Merge pull request #2 from bzhanglab/cran_comments

Address cran comments

.Rbuildignore

@@ -9,4 +9,5 @@
 ^pkgdown$
 ^\.github$
 ^man\\figures\.gitkeep$
-^man/figures/\.gitkeep$
+^man/figures/\.gitkeep$
+^CRAN-SUBMISSION$

CRAN-SUBMISSION

@@ -0,0 +1,3 @@
+Version: 1.0.4
+Date: 2024-06-18 18:58:59 UTC
+SHA: 584cc5189e1e0674fdbb7b28fedda3b4de5a2d87

DESCRIPTION

@@ -7,6 +7,6 @@ Description: Provides an interface to the 'ClinicalOmicsDB' API, allowing for ea
 License: MIT + file LICENSE
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 Imports: httr2, R6, dplyr, utils, jsonlite
 BugReports: https://github.com/bzhanglab/clinicalomicsdbR/issues/new

R/clinicalomicsdbR.R

@@ -13,6 +13,8 @@ clinicalomicsdbR <- R6Class("clinicalomicsdbR", list(
   hostname = "https://trials.linkedomics.org",
   #' @field study_list The list of all the studies that are a result of filtering.
   study_list = c(),
+  #' @field verbosity The level of messages wanted for downloads (defaults to 0: No Output). Follows httr2 documentatation for `req_perform`
+  verbosity = 0,
   #' @description
   #' filter objects according to the specified drugs and cancers
   #' @param drugs list or vector containing drugs that studies need to contain at least one of
@@ -52,10 +54,10 @@ clinicalomicsdbR <- R6Class("clinicalomicsdbR", list(
           \"cancers\": ", cancer_text, "
         }
         "))
-    resp <- req_perform(req)
+    resp <- req_perform(req, verbosity = self$verbosity)
     filter_res <- resp %>% resp_body_json()
     self$study_list <- unlist(filter_res$study_list)
-    print(paste0("Filtered to ", length(self$study_list), " studies."))
+    message(paste0("Filtered to ", length(self$study_list), " studies."))
     invisible(self)
   },
   #' @description
@@ -67,47 +69,47 @@ clinicalomicsdbR <- R6Class("clinicalomicsdbR", list(
     req <- req %>%
       req_method("GET") %>%
       req_headers("Accept" = "application/json, text/plain")
-    resp <- req_perform(req)
+    resp <- req_perform(req, verbosity = self$verbosity)
     resp_json <- resp %>% resp_body_json()
     return(resp_json$download_url)
   },
   #' @description
   #' Download all files of the studies in `self$study_list`. Use `filter` function first
-  #' @param output_dir Directory to download files to. Default to `clindb`
+  #' @param output_dir Directory to download files to.
   #' @return unmodifed clinicalomicsdbR object
-  download = function(output_dir = "clindb") {
+  download = function(output_dir) {
     cidr <- getwd()
     dir.create(file.path(cidr, output_dir), recursive = TRUE, showWarnings = FALSE)
     for (study_id in self$study_list) {
       dl_url <- self$get_download_url(study_id)
-      print(paste0("Downloading study ", study_id, " from ", dl_url))
+      message(paste0("Downloading study ", study_id, " from ", dl_url))
       download.file(dl_url, paste0(output_dir, "/", study_id))
     }
-    print(paste0("Downloaded ", length(self$study_list), " studies."))
+    message(paste0("Downloaded ", length(self$study_list), " studies."))
     invisible(self)
   },
   #' @description
   #' Download all file from `study_id` into `output_dir` directory
   #' @param study_id String containing the ID of the study to download
-  #' @param output_dir Directory to download files to. Default to `clindb`
+  #' @param output_dir Directory to download files to.
   #' @return unmodifed clinicalomicsdbR object
-  download_from_id = function(study_id, output_dir = "clindb") {
+  download_from_id = function(study_id) {
     cidr <- getwd()
     dir.create(file.path(cidr, output_dir), recursive = TRUE, showWarnings = FALSE)
     dl_url <- self$get_download_url(study_id)
     tryCatch(
       {
-        print(paste0("Downloading study ", study_id, " from ", dl_url))
+        message(paste0("Downloading study ", study_id, " from ", dl_url))
         download.file(dl_url, paste0(output_dir, "/", study_id))
-        print("Done downloading study.")
+        message("Done downloading study.")
         invisible(self)
       },
       error = function(err) {
-        print(paste0("Error fetching study with ID: ", study_id, ".\nVerify ID is correct or change hostname."))
+        message(paste0("Error fetching study with ID: ", study_id, ".\nVerify ID is correct or change hostname."))
         stop(paste0("Could not fetch study: ", study_id))
       },
       warning = function(warn) {
-        print(paste0("Warning fetching study with ID: ", study_id, ".\nVerify ID is correct or change hostname."))
+        message(paste0("Warning fetching study with ID: ", study_id, ".\nVerify ID is correct or change hostname."))
         warn(paste0("Warning with study: ", study_id))
       }
     )
@@ -130,15 +132,15 @@ clinicalomicsdbR <- R6Class("clinicalomicsdbR", list(
     tryCatch(
       {
         dl_url <- self$get_download_url(study_id)
-        print(paste0("Getting dataframe of study ", study_id, " from ", dl_url))
+        message(paste0("Getting dataframe of study ", study_id, " from ", dl_url))
         return(read.csv(dl_url))
       },
       error = function(err) {
-        print(paste0("Error fetching study with ID: ", study_id, ".\nVerify ID is correct or change hostname."))
+        message(paste0("Error fetching study with ID: ", study_id, ".\nVerify ID is correct or change hostname."))
         stop(paste0("Could not fetch study: ", study_id))
       },
       warning = function(warn) {
-        print(paste0("Warning fetching study with ID: ", study_id, ".\nVerify ID is correct or change hostname."))
+        message(paste0("Warning fetching study with ID: ", study_id, ".\nVerify ID is correct or change hostname."))
         warn(paste0("Warning with study: ", study_id))
       }
     )

README.Rmd

@@ -54,13 +54,12 @@ See Examples below to see how to use.
   combinations. See the ClinicalOmicsDB website for all options.
   `cancers` can contain multiple cancers.
 - `download(output_dir)` - downloads all studies from `filter()` into
-  `output_dir`. `output_dir` is optional, and defaults to `clindb`
+  `output_dir`.
 - `dataframe()` - loads all the studies from `filter()` into a
   list, with column `study_list` that contains the names of the
   studies and `df` that contains a list of the study data information.
 - `dataframe_from_id(study_id)` - loads a study with id from `study_id` into a dataframe
-- `downlaod_from_id(study_id, output_dir)` - downsloads a study with id from `study_id` into a folder `output_dir`. `output_dir` defaults to `clindb`
-
+- `download_from_id(study_id, output_dir)` - downsloads a study with id from `study_id` into a folder `output_dir`.
 See the examples below for more information on how to use.
 
 ## Examples
@@ -69,12 +68,10 @@ See the examples below for more information on how to use.
 
 Filters studies for those which used rituximab or ipilimumab then downloads them to the `studies` folder.
 
-*Notes*: `output_dir` is optional. Defaults to `clindb`.
-
 ```{r example}
 library(clinicalomicsdbR)
 
-clinicalomicsdbR$new()$filter(drugs = c("ipilimumab", "rituximab"))$download(output_dir = "studies") # downloads all files
+clinicalomicsdbR$new()$filter(drugs = c("ipilimumab", "rituximab"))$download(output_dir = tempdir()) # downloads all files
 ```
 
 ### Filter and Get Data Frame

README.md

@@ -48,17 +48,15 @@ See Examples below to see how to use.
   combinations. See the ClinicalOmicsDB website for all options.
   `cancers` can contain multiple cancers.
 - `download(output_dir)` - downloads all studies from `filter()` into
-  `output_dir`. `output_dir` is optional, and defaults to `clindb`
+  `output_dir`.
 - `dataframe()` - loads all the studies from `filter()` into a list,
   with column `study_list` that contains the names of the studies and
   `df` that contains a list of the study data information.
 - `dataframe_from_id(study_id)` - loads a study with id from `study_id`
   into a dataframe
-- `downlaod_from_id(study_id, output_dir)` - downsloads a study with id
-  from `study_id` into a folder `output_dir`. `output_dir` defaults to
-  `clindb`
-
-See the examples below for more information on how to use.
+- `download_from_id(study_id, output_dir)` - downsloads a study with id
+  from `study_id` into a folder `output_dir`. See the examples below for
+  more information on how to use.
 
 ## Examples
 
@@ -67,18 +65,16 @@ See the examples below for more information on how to use.
 Filters studies for those which used rituximab or ipilimumab then
 downloads them to the `studies` folder.
 
-*Notes*: `output_dir` is optional. Defaults to `clindb`.
-
 ``` r
 library(clinicalomicsdbR)
 
-clinicalomicsdbR$new()$filter(drugs = c("ipilimumab", "rituximab"))$download(output_dir = "studies") # downloads all files
-#> [1] "Filtered to 4 studies."
-#> [1] "Downloading study Gide_Cell_2019_pembro_ipi.csv from https://bcm.box.com/shared/static/swf5fywqcqmf75600g7v8irt2a9agnqo.csv"
-#> [1] "Downloading study VanAllen_antiCTLA4_2015.csv from https://bcm.box.com/shared/static/v0sphd7ht487qk96xbwjokgkbkjpexom.csv"
-#> [1] "Downloading study Gide_Cell_2019_nivo_ipi.csv from https://bcm.box.com/shared/static/jwv108f6cy4kvyeqer95jdugla53m1zt.csv"
-#> [1] "Downloading study GSE35935.csv from https://bcm.box.com/shared/static/8icr4i6gbbp6lgd01iscbss4v7lnj6c5.csv"
-#> [1] "Downloaded 4 studies."
+clinicalomicsdbR$new()$filter(drugs = c("ipilimumab", "rituximab"))$download(output_dir = tempdir()) # downloads all files
+#> Filtered to 4 studies.
+#> Downloading study Gide_Cell_2019_pembro_ipi.csv from https://bcm.box.com/shared/static/swf5fywqcqmf75600g7v8irt2a9agnqo.csv
+#> Downloading study VanAllen_antiCTLA4_2015.csv from https://bcm.box.com/shared/static/v0sphd7ht487qk96xbwjokgkbkjpexom.csv
+#> Downloading study Gide_Cell_2019_nivo_ipi.csv from https://bcm.box.com/shared/static/jwv108f6cy4kvyeqer95jdugla53m1zt.csv
+#> Downloading study GSE35935.csv from https://bcm.box.com/shared/static/8icr4i6gbbp6lgd01iscbss4v7lnj6c5.csv
+#> Downloaded 4 studies.
 ```
 
 ### Filter and Get Data Frame
@@ -92,11 +88,14 @@ data frame.
 library(clinicalomicsdbR)
 
 res <- clinicalomicsdbR$new()$filter(drugs = c("ipilimumab", "rituximab"))$dataframe(); # downloads all files
-#> [1] "Filtered to 4 studies."
-#> [1] "Getting dataframe of study Gide_Cell_2019_pembro_ipi.csv from https://bcm.box.com/shared/static/swf5fywqcqmf75600g7v8irt2a9agnqo.csv"
-#> [1] "Getting dataframe of study VanAllen_antiCTLA4_2015.csv from https://bcm.box.com/shared/static/v0sphd7ht487qk96xbwjokgkbkjpexom.csv"
-#> [1] "Getting dataframe of study Gide_Cell_2019_nivo_ipi.csv from https://bcm.box.com/shared/static/jwv108f6cy4kvyeqer95jdugla53m1zt.csv"
-#> [1] "Getting dataframe of study GSE35935.csv from https://bcm.box.com/shared/static/8icr4i6gbbp6lgd01iscbss4v7lnj6c5.csv"
+#> Filtered to 4 studies.
+#> Getting dataframe of study Gide_Cell_2019_pembro_ipi.csv from https://bcm.box.com/shared/static/swf5fywqcqmf75600g7v8irt2a9agnqo.csv
+#> Getting dataframe of study VanAllen_antiCTLA4_2015.csv from https://bcm.box.com/shared/static/v0sphd7ht487qk96xbwjokgkbkjpexom.csv
+#> Getting dataframe of study Gide_Cell_2019_nivo_ipi.csv from https://bcm.box.com/shared/static/jwv108f6cy4kvyeqer95jdugla53m1zt.csv
+#> Getting dataframe of study GSE35935.csv from https://bcm.box.com/shared/static/8icr4i6gbbp6lgd01iscbss4v7lnj6c5.csv
+```
+
+``` r
 
 for (study in res[["study_list"]]) {
   print(ncol(res[["df"]][[study]]))