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Merge pull request #942 from davebx/docker

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Enable dockerized toolshed tests.
This commit is contained in:
Martin Cech
2015-11-13 11:26:24 -05:00
parent 625d49e2de 1766b896e3
commit 2dcb92aa0e
7 changed files with 75 additions and 20 deletions
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lib/galaxy/model/orm/scripts.py
+5 -1
View File
@@ -19,6 +19,7 @@ DATABASE = {
'repo': 'lib/galaxy/model/migrate',
'old_config_file': 'universe_wsgi.ini',
'default_sqlite_file': './database/universe.sqlite',
'config_override': 'GALAXY_CONFIG_',
},
"tool_shed":
{
@@ -26,6 +27,7 @@ DATABASE = {
'config_file': 'config/tool_shed.ini',
'old_config_file': 'tool_shed_wsgi.ini',
'default_sqlite_file': './database/community.sqlite',
'config_override': 'TOOL_SHED_CONFIG_',
},
"install":
{
@@ -33,6 +35,7 @@ DATABASE = {
'old_config_file': 'universe_wsgi.ini',
'config_prefix': 'install_',
'default_sqlite_file': './database/install.sqlite',
'config_override': 'GALAXY_INSTALL_CONFIG_',
},
}
@@ -92,11 +95,12 @@ def get_config( argv, cwd=None ):
config_file = read_config_file_arg( argv, default, old_default )
repo = database_defaults[ 'repo' ]
config_prefix = database_defaults.get( 'config_prefix', DEFAULT_CONFIG_PREFIX )
config_override = database_defaults.get( 'config_override', 'GALAXY_CONFIG_' )
default_sqlite_file = database_defaults[ 'default_sqlite_file' ]
if cwd:
config_file = os.path.join( cwd, config_file )
properties = load_app_properties( ini_file=config_file )
properties = load_app_properties( ini_file=config_file, config_prefix=config_override )
if ("%sdatabase_connection" % config_prefix) in properties:
db_url = properties[ "%sdatabase_connection" % config_prefix ]
lib/galaxy/webapps/tool_shed/buildapp.py
+5
View File
@@ -16,6 +16,7 @@ from galaxy.webapps.util import build_template_error_formatters
from galaxy.webapps.tool_shed.framework.middleware import hg
from galaxy import util
from galaxy.config import process_is_uwsgi
from galaxy.util.properties import load_app_properties
log = logging.getLogger( __name__ )
@@ -49,6 +50,10 @@ def add_ui_controllers( webapp, app ):
def app_factory( global_conf, **kwargs ):
"""Return a wsgi application serving the root object"""
# Create the Galaxy tool shed application unless passed in
kwargs = load_app_properties(
kwds=kwargs,
config_prefix='TOOL_SHED_CONFIG_'
)
if 'app' in kwargs:
app = kwargs.pop( 'app' )
else:
test/docker/base/Dockerfile
+29 -11
View File
@@ -18,9 +18,15 @@ RUN apt-get update -y && apt-get install -y software-properties-common curl && \
} | debconf-set-selections && \
apt-get update -y && \
apt-get install -y libpq-dev postgresql postgresql-client postgresql-plpython-9.3 \
ansible postgresql-server-dev-9.3 wget mysql-server="${MYSQL_MAJOR}"* \
slurm-llnl libmunge-dev slurm-drmaa-dev \
nodejs && \
ansible postgresql-server-dev-9.3 wget mysql-server="${MYSQL_MAJOR}"* \
slurm-llnl libmunge-dev slurm-drmaa-dev ant atop axel bioperl cmake curl \
g++ gcc gfortran git-core htop iftop iotop ipython libffi-dev liblapack-dev \
libncurses5-dev libopenblas-dev libpam0g-dev libpq-dev libsparsehash-dev make \
mercurial nginx-extras nmon patch postgresql postgresql \
postgresql-client postgresql-plpython-9.3 python-boto python-dev \
python-prettytable python-psycopg2 python-virtualenv python-pip \
postgresql-server-dev-9.3 rsync slurm-drmaa-dev supervisor swig sysstat unzip \
wget zlib1g-dev nodejs && \
npm install -g grunt-contrib-qunit grunt grunt-cli casperjs phantomjs && \
apt-get autoremove -y && apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
@@ -35,20 +41,21 @@ ADD provision.yml /tmp/ansible/provision.yml
ENV GALAXY_ROOT=/galaxy
RUN mkdir /etc/galaxy && \
cd /tmp/ansible && \
mkdir roles && \
RUN mkdir /etc/galaxy && cd /tmp/ansible && mkdir roles && \
mkdir roles/galaxyprojectdotorg.galaxy-os && \
wget -qO- https://github.com/galaxyproject/ansible-galaxy-os/archive/master.tar.gz | tar -xzf- --strip-components=1 -C roles/galaxyprojectdotorg.galaxy-os && \
wget --quiet -O- https://github.com/galaxyproject/ansible-galaxy-os/archive/master.tar.gz | tar -xzf- --strip-components=1 -C roles/galaxyprojectdotorg.galaxy-os && \
mkdir roles/galaxyprojectdotorg.cloudman-database && \
wget -qO- https://github.com/galaxyproject/ansible-cloudman-database/archive/master.tar.gz | tar -xzf- --strip-components=1 -C roles/galaxyprojectdotorg.cloudman-database && \
wget --quiet -O- https://github.com/galaxyproject/ansible-cloudman-database/archive/master.tar.gz | tar -xzf- --strip-components=1 -C roles/galaxyprojectdotorg.cloudman-database && \
mkdir roles/galaxyprojectdotorg.galaxy && \
wget -qO- https://github.com/galaxyproject/ansible-galaxy/archive/master.tar.gz | tar -xzf- --strip-components=1 -C roles/galaxyprojectdotorg.galaxy && \
wget --quiet -O- https://github.com/galaxyproject/ansible-galaxy/archive/master.tar.gz | tar -xzf- --strip-components=1 -C roles/galaxyprojectdotorg.galaxy && \
mkdir roles/galaxyprojectdotorg.galaxy-extras && \
wget -qO- https://github.com/galaxyproject/ansible-galaxy-extras/archive/dynamic_uwsgi_config.tar.gz | tar -xzf- --strip-components=1 -C roles/galaxyprojectdotorg.galaxy-extras && \
wget --quiet -O- https://github.com/galaxyproject/ansible-galaxy-extras/archive/dynamic_uwsgi_config.tar.gz | tar -xzf- --strip-components=1 -C roles/galaxyprojectdotorg.galaxy-extras && \
mkdir roles/galaxyprojectdotorg.galaxy-toolshed && \
wget --quiet -O- https://github.com/galaxyproject/ansible-galaxy-toolshed/archive/master.tar.gz | tar -xzf- --strip-components=1 -C roles/galaxyprojectdotorg.galaxy-toolshed && \
ANSIBLE_FORCE_COLOR=1 PYTHONUNBUFFERED=1 ansible-playbook /tmp/ansible/provision.yml --tags=image -c local -e "@ansible_vars.yml" && \
ANSIBLE_FORCE_COLOR=1 PYTHONUNBUFFERED=1 ansible-playbook /tmp/ansible/provision.yml --tags=database -c local -e "@ansible_vars.yml" && \
ANSIBLE_FORCE_COLOR=1 PYTHONUNBUFFERED=1 ansible-playbook /tmp/ansible/provision.yml --tags=galaxy -c local -e "@ansible_vars.yml" && \
ANSIBLE_FORCE_COLOR=1 PYTHONUNBUFFERED=1 ansible-playbook /tmp/ansible/provision.yml --tags=toolshed -c local -e "@ansible_vars.yml" && \
apt-get autoremove -y && apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
RUN cd $GALAXY_ROOT && \
@@ -59,7 +66,16 @@ RUN cd $GALAXY_ROOT && \
echo "Prepopuating sqlite database" && \
GALAXY_CONFIG_DATABASE_CONNECTION="sqlite:////opt/galaxy/galaxy.sqlite" sh create_db.sh && \
sh /opt/galaxy/start_mysql.sh && \
GALAXY_CONFIG_DATABASE_CONNECTION="mysql://galaxy:galaxy@localhost/galaxy?unix_socket=/var/run/mysqld/mysqld.sock" sh create_db.sh
echo "Prepopuating mysql database" && \
GALAXY_CONFIG_DATABASE_CONNECTION="mysql://galaxy:galaxy@localhost/galaxy?unix_socket=/var/run/mysqld/mysqld.sock" sh create_db.sh && \
echo "Prepopulating toolshed postgres database" && \
su -c '/usr/lib/postgresql/9.3/bin/pg_ctl -o "-F" start -D /opt/galaxy/db' postgres && \
GALAXY_CONFIG_DATABASE_CONNECTION="postgresql://root@localhost:5930/toolshed" sh create_db.sh tool_shed && \
echo "Prepopuating toolshed sqlite database" && \
GALAXY_CONFIG_DATABASE_CONNECTION="sqlite:////opt/galaxy/toolshed.sqlite" sh create_db.sh tool_shed && \
sh /opt/galaxy/start_mysql.sh && \
echo "Prepopuating toolshed mysql database" && \
GALAXY_CONFIG_DATABASE_CONNECTION="mysql://galaxy:galaxy@localhost/toolshed?unix_socket=/var/run/mysqld/mysqld.sock" sh create_db.sh tool_shed
# bcftools for Galaxy.
RUN mkdir -p /tmp/install && \
@@ -72,6 +88,8 @@ RUN mkdir -p /tmp/install && \
cd && rm -rf /tmp/install
ADD run_test_wrapper.sh /usr/local/bin/run_test_wrapper.sh
EXPOSE :9009
EXPOSE :8080
EXPOSE :80
ENTRYPOINT ["/bin/bash", "/usr/local/bin/run_test_wrapper.sh"]
test/docker/base/ansible_vars.yml
+10 -1
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@@ -21,7 +21,6 @@ galaxy_manage_database: no
galaxy_user_name: "root"
galaxy_extras_install_packages: true
galaxy_job_conf_path: "/etc/galaxy/job_conf.xml"
galxy_config_file: "/galaxy/config/galaxy.ini.sample"
galaxy_web_processes: 1
galaxy_handler_processes: 2
@@ -37,3 +36,13 @@ galaxy_extras_config_supervisor: true
galaxy_extras_config_galaxy_root: false
galaxy_extras_config_galaxy_job_metrics: false
galaxy_extras_config_uwsgi: true
manage_shed_db: yes
galaxy_toolshed_manage_static_setup: yes
galaxy_toolshed_manage_database: no
galaxy_toolshed_server_dir: "/galaxy"
galaxy_toolshed_venv_dir: "{{ galaxy_venv_dir }}"
galaxy_toolshed_config_file: "{{ galaxy_toolshed_server_dir }}/config/tool_shed.ini"
galaxy_toolshed_config_templates:
- {dest: '{{ galaxy_toolshed_config_file }}', src: tool_shed.ini.j2}
test/docker/base/provision.yml
+3 -2
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@@ -11,5 +11,6 @@
- role: galaxyprojectdotorg.galaxy
sudo: yes
tags: galaxy
- role: galaxyprojectdotorg.galaxy-toolshed
sudo: yes
tags: toolshed
test/docker/base/run_test_wrapper.sh
+10
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@@ -6,19 +6,27 @@ if [ "$GALAXY_TEST_DATABASE_TYPE" = "postgres" ];
then
su -c '/usr/lib/postgresql/9.3/bin/pg_ctl -o "-F" start -D /opt/galaxy/db' postgres
sleep 3
GALAXY_TEST_INSTALL_DB_MERGED="true"
GALAXY_TEST_DBURI="postgres://root@localhost:5930/galaxy?client_encoding=utf8"
TOOL_SHED_TEST_DBURI="postgres://root@localhost:5930/toolshed"
elif [ "$GALAXY_TEST_DATABASE_TYPE" = "mysql" ];
then
sh /opt/galaxy/start_mysql.sh
GALAXY_TEST_INSTALL_DB_MERGED="true"
GALAXY_TEST_DBURI="mysql://galaxy:galaxy@localhost/galaxy?unix_socket=/var/run/mysqld/mysqld.sock"
TOOL_SHED_TEST_DBURI="mysql://galaxy:galaxy@localhost/toolshed?unix_socket=/var/run/mysqld/mysqld.sock"
elif [ "$GALAXY_TEST_DATABASE_TYPE" = "sqlite" ];
then
GALAXY_TEST_INSTALL_DB_MERGED="true"
GALAXY_TEST_DBURI="sqlite:////opt/galaxy/galaxy.sqlite"
TOOL_SHED_TEST_DBURI="sqlite:////opt/galaxy/toolshed.sqlite"
else
echo "Unknown database type"
exit 1
fi
export GALAXY_TEST_DBURI
export TOOL_SHED_TEST_DBURI
export GALAXY_TEST_INSTALL_DB_MERGED
cd /galaxy
GALAXY_CONFIG_OVERRIDE_DATABASE_CONNECTION="$GALAXY_TEST_DBURI";
@@ -37,6 +45,7 @@ then
else
GALAXY_CONFIG_MASTER_API_KEY=${GALAXY_CONFIG_MASTER_API_KEY:-"testmasterapikey"}
GALAXY_CONFIG_FILE=${GALAXY_CONFIG_FILE:-config/galaxy.ini.sample}
TOOL_SHED_CONFIG_FILE=${GALAXY_CONFIG_FILE:-config/tool_shed.ini.sample}
GALAXY_CONFIG_CHECK_MIGRATE_TOOLS=false
if [ -z "$GALAXY_MULTI_PROCESS" ];
then
@@ -49,6 +58,7 @@ else
export GALAXY_CONFIG_MASTER_API_KEY
export GALAXY_CONFIG_FILE
export TOOL_SHED_CONFIG_FILE
export GALAXY_CONFIG_CHECK_MIGRATE_TOOLS
export GALAXY_CONFIG_JOB_CONFIG_FILE
export GALAXY_CONFIG_FILE_PATH
test/docker/base/start_mysql.sh
+13 -5
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@@ -4,6 +4,7 @@ set -e
MYSQL_USER=galaxy
MYSQL_PASSWORD=galaxy
MYSQL_DATABASE=galaxy
SHED_MYSQL_DATABASE=toolshed
mkdir -p /var/lib/mysql
chown -R mysql:mysql /var/lib/mysql
@@ -22,15 +23,22 @@ cat > "$tempSqlFile" <<-EOSQL
EOSQL
if [ "$MYSQL_DATABASE" ]; then
echo "CREATE DATABASE IF NOT EXISTS \`$MYSQL_DATABASE\` ;" >> "$tempSqlFile"
echo "CREATE DATABASE IF NOT EXISTS \`$MYSQL_DATABASE\` ;" >> "$tempSqlFile"
fi
if [ "$SHED_MYSQL_DATABASE" ]; then
echo "CREATE DATABASE IF NOT EXISTS \`$SHED_MYSQL_DATABASE\` ;" >> "$tempSqlFile"
fi
if [ "$MYSQL_USER" -a "$MYSQL_PASSWORD" ]; then
echo "CREATE USER '$MYSQL_USER'@'%' IDENTIFIED BY '$MYSQL_PASSWORD' ;" >> "$tempSqlFile"
echo "CREATE USER '$MYSQL_USER'@'%' IDENTIFIED BY '$MYSQL_PASSWORD' ;" >> "$tempSqlFile"
if [ "$MYSQL_DATABASE" ]; then
echo "GRANT ALL ON \`$MYSQL_DATABASE\`.* TO '$MYSQL_USER'@'%' ;" >> "$tempSqlFile"
fi
if [ "$MYSQL_DATABASE" ]; then
echo "GRANT ALL ON \`$MYSQL_DATABASE\`.* TO '$MYSQL_USER'@'%' ;" >> "$tempSqlFile"
fi
if [ "$SHED_MYSQL_DATABASE" ]; then
echo "GRANT ALL ON \`$SHED_MYSQL_DATABASE\`.* TO '$MYSQL_USER'@'%' ;" >> "$tempSqlFile"
fi
fi
echo 'FLUSH PRIVILEGES ;' >> "$tempSqlFile"