Merge pull request #1 from manics/devel

Refactor startup scripts, envvars for all omero parameter

50-config.py

@@ -0,0 +1,26 @@
+#!/usr/bin/env python
+# 1. Run .omero files from /opt/omero/server/config/
+# 2. Set omero config properties from CONFIG_ envvars
+#    Variable names should replace "." with "_" and "_" with "__"
+#    E.g. CONFIG_omero_web_public_enabled=false
+
+import os
+from subprocess import call
+from re import sub
+
+
+CONFIG_OMERO = '/opt/omero/server/config/omero-server-config-update.sh'
+OMERO = '/opt/omero/server/OMERO.server/bin/omero'
+
+if os.access(CONFIG_OMERO, os.X_OK):
+    rc = call([CONFIG_OMERO])
+    assert rc == 0
+
+for (k, v) in os.environ.iteritems():
+    if k.startswith('CONFIG_'):
+        prop = k[7:]
+        prop = sub('([^_])_([^_])', r'\1.\2', prop)
+        prop = sub('__', '_', prop)
+        value = v
+        rc = call([OMERO, 'config', 'set', '--', prop, value])
+        assert rc == 0

60-database.sh

@@ -0,0 +1,45 @@
+#!/bin/bash
+# 50-config.py or equivalent must be run first to set all omero.db.*
+# omero.db.host may require special handling since the default is
+# to use `--link postgres:db`
+
+set -eu
+
+omero=/opt/omero/server/OMERO.server/bin/omero
+omego=/opt/omero/omego/bin/omego
+cd /opt/omero/server
+
+CONFIG_omero_db_host=${CONFIG_omero_db_host:-}
+if [ -n "$CONFIG_omero_db_host" ]; then
+    DBHOST="$CONFIG_omero_db_host"
+else
+    DBHOST=db
+    $omero config set omero.db.host "$DBHOST"
+fi
+DBUSER="${CONFIG_omero_db_user:-omero}"
+DBNAME="${CONFIG_omero_db_name:-omero}"
+DBPASS="${CONFIG_omero_db_pass:-omero}"
+ROOTPASS="${ROOTPASS:-omero}"
+
+export PGPASSWORD="$DBPASS"
+
+i=0
+while ! psql -h "$DBHOST" -U "$DBUSER" "$DBNAME" >/dev/null 2>&1 < /dev/null; do
+    i=$(($i+1))
+    if [ $i -ge 50 ]; then
+        echo "$(date) - postgres:5432 still not reachable, giving up"
+        exit 1
+    fi
+    echo "$(date) - waiting for postgres:5432..."
+    sleep 1
+done
+echo "postgres connection established"
+
+psql -w -h "$DBHOST" -U "$DBUSER" "$DBNAME" -c \
+    "select * from dbpatch" 2> /dev/null && {
+    echo "Upgrading database"
+    $omego db upgrade --serverdir=OMERO.server
+} || {
+    echo "Initialising database"
+    $omego db init --rootpass "$ROOTPASS" --serverdir=OMERO.server
+}

99-run.sh

@@ -0,0 +1,8 @@
+#!/bin/bash
+
+set -eu
+
+omero=/opt/omero/server/OMERO.server/bin/omero
+cd /opt/omero/server
+echo "Starting OMERO.server"
+exec $omero admin start --foreground

Dockerfile

@@ -12,13 +12,15 @@ RUN yum -y install epel-release \
 ARG OMERO_VERSION=latest
 RUN ansible-playbook playbook.yml -e omero_server_release=$OMERO_VERSION
 
-USER omero-server
+RUN curl -L -o /usr/local/bin/dumb-init \
+    https://github.com/Yelp/dumb-init/releases/download/v1.2.0/dumb-init_1.2.0_amd64 && \
+    chmod +x /usr/local/bin/dumb-init
+ADD entrypoint.sh /usr/local/bin/
+ADD 50-config.py 60-database.sh 99-run.sh /startup/
 
-# default.xml may be modified at runtime for a multinode configuration
-RUN cp /opt/omero/server/OMERO.server/etc/templates/grid/default.xml /opt/omero/server/OMERO.server/etc/templates/grid/default.xml.orig
+USER omero-server
 
-EXPOSE 4061 4063 4064
+EXPOSE 4063 4064
 VOLUME ["/OMERO", "/opt/omero/server/OMERO.server/var"]
 
-ADD slave.cfg run.sh process_defaultxml.py /opt/omero/server/
-ENTRYPOINT ["/opt/omero/server/run.sh"]
+ENTRYPOINT ["/usr/local/bin/entrypoint.sh"]

README.md

@@ -0,0 +1,80 @@
+OMERO.server Docker
+===================
+
+A CentOS 7 based Docker image for OMERO.server.
+
+
+Running the images
+------------------
+
+To run the Docker images start a postgres DB:
+
+    docker run -d --name postgres -e POSTGRES_PASSWORD=postgres postgres
+
+Then run OMERO.server passing the database configuration parameters if they differ from the defaults.
+This example uses the default `postgres` system database for convenience, in practice you may want to create your own database.
+
+    docker run -d --name omero-server --link postgres:db
+        -e CONFIG_omero_db_user=postgres \
+        -e CONFIG_omero_db_pass=postgres \
+        -e CONFIG_omero_db_name=postgres \
+        -e ROOTPASS=omero-root-password \
+        -p 4063:4063 -p 4064:4064 \
+        openmicroscopy/omero-server
+
+
+Configuration variables
+-----------------------
+
+All [OMERO configuration properties](www.openmicroscopy.org/site/support/omero/sysadmins/config.html) can be set be defining environment variables `CONFIG_omero_property_name=`.
+Since `.` is not allowed in a variable name `.` must be replaced by `_`, and `_` by `__`, for example
+
+    -e CONFIG_omero_web_public_enabled=false
+
+
+Configuration files
+-------------------
+
+Additional configuration files for OMERO can be provided by mounting files into `/opt/omero/server/config/`.
+Files will be loaded with `omero load`.
+For example:
+
+    docker run -d -v
+        /config/extra.omero:/opt/omero/server/config/extra.omero:ro
+        openmicroscopy/omero-server
+
+Parameters required for initializing the server such as database configuration *must* be set using environment variables.
+
+
+Default volumes
+---------------
+
+- `/opt/omero/server/OMERO.server/var`: The OMERO.server `var` directory, including logs
+- `/OMERO`: The OMERO data directory
+
+
+Exposed ports
+-------------
+
+- 4063
+- 4064
+
+
+Example with named volumes
+--------------------------
+
+    docker volume create --name omero-db
+    docker volume create --name omero-data
+
+    docker run -d --name postgres -e POSTGRES_PASSWORD=postgres
+        -v omero-db:/var/lib/postgresql/data postgres
+    docker run -d --name omero-server --link postgres:db
+        <-e CONFIG_omero_db_ ...>
+        -v omero-data:/OMERO
+        -p 4063:4063 -p 4064:4064 openmicroscopy/omero-server
+
+
+Running without links
+---------------------
+
+As an alternative to running with `--link` the address of the database can be specified using the variable `CONFIG_omero_db_host`

entrypoint.sh

@@ -0,0 +1,10 @@
+#!/usr/local/bin/dumb-init /bin/bash
+
+set -e
+
+for f in /startup/*; do
+    if [ -f "$f" -a -x "$f" ]; then
+        echo "Running $f $@"
+        "$f" "$@"
+    fi
+done

playbook.yml

@@ -3,5 +3,10 @@
   - role: openmicroscopy.omero-server
   vars:
     ice_version: "3.6"
+    ice_install_devel: False
     omero_server_database_manage: False
     omero_server_systemd_setup: False
+    omero_server_system_uid: 1000
+    # You can reduce the size of the image by providing the URL to a
+    # precompiled Ice Python wheel
+    #ice_python_wheel:

requirements.yml

@@ -4,10 +4,10 @@
   version: 1.0.0
 
 - src: openmicroscopy.ice
-  version: 2.0.0
+  version: 2.1.0
 
 - src: openmicroscopy.java
-  version: 2.0.0
+  version: 2.0.1
 
 - src: openmicroscopy.omego
   version: 0.1.0
@@ -18,9 +18,8 @@
 - src: openmicroscopy.omero-python-deps
   version: 1.1.0
 
-- name: openmicroscopy.omero-server
-#  version: 2.0.0-m1
-  src: https://github.com/manics/ansible-role-omero-server/archive/devel.tar.gz
+- src: openmicroscopy.omero-server
+  version: 2.0.0-m2
 
 - src: openmicroscopy.postgresql
   version: 2.0.0