omero-grid now builds separate master and slave images only

This is based on ome/omero-server-docker#1

Author: manics

build.py

@@ -0,0 +1,13 @@
+#!/bin/bash
+
+set -eu
+
+omero=/opt/omero/server/OMERO.server/bin/omero
+cd /opt/omero/server
+
+# Args are the servers to run, default (no args) is to run all
+./process_defaultxml.py OMERO.server/etc/templates/grid/default.xml.orig \
+    "$@" > OMERO.server/etc/templates/grid/default.xml
+
+MASTER_IP=$(hostname -i)
+$omero config set omero.master.host "$MASTER_IP"

master/70-grid-xml.sh

@@ -0,0 +1,15 @@
+# TODO: Switch to openmicroscopy/omero-server when it's merged
+FROM test-omero-server
+MAINTAINER [email protected]
+
+USER root
+ADD process_defaultxml.py /opt/omero/server/
+ADD 70-grid-xml.sh /startup/
+
+USER omero-server
+
+# 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
+
+# TODO: Don't expose 4061 (internal links only)
+EXPOSE 4061 4063 4064

master/Dockerfile

@@ -0,0 +1,41 @@
+#!/bin/bash
+
+set -eu
+
+TARGET="${1}"
+if [ -z "$TARGET" ]; then
+    echo "ERROR: Slave-name required"
+    exit 2
+fi
+
+omero=/opt/omero/server/OMERO.server/bin/omero
+cd /opt/omero/server
+
+CONFIG_omero_master_host=${CONFIG_omero_master_host:-}
+if [ -n "$CONFIG_omero_master_host" ]; then
+    MASTER_ADDR="$CONFIG_omero_master_host"
+else
+    MASTER_ADDR=master
+    $omero config set omero.master.host "$MASTER_ADDR"
+fi
+
+SLAVE_ADDR=$(hostname -i)
+
+# Is this needed on a slave?
+#if stat -t /config/* > /dev/null 2>&1; then
+#    for f in /config/*; do
+#        echo "Loading $f"
+#        $omero load "$f"
+#    done
+#fi
+
+echo "Master addr: $MASTER_ADDR Slave addr: $SLAVE_ADDR"
+sed -e "s/@omero.slave.host@/$SLAVE_ADDR/" -e "s/@slave.name@/$TARGET/" \
+    slave.cfg > OMERO.server/etc/$TARGET.cfg
+grep '^Ice.Default.Router=' OMERO.server/etc/ice.config || \
+    echo Ice.Default.Router= >> OMERO.server/etc/ice.config
+sed -i -r "s|^(Ice.Default.Router=).*|\1OMERO.Glacier2/router:tcp -p 4063 -h $MASTER_ADDR|" \
+    OMERO.server/etc/ice.config
+
+echo "Starting node $TARGET"
+exec $omero node $TARGET start --foreground

omero-grid/process_defaultxml.py renamed to master/process_defaultxml.py

@@ -0,0 +1,15 @@
+# TODO: Switch to openmicroscopy/omero-server when it's merged
+FROM test-omero-server
+MAINTAINER [email protected]
+
+USER root
+ADD slave.cfg /opt/omero/server/
+# Don't configure database in a slave
+RUN rm /startup/60-database.sh
+# Replace existing 99-run.sh
+ADD 99-run.sh /startup/
+
+USER omero-server
+
+# TODO: Not needed?
+EXPOSE 4063 4064

slave/99-run.sh

@@ -2,19 +2,15 @@
 
 set -e
 set -u
-set -x
 
-PREFIX=omero-grid-test
-IMAGE=omero-grid:$PREFIX
-IMAGEWEB=omero-grid-web:$PREFIX
-BUILD=${BUILD:-}
-CLEAN=${CLEAN:-y}
+PREFIX=test
+IMAGEMASTER=omero-master:$PREFIX
+IMAGESLAVE=omero-slave:$PREFIX
 
-# Script must be run from omero-grid/
-cd "$(dirname $0)"
+CLEAN=${CLEAN:-y}
 
 cleanup() {
-    docker rm -f -v $PREFIX-db $PREFIX-master $PREFIX-slave-1 $PREFIX-web
+    docker rm -f -v $PREFIX-db $PREFIX-server $PREFIX-slave-1
 }
 
 if [ "$CLEAN" = y ]; then
@@ -23,29 +19,32 @@ fi
 
 cleanup || true
 
-# From the README
-./build.py --tag $IMAGE $BUILD omero-grid
-./build.py --tag $IMAGEWEB $BUILD omero-grid-web
+
+docker build -t $IMAGEMASTER master
+docker build -t $IMAGESLAVE slave
 docker run -d --name $PREFIX-db -e POSTGRES_PASSWORD=postgres postgres
-docker run -d --name $PREFIX-master --link $PREFIX-db:db \
-    -e DBUSER=postgres -e DBPASS=postgres -e DBNAME=postgres $IMAGE master \
+docker run -d --name $PREFIX-server --link $PREFIX-db:db \
+    -p 4063:4063 -p 4064:4064 \
+    -e CONFIG_omero_db_user=postgres \
+    -e CONFIG_omero_db_pass=postgres \
+    -e CONFIG_omero_db_name=postgres \
+    -e ROOTPASS=omero-root-password \
+    $IMAGEMASTER \
     master:Blitz-0,Indexer-0,DropBox,MonitorServer,FileServer,Storm,PixelData-0,Tables-0 \
     slave-1:Processor-0
 
-docker run -d --name $PREFIX-slave-1 --link $PREFIX-master:master $IMAGE slave-1
-docker run -d --name $PREFIX-web --link $PREFIX-master:master -P $IMAGEWEB
-
-echo "Exposed web port:"
-docker port $PREFIX-web
+docker run -d --name $PREFIX-slave-1 --link $PREFIX-server:master $IMAGESLAVE slave-1
 
 # Smoke tests
 
 export OMERO_USER=root
-export OMERO_PASS=omero
+export OMERO_PASS=omero-root-password
 export PREFIX
 
-# Login to web
+# Login to server
 bash test_login.sh
+# Wait a minute to ensure other servers are running
+sleep 60
 # Now that we know the server is up, test Dropbox
 bash test_dropbox.sh
 # And Processor (slave-1)

slave/Dockerfile

@@ -7,8 +7,9 @@ set -x
 # Must be exported by the caller:
 # OMERO_USER OMERO_PASS PREFIX
 
+OMERO=/opt/omero/server/OMERO.server/bin/omero
 FILENAME=$(date +%Y%m%d-%H%M%S-%N).fake
-docker exec $PREFIX-master sh -c \
+docker exec $PREFIX-server sh -c \
     "mkdir -p /OMERO/DropBox/root && touch /OMERO/DropBox/root/$FILENAME"
 
 echo -n "Checking for imported DropBox image $FILENAME "
@@ -17,7 +18,7 @@ i=0
 result=
 while [ $i -lt 60 ]; do
     sleep 4
-    result=$(docker exec $PREFIX-master OMERO.server/bin/omero hql -q -s localhost -u $OMERO_USER -w $OMERO_PASS "SELECT COUNT (*) FROM Image WHERE name='$FILENAME'" --style plain)
+    result=$(docker exec $PREFIX-server $OMERO hql -q -s localhost -u $OMERO_USER -w $OMERO_PASS "SELECT COUNT (*) FROM Image WHERE name='$FILENAME'" --style plain)
     if [ "$result" = "0,1" ]; then
         echo
         echo "Found image: $result"

omero-grid/slave.cfg renamed to slave/slave.cfg

@@ -7,56 +7,17 @@ set -x
 # Must be exported by the caller:
 # OMERO_USER OMERO_PASS PREFIX
 
-WEB_PORT=$(docker inspect --format='{{(index (index .NetworkSettings.Ports "8080/tcp") 0).HostPort}}' $PREFIX-web)
+OMERO=/opt/omero/server/OMERO.server/bin/omero
 
-LOGIN_URL="http://localhost:$WEB_PORT/webclient/login/"
-SERVER="1"
-URL="url=%2Fwebclient%2F"
-COOKIES=cookies.txt
-
-rm -f $COOKIES
-CURL_BIN="curl -i -k -s -c $COOKIES -b $COOKIES -e $LOGIN_URL"
-
-echo -n "Getting CRSF token "
-# Retry for 2 mins
-i=0
-csrf_token=
-while [ -z "$csrf_token" -a $i -lt 60 ]; do
-    sleep 2
-    $CURL_BIN $LOGIN_URL > /dev/null || true
-    csrf_token=$(grep csrftoken cookies.txt | awk '{print $7}')
-    echo -n "."
-    let ++i
-done
-echo
-
-if [ -z "$csrf_token" ]; then
-    echo "Failed to get CSRF token"
-    exit 2
-fi
-
-echo "CSRF token: $csrf_token"
-echo -n "Attempting to login "
-# Retry for 2 mins
-DJANGO_TOKEN="csrfmiddlewaretoken=$csrf_token"
+# Wait up to 2 mins
 i=0
-session_id=
-# Retry for 2 mins
-while [ -z "$session_id" -a $i -lt 60 ]; do
-    sleep 2
-    $CURL_BIN -d \
-        "$DJANGO_TOKEN&username=$OMERO_USER&password=$OMERO_PASS&server=$SERVER&url=$URL" \
-    -X POST $LOGIN_URL > /dev/null || true
-    session_id=$(grep sessionid cookies.txt | awk '{print $7}')
-    echo -n "."
-    let ++i
+while ! docker exec test-server $OMERO login -C -s localhost -u "$OMERO_USER" -q -w "$OMERO_PASS"; do
+    i=$(($i+1))
+    if [ $i -ge 24 ]; then
+        echo "$(date) - OMERO.server still not reachable, giving up"
+        exit 1
+    fi
+    echo "$(date) - waiting for OMERO.server..."
+    sleep 5
 done
-echo
-
-if [ -z "$session_id" ]; then
-    echo "Failed to login"
-    exit 2
-fi
-
-echo "Session id: $session_id"
-rm -f $COOKIES
+echo "OMERO.server connection established"

test.sh

@@ -7,20 +7,20 @@ set -x
 # Must be exported by the caller:
 # OMERO_USER OMERO_PASS PREFIX
 
+OMERO=/opt/omero/server/OMERO.server/bin/omero
 DSNAME=$(date +%Y%m%d-%H%M%S-%N)
 FILENAME=$(date +%Y%m%d-%H%M%S-%N).fake
 SCRIPT=/omero/util_scripts/Dataset_To_Plate.py
 
-dataset_id=$(docker exec $PREFIX-master OMERO.server/bin/omero obj -q -s localhost -u $OMERO_USER -w $OMERO_PASS new Dataset name=$DSNAME | cut -d: -f2)
+dataset_id=$(docker exec $PREFIX-server $OMERO obj -q -s localhost -u $OMERO_USER -w $OMERO_PASS new Dataset name=$DSNAME | cut -d: -f2)
 
-docker exec $PREFIX-master sh -c \
-    "touch $FILENAME && OMERO.server/bin/omero import -d $dataset_id $FILENAME"
+docker exec $PREFIX-server sh -c \
+    "touch /tmp/$FILENAME && $OMERO import -d $dataset_id /tmp/$FILENAME"
 
-docker exec $PREFIX-master OMERO.server/bin/omero script launch $SCRIPT \
-    IDs=$dataset_id
+docker exec $PREFIX-server $OMERO script launch $SCRIPT IDs=$dataset_id
 echo "Completed with code $?"
 
-result=$(docker exec $PREFIX-master OMERO.server/bin/omero hql -q -s localhost -u $OMERO_USER -w $OMERO_PASS "SELECT COUNT(w) FROM WellSample w WHERE w.well.plate.name='$DSNAME' AND w.image.name='$FILENAME'" --style plain)
+result=$(docker exec $PREFIX-server $OMERO hql -q -s localhost -u $OMERO_USER -w $OMERO_PASS "SELECT COUNT(w) FROM WellSample w WHERE w.well.plate.name='$DSNAME' AND w.image.name='$FILENAME'" --style plain)
 if [ "$result" != "0,1" ]; then
     echo "Script failed: $result"
     exit 2