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anthonysenaanthonysena
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Fix merge problems
1 parent 8dca2cc commit e118c5d

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Lines changed: 35 additions & 37 deletions

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‎DESCRIPTION‎

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Original file line numberDiff line numberDiff line change
@@ -46,6 +46,6 @@ VignetteBuilder: knitr
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URL: https://github.com/OHDSI/FeatureExtraction
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BugReports: https://github.com/OHDSI/FeatureExtraction/issues
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NeedsCompilation: no
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RoxygenNote: 7.3.2
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RoxygenNote: 7.3.3
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Encoding: UTF-8
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Language: en-US

‎R/GetDefaultCovariates.R‎

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Original file line numberDiff line numberDiff line change
@@ -280,8 +280,7 @@ getDbDefaultCovariateData <- function(connection,
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}
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}
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283-
if (missing(targetCovariateTable) || is.null(targetCovariateTable)) {
284-
if ((missing(targetDatabaseSchema) | is.null(targetDatabaseSchema)) & !allTempTables) {
283+
if ((missing(targetDatabaseSchema) || is.null(targetDatabaseSchema)) & !allTempTables) {
285284
attr(covariateData, "metaData") <- list()
286285
if (is.null(covariateData$covariates) && is.null(covariateData$covariatesContinuous)) {
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warning("No data found, probably because no covariates were specified.")

‎man/getDbDefaultCovariateData.Rd‎

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‎tests/testthat/setup.R‎

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Original file line numberDiff line numberDiff line change
@@ -217,6 +217,7 @@ if (dbms == "sql server") {
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# eunomia
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if (dbms == "sqlite") {
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if (!is.null(checkRemoteFileAvailable("https://raw.githubusercontent.com/OHDSI/EunomiaDatasets/main/datasets/GiBleed/GiBleed_5.3.zip"))) {
220+
print('got here')
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eunomiaConnectionDetails <- Eunomia::getEunomiaConnectionDetails(databaseFile = "testEunomia.sqlite")
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eunomiaCdmDatabaseSchema <- "main"
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eunomiaOhdsiDatabaseSchema <- "main"

‎tests/testthat/test-GetDefaultCovariates.R‎

Lines changed: 27 additions & 30 deletions
Original file line numberDiff line numberDiff line change
@@ -43,11 +43,10 @@ test_that("Test exit conditions", {
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})
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4545
test_that("Test target table", {
46-
connection <- DatabaseConnector::connect(connectionDetails)
47-
on.exit(DatabaseConnector::disconnect(connection))
48-
Eunomia::createCohorts(connectionDetails)
49-
50-
results <- getDbDefaultCovariateData(connection = connection,
46+
skip_on_cran()
47+
skip_if_not(dbms == "sqlite" && exists("eunomiaConnection"))
48+
49+
results <- getDbDefaultCovariateData(connection = eunomiaConnection,
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cdmDatabaseSchema = "main",
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cohortTable = "cohort",
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covariateSettings = createDefaultCovariateSettings(),
@@ -56,11 +55,11 @@ test_that("Test target table", {
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covariateRef = "ut_cov_ref",
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analysisRef = "ut_cov_analysis_ref"))
5857

59-
expect_gt(DatabaseConnector::renderTranslateQuerySql(connection, "SELECT COUNT(*) FROM main.ut_cov")[1], 1)
60-
expect_gt(DatabaseConnector::renderTranslateQuerySql(connection, "SELECT COUNT(*) FROM main.ut_cov_ref")[1], 1)
61-
expect_gt(DatabaseConnector::renderTranslateQuerySql(connection, "SELECT COUNT(*) FROM main.ut_cov_analysis_ref")[1], 1)
58+
expect_gt(DatabaseConnector::renderTranslateQuerySql(eunomiaConnection, "SELECT COUNT(*) FROM main.ut_cov")[1], 1)
59+
expect_gt(DatabaseConnector::renderTranslateQuerySql(eunomiaConnection, "SELECT COUNT(*) FROM main.ut_cov_ref")[1], 1)
60+
expect_gt(DatabaseConnector::renderTranslateQuerySql(eunomiaConnection, "SELECT COUNT(*) FROM main.ut_cov_analysis_ref")[1], 1)
6261

63-
results <- getDbDefaultCovariateData(connection = connection,
62+
results <- getDbDefaultCovariateData(connection = eunomiaConnection,
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cdmDatabaseSchema = "main",
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cohortTable = "cohort",
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covariateSettings = createDefaultCovariateSettings(),
@@ -70,12 +69,12 @@ test_that("Test target table", {
7069
covariateRef = "ut_cov_ref_agg",
7170
analysisRef = "ut_cov_analysis_ref_agg"))
7271

73-
expect_gt(DatabaseConnector::renderTranslateQuerySql(connection, "SELECT COUNT(*) FROM main.ut_cov_agg")[1], 1)
74-
expect_gt(DatabaseConnector::renderTranslateQuerySql(connection, "SELECT COUNT(*) FROM main.ut_cov_ref_agg")[1], 1)
75-
expect_gt(DatabaseConnector::renderTranslateQuerySql(connection, "SELECT COUNT(*) FROM main.ut_cov_analysis_ref_agg")[1], 1)
72+
expect_gt(DatabaseConnector::renderTranslateQuerySql(eunomiaConnection, "SELECT COUNT(*) FROM main.ut_cov_agg")[1], 1)
73+
expect_gt(DatabaseConnector::renderTranslateQuerySql(eunomiaConnection, "SELECT COUNT(*) FROM main.ut_cov_ref_agg")[1], 1)
74+
expect_gt(DatabaseConnector::renderTranslateQuerySql(eunomiaConnection, "SELECT COUNT(*) FROM main.ut_cov_analysis_ref_agg")[1], 1)
7675

7776
# Temp tables with old prototype
78-
results <- getDbDefaultCovariateData(connection = connection,
77+
results <- getDbDefaultCovariateData(connection = eunomiaConnection,
7978
cdmDatabaseSchema = "main",
8079
cohortTable = "cohort",
8180
covariateSettings = createDefaultCovariateSettings(),
@@ -84,27 +83,27 @@ test_that("Test target table", {
8483
targetAnalysisRefTable = "#ut_cov_ref_agg",
8584
targetCovariateRefTable = "#ut_cov_anal_ref_agg")
8685

87-
expect_gt(DatabaseConnector::renderTranslateQuerySql(connection, "SELECT COUNT(*) FROM #ut_cov_agg")[1], 1)
88-
expect_gt(DatabaseConnector::renderTranslateQuerySql(connection, "SELECT COUNT(*) FROM #ut_cov_ref_agg")[1], 1)
89-
expect_gt(DatabaseConnector::renderTranslateQuerySql(connection, "SELECT COUNT(*) FROM #ut_cov_anal_ref_agg")[1], 1)
86+
expect_gt(DatabaseConnector::renderTranslateQuerySql(eunomiaConnection, "SELECT COUNT(*) FROM #ut_cov_agg")[1], 1)
87+
expect_gt(DatabaseConnector::renderTranslateQuerySql(eunomiaConnection, "SELECT COUNT(*) FROM #ut_cov_ref_agg")[1], 1)
88+
expect_gt(DatabaseConnector::renderTranslateQuerySql(eunomiaConnection, "SELECT COUNT(*) FROM #ut_cov_anal_ref_agg")[1], 1)
9089

91-
results <- getDbDefaultCovariateData(connection = connection,
90+
results <- getDbDefaultCovariateData(connection = eunomiaConnection,
9291
cdmDatabaseSchema = "main",
9392
cohortTable = "cohort",
9493
covariateSettings = createDefaultCovariateSettings(),
9594
targetCovariateTable = "#ut_cov",
9695
targetAnalysisRefTable = "#ut_cov_ref",
9796
targetCovariateRefTable = "#ut_cov_analysis_ref")
9897

99-
covCt <- DatabaseConnector::renderTranslateQuerySql(connection, "SELECT COUNT(*) FROM #ut_cov")[1]
98+
covCt <- DatabaseConnector::renderTranslateQuerySql(eunomiaConnection, "SELECT COUNT(*) FROM #ut_cov")[1]
10099
expect_gt(covCt, 1)
101-
covRefCt <- DatabaseConnector::renderTranslateQuerySql(connection, "SELECT COUNT(*) FROM #ut_cov_ref")[1]
100+
covRefCt <- DatabaseConnector::renderTranslateQuerySql(eunomiaConnection, "SELECT COUNT(*) FROM #ut_cov_ref")[1]
102101
expect_gt(covRefCt, 1)
103-
anlRefCt <- DatabaseConnector::renderTranslateQuerySql(connection, "SELECT COUNT(*) FROM #ut_cov_analysis_ref")[1]
102+
anlRefCt <- DatabaseConnector::renderTranslateQuerySql(eunomiaConnection, "SELECT COUNT(*) FROM #ut_cov_analysis_ref")[1]
104103
expect_gt(anlRefCt, 1)
105104

106105
# append results rather than deleting the tables
107-
results <- getDbDefaultCovariateData(connection = connection,
106+
results <- getDbDefaultCovariateData(connection = eunomiaConnection,
108107
cdmDatabaseSchema = "main",
109108
cohortTable = "cohort",
110109
covariateSettings = createDefaultCovariateSettings(),
@@ -114,12 +113,12 @@ test_that("Test target table", {
114113
targetAnalysisRefTable = "#ut_cov_ref",
115114
targetCovariateRefTable = "#ut_cov_analysis_ref")
116115

117-
expect_equal(DatabaseConnector::renderTranslateQuerySql(connection, "SELECT COUNT(*) FROM #ut_cov")[1], covCt * 2)
118-
expect_equal(DatabaseConnector::renderTranslateQuerySql(connection, "SELECT COUNT(*) FROM #ut_cov_ref")[1], covRefCt * 2)
119-
expect_equal(DatabaseConnector::renderTranslateQuerySql(connection, "SELECT COUNT(*) FROM #ut_cov_analysis_ref")[1], anlRefCt * 2)
116+
expect_equal(DatabaseConnector::renderTranslateQuerySql(eunomiaConnection, "SELECT COUNT(*) FROM #ut_cov")[1], covCt * 2)
117+
expect_equal(DatabaseConnector::renderTranslateQuerySql(eunomiaConnection, "SELECT COUNT(*) FROM #ut_cov_ref")[1], covRefCt * 2)
118+
expect_equal(DatabaseConnector::renderTranslateQuerySql(eunomiaConnection, "SELECT COUNT(*) FROM #ut_cov_analysis_ref")[1], anlRefCt * 2)
120119

121120
# Recreate tables (and check create override works)
122-
results <- getDbDefaultCovariateData(connection = connection,
121+
results <- getDbDefaultCovariateData(connection = eunomiaConnection,
123122
cdmDatabaseSchema = "main",
124123
cohortTable = "cohort",
125124
covariateSettings = createDefaultCovariateSettings(),
@@ -129,9 +128,7 @@ test_that("Test target table", {
129128
targetAnalysisRefTable = "#ut_cov_ref",
130129
targetCovariateRefTable = "#ut_cov_analysis_ref")
131130

132-
expect_equal(DatabaseConnector::renderTranslateQuerySql(connection, "SELECT COUNT(*) FROM #ut_cov")[1], covCt)
133-
expect_equal(DatabaseConnector::renderTranslateQuerySql(connection, "SELECT COUNT(*) FROM #ut_cov_ref")[1], covRefCt)
134-
expect_equal(DatabaseConnector::renderTranslateQuerySql(connection, "SELECT COUNT(*) FROM #ut_cov_analysis_ref")[1], anlRefCt)
131+
expect_equal(DatabaseConnector::renderTranslateQuerySql(eunomiaConnection, "SELECT COUNT(*) FROM #ut_cov")[1], covCt)
132+
expect_equal(DatabaseConnector::renderTranslateQuerySql(eunomiaConnection, "SELECT COUNT(*) FROM #ut_cov_ref")[1], covRefCt)
133+
expect_equal(DatabaseConnector::renderTranslateQuerySql(eunomiaConnection, "SELECT COUNT(*) FROM #ut_cov_analysis_ref")[1], anlRefCt)
135134
})
136-
137-
unlink(connectionDetails$server())

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