Feat/logger - add stream handler (#33)

* fix(sqlite): create sqlite file on docker start

* feat(logger): add default stdout logger

* fix(setup): disallow zip

.travis.yml

@@ -7,6 +7,6 @@ python:
 sudo: false
 
 install:
-    - "pip install . --force --upgrade"
+    - "python setup.py install --force"
 
 script: "py.test -vv tests"

Dockerfile

@@ -1,11 +1,11 @@
 FROM ubuntu:16.04
 MAINTAINER CDIS <[email protected]>
 
-RUN apt-get update && apt-get install -y python-pip git python-dev libpq-dev apache2 libapache2-mod-wsgi vim \ 
+RUN apt-get update && apt-get install -y sudo python-pip git python-dev libpq-dev apache2 libapache2-mod-wsgi vim \ 
  && apt-get clean && apt-get autoremove \
  && rm -rf /var/lib/apt/lists/*
 ADD . /indexd
-RUN cd /indexd && pip install .
+RUN cd /indexd && python setup.py install
 
 RUN mkdir -p /var/www/indexd/ && chmod 777 /var/www/indexd && cp /indexd/wsgi.py /var/www/indexd/wsgi.py && cp /indexd/bin/indexd /var/www/indexd/indexd
 
@@ -35,6 +35,7 @@ EXPOSE 80
 
 WORKDIR /var/www/indexd
 
+
 # this allows container to be restarted
 RUN rm -f /var/run/apache2/apache2.pid
 

dockerrun.bash

@@ -1,4 +1,5 @@
 #!/bin/bash
 
 sed -i.bak -e 's/WSGIDaemonProcess indexd processes=1 threads=3/WSGIDaemonProcess indexd processes='${WSGI_PROCESSES:-1}' threads='${WSGI_THREADS:-3}'/g' /etc/apache2/sites-available/apache-indexd.conf
+cd /var/www/indexd; sudo -u www-data python wsgi.py
 /usr/sbin/apache2ctl -D FOREGROUND

indexd/app.py

@@ -4,7 +4,10 @@
 from .blueprint import blueprint as cross_blueprint
 import os
 import sys
+from cdispyutils.log import get_handler
+
 def app_init(app, settings=None):
+    app.logger.addHandler(get_handler())
     if not settings:
         from default_settings import settings 
     app.config.update(settings['config'])

setup.cfg

@@ -0,0 +1,2 @@
+[easy_install]
+zip_ok = false

setup.py

@@ -21,6 +21,10 @@
         'flask==0.10.1',
         'jsonschema==2.5.1',
         'sqlalchemy==1.0.8',
-	'psycopg2==2.6.1',
+    	'psycopg2==2.6.1',
+        'cdispyutils',
+    ],
+    dependency_links=[
+        "git+https://github.com/uc-cdis/[email protected]#egg=cdispyutils",
     ],
 )