Merge pull request #121 from RGLab/dev

Dev
RGLab · Dec 13, 2022 · 3372fe8 · 3372fe8
2 parents 7a9f0da + 8720a6a
commit 3372fe8
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diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -41,9 +41,9 @@ jobs:
       - name: Set environment for branch
         run: |
           if [[ $GITHUB_REF == "refs/heads/main" ]]; then
-              echo "ISR_machine=www.immunespace.org" >> "$GITHUB_ENV"
+              echo "ISR_machine=datatools.immunespace.org" >> "$GITHUB_ENV"
           else
-              echo "ISR_machine=test.immunespace.org" >> "$GITHUB_ENV"
+              echo "ISR_machine=datatools-dev.immunespace.org" >> "$GITHUB_ENV"
           fi
         shell: bash
 

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: ImmuneSpaceR
 Type: Package
-Title: A Thin Wrapper around the ImmuneSpace Database
-Version: 1.25.1
+Title: A Thin Wrapper around the ImmuneSpace Data and Tools Portal
+Version: 1.25.2
 Date: 2014-06-12
 Authors@R: c(person("Greg", "Finak", role = "aut"),
              person("Renan", "Sauteraud", role = "aut"),
@@ -18,8 +18,8 @@ Authors@R: c(person("Greg", "Finak", role = "aut"),
                     role = c("cre", "cph")))
 VignetteBuilder: knitr
 Description: Provides a convenient API for accessing data sets within
-    ImmuneSpace (www.immunespace.org), the data repository and
-    analysis platform of the Human Immunology Project Consortium
+    ImmuneSpace Data and Tools Portal (datatools.immunespace.org), the data
+    repository and analysis platform of the Human Immunology Project Consortium
     (HIPC).
 biocViews: DataImport, DataRepresentation, ThirdPartyClient
 URL: https://github.com/RGLab/ImmuneSpaceR
@@ -51,7 +51,7 @@ Imports:
     flowCore,
     flowWorkspace,
     digest
-RoxygenNote: 7.2.1
+RoxygenNote: 7.2.2
 Encoding: UTF-8
 Collate: 
     'CreateConnection.R'

diff --git a/R/CreateConnection.R b/R/CreateConnection.R
@@ -11,8 +11,8 @@
 #' @param verbose A \code{"logical"} whether to print the extra details for
 #' troubleshooting.
 #' @param onTest A \code{"logical"} whether to connect to the test server
-#' (https://test.immunespace.org/) instead of the production server
-#' (https://www.immunespace.org/).
+#' (https://datatools-dev.immunespace.org/) instead of the production server
+#' (https://datatools.immunespace.org/).
 #'
 #' @description Constructor for \code{ImmuneSpaceConnection} class.
 #'

diff --git a/R/ISCon.R b/R/ISCon.R
@@ -33,11 +33,11 @@
 #' \code{.netrc} file in \code{"~/"} the user's home directory. The
 #' \code{.netrc} file should contain a \code{machine}, \code{login}, and
 #' \code{password} entry to allow access to ImmuneSpace, where \code{machine} is
-#' the host name like "www.immunespace.org".
+#' the host name like "datatools.immunespace.org".
 #'
 #' It can also use global variables \code{labkey.url.base}, and
 #' \code{labkey.url.path}, to access a study. \code{labkey.url.base} should be
-#' \code{https://www.immunespace.org/}. \code{labkey.url.path} should be
+#' \code{https://datatools.immunespace.org/}. \code{labkey.url.path} should be
 #' \code{/Studies/studyname}, where 'studyname' is the accession number of the
 #' study.
 #'
@@ -403,7 +403,7 @@ ISCon$set(
 
 
 .get_host <- function(onTest = FALSE) {
-  ifelse(onTest, "test.immunespace.org", "www.immunespace.org")
+  ifelse(onTest, "datatools-dev.immunespace.org", "datatools.immunespace.org")
 }
 
 
@@ -511,15 +511,11 @@ ISCon$set(
 
   if (!inherits(nf, "try-error") && !is.null(nf)) {
     curlOptions <- labkey.setCurlOptions(
-      ssl_verifyhost = 2,
-      sslversion = 1,
       netrc_file = nf,
       useragent = useragent
     )
   } else {
     curlOptions <- labkey.setCurlOptions(
-      ssl_verifyhost = 2,
-      sslversion = 1,
       useragent = useragent
     )
   }

diff --git a/R/netrc.R b/R/netrc.R
@@ -31,7 +31,7 @@ interactive_netrc <- function() {
 
     if (chk == TRUE) {
       message("writing netrc to ", filepath)
-      cat("machine www.immunespace.org\nlogin ", login, "\npassword ", password, "\n", file = filepath)
+      cat("machine datatools.immunespace.org\nlogin ", login, "\npassword ", password, "\n", file = filepath)
     }
   } else {
     # don't overwrite - validate available netrc
@@ -58,7 +58,7 @@ interactive_netrc <- function() {
 #' @export
 write_netrc <- function(login,
                         password,
-                        machine = "www.immunespace.org",
+                        machine = "datatools.immunespace.org",
                         file = NULL) {
   string <- paste0(
     "machine ", machine, "\n",
@@ -109,8 +109,8 @@ check_netrc <- function() {
   }
   lines <- readLines(netrc_file)
   lines <- gsub("http.*//", "", lines)
-  if (length(grep("machine\\swww.immunespace.org", lines)) == 0) {
-    stop("No entry found for www.immunespace.org in the netrc file.")
+  if (length(grep("machine\\sdatatools.immunespace.org", lines)) == 0) {
+    stop("No entry found for datatools.immunespace.org in the netrc file.")
   }
   print("The netrc looks valid.")
   return(netrc_file)
@@ -122,7 +122,7 @@ check_netrc <- function() {
   ISR_login <- Sys.getenv("ISR_login")
   ISR_pwd <- Sys.getenv("ISR_pwd")
   ISR_machine <- ifelse(Sys.getenv("ISR_machine") == "",
-    "www.immunespace.org",
+    "datatools.immunespace.org",
     Sys.getenv("ISR_machine")
   )
   if (ISR_login != "" & ISR_pwd != "") {
@@ -139,7 +139,7 @@ check_netrc <- function() {
   machine <- Sys.getenv("ISR_machine")
   # if blank, then use production
   if (machine == "") {
-    return("https://www.immunespace.org")
+    return("https://datatools.immunespace.org")
   }
 
   if (grepl("immunespace", machine)) {

diff --git a/README.md b/README.md
@@ -11,8 +11,9 @@
 [![Updated](https://bioconductor.org/shields/lastcommit/release/bioc/ImmuneSpaceR.svg)](http://bioconductor.org/packages/release/bioc/news/ImmuneSpaceR/NEWS)
 <!-- badges: end -->
 
+> Please update the URL (machine name) to `datatools.immunespace.org` from `www.immunespace.org` in your `.netrc` file.
 
-A thin wrapper around Rlabkey to access the [ImmuneSpace](https://www.immunespace.org) database from R.
+A thin wrapper around Rlabkey to access the [ImmuneSpace Data & Tools Portal](https://datatools.immunespace.org) from R.
 
 This package simplifies access to the [HIPC](https://www.immuneprofiling.org/) ImmuneSpace database for R programmers. It takes advantage of the standardization of the database to hide all the [`Rlabkey`](https://cran.r-project.org/web/packages/Rlabkey/index.html) specific code away from the user. The study-specific datasets can be accessed via an object-oriented paradigm.
 
@@ -40,7 +41,7 @@ remotes::install_github("RGLab/ImmuneSpaceR")
 
 The ImmuneSpace Portal can be accessed via `ImmuneSpaceR` with the user's credentials. A `.netrc` file storing login and password information is required.
 
-1. [Register](https://www.immunespace.org/login/home/register.view?)
+1. [Register](https://datatools.immunespace.org/login/home/register.view?)
 1. Create a netrc file with your ImmuneSpace credetntials using `interactive_netrc()` function in R:
 
 ``` r
@@ -103,7 +104,7 @@ con$plot("hai")
 
 ## Examples & Documentation
 
-For more advanced examples and detailed documentation, see [the package vignettes](http://rglab.github.io/ImmuneSpaceR/articles/) and the reports available on [ImmuneSpace](https://www.immunespace.org/).
+For more advanced examples and detailed documentation, see [the package vignettes](http://rglab.github.io/ImmuneSpaceR/articles/) and the reports available on [ImmuneSpace](https://datatools.immunespace.org/).
 
 
 

diff --git a/_pkgdown.yml b/_pkgdown.yml
@@ -6,7 +6,7 @@ template:
 navbar:
   right:
     - icon: fa-globe
-      href: https://www.immunespace.org/
+      href: https://datatools.immunespace.org/
     - icon: fa-twitter
       href: https://twitter.com/ImmuneSpace
     - icon: fa-github

diff --git a/man/CreateConnection.Rd b/man/CreateConnection.Rd
diff --git a/man/ImmuneSpaceConnection.Rd b/man/ImmuneSpaceConnection.Rd
diff --git a/man/write_netrc.Rd b/man/write_netrc.Rd
diff --git a/vignettes/Intro_to_ImmuneSpaceR.Rmd b/vignettes/Intro_to_ImmuneSpaceR.Rmd
@@ -26,7 +26,7 @@ if (!any(file.exists("~/.netrc", "~/_netrc"))) {
 ```
 
 
-This package provides a *thin* wrapper around [`Rlabkey`](https://cran.r-project.org/web/packages/Rlabkey/index.html) and connects to the [ImmuneSpace](https://www.immunespace.org) database, making it easier to fetch datasets, including gene expression data, HAI, and so forth, from specific studies. 
+This package provides a *thin* wrapper around [`Rlabkey`](https://cran.r-project.org/web/packages/Rlabkey/index.html) and connects to the [ImmuneSpace](https://datatools.immunespace.org) database, making it easier to fetch datasets, including gene expression data, HAI, and so forth, from specific studies. 
 
 
 
@@ -49,12 +49,12 @@ Or create netrc file in the computer running R:
 The following three lines must be included in the `.netrc` or `_netrc` file either separated by white space (spaces, tabs, or newlines) or commas.
 
 ```
-machine www.immunespace.org
+machine datatools.immunespace.org
 login [email protected]
 password superSecretPassword
 ```
 
-Multiple such blocks can exist in one file. Please ensure that the machine name in the netrc file contains the "www" prefix as that is how the package connects to immunespace by default. A mismatch will lead to connection failures.
+Multiple such blocks can exist in one file. Please ensure that the machine name in the netrc file contains the "datatools" subdomain as that is how the package connects to immunespace by default. A mismatch will lead to connection failures.
 
 See [the official LabKey documentation](https://www.labkey.org/wiki/home/Documentation/page.view?name=netrc) for more information.
 

diff --git a/vignettes/interactiveNetrc.Rmd b/vignettes/interactiveNetrc.Rmd
@@ -29,7 +29,7 @@ In order to connect to ImmuneSpace, you will need a `.netrc` file in your home d
 A netrc file may look like this:
 
 ```
-machine www.immunespace.org
+machine datatools.immunespace.org
 login [email protected]
 password supersecretpassword
 ```
@@ -58,7 +58,7 @@ Below is a gif demonstrating how to use this function:
 
 In the case that the user did not provide login information that results in a connection to ImmuneSpace, a netrc file will not be written to the user's home directory, and the user can try the method again checking for typos.
 
-If the user still cannot connect to ImmuneSpace via the API, they might want to double check that they are registered and that their login information works for [ImmuneSpace](https://immunespace.org/).
+If the user still cannot connect to ImmuneSpace via the API, they might want to double check that they are registered and that their login information works for [ImmuneSpace](https://datatools.immunespace.org/).
 
 If a netrc file already exists, `interactive_netrc` will print the existing file to the console and ask the user if they wish to overwrite that file.
 

diff --git a/vignettes/report_SDY180.Rmd b/vignettes/report_SDY180.Rmd
@@ -27,7 +27,7 @@ if (!any(file.exists("~/.netrc", "~/_netrc"))) {
 
 
 
-`ImmuneSpaceR` code produces consistent results, regardless of whether it is being executed from a module or a UI based report on the server or on a local machine. This vignette reproduces a report available on <a href="https://www.immunespace.org/reports/Studies/SDY180/runReport.view?reportId=module %3ASDY180%2Freports%2Fschemas%2Fstudy%2Fdemographics%2Fplasmablast_abundance.Rmd">the ImmuneSpace portal</a> using the same code.
+`ImmuneSpaceR` code produces consistent results, regardless of whether it is being executed from a module or a UI based report on the server or on a local machine. This vignette reproduces a report available on <a href="https://datatools.immunespace.org/reports/Studies/SDY180/runReport.view?reportId=module %3ASDY180%2Freports%2Fschemas%2Fstudy%2Fdemographics%2Fplasmablast_abundance.Rmd">the ImmuneSpace portal</a> using the same code.
 
 
 

diff --git a/vignettes/report_SDY269.Rmd b/vignettes/report_SDY269.Rmd
@@ -27,7 +27,7 @@ if (!any(file.exists("~/.netrc", "~/_netrc"))) {
 
 
 
-`ImmuneSpaceR` code produces consistent results, regardless of whether it is being executed from a module or UI based report on the server or on a local machine. This vignette reproduces a report available on <a href="https://www.immunespace.org/reports/Studies/SDY269/runReport.view?reportId=module%3ASDY269%2Freports%2Fschemas%2Fhai_flow_elispot.Rmd">the ImmuneSpace portal</a> using the same code.
+`ImmuneSpaceR` code produces consistent results, regardless of whether it is being executed from a module or UI based report on the server or on a local machine. This vignette reproduces a report available on <a href="https://datatools.immunespace.org/reports/Studies/SDY269/runReport.view?reportId=module%3ASDY269%2Freports%2Fschemas%2Fhai_flow_elispot.Rmd">the ImmuneSpace portal</a> using the same code.