napistu 0.2.5.dev6__py3-none-any.whl → 0.3.1__py3-none-any.whl

napistu/network/data_handling.py

@@ -0,0 +1,388 @@
+import logging
+import re
+from typing import Union, List, Optional, Callable, Dict
+
+import pandas as pd
+
+from napistu import sbml_dfs_core
+from napistu.network import net_create
+from napistu.network.napistu_graph_core import NapistuGraph
+
+from napistu.constants import SBML_DFS, ENTITIES_W_DATA
+from napistu.network.constants import NAPISTU_GRAPH, DEFAULT_WT_TRANS, WEIGHTING_SPEC
+
+logger = logging.getLogger(__name__)
+
+
+def add_results_table_to_graph(
+    napistu_graph: NapistuGraph,
+    sbml_dfs: sbml_dfs_core.SBML_dfs,
+    attribute_names: Optional[Union[str, List[str]]] = None,
+    table_name: str = None,
+    table_type: str = SBML_DFS.SPECIES,
+    graph_attr_modified: str = NAPISTU_GRAPH.VERTICES,
+    transformation: Optional[Callable] = None,
+    custom_transformations: Optional[Dict[str, Callable]] = None,
+    inplace: bool = True,
+):
+    """
+    Add Results Table to Graph
+
+    This function extracts one or more attributes from an sbml_dfs species_data table, applies an optional transformation, and adds the result as a vertex attributes to a Napistu graph.
+
+    Parameters
+    ----------
+    napistu_graph: NapistuGraph
+        The Napistu graph to which attributes will be added.
+    sbml_dfs: sbml_dfs_core.SBML_dfs
+        The sbml_dfs object containing the species_data table.
+    attribute_names: str or list of str, optional
+        Either:
+            - The name of the attribute to add to the graph.
+            - A list of attribute names to add to the graph.
+            - A regular expression pattern to match attribute names.
+            - If None, all attributes in the species_data table will be added.
+    table_name: str, optional
+        The name of the species_data table to use. If not provided, then a single table will be expected in species_data.
+    table_type: str, optional
+        The type of table to use (e.g., species for species_data, reactions for reaction_data). Currently, only species is supproted.
+    graph_attr_modified: str, optional
+        The type of graph attribute to modify: vertices or edges. Certain table_types can only modify vertices (species) while others can modify either vertices or edges (reactions). Currently, ignore.
+    transformation: str or Callable, optional
+        Either:
+            - the name of a function in custom_transformations or DEFINED_WEIGHT_TRANSFORMATION.
+            - A function to apply to the attribute.
+        If not provided, the attribute will not be transformed.
+    custom_transformations: dict, optional
+        A dictionary of custom transformations which could be applied to the attributes. The keys are the transformation names and the values are the transformation functions.
+    inplace: bool, optional
+        If True, the attribute will be added to the graph in place. If False, a new graph will be returned.
+
+    Returns
+    -------
+    napistu_graph: NapistuGraph
+        If inplace is False, the Napistu graph with attributes added.
+    """
+
+    if not inplace:
+        napistu_graph = napistu_graph.copy()
+
+    if table_type not in ENTITIES_W_DATA:
+        raise ValueError(
+            f"Invalid table_type: {table_type}. Must be one of {ENTITIES_W_DATA}"
+        )
+    if table_type == SBML_DFS.REACTIONS:
+        raise NotImplementedError("Reactions are not yet supported")
+
+    if graph_attr_modified != NAPISTU_GRAPH.VERTICES:
+        raise NotImplementedError(
+            f"graph_attr_modified must be {NAPISTU_GRAPH.VERTICES}"
+        )
+
+    # load the to-be-added table
+    logger.debug(f"Loading table {table_name} from {table_type}_data")
+    data_table = _select_sbml_dfs_data_table(sbml_dfs, table_name, table_type)
+
+    # filter to attributes of interest
+    logger.debug("Creating a mapping of attributes to add")
+    attribute_mapping = _create_data_table_column_mapping(
+        data_table, attribute_names, table_type
+    )
+
+    if transformation is None:
+        transformation = DEFAULT_WT_TRANS
+
+    # create the configuration dict which is used by lower-level functions
+    reaction_attrs = _create_graph_attrs_config(
+        column_mapping=attribute_mapping,
+        data_type=table_type,
+        table_name=table_name,
+        transformation=transformation,
+    )
+
+    # add the attribute to the graph
+    napistu_graph = _add_graph_species_attribute(
+        napistu_graph,
+        sbml_dfs,
+        species_graph_attrs=reaction_attrs,
+        custom_transformations=custom_transformations,
+    )
+
+    return napistu_graph if not inplace else None
+
+
+def _add_graph_species_attribute(
+    napistu_graph: NapistuGraph,
+    sbml_dfs: sbml_dfs_core.SBML_dfs,
+    species_graph_attrs: dict,
+    custom_transformations: Optional[dict] = None,
+) -> NapistuGraph:
+    """
+    Add meta-data from species_data to existing igraph's vertices.
+
+    This function augments the vertices of an igraph network with additional attributes
+    derived from the species-level data in the provided SBML_dfs object. The attributes
+    to add are specified in the species_graph_attrs dictionary, and can be transformed
+    using either built-in or user-supplied transformation functions.
+
+    Parameters
+    ----------
+    napistu_graph : NapistuGraph
+        The igraph network to augment.
+    sbml_dfs : sbml_dfs_core.SBML_dfs
+        The SBML_dfs object containing species data.
+    species_graph_attrs : dict
+        Dictionary specifying which attributes to pull from species_data and how to transform them.
+        The structure should be {attribute_name: {"table": ..., "variable": ..., "trans": ...}}.
+    custom_transformations : dict, optional
+        Dictionary mapping transformation names to functions. If provided, these will be checked
+        before built-in transformations. Example: {"square": lambda x: x**2}
+
+    Returns
+    -------
+    NapistuGraph
+        The input igraph network with additional vertex attributes added from species_data.
+    """
+    if not isinstance(species_graph_attrs, dict):
+        raise TypeError(
+            f"species_graph_attrs must be a dict, but was {type(species_graph_attrs)}"
+        )
+
+    # fail fast if species_graph_attrs is not properly formatted
+    # also flatten attribute list to be added to vertex nodes
+    sp_graph_key_list = []
+    sp_node_attr_list = []
+    for k in species_graph_attrs.keys():
+        net_create._validate_entity_attrs(
+            species_graph_attrs[k], custom_transformations=custom_transformations
+        )
+
+        sp_graph_key_list.append(k)
+        sp_node_attr_list.append(list(species_graph_attrs[k].keys()))
+
+    # flatten sp_node_attr_list
+    flat_sp_node_attr_list = [item for items in sp_node_attr_list for item in items]
+
+    # Check for attribute collisions before proceeding
+    existing_attrs = set(napistu_graph.vs.attributes())
+    for attr in flat_sp_node_attr_list:
+        if attr in existing_attrs:
+            raise ValueError(f"Attribute '{attr}' already exists in graph vertices")
+
+    logger.info("Adding meta-data from species_data")
+
+    curr_network_nodes_df = napistu_graph.get_vertex_dataframe()
+
+    # add species-level attributes to nodes dataframe
+    augmented_network_nodes_df = net_create._augment_network_nodes(
+        curr_network_nodes_df,
+        sbml_dfs,
+        species_graph_attrs,
+        custom_transformations=custom_transformations,
+    )
+
+    # Add each attribute to the graph vertices
+    for vs_attr in flat_sp_node_attr_list:
+        logger.info(f"Adding new attribute {vs_attr} to vertices")
+        napistu_graph.vs[vs_attr] = augmented_network_nodes_df[vs_attr].values
+
+    return napistu_graph
+
+
+def _select_sbml_dfs_data_table(
+    sbml_dfs: sbml_dfs_core.SBML_dfs,
+    table_name: Optional[str] = None,
+    table_type: str = SBML_DFS.SPECIES,
+) -> pd.DataFrame:
+    """
+    Select an SBML_dfs data table by name and type.
+
+    This function validates the table type and name and returns the table.
+
+    Parameters
+    ----------
+    sbml_dfs: sbml_dfs_core.SBML_dfs
+        The sbml_dfs object containing the data tables.
+    table_name: str, optional
+        The name of the table to select. If not provided, the first table of the given type will be returned.
+    table_type: str, optional
+        The type of table to select. Must be one of {VALID_SBML_DFS_DATA_TYPES}.
+
+    Returns
+    -------
+    entity_data: pd.DataFrame
+    """
+
+    # validate table_type
+    if table_type not in ENTITIES_W_DATA:
+        raise ValueError(
+            f"Invalid table_type: {table_type}. Must be one of {ENTITIES_W_DATA}"
+        )
+    table_type_data_attr = f"{table_type}_data"
+
+    # validate table_name
+    data_attr = getattr(sbml_dfs, table_type_data_attr)
+
+    if len(data_attr) == 0:
+        raise ValueError(f"No {table_type} data found in sbml_dfs")
+    valid_table_names = list(data_attr.keys())
+
+    if table_name is None:
+        if len(data_attr) != 1:
+            raise ValueError(
+                f"Expected a single {table_type} data table but found {len(data_attr)}"
+            )
+        table_name = valid_table_names[0]
+
+    if table_name not in valid_table_names:
+        raise ValueError(
+            f"Invalid table_name: {table_name}. Must be one of {valid_table_names}"
+        )
+
+    entity_data = data_attr[table_name]
+
+    return entity_data
+
+
+def _create_data_table_column_mapping(
+    entity_data: pd.DataFrame,
+    attribute_names: Union[str, List[str], Dict[str, str]],
+    table_type: Optional[str] = SBML_DFS.SPECIES,
+) -> Dict[str, str]:
+    """
+    Select attributes from an sbml_dfs data table.
+
+    This function validates the attribute names and returns a mapping of original names to new names.
+
+    Parameters
+    ----------
+    entity_data: pd.DataFrame
+        The data table to select attributes from.
+    attribute_names: str or list of str, optional
+        Either:
+            - The name of the attribute to add to the graph.
+            - A list of attribute names to add to the graph.
+            - A regular expression pattern to match attribute names.
+            - A dictionary with attributes as names and re-named attributes as values.
+            - If None, all attributes in the species_data table will be added.
+    table_type: str, optional
+        The type of table to use. Must be one of {VALID_SBML_DFS_DATA_TYPES}. (Only used for error messages).
+
+    Returns
+    -------
+    Dict[str, str]
+        A dictionary mapping original column names to their new names.
+        For non-renamed columns, the mapping will be identity (original -> original).
+    """
+    valid_data_table_columns = entity_data.columns.tolist()
+
+    # select the attributes to add
+    if attribute_names is None:
+        # For None, create identity mapping for all columns
+        return {col: col for col in valid_data_table_columns}
+    elif isinstance(attribute_names, str):
+        # try to find an exact match
+        if attribute_names in valid_data_table_columns:
+            return {attribute_names: attribute_names}
+        else:
+            # try to find a regex match
+            matching_attrs = [
+                attr
+                for attr in valid_data_table_columns
+                if re.match(attribute_names, attr)
+            ]
+            if len(matching_attrs) == 0:
+                raise ValueError(
+                    f"No attributes found matching {attribute_names} as a literal or regular expression. Valid attributes: {valid_data_table_columns}"
+                )
+            return {attr: attr for attr in matching_attrs}
+    elif isinstance(attribute_names, list):
+        # Validate that all attributes exist
+        invalid_attributes = [
+            attr for attr in attribute_names if attr not in valid_data_table_columns
+        ]
+        if len(invalid_attributes) > 0:
+            raise ValueError(
+                f"The following attributes were missing from the {table_type}_data table: {invalid_attributes}. Valid attributes: {valid_data_table_columns}"
+            )
+        return {attr: attr for attr in attribute_names}
+    elif isinstance(attribute_names, dict):
+        # validate the keys exist in the table
+        invalid_keys = [
+            key for key in attribute_names.keys() if key not in valid_data_table_columns
+        ]
+        if len(invalid_keys) > 0:
+            raise ValueError(
+                f"The following source columns were missing from the {table_type}_data table: {invalid_keys}. Valid columns: {valid_data_table_columns}"
+            )
+
+        # validate that new column names don't conflict with existing ones
+        # except when a column is being renamed to itself
+        conflicting_names = [
+            new_name
+            for old_name, new_name in attribute_names.items()
+            if new_name in valid_data_table_columns and new_name != old_name
+        ]
+        if conflicting_names:
+            raise ValueError(
+                f"The following new column names conflict with existing columns: {conflicting_names}"
+            )
+
+        if len(attribute_names) == 0:
+            raise ValueError(
+                f"No attributes found in the dictionary. Valid attributes: {valid_data_table_columns}"
+            )
+
+        return attribute_names
+    else:
+        # shouldn't be reached - for clarity
+        raise ValueError(
+            f"Invalid type for attribute_names: {type(attribute_names)}. Must be str, list, dict, or None."
+        )
+
+
+def _create_graph_attrs_config(
+    column_mapping: Dict[str, str],
+    data_type: str,
+    table_name: str,
+    transformation: str = DEFAULT_WT_TRANS,
+) -> Dict[str, Dict[str, Dict[str, str]]]:
+    """
+    Create a configuration dictionary for graph attributes.
+
+    Parameters
+    ----------
+    column_mapping : Dict[str, str]
+        A dictionary mapping original column names to their new names in the graph
+    data_type : str
+        The type of data (e.g. "species", "reactions")
+    table_name : str
+        The name of the table containing the data
+    transformation : str, optional
+        The transformation to apply to the data, by default "identity"
+
+    Returns
+    -------
+    Dict[str, Dict[str, Dict[str, str]]]
+        A nested dictionary containing the graph attributes configuration
+        Format:
+        {
+            data_type: {
+                new_col_name: {
+                    "table": table_name,
+                    "variable": original_col_name,
+                    "trans": transformation
+                }
+            }
+        }
+    """
+    graph_attrs = {data_type: {}}
+
+    for original_col, new_col in column_mapping.items():
+        graph_attrs[data_type][new_col] = {
+            WEIGHTING_SPEC.TABLE: table_name,
+            WEIGHTING_SPEC.VARIABLE: original_col,
+            WEIGHTING_SPEC.TRANSFORMATION: transformation,
+        }
+
+    return graph_attrs