fix and improvements in ES upgrade script

CHANGELOG.md

@@ -1,5 +1,9 @@
 # Changelog Fab Manager
 
+- Allow running the ElasticSearch upgrade script while being root
+- Fix an issue with ES upgrade script, preventing reindexing in some cases
+- Improved ES upgrade documentation
+
 # v2.7.1 2018 November 27
 
 - Updated angular.js to 1.6

doc/elastic_upgrade.md

@@ -1,5 +1,7 @@
 # Instructions for upgrading ElasticSearch
 
+## Automatic upgrade
+
 Fab-manager release 2.6.5 has upgraded its dependency to ElasticSearch from version 1.7 to version 5.6 as the previous was unsupported for months.
 To keep using fab-manager you need to upgrade your installation with the new version.
 We've wrote a script to automate the process while keeping your data integrity, but there's some requirements to understand before running it.
@@ -22,6 +24,93 @@ cd /apps/fabmanager
 \curl https://raw.githubusercontent.com/LaCasemate/fab-manager/master/scripts/elastic-upgrade.sh | bash
 ```
 
+## Manual upgrade
+
 For instructions regarding a manual upgrade, please refer to the official documentation:
+
 - https://www.elastic.co/guide/en/elasticsearch/reference/2.4/restart-upgrade.html
-- https://www.elastic.co/guide/en/elasticsearch/reference/5.6/restart-upgrade.html
+- https://www.elastic.co/guide/en/elasticsearch/reference/5.6/restart-upgrade.html
+
+## Revert the upgrade
+
+So something goes wrong and the upgrade was not successful. 
+Sad news, but everything isn't lost, follow this procedure to downgrade to ElasticSearch 1.7.
+
+First, check the status of your indices:
+
+```bash
+# Replace fabmanager_elasticsearch_1 in the next command with your container's name. 
+# You can get it running `docker ps`
+ES_IP=$(docker inspect -f '{{range .NetworkSettings.Networks}}{{.IPAddress}}{{end}}' fabmanager_elasticsearch_1)
+curl "$ES_IP:9200/_cat/indices?v"
+```
+
+You should get something like this:
+```
+health status index     pri rep docs.count docs.deleted store.size pri.store.size 
+green  open   fablab_24   1   0       1944            0        1mb            1mb 
+green  open   stats_24    1   0          0            0      2.8mb           104b 
+green  open   stats       5   0      13515            0      2.7mb          2.7mb 
+green  open   fablab      5   0       1944            4      1.2mb          1.2mb 
+```
+
+Here, we can see that the migration is not complete, as *docs.count* are not equal for `stat_24` and `stats`.
+
+
+Now let's stop and remove the ElasticSearch container.
+
+```bash
+docker-compose stop elasticsearch
+docker-compose rm -f elasticsearch
+docker-compose down
+```
+
+Then, edit your [docker-compose.yml](../docker/docker-compose.yml) and change the *elasticsearch* block according to the following: 
+
+<table>
+<tr><td>
+<pre style="max-width:350px; overflow-y: scroll">
+  elasticsearch:
+    image: elasticsearch:2.4
+    ulimits:
+      memlock:
+        soft: -1
+        hard: -1
+    environment:
+      - "ES_JAVA_OPTS=-Xms512m -Xmx512m"
+    volumes:
+      - ${PWD}/elasticsearch/config:/usr/share/elasticsearch/config
+      - ${PWD}/elasticsearch:/usr/share/elasticsearch/data
+    restart: always
+</pre>
+</td>
+<td>
+=>
+</td>
+<td>
+<pre style="max-width:350px; overflow-y: scroll">
+  elasticsearch:
+    image: elasticsearch:1.7
+    volumes:
+      - ${PWD}/elasticsearch:/usr/share/elasticsearch/data
+    restart: always
+</pre>
+</td></tr>
+</table>
+
+Restart your containers:
+
+```bash
+docker-compose pull
+docker-compose up -d
+```
+
+Now you're back with ElasticSearch 1.7. You can safely restart the upgrade script.
+
+## Debugging the upgrade
+
+You can check for any error during container startup, using:
+
+```bash
+docker-compose logs elasticsearch 
+```

docker/elasticsearch.yml

@@ -1,6 +1,5 @@
 http.host: 0.0.0.0
 script.inline: true
-script.stored: true
-script.painless.regex.enabled: true
+script.engine.groovy.inline.update: true
 path.repo: /usr/share/elasticsearch
 

scripts/elastic-upgrade.sh

@@ -308,6 +308,19 @@ upgrade_compose()
   then
     sed -i.bak "/image: $image/s/.*/&\n    ulimits:\n      memlock:\n        soft: -1\n        hard: -1/" "$FM_PATH/docker-compose.yml"
   fi
+  if [ $target = '2.4' ]
+  then
+    # get current data directory
+    dir=$(awk 'BEGIN { FS="\n"; RS="";} { match($0, /image: elasticsearch:2\.4(\n|.)+volumes:(\n|.)+(-.*elasticsearch\/data)/, lines); FS="[ :]+"; RS="\r\n"; split(lines[3], line); print line[2] }' "$FM_PATH/docker-compose.yml")
+    # set the configuration directory
+    dir=$(echo "${dir//[$'\t\r\n ']}/config")
+    # insert configuration directory into docker-compose bindings
+    awk "BEGIN { FS=\"\n\"; RS=\"\";} { print gensub(/(image: elasticsearch:2\.4(\n|.)+)volumes:\n/, \"\\1volumes:\n      - ${dir}:/usr/share/elasticsearch/config\n\", \"g\") }" "$FM_PATH/docker-compose.yml" > "$FM_PATH/.awktmpfile" && mv "$FM_PATH/.awktmpfile" "$FM_PATH/docker-compose.yml"
+    echo -e "\nCopying ElasticSearch 2.4 configuration files from $(pwd)/docker to $dir..."
+    mkdir -p "$dir"
+    curl -sSL https://raw.githubusercontent.com/LaCasemate/fab-manager/master/docker/elasticsearch.yml > "$dir/elasticsearch.yml"
+    curl -sSL https://raw.githubusercontent.com/LaCasemate/fab-manager/master/docker/log4j2.properties > "$dir/log4j2.properties"
+  fi
   docker-compose pull
   docker-compose up -d
   wait_for_online
@@ -351,7 +364,7 @@ upgrade_docker()
   then
     image_name="elasticsearch-oss:$target"
     image="docker.elastic.co/elasticsearch/$image_name"
-  elif [ $target = '5.6' ]
+  elif [ $target = '2.4' ]
   then
     configdir=$(echo "$volumes" | grep config | awk -F'[ :]' '{print $2}')
     echo -e "\nCopying ElasticSearch 2.4 configuration files from $(pwd)/docker to $configdir..."
@@ -497,6 +510,9 @@ reindex_indices()
       },
       "dest": {
         "index": "'"$migration_index"'"
+      },
+      "script": {
+        "inline": "ctx._source.remove('"'"'_id'"'"')"
       }
     }'
   done