Replace --no_overwrite with --exists in zarrs_{filter,ome}

Adds overwrite option to `zarrs_ome`.

CHANGELOG.md

@@ -7,6 +7,11 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased]
 
+### Changed
+ - Replace `--no_overwrite` with `--exists` in `zarrs_filter` and `zarrs_ome`
+   - Both support `erase` and `exit` options
+   - `zarrs_ome` also supports an `overwrite` option
+
 ## [0.4.0] - 2024-04-20
 
 ### Added

Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "zarrs_tools"
-version = "0.4.0"
+version = "0.4.1"
 authors = ["Lachlan Deakin <ljdgit@gmail.com>"]
 edition = "2021"
 rust-version = "1.75"

docs/zarrs_ome.md

@@ -66,8 +66,15 @@ Options:
       --discrete
           Do majority downsampling and do not apply gaussian smoothing
 
-      --no-overwrite
-          Exit instead of overwriting an existing array
+      --exists <EXISTS>
+          Behaviour if the output exists
+          
+          [default: overwrite]
+
+          Possible values:
+          - overwrite: Overwrite existing files. Useful if the output includes additional non-zarr files to be preserved
+          - erase:     Erase the output
+          - exit:      Exit if the output already exists
 
       --group-attributes <GROUP_ATTRIBUTES>
           Attributes (optional).

src/bin/zarrs_filter.rs

@@ -22,6 +22,14 @@ use zarrs_tools::{
     ZarrReencodingArgs,
 };
 
+#[derive(clap::ValueEnum, Debug, Clone)]
+enum OutputExists {
+    /// Erase the output
+    Erase,
+    /// Exit if the output already exists
+    Exit,
+}
+
 /// Apply simple image filters (transformations) to a Zarr V3 array.
 #[derive(Parser, Debug)]
 #[command(author, version)]
@@ -30,9 +38,10 @@ struct Cli {
     #[arg(long)]
     hide_progress: bool,
 
-    /// Exit instead of overwriting an existing array.
+    /// Behaviour if the output exists.
     #[arg(long)]
-    no_overwrite: bool,
+    #[clap(value_enum, default_value_t=OutputExists::Erase)]
+    exists: OutputExists,
 
     /// Directory for temporary arrays.
     ///
@@ -211,11 +220,15 @@ fn run() -> Result<(), Box<dyn Error>> {
         output_paths,
         exists,
     } = get_input_output_paths(&filter_commands, tmp_dir.path())?;
-    // println!("{output_paths:?}");
-    if cli.no_overwrite && exists.iter().any(|i| *i) {
-        Err(FilterError::Other(
-            "Run without --no-overwrite to overwrite".to_string(),
-        ))?;
+
+    // Handle an existing output
+    match cli.exists {
+        OutputExists::Exit => {
+            if exists.iter().any(|i| *i) {
+                Err(FilterError::Other("Output exists, exiting".to_string()))?;
+            }
+        }
+        OutputExists::Erase => {}
     }
 
     // Instantiate the filters

src/bin/zarrs_ome.rs

@@ -28,6 +28,16 @@ use zarrs_tools::{
     ZarrReEncodingChangeType, ZarrReencodingArgs,
 };
 
+#[derive(clap::ValueEnum, Debug, Clone)]
+enum OutputExists {
+    /// Overwrite existing files. Useful if the output includes additional non-zarr files to be preserved.
+    Overwrite,
+    /// Erase the output
+    Erase,
+    /// Exit if the output already exists
+    Exit,
+}
+
 /// Convert a Zarr V3 array to OME-Zarr (0.5-dev).
 #[derive(Parser, Debug)]
 #[command(author, version)]
@@ -67,9 +77,10 @@ struct Cli {
     #[arg(long)]
     discrete: bool,
 
-    /// Exit instead of overwriting an existing array.
+    /// Behaviour if the output exists.
     #[arg(long)]
-    no_overwrite: bool,
+    #[clap(value_enum, default_value_t=OutputExists::Overwrite)]
+    exists: OutputExists,
 
     /// Attributes (optional).
     ///
@@ -251,13 +262,18 @@ fn run() -> Result<(), Box<dyn Error>> {
         group.attributes_mut().append(&mut group_attributes);
     }
 
-    // Check for overwrite
-    if cli.no_overwrite && cli.output.exists() {
-        Err(FilterError::Other(
-            "Run without --no-overwrite to overwrite".to_string(),
-        ))?;
+    // Handle an existing output
+    match cli.exists {
+        OutputExists::Exit => {
+            if cli.output.exists() {
+                Err(FilterError::Other("Output exists, exiting".to_string()))?;
+            }
+        }
+        OutputExists::Erase => {
+            store.erase_prefix(&StorePrefix::root()).unwrap();
+        }
+        OutputExists::Overwrite => {}
     }
-    store.erase_prefix(&StorePrefix::root()).unwrap();
 
     {
         let output_0_path = cli.output.join("0");