# HG changeset patch
# User lain
# Date 1611233733 0
# Node ID 5be8a770a11dfd6b8cb271810c7e1f73c7d214ce
# Parent  207e36770d181f7548f2de359468751158b4855f
" master branch Updating"

diff -r 207e36770d18 -r 5be8a770a11d XSeekerPreparator.R
--- a/XSeekerPreparator.R	Wed Jan 20 17:47:51 2021 +0000
+++ b/XSeekerPreparator.R	Thu Jan 21 12:55:33 2021 +0000
@@ -565,7 +565,7 @@
     if (length(classes) > 1) {
         stop(sprintf("Only one class expected in the variable metadata. Found %d .", length(classes)))
     }
-    if (length(classes) === 0) {
+    if (length(classes) == 0) {
         stop("Could not find any class column in your variableMetadata.")
     }
     return (classes[[1]])
diff -r 207e36770d18 -r 5be8a770a11d galaxy/tools/LC-MSMS/XSeekerPreparator.R
--- a/galaxy/tools/LC-MSMS/XSeekerPreparator.R	Wed Jan 20 17:47:51 2021 +0000
+++ b/galaxy/tools/LC-MSMS/XSeekerPreparator.R	Thu Jan 21 12:55:33 2021 +0000
@@ -565,7 +565,7 @@
     if (length(classes) > 1) {
         stop(sprintf("Only one class expected in the variable metadata. Found %d .", length(classes)))
     }
-    if (length(classes) === 0) {
+    if (length(classes) == 0) {
         stop("Could not find any class column in your variableMetadata.")
     }
     return (classes[[1]])
diff -r 207e36770d18 -r 5be8a770a11d test/recreate_full.R
--- a/test/recreate_full.R	Wed Jan 20 17:47:51 2021 +0000
+++ b/test/recreate_full.R	Thu Jan 21 12:55:33 2021 +0000
@@ -2,22 +2,23 @@
 
 ZIP <- FALSE
 
-file.copy("../convert/yann.rdata", "../convert/yann.rdata.old")
-load("../convert/yann.rdata", rdata <- new.env())
+file.copy("../convert/recreate_rdata_from_galaxy/20-01-2021.rdata", "../convert/recreate_rdata_from_galaxy/20-01-2021.rdata.old")
+load("../convert/recreate_rdata_from_galaxy/20-01-2021.rdata", rdata <- new.env())
 
 listOFlistArguments <- rdata$listOFlistArguments
 diffrep <- rdata$diffrep
 variableMetadata <- rdata$variableMetadata
 xa <- rdata$xa
 if (ZIP) {
-	zipfile <- normalizePath("../convert/yann.zip", mustWork=TRUE)
+	zipfile <- normalizePath("../convert/recreate_rdata_from_galaxy/20-01-2021.zip", mustWork=TRUE)
 	singlefile <- rdata$singlefile
 } else {
-	singles <- list.files("../convert/")
-	singles <- singles[singles != "yann.rdata"]
+	singles <- list.files("../convert/recreate_rdata_from_galaxy/")
+	singles <- singles[singles != "20-01-2021.rdata"]
+    singles <- singles[singles != "20-01-2021.rdata.old"]
 	singlefile <- list()
 	for (single in singles) {
-		singlefile[tools::file_path_sans_ext(single)] <- normalizePath(paste0("../convert/", single))
+		singlefile[tools::file_path_sans_ext(single)] <- normalizePath(paste0("../convert/recreate_rdata_from_galaxy/", single))
 	}
 	zipfile <- NULL
 	print(singlefile)
@@ -30,6 +31,6 @@
     variableMetadata,
     xa,
     singlefile,
-    file="../convert/yann.rdata"
+    file="../convert/recreate_rdata_from_galaxy/20-01-2021.rdata"
     ,version=2
 )
\ No newline at end of file
diff -r 207e36770d18 -r 5be8a770a11d test/test.sh
--- a/test/test.sh	Wed Jan 20 17:47:51 2021 +0000
+++ b/test/test.sh	Thu Jan 21 12:55:33 2021 +0000
@@ -6,7 +6,7 @@
 ln -s ../data/ ./data
 
 ~/R/bin/Rscript $(realpath ../XSeekerPreparator.R)  \
-    -i $(realpath ../data/full.rdata)               \
+    -i $(realpath ../data/20-01-2021.rdata)         \
     -m $(realpath ../data/models.R)                 \
     -c $(realpath ../data/SERUM_v2019Jan17.tabular) \
     -o $(realpath ../test.sqlite)                   \