make gdcapiwrapper pip installable

Author: ernestoarbitrio

LICENSE renamed to LICENSE.txt

@@ -9,4 +9,7 @@ The GDC API drives the GDC Data and Submission Portals and provides programmatic
 
 ## Features implemented
 - Downloading a Single File using GET 
-- Downloading Multiple Files using POST
+- Downloading Multiple Files using POST
+
+## Usage
+`pip install gdc-api-wrapper`

MANIFEST.in

@@ -0,0 +1,63 @@
+# coding: utf-8
+
+import os
+import re
+
+import setuptools
+
+
+def ascii_bytes_from(path, *paths):
+    """
+    Return the ASCII characters in the file specified by *path* and *paths*.
+    The file path is determined by concatenating *path* and any members of
+    *paths* with a directory separator in between.
+    """
+    file_path = os.path.join(path, *paths)
+    with open(file_path) as f:
+        ascii_bytes = f.read()
+    return ascii_bytes
+
+
+# read required text from files
+thisdir = os.path.dirname(__file__)
+init_py = ascii_bytes_from(thisdir, "src", "gdcapiwrapper", "__init__.py")
+readme = ascii_bytes_from(thisdir, "README.md")
+# This allows users to check installed version with:
+# `python -c 'from gdcapiwrapper import __version__; print(__version__)'`
+version = re.search('__version__ = "([^"]+)"', init_py).group(1)
+
+install_requires = ["requests[security]", "responses", "tqdm"]
+
+test_requires = ["pytest", "pytest-xdist", "coverage", "pytest-cov", "coveralls"]
+
+setuptools.setup(
+    name="gdc-api-wrapper",
+    version=version,
+    maintainer="Histolab Developers",
+    maintainer_email="[email protected]",
+    author="E. Arbitrio",
+    description="A simple Python wrapper for the GDC Application Programming Interface",
+    long_description=readme,
+    long_description_content_type="text/markdown",
+    url="https://github.com/histolab/gdc-api-wrapper",
+    download_url="https://github.com/histolab/gdc-api-wrapper",
+    install_requires=install_requires,
+    tests_require=test_requires,
+    extras_require={"testing": test_requires},
+    packages=setuptools.find_packages("src", exclude=["tests"]),
+    classifiers=[
+        "Programming Language :: Python :: 3",
+        "Programming Language :: Python :: 3.6",
+        "Programming Language :: Python :: 3.7",
+        "Programming Language :: Python :: 3.8",
+        "License :: OSI Approved :: Apache Software License",
+        "Operating System :: OS Independent",
+        "Intended Audience :: Science/Research",
+    ],
+    package_dir={"": "src"},
+    include_package_data=True,
+    entry_points={},
+    test_suite="pytest",
+    zip_safe=True,
+    python_requires=">=3.6",
+)

README.md

@@ -1,9 +1,9 @@
 # encoding: utf-8
 
 import os
-
 import requests
 
+__version__ = "0.1"
 GDC_API_TOKEN = os.environ.get("GCC_API_TOKEN", None)
 GDC_API_BASE_URL = os.environ.get("GDC_API_BASE_URL", "https://api.gdc.cancer.gov/")
 
@@ -17,6 +17,8 @@ class APITokenMissingError(Exception):
 
 
 request = requests.get(f"{GDC_API_BASE_URL}/status")
+
+
 if request.status_code != 200:
     raise APIBaseURLStatusError(
         f"{GDC_API_BASE_URL} status: {request.status_code}."

setup.py

@@ -19,11 +19,33 @@
 
 
 class Data(object):
+    """ Provides Data objects for https://api.gdc.cancer.gov/data/ `Data Endpoints`
+
+    Includes endpoints for file(s) download
+    """
+
     @classmethod
     def download(
         cls, uuid: str, path: str = ".", name: str = None
     ) -> Tuple[Response, str]:
+        """Download file and return the related api response and the file path
+
+        Parameters
+        ---------
+        uuid : str
+            File UUID
+        path: str
+            Local path where save file (default: current path)
+        name: str
+            Filename. If not provided it will be saved with UUID as name
+
+        Returns
+        -------
+        tuple
+            response, filename absolute path
+        """
         url = f"{base_url}/{uuid}"
+
         local_filename = uuid if not name else name
         with requests.get(url, stream=True) as r:
             total_size = int(r.headers.get("content-length", 0))
@@ -36,6 +58,20 @@ def download(
     def download_multiple(
         cls, uuid_list: list, path: str = "."
     ) -> Tuple[Response, str]:
+        """Download multiple files and return the related api response and the file path
+
+        Parameters
+        ---------
+        uuid_list : list
+            List of UUID(s) to save
+        path: str
+            Local path where save file (default: current path)
+
+        Returns
+        -------
+        tuple
+            response, filename absolute path
+        """
         with requests.post(base_url, stream=True, data={"ids": uuid_list}) as r:
             d = r.headers["content-disposition"]
             fname = re.findall("filename=(.+)", d)[0]

src/__init__.py

@@ -1,7 +1,7 @@
 # encoding: utf-8
 
 import os
-from unittest.mock import patch
+from unittest import mock
 
 import pytest
 from requests.exceptions import ChunkedEncodingError
@@ -20,7 +20,7 @@ def setup_class(cls):
     def test_download(self, tmpdir):
         base_url = "http://localhost:{port}/data".format(port=self.mock_server_port)
 
-        with patch.dict("gdcapiwrapper.data.__dict__", {"base_url": base_url}):
+        with mock.patch.dict("gdcapiwrapper.data.__dict__", {"base_url": base_url}):
             response, filename = Data.download(
                 uuid="fakeuuid", path=tmpdir, name="fakefilename"
             )
@@ -31,7 +31,7 @@ def test_download(self, tmpdir):
     def test_download_multiple(self, tmpdir):
         base_url = "http://localhost:{port}".format(port=self.mock_server_port)
         try:
-            with patch.dict("gdcapiwrapper.data.__dict__", {"base_url": base_url}):
+            with mock.patch.dict("gdcapiwrapper.data.__dict__", {"base_url": base_url}):
                 response, filename = Data.download_multiple(
                     uuid_list=["1", "2"], path=tmpdir
                 )