OHDSI / OHDSI/FeatureExtraction

Option to turn off messages FeatureExtraction::getDbCovariateData

Open
#135 1 comment 0 reactions 0 assignees View on GitHub

Nobody has claimed this yet.

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

No contributing guide indexed for this repository

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. 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

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.