isajson-ena

THIS README IS OUTDATED ### WATCH THIS SPACE FOR A NEW README ### LIBRARY TRANSFORMED TO SERVICE IN BH 2023

ISA Json to BioSample and ENA SRA converter and submitter command line tool

Run locally

Prerequisites

1. Java 11 (to run locally)
2. Gradle (to build the executable)

Steps to set up

Download and install Java 11

Oracle's OpenJDK JDK binary for Windows and Linux is available on release-specific pages of jdk.java.net as .zip archive.

Navigate in Web Browser to: https://jdk.java.net/java-se-ri/11

Look for the RI Binary (build 11+28) under the GNU General Public License version 2 section.

Click on the zip link right next to Windows/x64/ Linux.

At the time of writing the latest Oracle OpenJDK release was version: 11.0.28

Download and extract the file

Select an extract destination for the JDK files.

Setup JAVA_HOME and PATH environment variables

Setup JAVA_HOME on a Windows System

Right-click My Computer and select Properties.

On the Advanced tab, select Environment Variables, and then edit JAVA_HOME to point to where the JDK software is located, for example, C:\Program Files\Java\jdk1.6.0_02.

Setup JAVA_HOME on LINUX/ UNIX system

To set JAVA_HOME, do one of the following:

For Korn and bash shells, run the following commands:

export JAVA_HOME=jdk-install-dir

export PATH=$JAVA_HOME/bin:$PATH

For the bourne shell, run the following commands:

JAVA_HOME=jdk-install-dir

export JAVA_HOME

PATH=$JAVA_HOME/bin:$PATH

export PATH

For the C shell, run the following commands:

setenv JAVA_HOME jdk-install-dir

setenv PATH $JAVA_HOME/bin:$PATH

export PATH=$JAVA_HOME/bin:$PATH

Gradle setup

Please follow - https://gradle.org/install/

Gradle build

./gradlew build -x test

A JAR (Java archive) by the name ISASRAProject27-0.0.1-SNAPSHOT.jar will get created in the project directory biohackathon-projects-2022\27\ISASRAProject27\build\libs\ISASRAProject27-0.0.1-SNAPSHOT.jar

Command line arguments

The tool needs 4 command line arguments:

1. webinJwt
2. webinUserName
3. webinPassword
4. isaJsonFilePath

Command line arguments values:

1. webinJwt - get the JWT token using the below curl:

TOKEN=$(curl --location --request POST 'https://www.ebi.ac.uk/ena/submit/webin/auth/token' --header 'Content-Type: application/json' --data-raw '{ "authRealms": [ "ENA" ], "password": "EBIN_PASSWORD", "username": "WEBIN-ID" }')

2. webinUserName: Webin user name
3. webinPassword: Webin account password
4. isaJsonFilePath: File path of the ISA Json file

Running the application

java -jar ISASRAProject27-0.0.1-SNAPSHOT.jar --webinJwt=webin_token --webinUserName=webin_username --webinPassword=webin_password --isaJsonFilePath=file_path_in_local_system