diff --git a/NEWS.md b/NEWS.md index 3f8a827c..6607b8a1 100644 --- a/NEWS.md +++ b/NEWS.md @@ -15,6 +15,10 @@ Version 1.4.x (Not yet released on CRAN) These features are not yet on CRAN. Install with `remotes::install_github("OuhscBbmc/REDCapR")` +### New Features + +* `redcap_file_repo_list_oneshot()` export a list of files/folders from the file repository (requested by @agdamsbo, #549) + Version 1.3.0 (released 2024-10-22) ========================================================== diff --git a/R/redcap-file-repo-list.R b/R/redcap-file-repo-list.R index 1b97353b..08551e7f 100644 --- a/R/redcap-file-repo-list.R +++ b/R/redcap-file-repo-list.R @@ -1,13 +1,13 @@ #' @title #' Export a List of Files/Folders from the File Repository -#'#' +#' #' @description #' Allows you to export a list of all files and sub-folders from a specific #' folder in a project's File Repository. #' Each sub-folder will have an associated folder_id number, #' and each file will have an associated doc_id number. #' -#' @param folder_id the `folder_id` of a specific folder in the +#' @param folder_id the integer of a specific folder in the #' File Repository for which you wish to export a list of its #' files and sub-folders. #' If `NA` (the default), diff --git a/_pkgdown.yml b/_pkgdown.yml index f0ac4515..42267218 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -46,8 +46,14 @@ reference: - redcap_write_oneshot - redcap_delete - redcap_report + + - title: "File API Operations" + desc: > + Manipulating files in the REDCap records and in the file repository. + contents: - redcap_file_download_oneshot - redcap_file_upload_oneshot + - redcap_file_repo_list_oneshot - title: "Additional API Methods" desc: > diff --git a/man/redcap_file_repo_list_oneshot.Rd b/man/redcap_file_repo_list_oneshot.Rd index 33a888fc..6e072e70 100644 --- a/man/redcap_file_repo_list_oneshot.Rd +++ b/man/redcap_file_repo_list_oneshot.Rd @@ -2,8 +2,7 @@ % Please edit documentation in R/redcap-file-repo-list.R \name{redcap_file_repo_list_oneshot} \alias{redcap_file_repo_list_oneshot} -\title{Export a List of Files/Folders from the File Repository -#'} +\title{Export a List of Files/Folders from the File Repository} \usage{ redcap_file_repo_list_oneshot( redcap_uri, @@ -24,7 +23,7 @@ Required.} \item{token}{The user-specific string that serves as the password for a project. Required.} -\item{folder_id}{the \code{folder_id} of a specific folder in the +\item{folder_id}{the integer of a specific folder in the File Repository for which you wish to export a list of its files and sub-folders. If \code{NA} (the default), diff --git a/vignettes/TroubleshootingApiCalls.Rmd b/vignettes/TroubleshootingApiCalls.Rmd index caa1fd21..6bb89501 100644 --- a/vignettes/TroubleshootingApiCalls.Rmd +++ b/vignettes/TroubleshootingApiCalls.Rmd @@ -44,6 +44,7 @@ This first group of checks primarily focuses on the server and the logins accoun ```{r EmailVerified} #| echo = FALSE, + #| fig.alt = 'verified email screen shot', #| out.extra = 'style = "fig.width=400px"' knitr::include_graphics("images/EmailVerified.png") ``` @@ -54,6 +55,7 @@ This first group of checks primarily focuses on the server and the logins accoun ```{r ApiPrivilegeDashboard} #| echo = FALSE, + #| fig.alt = 'tokens screen shot', #| out.extra = 'style = "fig.width=600px"' knitr::include_graphics("images/ApiPrivilegeDashboard.png") ``` @@ -64,6 +66,7 @@ This first group of checks primarily focuses on the server and the logins accoun ```{r MagnifyingGlass} #| echo = FALSE, + #| fig.alt = 'magnifying screen shot', #| out.extra = 'style = "fig.width=550px"' knitr::include_graphics("images/MagnifyingGlass.png") ``` @@ -79,6 +82,7 @@ This section examines potential problems that occur after data leaves a working ```{r PostmanScreenshot} #| echo = FALSE, +#| fig.alt = 'PostMan screen shot', #| out.extra = 'style = "fig.width=800px"' knitr::include_graphics("images/PostmanScreenshot.png") ``` diff --git a/vignettes/workflow-read.Rmd b/vignettes/workflow-read.Rmd index ac9ab4de..e3cb0193 100644 --- a/vignettes/workflow-read.Rmd +++ b/vignettes/workflow-read.Rmd @@ -202,7 +202,7 @@ ds_1 <- At this point, the data.frame `ds_1` has everything you need to start analyzing the project. -```{r unstructured-2} +```{r unstructured-2, fig.alt = "histogram of patient weight"} ds_1 hist(ds_1$weight) diff --git a/vignettes/workflow-write.Rmd b/vignettes/workflow-write.Rmd index 331453cf..a6c4da7d 100644 --- a/vignettes/workflow-write.Rmd +++ b/vignettes/workflow-write.Rmd @@ -7,8 +7,8 @@ vignette: > %\VignetteIndexEntry{Writing to a REDCap Project} %\VignetteEncoding{UTF-8} %\VignetteEngine{knitr::rmarkdown} -editor_options: - markdown: +editor_options: + markdown: wrap: 72 --- @@ -241,6 +241,7 @@ ds_patient <- ```{r codebook-race} #| echo = FALSE, +#| fig.alt = 'codebook race variable screen shot', #| out.extra = 'style = "fig.width=1200px"' knitr::include_graphics("images/codebook-race.png") ``` @@ -364,16 +365,16 @@ format (*i.e.*, everything jammed into one rectangle.) ## REDCap's CDIS -The [Clinical Data Interoperability Services](https://projectredcap.org/software/cdis/) (CDIS) +The [Clinical Data Interoperability Services](https://projectredcap.org/software/cdis/) (CDIS) use [FHIR](https://www.hl7.org/fhir/overview.html) to move data from your institution's [EMR/EHR](https://www.healthit.gov/faq/what-are-differences-between-electronic-medical-records-electronic-health-records-and-personal) -(eg, Epic, Cerner) to REDCap. +(eg, Epic, Cerner) to REDCap. Research staff have control over which patient records are selected or eligible. -Conceptually it's similar to writing to REDCap's with the API, +Conceptually it's similar to writing to REDCap's with the API, but at much bigger scale. Realistically, it takes months to get through your institution's human layers. -Once established, a project would be populated with EMR data -in much less development time +Once established, a project would be populated with EMR data +in much less development time --assuming the desired data models corresponds with FHIR [endpoints](https://hl7.org/fhir/endpoint.html).