Add new tests and reformat code

zefiro-core/zefiro-cwl-parser/src/schema/command_line_tool.rs

@@ -1,26 +1,42 @@
-use crate::schema::requirements::CommandLineToolRequirement;
+use crate::schema::requirements::{CommandLineToolRequirement, SUPPORTED_CWL_VERSIONS};
 use crate::schema::types::{Any, CwlSchemaType, Documentation};
 use serde::{Deserialize, Serialize};
 use serde_with::skip_serializing_none;
 
 /// This defines the schema of the CWL Command Line Tool Description document.
 /// See: https://www.commonwl.org/v1.2/CommandLineTool.html
 #[skip_serializing_none]
-#[derive(Clone, Debug, Deserialize, Serialize)]
+#[derive(Clone, Debug, Deserialize, Serialize, Default)]
 #[serde(rename_all = "camelCase")]
 pub struct CommandLineTool {
+    #[serde(default = "CommandLineTool::default_cwl_version")]
     pub cwl_version: String,
+    #[serde(default = "CommandLineTool::default_class")]
     pub class: String,
     #[serde(skip_serializing_if = "Option::is_none")]
     pub doc: Option<Documentation>,
+    #[serde(default)]
     pub id: String,
     #[serde(skip_serializing_if = "Option::is_none")]
     pub label: Option<String>,
+    #[serde(default)]
     pub inputs: Vec<CommandInputParameter>,
+    #[serde(default)]
     pub outputs: Vec<CommandOutputParameter>,
+    #[serde(default)]
     pub requirements: Vec<CommandLineToolRequirement>,
 }
 
+impl CommandLineTool {
+    fn default_cwl_version() -> String {
+        SUPPORTED_CWL_VERSIONS[0].to_string()
+    }
+
+    fn default_class() -> String {
+        "CommandLineTool".to_string()
+    }
+}
+
 /// Represents an input parameter for a `CommandLineTool`.
 /// See: https://www.commonwl.org/v1.2/CommandLineTool.html#CommandInputParameter
 #[skip_serializing_none]

zefiro-core/zefiro-cwl-parser/src/schema/document.rs

@@ -1,4 +1,6 @@
-use crate::schema::{command_line_tool::CommandLineTool, workflow::Workflow};
+use crate::schema::{
+    command_line_tool::CommandLineTool, requirements::SUPPORTED_CWL_VERSIONS, workflow::Workflow,
+};
 use anyhow::{bail, ensure, Error, Result};
 use serde::{Deserialize, Serialize};
 use serde_yaml::{self, Value};
@@ -8,8 +10,6 @@ use std::{
     str::FromStr,
 };
 
-const SUPPORTED_VERSIONS: &[&str] = &["v1.2"];
-
 /// Represents a CWL Schema which can be either a CommandLineTool or a Workflow
 #[derive(Clone, Debug, Deserialize, Serialize)]
 #[serde(untagged)]
@@ -40,7 +40,7 @@ impl CwlSchema {
             .and_then(Value::as_str)
             .ok_or_else(|| anyhow::anyhow!("Failed to determine CWL specification version."))?;
         ensure!(
-            SUPPORTED_VERSIONS.contains(&version),
+            SUPPORTED_CWL_VERSIONS.contains(&version),
             "Unsupported CWL version: {version}"
         );
 
@@ -158,4 +158,40 @@ mod tests {
             serde_yaml::to_value(&written_values).unwrap()
         );
     }
+
+    #[test]
+    fn test_clt_to_yaml_write_error() {
+        use std::io::{Error, ErrorKind, Write};
+
+        struct FailingWriter;
+        impl Write for FailingWriter {
+            fn write(&mut self, _: &[u8]) -> std::io::Result<usize> {
+                Err(Error::new(ErrorKind::Other, "Simulated write error"))
+            }
+            fn flush(&mut self) -> std::io::Result<()> {
+                Ok(())
+            }
+        }
+
+        let schema = CwlSchema::CommandLineTool(CommandLineTool::default());
+        assert!(schema.to_yaml(FailingWriter).is_err());
+    }
+
+    #[test]
+    fn test_wf_to_yaml_write_error() {
+        use std::io::{Error, ErrorKind, Write};
+
+        struct FailingWriter;
+        impl Write for FailingWriter {
+            fn write(&mut self, _: &[u8]) -> std::io::Result<usize> {
+                Err(Error::new(ErrorKind::Other, "Simulated write error"))
+            }
+            fn flush(&mut self) -> std::io::Result<()> {
+                Ok(())
+            }
+        }
+
+        let schema = CwlSchema::Workflow(Workflow::default());
+        assert!(schema.to_yaml(FailingWriter).is_err());
+    }
 }

zefiro-core/zefiro-cwl-parser/src/schema/requirements.rs

@@ -1,6 +1,8 @@
 use serde::{Deserialize, Serialize};
 use serde_with::skip_serializing_none;
 
+pub const SUPPORTED_CWL_VERSIONS: [&str; 1] = ["v1.2"];
+
 const CPU_NUM_DEFAULT: u32 = 1;
 const RAM_SIZE_IN_MB_DEFAULT: u32 = 1024;
 const TMPDIR_MIN_IN_MB_DEFAULT: u32 = 1024;

zefiro-core/zefiro-cwl-parser/src/schema/workflow.rs

@@ -1,18 +1,21 @@
 use crate::schema::command_line_tool::CommandLineTool;
-use crate::schema::requirements::WorkflowRequirement;
+use crate::schema::requirements::{WorkflowRequirement, SUPPORTED_CWL_VERSIONS};
 use crate::schema::types::{Any, CwlSchemaType, Documentation, Scatter, Source};
 use serde::{Deserialize, Serialize};
 use serde_with::skip_serializing_none;
 
 /// This defines the schema of the CWL Workflow Description document.
 /// See: https://www.commonwl.org/v1.2/Workflow.html
 #[skip_serializing_none]
-#[derive(Clone, Debug, Deserialize, Serialize)]
+#[derive(Clone, Debug, Deserialize, Serialize, Default)]
 #[serde(rename_all = "camelCase")]
 pub struct Workflow {
-    pub class: String,
+    #[serde(default = "Workflow::default_cwl_version")]
     pub cwl_version: String,
+    #[serde(default = "Workflow::default_class")]
+    pub class: String,
     pub doc: Option<Documentation>,
+    #[serde(default)]
     pub id: String,
     pub label: Option<String>,
     pub inputs: Vec<WorkflowInputParameter>,
@@ -21,6 +24,16 @@ pub struct Workflow {
     pub requirements: Vec<WorkflowRequirement>,
 }
 
+impl Workflow {
+    fn default_cwl_version() -> String {
+        SUPPORTED_CWL_VERSIONS[0].to_string()
+    }
+
+    fn default_class() -> String {
+        "Workflow".to_string()
+    }
+}
+
 /// Represents an input parameter for a `Workflow`.
 /// See: https://www.commonwl.org/v1.2/Workflow.html#WorkflowInputParameter
 #[skip_serializing_none]