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Adds new end-points and improves to existing ones (#5)
* adds new end-points and impv to previous ones * adds pkgdown html links * linting correction * R-cmd-check in every push and PR * minor correction to title * updates doc * chnages to snakecase for team_id and base_url * error message() -> stop() which will exit with message. * minor corrections * local build and check * --no-build-vignettes added for R-CMD-Check as it require api-key to build * Attempt to fix tests (respect --no-build) * Attempt to address #5 (comment) * syntax fix in YAML * vignette oved to README * cleaning * no else based on @cgpu 's review Co-authored-by: cgpu <38183826+cgpu@users.noreply.github.com>
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| ^docs$ | ||
| ^pkgdown$ | ||
| ^local* | ||
| README* | ||
| ^check$ | ||
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| .Rproj.user | ||
| .Rhistory | ||
| .RData | ||
| local* | ||
| local* | ||
| inst/doc | ||
| check* |
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| # Generated by roxygen2: do not edit by hand | ||
|
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| export(create_cohort) | ||
| export(extract_genotypic_data) | ||
| export(extract_participants) | ||
| export(list_cohorts) |
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| #' @title Create Cohort | ||
| #' | ||
| #' @description Creates a new Cohort | ||
| #' | ||
| #' @param base_url Base URL of the CloudOS server. (Required) | ||
| #' @param auth An authentication method. (Required) | ||
| #' Example - Bearer token or API key. | ||
| #' @param team_id 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(base_url= "https://cloudos.lifebit.ai", | ||
| #' auth = "Bearer ***token***", | ||
| #' team_id = "***team_id***", | ||
| #' cohort_name = "my cohort", | ||
| #' cohort_desc = "my cohort description") | ||
| #' } | ||
| #' @export | ||
| create_cohort <- function(base_url, auth, team_id, | ||
| cohort_name, cohort_desc, filters = "") { | ||
| url <- paste(base_url, "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" = team_id), | ||
| body = list("name" = cohort_name, | ||
| "description" = cohort_desc, | ||
| "moreFilters" = filters), | ||
| encode = "json" | ||
| ) | ||
| if (!r$status_code == 200) { | ||
| stop("Something went wrong. Not able to create a cohort") | ||
| } | ||
| # parse the content | ||
| message("Cohort named ", cohort_name, " created successfully. Bellow are the details") | ||
| res <- httr::content(r) | ||
| # into a dataframe | ||
| res_df <- do.call(rbind, res) | ||
| colnames(res_df) <- "details" | ||
| return(res_df) | ||
| } |
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| #' @title Extract Genotypic Data | ||
| #' | ||
| #' @description Extract Genotypic Data with filter. | ||
| #' | ||
| #' @param base_url Base URL of the CloudOS server. (Required) | ||
| #' @param auth An authentication method. (Required) | ||
| #' Example - Bearer token or API key. | ||
| #' @param team_id Team ID in CloudOS account. (Required) | ||
| #' @param page_number Number of page. (Optional) Default - 0 | ||
| #' @param page_size Number of entries in a page. (Optional) Default - 10 | ||
| #' @param filters WIP - details will be added. | ||
| #' | ||
| #' @return A dataframe. | ||
| #' | ||
| #' @examples | ||
| #' \dontrun{ | ||
| #' extract_genotypic_data(base_url= "https://cloudos.lifebit.ai", | ||
| #' auth = "Bearer ***token***", | ||
| #' team_id = "***team_id***") | ||
| #' } | ||
| #' @export | ||
| extract_genotypic_data <- function(base_url, auth, team_id, | ||
| page_number = 0, | ||
| page_size = 10, | ||
| filters = "") { | ||
| url <- paste(base_url, "api/v1/cohort/genotypic-data", sep = "/") | ||
| r <- httr::POST(url, | ||
| httr::add_headers(.headers = c("Authorization" = auth, | ||
| "accept" = "application/json, text/plain, */*", | ||
| "content-type" = "application/json;charset=UTF-8")), | ||
| query = list("teamId" = team_id), | ||
| body = list("pageNumber" = page_number, | ||
| "pageSize" = page_size, | ||
| "filters" = filters), | ||
| encode = "json" | ||
| ) | ||
| if (!r$status_code == 200) { | ||
| stop("Something went wrong.") | ||
| } | ||
| # parse the content | ||
| res <- httr::content(r) | ||
| return(res$participants) | ||
| } |
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| #' @title Limited Cohort Data Extractor | ||
| #' @title List cohorts | ||
| #' | ||
| #' @description Extracts the data frame with limited cohort data columns. | ||
| #' | ||
| #' @param baseurl Base URL of the CloudOS server. (Required) | ||
| #' @param base_url Base URL of the CloudOS server. (Required) | ||
| #' @param auth An authentication method. (Required) | ||
| #' Example - Bearer token or API key. | ||
| #' @param teamid Team ID in CloudOS account. (Required) | ||
| #' @param team_id Team ID in CloudOS account. (Required) | ||
| #' @param page_number Number of page. (Optional) Default - 0 | ||
| #' @param page_size Number of entries in a page. (Optional) Default - 10 | ||
| #' | ||
| #' @return A data frame with available cohorts. | ||
| #' | ||
| #' @examples | ||
| #' \dontrun{ | ||
| #' list_cohorts(baseurl= "https://cloudos.lifebit.ai", | ||
| #' list_cohorts(base_url= "https://cloudos.lifebit.ai", | ||
| #' auth = "Bearer ***token***", | ||
| #' teamid = "***teamid***") | ||
| #' team_id = "***team_id***") | ||
| #' } | ||
| #' @export | ||
| list_cohorts <- function(baseurl, | ||
| list_cohorts <- function(base_url, | ||
| auth, | ||
| teamid, | ||
| team_id, | ||
| page_number = 0, | ||
| page_size = 10) { | ||
| url <- paste(baseurl, "api/v1/cohort", sep = "/") | ||
| url <- paste(base_url, "api/v1/cohort", sep = "/") | ||
| r <- httr::GET(url, | ||
| httr::add_headers("Authorization" = auth), | ||
| query = list("teamId" = teamid, | ||
| query = list("teamId" = team_id, | ||
| "pageNumber" = page_number, | ||
| "pageSize" = page_size)) | ||
| if (!r$status_code == 200) { | ||
| stop("No cohorts found. Or not able to connect with server.") | ||
| } | ||
| # parse the content | ||
| res <- httr::content(r) | ||
| if(length(res) == 0){ | ||
| message("No cohorts found. Or not able to connect with server.") | ||
| } else { | ||
| message("Total number of cohorts found - ", res$total) | ||
| cohorts <- res$cohort | ||
| # make in to a list | ||
| cohorts_list <- list() | ||
| for(n in 1:res$total){ | ||
| dta <- data.frame(id = cohorts[[n]]$`_id`, | ||
| name = cohorts[[n]]$`name`, | ||
| description = cohorts[[n]]$`description`, | ||
| number_of_participants = cohorts[[n]]$`numberOfParticipants`, | ||
| number_of_filters = cohorts[[n]]$`numberOfFilters`, | ||
| created_at = cohorts[[n]]$`createdAt`, | ||
| updated_at = cohorts[[n]]$`updatedAt`) | ||
| cohorts_list[[n]] <- dta | ||
| # filter | ||
| # cohorts[[1]]$`filters` | ||
| } | ||
| # make in to a dataframe | ||
| cohorts_df = do.call(rbind, cohorts_list) | ||
| return(cohorts_df) | ||
| message("Total number of cohorts found-", res$total, | ||
| ". But here is 10. For more, change 'page_number' and 'page_size'") | ||
| cohorts <- res$cohorts | ||
| # make in to a list | ||
| cohorts_list <- list() | ||
| for (n in 1:page_size) { | ||
| dta <- data.frame(id = cohorts[[n]]$`_id`, | ||
| name = cohorts[[n]]$`name`, | ||
| description = cohorts[[n]]$`description`, | ||
| number_of_participants = cohorts[[n]]$`numberOfParticipants`, | ||
| number_of_filters = cohorts[[n]]$`numberOfFilters`, | ||
| created_at = cohorts[[n]]$`createdAt`, | ||
| updated_at = cohorts[[n]]$`updatedAt`) | ||
| cohorts_list[[n]] <- dta | ||
| # filter | ||
| # cohorts[[1]]$`filters` | ||
| } | ||
| # make in to a dataframe | ||
| cohorts_df <- do.call(rbind, cohorts_list) | ||
| return(cohorts_df) | ||
| } |
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| --- | ||
| output: github_document | ||
| --- | ||
|
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| <!-- README.md is generated from README.Rmd. Please edit that file --> | ||
|
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| ```{r setup, include = FALSE} | ||
| knitr::opts_chunk$set( | ||
| collapse = TRUE, | ||
| comment = "#>", | ||
| fig.path = "man/figures/README-", | ||
| out.width = "100%" | ||
| ) | ||
| ``` | ||
|
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| # cloudos | ||
|
|
||
| <!-- badges: start --> | ||
| [](https://www.tidyverse.org/lifecycle/#experimental) | ||
| [](https://github.com/lifebit-ai/cloudos/actions) | ||
| <!-- badges: end --> | ||
|
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| The 'CloudOS' client library for R makes it easy to interact with CloudOS <https://cloudos.lifebit.ai/> in the R environment for analysis. | ||
|
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| ## Installation | ||
|
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| You can install the released version of cloudos from [GitHub](https://github.com/lifebit-ai/cloudos/) at this moment. (Will be listed on [CRAN](https://CRAN.R-project.org) as well) | ||
|
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| ```{r, eval=FALSE} | ||
| if (!require(remotes)) { install.packages("remotes") } | ||
| remotes::install_github("lifebit-ai/cloudos") | ||
| ``` | ||
|
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| ## Usage | ||
|
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| ### Load the cloudos R-client library | ||
|
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| ```{r} | ||
| library(cloudos) | ||
| ``` | ||
|
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| ### Setup essentials | ||
|
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| ```{r} | ||
| cb_base_url <- "http://cohort-browser-766010452.eu-west-1.elb.amazonaws.com" | ||
| my_auth <- "*************************" | ||
| my_team_id <- "***************************" | ||
| ``` | ||
|
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| ```{r secrets, echo=FALSE} | ||
| my_auth <- Sys.getenv("cloudos_Bearer_token") | ||
| my_team_id <- Sys.getenv("cloudos_team_id") | ||
| ``` | ||
|
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| ### Create a cohort | ||
|
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| ```{r} | ||
| cloudos::create_cohort(base_url = cb_base_url, | ||
| auth = my_auth, | ||
| team_id = my_team_id, | ||
| cohort_name = "Cohort-R", | ||
| cohort_desc = "This cohort is for testing purpose, created from R.") | ||
| ``` | ||
|
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| ### List Cohorts | ||
|
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| List available cohorts in a workspace. | ||
|
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| ```{r} | ||
| cohorts <- cloudos::list_cohorts(base_url = cb_base_url, | ||
| auth = my_auth, | ||
| team_id = my_team_id) | ||
| kableExtra::kable(cohorts) | ||
| ``` | ||
|
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| ### Extract participants | ||
|
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| Create a RAW data string. This usually generates after selecting participants on UI. (more information will be added how to create this in R) | ||
|
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| ```{r} | ||
| new_raw_data <- '{"columns":[{"id":34,"instance":0,"array":{"type":"exact","value":0}},{"id":31,"instance":0,"array":{"type":"exact","value":0}},{"id":52,"instance":0,"array":{"type":"exact","value":0}},{"id":5984,"instance":0,"array":{"type":"avg"}},{"id":5984,"instance":0,"array":{"type":"min"}},{"id":5984,"instance":0,"array":{"type":"max"}},{"id":20001,"instance":0,"array":{"type":"exact","value":0}}],"ids":["5f185b92bf92ed4d3be9637d","5edbdd689d700db709af0c2f","5f185b91bf92ed4d3be9587e","5f185b91bf92ed4d3be95984","5edbdd689d700db709af0c3e","5edbdd689d700db709af0c2b","5edbdd689d700db709af0c2d","5f185b93bf92ed4d3be982e9","5edbdd689d700db709af0c2a","5edbdd689d700db709af0c4d"],"type":"csv","base_url":"http://cohort-browser-766010452.eu-west-1.elb.amazonaws.com"}' | ||
| ``` | ||
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| Using this above raw data lets extract selected participants. | ||
|
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| ```{r} | ||
| df <- cloudos::extract_participants(base_url= cb_base_url, | ||
| auth = my_auth, | ||
| raw_data = new_raw_data) | ||
| kableExtra::kable(df) | ||
| ``` | ||
|
|
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