get up to date with main

Merge branch 'main' of https://github.com/karissawhiting/cbioportalR into get-study-id-for-samples

# Conflicts:
#	vignettes/overview-of-workflow.Rmd

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: cbioportalR
 Title: Browse and Query Clinical and Genomic Data from cBioPortal
-Version: 1.0.1.9002
+Version: 1.1.0
 Authors@R: 
     c(person(given = "Karissa",
            family = "Whiting",

NAMESPACE

@@ -1,20 +1,10 @@
 # Generated by roxygen2: do not edit by hand
 
 export("%>%")
-export(.check_for_patient_id)
-export(.check_for_study_id)
-export(.check_input_pair_df)
-export(.get_cbioportal_url)
 export(.get_clinical_by_list_item)
 export(.get_clinical_pat_by_list_item)
 export(.get_data_by_sample)
 export(.get_data_by_study)
-export(.get_panel_entrez)
-export(.guess_study_id)
-export(.lookup_hugo)
-export(.lookup_profile_name)
-export(.lookup_study_name)
-export(.resolve_url)
 export(available_clinical_attributes)
 export(available_gene_panels)
 export(available_patients)

NEWS.md

@@ -1,8 +1,8 @@
-# cbioportalR (development version)
+# cbioportalR 1.1.0
 
 * Added `available_sample_lists()` function which returns all available sample list IDs for a given study ID
 * Added `sample_list_id` argument to `available_samples()` which returns all samples IDs in specific sample list within a study (#53).
-* Fixed {cli} errors to make package compatible with {cli} v3.4.1.
+* Fixed {cli} errors to make package compatible with {cli} ≥ v3.4.1.
 * Added CNA segmentation retrieval endpoint accessible via `get_segments_by_sample()` and `get_segments_by_study()`). You can use `get_genomics_by_*(return_segments = TRUE)` as well to access this data.
 
 # cbioportalR 1.0.1

R/authenticate.R

@@ -101,7 +101,6 @@ test_cbioportal_db <- function() {
 #' Pulls the set URL from the internal package environment
 #'
 #' @return a string indicating the saved URL in the `cbioportal_env` environment or an error if no URL found.
-#' @export
 #' @author Karissa Whiting, Daniel D. Sjoberg
 #' @keywords internal
 #' @noRd
@@ -126,9 +125,7 @@ test_cbioportal_db <- function() {
 #' Process and make a best guess of URL string passed to authentication functions
 #'
 #' @param raw_url The URL passed to a function by a user
-#'
 #' @return A string with a final URL to be used in the given query.
-#' @export
 #' @author Karissa Whiting, Daniel D. Sjoberg
 #' @keywords internal
 #' @noRd

R/utils.R

@@ -5,7 +5,6 @@
 #' @return stop if no arg
 #' @keywords internal
 #' @noRd
-#' @export
 #'
 .check_for_study_id <- function(study_id) {
 
@@ -27,7 +26,6 @@
 #' @return stop if no sample_id arg
 #' @keywords internal
 #' @noRd
-#' @export
 #'
 .check_for_patient_id <- function(patient_id) {
   if (is.null(patient_id)) {
@@ -43,7 +41,6 @@
 #' @return A valid `sample_study_pairs` or `patient_study_pairs` data frame. If `input_df` is NULL, it will return NULL.
 #' @keywords internal
 #' @noRd
-#' @export
 #'
 .check_input_pair_df <- function(input_df) {
 
@@ -113,7 +110,6 @@
 #' @return a guess at which study_id a user may want to use
 #' @keywords internal
 #' @noRd
-#' @export
 #'
 .guess_study_id <- function(study_id, resolved_url) {
 
@@ -125,7 +121,7 @@
   study_id_guess %||% cli::cli_abort("Unable to guess a {.code study_id} for your database.
                                    Please provide a {.code study_id}.")
 
-  cli::cli_alert_info("No {.code study_id} provided. Using {.val {study_id_guess}} as default study")
+  study_id %||% cli::cli_alert_info("No {.code study_id} provided. Using {.val {study_id_guess}} as default study")
 
   return(study_id_guess)
 }
@@ -144,7 +140,6 @@
 #' @return find molecular profile name for a specified data type
 #' @keywords internal
 #' @noRd
-#' @export
 #'
 .lookup_profile_name <- function(data_type, study_id, base_url) {
 
@@ -178,7 +173,6 @@
 #' @return find study ID for a specified molecular profile
 #' @keywords internal
 #' @noRd
-#' @export
 #'
 .lookup_study_name <- function(molecular_profile_id, study_id, base_url) {
 
@@ -217,7 +211,6 @@
 #' @return a dataframe that matches input data frame but with hugoGeneSymbol column
 #' @keywords internal
 #' @noRd
-#' @export
 #'
 .lookup_hugo <- function(df, base_url) {
 
@@ -262,7 +255,6 @@
 #' @return a vector of Entrez Gene IDs
 #' @keywords internal
 #' @noRd
-#' @export
 #'
 .get_panel_entrez <- function(panel_id, base_url) {
 
@@ -286,7 +278,6 @@
 #' Check if NULL
 #'
 #' @param x any R object or expression
-#'
 #' @noRd
 #' @keywords internal
 #'

README.Rmd

@@ -32,7 +32,7 @@ library(tidyverse)
 
 This package was created to work with both the public [cBioPortal website](https://www.cbioportal.org/), as well as private institutional cBioPortal instances (e.g. MSKCC, GENIE) with appropriate credentials and [authentication]. 
 
-This package is compatible with cBioPortal v5.0, but is subject to change as [cBioPortal updates are released](https://github.com/cBioPortal/cbioportal/releases). For more information on cBioPortal, see the following publications:
+This package is compatible with cBioPortal v5, but is subject to change as [cBioPortal updates are released](https://github.com/cBioPortal/cbioportal/releases). To see if your cBioPortal instance is compatible, look for its version in the footer of the homepage or check `portalVersion` in the output of `YOUR_CBIOPORTAL_INSTANCE/api/info`. For more information on cBioPortal, see the following publications:
 
 - [Gao et al. Sci. Signal. 2013](https://pubmed.ncbi.nlm.nih.gov/23550210/)
 - [ Cerami et al. Cancer Discov. 2012](https://aacrjournals.org/cancerdiscovery/article/2/5/401/3246/The-cBio-Cancer-Genomics-Portal-An-Open-Platform)