deriva-ml 1.12.3__py3-none-any.whl → 1.13.0__py3-none-any.whl

deriva_ml/__init__.py

@@ -14,6 +14,7 @@ __all__ = [
     "BuiltinTypes",
     "UploadState",
     "MLVocab",
+    "MLAsset",
     "ExecMetadataVocab",
     "RID",
     "DerivaSystemColumns",
@@ -32,6 +33,7 @@ from .deriva_definitions import (
     RID,
     DerivaMLException,
     MLVocab,
+    MLAsset,
     ExecMetadataVocab,
     DerivaSystemColumns,
 )
@@ -49,4 +51,3 @@ try:
 except PackageNotFoundError:
     # package is not installed
     pass
-

deriva_ml/deriva_definitions.py

@@ -192,6 +192,11 @@ class MLVocab(StrEnum):
     asset_role = "Asset_Role"
 
 
+class MLAsset(StrEnum):
+    execution_metadata = "Execution_Metadata"
+    execution_asset = "Execution_Asset"
+
+
 class ExecMetadataVocab(StrEnum):
     """
     Predefined execution metadata types.

deriva_ml/deriva_ml_base.py

@@ -14,17 +14,16 @@ import getpass
 import logging
 from datetime import datetime
 from itertools import chain
-import inspect
-import setuptools_scm
 from pathlib import Path
 import requests
-import subprocess
+
 from typing import Optional, Any, Iterable, TYPE_CHECKING
+
 from deriva.core import (
     get_credential,
     urlquote,
-    DEFAULT_SESSION_CONFIG,
     format_exception,
+    DEFAULT_SESSION_CONFIG,
 )
 import deriva.core.datapath as datapath
 from deriva.core.datapath import DataPathException
@@ -33,7 +32,6 @@ from deriva.core.ermrest_catalog import ResolveRidResult
 from deriva.core.ermrest_model import Key, Table
 from deriva.core.utils.globus_auth_utils import GlobusNativeLogin
 from pydantic import validate_call, ConfigDict
-from requests import RequestException
 
 from .execution_configuration import ExecutionConfiguration, Workflow
 from .feature import Feature, FeatureRecord
@@ -60,33 +58,6 @@ 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
 
 
-try:
-    from IPython import get_ipython
-except ImportError:  # Graceful fallback if IPython isn't installed.
-
-    def get_ipython():
-        """Dummy routine in case you are not running in IPython."""
-        return None
-
-
-try:
-    from jupyter_server.serverapp import list_running_servers
-except ImportError:
-
-    def list_running_servers():
-        """Dummy routine in case you are not running in Jupyter."""
-        return []
-
-
-try:
-    from ipykernel import get_connection_file
-except ImportError:
-
-    def get_connection_file():
-        """Dummy routine in case you are not running in Jupyter."""
-        return ""
-
-
 if TYPE_CHECKING:
     from .execution import Execution
 
@@ -165,7 +136,6 @@ class DerivaML(Dataset):
         self.version = model_version
         self.configuration = None
         self._execution: Optional[Execution] = None
-        self.executable_path, self._is_notebook = self._get_python_script()
         self.domain_schema = self.model.domain_schema
         self.project_name = project_name or self.domain_schema
         self.start_time = datetime.now()
@@ -192,102 +162,6 @@ class DerivaML(Dataset):
         except (AttributeError, requests.HTTPError):
             pass
 
-    def _check_nbstrip_status(self) -> None:
-        """Check to see if nbstrip is installed"""
-        try:
-            if subprocess.run(
-                ["nbstripout", "--is-installed"],
-                check=False,
-                capture_output=True,
-            ).returncode:
-                self._logger.warning(
-                    "nbstripout is not installed in repository. Please run nbstripout --install"
-                )
-        except subprocess.CalledProcessError:
-            self._logger.error("nbstripout is not found.")
-
-    @staticmethod
-    def _get_notebook_session() -> tuple[dict[str, Any] | None, dict[str, Any] | None]:
-        """Return the absolute path of the current notebook."""
-        # Get the kernel's connection file and extract the kernel ID
-        try:
-            if not (connection_file := Path(get_connection_file()).name):
-                return None, None
-        except RuntimeError:
-            return None, None
-
-        kernel_id = connection_file.split("-", 1)[1].split(".")[0]
-
-        # Look through the running server sessions to find the matching kernel ID
-        for server in list_running_servers():
-            try:
-                # If a token is required for authentication, include it in headers
-                token = server.get("token", "")
-                headers = {}
-                if token:
-                    headers["Authorization"] = f"token {token}"
-
-                try:
-                    sessions_url = server["url"] + "api/sessions"
-                    response = requests.get(sessions_url, headers=headers)
-                    response.raise_for_status()
-                    sessions = response.json()
-                except RequestException as e:
-                    raise e
-                for sess in sessions:
-                    if sess["kernel"]["id"] == kernel_id:
-                        return server, sess
-            except Exception as _e:
-                # Ignore servers we can't connect to.
-                pass
-        return None, None
-
-    def _get_notebook_path(self) -> Path | None:
-        """Return the absolute path of the current notebook."""
-
-        server, session = DerivaML._get_notebook_session()
-        if server and session:
-            self._check_nbstrip_status()
-            relative_path = session["notebook"]["path"]
-            # Join the notebook directory with the relative path
-            return Path(server["root_dir"]) / relative_path
-        else:
-            return None
-
-    def _get_python_script(self) -> tuple[Path, bool]:
-        """Return the path to the currently executing script"""
-        is_notebook = False
-        if filename := self._get_notebook_path():
-            is_notebook = True
-        else:
-            stack = inspect.stack()
-            # Get the caller's filename, which is two up the stack from here.
-            if len(stack) > 1:
-                filename = Path(stack[2].filename)
-                if not filename.exists():
-                    # Begin called from command line interpreter.
-                    filename = "REPL"
-                # Get the caller's filename, which is two up the stack from here.
-            else:
-                raise DerivaMLException(
-                    "Looking for caller failed"
-                )  # Stack is too shallow
-        return filename, is_notebook
-
-    def _get_git_root(self):
-        try:
-            result = subprocess.run(
-                ["git", "rev-parse", "--show-toplevel"],
-                cwd=self.executable_path.parent,
-                stdout=subprocess.PIPE,
-                stderr=subprocess.DEVNULL,
-                text=True,
-                check=True,
-            )
-            return result.stdout.strip()
-        except subprocess.CalledProcessError:
-            return None  # Not in a git repository
-
     @staticmethod
     def _get_session_config():
         """ """
@@ -311,10 +185,6 @@ class DerivaML(Dataset):
         """Get a new instance of a pathBuilder object."""
         return self.catalog.getPathBuilder()
 
-    def get_version(self) -> str:
-        """Return the version number of the executable"""
-        return setuptools_scm.get_version(root=self._get_git_root())
-
     @property
     def domain_path(self):
         """Get a new instance of a pathBuilder object to the domain schema"""
@@ -1117,105 +987,7 @@ class DerivaML(Dataset):
         # Make sure type is correct.
         self.lookup_term(MLVocab.workflow_type, workflow_type)
 
-        try:
-            subprocess.run(
-                "git rev-parse --is-inside-work-tree",
-                capture_output=True,
-                text=True,
-                shell=True,
-                check=True,
-            )
-        except subprocess.CalledProcessError:
-            raise DerivaMLException("Not executing in a Git repository.")
-
-        github_url, is_dirty = self._github_url()
-
-        if is_dirty:
-            self._logger.warning(
-                f"File {self.executable_path} has been modified since last commit. Consider commiting before executing"
-            )
-
-        # If you are in a notebook, strip out the outputs before computing the checksum.
-        cmd = (
-            f"nbstripout {self.executable_path} | git hash-object --stdin"
-            if self._is_notebook
-            else f"git hash-object {self.executable_path}"
-        )
-        checksum = (
-            subprocess.run(
-                cmd,
-                capture_output=True,
-                text=True,
-                check=False,
-                shell=True,
-            ).stdout.strip()
-            if self.executable_path != "REPL"
-            else "1"
-        )
-
-        return Workflow(
-            name=name,
-            url=github_url,
-            checksum=checksum,
-            description=description,
-            workflow_type=workflow_type,
-        )
-
-    def _github_url(self) -> tuple[str, bool]:
-        """Return a GitHUB URL for the latest commit of the script from which this routine is called.
-
-        This routine is used to be called from a script or notebook (e.g. python -m file). It assumes that
-        the file is in a gitHUB repository and commited.  It returns a URL to the last commited version of this
-        file in GitHUB.
-
-        Returns: A tuple with the gethub_url and a boolean to indicated if uncommited changes
-            have been made to the file.
-
-        """
-
-        # Get repo URL from local gitHub repo.
-        if self.executable_path == "REPL":
-            return "REPL", True
-        try:
-            result = subprocess.run(
-                ["git", "remote", "get-url", "origin"],
-                capture_output=True,
-                text=True,
-                cwd=self.executable_path.parent,
-            )
-            github_url = result.stdout.strip().removesuffix(".git")
-        except subprocess.CalledProcessError:
-            raise DerivaMLException("No GIT remote found")
-
-        # Find the root directory for the repository
-        repo_root = self._get_git_root()
-
-        # Now check to see if file has been modified since the last commit.
-        try:
-            result = subprocess.run(
-                ["git", "status", "--porcelain"],
-                cwd=self.executable_path.parent,
-                capture_output=True,
-                text=True,
-                check=True,
-            )
-            is_dirty = bool(
-                "M " in result.stdout.strip()
-            )  # Returns True if output indicates a modified file
-        except subprocess.CalledProcessError:
-            is_dirty = False  # If Git command fails, assume no changes
-
-        """Get SHA-1 hash of latest commit of the file in the repository"""
-        result = subprocess.run(
-            ["git", "log", "-n", "1", "--pretty=format:%H--", self.executable_path],
-            cwd=self.executable_path.parent,
-            capture_output=True,
-            text=True,
-            check=True,
-        )
-        sha = result.stdout.strip()
-        url = f"{github_url}/blob/{sha}/{self.executable_path.relative_to(repo_root)}"
-        return url, is_dirty
+        return Workflow.create_workflow(name, workflow_type, description)
 
     # @validate_call
     def create_execution(
@@ -1259,6 +1031,15 @@ class DerivaML(Dataset):
             exec_rid=execution_rid,
             file_name="configuration.json",
             asset_table=self.model.name_to_table("Execution_Metadata"),
+            metadata={},
         )
-        configuration = ExecutionConfiguration.load_configuration(cfile)
+
+        if cfile.exists():
+            configuration = ExecutionConfiguration.load_configuration(cfile)
+        else:
+            execution = self.retrieve_rid(execution_rid)
+            configuration = ExecutionConfiguration(
+                workflow=execution["Workflow"],
+                description=execution["Description"],
+            )
         return Execution(configuration, self, reload=execution_rid)

deriva_ml/execution.py

@@ -27,6 +27,7 @@ from .deriva_definitions import (
     FileUploadState,
     DerivaMLException,
     MLVocab,
+    MLAsset,
     DRY_RUN_RID,
 )
 from .deriva_ml_base import DerivaML, FeatureRecord
@@ -54,11 +55,14 @@ except ImportError:  # Graceful fallback if IceCream isn't installed.
 
 
 try:
-    from jupyter_server.serverapp import list_running_servers
+    from IPython.display import display, Markdown
 except ImportError:
 
-    def list_running_servers():
-        return []
+    def display(s):
+        print(s)
+
+    def Markdown(s):
+        return s
 
 
 class AssetFilePath(type(Path())):
@@ -218,6 +222,15 @@ class Execution:
                 ]
             )[0]["RID"]
 
+        if (
+            isinstance(self.configuration.workflow, Workflow)
+            and self.configuration.workflow.is_notebook
+        ):
+            # Put execution_rid into cell output so we can find it later.
+            display(
+                Markdown(f"Execution RID: {self._ml_object.cite(self.execution_rid)}")
+            )
+
         # Create a directory for execution rid so we can recover state in case of a crash.
         execution_root(prefix=self._ml_object.working_dir, exec_rid=self.execution_rid)
         self._initialize_execution(reload)
@@ -281,16 +294,20 @@ class Execution:
             )
 
         # Save configuration details for later upload
-        cfile = self.asset_file_path(
-            asset_name="Execution_Metadata",
-            file_name="configuration.json",
-            asset_types=ExecMetadataVocab.execution_config.value,
-        )
-        with open(cfile.as_posix(), "w", encoding="utf-8") as config_file:
-            json.dump(self.configuration.model_dump(), config_file)
+        if not reload:
+            cfile = self.asset_file_path(
+                asset_name=MLAsset.execution_metadata,
+                file_name="configuration.json",
+                asset_types=ExecMetadataVocab.execution_config.value,
+            )
+            with open(cfile.as_posix(), "w", encoding="utf-8") as config_file:
+                json.dump(self.configuration.model_dump(), config_file)
 
-        # save runtime env
-        self._save_runtime_environment()
+            for parameter_file in self.configuration.parameters:
+                self.asset_file_path(MLAsset.execution_assets, parameter_file)
+
+            # save runtime env
+            self._save_runtime_environment()
 
         self.start_time = datetime.now()
         self.update_status(Status.pending, "Initialize status finished.")
@@ -741,7 +758,7 @@ class Execution:
     def asset_file_path(
         self,
         asset_name: str,
-        file_name: str,
+        file_name: str | Path,
         asset_types: Optional[list[str] | str] = None,
         copy_file=False,
         **kwargs,

deriva_ml/execution_configuration.py

@@ -4,16 +4,56 @@ Classes that are used to define an execution configuration.
 
 from __future__ import annotations
 
+import inspect
 import json
+import logging
+import os
+
+from requests import RequestException
+import requests
+import subprocess
 from typing import Optional, Any
 
-from pydantic import BaseModel, conlist, ConfigDict, field_validator, Field
+from pydantic import (
+    BaseModel,
+    conlist,
+    ConfigDict,
+    field_validator,
+    Field,
+    PrivateAttr,
+)
 from pathlib import Path
 import sys
 
 
 from .dataset_aux_classes import DatasetSpec
-from .deriva_definitions import RID
+from .deriva_definitions import RID, DerivaMLException
+
+try:
+    from IPython import get_ipython
+except ImportError:  # Graceful fallback if IPython isn't installed.
+
+    def get_ipython():
+        """Dummy routine in case you are not running in IPython."""
+        return None
+
+
+try:
+    from jupyter_server.serverapp import list_running_servers
+except ImportError:
+
+    def list_running_servers():
+        """Dummy routine in case you are not running in Jupyter."""
+        return []
+
+
+try:
+    from ipykernel import get_connection_file
+except ImportError:
+
+    def get_connection_file():
+        """Dummy routine in case you are not running in Jupyter."""
+        return ""
 
 
 class Workflow(BaseModel):
@@ -26,15 +66,255 @@ class Workflow(BaseModel):
         workflow_type: The type of the workflow.  Must be an existing controlled vocabulary term.
         version: The version of the workflow instance.  Should follow semantic versioning.
         description: A description of the workflow instance.  Can be in Markdown format.
+        is_notebook: A boolean indicating whether this workflow instance is a notebook or not.
     """
 
     name: str
     url: str
     workflow_type: str
     version: Optional[str] = None
-    description: Optional[str] = ""
+    description: str = None
     rid: Optional[RID] = None
-    checksum: Optional[str]
+    checksum: Optional[str] = None
+    is_notebook: bool = False
+
+    _logger: Any = PrivateAttr()
+
+    def __post_init__(self):
+        self._logger = logging.getLogger("deriva_ml")
+
+    @staticmethod
+    def _check_nbstrip_status() -> None:
+        """Check to see if nbstrip is installed"""
+        logger = logging.getLogger("deriva_ml")
+        try:
+            if subprocess.run(
+                ["nbstripout", "--is-installed"],
+                check=False,
+                capture_output=True,
+            ).returncode:
+                logger.warning(
+                    "nbstripout is not installed in repository. Please run nbstripout --install"
+                )
+        except subprocess.CalledProcessError:
+            logger.error("nbstripout is not found.")
+
+    @staticmethod
+    def _get_notebook_path() -> Path | None:
+        """Return the absolute path of the current notebook."""
+
+        server, session = Workflow._get_notebook_session()
+        if server and session:
+            relative_path = session["notebook"]["path"]
+            # Join the notebook directory with the relative path
+            return Path(server["root_dir"]) / relative_path
+        else:
+            return None
+
+    @staticmethod
+    def _get_notebook_session() -> tuple[dict[str, Any] | None, dict[str, Any] | None]:
+        """Return the absolute path of the current notebook."""
+        # Get the kernel's connection file and extract the kernel ID
+        try:
+            if not (connection_file := Path(get_connection_file()).name):
+                return None, None
+        except RuntimeError:
+            return None, None
+
+        kernel_id = connection_file.split("-", 1)[1].split(".")[0]
+
+        # Look through the running server sessions to find the matching kernel ID
+        for server in list_running_servers():
+            try:
+                # If a token is required for authentication, include it in headers
+                token = server.get("token", "")
+                headers = {}
+                if token:
+                    headers["Authorization"] = f"token {token}"
+
+                try:
+                    sessions_url = server["url"] + "api/sessions"
+                    response = requests.get(sessions_url, headers=headers)
+                    response.raise_for_status()
+                    sessions = response.json()
+                except RequestException as e:
+                    raise e
+                for sess in sessions:
+                    if sess["kernel"]["id"] == kernel_id:
+                        return server, sess
+            except Exception as _e:
+                # Ignore servers we can't connect to.
+                pass
+        return None, None
+
+    @staticmethod
+    def _get_python_script() -> tuple[Path, bool]:
+        """Return the path to the currently executing script"""
+        is_notebook = True
+        if not (filename := Workflow._get_notebook_path()):
+            is_notebook = False
+            stack = inspect.stack()
+            # Get the caller's filename, which is two up the stack from here.
+            if len(stack) > 1:
+                filename = Path(stack[2].filename)
+                if not filename.exists():
+                    # Begin called from command line interpreter.
+                    filename = Path("REPL")
+                # Get the caller's filename, which is two up the stack from here.
+            else:
+                raise DerivaMLException(
+                    "Looking for caller failed"
+                )  # Stack is too shallow
+        return filename, is_notebook
+
+    @staticmethod
+    def _github_url(executable_path: Path) -> tuple[str, bool]:
+        """Return a GitHUB URL for the latest commit of the script from which this routine is called.
+
+        This routine is used to be called from a script or notebook (e.g. python -m file). It assumes that
+        the file is in a gitHUB repository and commited.  It returns a URL to the last commited version of this
+        file in GitHUB.
+
+        Returns: A tuple with the gethub_url and a boolean to indicated if uncommited changes
+            have been made to the file.
+
+        """
+
+        # Get repo URL from local gitHub repo.
+        if executable_path == "REPL":
+            return "REPL", True
+        try:
+            result = subprocess.run(
+                ["git", "remote", "get-url", "origin"],
+                capture_output=True,
+                text=True,
+                cwd=executable_path.parent,
+            )
+            github_url = result.stdout.strip().removesuffix(".git")
+        except subprocess.CalledProcessError:
+            raise DerivaMLException("No GIT remote found")
+
+        # Find the root directory for the repository
+        repo_root = Workflow._get_git_root(executable_path)
+
+        # Now check to see if file has been modified since the last commit.
+        try:
+            result = subprocess.run(
+                ["git", "status", "--porcelain"],
+                cwd=executable_path.parent,
+                capture_output=True,
+                text=True,
+                check=True,
+            )
+            is_dirty = bool(
+                "M " in result.stdout.strip()
+            )  # Returns True if output indicates a modified file
+        except subprocess.CalledProcessError:
+            is_dirty = False  # If Git command fails, assume no changes
+
+        """Get SHA-1 hash of latest commit of the file in the repository"""
+        result = subprocess.run(
+            ["git", "log", "-n", "1", "--pretty=format:%H--", executable_path],
+            cwd=executable_path.parent,
+            capture_output=True,
+            text=True,
+            check=True,
+        )
+        sha = result.stdout.strip()
+        url = f"{github_url}/blob/{sha}/{executable_path.relative_to(repo_root)}"
+        return url, is_dirty
+
+    @staticmethod
+    def _get_git_root(executable_path: Path):
+        try:
+            result = subprocess.run(
+                ["git", "rev-parse", "--show-toplevel"],
+                cwd=executable_path.parent,
+                stdout=subprocess.PIPE,
+                stderr=subprocess.DEVNULL,
+                text=True,
+                check=True,
+            )
+            return result.stdout.strip()
+        except subprocess.CalledProcessError:
+            return None  # Not in a git repository
+
+    @staticmethod
+    def create_workflow(
+        name: str,
+        workflow_type: str,
+        description: str = "",
+    ) -> Workflow:
+        """Identify current executing program and return a workflow RID for it
+
+        Determine the notebook or script that is currently being executed. Assume that  this is
+        being executed from a cloned GitHub repository.  Determine the remote repository name for
+        this object.  Then either retrieve an existing workflow for this executable or create
+        a new one.
+
+        Args:
+            name: The name of the workflow.
+            workflow_type: The type of the workflow.
+            description: The description of the workflow.
+        """
+
+        # Check to see if execution file info is being passed in by calling program.
+        if "DERIVA_ML_WORKFLOW_URL" in os.environ:
+            github_url = os.environ["DERIVA_ML_WORKFLOW_URL"]
+            checksum = os.environ["DERIVA_ML_WORKFLOW_CHECKSUM"]
+            is_notebook = True
+        else:
+            path, is_notebook = Workflow._get_notebook_path()
+            github_url, checksum = Workflow.get_url_and_checksum(path)
+
+        return Workflow(
+            name=name,
+            url=github_url,
+            checksum=checksum,
+            description=description,
+            workflow_type=workflow_type,
+            is_notebook=is_notebook,
+        )
+
+    @staticmethod
+    def get_url_and_checksum(executable_path: Path) -> tuple[str, str]:
+        """Determine the checksum for a specified executable"""
+        try:
+            subprocess.run(
+                "git rev-parse --is-inside-work-tree",
+                capture_output=True,
+                text=True,
+                shell=True,
+                check=True,
+            )
+        except subprocess.CalledProcessError:
+            raise DerivaMLException("Not executing in a Git repository.")
+
+        github_url, is_dirty = Workflow._github_url(executable_path)
+
+        if is_dirty:
+            logging.getLogger("deriva_ml").warning(
+                f"File {executable_path} has been modified since last commit. Consider commiting before executing"
+            )
+
+        # If you are in a notebook, strip out the outputs before computing the checksum.
+        cmd = (
+            f"nbstripout -t {executable_path} | git hash-object --stdin"
+            if "ipynb" == executable_path.suffix
+            else f"git hash-object {executable_path}"
+        )
+        checksum = (
+            subprocess.run(
+                cmd,
+                capture_output=True,
+                text=True,
+                check=False,
+                shell=True,
+            ).stdout.strip()
+            if executable_path != "REPL"
+            else "1"
+        )
+        return github_url, checksum
 
 
 class ExecutionConfiguration(BaseModel):

deriva_ml/run_notebook.py

@@ -0,0 +1,155 @@
+"""Module to run a notebook using papermill"""
+
+import json
+import os
+import papermill as pm
+from pathlib import Path
+import regex as re
+import tempfile
+
+from deriva_ml import Workflow, DerivaML, MLVocab
+from deriva.core import BaseCLI
+from deriva_ml import MLAsset
+
+
+class DerivaMLRunNotebookCLI(BaseCLI):
+    """Main class to part command line arguments and call model"""
+
+    def __init__(self, description, epilog, **kwargs):
+        BaseCLI.__init__(self, description, epilog, **kwargs)
+        Workflow._check_nbstrip_status()
+        self.parser.add_argument(
+            "notebook_file", type=Path, help="Path to the notebook file"
+        )
+
+        self.parser.add_argument(
+            "--file",
+            "-f",
+            type=Path,
+            default=None,
+            help="JSON file with parameter values to inject into the notebook.",
+        )
+
+        self.parser.add_argument(
+            "--inspect",
+            action="store_true",
+            help="Display parameters information for the given notebook path.",
+        )
+
+        self.parser.add_argument(
+            "--parameter",
+            "-p",
+            nargs=2,
+            action="append",
+            metavar=("KEY", "VALUE"),
+            default=[],
+            help="Provide a parameter name band value to inject into the notebook.",
+        )
+
+        self.parser.add_argument(
+            "--kernel", "-k", nargs=1, help="Name of kernel to run..", default=None
+        )
+
+    @staticmethod
+    def _coerce_number(val: str):
+        """
+        Try to convert a string to int, then float; otherwise return str.
+        """
+        try:
+            return int(val)
+        except ValueError:
+            try:
+                return float(val)
+            except ValueError:
+                return val
+
+    def main(self):
+        """Parse arguments and set up execution environment."""
+        args = self.parse_cli()
+        notebook_file = args.notebook_file
+        parameter_file = args.file
+
+        # args.parameter is now a list of [KEY, VALUE] lists
+        # e.g. [['timeout', '30'], ['name', 'Alice'], ...]
+        parameters = {key: self._coerce_number(val) for key, val in args.parameter}
+
+        if parameter_file:
+            if not (parameter_file.is_file() and parameter_file.suffix == ".json"):
+                print("Parameter file must be an json file.")
+                exit(1)
+            with open(parameter_file, "r") as f:
+                parameters |= json.load(f)
+
+        if not (notebook_file.is_file() and notebook_file.suffix == ".ipynb"):
+            print("Notebook file must be an ipynb file.")
+            exit(1)
+
+        # 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:
+                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:")
+            for param, value in notebook_parameters.items():
+                print(f"  {param}:{value}")
+            self.run_notebook(notebook_file.resolve(), parameters, args.kernel)
+
+    def run_notebook(self, notebook_file, parameters, kernel=None):
+        url, checksum = Workflow.get_url_and_checksum(Path(notebook_file))
+        os.environ["DERIVA_ML_WORKFLOW_URL"] = url
+        os.environ["DERIVA_ML_WORKFLOW_CHECKSUM"] = checksum
+
+        with tempfile.TemporaryDirectory() as tmpdirname:
+            notebook_output = Path(tmpdirname) / Path(notebook_file).name
+            pm.execute_notebook(
+                input_path=notebook_file,
+                output_path=notebook_output,
+                parameters=parameters,
+                kernel_name=kernel,
+            )
+            host = catalog_id = execution_rid = None
+            with open(notebook_output, "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,
+                    ):
+                        host = m["host"]
+                        catalog_id = m["catalog_id"]
+                        execution_rid = m["execution_rid"]
+            if not execution_rid:
+                print("Execution RID not found.")
+                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",
+            )
+            execution = ml_instance.restore_execution(execution_rid)
+            execution.asset_file_path(
+                asset_name=MLAsset.execution_asset,
+                file_name=notebook_output,
+                asset_types=["Notebook_Output"],
+            )
+            execution.upload_execution_outputs()
+
+
+def main():
+    cli = DerivaMLRunNotebookCLI(
+        description="Deriva ML Execution Script Demo", epilog=""
+    )
+    cli.main()
+
+
+if __name__ == "__main__":
+    main()

deriva_ml/test_notebook.ipynb

@@ -0,0 +1,124 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "id": "0",
+   "metadata": {},
+   "source": [
+    "import builtins\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"
+   ],
+   "outputs": [],
+   "execution_count": null
+  },
+  {
+   "cell_type": "code",
+   "id": "1",
+   "metadata": {
+    "tags": [
+     "parameters"
+    ]
+   },
+   "source": [
+    "foo: int = 1\n",
+    "bar: str = \"hello\"\n",
+    "list_parameter: list[float] = [1, 2, 3]"
+   ],
+   "outputs": [],
+   "execution_count": null
+  },
+  {
+   "metadata": {},
+   "cell_type": "code",
+   "outputs": [],
+   "execution_count": null,
+   "source": [
+    "print('foo', foo)\n",
+    "print('bar', bar)\n",
+    "print('list_parameter', list_parameter)"
+   ],
+   "id": "70b23cdd933ce669"
+  },
+  {
+   "metadata": {},
+   "cell_type": "code",
+   "outputs": [],
+   "execution_count": null,
+   "source": [
+    "hostname = 'dev.eye-ai.org'\n",
+    "domain_schema = 'eye-ai'\n",
+    "\n",
+    "gnl = GlobusNativeLogin(host=hostname)\n",
+    "if gnl.is_logged_in([hostname]):\n",
+    "    print(\"You are already logged in.\")\n",
+    "else:\n",
+    "    gnl.login([hostname], no_local_server=True, no_browser=True, refresh_tokens=True, update_bdbag_keychain=True)\n",
+    "    print(\"Login Successful\")\n"
+   ],
+   "id": "2"
+  },
+  {
+   "cell_type": "code",
+   "id": "3",
+   "metadata": {},
+   "source": [
+    "ml_instance = DemoML(hostname, domain_schema)\n",
+    "print(f'Creating catalog at {ml_instance.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\")"
+   ],
+   "outputs": [],
+   "execution_count": null
+  },
+  {
+   "metadata": {},
+   "cell_type": "code",
+   "source": [
+    "api_workflow = ml_instance.create_workflow(\n",
+    "    name=\"Manual Workflow\",\n",
+    "    workflow_type=\"Manual Workflow\",\n",
+    "    description=\"A manual operation\"\n",
+    ")"
+   ],
+   "id": "5",
+   "outputs": [],
+   "execution_count": null
+  },
+  {
+   "cell_type": "code",
+   "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."
+   ],
+   "outputs": [],
+   "execution_count": null
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "deriva-test",
+   "language": "python",
+   "name": "deriva-test"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 2
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython2",
+   "version": "2.7.6"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

{deriva_ml-1.12.3.dist-info → deriva_ml-1.13.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: deriva-ml
-Version: 1.12.3
+Version: 1.13.0
 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
@@ -15,6 +15,7 @@ Requires-Dist: semver>3.0.0
 Requires-Dist: setuptools>=64
 Requires-Dist: setuptools-scm<=6.0
 Requires-Dist: nbstripout
+Requires-Dist: papermill
 Dynamic: license-file
 
 # DerivaML

{deriva_ml-1.12.3.dist-info → deriva_ml-1.13.0.dist-info}/RECORD

@@ -1,27 +1,29 @@
-deriva_ml/__init__.py,sha256=r1Z9N5vtZkAET7emqhpAx2bf_xJUp5wHOc4_DIplsG8,1082
+deriva_ml/__init__.py,sha256=2sRcX2s72Guo4M7IGW_0_ZyKokZNCbVE6de65tvHBlw,1109
 deriva_ml/database_model.py,sha256=lMbAEqn4n0m7h_JstMX_LX9gbvBIEydG3sRilPn3eLU,14885
 deriva_ml/dataset.py,sha256=OyWUKWnYeP0ctimSBQ4em-uJrzCNOohx4GPT2uIl6R4,60649
 deriva_ml/dataset_aux_classes.py,sha256=YxjQnu2kS9kK_f8bGqhmgE6ty9GNeitCxfvReT9vaM0,6537
 deriva_ml/dataset_bag.py,sha256=yS8oYVshfFtRDyhGPRqtbvxjyd3ZFF29lrB783OP4vM,11849
 deriva_ml/demo_catalog.py,sha256=9Qo3JD4bUIwnL3ngPctc2QBeWApvMR_5UyaK9ockTrY,11536
-deriva_ml/deriva_definitions.py,sha256=HLaQ0zWO-Yd17Yp8hvqFSGkvjANJ52Ws5yHCVYMhfGA,8918
-deriva_ml/deriva_ml_base.py,sha256=rrImShp1RXvMuXVLft5GfTnxf_PfF1LONHgV1Ee_E9I,46517
+deriva_ml/deriva_definitions.py,sha256=MZl3c23gArbS-0HZ24VDAyb8HI2Kcb8hFdhSnBLOLfo,9030
+deriva_ml/deriva_ml_base.py,sha256=JYTG_a8SURhrPQBTz6OaGMk0D0sSPWpXqCnoVnSNViI,38501
 deriva_ml/deriva_model.py,sha256=wytGCAHutiUaRfnRKr80Ks_P6ci0_wXRU3vq3lthfYU,13260
-deriva_ml/execution.py,sha256=xYS4wYRYcksNjUZ-Rwys_H4jZchW3YVu-uWg7ySJMjk,37510
-deriva_ml/execution_configuration.py,sha256=XQeXzPz9Gh_AGa_iYW8zF95niwHed3ojv4gnibB0thA,4082
+deriva_ml/execution.py,sha256=t20sGqPRcUaG-5LLHPaQ01pPP8XpqiCveS1h-Fw_XbQ,38093
+deriva_ml/execution_configuration.py,sha256=WiA4PPijNZUftExN6Qm1YScVD1OY3depNKTutIwOfUg,14063
 deriva_ml/execution_environment.py,sha256=bCRKrCELDbGQDo7_FKfw7e8iMzVjSRZK3baKkqH5-_0,3264
 deriva_ml/feature.py,sha256=07g0uSrhumdopJluWuWSRMrzagaikAOihqB09bzXBP4,5475
 deriva_ml/history.py,sha256=qTDLDs8Ow_6r7mDO0gZm0Fg81SWKOAgtCU5pzZoDRgM,2828
+deriva_ml/run_notebook.py,sha256=XzI38WNsu9CKDYbWMt8b5ODtlp27dsWsSuMkKwfeWOE,5484
 deriva_ml/test_functions.py,sha256=-eqLHjjCQCLBNAr1ofbZekNiCOfMISSACRxT_YHER8I,4396
+deriva_ml/test_notebook.ipynb,sha256=CatQIh9whsmYWGpwuyw9XMggQ9-TlCueTyH3Wiv4aBc,3116
 deriva_ml/upload.py,sha256=gHTGXAVlf56EwNzmw5zY0gbBf8h08eU2q2GBbb2FdVc,16087
 deriva_ml/schema_setup/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 deriva_ml/schema_setup/annotations.py,sha256=v0gTpmWYxRqsQ-bcnQzsr8WowGv2pi9pZUsO3WWnu1U,9528
 deriva_ml/schema_setup/create_schema.py,sha256=hNMc-v5tferd0UjfdB6nBw7Rc_o-Mg6NkPqQGie9YOw,11700
 deriva_ml/schema_setup/policy.json,sha256=77sf0Imy6CAQV0_VwwbA56_KROJ05WXsvT-Wjtkk538,1633
 deriva_ml/schema_setup/table_comments_utils.py,sha256=-2_ubEpoH7ViLVb-ZfW9wZbQ26DTKNgjkCABMzGu4i4,2140
-deriva_ml-1.12.3.dist-info/licenses/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
-deriva_ml-1.12.3.dist-info/METADATA,sha256=CNoKyLpxijU8MrLj4VQzrOQLAU3oIT232DF9RI-eFbw,974
-deriva_ml-1.12.3.dist-info/WHEEL,sha256=CmyFI0kx5cdEMTLiONQRbGQwjIoR1aIYB7eCAQ4KPJ0,91
-deriva_ml-1.12.3.dist-info/entry_points.txt,sha256=ZiOvrYj022x544TQwi018ujeHRRDahNmwJnzn5ThacM,242
-deriva_ml-1.12.3.dist-info/top_level.txt,sha256=I1Q1dkH96cRghdsFRVqwpa2M7IqJpR2QPUNNc5-Bnpw,10
-deriva_ml-1.12.3.dist-info/RECORD,,
+deriva_ml-1.13.0.dist-info/licenses/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
+deriva_ml-1.13.0.dist-info/METADATA,sha256=YxPB1VnpB-Y8KL4Yp3VKAYq7F5EUp-R7MfZ1uhWpRZs,999
+deriva_ml-1.13.0.dist-info/WHEEL,sha256=CmyFI0kx5cdEMTLiONQRbGQwjIoR1aIYB7eCAQ4KPJ0,91
+deriva_ml-1.13.0.dist-info/entry_points.txt,sha256=cJnALMa6pjdk6RQCt4HFbKHqALpVa0k6wPeQDPedLJI,295
+deriva_ml-1.13.0.dist-info/top_level.txt,sha256=I1Q1dkH96cRghdsFRVqwpa2M7IqJpR2QPUNNc5-Bnpw,10
+deriva_ml-1.13.0.dist-info/RECORD,,

{deriva_ml-1.12.3.dist-info → deriva_ml-1.13.0.dist-info}/entry_points.txt

@@ -1,4 +1,5 @@
 [console_scripts]
 deriva-ml-alter-annotation = deriva_ml.schema_setup.alter_annotation:main
 deriva-ml-create-schema = deriva_ml.schema_setup.create_schema:main
+deriva-ml-run-notebook = deriva_ml.run_notebook:main
 deriva-ml-table-comments-utils = deriva_ml.schema_setup.table_comments_utils:main