Adds new end-points and improves to existing ones

.github/workflows/R-CMD-check.yaml

@@ -1,12 +1,5 @@
-on:
-  push:
-    branches:
-      - master
-  pull_request:
-    branches:
-      - master
-
 name: R-CMD-check
+on: [push, pull_request]
 
 jobs:
   R-CMD-check:

NAMESPACE

@@ -1,4 +1,6 @@
 # Generated by roxygen2: do not edit by hand
 
+export(create_cohort)
+export(extract_genotypic_data)
 export(extract_participants)
 export(list_cohorts)

R/create_cohort.R

@@ -0,0 +1,47 @@
+#' @title Create Cohort
+#'
+#' @description Creates a new Cohort
+#'
+#' @param baseurl Base URL of the CloudOS server. (Required)
+#' @param auth  An authentication method. (Required)
+#' Example - Bearer token or API key.
+#' @param teamid Team ID in CloudOS account. (Required)
+#' @param cohort_name New cohort name to be created. (Required)
+#' @param cohort_desc New cohort description to be created. (Required)
+#' @param filters WIP - details will be added.
+#'
+#' @return A dataframe.
+#'
+#' @examples
+#' \dontrun{
+#' create_cohort(baseurl= "https://cloudos.lifebit.ai",
+#'              auth = "Bearer ***token***",
+#'              teamid = "***teamid***",
+#'              cohort_name = "my cohort",
+#'              cohort_desc = "my cohort description")
+#' }
+#' @export
+create_cohort <- function(baseurl, auth, teamid,
+                          cohort_name, cohort_desc, filters = "") {
+  url <- paste(baseurl, "api/v1/cohort/", sep = "/")
+  r <- httr::POST(url,
+                  httr::add_headers(.headers = c("Authorization" = auth,
+                                                 "accept" = "application/json, text/plain, */*",
+                                                 "content-type" = "application/json;charset=UTF-8")),
+                  query = list("teamId" = teamid),
+                  body = list("name" = cohort_name,
+                              "description" = cohort_desc,
+                              "moreFilters" = filters),
+                  encode = "json"
+  )
+  if (!r$status_code == 200) {
+    message("Something went wrong. Not able to create a cohort")
+  }else{
+    message("Cohort named ", cohort_name, " created successfully. Bellow are the details")
+    res <- httr::content(r)
+    # into a dataframe
+    res_df <- do.call(rbind, res)
+    colnames(res_df) <- "details"
+    return(res_df)
+  }
+}

R/extract_genotypic_data.R

@@ -0,0 +1,43 @@
+#' @title Extract Genotypic Data
+#'
+#' @description Extract Genotypic Data with filter.
+#'
+#' @param baseurl Base URL of the CloudOS server. (Required)
+#' @param auth  An authentication method. (Required)
+#' Example - Bearer token or API key.
+#' @param teamid Team ID in CloudOS account. (Required)
+#' @param page_number Number of page. (Optional) Default - 0
+#' @param page_size Number of entries in a page. (Optional) Default - 10
+#' @param filters WIP - details will be added.
+#'
+#' @return A dataframe.
+#'
+#' @examples
+#' \dontrun{
+#' extract_genotypic_data(baseurl= "https://cloudos.lifebit.ai",
+#'              auth = "Bearer ***token***",
+#'              teamid = "***teamid***")
+#' }
+#' @export
+extract_genotypic_data <- function(baseurl, auth, teamid,
+                               page_number = 0,
+                               page_size = 10,
+                               filters = "") {
+  url <- paste(baseurl, "api/v1/cohort/genotypic-data", sep = "/")
+  r <- httr::POST(url,
+                  httr::add_headers(.headers = c("Authorization" = auth,
+                                                 "accept" = "application/json, text/plain, */*",
+                                                 "content-type" = "application/json;charset=UTF-8")),
+                  query = list("teamId" = teamid),
+                  body = list("pageNumber" = page_number,
+                              "pageSize" = page_size,
+                              "filters" = filters),
+                  encode = "json"
+  )
+  if (!r$status_code == 200) {
+    message("Something went wrong.")
+  }else{
+    res <- httr::content(r)
+    return(res$participants)
+  }
+}

R/extract_participants.R

@@ -25,7 +25,11 @@ extract_participants <- function(baseurl, auth, raw_data) {
                   body = raw_data,
                   encode = "json"
         )
-  res <- httr::content(r, as = "text")
-  df <- utils::read.csv(textConnection(res))
-  return(df)
+  if (!r$status_code == 200) {
+    message("Something went wrong.")
+  }else{
+    res <- httr::content(r, as = "text")
+    df <- utils::read.csv(textConnection(res))
+    return(df)
+  }
 }

R/list_cohorts.R

@@ -1,4 +1,4 @@
-#' @title Limited Cohort Data Extractor
+#' @title List cohorts
 #'
 #' @description Extracts the data frame with limited cohort data columns.
 #'
@@ -29,15 +29,15 @@ list_cohorts <- function(baseurl,
                  query = list("teamId" = teamid,
                               "pageNumber" = page_number,
                               "pageSize" = page_size))
-  res <- httr::content(r)
-  if(length(res) == 0){
+  if (!r$status_code == 200) {
     message("No cohorts found. Or not able to connect with server.")
   } else {
+    res <- httr::content(r)
     message("Total number of cohorts found - ", res$total)
     cohorts <- res$cohort
     # make in to a list
     cohorts_list <- list()
-    for(n in 1:res$total){
+    for (n in 1:res$total) {
       dta <- data.frame(id = cohorts[[n]]$`_id`,
                         name = cohorts[[n]]$`name`,
                         description = cohorts[[n]]$`description`,
@@ -50,7 +50,7 @@ list_cohorts <- function(baseurl,
       # cohorts[[1]]$`filters`
     }
     # make in to a dataframe
-    cohorts_df = do.call(rbind, cohorts_list)
+    cohorts_df <- do.call(rbind, cohorts_list)
     return(cohorts_df)
   }
 }

README.md

@@ -17,16 +17,12 @@ if (!require(remotes)) { install.packages("remotes") }
   remotes::install_github("lifebit-ai/cloudos")
 ```
 
-## Example
+## Documentation
 
-This is a basic example.
+Online pkgdown generated doc - https://lifebit-ai.github.io/cloudos/
 
-``` r
-library(cloudos)
+All the avaiable functions - https://lifebit-ai.github.io/cloudos/reference/index.html
 
-extract_participants(baseurl= "https://cloudos.lifebit.ai", 
-              auth = "Bearer ***token***",
-              raw_data = "a JSON string for selected participants")
+A vignette with examples on - [Access Lifebit’s cohort broswer in R](https://lifebit-ai.github.io/cloudos/articles/cohort_browser.html)
 
-```
 

_pkgdown.yml

@@ -0,0 +1,6 @@
+url: https://lifebit-ai.github.io/cloudos/
+authors:
+  Lifebit:
+    href: https://lifebit.ai
+development:
+  mode: auto