added setup, license, requirements

Author: khoroshevskyi

LICENSE.txt

@@ -0,0 +1,9 @@
+Copyright 2023 Nathan Sheffield
+
+Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

MANIFEST.in

@@ -0,0 +1,3 @@
+include requirements/*
+include README.md
+include pephubclient/pephub_oauth/*

error_handling/constants.py

@@ -1,5 +1,5 @@
 __app_name__ = "pephubclient"
 __version__ = "0.1.0"
+__author__ = "Oleksandr Khoroshevskyi, Rafal Stepien"
 
-
-__all__ = ["__app_name__", "__version__"]
+__all__ = ["__app_name__", "__version__", "__author__"]

error_handling/error_handler.py

@@ -1,5 +1,5 @@
 from typing import Optional
-
+from enum import Enum
 from pydantic import BaseModel
 
 # PEPHUB_BASE_URL = "https://pephub.databio.org/"
@@ -15,3 +15,9 @@ class RegistryPath(BaseModel):
     item: str
     subitem: Optional[str]
     tag: Optional[str]
+
+
+class ResponseStatusCodes(int, Enum):
+    FORBIDDEN_403 = 403
+    NOT_EXIST_404 = 404
+    OK_200 = 200

error_handling/models.py

@@ -0,0 +1,2 @@
+# Here should be error handler
+

pephubclient/__init__.py

@@ -3,7 +3,7 @@
 
 import requests
 
-from error_handling.exceptions import ResponseError
+from pephubclient.exceptions import ResponseError
 
 
 class RequestManager:

pephubclient/constants.py

@@ -11,11 +11,10 @@
     PEPHUB_BASE_URL,
     PEPHUB_PEP_API_BASE_URL,
     RegistryPath,
+    ResponseStatusCodes
 )
 from pephubclient.models import JWTDataResponse
 from pephubclient.models import ClientData
-# from error_handling.exceptions import ResponseError, IncorrectQueryStringError
-# from error_handling.constants import ResponseStatusCodes
 from pephubclient.files_manager import FilesManager
 from pephubclient.helpers import RequestManager
 
@@ -109,10 +108,10 @@ def _load_pep(
     def _handle_pephub_response(pephub_response: requests.Response):
         decoded_response = PEPHubClient.decode_response(pephub_response)
 
-        # if pephub_response.status_code != ResponseStatusCodes.OK_200:
-        #     raise ResponseError(message=json.loads(decoded_response).get("detail"))
-        # else:
-        return decoded_response
+        if pephub_response.status_code != ResponseStatusCodes.OK_200:
+            raise ResponseError(message=json.loads(decoded_response).get("detail"))
+        else:
+            return decoded_response
 
     def _request_jwt_from_pephub(self, client_data: ClientData) -> str:
         pephub_response = self.send_request(

pephubclient/error_handler.py

@@ -0,0 +1,64 @@
+import sys
+import os
+from setuptools import find_packages, setup
+from pephubclient import __app_name__, __version__, __author__
+
+PACKAGE = __app_name__
+REQDIR = "requirements"
+
+# Additional keyword arguments for setup().
+extra = {}
+
+# Ordinary dependencies
+def read_reqs(reqs_name):
+    deps = []
+    with open(os.path.join(REQDIR, f"requirements-{reqs_name}.txt"), "r") as f:
+        for l in f:
+            if not l.strip():
+                continue
+            deps.append(l)
+    return deps
+
+
+DEPENDENCIES = read_reqs("all")
+extra["install_requires"] = DEPENDENCIES
+
+scripts = None
+
+with open("README.md") as f:
+    long_description = f.read()
+
+setup(
+    name=PACKAGE,
+    packages=[PACKAGE],
+    version=__version__,
+    description="PEPhub command line interface.",
+    long_description=long_description,
+    long_description_content_type="text/markdown",
+    classifiers=[
+        "Development Status :: 1 - Planing",
+        "License :: OSI Approved :: BSD License",
+        "Programming Language :: Python :: 3.8",
+        "Programming Language :: Python :: 3.9",
+        "Programming Language :: Python :: 3.10",
+        "Topic :: Scientific/Engineering :: Bio-Informatics",
+    ],
+    keywords="project, bioinformatics, metadata",
+    url=f"https://github.com/databio/{PACKAGE}/",
+    author=__author__,
+    license="BSD2",
+    entry_points={
+        "console_scripts": [
+            "pephubclient = pephubclient.__main__:main",
+        ],
+    },
+    package_data={PACKAGE: ["templates/*"]},
+    scripts=scripts,
+    include_package_data=True,
+    test_suite="tests",
+    tests_require=read_reqs("dev"),
+    setup_requires=(
+        ["pytest-runner"] if {"test", "pytest", "ptr"} & set(sys.argv) else []
+    ),
+    **extra,
+)

error_handling/exceptions.py pephubclient/exceptions.py

@@ -1,7 +1,7 @@
 import pytest
 from unittest.mock import Mock, patch, mock_open
 from pephubclient.pephubclient import PEPHubClient
-from error_handling.exceptions import ResponseError
+from pephubclient.exceptions import ResponseError
 
 
 def test_login(mocker, test_jwt_response, test_client_data, test_access_token):