including the sub-folder directory commands for where the harmonised …

…datasets will be stored
nfdi4health · Dec 18, 2024 · 2c51829 · 2c51829
1 parent a5617f5
commit 2c51829
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Showing 8 changed files with 24 additions and 8 deletions.
diff --git a/scripts/GINI_P1.R b/scripts/GINI_P1.R
@@ -104,8 +104,10 @@ fabR::bookdown_open(bookdown_path)
 #### Step 9: Extract and save harmonized data into a pre-set folder
 harmonized_dataset <- Rmonize::pooled_harmonized_dataset_create(harmonized_dossier)
 
+ifelse(!dir.exists(file.path(here::here("output/harmonised_dataset/", paste0(dataset_name, "_", system_name)))),dir.create(here::here("output/harmonised_dataset/", paste0(dataset_name, "_", system_name))), FALSE)
+
 readr::write_delim(x = harmonized_dataset, 
-                   file = here::here(paste0("output/harmonised_dataset/", dataset_name, "_harmonized.csv")),
+                   file = here::here(paste0("output/harmonised_dataset/", dataset_name, "_", system_name, "/", dataset_name,"_harmonized.csv")),
                    delim = ",",
                    na = "")
 

diff --git a/scripts/GINI_P2.R b/scripts/GINI_P2.R
@@ -104,7 +104,9 @@ fabR::bookdown_open(bookdown_path)
 #### Step 9: Extract and save harmonized data into a pre-set folder
 harmonized_dataset <- Rmonize::pooled_harmonized_dataset_create(harmonized_dossier)
 
+ifelse(!dir.exists(file.path(here::here("output/harmonised_dataset/", paste0(dataset_name, "_", system_name)))),dir.create(here::here("output/harmonised_dataset/", paste0(dataset_name, "_", system_name))), FALSE)
+
 readr::write_delim(x = harmonized_dataset, 
-                   file = here::here(paste0("output/harmonised_dataset/", dataset_name, "_harmonized.csv")),
+                   file = here::here(paste0("output/harmonised_dataset/", dataset_name, "_", system_name, "/", dataset_name,"_harmonized.csv")),
                    delim = ",",
                    na = "")
diff --git a/scripts/KORA_S1_P1.R b/scripts/KORA_S1_P1.R
@@ -104,8 +104,10 @@ fabR::bookdown_open(bookdown_path)
 #### Step 9: Extract and save harmonized data into a pre-set folder
 harmonized_dataset <- Rmonize::pooled_harmonized_dataset_create(harmonized_dossier)
 
+ifelse(!dir.exists(file.path(here::here("output/harmonised_dataset/", paste0(dataset_name, "_", system_name)))),dir.create(here::here("output/harmonised_dataset/", paste0(dataset_name, "_", system_name))), FALSE)
+
 readr::write_delim(x = harmonized_dataset, 
-                   file = here::here(paste0("output/harmonised_dataset/", dataset_name, "_harmonized.csv")),
+                   file = here::here(paste0("output/harmonised_dataset/", dataset_name, "_", system_name, "/", dataset_name,"_harmonized.csv")),
                    delim = ",",
                    na = "")
 

diff --git a/scripts/KORA_S1_P2.R b/scripts/KORA_S1_P2.R
@@ -104,7 +104,9 @@ fabR::bookdown_open(bookdown_path)
 #### Step 9: Extract and save harmonized data into a pre-set folder
 harmonized_dataset <- Rmonize::pooled_harmonized_dataset_create(harmonized_dossier)
 
+ifelse(!dir.exists(file.path(here::here("output/harmonised_dataset/", paste0(dataset_name, "_", system_name)))),dir.create(here::here("output/harmonised_dataset/", paste0(dataset_name, "_", system_name))), FALSE)
+
 readr::write_delim(x = harmonized_dataset, 
-                   file = here::here(paste0("output/harmonised_dataset/", dataset_name, "_harmonized.csv")),
+                   file = here::here(paste0("output/harmonised_dataset/", dataset_name, "_", system_name, "/", dataset_name,"_harmonized.csv")),
                    delim = ",",
                    na = "")
diff --git a/scripts/KORA_S3_P1.R b/scripts/KORA_S3_P1.R
@@ -104,7 +104,9 @@ fabR::bookdown_open(bookdown_path)
 #### Step 9: Extract and save harmonized data into a pre-set folder
 harmonized_dataset <- Rmonize::pooled_harmonized_dataset_create(harmonized_dossier)
 
+ifelse(!dir.exists(file.path(here::here("output/harmonised_dataset/", paste0(dataset_name, "_", system_name)))),dir.create(here::here("output/harmonised_dataset/", paste0(dataset_name, "_", system_name))), FALSE)
+
 readr::write_delim(x = harmonized_dataset, 
-                   file = here::here(paste0("output/harmonised_dataset/", dataset_name, "_harmonized.csv")),
+                   file = here::here(paste0("output/harmonised_dataset/", dataset_name, "_", system_name, "/", dataset_name,"_harmonized.csv")),
                    delim = ",",
                    na = "")
diff --git a/scripts/KORA_S3_P2.R b/scripts/KORA_S3_P2.R
@@ -104,7 +104,9 @@ fabR::bookdown_open(bookdown_path)
 #### Step 9: Extract and save harmonized data into a pre-set folder
 harmonized_dataset <- Rmonize::pooled_harmonized_dataset_create(harmonized_dossier)
 
+ifelse(!dir.exists(file.path(here::here("output/harmonised_dataset/", paste0(dataset_name, "_", system_name)))),dir.create(here::here("output/harmonised_dataset/", paste0(dataset_name, "_", system_name))), FALSE)
+
 readr::write_delim(x = harmonized_dataset, 
-                   file = here::here(paste0("output/harmonised_dataset/", dataset_name, "_harmonized.csv")),
+                   file = here::here(paste0("output/harmonised_dataset/", dataset_name, "_", system_name, "/", dataset_name,"_harmonized.csv")),
                    delim = ",",
                    na = "")
diff --git a/scripts/LISA_P1.R b/scripts/LISA_P1.R
@@ -104,8 +104,10 @@ fabR::bookdown_open(bookdown_path)
 #### Step 9: Extract and save harmonized data into a pre-set folder
 harmonized_dataset <- Rmonize::pooled_harmonized_dataset_create(harmonized_dossier)
 
+ifelse(!dir.exists(file.path(here::here("output/harmonised_dataset/", paste0(dataset_name, "_", system_name)))),dir.create(here::here("output/harmonised_dataset/", paste0(dataset_name, "_", system_name))), FALSE)
+
 readr::write_delim(x = harmonized_dataset, 
-                   file = here::here(paste0("output/harmonised_dataset/", dataset_name, "_harmonized.csv")),
+                   file = here::here(paste0("output/harmonised_dataset/", dataset_name, "_", system_name, "/", dataset_name,"_harmonized.csv")),
                    delim = ",",
                    na = "")
 

diff --git a/scripts/LISA_P2.R b/scripts/LISA_P2.R
@@ -104,8 +104,10 @@ fabR::bookdown_open(bookdown_path)
 #### Step 9: Extract and save harmonized data into a pre-set folder
 harmonized_dataset <- Rmonize::pooled_harmonized_dataset_create(harmonized_dossier)
 
+ifelse(!dir.exists(file.path(here::here("output/harmonised_dataset/", paste0(dataset_name, "_", system_name)))),dir.create(here::here("output/harmonised_dataset/", paste0(dataset_name, "_", system_name))), FALSE)
+
 readr::write_delim(x = harmonized_dataset, 
-                   file = here::here(paste0("output/harmonised_dataset/", dataset_name, "_harmonized.csv")),
+                   file = here::here(paste0("output/harmonised_dataset/", dataset_name, "_", system_name, "/", dataset_name,"_harmonized.csv")),
                    delim = ",",
                    na = "")