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Upload the results into a result database

Source: R/Database.R
insertResultsToDatabase.Rd

This function uploads results in csv format into a result database

Usage

insertResultsToDatabase(
  connectionDetails,
  schema,
  resultsFolder,
  tablePrefix = "",
  csvTablePrefix = "c_",
  includedFiles = NULL
)

Arguments

connectionDetails

The connection details to the result database

schema

The schema for the result database

resultsFolder

The folder containing the csv results

tablePrefix

A prefix to append to the result tables for the characterization results

csvTablePrefix

The prefix added to the csv results - default is 'c_'

includedFiles

Specify the csv files to upload or NULL to upload all in directory

Value

Returns the connection to the sqlite database

Details

Calls ResultModelManager uploadResults function to upload the csv files

See also

Other Database: createCharacterizationTables(), createSqliteDatabase()

Examples


# generate results into resultsFolder
conDet <- exampleOmopConnectionDetails()

tteSet <- createTimeToEventSettings(
targetIds = c(1,2),
  outcomeIds = 3
  )

cSet <- createCharacterizationSettings(
  timeToEventSettings = tteSet
)

runCharacterizationAnalyses(
  connectionDetails = conDet,
  targetDatabaseSchema = 'main',
  targetTable = 'cohort',
  outcomeDatabaseSchema = 'main',
  outcomeTable = 'cohort',
  cdmDatabaseSchema = 'main',
  characterizationSettings = cSet,
  outputDirectory = file.path(tempdir(),'database')
)
#> Creating directory /tmp/Rtmpgkb1Yb/database
#> Creating directory /tmp/Rtmpgkb1Yb/database/execution
#> Currently in a tryCatch or withCallingHandlers block, so unable to add global calling handlers. ParallelLogger will not capture R messages, errors, and warnings, only explicit calls to ParallelLogger. (This message will not be shown again this R session)
#> Connecting using SQLite driver
#> Extracting cohort jobs
#> Connecting using SQLite driver
#> Creating new cluster
#> Connecting using SQLite driver
#> Uploading #cohort_settings
#> Inserting data took 0.037 secs
#> Computing time to event results
#> Executing SQL took 0.0217 secs
#> Computing time-to-event for 2 T-O pairs took 0.243 secs
#> exporting to andromeda
#> Disconnected Andromeda. This data object can no longer be used
#> Removing any existing results in outputFolder directory
#> Loading andromeda result at /tmp/Rtmpgkb1Yb/database/execution/tte_1

# create sqlite database
charResultDbCD <- createSqliteDatabase()

# create database results tables
createCharacterizationTables(
   connectionDetails = charResultDbCD,
   resultSchema = 'main'
 )
#> Connecting using SQLite driver
#> Deleting existing tables
#> Executing SQL took 0.00264 secs
#> Executing SQL took 0.00261 secs
#> Executing SQL took 0.00258 secs
#> Executing SQL took 0.00276 secs
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#> Executing SQL took 0.0027 secs
#> Executing SQL took 0.00248 secs
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#> Executing SQL took 0.0025 secs
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#> Executing SQL took 0.00252 secs
#> Executing SQL took 0.00261 secs
#> Creating characterization results tables
#> Executing SQL took 0.0154 secs
#> Migrating data set
#> Migrator using SQL files in Characterization
#> Connecting using SQLite driver
#> Creating migrations table
#>   |                                                                              |                                                                      |   0%  |                                                                              |======================================================================| 100%
#> Executing SQL took 0.00277 secs
#> Migrations table created
#> Executing migration: Migration_1-v3_0_0_store_version.sql
#>   |                                                                              |                                                                      |   0%  |                                                                              |===================================                                   |  50%  |                                                                              |======================================================================| 100%
#> Executing SQL took 0.00311 secs
#> Saving migration: Migration_1-v3_0_0_store_version.sql
#>   |                                                                              |                                                                      |   0%  |                                                                              |======================================================================| 100%
#> Executing SQL took 0.0027 secs
#> Migration complete Migration_1-v3_0_0_store_version.sql
#> Closing database connection
#> Updating version number
#> Executing SQL took 0.00327 secs

# insert results
insertResultsToDatabase(
 connectionDetails = charResultDbCD,
 schema = 'main',
 resultsFolder = file.path(tempdir(),'database'),
 includedFiles = c('time_to_event')
)
#> Connecting using SQLite driver
#> Uploading file: c_time_to_event.csv to table: c_time_to_event
#> - Preparing to upload rows 1 through 96
#> Inserting data took 0.0108 secs
#> Uploading data took 1.23 secs