Merge pull request #42 from TheJacksonLaboratory/G3-193-species-by-id…

…-endpoint

G3 193 species by id endpoint

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "geneweaver-api"
-version = "0.4.0a4"
+version = "0.4.0a5"
 description = "The Geneweaver API"
 authors = [
     "Alexander Berger <alexander.berger@jax.org>",

src/geneweaver/api/controller/species.py

@@ -4,7 +4,7 @@
 from fastapi import APIRouter, Depends, Query
 from geneweaver.api import dependencies as deps
 from geneweaver.api.services import species as species_service
-from geneweaver.core.enum import GeneIdentifier
+from geneweaver.core.enum import GeneIdentifier, Species
 from typing_extensions import Annotated
 
 router = APIRouter(prefix="/species", tags=["species"])
@@ -22,3 +22,13 @@ def get_species(
     response = species_service.get_species(cursor, taxonomy_id, reference_gene_id_type)
 
     return response
+
+
+@router.get("/{species_id}")
+def get_species_by_id(
+    species_id: Species, cursor: Optional[deps.Cursor] = Depends(deps.cursor)
+) -> dict:
+    """Get species."""
+    response = species_service.get_species_by_id(cursor, species_id)
+
+    return response

src/geneweaver/api/services/species.py

@@ -3,7 +3,7 @@
 from typing import Optional
 
 from fastapi.logger import logger
-from geneweaver.core.enum import GeneIdentifier
+from geneweaver.core.enum import GeneIdentifier, Species
 from geneweaver.db import species as db_species
 from psycopg import Cursor
 
@@ -23,14 +23,35 @@ def get_species(
     try:
         species = db_species.get(cursor, taxonomy_id, reference_gene_id_type)
         for species_record in species:
-            ref_gene_id_type = species_record.get("reference_gene_identifier", None)
-            if ref_gene_id_type:
-                species_record["reference_gene_identifier"] = GeneIdentifier(
-                    ref_gene_id_type
-                )
+            decode_gene_identifier(species_record)
 
         return {"species": species}
 
     except Exception as err:
         logger.error(err)
         raise err
+
+
+def get_species_by_id(cursor: Cursor, species: Species) -> dict:
+    """Get species from DB.
+
+    @param cursor: DB cursor
+    @param species: species id
+    @return: dictionary response (species).
+    """
+    try:
+        species_rsp = db_species.get_by_id(cursor, species)
+        decode_gene_identifier(species_rsp)
+
+        return {"species": species_rsp}
+
+    except Exception as err:
+        logger.error(err)
+        raise err
+
+
+def decode_gene_identifier(species: Species) -> None:
+    """Decode gene identifier from DB to Enum str value."""
+    ref_gene_id_type = species.get("reference_gene_identifier", None)
+    if ref_gene_id_type:
+        species["reference_gene_identifier"] = GeneIdentifier(ref_gene_id_type)

tests/controllers/test_species.py

@@ -41,3 +41,14 @@ def test_valid_species_url_gene_id_type_req(mock_species_service_call, client):
 
     assert response.status_code == 200
     assert response.json() == species_by_gene_id_type_flybase
+
+
+@patch("geneweaver.api.services.species.get_species_by_id")
+def test_valid_url_species_by_id(mock_species_service_call, client):
+    """Test valid url request to get species by id."""
+    mock_species_service_call.return_value = species_by_gene_id_type_flybase
+
+    response = client.get(url="/api/species/5")
+
+    assert response.status_code == 200
+    assert response.json() == species_by_gene_id_type_flybase

tests/services/test_species.py

@@ -4,7 +4,7 @@
 
 import pytest
 from geneweaver.api.services import species as species_service
-from geneweaver.core.enum import GeneIdentifier
+from geneweaver.core.enum import GeneIdentifier, Species
 
 from tests.data import get_species_db_resp, test_species_data
 
@@ -63,8 +63,38 @@ def test_get_species_by_gene_id_type_and_taxonomy(mock_db_species):
 
 @patch("geneweaver.api.services.species.db_species")
 def test_get_species_with_error(mock_db_species):
-    """Test error in DB call."""
+    """Test get species error in DB call."""
     mock_db_species.get.side_effect = Exception("ERROR")
 
     with pytest.raises(expected_exception=Exception):
         species_service.get(None)
+
+
+@patch("geneweaver.api.services.species.db_species")
+def test_get_species_by_id(mock_db_species):
+    """Test speccies by species id."""
+    mock_db_species.get_by_id.return_value = species_by_gene_id_type_flybase[0]
+
+    response = species_service.get_species_by_id(None, Species(5))
+
+    assert response.get("species") == species_by_gene_id_type_flybase[0]
+
+
+@patch("geneweaver.api.services.species.db_species")
+def test_get_species_by_id_with_error(mock_db_species):
+    """Test species by id error in DB call."""
+    mock_db_species.get_by_id.side_effect = Exception("ERROR")
+
+    with pytest.raises(expected_exception=Exception):
+        species_service.get_species_by_id(None, Species(5))
+
+
+def test_get_decode_gene_identifier():
+    """Test decode gene identifier."""
+    species = species_by_gene_id_type_flybase[0].copy()
+    species_service.decode_gene_identifier(species)
+
+    assert (
+        species
+        == test_species_data.get("species_by_gene_id_type_flybase").get("species")[0]
+    )