add metadata to vpipe module

.gitignore

@@ -136,3 +136,6 @@ poetry.lock
 
 # Output folder
 output
+
+# Secret files
+secrets

scripts/vp_transformer.py

@@ -18,6 +18,7 @@
 from sr2silo.process import pair_normalize_reads
 from sr2silo.s3 import compress_bz2, upload_file_to_s3
 from sr2silo.translation import translate
+from sr2silo.vpipe.metadata import sample_id_decoder
 
 logging.basicConfig(
     level=logging.DEBUG, format="%(asctime)s - %(levelname)s - %(message)s"
@@ -37,31 +38,6 @@ def load_config(config_file: Path) -> dict:
         raise
 
 
-def sample_id_decoder(sample_id: str) -> dict:
-    """Decode the sample ID into individual components.
-
-    Args:
-        sample_id (str): The sample ID to decode.
-
-    Returns:
-        dict: A dictionary containing the decoded components.
-              containing the following keys:
-                - sequencing_well_position (str : sequencing well position)
-                - location_code (int : code of the location)
-                - sampling_date (str : date of the sampling)
-    """
-    components = sample_id.split("_")
-    # Assign components to meaningful variable names
-    well_position = components[0]  # A1
-    location_code = components[1]  # 10
-    sampling_date = f"{components[2]}-{components[3]}-{components[4]}"  # 2024-09-30
-    return {
-        "sequencing_well_position": well_position,
-        "location_code": location_code,
-        "sampling_date": sampling_date,
-    }
-
-
 def batch_id_decoder(batch_id: str) -> dict:
     """Decode the batch ID into individual components.
 

src/sr2silo/__init__.py

@@ -5,4 +5,8 @@
 """sr2silo connects pairs, normalizes reads, and converts BAM to SAM files."""
 from __future__ import annotations
 
+import sr2silo.vpipe as vpipe
+
 __version__ = "0.0.2"
+
+__all__ = ["vpipe"]

src/sr2silo/vpipe/__init__.py

@@ -0,0 +1,4 @@
+"""Implements V-Pipe specific utilities.
+
+  i.e. extracting metadata from V-Pipe Filenaming Conventions.
+  """

src/sr2silo/vpipe/metadata.py

@@ -0,0 +1,28 @@
+"""Extract metadata from V-Pipe Filenaming Conventions."""
+
+from __future__ import annotations
+
+
+def sample_id_decoder(sample_id: str) -> dict:
+    """Decode the sample ID into individual components.
+
+    Args:
+        sample_id (str): The sample ID to decode.
+
+    Returns:
+        dict: A dictionary containing the decoded components.
+              containing the following keys:
+                - sequencing_well_position (str : sequencing well position)
+                - location_code (int : code of the location)
+                - sampling_date (str : date of the sampling)
+    """
+    components = sample_id.split("_")
+    # Assign components to meaningful variable names
+    well_position = components[0]  # A1
+    location_code = components[1]  # 10
+    sampling_date = f"{components[2]}-{components[3]}-{components[4]}"  # 2024-09-30
+    return {
+        "sequencing_well_position": well_position,
+        "location_code": location_code,
+        "sampling_date": sampling_date,
+    }

tests/vpipe/test_metadata.py

@@ -0,0 +1,18 @@
+"""Implement tests for the metadata extraction functions."""
+
+
+from __future__ import annotations
+
+from sr2silo.vpipe.metadata import sample_id_decoder
+
+
+def test_sample_id_decoder():
+    """Test the sample_id_decoder function."""
+    sample_id = "A1_10_2024_09_30"
+    result = sample_id_decoder(sample_id)
+    expected = {
+        "sequencing_well_position": "A1",
+        "location_code": "10",
+        "sampling_date": "2024-09-30",
+    }
+    assert result == expected