Update Pipeline Config and Fix Unit Test Execution in GitHub Actions (#97)

* Update pipeline with latest r-lib actions. * Update readme to include build status GHA * force upated testthat package to >= 2.0.1 * remove snapshot reference. * new cache * Fix cause of Invalid Cursor State * Add fix for failing tests in CI * Remove commented code in ci yaml
2022-02-25 12:18:10 -08:00 · 2022-02-25 12:18:10 -08:00 · f27e8f1495
--- a/.github/workflows/ci.yaml
+++ b/.github/workflows/ci.yaml
@ -29,7 +29,7 @@ jobs:
    strategy:
      fail-fast: false
      matrix:
-        r-version: [3.5]
+        r-version: ["3.5.2"]

    env:
      # Define CI to skip some test case.
@ -43,22 +43,25 @@ jobs:
    steps:
      - uses: actions/checkout@v2

-      - name: Set up R ${{ matrix.r-version }}
-        uses: r-lib/actions/setup-r@v1
+      - name: Set up R ${{ matrix.r-version }} Runtime
+        uses: r-lib/actions/setup-r@v2
        with:
          r-version: ${{ matrix.r-version }}
-          extra-repositories: 'https://mran.microsoft.com/snapshot/2019-02-01'

-      - name: Install dependencies
-        working-directory: ./R
-        run: |
-          install.packages(c("remotes", "rcmdcheck"))
-          remotes::install_deps(dependencies = TRUE)
-        shell: Rscript {0}
-      - name: Check
-        working-directory: ./R
-        run: rcmdcheck::rcmdcheck(args = "--no-manual", error_on = "error")
-        shell: Rscript {0}
+      - name: Install R Package Dependencies
+        uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          cache-version: 2
+          working-directory: ./R
+          extra-packages:
+            #Retrieves most recent odbc pkg from cran to avoid errors seen in older versions.
+            #Updated odbc pkg is still compatible with R >= 3.2.0
+            cran::odbc
+            rcmdcheck
+          
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          working-directory: ./R

  Python:
    runs-on: windows-latest
--- a/R/R/sqlPackage.R
+++ b/R/R/sqlPackage.R
@ -449,7 +449,7 @@ sqlRemoteExecuteFun <- function(connection, FUN, ..., useRemoteFun = FALSE, asus
                                 withCallingHandlers({
                                 binArgList <- unlist(lapply(lapply(strsplit(\"%s\",\";\")[[1]], as.hexmode), as.raw))
                                 argList <- as.list(unserialize(binArgList))
-                                 result <- do.call(%s, argList)
+                                 result <- suppressPackageStartupMessages(do.call(%s, argList))
                             },
                             error = function(err)
                             {
@ -458,6 +458,7 @@ sqlRemoteExecuteFun <- function(connection, FUN, ..., useRemoteFun = FALSE, asus
                             warning = function(warn)
                             {
                                funwarnings <<- c(funwarnings, warn$message)
+                                invokeRestart(\"muffleWarning\")
                             }
                             ), silent = TRUE
                             ))
@ -543,6 +544,11 @@ sqlRemoteExecuteFun <- function(connection, FUN, ..., useRemoteFun = FALSE, asus
        funwarnings <-lst[[3]]
        output <- lst[[4]]

+        if (is.null(result))
+        {
+            result <- FALSE
+        }
+        
        if (!is.null(output))
        {
            for(o in output)
--- a/R/tests/testthat/helper-Setup.R
+++ b/R/tests/testthat/helper-Setup.R
@ -51,7 +51,7 @@ testthatDir <- getwd()
 R_Root <- file.path(testthatDir, "../..")
 scriptDirectory <- file.path(testthatDir, "scripts")

-options(repos = c(CRAN="https://cran.microsoft.com", CRANextra = "http://www.stats.ox.ac.uk/pub/RWin"))
+options(repos = c(CRAN="https://cran.microsoft.com", CRANextra = "https://mran.microsoft.com/snapshot/2019-02-01"))
 cat("INFO: repos = ", getOption("repos"), sep="\n")

 # Compute context specifications
--- a/R/tests/testthat/test.sqlPackage.basic.R
+++ b/R/tests/testthat/test.sqlPackage.basic.R
@ -8,10 +8,6 @@ context("Tests for sqlmlutils package management")

 test_that( "successfull install and remove of package with special char in name that requires [] in t-sql",
 {
-    # There is an issue running this test in github actions CI environment.
-    # We will need to investigate why it failed. For now, we will disable the test in CI.
-    skip_on_ci()
-
    #
    # Set scope to public for trusted connection on Windows
    #
--- a/R/tests/testthat/test.sqlPackage.createExternalLibrary.R
+++ b/R/tests/testthat/test.sqlPackage.createExternalLibrary.R
@ -8,10 +8,6 @@ context("Tests for sqlmlutils package management create external library")

 test_that("Package APIs interop with Create External Library",
 {
-    # There is an issue running this test in github actions CI environment.
-    # We will need to investigate why it failed. For now, we will disable the test in CI.
-    skip_on_ci()
-
    cat("\nINFO: test if package management interops properly with packages installed directly with CREATE EXTERNAL LIBRARY\n
      Note:\n
        packages installed with CREATE EXTERNAL LIBRARY won't have top-level attribute set in extended properties\n
--- a/R/tests/testthat/test.sqlPackage.dependencies.R
+++ b/R/tests/testthat/test.sqlPackage.dependencies.R
@ -8,10 +8,6 @@ context("Tests for sqlmlutils package management dependencies")

 test_that("single package install and removal with no dependencies",
 {
-    # There is an issue running this test in github actions CI environment.
-    # We will need to investigate why it failed. For now, we will disable the test in CI.
-    skip_on_ci()
-
    #
    # Set scope to public for trusted connection on Windows
    #
@ -66,10 +62,6 @@ test_that("single package install and removal with no dependencies",

 test_that( "package install and uninstall with dependency",
 {
-    # There is an issue running this test in github actions CI environment.
-    # We will need to investigate why it failed. For now, we will disable the test in CI.
-    skip_on_ci()
-
    connectionStringAirlineUserdbowner <- helper_getSetting("connectionStringAirlineUserdbowner")
    scope <- "private"
    
--- a/R/tests/testthat/test.sqlPackage.scope.R
+++ b/R/tests/testthat/test.sqlPackage.scope.R
@ -8,10 +8,6 @@ context("Tests for sqlmlutils package management scope")

 test_that("dbo cannot install package into private scope",
 {
-    # There is an issue running this test in github actions CI environment.
-    # We will need to investigate why it failed. For now, we will disable the test in CI.
-    skip_on_ci()
-
    skip_if(helper_isServerLinux(), "Linux tests do not have support for Trusted user." )

    connectionStringDBO <- helper_getSetting("connectionStringDBO")
--- a/R/tests/testthat/test.sqlPackage.toplevel.R
+++ b/R/tests/testthat/test.sqlPackage.toplevel.R
@ -8,10 +8,6 @@ context("Tests for sqlmlutils package management top level")

 test_that("package top level install and remove",
 {
-    # There is an issue running this test in github actions CI environment.
-    # We will need to investigate why it failed. For now, we will disable the test in CI.
-    skip_on_ci()
-
    connectionStringAirlineUserdbowner <- helper_getSetting("connectionStringAirlineUserdbowner")
    scope <- "private"

--- a/R/tests/testthat/test.storedProcedureTests.R
+++ b/R/tests/testthat/test.storedProcedureTests.R
@ -90,7 +90,7 @@ test_that("Simple InputDataSet test",
    capture.output(createSprocFromFunction(name, inData, connectionString = connection, inputParams = inputParams))
    expect_true(checkSproc(name, connectionString = connection))

-    res <- executeSproc(name, in_df = "SELECT TOP 10 Id, CarrierDelay, TailNum, CancellationCode FROM airline5000", connectionString = connection)
+    res <- executeSproc(name, in_df = "SELECT TOP 10 Id, CarrierDelay, FlightNum, ActualElapsedTime FROM airline5000", connectionString = connection)
    expect_equal(nrow(res), 10)
    expect_equal(ncol(res), 4)

@ -119,7 +119,7 @@ test_that("InputDataSet to OutputDataSet test",
    capture.output(createSprocFromFunction(name, inOutData, connectionString = connection, inputParams = inputParams, outputParams = outputParams))
    expect_true(checkSproc(name, connectionString = connection))

-    res <- executeSproc(name, in_df = "SELECT TOP 10 Id, CarrierDelay, TailNum, CancellationCode FROM airline5000", connectionString = connection)
+    res <- executeSproc(name, in_df = "SELECT TOP 10 Id, CarrierDelay, FlightNum, ActualElapsedTime FROM airline5000", connectionString = connection)
    expect_equal(nrow(res), 10)
    expect_equal(ncol(res), 4)

@ -146,12 +146,12 @@ test_that("InputDataSet with InputParameter test",
    capture.output(createSprocFromFunction(name, inDataParams, connectionString = connection, inputParams = inputParams))
    expect_true(checkSproc(name, connectionString = connection))

-    res <- executeSproc(name, id = "SELECT TOP 10 Id, CarrierDelay, TailNum, CancellationCode FROM airline5000", ip = 4, connectionString = connection)
+    res <- executeSproc(name, id = "SELECT TOP 10 Id, CarrierDelay, FlightNum, ActualElapsedTime FROM airline5000", ip = 4, connectionString = connection)

    expect_equal(nrow(res), 11)
    expect_equal(ncol(res), 4)

-    expect_error(executeSproc(name, "SELECT TOP 10 Id, CarrierDelay, TailNum, CancellationCode FROM airline5000", ip = 4, connectionString = connection))
+    expect_error(executeSproc(name, "SELECT TOP 10 Id, CarrierDelay, FlightNum, ActualElapsedTime FROM airline5000", ip = 4, connectionString = connection))

    dropIfExists(name, connectionString = connection)
    expect_false(checkSproc(name, connectionString = connection))
@ -177,12 +177,12 @@ test_that("InputDataSet with InputParameter test, out of order",
    capture.output(createSprocFromFunction(name, inDataParams, connectionString = connection, inputParams = inputParams))
    expect_true(checkSproc(name, connectionString = connection))

-    res <- executeSproc(name, ip2 = "Hello", ip = 4, id = "SELECT TOP 10 Id, CarrierDelay, TailNum, CancellationCode FROM airline5000",  connectionString = connection)
+    res <- executeSproc(name, ip2 = "Hello", ip = 4, id = "SELECT TOP 10 Id, CarrierDelay, FlightNum, ActualElapsedTime FROM airline5000",  connectionString = connection)

    expect_equal(nrow(res), 11)
    expect_equal(ncol(res), 4)

-    expect_error(executeSproc(name,ip = 4,  "SELECT TOP 10 Id, CarrierDelay, TailNum, CancellationCode FROM airline5000", connectionString = connection))
+    expect_error(executeSproc(name,ip = 4,  "SELECT TOP 10 Id, CarrierDelay, FlightNum, ActualElapsedTime FROM airline5000", connectionString = connection))

    dropIfExists(name, connectionString = connection)
    expect_false(checkSproc(name, connectionString = connection))
@ -205,7 +205,7 @@ test_that("Stored Procedure with Scripts",
        connectionString = connection, name=name, file.path(scriptDir, "script3.R"), inputParams = inputParams, outputParams = outputParams))
    expect_true(checkSproc(connectionString = connection, name = name))

-    retVal <- executeSproc(connectionString = connection, name, num1 = 3, num2 = 4, in_df = "SELECT TOP 10 Id, CarrierDelay, TailNum, CancellationCode FROM airline5000")
+    retVal <- executeSproc(connectionString = connection, name, num1 = 3, num2 = 4, in_df = "SELECT TOP 10 Id, CarrierDelay, FlightNum, ActualElapsedTime FROM airline5000")

    expect_equal(nrow(retVal), 11)
    expect_equal(ncol(retVal), 4)
@ -333,7 +333,7 @@ test_that("Bad input param types or usage",
    expect_true(checkSproc(connection, name))

    expect_error(expect_warning(executeSproc(connection, name, arg1=12314532)))
-    res <- executeSproc(connection, name, arg1="SELECT TOP 5 Id, CarrierDelay, TailNum, CancellationCode FROM airline5000")
+    res <- executeSproc(connection, name, arg1="SELECT TOP 5 Id, CarrierDelay, FlightNum, ActualElapsedTime FROM airline5000")

    expect_equal(ncol(res), 4)
    expect_equal(nrow(res), 5)
--- a/README.md
+++ b/README.md
@ -1,7 +1,6 @@
 # sqlmlutils

-[![Build Status](https://travis-ci.com/Microsoft/sqlmlutils.svg?branch=master)](https://travis-ci.com/Microsoft/sqlmlutils)
-![Github action CI](https://github.com/Microsoft/sqlmlutils/actions/workflows/main.yml/badge.svg)
+[![BuildAndTest](https://github.com/microsoft/sqlmlutils/actions/workflows/ci.yaml/badge.svg)](https://github.com/microsoft/sqlmlutils/actions/workflows/ci.yaml)

 sqlmlutils is a package designed to help users interact with SQL databases (SQL Server and Azure SQL Database) and execute R or Python code in SQL from an R/Python client. 
 Currently, only the R version of sqlmlutils is supported in Azure SQL Database. Python support will be added later.