service-ars

RESTful Service for Antigen Recognition Site Reduction

Build

Docker Image

Further documentation is available at service-ars.readthedocs.io

Using service-ars

    
    # Do ARS reduction on a typing #
    curl http://localhost:3000/api/v1/redux?typing=A*01:01?dbversion=3.20

    # Do ARS reduction on multiple subjects # 
    curl --header "Content-type: application/json" --request POST 
    --data '{"arsFile":"hla_nom_g.txt","dbversion":"3.20.0","arsType":"G",
    "Subjects":[{"SubjectID":1,"typing":["A*01:01+A*01:02","B*08:01+B*07:02","C*07:01+C*07:01"]},
    {"SubjectID":1,"typing":["A*01:01+A*01:02","B*08:01+B*07:02","C*07:01+C*07:01"]}]}' 
    http://localhost:3000/api/v1/reduxSubjects
    
    # Get all the ARS data #
    curl http://localhost:3000/api/v1/ars
    
    # Get all the ARS data for IMGTDB 3.20.0 #
    curl http://localhost:3000/api/v1/ars?dbversion=3.20.0

Tools

ex. config.json

{  
   "arsFile":"hla_nom_g.txt",
   "dbversion":"3.20.0",
   "arsUrl":"http://localhost:3000",
   "macUrl":"http://devgenomicservices1.nmdp.org/mac",
   "arsType":"g"
}

Java

hml-typing-resolution

arguments:
   -a, --about  display about message [optional]
   -h, --help  display help message [optional]
   -i, --input-file [class java.io.File]  input file, default stdin [optional]
   -j, --json-file [class java.io.File]  json configuration file [required]
   -x, --xml  print output as xml [optional]
   -s, --json  print output as json [optional]
   -c, --csv  print output as csv [optional]

hml-typing-resolution -j config.json -x < inputFile.xml > outputFile.xml
hml-typing-resolution -j config.json -x -i inputFile.xml > outputFile.xml
hml-typing-resolution -j config.json -c -i inputFile.xml > outputFile.csv
hml-typing-resolution -j config.json -s -i inputFile.xml > outputFile.json

Perl

./ars-resolution [--config] [--verbos] [--help]
    -c/--config
    -v/--verbose
    -h/--help

ars-resolution -c config.json < testInput.csv > testOutput.csv

Installing

./build.sh

Required Software

• JDK 1.7 or later, http://openjdk.java.net
• Apache Maven 3.2.5 or later, http://maven.apache.org
• Git, http://git.org
• perl 5.18 or later, http://perl.org

Perl Modules

• YAML
• Plack
• Plack::Handler::Starman
• Template
• JSON
• Getopt::Long
• LWP::UserAgent
• Test::More Dancer

Related Pages

• docker-ars
• dockerhub