add functionality for custom pkl file

osp/models/catalytic/co_catalyticfoam.py

@@ -248,6 +248,9 @@ def __post_init_post_parse__(self):
                 calc.add(self._make_species(species), rel=emmo.hasCalculationInput)
             calc.add(self._make_continuum_model(), rel=emmo.hasCalculationInput)
             calc.add(self._make_catalyist_amount(), rel=emmo.hasCalculationInput)
+            if self.species_from_upload:
+                pkl = emmo.PKLFile(uid=self.species_from_upload)
+                calc.add(pkl, rel=emmo.hasCalculationInput)
         file = tempfile.NamedTemporaryFile(suffix=".ttl")
         export_cuds(session, file.name)
         self._uuid = get_upload(file)

osp/wrappers/simcatalyticfoam/catalyticfoam_engine.py

@@ -3,7 +3,7 @@
 import shutil
 import subprocess  # nosec
 import tempfile
-from typing import TYPE_CHECKING
+from typing import TYPE_CHECKING, Optional
 
 import osp.dictionaries.catalyticFoam as case
 
@@ -37,6 +37,7 @@ def __init__(self, case: str, config: dict = {}):
                 directory=runtime,
                 filename=tar,
             )
+        self._pkl: Optional[str] = None
         self._parse_files = dict()
         self._config: dict = config
         self._current_process: subprocess.Popen = None
@@ -66,6 +67,12 @@ def run(self) -> None:
             with open(path, "w+") as file:
                 file_content = serialize(content)
                 file.write(file_content)
+        if self._pkl:
+            logger.info("Will use custom PKL for catalytic wall: `%s`", self._pkl)
+            dest_pkl = os.path.join(
+                self._config["directory"], "ml_ExtraTrees_forCFD.pkl"
+            )
+            shutil.copy(self._pkl, dest_pkl)
         for command in self._config["commands"]:
             cmd = self._prepare_command(command)
             logger.info(
@@ -221,3 +228,7 @@ def exit_code(cls):
     @property
     def tarball(cls):
         return f"{cls._config['filename']}.tar"
+
+    @property
+    def pkl(cls):
+        return cls._pkl

osp/wrappers/simcatalyticfoam/simcatalyticfoam.py

@@ -5,6 +5,7 @@
 from osp.core.namespaces import emmo
 from osp.core.session import SimWrapperSession
 from osp.models.catalytic.utils import check_arcp, wrap_arcp
+from osp.models.utils.general import get_download
 
 from .catalyticfoam_engine import CatalyticFoamEngine, settings
 
@@ -68,6 +69,8 @@ def _wrap(self, cuds: "Cuds") -> None:
             self._check_for_value(cuds)
         elif cuds.is_a(emmo.AdjustableSimulationTimeStep):
             self._wrap_arcp(cuds, "yes")
+        elif cuds.is_a(emmo.PKLFile):
+            self._engine.pkl = get_download(str(cuds.uid), as_file=True)
 
     def _make_new_chemical(self, composition: "Cuds") -> None:
         species = composition.get(oclass=emmo.ChemicalSpecies)