Merge pull request #96 from stemangiola/fix-74

Create `update_database()` for updating metadata

Author: multimeric

DESCRIPTION

@@ -106,7 +106,10 @@ Suggests:
     knitr,
     testthat,
     tidySingleCellExperiment,
-    ggplot2
+    ggplot2,
+    basilisk,
+    arrow,
+    reticulate
 Biarch: true
 biocViews: 
     AssayDomain,

R/dev.R

@@ -0,0 +1,69 @@
+# Utility scripts for development purposes, that are not exported to users
+
+#' Update the metadata database in nectar using a newly created data frame
+#' @param metadata The data frame to upload
+#' @param version The version for the new metadata as a character scalar, e.g.
+#'   "0.2.3"
+#' @param credential_id The OpenStack application credential ID as a character
+#'   scalar. This is optional because you can alternatively source a
+#'   `-openrc.sh` file instead of providing it here.
+#' @param credential_id The OpenStack application credential secret as a
+#'   character scalar
+#' @noRd
+#' @example 
+#' \dontrun{
+#'  metadata = CuratedAtlasQueryR::get_metadata() |> head(10) |> dplyr::collect()
+#'  update_database(metadata, "0.2.3", "rfypdlunhrfopdnkrs", "3q5lw3qntafptdfsrdh-wa4p8h")
+#'  # Prints "metadata.0.2.3.parquet" if successful
+#' }
+update_database = function(metadata, version, credential_id = NULL, credential_secret = NULL){
+    # These are optional dev packages
+    rlang::check_installed(c("arrow", "glue", "basilisk"))
+    
+    # Create parquet
+    dir <- tempdir()
+    parquet_name <- glue::glue("metadata.{version}.parquet")
+    parquet_path <- file.path(dir, parquet_name)
+    arrow::write_parquet(metadata, sink=parquet_path)
+    
+    # Create the basilisk environment
+    swift_env <- basilisk::BasiliskEnvironment(
+        envname="swift-nectar-upload",
+        pkgname=packageName(),
+        packages=c("python-swiftclient==4.2.0", "python-keystoneclient==5.1.0", "python==3.10.9")
+    )
+    proc <- basilisk::basiliskStart(swift_env)
+    
+    # Build the CLI args
+    if (!is.null(credential_id) && !is.null(credential_secret)){
+        auth <- c(
+            "--os-auth-type",
+            "v3applicationcredential",
+            "--os-application-credential-id",
+            credential_id,
+            "--os-application-credential-secret",
+            credential_secret
+        )
+    }
+    else {
+        auth <- character()
+    }
+    args = c(
+        "-m", 
+        "swiftclient.shell",
+        "--os-auth-url",
+        "https://keystone.rc.nectar.org.au:5000/v3/",
+        "--os-project-id",
+        "06d6e008e3e642da99d806ba3ea629c5",
+        auth,
+        "upload",
+        "metadata",
+        parquet_path,
+        "--object-name",
+        parquet_name
+    )
+    
+    # Perform the upload
+    system2(reticulate::py_exe(), args=args)
+    basilisk::basiliskStop(proc)
+}