Dev (#119)

* Fix test expectations, R-CMD-Check notes, and suppress warning message in labkey.getFolders

* Allow lji servers

* Update saved dataset

.Rbuildignore

@@ -1,6 +1,6 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
-^docs$
+^pkgdown$
 ^CONTRIBUTING.md$
 ^_pkgdown\.yml$
 ^\.github$

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: ImmuneSpaceR
 Type: Package
 Title: A Thin Wrapper around the ImmuneSpace Database
-Version: 1.19.2
+Version: 1.25.1
 Date: 2014-06-12
 Authors@R: c(person("Greg", "Finak", role = "aut"),
              person("Renan", "Sauteraud", role = "aut"),
@@ -28,7 +28,8 @@ License: GPL-2
 Suggests:
     knitr,
     testthat,
-    covr
+    covr,
+    withr
 Imports:
     utils,
     R6,
@@ -50,7 +51,8 @@ Imports:
     flowCore,
     flowWorkspace,
     digest
-RoxygenNote: 7.1.1
+RoxygenNote: 7.2.1
+Encoding: UTF-8
 Collate: 
     'CreateConnection.R'
     'ISCon.R'

R/ISCon-geneExpression.R

@@ -511,14 +511,12 @@ ISCon$set(
       fileSuffix <- ".immsig"
     } else {
       if (outputType == "summary") {
-        fileSuffix <- switch(
-          annotation,
+        fileSuffix <- switch(annotation,
           "latest" = ".summary",
           "default" = ".summary.orig"
         )
       } else {
-        fileSuffix <- switch(
-          outputType,
+        fileSuffix <- switch(outputType,
           "normalized" = "",
           "raw" = ".raw"
         )
@@ -877,14 +875,12 @@ ISCon$set(
 
 # Get the cache name of expression matrix by output type and annotation
 .getMatrixCacheName <- function(matrixName, outputType, annotation) {
-  outputSuffix <- switch(
-    outputType,
+  outputSuffix <- switch(outputType,
     "summary" = "_sum",
     "normalized" = "_norm",
     "raw" = "_raw"
   )
-  annotationSuffix <- switch(
-    annotation,
+  annotationSuffix <- switch(annotation,
     "latest" = "_latest",
     "default" = "_default",
     "ImmSig" = "_immsig"

R/ISCon-utils.R

@@ -58,12 +58,12 @@ ISCon$set(
   which = "private",
   name = ".checkStudy",
   value = function(verbose = FALSE) {
-    folders <- labkey.getFolders(
+    folders <- suppressWarnings(labkey.getFolders(
       baseUrl = self$config$labkey.url.base,
       folderPath = "",
       includeSubfolders = TRUE,
       includeEffectivePermissions = TRUE
-    )
+    ))
     folders <- folders[grepl("IS\\d{1}|SDY\\d{2,4}", folders$name), ]
     study <- basename(self$config$labkey.url.path)
 

R/ISCon.R

@@ -355,7 +355,7 @@ ISCon$set(
     .check_portal(onTest)
 
     # fetch config variables
-    labkey.url.base <- .get_url_base(onTest)
+    labkey.url.base <- .get_url_base(onTest, verbose)
     labkey.user.email <- .get_user_email()
     labkey.url.path <- .get_url_path(study)
     curlOptions <- .set_curl_options(login, password)
@@ -420,7 +420,7 @@ ISCon$set(
 # which really should have been done through option()/getOption() mechanism
 # Here we do this to be compatible to labkey online report system
 # that automatically assigns these variables in global environment
-.get_url_base <- function(onTest = FALSE) {
+.get_url_base <- function(onTest = FALSE, verbose = FALSE) {
   labkey.url.base <- try(get("labkey.url.base", .GlobalEnv), silent = TRUE)
   if (inherits(labkey.url.base, "try-error")) {
     labkey.url.base <- paste0("https://", .get_host(onTest))
@@ -431,7 +431,7 @@ ISCon$set(
   }
 
   # Allow http (no SSL) for local
-  if (grepl("immunespace", labkey.url.base)) {
+  if (grepl("(immunespace|lji)", labkey.url.base)) {
     labkey.url.base <- gsub("http:", "https:", labkey.url.base)
     if (length(grep("^https://", labkey.url.base)) == 0) {
       labkey.url.base <- paste0("https://", labkey.url.base)
@@ -442,6 +442,8 @@ ISCon$set(
     }
   }
 
+  if (isTRUE(verbose)) message(sprintf("URL base: %s", labkey.url.base))
+
   labkey.url.base
 }
 

R/ImmuneSpaceR.R

@@ -42,6 +42,7 @@ globalVariables(
     "geo_accession",
     "expsample_accession",
     "feature_id",
-    "labkey.netrc.file"
+    "labkey.netrc.file",
+    "cell_number_preferred"
   )
 )