deriva-ml 1.14.47__py3-none-any.whl → 1.17.0__py3-none-any.whl

deriva_ml/protocols/dataset.py

@@ -0,0 +1,19 @@
+"""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/run_notebook.py

@@ -3,14 +3,13 @@
 import json
 import os
 import tempfile
-from datetime import datetime
 from pathlib import Path
 
 import nbformat
 import papermill as pm
-import regex as re
 import yaml
 from deriva.core import BaseCLI
+from jupyter_client.kernelspec import KernelSpecManager
 from nbconvert import MarkdownExporter
 
 from deriva_ml import DerivaML, ExecAssetType, Execution, ExecutionConfiguration, MLAsset, Workflow
@@ -44,13 +43,6 @@ class DerivaMLRunNotebookCLI(BaseCLI):
             help="Display logging output from notebook.",
         )
 
-        self.parser.add_argument(
-            "--catalog",
-            metavar="<1>",
-            default=1,
-            help="Catalog number. Default 1",
-        )
-
         self.parser.add_argument(
             "--parameter",
             "-p",
@@ -61,7 +53,13 @@ class DerivaMLRunNotebookCLI(BaseCLI):
             help="Provide a parameter name and value to inject into the notebook.",
         )
 
-        self.parser.add_argument("--kernel", "-k", nargs=1, help="Name of kernel to run..", default=None)
+        self.parser.add_argument(
+            "--kernel",
+            "-k",
+            type=str,
+            help="Name of kernel to run..",
+            default=self._find_kernel_for_venv(),
+        )
 
     @staticmethod
     def _coerce_number(val: str):
@@ -100,26 +98,50 @@ class DerivaMLRunNotebookCLI(BaseCLI):
             print(f"Notebook file must be an ipynb file: {notebook_file.name}.")
             exit(1)
 
-        os.environ["DERIVA_HOST"] = args.host
-        os.environ["DERIVA_CATALOG"] = args.catalog
-
         # Create a workflow instance for this specific version of the script.
         # Return an existing workflow if one is found.
         notebook_parameters = pm.inspect_notebook(notebook_file)
+
         if args.inspect:
             for param, value in notebook_parameters.items():
                 print(f"{param}:{value['inferred_type_name']}  (default {value['default']})")
             return
         else:
-            notebook_parameters = (
-                {k: v["default"] for k, v in notebook_parameters.items()}
-                | {"host": args.host, "hostname": args.host, "catalog_id": args.catalog, "catalog": args.catalog}
-                | parameters
-            )
-            print(f"Running notebook {notebook_file.name} with parameters:")
-            for param, value in notebook_parameters.items():
-                print(f"  {param}:{value}")
-            self.run_notebook(notebook_file.resolve(), parameters, kernel=args.kernel[0], log=args.log_output)
+            notebook_parameters = {k: v["default"] for k, v in notebook_parameters.items()} | parameters
+            self.run_notebook(notebook_file.resolve(), parameters, kernel=args.kernel, log=args.log_output)
+
+    @staticmethod
+    def _find_kernel_for_venv() -> str | None:
+        """
+        Return the name and spec of an existing Jupyter kernel corresponding
+        to a given Python virtual environment path.
+
+        Parameters
+        ----------
+        venv_path : str
+            Absolute or relative path to the virtual environment.
+
+        Returns
+        -------
+        dict | None
+            The kernel spec (as a dict) if found, or None if not found.
+        """
+        venv = os.environ.get("VIRTUAL_ENV")
+        if not venv:
+            return None
+        venv_path = Path(venv).resolve()
+        ksm = KernelSpecManager()
+        for name, spec in ksm.get_all_specs().items():
+            kernel_json = spec.get("spec", {})
+            argv = kernel_json.get("argv", [])
+            # check for python executable path inside argv
+            for arg in argv:
+                try:
+                    if Path(arg).resolve() == venv_path.joinpath("bin", "python").resolve():
+                        return name
+                except Exception:
+                    continue
+        return None
 
     def run_notebook(self, notebook_file: Path, parameters, kernel=None, log=False):
         url, checksum = Workflow.get_url_and_checksum(Path(notebook_file))
@@ -127,8 +149,9 @@ class DerivaMLRunNotebookCLI(BaseCLI):
         os.environ["DERIVA_ML_WORKFLOW_CHECKSUM"] = checksum
         os.environ["DERIVA_ML_NOTEBOOK_PATH"] = notebook_file.as_posix()
         with tempfile.TemporaryDirectory() as tmpdirname:
-            print(f"Running notebook {notebook_file.name} with parameters:")
             notebook_output = Path(tmpdirname) / Path(notebook_file).name
+            execution_rid_path = Path(tmpdirname) / "execution_rid.json"
+            os.environ["DERIVA_ML_SAVE_EXECUTION_RID"] = execution_rid_path.as_posix()
             pm.execute_notebook(
                 input_path=notebook_file,
                 output_path=notebook_output,
@@ -137,22 +160,19 @@ class DerivaMLRunNotebookCLI(BaseCLI):
                 log_output=log,
             )
             print(f"Notebook output saved to {notebook_output}")
-            catalog_id = execution_rid = None
-            with Path(notebook_output).open("r") as f:
-                for line in f:
-                    if m := re.search(
-                        r"Execution RID: https://(?P<host>.*)/id/(?P<catalog_id>.*)/(?P<execution_rid>[\w-]+)",
-                        line,
-                    ):
-                        hostname = m["host"]
-                        catalog_id = m["catalog_id"]
-                        execution_rid = m["execution_rid"]
-            if not execution_rid:
+            with execution_rid_path.open("r") as f:
+                execution_config = json.load(f)
+
+            if not execution_config:
                 print("Execution RID not found.")
                 exit(1)
 
+            execution_rid = execution_config["execution_rid"]
+            hostname = execution_config["hostname"]
+            catalog_id = execution_config["catalog_id"]
+            workflow_rid = execution_config["workflow_rid"]
             ml_instance = DerivaML(hostname=hostname, catalog_id=catalog_id, working_dir=tmpdirname)
-            workflow_rid = ml_instance.retrieve_rid(execution_rid)["Workflow"]
+            workflow_rid = ml_instance.retrieve_rid(execution_config["execution_rid"])["Workflow"]
 
             execution = Execution(
                 configuration=ExecutionConfiguration(workflow=workflow_rid),
@@ -183,21 +203,6 @@ class DerivaMLRunNotebookCLI(BaseCLI):
                 file_name=notebook_output_md,
                 asset_types=ExecAssetType.notebook_output,
             )
-            execution.asset_file_path(
-                asset_name=MLAsset.execution_asset,
-                file_name=notebook_output_md,
-                asset_types=ExecAssetType.notebook_output,
-            )
-            print("parameter....")
-
-            parameter_file = execution.asset_file_path(
-                asset_name=MLAsset.execution_asset,
-                file_name=f"notebook-parameters-{datetime.now().strftime('%Y%m%d-%H%M%S')}.json",
-                asset_types=ExecAssetType.input_file.value,
-            )
-
-            with Path(parameter_file).open("w") as f:
-                json.dump(parameters, f)
             execution.upload_execution_outputs()
 
             print(ml_instance.cite(execution_rid))

deriva_ml/schema/annotations.py

@@ -1,4 +1,5 @@
 import argparse
+import sys
 
 from deriva.core.ermrest_model import Model, Table
 from deriva.core.utils.core_utils import tag as deriva_tags
@@ -183,10 +184,10 @@ def catalog_annotation(model: DerivaModel) -> None:
 
 def asset_annotation(asset_table: Table):
     """Generate annotations for an asset table.
-    
+
     Args:
         asset_table: The Table object representing the asset table.
-        
+
     Returns:
         A dictionary containing the annotations for the asset table.
     """
@@ -316,7 +317,8 @@ def generate_annotation(model: Model, schema: str) -> dict:
                 },
                 {
                     "source": [
-                        {"inbound": [schema, "Execution_Metadata_Execution_fkey"]},
+                        {"inbound": [schema, "Execution_Metadata_Execution_Execution_fkey"]},
+                        {"outbound": [schema, "Execution_Metadata_Execution_Execution_Metadata_fkey"]},
                         "RID",
                     ],
                     "markdown_name": "Execution Metadata",
@@ -453,9 +455,9 @@ def generate_annotation(model: Model, schema: str) -> dict:
 
 def main():
     """Main entry point for the annotations CLI.
-    
+
     Applies annotations to the ML schema based on command line arguments.
-    
+
     Returns:
         None. Executes the CLI.
     """

deriva_ml/test.py

@@ -0,0 +1,94 @@
+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-1.14.47.dist-info → deriva_ml-1.17.0.dist-info}/METADATA

@@ -1,9 +1,9 @@
 Metadata-Version: 2.4
 Name: deriva-ml
-Version: 1.14.47
+Version: 1.17.0
 Summary: Utilities to simplify use of Dervia and Pandas to create reproducable ML pipelines
 Author-email: ISRD <isrd-dev@isi.edu>
-Requires-Python: >=3.10
+Requires-Python: >=3.11
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: bump-my-version
@@ -12,15 +12,18 @@ Requires-Dist: deriva~=1.7.10
 Requires-Dist: deepdiff
 Requires-Dist: nbconvert
 Requires-Dist: pandas
-Requires-Dist: regex~=2024.7.24
+Requires-Dist: pip-system-certs
 Requires-Dist: pydantic>=2.11
-Requires-Dist: semver>3.0.0
-Requires-Dist: setuptools>=64
-Requires-Dist: setuptools-scm>=8.0
-Requires-Dist: nbstripout
 Requires-Dist: papermill
 Requires-Dist: pandas-stubs==2.2.3.250527
 Requires-Dist: pyyaml
+Requires-Dist: regex~=2024.7.24
+Requires-Dist: semver>3.0.0
+Requires-Dist: setuptools>=80
+Requires-Dist: setuptools-scm>=8.0
+Requires-Dist: nbstripout
+Requires-Dist: hydra_zen
+Requires-Dist: SQLAlchemy
 Dynamic: license-file
 
 # DerivaML

deriva_ml-1.17.0.dist-info/RECORD

@@ -0,0 +1,45 @@
+deriva_ml/.DS_Store,sha256=gb-f5IXVed_gS5Be1Z6WxCYjrI_r5SdblvfFpIOY4ro,8196
+deriva_ml/__init__.py,sha256=YCG7P4PUtO_b-aIIYb4KhKHcfnb8Wz_YeAL-c0HiQlA,1775
+deriva_ml/bump_version.py,sha256=eN2G5G_OeiuFxhOdjjwfxD8Rmv6dFvzIm0y_1x4Mif4,4020
+deriva_ml/demo_catalog.py,sha256=FfXPlDfzy29K9g2Fr_KmYyRhmxP2eSaqm8_Xcji8fUM,15352
+deriva_ml/feature.py,sha256=6-aphkxdKjWa9oPSGFWxHcwAc_8hmWj-7I4M178YG5Y,8470
+deriva_ml/install_kernel.py,sha256=b62XY0SLViYO_Zye5r1Pl9qhYZyu_fk4KAO8NS1pxgM,2165
+deriva_ml/run_notebook.py,sha256=_pds1q3WcfWqhCBqKeznbwSv5n7OND8FkL6JQ2Jkfmc,8093
+deriva_ml/test.py,sha256=BqmQXR9IyQP9h8pWttk0dzyJod2CwcfYbSUZS-Q5r4k,4460
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+deriva_ml/core/base.py,sha256=KzZW310J0YmvCUhuCWxd42LNCM_JSzR__ObtT7zgcsU,62525
+deriva_ml/core/config.py,sha256=dF4rOLFmbk1DEkQimqbiH4pC519nRZWpwKItARNMiZ4,2244
+deriva_ml/core/constants.py,sha256=6wBJ8qMxe-dbCjRGrjUIX-RK0mTWrLDTeUpaVbLFoM8,888
+deriva_ml/core/definitions.py,sha256=uq_8uYFBVBVHS691Ri2kdQsN37z0GNYTaZskJIb_ocM,1385
+deriva_ml/core/enums.py,sha256=sSN4B4OynbB-AXwxRszoFr-KWIWIAfhVa06EzAEHwVc,7194
+deriva_ml/core/ermrest.py,sha256=N0IJ3TE87jElaBChEIo5AFDTr0SIrb6F90yiimRfPr4,10182
+deriva_ml/core/exceptions.py,sha256=4MZNPOyN-UMaGeY9sqJDVwh_iOmz1ntp4usSyCNqVMg,934
+deriva_ml/core/filespec.py,sha256=BQAAcRXfXq1lDcsKlokLOOXCBtEZpPgXxrFOIZYAgLg,4229
+deriva_ml/dataset/__init__.py,sha256=wTCQaWGfRYEiUoOOxerKSpkbl1T5YFhoCyemlxGTk8k,283
+deriva_ml/dataset/aux_classes.py,sha256=ojqe7gyK4KQVz_xfIillXS_HJ1PMsyr47pb2tFOXO_c,7855
+deriva_ml/dataset/dataset.py,sha256=d860WuCL0-Pz6TyRpGVzhpPWDMco01-I5LT4dZjYxsQ,64728
+deriva_ml/dataset/dataset_bag.py,sha256=ori3BuYVqfeHkVCjNSKuZh7oMdC6uufsszicpTPODiw,19944
+deriva_ml/dataset/history.py,sha256=FK5AYYz11p4E4FWMVg4r7UPWOD4eobrq3b3xMjWF59g,3197
+deriva_ml/dataset/upload.py,sha256=n1aXSbOx1hghCDxuF8yf03jZmOLMueXL-rSnQMrfHq0,16535
+deriva_ml/execution/__init__.py,sha256=5kKpPwQbxhmRn7Npz7DpavuCxYwCQaDdl4-6z62hbds,705
+deriva_ml/execution/environment.py,sha256=B7nywqxFTRUWgyu8n7rFoKcVC9on422kjeFG2FPQfvg,9302
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+deriva_ml/execution/workflow.py,sha256=rTlspICp2Q6prUwPCeukjhO64rbcJivcFs4zH60B16U,13906
+deriva_ml/model/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+deriva_ml/model/catalog.py,sha256=O6_Ll4Uxg6DyxoBXT9P9CPTt9jx1guVTeX1L3KW1A5c,19645
+deriva_ml/model/database.py,sha256=BG5FSisl9tWTBnf5k9dNnijOIDyCUDeRhN_inkmIqTw,31132
+deriva_ml/protocols/dataset.py,sha256=1TyaT--89Elcs-nCvVyJxUj4cDaLztZOuSOzzj1cBMk,699
+deriva_ml/schema/__init__.py,sha256=yV-MfzCF3FA4OOz7mZwMM2q6-x1vgOJ057kUvikFF6E,130
+deriva_ml/schema/annotations.py,sha256=CMcRqYUlyW8iLCYp6sYJsncaRNtp4kFKoxcg-i-t-50,18302
+deriva_ml/schema/check_schema.py,sha256=6dadLYHPqRex6AYVClmsESI8WhC7-rb-XnGf2G298xw,3609
+deriva_ml/schema/create_schema.py,sha256=9qK9_8SRQT-DwcEwTGSkhi3j2NaoH5EVgthvV2kO-gg,13042
+deriva_ml/schema/deriva-ml-reference.json,sha256=AEOMIgwKO3dNMMWHb0lxaXyamvfAEbUPh8qw0aAtsUQ,242460
+deriva_ml/schema/policy.json,sha256=5ykB8nnZFl-oCHzlAwppCFKJHWJFIkYognUMVEanfY8,1826
+deriva_ml/schema/table_comments_utils.py,sha256=4flCqnZAaqg_uSZ9I18pNUWAZoLfmMCXbmI5uERY5vM,2007
+deriva_ml-1.17.0.dist-info/licenses/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
+deriva_ml-1.17.0.dist-info/METADATA,sha256=gvz8ApFj8xylH1r4Nr-X_QiHChj6wRNJE7pLzI2sB8E,1272
+deriva_ml-1.17.0.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
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+deriva_ml-1.17.0.dist-info/top_level.txt,sha256=I1Q1dkH96cRghdsFRVqwpa2M7IqJpR2QPUNNc5-Bnpw,10
+deriva_ml-1.17.0.dist-info/RECORD,,

deriva_ml/model/sql_mapper.py

@@ -1,44 +0,0 @@
-from datetime import datetime, timezone
-from typing import TYPE_CHECKING, Any, Sequence
-
-if TYPE_CHECKING:
-    from deriva_ml.model.database import DatabaseModel
-
-try:
-    from icecream import ic
-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
-
-
-class SQLMapper:
-    def __init__(self, database: "DatabaseModel", table: str) -> None:
-        table_name = database.normalize_table_name(table)
-        schema, table = table_name.split(":")
-
-        with database.dbase as dbase:
-            self.col_names = [c[1] for c in dbase.execute(f'PRAGMA table_info("{table_name}")').fetchall()]
-
-        self.boolean_columns = [
-            self.col_names.index(c.name)
-            for c in database.model.schemas[schema].tables[table].columns
-            if c.type.typename == "boolean"
-        ]
-        self.time_columns = [
-            self.col_names.index(c.name)
-            for c in database.model.schemas[schema].tables[table].columns
-            if c.type.typename in ["ermrest_rct", "ermrest_rmt"]
-        ]
-
-    def _map_value(self, idx: int, v: Any) -> Any:
-        """
-        Return a new value based on `data` where, for each index in `idxs`,
-        """
-        tf_map = {"t": True, "f": False}
-        if idx in self.boolean_columns:
-            return tf_map.get(v, v)
-        if idx in self.time_columns:
-            return datetime.strptime(v, "%Y-%m-%d %H:%M:%S.%f+00").replace(tzinfo=timezone.utc).isoformat()
-        return v
-
-    def transform_tuple(self, data: Sequence[Any]) -> Any:
-        return dict(zip(self.col_names, tuple(self._map_value(i, v) for i, v in enumerate(data))))

deriva_ml-1.14.47.dist-info/RECORD

@@ -1,42 +0,0 @@
-deriva_ml/__init__.py,sha256=_aMdxGG4mRTcXodLZLNpXqH8v5uqMbqFUryE9KqNSB8,1158
-deriva_ml/bump_version.py,sha256=eN2G5G_OeiuFxhOdjjwfxD8Rmv6dFvzIm0y_1x4Mif4,4020
-deriva_ml/demo_catalog.py,sha256=JjPAIac_hKPh5krEhGJydjXquRnivi7kQoR8W4Khp-s,14928
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