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StuartWheaterStuartWheater
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‎azure-pipelines.yml‎

Lines changed: 59 additions & 45 deletions
Original file line numberDiff line numberDiff line change
@@ -132,6 +132,9 @@ jobs:
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sudo R -q -e "install.packages(c('devtools','metafor','fields','covr'), dependencies=TRUE, repos='https://cloud.r-project.org')"
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sudo R -q -e "install.packages(c('DSI','DSOpal','DSLite'), dependencies=TRUE, repos='https://cloud.r-project.org')"
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# XML grep for coverage report merging
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sudo apt-get install -qq xml-twig-tools -y
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displayName: 'Install all dependencies for dsBaseClient'
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condition: succeeded()
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@@ -157,8 +160,8 @@ jobs:
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echo "Run devtools::document() locally then commit again."
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exit 1
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else
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echo "Documentation up to date."
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exit 0
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echo "Documentation up to date."
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exit 0
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fi
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workingDirectory: $(Pipeline.Workspace)/dsBaseClient
@@ -241,34 +244,32 @@ jobs:
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# testthat::testpackage uses a MultiReporter, comprised of a ProgressReporter and JunitReporter
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# R output and messages are redirected by sink() to test_console_output.txt
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# junit reporter output is to test_results.xml
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#
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# "_-|arg-|smk-|datachk-|disc-|math-|expt-|expt_smk-"
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sudo R -q -e '
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library(covr);
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write.csv(
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coverage_to_list(
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covr::package_coverage(
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type = c("none"),
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code = c(
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'"'"'library(testthat);
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output_file <- file("test_console_output.txt");
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sink(output_file);
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sink(output_file, type = "message");
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library(testthat);
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junit_rep <- JunitReporter$new(file = "test_results.xml");
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progress_rep <- ProgressReporter$new(max_failures = 999999);
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multi_rep <- MultiReporter$new(reporters = list(progress_rep, junit_rep));
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testthat::test_package("$(projectName)", filter = "_-|arg-|smk-|datachk-|disc-|math-|expt-|expt_smk-",reporter = multi_rep, stop_on_failure = FALSE)'"'"')
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)
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),
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"coveragelist.csv"
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)'
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dsbase.res <- covr::package_coverage(
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type = c("none"),
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code = c(
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'"'"'library(testthat);
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output_file <- file("test_console_output_dsbase.txt");
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sink(output_file);
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sink(output_file, type = "message");
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library(testthat);
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junit_rep <- JunitReporter$new(
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file = "test_results_dsbase.xml");
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progress_rep <- ProgressReporter$new(max_failures = 999999);
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multi_rep <- MultiReporter$new(reporters = list(progress_rep, junit_rep));
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testthat::test_package("$(projectName)", filter = "_-", reporter = multi_rep, stop_on_failure = FALSE)'"'"')
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)
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)
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)
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base::saveRDS(dsbase.res, "test_results_dsbase.rds")'
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# display the test console output
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cat test_console_output.txt
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mv coveragelist.csv $(Pipeline.Workspace)/logs
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mv test_results.xml $(Pipeline.Workspace)/logs
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mv test_console_output.txt $(Pipeline.Workspace)/logs
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cat test_console_output_dsbase.txt
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grep --quiet "Failed: 0" $(Pipeline.Workspace)/logs/test_console_output.txt
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grep --quiet "Failed: 0" test_console_output_dsbase.txt
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workingDirectory: $(Pipeline.Workspace)/dsBaseClient
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displayName: 'Code coverage and JUnit report output, with dsBase'
@@ -320,32 +321,45 @@ jobs:
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# junit reporter output is to test_results.xml
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sudo R -q -e '
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library(covr);
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dsdanger.res <- covr::package_coverage(
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type = c("none"),
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code = c(
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'"'"'library(testthat);
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output_file <- file("test_console_output_dsdanger.txt");
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sink(output_file);
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sink(output_file, type = "message");
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library(testthat);
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junit_rep <- JunitReporter$new(file = "test_results_dsdanger.xml");
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progress_rep <- ProgressReporter$new(max_failures = 999999);
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multi_rep <- MultiReporter$new(reporters = list(progress_rep, junit_rep));
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testthat::test_package("$(projectName)", filter = "smk_dgr-",reporter = multi_rep, stop_on_failure = FALSE)'"'"')
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)
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)
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base::saveRDS(dsdanger.res, "test_results_dsdanger.rds")'
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# Merge coverage results
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cat test_results_dsbase.txt test_results_dsdanger.txt > $(Pipeline.Workspace)/logs/test_console_output.txt
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xml_grep --pretty_print indented --wrap "testsuites" --descr "" --cond "testsuite" test_results_dsbase.xml test_results_dsdanger.xml > test_results.xml
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344+
# Create 'coveragelist.csv'
345+
sudo R -q -e '
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library(covr);
347+
dsbase.res <- base::readRDS("test_results_dsbase.rds")
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dsdanger.res <- base::readRDS("test_results_dsdanger.rds")
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write.csv(
324-
coverage_to_list(
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covr::package_coverage(
326-
type = c("none"),
327-
code = c(
328-
'"'"'library(testthat);
329-
output_file <- file("test_console_output.txt");
330-
sink(output_file);
331-
sink(output_file, type = "message");
332-
library(testthat);
333-
junit_rep <- JunitReporter$new(file = "test_results.xml");
334-
progress_rep <- ProgressReporter$new(max_failures = 999999);
335-
multi_rep <- MultiReporter$new(reporters = list(progress_rep, junit_rep));
336-
testthat::test_package("$(projectName)", filter = "_-|smk_dgr-",reporter = multi_rep, stop_on_failure = FALSE)'"'"')
337-
)
338-
),
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"coveragelist.csv"
340-
)'
350+
coverage_to_list(
351+
c(dsbase.res, dsdanger.res)
352+
"coveragelist.csv"
353+
)
354+
)'
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# display the test console output
343-
cat test_console_output.txt
357+
cat test_console_output_dsdanger.txt
358+
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mv coveragelist.csv $(Pipeline.Workspace)/logs
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mv test_results.xml $(Pipeline.Workspace)/logs
346-
mv test_console_output.txt $(Pipeline.Workspace)/logs
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grep --quiet "Failed: 0" $(Pipeline.Workspace)/logs/test_console_output.txt
362+
grep --quiet "Failed: 0" test_console_output_dsdanger.txt
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workingDirectory: $(Pipeline.Workspace)/dsBaseClient
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displayName: 'Code coverage and JUnit report output, with dsBase and dsDanger'

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