[Webapp] Synchronization failure as of new MaveDB version

[jweile]

2018-07-11 03:14:07 Starting new synchronization cycle.
2018-07-11 03:14:15 ERROR: Synchronization failed!
2018-07-11 03:14:15 Error in FUN(X[[i]], ...): attempt to apply non-function

[jweile]

Caused by missing Uniprot reference in the new BRCA1 dataset.

[jweile]

Synchronization now stores NA values where xref is missing.
Adding manual offset field to the interface to account for it.

Test run results in error:
Error in if (s < stop.med) { : missing value where TRUE/FALSE needed
Calls: dashboard ... genophenogram -> scoreToColIdx -> sapply -> lapply -> FUN
In addition: Warning messages:
1: In mean.default(sort(x, partial = half + 0L:1L)[half + 0L:1L]) : argument is not numeric or logical: returning NA
2: NAs introduced by coercion 3: NAs introduced by coercion Execution halted

[jweile]

This seems to be caused by variants with score "None" in the dataset. Will need to add filtering.
Also, the error column is called "SE" instead of "se". Will need to add a smart recognition function for error column names.

[jweile]

More problems:

2018-07-12 21:04:36 Starting new synchronization cycle.
2018-07-12 21:04:45 Index successfully updated.
2018-07-12 21:04:45 Starting caching cycle.
2018-07-12 21:04:45 Caching alignment for NA
2018-07-12 21:04:45 ERROR: Synchronization failed!
2018-07-12 21:04:45 Error in calc.conservation(acc): Unable to access Uniref!
Client error: (404) Not Found

This seems to be due to trying to find orthologs for Uniprot ID 'NA'. Need to skip those

2018-07-13 16:03:35 Caching structures for P63279
2018-07-13 16:03:43 ERROR: Synchronization failed!
2018-07-13 16:03:43 Error in calc.conservation(acc): ClustalOmega failed!

Will have to investigate that one.

[jweile]

Should be fixed now