[Galaxy-user] Error with ENCODEdb

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[Galaxy-user] Error with ENCODEdb

Prachi Shah
ENCODEdb queries don't work well. Here's the error message generated:

error, format: interval, database: hg16
Info: 'module' object has no attribute 'BASEURL'

Thanks,
Prachi


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Re: Error with ENCODEdb

Istvan Albert
On 2/28/06, Prachi Shah <[hidden email]> wrote:
> ENCODEdb queries don't work well. Here's the error message generated:
>
> error, format: interval, database: hg16
> Info: 'module' object has no attribute 'BASEURL'

we've been changing a bunch of things lately. I'll take a look.

--
Istvan Albert,
Research Associate,
Bioinformatics Consulting Center,
Huck Institute for Life Sciences,
Pennsylvania State University
http://www.personal.psu.edu/iua1

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Re: Error with ENCODEdb

Prachi Shah
> From: [hidden email]
> [mailto:[hidden email]] On Behalf Of Istvan Albert
> Sent: Wednesday, March 01, 2006 5:42 AM
> To: [hidden email]
> Cc: [hidden email]
> Subject: Re: [Galaxy-user] Error with ENCODEdb
>
> On 2/28/06, Prachi Shah <[hidden email]> wrote:
> > ENCODEdb queries don't work well. Here's the error message
> generated:
> >
> > error, format: interval, database: hg16
> > Info: 'module' object has no attribute 'BASEURL'
>
> we've been changing a bunch of things lately. I'll take a look.

Thanks for looking in it. I hope we can have it resolved before Friday. That
is my last day at work.
And can you somehow add the ENCODEdb queries into your test so that next
time there are some changes that indirectly affect the connection, you would
know about it.

Prachi


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Re: Error with ENCODEdb

Istvan Albert
On 3/1/06, Prachi Shah <[hidden email]> wrote:
> And can you somehow add the ENCODEdb queries into your test so that next
> time there are some changes that indirectly affect the connection, you would
> know about it.

I believe I've fixed the problem, we'll ask Anton to make it live on
the test server.

As for automated tests, it is easy to write tests for local tools or
static forms, but for external sites that use dynamic features like
javascript or DHTML it can be very tedious to analyze the content of
each page and manually trigger the proper page updates, so that the
pages look and contain the same things as when using the browser.

Istvan

--
Istvan Albert,
Research Associate,
Bioinformatics Consulting Center,
Huck Institute for Life Sciences,
Pennsylvania State University
http://www.personal.psu.edu/iua1

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Re: Error with ENCODEdb

James Taylor
> As for automated tests, it is easy to write tests for local tools or
> static forms, but for external sites that use dynamic features like
> javascript or DHTML it can be very tedious to analyze the content of
> each page and manually trigger the proper page updates, so that the
> pages look and contain the same things as when using the browser.

Can't we mock it though? Run the tool but don't actually have it send  
anything to ENCODE db, instead intercept what would be sent and make  
sure it looks good, then send back a pre-canned response.

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Re: Error with ENCODEdb

Istvan Albert
On 3/2/06, James Taylor <[hidden email]> wrote:

> Can't we mock it though? Run the tool but don't actually have it send
> anything to ENCODE db, instead intercept what would be sent and make
> sure it looks good, then send back a pre-canned response.

Yes we can mock it, though this one is more complicated to properly emulate.

If I recall it correctly, to cover it fully it would need to receive
two responses, once to create the data, then later get a second
request to inform it about the location of the download,  then allow
the system to connect to this location to fetch the data,

On the other hand, even partial tests would help to catch many errors
like the ones we just had.

Istvan

--
Istvan Albert,
Research Associate,
Bioinformatics Consulting Center,
Huck Institute for Life Sciences,
Pennsylvania State University
http://www.personal.psu.edu/iua1

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Re: Error with ENCODEdb

Prachi Shah
In reply to this post by Istvan Albert
Istvan,

Please let me, Lowell and Laura know when the changes go up to the galaxy
public site, because that is the one linked to ENCODEdb.

You can reach me at [hidden email] after Sunday.

Lowell, there is nothing to be done at the ENCODEdb end. Just run a couple
of test queries and make sure everything is alright with the connection to
Galaxy.

Prachi

> -----Original Message-----
> From: [hidden email]
> [mailto:[hidden email]] On Behalf Of Istvan Albert
> Sent: Thursday, March 02, 2006 6:42 AM
> To: [hidden email]
> Cc: [hidden email]
> Subject: Re: [Galaxy-user] Error with ENCODEdb
>
> On 3/1/06, Prachi Shah <[hidden email]> wrote:
> > And can you somehow add the ENCODEdb queries into your test so that
> > next time there are some changes that indirectly affect the
> > connection, you would know about it.
>
> I believe I've fixed the problem, we'll ask Anton to make it
> live on the test server.
>
> As for automated tests, it is easy to write tests for local
> tools or static forms, but for external sites that use
> dynamic features like javascript or DHTML it can be very
> tedious to analyze the content of each page and manually
> trigger the proper page updates, so that the pages look and
> contain the same things as when using the browser.
>
> Istvan
>
> --
> Istvan Albert,
> Research Associate,
> Bioinformatics Consulting Center,
> Huck Institute for Life Sciences,
> Pennsylvania State University
> http://www.personal.psu.edu/iua1
>