// ldapsearch.java

import java.io.*;
import java.util.*;
import javax.naming.*;
import javax.naming.directory.*;

/**
  
  <h4>ldapsearch.java NOTES</h4> <p>
  Test LDAP directory of genome data at http://euGenes.org/ <p>
  
  This script fetches and prints sequence and associated gene
  features from an ldap directory of genome annotations at euGenes.org
  The species, chromosome, feature kind and base range can be specified.
  Search of high level directories provide information on contents
  of the specific attributes available in species-chromosome directories. <p>
  
  Compile with 'javac ldapsearch.java'
  Run with 'java ldapsearch'
  <p>

  * @author Don Gilbert
  * @version 1.0 05/01/2002
  */
  
public class ldapsearch
{

  public static void main(String[] args)
  {
    int ns= 0;
    ldapsearch ldap= new ldapsearch();
    for (int i=0; i<args.length; i++) {
      if (args[i].startsWith("ldap://"))
        { ldap.search( args[i] ); ns++; }
      else if (args[i].startsWith("test")) ldap.test();
      else if (args[i].startsWith("h")) ldap.help();
      }
    if (ns==0) ldap.help();  
  }

  boolean helping;
  PrintStream out= System.out;
  
  public void help() {
    out.println("ldapsearch [ help | test | ldap://url.../?... ]");
    out.println("  Simple client for LDAP, testing Bio-data directory servers");
    out.println("  Call with ldap url or 'test' to test these bio-directories:");
    out.println();
    helping= true; 
    test();
    }
    
  public void test() 
  {     
		String url;
		out.println("Biosequence directory - top level (SRS-LDAP, service srv=srs)");
  	url= "ldap://iubio.bio.indiana.edu:3895/srv=srs";
    this.search( url );  
  	
		out.println("Biosequence directory (search for protein kinesin)");
  	url= "ldap://iubio.bio.indiana.edu:3895/srv=srs??sub"
  		+"?(&(objectClass=*)(lib=swissprot trembl refseq)(des=kinesin))"
  		+"?sizelimit=2";
    this.search( url );  
 
    out.println("Top level genome map directory (service srv=srsgnomap)");
    url= "ldap://eugenes.org:3891/srv=srsgnomap??one?(objectClass=*)";
    this.search( url ); 
    
    out.println("One level directory of worm species data");
    url= "ldap://eugenes.org:3891/spp=worm,srv=srsgnomap??one?(objectClass=*)";
    this.search( url );
     
    out.println("Search directory of fly species, chromosome 2L, and all subdirectories ");
    out.println("for Feature and NA-Sequence objects, for the chromosome base range");
    out.println("and limit search to specific feature (ft) kinds");
    url= "ldap://eugenes.org:3891/chr=2L,spp=fly,srv=srsgnomap"
    +"?" // select attributes to return, or all, e.g. "id,loc,name" 
    +"?sub" // search scope - base,one,sub(directories)
    +"?(&(|(objectClass=Feature)(objectClass=NA-Sequence))" // search filter
       +"(|(ft=gene)(ft=CDS)(ft=insertion))"
       +"(start=>50000)(stop=<80000))"
    +"?sizelimit=10,deref=always" // other ldap options
    ;
    
    this.search( url );

    System.exit(0);
  }
      
  public int search(String url)
  {
    out.println("Search URL: " +url); out.println(); 
    if (helping) return 0;
    int counter= 0;  
    try {
  		// ldap://host:port/dn?attributes?scope?filter?extensions
    com.sun.jndi.ldap.LdapURL lu=  new com.sun.jndi.ldap.LdapURL(url);
    String aurl= lu.toString();
    int q= aurl.indexOf('?'); if (q>0) aurl= aurl.substring(0,q); 
    Properties env= new Properties();
    env.put( Context.PROVIDER_URL, aurl);
    env.put( Context.INITIAL_CONTEXT_FACTORY, "com.sun.jndi.ldap.LdapCtxFactory");

    String dn= lu.getDN();
    String base= "";  
    String scope= lu.getScope();
    String filter= lu.getFilter(); 
    String[] attr= splitString( lu.getAttributes(),",;");

    SearchControls scontrols = new SearchControls();
    int iscope= SearchControls.OBJECT_SCOPE;  //  should this be default?
    if ("sub".equalsIgnoreCase(scope)) iscope= SearchControls.SUBTREE_SCOPE;
    else if ("base".equalsIgnoreCase(scope)) iscope= SearchControls.OBJECT_SCOPE;
    else if ("one".equalsIgnoreCase(scope)) iscope= SearchControls.ONELEVEL_SCOPE;
    scontrols.setSearchScope(iscope);
    if (attr.length>0) scontrols.setReturningAttributes(attr);
		if (filter==null) filter="(objectClass=*)";

  	String[] extn= splitString( lu.getExtensions(),"=,;");
  	for (int i=0; i<extn.length-1; i++) try {
  		if ("sizelimit".equalsIgnoreCase(extn[i]))
   			scontrols.setCountLimit( Long.parseLong(extn[++i]) );
  		else if ("timelimit".equalsIgnoreCase(extn[i]))
   			scontrols.setTimeLimit( Integer.parseInt(extn[++i]) );
  		else if ("deref".equalsIgnoreCase(extn[i]))
   			scontrols.setDerefLinkFlag( ! "never".equalsIgnoreCase(extn[++i]) );
 			} catch (Exception e) {}
 			
    DirContext dir = (DirContext) new InitialDirContext(env);
    NamingEnumeration results;
 		results = dir.search( base, filter, scontrols);
    while (results != null && results.hasMore()) {
      SearchResult nc = (SearchResult) results.next();
      processSearchResult(dn, nc); counter++;
      }
    dir.close();
    } 
    catch (Exception e) { System.err.println("Search failed: "+e); }   
    out.println(); 
    return counter;
  }

  void processSearchResult(String base, SearchResult si) { 
    String name = si.getName();             
    out.print("dn: "+name);
  	if (si.isRelative()) { 
  		if (name.length()>0) out.print(","); 
  		out.print(base);  
  		}
    out.println();
    Attributes attrs= si.getAttributes();
    if (attrs.size()>0) out.println( attrs);  // otherwise get "No attributes"
    out.println();
    }
    
  String[] splitString(String s, String del) {
    if (s==null) return new String[0];
    StringTokenizer st= new StringTokenizer(s, del);
    int n= st.countTokens(); String[] ss= new String[n];
    for (int i=0; i<n; i++) ss[i]= st.nextToken();
    return ss;
    }
 }