deriva-ml 1.17.10__py3-none-any.whl → 1.17.11__py3-none-any.whl

deriva_ml-1.17.11.dist-info/RECORD

@@ -0,0 +1,77 @@
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+deriva_ml-1.17.11.dist-info/RECORD,,

{deriva_ml-1.17.10.dist-info → deriva_ml-1.17.11.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (80.9.0)
+Generator: setuptools (80.10.2)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

{deriva_ml-1.17.10.dist-info → deriva_ml-1.17.11.dist-info}/entry_points.txt

@@ -5,5 +5,6 @@ deriva-ml-alter-annotation = deriva_ml.schema_setup.alter_annotation:main
 deriva-ml-check-catalog-schema = deriva_ml.schema.check_schema:main
 deriva-ml-create-schema = deriva_ml.schema_setup.create_schema:main
 deriva-ml-install-kernel = deriva_ml.install_kernel:main
+deriva-ml-run = deriva_ml.run_model:main
 deriva-ml-run-notebook = deriva_ml.run_notebook:main
 deriva-ml-table-comments-utils = deriva_ml.schema_setup.table_comments_utils:main

deriva_ml/protocols/dataset.py

@@ -1,19 +0,0 @@
-"""A module defining the DatasetLike protocol for dataset operations.
-
-This module contains the definition of the DatasetLike protocol, which
-provides an interface for datasets to implement specific functionality related
-to listing dataset children. It is particularly useful for ensuring type
-compatibility for objects that mimic datasets in their behavior.
-
-Classes:
-    DatasetLike: A protocol that specifies methods required for dataset-like
-    objects.
-"""
-from typing import Protocol, runtime_checkable
-
-from deriva_ml.core.definitions import RID
-
-
-@runtime_checkable
-class DatasetLike(Protocol):
-    def list_dataset_children(self, dataset_rid: RID, recurse: bool = False) -> list[RID]: ...

deriva_ml/test.py

@@ -1,94 +0,0 @@
-from typing import Any, Type
-from deriva_ml import RID
-from sqlalchemy import UniqueConstraint, inspect
-from collections import defaultdict
-from graphlib import CycleError, TopologicalSorter
-
-def _prepare_wide_table(self, dataset, dataset_rid: RID, include_tables: list[str]) -> tuple:
-    """
-    Generates details of a wide table from the model
-
-    Args:
-        include_tables (list[str] | None): List of table names to include in the denormalized dataset. If None,
-            all tables from the dataset will be included.
-
-    Returns:
-        str: SQL query string that represents the process of denormalization.
-    """
-
-    # Skip over tables that we don't want to include in the denormalized dataset.
-    # Also, strip off the Dataset/Dataset_X part of the path so we don't include dataset columns in the denormalized
-    # table.
-    include_tables = set(include_tables)
-    for t in include_tables:
-        # Check to make sure the table is in the catalog.
-        _ = self.name_to_table(t)
-
-    table_paths = [
-        path
-        for path in self._schema_to_paths()
-        if path[-1].name in include_tables and include_tables.intersection({p.name for p in path})
-    ]
-    paths_by_element = defaultdict(list)
-    for p in table_paths:
-        paths_by_element[p[2].name].append(p)
-
-    # Get the names of all of the tables that can be dataset elements.
-    dataset_element_tables = {e.name for e in self.list_dataset_element_types() if e.schema.name == self.domain_schema}
-
-    skip_columns = {"RCT", "RMT", "RCB", "RMB"}
-    join_conditions = {}
-    join_tables = {}
-    for element_table, paths in paths_by_element.items():
-        graph = {}
-        for path in paths:
-            for left, right in zip(path[0:], path[1:]):
-                graph.setdefault(left.name, set()).add(right.name)
-
-        # New lets remove any cycles that we may have in the graph.
-        # We will use a topological sort to find the order in which we need to join the tables.
-        # If we find a cycle, we will remove the table from the graph and splice in an additional ON clause.
-        # We will then repeat the process until there are no cycles.
-        graph_has_cycles = True
-        element_join_tables = []
-        element_join_conditions = {}
-        while graph_has_cycles:
-            try:
-                ts = TopologicalSorter(graph)
-                element_join_tables = list(reversed(list(ts.static_order())))
-                graph_has_cycles = False
-            except CycleError as e:
-                cycle_nodes = e.args[1]
-                if len(cycle_nodes) > 3:
-                    raise DerivaMLException(f"Unexpected cycle found when normalizing dataset {cycle_nodes}")
-                # Remove cycle from graph and splice in additional ON constraint.
-                graph[cycle_nodes[1]].remove(cycle_nodes[0])
-
-    # The Dataset_Version table is a special case as it points to dataset and dataset to version.
-        if "Dataset_Version" in join_tables:
-            element_join_tables.remove("Dataset_Version")
-
-        for path in paths:
-            for left, right in zip(path[0:], path[1:]):
-                if right.name == "Dataset_Version":
-                    # The Dataset_Version table is a special case as it points to dataset and dataset to version.
-                    continue
-                if element_join_tables.index(right.name) < element_join_tables.index(left.name):
-                    continue
-                table_relationship = self._table_relationship(left, right)
-                element_join_conditions.setdefault(right.name, set()).add((table_relationship[0], table_relationship[1]))
-        join_tables[element_table] = element_join_tables
-        join_conditions[element_table] = element_join_conditions
-    # Get the list of columns that will appear in the final denormalized dataset.
-    denormalized_columns = [
-        (table_name, c.name)
-        for table_name in join_tables
-        if not self.is_association(table_name)  # Don't include association columns in the denormalized view.'
-        for c in self.name_to_table(table_name).columns
-        if (not include_tables or table_name in include_tables) and (c.name not in skip_columns)
-    ]
-
-    # List of dataset ids to include in the denormalized view.
-    dataset_rids = [dataset_rid] + dataset.list_dataset_children(recurse=True)
-    return join_tables, join_conditions, denormalized_columns, dataset_rids, dataset_element_tables
-

deriva_ml-1.17.10.dist-info/RECORD

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