Merge pull request #38 from wkumler/enc_hotfix

Fixed encoding usage for multi-encoding files
wkumler · Jun 27, 2024 · 89c01b7 · 89c01b7
2 parents 04ce48a + 17f9709
commit 89c01b7
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Showing 14 changed files with 11 additions and 4 deletions.
diff --git a/.gitignore b/.gitignore
@@ -5,6 +5,8 @@
 
 *.mzML
 *.mzXML
+*.sqlite
+*.parquet
 
 .Rproj.user
 README.Rmd

diff --git a/R/grabMzxmlFunctions.R b/R/grabMzxmlFunctions.R
@@ -638,17 +638,22 @@ grabMzxmlSpectraVoltage <- function(xml_nodes){
 
 grabMzxmlSpectraMzInt <- function(xml_nodes, file_metadata){
   all_peak_nodes <- xml2::xml_text(xml2::xml_find_all(xml_nodes, xpath = "d1:peaks"))
-  vals <- lapply(all_peak_nodes, function(binary){
+  init_peak_encs <- xml2::xml_attr(xml2::xml_find_all(xml_nodes, xpath = "d1:peaks"), "compressionType")
+  all_peak_encs <- rep("none", length(init_peak_encs))
+  all_peak_encs[init_peak_encs=="zlib"] <- "gzip"
+  all_peak_encs[init_peak_encs=="zlib compression"] <- "gzip"
+
+  vals <- mapply(function(binary, encoding_i){
     if(!nchar(binary))return(matrix(ncol = 2, nrow = 0))
     decoded_binary <- base64enc::base64decode(binary)
     raw_binary <- as.raw(decoded_binary)
-    decomp_binary <- memDecompress(raw_binary, type = file_metadata$compression)
+    decomp_binary <- memDecompress(raw_binary, type = encoding_i)
     final_binary <- readBin(decomp_binary, what = "numeric",
                             n=length(decomp_binary)/file_metadata$precision,
                             size = file_metadata$precision,
                             endian = file_metadata$endi_enc)
     matrix(final_binary, ncol = 2, byrow = TRUE)
-  })
+  }, all_peak_nodes, all_peak_encs)
 }
 
 

diff --git a/vignettes/figures/ssc_vignette_renders/make_time_gp.png b/vignettes/figures/ssc_vignette_renders/make_time_gp.png
diff --git a/vignettes/figures/ssc_vignette_renders/make_timings.rds b/vignettes/figures/ssc_vignette_renders/make_timings.rds
diff --git a/vignettes/figures/ssc_vignette_renders/multichrom_gp.png b/vignettes/figures/ssc_vignette_renders/multichrom_gp.png
diff --git a/vignettes/figures/ssc_vignette_renders/multichrom_timings.rds b/vignettes/figures/ssc_vignette_renders/multichrom_timings.rds
diff --git a/vignettes/figures/ssc_vignette_renders/par_time_gp.png b/vignettes/figures/ssc_vignette_renders/par_time_gp.png
diff --git a/vignettes/figures/ssc_vignette_renders/par_timings.rds b/vignettes/figures/ssc_vignette_renders/par_timings.rds
diff --git a/vignettes/figures/ssc_vignette_renders/query_time_gp.png b/vignettes/figures/ssc_vignette_renders/query_time_gp.png
diff --git a/vignettes/figures/ssc_vignette_renders/query_timings.rds b/vignettes/figures/ssc_vignette_renders/query_timings.rds
diff --git a/vignettes/figures/ssc_vignette_renders/size_cons.png b/vignettes/figures/ssc_vignette_renders/size_cons.png
diff --git a/vignettes/figures/ssc_vignette_renders/size_list.rds b/vignettes/figures/ssc_vignette_renders/size_list.rds
diff --git a/vignettes/figures/ssc_vignette_renders/sum_plot.png b/vignettes/figures/ssc_vignette_renders/sum_plot.png
diff --git a/vignettes/speed_size_comparison.Rmd b/vignettes/speed_size_comparison.Rmd
@@ -12,7 +12,7 @@ vignette: >
 ---
 
 ```{r setup, include=FALSE}
-knitr::opts_chunk$set(echo = TRUE, eval=FALSE)
+knitr::opts_chunk$set(echo = TRUE, eval=TRUE)
 options(rmarkdown.html_vignette.check_title = FALSE)
 data.table::setDTthreads(2)
 ```