Merge branch 'release/1.22.0'

Author: pbchase

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: redcapcustodian
 Type: Package
 Title: Data automation for R-centric workflows with a nod towards REDCap
-Version: 1.21.0
+Version: 1.22.0
 Authors@R: c(
   person("Philip", "Chase",
         email = "pbc@ufl.edu",
@@ -70,6 +70,6 @@ Suggests:
     tidyverse
 VignetteBuilder: knitr
 Config/testthat/edition: 3
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 Depends: 
     R (>= 3.5.0)

Dockerfile

@@ -1,10 +1,13 @@
-FROM --platform=linux/amd64 rocker/verse:4.3.2
+FROM --platform=linux/amd64 rocker/verse:4.3.3
 
 WORKDIR /home/rocker
 
 RUN apt update -y && apt install -y libmariadb-dev libmariadb-dev-compat
 RUN apt install -y --no-install-recommends libxt6
 
+# returns an error but tlmgr is updated to 2024 regardless
+RUN wget ${CTAN_REPO}/update-tlmgr-latest.sh && bash update-tlmgr-latest.sh; exit 0
+
 # install necessary libraries
 RUN R -e "install.packages(c( \
   'DBI', \

NEWS.md

@@ -1,3 +1,9 @@
+# redcapcustodian 1.22.0 (released 2024-03-26)
+- Implement hacky fix for tlmgr 2023 being unable to install packages (@ChemiKyle, #156)
+- Fix bug that prevented email_body from being included in email (@ljwoodley, @ChemiKyle, #155)
+- Add 'Scraping one user's API tokens' section to vignettes/credential-scraping.Rmd (@pbchase, @ChemiKyle, #154)
+- Update scrape_user_api_tokens() to tidyselect 1.2 standards (@pbchase, #154)
+
 # redcapcustodian 1.21.0 (released 2024-03-15)
 - Add attachment management to send_email() allowing lists of files or dataframes to be attached to an email (@ljwoodley, #152, #153)
 

R/credential_management.R

@@ -22,7 +22,7 @@ scrape_user_api_tokens <- function(conn, username_to_scrape = Sys.info()[["user"
   # collect super API token if one exists
   super_credentials <- dplyr::tbl(conn, "redcap_user_information") %>%
     dplyr::filter(.data$username == username_to_scrape) %>%
-    dplyr::select(.data$username, .data$api_token) %>%
+    dplyr::select("username", "api_token") %>%
     dplyr::collect() %>%
     dplyr::mutate(project_id = 0) %>%
     dplyr::filter(!is.na(.data$api_token)) %>%
@@ -32,25 +32,25 @@ scrape_user_api_tokens <- function(conn, username_to_scrape = Sys.info()[["user"
     dplyr::filter(.data$username == username_to_scrape) %>%
     dplyr::filter(!is.na(.data$api_token)) %>%
     dplyr::select(
-      .data$project_id,
-      .data$username,
-      .data$api_token
+      "project_id",
+      "username",
+      "api_token"
     ) %>%
     # add project information
     dplyr::left_join(
       dplyr::tbl(conn, "redcap_projects") %>%
         dplyr::select(
-          .data$project_id,
-          .data$app_title
+          "project_id",
+          "app_title"
         ),
       by = "project_id"
     ) %>%
     dplyr::collect() %>%
     # bind_rows used over rbind to avoid need to align column order
     dplyr::bind_rows(super_credentials) %>%
     dplyr::rename(
-      project_display_name = .data$app_title,
-      token = .data$api_token # rename for compatibility with REDCapR credential objects
+      project_display_name = "app_title",
+      token = "api_token" # rename for compatibility with REDCapR credential objects
     )
 
   return(credentials)

R/logging.R

@@ -689,9 +689,10 @@ send_email <-
       email_to <- unlist(strsplit(email_to, " "))
     }
 
+    email_content <- email_body
+
     if (!is.null(file_name)) {
       output_dir <- tempdir()
-      email_content <- list()
 
       if (!is.null(df_to_email) && is.data.frame(df_to_email)) {
         df_to_email <- list(df_to_email)

VERSION

@@ -1 +1 @@
-1.21.0
+1.22.0

vignettes/credential-scraping.Rmd

@@ -115,6 +115,79 @@ dbDisconnect(file_conn)
 dbDisconnect(source_conn)
 ```
 
+### Scraping one user's API tokens
+
+Scraping one user's API tokens and putting them in a new, local sqlite DB for use. 
+
+You must provide the username in the API_USER environment variable or on the command line. To specify it on the command line via `Rscript` and specify a REDCap username. e.g.
+
+```sh
+Rscript scrape_one_user.R jane_doe
+```
+
+```{r, eval = FALSE}
+library(redcapcustodian)
+library(DBI)
+library(tidyverse)
+library(dotenv)
+
+# Get the username provided on the command line if one is provided. 
+# Otherwise, get the username form the environment.
+# Otherwise, exit.
+args <- commandArgs(trailingOnly = TRUE)
+if (length(args) > 0) {
+  # Use the command line argument
+  username <- args
+} else if (Sys.getenv("API_USER") != "") {
+  # Use the environment variable
+  username <- Sys.getenv("API_USER")
+} else {
+  # Exit
+  warning("Please provide a username that whose API tokens you want to read either on the command line or via the API_USER environment variable. No action taken.")
+  quit()
+}
+
+# Creates the credentials file if one does not exists.
+# Otherwise it deletes the credentials file
+credentials_db_path <- here::here(paste0("credentials-", username, ".db"))
+if (fs::file_exists(credentials_db_path)) fs::file_delete(credentials_db_path)
+file_conn <- DBI::dbConnect(RSQLite::SQLite(), credentials_db_path)
+
+# SQLite friendly schema
+credentials_sql <- "CREATE TABLE IF NOT EXISTS `credentials` (
+  `redcap_uri` TEXT NOT NULL,
+  `server_short_name` varchar(128) NOT NULL,
+  `username` varchar(191) NOT NULL,
+  `project_id` int(10) NOT NULL,
+  `project_display_name` TEXT NOT NULL,
+  `project_short_name` varchar(128) DEFAULT NULL,
+  `token` varchar(64) NOT NULL,
+  `comment` varchar(256) DEFAULT NULL
+);
+"
+
+dbExecute(file_conn, credentials_sql)
+
+# Connect to the REDCap database specified in the environment
+# loaded by the dotenv library
+source_conn <- connect_to_redcap_db()
+source_credentials <- scrape_user_api_tokens(
+  conn = source_conn,
+  username_to_scrape = username
+)
+
+# alter credentials to match local schema
+source_credentials_upload <- source_credentials %>%
+  mutate(
+    redcap_uri = Sys.getenv("URI"),
+    server_short_name = tolower(Sys.getenv("INSTANCE"))
+  )
+
+dbAppendTable(file_conn, "credentials", source_credentials_upload)
+
+dbDisconnect(file_conn)
+dbDisconnect(source_conn)
+```
 ### Creating API tokens for all local projects
 
 ```{r, eval = FALSE}