package com.cipres.mrBayesPlugin;

import java.io.File;
import java.util.ArrayList;
import java.util.Collection;
import java.util.List;
import java.util.Map;

import org.ngbw.directclient.CiCipresException;
import org.ngbw.restdatatypes.ErrorData;
import org.ngbw.restdatatypes.LimitStatus;
import org.ngbw.restdatatypes.ParamError;

import com.biomatters.geneious.publicapi.components.Dialogs;
import com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument;
import com.biomatters.geneious.publicapi.documents.sequence.SequenceAlignmentDocument;
import com.biomatters.geneious.publicapi.documents.sequence.SequenceDocument;
import com.biomatters.geneious.publicapi.plugin.DocumentOperation;
import com.biomatters.geneious.publicapi.plugin.DocumentOperationException;
import com.biomatters.geneious.publicapi.plugin.DocumentSelectionSignature;
import com.biomatters.geneious.publicapi.plugin.GeneiousActionOptions;
import com.biomatters.geneious.publicapi.plugin.Icons;
import com.biomatters.geneious.publicapi.plugin.Options;
import com.biomatters.geneious.publicapi.utilities.IconUtilities;
import com.cipres.mrBayesPlugin.ui.LoginOptions;
import com.cipres.mrBayesPlugin.ui.RAxMLRESTXSEDEOptions;
import com.cipres.mrBayesPlugin.utilities.CipresUtilities;

import jebl.util.ProgressListener;

public class CipresRAxMLRESTXSEDETree extends DocumentOperation {
	private static final String NEWLINE = System.getProperty("line.separator");
	
	@Override
	public GeneiousActionOptions getActionOptions() {
		Icons icon= IconUtilities.getIcons("tree24.png");
		
        return new GeneiousActionOptions("RAxML_CIPRES",
                "RAxML is a program for sequential and parallel maximum likelihood based inference of large phylogenetic trees.", 
                icon, GeneiousActionOptions.Category.TreeBuilding);
	}

	@Override
	public String getHelp() {
		return "RAxML (Randomized Axelerated Maximum Likelihood) is a program for sequential and parallel " + 
				"Maximum Likelihood based inference of large phylogenetic trees.\r\nIt can also be used for postanalyses of sets of phylogenetic trees, analyses of alignments and, evolutionary placement of short reads."; 
	}

	@Override
	public DocumentSelectionSignature[] getSelectionSignatures() {
		DocumentSelectionSignature singleAlignmentSignature = new DocumentSelectionSignature(
                SequenceAlignmentDocument.class, 1, 1);
		//DocumentSelectionSignature singleSequenceSignature = new DocumentSelectionSignature(
		//		SequenceDocument.class, 1, 1);
		
        return new DocumentSelectionSignature[]{singleAlignmentSignature/*, nucleotideSequenceSelectionSignature, proteinSequenceSelectionSignature*/};
        //return new DocumentSelectionSignature[]{singleSequenceSignature};
	}

	public Options getOptions(final AnnotatedPluginDocument[] docs) throws DocumentOperationException{
        Options options = null;
        if (CipresUtilities.isNewUser())
        {
			options = new LoginOptions();
	        options.canRestoreDefaults();
        }
        else
        {
        	options = new RAxMLRESTXSEDEOptions(docs);
        }
        return options;            
        	
    }
	
	public List performOperation(AnnotatedPluginDocument[] docs, ProgressListener progress, Options options) throws DocumentOperationException{
    	String userName = null;
    	String password = null;  
    	if (options instanceof LoginOptions)
    	{
    		LoginOptions loginOpt = (LoginOptions)options;
    		userName = loginOpt.getUsername();
    		password = loginOpt.getPassword();
    	}
    	
    	if (CipresMrBayesInitializer.Instance.initialize(userName, password) == false)
    		return null;
    	else
    	{
    		if (options instanceof LoginOptions)
    		{
    			Dialogs.showMessageDialog("Your login credentials have been saved. Please right click on your data and select Tree... again.");
    			return null;
    		}
    	}
    	RAxMLRESTXSEDEOptions raxmlRESTXSEDEOptions = (RAxMLRESTXSEDEOptions)options;
		List<File> files = new ArrayList<File>();
        final AnnotatedPluginDocument doc = docs[0];
        final SequenceAlignmentDocument alignmentDoc = (SequenceAlignmentDocument) doc.getDocument();
        
        
        if (alignmentDoc.getNumberOfSequences() < 4) {
            throw new DocumentOperationException("MrBayes requires at least 4 sequences." + NEWLINE + "Please select an alignment" +
                    " containing 4 or more sequences.");            
        }
        
        raxmlRESTXSEDEOptions.populateJsonCommand();
		Map<String, Collection<String>> vParams = raxmlRESTXSEDEOptions.getVParams();
		Map<String, String> inputParams = raxmlRESTXSEDEOptions.getInputParams();
		Map<String, String> metadata = raxmlRESTXSEDEOptions.getMetadata(docs[0].getName());
		
		System.out.println("The size of vParams = " + vParams.size());
		System.out.println("vParams = " + vParams);
		System.out.println("inputParams = " + inputParams);
		System.out.println("metadata = " + metadata);
		
        try {
			CipresUtilities.submitJob("RAXMLHPC8_REST_XSEDE", vParams, inputParams, metadata);
		} catch (CiCipresException ce) {
			System.err.println("Caught in SubmitJob");
			
            ErrorData ed = ce.getErrorData();
            System.out.println("Cipres error code=" + ed.code + ", message=" + ed.displayMessage);
            if (ed.code == ErrorData.FORM_VALIDATION)
            {
                for (ParamError pe : ed.paramError)
                {
                    System.out.println(pe.param + ": " + pe.error);
                }
            } else if (ed.code == ErrorData.USAGE_LIMIT)
            {
                LimitStatus ls = ed.limitStatus;
                System.out.println("Usage Limit Error, type=" + ls.type + ", ceiling=" + ls.ceiling);
            }
		}

    	return null;
	}
}