added gitlab-ci, added sitename to filenames, fixed r cmd check results

.Rbuildignore

@@ -4,3 +4,4 @@
 ^LICENSE\.md$
 ^docker$
 ^inst/application/_settings$
+^\.gitlab-ci\.yml$

.gitlab-ci.yml

+variables:
+  _R_CHECK_CRAN_INCOMING_: "false"
+  _R_CHECK_FORCE_SUGGESTS_: "true"
+  CI_IMAGE_NAME: "rocker/verse"
+  CI_IMAGE_TAG: "3.6.1"
+  R_PKG_NAME: "DQAgui"
+
+default:
+  image: ${CI_IMAGE_NAME}:${CI_IMAGE_TAG}
+  before_script:
+    - echo "options('repos' = 'https://ftp.fau.de/cran/')" >> /usr/local/lib/R/etc/Rprofile.site
+    - R -e "devtools::install_deps(pkg = '.', upgrade = 'always')"
+    - R -e "devtools::install_dev_deps(pkg = '.', upgrade = 'always')"
+    - mkdir -p ci
+
+stages:
+  - build
+  - test
+  - deploy
+
+check:
+  stage: build
+  script:
+    - R -e "devtools::check(pkg = '.', args = c('--no-tests'), build_args = c('--no-build-vignettes'), check_dir = '${CI_PROJECT_DIR}/ci')"
+  artifacts:
+    paths:
+      - "${CI_PROJECT_DIR}/ci/*.Rcheck"
+    when: on_failure # upload check artifacts when job fails!
+    expire_in: 1 week
+
+create_manual:
+  stage: build
+  script:
+    - R -e "devtools::build_manual(pkg = '.', path = '${CI_PROJECT_DIR}/ci')"
+  artifacts:
+    paths:
+      - "${CI_PROJECT_DIR}/ci/*.pdf"
+    expire_in: 1 week
+
+build_source:
+  stage: build
+  script:
+    - R -e "devtools::build(pkg = '.', path = '${CI_PROJECT_DIR}/ci', binary = FALSE, vignettes = FALSE)"
+  artifacts:
+    paths:
+      - "${CI_PROJECT_DIR}/ci/*.tar.gz"
+    expire_in: 1 week
+
+build_binary:
+  stage: build
+  script:
+    - R -e "devtools::build(pkg = '.', path = '${CI_PROJECT_DIR}/ci', binary = TRUE, vignettes = FALSE)"
+  artifacts:
+    paths:
+      - "${CI_PROJECT_DIR}/ci/*.tar.gz"
+    expire_in: 1 week
+
+# To have the coverage percentage appear as a gitlab badge follow these
+# instructions:
+# https://docs.gitlab.com/ee/user/project/pipelines/settings.html#test-coverage-parsing
+# The coverage parsing string is
+# Coverage: \d+\.\d+
+
+coverage:
+  stage: test
+  allow_failure: true
+  when: on_success
+  script:
+    - R -e "install.packages('DT')"
+    - R -e "covr::gitlab(quiet = FALSE)"
+  artifacts:
+    paths:
+      - public
+
+testing:
+  stage: test
+  allow_failure: true
+  when: on_success
+  script:
+    - R -e "devtools::test(pkg = '.')"
+
+# To produce a code coverage report as a GitLab page see
+# https://about.gitlab.com/2016/11/03/publish-code-coverage-report-with-gitlab-pages/
+
+install:
+  stage: deploy
+  script:
+    - R -e "devtools::install(pkg = '.', upgrade = 'always')"

DESCRIPTION

@@ -13,7 +13,7 @@ URL: https://gitlab.miracum.org/miracum-dqa/dqagui
 BugReports: https://gitlab.miracum.org/miracum-dqa/dqagui/issues
 Encoding: UTF-8
 Copyright: Universitätsklinikum Erlangen
-Date/Publication: 2019-11-05 15:25:31 UTC
+Date: 2019-11-11
 Imports: 
     data.table,
     magrittr,
@@ -30,3 +30,6 @@ Imports:
 Suggests: 
     testthat,
     processx
+Remotes: 
+    git::git@gitlab.miracum.org:miracumdqa/dqastats.git
+RoxygenNote: 6.1.1

R/launch_app.R

-# DQAgui - A graphical user interface (GUI) to the functions implemented in the R package 'DQAstats'.
+# DQAgui - A graphical user interface (GUI) to the functions implemented in the
+# R package 'DQAstats'.
 # Copyright (C) 2019 Universitätsklinikum Erlangen
 #
 # This program is free software: you can redistribute it and/or modify
@@ -18,12 +19,16 @@
 #' @title Launch the DQA graphical user interface (GUI)
 #'
 #' @param port The port, the MIRACUM DQA Tool is running on (default: 3838)
-#' @param utilspath The path to the utilities-folder, containing the metadata repository files (`mdr.csv` inside the folder `MDR`),
-#'   JSON files with SQL statements (inside the folder `SQL`), config files for the database connection (`settings_default.yml`)
-#'   and the email address used for the data map (`email.yml`), a JSON file containing site names (inside the folder `MISC`) and a
-#'   markdown templated to create the PDF report (`DQA_report.Rmd` inside the folder `RMD`).
-#' @param db_source The name of the source database. Currently, the only allowed argument is `p21csv` used for the import of the
-#'   corresponding csv files.
+#' @param utilspath The path to the utilities-folder, containing the metadata
+#'   repository files (`mdr.csv` inside the folder `MDR`), JSON files with SQL
+#'   statements (inside the folder `SQL`), config files for the database
+#'   connection (`settings_default.yml`) and the email address used for the
+#'   data map (`email.yml`), a JSON file containing site names (inside the
+#'   folder `MISC`) and a markdown templated to create the PDF report
+#'   (`DQA_report.Rmd` inside the folder `RMD`).
+#' @param db_source The name of the source database. Currently, the only
+#'   allowed argument is `p21csv` used for the import of the corresponding
+#'   csv files.
 #'
 #' @return DQAgui Shiny application
 #'
@@ -34,10 +39,34 @@
 #' @export
 #'
 
-launchApp <- function(port=3838, utilspath, db_source){
+launchApp <- function(port=3838,
+                      utilspath,
+                      db_source) {
+
+  global_env_hack <- function(key,
+                              val,
+                              pos) {
+    assign(
+      key,
+      val,
+      envir = as.environment(pos)
+    )
+  }
+
+  global_env_hack(
+    key = "utilspath",
+    val = utilspath,
+    pos = 1L
+  )
+
+  global_env_hack(
+    key = "db_source",
+    val = db_source,
+    pos = 1L
+  )
+
   options(shiny.port = port)
-  assign("utilspath", utilspath, envir = .GlobalEnv)
-  assign("db_source", db_source, envir = .GlobalEnv)
+
   shiny::shinyAppDir(appDir = system.file("application", package = "DQAgui"))
 }
 

R/moduleReport.R

@@ -93,6 +93,8 @@ moduleReportServer <- function(input,
              gsub("\\-|\\:| ",
                   "",
                   substr(rv$start.time, 1, 16)),
+             "_",
+             rv$sitename,
              ".pdf")
     },
     content = function(file){
@@ -116,6 +118,8 @@ moduleReportServer <- function(input,
              gsub("\\-|\\:| ",
                   "",
                   substr(rv$start.time, 1, 16)),
+             "_",
+             rv$sitename,
              ".zip")
     },
     content = function(fname) {

data-raw/devstuffs.R

@@ -21,7 +21,7 @@ my_desc$set(Title = "DQA GUI")
 # The description of your package
 my_desc$set(Description = "A graphical user interface (GUI) to the functions implemented in the R package 'DQAstats'.")
 # The description of your package
-my_desc$set("Date/Publication" = paste(as.character(Sys.time()), "UTC"))
+my_desc$set("Date" = as.character(Sys.Date()))
 # The urls
 my_desc$set("URL", "https://gitlab.miracum.org/miracum-dqa/dqagui")
 my_desc$set("BugReports",
@@ -67,8 +67,10 @@ usethis::use_package("testthat", type = "Suggests")
 usethis::use_package("processx", type = "Suggests")
 
 # Development package
-# https://remotes.r-lib.org/articles/dependencies.html
+devtools::install_git(url = "https://gitlab.miracum.org/miracum-dqa/dqastats.git", ref = "master", upgrade = "always")
 usethis::use_dev_package("DQAstats", type = "Imports")
+# https://cran.r-project.org/web/packages/devtools/vignettes/dependencies.html
+desc::desc_set_remotes("git::git@gitlab.miracum.org:miracumdqa/dqastats.git", file = usethis::proj_get())
 
 # buildignore and gitignore
 usethis::use_build_ignore("docker")

man/launchApp.Rd

@@ -9,13 +9,17 @@ launchApp(port = 3838, utilspath, db_source)
 \arguments{
 \item{port}{The port, the MIRACUM DQA Tool is running on (default: 3838)}
 
-\item{utilspath}{The path to the utilities-folder, containing the metadata repository files (`mdr.csv` inside the folder `MDR`),
-JSON files with SQL statements (inside the folder `SQL`), config files for the database connection (`settings_default.yml`)
-and the email address used for the data map (`email.yml`), a JSON file containing site names (inside the folder `MISC`) and a
-markdown templated to create the PDF report (`DQA_report.Rmd` inside the folder `RMD`).}
+\item{utilspath}{The path to the utilities-folder, containing the metadata
+repository files (`mdr.csv` inside the folder `MDR`), JSON files with SQL
+statements (inside the folder `SQL`), config files for the database
+connection (`settings_default.yml`) and the email address used for the
+data map (`email.yml`), a JSON file containing site names (inside the
+folder `MISC`) and a markdown templated to create the PDF report
+(`DQA_report.Rmd` inside the folder `RMD`).}
 
-\item{db_source}{The name of the source database. Currently, the only allowed argument is `p21csv` used for the import of the
-corresponding csv files.}
+\item{db_source}{The name of the source database. Currently, the only
+allowed argument is `p21csv` used for the import of the corresponding
+csv files.}
 }
 \value{
 DQAgui Shiny application