stage correctly if Dirent.entry_name is None

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 199/378
+- ramping up runner conformance from 160/378 to 202/378
 
 # v0.5.2
 ## 🐛 Bugfixes

crates/cwl-execution/src/expression.rs

@@ -197,7 +197,9 @@ pub(crate) fn process_expressions(tool: &mut CWLDocument, input_values: &mut Inp
         if let Requirement::InitialWorkDirRequirement(wd_req) = requirement {
             for listing in &mut wd_req.listing {
                 if let WorkDirItem::Dirent(dirent) = listing {
-                    dirent.entryname = replace_expressions(&dirent.entryname)?;
+                    if let Some(entryname) = &mut dirent.entryname {
+                        *entryname = replace_expressions(entryname)?;
+                    }
                     dirent.entry = match &mut dirent.entry {
                         Entry::Source(src) => {
                             *src = replace_expressions(src)?;

crates/cwl-execution/src/staging.rs

@@ -55,7 +55,17 @@ fn stage_requirements(requirements: &[Requirement], tool_path: &Path, path: &Pat
         if let Requirement::InitialWorkDirRequirement(iwdr) = requirement {
             for listing in &iwdr.listing {
                 let into_path = match listing {
-                    WorkDirItem::Dirent(dirent) => path.join(&dirent.entryname),
+                    WorkDirItem::Dirent(dirent) => {
+                        if let Some(entryname) = &dirent.entryname {
+                            path.join(entryname)
+                        } else {
+                            let eval = match &dirent.entry {
+                                Entry::Source(src) => Path::new(src),
+                                Entry::Include(include) => &get_iwdr_src(tool_path, &include.include)?,
+                            };
+                            path.join(eval.file_name().unwrap())
+                        }
+                    }
                     WorkDirItem::FileOrDirectory(val) => match &**val {
                         DefaultValue::File(file) => {
                             let location = Path::new(file.location.as_ref().unwrap());
@@ -75,7 +85,12 @@ fn stage_requirements(requirements: &[Requirement], tool_path: &Path, path: &Pat
                     WorkDirItem::Dirent(dirent) => match &dirent.entry {
                         Entry::Source(src) => {
                             if fs::exists(src).unwrap_or(false) {
-                                copy_file(src, &into_path).map_err(|e| format!("Failed to copy file from {} to {}: {}", src, path_str, e))?;
+                                let src = Path::new(src); //is safer ;)
+                                if src.is_file() {
+                                    copy_file(src, &into_path).map_err(|e| format!("Failed to copy file from {:?} to {}: {}", src, path_str, e))?;
+                                } else {
+                                    copy_dir(src, &into_path).map_err(|e| format!("Failed to copy dir from {:?} to {}: {}", src, path_str, e))?;
+                                }
                             } else {
                                 create_and_write_file(&into_path, src).map_err(|e| format!("Failed to create file {:?}: {}", into_path, e))?;
                             }
@@ -251,7 +266,7 @@ fn stage_secondary_inputs(incoming_data: &DefaultValue, path: &Path, input: &Com
                 &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);

crates/cwl-execution/src/validate.rs

@@ -111,7 +111,9 @@ pub(crate) fn set_placeholder_values_requirements(
         if let Requirement::InitialWorkDirRequirement(wd_req) = requirement {
             for listing in &mut wd_req.listing {
                 if let WorkDirItem::Dirent(dirent) = listing {
-                    dirent.entryname = set_placeholder_values_in_string(&dirent.entryname, runtime, inputs);
+                    if let Some(entryname) = &mut dirent.entryname {
+                        *entryname = set_placeholder_values_in_string(entryname, runtime, inputs);
+                    }
                     dirent.entry = match &mut dirent.entry {
                         Entry::Source(src) => {
                             *src = set_placeholder_values_in_string(src, runtime, inputs);

crates/cwl/src/requirements.rs

@@ -147,8 +147,9 @@ impl InitialWorkDirRequirement {
     pub fn from_file(filename: &str) -> Self {
         InitialWorkDirRequirement {
             listing: vec![WorkDirItem::Dirent(Dirent {
-                entryname: filename.to_string(),
+                entryname: Some(filename.to_string()),
                 entry: Entry::from_file(filename),
+                ..Default::default()
             })],
         }
     }
@@ -158,8 +159,9 @@ impl InitialWorkDirRequirement {
                 .iter()
                 .map(|&filename| {
                     WorkDirItem::Dirent(Dirent {
-                        entryname: filename.to_string(),
+                        entryname: Some(filename.to_string()),
                         entry: Entry::Source(get_entry_name(filename)),
+                        ..Default::default()
                     })
                 })
                 .collect(),
@@ -168,17 +170,19 @@ impl InitialWorkDirRequirement {
     pub fn from_contents(entryname: &str, contents: &str) -> Self {
         InitialWorkDirRequirement {
             listing: vec![WorkDirItem::Dirent(Dirent {
-                entryname: entryname.to_string(),
+                entryname: Some(entryname.to_string()),
                 entry: Entry::Source(contents.to_string()),
+                ..Default::default()
             })],
         }
     }
 
     pub fn add_files(&mut self, filenames: &[&str]) {
         self.listing.extend(filenames.iter().map(|&f| {
             WorkDirItem::Dirent(Dirent {
-                entryname: f.to_string(),
+                entryname: Some(f.to_string()),
                 entry: Entry::Source(get_entry_name(f)),
+                ..Default::default()
             })
         }));
     }
@@ -275,7 +279,7 @@ mod tests {
         assert_eq!(req.listing.len(), 1);
         assert!(matches!(req.listing[0], WorkDirItem::Dirent(_)));
         if let WorkDirItem::Dirent(dirent) = &req.listing[0] {
-            assert_eq!(dirent.entryname, "../../tests/test_data/echo.py".to_string());
+            assert_eq!(dirent.entryname, Some("../../tests/test_data/echo.py".to_string()));
         }
     }
 

crates/cwl/src/types.rs

@@ -604,9 +604,22 @@ pub enum EnviromentDefs {
 #[derive(Serialize, Deserialize, Debug, PartialEq, Clone)]
 #[serde(rename_all = "camelCase")]
 pub struct Dirent {
-    pub entryname: String,
+    pub entryname: Option<String>,
     pub entry: Entry,
+    #[serde(skip_serializing_if = "Option::is_none")]
+    pub writeable: Option<bool>,
+}
+
+impl Default for Dirent {
+    fn default() -> Self {
+        Self {
+            entryname: None,
+            entry: Entry::Source(String::new()),
+            writeable: None,
+        }
+    }
 }
+
 #[derive(Serialize, Deserialize, Debug, PartialEq, Clone)]
 #[serde(untagged)]
 pub enum Entry {

src/cwl.rs

@@ -339,7 +339,8 @@ mod tests {
             Requirement::InitialWorkDirRequirement(InitialWorkDirRequirement {
                 listing: vec![WorkDirItem::Dirent(Dirent {
                     entry: Entry::from_file(os_path("../../test/script.py")),
-                    entryname: "test/script.py".to_string()
+                    entryname: Some("test/script.py".to_string()),
+                    ..Default::default()
                 })]
             })
         );