Feat/base peregrine (#110)

* feat(base-peregrine): alpine image changes

* feat(base-peregrine): unify uwsgi and nginx confs

* feat(base-peregrine): use generic dockerrun

* feat(base-peregrine): updated uwsgi.ini with timeouts

* feat(base-peregrine): remove extraneous deployment files

* feat(base-peregrine): update cdispyutils pin

Dockerfile

@@ -1,60 +1,27 @@
 # To run: docker run -v /path/to/wsgi.py:/var/www/peregrine/wsgi.py --name=peregrine -p 81:80 peregrine
-# To check running container: docker exec -it peregrine /bin/bash
+# To check running container: docker exec -it peregrine /bin/bash 
 
-FROM ubuntu:16.04
+FROM quay.io/cdis/py27base:pybase2-1.0.0
 
 ENV DEBIAN_FRONTEND=noninteractive
 
-RUN apt-get update && apt-get install -y --no-install-recommends \
-    build-essential \
-    curl \
-    git \
-    # dependency for cryptography
-    libffi-dev \
-    # dependency for pyscopg2 - which is dependency for sqlalchemy postgres engine
-    libpq-dev \
-    # dependency for cryptography
-    libssl-dev \
-    libxml2-dev \
-    libxslt1-dev \
-    nginx \
-    python2.7 \
-    python-dev \
-    python-pip \
-    python-setuptools \
-    sudo \
-    vim \
-    && python -m pip install --upgrade pip \
-    && python -m pip install --upgrade setuptools \
-    && python -m pip install --upgrade uwsgi \
-    && mkdir /var/www/peregrine \
-    && mkdir -p /var/www/.cache/Python-Eggs/ \
-    && chown www-data -R /var/www/.cache/Python-Eggs/ \
-    && mkdir /run/nginx/ \
-    && mkdir -m 075 /var/run/gen3 \
-    && chown root:www-data /var/run/gen3
+RUN mkdir /var/www/peregrine \
+    && chown www-data /var/www/peregrine
 
 COPY . /peregrine
 COPY ./deployment/uwsgi/uwsgi.ini /etc/uwsgi/uwsgi.ini
-COPY ./deployment/nginx/nginx.conf /etc/nginx/
-COPY ./deployment/nginx/uwsgi.conf /etc/nginx/sites-available/
 WORKDIR /peregrine
 
 RUN pip install -r requirements.txt \
     && COMMIT=`git rev-parse HEAD` && echo "COMMIT=\"${COMMIT}\"" >peregrine/version_data.py \
     && VERSION=`git describe --always --tags` && echo "VERSION=\"${VERSION}\"" >>peregrine/version_data.py \
     && cd /peregrine/src/gdcdictionary && DICTCOMMIT=`git rev-parse HEAD` && echo "DICTCOMMIT=\"${DICTCOMMIT}\"" >>/peregrine/peregrine/version_data.py \
     && DICTVERSION=`git describe --always --tags` && echo "DICTVERSION=\"${DICTVERSION}\"" >>/peregrine/peregrine/version_data.py \
-    && python setup.py install \
-    && rm /etc/nginx/sites-enabled/default \
-    && ln -s /etc/nginx/sites-available/uwsgi.conf /etc/nginx/sites-enabled/uwsgi.conf \
-    && ln -sf /dev/stdout /var/log/nginx/access.log \
-    && ln -sf /dev/stderr /var/log/nginx/error.log \
-    && chown www-data /var/www/peregrine
+    && python setup.py install
 
 EXPOSE 80
 
-WORKDIR /var/www/peregrine
+WORKDIR /var/www/peregrine 
 
-ENTRYPOINT [ "/bin/sh", "/peregrine/dockerrun.sh" ]
+ENTRYPOINT [ "/bin/sh", "/dockerrun.sh" ]
 CMD []

deployment/uwsgi/uwsgi.ini

@@ -5,13 +5,14 @@ buffer-size = 32768
 chmod-socket = 666
 master = true
 processes = 2
-harakiri-verbose = true
+harakiki-verbose = 20
 harakiri = 45
 http-timeout = 45
 socket-timeout = 45
 worker-reload-mercy = 45
 reload-mercy = 45
 mule-reload-mercy = 45
+disable-logging = true
 wsgi-file=/var/www/peregrine/wsgi.py
 plugins = python
 vacuum = true

requirements.txt

@@ -1,5 +1,4 @@
 defusedxml==0.5.0
-scipy==0.18.1
 SurvivalPy==1.0.2
 simplejson==3.8.1
 stopit==1.1.1
@@ -35,7 +34,7 @@ Flask-SQLAlchemy-Session==1.1
 -e git+https://git@github.com/uc-cdis/gdcdatamodel.git@1.3.6#egg=gdcdatamodel
 -e git+https://git@github.com/NCI-GDC/psqlgraph.git@5cddf49dd03a25bd4e553161d7ad7b9a6fe0ac0d#egg=psqlgraph
 -e git+https://git@github.com/NCI-GDC/cdisutils.git@8a8e599fdab5ade9bd8c586132d974a102e5d72d#egg=cdisutils
-cdispyutils==0.2.12
+cdispyutils==0.2.13
 -e git+https://git@github.com/uc-cdis/storage-client.git@0.1.1#egg=storageclient
 -e git+https://git@github.com/uc-cdis/dictionaryutils.git@2.0.4#egg=dictionaryutils
 -e git+https://git@github.com/uc-cdis/datamodelutils.git@0.4.0#egg=datamodelutils