option to skip individual preprocessing steps by using dummy files

michaelwitting · Aug 2, 2023 · c6b6522 · c6b6522
1 parent 6766eac
commit c6b6522
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Showing 4 changed files with 29 additions and 0 deletions.
diff --git a/scripts/R_ci/compounds_classyfire.R b/scripts/R_ci/compounds_classyfire.R
@@ -37,6 +37,13 @@ for(data_folder in data_folders) {
 
   cat(paste(Sys.time(), "processing", data_folder, "\n"))
 
+  # step will be skipped when ".classyfire_done" file is present in folder
+  if(file.exists(file.path(data_folder, ".classyfire_done"))){
+    cat(paste("skipping ", data_folder, "\n"))
+    next
+  }
+
+
   # canconical smiles data -----------------------------------------------------
   # read canonical smiles data
   rt_data_file <- list.files(data_folder,

diff --git a/scripts/R_ci/compounds_descriptors.R b/scripts/R_ci/compounds_descriptors.R
@@ -41,6 +41,13 @@ for(data_folder in data_folders) {
 
   cat(paste(Sys.time(), "processing", data_folder, "\n"))
 
+  # step will be skipped when ".descriptors_done" file is present in folder
+  if(file.exists(file.path(data_folder, ".descriptors_done"))){
+    cat(paste("skipping ", data_folder, "\n"))
+    next
+  }
+
+
   # canconical smiles data -----------------------------------------------------
   # read canonical smiles data
   rt_data_file <- list.files(data_folder,

diff --git a/scripts/R_ci/compounds_fingerprints.R b/scripts/R_ci/compounds_fingerprints.R
@@ -29,6 +29,13 @@ for(data_folder in data_folders) {
 
   cat(paste(Sys.time(), "processing", data_folder, "\n"))
 
+  # step will be skipped when ".fingerprints_done" file is present in folder
+  if(file.exists(file.path(data_folder, ".fingerprints_done"))){
+    cat(paste("skipping ", data_folder, "\n"))
+    next
+  }
+
+
   # canconical smiles data -----------------------------------------------------
   # read canonical smiles data
   rt_data_file <- list.files(data_folder,

diff --git a/scripts/R_ci/compounds_standardize.R b/scripts/R_ci/compounds_standardize.R
@@ -39,6 +39,14 @@ for(data_folder in data_folders) {
 
   cat(paste(Sys.time(), "processing", data_folder, "\n"))
 
+  # step will be skipped when ".standardization_done" file is present in folder
+  if(file.exists(file.path(data_folder, ".standardization_done"))){
+    cat(paste("skipping ", data_folder, "\n"))
+    next
+  }
+
+
+
   # ============================================================================
   # read and standardize compound data
   # ============================================================================