Initial commit

Initially gwaportal-gwas-server supports retrieving LD data and calculating LD. I

.gitignore

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+*.py[cod]
+
+# C extensions
+*.c
+*.so
+
+# Jython
+*$py.class
+
+# Packages
+*.egg
+*.egg-info
+dist
+build
+eggs
+parts
+var
+sdist
+develop-eggs
+.installed.cfg
+lib
+lib64
+
+# Installer logs
+pip-log.txt
+
+# Unit test / coverage reports
+.coverage
+.coverage_*
+.tox
+nosetests.xml
+htmlcov
+*.dat
+
+# Docs
+doc/_build
+
+# Translations
+*.mo
+
+# Idea
+.idea
+
+# System
+.DS_Store
+
+# VIM swap files
+.*.swp
+
+# VIM temp files
+*~

Dockerfile

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+# Dockerfile for docker-gwaportal-gwas-server
+# Version 0.1
+
+FROM timeu/docker-gwas-base
+MAINTAINER Uemit Seren <[email protected]>
+
+WORKDIR /tmp 
+
+RUN mkdir /GWAS_STUDY_FOLDER && mkdir /GENOTYPE_FOLDER
+
+COPY . /tmp
+
+RUN /env/bin/pip install . && rm -fr /tmp/*
+
+VOLUME ["/GWAS_STUDY_FOLDER","/GENOTYPE_FOLDER"]
+
+
+ENV GWAS_STUDY_FOLDER /GWAS_STUDY_FOLDER
+
+ENV GENOTYPE_FOLDER /GENOTYPE_FOLDER
+
+CMD ["/env/bin/gunicorn","gwasrv:api"]

LICENSE

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+The MIT License (MIT)
+
+Copyright (c) 2014 Ümit Seren
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of
+this software and associated documentation files (the "Software"), to deal in
+the Software without restriction, including without limitation the rights to
+use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of
+the Software, and to permit persons to whom the Software is furnished to do so,
+subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS
+FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR
+COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER
+IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

MANIFEST.in

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+include README.rst

README.rst

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+gwaportal-hdf5-server

gwasrv.py

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+import falcon
+import json
+import logging
+import os
+from pygwas.core import ld
+from pygwas.core import genotype
+from wsgiref import simple_server
+
+GWAS_STUDY_FOLDER=os.environ['GWAS_STUDY_FOLDER']
+GENOTYPE_FOLDER=os.environ['GENOTYPE_FOLDER']
+
+
+
+
+class RequireJSON(object):
+
+    def process_request(self, req, resp):
+        if not req.client_accepts_json:
+            raise falcon.HTTPNotAcceptable(
+                'This API only supports responses encoded as JSON.',
+                href='http://docs.examples.com/api/json')
+
+        if req.method in ('POST', 'PUT'):
+            if 'application/json' not in req.content_type:
+                raise falcon.HTTPUnsupportedMediaType(
+                    'This API only supports requests encoded as JSON.',
+                    href='http://docs.examples.com/api/json')
+
+
+class JSONTranslator(object):
+
+    def process_request(self, req, resp):
+        # req.stream corresponds to the WSGI wsgi.input environ variable,
+        # and allows you to read bytes from the request body.
+        #
+        # See also: PEP 3333
+        if req.content_length in (None, 0):
+            # Nothing to do
+            return
+
+        body = req.stream.read()
+        if not body:
+            raise falcon.HTTPBadRequest('Empty request body',
+                                        'A valid JSON document is required.')
+
+        try:
+            req.context['doc'] = json.loads(body.decode('utf-8'))
+
+        except (ValueError, UnicodeDecodeError):
+            raise falcon.HTTPError(falcon.HTTP_753,
+                                   'Malformed JSON',
+                                   'Could not decode the request body. The '
+                                   'JSON was incorrect or not encoded as '
+                                   'UTF-8.')
+
+    def process_response(self, req, resp, resource):
+        if 'result' not in req.context:
+            return
+
+        resp.body = json.dumps(req.context['result'])
+
+
+class LdForSnpResource(object):
+
+    def __init__(self, storage_path):
+        self.storage_path = storage_path
+        self.logger = logging.getLogger(__name__)
+
+    def on_get(self, req, resp,analysis_id,chr,position):
+        position = int(position)
+        ld_data = ld.get_ld_for_snp('%s/%s.hdf5' % (self.storage_path,analysis_id),chr,position)
+        req.context['result'] = ld_data
+        resp.status = falcon.HTTP_200
+
+class LdForRegionResource(object):
+    def __init__(self, storage_path):
+        self.storage_path = storage_path
+        self.logger = logging.getLogger(__name__)
+
+    def on_get(self, req, resp,analysis_id,chr,start_pos,end_pos):
+        start_pos = int(start_pos)
+        end_pos = int(end_pos)
+        ld_data = ld.get_ld_for_region('%s/%s.hdf5' % (self.storage_path,analysis_id),chr,start_pos,end_pos)
+        req.context['result'] = ld_data
+        resp.status = falcon.HTTP_200
+
+class LdExactForRegionResource(object):
+    def __init__(self, storage_path):
+        self.storage_path = storage_path
+        self.logger = logging.getLogger(__name__)
+
+    def on_post(self, req, resp,genotype_id,chr,position):
+        #filter nan
+        position = int(position)
+        genotypeData = genotype.load_hdf5_genotype_data('%s/%s/all_chromosomes_binary.hdf5' % (self.storage_path,genotype_id))
+        num_snps = int(req.params.get('num_snps',250))
+        accessions =  req.context.get('doc',[])
+
+        ld_data = ld.calculate_ld_for_region(genotypeData,accessions,chr,position,num_snps=num_snps)
+        req.context['result'] = ld_data
+        resp.status = falcon.HTTP_200
+
+
+
+api = falcon.API(middleware=[
+    RequireJSON(),
+    JSONTranslator(),
+])
+
+ldForSnp = LdForSnpResource(GWAS_STUDY_FOLDER)
+ldForRegion = LdForRegionResource(GWAS_STUDY_FOLDER)
+ldForExactRegion = LdExactForRegionResource(GENOTYPE_FOLDER)
+
+api.add_route('/analysis/{analysis_id}/ld/{chr}/{position}', ldForSnp)
+api.add_route('/analysis/{analysis_id}/ld/region/{chr}/{start_pos}/{end_pos}', ldForRegion)
+api.add_route('/ld/{genotype_id}/{chr}/{position}',ldForExactRegion)
+
+def main():
+    httpd = simple_server.make_server('127.0.0.1', 8000, api)
+    httpd.serve_forever()
+
+if __name__ == '__main__':
+    main()

setup.cfg

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+[bdist_wheel]
+# This flag says that the code is written to work on both Python 2 and Python
+# 3. If at all possible, it is good practice to do this. If you cannot, you
+# will need to generate wheels for each Python version that you support.
+universal=1

setup.py

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+from setuptools import setup, find_packages  # Always prefer setuptools over distutils
+from codecs import open  # To use a consistent encoding
+from os import path
+
+here = path.abspath(path.dirname(__file__))
+
+# Get the long description from the relevant file
+with open(path.join(here, 'README.rst'), encoding='utf-8') as f:
+    long_description = f.read()
+
+setup(
+    name='gwasrv',
+    version="0.0.1",
+    description='A RESTful backend for accessing GWAS HDF5 files GWA-Portal',
+    long_description=long_description,
+    url='https://github.com/timeu/gwaportal-gwas-server',
+    author='Uemit Seren',
+    author_email='[email protected]',
+    license='MIT',
+    classifiers=[
+        'Development Status :: 5 - Production/Stable',
+        'Intended Audience :: Developers',
+	'Topic :: Scientific/Engineering :: Bio-Informatics',
+        'License :: OSI Approved :: MIT License',
+        'Programming Language :: Python :: 2',
+        'Programming Language :: Python :: 2.6',
+        'Programming Language :: Python :: 2.7',
+        'Programming Language :: Python :: 3',
+        'Programming Language :: Python :: 3.2',
+        'Programming Language :: Python :: 3.3',
+        'Programming Language :: Python :: 3.4',
+    ],
+    keywords='GWAS hdf5 GWA-Portal',
+    py_modules=['gwasrv'],
+    install_requires=[
+        "PyGWAS >= 1.1.0",
+        "gunicorn >=19.0.0",
+        "falcon >= 0.3.0",
+    ],
+    entry_points={
+        'console_scripts': [
+            'gwasrv=gwasrv:main'
+        ],
+    },
+)
+