Hi,
I am trying to ingest a large number of files. The metadata for these files
exist in .met files.
Many of the metadata fields contain characters like '$' etc.
Running crawler on these metadata results in failure.
When I try to escape the characters using HTML encode e.g. '' becomes gt etc
Hi Kos,
I take you up on your challenge ;) However I don't know if this will fix it.
On Tue, Oct 7, 2014 at 11:31 PM, Konstantinos Mavrommatis
kmavromma...@celgene.com wrote:
valsailfish quant --index
/reference/v1/Homo-sapiens/GRCh37.p12/SailFishIndex --libtype
'T=PE:O=:S=AS' -1 (gunzip -c
Hello,
I am still having trouble getting my CAS PGE crawler task to run due to
http://localhost:2001 being down. I have spent the last 2 days tracing
through the resource manager code and tracked this down to line 146 of
LRUScheduler where the XmlRpcBatchMgr is failing to execute the task
Well then, I'm proud to be a member :) (I think )
Valerie A. Mallder
New Horizons Deputy Mission System Engineer
Johns Hopkins University/Applied Physics Laboratory
-Original Message-
From: Bruce Barkstrom [mailto:brbarkst...@gmail.com]
Sent: Wednesday, October 08, 2014 4:54
Valerie,
I would have thought it would have just not used a batch stub by default. That
said if you go into the $OODT_HOME/resmgr/bin there should be a script to start
a batch stub. Right now on my phone I forget the name of the script but if you
more the file you will see the Java class name
Hi Paul,
Thank you for replying. I found the batch_stub script (Duh!). I was so busy
looking at java code that I never looked in the bin dir. So, I ran batch_stub
with the expected port number, and I made a little more progress, batch_stub
actually received the job! The learn by example
Dynamite Angela.
Thanks for your persistence.
On Sat, Oct 4, 2014 at 8:22 PM, MengYing Wang mengyingwa...@gmail.com
wrote:
Dear Lewis,
Done. This is the jira url: https://issues.apache.org/jira/browse/OODT-756
Best,
Mengying Wang
On Tue, Sep 30, 2014 at 6:59 PM, Lewis John Mcgibbney
Hi Valerie,
All I am trying to do is run crawler_launcher as a workflow task in
the CAS PGE environment.
Interesting. I have a working example here [1] you can look at that does this
exact thing.
So, if batchstub is necessary in this scenario, pleast tell me what
it is, why it is
Hi Rishi,
Thank you very much for pointing me to your working example. This is very
helpful. My pgeConfig looks very similar to yours. So, I commented out the
resource manager like you suggested and tried running again without the
resource manager. And my problem still exists. The problem is
Hi Lewis
I escaped the characters using the CGI::escapeHTML function from the CGI perl
module.
The differences between the two versions (mine escaped vs yours escaped) is in
the encoding of the single quote ' character, if I am not mistaken. I want to
clarify this because your email come as
Take courage. It's essential.
Believe it or not you have a new persona.
Welcome to your new community.
On Wed, Oct 8, 2014 at 5:03 PM, Mallder, Valerie valerie.mall...@jhuapl.edu
wrote:
Well then, I'm proud to be a member :) (I think )
Valerie A. Mallder
New Horizons Deputy Mission
Hi Val,
Yep - here’s a link to the tasks.xml file:
https://github.com/riverma/xdata-jpl-netscan/blob/master/oodt-netscan/workflow/src/main/resources/policy/tasks.xml
The problem is that the ExternScriptTaskInstance is unable to recognize the
command line arguments that I want to pass to the
Folks,
Is it possible to create a parent issue for defining XSD's for all of the
XML file we need ti OODT?
I do not know them all, but from this thread alone, it is clear that we
could do with setting some kind of restrictions on what can be included
within task and configuration XML within OODT.
During the last month, I managed to get a fairly difficult installation task
to work on software I felt I had a critical need for. I've attached the
documentation I wrote as I went through the experience describing
what I had to do. I think we often denigrate writing documentation at
the level
Hi Kos,
Thanks for reply
On Wed, Oct 8, 2014 at 5:16 PM, Konstantinos Mavrommatis
kmavromma...@celgene.com wrote:
I escaped the characters using the CGI::escapeHTML function from the CGI
perl module.
Wow. I am surpised at this one. I wonder if this is a bug which results in
the discrepancy
In addition, if you can get to the bottom of what you think the intended
behaviour is here, please feel free to log a ticket in Jira
https://issues.apache.org/jira/browse/OODT/?selectedTab=com.atlassian.jira.jira-projects-plugin:issues-panel
On Wed, Oct 8, 2014 at 5:59 PM, Lewis John Mcgibbney
+1 billion
--Paul
Sent from my iPhone
On Oct 8, 2014, at 5:55 PM, Lewis John Mcgibbney lewis.mcgibb...@gmail.com
wrote:
Folks,
Is it possible to create a parent issue for defining XSD's for all of the
XML file we need ti OODT?
I do not know them all, but from this thread alone, it is
Yep woot! Committed!
Chris Mattmann
chris.mattm...@gmail.com
-Original Message-
From: Lewis John Mcgibbney lewis.mcgibb...@gmail.com
Reply-To: dev@oodt.apache.org
Date: Thursday, October 9, 2014 at 12:01 AM
To: MengYing Wang mengyingwa...@gmail.com
Cc: Chris
cas-metadata should handle this escaping/unescaping in its
SerDe capabilities.
Kostsas, can yo provide the exact file that I can test on and upload it to
JIRA?
Chris Mattmann
chris.mattm...@gmail.com
-Original Message-
From: Lewis John Mcgibbney
Thanks Chris,
attached is an offending file before escape.
For the record perl module HTML::Entities does provide an escapeHTML
alternative that produces acceptable files.
Thanks
K
-Original Message-
From: Chris Mattmann [mailto:chris.mattm...@gmail.com]
Sent: Wednesday, October
Hi Val,
I don¹t think you need to run a CAS-PGE task to call
crawler_launcher. If you define blocks in the output../output
section of the XML file, a crawler will be forked in the job working
directory of CAS-PGE and crawl your specified output.
I believe that will accomplish the same goal of
ack, git push
Chris Mattmann
chris.mattm...@gmail.com
-Original Message-
From: Ramirez, Paul M (398J) paul.m.rami...@jpl.nasa.gov
Reply-To: dev@oodt.apache.org
Date: Thursday, October 9, 2014 at 4:37 AM
To: dev@oodt.apache.org dev@oodt.apache.org
Subject: Re:
Thanks Kostas. Can you upload somewhere and then point here, the
message list strips attachments..
Cheers,
Chris
Chris Mattmann
chris.mattm...@gmail.com
-Original Message-
From: Konstantinos Mavrommatis kmavromma...@celgene.com
Reply-To: dev@oodt.apache.org
Valerie,
This could be nothing, or it could be the root cause...your output XML tags
are malformed.
!-- Files to ingest --
output/
/output
Should be:
!-- Files to ingest --
output
/output
No trailing slash in the opening tag. It might be failing since it cannot
parse the XML
Here is the offending file before escape:
cas:metadata xmlns:cas=http://oodt.jpl.nasa.gov/1.0/cas;
keyval
keyderived_from/key
val/gpfs/celgene/reference/v1/Homo-sapiens/GRCh37.p12/SailFishIndex/val
25 matches
Mail list logo
