: Class Biogridlet

public class Biogridlet
extends java.lang.Object

Biogridlet - basic biogrid toolkit component

a basic directory access component for bioinformatics grids.

Simple test of a "Gridlet" for bio data directory access. For each compute node on your test grid, do this:

Install/test/locate NCBI BLAST software (yet to do as a gridlet), set bl=/path/to/blastall
Download Biogridlet .class and .prop files, edit Biogridlet.prop properties to taste, especially QUERY selection. Make sure Java 1.3+ runtime is available

Find a query biosequence in fasta format to test. A sample query set is

java Biogridlet count=100 ldap://bio-mirror.net:3895/srv=srs out=query \
'query=(lib=genbank)(org=Anopheles gambiae)'

Use Biogridlet to copy a databank subset to each node and run blast:

node1:

java Biogridlet start=0 count=1000 | $bl/formatdb -i stdin -p F -o T -n databank1 
$bl/blastall -p blastn -d databank1 -i query -m 8 -o databank1.out

node2:

java Biogridlet start=1000 count=1000 | $bl/formatdb -i stdin -p F -o T -n databank2  
$bl/blastall -p blastn -d databank2 -i query -m 8 -o databank2.out

node3 .. n

Copy blast results from each node and assemble to full result (yet to do; see NBLAST)

The runtime cost for this grid example, from a few quick tests, is approximately the time it takes to run on one computer with a full databank, divided by the number of nodes and subset databanks you use.

Gridlet defined

From Jan K. Labanowski: Computational Portals for Chemistry Gridlets and XMLets

I found a new word gridlet in papers by Rajkumar Buyya and Manzur Murshed from Monash University: http://www.csse.monash.edu.au/~rajkumar/. By gridlet they understand the tiny GridApp that contains all information related to jobs and job execution management details such as jobs processing requirements.

Note: this should become part of existing package iubio.grid used by BioGridRunner -- maybe subpackage iubio.grid.gridlet ?

Design

 
 Design for basic biogrid - partway between seti@home and globus  grid methods
Data grid components - serve data via simple directory search/retrieval methods
Compute grid components - run applications, fetching data from Data grid components 
Runner - client app used by biologist to select data, allocate cpu grid nodes,
run analysis, assemble results
Central/Home (?) - master directory services registry 
for registering and identifying data and compute grid components

 Basic Components
Biogridlet - Compute-Grid component handler
Biogridrun - basic controller app for running list of available programs (start w/ BLAST?)
Biodirectory - data & software directory services - for Data-Grid servers
-- ldap, http?
Biogridhome - ? central directory for listing & using data & compute grid components


  Biogridlet:	
-- ? split into 3 gridlets for cpu-node: node-manager, copy-url, run-app ?
... need simple execute() method to run programs
... need methods for handling Binary objects - gunzip for data
... possible use of java (.class,.jar), perl objects (script)
... should this become a 'screen-saver' type background app run on each compute node
with messaging to Biogridhome to keep node resources up to date?
... need to add different directory access choices: ldap, soap, http-cgi, others

 Biodirectory:
-- basic directory node server (data + applications)
-- use javaldap now for simplicity
-- ldap-srs interface for SRS data providers.
Find here.

  Biogridrun:
-- select compute nodes from compute grid list known to Biogridhome
--- need parameters of node: os flavor, cpu, disk, memory available at mimimum

-- select application to run (for now from list provided by  Biogridhome)
--- will include app binary url (no source compiles?)

-- select data from data grid, using search of data directories known to Biogridhome
-- foreach grid cpu node:
--- package up Biogridlet.class + message w/ app and data parameters
--- send to node & start Biogridlet on node
--- either poll node repeatedly, or have 

  Biogridhome:
-- mainly a central directory server, with dynamic registration and updates of
available data, software and compute grid nodes, their resources and allowed 
users and application running choices
-- Biogridrun interacts w/ this, gets referrals to other data, app and cpu directories

-- use existing bio name service, 
ldap://bio-mirror.net/ --  add new o=Biogrid ... ou=Bio,o=Grid ??
ldap://bio-mirror.net:3891/o=Bions
ldap://bio-mirror.net:3891/bc=Package,bc=Catalog,o=Bions

Notes

For now security & authentication will wait, as other globus-type components of grid. Design for restricted list of applications that can be run.

Author:: d.gilbert, nov 2002, gilbertd@bio.indiana.edu

Field Summary

static java.lang.String ATTRIBUTES
          properties key: which object fields to return = all, others are defined in http://iubio.bio.indiana.edu/biogrid/directories/schema/bioseq.schema

static java.lang.String COUNT
          properties key: number of objects to retrieve

static java.lang.String DEBUG


static java.lang.String DN
          url component

static java.lang.String EXTENSIONS
          properties key: ldap extension controls, sizelimit=10, timelimit=1000 being useful

static java.lang.String FILE
          url component

static java.lang.String FORMAT
          properties key: result biosequence format limited choices now: fasta, native (e.g.

static java.lang.String HOST
          url component

static java.lang.String LISTDN
          properties key: output control; listdn=false for no name

static java.lang.String LISTKEY
          properties key: output control; listkey=false for no field key

static java.lang.String LISTVAL
          properties key: output control; listkey=false for no field value

static java.lang.String OBJECT
          properties key: objectClass to search/retrieve default * gets query summary, objectClasses should be defined in http://iubio.bio.indiana.edu/biogrid/directories/schema/bioseq.schema

static java.lang.String OUTPUT
          properties key: output file, standard output is default

static java.lang.String PATH
          url component

static java.lang.String PORT
          url component

static java.lang.String PROPERTIES
          default properties file

static java.lang.String PROTOCOL
          url component

static java.lang.String QUERY
          properties key: query for databank, data field, etc.

static java.lang.String REF
          url component

static java.lang.String SCOPE
          properties key: search scope, option, sub is default

static java.lang.String START
          properties key: start object number to retrieve from query result

static java.lang.String TITLE
          visible title for url

static java.lang.String URL
          properties key: data directory url; must have

Constructor Summary

Biogridlet()


Biogridlet(java.util.Properties env)


Method Summary

(package private) boolean ldapsearch(java.util.Properties env)


(package private) boolean ldapsearch(java.util.Properties env, java.lang.String ldapurl, java.lang.String scope, java.lang.String filter, java.lang.String[] attr, long sizelimit, int timelimit, boolean derefLinks)


(package private) boolean ldapsearch(java.util.Properties env, java.lang.String ldapurl, java.lang.String scope, java.lang.String filter, java.lang.String[] attr, java.lang.String[] extn)


static void main(java.lang.String[] args)
          run with Biogridlet.props properties and/or command-line options

java.util.Properties parseUrl(java.lang.String url, java.util.Properties h)


void retrieve()


boolean search(java.lang.String url)


void setProperties(java.util.Properties env)


void usage()


Methods inherited from class java.lang.Object

, clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

URL

public static final java.lang.String URL

properties key: data directory url; must have

PROTOCOL

public static final java.lang.String PROTOCOL

url component

HOST

public static final java.lang.String HOST

url component

PORT

public static final java.lang.String PORT

url component

DN

public static final java.lang.String DN

url component

PATH

public static final java.lang.String PATH

url component

FILE

public static final java.lang.String FILE

url component

REF

public static final java.lang.String REF

url component

SCOPE

public static final java.lang.String SCOPE

properties key: search scope, option, sub is default

QUERY

public static final java.lang.String QUERY

properties key: query for databank, data field, etc. to search, ldap query syntax for now

START

public static final java.lang.String START

properties key: start object number to retrieve from query result

COUNT

public static final java.lang.String COUNT

properties key: number of objects to retrieve

OBJECT

public static final java.lang.String OBJECT

properties key: objectClass to search/retrieve default * gets query summary, objectClasses should be defined in http://iubio.bio.indiana.edu/biogrid/directories/schema/bioseq.schema

FORMAT

public static final java.lang.String FORMAT

properties key: result biosequence format limited choices now: fasta, native (e.g. genbank, embl, swissprot, other biosequence formats)

ATTRIBUTES

public static final java.lang.String ATTRIBUTES

properties key: which object fields to return = all, others are defined in http://iubio.bio.indiana.edu/biogrid/directories/schema/bioseq.schema

EXTENSIONS

public static final java.lang.String EXTENSIONS

properties key: ldap extension controls, sizelimit=10, timelimit=1000 being useful

TITLE

public static final java.lang.String TITLE

visible title for url

LISTDN

public static final java.lang.String LISTDN

properties key: output control; listdn=false for no name

LISTKEY

public static final java.lang.String LISTKEY

properties key: output control; listkey=false for no field key

LISTVAL

public static final java.lang.String LISTVAL

properties key: output control; listkey=false for no field value

DEBUG

public static final java.lang.String DEBUG

OUTPUT

public static final java.lang.String OUTPUT

properties key: output file, standard output is default

PROPERTIES

public static final java.lang.String PROPERTIES

default properties file

Constructor Detail

Biogridlet

public Biogridlet()

Biogridlet

public Biogridlet(java.util.Properties env)

Method Detail

main

public static void main(java.lang.String[] args)

run with Biogridlet.props properties and/or command-line options

usage

public void usage()

setProperties

public void setProperties(java.util.Properties env)

search

public boolean search(java.lang.String url)

retrieve

public void retrieve()

ldapsearch

boolean ldapsearch(java.util.Properties env)

ldapsearch

boolean ldapsearch(java.util.Properties env,
                   java.lang.String ldapurl,
                   java.lang.String scope,
                   java.lang.String filter,
                   java.lang.String[] attr,
                   java.lang.String[] extn)

ldapsearch

boolean ldapsearch(java.util.Properties env,
                   java.lang.String ldapurl,
                   java.lang.String scope,
                   java.lang.String filter,
                   java.lang.String[] attr,
                   long sizelimit,
                   int timelimit,
                   boolean derefLinks)

parseUrl

public java.util.Properties parseUrl(java.lang.String url,
                                     java.util.Properties h)

Field Summary
`static java.lang.String`	`ATTRIBUTES` properties key: which object fields to return = all, others are defined in http://iubio.bio.indiana.edu/biogrid/directories/schema/bioseq.schema
`static java.lang.String`	`COUNT` properties key: number of objects to retrieve
`static java.lang.String`	`DEBUG`
`static java.lang.String`	`DN` url component
`static java.lang.String`	`EXTENSIONS` properties key: ldap extension controls, sizelimit=10, timelimit=1000 being useful
`static java.lang.String`	`FILE` url component
`static java.lang.String`	`FORMAT` properties key: result biosequence format limited choices now: fasta, native (e.g.
`static java.lang.String`	`HOST` url component
`static java.lang.String`	`LISTDN` properties key: output control; listdn=false for no name
`static java.lang.String`	`LISTKEY` properties key: output control; listkey=false for no field key
`static java.lang.String`	`LISTVAL` properties key: output control; listkey=false for no field value
`static java.lang.String`	`OBJECT` properties key: objectClass to search/retrieve default * gets query summary, objectClasses should be defined in http://iubio.bio.indiana.edu/biogrid/directories/schema/bioseq.schema
`static java.lang.String`	`OUTPUT` properties key: output file, standard output is default
`static java.lang.String`	`PATH` url component
`static java.lang.String`	`PORT` url component
`static java.lang.String`	`PROPERTIES` default properties file
`static java.lang.String`	`PROTOCOL` url component
`static java.lang.String`	`QUERY` properties key: query for databank, data field, etc.
`static java.lang.String`	`REF` url component
`static java.lang.String`	`SCOPE` properties key: search scope, option, sub is default
`static java.lang.String`	`START` properties key: start object number to retrieve from query result
`static java.lang.String`	`TITLE` visible title for url
`static java.lang.String`	`URL` properties key: data directory url; must have

Constructor Summary
`Biogridlet()`
`Biogridlet(java.util.Properties env)`

Method Summary
`(package private) boolean`	`ldapsearch(java.util.Properties env)`
`(package private) boolean`	`ldapsearch(java.util.Properties env, java.lang.String ldapurl, java.lang.String scope, java.lang.String filter, java.lang.String[] attr, long sizelimit, int timelimit, boolean derefLinks)`
`(package private) boolean`	`ldapsearch(java.util.Properties env, java.lang.String ldapurl, java.lang.String scope, java.lang.String filter, java.lang.String[] attr, java.lang.String[] extn)`
`static void`	`main(java.lang.String[] args)` run with Biogridlet.props properties and/or command-line options
`java.util.Properties`	`parseUrl(java.lang.String url, java.util.Properties h)`
`void`	`retrieve()`
`boolean`	`search(java.lang.String url)`
`void`	`setProperties(java.util.Properties env)`
`void`	`usage()`