isAndromedaTable fails on covariateData tables

[egillax]

@schuemie I'm not sure in what package exactly I should raise this issue.

The issue is that BigKnn only receives an Andromeda table originating from covariateData. Then it checks the table with Andromeda::isAndromedaTable but that fails since FeatureExtraction adds the class covariateData to covariateData, which makes the class of the table tbl_covariateData (among others).

I'm not sure what is the best solution, add more classes to check in isAndromedaTable or handle this somehow in either BigKnn or FeaturExtraction.

This is currently breaking the PLP GA.

See reprex below:

connectionDetails <- Eunomia::getEunomiaConnectionDetails()
#> attempting to download GiBleed
#> attempting to extract and load: /tmp/RtmpZlTE0l/GiBleed_5.3.zip to: /tmp/RtmpZlTE0l/GiBleed_5.3.sqlite
Eunomia::createCohorts(connectionDetails)
#> Cohorts created in table main.cohort
#>   cohortId       name
#> 1        1  Celecoxib
#> 2        2 Diclofenac
#> 3        3    GiBleed
#> 4        4     NSAIDs
#>                                                                                        description
#> 1    A simplified cohort definition for new users of celecoxib, designed specifically for Eunomia.
#> 2    A simplified cohort definition for new users ofdiclofenac, designed specifically for Eunomia.
#> 3 A simplified cohort definition for gastrointestinal bleeding, designed specifically for Eunomia.
#> 4       A simplified cohort definition for new users of NSAIDs, designed specifically for Eunomia.
#>   count
#> 1  1844
#> 2   850
#> 3   479
#> 4  2694

covSettings <- FeatureExtraction::createDefaultCovariateSettings()

connection <- DatabaseConnector::connect(connectionDetails)
#> Connecting using SQLite driver
covariateData <- FeatureExtraction::getDbDefaultCovariateData(connection,
                                                              cohortIds = 1,
                                                              covariateSettings = covSettings,
                                                              cdmDatabaseSchema = "main",
                                                              cohortTable = "cohort")
#> Constructing features on server
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#> Executing SQL took 5.18 secs
#> Fetching data from server
#> Fetching data took 0.774 secs
Andromeda::isAndromedaTable(covariateData$covariates)
#> [1] FALSE

class(covariateData$covariates)
#> [1] "tbl_CovariateData" "tbl_dbi"           "tbl_sql"          
#> [4] "tbl_lazy"          "tbl"

^{Created on 2024-05-31 with reprex v2.1.0}

[schuemie]

Weird! CovariateData inherits from Andromeda, but for some reason that changes the table class too, from tbl_Andromeda to tbl_CovariateData, and tbl_CovariateData does not inherit from tbl_Andromeda.

I've now changed the implementation of the isAndromedaTable() function in the develop branch. Could you give that a try?

[egillax]

Yes it works now with develop! Thanks.