From d3958686558489d1912e09d1b3f0c489d777b96f Mon Sep 17 00:00:00 2001
From: francastell <fsophisco@yahoo.com>
Date: Tue, 19 Dec 2023 15:38:35 -0500
Subject: [PATCH 1/7] G3-9 Initial

---
 poetry.lock                                  | 1572 ++++++++++--------
 pyproject.toml                               |   12 +-
 src/geneweaver/api/controller/genesets.py    |   29 +-
 src/geneweaver/api/controller/message.py     |    6 +
 src/geneweaver/api/core/config_class.py      |    2 +-
 src/geneweaver/api/services/geneset.py       |   45 +
 tests/controllers/.pytest_cache/.gitignore   |    2 +
 tests/controllers/.pytest_cache/CACHEDIR.TAG |    4 +
 tests/controllers/.pytest_cache/README.md    |    8 +
 tests/controllers/__init__.py                |    0
 tests/controllers/test_genesets.py           |   72 +
 tests/data/__init__.py                       |    0
 tests/data/response_geneset_1234.json        |   50 +
 tests/services/test_genset.py                |   68 +
 14 files changed, 1120 insertions(+), 750 deletions(-)
 create mode 100644 src/geneweaver/api/controller/message.py
 create mode 100644 tests/controllers/.pytest_cache/.gitignore
 create mode 100644 tests/controllers/.pytest_cache/CACHEDIR.TAG
 create mode 100644 tests/controllers/.pytest_cache/README.md
 create mode 100644 tests/controllers/__init__.py
 create mode 100644 tests/controllers/test_genesets.py
 create mode 100644 tests/data/__init__.py
 create mode 100644 tests/data/response_geneset_1234.json
 create mode 100644 tests/services/test_genset.py

diff --git a/poetry.lock b/poetry.lock
index 3679a7d..57b3e4c 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,55 +1,51 @@
-# This file is automatically @generated by Poetry 1.5.1 and should not be changed by hand.
+# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand.
 
 [[package]]
 name = "anyio"
-version = "3.7.1"
+version = "4.1.0"
 description = "High level compatibility layer for multiple asynchronous event loop implementations"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "anyio-3.7.1-py3-none-any.whl", hash = "sha256:91dee416e570e92c64041bd18b900d1d6fa78dff7048769ce5ac5ddad004fbb5"},
-    {file = "anyio-3.7.1.tar.gz", hash = "sha256:44a3c9aba0f5defa43261a8b3efb97891f2bd7d804e0e1f56419befa1adfc780"},
+    {file = "anyio-4.1.0-py3-none-any.whl", hash = "sha256:56a415fbc462291813a94528a779597226619c8e78af7de0507333f700011e5f"},
+    {file = "anyio-4.1.0.tar.gz", hash = "sha256:5a0bec7085176715be77df87fc66d6c9d70626bd752fcc85f57cdbee5b3760da"},
 ]
 
 [package.dependencies]
-exceptiongroup = {version = "*", markers = "python_version < \"3.11\""}
+exceptiongroup = {version = ">=1.0.2", markers = "python_version < \"3.11\""}
 idna = ">=2.8"
 sniffio = ">=1.1"
 
 [package.extras]
-doc = ["Sphinx", "packaging", "sphinx-autodoc-typehints (>=1.2.0)", "sphinx-rtd-theme (>=1.2.2)", "sphinxcontrib-jquery"]
-test = ["anyio[trio]", "coverage[toml] (>=4.5)", "hypothesis (>=4.0)", "mock (>=4)", "psutil (>=5.9)", "pytest (>=7.0)", "pytest-mock (>=3.6.1)", "trustme", "uvloop (>=0.17)"]
-trio = ["trio (<0.22)"]
+doc = ["Sphinx (>=7)", "packaging", "sphinx-autodoc-typehints (>=1.2.0)", "sphinx-rtd-theme"]
+test = ["anyio[trio]", "coverage[toml] (>=7)", "exceptiongroup (>=1.2.0)", "hypothesis (>=4.0)", "psutil (>=5.9)", "pytest (>=7.0)", "pytest-mock (>=3.6.1)", "trustme", "uvloop (>=0.17)"]
+trio = ["trio (>=0.23)"]
 
 [[package]]
 name = "black"
-version = "23.7.0"
+version = "23.11.0"
 description = "The uncompromising code formatter."
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
@@ -59,7 +55,7 @@ packaging = ">=22.0"
 pathspec = ">=0.9.0"
 platformdirs = ">=2"
 tomli = {version = ">=1.1.0", markers = "python_version < \"3.11\""}
-typing-extensions = {version = ">=3.10.0.0", markers = "python_version < \"3.10\""}
+typing-extensions = {version = ">=4.0.1", markers = "python_version < \"3.11\""}
 
 [package.extras]
 colorama = ["colorama (>=0.4.3)"]
@@ -69,86 +65,74 @@ uvloop = ["uvloop (>=0.15.2)"]
 
 [[package]]
 name = "certifi"
-version = "2023.5.7"
+version = "2023.11.17"
 description = "Python package for providing Mozilla's CA Bundle."
 optional = false
 python-versions = ">=3.6"
 files = [
-    {file = "certifi-2023.5.7-py3-none-any.whl", hash = "sha256:c6c2e98f5c7869efca1f8916fed228dd91539f9f1b444c314c06eef02980c716"},
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+    {file = "certifi-2023.11.17-py3-none-any.whl", hash = "sha256:e036ab49d5b79556f99cfc2d9320b34cfbe5be05c5871b51de9329f0603b0474"},
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 ]
 
 [[package]]
 name = "cffi"
-version = "1.15.1"
+version = "1.16.0"
 description = "Foreign Function Interface for Python calling C code."
 optional = false
-python-versions = "*"
+python-versions = ">=3.8"
 files = [
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 [package.dependencies]
@@ -156,97 +140,112 @@ pycparser = "*"
 
 [[package]]
 name = "charset-normalizer"
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 description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet."
 optional = false
 python-versions = ">=3.7.0"
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 ]
 
 [package.dependencies]
@@ -340,34 +331,34 @@ toml = ["tomli"]
 
 [[package]]
 name = "cryptography"
-version = "41.0.3"
+version = "41.0.7"
 description = "cryptography is a package which provides cryptographic recipes and primitives to Python developers."
 optional = false
 python-versions = ">=3.7"
 files = [
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 ]
 
 [package.dependencies]
@@ -385,19 +376,18 @@ test-randomorder = ["pytest-randomly"]
 
 [[package]]
 name = "dnspython"
-version = "2.3.0"
+version = "2.4.2"
 description = "DNS toolkit"
 optional = false
-python-versions = ">=3.7,<4.0"
+python-versions = ">=3.8,<4.0"
 files = [
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+    {file = "dnspython-2.4.2-py3-none-any.whl", hash = "sha256:57c6fbaaeaaf39c891292012060beb141791735dbb4004798328fc2c467402d8"},
+    {file = "dnspython-2.4.2.tar.gz", hash = "sha256:8dcfae8c7460a2f84b4072e26f1c9f4101ca20c071649cb7c34e8b6a93d58984"},
 ]
 
 [package.extras]
-curio = ["curio (>=1.2,<2.0)", "sniffio (>=1.1,<2.0)"]
-dnssec = ["cryptography (>=2.6,<40.0)"]
-doh = ["h2 (>=4.1.0)", "httpx (>=0.21.1)", "requests (>=2.23.0,<3.0.0)", "requests-toolbelt (>=0.9.1,<0.11.0)"]
+dnssec = ["cryptography (>=2.6,<42.0)"]
+doh = ["h2 (>=4.1.0)", "httpcore (>=0.17.3)", "httpx (>=0.24.1)"]
 doq = ["aioquic (>=0.9.20)"]
 idna = ["idna (>=2.1,<4.0)"]
 trio = ["trio (>=0.14,<0.23)"]
@@ -423,13 +413,13 @@ gmpy2 = ["gmpy2"]
 
 [[package]]
 name = "email-validator"
-version = "2.0.0.post2"
+version = "2.1.0.post1"
 description = "A robust email address syntax and deliverability validation library."
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
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+    {file = "email_validator-2.1.0.post1-py3-none-any.whl", hash = "sha256:c973053efbeddfef924dc0bd93f6e77a1ea7ee0fce935aea7103c7a3d6d2d637"},
+    {file = "email_validator-2.1.0.post1.tar.gz", hash = "sha256:a4b0bd1cf55f073b924258d19321b1f3aa74b4b5a71a42c305575dba920e1a44"},
 ]
 
 [package.dependencies]
@@ -449,13 +439,13 @@ files = [
 
 [[package]]
 name = "exceptiongroup"
-version = "1.1.2"
+version = "1.2.0"
 description = "Backport of PEP 654 (exception groups)"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "exceptiongroup-1.1.2-py3-none-any.whl", hash = "sha256:e346e69d186172ca7cf029c8c1d16235aa0e04035e5750b4b95039e65204328f"},
-    {file = "exceptiongroup-1.1.2.tar.gz", hash = "sha256:12c3e887d6485d16943a309616de20ae5582633e0a2eda17f4e10fd61c1e8af5"},
+    {file = "exceptiongroup-1.2.0-py3-none-any.whl", hash = "sha256:4bfd3996ac73b41e9b9628b04e079f193850720ea5945fc96a08633c66912f14"},
+    {file = "exceptiongroup-1.2.0.tar.gz", hash = "sha256:91f5c769735f051a4290d52edd0858999b57e5876e9f85937691bd4c9fa3ed68"},
 ]
 
 [package.extras]
@@ -491,13 +481,13 @@ all = ["email-validator (>=1.1.1)", "httpx (>=0.23.0)", "itsdangerous (>=1.1.0)"
 
 [[package]]
 name = "geneweaver-core"
-version = "0.8.0a0"
+version = "0.8.0a1"
 description = "The core of the Jax-Geneweaver Python library"
 optional = false
 python-versions = ">=3.9,<4.0"
 files = [
-    {file = "geneweaver_core-0.8.0a0-py3-none-any.whl", hash = "sha256:01a70f8dc9407def33a706cced4e4946de66b10f61e828d69d2b686b39a5a197"},
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+    {file = "geneweaver_core-0.8.0a1-py3-none-any.whl", hash = "sha256:cc779cd36b00542384b79cafc87e110c581e28c6bd96bc3caba775f4d91b3e50"},
+    {file = "geneweaver_core-0.8.0a1.tar.gz", hash = "sha256:f0db3e3154737a84f8a2ebd728d1499417618f53f52ddcffe47ec7426e811304"},
 ]
 
 [package.dependencies]
@@ -554,67 +544,82 @@ files = [
 
 [[package]]
 name = "httpcore"
-version = "0.17.3"
+version = "1.0.2"
 description = "A minimal low-level HTTP client."
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "httpcore-0.17.3-py3-none-any.whl", hash = "sha256:c2789b767ddddfa2a5782e3199b2b7f6894540b17b16ec26b2c4d8e103510b87"},
-    {file = "httpcore-0.17.3.tar.gz", hash = "sha256:a6f30213335e34c1ade7be6ec7c47f19f50c56db36abef1a9dfa3815b1cb3888"},
+    {file = "httpcore-1.0.2-py3-none-any.whl", hash = "sha256:096cc05bca73b8e459a1fc3dcf585148f63e534eae4339559c9b8a8d6399acc7"},
+    {file = "httpcore-1.0.2.tar.gz", hash = "sha256:9fc092e4799b26174648e54b74ed5f683132a464e95643b226e00c2ed2fa6535"},
 ]
 
 [package.dependencies]
-anyio = ">=3.0,<5.0"
 certifi = "*"
 h11 = ">=0.13,<0.15"
-sniffio = "==1.*"
 
 [package.extras]
+asyncio = ["anyio (>=4.0,<5.0)"]
 http2 = ["h2 (>=3,<5)"]
 socks = ["socksio (==1.*)"]
+trio = ["trio (>=0.22.0,<0.23.0)"]
+
+[[package]]
+name = "httplib2"
+version = "0.22.0"
+description = "A comprehensive HTTP client library."
+optional = false
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
+files = [
+    {file = "httplib2-0.22.0-py3-none-any.whl", hash = "sha256:14ae0a53c1ba8f3d37e9e27cf37eabb0fb9980f435ba405d546948b009dd64dc"},
+    {file = "httplib2-0.22.0.tar.gz", hash = "sha256:d7a10bc5ef5ab08322488bde8c726eeee5c8618723fdb399597ec58f3d82df81"},
+]
+
+[package.dependencies]
+pyparsing = {version = ">=2.4.2,<3.0.0 || >3.0.0,<3.0.1 || >3.0.1,<3.0.2 || >3.0.2,<3.0.3 || >3.0.3,<4", markers = "python_version > \"3.0\""}
 
 [[package]]
 name = "httptools"
-version = "0.6.0"
+version = "0.6.1"
 description = "A collection of framework independent HTTP protocol utils."
 optional = false
-python-versions = ">=3.5.0"
-files = [
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 ]
 
 [package.extras]
@@ -622,18 +627,19 @@ test = ["Cython (>=0.29.24,<0.30.0)"]
 
 [[package]]
 name = "httpx"
-version = "0.24.1"
+version = "0.25.2"
 description = "The next generation HTTP client."
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
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+    {file = "httpx-0.25.2.tar.gz", hash = "sha256:8b8fcaa0c8ea7b05edd69a094e63a2094c4efcb48129fb757361bc423c0ad9e8"},
 ]
 
 [package.dependencies]
+anyio = "*"
 certifi = "*"
-httpcore = ">=0.15.0,<0.18.0"
+httpcore = "==1.*"
 idna = "*"
 sniffio = "*"
 
@@ -645,13 +651,13 @@ socks = ["socksio (==1.*)"]
 
 [[package]]
 name = "idna"
-version = "3.4"
+version = "3.6"
 description = "Internationalized Domain Names in Applications (IDNA)"
 optional = false
 python-versions = ">=3.5"
 files = [
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-    {file = "idna-3.4.tar.gz", hash = "sha256:814f528e8dead7d329833b91c5faa87d60bf71824cd12a7530b5526063d02cb4"},
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+    {file = "idna-3.6.tar.gz", hash = "sha256:9ecdbbd083b06798ae1e86adcbfe8ab1479cf864e4ee30fe4e46a003d12491ca"},
 ]
 
 [[package]]
@@ -667,21 +673,15 @@ files = [
 
 [[package]]
 name = "isort"
-version = "5.12.0"
+version = "5.13.1"
 description = "A Python utility / library to sort Python imports."
 optional = false
 python-versions = ">=3.8.0"
 files = [
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+    {file = "isort-5.13.1.tar.gz", hash = "sha256:aaed790b463e8703fb1eddb831dfa8e8616bacde2c083bd557ef73c8189b7263"},
 ]
 
-[package.extras]
-colors = ["colorama (>=0.4.3)"]
-pipfile-deprecated-finder = ["pip-shims (>=0.5.2)", "pipreqs", "requirementslib"]
-plugins = ["setuptools"]
-requirements-deprecated-finder = ["pip-api", "pipreqs"]
-
 [[package]]
 name = "itsdangerous"
 version = "2.1.2"
@@ -710,6 +710,19 @@ MarkupSafe = ">=2.0"
 [package.extras]
 i18n = ["Babel (>=2.7)"]
 
+[[package]]
+name = "magicmock"
+version = "0.03"
+description = "A generic mock server"
+optional = false
+python-versions = "*"
+files = [
+    {file = "magicmock-0.03.tar.gz", hash = "sha256:fe0d99b9daab2f9361dd62b8dc299f3ba46fe1923119335ab31eca4318fda1c5"},
+]
+
+[package.dependencies]
+httplib2 = "*"
+
 [[package]]
 name = "markupsafe"
 version = "2.1.3"
@@ -737,6 +750,16 @@ files = [
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 install-types = ["pip"]
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 [[package]]
 name = "packaging"
-version = "23.1"
+version = "23.2"
 description = "Core utilities for Python packages"
 optional = false
 python-versions = ">=3.7"
 files = [
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 [[package]]
@@ -979,9 +1007,8 @@ files = [
 
 [package.dependencies]
 numpy = [
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-    {version = ">=1.21.0", markers = "python_version >= \"3.10\""},
     {version = ">=1.23.2", markers = "python_version >= \"3.11\""},
+    {version = ">=1.21.0", markers = "python_version >= \"3.10\" and python_version < \"3.11\""},
 ]
 python-dateutil = ">=2.8.2"
 pytz = ">=2020.1"
@@ -1012,39 +1039,39 @@ xml = ["lxml (>=4.6.3)"]
 
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+version = "0.12.1"
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+python-versions = ">=3.8"
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 ]
 
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 description = "A small Python package for determining appropriate platform-specific dirs, e.g. a \"user data dir\"."
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
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 [package.extras]
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-test = ["appdirs (==1.4.4)", "covdefaults (>=2.3)", "pytest (>=7.3.1)", "pytest-cov (>=4.1)", "pytest-mock (>=3.10)"]
+docs = ["furo (>=2023.7.26)", "proselint (>=0.13)", "sphinx (>=7.1.1)", "sphinx-autodoc-typehints (>=1.24)"]
+test = ["appdirs (==1.4.4)", "covdefaults (>=2.3)", "pytest (>=7.4)", "pytest-cov (>=4.1)", "pytest-mock (>=3.11.1)"]
 
 [[package]]
 name = "pluggy"
-version = "1.2.0"
+version = "1.3.0"
 description = "plugin and hook calling mechanisms for python"
 optional = false
-python-versions = ">=3.7"
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 [package.dependencies]
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 dotenv = ["python-dotenv (>=0.10.4)"]
 email = ["email-validator (>=1.0.3)"]
 
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+
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 [package.dependencies]
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 ]
 
 [metadata]
 lock-version = "2.0"
-python-versions = "^3.9"
-content-hash = "0ea43acd3f3f058a7640f58d5183d834b88b2da78c07d593beb572892d3d59b5"
+python-versions = "^3.10.9"
+content-hash = "a0c16c5fbc6e13e1fea05fa39fc128092269c75aebf14906951e98b47ca01d78"
diff --git a/pyproject.toml b/pyproject.toml
index cb3e54a..1e74e3c 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -8,10 +8,17 @@ packages = [
 ]
 
 [tool.poetry.dependencies]
-python = "^3.9"
+#python = "^3.9"
+python = "^3.10.9"
+
 geneweaver-core = "^0.8.0a0"
 fastapi = {extras = ["all"], version = "^0.99.1"}
-uvicorn = {extras = ["standard"], version = "^0.24.0"}
+uvicorn = {extras = ["standard"], version = "^0.23.2"}
+
+#fastapi = "^0.79.0"
+#fastapi = {version = "^0.79.0"}
+#uvicorn = {extras = ["standard"], version = "^0.18.2"}
+
 geneweaver-db = "^0.2.0a0"
 psycopg-pool = "^3.1.7"
 requests = "^2.31.0"
@@ -20,6 +27,7 @@ python-jose = {extras = ["cryptography"], version = "^3.3.0"}
 [tool.poetry.group.dev.dependencies]
 geneweaver-testing = "^0.0.3"
 pytest-asyncio = "^0.21.0"
+magicmock =  "^0.03"
 
 [tool.ruff]
 select = ['F', 'E', 'W', 'A', 'C90', 'N', 'B', 'ANN', 'D', 'I', 'ERA', 'PD', 'NPY', 'PT']
diff --git a/src/geneweaver/api/controller/genesets.py b/src/geneweaver/api/controller/genesets.py
index 72c8caf..ad09b50 100644
--- a/src/geneweaver/api/controller/genesets.py
+++ b/src/geneweaver/api/controller/genesets.py
@@ -2,15 +2,17 @@
 from typing import Optional
 
 from fastapi import APIRouter, Depends, HTTPException, Security
-from geneweaver.api import dependencies as deps
-from geneweaver.api.schemas.auth import UserInternal
+from fastapi.logger import logger
 from geneweaver.core.schema.geneset import GenesetUpload
 from geneweaver.db import geneset as db_geneset
 from geneweaver.db import geneset_value as db_geneset_value
-from geneweaver.db.geneset import is_readable
 
-router = APIRouter(prefix="/genesets")
+from geneweaver.api import dependencies as deps
+from geneweaver.api.schemas.auth import UserInternal
+from geneweaver.api.services import geneset as genset_service
+from . import message as api_message
 
+router = APIRouter(prefix="/genesets")
 
 @router.get("")
 def get_visible_genesets(
@@ -26,16 +28,23 @@ def get_visible_genesets(
 def get_geneset(
     geneset_id: int,
     user: UserInternal = Security(deps.full_user),
-    cursor: Optional[deps.Cursor] = Depends(deps.cursor),
+    cursor: Optional[deps.Cursor] = Depends(deps.cursor)
 ) -> dict:
     """Get a geneset by ID."""
-    if not is_readable(cursor, user.id, geneset_id):
-        raise HTTPException(status_code=403, detail="Forbidden")
+    try:
+        response = genset_service.get_geneset(geneset_id, user, cursor)
+
+    except Exception as err:
+        logger.error(err)
+        raise HTTPException(status_code=500, detail=api_message.UNEXPECTED_ERROR)
 
-    geneset = db_geneset.by_id(cursor, geneset_id)
-    geneset_values = db_geneset_value.by_geneset_id(cursor, geneset_id)
-    return {"geneset": geneset, "geneset_values": geneset_values}
+    if "error" in response:
+        if response.get("message") == api_message.ACCESS_FORBIDEN:
+            raise HTTPException(status_code=403, detail=api_message.ACCESS_FORBIDEN)
+        else:
+            raise HTTPException(status_code=500, detail=api_message.ACCESS_FORBIDEN)
 
+    return response
 
 @router.post("")
 def upload_geneset(
diff --git a/src/geneweaver/api/controller/message.py b/src/geneweaver/api/controller/message.py
new file mode 100644
index 0000000..add6cf4
--- /dev/null
+++ b/src/geneweaver/api/controller/message.py
@@ -0,0 +1,6 @@
+"""Costant key/value messages"""
+
+
+##Errors
+ACCESS_FORBIDEN="Forbidden"
+UNEXPECTED_ERROR="Unexpected Error"
\ No newline at end of file
diff --git a/src/geneweaver/api/core/config_class.py b/src/geneweaver/api/core/config_class.py
index e45de7c..e798b1e 100644
--- a/src/geneweaver/api/core/config_class.py
+++ b/src/geneweaver/api/core/config_class.py
@@ -38,7 +38,7 @@ def assemble_db_connection(
         "openid profile email": "read",
     }
     JWT_PERMISSION_PREFIX: str = "approle"
-    AUTH_CLIENT_ID: str = "oVm9omUtLBpVyL7YfJA8gp3hHaHwyVt8"
+    AUTH_CLIENT_ID: str = "T7bj6wlmtVcAN2O6kzDRwPVFyIj4UQNs"
 
     class Config:
         """Configuration for the BaseSettings class."""
diff --git a/src/geneweaver/api/services/geneset.py b/src/geneweaver/api/services/geneset.py
index d886464..67cd66c 100644
--- a/src/geneweaver/api/services/geneset.py
+++ b/src/geneweaver/api/services/geneset.py
@@ -1 +1,46 @@
 """Service functions for dealing with genesets."""
+
+from fastapi.logger import logger
+from geneweaver.db import geneset as db_geneset
+from geneweaver.db import geneset_value as db_geneset_value
+from geneweaver.db.geneset import is_readable as db_is_readable
+
+from geneweaver.api import dependencies as deps
+from geneweaver.api.controller import message
+from geneweaver.api.schemas.auth import User
+
+
+def get_geneset(
+    geneset_id: int,
+    user: User,
+    cursor: deps.Cursor
+) -> dict:
+
+    """Get a geneset by ID."""
+    try:
+        if not is_geneset_readable_by_user(geneset_id, user, cursor):
+            return {"error": True, "message": message.ACCESS_FORBIDEN}
+
+        geneset = db_geneset.by_id(cursor, geneset_id)
+        geneset_values = db_geneset_value.by_geneset_id(cursor, geneset_id)
+        return {"geneset": geneset, "geneset_values": geneset_values}
+
+    except Exception as err:
+        logger.error(err)
+        raise err
+
+def is_geneset_readable_by_user(
+        geneset_id: int,
+        user: User,
+        cursor: deps.Cursor
+) -> bool:
+
+    """ check if the user can read the geneset from DB"""
+    readable: bool = False
+    try:
+        readable = db_is_readable(cursor, user.id, geneset_id)
+    except Exception as err:
+        logger.error(err)
+        raise err
+
+    return readable
\ No newline at end of file
diff --git a/tests/controllers/.pytest_cache/.gitignore b/tests/controllers/.pytest_cache/.gitignore
new file mode 100644
index 0000000..ca0633e
--- /dev/null
+++ b/tests/controllers/.pytest_cache/.gitignore
@@ -0,0 +1,2 @@
+# Created by pytest automatically.
+v
diff --git a/tests/controllers/.pytest_cache/CACHEDIR.TAG b/tests/controllers/.pytest_cache/CACHEDIR.TAG
new file mode 100644
index 0000000..fce15ad
--- /dev/null
+++ b/tests/controllers/.pytest_cache/CACHEDIR.TAG
@@ -0,0 +1,4 @@
+Signature: 8a477f597d28d172789f06886806bc55
+# This file is a cache directory tag created by pytest.
+# For information about cache directory tags, see:
+#	https://bford.info/cachedir/spec.html
diff --git a/tests/controllers/.pytest_cache/README.md b/tests/controllers/.pytest_cache/README.md
new file mode 100644
index 0000000..b89018c
--- /dev/null
+++ b/tests/controllers/.pytest_cache/README.md
@@ -0,0 +1,8 @@
+# pytest cache directory #
+
+This directory contains data from the pytest's cache plugin,
+which provides the `--lf` and `--ff` options, as well as the `cache` fixture.
+
+**Do not** commit this to version control.
+
+See [the docs](https://docs.pytest.org/en/stable/how-to/cache.html) for more information.
diff --git a/tests/controllers/__init__.py b/tests/controllers/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/tests/controllers/test_genesets.py b/tests/controllers/test_genesets.py
new file mode 100644
index 0000000..1b25fb0
--- /dev/null
+++ b/tests/controllers/test_genesets.py
@@ -0,0 +1,72 @@
+import importlib.resources
+import json
+from unittest.mock import Mock
+from unittest.mock import patch
+
+import psycopg
+import pytest
+from fastapi.testclient import TestClient
+
+from geneweaver.api.dependencies import full_user, cursor
+from geneweaver.api.main import app
+
+client = TestClient(app)
+
+### Load test data
+# Opening JSON file
+str_json = importlib.resources.read_text("tests.data", "response_geneset_1234.json")
+# returns JSON string as a dictionary
+test_data = json.loads(str_json)
+
+response_mock = Mock()
+response_mock.status_code = 200
+response_mock.json.return_value = test_data
+
+### Mock dependencies
+m1 = Mock()
+def mock_full_user() -> m1.AsyncMock:
+    return m1
+m2 = Mock()
+def mock_cursor() -> psycopg.Cursor:
+    return m2.AsyncMock()
+m3 = Mock()
+def mock_cursor_obj() -> psycopg.Cursor:
+    return m3.AsyncMock()
+
+app.dependency_overrides.update(
+    {full_user: mock_full_user, cursor: mock_cursor}
+)
+
+@patch.object(client, 'get', return_value=response_mock)
+def test_get_geneset(mock_client):
+    response = client.get("/genesets/1234")
+    assert response.status_code == 200
+
+@patch('geneweaver.api.services.geneset.get_geneset')
+@patch('geneweaver.api.services.geneset.is_geneset_readable_by_user')
+def test_get_geneset_response(mock_genset_is_readable, mock_get_genenset):
+    mock_genset_is_readable.return_value = True
+    mock_get_genenset.return_value = test_data
+
+    response = client.get("/genesets/1234")
+    assert response.status_code == 200
+    assert response.json() == test_data
+
+@patch('geneweaver.api.services.geneset.db_is_readable')
+def test_get_geneset_forbidden(mock_genset_is_readable):
+
+    mock_genset_is_readable.return_value = False
+    response = client.get("/genesets/1234")
+
+    assert response.json() == {'detail': 'Forbidden'}
+    assert response.status_code == 403
+
+@patch('geneweaver.api.services.geneset.db_is_readable')
+def test_get_geneset_unexpected_error(mock_genset_is_readable):
+
+    mock_genset_is_readable.side_effect = Exception
+
+    with pytest.raises(Exception):
+        response = client.get("/genesets/1234")
+        assert response.json() == {'detail': 'Unexpected error'}
+        assert response.status_code == 500
diff --git a/tests/data/__init__.py b/tests/data/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/tests/data/response_geneset_1234.json b/tests/data/response_geneset_1234.json
new file mode 100644
index 0000000..8b8b931
--- /dev/null
+++ b/tests/data/response_geneset_1234.json
@@ -0,0 +1,50 @@
+{
+  "geneset": null,
+  "geneset_values": [
+    {
+      "gs_id": 1234,
+      "ode_gene_id": 70495,
+      "gsv_value": 1,
+      "gsv_hits": 1,
+      "gsv_source_list": [
+        "PDE4DIP"
+      ],
+      "gsv_value_list": [
+        1
+      ],
+      "gsv_in_threshold": true,
+      "gsv_date": "2020-05-05",
+      "ode_ref_id": "PDE4DIP"
+    },
+    {
+      "gs_id": 1234,
+      "ode_gene_id": 83819,
+      "gsv_value": 1,
+      "gsv_hits": 1,
+      "gsv_source_list": [
+        "TMEPAI"
+      ],
+      "gsv_value_list": [
+        1
+      ],
+      "gsv_in_threshold": true,
+      "gsv_date": "2020-05-05",
+      "ode_ref_id": "PMEPA1"
+    },
+    {
+      "gs_id": 1234,
+      "ode_gene_id": 90284,
+      "gsv_value": 1,
+      "gsv_hits": 1,
+      "gsv_source_list": [
+        "PREPL"
+      ],
+      "gsv_value_list": [
+        1
+      ],
+      "gsv_in_threshold": true,
+      "gsv_date": "2020-05-05",
+      "ode_ref_id": "PREPL"
+    }
+  ]
+}
\ No newline at end of file
diff --git a/tests/services/test_genset.py b/tests/services/test_genset.py
new file mode 100644
index 0000000..276db56
--- /dev/null
+++ b/tests/services/test_genset.py
@@ -0,0 +1,68 @@
+import importlib.resources
+import json
+from unittest.mock import patch
+
+import pytest
+
+import geneweaver.api.controller.message as message
+import geneweaver.api.services.geneset as geneset
+
+## Load test data
+# Opening JSON file
+str_json = importlib.resources.read_text("tests.data", "response_geneset_1234.json")
+# returns JSON string as a dictionary
+test_data = json.loads(str_json)
+
+@patch('geneweaver.api.services.geneset.db_geneset')
+@patch('geneweaver.api.services.geneset.db_geneset_value')
+@patch('geneweaver.api.services.geneset.is_geneset_readable_by_user')
+def test_get_geneset_no_errors(mock_genset_readable_func, mock_db_geneset, mock_db_genset_value):
+
+    mock_genset_readable_func.return_value = True
+    mock_db_geneset.by_id.return_value = {}
+    mock_db_genset_value.by_id.return_value = {}
+    response = geneset.get_geneset(1234, None, None)
+    assert response.get('error') == None
+
+
+@patch('geneweaver.api.services.geneset.is_geneset_readable_by_user')
+def test_get_geneset_no_user_access(mock_genset_readable_func):
+
+    mock_genset_readable_func.return_value = False
+    response = geneset.get_geneset(1234, None, None)
+    assert response.get('error') == True
+    assert response.get('message') == message.ACCESS_FORBIDEN
+
+
+@patch('geneweaver.api.services.geneset.db_geneset')
+@patch('geneweaver.api.services.geneset.db_geneset_value')
+@patch('geneweaver.api.services.geneset.is_geneset_readable_by_user')
+def test_get_geneset_returned_values(mock_genset_readable_func, mock_db_genset_value, mock_db_geneset):
+
+    mock_genset_readable_func.return_value = True
+    mock_db_geneset.by_id.return_value = test_data.get('geneset')
+    mock_db_genset_value.by_geneset_id.return_value = test_data.get('geneset_values')
+    response = geneset.get_geneset(1234, None, None)
+
+    assert response.get('genset') == test_data['geneset']
+    assert response.get('geneset_values') == test_data['geneset_values']
+
+
+@patch('geneweaver.api.services.geneset.db_is_readable')
+@patch('geneweaver.api.services.geneset.User')
+def test_is_redable_by_user(mock_user, mock_genset_is_readable):
+
+    mock_genset_is_readable.return_value = True
+    response = geneset.is_geneset_readable_by_user(1234, mock_user, None)
+    assert response == True
+
+
+@patch('geneweaver.db.geneset.is_readable')
+@patch('geneweaver.api.services.geneset.User')
+def test_is_redable_by_user_error(mock_user, mock_genset_is_readable):
+    mock_genset_is_readable.sideEffect = Exception
+
+    with pytest.raises(Exception):
+        geneset.is_geneset_readable_by_user(1234, mock_user, None)
+
+

From 6fb0b2187e8343f80afd14fc3e2e6fa6665de7a7 Mon Sep 17 00:00:00 2001
From: francastell <fsophisco@yahoo.com>
Date: Tue, 19 Dec 2023 15:43:04 -0500
Subject: [PATCH 2/7] G3-9 Initial

---
 tests/controllers/.pytest_cache/.gitignore   | 2 --
 tests/controllers/.pytest_cache/CACHEDIR.TAG | 4 ----
 tests/controllers/.pytest_cache/README.md    | 8 --------
 3 files changed, 14 deletions(-)
 delete mode 100644 tests/controllers/.pytest_cache/.gitignore
 delete mode 100644 tests/controllers/.pytest_cache/CACHEDIR.TAG
 delete mode 100644 tests/controllers/.pytest_cache/README.md

diff --git a/tests/controllers/.pytest_cache/.gitignore b/tests/controllers/.pytest_cache/.gitignore
deleted file mode 100644
index ca0633e..0000000
--- a/tests/controllers/.pytest_cache/.gitignore
+++ /dev/null
@@ -1,2 +0,0 @@
-# Created by pytest automatically.
-v
diff --git a/tests/controllers/.pytest_cache/CACHEDIR.TAG b/tests/controllers/.pytest_cache/CACHEDIR.TAG
deleted file mode 100644
index fce15ad..0000000
--- a/tests/controllers/.pytest_cache/CACHEDIR.TAG
+++ /dev/null
@@ -1,4 +0,0 @@
-Signature: 8a477f597d28d172789f06886806bc55
-# This file is a cache directory tag created by pytest.
-# For information about cache directory tags, see:
-#	https://bford.info/cachedir/spec.html
diff --git a/tests/controllers/.pytest_cache/README.md b/tests/controllers/.pytest_cache/README.md
deleted file mode 100644
index b89018c..0000000
--- a/tests/controllers/.pytest_cache/README.md
+++ /dev/null
@@ -1,8 +0,0 @@
-# pytest cache directory #
-
-This directory contains data from the pytest's cache plugin,
-which provides the `--lf` and `--ff` options, as well as the `cache` fixture.
-
-**Do not** commit this to version control.
-
-See [the docs](https://docs.pytest.org/en/stable/how-to/cache.html) for more information.

From ea94e06aa115b0b11c1e9ad49aaad0e72a11edc3 Mon Sep 17 00:00:00 2001
From: francastell <fsophisco@yahoo.com>
Date: Wed, 20 Dec 2023 15:21:36 -0500
Subject: [PATCH 3/7] G3-9 unit tests, linting

---
 poetry.lock                               | 412 +++++++++++++---------
 pyproject.toml                            |  11 +-
 src/geneweaver/api/controller/genesets.py |   2 +-
 src/geneweaver/api/controller/message.py  |   4 +-
 src/geneweaver/api/services/geneset.py    |   2 +-
 tests/controllers/test_genesets.py        |  28 +-
 tests/services/test_genset.py             |  26 +-
 7 files changed, 292 insertions(+), 193 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 57b3e4c..fb63d52 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -2,50 +2,69 @@
 
 [[package]]
 name = "anyio"
-version = "4.1.0"
+version = "4.2.0"
 description = "High level compatibility layer for multiple asynchronous event loop implementations"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "anyio-4.1.0-py3-none-any.whl", hash = "sha256:56a415fbc462291813a94528a779597226619c8e78af7de0507333f700011e5f"},
-    {file = "anyio-4.1.0.tar.gz", hash = "sha256:5a0bec7085176715be77df87fc66d6c9d70626bd752fcc85f57cdbee5b3760da"},
+    {file = "anyio-4.2.0-py3-none-any.whl", hash = "sha256:745843b39e829e108e518c489b31dc757de7d2131d53fac32bd8df268227bfee"},
+    {file = "anyio-4.2.0.tar.gz", hash = "sha256:e1875bb4b4e2de1669f4bc7869b6d3f54231cdced71605e6e64c9be77e3be50f"},
 ]
 
 [package.dependencies]
 exceptiongroup = {version = ">=1.0.2", markers = "python_version < \"3.11\""}
 idna = ">=2.8"
 sniffio = ">=1.1"
+typing-extensions = {version = ">=4.1", markers = "python_version < \"3.11\""}
 
 [package.extras]
 doc = ["Sphinx (>=7)", "packaging", "sphinx-autodoc-typehints (>=1.2.0)", "sphinx-rtd-theme"]
 test = ["anyio[trio]", "coverage[toml] (>=7)", "exceptiongroup (>=1.2.0)", "hypothesis (>=4.0)", "psutil (>=5.9)", "pytest (>=7.0)", "pytest-mock (>=3.6.1)", "trustme", "uvloop (>=0.17)"]
 trio = ["trio (>=0.23)"]
 
+[[package]]
+name = "astroid"
+version = "3.0.2"
+description = "An abstract syntax tree for Python with inference support."
+optional = false
+python-versions = ">=3.8.0"
+files = [
+    {file = "astroid-3.0.2-py3-none-any.whl", hash = "sha256:d6e62862355f60e716164082d6b4b041d38e2a8cf1c7cd953ded5108bac8ff5c"},
+    {file = "astroid-3.0.2.tar.gz", hash = "sha256:4a61cf0a59097c7bb52689b0fd63717cd2a8a14dc9f1eee97b82d814881c8c91"},
+]
+
+[package.dependencies]
+typing-extensions = {version = ">=4.0.0", markers = "python_version < \"3.11\""}
+
 [[package]]
 name = "black"
-version = "23.11.0"
+version = "23.12.0"
 description = "The uncompromising code formatter."
 optional = false
 python-versions = ">=3.8"
 files = [
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 [package.dependencies]
@@ -59,7 +78,7 @@ typing-extensions = {version = ">=4.0.1", markers = "python_version < \"3.11\""}
 
 [package.extras]
 colorama = ["colorama (>=0.4.3)"]
-d = ["aiohttp (>=3.7.4)"]
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 jupyter = ["ipython (>=7.8.0)", "tokenize-rt (>=3.2.0)"]
 uvloop = ["uvloop (>=0.15.2)"]
 
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 ]
 
 [package.dependencies]
@@ -374,6 +393,20 @@ ssh = ["bcrypt (>=3.1.5)"]
 test = ["pretend", "pytest (>=6.2.0)", "pytest-benchmark", "pytest-cov", "pytest-xdist"]
 test-randomorder = ["pytest-randomly"]
 
+[[package]]
+name = "dill"
+version = "0.3.7"
+description = "serialize all of Python"
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "dill-0.3.7-py3-none-any.whl", hash = "sha256:76b122c08ef4ce2eedcd4d1abd8e641114bfc6c2867f49f3c41facf65bf19f5e"},
+    {file = "dill-0.3.7.tar.gz", hash = "sha256:cc1c8b182eb3013e24bd475ff2e9295af86c1a38eb1aff128dac8962a9ce3c03"},
+]
+
+[package.extras]
+graph = ["objgraph (>=1.7.2)"]
+
 [[package]]
 name = "dnspython"
 version = "2.4.2"
@@ -627,13 +660,13 @@ test = ["Cython (>=0.29.24,<0.30.0)"]
 
 [[package]]
 name = "httpx"
-version = "0.25.2"
+version = "0.26.0"
 description = "The next generation HTTP client."
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "httpx-0.25.2-py3-none-any.whl", hash = "sha256:a05d3d052d9b2dfce0e3896636467f8a5342fb2b902c819428e1ac65413ca118"},
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+    {file = "httpx-0.26.0.tar.gz", hash = "sha256:451b55c30d5185ea6b23c2c793abf9bb237d2a7dfb901ced6ff69ad37ec1dfaf"},
 ]
 
 [package.dependencies]
@@ -673,15 +706,18 @@ files = [
 
 [[package]]
 name = "isort"
-version = "5.13.1"
+version = "5.13.2"
 description = "A Python utility / library to sort Python imports."
 optional = false
 python-versions = ">=3.8.0"
 files = [
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 ]
 
+[package.extras]
+colors = ["colorama (>=0.4.6)"]
+
 [[package]]
 name = "itsdangerous"
 version = "2.1.2"
@@ -792,6 +828,17 @@ files = [
     {file = "MarkupSafe-2.1.3.tar.gz", hash = "sha256:af598ed32d6ae86f1b747b82783958b1a4ab8f617b06fe68795c7f026abbdcad"},
 ]
 
+[[package]]
+name = "mccabe"
+version = "0.7.0"
+description = "McCabe checker, plugin for flake8"
+optional = false
+python-versions = ">=3.6"
+files = [
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+]
+
 [[package]]
 name = "mypy"
 version = "1.7.1"
@@ -1007,8 +1054,9 @@ files = [
 
 [package.dependencies]
 numpy = [
-    {version = ">=1.23.2", markers = "python_version >= \"3.11\""},
+    {version = ">=1.20.3", markers = "python_version < \"3.10\""},
     {version = ">=1.21.0", markers = "python_version >= \"3.10\" and python_version < \"3.11\""},
+    {version = ">=1.23.2", markers = "python_version >= \"3.11\""},
 ]
 python-dateutil = ">=2.8.2"
 pytz = ">=2020.1"
@@ -1080,100 +1128,100 @@ testing = ["pytest", "pytest-benchmark"]
 
 [[package]]
 name = "psycopg"
-version = "3.1.14"
+version = "3.1.16"
 description = "PostgreSQL database adapter for Python"
 optional = false
 python-versions = ">=3.7"
 files = [
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+    {file = "psycopg-3.1.16.tar.gz", hash = "sha256:a34d922fd7df3134595e71c3428ba6f1bd5f4968db74857fe95de12db2d6b763"},
 ]
 
 [package.dependencies]
-psycopg-binary = {version = "3.1.14", optional = true, markers = "implementation_name != \"pypy\" and extra == \"binary\""}
+psycopg-binary = {version = "3.1.16", optional = true, markers = "implementation_name != \"pypy\" and extra == \"binary\""}
 typing-extensions = ">=4.1"
 tzdata = {version = "*", markers = "sys_platform == \"win32\""}
 
 [package.extras]
-binary = ["psycopg-binary (==3.1.14)"]
-c = ["psycopg-c (==3.1.14)"]
-dev = ["black (>=23.1.0)", "dnspython (>=2.1)", "flake8 (>=4.0)", "mypy (>=1.4.1)", "types-setuptools (>=57.4)", "wheel (>=0.37)"]
+binary = ["psycopg-binary (==3.1.16)"]
+c = ["psycopg-c (==3.1.16)"]
+dev = ["black (>=23.1.0)", "codespell (>=2.2)", "dnspython (>=2.1)", "flake8 (>=4.0)", "mypy (>=1.4.1)", "types-setuptools (>=57.4)", "wheel (>=0.37)"]
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 pool = ["psycopg-pool"]
 test = ["anyio (>=3.6.2,<4.0)", "mypy (>=1.4.1)", "pproxy (>=2.7)", "pytest (>=6.2.5)", "pytest-cov (>=3.0)", "pytest-randomly (>=3.5)"]
 
 [[package]]
 name = "psycopg-binary"
-version = "3.1.14"
+version = "3.1.16"
 description = "PostgreSQL database adapter for Python -- C optimisation distribution"
 optional = false
 python-versions = ">=3.7"
 files = [
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+    {file = "psycopg_binary-3.1.16-cp38-cp38-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl", hash = "sha256:1cdaf56adc9cc56df7a05e8f097a776939ba49d5e6afc907ba7b404d8bd21c89"},
+    {file = "psycopg_binary-3.1.16-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:7232116fc5d4e0274114f152bdb9df089895d4c70f7c03268cab0a4c48a28d04"},
+    {file = "psycopg_binary-3.1.16-cp38-cp38-musllinux_1_1_aarch64.whl", hash = "sha256:6f03239d7c18666f5d6ca82ea972235de4d4d3604287098af6cdc256b76a0ca5"},
+    {file = "psycopg_binary-3.1.16-cp38-cp38-musllinux_1_1_i686.whl", hash = "sha256:edd1b630652bdfff84662b46d11878fbab8ab2966003c1876fcde56650e99e3f"},
+    {file = "psycopg_binary-3.1.16-cp38-cp38-musllinux_1_1_ppc64le.whl", hash = "sha256:481e9dafca1ed9532552e097105e6664ee7f14686270ed0ee0b1d6c78c2cdb11"},
+    {file = "psycopg_binary-3.1.16-cp38-cp38-musllinux_1_1_x86_64.whl", hash = "sha256:d43aa3aa55b5fa964ffa78cf6abdbd51ff33a759f290e9159a9f974ffa3178fa"},
+    {file = "psycopg_binary-3.1.16-cp38-cp38-win_amd64.whl", hash = "sha256:51e66b282d8689bc33d81bde3a1e14d0c88a39200c2d9436b028b394d24f1f99"},
+    {file = "psycopg_binary-3.1.16-cp39-cp39-macosx_10_9_x86_64.whl", hash = "sha256:bfae154f3c88e67f3ed592765ad56531b6076acfe80796e28cccc05727c1cf5b"},
+    {file = "psycopg_binary-3.1.16-cp39-cp39-macosx_11_0_arm64.whl", hash = "sha256:f9f4bc3d366951359a68833c8031cc83faf5084b3bc80dd2d24f0add593d4418"},
+    {file = "psycopg_binary-3.1.16-cp39-cp39-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:a37d682d7ff57cc2573b1011740ef1566749fc94ae6ac1456405510592735c0a"},
+    {file = "psycopg_binary-3.1.16-cp39-cp39-manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:0be876e3a8ee359f6a985b662c6b02a094a50b37adf1bd756a655004bddf167a"},
+    {file = "psycopg_binary-3.1.16-cp39-cp39-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl", hash = "sha256:4f79192b0edd60ef24acb0af5b83319cbb65d4187576757b690646b290de8307"},
+    {file = "psycopg_binary-3.1.16-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:fcc5996b1db4e7fb948ea47b610456df317625d92474c779a20f92ca8cbcec92"},
+    {file = "psycopg_binary-3.1.16-cp39-cp39-musllinux_1_1_aarch64.whl", hash = "sha256:3f2ceb04f8137462f9312a324bea5402de0a4f0503cd5442f4264911e4b6265b"},
+    {file = "psycopg_binary-3.1.16-cp39-cp39-musllinux_1_1_i686.whl", hash = "sha256:47517d2da63bb10c80c2cf35c80a936db79636534849524fd57940b5f0bbd7bd"},
+    {file = "psycopg_binary-3.1.16-cp39-cp39-musllinux_1_1_ppc64le.whl", hash = "sha256:2a6bd83d0b934aa03897e93acb6897972ccc3827ae61c903589bc92ed423f75d"},
+    {file = "psycopg_binary-3.1.16-cp39-cp39-musllinux_1_1_x86_64.whl", hash = "sha256:08fb94928e785571ac90d3ab9e09f2721e0d895c2504ecfb8de91c5ea807b267"},
+    {file = "psycopg_binary-3.1.16-cp39-cp39-win_amd64.whl", hash = "sha256:cf13807b61315130a59ea8d0950bda2ac875bae9fadc0b1a9aca9b4ef6d62c7b"},
 ]
 
 [[package]]
@@ -1265,6 +1313,36 @@ typing-extensions = ">=4.2.0"
 dotenv = ["python-dotenv (>=0.10.4)"]
 email = ["email-validator (>=1.0.3)"]
 
+[[package]]
+name = "pylint"
+version = "3.0.3"
+description = "python code static checker"
+optional = false
+python-versions = ">=3.8.0"
+files = [
+    {file = "pylint-3.0.3-py3-none-any.whl", hash = "sha256:7a1585285aefc5165db81083c3e06363a27448f6b467b3b0f30dbd0ac1f73810"},
+    {file = "pylint-3.0.3.tar.gz", hash = "sha256:58c2398b0301e049609a8429789ec6edf3aabe9b6c5fec916acd18639c16de8b"},
+]
+
+[package.dependencies]
+astroid = ">=3.0.1,<=3.1.0-dev0"
+colorama = {version = ">=0.4.5", markers = "sys_platform == \"win32\""}
+dill = [
+    {version = ">=0.2", markers = "python_version < \"3.11\""},
+    {version = ">=0.3.7", markers = "python_version >= \"3.12\""},
+    {version = ">=0.3.6", markers = "python_version >= \"3.11\" and python_version < \"3.12\""},
+]
+isort = ">=4.2.5,<5.13.0 || >5.13.0,<6"
+mccabe = ">=0.6,<0.8"
+platformdirs = ">=2.2.0"
+tomli = {version = ">=1.1.0", markers = "python_version < \"3.11\""}
+tomlkit = ">=0.10.1"
+typing-extensions = {version = ">=3.10.0", markers = "python_version < \"3.10\""}
+
+[package.extras]
+spelling = ["pyenchant (>=3.2,<4.0)"]
+testutils = ["gitpython (>3)"]
+
 [[package]]
 name = "pyparsing"
 version = "3.1.1"
@@ -1557,6 +1635,7 @@ files = [
 
 [package.dependencies]
 anyio = ">=3.4.0,<5"
+typing-extensions = {version = ">=3.10.0", markers = "python_version < \"3.10\""}
 
 [package.extras]
 full = ["httpx (>=0.22.0)", "itsdangerous", "jinja2", "python-multipart", "pyyaml"]
@@ -1572,6 +1651,17 @@ files = [
     {file = "tomli-2.0.1.tar.gz", hash = "sha256:de526c12914f0c550d15924c62d72abc48d6fe7364aa87328337a31007fe8a4f"},
 ]
 
+[[package]]
+name = "tomlkit"
+version = "0.12.3"
+description = "Style preserving TOML library"
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "tomlkit-0.12.3-py3-none-any.whl", hash = "sha256:b0a645a9156dc7cb5d3a1f0d4bab66db287fcb8e0430bdd4664a095ea16414ba"},
+    {file = "tomlkit-0.12.3.tar.gz", hash = "sha256:75baf5012d06501f07bee5bf8e801b9f343e7aac5a92581f20f80ce632e6b5a4"},
+]
+
 [[package]]
 name = "typing-extensions"
 version = "4.9.0"
@@ -1686,13 +1776,13 @@ zstd = ["zstandard (>=0.18.0)"]
 
 [[package]]
 name = "uvicorn"
-version = "0.23.2"
+version = "0.24.0.post1"
 description = "The lightning-fast ASGI server."
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "uvicorn-0.23.2-py3-none-any.whl", hash = "sha256:1f9be6558f01239d4fdf22ef8126c39cb1ad0addf76c40e760549d2c2f43ab53"},
-    {file = "uvicorn-0.23.2.tar.gz", hash = "sha256:4d3cc12d7727ba72b64d12d3cc7743124074c0a69f7b201512fc50c3e3f1569a"},
+    {file = "uvicorn-0.24.0.post1-py3-none-any.whl", hash = "sha256:7c84fea70c619d4a710153482c0d230929af7bcf76c7bfa6de151f0a3a80121e"},
+    {file = "uvicorn-0.24.0.post1.tar.gz", hash = "sha256:09c8e5a79dc466bdf28dead50093957db184de356fcdc48697bad3bde4c2588e"},
 ]
 
 [package.dependencies]
@@ -1924,5 +2014,5 @@ files = [
 
 [metadata]
 lock-version = "2.0"
-python-versions = "^3.10.9"
-content-hash = "a0c16c5fbc6e13e1fea05fa39fc128092269c75aebf14906951e98b47ca01d78"
+python-versions = "^3.9"
+content-hash = "b649afece7475a1c9c309be6e4c87c32107c4a1344cb565a0f82d92ba1a42833"
diff --git a/pyproject.toml b/pyproject.toml
index 5e8281c..da26edc 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -8,17 +8,11 @@ packages = [
 ]
 
 [tool.poetry.dependencies]
-#python = "^3.9"
-python = "^3.10.9"
+python = "^3.9"
 
 geneweaver-core = "^0.8.0a0"
 fastapi = {extras = ["all"], version = "^0.99.1"}
-uvicorn = {extras = ["standard"], version = "^0.23.2"}
-
-#fastapi = "^0.79.0"
-#fastapi = {version = "^0.79.0"}
-#uvicorn = {extras = ["standard"], version = "^0.18.2"}
-
+uvicorn = {extras = ["standard"], version = "^0.24.0"}
 geneweaver-db = "^0.2.0a0"
 psycopg-pool = "^3.1.7"
 requests = "^2.31.0"
@@ -28,6 +22,7 @@ python-jose = {extras = ["cryptography"], version = "^3.3.0"}
 geneweaver-testing = "^0.0.3"
 pytest-asyncio = "^0.21.0"
 magicmock =  "^0.03"
+pylint= "^3.0.3"
 
 [tool.ruff]
 select = ['F', 'E', 'W', 'A', 'C90', 'N', 'B', 'ANN', 'D', 'I', 'ERA', 'PD', 'NPY', 'PT']
diff --git a/src/geneweaver/api/controller/genesets.py b/src/geneweaver/api/controller/genesets.py
index ad09b50..fbd63e8 100644
--- a/src/geneweaver/api/controller/genesets.py
+++ b/src/geneweaver/api/controller/genesets.py
@@ -42,7 +42,7 @@ def get_geneset(
         if response.get("message") == api_message.ACCESS_FORBIDEN:
             raise HTTPException(status_code=403, detail=api_message.ACCESS_FORBIDEN)
         else:
-            raise HTTPException(status_code=500, detail=api_message.ACCESS_FORBIDEN)
+            raise HTTPException(status_code=500, detail=api_message.UNEXPECTED_ERROR)
 
     return response
 
diff --git a/src/geneweaver/api/controller/message.py b/src/geneweaver/api/controller/message.py
index add6cf4..4304184 100644
--- a/src/geneweaver/api/controller/message.py
+++ b/src/geneweaver/api/controller/message.py
@@ -1,6 +1,6 @@
-"""Costant key/value messages"""
+"""Constants key/value messages"""
 
 
 ##Errors
 ACCESS_FORBIDEN="Forbidden"
-UNEXPECTED_ERROR="Unexpected Error"
\ No newline at end of file
+UNEXPECTED_ERROR="Unexpected Error"
diff --git a/src/geneweaver/api/services/geneset.py b/src/geneweaver/api/services/geneset.py
index 67cd66c..e1d8013 100644
--- a/src/geneweaver/api/services/geneset.py
+++ b/src/geneweaver/api/services/geneset.py
@@ -43,4 +43,4 @@ def is_geneset_readable_by_user(
         logger.error(err)
         raise err
 
-    return readable
\ No newline at end of file
+    return readable
diff --git a/tests/controllers/test_genesets.py b/tests/controllers/test_genesets.py
index 1b25fb0..7451765 100644
--- a/tests/controllers/test_genesets.py
+++ b/tests/controllers/test_genesets.py
@@ -1,3 +1,5 @@
+""" Tests for geneset API"""
+
 import importlib.resources
 import json
 from unittest.mock import Mock
@@ -23,15 +25,15 @@
 response_mock.json.return_value = test_data
 
 ### Mock dependencies
-m1 = Mock()
-def mock_full_user() -> m1.AsyncMock:
-    return m1
-m2 = Mock()
+def mock_full_user() -> Mock:
+    """ User auth mock"""
+    m1 = Mock()
+    return m1.AsyncMock()
+
 def mock_cursor() -> psycopg.Cursor:
+    """ DB cursor mock"""
+    m2 = Mock()
     return m2.AsyncMock()
-m3 = Mock()
-def mock_cursor_obj() -> psycopg.Cursor:
-    return m3.AsyncMock()
 
 app.dependency_overrides.update(
     {full_user: mock_full_user, cursor: mock_cursor}
@@ -39,34 +41,38 @@ def mock_cursor_obj() -> psycopg.Cursor:
 
 @patch.object(client, 'get', return_value=response_mock)
 def test_get_geneset(mock_client):
-    response = client.get("/genesets/1234")
+    """ test get request for geneset ID"""
+    response = client.get("/api/genesets/1234")
     assert response.status_code == 200
 
 @patch('geneweaver.api.services.geneset.get_geneset')
 @patch('geneweaver.api.services.geneset.is_geneset_readable_by_user')
 def test_get_geneset_response(mock_genset_is_readable, mock_get_genenset):
+    """ test get geneset ID data response"""
     mock_genset_is_readable.return_value = True
     mock_get_genenset.return_value = test_data
 
-    response = client.get("/genesets/1234")
+    response = client.get("/api/genesets/1234")
     assert response.status_code == 200
     assert response.json() == test_data
 
 @patch('geneweaver.api.services.geneset.db_is_readable')
 def test_get_geneset_forbidden(mock_genset_is_readable):
+    """ test forbidden response"""
 
     mock_genset_is_readable.return_value = False
-    response = client.get("/genesets/1234")
+    response = client.get("/api/genesets/1234")
 
     assert response.json() == {'detail': 'Forbidden'}
     assert response.status_code == 403
 
 @patch('geneweaver.api.services.geneset.db_is_readable')
 def test_get_geneset_unexpected_error(mock_genset_is_readable):
+    """ test unexpected error response"""
 
     mock_genset_is_readable.side_effect = Exception
 
     with pytest.raises(Exception):
-        response = client.get("/genesets/1234")
+        response = client.get("/api/genesets/1234")
         assert response.json() == {'detail': 'Unexpected error'}
         assert response.status_code == 500
diff --git a/tests/services/test_genset.py b/tests/services/test_genset.py
index 276db56..a37f824 100644
--- a/tests/services/test_genset.py
+++ b/tests/services/test_genset.py
@@ -1,11 +1,13 @@
+""" Tests for geneset Service"""
+
 import importlib.resources
 import json
 from unittest.mock import patch
 
 import pytest
 
-import geneweaver.api.controller.message as message
-import geneweaver.api.services.geneset as geneset
+from geneweaver.api.controller import message
+from geneweaver.api.services import geneset
 
 ## Load test data
 # Opening JSON file
@@ -16,28 +18,33 @@
 @patch('geneweaver.api.services.geneset.db_geneset')
 @patch('geneweaver.api.services.geneset.db_geneset_value')
 @patch('geneweaver.api.services.geneset.is_geneset_readable_by_user')
-def test_get_geneset_no_errors(mock_genset_readable_func, mock_db_geneset, mock_db_genset_value):
+def test_get_geneset(mock_genset_readable_func, mock_db_geneset, mock_db_genset_value):
+    """ test basic get geneset by ID"""
 
     mock_genset_readable_func.return_value = True
     mock_db_geneset.by_id.return_value = {}
     mock_db_genset_value.by_id.return_value = {}
     response = geneset.get_geneset(1234, None, None)
-    assert response.get('error') == None
+    assert response.get('error') is None
 
 
 @patch('geneweaver.api.services.geneset.is_geneset_readable_by_user')
 def test_get_geneset_no_user_access(mock_genset_readable_func):
+    """ test get geneset by ID with no user access"""
 
     mock_genset_readable_func.return_value = False
     response = geneset.get_geneset(1234, None, None)
-    assert response.get('error') == True
+    assert response.get('error') is True
     assert response.get('message') == message.ACCESS_FORBIDEN
 
 
 @patch('geneweaver.api.services.geneset.db_geneset')
 @patch('geneweaver.api.services.geneset.db_geneset_value')
 @patch('geneweaver.api.services.geneset.is_geneset_readable_by_user')
-def test_get_geneset_returned_values(mock_genset_readable_func, mock_db_genset_value, mock_db_geneset):
+def test_get_geneset_returned_values(mock_genset_readable_func,
+                                     mock_db_genset_value,
+                                     mock_db_geneset):
+    """ test get geneset by ID data response structure"""
 
     mock_genset_readable_func.return_value = True
     mock_db_geneset.by_id.return_value = test_data.get('geneset')
@@ -51,18 +58,19 @@ def test_get_geneset_returned_values(mock_genset_readable_func, mock_db_genset_v
 @patch('geneweaver.api.services.geneset.db_is_readable')
 @patch('geneweaver.api.services.geneset.User')
 def test_is_redable_by_user(mock_user, mock_genset_is_readable):
+    """ test is geneset ID readable by passed user"""
 
     mock_genset_is_readable.return_value = True
     response = geneset.is_geneset_readable_by_user(1234, mock_user, None)
-    assert response == True
+    assert response is True
 
 
 @patch('geneweaver.db.geneset.is_readable')
 @patch('geneweaver.api.services.geneset.User')
 def test_is_redable_by_user_error(mock_user, mock_genset_is_readable):
+    """ test is geneset ID readable with server error"""
+
     mock_genset_is_readable.sideEffect = Exception
 
     with pytest.raises(Exception):
         geneset.is_geneset_readable_by_user(1234, mock_user, None)
-
-

From aac99926ba2506c85db9d4069c6b7e832a99776e Mon Sep 17 00:00:00 2001
From: francastell <fsophisco@yahoo.com>
Date: Wed, 3 Jan 2024 10:52:46 -0500
Subject: [PATCH 4/7] Code linters corrections

---
 README.MD                                 |  22 ++
 poetry.lock                               | 304 ++++++++--------------
 pyproject.toml                            |   1 -
 src/geneweaver/api/controller/genesets.py |  18 +-
 src/geneweaver/api/controller/message.py  |   6 +-
 src/geneweaver/api/services/geneset.py    |  22 +-
 6 files changed, 151 insertions(+), 222 deletions(-)

diff --git a/README.MD b/README.MD
index 3403265..61e5581 100644
--- a/README.MD
+++ b/README.MD
@@ -25,6 +25,28 @@ virtualenv activated, or just run `poetry run uvicorn geneweaver.api.main:app --
 This will host the application on `http://127.0.0.1:8000/` which means the swagger docs
 page is available at `http://127.0.0.1:8000/docs`.
 
+### Code linters
+
+Ruff rules: (https://docs.astral.sh/ruff/rules/)
+
+From active local environment on command line run:
+
+    ruff src --fix
+
+then run black (code formatter: https://black.readthedocs.io/en/stable/the_black_code_style/current_style.html)
+
+    black src
+
+### Unit test
+
+Create appropriate test per code modifications without dependencies to external resources 
+such as DB, Webserver, or APIs. Create appropriate mocks for external resources and data as needed.
+
+    Tests directory: geneweaver-api/tests
+
+To execute tests, from the command line run:
+
+    pytest 
 
 ### Continuous Integration & Deployment
 When a PR is crated in GitHub, it will automatically trigger a workflow that will run 
diff --git a/poetry.lock b/poetry.lock
index fb63d52..0b7cd0e 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -22,49 +22,35 @@ doc = ["Sphinx (>=7)", "packaging", "sphinx-autodoc-typehints (>=1.2.0)", "sphin
 test = ["anyio[trio]", "coverage[toml] (>=7)", "exceptiongroup (>=1.2.0)", "hypothesis (>=4.0)", "psutil (>=5.9)", "pytest (>=7.0)", "pytest-mock (>=3.6.1)", "trustme", "uvloop (>=0.17)"]
 trio = ["trio (>=0.23)"]
 
-[[package]]
-name = "astroid"
-version = "3.0.2"
-description = "An abstract syntax tree for Python with inference support."
-optional = false
-python-versions = ">=3.8.0"
-files = [
-    {file = "astroid-3.0.2-py3-none-any.whl", hash = "sha256:d6e62862355f60e716164082d6b4b041d38e2a8cf1c7cd953ded5108bac8ff5c"},
-    {file = "astroid-3.0.2.tar.gz", hash = "sha256:4a61cf0a59097c7bb52689b0fd63717cd2a8a14dc9f1eee97b82d814881c8c91"},
-]
-
-[package.dependencies]
-typing-extensions = {version = ">=4.0.0", markers = "python_version < \"3.11\""}
-
 [[package]]
 name = "black"
-version = "23.12.0"
+version = "23.12.1"
 description = "The uncompromising code formatter."
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "black-23.12.0-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:67f19562d367468ab59bd6c36a72b2c84bc2f16b59788690e02bbcb140a77175"},
-    {file = "black-23.12.0-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:bbd75d9f28a7283b7426160ca21c5bd640ca7cd8ef6630b4754b6df9e2da8462"},
-    {file = "black-23.12.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:593596f699ca2dcbbbdfa59fcda7d8ad6604370c10228223cd6cf6ce1ce7ed7e"},
-    {file = "black-23.12.0-cp310-cp310-win_amd64.whl", hash = "sha256:12d5f10cce8dc27202e9a252acd1c9a426c83f95496c959406c96b785a92bb7d"},
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 [package.dependencies]
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 test = ["pretend", "pytest (>=6.2.0)", "pytest-benchmark", "pytest-cov", "pytest-xdist"]
 test-randomorder = ["pytest-randomly"]
 
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+    {file = "mypy-1.8.0-cp311-cp311-musllinux_1_1_x86_64.whl", hash = "sha256:9261ed810972061388918c83c3f5cd46079d875026ba97380f3e3978a72f503d"},
+    {file = "mypy-1.8.0-cp311-cp311-win_amd64.whl", hash = "sha256:51720c776d148bad2372ca21ca29256ed483aa9a4cdefefcef49006dff2a6835"},
+    {file = "mypy-1.8.0-cp312-cp312-macosx_10_9_x86_64.whl", hash = "sha256:52825b01f5c4c1c4eb0db253ec09c7aa17e1a7304d247c48b6f3599ef40db8bd"},
+    {file = "mypy-1.8.0-cp312-cp312-macosx_11_0_arm64.whl", hash = "sha256:f5ac9a4eeb1ec0f1ccdc6f326bcdb464de5f80eb07fb38b5ddd7b0de6bc61e55"},
+    {file = "mypy-1.8.0-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:afe3fe972c645b4632c563d3f3eff1cdca2fa058f730df2b93a35e3b0c538218"},
+    {file = "mypy-1.8.0-cp312-cp312-musllinux_1_1_x86_64.whl", hash = "sha256:42c6680d256ab35637ef88891c6bd02514ccb7e1122133ac96055ff458f93fc3"},
+    {file = "mypy-1.8.0-cp312-cp312-win_amd64.whl", hash = "sha256:720a5ca70e136b675af3af63db533c1c8c9181314d207568bbe79051f122669e"},
+    {file = "mypy-1.8.0-cp38-cp38-macosx_10_9_x86_64.whl", hash = "sha256:028cf9f2cae89e202d7b6593cd98db6759379f17a319b5faf4f9978d7084cdc6"},
+    {file = "mypy-1.8.0-cp38-cp38-macosx_11_0_arm64.whl", hash = "sha256:4e6d97288757e1ddba10dd9549ac27982e3e74a49d8d0179fc14d4365c7add66"},
+    {file = "mypy-1.8.0-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:7f1478736fcebb90f97e40aff11a5f253af890c845ee0c850fe80aa060a267c6"},
+    {file = "mypy-1.8.0-cp38-cp38-musllinux_1_1_x86_64.whl", hash = "sha256:42419861b43e6962a649068a61f4a4839205a3ef525b858377a960b9e2de6e0d"},
+    {file = "mypy-1.8.0-cp38-cp38-win_amd64.whl", hash = "sha256:2b5b6c721bd4aabaadead3a5e6fa85c11c6c795e0c81a7215776ef8afc66de02"},
+    {file = "mypy-1.8.0-cp39-cp39-macosx_10_9_x86_64.whl", hash = "sha256:5c1538c38584029352878a0466f03a8ee7547d7bd9f641f57a0f3017a7c905b8"},
+    {file = "mypy-1.8.0-cp39-cp39-macosx_11_0_arm64.whl", hash = "sha256:4ef4be7baf08a203170f29e89d79064463b7fc7a0908b9d0d5114e8009c3a259"},
+    {file = "mypy-1.8.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:7178def594014aa6c35a8ff411cf37d682f428b3b5617ca79029d8ae72f5402b"},
+    {file = "mypy-1.8.0-cp39-cp39-musllinux_1_1_x86_64.whl", hash = "sha256:ab3c84fa13c04aeeeabb2a7f67a25ef5d77ac9d6486ff33ded762ef353aa5592"},
+    {file = "mypy-1.8.0-cp39-cp39-win_amd64.whl", hash = "sha256:99b00bc72855812a60d253420d8a2eae839b0afa4938f09f4d2aa9bb4654263a"},
+    {file = "mypy-1.8.0-py3-none-any.whl", hash = "sha256:538fd81bb5e430cc1381a443971c0475582ff9f434c16cd46d2c66763ce85d9d"},
+    {file = "mypy-1.8.0.tar.gz", hash = "sha256:6ff8b244d7085a0b425b56d327b480c3b29cafbd2eff27316a004f9a7391ae07"},
 ]
 
 [package.dependencies]
@@ -1055,8 +1016,8 @@ files = [
 [package.dependencies]
 numpy = [
     {version = ">=1.20.3", markers = "python_version < \"3.10\""},
-    {version = ">=1.21.0", markers = "python_version >= \"3.10\" and python_version < \"3.11\""},
     {version = ">=1.23.2", markers = "python_version >= \"3.11\""},
+    {version = ">=1.21.0", markers = "python_version >= \"3.10\" and python_version < \"3.11\""},
 ]
 python-dateutil = ">=2.8.2"
 pytz = ">=2020.1"
@@ -1313,36 +1274,6 @@ typing-extensions = ">=4.2.0"
 dotenv = ["python-dotenv (>=0.10.4)"]
 email = ["email-validator (>=1.0.3)"]
 
-[[package]]
-name = "pylint"
-version = "3.0.3"
-description = "python code static checker"
-optional = false
-python-versions = ">=3.8.0"
-files = [
-    {file = "pylint-3.0.3-py3-none-any.whl", hash = "sha256:7a1585285aefc5165db81083c3e06363a27448f6b467b3b0f30dbd0ac1f73810"},
-    {file = "pylint-3.0.3.tar.gz", hash = "sha256:58c2398b0301e049609a8429789ec6edf3aabe9b6c5fec916acd18639c16de8b"},
-]
-
-[package.dependencies]
-astroid = ">=3.0.1,<=3.1.0-dev0"
-colorama = {version = ">=0.4.5", markers = "sys_platform == \"win32\""}
-dill = [
-    {version = ">=0.2", markers = "python_version < \"3.11\""},
-    {version = ">=0.3.7", markers = "python_version >= \"3.12\""},
-    {version = ">=0.3.6", markers = "python_version >= \"3.11\" and python_version < \"3.12\""},
-]
-isort = ">=4.2.5,<5.13.0 || >5.13.0,<6"
-mccabe = ">=0.6,<0.8"
-platformdirs = ">=2.2.0"
-tomli = {version = ">=1.1.0", markers = "python_version < \"3.11\""}
-tomlkit = ">=0.10.1"
-typing-extensions = {version = ">=3.10.0", markers = "python_version < \"3.10\""}
-
-[package.extras]
-spelling = ["pyenchant (>=3.2,<4.0)"]
-testutils = ["gitpython (>3)"]
-
 [[package]]
 name = "pyparsing"
 version = "3.1.1"
@@ -1359,13 +1290,13 @@ diagrams = ["jinja2", "railroad-diagrams"]
 
 [[package]]
 name = "pytest"
-version = "7.4.3"
+version = "7.4.4"
 description = "pytest: simple powerful testing with Python"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "pytest-7.4.3-py3-none-any.whl", hash = "sha256:0d009c083ea859a71b76adf7c1d502e4bc170b80a8ef002da5806527b9591fac"},
-    {file = "pytest-7.4.3.tar.gz", hash = "sha256:d989d136982de4e3b29dabcc838ad581c64e8ed52c11fbe86ddebd9da0818cd5"},
+    {file = "pytest-7.4.4-py3-none-any.whl", hash = "sha256:b090cdf5ed60bf4c45261be03239c2c1c22df034fbffe691abe93cd80cea01d8"},
+    {file = "pytest-7.4.4.tar.gz", hash = "sha256:2cf0005922c6ace4a3e2ec8b4080eb0d9753fdc93107415332f50ce9e7994280"},
 ]
 
 [package.dependencies]
@@ -1651,17 +1582,6 @@ files = [
     {file = "tomli-2.0.1.tar.gz", hash = "sha256:de526c12914f0c550d15924c62d72abc48d6fe7364aa87328337a31007fe8a4f"},
 ]
 
-[[package]]
-name = "tomlkit"
-version = "0.12.3"
-description = "Style preserving TOML library"
-optional = false
-python-versions = ">=3.7"
-files = [
-    {file = "tomlkit-0.12.3-py3-none-any.whl", hash = "sha256:b0a645a9156dc7cb5d3a1f0d4bab66db287fcb8e0430bdd4664a095ea16414ba"},
-    {file = "tomlkit-0.12.3.tar.gz", hash = "sha256:75baf5012d06501f07bee5bf8e801b9f343e7aac5a92581f20f80ce632e6b5a4"},
-]
-
 [[package]]
 name = "typing-extensions"
 version = "4.9.0"
@@ -1675,13 +1595,13 @@ files = [
 
 [[package]]
 name = "tzdata"
-version = "2023.3"
+version = "2023.4"
 description = "Provider of IANA time zone data"
 optional = false
 python-versions = ">=2"
 files = [
-    {file = "tzdata-2023.3-py2.py3-none-any.whl", hash = "sha256:7e65763eef3120314099b6939b5546db7adce1e7d6f2e179e3df563c70511eda"},
-    {file = "tzdata-2023.3.tar.gz", hash = "sha256:11ef1e08e54acb0d4f95bdb1be05da659673de4acbd21bf9c69e94cc5e907a3a"},
+    {file = "tzdata-2023.4-py2.py3-none-any.whl", hash = "sha256:aa3ace4329eeacda5b7beb7ea08ece826c28d761cda36e747cfbf97996d39bf3"},
+    {file = "tzdata-2023.4.tar.gz", hash = "sha256:dd54c94f294765522c77399649b4fefd95522479a664a0cec87f41bebc6148c9"},
 ]
 
 [[package]]
@@ -2015,4 +1935,4 @@ files = [
 [metadata]
 lock-version = "2.0"
 python-versions = "^3.9"
-content-hash = "b649afece7475a1c9c309be6e4c87c32107c4a1344cb565a0f82d92ba1a42833"
+content-hash = "40397bcf89831665111b703753585483532a606b50f077dc931d072def417d66"
diff --git a/pyproject.toml b/pyproject.toml
index da26edc..c2a2949 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -22,7 +22,6 @@ python-jose = {extras = ["cryptography"], version = "^3.3.0"}
 geneweaver-testing = "^0.0.3"
 pytest-asyncio = "^0.21.0"
 magicmock =  "^0.03"
-pylint= "^3.0.3"
 
 [tool.ruff]
 select = ['F', 'E', 'W', 'A', 'C90', 'N', 'B', 'ANN', 'D', 'I', 'ERA', 'PD', 'NPY', 'PT']
diff --git a/src/geneweaver/api/controller/genesets.py b/src/geneweaver/api/controller/genesets.py
index fbd63e8..0578ac5 100644
--- a/src/geneweaver/api/controller/genesets.py
+++ b/src/geneweaver/api/controller/genesets.py
@@ -2,18 +2,18 @@
 from typing import Optional
 
 from fastapi import APIRouter, Depends, HTTPException, Security
-from fastapi.logger import logger
+from geneweaver.api import dependencies as deps
+from geneweaver.api.schemas.auth import UserInternal
+from geneweaver.api.services import geneset as genset_service
 from geneweaver.core.schema.geneset import GenesetUpload
 from geneweaver.db import geneset as db_geneset
 from geneweaver.db import geneset_value as db_geneset_value
 
-from geneweaver.api import dependencies as deps
-from geneweaver.api.schemas.auth import UserInternal
-from geneweaver.api.services import geneset as genset_service
 from . import message as api_message
 
 router = APIRouter(prefix="/genesets")
 
+
 @router.get("")
 def get_visible_genesets(
     user: UserInternal = Security(deps.full_user),
@@ -28,15 +28,10 @@ def get_visible_genesets(
 def get_geneset(
     geneset_id: int,
     user: UserInternal = Security(deps.full_user),
-    cursor: Optional[deps.Cursor] = Depends(deps.cursor)
+    cursor: Optional[deps.Cursor] = Depends(deps.cursor),
 ) -> dict:
     """Get a geneset by ID."""
-    try:
-        response = genset_service.get_geneset(geneset_id, user, cursor)
-
-    except Exception as err:
-        logger.error(err)
-        raise HTTPException(status_code=500, detail=api_message.UNEXPECTED_ERROR)
+    response = genset_service.get_geneset(geneset_id, user, cursor)
 
     if "error" in response:
         if response.get("message") == api_message.ACCESS_FORBIDEN:
@@ -46,6 +41,7 @@ def get_geneset(
 
     return response
 
+
 @router.post("")
 def upload_geneset(
     geneset: GenesetUpload,
diff --git a/src/geneweaver/api/controller/message.py b/src/geneweaver/api/controller/message.py
index 4304184..553f50f 100644
--- a/src/geneweaver/api/controller/message.py
+++ b/src/geneweaver/api/controller/message.py
@@ -1,6 +1,6 @@
-"""Constants key/value messages"""
+"""Constants key/value messages."""
 
 
 ##Errors
-ACCESS_FORBIDEN="Forbidden"
-UNEXPECTED_ERROR="Unexpected Error"
+ACCESS_FORBIDEN = "Forbidden"
+UNEXPECTED_ERROR = "Unexpected Error"
diff --git a/src/geneweaver/api/services/geneset.py b/src/geneweaver/api/services/geneset.py
index e1d8013..9c80ffc 100644
--- a/src/geneweaver/api/services/geneset.py
+++ b/src/geneweaver/api/services/geneset.py
@@ -1,21 +1,15 @@
 """Service functions for dealing with genesets."""
 
 from fastapi.logger import logger
-from geneweaver.db import geneset as db_geneset
-from geneweaver.db import geneset_value as db_geneset_value
-from geneweaver.db.geneset import is_readable as db_is_readable
-
 from geneweaver.api import dependencies as deps
 from geneweaver.api.controller import message
 from geneweaver.api.schemas.auth import User
+from geneweaver.db import geneset as db_geneset
+from geneweaver.db import geneset_value as db_geneset_value
+from geneweaver.db.geneset import is_readable as db_is_readable
 
 
-def get_geneset(
-    geneset_id: int,
-    user: User,
-    cursor: deps.Cursor
-) -> dict:
-
+def get_geneset(geneset_id: int, user: User, cursor: deps.Cursor) -> dict:
     """Get a geneset by ID."""
     try:
         if not is_geneset_readable_by_user(geneset_id, user, cursor):
@@ -29,13 +23,11 @@ def get_geneset(
         logger.error(err)
         raise err
 
+
 def is_geneset_readable_by_user(
-        geneset_id: int,
-        user: User,
-        cursor: deps.Cursor
+    geneset_id: int, user: User, cursor: deps.Cursor
 ) -> bool:
-
-    """ check if the user can read the geneset from DB"""
+    """Check if the user can read the geneset from DB."""
     readable: bool = False
     try:
         readable = db_is_readable(cursor, user.id, geneset_id)

From a469e19d543b0263a800d7b8332b338b7a10588d Mon Sep 17 00:00:00 2001
From: francastell <fsophisco@yahoo.com>
Date: Wed, 3 Jan 2024 12:05:50 -0500
Subject: [PATCH 5/7] code linting for tests, README udpates

---
 README.MD                          |  4 +-
 tests/controllers/__init__.py      |  1 +
 tests/controllers/test_genesets.py | 51 ++++++++++++------------
 tests/data/__init__.py             |  1 +
 tests/services/test_genset.py      | 63 ++++++++++++++----------------
 5 files changed, 58 insertions(+), 62 deletions(-)

diff --git a/README.MD b/README.MD
index 61e5581..6511c74 100644
--- a/README.MD
+++ b/README.MD
@@ -31,11 +31,11 @@ Ruff rules: (https://docs.astral.sh/ruff/rules/)
 
 From active local environment on command line run:
 
-    ruff src --fix
+    ruff src/ tests/ --fix
 
 then run black (code formatter: https://black.readthedocs.io/en/stable/the_black_code_style/current_style.html)
 
-    black src
+    black src/ tests/
 
 ### Unit test
 
diff --git a/tests/controllers/__init__.py b/tests/controllers/__init__.py
index e69de29..ce6d944 100644
--- a/tests/controllers/__init__.py
+++ b/tests/controllers/__init__.py
@@ -0,0 +1 @@
+"""Tests for controllers."""
diff --git a/tests/controllers/test_genesets.py b/tests/controllers/test_genesets.py
index 7451765..e0103ad 100644
--- a/tests/controllers/test_genesets.py
+++ b/tests/controllers/test_genesets.py
@@ -1,15 +1,13 @@
-""" Tests for geneset API"""
+"""Tests for geneset API."""
 
 import importlib.resources
 import json
-from unittest.mock import Mock
-from unittest.mock import patch
+from unittest.mock import Mock, patch
 
 import psycopg
 import pytest
 from fastapi.testclient import TestClient
-
-from geneweaver.api.dependencies import full_user, cursor
+from geneweaver.api.dependencies import cursor, full_user
 from geneweaver.api.main import app
 
 client = TestClient(app)
@@ -24,31 +22,34 @@
 response_mock.status_code = 200
 response_mock.json.return_value = test_data
 
+
 ### Mock dependencies
 def mock_full_user() -> Mock:
-    """ User auth mock"""
+    """User auth mock."""
     m1 = Mock()
     return m1.AsyncMock()
 
+
 def mock_cursor() -> psycopg.Cursor:
-    """ DB cursor mock"""
+    """DB cursor mock."""
     m2 = Mock()
     return m2.AsyncMock()
 
-app.dependency_overrides.update(
-    {full_user: mock_full_user, cursor: mock_cursor}
-)
 
-@patch.object(client, 'get', return_value=response_mock)
+app.dependency_overrides.update({full_user: mock_full_user, cursor: mock_cursor})
+
+
+@patch.object(client, "get", return_value=response_mock)
 def test_get_geneset(mock_client):
-    """ test get request for geneset ID"""
+    """Test get request for geneset ID."""
     response = client.get("/api/genesets/1234")
     assert response.status_code == 200
 
-@patch('geneweaver.api.services.geneset.get_geneset')
-@patch('geneweaver.api.services.geneset.is_geneset_readable_by_user')
+
+@patch("geneweaver.api.services.geneset.get_geneset")
+@patch("geneweaver.api.services.geneset.is_geneset_readable_by_user")
 def test_get_geneset_response(mock_genset_is_readable, mock_get_genenset):
-    """ test get geneset ID data response"""
+    """Test get geneset ID data response."""
     mock_genset_is_readable.return_value = True
     mock_get_genenset.return_value = test_data
 
@@ -56,23 +57,21 @@ def test_get_geneset_response(mock_genset_is_readable, mock_get_genenset):
     assert response.status_code == 200
     assert response.json() == test_data
 
-@patch('geneweaver.api.services.geneset.db_is_readable')
-def test_get_geneset_forbidden(mock_genset_is_readable):
-    """ test forbidden response"""
 
+@patch("geneweaver.api.services.geneset.db_is_readable")
+def test_get_geneset_forbidden(mock_genset_is_readable):
+    """Test forbidden response."""
     mock_genset_is_readable.return_value = False
     response = client.get("/api/genesets/1234")
 
-    assert response.json() == {'detail': 'Forbidden'}
+    assert response.json() == {"detail": "Forbidden"}
     assert response.status_code == 403
 
-@patch('geneweaver.api.services.geneset.db_is_readable')
-def test_get_geneset_unexpected_error(mock_genset_is_readable):
-    """ test unexpected error response"""
 
+@patch("geneweaver.api.services.geneset.db_is_readable")
+def test_get_geneset_unexpected_error(mock_genset_is_readable):
+    """Test unexpected error response."""
     mock_genset_is_readable.side_effect = Exception
 
-    with pytest.raises(Exception):
-        response = client.get("/api/genesets/1234")
-        assert response.json() == {'detail': 'Unexpected error'}
-        assert response.status_code == 500
+    with pytest.raises(expected_exception=Exception):
+        client.get("/api/genesets/1234")
diff --git a/tests/data/__init__.py b/tests/data/__init__.py
index e69de29..2d1c0a9 100644
--- a/tests/data/__init__.py
+++ b/tests/data/__init__.py
@@ -0,0 +1 @@
+"""Data package for tests."""
diff --git a/tests/services/test_genset.py b/tests/services/test_genset.py
index a37f824..d18d720 100644
--- a/tests/services/test_genset.py
+++ b/tests/services/test_genset.py
@@ -1,11 +1,10 @@
-""" Tests for geneset Service"""
+"""Tests for geneset Service."""
 
 import importlib.resources
 import json
 from unittest.mock import patch
 
 import pytest
-
 from geneweaver.api.controller import message
 from geneweaver.api.services import geneset
 
@@ -15,62 +14,58 @@
 # returns JSON string as a dictionary
 test_data = json.loads(str_json)
 
-@patch('geneweaver.api.services.geneset.db_geneset')
-@patch('geneweaver.api.services.geneset.db_geneset_value')
-@patch('geneweaver.api.services.geneset.is_geneset_readable_by_user')
-def test_get_geneset(mock_genset_readable_func, mock_db_geneset, mock_db_genset_value):
-    """ test basic get geneset by ID"""
 
+@patch("geneweaver.api.services.geneset.db_geneset")
+@patch("geneweaver.api.services.geneset.db_geneset_value")
+@patch("geneweaver.api.services.geneset.is_geneset_readable_by_user")
+def test_get_geneset(mock_genset_readable_func, mock_db_geneset, mock_db_genset_value):
+    """Test basic get geneset by ID."""
     mock_genset_readable_func.return_value = True
     mock_db_geneset.by_id.return_value = {}
     mock_db_genset_value.by_id.return_value = {}
     response = geneset.get_geneset(1234, None, None)
-    assert response.get('error') is None
+    assert response.get("error") is None
 
 
-@patch('geneweaver.api.services.geneset.is_geneset_readable_by_user')
+@patch("geneweaver.api.services.geneset.is_geneset_readable_by_user")
 def test_get_geneset_no_user_access(mock_genset_readable_func):
-    """ test get geneset by ID with no user access"""
-
+    """Test get geneset by ID with no user access."""
     mock_genset_readable_func.return_value = False
     response = geneset.get_geneset(1234, None, None)
-    assert response.get('error') is True
-    assert response.get('message') == message.ACCESS_FORBIDEN
+    assert response.get("error") is True
+    assert response.get("message") == message.ACCESS_FORBIDEN
 
 
-@patch('geneweaver.api.services.geneset.db_geneset')
-@patch('geneweaver.api.services.geneset.db_geneset_value')
-@patch('geneweaver.api.services.geneset.is_geneset_readable_by_user')
-def test_get_geneset_returned_values(mock_genset_readable_func,
-                                     mock_db_genset_value,
-                                     mock_db_geneset):
-    """ test get geneset by ID data response structure"""
-
+@patch("geneweaver.api.services.geneset.db_geneset")
+@patch("geneweaver.api.services.geneset.db_geneset_value")
+@patch("geneweaver.api.services.geneset.is_geneset_readable_by_user")
+def test_get_geneset_returned_values(
+    mock_genset_readable_func, mock_db_genset_value, mock_db_geneset
+):
+    """Test get geneset by ID data response structure."""
     mock_genset_readable_func.return_value = True
-    mock_db_geneset.by_id.return_value = test_data.get('geneset')
-    mock_db_genset_value.by_geneset_id.return_value = test_data.get('geneset_values')
+    mock_db_geneset.by_id.return_value = test_data.get("geneset")
+    mock_db_genset_value.by_geneset_id.return_value = test_data.get("geneset_values")
     response = geneset.get_geneset(1234, None, None)
 
-    assert response.get('genset') == test_data['geneset']
-    assert response.get('geneset_values') == test_data['geneset_values']
+    assert response.get("genset") == test_data["geneset"]
+    assert response.get("geneset_values") == test_data["geneset_values"]
 
 
-@patch('geneweaver.api.services.geneset.db_is_readable')
-@patch('geneweaver.api.services.geneset.User')
+@patch("geneweaver.api.services.geneset.db_is_readable")
+@patch("geneweaver.api.services.geneset.User")
 def test_is_redable_by_user(mock_user, mock_genset_is_readable):
-    """ test is geneset ID readable by passed user"""
-
+    """Test is geneset ID readable by passed user."""
     mock_genset_is_readable.return_value = True
     response = geneset.is_geneset_readable_by_user(1234, mock_user, None)
     assert response is True
 
 
-@patch('geneweaver.db.geneset.is_readable')
-@patch('geneweaver.api.services.geneset.User')
+@patch("geneweaver.db.geneset.is_readable")
+@patch("geneweaver.api.services.geneset.User")
 def test_is_redable_by_user_error(mock_user, mock_genset_is_readable):
-    """ test is geneset ID readable with server error"""
-
+    """Test is geneset ID readable with server error."""
     mock_genset_is_readable.sideEffect = Exception
 
-    with pytest.raises(Exception):
+    with pytest.raises(expected_exception=Exception):
         geneset.is_geneset_readable_by_user(1234, mock_user, None)

From dc7af3a9872a782b11954a6f0ef73ea3616a9cd4 Mon Sep 17 00:00:00 2001
From: francastell <fsophisco@yahoo.com>
Date: Wed, 3 Jan 2024 18:09:19 -0500
Subject: [PATCH 6/7] tests refactoring. Mocking config

---
 src/geneweaver/api/controller/genesets.py |  2 +-
 src/geneweaver/api/services/geneset.py    | 10 ++--
 tests/controllers/conftest.py             | 68 +++++++++++++++++++++++
 tests/controllers/test_genesets.py        | 50 ++---------------
 tests/services/test_genset.py             | 10 ++--
 5 files changed, 83 insertions(+), 57 deletions(-)
 create mode 100644 tests/controllers/conftest.py

diff --git a/src/geneweaver/api/controller/genesets.py b/src/geneweaver/api/controller/genesets.py
index 0578ac5..e454169 100644
--- a/src/geneweaver/api/controller/genesets.py
+++ b/src/geneweaver/api/controller/genesets.py
@@ -31,7 +31,7 @@ def get_geneset(
     cursor: Optional[deps.Cursor] = Depends(deps.cursor),
 ) -> dict:
     """Get a geneset by ID."""
-    response = genset_service.get_geneset(geneset_id, user, cursor)
+    response = genset_service.get_geneset(cursor, geneset_id, user)
 
     if "error" in response:
         if response.get("message") == api_message.ACCESS_FORBIDEN:
diff --git a/src/geneweaver/api/services/geneset.py b/src/geneweaver/api/services/geneset.py
index 9c80ffc..ce710b7 100644
--- a/src/geneweaver/api/services/geneset.py
+++ b/src/geneweaver/api/services/geneset.py
@@ -1,18 +1,18 @@
 """Service functions for dealing with genesets."""
 
 from fastapi.logger import logger
-from geneweaver.api import dependencies as deps
 from geneweaver.api.controller import message
 from geneweaver.api.schemas.auth import User
 from geneweaver.db import geneset as db_geneset
 from geneweaver.db import geneset_value as db_geneset_value
 from geneweaver.db.geneset import is_readable as db_is_readable
+from psycopg import Cursor
 
 
-def get_geneset(geneset_id: int, user: User, cursor: deps.Cursor) -> dict:
+def get_geneset(cursor: Cursor, geneset_id: int, user: User) -> dict:
     """Get a geneset by ID."""
     try:
-        if not is_geneset_readable_by_user(geneset_id, user, cursor):
+        if not is_geneset_readable_by_user(cursor, geneset_id, user):
             return {"error": True, "message": message.ACCESS_FORBIDEN}
 
         geneset = db_geneset.by_id(cursor, geneset_id)
@@ -24,9 +24,7 @@ def get_geneset(geneset_id: int, user: User, cursor: deps.Cursor) -> dict:
         raise err
 
 
-def is_geneset_readable_by_user(
-    geneset_id: int, user: User, cursor: deps.Cursor
-) -> bool:
+def is_geneset_readable_by_user(cursor: Cursor, geneset_id: int, user: User) -> bool:
     """Check if the user can read the geneset from DB."""
     readable: bool = False
     try:
diff --git a/tests/controllers/conftest.py b/tests/controllers/conftest.py
new file mode 100644
index 0000000..2643700
--- /dev/null
+++ b/tests/controllers/conftest.py
@@ -0,0 +1,68 @@
+"""Fixtures for the controller tests."""
+import importlib.resources
+import json
+from unittest.mock import Mock
+
+import psycopg
+import pytest
+from fastapi.testclient import TestClient
+from geneweaver.api.core.config_class import GeneweaverAPIConfig
+
+# Load test data
+# Opening JSON file
+str_json = importlib.resources.read_text("tests.data", "response_geneset_1234.json")
+# returns JSON string as a dictionary
+test_data = json.loads(str_json)
+
+response_mock = Mock()
+response_mock.status_code = 200
+response_mock.json.return_value = test_data
+
+
+# Mock dependencies
+def mock_full_user() -> Mock:
+    """User auth mock."""
+    m1 = Mock()
+    return m1.AsyncMock()
+
+
+def mock_cursor() -> psycopg.Cursor:
+    """DB cursor mock."""
+    m2 = Mock()
+    return m2.AsyncMock()
+
+
+@pytest.fixture()
+def mock_settings(monkeypatch) -> GeneweaverAPIConfig:
+    """Patch the settings class to return a test settings instance.
+
+    returns: A patched settings instance.
+    """
+    test_settings = GeneweaverAPIConfig(
+        DB_HOST="localhost",
+        DB_USERNAME="postgres",
+        DB_PASSWORD="postgres",
+        DB_NAME="geneweaver",
+    )
+
+    monkeypatch.setattr(
+        "geneweaver.api.core.config_class.GeneweaverAPIConfig", lambda: test_settings
+    )
+
+    return test_settings
+
+
+@pytest.fixture()
+def client(mock_settings) -> TestClient:
+    """Provide a mocked FastAPI application.
+
+    returns: A mocked FastAPI application.
+    """
+    from geneweaver.api.dependencies import cursor, full_user
+    from geneweaver.api.main import app
+
+    test_app = TestClient(app)
+
+    app.dependency_overrides.update({full_user: mock_full_user, cursor: mock_cursor})
+
+    return test_app
diff --git a/tests/controllers/test_genesets.py b/tests/controllers/test_genesets.py
index e0103ad..219dbf6 100644
--- a/tests/controllers/test_genesets.py
+++ b/tests/controllers/test_genesets.py
@@ -1,54 +1,14 @@
 """Tests for geneset API."""
+from unittest.mock import patch
 
-import importlib.resources
-import json
-from unittest.mock import Mock, patch
-
-import psycopg
 import pytest
-from fastapi.testclient import TestClient
-from geneweaver.api.dependencies import cursor, full_user
-from geneweaver.api.main import app
-
-client = TestClient(app)
-
-### Load test data
-# Opening JSON file
-str_json = importlib.resources.read_text("tests.data", "response_geneset_1234.json")
-# returns JSON string as a dictionary
-test_data = json.loads(str_json)
-
-response_mock = Mock()
-response_mock.status_code = 200
-response_mock.json.return_value = test_data
-
-
-### Mock dependencies
-def mock_full_user() -> Mock:
-    """User auth mock."""
-    m1 = Mock()
-    return m1.AsyncMock()
-
 
-def mock_cursor() -> psycopg.Cursor:
-    """DB cursor mock."""
-    m2 = Mock()
-    return m2.AsyncMock()
-
-
-app.dependency_overrides.update({full_user: mock_full_user, cursor: mock_cursor})
-
-
-@patch.object(client, "get", return_value=response_mock)
-def test_get_geneset(mock_client):
-    """Test get request for geneset ID."""
-    response = client.get("/api/genesets/1234")
-    assert response.status_code == 200
+from tests.controllers.conftest import test_data
 
 
 @patch("geneweaver.api.services.geneset.get_geneset")
 @patch("geneweaver.api.services.geneset.is_geneset_readable_by_user")
-def test_get_geneset_response(mock_genset_is_readable, mock_get_genenset):
+def test_get_geneset_response(mock_genset_is_readable, mock_get_genenset, client):
     """Test get geneset ID data response."""
     mock_genset_is_readable.return_value = True
     mock_get_genenset.return_value = test_data
@@ -59,7 +19,7 @@ def test_get_geneset_response(mock_genset_is_readable, mock_get_genenset):
 
 
 @patch("geneweaver.api.services.geneset.db_is_readable")
-def test_get_geneset_forbidden(mock_genset_is_readable):
+def test_get_geneset_forbidden(mock_genset_is_readable, client):
     """Test forbidden response."""
     mock_genset_is_readable.return_value = False
     response = client.get("/api/genesets/1234")
@@ -69,7 +29,7 @@ def test_get_geneset_forbidden(mock_genset_is_readable):
 
 
 @patch("geneweaver.api.services.geneset.db_is_readable")
-def test_get_geneset_unexpected_error(mock_genset_is_readable):
+def test_get_geneset_unexpected_error(mock_genset_is_readable, client):
     """Test unexpected error response."""
     mock_genset_is_readable.side_effect = Exception
 
diff --git a/tests/services/test_genset.py b/tests/services/test_genset.py
index d18d720..2db35f8 100644
--- a/tests/services/test_genset.py
+++ b/tests/services/test_genset.py
@@ -23,7 +23,7 @@ def test_get_geneset(mock_genset_readable_func, mock_db_geneset, mock_db_genset_
     mock_genset_readable_func.return_value = True
     mock_db_geneset.by_id.return_value = {}
     mock_db_genset_value.by_id.return_value = {}
-    response = geneset.get_geneset(1234, None, None)
+    response = geneset.get_geneset(None, 1234, None)
     assert response.get("error") is None
 
 
@@ -31,7 +31,7 @@ def test_get_geneset(mock_genset_readable_func, mock_db_geneset, mock_db_genset_
 def test_get_geneset_no_user_access(mock_genset_readable_func):
     """Test get geneset by ID with no user access."""
     mock_genset_readable_func.return_value = False
-    response = geneset.get_geneset(1234, None, None)
+    response = geneset.get_geneset(None, 1234, None)
     assert response.get("error") is True
     assert response.get("message") == message.ACCESS_FORBIDEN
 
@@ -46,7 +46,7 @@ def test_get_geneset_returned_values(
     mock_genset_readable_func.return_value = True
     mock_db_geneset.by_id.return_value = test_data.get("geneset")
     mock_db_genset_value.by_geneset_id.return_value = test_data.get("geneset_values")
-    response = geneset.get_geneset(1234, None, None)
+    response = geneset.get_geneset(None, 1234, None)
 
     assert response.get("genset") == test_data["geneset"]
     assert response.get("geneset_values") == test_data["geneset_values"]
@@ -57,7 +57,7 @@ def test_get_geneset_returned_values(
 def test_is_redable_by_user(mock_user, mock_genset_is_readable):
     """Test is geneset ID readable by passed user."""
     mock_genset_is_readable.return_value = True
-    response = geneset.is_geneset_readable_by_user(1234, mock_user, None)
+    response = geneset.is_geneset_readable_by_user(None, 1234, mock_user)
     assert response is True
 
 
@@ -68,4 +68,4 @@ def test_is_redable_by_user_error(mock_user, mock_genset_is_readable):
     mock_genset_is_readable.sideEffect = Exception
 
     with pytest.raises(expected_exception=Exception):
-        geneset.is_geneset_readable_by_user(1234, mock_user, None)
+        geneset.is_geneset_readable_by_user(None, 1234, mock_user)

From 6183b22fe10ca6af9b7f0cf30e1a05faa3af3f67 Mon Sep 17 00:00:00 2001
From: francastell <fsophisco@yahoo.com>
Date: Thu, 4 Jan 2024 11:22:07 -0500
Subject: [PATCH 7/7] removing unnecessary dependency

---
 poetry.lock    | 43 +------------------------------------------
 pyproject.toml |  1 -
 2 files changed, 1 insertion(+), 43 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 0b7cd0e..dc67b0d 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -568,20 +568,6 @@ http2 = ["h2 (>=3,<5)"]
 socks = ["socksio (==1.*)"]
 trio = ["trio (>=0.22.0,<0.23.0)"]
 
-[[package]]
-name = "httplib2"
-version = "0.22.0"
-description = "A comprehensive HTTP client library."
-optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
-files = [
-    {file = "httplib2-0.22.0-py3-none-any.whl", hash = "sha256:14ae0a53c1ba8f3d37e9e27cf37eabb0fb9980f435ba405d546948b009dd64dc"},
-    {file = "httplib2-0.22.0.tar.gz", hash = "sha256:d7a10bc5ef5ab08322488bde8c726eeee5c8618723fdb399597ec58f3d82df81"},
-]
-
-[package.dependencies]
-pyparsing = {version = ">=2.4.2,<3.0.0 || >3.0.0,<3.0.1 || >3.0.1,<3.0.2 || >3.0.2,<3.0.3 || >3.0.3,<4", markers = "python_version > \"3.0\""}
-
 [[package]]
 name = "httptools"
 version = "0.6.1"
@@ -718,19 +704,6 @@ MarkupSafe = ">=2.0"
 [package.extras]
 i18n = ["Babel (>=2.7)"]
 
-[[package]]
-name = "magicmock"
-version = "0.03"
-description = "A generic mock server"
-optional = false
-python-versions = "*"
-files = [
-    {file = "magicmock-0.03.tar.gz", hash = "sha256:fe0d99b9daab2f9361dd62b8dc299f3ba46fe1923119335ab31eca4318fda1c5"},
-]
-
-[package.dependencies]
-httplib2 = "*"
-
 [[package]]
 name = "markupsafe"
 version = "2.1.3"
@@ -1274,20 +1247,6 @@ typing-extensions = ">=4.2.0"
 dotenv = ["python-dotenv (>=0.10.4)"]
 email = ["email-validator (>=1.0.3)"]
 
-[[package]]
-name = "pyparsing"
-version = "3.1.1"
-description = "pyparsing module - Classes and methods to define and execute parsing grammars"
-optional = false
-python-versions = ">=3.6.8"
-files = [
-    {file = "pyparsing-3.1.1-py3-none-any.whl", hash = "sha256:32c7c0b711493c72ff18a981d24f28aaf9c1fb7ed5e9667c9e84e3db623bdbfb"},
-    {file = "pyparsing-3.1.1.tar.gz", hash = "sha256:ede28a1a32462f5a9705e07aea48001a08f7cf81a021585011deba701581a0db"},
-]
-
-[package.extras]
-diagrams = ["jinja2", "railroad-diagrams"]
-
 [[package]]
 name = "pytest"
 version = "7.4.4"
@@ -1935,4 +1894,4 @@ files = [
 [metadata]
 lock-version = "2.0"
 python-versions = "^3.9"
-content-hash = "40397bcf89831665111b703753585483532a606b50f077dc931d072def417d66"
+content-hash = "0ea43acd3f3f058a7640f58d5183d834b88b2da78c07d593beb572892d3d59b5"
diff --git a/pyproject.toml b/pyproject.toml
index c2a2949..65bd346 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -21,7 +21,6 @@ python-jose = {extras = ["cryptography"], version = "^3.3.0"}
 [tool.poetry.group.dev.dependencies]
 geneweaver-testing = "^0.0.3"
 pytest-asyncio = "^0.21.0"
-magicmock =  "^0.03"
 
 [tool.ruff]
 select = ['F', 'E', 'W', 'A', 'C90', 'N', 'B', 'ANN', 'D', 'I', 'ERA', 'PD', 'NPY', 'PT']