nerdd-module 0.3.24__tar.gz → 0.3.25__tar.gz

{nerdd_module-0.3.24 → nerdd_module-0.3.25}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: nerdd-module
-Version: 0.3.24
+Version: 0.3.25
 Summary: Base package to create NERDD modules
 Author-email: Steffen Hirte <steffen.hirte@univie.ac.at>
 Maintainer-email: Steffen Hirte <steffen.hirte@univie.ac.at>

{nerdd_module-0.3.24 → nerdd_module-0.3.25}/nerdd_module/model/__init__.py

@@ -1,4 +1,3 @@
-from .assign_mol_id_step import *
 from .assign_name_step import *
 from .convert_representations_step import *
 from .model import *

{nerdd_module-0.3.24 → nerdd_module-0.3.25}/nerdd_module/model/read_input_step.py

@@ -13,8 +13,9 @@ class ReadInputStep(Step):
         self._input = input
 
     def _run(self, source: Iterator[dict]) -> Iterator[dict]:
-        for entry in self._explorer.explore(self._input):
+        for mol_id, entry in enumerate(self._explorer.explore(self._input)):
             record = dict(
+                mol_id=mol_id,
                 input_text=entry.raw_input,
                 source=entry.source,
                 input_type=entry.input_type,

{nerdd_module-0.3.24 → nerdd_module-0.3.25}/nerdd_module/model/simple_model.py

@@ -18,7 +18,6 @@ from ..preprocessing import PreprocessingStep
 from ..problem import Problem
 from ..steps import Step
 from ..util import get_file_path_to_instance
-from .assign_mol_id_step import AssignMolIdStep
 from .assign_name_step import AssignNameStep
 from .convert_representations_step import ConvertRepresentationsStep
 from .enforce_schema_step import EnforceSchemaStep
@@ -52,11 +51,10 @@ class SimpleModel(Model):
         self, input: Any, input_format: Optional[str], **kwargs: Any
     ) -> List[Step]:
         return [
-            AssignMolIdStep(),
             AssignNameStep(),
             *self._preprocessing_steps,
             # the following step ensures that the column preprocessed_mol is created
-            # (even is self._preprocessing_steps is empty)
+            # (even if self._preprocessing_steps is empty)
             CustomPreprocessingStep(self),
         ]
 
@@ -214,4 +212,7 @@ class CustomPreprocessingStep(PreprocessingStep):
         self.model = model
 
     def _preprocess(self, mol: Mol) -> Tuple[Optional[Mol], List[Problem]]:
-        return self.model._preprocess(mol)
+        try:
+            return self.model._preprocess(mol)
+        except Exception as e:
+            return None, [Problem(type="preprocessing_error", message=str(e))]

{nerdd_module-0.3.24 → nerdd_module-0.3.25}/nerdd_module.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: nerdd-module
-Version: 0.3.24
+Version: 0.3.25
 Summary: Base package to create NERDD modules
 Author-email: Steffen Hirte <steffen.hirte@univie.ac.at>
 Maintainer-email: Steffen Hirte <steffen.hirte@univie.ac.at>

{nerdd_module-0.3.24 → nerdd_module-0.3.25}/nerdd_module.egg-info/SOURCES.txt

@@ -45,7 +45,6 @@ nerdd_module/input/string_reader.py
 nerdd_module/input/tar_reader.py
 nerdd_module/input/zip_reader.py
 nerdd_module/model/__init__.py
-nerdd_module/model/assign_mol_id_step.py
 nerdd_module/model/assign_name_step.py
 nerdd_module/model/convert_representations_step.py
 nerdd_module/model/enforce_schema_step.py

{nerdd_module-0.3.24 → nerdd_module-0.3.25}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "nerdd-module"
-version = "0.3.24"
+version = "0.3.25"
 description = "Base package to create NERDD modules"
 readme = "README.md"
 license = { file = "LICENSE" }

nerdd_module-0.3.24/nerdd_module/model/assign_mol_id_step.py

@@ -1,17 +0,0 @@
-from typing import Iterator
-
-from ..steps import Step
-
-__all__ = ["AssignMolIdStep"]
-
-
-class AssignMolIdStep(Step):
-    def __init__(self) -> None:
-        super().__init__()
-
-    def _run(self, source: Iterator[dict]) -> Iterator[dict]:
-        mol_id = 0
-        for record in source:
-            record["mol_id"] = mol_id
-            mol_id += 1
-            yield record