Merging

.gitignore

@@ -1,8 +1,9 @@
 target/
 debug/
+
 Cargo.lock
+
 openapitools.json
 *.log
 funnel-work-dir/
 funnel/
-lib/src/*/models

Cargo.toml

@@ -6,8 +6,8 @@ members = [
 
 [workspace.package]
 version = "0.1.0"
-authors = ["Aarav Mehta <[email protected]> (Google Summer of Code Participant)", "Pavel Nikonorov <[email protected]> (Google Summer of Code Mentor; GENXT)", "ELIXIR Cloud & AAI <[email protected]> (ELIXIR Europe)"]
+authors = ["Aarav Mehta <[email protected]>", "Pavel Nikonorov <[email protected]>", "ELIXIR Cloud & AAI <[email protected]> (ELIXIR Europe)"]
 edition = "2021"
 readme = "./README.md"
-license-file = "LICENSE.txt"
+license-file = "LICENSE"
 repository = "https://github.com/elixir-cloud-aai/ga4gh-sdk.git"

README.md

@@ -1,4 +1,15 @@
-# A Generic SDK and CLI for GA4GH API services
+# GA4GH SDK
+[![License](https://img.shields.io/badge/License-Apache_2.0-blue.svg)](./LICENSE)
+
+## Synopsis
+
+A Generic SDK and CLI for GA4GH API services.
+
+## Basic usage
+TBA
+
+## Installation
+TBA
 
 ## Building
 
@@ -12,25 +23,82 @@ To build the project:
 cargo build
 ```
 
-## Running the tests
+## Testing
+There are 2 types of Tests: Unit tests and integration tests.
+
+To run the unit tests, which are being tested with mock servers, you can simply run
+```
+cargo test
+```
 
-Before running the tests, you need to install Funnel, a task execution system that is compatible with the GA4GH TES API. Follow the instructions in the [Funnel Developer's Guide](https://ohsu-comp-bio.github.io/funnel/docs/development/developers/) to install Funnel.
+To test the integration tests:
+Before running the integration tests, you need to install Funnel, a task execution system that is compatible with the GA4GH TES API. Follow the instructions in the Funnel Developer's Guide to install Funnel: https://ohsu-comp-bio.github.io/funnel/docs/development/developers/. Note that the link may change over time, so refer to the official Funnel repository or website for the most up-to-date information.
 
 Once you have installed Funnel, you can run the tests. This will automatically run Funnel as well:
 
 ```
 bash ./run-tests.sh
 ```
-or, you can run using cargo nextest using
+or, you can run using:
 ```
 cargo nextest run
 ```
-For checking the unit converage, you can run:
+For checking the unit coverage, you can run:
 ```
 cargo llvm-cov nextest
 ```
 
 To test the CI/CD workflow locally, install `act` and run the following command:
 ```
 act -j build --container-architecture linux/amd64 -P ubuntu-latest=ubuntu:24.04 --reuse
-```
+# Note: The specified Ubuntu version (24.04) may change in the future. 
+# Please check for the latest version when running this command.
+```
+
+## Versioning
+The project adopts the [semver] scheme for versioning.
+Currently the software is in a pre-release stage, so changes to the API,
+including breaking changes, may occur at any time without further notice.
+
+## Contributing
+
+This project is a community effort and lives off your contributions, be it in
+the form of bug reports, feature requests, discussions, ideas, fixes, or other
+code changes. Please read [these guidelines][docs-contributing] if you want to
+contribute. And please mind the [code of conduct][docs-coc] for all
+interactions with the community.
+
+## License
+
+This project is covered by the [Apache License 2.0](badge-url-license) also
+[shipped with this repository][license].
+
+## Contact
+The project is maintained by [ELIXIR Cloud & AAI][elixir-cloud-aai], a Driver
+Project of the [Global Alliance for Genomics and Health (GA4GH)][ga4gh], under
+the umbrella of the [ELIXIR] [Compute Platform][elixir-compute].
+
+To get in touch with us, please use one of the following routes:
+
+- For filing bug reports, feature requests or other code-related issues, please
+  make use of the project's [issue tracker][issue-tracker].
+- For private/personal issues, more involved communication, or if you would like
+  to join our team as a regular contributor, you can either join our
+  [chat board][badge-chat-url] or [email] the community leaders.
+
+
+[![logo-elixir]][elixir] [![logo-elixir-cloud-aai]][elixir-cloud-aai]
+
+[badge-chat-url]: https://join.slack.com/t/elixir-cloud/shared_invite/enQtNzA3NTQ5Mzg2NjQ3LTZjZGI1OGQ5ZTRiOTRkY2ExMGUxNmQyODAxMDdjM2EyZDQ1YWM0ZGFjOTJhNzg5NjE0YmJiZTZhZDVhOWE4MWM
+[badge-license-url]: http://www.apache.org/licenses/LICENSE-2.0
+[code-of-conduct]: https://elixir-cloud-aai.github.io/about/code-of-conduct/
+[contributing]: https://elixir-cloud-aai.github.io/guides/guide-contributor/
+[elixir]: https://elixir-europe.org/
+[elixir-cloud-aai]: https://elixir-cloud.dcc.sib.swiss/
+[elixir-compute]: https://elixir-europe.org/platforms/compute
+[email]: mailto:[email protected]
+[ga4gh]: https://ga4gh.org/
+[license]: LICENSE
+[logo-elixir]: ./images/logo-elixir.svg
+[logo-elixir-cloud-aai]: ./images/logo-elixir-cloud-aai.svg
+[semver]: https://semver.org/

cli/Cargo.toml

@@ -19,6 +19,7 @@ serde_json = "^1.0"
 tempfile = "3.2"
 dirs = "5.0.1"
 anyhow = "1.0.86"
+url = "2.5.2"
 
 [[bin]]
 name = "cli"

cli/src/main.rs

@@ -1,15 +1,15 @@
 use clap::{arg, Command};
-use ga4gh_sdk::configuration::Configuration;
-use ga4gh_sdk::tes::model::ListTasksParams;
-use ga4gh_sdk::transport::Transport;
+use ga4gh_sdk::clients::tes::models::ListTasksParams;
 use std::collections::HashMap;
 use std::error::Error;
-use ga4gh_sdk::tes::{Task, TES};
-use ga4gh_sdk::tes::models::TesTask;
-use ga4gh_sdk::test_utils::ensure_funnel_running;
 use std::fs;
 use std::path::Path;
-use ga4gh_sdk::configuration::BasicAuth;
+use ga4gh_sdk::clients::tes::models::TesTask;
+use ga4gh_sdk::clients::tes::{Task, TES};
+use ga4gh_sdk::utils::configuration::Configuration;
+use ga4gh_sdk::utils::test_utils::ensure_funnel_running;
+use ga4gh_sdk::utils::transport::Transport;
+use ga4gh_sdk::utils::configuration::BasicAuth;
 use std::fs::File;
 use serde_json::Value;
 use std::io::Read;
@@ -126,9 +126,10 @@ async fn main() -> Result<(), Box<dyn Error>> {
                 let testask: TesTask = serde_json::from_str(&task_json)
                     .map_err(|e| format!("Failed to parse JSON: {}", e))?;
                 let mut config = load_configuration();
-                if config.base_path == "localhost" {
+                if config.base_path.as_str() == "localhost" {
                     let funnel_url = ensure_funnel_running().await;
-                    config.set_base_path(&funnel_url);
+                    let funnel_url = url::Url::parse(&funnel_url).expect("Invalid URL");
+                    config.set_base_path(funnel_url);
                 }
                 match TES::new(&config).await {
                         Ok(tes) => {
@@ -166,9 +167,10 @@ async fn main() -> Result<(), Box<dyn Error>> {
                 };
                 println!("parameters are: {:?}",parameters);
                 let mut config = load_configuration();
-                if config.base_path == "localhost" {
+                if config.base_path.as_str() == "localhost" {
                     let funnel_url = ensure_funnel_running().await;
-                    config.set_base_path(&funnel_url);
+                    let funnel_url = url::Url::parse(&funnel_url).expect("Invalid URL");
+                    config.set_base_path(funnel_url);
                 }
                 match TES::new(&config).await {
                     Ok(tes) => {
@@ -186,9 +188,10 @@ async fn main() -> Result<(), Box<dyn Error>> {
                 let view = sub.value_of("view").unwrap();
 
                 let mut config = load_configuration();
-                if config.base_path == "localhost" {
+                if config.base_path.as_str() == "localhost" {
                     let funnel_url = ensure_funnel_running().await;
-                    config.set_base_path(&funnel_url);
+                    let funnel_url = url::Url::parse(&funnel_url).expect("Invalid URL");
+                    config.set_base_path(funnel_url);
                 }
 
                 match TES::new(&config).await {
@@ -206,9 +209,10 @@ async fn main() -> Result<(), Box<dyn Error>> {
                 let id = sub.value_of("id").unwrap().to_string();
 
                 let mut config = load_configuration();   
-                if config.base_path == "localhost" {
+                if config.base_path.as_str() == "localhost" {
                     let funnel_url = ensure_funnel_running().await;
-                    config.set_base_path(&funnel_url);
+                    let funnel_url = url::Url::parse(&funnel_url).expect("Invalid URL");
+                    config.set_base_path(funnel_url);
                 }
                 let transport = Transport::new(&config);
                 let task = Task::new(id, transport);
@@ -226,9 +230,10 @@ async fn main() -> Result<(), Box<dyn Error>> {
                 let id = sub.value_of("id").unwrap().to_string();
 
                 let mut config = load_configuration();
-                if config.base_path == "localhost" {
+                if config.base_path.as_str() == "localhost" {
                     let funnel_url = ensure_funnel_running().await;
-                    config.set_base_path(&funnel_url);
+                    let funnel_url = url::Url::parse(&funnel_url).expect("Invalid URL");
+                    config.set_base_path(funnel_url);
                 }
                 let transport = Transport::new(&config);
                 let task = Task::new(id, transport);
@@ -275,8 +280,11 @@ fn read_configuration_from_file(file_path: &str) -> Result<Configuration, Box<dy
             password: Some(auth["password"].as_str().unwrap_or_default().to_string()),
         });
     let oauth_access_token = json_value["oauth_access_token"].as_str().map(|s| s.to_string());
-
-    let config = Configuration::new(base_path, user_agent, basic_auth, oauth_access_token);
+    let base_path = url::Url::parse(&base_path).expect("Invalid URL");
+    let config = Configuration::new(base_path)
+        .with_user_agent(user_agent.expect("Invalid user agent"))
+        .with_basic_auth(basic_auth.expect("Invalid basic_auth"))
+        .with_oauth_access_token(oauth_access_token.expect("Invalid oauth access token"));
     Ok(config)
 }