From 94be9d5575c65d699d5f216c9e3c001314d5029d Mon Sep 17 00:00:00 2001
From: Silvio <s.waschina@nutrinf.uni-kiel.de>
Date: Sat, 8 Jun 2024 22:55:47 +0200
Subject: [PATCH] read and write gzipped SBML

Not super important, as libSBML can usually handle compressed model
file. However, in the homebrew/brewsci build of SBML, the gzip-support
is disables due to a conflict of libSBML and zlib:

https://github.com/brewsci/homebrew-bio/pull/1672

The change here, used R's build-in gz-file in/out support to read/write
gzipped SBML files.

Note: It is a little less efficient than the libSBML gz-support. When
zlib-connection in homebrew's libsbml is back, the lines added in this
commit could be removed again.
---
 R/io.R | 35 ++++++++++++++++++++++++++++++++++-
 1 file changed, 34 insertions(+), 1 deletion(-)

diff --git a/R/io.R b/R/io.R
index 082d85e..c70591a 100644
--- a/R/io.R
+++ b/R/io.R
@@ -12,9 +12,22 @@
 #' @import Matrix
 #' @export
 readSBMLmod <- function(file_path) {
+  is_compressed <- FALSE
+
+  file_path <- normalizePath(file_path)
+
+  if(grepl("\\.gz$",file_path)) {
+    is_compressed <- TRUE
+    fileconn <- gzfile(file_path)
+    tmpfile <- tempfile(fileext = ".xml")
+    writeLines(readLines(fileconn), tmpfile)
+    close(fileconn)
+    sbmldoc  <- readSBMLfile(tmpfile)
+  } else {
+    sbmldoc  <- readSBMLfile(file_path)
+  }
 
   # Pointers to SBML document and model (libSBML objects)
-  sbmldoc  <- readSBMLfile(normalizePath(file_path))
   modelPtr <- getModelObj(sbmldoc)
 
   #---------------#
@@ -78,6 +91,9 @@ readSBMLmod <- function(file_path) {
   })
   gpr_sbo <- getGeneProductSBOTerms(modelPtr)
 
+  if(is_compressed)
+    file.remove(tmpfile)
+
   return(
     new("ModelOrg",
         mod_id = mod_id,
@@ -144,6 +160,13 @@ sboterm2int <- function(sbo) {
 #' @export
 writeSBMLmod <- function(model, file_path = NULL) {
 
+  compress <- FALSE
+  if(grepl("\\.gz$",file_path)) {
+    compress <- TRUE
+    out_file <- file_path
+    file_path <- gsub("\\.gz$","", file_path)
+  }
+
   if(is.null(file_path))
     file_path <- paste0(model@mod_id, ".xml")
 
@@ -272,6 +295,16 @@ writeSBMLmod <- function(model, file_path = NULL) {
     obj_coef = model@obj_coef
   )
 
+  if(compress) {
+    input_conn <- file(file_path, "r")
+    output_conn <- gzfile(out_file, "w")
+    file_content <- readLines(input_conn)
+    writeLines(file_content, output_conn)
+    close(input_conn)
+    close(output_conn)
+    file.remove(file_path)
+  }
+
   return(out)
 }