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Added pkgdown documentation. Added one testthat test.
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Ajit Londhe
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Aug 23, 2019
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,34 @@ | ||
| language: r | ||
| sudo: false | ||
| cache: packages | ||
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| branches: | ||
| except: | ||
| - /^*-v[0-9]/ | ||
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| r_packages: | ||
| - covr | ||
| - drat | ||
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| before_script: | ||
| - export PKG_NAME=$(Rscript -e 'cat(paste0(devtools::as.package(".")$package))') | ||
| - export PKG_TARBALL=$(Rscript -e 'pkg <- devtools::as.package("."); cat(paste0(pkg$package,"_",pkg$version,".tar.gz"))') | ||
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| # Build and check package | ||
| script: | ||
| - R CMD build . | ||
| - _R_CHECK_CRAN_INCOMING_=FALSE R CMD check "${PKG_TARBALL}" --as-cran | ||
| - cat ${PKG_NAME}.Rcheck/00install.out # Print out install / compile log | ||
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| after_success: | ||
| - test $TRAVIS_PULL_REQUEST == "false" && test $TRAVIS_BRANCH == "master" && perl compare_versions --tag && bash deploy.sh && curl --data "build=true" -X POST https://registry.hub.docker.com/u/ohdsi/broadsea-methodslibrary/trigger/f0b51cec-4027-4781-9383-4b38b42dd4f5/ | ||
| - Rscript -e 'library(covr);codecov()' | ||
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| notifications: | ||
| recipients: | ||
| - alondhe2@its.jnj.com | ||
| - mblacke@its.jnj.com | ||
| - fdefalco@its.jnj.com | ||
| email: | ||
| on_success: change | ||
| on_failure: change |
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| Original file line number | Diff line number | Diff line change |
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| @@ -1,9 +1,5 @@ | ||
| # Generated by roxygen2: do not edit by hand | ||
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| export(dqDashPOC) | ||
| export(dqDashPOCOutput) | ||
| export(executeDqChecks) | ||
| export(renderDqDashPOC) | ||
| export(viewDqDashboard) | ||
| export(writeJsonResultsToTable) | ||
| import(htmlwidgets) |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,21 @@ | ||
| template: | ||
| params: | ||
| bootswatch: cosmo | ||
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| home: | ||
| links: | ||
| - text: Ask a question | ||
| href: http://forums.ohdsi.org | ||
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| reference: | ||
| - title: "Execution" | ||
| desc: > | ||
| Function for running data quality checks | ||
| contents: | ||
| - executeDqChecks | ||
| - writeJsonResultsToTable | ||
| - title: "View Dashboard" | ||
| desc: > | ||
| Function for viewing the data quality dashboard | ||
| contents: | ||
| - viewDqDashboard |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,68 @@ | ||
| #!/usr/bin/perl | ||
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| open(R_VERSION, "grep 'Version' DESCRIPTION |"); | ||
| $version = <R_VERSION>; | ||
| close(R_VERSION); | ||
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| $version =~ /(\d+)\.(\d+)\.(\d+)/; | ||
| $r_major = $1; | ||
| $r_minor = $2; | ||
| $r_mod = $3; | ||
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| print "New R version: $r_major-$r_minor-$r_mod\n"; | ||
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| open(GIT_VERSION, "git describe --tags |"); | ||
| $git = <GIT_VERSION>; | ||
| close(GIT_VERSION); | ||
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| $git =~ /v(\d+)\.(\d+)\.(\d+)/; | ||
| $git_major = $1; | ||
| $git_minor = $2; | ||
| $git_mod = $3; | ||
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| print "Current git version: $git_major-$git_minor-$git_mod\n"; | ||
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| if ($r_major > $git_major || $r_minor > $git_minor || $r_mod > $git_mod) { | ||
| $monotonic = 0; | ||
| } else { | ||
| $monotonic = -1; | ||
| } | ||
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| if ($monotonic != 0) { | ||
| print "Non-monotonically increasing versions numbers\n"; | ||
| } | ||
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| if ($monotonic == 0 & $ARGV[0] eq "--tag") { | ||
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| open(GIT_TAG, "git tag v$r_major.$r_minor.$r_mod |"); | ||
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| $fail = 0; | ||
| while ($line = <GIT_TAG>) { | ||
| if ($line =~ /fatal/) { | ||
| $fail = 1; | ||
| } | ||
| print "tag: $line"; | ||
| } # TODO Check for errors | ||
| close(GIT_TAG); | ||
| print "tag: END\n\n"; | ||
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| if ($fail eq 1) { | ||
| exit(-1); | ||
| } | ||
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| $cmd = "git config user.name \"alondhe\"; " . | ||
| "git config user.email \"alondhe2@its.jnj.com\"; " . | ||
| "git tag v$r_major.$r_minor.$r_mod ; " . | ||
| "git push -q https://\$GH_TOKEN\@github.com/OHDSI/\$PKG_NAME.git --tags"; | ||
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| print "cmd: $cmd\n"; | ||
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| open(GIT_PUSH, "$cmd |"); | ||
| while ($line = <GIT_PUSH>) { | ||
| print "push: $line"; | ||
| } # TODO Check for errors | ||
| close(GIT_PUSH); | ||
| print "push: END\n\n"; | ||
| } | ||
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| exit($monotonic); |
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