Opal 4.6 - enhanced logs

[Tom Bishop]

Hi,

 

For Opal 4.6, I think one of the new features was to provide more detailed DataSHIELD logs. On my test Opal 4.6 instance, my logs seem  to still be in the old format:

 

2023-07-18 14:43:21,755 INFO  datashield.user - parsed 'base::exists("df")'

2023-07-18 14:43:21,796 INFO  datashield.user - evaluated 'base::exists("df")'

2023-07-18 14:43:21,927 INFO  datashield.user - parsed 'dsBase::glmDS1(PM_BMI_CONTINUOUS~GENDER+DIS_DIAB, "poisson", NULL, NULL, "df")'

2023-07-18 14:43:22,057 ERROR datashield.user - evaluation failure 'dsBase::glmDS1(PM_BMI_CONTINUOUS~GENDER+DIS_DIAB, "poisson", NULL, NULL, "df")'

2023-07-18 14:43:26,683 INFO  datashield.user - parsed 'dsBase::asFactorDS1("x$GENDER")'

2023-07-18 14:43:26,733 ERROR datashield.user - evaluation failure 'dsBase::asFactorDS1("x$GENDER")'

2023-07-18 14:43:26,991 ERROR datashield.user - Script failed validation: No such DataSHIELD 'AGGREGATE' method with name: someFunc

2023-07-18 14:43:27,212 ERROR datashield.user - Script failed validation: No such DataSHIELD 'ASSIGN' method with name: someFunc

2023-07-18 14:43:32,413 INFO  datashield.user - closed datashield session 3641064e-4b53-4231-b958-eb9bce6fb7e9

 

 

Is there something else I need to do to get to the new format? Or have I misunderstood what the new format would look like?

 

Thanks

Tom

[Yannick Marcon]

Hi,

I have not written the upgrade instructions yet but the logback.xml is to be modified with a different encoder for the datashield log appender, to output json objects with all the fancy fields:

https://github.com/obiba/opal/blob/master/opal-server/src/main/conf/logback.xml#L73-L76

By the way I have added some R functions to opalr to get the different logs, especially the DS ones using dsadmin.log(), but the R package is not released yet (should be available soon, waiting for some other features validation). You can still try these log functions with the dev code:

remotes::install_github("obiba/opalr")

Regards

Yannick

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