diff --git a/DESCRIPTION b/DESCRIPTION
index 30c07d57e2b50a57f594da9df52ee9422f21c526..35342786cd6f9294fcc61d3747df5b5cf08fe9ea 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,11 +1,16 @@
Package: rlabkeyCLI
Type: Package
-Title: What the Package Does (Title Case)
-Version: 0.1.0
-Author: Who wrote it
-Maintainer: The package maintainer <yourself@somewhere.net>
-Description: More about what it does (maybe more than one line)
- Use four spaces when indenting paragraphs within the Description.
-License: What license is it under?
+Title: rlabkey CLI R package
+Version: 1.0.0
+Author: El Karchi Jad
+Maintainer: jad.el-karchi@u-bordeaux.fr
+Description: RLabKey CLI is a command-line interface designed for data managers to easily interact with the LabKey platform.
+ It allows fetching, pushing, and managing datasets and files using the Rlabkey package.
+License: NONE
+Imports:
+ Rlabkey (>= 3.2.2),
+ readxl (>= 1.4.3),
+ devtools (>= 2.4.5),
Encoding: UTF-8
LazyData: true
+RoxygenNote: 7.3.1
diff --git a/NAMESPACE b/NAMESPACE
index d75f824ec6278db24891505b14ab3d915514dba7..9842004e591aa78b1bb4b53391481b79e4e06d02 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -1 +1,5 @@
-exportPattern("^[[:alpha:]]+")
+# Generated by roxygen2: do not edit by hand
+
+export(fetch)
+export(push)
+export(status)
diff --git a/R/fetch.R b/R/fetch.R
index 65e5e80deea944775fa96ea03f0f37faa493ca3e..8d975b4cff7184109595c42ce4b51272d1aa24dc 100644
--- a/R/fetch.R
+++ b/R/fetch.R
@@ -1,6 +1,3 @@
-# Load necessary library
-library("Rlabkey")
-
# Base URLs
BASE_URL <- labkey.getBaseUrl()
@@ -14,7 +11,11 @@ check_path_exists <- function(folder_path, remote_file_path) {
# Download an entire project
download_project <- function(folder_path) {
+
local_base_dir <- file.path(Sys.getenv("HOME"), ".rlabkey")
+ if (!dir.exists(local_base_dir)) {
+ dir.create(local_base_dir, recursive = TRUE)
+ }
message("Downloading folder to ", local_base_dir)
labkey.webdav.downloadFolder(
baseUrl = BASE_URL,
@@ -23,19 +24,18 @@ download_project <- function(folder_path) {
remoteFilePath = ".",
overwriteFiles = TRUE,
mergeFolders = TRUE,
- fileSet = "@files",
- showProgressBar = TRUE
+ fileSet = "@files"
)
}
# Download a specific file
-download_file <- function(folder_path, file_name) {
- local_file_path <- file.path(Sys.getenv("HOME"), ".rlabkey", "_webdav", folder_path, file_name)
+download_file <- function(folder_path, remote_file_path) {
+ local_file_path <- file.path(Sys.getenv("HOME"), "_webdav", folder_path, remote_file_path)
message("Downloading file to ", local_file_path)
labkey.webdav.get(
baseUrl = BASE_URL,
folderPath = folder_path,
- remoteFilePath = file_name,
+ remoteFilePath = remote_file_path,
localFilePath = local_file_path,
overwrite = TRUE,
fileSet = "@files",
@@ -44,46 +44,43 @@ download_file <- function(folder_path, file_name) {
}
# fetch function
-fetch_data <- function(project_name, file_name = NULL) {
+fetch_data <- function(project_name, remote_file_path) {
folder_path <- paste0("/", project_name)
-
- if (is.null(file_name)) {
+
+ if (is.null(remote_file_path)) {
path_info <- check_path_exists(folder_path, ".")
} else {
- path_info <- check_path_exists(folder_path, file_name)
+ path_info <- check_path_exists(folder_path, remote_file_path)
}
-
+
if (!path_info$exists) {
stop("The specified path does not exist on any configured server.")
}
-
-
- if (is.null(file_name)) {
+
+
+ if (is.null(remote_file_path)) {
message("Fetching directory from: ", path_info$url, " ", path_info$project)
download_project(project_name)
} else {
message("Fetching file from: ", path_info$url, path_info$project, path_info$filename)
- download_file(folder_path, file_name)
+ download_file(folder_path, remote_file_path)
}
}
-# main function
-main <- function () {
- args <- commandArgs(trailingOnly = TRUE)
- if (length(args) < 1) {
- stop("Usage: Rscript fetch.R <project_name> [<file_name>]")
- }
-
- project_name <- args[1]
- file_name <- if (length(args) >= 2) args[2] else NULL
-
- project_name
- file_name
-
-
- fetch_data(project_name, file_name)
+#' Load a Matrix
+#'
+#' This function loads a file as a matrix. It assumes that the first column
+#' contains the rownames and the subsequent columns are the sample identifiers.
+#' Any rows with duplicated row names will be dropped with the first one being
+#' kepted.
+#'
+#' @param infile Path to the input file
+#' @return A matrix of the infile
+#' @export
+fetch <- function(projectName, remoteFilePath=NULL) {
+ project_name <- projectName
+ remote_file_path <- remoteFilePath
+
+ fetch_data(project_name, remote_file_path)
message("Data fetched successfully.")
}
-
-
-main()
\ No newline at end of file
diff --git a/R/push.R b/R/push.R
index a4bddbf11cef1a3bf4ff81167c509584cbcf6c25..c996b84529bd8bc86a3b1a0e49a20710a0817bcc 100644
--- a/R/push.R
+++ b/R/push.R
@@ -1,5 +1,4 @@
-# Load necessary library
-library("Rlabkey")
+library(readxl)
# Base URLs
BASE_URL <- labkey.getBaseUrl()
@@ -35,7 +34,7 @@ create_and_upload_dataset <- function(df, folder_path, schema_name, query_name)
description = ""
)
message("Domain created.")
-
+
message("Uploading data ...")
labkey.importRows(
baseUrl = BASE_URL,
@@ -44,19 +43,30 @@ create_and_upload_dataset <- function(df, folder_path, schema_name, query_name)
queryName = query_name,
toImport = df
)
-
+
message(paste("Data uploaded to", folder_path, ", schema:", schema_name, ", query:", query_name))
}
upload_data <- function(project_name, file_path, target_name, is_assay, is_dataset) {
# Load the data
- df <- read.csv(file_path, header = TRUE, sep = ",")
-
+ file_ext <- tools::file_ext(file_path)
+
+ # Read the file based on the extension
+ if (file_ext == "csv") {
+ df <- read.csv(file_path, header = TRUE, sep = ",")
+ } else if (file_ext == "tsv") {
+ df <- read.csv(file_path, header = TRUE, sep = "\t")
+ } else if (file_ext == "xlsx" || file_ext == "xls") {
+ df <- read_excel(file_path)
+ } else {
+ stop("Unsupported file type.")
+ }
+
# Initialize variables
folder_path <- project_name
schema_name <- ""
query_name <- NULL
-
+
# Define schema and queries based on the type
if (is_assay) {
upload_assay_data(df, folder_path, target_name)
@@ -67,19 +77,25 @@ upload_data <- function(project_name, file_path, target_name, is_assay, is_datas
}
}
-# main function
-main <- function () {
- args <- commandArgs(trailingOnly = TRUE)
- if (length(args) < 1) {
- stop("Usage: Rscript push.R <project_name> <file_path> <target_name> <is_assay> <is_dataset>")
- }
-
- project_name <- args[1]
- file_path <- if (length(args) >= 2) args[2] else NULL
- target_name <- if (length(args) >= 3) args[3] else NULL
- is_assay <- if (length(args) >= 4) as.logical(tolower(args[4])) else FALSE
- is_dataset <- if (length(args) >= 5) as.logical(tolower(args[5])) else FALSE
-
+#' Load a Matrix
+#'
+#' This function loads a file as a matrix. It assumes that the first column
+#' contains the rownames and the subsequent columns are the sample identifiers.
+#' Any rows with duplicated row names will be dropped with the first one being
+#' kepted.
+#'
+#' @param infile Path to the input file
+#' @return A matrix of the infile
+#' @export
+push <- function (projectName, filePath, targetName, dirPath=NULL, isAssay=FALSE, isDataset=FALSE) {
+
+ project_name <- projectName
+ file_path <- filePath
+ dir_path <- dirPath
+ target_name <- targetName
+ is_assay <- isAssay
+ is_dataset <- isDataset
+
if (!is.null(file_path) && !is.null(project_name) && !is.null(target_name) && xor(is_assay, is_dataset)) {
upload_data(project_name, file_path, target_name, is_assay, is_dataset)
message("Data uploaded successfully.")
@@ -93,5 +109,3 @@ main <- function () {
"\nis_dataset =", is_dataset))
}
}
-
-main()
\ No newline at end of file
diff --git a/R/status.R b/R/status.R
index 71be8e67d1f0c80987459a1253760687ae655d17..a3da47f0c9bff11591752ad60e436eb0b2857f99 100644
--- a/R/status.R
+++ b/R/status.R
@@ -1,12 +1,20 @@
-main <- function() {
+#' Load a Matrix
+#'
+#' This function loads a file as a matrix. It assumes that the first column
+#' contains the rownames and the subsequent columns are the sample identifiers.
+#' Any rows with duplicated row names will be dropped with the first one being
+#' kepted.
+#'
+#' @param infile Path to the input file
+#' @return A matrix of the infile
+#' @export
+status <- function() {
current_user_info <- labkey.whoAmI(baseUrl=NULL)
message(
paste("LabKey session status :"),
- paste("Name:", current_user_info$displayName),
- paste("Connected:", current_user_info$success),
- paste("ID:", current_user_info$id),
- paste("Email:", current_user_info$email)
+ paste("\n Name:", current_user_info$displayName),
+ paste("\n Connected:", current_user_info$success),
+ paste("\n ID:", current_user_info$id),
+ paste("\n Email:", current_user_info$email)
)
}
-
-main()
\ No newline at end of file
diff --git a/man/fetch.Rd b/man/fetch.Rd
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..d1d73e3ae2c243bdae9da0fb81a62ed9bbb518a4 100644
--- a/man/fetch.Rd
+++ b/man/fetch.Rd
@@ -0,0 +1,20 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/fetch.R
+\name{fetch}
+\alias{fetch}
+\title{Load a Matrix}
+\usage{
+fetch(projectName, remoteFilePath)
+}
+\arguments{
+\item{infile}{Path to the input file}
+}
+\value{
+A matrix of the infile
+}
+\description{
+This function loads a file as a matrix. It assumes that the first column
+contains the rownames and the subsequent columns are the sample identifiers.
+Any rows with duplicated row names will be dropped with the first one being
+kepted.
+}
diff --git a/man/push.Rd b/man/push.Rd
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..d4d3b4263f621774ff03a0bc9603a8d76c47ad9b 100644
--- a/man/push.Rd
+++ b/man/push.Rd
@@ -0,0 +1,27 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/push.R
+\name{push}
+\alias{push}
+\title{Load a Matrix}
+\usage{
+push(
+ projectName,
+ filePath,
+ targetName,
+ dirPath = NULL,
+ isAssay = FALSE,
+ isDataset = FALSE
+)
+}
+\arguments{
+\item{infile}{Path to the input file}
+}
+\value{
+A matrix of the infile
+}
+\description{
+This function loads a file as a matrix. It assumes that the first column
+contains the rownames and the subsequent columns are the sample identifiers.
+Any rows with duplicated row names will be dropped with the first one being
+kepted.
+}
diff --git a/man/status.Rd b/man/status.Rd
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..9576fec3383c92df9e2b3561919d980f14d982e3 100644
--- a/man/status.Rd
+++ b/man/status.Rd
@@ -0,0 +1,20 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/status.R
+\name{status}
+\alias{status}
+\title{Load a Matrix}
+\usage{
+status()
+}
+\arguments{
+\item{infile}{Path to the input file}
+}
+\value{
+A matrix of the infile
+}
+\description{
+This function loads a file as a matrix. It assumes that the first column
+contains the rownames and the subsequent columns are the sample identifiers.
+Any rows with duplicated row names will be dropped with the first one being
+kepted.
+}
diff --git a/renv.lock b/renv.lock
index d2b4a9cd0680ee2ccb4816f071ea1b80c1753226..db82af320ec09bc2febf14ac9974891d67795502 100644
--- a/renv.lock
+++ b/renv.lock
@@ -9,6 +9,104 @@
]
},
"Packages": {
+ "R6": {
+ "Package": "R6",
+ "Version": "2.5.1",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R"
+ ],
+ "Hash": "470851b6d5d0ac559e9d01bb352b4021"
+ },
+ "Rcpp": {
+ "Package": "Rcpp",
+ "Version": "1.0.12",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "methods",
+ "utils"
+ ],
+ "Hash": "5ea2700d21e038ace58269ecdbeb9ec0"
+ },
+ "Rlabkey": {
+ "Package": "Rlabkey",
+ "Version": "3.2.2",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "Rcpp",
+ "httr",
+ "jsonlite"
+ ],
+ "Hash": "4f57fb2006190d94ab53074a9fb7b5d4"
+ },
+ "askpass": {
+ "Package": "askpass",
+ "Version": "1.2.0",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "sys"
+ ],
+ "Hash": "cad6cf7f1d5f6e906700b9d3e718c796"
+ },
+ "curl": {
+ "Package": "curl",
+ "Version": "5.2.1",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R"
+ ],
+ "Hash": "411ca2c03b1ce5f548345d2fc2685f7a"
+ },
+ "httr": {
+ "Package": "httr",
+ "Version": "1.4.7",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "R6",
+ "curl",
+ "jsonlite",
+ "mime",
+ "openssl"
+ ],
+ "Hash": "ac107251d9d9fd72f0ca8049988f1d7f"
+ },
+ "jsonlite": {
+ "Package": "jsonlite",
+ "Version": "1.8.8",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "methods"
+ ],
+ "Hash": "e1b9c55281c5adc4dd113652d9e26768"
+ },
+ "mime": {
+ "Package": "mime",
+ "Version": "0.12",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "tools"
+ ],
+ "Hash": "18e9c28c1d3ca1560ce30658b22ce104"
+ },
+ "openssl": {
+ "Package": "openssl",
+ "Version": "2.2.0",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "askpass"
+ ],
+ "Hash": "2bcca3848e4734eb3b16103bc9aa4b8e"
+ },
"renv": {
"Package": "renv",
"Version": "1.0.7",
@@ -18,6 +116,13 @@
"utils"
],
"Hash": "397b7b2a265bc5a7a06852524dabae20"
+ },
+ "sys": {
+ "Package": "sys",
+ "Version": "3.4.2",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Hash": "3a1be13d68d47a8cd0bfd74739ca1555"
}
}
}
diff --git a/setup.R b/setup.R
new file mode 100644
index 0000000000000000000000000000000000000000..8205218ba5f0cc7ba2a7f9700e97fa0d12cdd4d7
--- /dev/null
+++ b/setup.R
@@ -0,0 +1,5 @@
+devtools::document()
+
+devtools::load_all()
+
+devtools::install()