Mercurial > repos > lain > xseekerpreparator

changeset 7:5be8a770a11d draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
" master branch Updating"
author lain
date Thu, 21 Jan 2021 12:55:33 +0000
parents 207e36770d18
children b7ebb4748e59
files XSeekerPreparator.R galaxy/tools/LC-MSMS/XSeekerPreparator.R test/recreate_full.R test/test.sh
diffstat 4 files changed, 11 insertions(+), 10 deletions(-) [+]
line wrap: on
line diff
--- 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]])
--- 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]])
--- 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
--- 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)                   \