deriva-ml 1.17.9__py3-none-any.whl → 1.17.11__py3-none-any.whl

deriva_ml/model/annotations.py

@@ -0,0 +1,1278 @@
+"""Annotation helper classes for DerivaML.
+
+This module provides lightweight helper classes for building Deriva catalog
+annotations that control how data is displayed in the Chaise web interface.
+
+These builders provide:
+
+- **IDE autocompletion** - Type hints for all annotation properties
+- **Validation** - Catches errors at construction time (e.g., mutually exclusive options)
+- **Reduced typos** - Use `Display(name="...")` instead of `{"name": "..."}`
+- **Self-documenting code** - Easier to read than raw dictionaries
+- **Method chaining** - Fluent API for building complex annotations
+
+For the full annotation schema, see the Deriva documentation at:
+https://docs.derivacloud.org/chaise/annotation/
+
+Quick Start
+-----------
+Basic usage with a TableHandle::
+
+    from deriva_ml.model import TableHandle, Display, VisibleColumns, TableDisplay
+
+    # Get a table handle
+    handle = TableHandle(table)
+
+    # Set display name
+    handle.set_annotation(Display(name="Research Subjects"))
+
+    # Configure visible columns
+    vc = VisibleColumns()
+    vc.compact(["RID", "Name", "Status"])
+    vc.detailed(["RID", "Name", "Status", "Description", "Created"])
+    handle.set_annotation(vc)
+
+    # Set row name pattern
+    td = TableDisplay()
+    td.row_name("{{{Name}}} ({{{RID}}})")
+    handle.set_annotation(td)
+
+Available Builders
+------------------
+**Main annotation builders:**
+
+- `Display` - Basic display properties (name, comment, show_null)
+- `VisibleColumns` - Which columns appear in each UI context
+- `VisibleForeignKeys` - Which related tables appear in detail view
+- `TableDisplay` - Row naming, ordering, and table-level options
+- `ColumnDisplay` - Column value formatting
+
+**Helper classes:**
+
+- `PseudoColumn` - Computed columns, FK traversals, aggregates
+- `Facet` / `FacetList` - Faceted search configuration
+- `SortKey` - Row ordering specification
+- `InboundFK` / `OutboundFK` - Foreign key path steps
+- `NameStyle` - Display name styling
+- `PreFormat` - Column pre-formatting (printf, boolean display)
+
+**Enums:**
+
+- `TemplateEngine` - HANDLEBARS or MUSTACHE
+- `Aggregate` - MIN, MAX, CNT, CNT_D, ARRAY, ARRAY_D
+- `ArrayUxMode` - RAW, CSV, OLIST, ULIST
+- `FacetUxMode` - CHOICES, RANGES, CHECK_PRESENCE
+
+**Context constants:**
+
+- `CONTEXT_DEFAULT` ("*") - Default for all contexts
+- `CONTEXT_COMPACT` - List/table views
+- `CONTEXT_DETAILED` - Single record view
+- `CONTEXT_ENTRY` - Create/edit forms
+- `CONTEXT_FILTER` - Faceted search
+
+Examples
+--------
+Display annotation with description::
+
+    display = Display(
+        name="Research Subjects",
+        comment="Individuals enrolled in the study"
+    )
+
+Visible columns with FK and pseudo-column::
+
+    from deriva_ml.model import fk_constraint, PseudoColumn, InboundFK, Aggregate
+
+    vc = VisibleColumns()
+    vc.compact([
+        "RID",
+        "Name",
+        fk_constraint("domain", "Subject_Species_fkey"),
+        PseudoColumn(
+            source=[InboundFK("domain", "Sample_Subject_fkey"), "RID"],
+            aggregate=Aggregate.CNT,
+            markdown_name="Samples"
+        ),
+    ])
+
+Table display with row name and ordering::
+
+    td = TableDisplay()
+    td.row_name("{{{Name}}} ({{{Species}}})")
+    td.compact(TableDisplayOptions(
+        row_order=[SortKey("Name"), SortKey("Created", descending=True)],
+        page_size=50
+    ))
+
+Faceted search configuration::
+
+    facets = FacetList()
+    facets.add(Facet(source="Species", open=True))
+    facets.add(Facet(source="Age", ux_mode=FacetUxMode.RANGES))
+
+    vc = VisibleColumns()
+    vc._contexts["filter"] = facets.to_dict()
+
+Using Raw Dictionaries
+----------------------
+The builders are optional. You can always use raw dictionaries::
+
+    table.annotations["tag:isrd.isi.edu,2016:visible-columns"] = {
+        "compact": ["RID", "Name"],
+        "detailed": ["RID", "Name", "Description"]
+    }
+    table.apply()
+"""
+
+from __future__ import annotations
+
+from dataclasses import dataclass, field
+from enum import Enum
+from typing import Any, Literal
+
+
+# =============================================================================
+# Enums for constrained values
+# =============================================================================
+
+class TemplateEngine(str, Enum):
+    """Template engine for markdown patterns.
+
+    Attributes:
+        HANDLEBARS: Use Handlebars.js templating (recommended, more features)
+        MUSTACHE: Use Mustache templating (simpler, fewer features)
+
+    Example:
+        >>> display = PseudoColumnDisplay(
+        ...     markdown_pattern="[{{{Name}}}]({{{URL}}})",
+        ...     template_engine=TemplateEngine.HANDLEBARS
+        ... )
+    """
+    HANDLEBARS = "handlebars"
+    MUSTACHE = "mustache"
+
+
+class Aggregate(str, Enum):
+    """Aggregation functions for pseudo-columns.
+
+    Used when a pseudo-column follows an inbound foreign key and returns
+    multiple values that need to be aggregated.
+
+    Attributes:
+        MIN: Minimum value
+        MAX: Maximum value
+        CNT: Count of values
+        CNT_D: Count of distinct values
+        ARRAY: Array of all values
+        ARRAY_D: Array of distinct values
+
+    Example:
+        >>> # Count related records
+        >>> pc = PseudoColumn(
+        ...     source=[InboundFK("domain", "Sample_Subject_fkey"), "RID"],
+        ...     aggregate=Aggregate.CNT,
+        ...     markdown_name="Sample Count"
+        ... )
+        >>>
+        >>> # Get distinct values as array
+        >>> pc = PseudoColumn(
+        ...     source=[InboundFK("domain", "Tag_Item_fkey"), "Name"],
+        ...     aggregate=Aggregate.ARRAY_D,
+        ...     markdown_name="Tags"
+        ... )
+    """
+    MIN = "min"
+    MAX = "max"
+    CNT = "cnt"
+    CNT_D = "cnt_d"
+    ARRAY = "array"
+    ARRAY_D = "array_d"
+
+
+class ArrayUxMode(str, Enum):
+    """Display modes for array values in pseudo-columns.
+
+    Controls how arrays of values are rendered in the UI.
+
+    Attributes:
+        RAW: Raw array display
+        CSV: Comma-separated values
+        OLIST: Ordered (numbered) list
+        ULIST: Unordered (bulleted) list
+
+    Example:
+        >>> pc = PseudoColumn(
+        ...     source=[InboundFK("domain", "Tag_Item_fkey"), "Name"],
+        ...     aggregate=Aggregate.ARRAY,
+        ...     display=PseudoColumnDisplay(array_ux_mode=ArrayUxMode.CSV)
+        ... )
+    """
+    RAW = "raw"
+    CSV = "csv"
+    OLIST = "olist"
+    ULIST = "ulist"
+
+
+class FacetUxMode(str, Enum):
+    """UX modes for facet filters in the search panel.
+
+    Controls how users interact with a facet filter.
+
+    Attributes:
+        CHOICES: Checkbox list for selecting values
+        RANGES: Range slider/inputs for numeric or date ranges
+        CHECK_PRESENCE: Check if value exists or is null
+
+    Example:
+        >>> # Choice-based facet
+        >>> Facet(source="Status", ux_mode=FacetUxMode.CHOICES)
+        >>>
+        >>> # Range-based facet for numeric values
+        >>> Facet(source="Age", ux_mode=FacetUxMode.RANGES)
+        >>>
+        >>> # Check presence (has value / no value)
+        >>> Facet(source="Notes", ux_mode=FacetUxMode.CHECK_PRESENCE)
+    """
+    CHOICES = "choices"
+    RANGES = "ranges"
+    CHECK_PRESENCE = "check_presence"
+
+
+# =============================================================================
+# Context Names
+# =============================================================================
+
+# Standard context names
+CONTEXT_DEFAULT = "*"
+CONTEXT_COMPACT = "compact"
+CONTEXT_COMPACT_BRIEF = "compact/brief"
+CONTEXT_COMPACT_BRIEF_INLINE = "compact/brief/inline"
+CONTEXT_COMPACT_SELECT = "compact/select"
+CONTEXT_DETAILED = "detailed"
+CONTEXT_ENTRY = "entry"
+CONTEXT_ENTRY_CREATE = "entry/create"
+CONTEXT_ENTRY_EDIT = "entry/edit"
+CONTEXT_EXPORT = "export"
+CONTEXT_FILTER = "filter"
+CONTEXT_ROW_NAME = "row_name"
+
+
+# =============================================================================
+# Annotation Tag URIs
+# =============================================================================
+
+TAG_DISPLAY = "tag:isrd.isi.edu,2015:display"
+TAG_VISIBLE_COLUMNS = "tag:isrd.isi.edu,2016:visible-columns"
+TAG_VISIBLE_FOREIGN_KEYS = "tag:isrd.isi.edu,2016:visible-foreign-keys"
+TAG_TABLE_DISPLAY = "tag:isrd.isi.edu,2016:table-display"
+TAG_COLUMN_DISPLAY = "tag:isrd.isi.edu,2016:column-display"
+TAG_SOURCE_DEFINITIONS = "tag:isrd.isi.edu,2019:source-definitions"
+
+
+# =============================================================================
+# Base Protocol for Annotations
+# =============================================================================
+
+class AnnotationBuilder:
+    """Base class for annotation builders.
+
+    Subclasses must implement:
+    - tag: The annotation tag URI
+    - to_dict(): Convert to dictionary representation
+    """
+
+    tag: str
+
+    def to_dict(self) -> dict[str, Any]:
+        """Convert to dictionary suitable for catalog annotation."""
+        raise NotImplementedError
+
+
+# =============================================================================
+# Display Annotation
+# =============================================================================
+
+@dataclass
+class NameStyle:
+    """Styling options for automatic display name formatting.
+
+    Applied to table or column names when no explicit display name is set.
+
+    Args:
+        underline_space: Replace underscores with spaces (e.g., "First_Name" -> "First Name")
+        title_case: Apply title case formatting (e.g., "firstname" -> "Firstname")
+        markdown: Render the name as markdown
+
+    Example:
+        >>> # Transform "Subject_ID" to "Subject Id" with title case
+        >>> display = Display(
+        ...     name_style=NameStyle(underline_space=True, title_case=True)
+        ... )
+    """
+    underline_space: bool | None = None
+    title_case: bool | None = None
+    markdown: bool | None = None
+
+    def to_dict(self) -> dict[str, bool]:
+        """Convert to dictionary, excluding None values."""
+        result = {}
+        if self.underline_space is not None:
+            result["underline_space"] = self.underline_space
+        if self.title_case is not None:
+            result["title_case"] = self.title_case
+        if self.markdown is not None:
+            result["markdown"] = self.markdown
+        return result
+
+
+@dataclass
+class Display(AnnotationBuilder):
+    """Display annotation for tables and columns.
+
+    Controls the display name, description/tooltip, and how null values
+    and foreign key links are rendered. Can be applied to both tables
+    and columns.
+
+    Args:
+        name: Display name shown in the UI (mutually exclusive with markdown_name)
+        markdown_name: Markdown-formatted display name (mutually exclusive with name)
+        name_style: Styling options for automatic name formatting
+        comment: Description text shown as tooltip/help text
+        show_null: How to display null values, per context
+        show_foreign_key_link: Whether to show FK values as links, per context
+
+    Raises:
+        ValueError: If both name and markdown_name are provided
+
+    Example:
+        Basic display name::
+
+            >>> display = Display(name="Research Subjects")
+            >>> handle.set_annotation(display)
+
+        With description/tooltip::
+
+            >>> display = Display(
+            ...     name="Subjects",
+            ...     comment="Individuals enrolled in research studies"
+            ... )
+
+        Markdown-formatted name::
+
+            >>> display = Display(markdown_name="**Bold** _Italic_ Name")
+
+        Context-specific null display::
+
+            >>> from deriva_ml.model import CONTEXT_COMPACT, CONTEXT_DETAILED
+            >>> display = Display(
+            ...     name="Value",
+            ...     show_null={
+            ...         CONTEXT_COMPACT: False,      # Hide nulls in lists
+            ...         CONTEXT_DETAILED: '"N/A"'    # Show "N/A" string
+            ...     }
+            ... )
+
+        Control foreign key link display::
+
+            >>> display = Display(
+            ...     name="Subject",
+            ...     show_foreign_key_link={CONTEXT_COMPACT: False}
+            ... )
+    """
+    tag = TAG_DISPLAY
+
+    name: str | None = None
+    markdown_name: str | None = None
+    name_style: NameStyle | None = None
+    comment: str | None = None
+    show_null: dict[str, bool | str] | None = None
+    show_foreign_key_link: dict[str, bool] | None = None
+
+    def __post_init__(self):
+        if self.name and self.markdown_name:
+            raise ValueError("name and markdown_name are mutually exclusive")
+
+    def to_dict(self) -> dict[str, Any]:
+        result = {}
+        if self.name is not None:
+            result["name"] = self.name
+        if self.markdown_name is not None:
+            result["markdown_name"] = self.markdown_name
+        if self.name_style is not None:
+            style_dict = self.name_style.to_dict()
+            if style_dict:
+                result["name_style"] = style_dict
+        if self.comment is not None:
+            result["comment"] = self.comment
+        if self.show_null is not None:
+            result["show_null"] = self.show_null
+        if self.show_foreign_key_link is not None:
+            result["show_foreign_key_link"] = self.show_foreign_key_link
+        return result
+
+
+# =============================================================================
+# Sort Key
+# =============================================================================
+
+@dataclass
+class SortKey:
+    """A sort key for row ordering.
+
+    Args:
+        column: Column name to sort by
+        descending: Sort in descending order (default False)
+
+    Example:
+        >>> SortKey("Name")  # Ascending
+        >>> SortKey("Created", descending=True)  # Descending
+    """
+    column: str
+    descending: bool = False
+
+    def to_dict(self) -> dict[str, Any] | str:
+        """Convert to dict or string (if ascending)."""
+        if self.descending:
+            return {"column": self.column, "descending": True}
+        return self.column
+
+
+# =============================================================================
+# Foreign Key Path Components
+# =============================================================================
+
+@dataclass
+class InboundFK:
+    """An inbound foreign key path step for pseudo-column source paths.
+
+    Use this when following a foreign key FROM another table TO the current table.
+    This is common when counting or aggregating related records.
+
+    Args:
+        schema: Schema name containing the FK constraint
+        constraint: Foreign key constraint name
+
+    Example:
+        Count images related to a subject (Image has FK to Subject)::
+
+            >>> # In Subject table, count related images
+            >>> pc = PseudoColumn(
+            ...     source=[InboundFK("domain", "Image_Subject_fkey"), "RID"],
+            ...     aggregate=Aggregate.CNT,
+            ...     markdown_name="Image Count"
+            ... )
+    """
+    schema: str
+    constraint: str
+
+    def to_dict(self) -> dict[str, list[str]]:
+        return {"inbound": [self.schema, self.constraint]}
+
+
+@dataclass
+class OutboundFK:
+    """An outbound foreign key path step for pseudo-column source paths.
+
+    Use this when following a foreign key FROM the current table TO another table.
+    This is common when displaying values from referenced tables.
+
+    Args:
+        schema: Schema name containing the FK constraint
+        constraint: Foreign key constraint name
+
+    Example:
+        Show species name from a related Species table::
+
+            >>> # Subject has FK to Species, display Species.Name
+            >>> pc = PseudoColumn(
+            ...     source=[OutboundFK("domain", "Subject_Species_fkey"), "Name"],
+            ...     markdown_name="Species"
+            ... )
+
+        Chain multiple outbound FKs::
+
+            >>> # Image -> Subject -> Species
+            >>> pc = PseudoColumn(
+            ...     source=[
+            ...         OutboundFK("domain", "Image_Subject_fkey"),
+            ...         OutboundFK("domain", "Subject_Species_fkey"),
+            ...         "Name"
+            ...     ],
+            ...     markdown_name="Species"
+            ... )
+    """
+    schema: str
+    constraint: str
+
+    def to_dict(self) -> dict[str, list[str]]:
+        return {"outbound": [self.schema, self.constraint]}
+
+
+def fk_constraint(schema: str, constraint: str) -> list[str]:
+    """Create a foreign key constraint reference for visible-columns.
+
+    Use this in visible-columns to include a foreign key column (showing the
+    referenced row's name/link). This is different from InboundFK/OutboundFK
+    which are used inside PseudoColumn source paths.
+
+    Args:
+        schema: Schema name containing the FK constraint
+        constraint: Foreign key constraint name
+
+    Returns:
+        [schema, constraint] list for use in visible-columns
+
+    Example:
+        Include a foreign key in visible columns::
+
+            >>> vc = VisibleColumns()
+            >>> vc.compact([
+            ...     "RID",
+            ...     "Name",
+            ...     fk_constraint("domain", "Subject_Species_fkey"),  # Shows Species
+            ... ])
+
+        This is equivalent to the raw format::
+
+            >>> vc.compact(["RID", "Name", ["domain", "Subject_Species_fkey"]])
+    """
+    return [schema, constraint]
+
+
+# =============================================================================
+# Pseudo-Column Display Options
+# =============================================================================
+
+@dataclass
+class PseudoColumnDisplay:
+    """Display options for a pseudo-column.
+
+    Args:
+        markdown_pattern: Handlebars/mustache template
+        template_engine: Template engine to use
+        show_foreign_key_link: Show as clickable link
+        array_ux_mode: How to render array values
+        column_order: Sort order for the column, or False to disable
+        wait_for: Template variables to wait for before rendering
+    """
+    markdown_pattern: str | None = None
+    template_engine: TemplateEngine | None = None
+    show_foreign_key_link: bool | None = None
+    array_ux_mode: ArrayUxMode | None = None
+    column_order: list[SortKey] | Literal[False] | None = None
+    wait_for: list[str] | None = None
+
+    def to_dict(self) -> dict[str, Any]:
+        result = {}
+        if self.markdown_pattern is not None:
+            result["markdown_pattern"] = self.markdown_pattern
+        if self.template_engine is not None:
+            result["template_engine"] = self.template_engine.value
+        if self.show_foreign_key_link is not None:
+            result["show_foreign_key_link"] = self.show_foreign_key_link
+        if self.array_ux_mode is not None:
+            result["array_ux_mode"] = self.array_ux_mode.value
+        if self.column_order is not None:
+            if self.column_order is False:
+                result["column_order"] = False
+            else:
+                result["column_order"] = [
+                    k.to_dict() if isinstance(k, SortKey) else k
+                    for k in self.column_order
+                ]
+        if self.wait_for is not None:
+            result["wait_for"] = self.wait_for
+        return result
+
+
+# =============================================================================
+# Pseudo-Column (for visible-columns and visible-foreign-keys)
+# =============================================================================
+
+@dataclass
+class PseudoColumn:
+    """A pseudo-column definition for visible columns and foreign keys.
+
+    Pseudo-columns display computed values, values from related tables,
+    or custom markdown patterns. They appear as columns in table views
+    but are not actual database columns.
+
+    Args:
+        source: Path to source data. Can be:
+            - A column name (string)
+            - A list of FK path steps ending with a column name
+        sourcekey: Reference to a named source in source-definitions annotation
+        markdown_name: Display name for the column (supports markdown)
+        comment: Description/tooltip text (or False to hide)
+        entity: Whether this represents an entity (affects rendering)
+        aggregate: Aggregation function when source returns multiple values
+        self_link: Make the value a link to the current row
+        display: Display formatting options
+        array_options: Options for array aggregates (max_length, order)
+
+    Note:
+        source and sourcekey are mutually exclusive. Use source for inline
+        definitions, sourcekey to reference pre-defined sources.
+
+    Raises:
+        ValueError: If both source and sourcekey are provided
+
+    Example:
+        Simple column with custom display name::
+
+            >>> PseudoColumn(source="Internal_ID", markdown_name="ID")
+
+        Outbound FK traversal (display value from referenced table)::
+
+            >>> # Subject has FK to Species - show Species.Name
+            >>> PseudoColumn(
+            ...     source=[OutboundFK("domain", "Subject_Species_fkey"), "Name"],
+            ...     markdown_name="Species"
+            ... )
+
+        Inbound FK with aggregation (count related records)::
+
+            >>> # Count images pointing to this subject
+            >>> PseudoColumn(
+            ...     source=[InboundFK("domain", "Image_Subject_fkey"), "RID"],
+            ...     aggregate=Aggregate.CNT,
+            ...     markdown_name="Images"
+            ... )
+
+        Multi-hop FK path::
+
+            >>> # Image -> Subject -> Species
+            >>> PseudoColumn(
+            ...     source=[
+            ...         OutboundFK("domain", "Image_Subject_fkey"),
+            ...         OutboundFK("domain", "Subject_Species_fkey"),
+            ...         "Name"
+            ...     ],
+            ...     markdown_name="Species"
+            ... )
+
+        With custom display formatting::
+
+            >>> PseudoColumn(
+            ...     source="URL",
+            ...     display=PseudoColumnDisplay(
+            ...         markdown_pattern="[Download]({{{_value}}})",
+            ...         show_foreign_key_link=False
+            ...     )
+            ... )
+
+        Array aggregate with display options::
+
+            >>> PseudoColumn(
+            ...     source=[InboundFK("domain", "Tag_Item_fkey"), "Name"],
+            ...     aggregate=Aggregate.ARRAY_D,
+            ...     display=PseudoColumnDisplay(array_ux_mode=ArrayUxMode.CSV),
+            ...     markdown_name="Tags"
+            ... )
+    """
+    source: str | list[str | InboundFK | OutboundFK] | None = None
+    sourcekey: str | None = None
+    markdown_name: str | None = None
+    comment: str | Literal[False] | None = None
+    entity: bool | None = None
+    aggregate: Aggregate | None = None
+    self_link: bool | None = None
+    display: PseudoColumnDisplay | None = None
+    array_options: dict[str, Any] | None = None  # Can be complex
+
+    def __post_init__(self):
+        if self.source is not None and self.sourcekey is not None:
+            raise ValueError("source and sourcekey are mutually exclusive")
+
+    def to_dict(self) -> dict[str, Any]:
+        result = {}
+
+        if self.source is not None:
+            if isinstance(self.source, str):
+                result["source"] = self.source
+            else:
+                # Convert path elements
+                result["source"] = [
+                    item.to_dict() if hasattr(item, "to_dict") else item
+                    for item in self.source
+                ]
+
+        if self.sourcekey is not None:
+            result["sourcekey"] = self.sourcekey
+        if self.markdown_name is not None:
+            result["markdown_name"] = self.markdown_name
+        if self.comment is not None:
+            result["comment"] = self.comment
+        if self.entity is not None:
+            result["entity"] = self.entity
+        if self.aggregate is not None:
+            result["aggregate"] = self.aggregate.value
+        if self.self_link is not None:
+            result["self_link"] = self.self_link
+        if self.display is not None:
+            result["display"] = self.display.to_dict()
+        if self.array_options is not None:
+            result["array_options"] = self.array_options
+
+        return result
+
+
+# =============================================================================
+# Visible Columns Annotation
+# =============================================================================
+
+# Type for a single column entry
+ColumnEntry = str | list[str] | PseudoColumn
+
+
+@dataclass
+class VisibleColumns(AnnotationBuilder):
+    """Visible-columns annotation builder.
+
+    Controls which columns appear in different UI contexts and their order.
+    This is one of the most commonly used annotations for customizing the
+    Chaise interface.
+
+    Column entries can be:
+    - Column names (strings): "Name", "RID", "Description"
+    - Foreign key references: fk_constraint("schema", "constraint_name")
+    - Pseudo-columns: PseudoColumn(...) for computed/derived values
+
+    Contexts:
+    - ``compact``: Table/list views (search results, data browser)
+    - ``detailed``: Single record view (full record page)
+    - ``entry``: Create/edit forms
+    - ``entry/create``: Create form only
+    - ``entry/edit``: Edit form only
+    - ``*``: Default for all contexts
+
+    Example:
+        Basic column lists for different contexts::
+
+            >>> vc = VisibleColumns()
+            >>> vc.compact(["RID", "Name", "Status"])
+            >>> vc.detailed(["RID", "Name", "Status", "Description", "Created"])
+            >>> vc.entry(["Name", "Status", "Description"])
+            >>> handle.set_annotation(vc)
+
+        Method chaining::
+
+            >>> vc = (VisibleColumns()
+            ...     .compact(["RID", "Name"])
+            ...     .detailed(["RID", "Name", "Description"])
+            ...     .entry(["Name", "Description"]))
+
+        Including foreign key references::
+
+            >>> vc = VisibleColumns()
+            >>> vc.compact([
+            ...     "RID",
+            ...     "Name",
+            ...     fk_constraint("domain", "Subject_Species_fkey"),
+            ... ])
+
+        With pseudo-columns for computed values::
+
+            >>> vc = VisibleColumns()
+            >>> vc.compact([
+            ...     "RID",
+            ...     "Name",
+            ...     PseudoColumn(
+            ...         source=[InboundFK("domain", "Sample_Subject_fkey"), "RID"],
+            ...         aggregate=Aggregate.CNT,
+            ...         markdown_name="Samples"
+            ...     ),
+            ... ])
+
+        Context inheritance (reference another context)::
+
+            >>> vc = VisibleColumns()
+            >>> vc.compact(["RID", "Name"])
+            >>> vc.set_context("compact/brief", "compact")  # Inherit from compact
+
+        With faceted search (filter context)::
+
+            >>> vc = VisibleColumns()
+            >>> vc.compact(["RID", "Name", "Status"])
+            >>> facets = FacetList()
+            >>> facets.add(Facet(source="Status", open=True))
+            >>> vc._contexts["filter"] = facets.to_dict()
+    """
+    tag = TAG_VISIBLE_COLUMNS
+
+    _contexts: dict[str, list[ColumnEntry] | str] = field(default_factory=dict)
+
+    def set_context(
+        self,
+        context: str,
+        columns: list[ColumnEntry] | str
+    ) -> "VisibleColumns":
+        """Set columns for a context.
+
+        Args:
+            context: Context name (e.g., "compact", "detailed", "*")
+            columns: List of columns, or string referencing another context
+
+        Returns:
+            Self for chaining
+        """
+        self._contexts[context] = columns
+        return self
+
+    def compact(self, columns: list[ColumnEntry]) -> "VisibleColumns":
+        """Set columns for compact (list) view."""
+        return self.set_context(CONTEXT_COMPACT, columns)
+
+    def detailed(self, columns: list[ColumnEntry]) -> "VisibleColumns":
+        """Set columns for detailed (record) view."""
+        return self.set_context(CONTEXT_DETAILED, columns)
+
+    def entry(self, columns: list[ColumnEntry]) -> "VisibleColumns":
+        """Set columns for entry (create/edit) forms."""
+        return self.set_context(CONTEXT_ENTRY, columns)
+
+    def entry_create(self, columns: list[ColumnEntry]) -> "VisibleColumns":
+        """Set columns for create form only."""
+        return self.set_context(CONTEXT_ENTRY_CREATE, columns)
+
+    def entry_edit(self, columns: list[ColumnEntry]) -> "VisibleColumns":
+        """Set columns for edit form only."""
+        return self.set_context(CONTEXT_ENTRY_EDIT, columns)
+
+    def default(self, columns: list[ColumnEntry]) -> "VisibleColumns":
+        """Set default columns for all contexts."""
+        return self.set_context(CONTEXT_DEFAULT, columns)
+
+    def to_dict(self) -> dict[str, Any]:
+        result = {}
+        for context, columns in self._contexts.items():
+            if isinstance(columns, str):
+                result[context] = columns
+            else:
+                result[context] = [
+                    c.to_dict() if isinstance(c, PseudoColumn) else c
+                    for c in columns
+                ]
+        return result
+
+
+# =============================================================================
+# Visible Foreign Keys Annotation
+# =============================================================================
+
+# Type for a single FK entry
+ForeignKeyEntry = list[str] | PseudoColumn
+
+
+@dataclass
+class VisibleForeignKeys(AnnotationBuilder):
+    """Visible-foreign-keys annotation builder.
+
+    Controls which related tables appear in the UI via inbound foreign keys.
+
+    Example:
+        >>> vfk = VisibleForeignKeys()
+        >>> vfk.detailed([
+        ...     fk_constraint("domain", "Image_Subject_fkey"),
+        ...     fk_constraint("domain", "Diagnosis_Subject_fkey")
+        ... ])
+    """
+    tag = TAG_VISIBLE_FOREIGN_KEYS
+
+    _contexts: dict[str, list[ForeignKeyEntry] | str] = field(default_factory=dict)
+
+    def set_context(
+        self,
+        context: str,
+        foreign_keys: list[ForeignKeyEntry] | str
+    ) -> "VisibleForeignKeys":
+        """Set foreign keys for a context."""
+        self._contexts[context] = foreign_keys
+        return self
+
+    def detailed(self, foreign_keys: list[ForeignKeyEntry]) -> "VisibleForeignKeys":
+        """Set foreign keys for detailed view."""
+        return self.set_context(CONTEXT_DETAILED, foreign_keys)
+
+    def default(self, foreign_keys: list[ForeignKeyEntry]) -> "VisibleForeignKeys":
+        """Set default foreign keys for all contexts."""
+        return self.set_context(CONTEXT_DEFAULT, foreign_keys)
+
+    def to_dict(self) -> dict[str, Any]:
+        result = {}
+        for context, fkeys in self._contexts.items():
+            if isinstance(fkeys, str):
+                result[context] = fkeys
+            else:
+                result[context] = [
+                    fk.to_dict() if isinstance(fk, PseudoColumn) else fk
+                    for fk in fkeys
+                ]
+        return result
+
+
+# =============================================================================
+# Table Display Annotation
+# =============================================================================
+
+@dataclass
+class TableDisplayOptions:
+    """Options for a single table display context.
+
+    Args:
+        row_order: Sort order for rows
+        page_size: Number of rows per page
+        row_markdown_pattern: Template for row names
+        page_markdown_pattern: Template for page header
+        separator_markdown: Template between rows
+        prefix_markdown: Template before rows
+        suffix_markdown: Template after rows
+        template_engine: Template engine for patterns
+        collapse_toc_panel: Collapse TOC panel
+        hide_column_headers: Hide column headers
+    """
+    row_order: list[SortKey] | None = None
+    page_size: int | None = None
+    row_markdown_pattern: str | None = None
+    page_markdown_pattern: str | None = None
+    separator_markdown: str | None = None
+    prefix_markdown: str | None = None
+    suffix_markdown: str | None = None
+    template_engine: TemplateEngine | None = None
+    collapse_toc_panel: bool | None = None
+    hide_column_headers: bool | None = None
+
+    def to_dict(self) -> dict[str, Any]:
+        result = {}
+        if self.row_order is not None:
+            result["row_order"] = [
+                k.to_dict() if isinstance(k, SortKey) else k
+                for k in self.row_order
+            ]
+        if self.page_size is not None:
+            result["page_size"] = self.page_size
+        if self.row_markdown_pattern is not None:
+            result["row_markdown_pattern"] = self.row_markdown_pattern
+        if self.page_markdown_pattern is not None:
+            result["page_markdown_pattern"] = self.page_markdown_pattern
+        if self.separator_markdown is not None:
+            result["separator_markdown"] = self.separator_markdown
+        if self.prefix_markdown is not None:
+            result["prefix_markdown"] = self.prefix_markdown
+        if self.suffix_markdown is not None:
+            result["suffix_markdown"] = self.suffix_markdown
+        if self.template_engine is not None:
+            result["template_engine"] = self.template_engine.value
+        if self.collapse_toc_panel is not None:
+            result["collapse_toc_panel"] = self.collapse_toc_panel
+        if self.hide_column_headers is not None:
+            result["hide_column_headers"] = self.hide_column_headers
+        return result
+
+
+@dataclass
+class TableDisplay(AnnotationBuilder):
+    """Table-display annotation builder.
+
+    Controls table-level display options like row naming and ordering.
+
+    Example:
+        >>> td = TableDisplay()
+        >>> td.row_name(row_markdown_pattern="{{{Name}}} ({{{Species}}})")
+        >>> td.compact(row_order=[SortKey("Name")])
+    """
+    tag = TAG_TABLE_DISPLAY
+
+    _contexts: dict[str, TableDisplayOptions | str | None] = field(default_factory=dict)
+
+    def set_context(
+        self,
+        context: str,
+        options: TableDisplayOptions | str | None
+    ) -> "TableDisplay":
+        """Set options for a context."""
+        self._contexts[context] = options
+        return self
+
+    def row_name(
+        self,
+        row_markdown_pattern: str,
+        template_engine: TemplateEngine | None = None
+    ) -> "TableDisplay":
+        """Set row name pattern (used in foreign key dropdowns, etc.)."""
+        return self.set_context(
+            CONTEXT_ROW_NAME,
+            TableDisplayOptions(
+                row_markdown_pattern=row_markdown_pattern,
+                template_engine=template_engine
+            )
+        )
+
+    def compact(self, options: TableDisplayOptions) -> "TableDisplay":
+        """Set options for compact (list) view."""
+        return self.set_context(CONTEXT_COMPACT, options)
+
+    def detailed(self, options: TableDisplayOptions) -> "TableDisplay":
+        """Set options for detailed (record) view."""
+        return self.set_context(CONTEXT_DETAILED, options)
+
+    def default(self, options: TableDisplayOptions) -> "TableDisplay":
+        """Set default options."""
+        return self.set_context(CONTEXT_DEFAULT, options)
+
+    def to_dict(self) -> dict[str, Any]:
+        result = {}
+        for context, options in self._contexts.items():
+            if options is None:
+                result[context] = None
+            elif isinstance(options, str):
+                result[context] = options
+            else:
+                result[context] = options.to_dict()
+        return result
+
+
+# =============================================================================
+# Column Display Annotation
+# =============================================================================
+
+@dataclass
+class PreFormat:
+    """Pre-formatting options for column values.
+
+    Args:
+        format: Printf-style format string (e.g., "%.2f")
+        bool_true_value: Display value for True
+        bool_false_value: Display value for False
+    """
+    format: str | None = None
+    bool_true_value: str | None = None
+    bool_false_value: str | None = None
+
+    def to_dict(self) -> dict[str, Any]:
+        result = {}
+        if self.format is not None:
+            result["format"] = self.format
+        if self.bool_true_value is not None:
+            result["bool_true_value"] = self.bool_true_value
+        if self.bool_false_value is not None:
+            result["bool_false_value"] = self.bool_false_value
+        return result
+
+
+@dataclass
+class ColumnDisplayOptions:
+    """Options for displaying a column in a specific context.
+
+    Args:
+        pre_format: Pre-formatting options
+        markdown_pattern: Template for rendering
+        template_engine: Template engine to use
+        column_order: Sort order, or False to disable
+    """
+    pre_format: PreFormat | None = None
+    markdown_pattern: str | None = None
+    template_engine: TemplateEngine | None = None
+    column_order: list[SortKey] | Literal[False] | None = None
+
+    def to_dict(self) -> dict[str, Any]:
+        result = {}
+        if self.pre_format is not None:
+            result["pre_format"] = self.pre_format.to_dict()
+        if self.markdown_pattern is not None:
+            result["markdown_pattern"] = self.markdown_pattern
+        if self.template_engine is not None:
+            result["template_engine"] = self.template_engine.value
+        if self.column_order is not None:
+            if self.column_order is False:
+                result["column_order"] = False
+            else:
+                result["column_order"] = [
+                    k.to_dict() if isinstance(k, SortKey) else k
+                    for k in self.column_order
+                ]
+        return result
+
+
+@dataclass
+class ColumnDisplay(AnnotationBuilder):
+    """Column-display annotation builder.
+
+    Controls how column values are rendered.
+
+    Example:
+        >>> cd = ColumnDisplay()
+        >>> cd.default(ColumnDisplayOptions(
+        ...     pre_format=PreFormat(format="%.2f")
+        ... ))
+        >>>
+        >>> # Markdown link
+        >>> cd = ColumnDisplay()
+        >>> cd.default(ColumnDisplayOptions(
+        ...     markdown_pattern="[Link]({{{_value}}})"
+        ... ))
+    """
+    tag = TAG_COLUMN_DISPLAY
+
+    _contexts: dict[str, ColumnDisplayOptions | str] = field(default_factory=dict)
+
+    def set_context(
+        self,
+        context: str,
+        options: ColumnDisplayOptions | str
+    ) -> "ColumnDisplay":
+        """Set options for a context."""
+        self._contexts[context] = options
+        return self
+
+    def default(self, options: ColumnDisplayOptions) -> "ColumnDisplay":
+        """Set default options."""
+        return self.set_context(CONTEXT_DEFAULT, options)
+
+    def compact(self, options: ColumnDisplayOptions) -> "ColumnDisplay":
+        """Set options for compact view."""
+        return self.set_context(CONTEXT_COMPACT, options)
+
+    def detailed(self, options: ColumnDisplayOptions) -> "ColumnDisplay":
+        """Set options for detailed view."""
+        return self.set_context(CONTEXT_DETAILED, options)
+
+    def to_dict(self) -> dict[str, Any]:
+        result = {}
+        for context, options in self._contexts.items():
+            if isinstance(options, str):
+                result[context] = options
+            else:
+                result[context] = options.to_dict()
+        return result
+
+
+# =============================================================================
+# Facet Entry (for filter context)
+# =============================================================================
+
+@dataclass
+class FacetRange:
+    """A range for facet filtering.
+
+    Args:
+        min: Minimum value
+        max: Maximum value
+        min_exclusive: Exclude min value
+        max_exclusive: Exclude max value
+    """
+    min: float | None = None
+    max: float | None = None
+    min_exclusive: bool | None = None
+    max_exclusive: bool | None = None
+
+    def to_dict(self) -> dict[str, Any]:
+        result = {}
+        if self.min is not None:
+            result["min"] = self.min
+        if self.max is not None:
+            result["max"] = self.max
+        if self.min_exclusive is not None:
+            result["min_exclusive"] = self.min_exclusive
+        if self.max_exclusive is not None:
+            result["max_exclusive"] = self.max_exclusive
+        return result
+
+
+@dataclass
+class Facet:
+    """A facet definition for filtering.
+
+    Args:
+        source: Path to source data
+        sourcekey: Reference to named source
+        markdown_name: Display name
+        comment: Description
+        entity: Whether this is an entity facet
+        open: Start expanded
+        ux_mode: UI mode (choices, ranges, check_presence)
+        bar_plot: Show bar plot
+        choices: Preset choice values
+        ranges: Preset range values
+        not_null: Filter to non-null values
+        hide_null_choice: Hide "null" option
+        hide_not_null_choice: Hide "not null" option
+        n_bins: Number of bins for histogram
+    """
+    source: str | list[str | InboundFK | OutboundFK] | None = None
+    sourcekey: str | None = None
+    markdown_name: str | None = None
+    comment: str | None = None
+    entity: bool | None = None
+    open: bool | None = None
+    ux_mode: FacetUxMode | None = None
+    bar_plot: bool | None = None
+    choices: list[Any] | None = None
+    ranges: list[FacetRange] | None = None
+    not_null: bool | None = None
+    hide_null_choice: bool | None = None
+    hide_not_null_choice: bool | None = None
+    n_bins: int | None = None
+
+    def to_dict(self) -> dict[str, Any]:
+        result = {}
+
+        if self.source is not None:
+            if isinstance(self.source, str):
+                result["source"] = self.source
+            else:
+                result["source"] = [
+                    item.to_dict() if hasattr(item, "to_dict") else item
+                    for item in self.source
+                ]
+
+        if self.sourcekey is not None:
+            result["sourcekey"] = self.sourcekey
+        if self.markdown_name is not None:
+            result["markdown_name"] = self.markdown_name
+        if self.comment is not None:
+            result["comment"] = self.comment
+        if self.entity is not None:
+            result["entity"] = self.entity
+        if self.open is not None:
+            result["open"] = self.open
+        if self.ux_mode is not None:
+            result["ux_mode"] = self.ux_mode.value
+        if self.bar_plot is not None:
+            result["bar_plot"] = self.bar_plot
+        if self.choices is not None:
+            result["choices"] = self.choices
+        if self.ranges is not None:
+            result["ranges"] = [r.to_dict() for r in self.ranges]
+        if self.not_null is not None:
+            result["not_null"] = self.not_null
+        if self.hide_null_choice is not None:
+            result["hide_null_choice"] = self.hide_null_choice
+        if self.hide_not_null_choice is not None:
+            result["hide_not_null_choice"] = self.hide_not_null_choice
+        if self.n_bins is not None:
+            result["n_bins"] = self.n_bins
+
+        return result
+
+
+@dataclass
+class FacetList:
+    """A list of facets for filtering (visible_columns.filter).
+
+    Example:
+        >>> facets = FacetList([
+        ...     Facet(source="Species", open=True),
+        ...     Facet(source="Age", ux_mode=FacetUxMode.RANGES)
+        ... ])
+    """
+    facets: list[Facet] = field(default_factory=list)
+
+    def add(self, facet: Facet) -> "FacetList":
+        """Add a facet to the list."""
+        self.facets.append(facet)
+        return self
+
+    def to_dict(self) -> dict[str, list[dict]]:
+        return {"and": [f.to_dict() for f in self.facets]}