✨ Reintroduce taxa (#168)

Signed-off-by: zethson <[email protected]>

bionty/base/entities/_gene.py

@@ -1,6 +1,5 @@
 from __future__ import annotations
 
-from collections.abc import Iterable
 from typing import TYPE_CHECKING, Literal, NamedTuple
 
 import pandas as pd
@@ -97,23 +96,34 @@ def map_legacy_ids(self, values: Iterable) -> MappingResult:
 
 
 class EnsemblGene:
-    def __init__(self, organism: str, version: str) -> None:
+    def __init__(
+        self,
+        organism: str,
+        version: str,
+        taxa: Literal[
+            "vertebrates", "bacteria", "fungi", "metazoa", "plants", "all"
+        ] = "vertebrates",
+    ) -> None:
         """Ensembl Gene mysql.
 
         Args:
-            organism: a bionty.Organism object
-            version: name of the ensembl DB version, e.g. "release-110"
+            organism: Name of the organism
+            version: Name of the ensembl DB version, e.g. "release-110"
+            taxa: The taxa of the organism to fetch genes for.
         """
         self._import()
         import mysql.connector as sql
         from sqlalchemy import create_engine
 
         self._organism = (
-            Organism(version=version).lookup().dict().get(organism)  # type:ignore
-        )
-        self._url = (
-            f"mysql+mysqldb://anonymous:@ensembldb.ensembl.org/{self._organism.core_db}"
+            Organism(version=version, taxa=taxa).lookup().dict().get(organism)  # type:ignore
         )
+        # vertebrates and plants use different ports
+        if taxa == "plants":
+            port = 4157
+        else:
+            port = 3306
+        self._url = f"mysql+mysqldb://anonymous:@ensembldb.ensembl.org:{port}/{self._organism.core_db}"
         self._engine = create_engine(url=self._url)
 
     def _import(self):
@@ -232,8 +242,10 @@ def add_external_db_column(df: pd.DataFrame, ext_db: str, df_col: str):
         df_res = df_res[~df_res["ensembl_gene_id"].isna()]
 
         # if stable_id is not ensembl_gene_id, keep a stable_id column
-        if not any(df_res["ensembl_gene_id"].str.startswith("ENS")):
-            logger.warning("no ensembl_gene_id found, writing to table_id column.")
+        if not all(df_res["ensembl_gene_id"].str.startswith("ENS")):
+            logger.warning(
+                "ensembl_gene_id column not all ENS-prefixed, writing to stable_id column."
+            )
             df_res.insert(0, "stable_id", df_res.pop("ensembl_gene_id"))
             df_res = df_res.sort_values("stable_id").reset_index(drop=True)
         else:

bionty/base/entities/_organism.py

@@ -22,9 +22,7 @@ class Organism(PublicOntology):
 
     def __init__(
         self,
-        organism: Literal[
-            "vertebrates", "bacteria", "fungi", "metazoa", "plants", "all"
-        ]
+        taxa: Literal["vertebrates", "bacteria", "fungi", "metazoa", "plants", "all"]
         | None = None,
         source: Literal["ensembl", "ncbitaxon"] | None = None,
         version: Literal[
@@ -39,7 +37,11 @@ def __init__(
         | None = None,
         **kwargs,
     ):
-        super().__init__(organism=organism, source=source, version=version, **kwargs)
+        # To support the organism kwarg being passed in getattr access in other parts of the code
+        # https://github.com/laminlabs/bionty/issues/163
+        if "organism" in kwargs and taxa is None:
+            taxa = kwargs.pop("organism")
+        super().__init__(organism=taxa, source=source, version=version, **kwargs)
 
     def _load_df(self) -> pd.DataFrame:
         if self.source == "ensembl":