From 669ba414c9e70829816b89b5c5511266646f75a5 Mon Sep 17 00:00:00 2001
From: mrustl <michael.rustler@kompetenz-wasser.de>
Date: Tue, 4 Jun 2024 17:55:13 +0200
Subject: [PATCH] Add read_profile() and improve read_obsnode()

naming (using "node_id")
---
 NAMESPACE           |  1 +
 R/read_obsnode.R    |  3 ++-
 R/read_profile.R    | 48 +++++++++++++++++++++++++++++++++++++++++++++
 man/read_obsnode.Rd |  3 +++
 man/read_profile.Rd | 17 ++++++++++++++++
 5 files changed, 71 insertions(+), 1 deletion(-)
 create mode 100644 R/read_profile.R
 create mode 100644 man/read_profile.Rd

diff --git a/NAMESPACE b/NAMESPACE
index 018656e..09c6819 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -11,6 +11,7 @@ export(read_alevel)
 export(read_atmosph)
 export(read_meta_general)
 export(read_obsnode)
+export(read_profile)
 export(read_runinf)
 export(read_solute)
 export(read_tlevel)
diff --git a/R/read_obsnode.R b/R/read_obsnode.R
index 13b75b5..bc44a0f 100644
--- a/R/read_obsnode.R
+++ b/R/read_obsnode.R
@@ -2,6 +2,7 @@
 #'
 #' @param path path to Obs_Node.out
 #' @param to_longer convert table to longer format (default: TRUE)
+#' @return tibble with Obs_Node time series data
 #' @importFrom stringr str_trim str_split str_replace_all str_remove
 #' @importFrom readr read_csv
 #' @export
@@ -66,7 +67,7 @@ read_obsnode <- function(path, to_longer = TRUE) {
   if(to_longer) {
     dat %>%
       tidyr::pivot_longer( - time) %>%
-      tidyr::separate(col = "name", into = c("node", "variable"), sep = "_") %>%
+      tidyr::separate(col = "name", into = c("node_id", "variable"), sep = "_") %>%
       dplyr::mutate(node = stringr::str_remove(node, "node") %>% as.integer())
   } else {
     dat
diff --git a/R/read_profile.R b/R/read_profile.R
new file mode 100644
index 0000000..81f5785
--- /dev/null
+++ b/R/read_profile.R
@@ -0,0 +1,48 @@
+#' Read PROFILE.out
+#'
+#' @param path path to PROFILE.out
+#'
+#' @return tibble with PROFILE.out data
+#' @export
+#' @importFrom stringr str_replace
+read_profile <- function(path) {
+
+  lines <- readLines(paths$profile)
+
+  header_idx <- grep("x", lines)
+
+  dat <- lines[(header_idx+1):length(lines)] %>%
+    stringr::str_trim() %>%
+    stringr::str_replace_all("\\s+", ",")
+
+  ncols <- sapply(seq_along(dat), function(i) length(gregexpr(",", dat[i])[[1]])) + 1
+
+
+  header_names_file <- c("node_id", stringr::str_sub(lines[header_idx],
+                                                     start = gregexpr("x", lines[header_idx])[[1]][1],
+                                                     end = nchar(lines[header_idx])) %>%
+                           stringr::str_trim() %>%
+                           stringr::str_replace_all("\\s+", " ") %>%
+                           stringr::str_split(" ", simplify = TRUE) %>%
+                           as.vector() %>% tolower())
+
+  header_clean <- if(median(ncols) > length(header_names_file)) {
+    string_conc <- sprintf("conc_%d", seq_len(median(ncols) - length(header_names_file))+1)
+
+    c(stringr::str_replace(header_names_file, "conc", "conc_1"),
+      string_conc)
+
+  } else {
+    header_names_file
+  }
+
+  header_clean
+
+  path_profile <- file.path(tempdir(), "profile.csv")
+
+  c(paste0(header_clean, collapse = ","),
+    dat[ncols == median(ncols)]) %>%
+    writeLines(path_profile)
+
+  readr::read_csv(path_profile)
+}
diff --git a/man/read_obsnode.Rd b/man/read_obsnode.Rd
index 8a65936..ea2372c 100644
--- a/man/read_obsnode.Rd
+++ b/man/read_obsnode.Rd
@@ -11,6 +11,9 @@ read_obsnode(path, to_longer = TRUE)
 
 \item{to_longer}{convert table to longer format (default: TRUE)}
 }
+\value{
+tibble with Obs_Node time series data
+}
 \description{
 Read Obs_Node.out
 }
diff --git a/man/read_profile.Rd b/man/read_profile.Rd
new file mode 100644
index 0000000..d5c0e1d
--- /dev/null
+++ b/man/read_profile.Rd
@@ -0,0 +1,17 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/read_profile.R
+\name{read_profile}
+\alias{read_profile}
+\title{Read PROFILE.out}
+\usage{
+read_profile(path)
+}
+\arguments{
+\item{path}{path to PROFILE.out}
+}
+\value{
+tibble with PROFILE.out data
+}
+\description{
+Read PROFILE.out
+}