Merge pull request #68 from molgenis/chore/fix-release

fix: update and fix vignettes

R/ArmadilloResult.R

@@ -30,7 +30,7 @@ methods::setClass("ArmadilloResult",
 #'
 #' @return The result information. This should include the R expression
 #' being executed (`expression`) and if the query is complete
-#' (`{ "status" = "COMPLETED" }`).
+#' (`\{ "status" = "COMPLETED" \}`).
 #'
 #' @importMethodsFrom DSI dsGetInfo
 #' @export

cran-comments.md

@@ -1,4 +1,4 @@
-## 2.0.4 Bugfix for update in armadillo
+## 2.0.5 Bugfix for update in armadillo
 * Bugfix to enable armadillo update (N.B. this version of DSMolgenisArmadillo 
 should be used when using armadillo 3.5)
 

vignettes/DSMolgenisArmadillo.Rmd.orig

@@ -27,7 +27,7 @@ library(dsBaseClient)
 library(DSMolgenisArmadillo)
 
 # specify server url
-armadillo_url <- "https://armadillo.dev.molgenis.org"
+armadillo_url <- "https://armadillo-demo.molgenis.net"
 
 # get token from central authentication server
 token <- armadillo.get_token(armadillo_url)
@@ -38,16 +38,19 @@ The important part is to specify the driver. This should be `ArmadilloDriver`.
 ```{r, login}
 # build the login dataframe
 builder <- DSI::newDSLoginBuilder()
-builder$append(server = "armadillo",
-               url = armadillo_url,
-               token = token,
-               driver = "ArmadilloDriver")
+builder$append(
+  server = "armadillo",
+  url = armadillo_url,
+  token = token,
+  driver = "ArmadilloDriver",
+  profile = "xenon",
+  )
 
 # create loginframe
-logindata <- builder$build()
+login_data <- builder$build()
 
 # login into server
-conns <- datashield.login(logins = logindata, assign = FALSE)
+conns <- DSI::datashield.login(logins = login_data, assign = FALSE)
 ```
 
 > You can append multiple servers to the login frame to perform an analysis
@@ -98,20 +101,20 @@ login.
 ```{r, assign data during login}
 # build the login dataframe
 builder <- DSI::newDSLoginBuilder()
-builder$append(server = "armadillo",
-               url = armadillo_url,
-               token = token,
-               driver = "ArmadilloDriver",
-               table = "gecko/2_1-core-1_0/nonrep")
+builder$append(
+  server = "armadillo",
+  url = armadillo_url,
+  token = token,
+  driver = "ArmadilloDriver",
+  table = "gecko/2_1-core-1_0/nonrep",
+  profile = "xenon",
+  )
 
 # create loginframe
-logindata <- builder$build()
+login_data <- builder$build()
 
 # login into server
-conns <- datashield.login(
-  logins = logindata,
-  assign = TRUE,
-  symbol = "core_nonrep")
+conns <- DSI::datashield.login(logins = login_data, assign = TRUE, symbol="core_nonrep")
 ```
 
 ### Subsetting data

vignettes/development.Rmd.orig

@@ -63,19 +63,23 @@ You can login with basic auth when you are developing. The default credentials a
 ```{r, login frame with basic authentication}
 library(DSMolgenisArmadillo)
 
-armadillo_url <- "https://armadillo.dev.molgenis.org"
+armadillo_url <- "https://armadillo-demo.molgenis.net"
 
 builder <- DSI::newDSLoginBuilder()
-builder$append(server = "armadillo",
-               url = armadillo_url,
-               user = "admin",
-               password = "admin",
-               table = "gecko/2_1-core-1_0/nonrep",
-               driver = "ArmadilloDriver")
 
-logindata <- builder$build()
+builder$append(
+  server = "armadillo",
+  url = armadillo_url,
+  user = "admin",
+  password = "password",
+  driver = "ArmadilloDriver",
+  table = "gecko/2_1-core-1_0/nonrep",
+  profile = "xenon",
+  )
 
-conns <- datashield.login(login = logindata, assign = TRUE)
+login_data <- builder$build()
+
+conns <- DSI::datashield.login(logins = login_data, assign = TRUE)
 ```
 
 #### Version of the package
@@ -112,7 +116,7 @@ In DataSHIELD you can use a variety of methods and packages. To check which are
 The available packages displayed by the method, are the serverside R-packages. Which means the packages available on the Armadillo.
 
 ```{r, check packages}
-conns <- datashield.login(logins = logindata, assign = F)
+conns <- DSI::datashield.login(logins = login_data, assign = F)
 dsListPackages(conns$armadillo)
 ```
 

vignettes/workspaces.Rmd

@@ -19,14 +19,14 @@ library(dsBaseClient)
 library(DSMolgenisArmadillo)
 
 # specify server url
-armadillo_url <- "https://armadillo.dev.molgenis.org"
+armadillo_url <- "https://armadillo-demo.molgenis.net/"
 
 # get token from central authentication server
 token <- armadillo.get_token(armadillo_url)
 ```
 
 ```
-## [1] "We're opening a browser so you can log in with code QR4XJ9"
+## [1] "We're opening a browser so you can log in with code R8VPYX"
 ```
 
 ```r
@@ -41,7 +41,7 @@ builder$append(server = "armadillo",
 # create loginframe
 logindata <- builder$build()
 
-conns <- datashield.login(login = logindata)
+conns <- DSI::datashield.login(login = logindata)
 ```
 
 ```
@@ -50,7 +50,7 @@ conns <- datashield.login(login = logindata)
 ```
 
 ```
-##   Logged in all servers [================================================================] 100% / 0s
+##    [-------------------------------------------------------------------------------------]   0% / 0s  Login armadillo [==================================>-----------------------------------]  50% / 0s  Logged in all servers [================================================================] 100% / 0s
 ```
 
 ```r
@@ -61,20 +61,27 @@ datashield.assign.table(conns = conns,
 ```
 
 ```
-##   Assigned all table (J <- ...) [========================================================] 100% / 0s
+##    [-------------------------------------------------------------------------------------]   0% / 0s  Checking armadillo (J <- `gecko/2_1-core-1_0/nonrep`) [--------------------------------]   0% / 0s  Waiting...  (J <- ...) [---------------------------------------------------------------]   0% / 0s  Checking armadillo (J <- `gecko/2_1-core-1_0/nonrep`) [--------------------------------]   0% / 0s  Waiting...  (J <- ...) [---------------------------------------------------------------]   0% / 0s  Checking armadillo (J <- `gecko/2_1-core-1_0/nonrep`) [--------------------------------]   0% / 0s  Waiting...  (J <- ...) [---------------------------------------------------------------]   0% / 0s  Checking armadillo (J <- `gecko/2_1-core-1_0/nonrep`) [--------------------------------]   0% / 0s  Waiting...  (J <- ...) [---------------------------------------------------------------]   0% / 0s  Checking armadillo (J <- `gecko/2_1-core-1_0/nonrep`) [--------------------------------]   0% / 0s  Finalizing assignment armadillo (J <- `gecko/2_1-core-1_0/nonrep`) [=========>---------]  50% / 0s  Assigned all table (J <- ...) [========================================================] 100% / 0s
 ```
 
 ```r
 datashield.logout(conns, save = "my-workspace")
+```
 
-conns <- datashield.login(logins = logindata,
+```
+##    [-------------------------------------------------------------------------------------]   0% / 0s  Logout armadillo [=================================>-----------------------------------]  50% / 0s  Logged out from all servers [==========================================================] 100% / 0s
+```
+
+```r
+conns <- DSI::datashield.login(logins = logindata,
                           assign = FALSE,
                           restore = "my-workspace")
 ```
 
 ```
 ## 
 ## Logging into the collaborating servers
+##    [-------------------------------------------------------------------------------------]   0% / 0s  Login armadillo [==================================>-----------------------------------]  50% / 0s  Logged in all servers [================================================================] 100% / 0s
 ```
 
 ```r
@@ -98,16 +105,17 @@ datashield.logout(conns)
 ```
 
 ```
-##   Logged out from all servers [==========================================================] 100% / 1s
+##    [-------------------------------------------------------------------------------------]   0% / 0s  Logout armadillo [=================================>-----------------------------------]  50% / 0s  Logged out from all servers [==========================================================] 100% / 0s
 ```
 
 ```r
-conns <- datashield.login(logins = logindata)
+conns <- DSI::datashield.login(logins = logindata)
 ```
 
 ```
 ## 
 ## Logging into the collaborating servers
+##    [-------------------------------------------------------------------------------------]   0% / 0s  Login armadillo [==================================>-----------------------------------]  50% / 0s  Logged in all servers [================================================================] 100% / 0s
 ```
 
 ```r
@@ -117,7 +125,7 @@ datashield.assign.table(conns = conns,
 ```
 
 ```
-##   Assigned all table (H <- ...) [========================================================] 100% / 0s
+##    [-------------------------------------------------------------------------------------]   0% / 0s  Checking armadillo (H <- `gecko/2_1-core-1_0/nonrep`) [--------------------------------]   0% / 0s  Waiting...  (H <- ...) [---------------------------------------------------------------]   0% / 0s  Checking armadillo (H <- `gecko/2_1-core-1_0/nonrep`) [--------------------------------]   0% / 0s  Waiting...  (H <- ...) [---------------------------------------------------------------]   0% / 0s  Checking armadillo (H <- `gecko/2_1-core-1_0/nonrep`) [--------------------------------]   0% / 0s  Waiting...  (H <- ...) [---------------------------------------------------------------]   0% / 0s  Checking armadillo (H <- `gecko/2_1-core-1_0/nonrep`) [--------------------------------]   0% / 0s  Waiting...  (H <- ...) [---------------------------------------------------------------]   0% / 0s  Checking armadillo (H <- `gecko/2_1-core-1_0/nonrep`) [--------------------------------]   0% / 0s  Finalizing assignment armadillo (H <- `gecko/2_1-core-1_0/nonrep`) [=========>---------]  50% / 0s  Assigned all table (H <- ...) [========================================================] 100% / 0s
 ```
 
 ```r
@@ -133,10 +141,10 @@ datashield.workspaces(conns$armadillo)
 ```
 
 ```
-##             lastAccessDate                               ETag                               name   size user
-## 1 2020-09-08T10:14:42.345Z "79ea8e26a41a0f43716040c5f09466c0" armadillo:my-workspace-overwritten 172072     
-## 2 2020-09-08T10:14:40.907Z "7de51b96e6d15e9ab13b9ef52fe3547f"   armadillo:my-workspace-version-2   3610     
-## 3 2020-09-08T10:14:40.524Z "7de51b96e6d15e9ab13b9ef52fe3547f"             armadillo:my-workspace   3610
+##                                 name   size           lastAccessDate user
+## 1 armadillo:my-workspace-overwritten 172073 2023-10-24T09:22:41.747Z     
+## 2             armadillo:my-workspace   3611 2023-10-24T09:22:40.615Z     
+## 3   armadillo:my-workspace-version-2   3611 2023-10-24T09:22:40.847Z
 ```
 
 Remove workspaces.
@@ -148,10 +156,10 @@ datashield.workspaces(conns)
 ```
 
 ```
-##      server name..armadillo.my.workspace.version.2. name..armadillo.my.workspace. user
-## 1 armadillo        armadillo:my-workspace-version-2        armadillo:my-workspace     
-## 2 armadillo        armadillo:my-workspace-version-2        armadillo:my-workspace     
-##   lastAccessDate..2020.09.08T10.14.40.907Z. lastAccessDate..2020.09.08T10.14.40.524Z. size.3610L size.3610L.1
-## 1                  2020-09-08T10:14:40.907Z                  2020-09-08T10:14:40.524Z       3610         3610
-## 2                  2020-09-08T10:14:40.907Z                  2020-09-08T10:14:40.524Z       3610         3610
+##      server name..armadillo.my.workspace. name..armadillo.my.workspace.version.2. user
+## 1 armadillo        armadillo:my-workspace        armadillo:my-workspace-version-2     
+## 2 armadillo        armadillo:my-workspace        armadillo:my-workspace-version-2     
+##   lastAccessDate..2023.10.24T09.22.40.615Z. lastAccessDate..2023.10.24T09.22.40.847Z. size.3611L size.3611L.1
+## 1                  2023-10-24T09:22:40.615Z                  2023-10-24T09:22:40.847Z       3611         3611
+## 2                  2023-10-24T09:22:40.615Z                  2023-10-24T09:22:40.847Z       3611         3611
 ```

vignettes/workspaces.Rmd.orig

@@ -20,7 +20,7 @@ library(dsBaseClient)
 library(DSMolgenisArmadillo)
 
 # specify server url
-armadillo_url <- "https://armadillo.dev.molgenis.org"
+armadillo_url <- "https://armadillo-demo.molgenis.net/"
 
 # get token from central authentication server
 token <- armadillo.get_token(armadillo_url)
@@ -36,7 +36,7 @@ builder$append(server = "armadillo",
 # create loginframe
 logindata <- builder$build()
 
-conns <- datashield.login(login = logindata)
+conns <- DSI::datashield.login(login = logindata)
 
 datashield.assign.table(conns = conns,
                         table = "gecko/2_1-core-1_0/nonrep",
@@ -45,7 +45,7 @@ datashield.assign.table(conns = conns,
 
 datashield.logout(conns, save = "my-workspace")
 
-conns <- datashield.login(logins = logindata,
+conns <- DSI::datashield.login(logins = logindata,
                           assign = FALSE,
                           restore = "my-workspace")
 
@@ -57,7 +57,7 @@ You can overwrite workspaces using the same name again when saving the workspace
 
 ```{r, overwrite using the same name}
 datashield.logout(conns)
-conns <- datashield.login(logins = logindata)
+conns <- DSI::datashield.login(logins = logindata)
 
 datashield.assign.table(conns = conns,
                         table = "gecko/2_1-core-1_0/nonrep",