' cache.",
     )
+
+    cache_compression: Optional[Literal["gzip", "lzf"]] = Field(
+        default=None,
+        description="See the h5py Filter pipeline. (Default: settings.cache_compression)",
+    )
+
     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."
+        description="Only keep 'Gene Expression' data and ignore other feature types, e.g. 'Antibody Capture', 'CRISPR Guide Capture', or 'Custom'",
     )
-    prefix: str = Field(
+
+    prefix: Optional[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."
+        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_. (Default: no prefix)",
     )
-    
-    @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+'")
+
+    @field_validator("path")
+    def validate_path(cls, v: str) -> str:
+        """Validate path is not empty"""
+        if not v.strip():
+            raise ValueError("path cannot be empty")
+        return v
+
+    @field_validator("var_names")
+    def validate_var_names(cls, v: str) -> str:
+        """Validate var_names is supported"""
+        if v not in ["gene_symbols", "gene_ids"]:
+            raise ValueError("var_names must be either 'gene_symbols' or 'gene_ids'")
         return v
-    
-    @field_validator('cache_compression')
+
+    @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']:
+        """Validate cache_compression is supported if provided"""
+        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 WriteParams(BaseModel):
+class WriteParam(BaseModel):
     """Input schema for the write tool."""
+
+    adata: str = Field(..., description="The AnnData object variable name.")
     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(
+    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."
+        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: Literal["gzip", "lzf"] = Field(
+        default="gzip", description="Compression format for h5 files."
     )
     compression_opts: int = Field(
-        default=None,
-        description="Compression options for h5 files."
+        default=None, description="Compression options for h5 files."
     )
-    
-    @field_validator('filename')
+
+    @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) -> 'WriteModel':
+
+    @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:
+        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