[seek-dev] ecogrid's put service for SRB is completed
Jing Tao
tao at nceas.ucsb.edu
Tue Sep 14 17:20:36 PDT 2004
Hi, Bing:
Only one issue I am thinking is how do you deploy the configure file to
$TOMCAT/webapps/ogsa/WEB-INF. Currently we use the build.xml in gt3 to
deploy our gar file to tomcat and I am not sure if the build.xml will copy
the configure file to that directory or not. You may take a look at it. If
it does, will be great. If it doesn't, we need put the configure file into
the jar file which will be deploied to tomcat/webapps/ogsa/WEB-INF/lib and
write a java file to read it from the jar file.
Hope this is helpful.
Thanks.
Jing
On Tue, 14 Sep 2004, Bing Zhu wrote:
> Date: Tue, 14 Sep 2004 10:32:52 -0700
> From: Bing Zhu <bzhu at sdsc.edu>
> To: Jing Tao <tao at nceas.ucsb.edu>
> Cc: Matt Jones <jones at nceas.ucsb.edu>, Arcot Rajasekar <sekar at sdsc.edu>,
> Seek-Dev <seek-dev at ecoinformatics.org>
> Subject: RE: [seek-dev] ecogrid's put service for SRB is completed
>
> Jing,
>
> I found a call in Globus to get the configuration directory, which
> returns the following directory, $TOMCAT//webapps/ogsa/WEB-INF.
> Please check the OpenEcogridConfigFile() in EcogridUtils.java.
>
> Therefore, I put the code to read some configuration info such as
> Metacat URL and debug flag from some configuration files
> for Metacat (MetacatConfig.xml) or SRB (SrbConfig.xml) under
> $TOMCAT//webapps/ogsa/WEB-INF/etc.
>
> Please also check out the MetacatPutImpl.java for reading config
> from a config file and debug message handling which I found ecogrid
> (I guess Rod did it) already had a way to dealing with in EcogridUtils.java.
>
> Bing
>
>
>
>
> -----Original Message-----
> From: Jing Tao [mailto:tao at nceas.ucsb.edu]
> Sent: Monday, September 13, 2004 9:16 AM
> To: Bing Zhu
> Cc: Matt Jones
> Subject: RE: [seek-dev] ecogrid's put service for SRB is completed
>
>
> Hi, Bing:
>
> I still think client user should have responsibility to assign a docid for
> the put document. Ecogrid service don't need to do anything for it.
>
> The MetacatClientTest append ".1" to a docid is because the code is client
> code :) and it has to generate a docid.
>
> The format of docid should look like bing.5.1 or bing.23.2
>
> The first part always is username in knb(but not have to), and second part
> is serial number and the last part is version number.
>
> By the way, the url of Metacat is hard code in the implementation. Do you
> think if is better to read it from a configure file?
>
> Thanks.
>
> Jing
>
> On Fri, 10 Sep 2004, Bing Zhu wrote:
>
> > Date: Fri, 10 Sep 2004 18:03:41 -0700
> > From: Bing Zhu <bzhu at sdsc.edu>
> > To: Jing Tao <tao at nceas.ucsb.edu>, Matt Jones <jones at nceas.ucsb.edu>
> > Subject: RE: [seek-dev] ecogrid's put service for SRB is completed
> >
> > Hi Jing,
> >
> > Thanks for your comments.
> >
> > For the docID, I did some experiments with MatacatClient code and realized
> > that the usage of '.1.' for a document name in Metacat. Actually, I
> > hesitated to
> > put code which appends a '.1' to a filename when uploading a file or
> > inserting a
> > xml document.
> >
> > So the question is which one of the following object ID we expect user
> will
> > use in calling Ecogrid 'put?
> > (1) bing.txt.1
> > (2) bing.txt
> >
> > Note that MetacatClientTest.java has code to append '.1' for each objID in
> > both
> > uploading a file and inserting a XML. Finally I decided to adopt this
> > approach.
> >
> > Let me know .
> >
> > Bing
> >
> >
> >
> >
> >
> >
> > -----Original Message-----
> > From: Jing Tao [mailto:tao at nceas.ucsb.edu]
> > Sent: Friday, September 10, 2004 3:59 PM
> > To: Matt Jones
> > Cc: bzhu at sdsc.edu
> > Subject: Re: [seek-dev] ecogrid's put service for SRB is completed
> >
> >
> > Hi, Bing:
> >
> > I took a look at the put implementation of metacat, it looks good. Thanks.
> >
> > But I have a issue about the docid. In uploadMetacatMetadata method, you
> > generte a new id by combine docid which specified in put operation and a
> > suffix - ".1". This new id will be insert into metacat. So the docid
> > stored in metacat will be different to the docid which user specified in
> > put operation.
> >
> > I guess the reseaon you want add the suffix to docid is because that if
> > docid which will be inserted (not update) into metacat is not end with
> > ".1", metacat will throw an exception. But I think the client user should
> > have
> > the responsibility to make the docid correct for metacat. How do you
> > think?
> >
> > I am still not clear why you don't call metacatClient.update(...) method.
> > If a docid user want put is bing.30.2(it is metacat data), either you
> > should call update() method in metacat client library or like you do now -
> > adding ".1" suffix to "bing.30.2" and call insert(). As I mentioned before
> > the id stored in metacat will be bing.30.2.1 and it is different to
> > bing.30.2
> >
> > If without the change of metacat implementation, I think we have to use
> > update in metacat client library to handle the docid which is not revision
> > one.
> >
> > By the way, above discussion only focus on local indentifier rather than
> > LSID indentifier.
> >
> > This is my two cents :)
> >
> > Jing
> >
> >
> > On Fri, 10 Sep 2004, Matt Jones wrote:
> >
> > > Date: Fri, 10 Sep 2004 07:15:44 -0800
> > > From: Matt Jones <jones at nceas.ucsb.edu>
> > > To: bzhu at sdsc.edu
> > > Cc: Jing Tao <tao at nceas.ucsb.edu>
> > > Subject: Re: [seek-dev] ecogrid's put service for SRB is completed
> > >
> > > Hi Bing,
> > >
> > > No, I didn't mean that. The metacat update command is superfluous given
> > > our decision to not allow revisions in the identifiers. Therefore, I
> > > think there should be three operations:
> > > > login(username, passwd) returns sessionID
> > > > put(...) as designed
> > > > logout(sessionID)
> > >
> > > This means that, depending on the ID, in metacat some put operations
> > > would call Metacat.insert(...) and others would call Metacat.upload(...)
> > > depending on whether its metadata or data that is being put. There
> > > might even be a reason to call Metacat.update(...) from the put routine,
> > > but I don't think so.
> > >
> > > Also, these same three operations should work identically for SRB and
> > > Metacat (ie, no signature differences there, right?).
> > >
> > > Can you ask Jing to take a look at your implementation when you're done
> > > testing? Have you developed some junit test for testing? You could
> > > probably modify the MetacatClientTest.java class pretty easily to do
> > > Ecogrid calls instead in testing.
> > >
> > > Matt
> > >
> > > Bing Zhu wrote:
> > > > Matt,
> > > >
> > > > I finished the coding 'put' for Metacat and checked in the code.
> > > > Currently I am testing the service.
> > > >
> > > > When I reviewed you mail below this morning, I wonder if you mean
> > > > there should be four operations in put service.
> > > > login(username, passwd) returns sessionID
> > > > put(...) as designed
> > > > update() similar to put()
> > > > logout(sessionID)
> > > >
> > > > Note that put actually call 'upload' or 'insert' depending the data
> > type.
> > > >
> > > > Bing
> > > >
> > > >
> > > >
> > > >
> > > >
> > > > -----Original Message-----
> > > > From: Matt Jones [mailto:jones at nceas.ucsb.edu]
> > > > Sent: Monday, August 23, 2004 1:25 PM
> > > > To: bzhu at sdsc.edu
> > > > Cc: Jing Tao; Saurabh Garg; Bertram Ludaescher
> > > > Subject: Re: [seek-dev] ecogrid's put service for SRB is completed
> > > >
> > > >
> > > > Hi Bing,
> > > >
> > > > Welcome back.
> > > >
> > > > The 'get' implementation for metacat's ecogrid interface uses our
> > > > metacat client library. So, I think 'put' should be implemented in a
> > > > parallel way. To do so, you need metacat-client.jar, not
> metacat.jar.
> > > > The easiest way for you to get everything that you need is to check
> > > > out a copy of the 'metacat' and the 'utilities' module out of cvs.
> Your
> > > > current SEEK cvs information should work fine with a command like
> this:
> > > >
> > > > cvs co -P metacat
> > > > cvs co -P utilities
> > > >
> > > > Then, to get the metacat-client.jar, type 'ant clientjar' from within
> > > > the metacat directory, which will create the jar for you in the build
> > > > directory.
> > > >
> > > > The metacat API has three interfaces that are relevant to your 'put'
> > > > implementation:
> > > > insert, update, and upload
> > > > You will also need to utilize the 'login' interface to establish
> > > > identity before being able to write to a service.
> > > >
> > > > These are all defined in the interface file:
> > > > metacat/src/edu/ucsb/nceas/metacat/client/Metacat.java
> > > >
> > > > You and Bertram and I need to discuss your activities for the next few
> > > > weeks -- Bertram and I came up with some possibly higher priority work
> > > > on the ecogrid registry, but I'd like to talk to you and Bertram about
> > > > it for a bit to decide how to prioritize stuff. Can we do that this
> > > > week? Thanks,
> > > >
> > > > Matt
> > > >
> > > > Saurabh Garg wrote:
> > > >
> > > >>Hi Bing,
> > > >>
> > > >>I am not sure about the particulars of put operation in Ecogrid. Hence
> I
> > > >>dont know about the format of the parameter 'object'.
> > > >>
> > > >>Session id is the id you get when you log into metacat. When you log
> > into
> > > >>metacat, the xml that is sent back contains the session id - the id
> that
> > > >
> > > > is
> > > >
> > > >>used to identify you (the user) during the life of the session. Once
> you
> > > >
> > > > log
> > > >
> > > >>out, the session id is deleted from the server. So to get that session
> > id,
> > > >>you will have to do a login first.
> > > >>
> > > >>The most recent jar file is attached. (I hope you were refering to
> this
> > > >
> > > > file
> > > >
> > > >>from the build directory and not an install jar for metacat)
> > > >>
> > > >>Hope that helps,
> > > >>Sid
> > > >>
> > > >>----- Original Message -----
> > > >>From: "Bing Zhu" <bzhu at sdsc.edu>
> > > >>To: "Matt Jones" <jones at nceas.ucsb.edu>; <sgarg at nceas.ucsb.edu>
> > > >>Cc: "Bertram Ludaescher" <ludaesch at sdsc.edu>; "Arcot Rajasekar"
> > > >><sekar at sdsc.edu>; "Jing Tao" <tao at nceas.ucsb.edu>; "Seek-Dev"
> > > >><seek-dev at ecoinformatics.org>
> > > >>Sent: Monday, August 23, 2004 12:03 PM
> > > >>Subject: RE: [seek-dev] ecogrid's put service for SRB is completed
> > > >>
> > > >>
> > > >>
> > > >>
> > > >>>Matt and Sid,
> > > >>>
> > > >>>I am back to my office and would like to start implementation of
> > Ecogrid
> > > >>>'put' for
> > > >>>Metacat. Would you send me the followings.
> > > >>>
> > > >>>1. APIs used for uploading a Metacat document or the metadata for a
> > > >>
> > > >>Metacat
> > > >>
> > > >>
> > > >>>document.
> > > >>>
> > > >>> Basically the 'put' operation in Ecogrid's put service has
> > > >>
> > > >>following
> > > >>
> > > >>
> > > >>>form.
> > > >>> put(object, objectId, type, sessionId)
> > > >>>
> > > >>> The type can be either 'data' or 'metadata'.
> > > >>> In Metacat case, I think, the 'object' will be a byte array
> > which
> > > >>
> > > >>is
> > > >>
> > > >>
> > > >>>actually
> > > >>> the XML string for a XML document or metadata.
> > > >>>
> > > >>>2. The usage of "session ID" in Metacat's uploading function.
> > > >>>3. Latest Metacat jar file.
> > > >>>
> > > >>>Thanks.
> > > >>>
> > > >>>Sincerely,
> > > >>>Bing
> > > >>>
> > > >>>
> > > >>>
> > > >>>
> > > >>>-----Original Message-----
> > > >>>From: seek-dev-admin at ecoinformatics.org
> > > >>>[mailto:seek-dev-admin at ecoinformatics.org]On Behalf Of Jing Tao
> > > >>>Sent: Friday, August 13, 2004 4:12 PM
> > > >>>To: Bing Zhu
> > > >>>Cc: Matt Jones; Bertram Ludaescher; Arcot Rajasekar; Seek-Dev;
> > > >>>sgarg at nceas.ucsb.edu
> > > >>>Subject: Re: [seek-dev] ecogrid's put service for SRB is completed
> > > >>>
> > > >>>
> > > >>>Hi, bing:
> > > >>>
> > > >>>Great! It is glad to know the implementation is done for srb.
> > > >>>
> > > >>>Unfortunately I will be off from Aug. 23 to Aug. 27. If you have some
> > > >>>thing about metacat, you may talk with matt or sid (who is in charge
> > > >>>metacat now and his email is sgarg at nceas.ucsb.edu)
> > > >>>
> > > >>>Have a good vaction!
> > > >>>
> > > >>>Jing
> > > >>>
> > > >>>On Fri, 13 Aug 2004, Bing Zhu wrote:
> > > >>>
> > > >>>
> > > >>>
> > > >>>>Date: Fri, 13 Aug 2004 15:31:27 -0700
> > > >>>>From: Bing Zhu <bzhu at sdsc.edu>
> > > >>>>To: Matt Jones <jones at nceas.ucsb.edu>
> > > >>>>Cc: Bertram Ludaescher <ludaesch at sdsc.edu>, Arcot Rajasekar
> > > >>>
> > > >>><sekar at sdsc.edu>,
> > > >>>
> > > >>>
> > > >>>> Jing Tao <tao at nceas.ucsb.edu>, Seek-Dev
> > > >>
> > > >><seek-dev at ecoinformatics.org>
> > > >>
> > > >>>>Subject: [seek-dev] ecogrid's put service for SRB is completed
> > > >>>>
> > > >>>>Matt,
> > > >>>>
> > > >>>>The 'put' service for SRB has been implemented and tested. I have
> > > >>
> > > >>checked
> > > >>
> > > >>
> > > >>>in
> > > >>>
> > > >>>
> > > >>>>all code, stubs, SRB implementation code and a ecogrid put client.
> > > >>>>
> > > >>>>I will take next week off for a vacation break and will contact you
> > and
> > > >>>
> > > >>>Jing
> > > >>>
> > > >>>
> > > >>>>for the Metacat implementation after I come back (Aug 23).
> > > >>>>
> > > >>>>Sincerely,
> > > >>>>Bing
> > > >>>>
> > > >>>>
> > > >>>>BWT,
> > > >>>>The SRB implementation files:
> > > >>>>src\org\ecoinformatics\ecogrid\srb\put\SrbPutImpl.java
> > > >>>>
> > > >>>
> > > >>>src\org\ecoinformatics\ecogrid\srb\SRBuri.java
> > > >>>
> > > >>>
> > > >>>>Ecogrid put client:
> > > >>>>src\org\ecoinformatics\ecogrid\client\EcogridPutClient.java
> > > >>>>Ecogrid Put stubs from gwsdl:
> src\org\ecoinformatics\ecogrid\stub\...
> > > >>>>
> > > >>>>Currently the put service for SRB system is running in the test
> > machine:
> > > >>>>
> > > >>>>
> > > >>>
> > > >
> >
> http://sasa.sdsc.edu:8080/ogsa/services/org/ecoinformatics/ecogrid/EcoGridLe
> > > >
> > > >>>>velOnePutService
> > > >>>> (for web browser: http://sasa.sdsc.edu:8080/ogsa/services)
> > > >>>>
> > > >>>>_______________________________________________
> > > >>>>seek-dev mailing list
> > > >>>>seek-dev at ecoinformatics.org
> > > >>>>http://www.ecoinformatics.org/mailman/listinfo/seek-dev
> > > >>>>
> > > >>>
> > > >>>--
> > > >>>Jing Tao
> > > >>>National Center for Ecological
> > > >>>Analysis and Synthesis (NCEAS)
> > > >>>735 State St. Suite 204
> > > >>>Santa Barbara, CA 93101
> > > >>>
> > > >>>_______________________________________________
> > > >>>seek-dev mailing list
> > > >>>seek-dev at ecoinformatics.org
> > > >>>http://www.ecoinformatics.org/mailman/listinfo/seek-dev
> > > >>
> > > >
> > > > --
> > > > -------------------------------------------------------------------
> > > > Matt Jones jones at nceas.ucsb.edu
> > > > http://www.nceas.ucsb.edu/ Fax: 425-920-2439 Ph: 907-789-0496
> > > > National Center for Ecological Analysis and Synthesis (NCEAS)
> > > > University of California Santa Barbara
> > > > Interested in ecological informatics? http://www.ecoinformatics.org
> > > > -------------------------------------------------------------------
> > >
> > >
> >
> > --
> > Jing Tao
> > National Center for Ecological
> > Analysis and Synthesis (NCEAS)
> > 735 State St. Suite 204
> > Santa Barbara, CA 93101
> >
> >
>
> --
> Jing Tao
> National Center for Ecological
> Analysis and Synthesis (NCEAS)
> 735 State St. Suite 204
> Santa Barbara, CA 93101
>
> _______________________________________________
> seek-dev mailing list
> seek-dev at ecoinformatics.org
> http://www.ecoinformatics.org/mailman/listinfo/seek-dev
>
--
Jing Tao
National Center for Ecological
Analysis and Synthesis (NCEAS)
735 State St. Suite 204
Santa Barbara, CA 93101
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