Update storage handling

Author: kzollove

R/setup.R

@@ -0,0 +1,26 @@
+setup_offline_storage <- function(dir = "/opt/data", persist_data = FALSE) {
+    # Copy the storage.yml from inst/config to the working directory
+    if (!file.exists("storage.yml")) {
+        file.copy("inst/config/storage.yml", "storage.yml", overwrite = TRUE)
+    }
+    # Edit the storage.yml file to set the directory and change 
+    storage_config <- readLines("storage.yml")
+    storage_config <- gsub("directory: .*", paste0("directory: ", dir), storage_config)
+    writeLines(storage_config, "storage.yml")
+    message("storage.yml created with directory: ", dir, ". Local files can now be read from this directory.")
+    # If persist_data is TRUE, set up the offline storage directory
+    if (persist_data) {
+        storage_config <- readLines("storage.yml")
+        storage_config <- gsub("persist_data: .*", "persist_data: true", storage_config)
+        writeLines(storage_config, "storage.yml")
+        # make sure the directory exists
+        if (!dir.exists(dir)) {
+            dir.create(dir, recursive = TRUE)
+            message("Directory created: ", dir)
+        }
+        message("storage.yml created with persist_data: true. Downloaded files will now be written to this directory and persist indefinitely.")
+    } else {    
+        message("storage.yml created with persist_data: false. Downloaded files will not persist after the session ends.")
+    }
+    message("Offline storage setup complete.")
+}

R/stageData.R

@@ -135,7 +135,7 @@ getStaged <- function(rec, storageConfig = readStorageConfig()) {
 #' 
 
 readStorageConfig <- function() {
-  yaml::read_yaml(system.file('config/storage.yml', package = 'gaiaCore'))
+  yaml::read_yaml('./storage.yml')
 }
 
 

README.md

@@ -27,3 +27,18 @@ connectionDetails <- DatabaseConnector::createConnectionDetails(
 
 # Support
 -   Please use the <a href="https://github.com/OHDSI/gaiaCore/issues?q=sort%3Aupdated-desc+is%3Aissue+is%3Aopen">GitHub issue tracker</a> for all bugs, issues, and feature requests
+
+# Details
+## Offline Storage
+
+Offline storage can be set up for the purpose of loading local datasets in gaiaDB and persisting downloaded source datasets.
+
+Offline storage is configured using a file `storage.yml` to specify a directory and whether or not to persist downloaded datasets.
+
+You can create this file using the helper function `setup_offline_storage()`:
+
+```R
+setup_offline_storage(dir = "/path/to/data", persist_data = TRUE)
+```
+
+The above command will create a file named `storage.yml` in your working directory. It will also create a directory `path/to/data` if one does not already exist. Any datasets downloaded using `loadGeometry()` or `loadVariable()` will be saved to this directory!

inst/config/storage.yml

@@ -0,0 +1,3 @@
+offline_storage:
+  directory: /opt/data
+  persist_data: false