igblastr 1.1.4: Add utilities to update IgBLAST auxiliary and internal data

NCBI occasionally updates some of the files in the 'internal_data/'
and 'optional_file/' directories between IgBLAST releases, and it is
recommended to use the new files. They make the new files available
at https://ftp.ncbi.nih.gov/blast/executables/igblast/release/patch/

The user can now install these new files by calling update_live_igdata().
See '?update_live_igdata' for more information.

Author: hpages

DESCRIPTION

@@ -7,7 +7,7 @@ Description: The igblastr package provides functions to conveniently install
 biocViews: Immunology, Immunogenetics, ImmunoOncology, CellBiology
 URL: https://bioconductor.org/packages/igblastr
 BugReports: https://github.com/HyrienLab/igblastr/issues
-Version: 1.1.3
+Version: 1.1.4
 License: Artistic-2.0
 Encoding: UTF-8
 Authors@R: c(
@@ -24,7 +24,7 @@ Authors@R: c(
 Depends: R (>= 4.2.0), tibble, Biostrings
 Imports: methods, utils, stats, tools,
 	R.utils, curl, httr, xml2, rvest, xtable, jsonlite,
-	S4Vectors, IRanges, GenomeInfoDb
+	S4Vectors, IRanges, GenomeInfoDb (>= 1.47.2)
 Suggests: GenomicAlignments, parallel, testthat, knitr, rmarkdown,
 	BiocStyle, ggplot2, dplyr, scales, ggseqlogo
 VignetteBuilder: knitr
@@ -43,7 +43,7 @@ Collate:
 	get_igblast_root.R
 	edit_imgt_file.R
 	igblast_info.R
-	auxiliary-data-utils.R
+	igdata-utils.R
 	install_igblast.R
 	make_blastdbs.R
 	create_region_db.R

NAMESPACE

@@ -2,7 +2,7 @@ import(methods)
 
 importFrom(utils, download.file, untar, unzip, read.table, browseURL, URLencode)
 importFrom(stats, setNames)
-importFrom(tools, R_user_dir, file_path_as_absolute)
+importFrom(tools, R_user_dir, file_path_as_absolute, md5sum)
 
 importFrom(R.utils, gunzip)
 importFrom(curl, has_internet)
@@ -15,7 +15,7 @@ import(tibble)
 
 import(S4Vectors)
 import(IRanges)
-import(GenomeInfoDb)
+importFrom(GenomeInfoDb, list_ftp_dir)
 import(Biostrings)
 
 
@@ -27,11 +27,12 @@ S3method(print, alignment_summary)
 S3method(print, c_region_dbs_df)
 S3method(print, fmt7footer)
 S3method(print, fmt7record)
-S3method(print, outfmt7_specifiers)
 S3method(print, germline_dbs_df)
 S3method(print, hit_table)
 S3method(print, igblast_info)
 S3method(print, igblastn_raw_output)
+S3method(print, igdata_info)
+S3method(print, outfmt7_specifiers)
 S3method(print, query_details)
 S3method(print, subregion_sequence_details)
 S3method(print, VDJ_junction_details)
@@ -48,11 +49,12 @@ export(
     print.c_region_dbs_df,
     print.fmt7footer,
     print.fmt7record,
-    print.outfmt7_specifiers,
     print.germline_dbs_df,
     print.hit_table,
     print.igblast_info,
     print.igblastn_raw_output,
+    print.igdata_info,
+    print.outfmt7_specifiers,
     print.query_details,
     print.subregion_sequence_details,
     print.VDJ_junction_details,
@@ -75,9 +77,10 @@ export(
     list_igblast_organisms,
     igblastn_version, makeblastdb_version, igblast_build, igblast_info,
 
-    ## auxiliary-data-utils.R:
-    get_igblast_auxiliary_data,
-    load_igblast_auxiliary_data,
+    ## igdata-utils.R:
+    reset_live_igdata, update_live_igdata,
+    time_since_live_igdata_last_checked, igdata_info,
+    get_igblast_auxiliary_data, load_igblast_auxiliary_data,
 
     ## install_igblast.R:
     install_igblast,

R/auxiliary-data-utils.R

@@ -128,7 +128,7 @@ create_all_builtin_germline_dbs <- function(destdir)
     ## rename the temporary folder to 'destdir'. Otherwise we destroy the
     ## temporary folder and raise an error. This achieves atomicity.
     tmp_destdir <- tempfile("builtin_germline_dbs_")
-    dir.create(tmp_destdir, recursive=TRUE)
+    dir.create(tmp_destdir)
     on.exit(nuke_file(tmp_destdir))
 
     create_missing_builtin_germline_dbs(tmp_destdir)
@@ -186,7 +186,7 @@ create_all_builtin_c_region_dbs <- function(destdir)
     ## rename the temporary folder to 'destdir'. Otherwise we destroy the
     ## temporary folder and raise an error. This achieves atomicity.
     tmp_destdir <- tempfile("builtin_c_region_dbs_")
-    dir.create(tmp_destdir, recursive=TRUE)
+    dir.create(tmp_destdir)
     on.exit(nuke_file(tmp_destdir))
 
     ## Create IMGT C-region dbs.

R/builtin_db-utils.R

@@ -10,27 +10,28 @@
 ###   compartment       path
 ###   ----------------  ------------------------------------
 ###   IGBLAST_ROOTS     <igblastr-cache>/igblast_roots
+###   LIVE_IGDATA       <igblastr-cache>/live_igdata
 ###   GERMLINE_DBS      <igblastr-cache>/germline_dbs
 ###   C_REGION_DBS      <igblastr-cache>/c_region_dbs
 ###   IMGT_LOCAL_STORE  <igblastr-cache>/store/IMGT-releases
 ###
 ### Always use the igblastr_cache() function implemented in this file to
-### construct these paths.
+### obtain these paths.
 
 IGBLAST_ROOTS    <- "IGBLAST_ROOTS"
+LIVE_IGDATA      <- "LIVE_IGDATA"
 GERMLINE_DBS     <- "GERMLINE_DBS"
 C_REGION_DBS     <- "C_REGION_DBS"
 IMGT_LOCAL_STORE <- "IMGT_LOCAL_STORE"
 
-
 ### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
 ### igblastr_cache()
 ###
 
-.IGBLASTR_CACHES <- c(IGBLAST_ROOTS, GERMLINE_DBS,
-                      C_REGION_DBS, IMGT_LOCAL_STORE)
+.IGBLASTR_CACHES <- c(IGBLAST_ROOTS, LIVE_IGDATA,
+                      GERMLINE_DBS, C_REGION_DBS, IMGT_LOCAL_STORE)
 
-### Returns the path to the cache compartment specified via 'which'.
+### Returns **absolute** path to the cache compartment specified via 'which'.
 igblastr_cache <- function(which=NULL)
 {
     path <- getOption("igblastr_cache", R_user_dir("igblastr", "cache"))
@@ -39,6 +40,7 @@ igblastr_cache <- function(which=NULL)
     stopifnot(isSingleNonWhiteString(which))
     switch(which,
         IGBLAST_ROOTS   =file.path(path, "igblast_roots"),
+        LIVE_IGDATA     =file.path(path, "live_igdata"),
         GERMLINE_DBS    =file.path(path, "germline_dbs"),
         C_REGION_DBS    =file.path(path, "c_region_dbs"),
         IMGT_LOCAL_STORE=file.path(path, "store", "IMGT-releases"),

R/cache-utils.R

@@ -91,7 +91,7 @@ create_c_region_db <- function(fasta_dir, loci, destdir, force=FALSE)
     ## avoids loosing the content of the existing 'destdir' in case something
     ## goes wrong.
     tmp_destdir <- tempfile("c_region_db_")
-    dir.create(tmp_destdir, recursive=TRUE)
+    dir.create(tmp_destdir)
     on.exit(nuke_file(tmp_destdir))
     create_region_db(fasta_files, tmp_destdir, region_type="C")
     rename_file(tmp_destdir, destdir, replace=TRUE)

R/create_c_region_db.R

@@ -160,7 +160,7 @@ create_germline_db <- function(fasta_dir, loci, destdir, force=FALSE)
     ## atomicity and avoids loosing the content of the existing 'destdir' in
     ## case something goes wrong.
     tmp_destdir <- tempfile("germline_db_")
-    dir.create(tmp_destdir, recursive=TRUE)
+    dir.create(tmp_destdir)
     on.exit(nuke_file(tmp_destdir))
     .create_VDJ_region_dbs(fasta_dir, loci, tmp_destdir)
     rename_file(tmp_destdir, destdir, replace=TRUE)

R/create_germline_db.R

@@ -103,9 +103,7 @@ igblast_build <- function(igblast_root=get_igblast_root())
 
 print.igblast_info <- function(x, ...)
 {
-    x <- lapply(x, function(x) paste(x, collapse="; "))
-    x <- paste0(names(x), ": ", as.character(x))
-    cat(x, sep="\n")
+    cat(named_list_as_character(x), sep="\n")
 }
 
 igblast_info <- function(igblast_root=get_igblast_root())

R/igblast_info.R

@@ -233,7 +233,7 @@ print.igblastn_raw_output <- function(x, ...) cat(x, sep="\n")
     stopifnot(is.character(exe_args))
     igblastn_exe <- get_igblast_exe("igblastn", igblast_root=igblast_root)
     oldwd <- getwd()
-    setwd(igblast_root)
+    setwd(igblastr_cache(LIVE_IGDATA))
     on.exit(setwd(oldwd))
 
     stderr_file <- tempfile("igblastn_stderr_", fileext=".txt")