deriva-ml 1.14.0__py3-none-any.whl → 1.14.27__py3-none-any.whl

deriva_ml/{dataset.py → dataset/dataset.py}

@@ -1,74 +1,110 @@
-"""
-This module defines the DataSet class with is used to manipulate datasets in DerivaML.
-The intended use of this class is as a base class in DerivaML, so all the methods documented here are
-accessible via a DerivaML class instance.
-
+"""Dataset management for DerivaML.
+
+This module provides functionality for managing datasets in DerivaML. A dataset represents a collection
+of related data that can be versioned, downloaded, and tracked. The module includes:
+
+- Dataset class: Core class for dataset operations
+- Version management: Track and update dataset versions
+- History tracking: Record dataset changes over time
+- Download capabilities: Export datasets as BDBags
+- Relationship management: Handle dataset dependencies and hierarchies
+
+The Dataset class serves as a base class in DerivaML, making its methods accessible through
+DerivaML class instances.
+
+Typical usage example:
+    >>> ml = DerivaML('deriva.example.org', 'my_catalog')
+    >>> dataset_rid = ml.create_dataset('experiment', 'Experimental data')
+    >>> ml.add_dataset_members(dataset_rid=dataset_rid, members=['1-abc123', '1-def456'])
+    >>> ml.increment_dataset_version(datset_rid=dataset_rid, component=VersionPart.minor,
+    ...     description='Added new samples')
 """
 
 from __future__ import annotations
-from bdbag import bdbag_api as bdb
-from bdbag.fetch.fetcher import fetch_single_file
-from collections import defaultdict
-from graphlib import TopologicalSorter
+
+# Standard library imports
 import json
 import logging
+from collections import defaultdict
+from graphlib import TopologicalSorter
 from pathlib import Path
-from pydantic import (
-    validate_call,
-    ConfigDict,
-)
-import requests
 from tempfile import TemporaryDirectory
-from typing import Any, Callable, Optional, Iterable, Iterator, TYPE_CHECKING
+from typing import TYPE_CHECKING, Any, Callable, Iterable, Iterator
 
-from .history import iso_to_snap
-from deriva.core.ermrest_model import Table
-from deriva.core.utils.core_utils import tag as deriva_tags, format_exception
 import deriva.core.utils.hash_utils as hash_utils
-from deriva.transfer.download.deriva_export import DerivaExport
+import requests
+
+# Third-party imports
+from bdbag import bdbag_api as bdb
+from bdbag.fetch.fetcher import fetch_single_file
+
+# Deriva imports
+from deriva.core.ermrest_model import Table
+from deriva.core.utils.core_utils import format_exception
+from deriva.core.utils.core_utils import tag as deriva_tags
 from deriva.transfer.download.deriva_download import (
-    DerivaDownloadConfigurationError,
-    DerivaDownloadError,
     DerivaDownloadAuthenticationError,
     DerivaDownloadAuthorizationError,
+    DerivaDownloadConfigurationError,
+    DerivaDownloadError,
     DerivaDownloadTimeoutError,
 )
+from deriva.transfer.download.deriva_export import DerivaExport
+from pydantic import ConfigDict, validate_call
 
-
+# Local imports
 try:
     from icecream import ic
+
+    ic.configureOutput(includeContext=True)
 except ImportError:  # Graceful fallback if IceCream isn't installed.
     ic = lambda *a: None if not a else (a[0] if len(a) == 1 else a)  # noqa
 
-from deriva_ml import DatasetBag
-from .deriva_definitions import (
+from deriva_ml.core.constants import RID
+from deriva_ml.core.definitions import (
+    DRY_RUN_RID,
     ML_SCHEMA,
-    DerivaMLException,
     MLVocab,
     Status,
-    RID,
-    DRY_RUN_RID,
 )
-from .deriva_model import DerivaModel
-from .database_model import DatabaseModel
-from .dataset_aux_classes import (
-    DatasetVersion,
-    DatasetMinid,
+from deriva_ml.core.exceptions import DerivaMLException, DerivaMLTableTypeError
+from deriva_ml.dataset.aux_classes import (
     DatasetHistory,
-    VersionPart,
+    DatasetMinid,
     DatasetSpec,
+    DatasetVersion,
+    VersionPart,
 )
+from deriva_ml.dataset.dataset_bag import DatasetBag
+from deriva_ml.model.catalog import DerivaModel
+from deriva_ml.model.database import DatabaseModel
+
+from .history import iso_to_snap
+
+# Stop pycharm from complaining about undefined reference in docstring....
+ml: DerivaML
 
 if TYPE_CHECKING:
-    from .deriva_ml_base import DerivaML
+    from deriva_ml.core.base import DerivaML
 
 
 class Dataset:
-    """
-    Class to manipulate a dataset.
+    """Manages dataset operations in a Deriva catalog.
+
+    The Dataset class provides functionality for creating, modifying, and tracking datasets
+    in a Deriva catalog. It handles versioning, relationships between datasets, and data export.
 
     Attributes:
-        dataset_table (Table): ERMRest table holding dataset information.
+        dataset_table (Table): ERMrest table storing dataset information.
+        _model (DerivaModel): Catalog model instance.
+        _ml_schema (str): Schema name for ML-specific tables.
+        _cache_dir (Path): Directory for caching downloaded datasets.
+        _working_dir (Path): Directory for working data.
+        _use_minid (bool): Whether to use MINID service for dataset identification.
+
+    Note:
+        This class is typically used as a base class, with its methods accessed through
+        DerivaML class instances rather than directly.
     """
 
     _Logger = logging.getLogger("deriva_ml")
@@ -80,20 +116,31 @@ class Dataset:
         working_dir: Path,
         use_minid: bool = True,
     ):
+        """Initializes a Dataset instance.
+
+        Args:
+            model: DerivaModel instance representing the catalog.
+            cache_dir: Directory path for caching downloaded datasets.
+            working_dir: Directory path for working data.
+            use_minid: Whether to use MINID service for dataset identification.
+        """
         self._model = model
         self._ml_schema = ML_SCHEMA
-        self.dataset_table = self._model.schemas[self._ml_schema].tables["Dataset"]
         self._cache_dir = cache_dir
         self._working_dir = working_dir
         self._logger = logging.getLogger("deriva_ml")
         self._use_minid = use_minid
 
+    @property
+    def _dataset_table(self):
+        return self._model.schemas[self._ml_schema].tables["Dataset"]
+
     def _is_dataset_rid(self, dataset_rid: RID, deleted: bool = False) -> bool:
         try:
             rid_info = self._model.catalog.resolve_rid(dataset_rid, self._model.model)
         except KeyError as _e:
             raise DerivaMLException(f"Invalid RID {dataset_rid}")
-        if rid_info.table != self.dataset_table:
+        if rid_info.table != self._dataset_table:
             return False
         elif deleted:
             # Got a dataset rid. Now check to see if its deleted or not.
@@ -104,12 +151,12 @@ class Dataset:
     def _insert_dataset_versions(
         self,
         dataset_list: list[DatasetSpec],
-        description: Optional[str] = "",
-        execution_rid: Optional[RID] = None,
+        description: str | None = "",
+        execution_rid: RID | None = None,
     ) -> None:
         schema_path = self._model.catalog.getPathBuilder().schemas[self._ml_schema]
         # determine snapshot after changes were made
-        snap = self._model.catalog.get("/").json()["snaptime"]
+
         # Construct version records for insert
         version_records = schema_path.tables["Dataset_Version"].insert(
             [
@@ -118,16 +165,18 @@ class Dataset:
                     "Version": str(dataset.version),
                     "Description": description,
                     "Execution": execution_rid,
-                    "Snapshot": snap,
                 }
                 for dataset in dataset_list
             ]
         )
+        version_records = list(version_records)
+        snap = self._model.catalog.get("/").json()["snaptime"]
+        schema_path.tables["Dataset_Version"].update(
+            [{"RID": v["RID"], "Dataset": v["Dataset"], "Snapshot": snap} for v in version_records]
+        )
 
         # And update the dataset records.
-        schema_path.tables["Dataset"].update(
-            [{"Version": v["RID"], "RID": v["Dataset"]} for v in version_records]
-        )
+        schema_path.tables["Dataset"].update([{"Version": v["RID"], "RID": v["Dataset"]} for v in version_records])
 
     def _bootstrap_versions(self):
         datasets = [ds["RID"] for ds in self.find_datasets()]
@@ -143,9 +192,7 @@ class Dataset:
         version_path = schema_path.tables["Dataset_Version"]
         dataset_path = schema_path.tables["Dataset"]
         history = list(version_path.insert(ds_version))
-        dataset_versions = [
-            {"RID": h["Dataset"], "Version": h["Version"]} for h in history
-        ]
+        dataset_versions = [{"RID": h["Dataset"], "Version": h["Version"]} for h in history]
         dataset_path.update(dataset_versions)
 
     def _synchronize_dataset_versions(self):
@@ -161,45 +208,47 @@ class Dataset:
                 versions[v["Dataset"]] = v
         dataset_path = schema_path.tables["Dataset"]
 
-        dataset_path.update(
-            [
-                {"RID": dataset, "Version": version["RID"]}
-                for dataset, version in versions.items()
-            ]
-        )
+        dataset_path.update([{"RID": dataset, "Version": version["RID"]} for dataset, version in versions.items()])
 
     def _set_version_snapshot(self):
-        dataset_version_path = (
-            self._model.catalog.getPathBuilder()
-            .schemas[self._ml_schema]
-            .tables["Dataset_Version"]
-        )
+        """Update the Snapshot column of the Dataset_Version table to the correct time."""
+        dataset_version_path = self._model.catalog.getPathBuilder().schemas[self._ml_schema].tables["Dataset_Version"]
         versions = dataset_version_path.entities().fetch()
         dataset_version_path.update(
-            [
-                {"RID": h["RID"], "Snapshot": iso_to_snap(h["RCT"])}
-                for h in versions
-                if not h["Snapshot"]
-            ]
+            [{"RID": h["RID"], "Snapshot": iso_to_snap(h["RCT"])} for h in versions if not h["Snapshot"]]
         )
 
     def dataset_history(self, dataset_rid: RID) -> list[DatasetHistory]:
-        """Return a list of DatasetHistory objects representing the dataset
+        """Retrieves the version history of a dataset.
+
+        Returns a chronological list of dataset versions, including their version numbers,
+        creation times, and associated metadata.
 
         Args:
-            dataset_rid: A RID to the dataset for which history is to be fetched.
+            dataset_rid: Resource Identifier of the dataset.
 
         Returns:
-            A list of DatasetHistory objects which indicate the version-number, creation time, and bag instantiation of the dataset.
+            list[DatasetHistory]: List of history entries, each containing:
+                - dataset_version: Version number (major.minor.patch)
+                - minid: Minimal Viable Identifier
+                - snapshot: Catalog snapshot time
+                - dataset_rid: Dataset Resource Identifier
+                - version_rid: Version Resource Identifier
+                - description: Version description
+                - execution_rid: Associated execution RID
+
+        Raises:
+            DerivaMLException: If dataset_rid is not a valid dataset RID.
+
+        Example:
+            >>> history = ml.dataset_history("1-abc123")
+            >>> for entry in history:
+            ...     print(f"Version {entry.dataset_version}: {entry.description}")
         """
 
         if not self._is_dataset_rid(dataset_rid):
             raise DerivaMLException(f"RID is not for a data set: {dataset_rid}")
-        version_path = (
-            self._model.catalog.getPathBuilder()
-            .schemas[self._ml_schema]
-            .tables["Dataset_Version"]
-        )
+        version_path = self._model.catalog.getPathBuilder().schemas[self._ml_schema].tables["Dataset_Version"]
         return [
             DatasetHistory(
                 dataset_version=DatasetVersion.parse(v["Version"]),
@@ -210,9 +259,7 @@ class Dataset:
                 description=v["Description"],
                 execution_rid=v["Execution"],
             )
-            for v in version_path.filter(version_path.Dataset == dataset_rid)
-            .entities()
-            .fetch()
+            for v in version_path.filter(version_path.Dataset == dataset_rid).entities().fetch()
         ]
 
     @validate_call
@@ -234,14 +281,16 @@ class Dataset:
         if not history:
             return DatasetVersion(0, 1, 0)
         else:
-            return max([h.dataset_version for h in self.dataset_history(dataset_rid)])
+            # Ensure we return a DatasetVersion, not a string
+            versions = [h.dataset_version for h in history]
+            return max(versions) if versions else DatasetVersion(0, 1, 0)
 
     def _build_dataset_graph(self, dataset_rid: RID) -> Iterable[RID]:
-        ts = TopologicalSorter()
+        ts: TopologicalSorter = TopologicalSorter()
         self._build_dataset_graph_1(dataset_rid, ts, set())
         return ts.static_order()
 
-    def _build_dataset_graph_1(self, dataset_rid: RID, ts, visited) -> None:
+    def _build_dataset_graph_1(self, dataset_rid: RID, ts: TopologicalSorter, visited) -> None:
         """Use topological sort to return bottom up list of nested datasets"""
         ts.add(dataset_rid)
         if dataset_rid not in visited:
@@ -249,7 +298,8 @@ class Dataset:
             children = self.list_dataset_children(dataset_rid=dataset_rid)
             parents = self.list_dataset_parents(dataset_rid=dataset_rid)
             for parent in parents:
-                self._build_dataset_graph_1(parent, ts, visited)
+                # Convert string to RID type
+                self._build_dataset_graph_1(RID(parent), ts, visited)
             for child in children:
                 self._build_dataset_graph_1(child, ts, visited)
 
@@ -258,22 +308,34 @@ class Dataset:
         self,
         dataset_rid: RID,
         component: VersionPart,
-        description: Optional[str] = "",
-        execution_rid: Optional[RID] = None,
+        description: str | None = "",
+        execution_rid: RID | None = None,
     ) -> DatasetVersion:
-        """Increment the version of the specified dataset_table.
+        """Increments a dataset's version number.
+
+        Creates a new version of the dataset by incrementing the specified version component
+        (major, minor, or patch). The new version is recorded with an optional description
+        and execution reference.
 
         Args:
-            dataset_rid: RID of the dataset whose version is to be incremented.
-            component: Which version of the dataset_table to increment. Major, Minor, or Patch
-            description: Description of the version update of the dataset_table.
-            execution_rid: Which execution is performing increment.
+            dataset_rid: Resource Identifier of the dataset to version.
+            component: Which version component to increment ('major', 'minor', or 'patch').
+            description: Optional description of the changes in this version.
+            execution_rid: Optional execution RID to associate with this version.
 
         Returns:
-          new semantic version of the dataset_table as a 3-tuple
+            DatasetVersion: The new version number.
 
         Raises:
-          DerivaMLException: if provided, RID is not to a dataset_table.
+            DerivaMLException: If dataset_rid is invalid or version increment fails.
+
+        Example:
+            >>> new_version = ml.increment_dataset_version(
+            ...     dataset_rid="1-abc123",
+            ...     component="minor",
+            ...     description="Added new samples"
+            ... )
+            >>> print(f"New version: {new_version}")  # e.g., "1.2.0"
         """
 
         # Find all the datasets that are reachable from this dataset and determine their new version numbers.
@@ -285,46 +347,51 @@ class Dataset:
             )
             for ds_rid in related_datasets
         ]
-        self._insert_dataset_versions(
-            version_update_list, description=description, execution_rid=execution_rid
-        )
-        return [d.version for d in version_update_list if d.rid == dataset_rid][0]
+        self._insert_dataset_versions(version_update_list, description=description, execution_rid=execution_rid)
+        return next((d.version for d in version_update_list if d.rid == dataset_rid))
 
     @validate_call(config=ConfigDict(arbitrary_types_allowed=True))
     def create_dataset(
         self,
-        dataset_types: str | list[str],
-        description: str,
-        execution_rid: Optional[RID] = None,
-        version: Optional[DatasetVersion] = None,
+        dataset_types: str | list[str] | None = None,
+        description: str = "",
+        execution_rid: RID | None = None,
+        version: DatasetVersion | None = None,
     ) -> RID:
-        """Create a new dataset_table from the specified list of RIDs.
+        """Creates a new dataset in the catalog.
+
+        Creates a dataset with specified types and description. The dataset can be associated
+        with an execution and initialized with a specific version.
 
         Args:
-            dataset_types: One or more dataset_table types.  Must be a term from the DatasetType controlled vocabulary.
-            description: Description of the dataset_table.
-            execution_rid: Execution under which the dataset_table will be created.
-            version: Version of the dataset_table.
+            dataset_types: One or more dataset type terms from Dataset_Type vocabulary.
+            description: Description of the dataset's purpose and contents.
+            execution_rid: Optional execution RID to associate with dataset creation.
+            version: Optional initial version number. Defaults to 0.1.0.
 
         Returns:
-            New dataset_table RID.
+            RID: Resource Identifier of the newly created dataset.
 
+        Raises:
+            DerivaMLException: If dataset_types are invalid or creation fails.
+
+        Example:
+            >>> rid = ml.create_dataset(
+            ...     dataset_types=["experiment", "raw_data"],
+            ...     description="RNA sequencing experiment data",
+            ...     version=DatasetVersion(1, 0, 0)
+            ... )
         """
 
         version = version or DatasetVersion(0, 1, 0)
+        dataset_types = dataset_types or []
 
-        type_path = (
-            self._model.catalog.getPathBuilder()
-            .schemas[self._ml_schema]
-            .tables[MLVocab.dataset_type.value]
-        )
+        type_path = self._model.catalog.getPathBuilder().schemas[self._ml_schema].tables[MLVocab.dataset_type.value]
         defined_types = list(type_path.entities().fetch())
 
         def check_dataset_type(dtype: str) -> bool:
             for term in defined_types:
-                if dtype == term["Name"] or (
-                    term["Synonyms"] and ds_type in term["Synonyms"]
-                ):
+                if dtype == term["Name"] or (term["Synonyms"] and ds_type in term["Synonyms"]):
                     return True
             return False
 
@@ -334,9 +401,7 @@ class Dataset:
         for ds_type in ds_types:
             if not check_dataset_type(ds_type):
                 raise DerivaMLException("Dataset type must be a vocabulary term.")
-        dataset_table_path = pb.schemas[self.dataset_table.schema.name].tables[
-            self.dataset_table.name
-        ]
+        dataset_table_path = pb.schemas[self._dataset_table.schema.name].tables[self._dataset_table.name]
         dataset_rid = dataset_table_path.insert(
             [
                 {
@@ -347,21 +412,13 @@ class Dataset:
         )[0]["RID"]
 
         # Get the name of the association table between dataset_table and dataset_type.
-        atable = next(
-            self._model.schemas[self._ml_schema]
-            .tables[MLVocab.dataset_type]
-            .find_associations()
-        ).name
+        associations = list(self._model.schemas[self._ml_schema].tables[MLVocab.dataset_type].find_associations())
+        atable = associations[0].name if associations else None
         pb.schemas[self._ml_schema].tables[atable].insert(
-            [
-                {MLVocab.dataset_type: ds_type, "Dataset": dataset_rid}
-                for ds_type in ds_types
-            ]
+            [{MLVocab.dataset_type: ds_type, "Dataset": dataset_rid} for ds_type in ds_types]
         )
         if execution_rid is not None:
-            pb.schemas[self._ml_schema].Dataset_Execution.insert(
-                [{"Dataset": dataset_rid, "Execution": execution_rid}]
-            )
+            pb.schemas[self._ml_schema].Dataset_Execution.insert([{"Dataset": dataset_rid, "Execution": execution_rid}])
         self._insert_dataset_versions(
             [DatasetSpec(rid=dataset_rid, version=version)],
             execution_rid=execution_rid,
@@ -383,18 +440,12 @@ class Dataset:
             raise DerivaMLException("Dataset_rid is not a dataset.")
 
         if parents := self.list_dataset_parents(dataset_rid):
-            raise DerivaMLException(
-                f'Dataset_rid "{dataset_rid}" is in a nested dataset: {parents}.'
-            )
+            raise DerivaMLException(f'Dataset_rid "{dataset_rid}" is in a nested dataset: {parents}.')
 
         pb = self._model.catalog.getPathBuilder()
-        dataset_path = pb.schemas[self.dataset_table.schema.name].tables[
-            self.dataset_table.name
-        ]
+        dataset_path = pb.schemas[self._dataset_table.schema.name].tables[self._dataset_table.name]
 
-        rid_list = [dataset_rid] + (
-            self.list_dataset_children(dataset_rid) if recurse else []
-        )
+        rid_list = [dataset_rid] + (self.list_dataset_children(dataset_rid=dataset_rid) if recurse else [])
         dataset_path.update([{"RID": r, "Deleted": True} for r in rid_list])
 
     def find_datasets(self, deleted: bool = False) -> Iterable[dict[str, Any]]:
@@ -408,14 +459,9 @@ class Dataset:
         """
         # Get datapath to all the tables we will need: Dataset, DatasetType and the association table.
         pb = self._model.catalog.getPathBuilder()
-        dataset_path = pb.schemas[self.dataset_table.schema.name].tables[
-            self.dataset_table.name
-        ]
-        atable = next(
-            self._model.schemas[self._ml_schema]
-            .tables[MLVocab.dataset_type]
-            .find_associations()
-        ).name
+        dataset_path = pb.schemas[self._dataset_table.schema.name].tables[self._dataset_table.name]
+        associations = list(self._model.schemas[self._ml_schema].tables[MLVocab.dataset_type].find_associations())
+        atable = associations[0].name if associations else None
         ml_path = pb.schemas[self._ml_schema]
         atable_path = ml_path.tables[atable]
 
@@ -423,21 +469,16 @@ class Dataset:
             filtered_path = dataset_path
         else:
             filtered_path = dataset_path.filter(
-                (dataset_path.Deleted == False) | (dataset_path.Deleted == None)  # noqa: E712
+                (dataset_path.Deleted == False) | (dataset_path.Deleted == None)  # noqa: E711, E712
             )
 
         # Get a list of all the dataset_type values associated with this dataset_table.
         datasets = []
         for dataset in filtered_path.entities().fetch():
             ds_types = (
-                atable_path.filter(atable_path.Dataset == dataset["RID"])
-                .attributes(atable_path.Dataset_Type)
-                .fetch()
-            )
-            datasets.append(
-                dataset
-                | {MLVocab.dataset_type: [ds[MLVocab.dataset_type] for ds in ds_types]}
+                atable_path.filter(atable_path.Dataset == dataset["RID"]).attributes(atable_path.Dataset_Type).fetch()
             )
+            datasets.append(dataset | {MLVocab.dataset_type: [ds[MLVocab.dataset_type] for ds in ds_types]})
         return datasets
 
     def list_dataset_element_types(self) -> Iterable[Table]:
@@ -448,16 +489,9 @@ class Dataset:
         """
 
         def domain_table(table: Table) -> bool:
-            return (
-                table.schema.name == self._model.domain_schema
-                or table.name == self.dataset_table.name
-            )
+            return table.schema.name == self._model.domain_schema or table.name == self._dataset_table.name
 
-        return [
-            t
-            for a in self.dataset_table.find_associations()
-            if domain_table(t := a.other_fkeys.pop().pk_table)
-        ]
+        return [t for a in self._dataset_table.find_associations() if domain_table(t := a.other_fkeys.pop().pk_table)]
 
     @validate_call(config=ConfigDict(arbitrary_types_allowed=True))
     def add_dataset_element_type(self, element: str | Table) -> Table:
@@ -472,31 +506,45 @@ class Dataset:
         """
         # Add table to map
         element_table = self._model.name_to_table(element)
-        table = self._model.schemas[self._model.domain_schema].create_table(
-            Table.define_association([self.dataset_table, element_table])
-        )
+        atable_def = Table.define_association([self._dataset_table, element_table])
+        try:
+            table = self._model.schemas[self._model.domain_schema].create_table(atable_def)
+        except ValueError as e:
+            if "already exists" in str(e):
+                table = self._model.name_to_table(atable_def["table_name"])
+            else:
+                raise e
 
         # self.model = self.catalog.getCatalogModel()
-        self.dataset_table.annotations.update(
-            self._generate_dataset_download_annotations()
-        )
+        self._dataset_table.annotations.update(self._generate_dataset_download_annotations())
         self._model.model.apply()
         return table
 
     # @validate_call
     def list_dataset_members(
-        self, dataset_rid: RID, recurse: bool = False, limit: Optional[int] = None
+        self, dataset_rid: RID, recurse: bool = False, limit: int | None = None
     ) -> dict[str, list[dict[str, Any]]]:
-        """Return a list of entities associated with a specific dataset_table.
+        """Lists members of a dataset.
+
+        Returns a dictionary mapping member types to lists of member records. Can optionally
+        recurse through nested datasets and limit the number of results.
 
         Args:
-            dataset_rid: param recurse: If this is a nested dataset_table, list the members of the contained datasets
-            recurse: (Default value = False)
-            limit: If provided, the maximum number of members to return for each element type.
+            dataset_rid: Resource Identifier of the dataset.
+            recurse: Whether to include members of nested datasets. Defaults to False.
+            limit: Maximum number of members to return per type. None for no limit.
 
         Returns:
-            Dictionary of entities associated with a specific dataset_table.  Key is the table from which the elements
-            were taken.
+            dict[str, list[dict[str, Any]]]: Dictionary mapping member types to lists of members.
+                Each member is a dictionary containing the record's attributes.
+
+        Raises:
+            DerivaMLException: If dataset_rid is invalid.
+
+        Example:
+            >>> members = ml.list_dataset_members("1-abc123", recurse=True)
+            >>> for type_name, records in members.items():
+            ...     print(f"{type_name}: {len(records)} records")
         """
 
         if not self._is_dataset_rid(dataset_rid):
@@ -506,21 +554,18 @@ class Dataset:
         # the appropriate association table.
         members = defaultdict(list)
         pb = self._model.catalog.getPathBuilder()
-        for assoc_table in self.dataset_table.find_associations():
+        for assoc_table in self._dataset_table.find_associations():
             other_fkey = assoc_table.other_fkeys.pop()
             target_table = other_fkey.pk_table
             member_table = assoc_table.table
 
             # Look at domain tables and nested datasets.
-            if (
-                target_table.schema.name != self._model.domain_schema
-                and target_table != self.dataset_table
+            if target_table.schema.name != self._model.domain_schema and not (
+                target_table == self._dataset_table or target_table.name == "File"
             ):
                 continue
             member_column = (
-                "Nested_Dataset"
-                if target_table == self.dataset_table
-                else other_fkey.foreign_key_columns[0].name
+                "Nested_Dataset" if target_table == self._dataset_table else other_fkey.foreign_key_columns[0].name
             )
 
             target_path = pb.schemas[target_table.schema.name].tables[target_table.name]
@@ -530,15 +575,13 @@ class Dataset:
                 target_path,
                 on=(member_path.columns[member_column] == target_path.columns["RID"]),
             )
-            target_entities = list(
-                path.entities().fetch(limit=limit) if limit else path.entities().fetch()
-            )
+            target_entities = list(path.entities().fetch(limit=limit) if limit else path.entities().fetch())
             members[target_table.name].extend(target_entities)
-            if recurse and target_table == self.dataset_table:
+            if recurse and target_table == self._dataset_table:
                 # Get the members for all the nested datasets and add to the member list.
                 nested_datasets = [d["RID"] for d in target_entities]
                 for ds in nested_datasets:
-                    for k, v in self.list_dataset_members(ds, recurse=False).items():
+                    for k, v in self.list_dataset_members(ds, recurse=recurse).items():
                         members[k].extend(v)
         return dict(members)
 
@@ -546,24 +589,38 @@ class Dataset:
     def add_dataset_members(
         self,
         dataset_rid: RID,
-        members: list[RID],
+        members: list[RID] | dict[str, list[RID]],
         validate: bool = True,
-        description: Optional[str] = "",
-        execution_rid: Optional[RID] = None,
+        description: str | None = "",
+        execution_rid: RID | None = None,
     ) -> None:
-        """Add additional elements to an existing dataset_table.
+        """Adds members to a dataset.
 
-        Add new elements to an existing dataset. In addition to adding new members, the minor version number of the
-        dataset is incremented and the description, if provide is applied to that new version.
+        Associates one or more records with a dataset. Can optionally validate member types
+        and create a new dataset version to track the changes.
 
         Args:
-            dataset_rid: RID of dataset_table to extend or None if a new dataset_table is to be created.
-            members: List of member RIDs to add to the dataset_table.
-            validate: Check rid_list to make sure elements are not already in the dataset_table.
-            description: Markdown description of the updated dataset.
-            execution_rid: Optional RID of execution associated with this dataset.
+            dataset_rid: Resource Identifier of the dataset.
+            members: List of RIDs to add as dataset members. Can be orginized into a dictionary that indicates the
+                table that the member rids belong to.
+            validate: Whether to validate member types. Defaults to True.
+            description: Optional description of the member additions.
+            execution_rid: Optional execution RID to associate with changes.
+
+        Raises:
+            DerivaMLException: If:
+                - dataset_rid is invalid
+                - members are invalid or of wrong type
+                - adding members would create a cycle
+                - validation fails
+
+        Example:
+            >>> ml.add_dataset_members(
+            ...     dataset_rid="1-abc123",
+            ...     members=["1-def456", "1-ghi789"],
+            ...     description="Added sample data"
+            ... )
         """
-        members = set(members)
         description = description or "Updated dataset via add_dataset_members"
 
         def check_dataset_cycle(member_rid, path=None):
@@ -580,43 +637,37 @@ class Dataset:
             return member_rid in path
 
         if validate:
-            existing_rids = set(
-                m["RID"]
-                for ms in self.list_dataset_members(dataset_rid).values()
-                for m in ms
-            )
+            existing_rids = set(m["RID"] for ms in self.list_dataset_members(dataset_rid).values() for m in ms)
             if overlap := set(existing_rids).intersection(members):
-                raise DerivaMLException(
-                    f"Attempting to add existing member to dataset_table {dataset_rid}: {overlap}"
-                )
+                raise DerivaMLException(f"Attempting to add existing member to dataset_table {dataset_rid}: {overlap}")
 
         # Now go through every rid to be added to the data set and sort them based on what association table entries
         # need to be made.
         dataset_elements = {}
         association_map = {
-            a.other_fkeys.pop().pk_table.name: a.table.name
-            for a in self.dataset_table.find_associations()
+            a.other_fkeys.pop().pk_table.name: a.table.name for a in self._dataset_table.find_associations()
         }
+
         # Get a list of all the object types that can be linked to a dataset_table.
-        for m in members:
-            try:
-                rid_info = self._model.catalog.resolve_rid(m)
-            except KeyError:
-                raise DerivaMLException(f"Invalid RID: {m}")
-            if rid_info.table.name not in association_map:
-                raise DerivaMLException(
-                    f"RID table: {rid_info.table.name} not part of dataset_table"
-                )
-            if rid_info.table == self.dataset_table and check_dataset_cycle(
-                rid_info.rid
-            ):
-                raise DerivaMLException("Creating cycle of datasets is not allowed")
-            dataset_elements.setdefault(rid_info.table.name, []).append(rid_info.rid)
+        if type(members) is list:
+            members = set(members)
+            for m in members:
+                try:
+                    rid_info = self._model.catalog.resolve_rid(m)
+                except KeyError:
+                    raise DerivaMLException(f"Invalid RID: {m}")
+                if rid_info.table.name not in association_map:
+                    raise DerivaMLException(f"RID table: {rid_info.table.name} not part of dataset_table")
+                if rid_info.table == self._dataset_table and check_dataset_cycle(rid_info.rid):
+                    raise DerivaMLException("Creating cycle of datasets is not allowed")
+                dataset_elements.setdefault(rid_info.table.name, []).append(rid_info.rid)
+        else:
+            dataset_elements = {t: set(ms) for t, ms in members.items()}
         # Now make the entries into the association tables.
         pb = self._model.catalog.getPathBuilder()
         for table, elements in dataset_elements.items():
             schema_path = pb.schemas[
-                self._ml_schema if table == "Dataset" else self._model.domain_schema
+                self._ml_schema if (table == "Dataset" or table == "File") else self._model.domain_schema
             ]
             fk_column = "Nested_Dataset" if table == "Dataset" else table
             if len(elements):
@@ -637,7 +688,7 @@ class Dataset:
         dataset_rid: RID,
         members: list[RID],
         description: str = "",
-        execution_rid: Optional[RID] = None,
+        execution_rid: RID | None = None,
     ) -> None:
         """Remove elements to an existing dataset_table.
 
@@ -658,8 +709,7 @@ class Dataset:
         # need to be made.
         dataset_elements = {}
         association_map = {
-            a.other_fkeys.pop().pk_table.name: a.table.name
-            for a in self.dataset_table.find_associations()
+            a.other_fkeys.pop().pk_table.name: a.table.name for a in self._dataset_table.find_associations()
         }
         # Get a list of all the object types that can be linked to a dataset_table.
         for m in members:
@@ -668,16 +718,12 @@ class Dataset:
             except KeyError:
                 raise DerivaMLException(f"Invalid RID: {m}")
             if rid_info.table.name not in association_map:
-                raise DerivaMLException(
-                    f"RID table: {rid_info.table.name} not part of dataset_table"
-                )
+                raise DerivaMLException(f"RID table: {rid_info.table.name} not part of dataset_table")
             dataset_elements.setdefault(rid_info.table.name, []).append(rid_info.rid)
         # Now make the entries into the association tables.
         pb = self._model.catalog.getPathBuilder()
         for table, elements in dataset_elements.items():
-            schema_path = pb.schemas[
-                self._ml_schema if table == "Dataset" else self._model.domain_schema
-            ]
+            schema_path = pb.schemas[self._ml_schema if table == "Dataset" else self._model.domain_schema]
             fk_column = "Nested_Dataset" if table == "Dataset" else table
 
             if len(elements):
@@ -685,8 +731,7 @@ class Dataset:
                 # Find out the name of the column in the association table.
                 for e in elements:
                     entity = atable_path.filter(
-                        (atable_path.Dataset == dataset_rid)
-                        & (atable_path.columns[fk_column] == e),
+                        (atable_path.Dataset == dataset_rid) & (atable_path.columns[fk_column] == e),
                     )
                     entity.delete()
         self.increment_dataset_version(
@@ -708,21 +753,14 @@ class Dataset:
             RID of the parent dataset_table.
         """
         if not self._is_dataset_rid(dataset_rid):
-            raise DerivaMLException(
-                f"RID: {dataset_rid} does not belong to dataset_table {self.dataset_table.name}"
-            )
+            raise DerivaMLException(f"RID: {dataset_rid} does not belong to dataset_table {self._dataset_table.name}")
         # Get association table for nested datasets
         pb = self._model.catalog.getPathBuilder()
         atable_path = pb.schemas[self._ml_schema].Dataset_Dataset
-        return [
-            p["Dataset"]
-            for p in atable_path.filter(atable_path.Nested_Dataset == dataset_rid)
-            .entities()
-            .fetch()
-        ]
+        return [p["Dataset"] for p in atable_path.filter(atable_path.Nested_Dataset == dataset_rid).entities().fetch()]
 
     @validate_call
-    def list_dataset_children(self, dataset_rid: RID, recurse=False) -> list[RID]:
+    def list_dataset_children(self, dataset_rid: RID, recurse: bool = False) -> list[RID]:
         """Given a dataset_table RID, return a list of RIDs for any nested datasets.
 
         Args:
@@ -733,19 +771,11 @@ class Dataset:
           list of nested dataset RIDs.
 
         """
-        dataset_dataset_path = (
-            self._model.catalog.getPathBuilder()
-            .schemas[self._ml_schema]
-            .tables["Dataset_Dataset"]
-        )
+        dataset_dataset_path = self._model.catalog.getPathBuilder().schemas[self._ml_schema].tables["Dataset_Dataset"]
         nested_datasets = list(dataset_dataset_path.entities().fetch())
 
         def find_children(rid: RID):
-            children = [
-                child["Nested_Dataset"]
-                for child in nested_datasets
-                if child["Dataset"] == rid
-            ]
+            children = [child["Nested_Dataset"] for child in nested_datasets if child["Dataset"] == rid]
             if recurse:
                 for child in children.copy():
                     children.extend(find_children(child))
@@ -753,9 +783,7 @@ class Dataset:
 
         return find_children(dataset_rid)
 
-    def _export_vocabulary(
-        self, writer: Callable[[str, str, Table], list[dict[str, Any]]]
-    ) -> list[dict[str, Any]]:
+    def _export_vocabulary(self, writer: Callable[[str, str, Table], list[dict[str, Any]]]) -> list[dict[str, Any]]:
         """
 
         Args:
@@ -770,16 +798,12 @@ class Dataset:
             for table in s.tables.values()
             if self._model.is_vocabulary(table)
         ]
-        return [
-            o
-            for table in vocabs
-            for o in writer(f"{table.schema.name}:{table.name}", table.name, table)
-        ]
+        return [o for table in vocabs for o in writer(f"{table.schema.name}:{table.name}", table.name, table)]
 
     def _table_paths(
         self,
-        dataset: Optional[DatasetSpec] = None,
-        snapshot_catalog: Optional[DerivaML] = None,
+        dataset: DatasetSpec | None = None,
+        snapshot_catalog: DerivaML | None = None,
     ) -> Iterator[tuple[str, str, Table]]:
         paths = self._collect_paths(dataset and dataset.rid, snapshot_catalog)
 
@@ -805,25 +829,20 @@ class Dataset:
 
     def _collect_paths(
         self,
-        dataset_rid: Optional[RID] = None,
-        snapshot: Optional[Dataset] = None,
-        dataset_nesting_depth: Optional[int] = None,
+        dataset_rid: RID | None = None,
+        snapshot: Dataset | None = None,
+        dataset_nesting_depth: int | None = None,
     ) -> set[tuple[Table, ...]]:
         snapshot_catalog = snapshot if snapshot else self
 
-        dataset_table = snapshot_catalog._model.schemas[self._ml_schema].tables[
-            "Dataset"
-        ]
-        dataset_dataset = snapshot_catalog._model.schemas[self._ml_schema].tables[
-            "Dataset_Dataset"
-        ]
+        dataset_table = snapshot_catalog._model.schemas[self._ml_schema].tables["Dataset"]
+        dataset_dataset = snapshot_catalog._model.schemas[self._ml_schema].tables["Dataset_Dataset"]
 
         # Figure out what types of elements the dataset contains.
         dataset_associations = [
             a
-            for a in self.dataset_table.find_associations()
-            if a.table.schema.name != self._ml_schema
-            or a.table.name == "Dataset_Dataset"
+            for a in self._dataset_table.find_associations()
+            if a.table.schema.name != self._ml_schema or a.table.name == "Dataset_Dataset"
         ]
         if dataset_rid:
             # Get a list of the members of the dataset so we can figure out which tables to query.
@@ -835,9 +854,7 @@ class Dataset:
                 if m
             ]
             included_associations = [
-                a.table
-                for a in dataset_table.find_associations()
-                if a.other_fkeys.pop().pk_table in dataset_elements
+                a.table for a in dataset_table.find_associations() if a.other_fkeys.pop().pk_table in dataset_elements
             ]
         else:
             included_associations = dataset_associations
@@ -848,9 +865,7 @@ class Dataset:
             for p in snapshot_catalog._model._schema_to_paths()
             if (len(p) == 1)
             or (p[1] not in dataset_associations)  # Tables in the domain schema
-            or (
-                p[1] in included_associations
-            )  # Tables that include members of the dataset
+            or (p[1] in included_associations)  # Tables that include members of the dataset
         }
         # Now get paths for nested datasets
         nested_paths = set()
@@ -860,56 +875,42 @@ class Dataset:
         else:
             # Initialize nesting depth if not already provided.
             dataset_nesting_depth = (
-                self._dataset_nesting_depth()
-                if dataset_nesting_depth is None
-                else dataset_nesting_depth
+                self._dataset_nesting_depth() if dataset_nesting_depth is None else dataset_nesting_depth
             )
             if dataset_nesting_depth:
-                nested_paths = self._collect_paths(
-                    dataset_nesting_depth=dataset_nesting_depth - 1
-                )
+                nested_paths = self._collect_paths(dataset_nesting_depth=dataset_nesting_depth - 1)
         if nested_paths:
             paths |= {
                 tuple([dataset_table]),
                 (dataset_table, dataset_dataset),
             }
-        paths |= {(self.dataset_table, dataset_dataset) + p for p in nested_paths}
+        paths |= {(self._dataset_table, dataset_dataset) + p for p in nested_paths}
         return paths
 
-    def _dataset_nesting_depth(self, dataset_rid: Optional[RID] = None) -> int:
+    def _dataset_nesting_depth(self, dataset_rid: RID | None = None) -> int:
         """Determine the maximum dataset nesting depth in the current catalog.
 
         Returns:
 
         """
 
-        def children_depth(
-            dataset_rid: RID, nested_datasets: dict[str, list[str]]
-        ) -> int:
+        def children_depth(dataset_rid: RID, nested_datasets: dict[str, list[str]]) -> int:
             """Return the number of nested datasets for the dataset_rid if provided, otherwise in the current catalog"""
             try:
                 children = nested_datasets[dataset_rid]
-                return (
-                    max(map(lambda x: children_depth(x, nested_datasets), children)) + 1
-                    if children
-                    else 1
-                )
+                return max(map(lambda x: children_depth(x, nested_datasets), children)) + 1 if children else 1
             except KeyError:
                 return 0
 
         # Build up the dataset_table nesting graph...
-        pb = (
-            self._model.catalog.getPathBuilder()
-            .schemas[self._ml_schema]
-            .tables["Dataset_Dataset"]
-        )
+        pb = self._model.catalog.getPathBuilder().schemas[self._ml_schema].tables["Dataset_Dataset"]
         dataset_children = (
             [
                 {
                     "Dataset": dataset_rid,
                     "Nested_Dataset": c,
                 }  # Make uniform with return from datapath
-                for c in self.list_dataset_children(dataset_rid)
+                for c in self.list_dataset_children(dataset_rid=dataset_rid)
             ]
             if dataset_rid
             else pb.entities().fetch()
@@ -917,30 +918,29 @@ class Dataset:
         nested_dataset = defaultdict(list)
         for ds in dataset_children:
             nested_dataset[ds["Dataset"]].append(ds["Nested_Dataset"])
-        return (
-            max(map(lambda d: children_depth(d, dict(nested_dataset)), nested_dataset))
-            if nested_dataset
-            else 0
-        )
+        return max(map(lambda d: children_depth(d, dict(nested_dataset)), nested_dataset)) if nested_dataset else 0
 
     def _dataset_specification(
         self,
         writer: Callable[[str, str, Table], list[dict[str, Any]]],
-        dataset: Optional[DatasetSpec] = None,
-        snapshot_catalog: Optional[DerivaML] = None,
+        dataset: DatasetSpec | None = None,
+        snapshot_catalog: DerivaML | None = None,
     ) -> list[dict[str, Any]]:
-        """Output a download/export specification for a dataset_table.  Each element of the dataset_table will be placed in its own dir
-        The top level data directory of the resulting BDBag will have one subdirectory for element type. The subdirectory
-        will contain the CSV indicating which elements of that type are present in the dataset_table, and then there will be a
-         subdirectory for each object that is reachable from the dataset_table members.
-
-        To simplify reconstructing the relationship between tables, the CVS for each
-        The top level data directory will also contain a subdirectory for any controlled vocabularies used in the dataset_table.
-        All assets will be placed into a directory named asset in a subdirectory with the asset table name.
-
-        For example, consider a dataset_table that consists of two element types, T1 and T2. T1 has foreign key relationships to
-        objects in tables T3 and T4.  There are also two controlled vocabularies, CV1 and CV2.  T2 is an asset table
-        which has two assets in it. The layout of the resulting bdbag would be:
+        """Output a download/export specification for a dataset_table.  Each element of the dataset_table
+        will be placed in its own directory.
+        The top level data directory of the resulting BDBag will have one subdirectory for element type.
+        The subdirectory will contain the CSV indicating which elements of that type are present in the
+        dataset_table, and then there will be a subdirectory for each object that is reachable from the
+        dataset_table members.
+
+        To simplify reconstructing the relationship between tables, the CVS for each element is included.
+        The top level data directory will also contain a subdirectory for any controlled vocabularies used in
+        the dataset_table. All assets will be placed into a directory named asset in a subdirectory with the
+        asset table name.
+
+        For example, consider a dataset_table that consists of two element types, T1 and T2. T1 has foreign
+        key relationships to objects in tables T3 and T4. There are also two controlled vocabularies, CV1 and
+        CV2. T2 is an asset table which has two assets in it. The layout of the resulting bdbag would be:
               data
                 CV1/
                     cv1.csv
@@ -967,17 +967,15 @@ class Dataset:
             A dataset_table specification.
         """
         element_spec = self._export_vocabulary(writer)
-        for path in self._table_paths(
-            dataset=dataset, snapshot_catalog=snapshot_catalog
-        ):
+        for path in self._table_paths(dataset=dataset, snapshot_catalog=snapshot_catalog):
             element_spec.extend(writer(*path))
         return element_spec
 
     def _download_dataset_bag(
         self,
         dataset: DatasetSpec,
-        execution_rid: Optional[RID] = None,
-        snapshot_catalog: Optional[DerivaML] = None,
+        execution_rid: RID | None = None,
+        snapshot_catalog: DerivaML | None = None,
     ) -> DatasetBag:
         """Download a dataset onto the local file system.  Create a MINID for the dataset if one doesn't already exist.
 
@@ -1007,27 +1005,29 @@ class Dataset:
 
     def _version_snapshot(self, dataset: DatasetSpec) -> str:
         """Return a catalog with snapshot for the specified dataset version"""
-        version_record = [
-            h
-            for h in self.dataset_history(dataset_rid=dataset.rid)
-            if h.dataset_version == dataset.version
-        ][0]
+        try:
+            version_record = next(
+                h for h in self.dataset_history(dataset_rid=dataset.rid) if h.dataset_version == dataset.version
+            )
+        except StopIteration:
+            raise DerivaMLException(f"Dataset version {dataset.version} not found for dataset {dataset.rid}")
         return f"{self._model.catalog.catalog_id}@{version_record.snapshot}"
 
-    def _create_dataset_minid(
-        self, dataset: DatasetSpec, snapshot_catalog: Optional[DerivaML] = None
-    ) -> str:
+    def _create_dataset_minid(self, dataset: DatasetSpec, snapshot_catalog: DerivaML | None = None) -> str:
         with TemporaryDirectory() as tmp_dir:
             # Generate a download specification file for the current catalog schema. By default, this spec
             # will generate a minid and place the bag into S3 storage.
-            spec_file = f"{tmp_dir}/download_spec.json"
-            with open(spec_file, "w", encoding="utf-8") as ds:
-                json.dump(
-                    self._generate_dataset_download_spec(dataset, snapshot_catalog), ds
-                )
+            spec_file = Path(tmp_dir) / "download_spec.json"
+            with spec_file.open("w", encoding="utf-8") as ds:
+                json.dump(self._generate_dataset_download_spec(dataset, snapshot_catalog), ds)
             try:
                 self._logger.info(
-                    f"Downloading dataset {'minid' if self._use_minid else 'bag'} for catalog: {dataset.rid}@{str(dataset.version)}"
+                    "Downloading dataset %s for catalog: %s@%s"
+                    % (
+                        "minid" if self._use_minid else "bag",
+                        dataset.rid,
+                        str(dataset.version),
+                    )
                 )
                 # Generate the bag and put into S3 storage.
                 exporter = DerivaExport(
@@ -1050,15 +1050,9 @@ class Dataset:
                 raise DerivaMLException(format_exception(e))
             # Update version table with MINID.
             if self._use_minid:
-                version_path = (
-                    self._model.catalog.getPathBuilder()
-                    .schemas[self._ml_schema]
-                    .tables["Dataset_Version"]
-                )
+                version_path = self._model.catalog.getPathBuilder().schemas[self._ml_schema].tables["Dataset_Version"]
                 version_rid = [
-                    h
-                    for h in self.dataset_history(dataset_rid=dataset.rid)
-                    if h.dataset_version == dataset.version
+                    h for h in self.dataset_history(dataset_rid=dataset.rid) if h.dataset_version == dataset.version
                 ][0].version_rid
                 version_path.update([{"RID": version_rid, "Minid": minid_page_url}])
         return minid_page_url
@@ -1066,10 +1060,10 @@ class Dataset:
     def _get_dataset_minid(
         self,
         dataset: DatasetSpec,
-        snapshot_catalog: Optional[DerivaML] = None,
+        snapshot_catalog: DerivaML | None = None,
         create: bool = True,
-    ) -> DatasetMinid:
-        """Return a MINID to the specified dataset.  If no version is specified, use the latest.
+    ) -> DatasetMinid | None:
+        """Return a MINID for the specified dataset. If no version is specified, use the latest.
 
         Args:
             dataset: Specification of the dataset.
@@ -1079,50 +1073,53 @@ class Dataset:
         Returns:
             New or existing MINID for the dataset.
         """
-        if dataset.rid.startswith("minid"):
-            minid_url = f"https://identifiers.org/{dataset.rid}"
-        elif dataset.rid.startswith("http"):
-            minid_url = dataset.rid
-        else:
-            if not any([dataset.rid == ds["RID"] for ds in self.find_datasets()]):
-                raise DerivaMLException(f"RID {dataset.rid} is not a dataset_table")
-
-            # Get the history record for the version we are looking for.
-            dataset_version_record = [
-                v
-                for v in self.dataset_history(dataset.rid)
-                if v.dataset_version == str(dataset.version)
-            ][0]
-            if not dataset_version_record:
-                raise DerivaMLException(
-                    f"Version {str(dataset.version)} does not exist for RID {dataset.rid}"
-                )
-            minid_url = dataset_version_record.minid
-            if not minid_url:
-                if not create:
-                    raise DerivaMLException(
-                        f"Minid for dataset {dataset.rid} doesn't exist"
-                    )
-                if self._use_minid:
-                    self._logger.info("Creating new MINID for dataset %s", dataset.rid)
-                minid_url = self._create_dataset_minid(dataset, snapshot_catalog)
-            # If provided a MINID, use the MINID metadata to get the checksum and download the bag.
+        rid = dataset.rid
+
+        # Case 1: RID is already a MINID or direct URL
+        if rid.startswith("minid"):
+            return self._fetch_minid_metadata(f"https://identifiers.org/{rid}", dataset.version)
+        if rid.startswith("http"):
+            return self._fetch_minid_metadata(rid, dataset.version)
+
+        # Case 2: RID is a dataset RID – validate existence
+        if not any(rid == ds["RID"] for ds in self.find_datasets()):
+            raise DerivaMLTableTypeError("Dataset", rid)
+
+        # Find dataset version record
+        version_str = str(dataset.version)
+        history = self.dataset_history(rid)
+        try:
+            version_record = next(v for v in history if v.dataset_version == version_str)
+        except StopIteration:
+            raise DerivaMLException(f"Version {version_str} does not exist for RID {rid}")
+
+        # Check or create MINID
+        minid_url = version_record.minid
+        if not minid_url:
+            if not create:
+                raise DerivaMLException(f"Minid for dataset {rid} doesn't exist")
             if self._use_minid:
-                r = requests.get(minid_url, headers={"accept": "application/json"})
-                dataset_minid = DatasetMinid(
-                    dataset_version=dataset.version, **r.json()
-                )
-            else:
-                dataset_minid = DatasetMinid(
-                    dataset_version=dataset.version,
-                    RID=f"{dataset.rid}@{dataset_version_record.snapshot}",
-                    location=minid_url,
-                )
-            return dataset_minid
+                self._logger.info("Creating new MINID for dataset %s", rid)
+            minid_url = self._create_dataset_minid(dataset, snapshot_catalog)
+
+        # Return based on MINID usage
+        if self._use_minid:
+            return self._fetch_minid_metadata(minid_url, dataset.version)
+
+        return DatasetMinid(
+            dataset_version=dataset.version,
+            RID=f"{rid}@{version_record.snapshot}",
+            location=minid_url,
+        )
+
+    def _fetch_minid_metadata(self, url: str, version: DatasetVersion) -> DatasetMinid:
+        r = requests.get(url, headers={"accept": "application/json"})
+        r.raise_for_status()
+        return DatasetMinid(dataset_version=version, **r.json())
 
     def _download_dataset_minid(self, minid: DatasetMinid) -> Path:
-        """Given a RID to a dataset_table, or a MINID to an existing bag, download the bag file, extract it, and validate
-        that all the metadata is correct
+        """Given a RID to a dataset_table, or a MINID to an existing bag, download the bag file, extract it, and
+        validate that all the metadata is correct
 
         Args:
             minid: The RID of a dataset_table or a minid to an existing bag.
@@ -1134,9 +1131,7 @@ class Dataset:
         # it.  If not, then we need to extract the contents of the archive into our cache directory.
         bag_dir = self._cache_dir / f"{minid.dataset_rid}_{minid.checksum}"
         if bag_dir.exists():
-            self._logger.info(
-                f"Using cached bag for  {minid.dataset_rid} Version:{minid.dataset_version}"
-            )
+            self._logger.info(f"Using cached bag for  {minid.dataset_rid} Version:{minid.dataset_version}")
             return Path(bag_dir / f"Dataset_{minid.dataset_rid}")
 
         # Either bag hasn't been downloaded yet, or we are not using a Minid, so we don't know the checksum yet.
@@ -1145,19 +1140,13 @@ class Dataset:
                 # Get bag from S3
                 archive_path = fetch_single_file(minid.bag_url)
             else:
-                exporter = DerivaExport(
-                    host=self._model.catalog.deriva_server.server, output_dir=tmp_dir
-                )
+                exporter = DerivaExport(host=self._model.catalog.deriva_server.server, output_dir=tmp_dir)
                 archive_path = exporter.retrieve_file(minid.bag_url)
-                hashes = hash_utils.compute_file_hashes(
-                    archive_path, hashes=["md5", "sha256"]
-                )
+                hashes = hash_utils.compute_file_hashes(archive_path, hashes=["md5", "sha256"])
                 checksum = hashes["sha256"][0]
                 bag_dir = self._cache_dir / f"{minid.dataset_rid}_{checksum}"
                 if bag_dir.exists():
-                    self._logger.info(
-                        f"Using cached bag for  {minid.dataset_rid} Version:{minid.dataset_version}"
-                    )
+                    self._logger.info(f"Using cached bag for  {minid.dataset_rid} Version:{minid.dataset_version}")
                     return Path(bag_dir / f"Dataset_{minid.dataset_rid}")
             bag_path = bdb.extract_bag(archive_path, bag_dir.as_posix())
         bdb.validate_bag_structure(bag_path)
@@ -1166,7 +1155,7 @@ class Dataset:
     def _materialize_dataset_bag(
         self,
         minid: DatasetMinid,
-        execution_rid: Optional[RID] = None,
+        execution_rid: RID | None = None,
     ) -> Path:
         """Materialize a dataset_table bag into a local directory
 
@@ -1180,9 +1169,7 @@ class Dataset:
         def update_status(status: Status, msg: str) -> None:
             """Update the current status for this execution in the catalog"""
             if execution_rid and execution_rid != DRY_RUN_RID:
-                self._model.catalog.getPathBuilder().schemas[
-                    self._ml_schema
-                ].Execution.update(
+                self._model.catalog.getPathBuilder().schemas[self._ml_schema].Execution.update(
                     [
                         {
                             "RID": execution_rid,
@@ -1212,9 +1199,7 @@ class Dataset:
 
         # If this bag has already been validated, our work is done.  Otherwise, materialize the bag.
         if not validated_check.exists():
-            self._logger.info(
-                f"Materializing bag {minid.dataset_rid} Version:{minid.dataset_version}"
-            )
+            self._logger.info(f"Materializing bag {minid.dataset_rid} Version:{minid.dataset_version}")
             bdb.materialize(
                 bag_path.as_posix(),
                 fetch_callback=fetch_progress_callback,
@@ -1225,7 +1210,7 @@ class Dataset:
 
     def _export_annotation(
         self,
-        snapshot_catalog: Optional[DerivaML] = None,
+        snapshot_catalog: DerivaML | None = None,
     ) -> list[dict[str, Any]]:
         """Return and output specification for the datasets in the provided model
 
@@ -1257,7 +1242,7 @@ class Dataset:
         )
 
     def _export_specification(
-        self, dataset: DatasetSpec, snapshot_catalog: Optional[DerivaML] = None
+        self, dataset: DatasetSpec, snapshot_catalog: DerivaML | None = None
     ) -> list[dict[str, Any]]:
         """
         Generate a specification for export engine for specific dataset.
@@ -1273,14 +1258,10 @@ class Dataset:
                 "processor": "json",
                 "processor_params": {"query_path": "/schema", "output_path": "schema"},
             }
-        ] + self._dataset_specification(
-            self._export_specification_dataset_element, dataset, snapshot_catalog
-        )
+        ] + self._dataset_specification(self._export_specification_dataset_element, dataset, snapshot_catalog)
 
     @staticmethod
-    def _export_specification_dataset_element(
-        spath: str, dpath: str, table: Table
-    ) -> list[dict[str, Any]]:
+    def _export_specification_dataset_element(spath: str, dpath: str, table: Table) -> list[dict[str, Any]]:
         """Return the download specification for the data object indicated by a path through the data model.
 
         Args:
@@ -1315,10 +1296,9 @@ class Dataset:
             )
         return exports
 
-    def _export_annotation_dataset_element(
-        self, spath: str, dpath: str, table: Table
-    ) -> list[dict[str, Any]]:
-        """Given a path in the data model, output an export specification for the path taken to get to the current table.
+    def _export_annotation_dataset_element(self, spath: str, dpath: str, table: Table) -> list[dict[str, Any]]:
+        """Given a path in the data model, output an export specification for the path taken to get to the
+        current table.
 
         Args:
           spath: Source path
@@ -1369,7 +1349,7 @@ class Dataset:
         return exports
 
     def _generate_dataset_download_spec(
-        self, dataset: DatasetSpec, snapshot_catalog: Optional[DerivaML] = None
+        self, dataset: DatasetSpec, snapshot_catalog: DerivaML | None = None
     ) -> dict[str, Any]:
         """
         Generate a specification for downloading a specific dataset.
@@ -1472,9 +1452,7 @@ class Dataset:
             else {}
         )
         return {
-            deriva_tags.export_fragment_definitions: {
-                "dataset_export_outputs": self._export_annotation()
-            },
+            deriva_tags.export_fragment_definitions: {"dataset_export_outputs": self._export_annotation()},
             deriva_tags.visible_foreign_keys: self._dataset_visible_fkeys(),
             deriva_tags.export_2019: {
                 "detailed": {