From 0ad2c8e0d996d58a33c22ca4557657f67aaeed69 Mon Sep 17 00:00:00 2001
From: francastell <fsophisco@yahoo.com>
Date: Wed, 13 Mar 2024 16:56:58 -0400
Subject: [PATCH 1/3] G3-192 species endpoint

---
 poetry.lock                              | 62 ++++++++--------
 pyproject.toml                           |  2 +-
 src/geneweaver/api/controller/api.py     |  3 +-
 src/geneweaver/api/controller/species.py | 24 +++++++
 src/geneweaver/api/services/species.py   | 29 ++++++++
 tests/controllers/test_species.py        | 43 +++++++++++
 tests/data/__init__.py                   | 13 ++++
 tests/data/species.json                  | 92 ++++++++++++++++++++++++
 tests/services/test_species.py           | 82 +++++++++++++++++++++
 9 files changed, 317 insertions(+), 33 deletions(-)
 create mode 100644 src/geneweaver/api/controller/species.py
 create mode 100644 src/geneweaver/api/services/species.py
 create mode 100644 tests/controllers/test_species.py
 create mode 100644 tests/data/species.json
 create mode 100644 tests/services/test_species.py

diff --git a/poetry.lock b/poetry.lock
index 594c348..37d9a20 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -785,38 +785,38 @@ files = [
 
 [[package]]
 name = "mypy"
-version = "1.8.0"
+version = "1.9.0"
 description = "Optional static typing for Python"
 optional = false
 python-versions = ">=3.8"
 files = [
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-    {file = "mypy-1.8.0-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:df9824ac11deaf007443e7ed2a4a26bebff98d2bc43c6da21b2b64185da011c4"},
-    {file = "mypy-1.8.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:2afecd6354bbfb6e0160f4e4ad9ba6e4e003b767dd80d85516e71f2e955ab50d"},
-    {file = "mypy-1.8.0-cp310-cp310-musllinux_1_1_x86_64.whl", hash = "sha256:8963b83d53ee733a6e4196954502b33567ad07dfd74851f32be18eb932fb1cb9"},
-    {file = "mypy-1.8.0-cp310-cp310-win_amd64.whl", hash = "sha256:e46f44b54ebddbeedbd3d5b289a893219065ef805d95094d16a0af6630f5d410"},
-    {file = "mypy-1.8.0-cp311-cp311-macosx_10_9_x86_64.whl", hash = "sha256:855fe27b80375e5c5878492f0729540db47b186509c98dae341254c8f45f42ae"},
-    {file = "mypy-1.8.0-cp311-cp311-macosx_11_0_arm64.whl", hash = "sha256:4c886c6cce2d070bd7df4ec4a05a13ee20c0aa60cb587e8d1265b6c03cf91da3"},
-    {file = "mypy-1.8.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:d19c413b3c07cbecf1f991e2221746b0d2a9410b59cb3f4fb9557f0365a1a817"},
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-    {file = "mypy-1.8.0-cp311-cp311-win_amd64.whl", hash = "sha256:51720c776d148bad2372ca21ca29256ed483aa9a4cdefefcef49006dff2a6835"},
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-    {file = "mypy-1.8.0-cp312-cp312-win_amd64.whl", hash = "sha256:720a5ca70e136b675af3af63db533c1c8c9181314d207568bbe79051f122669e"},
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-    {file = "mypy-1.8.0-cp39-cp39-musllinux_1_1_x86_64.whl", hash = "sha256:ab3c84fa13c04aeeeabb2a7f67a25ef5d77ac9d6486ff33ded762ef353aa5592"},
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-    {file = "mypy-1.8.0-py3-none-any.whl", hash = "sha256:538fd81bb5e430cc1381a443971c0475582ff9f434c16cd46d2c66763ce85d9d"},
-    {file = "mypy-1.8.0.tar.gz", hash = "sha256:6ff8b244d7085a0b425b56d327b480c3b29cafbd2eff27316a004f9a7391ae07"},
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+    {file = "mypy-1.9.0-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:d357423fa57a489e8c47b7c85dfb96698caba13d66e086b412298a1a0ea3b0ed"},
+    {file = "mypy-1.9.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:49c87c15aed320de9b438ae7b00c1ac91cd393c1b854c2ce538e2a72d55df150"},
+    {file = "mypy-1.9.0-cp310-cp310-musllinux_1_1_x86_64.whl", hash = "sha256:48533cdd345c3c2e5ef48ba3b0d3880b257b423e7995dada04248725c6f77374"},
+    {file = "mypy-1.9.0-cp310-cp310-win_amd64.whl", hash = "sha256:4d3dbd346cfec7cb98e6cbb6e0f3c23618af826316188d587d1c1bc34f0ede03"},
+    {file = "mypy-1.9.0-cp311-cp311-macosx_10_9_x86_64.whl", hash = "sha256:653265f9a2784db65bfca694d1edd23093ce49740b2244cde583aeb134c008f3"},
+    {file = "mypy-1.9.0-cp311-cp311-macosx_11_0_arm64.whl", hash = "sha256:3a3c007ff3ee90f69cf0a15cbcdf0995749569b86b6d2f327af01fd1b8aee9dc"},
+    {file = "mypy-1.9.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:2418488264eb41f69cc64a69a745fad4a8f86649af4b1041a4c64ee61fc61129"},
+    {file = "mypy-1.9.0-cp311-cp311-musllinux_1_1_x86_64.whl", hash = "sha256:68edad3dc7d70f2f17ae4c6c1b9471a56138ca22722487eebacfd1eb5321d612"},
+    {file = "mypy-1.9.0-cp311-cp311-win_amd64.whl", hash = "sha256:85ca5fcc24f0b4aeedc1d02f93707bccc04733f21d41c88334c5482219b1ccb3"},
+    {file = "mypy-1.9.0-cp312-cp312-macosx_10_9_x86_64.whl", hash = "sha256:aceb1db093b04db5cd390821464504111b8ec3e351eb85afd1433490163d60cd"},
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+    {file = "mypy-1.9.0-cp38-cp38-macosx_11_0_arm64.whl", hash = "sha256:5e6061f44f2313b94f920e91b204ec600982961e07a17e0f6cd83371cb23f5c2"},
+    {file = "mypy-1.9.0-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:81a10926e5473c5fc3da8abb04119a1f5811a236dc3a38d92015cb1e6ba4cb9e"},
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+    {file = "mypy-1.9.0-cp38-cp38-win_amd64.whl", hash = "sha256:5d741d3fc7c4da608764073089e5f58ef6352bedc223ff58f2f038c2c4698a89"},
+    {file = "mypy-1.9.0-cp39-cp39-macosx_10_9_x86_64.whl", hash = "sha256:587ce887f75dd9700252a3abbc9c97bbe165a4a630597845c61279cf32dfbf02"},
+    {file = "mypy-1.9.0-cp39-cp39-macosx_11_0_arm64.whl", hash = "sha256:f88566144752999351725ac623471661c9d1cd8caa0134ff98cceeea181789f4"},
+    {file = "mypy-1.9.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:61758fabd58ce4b0720ae1e2fea5cfd4431591d6d590b197775329264f86311d"},
+    {file = "mypy-1.9.0-cp39-cp39-musllinux_1_1_x86_64.whl", hash = "sha256:e49499be624dead83927e70c756970a0bc8240e9f769389cdf5714b0784ca6bf"},
+    {file = "mypy-1.9.0-cp39-cp39-win_amd64.whl", hash = "sha256:571741dc4194b4f82d344b15e8837e8c5fcc462d66d076748142327626a1b6e9"},
+    {file = "mypy-1.9.0-py3-none-any.whl", hash = "sha256:a260627a570559181a9ea5de61ac6297aa5af202f06fd7ab093ce74e7181e43e"},
+    {file = "mypy-1.9.0.tar.gz", hash = "sha256:3cc5da0127e6a478cddd906068496a97a7618a21ce9b54bde5bf7e539c7af974"},
 ]
 
 [package.dependencies]
@@ -953,13 +953,13 @@ files = [
 
 [[package]]
 name = "packaging"
-version = "23.2"
+version = "24.0"
 description = "Core utilities for Python packages"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "packaging-23.2-py3-none-any.whl", hash = "sha256:8c491190033a9af7e1d931d0b5dacc2ef47509b34dd0de67ed209b5203fc88c7"},
-    {file = "packaging-23.2.tar.gz", hash = "sha256:048fb0e9405036518eaaf48a55953c750c11e1a1b68e0dd1a9d62ed0c092cfc5"},
+    {file = "packaging-24.0-py3-none-any.whl", hash = "sha256:2ddfb553fdf02fb784c234c7ba6ccc288296ceabec964ad2eae3777778130bc5"},
+    {file = "packaging-24.0.tar.gz", hash = "sha256:eb82c5e3e56209074766e6885bb04b8c38a0c015d0a30036ebe7ece34c9989e9"},
 ]
 
 [[package]]
diff --git a/pyproject.toml b/pyproject.toml
index 2f44424..807ee10 100644
--- a/pyproject.toml
+++ b/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 <alexander.berger@jax.org>",
diff --git a/src/geneweaver/api/controller/api.py b/src/geneweaver/api/controller/api.py
index 0385bf7..808d4b4 100644
--- a/src/geneweaver/api/controller/api.py
+++ b/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)
diff --git a/src/geneweaver/api/controller/species.py b/src/geneweaver/api/controller/species.py
new file mode 100644
index 0000000..dd296bb
--- /dev/null
+++ b/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,
+    gene_id_type: Optional[GeneIdentifier] = None,
+) -> dict:
+    """Get species."""
+    response = species_service.get_species(cursor, taxonomy_id, gene_id_type)
+
+    return response
diff --git a/src/geneweaver/api/services/species.py b/src/geneweaver/api/services/species.py
new file mode 100644
index 0000000..d20c80d
--- /dev/null
+++ b/src/geneweaver/api/services/species.py
@@ -0,0 +1,29 @@
+"""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,
+    gene_id_type: Optional[GeneIdentifier] = None,
+) -> dict:
+    """Get species from DB.
+
+    @param cursor: DB cursor
+    @param taxonomy_id:
+    @param gene_id_type:
+    @return: dictionary response (species).
+    """
+    try:
+        species = db_species.get(cursor, taxonomy_id, gene_id_type)
+        return {"species": species}
+
+    except Exception as err:
+        logger.error(err)
+        raise err
diff --git a/tests/controllers/test_species.py b/tests/controllers/test_species.py
new file mode 100644
index 0000000..bf8ba4e
--- /dev/null
+++ b/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_params")
+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
diff --git a/tests/data/__init__.py b/tests/data/__init__.py
index f9388c7..b6ce854 100644
--- a/tests/data/__init__.py
+++ b/tests/data/__init__.py
@@ -24,6 +24,7 @@
     "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 +94,15 @@
     "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_params": 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"
+    ),
+}
diff --git a/tests/data/species.json b/tests/data/species.json
new file mode 100644
index 0000000..bab8f4f
--- /dev/null
+++ b/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": 12
+      },
+      {
+        "id": 4,
+        "name": "Danio rerio",
+        "taxonomic_id": 7955,
+        "reference_gene_identifier": 13
+      },
+      {
+        "id": 10,
+        "name": "Gallus gallus",
+        "taxonomic_id": 9031,
+        "reference_gene_identifier": 20
+      },
+      {
+        "id": 1,
+        "name": "Mus musculus",
+        "taxonomic_id": 10090,
+        "reference_gene_identifier": 10
+      },
+      {
+        "id": 5,
+        "name": "Drosophila melanogaster",
+        "taxonomic_id": 7227,
+        "reference_gene_identifier": 14
+      },
+      {
+        "id": 11,
+        "name": "Canis familiaris",
+        "taxonomic_id": 9615,
+        "reference_gene_identifier": 1
+      },
+      {
+        "id": 2,
+        "name": "Homo sapiens",
+        "taxonomic_id": 9606,
+        "reference_gene_identifier": 11
+      },
+      {
+        "id": 8,
+        "name": "Caenorhabditis elegans",
+        "taxonomic_id": 6239,
+        "reference_gene_identifier": 15
+      },
+      {
+        "id": 9,
+        "name": "Saccharomyces cerevisiae",
+        "taxonomic_id": 559292,
+        "reference_gene_identifier": 16
+      },
+      {
+        "id": 6,
+        "name": "Macaca mulatta",
+        "taxonomic_id": 9544,
+        "reference_gene_identifier": 1
+      }
+    ]
+  },
+  "species_by_taxonomy_id_10090": {
+    "species": [
+      {
+        "id": 1,
+        "name": "Mus musculus",
+        "taxonomic_id": 10090,
+        "reference_gene_identifier": 10
+      }
+    ]
+  },
+  "species_by_gene_id_type_flybase": {
+    "species": [
+      {
+        "id": 5,
+        "name": "Drosophila melanogaster",
+        "taxonomic_id": 7227,
+        "reference_gene_identifier": 14
+      }
+    ]
+  }
+}
\ No newline at end of file
diff --git a/tests/services/test_species.py b/tests/services/test_species.py
new file mode 100644
index 0000000..6fdca6c
--- /dev/null
+++ b/tests/services/test_species.py
@@ -0,0 +1,82 @@
+"""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 test_species_data
+
+species_no_params = test_species_data.get("species_no_params")
+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.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, 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, 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)
+
+
+@patch("geneweaver.api.services.species.db_species")
+def test_get_species_invalid_params(mock_db_species):
+    """Test speccies by taxonomy id."""
+    mock_db_species.get.return_value = species_no_params
+
+    # with pytest.raises(expected_exception=Exception):
+
+    response = species_service.get_species(
+        None, taxonomy_id="qweqw", gene_id_type="asdasd"
+    )
+
+    # with pytest.raises(expected_exception=TypeError):
+
+    assert response.get("species") == species_no_params

From fbcb259ae275777a81ca1747d95fd75f7683ce6f Mon Sep 17 00:00:00 2001
From: francastell <fsophisco@yahoo.com>
Date: Fri, 15 Mar 2024 15:20:24 -0400
Subject: [PATCH 2/3] db version update, udpates to api response and tests

---
 poetry.lock                              | 114 +++++++++++------------
 pyproject.toml                           |   2 +-
 src/geneweaver/api/controller/species.py |   4 +-
 src/geneweaver/api/services/species.py   |  13 ++-
 tests/controllers/test_species.py        |   2 +-
 tests/data/__init__.py                   |  17 +++-
 tests/data/species.json                  |  24 ++---
 tests/services/test_species.py           |  34 +++----
 8 files changed, 110 insertions(+), 100 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 37d9a20..2c89b22 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -269,63 +269,63 @@ files = [
 
 [[package]]
 name = "coverage"
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+version = "7.4.4"
 description = "Code coverage measurement for Python"
 optional = false
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+    {file = "coverage-7.4.4-cp39-cp39-win32.whl", hash = "sha256:d89d7b2974cae412400e88f35d86af72208e1ede1a541954af5d944a8ba46c57"},
+    {file = "coverage-7.4.4-cp39-cp39-win_amd64.whl", hash = "sha256:9ca28a302acb19b6af89e90f33ee3e1906961f94b54ea37de6737b7ca9d8827c"},
+    {file = "coverage-7.4.4-pp38.pp39.pp310-none-any.whl", hash = "sha256:b2c5edc4ac10a7ef6605a966c58929ec6c1bd0917fb8c15cb3363f65aa40e677"},
+    {file = "coverage-7.4.4.tar.gz", hash = "sha256:c901df83d097649e257e803be22592aedfd5182f07b3cc87d640bbb9afd50f49"},
 ]
 
 [package.dependencies]
@@ -513,13 +513,13 @@ pydantic = {version = ">=1.10.7,<2.0.0", extras = ["dotenv"]}
 
 [[package]]
 name = "geneweaver-db"
-version = "0.3.0a11"
+version = "0.3.0a12"
 description = "Database Interaction Services for GeneWeaver"
 optional = false
 python-versions = ">=3.9,<4.0"
 files = [
-    {file = "geneweaver_db-0.3.0a11-py3-none-any.whl", hash = "sha256:88e486fd5490884e91e99e0354ff899c21d5e18f60a547d700f8d077e28ee3f5"},
-    {file = "geneweaver_db-0.3.0a11.tar.gz", hash = "sha256:7c1875414ece157e03fe284b537a007ff69a4384253e6432289b85124f05b562"},
+    {file = "geneweaver_db-0.3.0a12-py3-none-any.whl", hash = "sha256:523e8c8f24863ab83f0953e9ee906b7462610746cdee53dc21ca16dc4409a679"},
+    {file = "geneweaver_db-0.3.0a12.tar.gz", hash = "sha256:4af5b12cf00ac54d7821bf90c9e668382b012a4db299fb2f7b0fd45be83030da"},
 ]
 
 [package.dependencies]
@@ -1905,4 +1905,4 @@ files = [
 [metadata]
 lock-version = "2.0"
 python-versions = "^3.9"
-content-hash = "53c418b2b7cd7f82dc46c6ad988aedb90d4c3a5941a89a4db69472c72164b6b4"
+content-hash = "73b9bbc2787a3db43f5a067aa5f4d4098f3401446c857543053d748ef7fab760"
diff --git a/pyproject.toml b/pyproject.toml
index 807ee10..0c04a2f 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -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"}
diff --git a/src/geneweaver/api/controller/species.py b/src/geneweaver/api/controller/species.py
index dd296bb..ec45a9f 100644
--- a/src/geneweaver/api/controller/species.py
+++ b/src/geneweaver/api/controller/species.py
@@ -16,9 +16,9 @@ def get_species(
     taxonomy_id: Annotated[
         Optional[int], Query(format="int64", minimum=0, maxiumum=9223372036854775807)
     ] = None,
-    gene_id_type: Optional[GeneIdentifier] = None,
+    reference_gene_id_type: Optional[GeneIdentifier] = None,
 ) -> dict:
     """Get species."""
-    response = species_service.get_species(cursor, taxonomy_id, gene_id_type)
+    response = species_service.get_species(cursor, taxonomy_id, reference_gene_id_type)
 
     return response
diff --git a/src/geneweaver/api/services/species.py b/src/geneweaver/api/services/species.py
index d20c80d..a619396 100644
--- a/src/geneweaver/api/services/species.py
+++ b/src/geneweaver/api/services/species.py
@@ -11,17 +11,24 @@
 def get_species(
     cursor: Cursor,
     taxonomy_id: Optional[int] = None,
-    gene_id_type: Optional[GeneIdentifier] = None,
+    reference_gene_id_type: Optional[GeneIdentifier] = None,
 ) -> dict:
     """Get species from DB.
 
     @param cursor: DB cursor
     @param taxonomy_id:
-    @param gene_id_type:
+    @param reference_gene_id_type:
     @return: dictionary response (species).
     """
     try:
-        species = db_species.get(cursor, taxonomy_id, gene_id_type)
+        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:
diff --git a/tests/controllers/test_species.py b/tests/controllers/test_species.py
index bf8ba4e..05ee2ee 100644
--- a/tests/controllers/test_species.py
+++ b/tests/controllers/test_species.py
@@ -3,7 +3,7 @@
 
 from tests.data import test_species_data
 
-species_no_params = test_species_data.get("species_no_params")
+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"
diff --git a/tests/data/__init__.py b/tests/data/__init__.py
index b6ce854..77d37ca 100644
--- a/tests/data/__init__.py
+++ b/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(
@@ -98,7 +100,7 @@
 
 ## Species test data
 test_species_data = {
-    "species_no_params": json.loads(species_json).get("species_no_parameters"),
+    "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"
     ),
@@ -106,3 +108,16 @@
         "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
diff --git a/tests/data/species.json b/tests/data/species.json
index bab8f4f..727d3f3 100644
--- a/tests/data/species.json
+++ b/tests/data/species.json
@@ -11,61 +11,61 @@
         "id": 3,
         "name": "Rattus norvegicus",
         "taxonomic_id": 10116,
-        "reference_gene_identifier": 12
+        "reference_gene_identifier": "RGD"
       },
       {
         "id": 4,
         "name": "Danio rerio",
         "taxonomic_id": 7955,
-        "reference_gene_identifier": 13
+        "reference_gene_identifier": "ZFIN"
       },
       {
         "id": 10,
         "name": "Gallus gallus",
         "taxonomic_id": 9031,
-        "reference_gene_identifier": 20
+        "reference_gene_identifier": "CGNC"
       },
       {
         "id": 1,
         "name": "Mus musculus",
         "taxonomic_id": 10090,
-        "reference_gene_identifier": 10
+        "reference_gene_identifier": "MGI"
       },
       {
         "id": 5,
         "name": "Drosophila melanogaster",
         "taxonomic_id": 7227,
-        "reference_gene_identifier": 14
+        "reference_gene_identifier": "FlyBase"
       },
       {
         "id": 11,
         "name": "Canis familiaris",
         "taxonomic_id": 9615,
-        "reference_gene_identifier": 1
+        "reference_gene_identifier": "Entrez"
       },
       {
         "id": 2,
         "name": "Homo sapiens",
         "taxonomic_id": 9606,
-        "reference_gene_identifier": 11
+        "reference_gene_identifier": "HGNC"
       },
       {
         "id": 8,
         "name": "Caenorhabditis elegans",
         "taxonomic_id": 6239,
-        "reference_gene_identifier": 15
+        "reference_gene_identifier": "Wormbase"
       },
       {
         "id": 9,
         "name": "Saccharomyces cerevisiae",
         "taxonomic_id": 559292,
-        "reference_gene_identifier": 16
+        "reference_gene_identifier": "SGD"
       },
       {
         "id": 6,
         "name": "Macaca mulatta",
         "taxonomic_id": 9544,
-        "reference_gene_identifier": 1
+        "reference_gene_identifier": "Entrez"
       }
     ]
   },
@@ -75,7 +75,7 @@
         "id": 1,
         "name": "Mus musculus",
         "taxonomic_id": 10090,
-        "reference_gene_identifier": 10
+        "reference_gene_identifier": "MGI"
       }
     ]
   },
@@ -85,7 +85,7 @@
         "id": 5,
         "name": "Drosophila melanogaster",
         "taxonomic_id": 7227,
-        "reference_gene_identifier": 14
+        "reference_gene_identifier": "FlyBase"
       }
     ]
   }
diff --git a/tests/services/test_species.py b/tests/services/test_species.py
index 6fdca6c..a65e6f9 100644
--- a/tests/services/test_species.py
+++ b/tests/services/test_species.py
@@ -6,12 +6,14 @@
 from geneweaver.api.services import species as species_service
 from geneweaver.core.enum import GeneIdentifier
 
-from tests.data import test_species_data
+from tests.data import get_species_db_resp, test_species_data
 
-species_no_params = test_species_data.get("species_no_params")
-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"
+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")
 )
 
 
@@ -40,7 +42,9 @@ 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, gene_id_type=GeneIdentifier("FlyBase"))
+    response = species_service.get_species(
+        None, reference_gene_id_type=GeneIdentifier("FlyBase")
+    )
 
     assert response.get("species") == species_by_gene_id_type_flybase
 
@@ -51,7 +55,7 @@ def test_get_species_by_gene_id_type_and_taxonomy(mock_db_species):
     mock_db_species.get.return_value = species_by_gene_id_type_flybase
 
     response = species_service.get_species(
-        None, gene_id_type=GeneIdentifier("FlyBase"), taxonomy_id=7227
+        None, reference_gene_id_type=GeneIdentifier("FlyBase"), taxonomy_id=7227
     )
 
     assert response.get("species") == species_by_gene_id_type_flybase
@@ -64,19 +68,3 @@ def test_get_species_with_error(mock_db_species):
 
     with pytest.raises(expected_exception=Exception):
         species_service.get(None)
-
-
-@patch("geneweaver.api.services.species.db_species")
-def test_get_species_invalid_params(mock_db_species):
-    """Test speccies by taxonomy id."""
-    mock_db_species.get.return_value = species_no_params
-
-    # with pytest.raises(expected_exception=Exception):
-
-    response = species_service.get_species(
-        None, taxonomy_id="qweqw", gene_id_type="asdasd"
-    )
-
-    # with pytest.raises(expected_exception=TypeError):
-
-    assert response.get("species") == species_no_params

From dbde2bea49c0f16f3129635dbde3317c949e10a6 Mon Sep 17 00:00:00 2001
From: francastell <fsophisco@yahoo.com>
Date: Fri, 15 Mar 2024 15:22:42 -0400
Subject: [PATCH 3/3] doc update

---
 tests/data/__init__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/data/__init__.py b/tests/data/__init__.py
index 77d37ca..86c34ee 100644
--- a/tests/data/__init__.py
+++ b/tests/data/__init__.py
@@ -111,7 +111,7 @@
 
 
 def get_species_db_resp(species_data: dict) -> dict:
-    """ " get species data as returned by DB."""
+    """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)