From f819e7d1cd8d0a5f9b1d7023deaae0b9bb9c9c24 Mon Sep 17 00:00:00 2001
From: ake <40662956+ake123@users.noreply.github.com>
Date: Sat, 10 Aug 2024 10:18:00 +0300
Subject: [PATCH] correction to DESCRIPTION file (#596)

---
 DESCRIPTION                     | 54 ++++++++++++++++-----------------
 inst/assets/bibliography.bib    |  2 +-
 oma_packages/extract_packages.R | 38 +++++++++++++++++++----
 oma_packages/oma_packages.csv   |  6 ++--
 4 files changed, 63 insertions(+), 37 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 260799172..f273bdf7b 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -27,49 +27,58 @@ biocViews:
 Depends:
     R (>= 4.0.0)
 Imports:
+    ape,
+    BiocManager,
+    BiocParallel,
+    Biostrings,
+    ComplexHeatmap,
+    dplyr,
+    ggplot2,
+    glue,
+    grid,
+    igraph,
+    knitr,
+    Maaslin2,
+    mia,
+    miaTime,
+    miaViz,
+    microbiome,
+    microbiomeDataSets,
+    phyloseq,
+    purrr,
+    reshape2,
+    scales,
+    sessioninfo,
+    stringr,
+    tidyverse,
+    vegan,
+    xgboost
 Suggests:
     ALDEx2,
     ANCOMBC,
-    ape,
     biclust,
     BiocBook,
-    BiocManager,
-    BiocParallel,
-    Biostrings,
     bluster,
     caret,
     circlize,
     cluster,
     cobiclust,
-    ComplexHeatmap,
     corpcor,
     curatedMetagenomicData,
     dada2,
     dendextend,
     devtools,
     DirichletMultinomial,
-    dplyr,
     DT,
     factoextra,
     forcats,
     fido,
-    ggplot2,
     ggpubr,
     ggtree,
     glmnet,
-    glue,
-    grid,
     gtools,
     gsEasy,
-    igraph,
     kableExtra,
-    knitr,
-    Maaslin2,
-    mia,
-    miaTime,
-    miaViz,
-    microbiome,
-    microbiomeDataSets,
     MicrobiomeStat,
     mikropml,
     MMUPHin,
@@ -79,31 +88,22 @@ Suggests:
     NbClust,
     NMF,
     patchwork,
-    phyloseq,
     plotly,
-    purrr,
     qgraph,
     RColorBrewer,
     rebook,
-    reshape2,
     reticulate,
     rgl,
     ROCR,
-    scales,
     scater,
     sechm,
-    sessioninfo,
     shadowtext,
     SpiecEasi,
     SPRING,
     stats,
-    stringr,
     SuperLearner,
-    tidyverse,
     topGO,
-    vegan,
-    WGCNA,
-    xgboost
+    WGCNA
 Remotes:
     github::microbiome/mia,
     github::microbiome/miaViz,
diff --git a/inst/assets/bibliography.bib b/inst/assets/bibliography.bib
index cdf058409..2d520ae57 100644
--- a/inst/assets/bibliography.bib
+++ b/inst/assets/bibliography.bib
@@ -18,7 +18,7 @@ @Article{Deng2024
   year =	 {2024},
   volume =	 18,
   number = {1},
-  pages = {wrae106}
+  pages = {wrae106},
   doi =		 {10.1093/ismejo/wrae106}
 }
 
diff --git a/oma_packages/extract_packages.R b/oma_packages/extract_packages.R
index 9f5d0e53d..9dd61daee 100644
--- a/oma_packages/extract_packages.R
+++ b/oma_packages/extract_packages.R
@@ -1,7 +1,19 @@
-packages <- function() {
-  lines <- readLines("../DESCRIPTION")
+extract_packages <- function(description_file_path = "~/OMA/DESCRIPTION", output_file_path = "~/OMA/oma_packages/oma_packages.csv") {
+  # Check if the DESCRIPTION file exists
+  if (!file.exists(description_file_path)) {
+    stop(paste("DESCRIPTION file not found at path:", description_file_path))
+  }
+  
+  # Read the DESCRIPTION file
+  lines <- tryCatch(readLines(description_file_path), error = function(e) {
+    message("Error reading DESCRIPTION file: ", e$message)
+    return(NULL)
+  })
+  
+  if (is.null(lines)) return()  # Exit if file could not be read
   
-  extract_packages <- function(lines, section_name) {
+  # Function to extract packages from a given section
+  extract_packages_from_section <- function(lines, section_name) {
     section_index <- grep(paste0("^", section_name, ":"), lines)
     if (length(section_index) > 0) {
       start_index <- section_index + 1
@@ -14,12 +26,26 @@ packages <- function() {
       packages <- trimws(packages)
       return(packages[packages != ""])
     } else {
+      message("Section '", section_name, "' not found in DESCRIPTION file.")
       return(character(0))
     }
   }
   
-  suggests_packages <- extract_packages(lines, "Suggests")
-  write.table(suggests_packages, "oma_packages.csv", row.names = FALSE, col.names = FALSE, sep = ",", quote = FALSE)
+  # Extract packages from the Imports and Suggests sections
+  imports_packages <- extract_packages_from_section(lines, "Imports")
+  suggests_packages <- extract_packages_from_section(lines, "Suggests")
+  
+  # Combine the packages into a single vector and sort alphabetically
+  combined_packages <- sort(c(imports_packages, suggests_packages))
+  
+  # Write the combined packages to a CSV file without headers
+  tryCatch({
+    write.table(combined_packages, output_file_path, row.names = FALSE, col.names = FALSE, sep = ",", quote = FALSE)
+    message("Combined packages written to ", output_file_path)
+  }, error = function(e) {
+    message("Error writing combined packages to CSV file: ", e$message)
+  })
 }
 
-packages()
+# Call the function with the default path to the DESCRIPTION file and output file path
+extract_packages()
diff --git a/oma_packages/oma_packages.csv b/oma_packages/oma_packages.csv
index 2b5a7962d..d9dc21a89 100644
--- a/oma_packages/oma_packages.csv
+++ b/oma_packages/oma_packages.csv
@@ -21,16 +21,16 @@ DirichletMultinomial
 dplyr
 DT
 factoextra
-forcats
 fido
+forcats
 ggplot2
 ggpubr
 ggtree
 glmnet
 glue
 grid
-gtools
 gsEasy
+gtools
 igraph
 kableExtra
 knitr
@@ -45,8 +45,8 @@ mikropml
 MMUPHin
 MOFA2
 multiview
-NetCoMi
 NbClust
+NetCoMi
 NMF
 patchwork
 phyloseq