SourceDisplayColumnFactory.java

package org.labkey.mgap.query;

import org.apache.commons.lang3.StringUtils;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.labkey.api.data.ColumnInfo;
import org.labkey.api.data.DataColumn;
import org.labkey.api.data.DisplayColumn;
import org.labkey.api.data.DisplayColumnFactory;
import org.labkey.api.data.RenderContext;
import org.labkey.api.query.FieldKey;
import org.labkey.api.util.PageFlowUtil;
import org.labkey.api.writer.HtmlWriter;

import java.util.Set;

public class SourceDisplayColumnFactory implements DisplayColumnFactory
{
    private static final Logger _log = LogManager.getLogger(SourceDisplayColumnFactory.class);

    @Override
    public DisplayColumn createRenderer(ColumnInfo colInfo)
    {
        return new DataColumn(colInfo)
        {
            @Override
            public void addQueryFieldKeys(Set<FieldKey> keys)
            {
                super.addQueryFieldKeys(keys);
                keys.add(getBoundKey("identifier"));
            }

            @Override
            public void renderGridCellContents(RenderContext ctx, HtmlWriter out)
            {
                String val = ctx.get(getBoundKey("source"), String.class);
                if (val == null)
                {
                    return;
                }

                String identifier = StringUtils.trimToNull(ctx.get(getBoundKey("identifier"), String.class));
                String url = null;
                if (identifier != null && identifier.contains(":"))
                {
                    String[] parts = identifier.split(":");
                    if (parts.length != 2)
                    {
                        _log.warn("Invalid variant identifier: " + val);
                    }
                    else
                    {
                        if (parts[0].equals("ClinVar"))
                        {
                            if (!StringUtils.isEmpty(parts[1]))
                            {
                                url = "https://www.ncbi.nlm.nih.gov/clinvar/variation/" + parts[1] + "/";
                            }
                        }
                    }
                }

                if (url == null)
                {
                    out.write(val);
                }
                else
                {
                    out.write(PageFlowUtil.link(val).href(url).clearClasses());
                }
            }

            private FieldKey getBoundKey(String colName)
            {
                return new FieldKey(getBoundColumn().getFieldKey().getParent(), colName);
            }
        };
    }
}