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-parsers

Installation

Configure your Scala Eclipse IDE by running sbt eclipse

Deployment

Deploying/publishing locally:

sbt publishLocal

Deploying/publishing on nexus

if you need credentials configured on ~/.sbt/x.x/sonatype.sbt:

credentials+=Credentials("Sonatype Nexus Repository Manager", "miniwatt.isb-sib.ch", "$sonatype_username", "$sonatype_password")

The syntax above works if in the build.sbt file but in sbt command line utility

It will go to either snapshot or production repository depending on your version suffix. If it ends with -SNAPSHOT it goes to the snapshot repository otherwise it will go to the production repository. Note that when you publish to the production repository you need to specify a new version within sbt with: set version:="x.x.x" .

sbt
> set version:="1.1.7"
> publish
> exit

NOTE

• about user / password for credential

1. See note above about sonatype
2. or use user /password for nexus on miniwatt (admin pwd)

• check on miniwatt if deployment is ok

1. check if defined version is available
2. check metadata files, they should have the date of the deployement. If not, 'rebuild metadata' and 'update index' of the nextprot-scala-parser (you have to be logged in to be able to do it)

Updating dependency in nextprot-loaders and build fat jar for NP1 data integration

1. Update artefact version in https://gitlab.isb-sib.ch/calipho/nextprot-loaders/blob/develop/tools.integration/pom.xml

<dependency>
  <groupId>org.nextprot.parser</groupId>
  <artifactId>nextprot-scala-parsers</artifactId>
  <version>1.1.6</version>
</dependency>

2. Commit / push your change

3. Rebuild the fat jar on cactus (NP1 data integration server)

> ssh npteam@cactus
> cd /work/projects/integration/nextprot-loaders/tools.integration
> git pull origin develop
> mvn package

The resulting fat jar is in:

> ls -l /work/projects/integration/nextprot-loaders/tools.integration/target 

TESTS

To test simply use sbt test If you want to specify only one test you can also use sbt "test:testOnly org.nextprot.parser.hpa.expression.FullFileEntryExpressionTest"

You can configure project dependencies in eclipse

On eclipse define project dependencies and remove library (the jar)