deriva-ml 1.13.0__py3-none-any.whl → 1.13.1__py3-none-any.whl

deriva_ml/__init__.py

@@ -15,7 +15,7 @@ __all__ = [
     "UploadState",
     "MLVocab",
     "MLAsset",
-    "ExecMetadataVocab",
+    "ExecAssetType",
     "RID",
     "DerivaSystemColumns",
     "VersionPart",
@@ -34,7 +34,7 @@ from .deriva_definitions import (
     DerivaMLException,
     MLVocab,
     MLAsset,
-    ExecMetadataVocab,
+    ExecAssetType,
     DerivaSystemColumns,
 )
 from .deriva_ml_base import DerivaML

deriva_ml/deriva_definitions.py

@@ -197,7 +197,7 @@ class MLAsset(StrEnum):
     execution_asset = "Execution_Asset"
 
 
-class ExecMetadataVocab(StrEnum):
+class ExecMetadataType(StrEnum):
     """
     Predefined execution metadata types.
     """
@@ -206,6 +206,16 @@ class ExecMetadataVocab(StrEnum):
     runtime_env = "Runtime_Env"
 
 
+class ExecAssetType(StrEnum):
+    """
+    Predefined execution metadata types.
+    """
+
+    input_file = "Input_File"
+    output_file = "Output_File"
+    notebook_output = "Notebook_Output"
+
+
 class ColumnDefinition(BaseModel):
     """Pydantic model for deriva_py Column.define"""
 

deriva_ml/execution.py

@@ -20,7 +20,6 @@ from typing import Iterable, Any, Optional
 from deriva.core import format_exception
 from deriva.core.datapath import DataPathException
 from deriva.core.hatrac_store import HatracStore
-from .deriva_definitions import ExecMetadataVocab
 from .deriva_definitions import (
     RID,
     Status,
@@ -28,6 +27,8 @@ from .deriva_definitions import (
     DerivaMLException,
     MLVocab,
     MLAsset,
+    ExecMetadataType,
+    ExecAssetType,
     DRY_RUN_RID,
 )
 from .deriva_ml_base import DerivaML, FeatureRecord
@@ -237,9 +238,9 @@ class Execution:
 
     def _save_runtime_environment(self):
         runtime_env_path = self.asset_file_path(
-            asset_name="Execution_Metadata",
-            file_name=f"environment_snapshot_{datetime.now().strftime('%Y%m%d_%H%M%S')}.txt",
-            asset_types=ExecMetadataVocab.runtime_env.value,
+            "Execution_Metadata",
+            f"environment_snapshot_{datetime.now().strftime('%Y%m%d_%H%M%S')}.txt",
+            ExecMetadataType.runtime_env.value,
         )
         with open(runtime_env_path, "w") as fp:
             json.dump(get_execution_environment(), fp)
@@ -296,15 +297,19 @@ class Execution:
         # Save configuration details for later upload
         if not reload:
             cfile = self.asset_file_path(
-                asset_name=MLAsset.execution_metadata,
-                file_name="configuration.json",
-                asset_types=ExecMetadataVocab.execution_config.value,
+                MLAsset.execution_metadata,
+                "configuration.json",
+                ExecMetadataType.execution_config.value,
             )
             with open(cfile.as_posix(), "w", encoding="utf-8") as config_file:
                 json.dump(self.configuration.model_dump(), config_file)
 
             for parameter_file in self.configuration.parameters:
-                self.asset_file_path(MLAsset.execution_assets, parameter_file)
+                self.asset_file_path(
+                    MLAsset.execution_asset,
+                    parameter_file,
+                    ExecAssetType.input_file.value,
+                )
 
             # save runtime env
             self._save_runtime_environment()

deriva_ml/execution_configuration.py

@@ -264,7 +264,7 @@ class Workflow(BaseModel):
             checksum = os.environ["DERIVA_ML_WORKFLOW_CHECKSUM"]
             is_notebook = True
         else:
-            path, is_notebook = Workflow._get_notebook_path()
+            path, is_notebook = Workflow._get_python_script()
             github_url, checksum = Workflow.get_url_and_checksum(path)
 
         return Workflow(
@@ -332,7 +332,7 @@ class ExecutionConfiguration(BaseModel):
     datasets: conlist(DatasetSpec) = []
     assets: list[RID | str] = []  # List of RIDs to model files.
     workflow: RID | Workflow
-    parameters: dict[str, Any] = {}
+    parameters: dict[str, Any] | Path = {}
     description: str = ""
     argv: conlist(str) = Field(default_factory=lambda: sys.argv)
 
@@ -341,7 +341,7 @@ class ExecutionConfiguration(BaseModel):
     @field_validator("parameters", mode="before")
     @classmethod
     def validate_parameters(cls, value: Any) -> Any:
-        """If parameter is a file, assume that it has JSON contents for configuration parameters"""
+        """If a parameter is a file, assume that it has JSON contents for configuration parameters"""
         if isinstance(value, str) or isinstance(value, Path):
             with open(value, "r") as f:
                 return json.load(f)

deriva_ml/run_notebook.py

@@ -1,5 +1,6 @@
 """Module to run a notebook using papermill"""
 
+from datetime import datetime
 import json
 import os
 import papermill as pm
@@ -7,9 +8,9 @@ from pathlib import Path
 import regex as re
 import tempfile
 
-from deriva_ml import Workflow, DerivaML, MLVocab
+from deriva_ml import Workflow, DerivaML
 from deriva.core import BaseCLI
-from deriva_ml import MLAsset
+from deriva_ml import MLAsset, ExecAssetType
 
 
 class DerivaMLRunNotebookCLI(BaseCLI):
@@ -36,6 +37,19 @@ class DerivaMLRunNotebookCLI(BaseCLI):
             help="Display parameters information for the given notebook path.",
         )
 
+        self.parser.add_argument(
+            "--log-output",
+            action="store_false",
+            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",
@@ -43,7 +57,7 @@ class DerivaMLRunNotebookCLI(BaseCLI):
             action="append",
             metavar=("KEY", "VALUE"),
             default=[],
-            help="Provide a parameter name band value to inject into the notebook.",
+            help="Provide a parameter name and value to inject into the notebook.",
         )
 
         self.parser.add_argument(
@@ -84,19 +98,24 @@ class DerivaMLRunNotebookCLI(BaseCLI):
             print("Notebook file must be an ipynb file.")
             exit(1)
 
+        os.environ["DERIVA_HOST"] = args.host
+        os.environ["DERIVA_CATALOG_ID"] = 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:
+            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()
-            } | parameters
-            print(f"Running notebook {notebook_file.name} with paremeters:")
+            notebook_parameters = (
+                {"host": args.host, "catalog": args.catalog}
+                | {k: v["default"] for k, v in notebook_parameters.items()}
+                | 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, args.kernel)
@@ -121,7 +140,7 @@ class DerivaMLRunNotebookCLI(BaseCLI):
                         r"Execution RID: https://(?P<host>.*)/id/(?P<catalog_id>.*)/(?P<execution_rid>[\w-]+)",
                         line,
                     ):
-                        host = m["host"]
+                        hostname = m["host"]
                         catalog_id = m["catalog_id"]
                         execution_rid = m["execution_rid"]
             if not execution_rid:
@@ -129,19 +148,24 @@ class DerivaMLRunNotebookCLI(BaseCLI):
                 exit(1)
             print("Uploaded notebook output for Execution RID:", execution_rid)
 
-            ml_instance = DerivaML(hostname=host, catalog_id=catalog_id)
-            ml_instance.add_term(
-                MLVocab.asset_type,
-                "Notebook_Output",
-                description="Jupyter Notebook Output",
-            )
+            ml_instance = DerivaML(hostname=hostname, catalog_id=catalog_id)
+
             execution = ml_instance.restore_execution(execution_rid)
             execution.asset_file_path(
                 asset_name=MLAsset.execution_asset,
                 file_name=notebook_output,
-                asset_types=["Notebook_Output"],
+                asset_types=ExecAssetType.notebook_output,
             )
+            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 open(parameter_file, "w") as f:
+                json.dump(parameters, f)
+
             execution.upload_execution_outputs()
+            print(ml_instance.cite(execution_rid))
 
 
 def main():

deriva_ml/test-files/execution-parameters.json

@@ -0,0 +1 @@
+{"local-file": "My local file.txt"}

deriva_ml/test-files/notebook-parameters.json

@@ -0,0 +1,5 @@
+{
+  "assets": ["2-7J8M"],
+  "datasets": ["2-7K8W"],
+  "parameters": "test-files/execution-parameters.json"
+}

deriva_ml/test_notebook.ipynb

@@ -3,15 +3,21 @@
   {
    "cell_type": "code",
    "id": "0",
-   "metadata": {},
+   "metadata": {
+    "ExecuteTime": {
+     "end_time": "2025-04-18T22:52:49.930351Z",
+     "start_time": "2025-04-18T22:52:48.926842Z"
+    }
+   },
    "source": [
     "import builtins\n",
+    "import os\n",
+    "\n",
     "from deriva.core.utils.globus_auth_utils import GlobusNativeLogin\n",
-    "from deriva_ml import ExecutionConfiguration, MLVocab, DerivaSystemColumns, DatasetSpec, DerivaML, Workflow\n",
-    "from deriva_ml.demo_catalog import create_demo_catalog, DemoML"
+    "from deriva_ml import ExecutionConfiguration, MLVocab, DerivaML, DatasetSpec"
    ],
    "outputs": [],
-   "execution_count": null
+   "execution_count": 1
   },
   {
    "cell_type": "code",
@@ -19,36 +25,61 @@
    "metadata": {
     "tags": [
      "parameters"
-    ]
+    ],
+    "ExecuteTime": {
+     "end_time": "2025-04-18T22:52:49.988873Z",
+     "start_time": "2025-04-18T22:52:49.986713Z"
+    }
    },
    "source": [
     "foo: int = 1\n",
-    "bar: str = \"hello\"\n",
-    "list_parameter: list[float] = [1, 2, 3]"
+    "assets = []\n",
+    "datasets = []\n",
+    "parameters = None"
    ],
    "outputs": [],
-   "execution_count": null
+   "execution_count": 2
   },
   {
-   "metadata": {},
+   "metadata": {
+    "ExecuteTime": {
+     "end_time": "2025-04-18T22:52:50.002808Z",
+     "start_time": "2025-04-18T22:52:49.999450Z"
+    }
+   },
    "cell_type": "code",
-   "outputs": [],
-   "execution_count": null,
    "source": [
-    "print('foo', foo)\n",
-    "print('bar', bar)\n",
-    "print('list_parameter', list_parameter)"
+    "print(\"foo\", foo)\n",
+    "print(\"assets\", assets)\n",
+    "print(\"datasets\", datasets)\n",
+    "print(\"parameters\", parameters)"
    ],
-   "id": "70b23cdd933ce669"
+   "id": "70b23cdd933ce669",
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "foo 1\n",
+      "assets []\n",
+      "datasets []\n",
+      "parameters None\n"
+     ]
+    }
+   ],
+   "execution_count": 3
   },
   {
-   "metadata": {},
+   "metadata": {
+    "ExecuteTime": {
+     "end_time": "2025-04-18T22:52:50.344660Z",
+     "start_time": "2025-04-18T22:52:50.013816Z"
+    }
+   },
    "cell_type": "code",
-   "outputs": [],
-   "execution_count": null,
    "source": [
-    "hostname = 'dev.eye-ai.org'\n",
-    "domain_schema = 'eye-ai'\n",
+    "hostname = os.environ.get(\"DERIVA_HOST\") #or \"dev.eye-ai.org\"\n",
+    "catalog_id = os.environ.get(\"DERIVA_CATALOG_ID\") #or 'eye-ai'\n",
     "\n",
     "gnl = GlobusNativeLogin(host=hostname)\n",
     "if gnl.is_logged_in([hostname]):\n",
@@ -57,15 +88,31 @@
     "    gnl.login([hostname], no_local_server=True, no_browser=True, refresh_tokens=True, update_bdbag_keychain=True)\n",
     "    print(\"Login Successful\")\n"
    ],
-   "id": "2"
+   "id": "2",
+   "outputs": [
+    {
+     "ename": "AttributeError",
+     "evalue": "'NoneType' object has no attribute 'lower'",
+     "output_type": "error",
+     "traceback": [
+      "\u001B[0;31m---------------------------------------------------------------------------\u001B[0m",
+      "\u001B[0;31mAttributeError\u001B[0m                            Traceback (most recent call last)",
+      "Cell \u001B[0;32mIn[4], line 5\u001B[0m\n\u001B[1;32m      2\u001B[0m catalog_id \u001B[38;5;241m=\u001B[39m os\u001B[38;5;241m.\u001B[39menviron\u001B[38;5;241m.\u001B[39mget(\u001B[38;5;124m\"\u001B[39m\u001B[38;5;124mDERIVA_CATALOG_ID\u001B[39m\u001B[38;5;124m\"\u001B[39m) \u001B[38;5;66;03m#or 'eye-ai'\u001B[39;00m\n\u001B[1;32m      4\u001B[0m gnl \u001B[38;5;241m=\u001B[39m GlobusNativeLogin(host\u001B[38;5;241m=\u001B[39mhostname)\n\u001B[0;32m----> 5\u001B[0m \u001B[38;5;28;01mif\u001B[39;00m \u001B[43mgnl\u001B[49m\u001B[38;5;241;43m.\u001B[39;49m\u001B[43mis_logged_in\u001B[49m\u001B[43m(\u001B[49m\u001B[43m[\u001B[49m\u001B[43mhostname\u001B[49m\u001B[43m]\u001B[49m\u001B[43m)\u001B[49m:\n\u001B[1;32m      6\u001B[0m     \u001B[38;5;28mprint\u001B[39m(\u001B[38;5;124m\"\u001B[39m\u001B[38;5;124mYou are already logged in.\u001B[39m\u001B[38;5;124m\"\u001B[39m)\n\u001B[1;32m      7\u001B[0m \u001B[38;5;28;01melse\u001B[39;00m:\n",
+      "File \u001B[0;32m~/opt/anaconda3/envs/deriva-test/lib/python3.10/site-packages/deriva/core/utils/globus_auth_utils.py:582\u001B[0m, in \u001B[0;36mGlobusNativeLogin.is_logged_in\u001B[0;34m(self, hosts, requested_scopes, hosts_to_scope_map, exclude_defaults)\u001B[0m\n\u001B[1;32m    576\u001B[0m \u001B[38;5;28;01mdef\u001B[39;00m\u001B[38;5;250m \u001B[39m\u001B[38;5;21mis_logged_in\u001B[39m(\u001B[38;5;28mself\u001B[39m,\n\u001B[1;32m    577\u001B[0m                  hosts\u001B[38;5;241m=\u001B[39m\u001B[38;5;28;01mNone\u001B[39;00m,\n\u001B[1;32m    578\u001B[0m                  requested_scopes\u001B[38;5;241m=\u001B[39m(),\n\u001B[1;32m    579\u001B[0m                  hosts_to_scope_map\u001B[38;5;241m=\u001B[39m\u001B[38;5;28;01mNone\u001B[39;00m,\n\u001B[1;32m    580\u001B[0m                  exclude_defaults\u001B[38;5;241m=\u001B[39m\u001B[38;5;28;01mFalse\u001B[39;00m):\n\u001B[1;32m    581\u001B[0m     scopes \u001B[38;5;241m=\u001B[39m \u001B[38;5;28mset\u001B[39m(requested_scopes)\n\u001B[0;32m--> 582\u001B[0m     scope_map \u001B[38;5;241m=\u001B[39m hosts_to_scope_map \u001B[38;5;28;01mif\u001B[39;00m hosts_to_scope_map \u001B[38;5;28;01melse\u001B[39;00m \u001B[38;5;28;43mself\u001B[39;49m\u001B[38;5;241;43m.\u001B[39;49m\u001B[43mhosts_to_scope_map\u001B[49m\u001B[43m(\u001B[49m\u001B[43mhosts\u001B[49m\u001B[43m \u001B[49m\u001B[38;5;129;43;01mor\u001B[39;49;00m\u001B[43m \u001B[49m\u001B[38;5;28;43mself\u001B[39;49m\u001B[38;5;241;43m.\u001B[39;49m\u001B[43mhosts\u001B[49m\u001B[43m)\u001B[49m\n\u001B[1;32m    583\u001B[0m     scopes\u001B[38;5;241m.\u001B[39mupdate(\u001B[38;5;28mself\u001B[39m\u001B[38;5;241m.\u001B[39mscope_set_from_scope_map(scope_map))\n\u001B[1;32m    584\u001B[0m     \u001B[38;5;28;01mif\u001B[39;00m \u001B[38;5;129;01mnot\u001B[39;00m exclude_defaults:\n",
+      "File \u001B[0;32m~/opt/anaconda3/envs/deriva-test/lib/python3.10/site-packages/deriva/core/utils/globus_auth_utils.py:607\u001B[0m, in \u001B[0;36mGlobusNativeLogin.hosts_to_scope_map\u001B[0;34m(self, hosts, match_scope_tag, all_tagged_scopes, force_refresh, warn_on_discovery_failure)\u001B[0m\n\u001B[1;32m    605\u001B[0m \u001B[38;5;28;01mfor\u001B[39;00m host \u001B[38;5;129;01min\u001B[39;00m hosts:\n\u001B[1;32m    606\u001B[0m     scope_map\u001B[38;5;241m.\u001B[39mupdate({host: []})\n\u001B[0;32m--> 607\u001B[0m     scopes \u001B[38;5;241m=\u001B[39m \u001B[43mget_oauth_scopes_for_host\u001B[49m\u001B[43m(\u001B[49m\u001B[43mhost\u001B[49m\u001B[43m,\u001B[49m\n\u001B[1;32m    608\u001B[0m \u001B[43m                                       \u001B[49m\u001B[43mconfig_file\u001B[49m\u001B[38;5;241;43m=\u001B[39;49m\u001B[38;5;28;43mself\u001B[39;49m\u001B[38;5;241;43m.\u001B[39;49m\u001B[43mconfig_file\u001B[49m\u001B[43m,\u001B[49m\n\u001B[1;32m    609\u001B[0m \u001B[43m                                       \u001B[49m\u001B[43mforce_refresh\u001B[49m\u001B[38;5;241;43m=\u001B[39;49m\u001B[43mforce_refresh\u001B[49m\u001B[43m,\u001B[49m\n\u001B[1;32m    610\u001B[0m \u001B[43m                                       \u001B[49m\u001B[43mwarn_on_discovery_failure\u001B[49m\u001B[38;5;241;43m=\u001B[39;49m\u001B[43mwarn_on_discovery_failure\u001B[49m\u001B[43m)\u001B[49m\n\u001B[1;32m    611\u001B[0m     scope_list \u001B[38;5;241m=\u001B[39m \u001B[38;5;28mlist\u001B[39m()\n\u001B[1;32m    612\u001B[0m     \u001B[38;5;28;01mif\u001B[39;00m scopes:\n",
+      "File \u001B[0;32m~/opt/anaconda3/envs/deriva-test/lib/python3.10/site-packages/deriva/core/utils/core_utils.py:300\u001B[0m, in \u001B[0;36mget_oauth_scopes_for_host\u001B[0;34m(host, config_file, force_refresh, warn_on_discovery_failure)\u001B[0m\n\u001B[1;32m    298\u001B[0m \u001B[38;5;28;01mif\u001B[39;00m required_scopes:\n\u001B[1;32m    299\u001B[0m     \u001B[38;5;28;01mfor\u001B[39;00m hostname, scopes \u001B[38;5;129;01min\u001B[39;00m required_scopes\u001B[38;5;241m.\u001B[39mitems():\n\u001B[0;32m--> 300\u001B[0m         \u001B[38;5;28;01mif\u001B[39;00m \u001B[43mhost\u001B[49m\u001B[38;5;241;43m.\u001B[39;49m\u001B[43mlower\u001B[49m() \u001B[38;5;241m==\u001B[39m hostname\u001B[38;5;241m.\u001B[39mlower():\n\u001B[1;32m    301\u001B[0m             result \u001B[38;5;241m=\u001B[39m scopes\n\u001B[1;32m    302\u001B[0m             \u001B[38;5;28;01mbreak\u001B[39;00m\n",
+      "\u001B[0;31mAttributeError\u001B[0m: 'NoneType' object has no attribute 'lower'"
+     ]
+    }
+   ],
+   "execution_count": 4
   },
   {
    "cell_type": "code",
    "id": "3",
    "metadata": {},
    "source": [
-    "ml_instance = DemoML(hostname, domain_schema)\n",
-    "print(f'Creating catalog at {ml_instance.catalog_id}')\n",
+    "ml_instance = DerivaML(hostname, catalog_id)\n",
     "\n",
     "ml_instance.add_term(MLVocab.workflow_type, \"Manual Workflow\", description=\"Initial setup of Model File\")\n",
     "ml_instance.add_term(MLVocab.asset_type, \"API_Model\", description=\"Model for our API workflow\")"
@@ -92,12 +139,38 @@
    "id": "6",
    "metadata": {},
    "source": [
-    "manual_execution = ml_instance.create_execution(ExecutionConfiguration( description=\"Sample Execution\", workflow=api_workflow))\n",
-    "manual_execution.upload_execution_outputs()\n",
-    "# Now lets create model configuration for our program."
+    "manual_execution = ml_instance.create_execution(\n",
+    "    ExecutionConfiguration(\n",
+    "        description=\"Sample Execution\",\n",
+    "        workflow=api_workflow,\n",
+    "        datasets=[DatasetSpec(rid=ds, version=ml_instance.dataset_version(ds)) for ds in datasets],\n",
+    "        assets=assets,\n",
+    "        parameters=parameters\n",
+    "    )\n",
+    ")"
    ],
    "outputs": [],
    "execution_count": null
+  },
+  {
+   "metadata": {},
+   "cell_type": "code",
+   "source": [
+    "print(f'parameters: {manual_execution.parameters}')\n",
+    "print(f'datasets: {manual_execution.datasets}')\n",
+    "print(f'assets: {manual_execution.asset_paths}')"
+   ],
+   "id": "4b2a3b8c16333645",
+   "outputs": [],
+   "execution_count": null
+  },
+  {
+   "metadata": {},
+   "cell_type": "code",
+   "source": "manual_execution.upload_execution_outputs()",
+   "id": "efa8cb1b0ed438bb",
+   "outputs": [],
+   "execution_count": null
   }
  ],
  "metadata": {

{deriva_ml-1.13.0.dist-info → deriva_ml-1.13.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: deriva-ml
-Version: 1.13.0
+Version: 1.13.1
 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

{deriva_ml-1.13.0.dist-info → deriva_ml-1.13.1.dist-info}/RECORD

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 deriva_ml/deriva_ml_base.py,sha256=JYTG_a8SURhrPQBTz6OaGMk0D0sSPWpXqCnoVnSNViI,38501
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