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Update instructions

Production branch is production, and should not be pushed as it contains the password.

Git changes from master via git pull origin master.

Update in order:

BioEntity.Link Production update

Production Trouble-shooting / info

The following ports should be open:

  netstat -tan | grep LISTEN
  tcp        0      0 0.0.0.0:80              0.0.0.0:*               LISTEN     
  tcp        0      0 0.0.0.0:22              0.0.0.0:*               LISTEN     
  tcp        0      0 0.0.0.0:443             0.0.0.0:*               LISTEN     
  tcp6       0      0 :::8080                 :::*                    LISTEN     
  tcp6       0      0 :::80                   :::*                    LISTEN     
  tcp6       0      0 :::7473                 :::*                    LISTEN     
  tcp6       0      0 :::7474                 :::*                    LISTEN     
  tcp6       0      0 :::21                   :::*                    LISTEN     
  tcp6       0      0 :::22                   :::*                    LISTEN     
  tcp6       0      0 127.0.0.1:8005          :::*                    LISTEN     
  tcp6       0      0 :::7687                 :::*                    LISTEN

or maybe

  neo4j start

To login to the neo4j server:

  cypher-shell

and then: neo4j/LAT8gjThKJ26TR

Use neo4j-admin dump and neo4j-admin load to dump and load.

To restart both the tomcat and neo4j server:

  sudo service tomcat8 stop 
  sudo service neo4j stop

Confirm that the servers are both down as above or use ps -ef | grep neo4j and ps -ef | grep catalina.

Then restart in this order:

  sudo service neo4j start
  sudo service tomcat8 start

If all else fails you may need to reboot the whole thing (which will be unusual):

  sudo init 6

When things come back up, make sure all of the services have started as above. If not, follow the instructions on how to restart them.

Unbuntu 16 production deployment

Install:

To run neo4j in docker:

docker run \                  
    --publish=7474:7474 --publish=7687:7687 \
    --volume=$HOME/neo4j/data:/data \
    --volume=$HOME/neo4j/logs:/logs \
    neo4j:3.1

GIT CLONE:

NEO4J INSTALLATION:

BUILD FOR TOMCAT

Getting started (Dev Environment)

Reference Documentation

Matching docs

From https://github.com/InSilicoLabs/dmc-grails/issues/157

Has a DOI ending in 200592:

TODO (move to GH / Asana later)

Angular2 with Grails profiles and Texture

Angular2

Use this doc to get the build going:

Install most recent stable node and npm and angular-cli.

npm install -g angular-cli

Texture

Texture is forked here: https://github.com/InSilicoLabs/texture

Putting it all together

Run them separately for best results:

# terminal 1, server port 8080
cd server 
./grailsw run-app

# terminal 2, ng port 4200
cd client 
ng serve

# terminal 3, ng port 5555
cd texture 
npm run start

All can be accessed at http://localhost:port/

Deploy production

Server

cd server 
./grailsw war
sudo systemctl stop tomcat8
sudo rm -rf /var/lib/tomcat8/webapps/dmc
sudo cp build/libs/dmc-0.1.war /var/lib/www/dmc.war
sudo systemctl start tomcat8

Note: I'm currently using run-app with screen instead of the proper war file.

NG2 Client

cd client 
ng build --prod 
sudo rm -rf /var/www/html/*
sudo cp -r dist/* /var/www/html/

Texture Client

If not available when you clone (would have to clone recursive) do:

git submodule update --recursive --remote
git pull --recurse-submodules

The build as normal:

cd texture
rm -rf dist
npm install 
node make 
# ctrl-c (will have built it)
sudo rm -rf /var/www/html/texture/
sudo cp -r dist /var/www/html/texture

Neo4j Production Notes

In neo4j.conf you have to set the address as follows:

dbms.connectors.default_advertised_address=dev.insilicodesigns.com

dbms.connectors.default_advertised_address=dev.insilico.link
dbms.memory.heap.max_size=8g

and I think these as well:

# With default configuration Neo4j only accepts local connections.
# To accept non-local connections, uncomment this line:
dbms.connectors.default_listen_address=0.0.0.0

These might already be set by default, but if not, they need to be exposed:

# Bolt connector
dbms.connector.bolt.enabled=true
#dbms.connector.bolt.tls_level=OPTIONAL
dbms.connector.bolt.listen_address=:7687

# HTTP Connector. There must be exactly one HTTP connector.
dbms.connector.http.enabled=true
dbms.connector.http.listen_address=:7474

Set the ulimit on some instances in the startup neo4j script:

ulimit -n 100000 # default is 1024

Clean out database

MATCH (n:Lexicon)-[s:LEXICONSOURCE]-(p:LexiconSource) return n limit 25 ;
MATCH (n:Lexicon)-[s:LEXICONSOURCE]-(p:LexiconSource) delete s  ;

MATCH (c:LexicaCapture)-[r:LEXICA]-(n:Lexicon) return c limit 5 ;
MATCH (n:LexicaCapture)-[r:SOURCE]-(q:LexiconSource) delete r,n;
match (s:Lexicon)-[r:LEXICA]-(c:LexicaCapture) delete s,r,c;

MATCH (n:Lexicon)-[r:LEXICA]-(k:KeyWord) return n limit 5 ;
MATCH (n:Lexicon)-[r:LEXICA]-(k:KeyWord)  delete r ;

MATCH (n:Lexicon) delete n ;

MATCH (n:KeyWord)-[r:KEYWORDSET]-(q:KeyWordSet) return n limit 25 ;
MATCH (n:KeyWord)-[r:KEYWORDSET]-(q:KeyWordSet) delete r;
MATCH (n:KeyWord) delete n ;
MATCH (n:KeyWordSet)-[r:SOURCES]-(s:LexiconSource) return n ;
MATCH (n:KeyWordSet)-[r:SOURCES]-(s:LexiconSource) delete n,r ;

MATCH (n:KeyWord) delete n ;

// delete markups
MATCH (n:Markup)-[r:PUBLICATION]-(p:Publication) delete r ;
MATCH (n:Markup)-[f:FINALLEXICON]-(l:Lexicon) delete n,f

Other Notes

Example configuration for Grails / Neo4j tests: https://github.com/grails/gorm-neo4j/tree/master/examples

Other Important Set

MATCH (kws:KeyWordSet)--(k:KeyWord)--(l:Lexicon)--(s:LexiconSource) where s.source='Source 3'  RETURN kws,k,l,s limit 25

License

CC BY-NC 4.0