Merge pull request #467 from katy-sadowski/katy__json_func

Fix function reference in Shiny app; fix vignette build issues
OHDSI · Jul 26, 2023 · 1ce9925 · 1ce9925
2 parents f1a46fe + 17d8703
commit 1ce9925
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Showing 6 changed files with 18 additions and 11 deletions.
diff --git a/.Rbuildignore b/.Rbuildignore
@@ -1,11 +1,12 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
-^\.github$
-^LICENSE$
-_pkgdown.yml/*
-compare_versions
+extras
+^\.git
+man-roxygen
+_pkgdown.yml
 deploy.sh
-docs/*
-extras/*
-^doc$
-^Meta$
+compare_versions
+.github
+docs
+^LICENSE$
+^inst/doc/.*\.pdf$
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -15,6 +15,7 @@ Authors@R: c(
 Maintainer: Katy Sadowski <sadowski@ohdsi.org>
 Description: An R package for assessing data quality in standardized OMOP Common Data Model data sources.
 License: Apache License (>= 2)
+Config/build/clean-inst-doc: FALSE
 VignetteBuilder: knitr
 Config/testthat/edition: 3
 URL: https://github.com/OHDSI/DataQualityDashboard

diff --git a/DataQualityDashboard.Rproj b/DataQualityDashboard.Rproj
@@ -13,6 +13,5 @@ RnwWeave: Sweave
 LaTeX: pdfLaTeX
 
 BuildType: Package
-PackageUseDevtools: Yes
 PackageInstallArgs: --no-multiarch --with-keep.source
-PackageRoxygenize: rd,collate,namespace,vignette
+PackageRoxygenize: rd,collate,namespace
diff --git a/extras/PackageMaintenance.R b/extras/PackageMaintenance.R
@@ -70,6 +70,12 @@ rmarkdown::render("vignettes/Thresholds.Rmd",
                                           number_sections = TRUE))
 unlink("inst/doc/Thresholds.tex")
 
+rmarkdown::render("vignettes/SqlOnly.Rmd",
+                  output_file = "../inst/doc/SqlOnly.pdf",
+                  rmarkdown::pdf_document(latex_engine = "pdflatex",
+                                          toc = TRUE,
+                                          number_sections = TRUE))
+unlink("inst/doc/SqlOnly.tex")
 
 pkgdown::build_site()
 OhdsiRTools::fixHadesLogo()
diff --git a/inst/doc/SqlOnly.pdf b/inst/doc/SqlOnly.pdf
diff --git a/inst/shinyApps/app.R b/inst/shinyApps/app.R
@@ -2,7 +2,7 @@ library(shiny)
 server <- function(input, output, session) {
   observe({
     jsonPath <- Sys.getenv("jsonPath")
-    results <- convertJsonResultsFileCase(jsonPath, writeToFile = FALSE, targetCase = "camel")
+    results <- DataQualityDashboard::convertJsonResultsFileCase(jsonPath, writeToFile = FALSE, targetCase = "camel")
     results <- jsonlite::parse_json(jsonlite::toJSON(results))
     session$sendCustomMessage("results", results)
   })