Error importing tabular metadata file - no samples displayed

[mccalluc]

• Specific code commit: f6b5665
• Version of the web browser and OS: MacOS FF
• Environment where the error occurred (Vagrant VM and site conf mode or AWS instance): Production Test

Steps to reproduce

Please list all the actions and the input data used:

1. Uploaded this CSV, accepted default column assignments, and associate a file for each row (Does the Data File Column refer to local files? --> Yes):

a,b,c
1,2,3
4,5,6

• But Scott says non trivial files work too.
• And I had thought I saw this when data was not associated, too.
• It can be reproduced on beta: 30567f8

Observed behavior

Empty table, and no facets:

In the console:

angular.js:14110 TypeError: Converting circular structure to JSON
    at JSON.stringify (<anonymous>)
    at angular.js:38
    at angular.js:30441
    at angular.js:17617
    at m.$digest (angular.js:17755)
    at m.$apply (angular.js:18021)
    at angular.js:18322
    at e (angular.js:6035)
    at angular.js:6314
(anonymous) @ angular.js:14110
3angular.js:14110 TypeError: Converting circular structure to JSON
    at JSON.stringify (<anonymous>)
    at angular.js:38
    at angular.js:30441
    at angular.js:17615
    at m.$digest (angular.js:17755)
    at m.$apply (angular.js:18021)
    at angular.js:18322
    at e (angular.js:6035)
    at angular.js:6314

Click to another tab and click back and it's there: Only a problem on initial load.

Assay/Files api returned duplicate attributes obj

[jkmarx]

Not an UI issue. Took a look at the api response and there's a duplicate attribute being returned. For some reason REFINERY_DATAFILE_s is being returned twice which is causing the circular import. Internal names should be unique and they are being used as keys.

[jkmarx]

• check if reproduced locally
• why a duplicate DATAFILE attribute is being associated (indexing issue?)

[hackdna]

I just got this behavior in Vagrant environment using hg19-metadata-local.txt and a single uploaded data file.

[jkmarx]

@scottx611x

[hackdna]

Still an issue in 42634ad (using hg19-metadata-local.txt and no data files).

[scottx611x]

@gmnelson Had a Tennen Lab member run into this same error again yesterday:

angular.js:14110 TypeError: Converting circular structure to JSON
    at JSON.stringify (<anonymous>)
    at angular.js:38
    at angular.js:30441
    at angular.js:17617
    at m.$digest (angular.js:17755)
    at m.$apply (angular.js:18021)
    at angular.js:18322
    at e (angular.js:6035)
    at angular.js:6314
(anonymous) @ angular.js:14110
3angular.js:14110 TypeError: Converting circular structure to JSON
    at JSON.stringify (<anonymous>)
    at angular.js:38
    at angular.js:30441
    at angular.js:17615
    at m.$digest (angular.js:17755)
    at m.$apply (angular.js:18021)
    at angular.js:18322
    at e (angular.js:6035)
    at angular.js:6314

[jkmarx]

@scottx611x Is the error (from Tennen lab) from a newly uploaded data set or a revised uploaded data set?

[scottx611x]

@jkmarx Tennen Lab was for a revised, but the original issue is for a fresh upload. I think they're closely related.

[jkmarx]

The above pull request #3196 should have resolved this issue. Has anyone encountered this bug since Feb? @hackdna @gmnelson If yes, please send me the data set you used. I'm unable to reproduce locally.

[gmnelson]

@jkmarx have not seen this recently