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Date: Fri, 14 Jun 2013 17:32:30 +0530
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Subject: Re: Apache Airavata-OODT Integration
From: Sanjaya Medonsa <sanjayamrt@gmail.com>
To: Airavata Dev <dev@airavata.apache.org>
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Thanks Chris for your input. I actually use the PGETaskInstance for file
staging with minimal additional code. But my issue issue not with the file
staging. As per my current implementation, application inputs product id.
Then using the capabilities in PGETaskInstance class, it does the file
staging. But my issue is that during the file staging product is mapped to
a file in specified working directory. I don't have a way to retrieve the
staged file name, as it is not recorded in Metadata (For this purpose, I
query the FileManager again to get the corresponding reference name for a
given product id). I need the staged file path, since I modify the input
product id into staged file path prior to actual workflow invocation.
Basically I am looking for some implementation where I can easily retrieve,
staged file path for a given product id.

Cheers,
Sanjaya


On Wed, Jun 12, 2013 at 10:04 PM, Mattmann, Chris A (398J) <
chris.a.mattmann@jpl.nasa.gov> wrote:

> Hi Sanjaya,
>
> -----Original Message-----
>
> From: Sanjaya Medonsa <sanjayamrt@gmail.com>
> Reply-To: "dev@airavata.apache.org" <dev@airavata.apache.org>
> Date: Monday, June 10, 2013 5:20 PM
> To: "dev@airavata.apache.org" <dev@airavata.apache.org>
> Cc: "dev@oodt.apache.org" <dev@oodt.apache.org>
> Subject: Re: Apache Airavata-OODT Integration
>
> >Hi Chris,
> >       On configuration, I have get rid of all the configuration files,
> >including pge-config.xml. All the required configurations are
> >programmatically set.  Configurations such FileManagerServer URL are
> >configured in the airavata-server.properties file. I'll update the review
> >request with modified details.
>
> Great work!
>
>
> >       Still I am not quite clear on how to retrieve staged file path
> >properly. Currently I am using getStagedFilePath method
> >in ApacheAiravataWorkFlowInstanceImpl to regenerate the staged file path.
> >While I am going through the OODT code that I have seen method in
> >DataTransferer to notify FileManagerServer once transfer is completed. But
> >I couldn't see the same for product retrieval.
>
> Example:
> http://svn.apache.org/repos/asf/oodt/trunk/pge/src/test/resources/pge-confi
> g.xml
>
>
> Review Board tickets:
> https://reviews.apache.org/r/4746/
>
> https://reviews.apache.org/r/5382/
>
>
> JIRA issue source (in OODT since 0.4):
>   https://issues.apache.org/jira/browse/OODT-443
>
>
> >       As you suggested I'll improve my workflow using Apache Tika. I'd
> >like to continue this as an Parallal task. While modifying staging
> >implementation based on community feedback, currently I am looking at
> >ingesting output back to OODT.
>
> See above for info on file staging. I would strongly encourage you not
> to reimplement CAS-PGE in Airavata -- it's pretty functional and expressive
> anyways and I would work to figure out how to make Airavata leverage
> CAS-PGE.
>
> Cheers,
> Chris
>
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> Chris Mattmann, Ph.D.
> Senior Computer Scientist
> NASA Jet Propulsion Laboratory Pasadena, CA 91109 USA
> Office: 171-266B, Mailstop: 171-246
> Email: chris.a.mattmann@nasa.gov
> WWW:  http://sunset.usc.edu/~mattmann/
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> Adjunct Assistant Professor, Computer Science Department
> University of Southern California, Los Angeles, CA 90089 USA
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
>
>
> >
> >
> >
> >On Wed, Jun 5, 2013 at 12:11 AM, Mattmann, Chris A (398J) <
> >chris.a.mattmann@jpl.nasa.gov> wrote:
> >
> >> Hi Sanjaya,
> >>
> >> I think starting out with /bin/ls would be good, maybe like a /bin/ls
> >> workflow, and then for each file returned, maybe run Apache Tika and
> >> extract its metadata and then pipe that to a file?
> >>
> >> How about that?
> >>
> >> Cheers,
> >> Chris
> >>
> >> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> >> Chris Mattmann, Ph.D.
> >> Senior Computer Scientist
> >> NASA Jet Propulsion Laboratory Pasadena, CA 91109 USA
> >> Office: 171-266B, Mailstop: 171-246
> >> Email: chris.a.mattmann@nasa.gov
> >> WWW:  http://sunset.usc.edu/~mattmann/
> >> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> >> Adjunct Assistant Professor, Computer Science Department
> >> University of Southern California, Los Angeles, CA 90089 USA
> >> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> >>
> >>
> >>
> >>
> >>
> >>
> >> -----Original Message-----
> >> From: Sanjaya Medonsa <sanjayamrt@gmail.com>
> >> Reply-To: "dev@airavata.apache.org" <dev@airavata.apache.org>
> >> Date: Tuesday, June 4, 2013 5:31 AM
> >> To: "dev@airavata.apache.org" <dev@airavata.apache.org>
> >> Cc: "dev@oodt.apache.org" <dev@oodt.apache.org>
> >> Subject: Re: Apache Airavata-OODT Integration
> >>
> >> >Hi Chris,
> >> >     Please see my comments below on the two items.
> >> >
> >> >Configuration : It should be possible to set them programmatically.
> >> >Actually I have implemented partly it for file staging information.
> >>I'll
> >> >work to get rid of the other configuration files.
> >> >
> >> >Staged File Path : I'll work on the suggested approach, though I am not
> >> >fully understand it at the moment. I guess I need to go through bit
> >>more
> >> >on
> >> >CAS-PGE and come back to you on the proposed approach.
> >> >
> >> >Currently I am testing this by wrapping /bin/ls command as GFac
> >>service. I
> >> >may need to test this with real workflow. Could you please provide me
> >>know
> >> >some guidance on better scenario to test this.
> >> >
> >> >Cheers,
> >> >Sanjaya
> >> >
> >> >
> >> >
> >> >
> >> >On Mon, Jun 3, 2013 at 8:17 PM, Mattmann, Chris A (398J) <
> >> >chris.a.mattmann@jpl.nasa.gov> wrote:
> >> >
> >> >> Hi Sanjaya,
> >> >>
> >> >> -----Original Message-----
> >> >>
> >> >> From: Sanjaya Medonsa <sanjayamrt@gmail.com>
> >> >> Reply-To: "dev@airavata.apache.org" <dev@airavata.apache.org>
> >> >> Date: Thursday, May 30, 2013 5:12 AM
> >> >> To: "dev@oodt.apache.org" <dev@oodt.apache.org>,
> >> >>"dev@airavata.apache.org"
> >> >> <dev@airavata.apache.org>
> >> >> Subject: Apache Airavata-OODT Integration
> >> >>
> >> >> >Hi,
> >> >> >     I have worked on the Apache Airavata integration with Apache
> >> >>OODT. As
> >> >> >a first step, I have implemented integration with Apache OODT file
> >> >> >manager component.
> >> >>
> >> >> Great work!!
> >> >>
> >> >> Comments below:
> >> >>
> >> >> >      1. Introduce a new GFac Schema type called OODTProduct which
> >> >>takes
> >> >> >APache OODT product IDs as input.
> >> >> >      2. Implemented new pre GFac Handler by extending Apache OODT
> >> >> >PgeTaskInstance to stage the corresponding file into the working
> >> >> >directory.
> >> >> >      3. Once file is staged, input parameter with OODT product id
> >>is
> >> >> >replaced with path of the staged file for downstream processing
> >> >> >
> >> >> >I have tested the implementation with Gfac application which wraps
> >> >>/bin/ls
> >> >> >command. Application takes product id as input and stage
> >>corresponding
> >> >> >file
> >> >> >into the working directory and /bin/ls is executed against the
> >>staged
> >> >> >file.
> >> >> >Hope this is a valid testing scenario.
> >> >> >
> >> >> >Concerns
> >> >> >- Configurations : I have added new configuration file named and
> >> >> >oodt-integration.properties in addition to dynamic_metadata.met and
> >> >> >pge-config.xml files used by OODT. But at the moment there is no
> >>item
> >> >> >configured with the oodt-integration.properties.
> >> >>
> >> >> You probably only need the pge-config.xml file. Dynamic metadata, and
> >> >>the
> >> >> task configuration properties can be specified programmatically,
> >>right?
> >> >>
> >> >> >- Staged File Name - With the current implementation of
> >> >>PgeTaskInstance it
> >> >> >is not possible to retrieve path of the staged file. Due to this
> >> >> >limitation, I have query the FileManagerServer with product id and
> >> >> >retrieve
> >> >> >the file name and computed the file path using information of
> >>working
> >> >> >directory.
> >> >>
> >> >> I'm not sure I understand this? If you store and record the Filename,
> >> >>and
> >> >> FileLocation
> >> >> metadata files, then you can easily retrieve the staged file path
> >>via a
> >> >> SQLquery
> >> >> via CAS-PGE by simply setting the FORMAT=('$FileLocation/$Filename')
> >>in
> >> >> the response.
> >> >> Can you comment on this?
> >> >>
> >> >> >- Currently it is not possible to execute the workflow using Xbaya
> >>due
> >> >>to
> >> >> >validation failure due to new schema type. I have commented out the
> >> >> >relevant validation code for testing purpose.
> >> >>
> >> >> OK, will probably need to work on this.
> >> >>
> >> >> >
> >> >> >Currently I am having an issue with review board client tool and
> >>need
> >> >>to
> >> >> >resolve it to upload the code for review.
> >> >>
> >> >> I see later that you got this working, so will head over and review
> >>that
> >> >> now.
> >> >>
> >> >> Thanks!
> >> >>
> >> >> Cheers,
> >> >> Chris
> >> >>
> >> >> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> >> >> Chris Mattmann, Ph.D.
> >> >> Senior Computer Scientist
> >> >> NASA Jet Propulsion Laboratory Pasadena, CA 91109 USA
> >> >> Office: 171-266B, Mailstop: 171-246
> >> >> Email: chris.a.mattmann@nasa.gov
> >> >> WWW:  http://sunset.usc.edu/~mattmann/
> >> >> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> >> >> Adjunct Assistant Professor, Computer Science Department
> >> >> University of Southern California, Los Angeles, CA 90089 USA
> >> >> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> >> >>
> >> >>
> >> >>
> >> >>
> >>
> >>
>
>

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