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
On 2/28/06, Prachi Shah prachis@mail.nih.gov 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
From: istvan.albert@gmail.com [mailto:istvan.albert@gmail.com] On Behalf Of Istvan Albert Sent: Wednesday, March 01, 2006 5:42 AM To: prachis@mail.nih.gov Cc: galaxy-user@bx.psu.edu Subject: Re: [Galaxy-user] Error with ENCODEdb
On 2/28/06, Prachi Shah prachis@mail.nih.gov 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
On 3/1/06, Prachi Shah prachis@mail.nih.gov 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
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.
On 3/2/06, James Taylor james@bx.psu.edu 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
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 pss11@psu.edu 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: istvan.albert@gmail.com [mailto:istvan.albert@gmail.com] On Behalf Of Istvan Albert Sent: Thursday, March 02, 2006 6:42 AM To: prachis@mail.nih.gov Cc: galaxy-user@bx.psu.edu Subject: Re: [Galaxy-user] Error with ENCODEdb
On 3/1/06, Prachi Shah prachis@mail.nih.gov 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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