update source on dataclasses that should contain children

src/cli/main.py

@@ -66,7 +66,8 @@
 )
 
 OPTION_CLONE_DIRECTORY = click.option(
-    "--duplicate_directory","-d",
+    "--duplicate_directory",
+    "-d",
     type=bool,
     is_flag=True,
     default=False,
@@ -183,7 +184,7 @@ def print_lab(
     bag_crate: Optional[bool],
     collect_all: Optional[bool],
     gpg_binary: Optional[Path],
-    duplicate_directory: Optional[Path]
+    duplicate_directory: Optional[bool],
 ) -> None:
     """
     Create an RO-Crate based on a Print Lab metadata file

src/ingestion_targets/print_lab_genomics/extractor.py

@@ -22,10 +22,10 @@
 import src.ingestion_targets.print_lab_genomics.consts as profile_consts
 from src.cli.mytardisconfig import SchemaConfig
 from src.ingestion_targets.print_lab_genomics.print_crate_dataclasses import (
+    ExtractionDataset,
     MedicalCondition,
     Participant,
     SampleExperiment,
-    ExtractionDataset
 )
 from src.metadata_extraction.metadata_extraction import (
     MetadataHanlder,
@@ -63,12 +63,6 @@ def __init__(
         self.metadata_handler = MetadataHanlder(self.api_agent, namespaces)
         self.collect_all = collect_all
 
-    #
-    # def _contruct_sensitive_dict(
-    #     self, sensitive_feild_names: list[str]
-    # ) -> dict[str, Callable[[str], str]]:
-    #     return {field_name: field_name for field_name in sensitive_feild_names}
-
     def datasheet_to_dataframe(
         self, input_data_source: Any, sheet_name: str
     ) -> pd.DataFrame:
@@ -289,7 +283,7 @@ def parse_dataset(row: pd.Series) -> ExtractionDataset:
                 additional_properties={},
                 schema_type="Dataset",
                 acls=None,
-                copy_unlisted=row["Crate Children"]
+                copy_unlisted=row["Crate Children"],
             )
             return new_dataset
 

src/ingestion_targets/print_lab_genomics/print_crate_builder.py

@@ -6,8 +6,8 @@
 
 from mytardis_rocrate_builder.rocrate_builder import ROBuilder
 from mytardis_rocrate_builder.rocrate_dataclasses.rocrate_dataclasses import (
+    Dataset,
     Experiment,
-    Dataset
 )
 from rocrate.model.contextentity import ContextEntity
 from rocrate.model.encryptedcontextentity import (  # pylint: disable=import-error, no-name-in-module
@@ -16,10 +16,10 @@
 from slugify import slugify
 
 from src.ingestion_targets.print_lab_genomics.print_crate_dataclasses import (
+    ExtractionDataset,
     MedicalCondition,
     Participant,
     SampleExperiment,
-    ExtractionDataset
 )
 
 logger = logging.getLogger(__name__)
@@ -143,8 +143,6 @@ def add_experiment(self, experiment: Experiment) -> ContextEntity:
         Args:
             experiment (Experiment): The experiment to be added to the crate
         """
-        # Note that this is being created as a data catalog object as there are no better
-        # fits
         if not isinstance(experiment, SampleExperiment):
             return super().add_experiment(experiment)
         properties: Dict[str, str | list[str] | dict[str, Any]] = {
@@ -183,7 +181,6 @@ def add_experiment(self, experiment: Experiment) -> ContextEntity:
         )
         return self._add_identifiers(experiment, experiment_obj)
 
-
     def add_dataset(self, dataset: Dataset) -> ContextEntity:
         """Add a dataset to the RO-Crate accounting for if unlisted cildren should be added
 
@@ -193,9 +190,12 @@ def add_dataset(self, dataset: Dataset) -> ContextEntity:
         # Note that this is being created as a data catalog object as there are no better
         # fits
         datset_entity = super().add_dataset(dataset)
-        if not isinstance(dataset,  ExtractionDataset):
+        if not isinstance(dataset, ExtractionDataset):
             return datset_entity
         if dataset.copy_unlisted:
-            datset_entity.source = self.crate.source / dataset.directory if self.crate.source else dataset.directory
+            datset_entity.source = (
+                self.crate.source / dataset.directory
+                if self.crate.source
+                else dataset.directory
+            )
         return datset_entity
-

src/ingestion_targets/print_lab_genomics/print_crate_dataclasses.py

@@ -67,7 +67,7 @@ class SampleExperiment(
     schema_type = "DataCatalog"
 
 @dataclass
-class ExtractionDataset(Dataset):  # type: ignore
+class ExtractionDataset(Dataset):
     """Dataset information for extraction of a dataset
      that may need to copy unlisted"""
     copy_unlisted : bool