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

napistu/rpy2/rids.py

@@ -3,697 +3,110 @@ from __future__ import annotations
 import logging
 
 import pandas as pd
-from napistu import constants
-from napistu import identifiers
-from napistu import sbml_dfs_core
-from napistu import source
-from napistu import utils
-from napistu.rpy2 import callr
-from napistu.rpy2 import report_r_exceptions
-from napistu.rpy2 import warn_if_no_rpy2
+from napistu.rpy2 import (
+    require_rpy2,
+    report_r_exceptions,
+)
+
+from napistu.rpy2.callr import bioconductor_org_r_function, r_dataframe_to_pandas
 
-from napistu.constants import SBML_DFS
-from napistu.constants import BQB
-from napistu.constants import IDENTIFIERS
 from napistu.constants import ONTOLOGIES
-from napistu.constants import ONTOLOGY_ALIASES
 from napistu.rpy2.constants import BIOC_VALID_EXPANDED_SPECIES_ONTOLOGIES
-from napistu.rpy2.constants import BIOC_DOGMATIC_MAPPING_ONTOLOGIES
-from napistu.rpy2.constants import BIOC_PROTEIN_ONTOLOGIES
-from napistu.rpy2.constants import BIOC_NAME_ONTOLOGIES
-from napistu.rpy2.constants import BIOC_GENE_ONTOLOGIES  # noqa
+from napistu.rpy2.constants import BIOC_ONTOLOGY_MAPPING
 from napistu.rpy2.constants import BIOC_NOMENCLATURE
 
 logger = logging.getLogger(__name__)
 
 
-@warn_if_no_rpy2
-@report_r_exceptions
-def expand_identifiers(
-    sbml_dfs: sbml_dfs_core.SBML_dfs,
-    id_type: str,
-    species: str,
-    expanded_ontologies: list[str],
-    r_paths: str | None = None,
-) -> pd.Series:
-    """
-    Expand Identifiers
-
-    Update a table's identifiers to include additional related ontologies
-
-    Ontologies are pulled from the bioconductor "org" packages. This is effective, but inelegant.
-
-    Parameters
-    ----------
-    sbml_dfs : SBML_dfs
-        A relational pathway model built around reactions interconverting compartmentalized species.
-    id_type: str
-        Identifiers to expand: species, compartments, or reactions
-    species: str
-        Species name
-    expanded_ontologies: list
-        Ontologies to add or complete
-    r_paths: str
-        Path to an R packages directory
-
-    Returns
-    -------
-    a pd.Series with identifiers as the index and updated Identifiers objects as values
-    """
-
-    if not isinstance(sbml_dfs, sbml_dfs_core.SBML_dfs):
-        raise TypeError("sbml_dfs is not an sbml_dfs_core.SBML_dfs object")
-
-    # pull out all identifiers as a pd.DataFrame
-    all_entity_identifiers = sbml_dfs.get_identifiers(id_type)
-    if not isinstance(all_entity_identifiers, pd.DataFrame):
-        raise TypeError("all_entity_identifiers must be a pandas DataFrame")
-
-    if id_type == "species":
-        all_entity_identifiers = _check_species_identifiers_entrez_gene_ontology(
-            all_entity_identifiers
-        )
-
-        valid_expanded_ontologies = BIOC_VALID_EXPANDED_SPECIES_ONTOLOGIES
-    elif id_type in ["reactions", "compartments"]:
-        raise NotImplementedError(
-            f"No converters implemented to expand {id_type} annotations"
-        )
-    else:
-        raise ValueError(f"{id_type} is an invalid id_type")
-
-    invalid_expanded_ontologies = set(expanded_ontologies).difference(
-        valid_expanded_ontologies
-    )
-
-    if len(invalid_expanded_ontologies) != 0:
-        raise NotImplementedError(
-            f"No converters implemented to expand {id_type} annotations to {', '.join(invalid_expanded_ontologies)}"
-        )
-
-    # find entries in valid_expanded_ontologies which are already present
-    # these are the entries that will be used to expand to other ontologies
-    # or fill in ontologies with incomplete annotations
-    starting_ontologies = valid_expanded_ontologies.intersection(
-        set(all_entity_identifiers["ontology"])
-    )
-
-    if len(starting_ontologies) == 0:
-        raise ValueError(f"No ontologies with {id_type} converters are present")
-
-    required_conversion_ontologies = set(starting_ontologies).union(
-        set(expanded_ontologies)
-    )
-
-    # pull down entrez ids + mapping to other ontologies
-    mapping_ontologies = required_conversion_ontologies.intersection(
-        BIOC_VALID_EXPANDED_SPECIES_ONTOLOGIES
-    )
-
-    mappings_dict = create_bioconductor_mapping_tables(
-        mappings=mapping_ontologies, species=species, r_paths=r_paths
-    )
-
-    # start with entrez IDs (since all other ontologies are mapped to them in the
-    # bioconductor "org" packages)
-
-    # get these values by just looking up the mappings between entrez genes and genomic loci
-    running_ids = merge_bioconductor_mappings(mappings_dict, mapping_ontologies)
-
-    # map from existing ontologies to expanded ontologies
-    ontology_mappings = list()
-    # starting w/
-    for start in starting_ontologies:
-        # ending w/
-        for end in expanded_ontologies:
-            if start == end:
-                continue
-            lookup = (
-                running_ids[[start, end]]
-                .rename(columns={start: IDENTIFIERS.IDENTIFIER, end: "new_identifier"})
-                .assign(ontology=start)
-                .assign(new_ontology=end)
-            )
-            ontology_mappings.append(lookup)
-
-    ontology_mappings_df = pd.concat(ontology_mappings).dropna()
-
-    # old identifiers joined with new identifiers
-
-    # first, define the names of keys and ids
-    table_pk_var = sbml_dfs.schema[id_type]["pk"]
-    table_id_var = sbml_dfs.schema[id_type]["id"]
-
-    # retain bqb terms to define how an identifier is related to sid
-    # this relation will be preserved for the new ids
-
-    merged_identifiers = all_entity_identifiers[
-        [
-            table_pk_var,
-            IDENTIFIERS.ONTOLOGY,
-            IDENTIFIERS.IDENTIFIER,
-            IDENTIFIERS.BQB,
-        ]
-    ].merge(ontology_mappings_df)
-
-    # new, possibly redundant identifiers
-    new_identifiers = merged_identifiers[
-        [table_pk_var, "new_ontology", "new_identifier", IDENTIFIERS.BQB]
-    ].rename(
-        columns={
-            "new_ontology": IDENTIFIERS.ONTOLOGY,
-            "new_identifier": IDENTIFIERS.IDENTIFIER,
-        }
-    )
-
-    expanded_identifiers_df = (
-        pd.concat(
-            [
-                all_entity_identifiers[
-                    [
-                        table_pk_var,
-                        IDENTIFIERS.ONTOLOGY,
-                        IDENTIFIERS.IDENTIFIER,
-                        IDENTIFIERS.URL,
-                        IDENTIFIERS.BQB,
-                    ]
-                ],
-                new_identifiers,
-                # ignore new identifier if it already exists
-            ]
-        )
-        # remove duplicated identifiers
-        .groupby([table_pk_var, IDENTIFIERS.ONTOLOGY, IDENTIFIERS.IDENTIFIER])
-        .first()
-        .reset_index()
-        .set_index(table_pk_var)
-    )
-
-    # create a dictionary of new Identifiers objects
-    expanded_identifiers_dict = {
-        i: _expand_identifiers_new_entries(i, expanded_identifiers_df)
-        for i in expanded_identifiers_df.index.unique()
-    }
-
-    output = pd.Series(expanded_identifiers_dict).rename(table_id_var)
-    output.index.name = table_pk_var
-
-    return output
-
-
-@warn_if_no_rpy2
+@require_rpy2
 @report_r_exceptions
 def create_bioconductor_mapping_tables(
     mappings: set[str], species: str, r_paths: str | None = None
 ) -> dict[str, pd.DataFrame]:
-    """
-    Create Bioconductor Mapping Tables
+    """Create Bioconductor Mapping Tables.
 
     Creating a dictionary of mappings between entrez and other ontologies.
 
-    Args:
-        mappings (set):
-            A set of ontologies to work with. The valid ontologies are:
-            "ensembl_gene", "ensembl_transcript", and "uniprot".
-        species (str):
-            The organismal species that we are working with (e.g., Homo sapiens).
-        r_paths (str, optional):
-            Optional path to a library of R packages.
+    Parameters
+    ----------
+    mappings : set[str]
+        A set of ontologies to work with. The valid ontologies are:
+        "ensembl_gene", "ensembl_transcript", and "uniprot".
+    species : str
+        The organismal species that we are working with (e.g., Homo sapiens).
+    r_paths : str | None, optional
+        Optional path to a library of R packages.
 
-    Returns:
-        mappings_dict (dict):
-            A table of entrez ids, and tables mapping from each ontology in "mappings" to entrez.
+    Returns
+    -------
+    dict[str, pd.DataFrame]
+        A table of entrez ids, and tables mapping from each ontology in "mappings" to entrez.
 
+    Raises
+    ------
+    ValueError
+        If any of the requested mappings are not supported
     """
-
-    if not isinstance(mappings, set):
-        raise TypeError(f"mappings must be a set, but got {type(mappings).__name__}")
-    if not isinstance(species, str):
-        raise TypeError(f"species must be a str, but got {type(species).__name__}")
-
     logger.info(
-        f"Creating mapping tables from entrez genes to/from {', '.join(mappings)}"
+        "Creating mapping tables from entrez genes to/from %s", ", ".join(mappings)
     )
 
     invalid_mappings = set(mappings).difference(BIOC_VALID_EXPANDED_SPECIES_ONTOLOGIES)
-
     if len(invalid_mappings) > 0:
         raise ValueError(
             f"{len(invalid_mappings)} mappings could not be created: {', '.join(invalid_mappings)}.\n"
             f"The valid mappings are {', '.join(BIOC_VALID_EXPANDED_SPECIES_ONTOLOGIES)}"
         )
 
-    mappings_dict = dict()
+    mappings_dict = {}
 
-    # all mappings are with respect to entrez. so we will always want to obtain entrez ids
-    mappings_dict[ONTOLOGIES.NCBI_ENTREZ_GENE] = (
-        callr.r_dataframe_to_pandas(
-            callr.bioconductor_org_r_function(
-                BIOC_NOMENCLATURE.CHR_TBL, species, r_paths=None
-            )
-        )
-        .drop(BIOC_NOMENCLATURE.CHROMOSOME, axis=1)
-        .rename(
-            columns={BIOC_NOMENCLATURE.NCBI_ENTREZ_GENE: ONTOLOGIES.NCBI_ENTREZ_GENE}
-        )
-        .set_index(ONTOLOGIES.NCBI_ENTREZ_GENE)
-    )
-
-    if ONTOLOGIES.ENSEMBL_GENE in mappings:
-        # "entrez <> ensembl genes"
-        mappings_dict[ONTOLOGIES.ENSEMBL_GENE] = (
-            callr.r_dataframe_to_pandas(
-                callr.bioconductor_org_r_function(
-                    BIOC_NOMENCLATURE.ENSG_TBL, species, r_paths=r_paths
-                )
-            )
-            .rename(
-                columns={
-                    BIOC_NOMENCLATURE.NCBI_ENTREZ_GENE: ONTOLOGIES.NCBI_ENTREZ_GENE,
-                    BIOC_NOMENCLATURE.ENSEMBL_GENE: ONTOLOGIES.ENSEMBL_GENE,
-                }
-            )
-            .set_index(ONTOLOGIES.NCBI_ENTREZ_GENE)
-        )
-
-    if ONTOLOGIES.ENSEMBL_TRANSCRIPT in mappings:
-        # "entrez <> ensembl transcripts"
-        mappings_dict[ONTOLOGIES.ENSEMBL_TRANSCRIPT] = (
-            callr.r_dataframe_to_pandas(
-                callr.bioconductor_org_r_function(
-                    BIOC_NOMENCLATURE.ENST_TBL, species, r_paths=r_paths
-                )
-            )
-            .rename(
-                columns={
-                    BIOC_NOMENCLATURE.NCBI_ENTREZ_GENE: ONTOLOGIES.NCBI_ENTREZ_GENE,
-                    BIOC_NOMENCLATURE.ENSEMBL_TRANSCRIPT: ONTOLOGIES.ENSEMBL_TRANSCRIPT,
-                }
-            )
-            .set_index(ONTOLOGIES.NCBI_ENTREZ_GENE)
-        )
-
-    if ONTOLOGIES.ENSEMBL_PROTEIN in mappings:
-        # "entrez <> ensembl proteins"
-        mappings_dict[ONTOLOGIES.ENSEMBL_PROTEIN] = (
-            callr.r_dataframe_to_pandas(
-                callr.bioconductor_org_r_function(
-                    BIOC_NOMENCLATURE.ENSP_TBL, species, r_paths=r_paths
-                )
-            )
-            .rename(
-                columns={
-                    BIOC_NOMENCLATURE.NCBI_ENTREZ_GENE: ONTOLOGIES.NCBI_ENTREZ_GENE,
-                    BIOC_NOMENCLATURE.ENSEMBL_PROTEIN: ONTOLOGIES.ENSEMBL_PROTEIN,
-                }
-            )
-            .set_index(ONTOLOGIES.NCBI_ENTREZ_GENE)
-        )
-
-    if ONTOLOGIES.UNIPROT in mappings:
-        # "entrez <> uniprot"
-        mappings_dict[ONTOLOGIES.UNIPROT] = (
-            callr.r_dataframe_to_pandas(
-                callr.bioconductor_org_r_function(
-                    BIOC_NOMENCLATURE.UNIPROT_TBL, species, r_paths=r_paths
-                )
-            )
-            .rename(
-                columns={
-                    BIOC_NOMENCLATURE.NCBI_ENTREZ_GENE: ONTOLOGIES.NCBI_ENTREZ_GENE,
-                    BIOC_NOMENCLATURE.UNIPROT: ONTOLOGIES.UNIPROT,
-                }
-            )
-            .set_index(ONTOLOGIES.NCBI_ENTREZ_GENE)
-        )
-
-    if ONTOLOGIES.GENE_NAME in mappings:
-        # "entrez <> gene name"
-        mappings_dict[ONTOLOGIES.GENE_NAME] = (
-            callr.r_dataframe_to_pandas(
-                callr.bioconductor_org_r_function(
-                    BIOC_NOMENCLATURE.NAME_TBL, species, r_paths=r_paths
-                )
-            )
-            .rename(
-                columns={
-                    BIOC_NOMENCLATURE.NCBI_ENTREZ_GENE: ONTOLOGIES.NCBI_ENTREZ_GENE,
-                    BIOC_NOMENCLATURE.GENE_NAME: ONTOLOGIES.GENE_NAME,
-                }
-            )
-            .set_index(ONTOLOGIES.NCBI_ENTREZ_GENE)
-        )
-
-    if ONTOLOGIES.SYMBOL in mappings:
-        # "entrez <> gene symbol"
-        mappings_dict[ONTOLOGIES.SYMBOL] = (
-            callr.r_dataframe_to_pandas(
-                callr.bioconductor_org_r_function(
-                    BIOC_NOMENCLATURE.SYMBOL_TBL, species, r_paths=r_paths
-                )
-            )
-            .rename(
-                columns={
-                    BIOC_NOMENCLATURE.NCBI_ENTREZ_GENE: ONTOLOGIES.NCBI_ENTREZ_GENE,
-                    BIOC_NOMENCLATURE.SYMBOL: ONTOLOGIES.SYMBOL,
-                }
-            )
-            .set_index(ONTOLOGIES.NCBI_ENTREZ_GENE)
-        )
+    # Create mapping tables for each requested ontology
+    for ontology in mappings:
+        mappings_dict[ontology] = _create_single_mapping(ontology, species, r_paths)
 
     return mappings_dict
 
 
-def merge_bioconductor_mappings(
-    mappings_dict: dict, mapping_ontologies: set[str]
+def _create_single_mapping(
+    ontology: str, species: str, r_paths: str | None = None
 ) -> pd.DataFrame:
-    """Combine multiple ontologies by recursively joining on Entrez Gene"""
-
-    running_ids = mappings_dict[ONTOLOGIES.NCBI_ENTREZ_GENE]
-
-    for mapping in mapping_ontologies:
-        logger.debug(f"adding entries for {mapping} to running_ids")
-        mapping_df = mappings_dict[mapping]
-
-        running_ids = running_ids.join(mapping_df)
+    """Create a single mapping table for a given ontology.
 
-    running_ids = running_ids.reset_index()
-
-    return running_ids
-
-
-def stack_bioconductor_mappings(
-    mappings_dict: dict[str, pd.DataFrame], mapping_ontologies: set[str]
-) -> pd.DataFrame:
-    """
-    Stack Bioconductor Mappings
-
-    Convert a dict of mappings between entrez identifiers and other identifiers to a single table.
-
-    Args:
-        mappings_dict (dict):
-            A dictionary containing mappings between entrez and other ontologies.
-        mapping_ontologies (set):
-            A set of mappings to combine.
-
-    Returns:
-        mappings_df (pd.DataFrame):
-            A table containing entrez_gene_id, ontology, and identifier.
-    """
-
-    mappings_list = list()
-    for ont in mapping_ontologies:
-        one_mapping_df = (
-            mappings_dict[ont].assign(ontology=ont).rename({ont: "identifier"}, axis=1)
-        )
-
-        mappings_list.append(one_mapping_df)
-
-    return pd.concat(mappings_list)
-
-
-def _check_species_identifiers_entrez_gene_ontology(
-    entity_identifiers_df: pd.DataFrame,
-) -> pd.DataFrame:
-    """
-    Check whether species ontologies contain ncbigene or ncbi_gene
-    If so, replaced them to ncbi_entrez_gene.
-    Return: entity_identifiers_df with proper gene ontology types.
-    """
-
-    intersect_gene_onto = set(entity_identifiers_df["ontology"]).intersection(
-        ONTOLOGY_ALIASES.NCBI_ENTREZ_GENE
-    )
-
-    # if entity_identifiers_df contains members of ENTREZ_ONTOLOGY_ALIASES,
-    # replace to ncbi_entrez_gene
-    if intersect_gene_onto:
-        logger.info(
-            f" Replace unmatching ontology {', '.join(intersect_gene_onto)} to {ONTOLOGIES.NCBI_ENTREZ_GENE}."
-        )
-
-        filtered_onto_df = entity_identifiers_df[
-            entity_identifiers_df["ontology"].isin(list(intersect_gene_onto))
-        ]
-
-        entity_identifiers_df.loc[filtered_onto_df.index, "ontology"] = (
-            ONTOLOGIES.NCBI_ENTREZ_GENE
-        )
-
-    return entity_identifiers_df
-
-
-def update_expanded_identifiers(
-    model: sbml_dfs_core.SBML_dfs, id_type: str, expanded_ids: pd.Series
-) -> sbml_dfs_core.SBML_dfs:
-    """Update the expanded identifiers for a model.
-
-    Args:
-        model (sbml_dfs_core.SBML_dfs): _description_
-        id_type (str): _description_
-        expanded_ids (str): _description_
-    """
-    ids = getattr(model, id_type)
-
-    # make sure expanded_ids and original model.species have same number of s_ids
-    # if a s_id only in model.species, adding it to expanded_ids.
-    if ids.shape[0] != expanded_ids.shape[0]:
-        matched_expanded_ids = expanded_ids.combine_first(ids[SBML_DFS.S_IDENTIFIERS])
-        logger.debug(
-            f"{ids.shape[0] - expanded_ids.shape[0]} "
-            "ids are not included in expanded ids"
-        )
-    else:
-        matched_expanded_ids = expanded_ids
-
-    updated_ids = ids.drop(SBML_DFS.S_IDENTIFIERS, axis=1).join(
-        pd.DataFrame(matched_expanded_ids)
-    )
-
-    setattr(model, id_type, updated_ids)
-
-    return model
-
-
-def create_dogmatic_sbml_dfs(
-    species: str, r_paths: str | None = None
-) -> sbml_dfs_core.SBML_dfs:
-    """
-    Create Dogmatic SMBL_DFs
-
-    Create an SBML_dfs model which is pretty much just proteins and no
-    reactions, as well as annotations linking proteins to genes, and
-    creating nice labels for genes/proteins.
-
-    Args:
-        species (str):
-            An organismal species (e.g., Homo sapiens)
-        r_paths (str or None)
-            Optional, p]ath to an R packages directory
+    Parameters
+    ----------
+    ontology : str
+        The ontology to map (e.g. ENSEMBL_GENE, UNIPROT)
+    species : str
+        The organismal species to map
+    r_paths : str | None, optional
+        Optional path to R packages directory
 
-    Returns:
-        dogmatic_sbml_dfs (sbml.SBML_dfs)
-            A pathway model which (pretty much) just contains proteins and
-            diverse identifiers
+    Returns
+    -------
+    pd.DataFrame
+        DataFrame containing the mapping between entrez and the target ontology
     """
 
-    dogmatic_mappings = connect_dogmatic_mappings(species)
+    if ontology not in BIOC_ONTOLOGY_MAPPING:
+        raise ValueError(f"Unsupported ontology: {ontology}")
 
-    logger.info("Creating inputs for sbml_dfs_from_edgelist()")
+    table_name, column_name = BIOC_ONTOLOGY_MAPPING[ontology]
 
-    # format entries for sbml_dfs_from_edgelist()
-    species_df = dogmatic_mappings["cluster_consensus_identifiers_df"].join(
-        dogmatic_mappings["s_name_series"]
+    df = r_dataframe_to_pandas(
+        bioconductor_org_r_function(table_name, species, r_paths=r_paths)
     )
 
-    # stub required but invariant variables
-    compartments_df = sbml_dfs_core._stub_compartments()
-    interaction_source = source.Source(init=True)
+    # Drop chromosome column if this is the chromosome table
+    # this was only introduced so we had a table with 1 row per unique entrez id
+    if table_name == BIOC_NOMENCLATURE.CHR_TBL:
+        df = df.drop(BIOC_NOMENCLATURE.CHROMOSOME, axis=1)
 
-    # interactions table. This is required to create the sbml_dfs but we'll drop the info later
-    interaction_edgelist = species_df.rename(
+    # Rename columns and set index
+    df = df.rename(
         columns={
-            "s_name": "upstream_name",
-            SBML_DFS.S_IDENTIFIERS: SBML_DFS.R_IDENTIFIERS,
+            BIOC_NOMENCLATURE.NCBI_ENTREZ_GENE: ONTOLOGIES.NCBI_ENTREZ_GENE,
+            column_name: ontology,
         }
-    )
-    interaction_edgelist["downstream_name"] = interaction_edgelist["upstream_name"]
-    interaction_edgelist["upstream_compartment"] = "cellular_component"
-    interaction_edgelist["downstream_compartment"] = "cellular_component"
-    interaction_edgelist["r_name"] = interaction_edgelist["upstream_name"]
-    interaction_edgelist["sbo_term"] = constants.MINI_SBO_FROM_NAME["reactant"]
-    interaction_edgelist["r_isreversible"] = False
-
-    dogmatic_sbml_dfs = sbml_dfs_core.sbml_dfs_from_edgelist(
-        interaction_edgelist=interaction_edgelist,
-        species_df=species_df,
-        compartments_df=compartments_df,
-        interaction_source=interaction_source,
-        upstream_stoichiometry=-1,
-        downstream_stoichiometry=1,
-        downstream_sbo_name="product",
-    )
-
-    # remove all reactions except 1 (so it still passes sbml_dfs.validate())
-    # this self reaction will be removed when creating the graph
-    dogmatic_sbml_dfs.remove_reactions(dogmatic_sbml_dfs.reactions.index.tolist()[1::])
-
-    return dogmatic_sbml_dfs
-
-
-def connect_dogmatic_mappings(species: str, r_paths: str | None = None) -> dict:
-    """
-    Connect Dogmatic Mappings
-
-    Merge all ontologies into greedy clusters based on shared associations to entrez ids
-
-    Args:
-        species (str):
-            An organismal species (e.g., Homo sapiens)
-        r_paths (str or None)
-            Optional, p]ath to an R packages directory
-
-    Returns:
-        dict with:
-        - s_name_series: a series where the index is distinct molecular species and the values are names.
-        - cluster_consensus_identifiers_df: a pd.DataFrame where the index is distinct molecular species
-          and values are identifiers objects.
-    """
-
-    mappings_dict = create_bioconductor_mapping_tables(
-        mappings=BIOC_DOGMATIC_MAPPING_ONTOLOGIES,
-        species=species,
-        r_paths=r_paths,
-    )
-
-    protein_mappings = stack_bioconductor_mappings(
-        mappings_dict, set(BIOC_PROTEIN_ONTOLOGIES)
-    )
-
-    # apply greedy graph-based clustering to connect proteins with a common mapping to entrez
-    edgelist_df = utils.format_identifiers_as_edgelist(
-        protein_mappings, [IDENTIFIERS.ONTOLOGY, IDENTIFIERS.IDENTIFIER]
-    )
-    connected_indices = utils.find_weakly_connected_subgraphs(
-        edgelist_df[["ind", "id"]]
-    )
-
-    # add clusters to proteins. Each cluster will be a distinct molecular species
-    protein_mappings_w_clusters = protein_mappings.reset_index().merge(
-        connected_indices
-    )
-
-    # combine entrez + cluster so we can pass cluster to non-protein attributes
-    entrez_clusters = protein_mappings_w_clusters[
-        [ONTOLOGIES.NCBI_ENTREZ_GENE, "cluster"]
-    ].drop_duplicates()
-    other_ontologies = BIOC_DOGMATIC_MAPPING_ONTOLOGIES.difference(
-        set(BIOC_PROTEIN_ONTOLOGIES)
-    )
-    other_mappings = stack_bioconductor_mappings(mappings_dict, other_ontologies)
-    other_mappings_w_clusters = entrez_clusters.merge(
-        other_mappings, left_on=ONTOLOGIES.NCBI_ENTREZ_GENE, right_index=True
-    )
-
-    possible_names = pd.concat(
-        [
-            protein_mappings_w_clusters.query(
-                "ontology in @BIOC_NAME_ONTOLOGIES.keys()"
-            ),
-            other_mappings_w_clusters.query("ontology in @BIOC_NAME_ONTOLOGIES.keys()"),
-        ]
-    )[["cluster", IDENTIFIERS.ONTOLOGY, IDENTIFIERS.IDENTIFIER]]
-
-    possible_names.loc[:, "ontology_preference"] = possible_names[
-        IDENTIFIERS.ONTOLOGY
-    ].map(BIOC_NAME_ONTOLOGIES)
-
-    # remove possible names which are present in multiple clusters.
-    # all clusters will need unique names to use sbml_dfs_from_edgelist()
-    id_counts = (
-        possible_names[["cluster", IDENTIFIERS.IDENTIFIER]]
-        .drop_duplicates()
-        .value_counts(IDENTIFIERS.IDENTIFIER)
-    )
-    possible_names = possible_names[
-        ~possible_names[IDENTIFIERS.IDENTIFIER].isin(
-            id_counts[id_counts > 1].index.tolist()
-        )
-    ]
-
-    s_name_series = (
-        utils._add_nameness_score(possible_names, IDENTIFIERS.IDENTIFIER)
-        .sort_values(["ontology_preference", "nameness_score"])
-        .groupby("cluster")
-        .first()
-        .rename(columns={IDENTIFIERS.IDENTIFIER: SBML_DFS.S_NAME})[SBML_DFS.S_NAME]
-    )
-
-    protein_ids = protein_mappings_w_clusters.assign(bqb=BQB.IS)[
-        ["cluster", IDENTIFIERS.IDENTIFIER, IDENTIFIERS.ONTOLOGY, IDENTIFIERS.BQB]
-    ]
-    gene_ids = other_mappings_w_clusters.query(
-        "ontology in @BIOC_GENE_ONTOLOGIES"
-    ).assign(bqb=BQB.IS_ENCODED_BY)[
-        ["cluster", IDENTIFIERS.IDENTIFIER, IDENTIFIERS.ONTOLOGY, IDENTIFIERS.BQB]
-    ]
-    entrez_ids = entrez_clusters.assign(
-        ontology=ONTOLOGIES.NCBI_ENTREZ_GENE, bqb=BQB.IS_ENCODED_BY
-    ).rename(columns={ONTOLOGIES.NCBI_ENTREZ_GENE: IDENTIFIERS.IDENTIFIER})[
-        ["cluster", IDENTIFIERS.IDENTIFIER, IDENTIFIERS.ONTOLOGY, IDENTIFIERS.BQB]
-    ]
-
-    # combine all ids to setup a single cluster-level Identifiers
-    all_ids = pd.concat([protein_ids, gene_ids, entrez_ids])
-    all_ids.loc[:, IDENTIFIERS.URL] = [
-        identifiers.create_uri_url(x, y)
-        for x, y in zip(all_ids[IDENTIFIERS.ONTOLOGY], all_ids[IDENTIFIERS.IDENTIFIER])
-    ]
-
-    # create one Identifiers object for each new species
-    cluster_consensus_identifiers = {
-        k: identifiers.Identifiers(
-            list(
-                v[
-                    [
-                        IDENTIFIERS.ONTOLOGY,
-                        IDENTIFIERS.IDENTIFIER,
-                        IDENTIFIERS.URL,
-                        IDENTIFIERS.BQB,
-                    ]
-                ]
-                .reset_index(drop=True)
-                .T.to_dict()
-                .values()
-            )
-        )
-        for k, v in all_ids.groupby("cluster")
-    }
-
-    cluster_consensus_identifiers_df = pd.DataFrame(
-        cluster_consensus_identifiers, index=[SBML_DFS.S_IDENTIFIERS]
-    ).T
-    cluster_consensus_identifiers_df.index.name = "cluster"
-
-    out_dict = {
-        "s_name_series": s_name_series,
-        "cluster_consensus_identifiers_df": cluster_consensus_identifiers_df,
-    }
-
-    return out_dict
-
-
-@warn_if_no_rpy2
-def _expand_identifiers_new_entries(
-    sysid: str, expanded_identifiers_df: pd.DataFrame
-) -> identifiers.Identifiers:
-    """Expand Identifiers to include Bioconductor annotations"""
-    entry = expanded_identifiers_df.loc[sysid]
-
-    if type(entry) is pd.Series:
-        sysis_id_list = [entry.to_dict()]
-    else:
-        # multiple annotations
-        sysis_id_list = list(entry.reset_index(drop=True).T.to_dict().values())
+    ).set_index(ONTOLOGIES.NCBI_ENTREZ_GENE)
 
-    return identifiers.Identifiers(sysis_id_list)
+    return df