deriva-ml 1.17.10__py3-none-any.whl → 1.17.12__py3-none-any.whl

deriva_ml/core/mixins/workflow.py

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+"""Workflow management mixin for DerivaML.
+
+This module provides the WorkflowMixin class which handles
+workflow operations including adding, looking up, listing,
+and creating workflows.
+"""
+
+from __future__ import annotations
+
+from typing import TYPE_CHECKING, Any, Callable
+
+# Deriva imports - use importlib to avoid shadowing by local 'deriva.py' files
+import importlib
+_deriva_core = importlib.import_module("deriva.core")
+format_exception = _deriva_core.format_exception
+
+from deriva_ml.core.definitions import RID, MLVocab, VocabularyTerm
+from deriva_ml.core.exceptions import DerivaMLException
+from deriva_ml.execution.workflow import Workflow
+
+if TYPE_CHECKING:
+    from deriva_ml.interfaces import DerivaMLCatalog
+
+
+class WorkflowMixin:
+    """Mixin providing workflow management operations.
+
+    This mixin requires the host class to have:
+        - ml_schema: str - name of the ML schema
+        - pathBuilder(): method returning catalog path builder
+        - lookup_term(): method for vocabulary term lookup (from VocabularyMixin)
+
+    Methods:
+        find_workflows: Find all workflows in the catalog
+        add_workflow: Add a workflow to the catalog
+        lookup_workflow: Look up a workflow by RID
+        find_workflow_by_url: Find a workflow by URL or checksum
+        create_workflow: Create a new workflow definition
+    """
+
+    # Type hints for IDE support - actual attributes/methods from host class
+    ml_schema: str
+    pathBuilder: Callable[[], Any]
+    lookup_term: Callable[[str, str], VocabularyTerm]
+
+    def find_workflows(self) -> list[Workflow]:
+        """Find all workflows in the catalog.
+
+        Catalog-level operation to find all workflow definitions, including their
+        names, URLs, types, versions, and descriptions. Each returned Workflow
+        is bound to the catalog, allowing its description to be updated.
+
+        Returns:
+            list[Workflow]: List of workflow objects, each containing:
+                - name: Workflow name
+                - url: Source code URL
+                - workflow_type: Type of workflow
+                - version: Version identifier
+                - description: Workflow description
+                - rid: Resource identifier
+                - checksum: Source code checksum
+
+        Examples:
+            List all workflows and their descriptions::
+
+                >>> workflows = ml.find_workflows()
+                >>> for w in workflows:
+                ...     print(f"{w.name} (v{w.version}): {w.description}")
+                ...     print(f"  Source: {w.url}")
+
+            Update a workflow's description (workflows are catalog-bound)::
+
+                >>> workflows = ml.find_workflows()
+                >>> workflows[0].description = "Updated description"
+        """
+        # Get a workflow table path and fetch all workflows
+        workflow_path = self.pathBuilder().schemas[self.ml_schema].Workflow
+        workflows = []
+        for w in workflow_path.entities().fetch():
+            workflow = Workflow(
+                name=w["Name"],
+                url=w["URL"],
+                workflow_type=w["Workflow_Type"],
+                version=w["Version"],
+                description=w["Description"],
+                rid=w["RID"],
+                checksum=w["Checksum"],
+            )
+            # Bind the workflow to this catalog instance
+            workflow._ml_instance = self  # type: ignore[assignment]
+            workflows.append(workflow)
+        return workflows
+
+    def add_workflow(self, workflow: Workflow) -> RID:
+        """Adds a workflow to the catalog.
+
+        Registers a new workflow in the catalog or returns the RID of an existing workflow with the same
+        URL or checksum.
+
+        Each workflow represents a specific computational process or analysis pipeline.
+
+        Args:
+            workflow: Workflow object containing name, URL, type, version, and description.
+
+        Returns:
+            RID: Resource Identifier of the added or existing workflow.
+
+        Raises:
+            DerivaMLException: If workflow insertion fails or required fields are missing.
+
+        Examples:
+            >>> workflow = Workflow(
+            ...     name="Gene Analysis",
+            ...     url="https://github.com/org/repo/workflows/gene_analysis.py",
+            ...     workflow_type="python_script",
+            ...     version="1.0.0",
+            ...     description="Analyzes gene expression patterns"
+            ... )
+            >>> workflow_rid = ml.add_workflow(workflow)
+        """
+        # Check if a workflow already exists by URL or checksum
+        if workflow_rid := self._find_workflow_rid_by_url(workflow.checksum or workflow.url):
+            return workflow_rid
+
+        # Get an ML schema path for the workflow table
+        ml_schema_path = self.pathBuilder().schemas[self.ml_schema]
+
+        try:
+            # Create a workflow record
+            workflow_record = {
+                "URL": workflow.url,
+                "Name": workflow.name,
+                "Description": workflow.description,
+                "Checksum": workflow.checksum,
+                "Version": workflow.version,
+                MLVocab.workflow_type: self.lookup_term(MLVocab.workflow_type, workflow.workflow_type).name,
+            }
+            # Insert a workflow and get its RID
+            workflow_rid = ml_schema_path.Workflow.insert([workflow_record])[0]["RID"]
+        except Exception as e:
+            error = format_exception(e)
+            raise DerivaMLException(f"Failed to insert workflow. Error: {error}")
+        return workflow_rid
+
+    def lookup_workflow(self, rid: RID) -> Workflow:
+        """Look up a workflow by its Resource Identifier (RID).
+
+        Retrieves a workflow from the catalog by its RID and returns a Workflow
+        object bound to the catalog. The returned Workflow can be modified (e.g.,
+        updating its description) and changes will be reflected in the catalog.
+
+        Args:
+            rid: Resource Identifier of the workflow to look up.
+
+        Returns:
+            Workflow: The workflow object bound to this catalog, allowing
+                properties like ``description`` to be updated.
+
+        Raises:
+            DerivaMLException: If the RID does not correspond to a workflow
+                in the catalog.
+
+        Examples:
+            Look up a workflow and read its properties::
+
+                >>> workflow = ml.lookup_workflow("2-ABC1")
+                >>> print(f"Name: {workflow.name}")
+                >>> print(f"Description: {workflow.description}")
+                >>> print(f"Type: {workflow.workflow_type}")
+
+            Update a workflow's description (persisted to catalog)::
+
+                >>> workflow = ml.lookup_workflow("2-ABC1")
+                >>> workflow.description = "Updated analysis pipeline for RNA sequences"
+                >>> # The change is immediately written to the catalog
+
+            Attempting to update on a read-only catalog raises an error::
+
+                >>> snapshot = ml.catalog_snapshot("2023-01-15T10:30:00")
+                >>> workflow = snapshot.lookup_workflow("2-ABC1")
+                >>> workflow.description = "New description"
+                DerivaMLException: Cannot update workflow description on a read-only
+                    catalog snapshot. Use a writable catalog connection instead.
+        """
+        # Get the workflow table path
+        workflow_path = self.pathBuilder().schemas[self.ml_schema].Workflow
+
+        # Filter by RID
+        records = list(workflow_path.filter(workflow_path.RID == rid).entities().fetch())
+
+        if not records:
+            raise DerivaMLException(f"Workflow with RID '{rid}' not found in the catalog")
+
+        w = records[0]
+        workflow = Workflow(
+            name=w["Name"],
+            url=w["URL"],
+            workflow_type=w["Workflow_Type"],
+            version=w["Version"],
+            description=w["Description"],
+            rid=w["RID"],
+            checksum=w["Checksum"],
+        )
+        # Bind the workflow to this catalog instance for write-back support
+        workflow._ml_instance = self  # type: ignore[assignment]
+        return workflow
+
+    def _find_workflow_rid_by_url(self, url_or_checksum: str) -> RID | None:
+        """Internal method to find a workflow RID by URL or checksum.
+
+        Args:
+            url_or_checksum: URL or checksum of the workflow to find.
+
+        Returns:
+            RID: Resource Identifier of the workflow if found, None otherwise.
+        """
+        # Get a workflow table path
+        workflow_path = self.pathBuilder().schemas[self.ml_schema].Workflow
+        workflow_rid = None
+        for w in workflow_path.path.entities().fetch():
+            if w['URL'] == url_or_checksum or w['Checksum'] == url_or_checksum:
+                workflow_rid = w['RID']
+
+        return workflow_rid
+
+    def lookup_workflow_by_url(self, url_or_checksum: str) -> Workflow:
+        """Look up a workflow by URL or checksum and return the full Workflow object.
+
+        Searches for a workflow in the catalog that matches the given URL or
+        checksum and returns a Workflow object bound to the catalog. This allows
+        you to both identify a workflow by its source code location and modify
+        its properties (e.g., description).
+
+        The URL should be a GitHub URL pointing to the specific version of the
+        workflow source code. The format typically includes the commit hash::
+
+            https://github.com/org/repo/blob/<commit_hash>/path/to/workflow.py
+
+        Alternatively, you can search by the Git object hash (checksum) of the
+        workflow file.
+
+        Args:
+            url_or_checksum: GitHub URL with commit hash, or Git object hash
+                (checksum) of the workflow file.
+
+        Returns:
+            Workflow: The workflow object bound to this catalog, allowing
+                properties like ``description`` to be updated.
+
+        Raises:
+            DerivaMLException: If no workflow with the given URL or checksum
+                is found in the catalog.
+
+        Examples:
+            Look up a workflow by its GitHub URL::
+
+                >>> url = "https://github.com/org/repo/blob/abc123/analysis.py"
+                >>> workflow = ml.lookup_workflow_by_url(url)
+                >>> print(f"Found: {workflow.name}")
+                >>> print(f"Version: {workflow.version}")
+
+            Look up by Git object hash (checksum)::
+
+                >>> workflow = ml.lookup_workflow_by_url("abc123def456789...")
+                >>> print(f"Name: {workflow.name}")
+                >>> print(f"URL: {workflow.url}")
+
+            Update the workflow's description after lookup::
+
+                >>> workflow = ml.lookup_workflow_by_url(url)
+                >>> workflow.description = "Updated analysis pipeline"
+                >>> # The change is persisted to the catalog
+
+            Typical GitHub URL formats supported::
+
+                # Full blob URL with commit hash
+                https://github.com/org/repo/blob/abc123def/src/workflow.py
+
+                # The URL is matched exactly, so ensure it matches what was
+                # recorded when the workflow was registered
+        """
+        # Find the RID first
+        rid = self._find_workflow_rid_by_url(url_or_checksum)
+        if rid is None:
+            raise DerivaMLException(
+                f"Workflow with URL or checksum '{url_or_checksum}' not found in the catalog"
+            )
+
+        # Use lookup_workflow to get the full object with catalog binding
+        return self.lookup_workflow(rid)
+
+    def create_workflow(self, name: str, workflow_type: str, description: str = "") -> Workflow:
+        """Creates a new workflow definition.
+
+        Creates a Workflow object that represents a computational process or analysis pipeline. The workflow type
+        must be a term from the controlled vocabulary. This method is typically used to define new analysis
+        workflows before execution.
+
+        Args:
+            name: Name of the workflow.
+            workflow_type: Type of workflow (must exist in workflow_type vocabulary).
+            description: Description of what the workflow does.
+
+        Returns:
+            Workflow: New workflow object ready for registration.
+
+        Raises:
+            DerivaMLException: If workflow_type is not in the vocabulary.
+
+        Examples:
+            >>> workflow = ml.create_workflow(
+            ...     name="RNA Analysis",
+            ...     workflow_type="python_notebook",
+            ...     description="RNA sequence analysis pipeline"
+            ... )
+            >>> rid = ml.add_workflow(workflow)
+        """
+        # Validate workflow type exists in vocabulary
+        self.lookup_term(MLVocab.workflow_type, workflow_type)
+
+        # Create and return a new workflow object
+        return Workflow(name=name, workflow_type=workflow_type, description=description)