Describe the bug
I am trying to reproduce the catalogue export for OMOP CDM v6, by removing analysis ids that use fields and tables not existent in the CDM v6.
The error it gives is Export query was not executed successfully with no further explanation
To Reproduce
Steps to reproduce the behavior:
See code:
run_catalogue_export <- function(dbms,
connectionString,
jdbcDriverFolder,
user,
password,
outputFolder,
cdmDatabaseSchema,
databaseInfoConfigFilePath
){
# Read the yaml file
data <- yaml::read_yaml(databaseInfoConfigFilePath)
# Access the values in the file
databaseName <- data$databaseName
parsed_uri <- urltools::url_parse(connectionString)
server <- paste0(parsed_uri$domain, "/", parsed_uri$path)
port <- as.integer(parsed_uri$port)
connectionDetails <- DatabaseConnector::createConnectionDetails(dbms = dbms,
user = user,
password = password,
server = server,
port = port,
pathToDriver = jdbcDriverFolder)
df <- CatalogueExport::getAnalysisDetails()
analysis_ids <- df$ANALYSIS_ID
filtered_ids <- analysis_ids[!(analysis_ids %in% c(920, 1020))]
CatalogueExport::catalogueExport(connectionDetails,
cdmDatabaseSchema = cdmDatabaseSchema,
resultsDatabaseSchema = cdmDatabaseSchema,
vocabDatabaseSchema = cdmDatabaseSchema,
numThreads = 1,
sourceName = databaseName,
outputFolder = file.path(getwd(), outputFolder),
cdmVersion = data$cdmVersion,
analysisIds=filtered_ids)
}
Describe the bug I am trying to reproduce the catalogue export for OMOP CDM v6, by removing analysis ids that use fields and tables not existent in the CDM v6.
The error it gives is
Export query was not executed successfully
with no further explanationTo Reproduce Steps to reproduce the behavior:
Expected behavior Should be exporting the file cataloge_results.csv