Error With Encodedb

12.8 years ago by

University Park

Istvan Albert ♦ 250 wrote:

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

ADD COMMENT • link written 12.8 years ago by Istvan Albert ♦ 250

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

ADD REPLY • link written 12.8 years ago by Prachi Shah • 30

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

ADD REPLY • link written 12.8 years ago by Istvan Albert ♦ 250

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.

ADD REPLY • link written 12.8 years ago by James Taylor • 320

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

ADD REPLY • link written 12.8 years ago by Istvan Albert ♦ 250

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

ADD REPLY • link written 12.8 years ago by Prachi Shah • 30

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