Initial client api deployment

.gitignore

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+# Created by .ignore support plugin (hsz.mobi)
+### VirtualEnv template
+# Virtualenv
+# http://iamzed.com/2009/05/07/a-primer-on-virtualenv/
+.Python
+[Bb]in
+[Ii]nclude
+[Ll]ib
+[Ll]ib64
+[Ll]ocal
+[Ss]cripts
+pyvenv.cfg
+.venv
+pip-selfcheck.json
+### Python template
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+__pycache__/
+*.py[cod]
+*$py.class
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+*.so
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+.Python
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+develop-eggs/
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+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+*.egg-info/
+.installed.cfg
+*.egg
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+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
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+#jetbrains ide
+
+.idea

MANIFEST.in

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+include LICENSE
+include MANIFEST.in
+include README.rst
+include setup.py
+include run.py
+recursive-exclude * __pycache__
+recursive-exclude * *.py[co]

README.md

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+# Variant API Client
+
+## A basic api client implementation for [api.varsome.com](https://api.varsome.com)
+
+This client is still in beta but it is a good start to start playing around with the API.
+
+### Installation
+
+Either download clone the repository from github and place the variantapi package
+within your code, or do
+
+    pip install https://github.com/saphetor/variant-api-client-python/archive/master.zip
+
+### API Documentation
+
+Please visit the [api documentation](http://docs.testapi2127.apiary.io/) to find out how to use the api and
+what values does the api provide as a response to lookup requests
+
+### Using the client in your code
+
+Using the api client is quite straightforward. Just install the api client package and from within
+your code use
+
+    from variantapi.client import VariantAPIClient
+    # api key is not required for single variant lookups
+    api_key = 'Your token'
+    api = VariantAPIClient(api_key)
+    # fetch information about a variant into a dictionary
+    result = api.lookup('chr19:20082943:1:G', ref_genome=1019)
+    # access results e.g. the sequence around the variant
+    sequence = result['ref_seq']['sequence']
+    # fetch information for multiple variants
+    variants = ['chr19:20082943:1:G','chr22:39777823::CAA']
+    # results will be an array of dictionaries an api key will be required for this request
+    results = api.batch_lookup(variants, ref_genome=1019)
+
+If errors occur while using the client an exception will be thrown.
+You may wish to catch this exception and proceed with your own code logic
+
+    from variantapi.client import VariantAPIClient, VariantApiException
+    api = VariantAPIClient()
+    try:
+       result = api.lookup('chr19:20082943:1:G', ref_genome=1054)
+    except VariantApiException as e:
+        # proceed with your code flow e.g.
+        print(e) # 404 (invalid reference genome)
+
+### Example Usage
+
+
+You may download and run the run.py python file after installation of the package
+to test the api client directly e.g.
+
+    ./run.py -g 1019 -q 'chr19:20082943:1:G'
+
+You may pass more than one values after the -q argument that will make a batch request
+to the API but you will need a token to do that e.g.
+
+    ./run.py -k 'your token' -g 1019 -q 'rs113488022' 'chr19:20082943:1:G'
+
+Run
+
+    ./run.py -h
+
+for a list of available options
+
+

run.py

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+#!/usr/bin/env python
+import argparse
+import json
+import logging
+import sys
+
+from variantapi.client import VariantAPIClient
+
+__author__ = 'ckopanos'
+logging.basicConfig(level=logging.DEBUG,
+                    format='[%(levelname)s]	%(threadName)s	%(message)s',
+                    )
+
+
+def main(argv):
+    parser = argparse.ArgumentParser(description='Sample Variant API calls')
+    parser.add_argument('-k', help='Your key to the API', type=str, metavar='API Key', required=False)
+    parser.add_argument('-g', help='Reference genome either 1019 or 1038', type=int, metavar='Reference Genome',
+                        required=False, default=1019)
+    parser.add_argument('-q',
+                        help='Query to lookup in the API e.g. chr19:20082943:1:G or in case of batch request '
+                             'e.g. chr19:20082943:1:G rs113488022',
+                        type=str, metavar='Query', required=True, nargs='+')
+    args = parser.parse_args()
+    api_key = args.k
+    query = args.q
+    ref_genome = args.g
+    api = VariantAPIClient(api_key)
+    if len(query) == 1:
+        result = api.lookup(query[0], ref_genome=ref_genome)
+    else:
+        if api_key is None:
+            sys.exit("You need to pass an api key to perform batch requests")
+        result = api.batch_lookup(query, ref_genome=ref_genome)
+    sys.stdout.write(json.dumps(result, indent=4, sort_keys=True) if result else "No result")
+    sys.stdout.write("\n")
+
+
+if __name__ == "__main__":
+    main(sys.argv[1:])

setup.cfg

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+[bdist_wheel]
+universal=1

setup.py

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+from setuptools import setup
+from os import path
+
+VERSION = (1, 0, '0b1')
+__version__ = VERSION
+__versionstr__ = '.'.join(map(str, VERSION))
+
+here = path.abspath(path.dirname(__file__))
+
+setup(
+    name='variant_api',
+    version=__versionstr__,
+    packages=['variantapi'],
+    url='https://github.com/saphetor/variant-api-client-python',
+    license='Apache License, Version 2.0',
+    author='Saphetor',
+    author_email='support@saphetor.com',
+    description='A basic python api client implementation for https://api.varsome.com',
+    classifiers=[
+        'Development Status :: 4 - Beta',
+        'Intended Audience :: Developers',
+        'Operating System :: OS Independent',
+        'License :: OSI Approved :: Apache License',
+        'Programming Language :: Python :: 2.7',
+        'Programming Language :: Python :: 3',
+        'Programming Language :: Python :: 3.2',
+        'Programming Language :: Python :: 3.3',
+        'Programming Language :: Python :: 3.4',
+        'Programming Language :: Python :: 3.5',
+    ],
+    install_requires=[
+        'requests>=2.0.0, <3.0.0'
+    ],
+)

variantapi/client.py

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+import logging
+
+import requests
+from requests.exceptions import HTTPError, Timeout, ConnectionError, RequestException
+
+
+
+class VariantApiException(Exception):
+    ERROR_CODES = {
+        400: "Bad request. A parameter you have passed is not valid, or something in your request is wrong",
+        401: "Not Authorized: either you need to provide authentication credentials, or the credentials provided aren't"
+             " valid.",
+        403: "Bad Request: your request is invalid, and we'll return an error message that tells you why. This is the "
+             "status code returned if you've exceeded the rate limit (see below).",
+        404: "Not Found: either you're requesting an invalid URI or the resource in question doesn't exist",
+        500: "Internal Server Error: we did something wrong.",
+        501: "Not implemented.",
+        502: "Bad Gateway: returned if VariantAPI is down or being upgraded.",
+        503: "Service Unavailable: the VariantAPI servers are up, but are overloaded with requests. Try again later.",
+        504: "Gateway Timeout",
+    }
+
+    def __init__(self, status, response=None):
+        self.status = status
+        self.response = response
+
+    def __str__(self):
+        return "%s (%s)" % (
+            self.status,
+            self.ERROR_CODES.get(self.status, 'Unknown error.') if self.response is None else self.response)
+
+    def __repr__(self):
+        return "%s(status=%s)" % (self.__class__.__name__, self.status)
+
+
+class VariantAPIClientBase(object):
+
+    _api_url = 'https://api.varsome.com'
+    _accepted_methods = ('GET', 'POST')
+
+    def __init__(self, api_key=None):
+        self.api_key = api_key
+        self._headers = {'Accept': 'application/json'}
+        if self.api_key is not None:
+            self._headers['Authorization'] = "Token " + self.api_key
+        self.session = requests.Session()
+        self.session.headers.update(self._headers)
+
+    def _make_request(self, path, method="GET", data=None, json_data=None):
+        if method not in self._accepted_methods:
+            raise VariantApiException('', "Unsupported method %s" % method)
+        try:
+            if method == "GET":
+                r = self.session.get(self._api_url + path, data=data)
+            if method == "POST":
+                r = self.session.post(self._api_url + path, data=data, json=json_data,
+                                      headers={'Content-Type': 'application/json'} if json_data is not None else None)
+                logging.debug('Time between request and response %s' % r.elapsed)
+                logging.debug('Content length %s' % len(r.content))
+            if r.status_code in VariantApiException.ERROR_CODES:
+                raise VariantApiException(
+                    r.status_code,
+                    r.json()['detail']
+                    if r.headers['Content-Type'] == "application/json" else None)
+            return r
+        except HTTPError as e:
+            raise VariantApiException('', "Unknown http error %s" % e)
+        except Timeout as e:
+            raise VariantApiException('', "Request timed out %s" % e)
+        except ConnectionError as e:
+            raise VariantApiException('', "Connection failure or connection refused %s" % e)
+        except RequestException as e:
+            raise VariantApiException('', "Unknown error %s" % e.response)
+
+    def get(self, path, data=None):
+        response = self._make_request(path, "GET", data=data)
+        return response.json()
+
+    def post(self, path, data=None, json_data=None):
+        response = self._make_request(path, "POST", data=data, json_data=json_data)
+        return response.json()
+
+
+class VariantAPIClient(VariantAPIClientBase):
+    schema_lookup_path = "/lookup/schema/"
+    lookup_path = "/lookup/%s/%s"
+    batch_lookup_path = "/lookup/batch/%s"
+    _max_variants_per_batch = 8000
+
+    def __init__(self, api_key=None):
+        super().__init__(api_key)
+
+    def schema(self):
+        return self.get(self.schema_lookup_path)
+
+    def lookup(self, query, ref_genome=1019):
+        return self.get(self.lookup_path % (query, ref_genome))
+
+    def batch_lookup(self, variants, ref_genome=1019):
+        results = []
+        for queries in [variants[x:x + self._max_variants_per_batch] for x in range(0, len(variants),
+                                                                                    self._max_variants_per_batch)]:
+            data = self.post(self.batch_lookup_path % ref_genome, json_data={'variants': queries})
+            results.extend(data)
+        return results