expression in sec-files

Author: JensKrumsieck

CHANGELOG.md

@@ -9,7 +9,7 @@
 - fixed a bug with Dockerfile path resolution
 - handle NetworkAccess Requirment in runner
 - inherit parents requirements correclty
-- ramping up runner conformance from 160/378 to 197/378
+- ramping up runner conformance from 160/378 to 198/378
 
 # v0.5.2
 ## 🐛 Bugfixes

crates/cwl-execution/src/expression.rs

@@ -76,7 +76,10 @@ pub(crate) fn evaluate_expression(input: &str) -> Result<Value, Box<dyn Error>>
 }
 
 pub(crate) fn evaluate_condition(input: &str, inputs: &HashMap<String, DefaultValue>) -> Result<bool, Box<dyn Error>> {
-    prepare_expression_engine(&RuntimeEnvironment { inputs: inputs.clone(), ..Default::default() })?;
+    prepare_expression_engine(&RuntimeEnvironment {
+        inputs: inputs.clone(),
+        ..Default::default()
+    })?;
     let result = evaluate_expression(input)?.as_bool().unwrap_or(false);
     reset_expression_engine()?;
     Ok(result)
@@ -209,6 +212,20 @@ pub(crate) fn process_expressions(tool: &mut CWLDocument, input_values: &mut Inp
             }
         }
     }
+    for input in &mut tool.inputs {
+        let tmp = input.id.clone();
+        if input.secondary_files.is_empty() {
+            continue;
+        }
+        
+        if let DefaultValue::File(file) = &input_values.inputs[&tmp] {            
+            set_self(&file.snapshot())?;
+            for sec_file in &mut input.secondary_files {
+                sec_file.pattern = replace_expressions(&sec_file.pattern)?;
+            }
+            unset_self()?;
+        }
+    }
     if let CWLDocument::CommandLineTool(clt) = tool {
         clt.base_command = match std::mem::take(&mut clt.base_command) {
             Command::Single(cmd) => Command::Single(replace_expressions(&cmd)?),

crates/cwl-execution/src/staging.rs

@@ -245,8 +245,14 @@ fn stage_secondary_inputs(incoming_data: &DefaultValue, path: &Path, input: &Com
         };
         for item in &input.secondary_files {
             let mut matched = false;
-            let pattern = file_dir.join(format!("*{}", item.pattern));
-            for res in glob(&pattern.to_string_lossy())? {
+            let pattern = if item.pattern.starts_with(file_dir.to_string_lossy().as_ref()) {
+                &item.pattern
+            } else {
+                &file_dir.join(format!("*{}", item.pattern)).to_string_lossy().into_owned()
+            };
+            let pattern = pattern.trim();
+            
+            for res in glob(pattern)? {
                 let res = res?;
                 let dest = path.join(&res);
                 copy_file(&res, &dest).map_err(|e| format!("Failed to copy file from {:?} to {:?}: {}", res, dest, e))?;