feat: Adding a script to generate schema (#198)

* Adding a script to generate pydantic class from GEOS XSD schema.
* Get the schema from github REST/API
* Fix hard coded variable
* Discard all but ProblemType
* Regen schema
* Update ReadMe
---------

Co-authored-by: jacques franc <jacquesfrancdev@gmail.com>

Author: paloma-martinez

geos-trame/pyproject.toml

@@ -42,7 +42,7 @@ dependencies = [
     "trame-matplotlib==2.0.3",
     "trame-components==2.4.2",
     "mpld3<0.5.11",
-    "xsdata==24.5",
+    "xsdata[cli]>=25.4",
     "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

@@ -20,7 +20,7 @@
 
 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, Included, File, Functions
 from geos.trame.app.utils.file_utils import normalize_path, format_xml
 
 import logging
@@ -127,14 +127,14 @@ def encode_data( data: BaseModel ) -> dict:
         return nodeDict
 
     @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
@@ -200,8 +200,8 @@ 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():
@@ -221,7 +221,7 @@ 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:
+    def _append_include_file( model: ProblemType, included_file_path: str ) -> None:
         """Append an Included object which follows this structure according to the documentation.
 
         <Included>
@@ -278,7 +278,7 @@ 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

@@ -113,7 +113,7 @@ def _update_vtkwell( self, well: Vtkwell, path: str, show: bool ) -> None:
         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.
+        """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()
 
@@ -112,7 +112,7 @@ 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

@@ -19,11 +19,11 @@ def __init__( self, mesh: pv.UnstructuredGrid, box: Box ) -> None:
         self._mesh: pv.UnstructuredGrid = mesh
 
         self._box: Box = box
-        self._box_polydata: pv.PolyData = None
-        self._box_polydata_actor: pv.Actor = None
+        self._box_polydata: pv.PolyData | None = None
+        self._box_polydata_actor: pv.Actor | None = None
 
-        self._extracted_cells: pv.UnstructuredGrid = None
-        self._extracted_cells_actor: pv.Actor = None
+        self._extracted_cells: pv.UnstructuredGrid | None = None
+        self._extracted_cells_actor: pv.Actor | None = None
 
         self._compute_box_as_polydata()
         self._compute_intersected_cell()
@@ -32,7 +32,7 @@ def get_box_polydata( self ) -> pv.PolyData | None:
         """Get the box polydata."""
         return self._box_polydata
 
-    def get_box_polydata_actor( self ) -> pv.Actor:
+    def get_box_polydata_actor( self ) -> pv.Actor | None:
         """Get the actor generated by a pv.Plotter for the box polydata."""
         return self._box_polydata_actor
 
@@ -86,16 +86,18 @@ def _retrieve_bounding_box( self ) -> list[ float ]:
 
     def _compute_intersected_cell( self ) -> None:
         """Extract the cells from the mesh that are inside the box."""
-        ids = self._mesh.find_cells_within_bounds( self._box_polydata.bounds )
+        if self._box_polydata:
+            ids = self._mesh.find_cells_within_bounds( self._box_polydata.bounds )
 
         saved_ids: list[ int ] = []
 
         for id in ids:
             cell: pv.vtkCell = self._mesh.GetCell( id )
 
-            is_inside = self._check_cell_inside_box( cell, self._box_polydata.bounds )
-            if is_inside:
-                saved_ids.append( id )
+            if self._box_polydata:
+                is_inside = self._check_cell_inside_box( cell, self._box_polydata.bounds )
+                if is_inside:
+                    saved_ids.append( id )
 
         if len( saved_ids ) > 0:
             self._extracted_cells = self._mesh.extract_cells( saved_ids )

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

@@ -50,7 +50,8 @@ def __init__(
         self._cell_data_array_names: list[ str ] = []
         self._source = source
         self._pl = pv.Plotter()
-        self._pl.iren.initialize()
+        if self._pl.iren:
+            self._pl.iren.initialize()
         self._mesh_actor: vtkActor | None = None
 
         self.CUT_PLANE = "on_cut_plane_visibility_change"
@@ -126,7 +127,7 @@ 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.
         """
@@ -253,7 +254,7 @@ 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.
         """
@@ -269,7 +270,7 @@ 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.
         """
@@ -308,7 +309,7 @@ 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.
 

geos-trame/src/geos/trame/schema_generated/README.md

@@ -11,49 +11,57 @@ to parse, serialize and deserialize these files in trame with `trame-simput`, we
 generate a serializable class for each balise described in the schema used by GEOS.
 
 For that we use a python module named `xsd-pydantic` which allows us to generate a file.
-It will contain all class for a given xsd schema file. 
+It will contain all class for a given xsd schema file.
 
 When starting the trame application, we can instantiate the expected dataclass when parsing
 the input file.
 
 ## How to generate a new file
 
-#### 1. Clone the GEOS Repository
+First, retrieve the `schema.xsd` corresponding to the GEOS version you want to use.
 
-```bash
-git clone git@github.com:GEOS-DEV/GEOS.git
-```
+> [!WARNING]
+> We advise to use GEOS version from commit [#1e617be](https://github.com/GEOS-DEV/GEOS/commit/1e617be8614817d92f0a7a159994cbed1661ff98). You may encounter compatibility issues with older versions.
 
-#### 2. Create a dedicate venv
+In a sourced virtual environement set for geos_trame,
 
 ```bash
-cd <path-to-geos-trame>
-python -m venv pydantic-venv
-source pydantic-venv/bin/activate
-pip install -e .
-pip install "xsdata[cli]"
-cd src/geos_trame/schema_generated
+(venv) cd geosPythonPackages/geos-trame/src/geos/trame/schema_generated
+(venv) python generate_schema.py -g
+(venv) mv schema_<GEOS-commit-sha>.xsd schema.xsd
+(venv) python generate_schema.py -v <GEOS-commit-sha>
 ```
 
-#### 3. Generate the new file
-
-The full documentation is [here](https://xsdata-pydantic.readthedocs.io/en/latest/codegen/).
+This two stage approach is defaulted:
 
-```bash
-xsdata <path-to-GEOS>/src/coreComponents/schema/schema.xsd --output pydantic --package generated_models --structure-style single-package --include-header
-```
+ 1. To take the latest commit on GEOS' `develop`. However, if a particular commit on `develop` is of interest,
+you can pass it through the option `-c <GEOS-commit-sha>`. It will generate `schema_<GEOS-commit-sha>.xsd`.
+ 2. To generate the `schema_mod.py` packages, metadata-ing the commit number in the header.
 
-Then update the generated file, at the beginning, by adding the geos commit used:
+In any other case, `schema.xsd` can be found in [GEOS Github repository](https://github.com/GEOS-DEV/GEOS) under `GEOS/src/coreComponents/schema/schema.xsd`
+and the first step can be skipped.
 
-For example:
+The second stage relies on `xsdata[cli]` interfaced with `pydantic` as driver.
+The full documentation can be found [here](https://xsdata-pydantic.readthedocs.io/en/latest/codegen/).
 
-```py
-"""This file was generated by xsdata, v24.6.1, on 2024-11-29
-
-Generator: PydanticGenerator
-See: https://xsdata.readthedocs.io/
-
-GEOS commit hash: <add-the-commit-hash-here>
-"""
-```
+Options to the helper script can be displayed with `--help` parameters:
 
+```bash
+$ python generate_schema.py --help
+
+Generate schema from schema.xsd file
+
+optional arguments:
+  -h, --help            show this help message and exit
+  -g, --get-schema      Get the latest schema files.
+  -c COMMIT, --commit COMMIT
+                        Force a specific GEOS develop's commit for schema
+                        download
+  -s SCHEMAFILE, --schemaFile SCHEMAFILE
+                        Filepath to GEOS schema file.
+  -cf CONFIGFILE, --configFile CONFIGFILE
+                        Filepath to xml configuration file for schema
+                        generation.
+  -v VERSION, --version VERSION
+                        GEOS commit sha or version identification.
+```

geos-trame/src/geos/trame/schema_generated/config_schema.xml

@@ -0,0 +1,16 @@
+<?xml version="1.0" encoding="UTF-8"?>
+
+
+<Config xmlns="http://pypi.org/project/xsdata" version="25.4">
+  <Output maxLineLength="79">
+    <Package>schema_mod</Package>
+    <Format repr="true" eq="true" order="false" unsafeHash="false" frozen="false" slots="false" kwOnly="false">pydantic</Format>
+    <Structure>single-package</Structure>
+    <IncludeHeader>false</IncludeHeader>
+    <DocstringStyle>reStructuredText</DocstringStyle>
+    <RelativeImports>false</RelativeImports>
+  </Output>
+  <Substitutions>
+    <Substitution type="class" search="(?&lt;!Problem)Type$" replace=""/>
+  </Substitutions>
+</Config>