neXtProt - The knowledge resource on human proteins

This is a code repository for the SIB - Swiss Institute of Bioinformatics CALIPHO group neXtProt project

See: https://www.nextprot.org/

neXtProt User Interface (UI)

CAUTION: neXtProt new UI is in early stages of development. Things are likely to change in ways that are not backwards compatible

AngularJS + Brunch + Bootstrap

Main Client Features:* Search* Basket

Backends

nextprot-api-web

Installation

npm install # node v6.10+ worked with polymer 1.0
./node_modules/.bin/bower install
./node_modules/.bin/brunch build
./node_modules/.bin/gulp # Gulp was included to run the polymer vulcanize. It is temporary solution, the polymer build procedure should be moved to nextprot-elements.

Updating nextprot-elements module dependency

Prerequisites: The new version of nextprot-elements must have been pushed on github

./node_modules/.bin/bower update
./node_modules/.bin/gulp node app

Usage

node app (this creates a build)

Maintenance Javascript Libraries

bower list (lists the current bower components and shows the latests)
bower install angular#1.4.0 --save (important to set the --save flag to update the bower.json accordingly)

Maintenance node modules

TODO !

Testing

Unit testing npm run-script unit Integration testing must start the application node app& >npm run-script integration Or use can directly work with karma >karma start test/karma.unit.js

Deploying

nxs-build-and-deploy-spa.sh (dev|alpha|pro) if pro is specified change the version.js in pro brunch -P is used (to minimize / uglify the javascript files)

Troubleshooting

On a mac the command node app may not throw any error or exception, in order to make sure to see the error compile the code using ./node_modules/.bin/brunch build instead.

build and minimize the project for production (do not use -m option to debug application)

./node_modules/.bin/brunch build -m

You can try to launch the build project using a simple http server like "serve ." or "mongoose"

Then deploy it in UAT

rsync -auv build/* npteam@uat-web2:/var/www/html/protosearch

start/kill solr

java -Dprotosearch.solr -Xmx512m -jar -Djetty.port=8985 start.jar & pkill -f protosearch.solr

update your local solr indexes for entries, publications and terms

LOCAL_SOLR=$HOME/application/solr-4.4.0/example/solr SOLR_INDEX="npentries1 npentries1gold npcvs1 nppublications1" for index in $SOLR_INDEX; do rsync -Lavz --delete npteam@crick:/work/devtools/solr-4.5.0/example/solr/$index/ $LOCAL_SOLR/$index/ done