minor bug fixes

Author: aaravm

Diff for: cli/src/main.rs

@@ -257,14 +257,26 @@ async fn main() -> Result<(), Box<dyn Error>> {
     Ok(())
 }
 
-/// Example `config.json` file:
+/// Loads the configuration from a JSON file.
+///
+/// # Example `config.json`
 ///
 /// ```json
 /// {
 ///   "base_path": "http://localhost:8000",
-///   "user_agent": "username"
+///   "user_agent": "Some(User)",
+///   "basic_auth": {
+///         "username": "your_username",
+///         "password": "your_password"
+///     },
+///   "oauth_access_token": "your_oauth_access_token"
 /// }
 /// ```
+///
+/// # Errors
+///
+/// This function will return an error if the configuration file is missing or malformed.
+
 
 fn read_configuration_from_file(file_path: &str) -> Result<Configuration, Box<dyn Error>> {
     let mut file = File::open(file_path)?;

Diff for: lib/src/clients/tes/mod.rs

@@ -76,7 +76,7 @@
 /// ```rust
 /// use ga4gh_sdk::clients::tes::TES;
 /// use ga4gh_sdk::utils::configuration::Configuration;
-/// use ga4gh_sdk::clients::tes::model::ListTasksParams;
+/// use ga4gh_sdk::clients::tes::models::ListTasksParams;
 ///
 /// # async fn test_tes_list_tasks() -> Result<(), Box<dyn std::error::Error>> {
 /// let config = Configuration::new(url::Url::parse("http://example.com")?);

Diff for: lib/src/tes/mod.rs

@@ -7,7 +7,7 @@ use crate::tes::models::TesListTasksResponse;
 use crate::tes::models::TesState;
 use crate::tes::models::TesTask;
 use crate::transport::Transport;
-use crate::tes::model::ListTasksParams;
+use crate::tes::models::ListTasksParams;
 use serde_json;
 use serde_json::from_str;
 use serde_json::json;

Diff for: lib/tests/funnel_tes.rs

@@ -1,12 +1,12 @@
 #[cfg(feature = "integration_tests")]
 #[cfg(test)]
 mod tests {
-    use ga4gh_sdk::utils::configuration::Configuration;
+    use ga4gh_sdk::clients::tes::models::ListTasksParams;
+    use ga4gh_sdk::clients::tes::models::TesState;
     use ga4gh_sdk::clients::tes::models::TesTask;
-    use ga4gh_sdk::clients::tes::model::ListTasksParams;
     use ga4gh_sdk::clients::tes::Task;
-    use ga4gh_sdk::clients::tes::models::TesState;
     use ga4gh_sdk::clients::tes::TES;
+    use ga4gh_sdk::utils::configuration::Configuration;
     use ga4gh_sdk::utils::test_utils::{ensure_funnel_running, setup};
 
     async fn create_task() -> Result<(Task, TES), Box<dyn std::error::Error>> {
@@ -26,8 +26,12 @@ mod tests {
         let task_json = match std::fs::read_to_string(&file_path) {
             Ok(content) => content,
             Err(e) => {
-                let current_dir = std::env::current_dir().unwrap_or_else(|_| std::path::PathBuf::from("unknown directory"));
-                panic!("Unable to read file in directory {:?}: {:?}", current_dir, e);
+                let current_dir = std::env::current_dir()
+                    .unwrap_or_else(|_| std::path::PathBuf::from("unknown directory"));
+                panic!(
+                    "Unable to read file in directory {:?}: {:?}",
+                    current_dir, e
+                );
             }
         };
         let task: TesTask = serde_json::from_str(&task_json).expect("JSON was not well-formatted");
@@ -54,7 +58,10 @@ mod tests {
         match status {
             Ok(state) => {
                 assert!(
-                    matches!(state, TesState::Initializing | TesState::Queued | TesState::Running),
+                    matches!(
+                        state,
+                        TesState::Initializing | TesState::Queued | TesState::Running
+                    ),
                     "Unexpected state: {:?}",
                     state
                 );
@@ -97,4 +104,4 @@ mod tests {
         assert!(list.is_ok());
         println!("{:?}", list);
     }
-}
+}