OHDSI / OHDSI/FeatureExtraction
Option to turn off messages FeatureExtraction::getDbCovariateData
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- Dominant language
- R
- Stars
- 74
- Forks
- 63
- PR merge metrics
- No merged PRs in 30d
Description
When running characterization on a large set of cohorts - especially when chunked over batches like below, FeatureExtraction::getDbCovariateData spits out a lot of messages into the console. These messages are not informative and add to clutter.
DatabaseConnector when executing SQL has options to turn off such messages e.g. reportOverallTime = FALSE, showProgressBar = FALSE.
The request is for an option in getDbCovariateData to turn off these messages - so that we can reduce R console being cluttered with messages that are negatively contributing to end-users experience.
I tried suppressMessage() & invisible() - it did not work for me
Constructing features on server
|==================================================================================================================================| 100%
Executing SQL took 56.4 secs
Fetching data from server
Fetching data took 15.8 secs
- Batch characterization. Processing cohorts 4 through 6
Sending temp tables to server
Constructing features on server
|==================================================================================================================================| 100%
Executing SQL took 49.5 secs
Fetching data from server
Fetching data took 10.4 secs
- Batch characterization. Processing cohorts 7 through 7
Sending temp tables to server
Constructing features on server
|==================================================================================================================================| 100%
Executing SQL took 14 secs
Fetching data from server
Fetching data took 4.61 secs
Contributor guide
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First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start at FeatureExtraction::getDbCovariateData and compare its messaging options with DatabaseConnector, particularly reportOverallTime and showProgressBar. Trace how the listed console messages are produced; done means callers can disable them through an option while the existing default behavior remains unchanged.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- r
- Domain
- databases
- Issue type
- Feature
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 42/100