I have a transformation script within a module-based assay that is written in R. Most of the time the import and transformation works fine. However, sometimes the runProperties.tsv file does not contain the line "runDataFile <filename> AssayRunTSVData <filename>". This causes my script to fail, as it doesn't know where to save the transformation output. Unfortunately I have not been able to find test case that always reproduces this problem. I have observed the problem about 10 times now, but with multiple attempts, the transformation has always been successful. Any ideas why those parameters are occasionally getting left out?
thanks,
-Will |
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| Jon (LabKey DevOps) responded: |
2015-03-05 19:32 |
Hi Will,
I haven't heard of anything like this before. Were there any error messages or anything unusual in your log files during the transformation script run?
Regards,
Jon |
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| Will Holtz responded: |
2015-03-05 19:50 |
Hi Jon,
I found this:
INFO DbScope 2015-03-04 10:04:20,594 http-bio-443-exec-2 : Loading DbSchema "labkey.assayresult" (Module)
INFO DbScope 2015-03-04 10:04:20,608 http-bio-443-exec-2 : no schema metadata xml file found for schema 'assayresult'
INFO DbScope 2015-03-04 10:04:20,609 http-bio-443-exec-2 : Shouldn't be loading metadata for Provisioned schema 'assayresult'
-Will |
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| Will Holtz responded: |
2015-03-06 14:30 |
I figured it out. My custom upload.html (sorry -- I forgot to mention that detail!) is based on the default from the general assay. My custom upload.html was supposed to have copied the behavior of the default of allowing multiple serial uploads without navigating way from or reloading the upload page. I realized today that the submission was always failing on the second serial submission without a page reload. Turns out I failed to reset all the properties of LABKEY.page.batch between submissions. Once I cleared all of those properties including lsid, it started working all the time.
-Will |
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