Dev 10 25 bis

energyml-utils/.flake8

@@ -1,6 +1,6 @@
 [flake8]
 # Ignore specific error codes (comma-separated list)
-ignore = E501, E722 #, W503, F403
+ignore = E501, E722, W503, F403, E203, E202
 
 # Max line length (default is 79, can be changed)
 max-line-length = 120

energyml-utils/example/epc_rels_management_example.py

@@ -0,0 +1,174 @@
+"""
+Example: Managing .rels files in EPC files using EpcStreamReader
+
+This example demonstrates the new .rels management capabilities:
+1. Removing objects without breaking .rels files
+2. Cleaning orphaned relationships
+3. Rebuilding all .rels files from scratch
+"""
+
+import sys
+from pathlib import Path
+
+# Add src directory to path
+src_path = Path(__file__).parent.parent / "src"
+sys.path.insert(0, str(src_path))
+
+from energyml.utils.epc_stream import EpcStreamReader
+
+
+def example_workflow(epc_path: str):
+    """
+    Complete workflow example for .rels management.
+    """
+    print(f"Opening EPC file: {epc_path}")
+    reader = EpcStreamReader(epc_path)
+    print(f"Loaded {len(reader)} objects\n")
+
+    # ============================================================
+    # Scenario 1: Remove objects without breaking .rels
+    # ============================================================
+    print("=" * 70)
+    print("SCENARIO 1: Remove objects (keeps .rels intact)")
+    print("=" * 70)
+
+    # Get some objects to remove
+    objects_to_remove = list(reader._metadata.keys())[-3:]
+    print(f"\nRemoving {len(objects_to_remove)} objects:")
+
+    for obj_id in objects_to_remove:
+        print(f"  - {obj_id}")
+        reader.remove_object(obj_id)
+
+    print(f"\nRemaining objects: {len(reader)}")
+    print("Note: .rels files still reference removed objects (orphaned relationships)")
+
+    # ============================================================
+    # Scenario 2: Clean orphaned relationships
+    # ============================================================
+    print("\n" + "=" * 70)
+    print("SCENARIO 2: Clean orphaned relationships")
+    print("=" * 70)
+
+    print("\nCalling clean_rels()...")
+    clean_stats = reader.clean_rels()
+
+    print("\nCleaning statistics:")
+    print(f"  • .rels files scanned: {clean_stats['rels_files_scanned']}")
+    print(f"  • Orphaned relationships removed: {clean_stats['relationships_removed']}")
+    print(f"  • Empty .rels files deleted: {clean_stats['rels_files_removed']}")
+
+    print("\n✓ Orphaned relationships cleaned!")
+
+    # ============================================================
+    # Scenario 3: Rebuild all .rels from scratch
+    # ============================================================
+    print("\n" + "=" * 70)
+    print("SCENARIO 3: Rebuild all .rels from scratch")
+    print("=" * 70)
+
+    print("\nCalling rebuild_all_rels()...")
+    rebuild_stats = reader.rebuild_all_rels(clean_first=True)
+
+    print("\nRebuild statistics:")
+    print(f"  • Objects processed: {rebuild_stats['objects_processed']}")
+    print(f"  • .rels files created: {rebuild_stats['rels_files_created']}")
+    print(f"  • SOURCE relationships: {rebuild_stats['source_relationships']}")
+    print(f"  • DESTINATION relationships: {rebuild_stats['destination_relationships']}")
+    print(
+        f"  • Total relationships: {rebuild_stats['source_relationships'] + rebuild_stats['destination_relationships']}"
+    )
+
+    print("\n✓ All .rels files rebuilt!")
+
+    # ============================================================
+    # Best Practices
+    # ============================================================
+    print("\n" + "=" * 70)
+    print("BEST PRACTICES")
+    print("=" * 70)
+
+    print(
+        """
+    1. After removing multiple objects:
+       → Call clean_rels() to remove orphaned relationships
+
+    2. After modifying many objects or complex operations:
+       → Call rebuild_all_rels() to ensure consistency
+
+    3. Regular maintenance:
+       → Periodically call clean_rels() to keep .rels files tidy
+
+    4. When in doubt:
+       → Use rebuild_all_rels() to guarantee correct relationships
+    """
+    )
+
+
+def quick_clean_example(epc_path: str):
+    """
+    Quick example: Just clean the .rels files.
+    """
+    print("\n" + "=" * 70)
+    print("QUICK EXAMPLE: Clean .rels in one line")
+    print("=" * 70)
+
+    reader = EpcStreamReader(epc_path)
+    stats = reader.clean_rels()
+
+    print(f"\n✓ Cleaned! Removed {stats['relationships_removed']} orphaned relationships")
+
+
+def quick_rebuild_example(epc_path: str):
+    """
+    Quick example: Rebuild all .rels files.
+    """
+    print("\n" + "=" * 70)
+    print("QUICK EXAMPLE: Rebuild all .rels in one line")
+    print("=" * 70)
+
+    reader = EpcStreamReader(epc_path)
+    stats = reader.rebuild_all_rels()
+
+    print(
+        f"\n✓ Rebuilt! Created {stats['rels_files_created']} .rels files with {stats['source_relationships'] + stats['destination_relationships']} relationships"
+    )
+
+
+if __name__ == "__main__":
+    # Use the test EPC file
+    test_epc = "wip/BRGM_AVRE_all_march_25.epc"
+
+    if not Path(test_epc).exists():
+        print(f"EPC file not found: {test_epc}")
+        print("Please provide a valid EPC file path")
+        sys.exit(1)
+
+    # Make a temporary copy for the example
+    import tempfile
+    import shutil
+
+    with tempfile.NamedTemporaryFile(delete=False, suffix=".epc") as tmp:
+        tmp_path = tmp.name
+
+    try:
+        shutil.copy(test_epc, tmp_path)
+
+        # Run the complete workflow
+        example_workflow(tmp_path)
+
+        # Show quick examples
+        shutil.copy(test_epc, tmp_path)
+        quick_clean_example(tmp_path)
+
+        shutil.copy(test_epc, tmp_path)
+        quick_rebuild_example(tmp_path)
+
+        print("\n" + "=" * 70)
+        print("Examples completed successfully!")
+        print("=" * 70)
+
+    finally:
+        # Cleanup
+        if Path(tmp_path).exists():
+            Path(tmp_path).unlink()

energyml-utils/example/main.py

@@ -1,9 +1,13 @@
 # Copyright (c) 2023-2024 Geosiris.
 # SPDX-License-Identifier: Apache-2.0
-import json
+import sys
+from pathlib import Path
 import re
 from dataclasses import fields
 
+src_path = Path(__file__).parent.parent / "src"
+sys.path.insert(0, str(src_path))
+
 from energyml.eml.v2_3.commonv2 import *
 from energyml.eml.v2_3.commonv2 import AbstractObject
 from energyml.resqml.v2_0_1.resqmlv2 import DoubleHdf5Array
@@ -17,19 +21,19 @@
 )
 
 # from src.energyml.utils.data.hdf import *
-from src.energyml.utils.data.helper import get_projected_uom, is_z_reversed
-from src.energyml.utils.epc import *
-from src.energyml.utils.introspection import *
-from src.energyml.utils.manager import *
-from src.energyml.utils.serialization import *
-from src.energyml.utils.validation import (
+from energyml.utils.data.helper import get_projected_uom, is_z_reversed
+from energyml.utils.epc import *
+from energyml.utils.introspection import *
+from energyml.utils.manager import *
+from energyml.utils.serialization import *
+from energyml.utils.validation import (
     patterns_validation,
     dor_validation,
     validate_epc,
     correct_dor,
 )
-from src.energyml.utils.xml import *
-from src.energyml.utils.data.datasets_io import HDF5FileReader, get_path_in_external_with_path
+from energyml.utils.xml import *
+from energyml.utils.data.datasets_io import HDF5FileReader, get_path_in_external_with_path
 
 fi_cit = Citation(
     title="An interpretation",
@@ -494,5 +498,22 @@ def test_dor_conversion():
     )
     # print(get_obj_uri(tr201, "coucou"))
 
-    print(get_usable_class(tr))
-    print(get_usable_class(tr201))
+    logging.basicConfig(level=logging.DEBUG)
+
+    emi = create_energyml_object("resqml20.ObjEarthModelInterpretation")
+    print(type(emi))
+    print(serialize_xml(emi))
+
+    from energyml.resqml.v2_0_1 import resqmlv2
+
+    emi = resqmlv2.ObjEarthModelInterpretation()
+    print(type(emi))
+    print(serialize_xml(emi))
+
+    emi = read_energyml_xml_file("C:/Users/Cryptaro/Downloads/emi.xml")
+    print(type(emi))
+    print(serialize_xml(emi))
+
+    emi = create_energyml_object("resqml20.EarthModelInterpretation")
+    print(type(emi))
+    print(serialize_xml(emi))

energyml-utils/example/main_hdf.py

@@ -0,0 +1,37 @@
+# Copyright (c) 2023-2024 Geosiris.
+# SPDX-License-Identifier: Apache-2.0
+import sys
+from pathlib import Path
+
+# Add src directory to path
+src_path = Path(__file__).parent.parent / "src"
+sys.path.insert(0, str(src_path))
+
+from energyml.utils.data.datasets_io import get_path_in_external_with_path
+from energyml.utils.introspection import get_obj_uri
+
+
+if __name__ == "__main__":
+    from energyml.utils.epc import Epc
+
+    # Create an EPC file
+    epc = Epc.read_file("wip/BRGM_AVRE_all_march_25.epc")
+
+    print("\n".join(map(lambda o: str(get_obj_uri(o)), epc.energyml_objects)))
+
+    print(epc.get_h5_file_paths("eml:///resqml22.PolylineSetRepresentation(e75db94d-a251-4f31-8a24-23b9573fbf39)"))
+
+    print(
+        get_path_in_external_with_path(
+            epc.get_object_by_identifier(
+                "eml:///resqml22.PolylineSetRepresentation(e75db94d-a251-4f31-8a24-23b9573fbf39)"
+            )
+        )
+    )
+
+    print(
+        epc.read_h5_dataset(
+            "eml:///resqml22.PolylineSetRepresentation(e75db94d-a251-4f31-8a24-23b9573fbf39)",
+            "/RESQML/e75db94d-a251-4f31-8a24-23b9573fbf39/points_patch0",
+        )
+    )