Move paths to SampleFileHandler and create get methods for some

lib/realms/tenx/run_sample.py

@@ -49,7 +49,7 @@ def __init__(
         self.file_handler: SampleFileHandler = SampleFileHandler(self)
 
         self.features: List[str] = self._collect_features()
-        self.pipeline_info: Optional[Dict[str, Any]] = self._get_pipeline_info()
+        self.pipeline_info: Optional[Dict[str, Any]] = self._get_pipeline_info() or {}
         self.reference_genomes: Dict[str, str] = (
             self.collect_reference_genomes()
         ) or {}
@@ -197,7 +197,7 @@ async def pre_process(self):
         slurm_metadata = {
             "sample_id": self.run_sample_id,
             "project_name": self.project_info.get("project_name", ""),
-            "output_dir": str(self.file_handler.base_dir),
+            "output_dir": str(self.file_handler.project_dir),
             "cellranger_command": cellranger_command,
         }
 
@@ -265,21 +265,14 @@ def assemble_cellranger_command(self) -> str:
         # Mapping of argument names to their values
         arg_values: Dict[str, Any] = {
             "--id": self.run_sample_id,
-            "--csv": str(
-                self.file_handler.base_dir / f"{self.run_sample_id}_multi.csv"
-            ),
+            "--csv": str(self.file_handler.get_multi_csv_path()),
             "--transcriptome": self.reference_genomes["gex"],
             "--fastqs": ",".join(
                 [",".join(paths) for paths in self.lab_samples[0].fastq_dirs.values()]
             ),
             "--sample": self.lab_samples[0].lab_sample_id,
-            "--libraries": str(
-                self.file_handler.base_dir / f"{self.run_sample_id}_libraries.csv"
-            ),
-            "--feature-ref": str(
-                self.file_handler.base_dir
-                / f"{self.run_sample_id}_feature_reference.csv"
-            ),
+            "--libraries": str(self.file_handler.get_libraries_csv_path()),
+            "--feature-ref": str(self.file_handler.get_feature_reference_csv_path()),
         }
 
         # Add references based on the pipeline
@@ -341,9 +334,7 @@ def collect_libraries_data(self) -> List[Dict[str, str]]:
     def generate_libraries_csv(self) -> None:
         """Generate the libraries CSV file required for processing."""
         logging.info(f"[{self.run_sample_id}] Generating library CSV")
-        library_csv_path = (
-            self.file_handler.base_dir / f"{self.run_sample_id}_libraries.csv"
-        )
+        library_csv_path = self.file_handler.get_libraries_csv_path()
 
         # Ensure the directory exists
         library_csv_path.parent.mkdir(parents=True, exist_ok=True)
@@ -365,12 +356,13 @@ def generate_libraries_csv(self) -> None:
     def generate_feature_reference_csv(self) -> None:
         """Generate the feature reference CSV file required for processing."""
         logging.info(f"[{self.run_sample_id}] Generating feature reference CSV")
+        # feature_ref_csv_path = self.file_handler.get_feature_reference_csv_path()
         pass
 
     def generate_multi_sample_csv(self) -> None:
         """Generate the multi-sample CSV file required for processing."""
         logging.info(f"[{self.run_sample_id}] Generating multi-sample CSV")
-        multi_csv_path = self.file_handler.base_dir / f"{self.run_sample_id}_multi.csv"
+        multi_csv_path = self.file_handler.get_multi_csv_path()
 
         # Ensure the directory exists
         multi_csv_path.parent.mkdir(parents=True, exist_ok=True)

lib/realms/tenx/tenx_project.py

@@ -46,6 +46,7 @@ def __init__(self, doc: Dict[str, Any], yggdrasil_db_manager: Any) -> None:
                 return
 
             self.project_dir: Optional[Path] = self.ensure_project_directory()
+            self.project_info["project_dir"] = self.project_dir
             self.samples: List[TenXRunSample] = []
             self.case_type: str = self.project_info.get("case_type", "unknown")
             logging.info(f"Case type: {self.case_type}")

lib/realms/tenx/utils/sample_file_handler.py

@@ -19,7 +19,7 @@ class SampleFileHandler:
         sample_ref (str): Reference genome for the sample.
         organism (str): Organism associated with the sample.
         config (Dict[str, Any]): Configuration settings.
-        base_dir (Path): Base directory path for the project.
+        project_dir (Path): Base directory path for the project.
         sample_dir (Path): Directory path for the sample.
         fastq_files_dir (Path): Directory path for FASTQ files.
         fastq_files (Dict[str, Any]): Dictionary of FASTQ file paths.
@@ -41,11 +41,9 @@ def __init__(self, sample: Any) -> None:
         self.config: Dict[str, Any] = sample.config
 
         # Define sample folder structure
-        self.base_dir: Path = (
-            Path(self.config["10x_dir"]) / "projects" / self.project_name
-        )
-        self.sample_dir: Path = self.base_dir / self.sample_id
-        self.fastq_files_dir: Path = self.base_dir / "fastq_files"
+        self.project_dir: Path = sample.project_info.get("project_dir", "")
+        self.sample_dir: Path = self.project_dir / self.sample_id
+        self.fastq_files_dir: Path = self.project_dir / "fastq_files"
 
         self.fastq_files: Dict[str, Any] = {}
 
@@ -56,9 +54,18 @@ def init_file_paths(self) -> None:
         """Initialize critical file paths."""
         # Files needed for processing
         self.slurm_script_path: Path = (
-            self.base_dir / f"{self.sample_id}_slurm_script.sh"
+            self.project_dir / f"{self.sample_id}_slurm_script.sh"
         )
 
         # Report output files
         # NOTE: Different pipelines may produce summaries in different locations
         self.summary_fpath: Path = self.sample_dir / "outs" / "web_summary.html"
+
+    def get_libraries_csv_path(self) -> Path:
+        return self.project_dir / f"{self.sample_id}_libraries.csv"
+
+    def get_multi_csv_path(self) -> Path:
+        return self.project_dir / f"{self.sample_id}_multi.csv"
+
+    def get_feature_reference_csv_path(self) -> Path:
+        return self.project_dir / f"{self.sample_id}_feature_reference.csv"