initial commit

docker/Dockerfile

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+####
+#### This docker file is trying to run and install AmiGO/GOlr
+#### minimally as root on localhost:
+####
+#### Build (from repo root):
+####   docker build -t geneontology/amigo-standalone:latest -t geneontology/amigo-standalone:`git log | head -1 | cut -d ' ' -f 2`_`date +%Y-%m-%dT%H%M%S` docker/amigo-standalone
+####
+#### To push:
+####  docker push geneontology/amigo-standalone:latest
+####  docker push geneontology/amigo-standalone:636b4aea877d2585be8d5e2d26f1a59422e43c45_2019-06-05T195931
+####
+#### Run with ports exposed:
+####  docker run -p 8080:8080 -p 9999:9999 -v /tmp/srv-solr-data:/srv/solr/data -t geneontology/amigo-standalone:636b4aea877d2585be8d5e2d26f1a59422e43c45_2019-06-05T195931
+####
+#### Check on AmiGO and with port exposed:
+####  docker run -it -p 9999:9999 -p 8080:8080 -v /tmp/srv-solr-data:/srv/solr/data geneontology/amigo-standalone:636b4aea877d2585be8d5e2d26f1a59422e43c45_2019-06-05T195931 /bin/bash
+####
+
+## Grab the latest(?) Ubuntu image.
+FROM ubuntu:18.04
+
+## Quiet it down a little bit.
+ENV DEBIAN_FRONTEND noninteractive
+ENV TERM linux
+
+###
+### Packages, repos, and location.
+###
+
+## Get the system updated and QoL.
+RUN apt-get -qq update && apt-get -qq -y install \
+	libterm-readline-gnu-perl apt-utils \
+	software-properties-common netcat rsync \
+	build-essential wget curl pigz subversion \
+	less mg byobu htop iotop di git make kwalify vim \
+	libcgi-application-perl \
+	libcgi-application-plugin-session-perl \
+	libcgi-application-plugin-tt-perl \
+	libcgi-application-server-perl \
+	libclone-perl libconfig-yaml-perl libdbi-perl \
+	libdbd-sqlite3-perl libdbd-mysql-perl \
+	libdata-formvalidator-perl libossp-uuid-perl \
+	libfile-type-perl libfile-slurp-perl \
+	libfreezethaw-perl libgraph-perl libgraphviz-perl \
+	libjson-xs-perl liburi-perl libwww-mechanize-perl \
+	liburi-encode-perl libxml-libxml-perl libxml-xpath-perl \
+	dh-make-perl apache2 openjdk-8-jdk openjdk-8-jre jetty9
+
+## AmiGO weirdness.
+ADD docker/libsql-tokenizer-perl_0.24-2_all.deb /tmp/libsql-tokenizer-perl_0.24-2_all.deb
+RUN dpkg -i /tmp/libsql-tokenizer-perl_0.24-2_all.deb
+
+## Node.
+RUN curl -sL https://deb.nodesource.com/setup_8.x | bash -
+RUN apt-get install -y nodejs
+
+## Grab the AmiGO/GOlr repo and change context.
+RUN mkdir -p /srv
+USER root:www-data
+# RUN git clone https://github.com/geneontology/amigo.git --branch master --single-branch /srv/amigo
+ADD . /srv/amigo
+WORKDIR /srv/amigo
+# RUN git pull
+USER root
+
+###
+### Apache.
+###
+
+## Get apache setup as a generic worker. Installation grouped above.
+RUN a2dismod mpm_event mpm_worker
+RUN a2enmod mpm_prefork
+RUN a2dismod cgid mpm_event mpm_worker
+RUN a2enmod alias mpm_prefork cgi rewrite proxy proxy_http proxy_html macro headers xml2enc
+
+###
+### GOlr/Jetty.
+###
+
+## GOlr/Jetty setup. Installation grouped above.
+RUN cp ./golr/solr/solr.war /var/lib/jetty9/webapps/
+RUN chown jetty /var/lib/jetty9/webapps/solr.war
+RUN chgrp adm /var/lib/jetty9/webapps/solr.war
+RUN cp ./golr/jetty/jetty /etc/default/jetty9
+RUN mkdir -p /srv/solr/data
+RUN mkdir -p /srv/solr/conf
+RUN cp ./golr/solr/conf/schema.xml /srv/solr/conf/schema.xml
+RUN cp ./golr/solr/conf/solrconfig.xml /srv/solr/conf/solrconfig.xml
+RUN chown -R jetty /srv/solr/
+RUN chgrp -R adm /srv/solr/
+
+## Custom runtime locations for jetty9/solr for the Docker environment.
+RUN mkdir -p /tmp/jetty9
+RUN chown -R jetty /tmp/jetty9
+RUN chgrp -R adm /tmp/jetty9
+
+###
+### AmiGO.
+###
+
+## Final Apache setup.
+RUN cp ./conf/examples/apache2.18_04.localhost_root.conf /etc/apache2/sites-available/001-inline-amigo.conf
+RUN cp /srv/amigo/conf/examples/apache2.ports.conf /etc/apache2/ports.conf
+RUN a2ensite 001-inline-amigo
+
+## Get AmiGO docker config into place.
+RUN cp ./conf/examples/amigo.yaml.localhost_docker_loader ./conf/amigo.yaml
+
+## AmiGO install.
+USER root:www-data
+RUN npm install
+RUN ./node_modules/.bin/gulp install
+USER root
+
+## The root environment seems to do something funny with the perl5
+## execution path; modify tp make sure everybody can get at it.
+RUN sed -i s,config.pl,/srv/amigo/perl/bin/config.pl,g /srv/amigo/perl/bin/*
+RUN sed -i s,config.pl,/srv/amigo/perl/bin/config.pl,g /srv/amigo/perl/lib/AmiGO.pm
+
+###
+### Finally.
+###
+
+##
+EXPOSE 8080 9999
+#WORKDIR /usr/share/jetty9
+
+#ADD docker/run-apache-solr.sh /tmp/run-apache-solr.sh
+#RUN ["chmod", "+x", "/tmp/run-apache-solr.sh"]
+#CMD "/tmp/run-apache-solr.sh"
+
+COPY ./docker/entrypoint.sh /
+RUN chmod +x /entrypoint.sh
+ENTRYPOINT [ "/entrypoint.sh" ]
+CMD ["tail", "-f", "/dev/null" ]

docker/entrypoint.sh

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+#!/usr/bin/env bash
+
+###
+### AmiGO on Apache first.
+###
+
+if [ -z $GULP_INSTALL ]; then
+   cp ./conf/examples/amigo.yaml.localhost_docker_loader ./conf/amigo.yaml
+   npm install
+   ./node_modules/.bin/gulp install
+   sed -i s,config.pl,/srv/amigo/perl/bin/config.pl,g /srv/amigo/perl/bin/*
+   sed -i s,config.pl,/srv/amigo/perl/bin/config.pl,g /srv/amigo/perl/lib/AmiGO.pm
+fi
+
+echo "Starting the apache2 server with amigo installed"
+cd /srv/amigo
+/etc/init.d/apache2 start
+
+echo "Launched, waiting for server response"
+
+COUNTER=0
+while ! nc -z localhost 9999; do
+  echo "Not found on 9999, rechecking after 2 sec"
+  sleep 2 # wait for 1 second before check again
+  COUNTER=$((COUNTER + 1))
+
+  if [ $COUNTER -gt 10 ]
+  then
+      echo "Something is wrong, exiting"
+      exit 1 ;
+  fi
+done
+
+echo "Server found on 9999"
+
+SOLR_MEM=${GOLR_SOLR_MEMORY:="4G"}
+
+echo "Starting the jetty server with Solr installed ($SOLR_MEM)"
+cd /usr/share/jetty9
+java -Xms$SOLR_MEM -Xmx$SOLR_MEM -DentityExpansionLimit=8172000 -Djava.awt.headless=true -Dsolr.solr.home=/srv/solr -Djava.io.tmpdir=/tmp/jetty9 -Djava.library.path=/usr/lib -Djetty.home=/usr/share/jetty9 -Djetty.logs=/var/log/jetty9 -Djetty.state=/tmp/jetty.state -Djetty.host=0.0.0.0 -Djetty.port=8080 -jar /usr/share/jetty9/start.jar --daemon /etc/jetty9/jetty-started.xml &
+
+cd /srv/amigo
+exec "$@"

provision/build_image.yaml

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+- name: build docker images
+  hosts: all
+  vars_files:
+  - vars.yaml
+  vars:
+    repo_dir: '{{ stage_dir }}/amigo'
+
+  tasks:
+  - name: Checkout repos
+    git:
+     repo: '{{ repo }}'
+     dest: '{{ repo_dir }}'
+     version: '{{ branch }}'
+     force: yes 
+
+  - name: build image
+    shell: "docker build -f {{ repo_dir }}/docker/Dockerfile -t 'amigo:{{ tag }}' {{ repo_dir }}"

provision/vars.yaml

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+---
+###############
+# Point stage_dir to a different locatiom. By default it will reside in the current directory.
+##############
+stage_dir: "{{ lookup('env', 'PWD') }}/stage_dir"
+branch: master
+tag: latest
+repo: https://github.com/geneontology/amigo.git