isa4j is a comprehensive and scalable Java Library for the programmatic generation of experimental metadata descriptions using the ISATab container format. We're assuming you're familiar with the ISA-Tab framework in the remainder of the manual; if you're not, please read up about it first.
The software provided as-is and made available under the terms of the MIT license (https://spdx.org/licenses/MIT.html), granting you the freedom to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software as long as you include the license and copyright notice in all copies or substantial portions of isa4j (details).
repositories {
mavenCentral()
}
dependencies {
implementation group: 'de.ipk-gatersleben', name:'isa4J', version:'###REPLACE-WITH-VERSION-NUMBER###'
}
<dependency>
<groupId>de.ipk-gatersleben</groupId>
<artifactId>isa4J</artifactId>
<version>###REPLACE-WITH-VERSION-NUMBER###</version>
</dependency>
If you don't use Gradle or Maven, please see the Installation page in the documentation for further instructions.
Here is a simple complete working example that you can just copy and paste into your favorite IDE and run. You can play with it and use it as a template to extend to your use case. More info on how to use isa4j can be found on the documentation website.
import java.io.IOException;
import de.ipk_gatersleben.bit.bi.isa4j.components.Assay;
import de.ipk_gatersleben.bit.bi.isa4j.components.DataFile;
import de.ipk_gatersleben.bit.bi.isa4j.components.Investigation;
import de.ipk_gatersleben.bit.bi.isa4j.components.Protocol;
import de.ipk_gatersleben.bit.bi.isa4j.components.Process;
import de.ipk_gatersleben.bit.bi.isa4j.components.Sample;
import de.ipk_gatersleben.bit.bi.isa4j.components.Source;
import de.ipk_gatersleben.bit.bi.isa4j.components.Study;
public class SimpleWorkingExample {
public static void main(String[] args) {
Investigation myInvestigation = new Investigation("myInvestigationID");
myInvestigation.setTitle("A very important Investigation");
/* Set further attributes, add Contacts, Publications, Ontologies...*/
Study myStudy = new Study("myStudyID", "s_study1.txt");
myStudy.setTitle("A very important study");
Protocol plantTalking = new Protocol("Plant Talking");
myStudy.addProtocol(plantTalking);
/* Set further Study attributes, add Contacts, Publications... */
myInvestigation.addStudy(myStudy);
Assay myAssay = new Assay("a_assay.txt");
/* Set further Assay attributes... */
myStudy.addAssay(myAssay);
/* Write the files */
try {
/* Investigation File */
myInvestigation.writeToFile("i_investigation.txt");
/* Study File */
myStudy.openFile();
/* Here you would loop through your database, CSV, JSON etc. */
for(int i = 0; i < 5; i++) {
Source source = new Source("Source " + i);
Sample sample = new Sample("Sample " + i);
/* plantTalking is a Protocol defined above */
Process talkingProcess = new Process(plantTalking);
talkingProcess.setInput(source);
talkingProcess.setOutput(sample);
myStudy.writeLine(source);
}
myStudy.closeFile();
/* Assay File */
myAssay.openFile();
for(int i = 0; i < 5; i++) {
Sample sample = new Sample("Sample " + i);
DataFile seqFile = new DataFile("Raw Data File", "seq-"+ i + ".fasta");
/* plantTalking is a Protocol defined above */
Process talkingProcess = new Process(plantTalking);
talkingProcess.setInput(sample);
talkingProcess.setOutput(seqFile);
myAssay.writeLine(sample);
}
myAssay.closeFile();
} catch (IOException e) {
System.err.println("Whoops, something went wrong!");
e.printStackTrace();
}
}
}Please see our GitHub Page for detailed documentation as well as an evaluation of isa4j's scalability.