Failure Thresholds and How to Change Them
Clair Blacketer
-2023-10-18
+2023-11-04
Source:vignettes/Thresholds.rmd
Thresholds.rmdConvert results JSON file case convertJsonResultsFileCase()
Convert JSON results file case
+ Write database results to a JSON file
+ Function to write DQD results from a database table into a JSON file
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+ Write DQD results database table to json
Write DQD results database table to json — writeDBResultsToJson • DataQualityDashboard
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+ Write DQD results database table to json
+ Source: R/writeDBResultsTo.R
+ writeDBResultsToJson.Rd
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+ Write DQD results database table to json
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+ writeDBResultsToJson(
+ connection,
+ resultsDatabaseSchema,
+ cdmDatabaseSchema,
+ writeTableName,
+ outputFolder,
+ outputFile
+)
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+ Arguments
+ - connection
+A connection object
- resultsDatabaseSchema
+The fully qualified database name of the results schema
- cdmDatabaseSchema
+The fully qualified database name of the CDM schema
- writeTableName
+Name of DQD results table in the database to read from
- outputFolder
+The folder to output the json results file to
- outputFile
+The output filename of the json results file
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diff --git a/docs/reference/writeJsonResultsToCsv.html b/docs/reference/writeJsonResultsToCsv.html
index 3083ad75..3bbd7d1f 100644
--- a/docs/reference/writeJsonResultsToCsv.html
+++ b/docs/reference/writeJsonResultsToCsv.html
@@ -17,7 +17,7 @@
diff --git a/docs/reference/writeJsonResultsToTable.html b/docs/reference/writeJsonResultsToTable.html
index 43b428f9..d23c3f39 100644
--- a/docs/reference/writeJsonResultsToTable.html
+++ b/docs/reference/writeJsonResultsToTable.html
@@ -17,7 +17,7 @@
diff --git a/docs/sitemap.xml b/docs/sitemap.xml
index 99f8a396..5ae0b4bc 100644
--- a/docs/sitemap.xml
+++ b/docs/sitemap.xml
@@ -117,6 +117,9 @@
/reference/viewDqDashboard.html
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+ /reference/writeDBResultsToJson.html
+
/reference/writeJsonResultsToCsv.html
diff --git a/extras/DataQualityDashboard.pdf b/extras/DataQualityDashboard.pdf
index 24a693fa..eb9dfa03 100644
Binary files a/extras/DataQualityDashboard.pdf and b/extras/DataQualityDashboard.pdf differ
diff --git a/inst/doc/AddNewCheck.pdf b/inst/doc/AddNewCheck.pdf
index ff24ed57..fe53eb2d 100644
Binary files a/inst/doc/AddNewCheck.pdf and b/inst/doc/AddNewCheck.pdf differ
diff --git a/inst/doc/CheckStatusDefinitions.pdf b/inst/doc/CheckStatusDefinitions.pdf
index b158d7cb..762f2594 100644
Binary files a/inst/doc/CheckStatusDefinitions.pdf and b/inst/doc/CheckStatusDefinitions.pdf differ
diff --git a/inst/doc/CheckTypeDescriptions.pdf b/inst/doc/CheckTypeDescriptions.pdf
index 4fc209fa..ff299a02 100644
Binary files a/inst/doc/CheckTypeDescriptions.pdf and b/inst/doc/CheckTypeDescriptions.pdf differ
diff --git a/inst/doc/DataQualityDashboard.pdf b/inst/doc/DataQualityDashboard.pdf
index 9d1faceb..062c6e2b 100644
Binary files a/inst/doc/DataQualityDashboard.pdf and b/inst/doc/DataQualityDashboard.pdf differ
diff --git a/inst/doc/DqdForCohorts.pdf b/inst/doc/DqdForCohorts.pdf
index dc381e31..9025cf6f 100644
Binary files a/inst/doc/DqdForCohorts.pdf and b/inst/doc/DqdForCohorts.pdf differ
diff --git a/inst/doc/SqlOnly.pdf b/inst/doc/SqlOnly.pdf
index f9107177..85328c66 100644
Binary files a/inst/doc/SqlOnly.pdf and b/inst/doc/SqlOnly.pdf differ
diff --git a/inst/doc/Thresholds.pdf b/inst/doc/Thresholds.pdf
index bb044544..a26b1308 100644
Binary files a/inst/doc/Thresholds.pdf and b/inst/doc/Thresholds.pdf differ
diff --git a/tests/testthat/test-executeDqChecks.R b/tests/testthat/test-executeDqChecks.R
index 35fbff93..1cafeff2 100644
--- a/tests/testthat/test-executeDqChecks.R
+++ b/tests/testthat/test-executeDqChecks.R
@@ -332,12 +332,12 @@ test_that("Incremental insert SQL is valid.", {
test_that("Multiple cdm_source rows triggers warning.", {
outputFolder <- tempfile("dqd_")
on.exit(unlink(outputFolder, recursive = TRUE))
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connectionDetailsEunomiaCS <- Eunomia::getEunomiaConnectionDetails()
connection <- DatabaseConnector::connect(connectionDetailsEunomiaCS)
on.exit(DatabaseConnector::disconnect(connection), add = TRUE)
DatabaseConnector::renderTranslateExecuteSql(connection, "INSERT INTO @database_schema.cdm_source VALUES ('foo',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL);", database_schema = cdmDatabaseSchemaEunomia)
-
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w <- capture_warnings(
results <- executeDqChecks(
connectionDetails = connectionDetailsEunomiaCS,
@@ -347,11 +347,11 @@ test_that("Multiple cdm_source rows triggers warning.", {
checkNames = "measurePersonCompleteness",
outputFolder = outputFolder,
writeToTable = F
- ))
-
+ )
+ )
+
expect_match(w, "Missing check names", all = FALSE)
expect_match(w, "The cdm_source table has", all = FALSE)
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expect_true(nrow(results$CheckResults) > 1)
})
-
diff --git a/tests/testthat/test-writeDBResultsTo.R b/tests/testthat/test-writeDBResultsTo.R
index 9cc11808..8d10e79a 100644
--- a/tests/testthat/test-writeDBResultsTo.R
+++ b/tests/testthat/test-writeDBResultsTo.R
@@ -38,10 +38,10 @@ test_that("Write DB results to json", {
on.exit(DatabaseConnector::disconnect(connection), add = TRUE)
# Check that file was exported properly
- expect_true(file.exists(file.path(outputFolder,testExportFile)))
+ expect_true(file.exists(file.path(outputFolder, testExportFile)))
# Check that export length matches length of db table
- results <- jsonlite::fromJSON(file.path(outputFolder,testExportFile))
+ results <- jsonlite::fromJSON(file.path(outputFolder, testExportFile))
table_rows <- DatabaseConnector::renderTranslateQuerySql(
connection,
sql = "select count(*) from @resultsDatabaseSchema.@writeTableName;",
@@ -50,5 +50,4 @@ test_that("Write DB results to json", {
snakeCaseToCamelCase = TRUE
)
expect_true(length(results$CheckResults) == table_rows)
-
-})
\ No newline at end of file
+})
Convert JSON results file case
Write database results to a JSON file
+Function to write DQD results from a database table into a JSON file
+Write DQD results database table to json
+
+
+
+
+
+
+
+
+
+
+ -
+
+
+
- + + + + + +
+
+
+
+
+
+
+
+
+
+
+ Write DQD results database table to json
+ Source:R/writeDBResultsTo.R
+ writeDBResultsToJson.Rd
+
+
+ Write DQD results database table to json
+
+
+
+
+ writeDBResultsToJson(
+ connection,
+ resultsDatabaseSchema,
+ cdmDatabaseSchema,
+ writeTableName,
+ outputFolder,
+ outputFile
+)
+
+
+ Arguments
+- connection +
A connection object
+
+
+- resultsDatabaseSchema +
The fully qualified database name of the results schema
+
+
+- cdmDatabaseSchema +
The fully qualified database name of the CDM schema
+
+
+- writeTableName +
Name of DQD results table in the database to read from
+
+
+- outputFolder +
The folder to output the json results file to
+
+
+- outputFile +
The output filename of the json results file
+
+