Provide command line interface to test parsing of any CIF

Currently, Demo.java has a nice command line interface to test parsing of 1acj PDB entry:

ciftools-java/src/main/java/org/rcsb/cif/Demo.java

Lines 17 to 23 in c589bd5

    
           public static void main(String[] args) throws IOException { 
        
               parseFile(); 
        
               System.out.println(); 
        
               buildModel(); 
        
               System.out.println(); 
        
               convertAlphaFold(); 
        
           }

It would be great if main in Demo.java could accept a filename to parse, and fallback on 1acj if not given anything.

I am doing a comparison of CIF readers and would like to include CIFTools (cod-developers/CIF-parsers#4). To do so I need a command line interface to parse a given file. I believe having such command line interface would benefit other purposes as well, for example, to see if a CIF file parses correctly.

Hi @merkys,

That's nice to hear. I've ran some of your test cases and this implementation looks quite forgiving when it comes to malformed files.

Something along these lines should allow you to test files via the command-line:

import java.nio.file.Paths;

public class Validate {
    public static void main(String[] args) {
        try {
            CifIO.readFromPath(Paths.get(args[0]));
        } catch (Exception e) {
            System.out.println("Not OK: " + e.getClass().getSimpleName() + " - " + e.getMessage());
        }
    }
}

Let me know if you'd like me to compile this into a runnable .jar and send it to you. I would rather not commit any changes related to this issue to the repo.

Best,
Sebastian

Thanks for prompt response, @JonStargaryen. I will look into adapting your code example into a test runner, I believe I will manage without a runnable JAR, but thanks.

I would rather not commit any changes related to this issue to the repo.

I saw Demo.java having a command line interface and thought this could make a nice backwards-compatible extension. But sure, I fully understand your choice.

I am closing this issue as I consider it solved. Thanks again!

Your example worked, thanks a lot. I have included ciftools-java in my comparison of CIF parsers. By the way, is ciftools-java able to read CIF v2.0 files?

No, neither reading nor writing of CIF2 files is supported.

OK, thanks for the answer.

	public static void main(String[] args) throws IOException {
	parseFile();
	System.out.println();
	buildModel();
	System.out.println();
	convertAlphaFold();
	}