v1.11.5 -- also use retries for geo_info()

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: recount
 Title: Explore and download data from the recount project
-Version: 1.11.4
+Version: 1.11.5
 Date: 2019-06-10
 Authors@R: c(person("Leonardo", "Collado-Torres", role = c("aut", "cre"),
     email = "lcolladotor@gmail.com", comment = c(ORCID = "0000-0003-2140-308X")),

R/geo_info.R

@@ -3,12 +3,12 @@
 #' This function uses GEOquery to extract information for a given sample. The
 #' GEO accession ids for the sample can be found in the study phenotype table.
 #'
-#' @return Returns a \link[S4Vectors]{DataFrame-class} with the information 
+#' @return Returns a \link[S4Vectors]{DataFrame-class} with the information
 #' from GEO available for the given sample.
 #'
 #' @param geoid A character vector of length 1 with the GEO accession id for
 #' a given sample.
-#' @param verbose If \code{TRUE} the \code{geoid} will be shown. 
+#' @param verbose If \code{TRUE} the \code{geoid} will be shown.
 #' @param sleep The number of seconds (or fraction) to wait before downloading
 #' data using \link[GEOquery]{getGEO}. This is important if you are looking over
 #' \code{geo_info()} given the constraints published at
@@ -30,41 +30,49 @@
 geo_info <- function(geoid, verbose = FALSE, sleep = 1/2, getGPL = FALSE,
     destdir = tempdir(), ...) {
     if(is.na(geoid)) return(NULL)
-    
+
     ## Check inputs
     stopifnot(is.character(geoid) & length(geoid) == 1)
 
     if(verbose) message(paste(Sys.time(),
         'finding GEO information for GEO accession id', geoid))
-    
+
     if(!file.exists(file.path(destdir, paste0(geoid, '.soft')))) {
         Sys.sleep(sleep)
     }
-
-    ## Get data from GEO
-    geo <- tryCatch(
-        GEOquery::getGEO(geoid, getGPL = getGPL, destdir = destdir, ...), 
-        error = function(e) {
-            soft <- paste0(geoid, '.soft')
-            soft_file <- file.path(destdir, soft)
-            if(any(grepl('private', readLines(soft_file)))) {
-                message(paste(geoid, 'is currently private'))
-                return(NA)
-            } else if (any(grepl('blocked', readLines(soft_file)))) {
-                warning(paste('It seems like your IP access is blocked. Please check the file', soft_file, 'for more details.'))
-                return(NA)
-            } else {
-                stop(e)
+
+    ## Get data from GEO, with 3 retries, waiting between 0 and 2 seconds in
+    ## between retries
+    N.TRIES <- 3L
+    while(N.TRIES > 0L) {
+        geo <- tryCatch(
+            GEOquery::getGEO(geoid, getGPL = getGPL, destdir = destdir, ...),
+            error = function(e) {
+                soft <- paste0(geoid, '.soft')
+                soft_file <- file.path(destdir, soft)
+                if(any(grepl('private', readLines(soft_file)))) {
+                    message(paste(geoid, 'is currently private'))
+                    return(NA)
+                } else if (any(grepl('blocked', readLines(soft_file)))) {
+                    warning(paste('It seems like your IP access is blocked. Please check the file', soft_file, 'for more details.'))
+                    return(NA)
+                } else {
+                    return(e)
+                }
             }
-        }
-    )
-
+        )
+        if(!inherits(geo, 'error'))
+            break
+        Sys.sleep(runif(n = 1, min = 0, max = 2))
+        N.TRIES <- N.TRIES - 1L
+    }
+
     ## Return and empty DataFrame if there was an issue with getGEO()
     if(!is(geo, 'GSM')) return(S4Vectors::DataFrame())
-    
+
     ## Extract the header information
 	result <- geo@header
-    
+
     ## Function for cleaning
     clean_geo <- function(pattern, varname, res) {
     	charIndex <- grep(pattern, names(res))
@@ -76,7 +84,7 @@ geo_info <- function(geoid, verbose = FALSE, sleep = 1/2, getGPL = FALSE,
     	}
         return(res)
     }
-    
+
     ## Clean up the header information
     df <- data.frame(
         pattern = c('characteristics_ch1', 'data_processing', 'contact_',
@@ -85,15 +93,15 @@ geo_info <- function(geoid, verbose = FALSE, sleep = 1/2, getGPL = FALSE,
         varname = c('characteristics', 'data_processing', 'contact', 'extract',
             'library', 'relation', 'series', 'supplementary_file'),
         stringsAsFactors = FALSE
-    )        
+    )
     for(i in seq_len(nrow(df))) result <- clean_geo(df$pattern[i],
         df$varname[i], result)
-    
+
     ## Make sure they are all length 1
     if(any(S4Vectors::elementNROWS(result) > 1)) {
         for(i in which(S4Vectors::elementNROWS(result) > 1)) result[i] <- IRanges::CharacterList(unlist(unname(result[i])))
     }
-    
+
     ## Finish
 	return(S4Vectors::DataFrame(result))
 }