deriva-ml 1.17.10__py3-none-any.whl

deriva_ml/schema/policy.json

@@ -0,0 +1,81 @@
+{
+  "groups": {
+    "isrd-systems": ["https://auth.globus.org/3938e0d0-ed35-11e5-8641-22000ab4b42b"],
+    "isrd-staff": ["https://auth.globus.org/176baec4-ed26-11e5-8e88-22000ab4b42b"],
+    "isrd-testers": ["https://auth.globus.org/9d596ac6-22b9-11e6-b519-22000aef184d"],
+    "eye-ai": ["https://auth.globus.org/d38e6f4d-ac96-11ed-8ab4-7b5a369c0a53"],
+
+    "local-admin": ["admin"],
+    "project-admins":   ["isrd-systems"],
+    "project-writers":  ["isrd-systems", "eye-ai"],
+
+    "project-curators": ["isrd-systems", "local-admin", "eye-ai" ],
+    "project-users":    ["isrd-systems", "local-admin", "eye-ai"],
+
+    "empty": [],
+    "public": ["*"],
+    "admins": [
+      "project-admins",
+      "local-admin",
+      "isrd-systems"
+    ],
+    "curators": ["project-curators"],
+    "writers": ["project-writers"],
+    "writers_and_curators": [
+      "curators",
+      "writers"
+    ],
+    "users": [
+      "isrd-staff",
+      "project-users",
+      "writers_and_curators"
+    ]
+  },
+
+  "acl_definitions": {
+    "read_only": {
+      "select": "users",
+      "enumerate": "users",
+      "insert": "empty",
+      "update": "empty",
+      "delete": "empty"
+    },
+    "self_serve": {
+      "select": "users",
+      "enumerate": "public",
+      "insert": "writers_and_curators",
+      "update": "curators",
+      "delete": "curators",
+      "owner": "admins"
+    }
+  },
+
+  "acl_bindings": {
+    "row_owner_guard": {
+      "types": ["update", "delete"],
+      "projection": ["RCB"],
+      "projection_type": "acl"
+    }
+  },
+
+  "catalog_acl": {
+    "acl": "self_serve"
+  },
+
+  "schema_acls": [
+    {
+      "schema": "public",
+      "acl": "read_only"
+    }
+  ],
+
+  "table_acls": [
+    {
+      "schema_pattern": "^(?!(^public)$).+$",
+      "table_pattern": ".*",
+      "acl_bindings": [
+        "row_owner_guard"
+      ]
+    }
+  ]
+}

deriva_ml/schema/table_comments_utils.py

@@ -0,0 +1,57 @@
+import argparse
+import sys
+from pathlib import Path
+
+from deriva.core import ErmrestCatalog, get_credential
+
+
+def update_table_comments(model, schema_name: str, table_name: str, comments_dir: str) -> None:
+    table = model.schemas[schema_name].tables[table_name]
+    table_comments_dir = Path(comments_dir)/Path(f"{schema_name}/{table_name}")
+    for file in table_comments_dir.iterdir():
+        file_path = table_comments_dir / file.name
+        with file_path.open("r") as f:
+            comment_str = f.read()
+            if file.name.split(".")[0] == table_name:
+                table.comment = comment_str
+            else:
+                table.columns[file.name.split(".")[0]].comment = comment_str
+
+
+def update_schema_comments(model, schema_name: str, comments_dir: str) -> None:
+    schema_comments_dir = Path(comments_dir)/Path(schema_name)
+    for table in schema_comments_dir.iterdir():
+        if not table.name.endswith(".DS_Store"):
+            update_table_comments(model, schema_name, table.name, comments_dir)
+
+
+def main():
+    """Main entry point for the table comments utility CLI.
+    
+    Parses command line arguments and updates table comments.
+    
+    Returns:
+        None. Executes the CLI.
+    """
+    parser = argparse.ArgumentParser(description="Update table comments from files")
+    parser.add_argument("host", help="Hostname")
+    parser.add_argument("catalog_id", help="Catalog ID")
+    parser.add_argument("comments_dir", help="Directory containing comment files")
+    
+    args = parser.parse_args()
+    
+    catalog = ErmrestCatalog("https", args.host, args.catalog_id, credentials=get_credential(args.host))
+    model = catalog.getCatalogModel()
+    
+    # Update comments for all schemas
+    for schema_name in model.schemas:
+        if schema_name not in ["public", "deriva-ml"]:
+            update_schema_comments(model, schema_name, args.comments_dir)
+
+
+if __name__ == '__main__':
+    sys.exit(main())
+
+
+
+# docs/<schema-name>/<table-name>/[table|<column-name>.Md

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-1.17.10.dist-info/METADATA

@@ -0,0 +1,38 @@
+Metadata-Version: 2.4
+Name: deriva-ml
+Version: 1.17.10
+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
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: bump-my-version
+Requires-Dist: bdbag
+Requires-Dist: deriva~=1.7.10
+Requires-Dist: deepdiff
+Requires-Dist: nbconvert
+Requires-Dist: pandas
+Requires-Dist: pydantic>=2.11
+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 is a python library to simplify the process of creating and executing reproducible machine learning workflows
+using a deriva catalog.
+
+
+Complete on-line documentation for DerivaML can be found [here](https://informatics-isi-edu.github.io/deriva-ml/)
+
+To get started using DerivaML, you can clone the [model template repository](https://github.com/informatics-isi-edu/deriva-ml-model-template), and modify it to suite your requirements.
+
+
+## References

deriva_ml-1.17.10.dist-info/RECORD

@@ -0,0 +1,45 @@
+deriva_ml/.DS_Store,sha256=gb-f5IXVed_gS5Be1Z6WxCYjrI_r5SdblvfFpIOY4ro,8196
+deriva_ml/__init__.py,sha256=OqhpZEC9xDpQ1vKNQSb_b0W32LlNGnfAyQaIkOXJNAs,1887
+deriva_ml/bump_version.py,sha256=eN2G5G_OeiuFxhOdjjwfxD8Rmv6dFvzIm0y_1x4Mif4,4020
+deriva_ml/demo_catalog.py,sha256=V0oJRfvAUQG_60-L3yweueKCtIGjDPXTWaAbM1nlOpY,17373
+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
+deriva_ml/core/__init__.py,sha256=Ko8GsWc7K_eDFW0-GaNS6gOWYP8cWHWir-ChSQaHntE,856
+deriva_ml/core/base.py,sha256=uy2wgQ41yakoKy0faRcrg9Z-yQ_t2hFwC_mLkJn3sck,62813
+deriva_ml/core/config.py,sha256=HKo_cTuPWbu-IMm5Nw57Wzn1B_Mhm7Wuiq6HC-Tmt2E,2423
+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=e0D83IEDvsSIx79lKoCsD-CcIFmnoinNtzvpdMMQ80E,7291
+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=7qDcW-ifrUbh6WTx_3TVs6jzZbbwxboz5X8je07jEww,16534
+deriva_ml/execution/__init__.py,sha256=1ngO7avVUqSOS1o09OzS8jFp5mf-rrLxEBHzlIm5R28,706
+deriva_ml/execution/environment.py,sha256=B7nywqxFTRUWgyu8n7rFoKcVC9on422kjeFG2FPQfvg,9302
+deriva_ml/execution/execution.py,sha256=NRu8N-KALUJIhX1YosK3vFijDPF9iwpNzvDU9HokF08,46828
+deriva_ml/execution/execution_configuration.py,sha256=Bxfa_JLbJoEkimRgJ0mDbCKyaKnsSn8j7XON0UbiP4I,5684
+deriva_ml/execution/workflow.py,sha256=moWvtXFzF_z0R44NkMGuBSaiXCqBcnbStU8bc9frkk8,14811
+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=jB6ZIlQVBMRTWOEnQN6XO6gxMNPdN3t4Q3VdDs8c6SE,13130
+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-1.17.10.dist-info/licenses/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
+deriva_ml-1.17.10.dist-info/METADATA,sha256=7QHhRlRwy1V5vclVB-ryN11dHlwdbJ941qaOJt1SDB4,1241
+deriva_ml-1.17.10.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+deriva_ml-1.17.10.dist-info/entry_points.txt,sha256=t4H-1_Cr_MTi9Sp_O4Bnq8d7YFTqLlzuHIxDODTwAt4,513
+deriva_ml-1.17.10.dist-info/top_level.txt,sha256=I1Q1dkH96cRghdsFRVqwpa2M7IqJpR2QPUNNc5-Bnpw,10
+deriva_ml-1.17.10.dist-info/RECORD,,

deriva_ml-1.17.10.dist-info/WHEEL

@@ -0,0 +1,5 @@
+Wheel-Version: 1.0
+Generator: setuptools (80.9.0)
+Root-Is-Purelib: true
+Tag: py3-none-any
+

deriva_ml-1.17.10.dist-info/entry_points.txt

@@ -0,0 +1,9 @@
+[console_scripts]
+bump-version = deriva_ml.bump_version:main
+create-demo-catalog = deriva_ml.demo_catalog:main
+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-notebook = deriva_ml.run_notebook:main
+deriva-ml-table-comments-utils = deriva_ml.schema_setup.table_comments_utils:main

deriva_ml-1.17.10.dist-info/licenses/LICENSE

@@ -0,0 +1,201 @@
+                                 Apache License
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+                        http://www.apache.org/licenses/
+
+   TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
+
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deriva_ml-1.17.10.dist-info/top_level.txt

@@ -0,0 +1 @@
+deriva_ml