feat: implement cwl js expressions executor

Cargo.toml

@@ -6,7 +6,8 @@ edition = "2021"
 [workspace]
 members = [
     "zefiro-cli",
-    "zefiro-core",
-    "zefiro-core/zefiro-cwl-parser",
+    "zefiro-pipeline-engine",
+    "zefiro-pipeline-engine/zefiro-cwl-parser",
+    "zefiro-pipeline-engine/zefiro-cwl-js-exec",
     "zefiro-ui"
 ]

README.md

@@ -1,3 +1,5 @@
 **Code**: [![codecov](https://codecov.io/gh/zefiroproj/zefiro/graph/badge.svg?token=5DgmM1KzuQ)](https://codecov.io/gh/zefiroproj/zefiro)
 
-# Zefiro - fast, scalable and simple engine to manage workflows
+# Zefiro - fast, scalable and simple engine to manage workflows
+
+⚠️ This project is a Work In Progress, and is very far from being suitable for use ⚠️

release.sh

@@ -36,11 +36,11 @@ export GIT_CLIFF_TEMPLATE="\
 		- {% if commit.breaking %}(breaking) {% endif %}{{ commit.message | upper_first }} ({{ commit.id | truncate(length=7, end=\"\") }})\
 	{% endfor %}
 	{% endfor %}"
-if [ ! -f "examples/detailed.toml" ]; then
-	echo "Error: examples/detailed.toml not found"
+if [ ! -f "test_data/detailed.toml" ]; then
+	echo "Error: test_data/detailed.toml not found"
 	exit 1
 fi
-changelog=$(git cliff --config examples/detailed.toml --unreleased --strip all)
+changelog=$(git cliff --config test_data/detailed.toml --unreleased --strip all)
 
 # create a signed tag
 git -c user.name="zefiro" \

zefiro-core/Cargo.toml → zefiro-pipeline-engine/Cargo.toml

@@ -1,5 +1,5 @@
 [package]
-name = "zefiro-core"
+name = "zefiro-pipeline-engine"
 version = "0.1.0"
 edition = "2021"
 rust-version = "1.83.0"

zefiro-pipeline-engine/zefiro-cwl-js-exec/Cargo.toml

@@ -0,0 +1,25 @@
+[package]
+name = "zefiro-cwl-js-exec"
+version = "0.1.0"
+description = """
+"The Common Workflow Language (CWL) object model that used in `zefiro`.
+"""
+authors = [
+  "Nikita Syzrantsev <[email protected]>"
+]
+categories = ["JavaScript", "CWL"]
+keywords = ["JavaScript", "CWL Expressions"]
+edition = "2021"
+homepage = "https://github.com/zefiroproj/zefiro/zefiro-core/zefiro-cwl-js-exec"
+license = "Apache-2.0"
+readme = "README.md"
+repository = "https://github.com/zefiroproj/zefiro"
+rust-version = "1.83.0"
+
+[dependencies]
+anyhow = "1.0.95"
+deno_core = "0.329.0"
+serde_json = "1.0.135"
+
+[dev-dependencies]
+rstest = "0.24.0"

zefiro-pipeline-engine/zefiro-cwl-js-exec/src/exec.rs

@@ -0,0 +1,79 @@
+use anyhow::{Context, Error};
+use deno_core::{serde_json, serde_v8, v8, JsRuntime};
+use serde_json::Value;
+
+pub struct JsExecutor {
+    runtime: JsRuntime,
+}
+
+impl JsExecutor {
+    /// Creates a new `JsExecutor` with given `cwl_inputs` and `cwl_self`.
+    pub fn new(cwl_inputs: &Value, cwl_self: &Value) -> Result<Self, Error> {
+        let mut runtime = JsRuntime::new(Default::default());
+        let init_script = format!(
+            r#"const inputs = {}; const self = {};"#,
+            cwl_inputs, cwl_self
+        );
+
+        runtime
+            .execute_script("<init>", init_script)
+            .context("Failed to initialize JavaScript context")?;
+
+        Ok(Self { runtime })
+    }
+
+    /// Executes JavaScript `script` and returns the result as a string.
+    pub fn run(&mut self, script: &str) -> Result<String, Error> {
+        let result = self
+            .runtime
+            .execute_script("<eval>", script.to_string())
+            .context("Failed to execute JavaScript expression")?;
+
+        let scope = &mut self.runtime.handle_scope();
+        let local_result = v8::Local::new(scope, result);
+        let result_json: serde_json::Value =
+            serde_v8::from_v8(scope, local_result).context("Failed to deserialize result")?;
+
+        Ok(result_json.to_string())
+    }
+}
+
+#[cfg(test)]
+mod tests {
+    use super::*;
+    use rstest::rstest;
+    use serde_json::json;
+
+    #[rstest]
+    #[case(
+        json!({
+            "in_fastq": {
+                "class": "File",
+                "location": "/path/to/input.fastq",
+                "size": 1024 * 1024 * 512
+            }
+        }),
+        json!([{ "location": "/path/to/output.fastq" }]),
+        "inputs.in_fastq.size / (1024 * 1024) * 2;",
+        "1024"
+    )]
+    #[case(
+        json!({ "output_location_subdir": "output/" }),
+        json!([{ "location": "/path/to/output.fastq", "nameroot": "output" }]),
+        "self[0].location = inputs.output_location_subdir + self[0].nameroot + '.fq'; self[0];",
+        json!({ "location": "output/output.fq", "nameroot": "output" }).to_string()
+    )]
+    fn test_jsexecutor_run(
+        #[case] cwl_inputs: Value,
+        #[case] cwl_self: Value,
+        #[case] js_script: &str,
+        #[case] expected_result: String,
+    ) {
+        let mut executor = JsExecutor::new(&cwl_inputs, &cwl_self)
+            .expect("Failed to initialize JavaScript engine");
+        let result = executor
+            .run(js_script)
+            .expect("JavaScript execution failed");
+        assert_eq!(result, expected_result);
+    }
+}

zefiro-pipeline-engine/zefiro-cwl-js-exec/src/lib.rs

@@ -0,0 +1,3 @@
+pub mod exec;
+
+pub use crate::exec::JsExecutor;

zefiro-core/zefiro-cwl-parser/Cargo.toml → zefiro-pipeline-engine/zefiro-cwl-parser/Cargo.toml

@@ -7,10 +7,10 @@ description = """
 authors = [
   "Nikita Syzrantsev <[email protected]>"
 ]
-categories = ["CWL serialization", "CWL deserialization", "Common Workflow Language"]
+categories = ["Serialization", "Deserialization", "Parsing"]
 keywords = ["CWL", "CommandLineTool", "Workflow"]
 edition = "2021"
-homepage = "https://github.com/zefiroproj/zefiro"
+homepage = "https://github.com/zefiroproj/zefiro/zefiro-core/zefiro-cwl-parser"
 license = "Apache-2.0"
 readme = "README.md"
 repository = "https://github.com/zefiroproj/zefiro"
@@ -21,6 +21,7 @@ anyhow = "1.0.95"
 serde = { version = "1.0.216", features = ["derive"] }
 serde_with = "3.12.0"
 serde_yaml = "0.9.34"
+sha1 = "0.10.6"
 
 [dev-dependencies]
 rstest = "0.24.0"

zefiro-pipeline-engine/zefiro-cwl-parser/README.md

@@ -0,0 +1,88 @@
+# zefiro-cwl-parser
+
+A Rust library for parsing and working with Common Workflow Language (CWL) documents.
+
+## Overview
+
+* Supports **only some fields** of CWL **v1.2** specification (see description of structures in the code)
+* Can serialize and deserialize [CommandLineTool](https://www.commonwl.org/v1.2/CommandLineTool.html) and [Workflow](https://www.commonwl.org/v1.2/Workflow.html) documents
+
+## Usage
+
+Add this to your `Cargo.toml`:
+
+```toml
+[dependencies]
+zefiro-cwl-parser = "0.1.0"
+```
+
+
+### How to parse CWL Schema document?
+
+```rust
+use zefiro_cwl_parser::CwlSchema;
+
+fn main() -> Result<(), Box<dyn std::error::Error>> {
+  // Parse from file
+  let schema = CwlSchema::from_path("test_data/cwl/clt-step-schema.yml").unwrap();
+
+  // Parse from string
+  let yaml_str = r#"
+  cwlVersion: v1.2
+  class: CommandLineTool
+  id: step
+  inputs:
+      - id: in_file
+        type: File
+        inputBinding:
+          prefix: --in-file
+      - id: out_file
+        type: string
+        default: "output.txt"
+        inputBinding:
+          prefix: --out-file
+      - id: output_location_subdir
+        type: string
+        default: output/
+  outputs:
+      - id: out_file
+        type: File
+        outputBinding:
+          glob: $(inputs.out_file)
+          outputEval: ${self[0].location += inputs.output_location_subdir; return self[0]}
+  requirements:
+      - class: DockerRequirement
+        dockerPull: step-image-uri:1.0
+      - class: InlineJavascriptRequirement
+  "#;
+  let schema = CwlSchema::from_string(yaml_str).unwrap();
+
+  Ok(())
+}
+```
+
+
+### How to parse CWL Values document?
+
+```rust
+use zefiro_cwl_parser::CwlValues;
+
+
+fn main() -> Result<(), Box<dyn std::error::Error>> {
+  // Parse input values from file
+  let values = CwlValues::from_path("test_data/cwl/clt-step-values.yml").unwrap();
+
+  // Create values from string
+  let yaml_input = r#"
+  input_file:
+      class: File
+      location: 's3://bucket/input.txt'
+  output_file: 'output.txt'
+  "#;
+  let values = CwlValues::from_string(yaml_input).unwrap();
+
+  Ok(())
+}
+```
+
+### How to execute JavaScript expressions?

zefiro-core/zefiro-cwl-parser/src/lib.rs → zefiro-pipeline-engine/zefiro-cwl-parser/src/lib.rs

@@ -1,3 +1,4 @@
+#[doc = include_str!("../README.md")]
 pub mod schema;
 pub mod values;