Publication Enrichment widget error

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Publication Enrichment widget error

kkarra@stanford.edu
Hi Julie,
That fixed it, thanks!
-Kalpana

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Sent: Tuesday, January 31, 2012 4:00:01 AM
Subject: dev Digest, Vol 32, Issue 20

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Today's Topics:

   1. read userprofile (jab250)
   2. Re: read userprofile (Julie Sullivan)
   3. Re: read userprofile (J.A. Blackshaw)
   4. Re: read userprofile (Julie Sullivan)
   5. Re: feature request tracker (Benjamin Hitz)
   6. Publication Enrichment widget error (Kalpana Karra)
   7. Re: Publication Enrichment widget error (Julie Sullivan)


----------------------------------------------------------------------

Message: 1
Date: Mon, 30 Jan 2012 12:45:17 +0000
From: jab250 <[hidden email]>
To: <[hidden email]>
Subject: [InterMine Dev] read userprofile
Message-ID: <[hidden email]>
Content-Type: text/plain; charset=UTF-8; format=flowed

 Hi,

 The MitoMiner Userprofile database currently stands at around 112MB.
 I've been trying to port it according to the instructions on the
 Intermine website, but it's needing around 8 GB of memory to do so,
 which means upgrading the release server. Is it normal to require so
 much memory? I've tried copying the database directly from the
 development server, but even when the data are the same in both records
 databases, the website fails to release. If I copy the userprofile
 database over as a gzip file and unpack it, does everything including
 the name of each database have to be identical? The data are, but the
 database names are different.

 Regards,
 James




------------------------------

Message: 2
Date: Mon, 30 Jan 2012 13:05:15 +0000
From: Julie Sullivan <[hidden email]>
To: [hidden email]
Subject: Re: [InterMine Dev] read userprofile
Message-ID: <[hidden email]>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Can you write/read the XML on the dev server?

On 30/01/12 12:45, jab250 wrote:
> Hi,
>
> The MitoMiner Userprofile database currently stands at around 112MB. I've been
> trying to port it according to the instructions on the Intermine website, but
> it's needing around 8 GB of memory to do so, which means upgrading the release
> server. Is it normal to require so much memory? I've tried copying the database

No, that's not really normal.

> directly from the development server, but even when the data are the same in
> both records databases, the website fails to release. If I copy the userprofile

Do you still have the error messages from when this failed?

> database over as a gzip file and unpack it, does everything including the name
> of each database have to be identical? The data are, but the database names are
> different.

The database names can be different, the webapp uses the properties file
(.intermine/mitomine.properties) to get the database names.

What's important is the InterMine IDs of the objects are the same.  eg.
`gene.id`, the ID you see in the URL.  This ID (eg. gene.id) is what's used in
the userprofile database.  This ID changes with each build of the database and
that's what the write/read userprofile XML process updates.

So you should be able to do this:

  1. write/read userprofile database XML on dev server
  2. dump userprofile database, copy dump over to release server, restore to
userprofile db
  3. release new webapp on release server
        - new production database
        - new userprofile
        - make sure mitomine.properties has correct database names

> Regards,
> James
>
>
> _______________________________________________
> dev mailing list
> [hidden email]
> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>



------------------------------

Message: 3
Date: 30 Jan 2012 15:05:49 +0000
From: "J.A. Blackshaw" <[hidden email]>
To: Julie Sullivan <[hidden email]>
Cc: [hidden email]
Subject: Re: [InterMine Dev] read userprofile
Message-ID: <[hidden email]>
Content-Type: text/plain; format=flowed; charset=ISO-8859-1

Yes, I can. My first thought was to read it on that one, dump the
userprofile there and export it to the release server. However, if I do
that, I get a blank website when I release the webapp. This doesn't happen
if I use a userprofile database I create from scratch.

-James

On Jan 30 2012, Julie Sullivan wrote:

>Can you write/read the XML on the dev server?
>
>On 30/01/12 12:45, jab250 wrote:
>> Hi,
>>
>> The MitoMiner Userprofile database currently stands at around 112MB.
>> I've been trying to port it according to the instructions on the
>> Intermine website, but it's needing around 8 GB of memory to do so,
>> which means upgrading the release server. Is it normal to require so
>> much memory? I've tried copying the database
>
>No, that's not really normal.
>
>> directly from the development server, but even when the data are the
>> same in both records databases, the website fails to release. If I copy
>> the userprofile
>
>Do you still have the error messages from when this failed?
>
>> database over as a gzip file and unpack it, does everything including
>> the name of each database have to be identical? The data are, but the
>> database names are different.
>
>The database names can be different, the webapp uses the properties file
>(.intermine/mitomine.properties) to get the database names.
>
> What's important is the InterMine IDs of the objects are the same. eg.
> `gene.id`, the ID you see in the URL. This ID (eg. gene.id) is what's
> used in the userprofile database. This ID changes with each build of the
> database and that's what the write/read userprofile XML process updates.
>
>So you should be able to do this:
>
>  1. write/read userprofile database XML on dev server
>  2. dump userprofile database, copy dump over to release server, restore
> to userprofile db
>  3. release new webapp on release server
> - new production database
> - new userprofile
> - make sure mitomine.properties has correct database names
>
>> Regards,
>> James
>>
>>
>> _______________________________________________
>> dev mailing list
>> [hidden email]
>> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>>
>
>_______________________________________________
>dev mailing list
>[hidden email]
>http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>



------------------------------

Message: 4
Date: Mon, 30 Jan 2012 15:18:34 +0000
From: Julie Sullivan <[hidden email]>
To: "J.A. Blackshaw" <[hidden email]>
Cc: [hidden email]
Subject: Re: [InterMine Dev] read userprofile
Message-ID: <[hidden email]>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Hmn, that should work, it doesn't like something in your userprofile.

Can you take a look in your webapp log files and tell me what error messages you
see?  Maybe you can just send them to me?  You want the error messages with the
timestamp matching when you tried to access your webapp.


        $TOMCAT/intermine.log
        $TOMCAT/logs/catalina.out
        $TOMCAT/logs/localhost-$DATE


I know you have custom code and it's time consuming, but I would start thinking
about upgrading to 0.98.  You won't have to upgrade your userprofile at all!
Also, you don't get that "blank page" anymore.  Instead, the webapp gives you a
nice helpful error message to let you know what's gone wrong.

On 30/01/12 15:05, J.A. Blackshaw wrote:

> Yes, I can. My first thought was to read it on that one, dump the userprofile
> there and export it to the release server. However, if I do that, I get a blank
> website when I release the webapp. This doesn't happen if I use a userprofile
> database I create from scratch.
>
> -James
>
> On Jan 30 2012, Julie Sullivan wrote:
>
>> Can you write/read the XML on the dev server?
>>
>> On 30/01/12 12:45, jab250 wrote:
>>> Hi,
>>>
>>> The MitoMiner Userprofile database currently stands at around 112MB. I've
>>> been trying to port it according to the instructions on the Intermine
>>> website, but it's needing around 8 GB of memory to do so, which means
>>> upgrading the release server. Is it normal to require so much memory? I've
>>> tried copying the database
>>
>> No, that's not really normal.
>>
>>> directly from the development server, but even when the data are the same in
>>> both records databases, the website fails to release. If I copy the userprofile
>>
>> Do you still have the error messages from when this failed?
>>
>>> database over as a gzip file and unpack it, does everything including the
>>> name of each database have to be identical? The data are, but the database
>>> names are different.
>>
>> The database names can be different, the webapp uses the properties file
>> (.intermine/mitomine.properties) to get the database names.
>>
>> What's important is the InterMine IDs of the objects are the same. eg.
>> `gene.id`, the ID you see in the URL. This ID (eg. gene.id) is what's used in
>> the userprofile database. This ID changes with each build of the database and
>> that's what the write/read userprofile XML process updates.
>>
>> So you should be able to do this:
>>
>> 1. write/read userprofile database XML on dev server
>> 2. dump userprofile database, copy dump over to release server, restore to
>> userprofile db
>> 3. release new webapp on release server
>> - new production database
>> - new userprofile
>> - make sure mitomine.properties has correct database names
>>
>>> Regards,
>>> James
>>>
>>>
>>> _______________________________________________
>>> dev mailing list
>>> [hidden email]
>>> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>>>
>>
>> _______________________________________________
>> dev mailing list
>> [hidden email]
>> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>>
>



------------------------------

Message: 5
Date: Mon, 30 Jan 2012 12:00:29 -0800
From: Benjamin Hitz <[hidden email]>
To: Julie Sullivan <[hidden email]>
Cc: [hidden email]
Subject: Re: [InterMine Dev] feature request tracker
Message-ID: <[hidden email]>
Content-Type: text/plain; charset=us-ascii


Both?  I sometimes can't remember if we've requested stuff.   Also, we are re-doing our internal tracker, and I imagine there will be feature/bug reports in "YeastMine" that Kalpana or I will pass up the chain to you guys, and I wanted to see if there was a tracker.  

Ben

On Jan 30, 2012, at 2:13 AM, Julie Sullivan wrote:

> Hi Ben
>
> Is there something specific you were going to request?  Or did you just want to see what was in the queue?
>
> We have an internal ticketing system that we are going to make public, but haven't yet for some reason.  I'm not sure why.  I'll ask with Richard.
>
> Cheers
> Julie
>
> On 28/01/12 00:05, Benjamin Hitz wrote:
>> Is there a general Intermine feature request tracker that ModMines can add to?
>> I poked around a bit but didn't see anything...  either that or I need to be logged in to see the trac tickets?
>>
>> Ben
>>
>>
>> --
>> Ben Hitz
>> Senior Scientific Programmer ** Saccharomyces Genome Database ** GO Consortium
>> Stanford University ** [hidden email]
>>
>>
>>
>>
>>
>> _______________________________________________
>> dev mailing list
>> [hidden email]
>> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>>
>
> _______________________________________________
> dev mailing list
> [hidden email]
> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev

--
Ben Hitz
Senior Scientific Programmer ** Saccharomyces Genome Database ** GO Consortium
Stanford University ** [hidden email]







------------------------------

Message: 6
Date: Mon, 30 Jan 2012 15:18:21 -0800
From: Kalpana Karra <[hidden email]>
To: Intermine <[hidden email]>
Subject: [InterMine Dev] Publication Enrichment widget error
Message-ID: <[hidden email]>
Content-Type: text/plain; charset="us-ascii"

in production yeastmine is throwing this error when you click either on 'View' or 'Download'.  I was checking it with the example 'List' of 20 genes. Do I have it configured wrongly? I don't see this being passed via URL in flymine?
Thanks,
-Kalpana


Request-URI Too Large

The requested URL's length exceeds the capacity limit for this server.
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Message: 7
Date: Tue, 31 Jan 2012 10:59:31 +0000
From: Julie Sullivan <[hidden email]>
To: [hidden email]
Subject: Re: [InterMine Dev] Publication Enrichment widget error
Message-ID: <[hidden email]>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Hi Kalpana

I've checked in a fix:

        http://intermine.org/changeset/29367

Can you update your checkout and try again?

Thanks!
Julie

On 30/01/12 23:18, Kalpana Karra wrote:

> in production yeastmine is throwing this error when you click either on 'View' or 'Download'.  I was checking it with the example 'List' of 20 genes. Do I have it configured wrongly? I don't see this being passed via URL in flymine?
> Thanks,
> -Kalpana
>
>
> Request-URI Too Large
>
> The requested URL's length exceeds the capacity limit for this server.
>
>
>
> _______________________________________________
> dev mailing list
> [hidden email]
> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev



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