feat: Adding a script to generate schema

geos-trame/pyproject.toml

@@ -42,7 +42,7 @@ dependencies = [
     "trame-components==2.4.2",
     "trame-gantt==0.1.5",
     "mpld3<0.5.11",
-    "xsdata==24.5",
+    "xsdata[cli]>24.5",
     "xsdata-pydantic[lxml]==24.5",
     "pyvista==0.45.2",
     "dpath==2.2.0",

geos-trame/src/geos/trame/app/deck/file.py

@@ -14,7 +14,7 @@
 from geos.trame.app.geosTrameException import GeosTrameException
 from geos.trame.app.io.xml_parser import XMLParser
 from geos.trame.app.utils.file_utils import normalize_path
-from geos.trame.schema_generated.schema_mod import Problem
+from geos.trame.schema_generated.schema_mod import ProblemType
 
 
 class DeckFile( object ):
@@ -30,7 +30,7 @@ def __init__( self, filename: str, **kwargs: Any ) -> None:
 
         self.inspect_tree: dict[ Any, Any ] | None = None
         self.pb_dict: dict[ str, Any ] | None = None
-        self.problem: Problem | None = None
+        self.problem: ProblemType | None = None
         self.xml_parser: XMLParser | None = None
         self.root_node = None
         self.filename = normalize_path( filename )
@@ -79,7 +79,7 @@ def open_deck_file( self, filename: str ) -> None:
         )
         parser = XmlParser( context=context, config=ParserConfig() )
         try:
-            self.problem = parser.parse( simulation_deck, Problem )
+            self.problem = parser.parse( simulation_deck, ProblemType )
         except ElementTree.XMLSyntaxError as e:
             msg = "Failed to parse input file %s:\n%s\n" % ( filename, e )
             raise GeosTrameException( msg ) from e

geos-trame/src/geos/trame/app/deck/tree.py

@@ -18,7 +18,7 @@
 
 from geos.trame.app.deck.file import DeckFile
 from geos.trame.app.geosTrameException import GeosTrameException
-from geos.trame.schema_generated.schema_mod import Problem, Included, File, Functions
+from geos.trame.schema_generated.schema_mod import ProblemType, IncludedType, FileType, FunctionsType
 from geos.trame.app.utils.file_utils import normalize_path, format_xml
 
 
@@ -100,14 +100,14 @@ def decode( self, path: str ) -> BaseModel | None:
         return decoder.decode( data[ 0 ] )
 
     @staticmethod
-    def decode_data( data: dict ) -> Problem:
+    def decode_data( data: dict ) -> ProblemType:
         """Convert a data to a xml serializable file."""
         context = XmlContext(
             element_name_generator=text.pascal_case,
             attribute_name_generator=text.camel_case,
         )
         decoder = DictDecoder( context=context, config=ParserConfig() )
-        node: Problem = decoder.decode( data )
+        node: ProblemType = decoder.decode( data )
         return node
 
     @staticmethod
@@ -144,7 +144,7 @@ def timeline( self ) -> list[ dict ] | None:
 
         return timeline
 
-    def plots( self ) -> list[ Functions ]:
+    def plots( self ) -> list[ FunctionsType ]:
         """Get the functions in the current problem."""
         assert self.input_file is not None and self.input_file.problem is not None
         return self.input_file.problem.functions
@@ -157,8 +157,8 @@ def write_files( self ) -> None:
         files = self._split( pb )
 
         for filepath, content in files.items():
-            model_loaded: Problem = DeckTree.decode_data( content )
-            model_with_changes: Problem = self._apply_changed_properties( model_loaded )
+            model_loaded: ProblemType = DeckTree.decode_data( content )
+            model_with_changes: ProblemType = self._apply_changed_properties( model_loaded )
 
             assert ( self.input_file is not None and self.input_file.xml_parser is not None )
             if self.input_file.xml_parser.contains_include_files():
@@ -178,8 +178,8 @@ def write_files( self ) -> None:
             self._ctrl.on_add_success( title="File saved", message=f"File {basename} has been saved." )
 
     @staticmethod
-    def _append_include_file( model: Problem, included_file_path: str ) -> None:
-        """Append an Included object which follows this structure according to the documentation.
+    def _append_include_file( model: ProblemType, included_file_path: str ) -> None:
+        """Append an IncludedType object which follows this structure according to the documentation.
 
         <Included>
             <File name="./included_file.xml" />
@@ -192,8 +192,8 @@ def _append_include_file( model: Problem, included_file_path: str ) -> None:
         if len( included_file_path ) == 0:
             return
 
-        includedTag = Included()
-        includedTag.file.append( File( name=DeckTree._append_id( included_file_path ) ) )
+        includedTag = IncludedType()
+        includedTag.file.append( FileType( name=DeckTree._append_id( included_file_path ) ) )
 
         model.included.append( includedTag )
 
@@ -235,7 +235,7 @@ def _convert_to_snake_case( content: str ) -> str:
         """
         return "".join( [ "_" + char.lower() if char.isupper() else char for char in content ] ).lstrip( "_" )
 
-    def _apply_changed_properties( self, model: Problem ) -> Problem:
+    def _apply_changed_properties( self, model: ProblemType ) -> ProblemType:
         """Retrieves all edited 'properties' from the simput_manager and apply it to a given model."""
         manager = get_simput_manager( self._sm_id )
         modified_proxy_ids: set[ str ] = manager.proxymanager.dirty_proxy_data

geos-trame/src/geos/trame/app/io/data_loader.py

@@ -13,10 +13,10 @@
 from geos.trame.app.ui.viewer.wellViewer import WellViewer
 from geos.trame.app.utils.pv_utils import read_unstructured_grid, split_vector_arrays
 from geos.trame.schema_generated.schema_mod import (
-    Vtkmesh,
-    Vtkwell,
-    Perforation,
-    InternalWell,
+    VtkmeshType,
+    VtkwellType,
+    PerforationType,
+    InternalWellType,
 )
 
 
@@ -44,7 +44,7 @@ def load_vtkmesh_from_id( self, node_id: str ) -> None:
         """Load the data at the given id if none is already loaded."""
         if self.region_viewer.input.number_of_cells == 0:
             active_block = self.source.decode( node_id )
-            if isinstance( active_block, Vtkmesh ):
+            if isinstance( active_block, VtkmeshType ):
                 self._read_mesh( active_block )
 
     def _update_object_state( self, object_state: tuple[ str, bool ], **_: dict ) -> None:
@@ -56,10 +56,10 @@ def _update_object_state( self, object_state: tuple[ str, bool ], **_: dict ) ->
 
         active_block = self.source.decode( path )
 
-        if isinstance( active_block, Vtkmesh ):
+        if isinstance( active_block, VtkmeshType ):
             self._update_vtkmesh( active_block, show_obj )
 
-        if isinstance( active_block, Vtkwell ):
+        if isinstance( active_block, VtkwellType ):
             if self.region_viewer.input.number_of_cells == 0 and show_obj:
                 self.ctrl.on_add_warning(
                     "Can't display " + active_block.name,
@@ -69,7 +69,7 @@ def _update_object_state( self, object_state: tuple[ str, bool ], **_: dict ) ->
 
             self._update_vtkwell( active_block, path, show_obj )
 
-        if isinstance( active_block, InternalWell ):
+        if isinstance( active_block, InternalWellType ):
             if self.region_viewer.input.number_of_cells == 0 and show_obj:
                 self.ctrl.on_add_warning(
                     "Can't display " + active_block.name,
@@ -79,7 +79,7 @@ def _update_object_state( self, object_state: tuple[ str, bool ], **_: dict ) ->
 
             self._update_internalwell( active_block, path, show_obj )
 
-        if ( isinstance( active_block, Perforation ) and self.well_viewer.get_number_of_wells() == 0 and show_obj ):
+        if ( isinstance( active_block, PerforationType ) and self.well_viewer.get_number_of_wells() == 0 and show_obj ):
             self.ctrl.on_add_warning(
                 "Can't display " + active_block.name,
                 "Please display a well before creating a perforation",
@@ -88,21 +88,21 @@ def _update_object_state( self, object_state: tuple[ str, bool ], **_: dict ) ->
 
         self.ctrl.update_viewer( active_block, path, show_obj )
 
-    def _update_vtkmesh( self, mesh: Vtkmesh, show: bool ) -> None:
+    def _update_vtkmesh( self, mesh: VtkmeshType, show: bool ) -> None:
         if not show:
             self.region_viewer.reset()
             return
 
         self._read_mesh( mesh )
 
-    def _read_mesh( self, mesh: Vtkmesh ) -> None:
+    def _read_mesh( self, mesh: VtkmeshType ) -> None:
         unstructured_grid = read_unstructured_grid( self.source.get_abs_path( mesh.file ) )
         split_vector_arrays( unstructured_grid )
 
         unstructured_grid.set_active_scalars( unstructured_grid.cell_data.keys()[ 0 ] )
         self.region_viewer.add_mesh( unstructured_grid )
 
-    def _update_vtkwell( self, well: Vtkwell, path: str, show: bool ) -> None:
+    def _update_vtkwell( self, well: VtkwellType, path: str, show: bool ) -> None:
         if not show:
             self.well_viewer.remove( path )
             return
@@ -112,8 +112,8 @@ def _update_vtkwell( self, well: Vtkwell, path: str, show: bool ) -> None:
             raise GeosTrameException( f"Expected PolyData, got {type(well_polydata).__name__}" )
         self.well_viewer.add_mesh( well_polydata, path )
 
-    def _update_internalwell( self, well: InternalWell, path: str, show: bool ) -> None:
-        """Used to control the visibility of the InternalWell.
+    def _update_internalwell( self, well: InternalWellType, path: str, show: bool ) -> None:
+        """Used to control the visibility of the InternalWellType.
 
         This method will create the mesh if it doesn't exist.
         """
@@ -134,7 +134,7 @@ def _update_internalwell( self, well: InternalWell, path: str, show: bool ) -> N
 
     @staticmethod
     def __parse_polyline_property( polyline_property: str, dtype: Type[ Any ] ) -> np.ndarray:
-        """Internal method used to parse and convert a property, such as polyline_node_coords, from an InternalWell.
+        """Internal method used to parse and convert a property, such as polyline_node_coords, from an InternalWellType.
 
         This string always follow this for :
             "{ { 800, 1450, 395.646 }, { 800, 1450, -554.354 } }"

geos-trame/src/geos/trame/app/ui/inspector.py

@@ -15,7 +15,7 @@
 from geos.trame.app.data_types.tree_node import TreeNode
 from geos.trame.app.deck.tree import DeckTree
 from geos.trame.app.utils.dict_utils import iterate_nested_dict
-from geos.trame.schema_generated.schema_mod import Problem
+from geos.trame.schema_generated.schema_mod import ProblemType
 
 vuetify.enable_lab()
 
@@ -113,7 +113,7 @@ def source( self ) -> dict | None:
     # TODO
     # v should be a proxy like the one in paraview simple
     # maybe it can be Any of schema_mod (e.g. Problem)
-    def _set_source( self, v: Problem | None ) -> None:
+    def _set_source( self, v: ProblemType | None ) -> None:
 
         # TODO replace this snippet
         from xsdata.formats.dataclass.serializers.config import SerializerConfig

geos-trame/src/geos/trame/app/ui/viewer/boxViewer.py

@@ -3,7 +3,7 @@
 # SPDX-FileContributor: Lucas Givord - Kitware
 import pyvista as pv
 
-from geos.trame.schema_generated.schema_mod import Box
+from geos.trame.schema_generated.schema_mod import BoxType
 
 import re
 
@@ -14,11 +14,11 @@ class BoxViewer:
     This mesh is represented in GEOS with a Box.
     """
 
-    def __init__( self, mesh: pv.UnstructuredGrid, box: Box ) -> None:
+    def __init__( self, mesh: pv.UnstructuredGrid, box: BoxType ) -> None:
         """Initialize the BoxViewer with a mesh and a box."""
         self._mesh: pv.UnstructuredGrid = mesh
 
-        self._box: Box = box
+        self._box: BoxType = box
         self._box_polydata: pv.PolyData = None
         self._box_polydata_actor: pv.Actor = None
 

geos-trame/src/geos/trame/app/ui/viewer/viewer.py

@@ -15,7 +15,7 @@
 from geos.trame.app.ui.viewer.perforationViewer import PerforationViewer
 from geos.trame.app.ui.viewer.regionViewer import RegionViewer
 from geos.trame.app.ui.viewer.wellViewer import WellViewer
-from geos.trame.schema_generated.schema_mod import Box, Vtkmesh, Vtkwell, InternalWell, Perforation
+from geos.trame.schema_generated.schema_mod import BoxType, VtkmeshType, VtkwellType, InternalWellType, PerforationType
 
 pv.OFF_SCREEN = True
 
@@ -32,17 +32,17 @@ def __init__(
         """Deck representing the 3D View using PyVista.
 
         This view can show:
-         - Vtkmesh,
-         - Vtkwell,
-         - Perforation,
-         - InternalWell
-         - Box
+         - VtkmeshType,
+         - VtkwellType,
+         - PerforationType,
+         - InternalWellType
+         - BoxType
 
         Everything is handle in the method 'update_viewer()' which is trigger when the
         'state.object_state' changed (see DeckTree).
 
         This View handle widgets, such as clip widget or slider to control Wells or
-        Perforation settings.
+        PerforationType settings.
         """
         super().__init__( **kwargs )
 
@@ -126,23 +126,23 @@ def rendering_menu_extra_items( self ) -> None:
     def update_viewer( self, active_block: BaseModel, path: str, show_obj: bool ) -> None:
         """Add from path the dataset given by the user.
 
-        Supported data type is: Vtkwell, Vtkmesh, InternalWell, Perforation, Box.
+        Supported data type is: VtkwellType, VtkmeshType, InternalWellType, PerforationType, BoxType.
 
         object_state  : array used to store path to the data and if we want to show it or not.
         """
-        if isinstance( active_block, Vtkmesh ):
+        if isinstance( active_block, VtkmeshType ):
             self._update_vtkmesh( show_obj )
 
-        if isinstance( active_block, Vtkwell ):
+        if isinstance( active_block, VtkwellType ):
             self._update_vtkwell( path, show_obj )
 
-        if isinstance( active_block, InternalWell ):
+        if isinstance( active_block, InternalWellType ):
             self._update_internalwell( path, show_obj )
 
-        if isinstance( active_block, Perforation ):
+        if isinstance( active_block, PerforationType ):
             self._update_perforation( active_block, show_obj, path )
 
-        if isinstance( active_block, Box ):
+        if isinstance( active_block, BoxType ):
             self._update_box( active_block, show_obj )
 
         # when data is added in the pv.Plotter, we need to refresh the scene to update
@@ -220,7 +220,7 @@ def _get_perforation_size( self ) -> float | None:
         return None
 
     def _update_internalwell( self, path: str, show: bool ) -> None:
-        """Used to control the visibility of the InternalWell.
+        """Used to control the visibility of the InternalWellType.
 
         This method will create the mesh if it doesn't exist.
         """
@@ -235,7 +235,7 @@ def _update_internalwell( self, path: str, show: bool ) -> None:
         self.ctrl.view_update()
 
     def _update_vtkwell( self, path: str, show: bool ) -> None:
-        """Used to control the visibility of the Vtkwell.
+        """Used to control the visibility of the VtkwellType.
 
         This method will create the mesh if it doesn't exist.
         """
@@ -273,7 +273,7 @@ def _update_actor_array( self, **_: Any ) -> None:
         self.ctrl.view_update()
 
     def _update_vtkmesh( self, show: bool ) -> None:
-        """Used to control the visibility of the Vtkmesh.
+        """Used to control the visibility of the VtkmeshType.
 
         This method will create the mesh if it doesn't exist.
 
@@ -298,7 +298,7 @@ def _update_vtkmesh( self, show: bool ) -> None:
                                        tubing=False,
                                        outline_translation=False )
 
-    def _update_perforation( self, perforation: Perforation, show: bool, path: str ) -> None:
+    def _update_perforation( self, perforation: PerforationType, show: bool, path: str ) -> None:
         """Generate VTK dataset from a perforation."""
         if not show:
             if path in self._perforations:
@@ -355,7 +355,7 @@ def _add_perforation( self, distance_from_head: float, path: str ) -> None:
 
         self._perforations[ path ] = saved_perforation
 
-    def _update_box( self, active_block: Box, show_obj: bool ) -> None:
+    def _update_box( self, active_block: BoxType, show_obj: bool ) -> None:
         """Generate and display a Box and inner cell(s) from the mesh."""
         if self.region_engine.input.number_of_cells == 0 and show_obj:
             self.ctrl.on_add_warning(
@@ -375,7 +375,7 @@ def _update_box( self, active_block: Box, show_obj: bool ) -> None:
             self._make_mesh_transparent( False )
             return
 
-        box: Box = active_block
+        box: BoxType = active_block
         self.box_engine[ active_block.name ] = BoxViewer( self.region_engine.input, box )
 
         box_polydata: pv.PolyData = self.box_engine[ active_block.name ].get_box_polydata()

geos-trame/src/geos/trame/app/ui/viewer/wellViewer.py

@@ -31,7 +31,7 @@ class WellViewer:
     def __init__( self, size: float, amplification: float ) -> None:
         """WellViewer stores all Well used in the pv.Plotter().
 
-        A Well in GEOS could a InternalWell or a Vtkwell.
+        A Well in GEOS could a InternalWellType or a VtkwellType.
         """
         self._wells: list[ Well ] = []
         self._wells_actors: list[ WellActor ] = []