changing detection of files

Author: gtfierro

cli/src/main.rs

@@ -121,7 +121,7 @@ enum Commands {
     Doctor,
     /// Reset the ontology environment by removing the .ontoenv directory
     Reset {
-        #[clap(long, short, action = clap::ArgAction::Set, default_value = "false")]
+        #[clap(long, short, action = clap::ArgAction::SetTrue, default_value = "false")]
         force: bool,
     },
 }
@@ -171,7 +171,11 @@ fn main() -> Result<()> {
     if cmd.verbose || cmd.debug {
         config.print();
     }
-    let ontoenv_exists = current_dir()?.join(".ontoenv").exists();
+    let ontoenv_exists = current_dir()?
+        .join(".ontoenv")
+        .join("ontoenv.json")
+        .exists();
+    println!("[INFO] OntoEnv exists: {}", ontoenv_exists);
 
     // create the env object to use in the subcommand.
     // - if temporary is true, create a new env object each time
@@ -181,12 +185,13 @@ fn main() -> Result<()> {
         let mut e = OntoEnv::init(config.clone(), false)?;
         e.update()?;
         Some(e)
-    } else if cmd.command.to_string() != "Init" && ontoenv_exists{
+    } else if cmd.command.to_string() != "Init" && ontoenv_exists {
         // if .ontoenv exists, load it
         Some(OntoEnv::load_from_directory(current_dir()?, false)?) // no read-only
     } else {
         None
     };
+    println!("[INFO] OntoEnv loaded: {}", env.is_some());
 
     match cmd.command {
         Commands::Init {
@@ -342,7 +347,7 @@ fn main() -> Result<()> {
             // remove .ontoenv directory
             let path = current_dir()?.join(".ontoenv");
             println!("Removing .ontoenv directory at {}...", path.display());
-            if path.exists() && !force {
+            if !force {
                 // check delete? [y/N]
                 let mut input = String::new();
                 println!("Are you sure you want to delete the .ontoenv directory? [y/N] ");
@@ -354,6 +359,8 @@ fn main() -> Result<()> {
                     println!("Aborting...");
                     return Ok(());
                 }
+            }
+            if path.exists() {
                 std::fs::remove_dir_all(path)?;
             }
         }

lib/src/api.rs

@@ -311,6 +311,7 @@ impl OntoEnv {
         let id = ont.id().clone();
         self.env.add_ontology(ont);
         self.add_ids_to_dependency_graph(vec![id.clone()])?;
+        self.save_to_directory()?;
         Ok(id)
     }
 
@@ -347,7 +348,24 @@ impl OntoEnv {
         // load all of these files into the environment
         let mut ontologies: Vec<Ontology> = vec![];
         for location in updated_files {
-            let ontology = self.io.add(location.clone(), true)?;
+            // if 'strict' mode then fail on any errors when adding the ontology
+            // otherwise just warn
+
+            let result = self.io.add(location.clone(), true);
+            if result.is_err() {
+                if self.config.strict {
+                    return Err(result.unwrap_err());
+                } else {
+                    warn!(
+                        "Failed to read ontology file {}: {}",
+                        location,
+                        result.unwrap_err()
+                    );
+                    continue;
+                }
+            }
+
+            let ontology = result.unwrap();
             ontologies.push(ontology);
         }
 
@@ -359,6 +377,7 @@ impl OntoEnv {
             update_ids.push(id);
         }
         self.add_ids_to_dependency_graph(update_ids)?;
+        self.save_to_directory()?;
         Ok(())
     }