[Biojava-dev] Biojava and webservices

Wed Jun 18 08:05:33 EDT 2003

Sounds great!

I think the only problem with including a new jar is if it is under a more restrictive lisence than biojava. It is also nice if it is optional (ie not needed for the core of biojava to build). We can for example make sub projects that are somewhat independent of the core biojava.

- Mark

	-----Original Message----- 
	From: Simon Foote [mailto:simon.foote at nrc-cnrc.gc.ca] 
	Sent: Tue 17/06/2003 6:30 a.m. 
	To: Carlisia P. Campos 
	Cc: Schreiber, Mark; biojava-dev at biojava.org 
	Subject: Re: [Biojava-dev] Biojava and webservices

	Hi Guys,

	To add further to this discussion, I've been working a lot with BioSQL
	recently and have implemented a web application/service for
	browsing/searching a BioSQL database.  It's in a beta stage right now,
	and appears to work fine under our loads.  Not sure how it will perform
	under heavy loads.

	In order to do this efficiently, I modified the BioSQLSequenceDB
	implementation to allow the use of an external database pooling system
	(instead of the simple one built into biojava).  This does in fact speed
	up the data access when compared to the existing pooling system.

	The only gotcha to this, is I'm not sure of the biojava take on
	including external libraries.  In this case, its based on the apache
	commons-dbcp and commons-pool packages.  I did notice a commons-cli.jar
	package in the biojava distribution, so I'm guessing it has been done.

	The changes I've made are basically:

	1) Replaced the JDBCConnectionPool class with a JDBCPoolingDataSource
	(backed the the commons-dbcp and -pool packages)

	2) Modified BioSQLSequenceDB to contain 2 constructors:
	        BioSQLSequenceDB(dbDriver, dbURL, dbUser, dbPass, biodatabase,
	create)
	             - this one creates a datasource using the
	JDBCPoolingDataSource class, then initializes the biodatabase
	       BioSQLSequenceDB(dataSource, biodatabase, create)
	             - this one takes an existing datasource and just
	initializes the biodatabase
	 Note: in order for this not break exisiting code, I would have to add a
	3rd constructor that doesn't take the dbDriver and then within the
	DbHelper class, have that set the driver based on the dbURL (this would
	work 99% of the time, probably would only fail with those using
	non-standard drivers)

	3) Made changes to all the biosql classes for getting connections from
	pool.takeConnection() to dataSource.getConnection()

	4) Made changes to all the biosql classes for closing connections from
	pool.putConnection(conn) to conn.close()

	I only just finished doing and testing this within the last hour, so
	probably still needs work, although it has worked for all the browsing
	and searching tests I've thrown at it so far.

	Thoughts,
	Simon Foote

	--
	Bioinformatics Specialist
	Institute for Biological Sciences
	National Research Council of Canada
	[T] 613-990-0561  [F] 613-952-9092
	simon.foote at nrc-cnrc.gc.ca

	Carlisia P. Campos wrote:

	>Hi Mark,
	>
	>Alright. I am at the very initial phase and should be done in two
	>months. I will be deploying it on my server so when it's done I'll let
	>you know and you can try it. I will most definitely give you all the
	>code and documentation, so in the case you try it and find it
	>interesting you can extend/maintain it for biojava. If in the mean time
	>you think of something super interesting that you would like to see
	>deployed as a web service pls let me know and I'll try to get it in.
	>
	>Best,
	>--Carlisia
	>
	>
	>On Sunday, June 15, 2003, at 03:15  AM, Schreiber, Mark wrote:
	>
	> 
	>
	>>Hi Carlista -
	>>
	>>I for one would be very interested. I think if you posted an example
	>>we could put it in the repository as an example or on the biojava in
	>>anger web page.
	>>
	>>- Mark
	>>
	>>
	>>-----Original Message-----
	>>From: Carlisia Campos [mailto:carlisia at bu.edu]
	>>Sent: Sat 14/06/2003 10:02 a.m.
	>>To:   biojava-dev at biojava.org
	>>Cc:  
	>>Subject:      [Biojava-dev] Biojava and webservices
	>>
	>>Hello there,
	>>
	>>
	>>I am working on a school project for my masters degree at Boston
	>>University and
	>>decided to use biojava as a basis for it. My project involves
	>>developing a set
	>>of web services that "serves" results of method calls to biojava over
	>>http. I
	>>don't intend to develop web services for the entire biojava API, but
	>>enough to
	>>put together a nice sample application.
	>>
	>>If you have any interest in this please let me know. I would love to
	>>donate
	>>whatever I develop to you if you think it is useful. I am looking to
	>>find out
	>>if there is anything in specific you would like to see deployed, or
	>>any other
	>>insight you wish to provide as I start thinking about what in specific
	>>I am
	>>going to implement.
	>>
	>>Best regards,
	>>--Carlisia Campos
	>>_______________________________________________
	>>biojava-dev mailing list
	>>biojava-dev at biojava.org
	>>http://biojava.org/mailman/listinfo/biojava-dev
	>>
	>>
	>>
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	>
	>::carlisia::
	>::www.carlisia.com::6178174587 at mobile.att.net::
	>
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	>biojava-dev at biojava.org
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	> 
	>

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