fix: Fix issue when metaDMG binary does not exist

src/metaDMG/cli/cli.py

@@ -57,20 +57,23 @@ def create_config(
         file_okay=True,
         help="Path to the (NCBI) names-mdmg.dmp.",
         rich_help_panel="LCA parameters",
+        callback=cli_utils.path_exists_or_None,
     ),
     nodes: Optional[Path] = typer.Option(
         None,
         exists=True,
         file_okay=True,
         help="Path to the (NCBI) nodes-mdmg.dmp.",
         rich_help_panel="LCA parameters",
+        callback=cli_utils.path_exists_or_None,
     ),
     acc2tax: Optional[Path] = typer.Option(
         None,
         exists=True,
         file_okay=True,
         help="Path to the (NCBI) acc2tax.gz.",
         rich_help_panel="LCA parameters",
+        callback=cli_utils.path_exists_or_None,
     ),
     min_similarity_score: Optional[float] = typer.Option(
         None,
@@ -135,6 +138,7 @@ def create_config(
         "-m",
         help="The command needed to run the metaDMG-cpp program.",
         rich_help_panel="General parameters",
+        callback=cli_utils.path_exists_or_None,
     ),
     max_position: int = typer.Option(
         15,

src/metaDMG/cli/cli_utils.py

@@ -1,7 +1,7 @@
 from enum import Enum
 from functools import partial
 from pathlib import Path
-from typing import Iterable, Optional
+from typing import Iterable, Optional, Union
 
 import click
 import typer
@@ -64,7 +64,7 @@ def is_in_range_or_None(
     """
 
     if x is None:
-        return x
+        return None
 
     if x < val_min or val_max < x:
         raise typer.BadParameter(
@@ -92,14 +92,46 @@ def is_positive_int_or_None(x: Optional[int]) -> Optional[int]:
     """
 
     if x is None:
-        return x
+        return None
 
     if x < 0:
         raise typer.BadParameter(f"x has to be positive. Got: {x}")
 
     return x
 
 
+def path_exists_or_None(x: Union[str, Path, None]) -> Union[str, Path, None]:
+    """Confirms that x exists or is None
+
+    Parameters
+    ----------
+    x
+        Value to check
+
+    Returns
+    -------
+        Confirmed value
+
+    Raises
+    ------
+    typer.BadParameter
+        If x is outside bounds
+    """
+
+    if x is None:
+        return None
+
+    if isinstance(x, str):
+        path = Path(x)
+    else:
+        path = x
+
+    if not path.is_file():
+        raise typer.BadParameter(f"The file {path} does not exists.")
+
+    return x
+
+
 #%%
 class RANKS(str, Enum):
     "Ranks allowed in the LCA"

src/metaDMG/fit/serial.py

@@ -293,6 +293,11 @@ def run_LCA(config: Config, force: bool = False) -> None:
                 f"{config['sample']}: The alignment file is invalid."
             )
 
+        if not metaDMG_cpp_is_valid(config):
+            raise metadamageError()
+
+        config["metaDMG_cpp"]
+
         logger.info(f"LCA has to be computed. This can take a while, please wait.")
 
         command_LCA = get_LCA_command(config)
@@ -332,6 +337,9 @@ def run_damage_no_lca(config: Config, force: bool = False) -> None:
                 f"{config['sample']}: The alignment file is invalid."
             )
 
+        if not metaDMG_cpp_is_valid(config):
+            raise metadamageError()
+
         logger.info(f"Computing damage. NOTE: NO LCA.")
 
         command_damage = get_damage_command(config)
@@ -491,6 +499,19 @@ def BAM_file_is_valid(config: Config) -> bool:
     return True
 
 
+def metaDMG_cpp_is_valid(config: Config) -> bool:
+
+    if not Path(config["metaDMG_cpp"]).is_file():
+        logger.error(f"The metaDMG-cpp binary does not exist: {config['metaDMG_cpp']}.")
+        return False
+
+    if config["bam"].stat().st_size == 0:
+        logger.error(f"The metaDMG-cpp binary is of size 0: {config['metaDMG_cpp']}.")
+        return False
+
+    return True
+
+
 #%%