oodt-dev mailing list archives

Site index · List index
Message view « Date » · « Thread »
Top « Date » · « Thread »
From "Mattmann, Chris A (398J)" <chris.a.mattm...@jpl.nasa.gov>
Subject Re: Apache Airavata-OODT Integration
Date Sat, 15 Jun 2013 19:21:57 GMT
Hey Sanjaya, sure +1 use the Filename. It's not guaranteed to be unique,
but you can easily just pop the first one off the top (latest) and take
that (since it's sorted by product received time). You may check out the
pcs-core module and some of its internal classes like FileManagerUtils
to see some cool helper functions that could aid in this regard.

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: Saturday, June 15, 2013 4:04 AM
To: Airavata Dev <dev@airavata.apache.org>
Subject: Re: Apache Airavata-OODT Integration

>Thanks Chris for your help! Working directory is available in
>JobExecutionContext in Airavata and directory can easily be retrieved.
>Issue in my case is that, from XBaya GUI I take product id as input not
>the
>file name. Internally file stager query the file manager using product id
>to retrieve product reference and corresponding file name to stage the
>file
>into input dir. Since this product id to file name mapping happens
>internally during the file staging, my implementation don't have access to
>filename unless I query the file manager to retrieve the corresponding
>file
>name using product id.
>
>One of the major issue in my implementation seems that I use OODT product
>id as input, not the file name. Should I change my implementation to use
>file name instead of product id ?
>
>Best Regards,
>Sanjaya
>
>
>On Fri, Jun 14, 2013 at 8:51 PM, Mattmann, Chris A (398J) <
>chris.a.mattmann@jpl.nasa.gov> wrote:
>
>> Hey Sanjaya,
>>
>> Easy, see the attached PGEConfig.xml here:
>>
>> http://paste.apache.org/6OGW
>>
>> In that file:
>>
>> 1. We compute the staged file path by computing JobDir
>> 2. We create in the exe block a staged input dir
>> 3. We stage the files just using cps in the exeBlock (could have
>> just as easily used fileStager)
>> 4. We know that the file is [JobInputDir]/[Filename]
>>
>> HTH.
>>
>> 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: Friday, June 14, 2013 5:02 AM
>> To: Airavata Dev <dev@airavata.apache.org>
>> Subject: Re: Apache Airavata-OODT Integration
>>
>> >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-con
>> >>fi
>> >> 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
>> >> >> >> 
>>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>> >> >> >>
>> >> >> >>
>> >> >> >>
>> >> >> >>
>> >> >>
>> >> >>
>> >>
>> >>
>>
>>


Mime
View raw message