Merge from master

.dockerignore

@@ -1,5 +1,5 @@
 Dockerfile
-.git
 .dockerignore
+./build
 *.swp
 ga4gh-env

.travis.yml

@@ -30,8 +30,9 @@ before_script:
 
 # run_tests.py runs everything under the script: tag so only put commands
 # under it that we want to run (and want to be able to run) as local tests
-script:
-  - flake8 *.py tests ga4gh scripts --exclude=ez_setup.py,ga4gh/*_pb2.py
+script: 
+  - flake8 *.py tests ga4gh scripts
+              --exclude=ez_setup.py,ga4gh/*_pb2.py,ga4gh/datamodel/obo_parser.py
   - nosetests --with-coverage --cover-package ga4gh
               --cover-inclusive --cover-min-percentage 80
               --cover-branches --cover-erase

Dockerfile

@@ -1,21 +1,61 @@
 ############################################################
 ## Dockerfile to build the ga4gh server on mod_wsgi-express
 ## Configurable to use a local dataset
-## Based on mod_wsgi-docker
-## Results of this build are available from Dockerhub as afirth/ga4gh_server_apache:prod
 ############################################################
-FROM grahamdumpleton/mod-wsgi-docker:python-2.7-onbuild
+FROM ubuntu
 
-# File Author / Maintainer
-MAINTAINER Alastair Firth
+# Originally created by Steve Hershman GitHub @hershman
+# previously maintained by Alastair Firth
+# currently maintained by Maciek Smuga-Otto at UCSC Genomics Institute
+MAINTAINER Maciek Smuga-Otto <[email protected]>
 
-# Place the config, if an existing config is not in place
-ADD deploy/config.py /app/ga4gh/docker_config.py
-RUN cp --no-clobber /app/ga4gh/docker_config.py /app/ga4gh/config.py
+# Update the sources list
+RUN apt-get update
 
-# Pass '-e GA4GH_DATA_SOURCE=/container/data/path' and '-v /host/data/path:/container/data/path:ro' to docker run to mount local data
-# See docs for more info
+# Install packages
+RUN apt-get install -y tar git curl wget dialog net-tools build-essential \
+    python python-dev python-distribute python-pip zlib1g-dev \
+    apache2 libapache2-mod-wsgi libxslt1-dev libffi-dev libssl-dev
 
-CMD [ "--working-directory", "ga4gh", \
-      "--log-to-terminal", \
-      "ga4gh/application.wsgi" ]
+# Enable wsgi module
+RUN a2enmod wsgi
+
+# Create cache directories
+RUN mkdir /var/cache/apache2/python-egg-cache && \
+    chown www-data:www-data /var/cache/apache2/python-egg-cache/
+
+# build the GA4GH server
+RUN mkdir -p /srv/ga4gh/server
+WORKDIR /srv/ga4gh/server
+
+# Configure the python requirements
+# Do this as a separate step prior to the build so that changes
+# to the GA4GH Server codebase do not trigger a full rebuild of the
+# pip requirements.
+COPY requirements.txt /srv/ga4gh/server/
+RUN pip install -r requirements.txt
+
+# Install the code
+COPY . /srv/ga4gh/server/
+RUN python setup.py install
+
+# Write new apache config
+COPY deploy/001-ga4gh.conf /etc/apache2/sites-available/001-ga4gh.conf
+
+# Write application.wsgi
+COPY deploy/application.wsgi /srv/ga4gh/application.wsgi
+COPY deploy/config.py /srv/ga4gh/config.py
+
+# Configure apache to serve GA4GH site
+WORKDIR /etc/apache2/sites-enabled
+RUN rm -f 000-default.conf && ln -s /etc/apache2/sites-available/001-ga4gh.conf 001-ga4gh.conf
+
+# Open port 80 for HTTP
+EXPOSE 80
+
+# Prepare container for deployment
+# The directory that the user will land in when executing an interactive shell
+WORKDIR /srv/ga4gh/server
+
+# Default action: Bring up a webserver instance to run as a daemon
+CMD ["/usr/sbin/apache2ctl", "-D", "FOREGROUND"]

deploy/001-ga4gh.conf

@@ -0,0 +1,14 @@
+<VirtualHost *:80>
+    ServerAdmin webmaster@localhost
+    DocumentRoot /var/www/html
+    ErrorLog ${APACHE_LOG_DIR}/error.log
+    CustomLog ${APACHE_LOG_DIR}/access.log combined
+    WSGIDaemonProcess ga4gh python-eggs=/var/cache/apache2/python-egg-cache \
+        processes=10 threads=1
+    WSGIScriptAlias /ga4gh /srv/ga4gh/application.wsgi
+    <Directory /srv/ga4gh>
+        WSGIProcessGroup ga4gh
+        WSGIApplicationGroup %{GLOBAL}
+        Require all granted
+    </Directory>
+</VirtualHost>

deploy/application.wsgi

@@ -2,4 +2,4 @@
 
 from ga4gh.frontend import app as application
 import ga4gh.frontend as frontend
-frontend.configure("/app/ga4gh/config.py")
+frontend.configure("/srv/ga4gh/config.py")

deploy/config.py

@@ -1,14 +1,3 @@
-# Configuration file for server, including Flask, see configuration documentation
-# for details
-# This file needs to be copied to /app/ga4gh/config.py by default
 import os
-
-#TODO this logic could move to frontend.configure() or BaseConfig
-# For docker, if/when a default is set in serverconfig.py, run -v /localdata:/default-path
-# If the env variable GA4GH_DATA_SOURCE is set, use that path. Otherwise, use the default path
-DATA_SOURCE = os.getenv('GA4GH_DATA_SOURCE', "/ga4gh-example-data")
-
-# If the env variable GA4GH_DEBUG is set, use that. Otherwise, use the empty string (False)
-# Enable with True.
-# WARNING: this enables Flask debugging and is insecure.
+DATA_SOURCE = os.getenv('GA4GH_DATA_SOURCE', "/data/repo.db")
 DEBUG = os.getenv('GA4GH_DEBUG', "")

docs/conf.py

@@ -35,6 +35,7 @@
     'sphinx.ext.autodoc',
     'sphinx.ext.intersphinx',
     'sphinx.ext.todo',
+    'sphinxarg.ext',
 ]
 
 # Add any paths that contain templates here, relative to this directory.