Adding pysal to Docker

Dockerfile

@@ -0,0 +1,187 @@
+# PostgreSQL GIS stack
+#
+# This image includes the following tools
+# - PostgreSQL 9.5
+# - PostGIS 2.2 with raster, topology and sfcgal support
+# - OGR Foreign Data Wrapper
+# - PgRouting
+# - PDAL master
+# - PostgreSQL PointCloud version master
+#
+# Version 1.7
+
+FROM phusion/baseimage
+MAINTAINER Vincent Picavet, vincent.picavet@oslandia.com
+
+# Set correct environment variables.
+ENV HOME /root
+
+# Regenerate SSH host keys. baseimage-docker does not contain any, so you
+# have to do that yourself. You may also comment out this instruction; the
+# init system will auto-generate one during boot.
+RUN /etc/my_init.d/00_regen_ssh_host_keys.sh
+
+# Use baseimage-docker's init system.
+CMD ["/sbin/my_init"]
+
+
+RUN apt-get update && apt-get install -y wget ca-certificates
+
+# Use APT postgresql repositories for 9.5 version
+RUN echo "deb http://apt.postgresql.org/pub/repos/apt/ wheezy-pgdg main 9.5" > /etc/apt/sources.list.d/pgdg.list && wget --quiet -O - https://www.postgresql.org/media/keys/ACCC4CF8.asc | sudo apt-key add -
+
+# packages needed for compilation
+RUN apt-get update
+
+RUN apt-get install -y autoconf build-essential cmake docbook-mathml docbook-xsl libboost-dev libboost-thread-dev libboost-filesystem-dev libboost-system-dev libboost-iostreams-dev libboost-program-options-dev libboost-timer-dev libcunit1-dev libgdal-dev libgeos++-dev libgeotiff-dev libgmp-dev libjson0-dev libjson-c-dev liblas-dev libmpfr-dev libopenscenegraph-dev libpq-dev libproj-dev libxml2-dev postgresql-server-dev-9.5 xsltproc git build-essential wget
+
+RUN add-apt-repository ppa:fkrull/deadsnakes &&\
+    apt-get update &&\
+    apt-get install -y python3.2
+
+
+
+
+# application packages
+RUN apt-get install -y postgresql-9.5 postgresql-plpython-9.5
+
+
+# Download and compile CGAL
+RUN wget https://gforge.inria.fr/frs/download.php/file/32994/CGAL-4.3.tar.gz &&\
+    tar -xzf CGAL-4.3.tar.gz &&\
+    cd CGAL-4.3 &&\
+    mkdir build && cd build &&\
+    cmake .. &&\
+    make -j3 && make install
+
+# orig sfcgal method
+# download and compile SFCGAL
+# RUN git clone https://github.com/Oslandia/SFCGAL.git
+# RUN cd SFCGAL && cmake . && make -j3 && make install
+# # cleanup
+# RUN rm -Rf SFCGAL
+
+# andrewxhill fix for stable sfcgal version
+RUN wget https://github.com/Oslandia/SFCGAL/archive/v1.2.0.tar.gz
+RUN tar -xzf v1.2.0.tar.gz
+RUN cd SFCGAL-1.2.0 && cmake . && make -j 1 && make install
+RUN rm -Rf v1.2.0.tar.gz SFCGAL-1.2.0
+
+# download and install GEOS 3.5
+RUN wget http://download.osgeo.org/geos/geos-3.5.0.tar.bz2 &&\
+    tar -xjf geos-3.5.0.tar.bz2 &&\
+    cd geos-3.5.0 &&\
+    ./configure && make && make install &&\
+    cd .. && rm -Rf geos-3.5.0 geos-3.5.0.tar.bz2
+
+# Download and compile PostGIS
+RUN wget http://download.osgeo.org/postgis/source/postgis-2.2.0.tar.gz
+RUN tar -xzf postgis-2.2.0.tar.gz
+RUN cd postgis-2.2.0 && ./configure --with-sfcgal=/usr/local/bin/sfcgal-config --with-geos=/usr/local/bin/geos-config
+RUN cd postgis-2.2.0 && make && make install
+# cleanup
+RUN rm -Rf postgis-2.2.0.tar.gz postgis-2.2.0
+
+# Download and compile pgrouting
+RUN git clone https://github.com/pgRouting/pgrouting.git &&\
+    cd pgrouting &&\
+    mkdir build && cd build &&\
+    cmake -DWITH_DOC=OFF -DWITH_DD=ON .. &&\
+    make -j3 && make install
+# cleanup
+RUN rm -Rf pgrouting
+
+
+
+# Download and compile ogr_fdw
+RUN git clone https://github.com/pramsey/pgsql-ogr-fdw.git &&\
+    cd pgsql-ogr-fdw &&\
+    make && make install &&\
+    cd .. && rm -Rf pgsql-ogr-fdw
+
+# Compile PDAL
+RUN git clone https://github.com/PDAL/PDAL.git pdal
+RUN mkdir PDAL-build && \
+    cd PDAL-build && \
+    cmake ../pdal && \
+    make -j3 && \
+    make install
+# cleanup
+RUN rm -Rf pdal && rm -Rf PDAL-build
+
+# Compile PointCloud
+RUN git clone https://github.com/pramsey/pointcloud.git
+RUN cd pointcloud && ./autogen.sh && ./configure && make -j3 && make install
+# cleanup
+RUN rm -Rf pointcloud
+
+
+RUN git clone https://github.com/CartoDB/cartodb-postgresql.git &&\
+    cd cartodb-postgresql &&\
+    make all install &&\
+    cd .. && rm -Rf cartodb-postgresql
+
+# install pip
+
+RUN apt-get -y  install python-dev python-pip  liblapack-dev gfortran libyaml-dev
+
+RUN pip install numpy pandas scipy theano keras sklearn
+RUN pip install pysal
+
+# get compiled libraries recognized
+RUN ldconfig
+
+# clean packages
+
+# all -dev packages
+# RUN apt-get remove -y --purge autotools-dev libgeos-dev libgif-dev libgl1-mesa-dev libglu1-mesa-dev libgnutls-dev libgpg-error-dev libhdf4-alt-dev libhdf5-dev libicu-dev libidn11-dev libjasper-dev libjbig-dev libjpeg8-dev libjpeg-dev libjpeg-turbo8-dev libkrb5-dev libldap2-dev libltdl-dev liblzma-dev libmysqlclient-dev libnetcdf-dev libopenthreads-dev libp11-kit-dev libpng12-dev libpthread-stubs0-dev librtmp-dev libspatialite-dev libsqlite3-dev libssl-dev libstdc++-4.8-dev libtasn1-6-dev libtiff5-dev libwebp-dev libx11-dev libx11-xcb-dev libxau-dev libxcb1-dev libxcb-dri2-0-dev libxcb-dri3-dev libxcb-glx0-dev libxcb-present-dev libxcb-randr0-dev libxcb-render0-dev libxcb-shape0-dev libxcb-sync-dev libxcb-xfixes0-dev libxdamage-dev libxdmcp-dev libxerces-c-dev libxext-dev libxfixes-dev libxshmfence-dev libxxf86vm-dev linux-libc-dev manpages-dev mesa-common-dev libgcrypt11-dev unixodbc-dev uuid-dev x11proto-core-dev x11proto-damage-dev x11proto-dri2-dev x11proto-fixes-dev x11proto-gl-dev x11proto-input-dev x11proto-kb-dev x11proto-xext-dev x11proto-xf86vidmode-dev xtrans-dev zlib1g-dev
+
+# installed packages
+# RUN apt-get remove -y --purge autoconf build-essential cmake docbook-mathml docbook-xsl libboost-dev libboost-filesystem-dev libboost-timer-dev libcgal-dev libcunit1-dev libgdal-dev libgeos++-dev libgeotiff-dev libgmp-dev libjson0-dev libjson-c-dev liblas-dev libmpfr-dev libopenscenegraph-dev libpq-dev libproj-dev libxml2-dev postgresql-server-dev-9.5 xsltproc git build-essential wget
+
+# additional compilation packages
+# RUN apt-get remove -y --purge automake m4 make
+
+
+
+
+# ---------- SETUP --------------
+
+# add a baseimage PostgreSQL init script
+RUN mkdir /etc/service/postgresql
+ADD postgresql.sh /etc/service/postgresql/run
+
+# Adjust PostgreSQL configuration so that remote connections to the
+# database are possible.
+RUN echo "host all  all    0.0.0.0/0  md5" >> /etc/postgresql/9.5/main/pg_hba.conf
+
+# And add ``listen_addresses`` to ``/etc/postgresql/9.5/main/postgresql.conf``
+RUN echo "listen_addresses='*'" >> /etc/postgresql/9.5/main/postgresql.conf
+
+# Expose PostgreSQL
+EXPOSE 5432
+
+# Add VOLUMEs to allow backup of config, logs and databases
+VOLUME  ["/data", "/etc/postgresql", "/var/log/postgresql", "/var/lib/postgresql"]
+
+# Add pip
+
+
+# http://bugs.python.org/issue19846
+# > At the moment, setting "LANG=C" on a Linux system *fundamentally breaks Python 3*, and that's not OK.
+ENV LANG C.UTF-8
+
+
+# add database setup upon image start
+ADD pgpass /root/.pgpass
+RUN chmod 700 /root/.pgpass
+RUN mkdir -p /etc/my_init.d
+ADD init_db_script.sh /etc/my_init.d/init_db_script.sh
+ADD init_db.sh /root/init_db.sh
+ADD run_tests.sh /root/run_tests.sh
+ADD run_tests.sh /root/run_server.sh
+
+# ---------- Final cleanup --------------
+#
+# Clean up APT when done.
+# RUN apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*

README.md

@@ -7,6 +7,34 @@ CartoDB Spatial Analysis extension for PostgreSQL.
 * *pg* contains the PostgreSQL extension source code
 * *python* Python module
 
+## Running with Docker
+
+Crankshaft comes with a Dockerfile to build and run a sandboxed machine for testing
+and development.
+
+First you have to build the docker container
+
+    docker build -t crankshaft .
+
+To run the pg tests run
+
+    docker run -it --rm -v $(pwd):/crankshaft  crankshaft /root/run_tests.sh
+
+if there are failures it will dump the reasion to the screen.
+
+To run a server you can develop on run
+
+    docker run -it --rm -v $(pwd):/crankshaft -p $(docker-machine ip default):5432:5432 /root/run_server.sh
+
+and connect from you host using
+
+    psql -U pggis -h $(docker-machine ip default) -p 5432 -W
+
+the password is pggis
+
+
+
+
 ## Requirements
 
 * pip

init_db.sh

@@ -0,0 +1,77 @@
+#!/bin/bash
+
+# wait for pg server to be ready
+echo "Waiting for PostgreSQL to run..."
+sleep 1
+while ! /usr/bin/pg_isready -q
+do
+    sleep 1
+    echo -n "."
+done
+
+# PostgreSQL running
+echo "PostgreSQL running, initializing database."
+
+# PostgreSQL user
+#
+# create postgresql user pggis
+
+/sbin/setuser postgres /usr/bin/psql -c "CREATE USER pggis with SUPERUSER PASSWORD 'pggis';"
+/sbin/setuser postgres /usr/bin/psql -c "CREATE role publicuser;"
+# == Auto restore dumps ==
+#
+# If we find some postgresql dumps in /data/restore, then we load it
+# in new databases
+shopt -s nullglob
+for f in /data/restore/*.backup
+do
+	echo "Found database dump to restore : $f"
+    DBNAME=$(basename -s ".backup" "$f")
+    echo "Creating a new database $DBNAME.."
+    /usr/bin/psql -U pggis -h localhost -c "CREATE DATABASE $DBNAME WITH OWNER = pggis     ENCODING = 'UTF8'     TEMPLATE = template0    CONNECTION LIMIT = -1;" postgres
+    /usr/bin/psql -U pggis -h localhost -w -c "CREATE EXTENSION citext; CREATE EXTENSION pg_trgm; CREATE EXTENSION btree_gist; CREATE EXTENSION hstore; CREATE EXTENSION fuzzystrmatch; CREATE EXTENSION unaccent; CREATE EXTENSION postgres_fdw; CREATE EXTENSION pgcrypto; CREATE EXTENSION plpythonu; CREATE EXTENSION postgis; CREATE EXTENSION postgis_topology; CREATE EXTENSION pgrouting; CREATE EXTENSION pointcloud; CREATE EXTENSION pointcloud_postgis; CREATE EXTENSION postgis_sfcgal; drop type if exists texture; create type texture as (url text,uv float[][]);CREATE ROLE publicuser;" $DBNAME
+
+#    /usr/bin/psql -U pggis -h localhost -w -f /usr/share/postgresql/9.5/contrib/postgis-2.1/sfcgal.sql -d $DBNAME
+
+
+    echo "Restoring database $DBNAME.."
+    /usr/bin/pg_restore -U pggis -h localhost -d $DBNAME -w "$f"
+
+    echo "creating public user"
+    /usr/bin/psql -U pggis -h localhost -w -c "CREATE ROLE publicuser;"
+
+    echo "Restore done."
+
+done
+
+# == Auto restore SQL backups ==
+#
+# If we find some postgresql sql scripts /data/restore, then we load it
+# in new databases
+shopt -s nullglob
+for f in /data/restore/*.sql
+do
+	echo "Found database SQL dump to restore : $f"
+    DBNAME=$(basename -s ".sql" "$f")
+    echo "Creating a new database $DBNAME.."
+    /usr/bin/psql -U pggis -h localhost -c "CREATE DATABASE $DBNAME WITH OWNER = pggis     ENCODING = 'UTF8'     TEMPLATE = template0    CONNECTION LIMIT = -1;" postgres
+    /usr/bin/psql -U pggis -h localhost -w -c "CREATE EXTENSION citext; CREATE EXTENSION pg_trgm; CREATE EXTENSION btree_gist; CREATE EXTENSION hstore; CREATE EXTENSION fuzzystrmatch; CREATE EXTENSION unaccent; CREATE EXTENSION postgres_fdw; CREATE EXTENSION pgcrypto; CREATE EXTENSION plpythonu; CREATE EXTENSION postgis; CREATE EXTENSION postgis_topology; CREATE EXTENSION postgis_sfcgal; CREATE EXTENSION pgrouting; CREATE EXTENSION pointcloud; CREATE EXTENSION pointcloud_postgis; drop type if exists texture; create type texture as (url text,uv float[][]);" $DBNAME
+#    /usr/bin/psql -U pggis -h localhost -w -f /usr/share/postgresql/9.5/contrib/postgis-2.1/sfcgal.sql -d $DBNAME
+    echo "Restoring database $DBNAME.."
+    /usr/bin/psql -U pggis -h localhost -d $DBNAME -w -f "$f"
+    echo "Restore done."
+done
+
+# == create new database pggis ==
+echo "Creating a new empty database..."
+# create user and main database
+/usr/bin/psql -U pggis -h localhost -c "CREATE DATABASE pggis WITH OWNER = pggis     ENCODING = 'UTF8'     TEMPLATE = template0    CONNECTION LIMIT = -1;" postgres
+
+# activate all needed extension in pggis database
+/usr/bin/psql -U pggis -h localhost -w -c "CREATE EXTENSION citext; CREATE EXTENSION pg_trgm; CREATE EXTENSION btree_gist; CREATE EXTENSION hstore; CREATE EXTENSION fuzzystrmatch; CREATE EXTENSION unaccent; CREATE EXTENSION postgres_fdw; CREATE EXTENSION pgcrypto; CREATE EXTENSION plpythonu; CREATE EXTENSION postgis; CREATE EXTENSION postgis_topology; CREATE EXTENSION postgis_sfcgal; CREATE EXTENSION pgrouting; CREATE EXTENSION pointcloud; CREATE EXTENSION pointcloud_postgis; drop type if exists texture;
+create type texture as (url text,uv float[][]);" pggis
+#/usr/bin/psql -U pggis -h localhost -w -f /usr/share/postgresql/9.5/contrib/postgis-2.1/sfcgal.sql -d pggis
+
+echo "Database initialized. Connect from host with :"
+echo "psql -h localhost -p <PORT> -U pggis -W pggis"
+echo "Get <PORT> value with 'docker ps'"

init_db_script.sh

@@ -0,0 +1,3 @@
+#!/bin/sh
+# Script for my_init.d, so as to run database init without blocking
+/root/init_db.sh &

pgpass

@@ -0,0 +1 @@
+localhost:5432:*:pggis:pggis

postgresql.sh

@@ -0,0 +1,5 @@
+#!/bin/sh
+# `/sbin/setuser postgres` runs the given command as the user `postgres`.
+# If you omit that part, the command will be run as root.
+rm -rf /etc/ssl/private-copy; mkdir /etc/ssl/private-copy; mv /etc/ssl/private/* /etc/ssl/private-copy/; rm -r /etc/ssl/private; mv /etc/ssl/private-copy /etc/ssl/private; chmod -R 0700 /etc/ssl/private; chown -R postgres /etc/ssl/private
+exec /sbin/setuser postgres /usr/lib/postgresql/9.5/bin/postgres -D /var/lib/postgresql/9.5/main -c config_file=/etc/postgresql/9.5/main/postgresql.conf >> /var/log/postgresql.log 2>&1

run_server.sh

@@ -0,0 +1,14 @@
+#!/bin/bash
+/sbin/my_init &
+
+echo "Waiting for PostgreSQL to run..."
+sleep 1
+while ! /usr/bin/pg_isready -q
+do
+    sleep 1
+    echo -n "."
+done
+
+cd /crankshaft/pg
+make install
+fg

run_tests.sh

@@ -0,0 +1,23 @@
+#!/bin/bash
+/sbin/my_init &
+
+echo "Waiting for PostgreSQL to run..."
+sleep 1
+while ! /usr/bin/pg_isready -q
+do
+    sleep 1
+    echo -n "."
+done
+
+cd /crankshaft/pg
+make install
+PGUSER=pggis PGPASSOWRD=pggis PGHOST=localhost make installcheck
+
+
+
+if [ "$?" -eq "0" ]
+then
+  echo "PASSED"
+else
+  cat /crankshaft/pg/test/0.0.1/regression.diffs
+fi