Merge pull request #37 from TheJacksonLaboratory/G3-192-species-list-…

…endpoint

G3-192 species endpoint

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "geneweaver-api"
-version = "0.3.0"
+version = "0.3.0a01"
 description = "The Geneweaver API"
 authors = [
     "Alexander Berger <[email protected]>",
@@ -21,7 +21,7 @@ python = "^3.9"
 geneweaver-core = "^0.9.0a1"
 fastapi = {extras = ["all"], version = "^0.99.1"}
 uvicorn = {extras = ["standard"], version = "^0.24.0"}
-geneweaver-db = "^0.3.0a11"
+geneweaver-db = "^0.3.0a12"
 psycopg-pool = "^3.1.7"
 requests = "^2.31.0"
 python-jose = {extras = ["cryptography"], version = "^3.3.0"}

src/geneweaver/api/controller/api.py

@@ -6,7 +6,7 @@
 from fastapi import APIRouter, FastAPI, Security
 from geneweaver.api import __version__
 from geneweaver.api import dependencies as deps
-from geneweaver.api.controller import genes, genesets, publications
+from geneweaver.api.controller import genes, genesets, publications, species
 from geneweaver.api.core.config import settings
 
 app = FastAPI(
@@ -28,5 +28,6 @@
 api_router.include_router(genesets.router)
 api_router.include_router(genes.router)
 api_router.include_router(publications.router)
+api_router.include_router(species.router)
 
 app.include_router(api_router, prefix=settings.API_PREFIX)

src/geneweaver/api/controller/species.py

@@ -0,0 +1,24 @@
+"""Endpoints related to species."""
+from typing import Optional
+
+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 typing_extensions import Annotated
+
+router = APIRouter(prefix="/species", tags=["species"])
+
+
+@router.get("/")
+def get_species(
+    cursor: Optional[deps.Cursor] = Depends(deps.cursor),
+    taxonomy_id: Annotated[
+        Optional[int], Query(format="int64", minimum=0, maxiumum=9223372036854775807)
+    ] = None,
+    reference_gene_id_type: Optional[GeneIdentifier] = None,
+) -> dict:
+    """Get species."""
+    response = species_service.get_species(cursor, taxonomy_id, reference_gene_id_type)
+
+    return response

src/geneweaver/api/services/species.py

@@ -0,0 +1,36 @@
+"""Service functions for Species."""
+
+from typing import Optional
+
+from fastapi.logger import logger
+from geneweaver.core.enum import GeneIdentifier
+from geneweaver.db import species as db_species
+from psycopg import Cursor
+
+
+def get_species(
+    cursor: Cursor,
+    taxonomy_id: Optional[int] = None,
+    reference_gene_id_type: Optional[GeneIdentifier] = None,
+) -> dict:
+    """Get species from DB.
+
+    @param cursor: DB cursor
+    @param taxonomy_id:
+    @param reference_gene_id_type:
+    @return: dictionary response (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
+                )
+
+        return {"species": species}
+
+    except Exception as err:
+        logger.error(err)
+        raise err

tests/controllers/test_species.py

@@ -0,0 +1,43 @@
+"""Tests for species API."""
+from unittest.mock import patch
+
+from tests.data import test_species_data
+
+species_no_params = test_species_data.get("species_no_parameters")
+species_by_taxonomy_id_10090 = test_species_data.get("species_by_taxonomy_id_10090")
+species_by_gene_id_type_flybase = test_species_data.get(
+    "species_by_gene_id_type_flybase"
+)
+
+
+@patch("geneweaver.api.services.species.get_species")
+def test_valid_species_url_req(mock_species_service_call, client):
+    """Test valid url request to get species."""
+    mock_species_service_call.return_value = species_no_params
+
+    response = client.get(url="/api/species")
+
+    assert response.status_code == 200
+    assert response.json() == species_no_params
+
+
+@patch("geneweaver.api.services.species.get_species")
+def test_species_url_taxonomy_req(mock_species_service_call, client):
+    """Test valid url request to get species."""
+    mock_species_service_call.return_value = species_by_taxonomy_id_10090
+
+    response = client.get(url="/api/species?taxonomy_id=10090")
+
+    assert response.status_code == 200
+    assert response.json() == species_by_taxonomy_id_10090
+
+
+@patch("geneweaver.api.services.species.get_species")
+def test_valid_species_url_gene_id_type_req(mock_species_service_call, client):
+    """Test valid url request to get species."""
+    mock_species_service_call.return_value = species_by_gene_id_type_flybase
+
+    response = client.get(url="/api/species?gene_id_type=14")
+
+    assert response.status_code == 200
+    assert response.json() == species_by_gene_id_type_flybase

tests/data/__init__.py

@@ -3,6 +3,8 @@
 import importlib.resources
 import json
 
+from geneweaver.core.enum import GeneIdentifier
+
 ## Load test data
 # Opening JSON files
 geneset_response_json = importlib.resources.read_text(
@@ -24,6 +26,7 @@
     "tests.data", "security_jwt_RS256_keys.json"
 )
 
+species_json = importlib.resources.read_text("tests.data", "species.json")
 
 ## laod and returns JSON string as a dictionary
 
@@ -93,3 +96,28 @@
     "test_private_key": json.loads(jwt_test_keys_json).get("private_key"),
     "test_public_key": json.loads(jwt_test_keys_json).get("public_key"),
 }
+
+
+## Species test data
+test_species_data = {
+    "species_no_parameters": json.loads(species_json).get("species_no_parameters"),
+    "species_by_taxonomy_id_10090": json.loads(species_json).get(
+        "species_by_taxonomy_id_10090"
+    ),
+    "species_by_gene_id_type_flybase": json.loads(species_json).get(
+        "species_by_gene_id_type_flybase"
+    ),
+}
+
+
+def get_species_db_resp(species_data: dict) -> dict:
+    """Get species data as returned by DB."""
+    species = species_data.get("species")
+    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
+            ).as_int()
+
+    return species

tests/data/species.json

@@ -0,0 +1,92 @@
+{
+  "species_no_parameters": {
+    "species": [
+      {
+        "id": 0,
+        "name": "",
+        "taxonomic_id": 0,
+        "reference_gene_identifier": null
+      },
+      {
+        "id": 3,
+        "name": "Rattus norvegicus",
+        "taxonomic_id": 10116,
+        "reference_gene_identifier": "RGD"
+      },
+      {
+        "id": 4,
+        "name": "Danio rerio",
+        "taxonomic_id": 7955,
+        "reference_gene_identifier": "ZFIN"
+      },
+      {
+        "id": 10,
+        "name": "Gallus gallus",
+        "taxonomic_id": 9031,
+        "reference_gene_identifier": "CGNC"
+      },
+      {
+        "id": 1,
+        "name": "Mus musculus",
+        "taxonomic_id": 10090,
+        "reference_gene_identifier": "MGI"
+      },
+      {
+        "id": 5,
+        "name": "Drosophila melanogaster",
+        "taxonomic_id": 7227,
+        "reference_gene_identifier": "FlyBase"
+      },
+      {
+        "id": 11,
+        "name": "Canis familiaris",
+        "taxonomic_id": 9615,
+        "reference_gene_identifier": "Entrez"
+      },
+      {
+        "id": 2,
+        "name": "Homo sapiens",
+        "taxonomic_id": 9606,
+        "reference_gene_identifier": "HGNC"
+      },
+      {
+        "id": 8,
+        "name": "Caenorhabditis elegans",
+        "taxonomic_id": 6239,
+        "reference_gene_identifier": "Wormbase"
+      },
+      {
+        "id": 9,
+        "name": "Saccharomyces cerevisiae",
+        "taxonomic_id": 559292,
+        "reference_gene_identifier": "SGD"
+      },
+      {
+        "id": 6,
+        "name": "Macaca mulatta",
+        "taxonomic_id": 9544,
+        "reference_gene_identifier": "Entrez"
+      }
+    ]
+  },
+  "species_by_taxonomy_id_10090": {
+    "species": [
+      {
+        "id": 1,
+        "name": "Mus musculus",
+        "taxonomic_id": 10090,
+        "reference_gene_identifier": "MGI"
+      }
+    ]
+  },
+  "species_by_gene_id_type_flybase": {
+    "species": [
+      {
+        "id": 5,
+        "name": "Drosophila melanogaster",
+        "taxonomic_id": 7227,
+        "reference_gene_identifier": "FlyBase"
+      }
+    ]
+  }
+}

tests/services/test_species.py

@@ -0,0 +1,70 @@
+"""Tests for publications Service."""
+
+from unittest.mock import patch
+
+import pytest
+from geneweaver.api.services import species as species_service
+from geneweaver.core.enum import GeneIdentifier
+
+from tests.data import get_species_db_resp, test_species_data
+
+species_no_params = get_species_db_resp(test_species_data.get("species_no_parameters"))
+species_by_taxonomy_id_10090 = get_species_db_resp(
+    test_species_data.get("species_by_taxonomy_id_10090")
+)
+species_by_gene_id_type_flybase = get_species_db_resp(
+    test_species_data.get("species_by_gene_id_type_flybase")
+)
+
+
+@patch("geneweaver.api.services.species.db_species")
+def test_get_species(mock_db_species):
+    """Test get species no paramaters."""
+    mock_db_species.get.return_value = species_no_params
+
+    response = species_service.get_species(None)
+
+    assert response.get("species") == species_no_params
+
+
+@patch("geneweaver.api.services.species.db_species")
+def test_get_species_by_taxonomy_id(mock_db_species):
+    """Test speccies by taxonomy id."""
+    mock_db_species.get.return_value = species_by_taxonomy_id_10090
+
+    response = species_service.get_species(None, taxonomy_id=10090)
+
+    assert response.get("species") == species_by_taxonomy_id_10090
+
+
+@patch("geneweaver.api.services.species.db_species")
+def test_get_species_by_gene_id_type(mock_db_species):
+    """Test speccies by taxonomy id."""
+    mock_db_species.get.return_value = species_by_gene_id_type_flybase
+
+    response = species_service.get_species(
+        None, reference_gene_id_type=GeneIdentifier("FlyBase")
+    )
+
+    assert response.get("species") == species_by_gene_id_type_flybase
+
+
+@patch("geneweaver.api.services.species.db_species")
+def test_get_species_by_gene_id_type_and_taxonomy(mock_db_species):
+    """Test speccies by taxonomy id."""
+    mock_db_species.get.return_value = species_by_gene_id_type_flybase
+
+    response = species_service.get_species(
+        None, reference_gene_id_type=GeneIdentifier("FlyBase"), taxonomy_id=7227
+    )
+
+    assert response.get("species") == species_by_gene_id_type_flybase
+
+
+@patch("geneweaver.api.services.species.db_species")
+def test_get_species_with_error(mock_db_species):
+    """Test error in DB call."""
+    mock_db_species.get.side_effect = Exception("ERROR")
+
+    with pytest.raises(expected_exception=Exception):
+        species_service.get(None)