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Merged
merged 5 commits into from
Nov 28, 2022
Merged

initial_docs: updates initial set of docs #2

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cee598e
initial_setup: removes python, initialise rust
cmaddux Nov 23, 2022
95b3850
initial_setup: initial Manager struct
cmaddux Nov 25, 2022
0897a24
initial...: adds lib docs
cmaddux Nov 27, 2022
327641b
initial...: adds docs
cmaddux Nov 28, 2022
0387230
Merge branch 'master' into initial_docs
cmaddux Nov 28, 2022
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21 changes: 21 additions & 0 deletions README.md
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Original file line number Diff line number Diff line change
@@ -0,0 +1,21 @@
# MinKNOW API Rust Client

*This is currently an early implementation and should not be used in production settings. This is NOT an official ONT project.*

A rust implementation of the minknow_api client for interacting with MinKNOW. More information on MinKNOW and minknow_api client, see [the minknow_api python client repository](https://github.com/nanoporetech/minknow_api).

## Contributing

Prequisites:

* Rust
* Cargo
* [MinKNOW](https://community.nanoporetech.com/docs/prepare/library_prep_protocols/Guppy-protocol/v/gpb_2003_v1_revan_14dec2018/guppy-for-macos) >=22.10.7 installed and running locally

End to end tests associated with the `minknow-api-rust` client currently interact directly with a running minknow instance to create simulated devices. The following setup must be performed prior to running tests:

1. Create a developer API token by opening the MinKNOW desktop application and navigating to 'Host Settings' -> 'API Access Tokens'.
1. An environment variable must reference this token, run `export MINKNOW_API_TEST_TOKEN={created_token}`
1. An environment variable must reference the self-signed certificate provided with the MinKNOW installation (for example, on MacOS run `export MIKNOW_TRUSTED_CA="/Applications/MinKNOW.app/Contents/Resources/conf/rpc-certs/ca.crt"`)

Once above prerequisites tests can be run with `cargo test --tests`.
24 changes: 20 additions & 4 deletions src/lib.rs
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@@ -1,3 +1,9 @@
//! A Rust implementation of the minknow_api client that supports communicating
//! with a MinKNOW server.
//!
//! For more information on MinKNOW and minknow_api clients, see [the minknow_api
//! python client repository].

use hyper::{
client::{HttpConnector, ResponseFuture},
header::HeaderValue,
Expand Down Expand Up @@ -58,7 +64,7 @@ pub mod minknow_api {
}
}

// A flow cell position
// A flow cell position.
//
// You should not normally construct this directly, but instead call
// `Manager.flow_cell_positions`. The constructor arguments may change between minor
Expand Down Expand Up @@ -303,6 +309,7 @@ impl Manager {
self.reset_positions(vec![position], force).await
}

// Reset flow cell positions.
async fn reset_positions(
&self,
positions: Vec<String>,
Expand All @@ -329,6 +336,9 @@ impl Manager {
Ok(response)
}

// Create a new developer api token, which expires at [expiry]
//
// Cannot be invoked when using a developer token as authorisation method.
async fn create_developer_api_token(
&self,
name: String
Expand All @@ -354,6 +364,7 @@ impl Manager {
Ok(response)
}

// Revoke an existing developer API token.
async fn revoke_developer_api_token(
&self,
id: String
Expand All @@ -378,6 +389,7 @@ impl Manager {
Ok(response)
}

// List existing developer API tokens.
async fn list_developer_api_tokens(
&self
) -> Result<minknow_api::manager::ListDeveloperApiTokensResponse, Status> {
Expand All @@ -399,6 +411,7 @@ impl Manager {
Ok(response)
}

// List available protocols for the given experiment type.
async fn find_protocols(
&self,
experiment_type: minknow_api::manager::ExperimentType
Expand Down Expand Up @@ -449,7 +462,8 @@ mod tests {
9502
).await;

manager.channel.set_token("5bd16355-3e52-4be0-8462-23eda1fb3c06".to_string());
let test_base_token = env::var("MINKNOW_API_TEST_TOKEN").ok().unwrap();
manager.channel.set_token(test_base_token);

let response = manager.create_developer_api_token(
"test_simulated_end_to_end".to_string()
Expand Down Expand Up @@ -494,7 +508,8 @@ mod tests {
9502
).await;

manager.channel.set_token("5bd16355-3e52-4be0-8462-23eda1fb3c06".to_string());
let test_base_token = env::var("MINKNOW_API_TEST_TOKEN").ok().unwrap();
manager.channel.set_token(test_base_token);

let response = manager.create_developer_api_token(
"test_developer_api_token_management".to_string()
Expand All @@ -519,7 +534,8 @@ mod tests {
9502
).await;

manager.channel.set_token("5bd16355-3e52-4be0-8462-23eda1fb3c06".to_string());
let test_base_token = env::var("MINKNOW_API_TEST_TOKEN").ok().unwrap();
manager.channel.set_token(test_base_token);

let response = manager.find_protocols(
minknow_api::manager::ExperimentType::Sequencing
Expand Down