[REFACTOR] Stage 2 & tests

data/test_mooring.yaml

@@ -0,0 +1,20 @@
+deployment_latitude: 60 00.000 N
+deployment_longitude: 030 00.000 W
+deployment_time: '2018-08-12T08:00:00'
+directory: moor/raw/test_deployment/
+instruments:
+- clock_offset: 300
+  depth: 100
+  end_time: '2018-08-26T20:47:24'
+  file_type: sbe-cnv
+  filename: test_data.cnv
+  instrument: microcat
+  serial: 7518
+  start_time: '2018-08-12T08:00:00'
+latitude: 60.0
+longitude: -30.0
+name: test_mooring
+recovery_time: '2018-08-26T20:47:24'
+seabed_latitude: 60 00.000 N
+seabed_longitude: 030 00.000 W
+waterdepth: 1000

oceanarray/generate_test_data.py

@@ -0,0 +1,107 @@
+#!/usr/bin/env python3
+"""
+Generate test_data_raw.nc from the real CNV file for Stage 2 testing.
+"""
+import yaml
+from pathlib import Path
+from oceanarray.stage1 import MooringProcessor
+
+
+def create_test_stage1_data():
+    """Create test data by running Stage 1 on the real CNV file."""
+
+    # Set up test directory structure
+    test_dir = Path("test_data_temp")
+    raw_dir = test_dir / "moor" / "raw" / "test_deployment" / "microcat"
+    proc_dir = test_dir / "moor" / "proc" / "test_mooring"
+
+    raw_dir.mkdir(parents=True, exist_ok=True)
+    proc_dir.mkdir(parents=True, exist_ok=True)
+
+    # Copy the real CNV file
+    source_cnv = Path("data/test_data.cnv")
+    dest_cnv = raw_dir / "test_data.cnv"
+
+    if not source_cnv.exists():
+        print(f"ERROR: Source CNV file not found at {source_cnv}")
+        print("Please ensure data/test_data.cnv exists")
+        return False
+
+    dest_cnv.write_text(source_cnv.read_text())
+    print(f"Copied CNV file to {dest_cnv}")
+
+    # Create YAML configuration
+    yaml_data = {
+        'name': 'test_mooring',
+        'waterdepth': 1000,
+        'longitude': -30.0,
+        'latitude': 60.0,
+        'deployment_latitude': '60 00.000 N',
+        'deployment_longitude': '030 00.000 W',
+        'deployment_time': '2018-08-12T08:00:00',  # Before data starts
+        'recovery_time': '2018-08-26T20:47:24',    # After data ends
+        'seabed_latitude': '60 00.000 N',
+        'seabed_longitude': '030 00.000 W',
+        'directory': 'moor/raw/test_deployment/',
+        'instruments': [
+            {
+                'instrument': 'microcat',
+                'serial': 7518,
+                'depth': 100,
+                'filename': 'test_data.cnv',
+                'file_type': 'sbe-cnv',
+                'clock_offset': 300,  # 5 minutes offset for testing
+                'start_time': '2018-08-12T08:00:00',
+                'end_time': '2018-08-26T20:47:24'
+            }
+        ]
+    }
+
+    config_file = proc_dir / "test_mooring.mooring.yaml"
+    with open(config_file, 'w') as f:
+        yaml.dump(yaml_data, f)
+
+    print(f"Created YAML config at {config_file}")
+
+    # Run Stage 1 processing
+    processor = MooringProcessor(str(test_dir))
+    success = processor.process_mooring("test_mooring")
+
+    if success:
+        # Move the generated file to data/ directory
+        generated_file = proc_dir / "microcat" / "test_mooring_7518_raw.nc"
+        target_file = Path("data/test_data_raw.nc")
+
+        if generated_file.exists():
+            target_file.write_bytes(generated_file.read_bytes())
+            print(f"Successfully created {target_file}")
+
+            # Also copy the YAML for Stage 2 tests
+            target_yaml = Path("data/test_mooring.yaml")
+            target_yaml.write_text(config_file.read_text())
+            print(f"Copied YAML config to {target_yaml}")
+
+            # Cleanup temp directory
+            import shutil
+            shutil.rmtree(test_dir)
+            print(f"Cleaned up temporary directory")
+
+            return True
+        else:
+            print(f"ERROR: Expected output file not found at {generated_file}")
+            return False
+    else:
+        print("ERROR: Stage 1 processing failed")
+        return False
+
+
+if __name__ == "__main__":
+    success = create_test_stage1_data()
+    if success:
+        print("\nTest data generation completed successfully!")
+        print("Files created:")
+        print("  - data/test_data_raw.nc")
+        print("  - data/test_mooring.yaml")
+        print("\nYou can now run Stage 2 tests with real data.")
+    else:
+        print("\nTest data generation failed.")

oceanarray/stage1.py

@@ -7,8 +7,7 @@
 from typing import Any, Dict, List, Optional, Tuple
 
 import yaml
-from ctd_tools.readers import (NortekAsciiReader,
-                               RbrAsciiReader,
+from ctd_tools.readers import (NortekAsciiReader, RbrAsciiReader,
                                RbrRskAutoReader, SbeAsciiReader, SbeCnvReader)
 from ctd_tools.writers import NetCdfWriter
 
@@ -22,9 +21,9 @@ class MooringProcessor:
         "nortek-aqd": NortekAsciiReader,
         "sbe-asc": SbeAsciiReader,
         "rbr-rsk": RbrRskAutoReader,
-        #"rbr-matlab": RbrMatlabReader,
+        # "rbr-matlab": RbrMatlabReader,
         "rbr-dat": RbrAsciiReader,
-        #"adcp-matlab": AdcpMatlabReader,
+        # "adcp-matlab": AdcpMatlabReader,
     }
 
     # Variables to remove for specific file types