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BiRG / Metabolomics-Analysis-Toolbox

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urlread timeout on large collection #13

Open pauleanderson opened 13 years ago

pauleanderson commented 13 years ago

To reproduce perform a urlread

[xml,status] = urlread('http://birg.cs.wright.edu/omics_analysis/collections/9472.xml','get',{'name',username,'password',password});

I believe this is a timeout issue, but I'm not sure how to fix it.

RadixSeven commented 13 years ago

If it is a timeout issue (which is likely - 3'rd google entry on a search for "matlab urlread"), we get to roll our own urlread.

Matlab is broken in http support. There is no way to set the time-out. The suggested work around on the Internet is to modify the source code of urlread. This won't work for us, so what I'll do after I wrap up my current stuff is copy urlread to a local file, modify the source to accept a time-out parameter and then search and replace all urlread calls to use the new one.

pauleanderson commented 13 years ago

Could it be the server that is timing out?

Paul

Paul E. Anderson, Ph.D. Bioinformatics Research Scientist Consortium of Universities Postdoctoral Fellow Biosciences & Protection Division Human Effectiveness Directorate Air Force Research Laboratory

On Fri, May 6, 2011 at 11:06 AM, RadixSeven reply@reply.github.com wrote:

If it is a timeout issue (which is likely - 3'rd google entry on a search for "matlab urlread"), we get to roll our own urlread.

Matlab is broken in http support.  There is no way to set the time-out.  The suggested work around on the Internet is to modify the source code of urlread.  This won't work for us, so what I'll do after I wrap up my current stuff is copy urlread to a local file, modify the source to accept a time-out parameter and then search and replace all urlread calls to use the new one.

Reply to this email directly or view it on GitHub: https://github.com/BiRG/Metabolomics-Analysis-Toolbox/issues/13#comment_1111729

RadixSeven commented 13 years ago

Good thought, I'll have to check that too.