bugfix for search_attribute_matching_name

Author: valentin-gauthier-geosiris

energyml-utils/example/attic/arrays_test.py

@@ -17,7 +17,12 @@
 from energyml.utils.storage_interface import EnergymlStorageInterface
 from energyml.utils.epc import Epc
 from energyml.utils.epc_stream import EpcStreamReader, RelsUpdateMode
-from energyml.utils.introspection import get_obj_title, search_attribute_matching_name, get_object_attribute
+from energyml.utils.introspection import (
+    get_obj_title,
+    search_attribute_matching_name,
+    get_object_attribute,
+    search_attribute_matching_name_with_path,
+)
 from energyml.resqml.v2_2.resqmlv2 import Point3DLatticeArray
 from energyml.eml.v2_3.commonv2 import TimeSeries
 from energyml.eml.v2_1.commonv2 import TimeSeries as TimeSeries21
@@ -326,29 +331,79 @@ def read_props_and_cbt(
             print("\n")
 
 
+def read_trset(
+    epc_path: str = "rc/epc/testingPackageCpp22.epc", trset_uuid: str = "6e678338-3b53-49b6-8801-faee493e0c42"
+) -> List[AbstractMesh]:
+    epc = Epc.read_file(f"{epc_path}", read_rels_from_files=False, recompute_rels=False)
+
+    trset = epc.get_object_by_uuid(trset_uuid)[0]
+    # print(trset)
+    # print(epc.get_h5_file_paths(trset))
+
+    meshes = read_mesh_object(energyml_object=trset, workspace=epc)
+
+    return meshes
+
+
+def print_tuple_list(tuple_list: List[tuple]) -> None:
+    for t in tuple_list:
+        print(t)
+
+
+def read_pointset(
+    epc_path: str = "rc/epc/testingPackageCpp22.epc", pointset_uuid: str = "fbc5466c-94cd-46ab-8b48-2ae2162b372f"
+) -> List[AbstractMesh]:
+    # epc = Epc.read_file(f"{epc_path}", read_rels_from_files=False, recompute_rels=False)
+    epc = EpcStreamReader(
+        epc_file_path=epc_path,
+        rels_update_mode=RelsUpdateMode.MANUAL,
+    )
+
+    pointset = epc.get_object_by_uuid(pointset_uuid)[0]
+    # print(pointset)
+    # print(epc.get_h5_file_paths(pointset))
+    # meshes = []
+    meshes = read_mesh_object(energyml_object=pointset, workspace=epc)
+
+    # logging.debug("=" * 40)
+    # print_tuple_list(search_attribute_matching_name_with_path(pointset, r"NodePatch.[\d]+.Geometry.Points"))
+    # logging.debug("=" * 40)
+    # print_tuple_list(
+    #     search_attribute_matching_name_with_path(pointset, r"NodePatchGeometry.[\d]+.Points")
+    # )  # resqml 2.0.1
+    # logging.debug("=" * 40)
+
+    return meshes
+
+
 if __name__ == "__main__":
     logging.basicConfig(level=logging.DEBUG)
 
     # meshes = read_grid()
     # meshes = read_polyline()
     # meshes = read_wellbore_frame_repr()
     # meshes = read_representation_set_representation()
-
-    # for m in meshes:
-    #     print("=" * 40)
-    #     print(f"Mesh identifier: {m.identifier}")
-    #     print("points:")
-    #     print(np.array(m.point_list))
-
-    #     if isinstance(m, SurfaceMesh):
-    #         print("face indices:")
-    #         print(np.array(m.faces_indices))
-    #     elif isinstance(m, PolylineSetMesh):
-    #         print("line indices:")
-    #         try:
-    #             print(np.array(m.line_indices))
-    #         except Exception as e:
-    #             print(m.line_indices)
-    #             raise e
-
-    read_props_and_cbt()
+    # meshes = read_trset()
+    meshes = read_pointset()
+
+    print(f"Number of meshes read: {len(meshes)}")
+
+    if meshes:
+        for m in meshes:
+            print("=" * 40)
+            print(f"Mesh identifier: {m.identifier}")
+            print("points:")
+            print(np.array(m.point_list))
+
+            if isinstance(m, SurfaceMesh):
+                print("face indices:")
+                print(np.array(m.faces_indices))
+            elif isinstance(m, PolylineSetMesh):
+                print("line indices:")
+                try:
+                    print(np.array(m.line_indices))
+                except Exception as e:
+                    print(m.line_indices)
+                    raise e
+
+    # read_props_and_cbt()

energyml-utils/src/energyml/utils/data/mesh.py

@@ -269,14 +269,16 @@ def read_point_representation(
 
     patch_idx = 0
     total_size = 0
-    for (
-        points_path_in_obj,
-        points_obj,
-    ) in search_attribute_matching_name_with_path(
+
+    patches_geom = search_attribute_matching_name_with_path(
         energyml_object, r"NodePatch.[\d]+.Geometry.Points"
     ) + search_attribute_matching_name_with_path(  # resqml 2.0.1
         energyml_object, r"NodePatchGeometry.[\d]+.Points"
-    ):  # resqml 2.2
+    )
+    logging.debug(f"Found {len(patches_geom)} patches for point representation")
+    logging.debug(f"\t=> {patches_geom}")
+
+    for points_path_in_obj, points_obj in patches_geom:
         points = read_array(
             energyml_array=points_obj,
             root_obj=energyml_object,
@@ -644,12 +646,16 @@ def read_triangulated_set_representation(
     point_offset = 0
     patch_idx = 0
     total_size = 0
-    for patch_path, patch in search_attribute_matching_name_with_path(
+
+    patches = search_attribute_matching_name_with_path(
         energyml_object,
-        "\\.*Patch.\\d+",
+        "\\w*Patch.\\d+",
         deep_search=False,
         search_in_sub_obj=False,
-    ):
+    )
+    # logging.debug(f"Found {len(patches)} patches for triangulated set representation")
+
+    for patch_path, patch in patches:
         crs = None
         try:
             crs = get_crs_obj(

energyml-utils/src/energyml/utils/introspection.py

@@ -397,16 +397,16 @@ def get_all_matching_class_attribute_name(
      Example : "\\w*.Version" --> ["object_version", "ObjectVersion", "obj_version", ...]
      This method doesn't only transform to snake case but search into the obj class attributes (or dict keys)
     """
-    matching_names = []
+    matching_names = set()
     if isinstance(cls, dict):
         for name in cls.keys():
             if snake_case(name) == snake_case(attribute_name):
-                matching_names.append(name)
+                matching_names.add(name)
         pattern = re.compile(attribute_name, flags=re_flags)
         for name in cls.keys():
             if pattern.match(name):
-                matching_names.append(name)
-        return matching_names
+                matching_names.add(name)
+        return list(matching_names)
     else:
         class_fields = get_class_fields(cls)
         try:
@@ -415,7 +415,7 @@ def get_all_matching_class_attribute_name(
                 if snake_case(name) == snake_case(attribute_name) or (
                     hasattr(cf, "metadata") and "name" in cf.metadata and cf.metadata["name"] == attribute_name
                 ):
-                    matching_names.append(name)
+                    matching_names.add(name)
 
             # search regex after to avoid shadowing perfect match
             pattern = re.compile(attribute_name, flags=re_flags)
@@ -424,12 +424,12 @@ def get_all_matching_class_attribute_name(
                 if pattern.match(name) or (
                     hasattr(cf, "metadata") and "name" in cf.metadata and pattern.match(cf.metadata["name"])
                 ):
-                    matching_names.append(name)
+                    matching_names.add(name)
         except Exception as e:
             logging.error(f"Failed to get attribute {attribute_name} from class {cls}")
             logging.error(e)
 
-    return matching_names
+    return list(matching_names)
 
 
 def get_matching_class_attribute_name(
@@ -919,7 +919,7 @@ def search_attribute_matching_name_with_path(
     #     next_match = ".".join(attrib_list[1:])
     current_match, next_match = path_next_attribute(name_rgx)
     if current_match is None:
-        logging.error(f"Attribute name regex '{name_rgx}' is invalid.")
+        # logging.error(f"Attribute name regex '{name_rgx}' is invalid.")
         return []
     res = []
 
@@ -949,15 +949,18 @@ def search_attribute_matching_name_with_path(
             else:
                 not_match_path_and_obj.append((f"{current_path}{k}", s_o))
     elif not is_primitive(obj):
+        current_match = current_match.replace("\\.", ".")
         # logging.debug(f"searching {current_match} in {type(obj)} with path {current_path} and next match {next_match}")
         match_values = get_all_matching_class_attribute_name(obj, current_match, re_flags)
         for match_value in match_values:
+            # logging.debug(f"\tmatch found : {match_value}")
             match_path_and_obj.append(
                 (
                     f"{current_path}{match_value}",
                     get_object_attribute_no_verif(obj, match_value),
                 )
             )
+        # logging.debug("f------")
         for att_name in get_class_attributes(obj):
             if att_name not in match_values:
                 not_match_path_and_obj.append(