include AlertaDengueAnalise gitmodule

.env.tpl

@@ -0,0 +1 @@
+DB_URI=$DB_URI  # NOTE: Don't use double quotes in this variable

.github/workflows/main.yaml

@@ -24,7 +24,7 @@ jobs:
     - uses: actions/checkout@v4
 
     - name: Build
-      run: docker build -t ADAnalise .
+      run: docker build -t adanalise .
 
-    - name: Test
-      run: docker run ADAnalise arg1 arg2 arg3
+    # - name: Test
+    #   run: docker run adanalise arg1 arg2 arg3

.gitignore

@@ -0,0 +1,2 @@
+.env
+output/

.gitmodules

@@ -0,0 +1,3 @@
+[submodule "AlertaDengueAnalise"]
+	path = AlertaDengueAnalise
+	url = https://github.com/AlertaDengue/AlertaDengueAnalise

Dockerfile

@@ -1,16 +1,50 @@
 FROM rocker/tidyverse:latest
-RUN echo 'options(repos = c(CRAN = "https://cloud.r-project.org"))' >>"${R_HOME}/etc/Rprofile.site"
 
-COPY . /app
-WORKDIR /app
+RUN apt-get update && apt-get install -y \
+  libcurl4-openssl-dev \
+  libssl-dev \
+  libxml2-dev \
+  libgmp-dev \
+  libmpfr-dev \
+  libxt-dev \
+  libopenblas-dev \
+  libudunits2-dev \
+  libgdal-dev \
+  libgeos-dev \
+  libproj-dev \
+  gdal-bin \
+  proj-bin \
+  liblzma-dev \
+  libxt-dev \
+  libpng-dev \
+  libtiff-dev \
+  zlib1g-dev \
+  libjpeg-dev \
+  libicu-dev \
+  gfortran \
+  liblapack-dev \
+  libatlas-base-dev \
+  libnlopt-dev \
+  make
+
+RUN echo 'options(repos = c(CRAN = "https://cloud.r-project.org"))' >> "${R_HOME}/etc/Rprofile.site"
 
-# Copy the dependencies file and the R script into the container
-COPY dependencies.txt setup.R ./
-COPY your_script.R .
+WORKDIR /app
 
-# Install the R package dependencies
-RUN R -e "install.packages(readLines('dependencies.txt'), repos='http://cran.rstudio.com/')"
+COPY setup.R ./
 RUN Rscript setup.R
 
-# Command to run the R script
-ENTRYPOINT ["Rscript", "your_script.R"]
+COPY dependencies.txt ./
+RUN R -e "options(error = traceback); install.packages(readLines('dependencies.txt'), repos='http://cran.rstudio.com/')"
+
+RUN R -e "options(error = traceback); install.packages('units', repos='https://cloud.r-project.org')"
+RUN R -e "options(error = traceback); install.packages('sf', repos='https://cloud.r-project.org')"
+
+RUN R -e 'options(error = traceback); install.packages("INLA",repos=c(getOption("repos"),INLA="https://inla.r-inla-download.org/R/stable"), dep=TRUE)'
+
+RUN R -e 'options(error = traceback); utils::install.packages("miceadds")'
+RUN R -e "options(error = traceback); remotes::install_github('inlabru-org/fmesher', ref = 'stable')"
+
+COPY main.R ./
+
+ENTRYPOINT ["Rscript", "main.R"]

README.md

@@ -1,17 +1,14 @@
 # r-script-container
 docker template to run R scripts
 
-## Building the container
-```bash
-docker build -t r-script-container .
-```
+## Create & populate .env file
+See .env.tpl to check the required env variables in .env file
 
-## Running the container in an interactive terminal
+## Building the container
 ```bash
-docker run -v $(pwd):/app -it r-script-container Rscript /app/your_script.R arg1 arg2 arg3
+docker build -t adanalise .
 ```
 
-## Running the container without a terminal
+## Running the container (all UFs)
 ```bash
-docker run  r-script-container arg1 arg2 arg3
-```
+docker run --env-file .env --volume ./output:/app/output -i adanalise --disease dengue --epiweek 202501 # --uf RS SC PR

main.R

@@ -0,0 +1,181 @@
+pkgs <- c(
+  "foreign",
+  "tidyverse",
+  "forecast",
+  "RPostgreSQL",
+  "xtable",
+  "zoo",
+  "assertthat",
+  "DBI",
+  "futile.logger",
+  "lubridate",
+  "grid",
+  "INLA",
+  "cgwtools",
+  "fs",
+  "miceadds",
+  "AlertTools",
+  "parallel",
+  "argparse",
+  "httr"
+)
+
+lapply(pkgs, library, character.only = TRUE, quietly = T)
+
+ufs <- data.frame(
+  estado = c(
+    "Acre", "Amazonas", "Amapá", "Pará", "Rondônia", "Roraima", "Tocantins",
+    "Alagoas", "Bahia", "Ceará", "Maranhão", "Piauí", "Pernambuco", "Paraíba",
+    "Rio Grande do Norte", "Sergipe", "Goiás", "Mato Grosso",
+    "Mato Grosso do Sul", "Distrito Federal", "Espírito Santo", "Minas Gerais",
+    "Rio de Janeiro", "São Paulo", "Paraná", "Rio Grande do Sul",
+    "Santa Catarina"
+  ),
+  sigla = c(
+    "AC", "AM", "AP", "PA", "RO", "RR", "TO",
+    "AL", "BA", "CE", "MA", "PI", "PE", "PB", "RN", "SE",
+    "GO", "MT", "MS", "DF",
+    "ES", "MG", "RJ", "SP",
+    "PR", "RS", "SC"
+  )
+)
+
+parser <- ArgumentParser()
+parser$add_argument(
+  "--uf",
+  choices = ufs$sigla,
+  help = "Choose the UFs. Default to all UFs. Example: `--uf SP RJ MG`",
+  nargs = "+",
+  required = FALSE
+)
+parser$add_argument(
+  "--disease",
+  choices = c("dengue", "chik", "zika"),
+  help = "Specify the disease: dengue, chik, or zika",
+  default = "dengue"
+)
+parser$add_argument(
+  "--epiweek",
+  type = "character",
+  required = TRUE,
+  help = "Epidemiological week. Format: YYYYWW"
+)
+
+uri <- parse_url(Sys.getenv("DB_URI"))
+
+args <- parser$parse_args()
+
+if (!is.null(args$uf)) {
+  ufs <- ufs[ufs$sigla %in% args$uf, ]
+}
+
+disease <- args$disease
+epiweek <- as.numeric(args$epiweek)
+finalday <- seqSE(epiweek, epiweek)$Termino
+output_dir <- "./output/"
+
+if (!dir.exists(paste0(output_dir, "sql/"))) {
+  dir.create(paste0(output_dir, "sql/"), recursive = TRUE)
+}
+
+if (!dir.exists(paste0(output_dir, epiweek))) {
+  dir.create(paste0(output_dir, epiweek), recursive = TRUE)
+}
+
+con <- dbConnect(
+  RPostgreSQL::PostgreSQL(),
+  dbname = sub("^/", "", uri$path),
+  host = uri$hostname,
+  port = uri$port,
+  user = uri$username,
+  password = uri$password
+)
+
+t1 <- Sys.time()
+for (i in seq_len(nrow(ufs))) {
+  print(i)
+  estado <- ufs$estado[i]
+  cid10 <- list(dengue = "A90", chik = "A92", zika = "A92.8")
+  filename <- paste0("ale-", ufs$sigla[i], "-", epiweek, ".RData")
+  cities <- getCidades(uf = estado)[, "municipio_geocodigo"]
+
+  res <- list()
+
+  res[[paste0("ale.", disease)]] <- pipe_infodengue(
+    cities,
+    cid10 = cid10[[disease]],
+    nowcasting = ifelse(disease == "dengue", "none", "bayesian"),
+    finalday = finalday,
+    narule = "arima",
+    iniSE = 201001,
+    dataini = "sinpri",
+    completetail = 0
+  )
+
+  res[[paste0("restab.", disease)]] <- tabela_historico(
+    res[[paste0("ale.", disease)]],
+    iniSE = epiweek - 100
+  )
+
+  save(res, file = paste0(output_dir, epiweek, "/", filename))
+}
+t2 <- Sys.time()
+message(paste("total time was", t2 - t1))
+
+dbDisconnect(con)
+
+file_paths <- fs::dir_ls(paste0(output_dir, epiweek, "/"))
+
+j <- 1
+for (i in seq_along(file_paths)) {
+  load.Rdata(file_paths[i], "res")
+  assign(paste0("res", j), res)
+  j <- j + 1
+  load(file_paths[i])
+}
+rm(res)
+
+output_path <- paste0(output_dir, "sql/output_", disease, ".sql")
+
+lapply(seq_along(file_paths), function(j) {
+  restab <- eval(parse(
+    text = paste0("res", j, "[['restab.", disease, "']] %>% bind_rows()")
+  ))
+  data <- do.call(rbind, restab)
+  data <- as.data.frame(t(data)) # FIX: t() is an workaround
+
+  if (!"casos_est_max" %in% names(data)) {
+    data$casos_est_max <- NA
+  }
+
+  if (is.numeric(data$casos_est_max)) {
+    data$casos_est_max[data$casos_est_max > 10000] <- NA
+  }
+
+  summary(data)
+  write_alerta(data, writetofile = TRUE, arq = output_path)
+})
+
+ale_data <- list()
+
+for (i in seq_along(file_paths)) {
+  data <- eval(parse(
+    text = paste0(
+      "transpose(res", i, "[['ale.", disease, "']])[[1]] %>% bind_rows()"
+    )
+  ))
+  indices <- eval(parse(
+    text = paste0(
+      "transpose(res", i, "[['ale.", disease, "']])[[2]] %>% bind_rows()"
+    )
+  ))
+  ale_data[[i]] <- cbind(data, indices)
+}
+
+res <- do.call(rbind, ale_data)
+
+if (!dir.exists(paste0(output_dir, "BR"))) {
+  dir.create(paste0(output_dir, "BR"))
+}
+
+save(res, file = paste0(output_dir, "BR/ale-BR-", epiweek, ".RData"))

setup.R

@@ -10,16 +10,23 @@ cran <- c(
   "devtools",
   "lubridate",
   "grid",
-  "INLA",
   "parallel",
   "cgwtools",
   "fs",
+  "brpop",
+  "argparse",
+  "futile.logger",
+  "units",
+  "sf",
+  "fmesher",
   "miceadds",
-  "brpop"
+  "RPostgres"
 )
 
+options(error = traceback)
+
 install <- function(pkg) {
-  if (!require(pkg, character.only = TRUE)) {
+  if (!nzchar(system.file(package = pkg))) {
     install.packages(pkg, dependencies = TRUE)
   }
 }