extras/PackageMaintenance.R

In OHDSI/CohortDiagnostics: Diagnostics for OHDSI Cohorts

# @file PackageMaintenance
#
# Copyright 2024 Observational Health Data Sciences and Informatics
#
# This file is part of CohortDiagnostics
# 
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# 
#     http://www.apache.org/licenses/LICENSE-2.0
# 
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.

# Format and check code
OhdsiRTools::checkUsagePackage("CohortDiagnostics")
OhdsiRTools::updateCopyrightYearFolder()
styler::style_pkg()
devtools::spell_check()

# Create manual and vignettes:
unlink("extras/CohortDiagnostics.pdf")
system("R CMD Rd2pdf ./ --output=extras/CohortDiagnostics.pdf")

dir.create(path = "./inst/doc/", showWarnings = FALSE)


rmarkdown::render("vignettes/ViewingResultsUsingDiagnosticsExplorer.Rmd",
                  output_file = "../inst/doc/ViewingResultsUsingDiagnosticsExplorer.pdf",
                  rmarkdown::pdf_document(latex_engine = "pdflatex",
                                          toc = TRUE,
                                          number_sections = TRUE))


rmarkdown::render("vignettes/WhatIsCohortDiagnostics.Rmd",
                  output_file = "../inst/doc/WhatIsCohortDiagnostics.pdf",
                  rmarkdown::pdf_document(latex_engine = "pdflatex",
                                          toc = TRUE,
                                          number_sections = TRUE))

rmarkdown::render("vignettes/RunningCohortDiagnostics.Rmd",
                  output_file = "../inst/doc/RunningCohortDiagnostics.pdf",
                  rmarkdown::pdf_document(latex_engine = "pdflatex",
                                          toc = TRUE,
                                          number_sections = TRUE))

pkgdown::build_site()
OhdsiRTools::fixHadesLogo()

# Change shiny app version number to current version
pattern <- "Version: (\\d+\\.\\d+\\.\\d+)"
text <- readChar("DESCRIPTION", file.info("DESCRIPTION")$size)
version <- stringi::stri_extract(text, regex = pattern)

filePath <- file.path("inst", "shiny", "DiagnosticsExplorer", "global.R")
text <- readChar(filePath, file.info(filePath)$size)
patternRep <- 'appVersionNum <- "Version: (\\d+\\.\\d+\\.\\d+)"'
text <- gsub(patternRep, paste0('appVersionNum <- "', version, '"'), text)
writeLines(text, con = file(filePath))


version <- gsub("Version: ", "", version)
filePath <- file.path("inst", "sql", "sql_server", "UpdateVersionNumber.sql")
text <- readChar(filePath, file.info(filePath)$size)
patternRep <- "\\{DEFAULT @version_number = '(\\d+\\.\\d+\\.\\d+)'\\}"
text <- gsub(patternRep, paste0("\\{DEFAULT @version_number = '", version, "'\\}"), text)
writeLines(text, con = file(filePath))