disable multiplex in another function for CTIS

R/ctrLoadQueryIntoDbCtgov2.R

@@ -289,7 +289,6 @@ ctrLoadQueryIntoDbCtgov2 <- function(
     tmp <- ctrMultiDownload(
       urlToDownload,
       fTrialJson,
-      progress = TRUE,
       verbose = verbose)
 
     # inform user
@@ -362,7 +361,6 @@ ctrLoadQueryIntoDbCtgov2 <- function(
     tmp <- ctrMultiDownload(
       urls = urls,
       destfiles = files,
-      resume = FALSE,
       verbose = verbose
     )
 
@@ -456,7 +454,6 @@ ctrLoadQueryIntoDbCtgov2 <- function(
     tmp <- ctrMultiDownload(
       urls = urls,
       destfiles = files,
-      resume = FALSE,
       verbose = verbose
     )
 

R/ctrLoadQueryIntoDbCtis.R

@@ -32,14 +32,6 @@ ctrLoadQueryIntoDbCtis <- function(
   ## create empty temporary directory
   tempDir <- ctrTempDir(verbose)
 
-  ## output mangle helper -----------------------------------------------
-
-  mangleText <- function(t) {
-
-    stringi::stri_replace_all_fixed(str = t, pattern = "'", replacement = "&apos;")
-
-  }
-
   ## ctis api -----------------------------------------------------------
 
   # https://euclinicaltrials.eu/ctis-public/assets/i18n/en.json
@@ -54,18 +46,18 @@ ctrLoadQueryIntoDbCtis <- function(
       # - 1 trial overview - post method
       "/search",
       #
-      # - 2 trial information - %s is ctNumber
-      "/retrieve/%s", # partI and partsII
+      # - 2 trial information, partI and partsII
+      "/retrieve/%s", # %s is ctNumber
       #
       # - 3 download files
-      "/documents/%s/%s/download" # trial _id, document[].uuid
+      "/documents/%s/%s/download" # %s are trial _id, document[].uuid
       #
     )
   )
 
   ## api_1: overviews ---------------------------------------------------------
 
-  # this is for importing overview (recruitment, status etc.) into database
+  # for importing overview (recruitment, status etc.) into database
   message("* Checking trials in CTIS...")
 
   # "HTTP server doesn't seem to support byte ranges. Cannot resume."
@@ -218,7 +210,7 @@ ctrLoadQueryIntoDbCtis <- function(
   # this is imported as the main data into the database
 
   message("(2/4) Downloading and processing trial data... (",
-          "estimate: ", signif(length(idsTrials) * 376 / 5117, 1L), " Mb)")
+          "estimate: ", signif(length(idsTrials) * 405 / 5505, 1L), " Mb)")
 
   urls <- sprintf(ctisEndpoints[2], idsTrials)
 
@@ -227,7 +219,9 @@ ctrLoadQueryIntoDbCtis <- function(
   }
 
   # "HTTP server doesn't seem to support byte ranges. Cannot resume."
-  tmp <- ctrMultiDownload(urls, fPartIPartsIIJson(idsTrials), verbose = verbose)
+  tmp <- ctrMultiDownload(
+    urls, fPartIPartsIIJson(idsTrials),
+    multiplex = FALSE, verbose = verbose)
 
   # convert partI and partsII details into ndjson file(s),
   # each approximately 10MB for nRecords = 100L

R/util_functions.R

@@ -811,6 +811,7 @@ ctrMultiDownload <- function(
     destfiles,
     progress = TRUE,
     resume = FALSE,
+    multiplex = TRUE,
     verbose = TRUE) {
 
   stopifnot(length(urls) == length(destfiles))
@@ -844,7 +845,7 @@ ctrMultiDownload <- function(
   # remove any duplicates
   downloadValue <- unique(downloadValue)
 
-  # does not error in case any of the individual requests fail
+  # does not error in case any of the individual requests fail.
   # inspect the return value to find out which were successful
   # make no more than 3 attempts to complete downloading
   while (any(toDo) && numI < 3L) {
@@ -855,7 +856,7 @@ ctrMultiDownload <- function(
       resume = canR,
       progress = progress,
       timeout = Inf,
-      multiplex = TRUE,
+      multiplex = multiplex,
       c(getOption("httr_config")[["options"]],
         accept_encoding = "gzip,deflate,zstd,br")
     )