Framework dependent code for a local instance of [htsget-rs], using Actix Web.
This crate is used for running a local instance of htsget-rs. It is based on: * Actix Web for endpoints, routes, and middleware. * [htsget-http] for htsget-rs specific HTTP responses
This crate uses [htsget-config] for configuration. See [htsget-config] for details on how to configure this crate.
To run an instance of this crate, execute the following command:
sh
cargo run -p htsget-actix --no-default-features
Using the default configuration, this will start a ticket server on 127.0.0.1:8080 and a data block server on 127.0.0.1:8081
with data accessible from the data directory.
To use AwsS3Storage, avoid compiling with no default features:
sh
cargo run -p htsget-actix
This will start a ticket server with AwsS3Storage using a bucket called "data".
See [htsget-search] for details on how to structure files.
There two server instances that are launched when running this crate. The ticket server, which returns a list of ticket URLs that a client must fetch. And the data block server, which responds to the URLs in the tickets. By default, the data block server runs without TLS. To run the data block server with TLS, pem formatted X.509 certificates are required.
For development and testing purposes, self-signed certificates can be used. For example, to generate self-signed certificates run:
sh
openssl req -x509 -newkey rsa:4096 -keyout key.pem -out cert.pem -sha256 -days 365 -nodes -subj '/CN=localhost'
It is not recommended to use self-signed certificates in a production environment as this is considered insecure.
Using default configuration settings, this crate responds to queries referencing files in the data directory.
Some example requests using curl are shown below:
sh
curl '127.0.0.1:8080/variants/data/vcf/sample1-bcbio-cancer'
sh
curl --header "Content-Type: application/json" -d '{}' '127.0.0.1:8080/variants/data/vcf/sample1-bcbio-cancer'
sh
curl '127.0.0.1:8080/variants/data/vcf/sample1-bcbio-cancer?format=VCF&class=header'
sh
curl --header "Content-Type: application/json" -d '{"format": "VCF", "regions": [{"referenceName": "chrM"}]}' '127.0.0.1:8080/variants/data/vcf/sample1-bcbio-cancer'
sh
curl '127.0.0.1:8080/variants/service-info'
There shouldn't be any need to interact with this crate as a library, however some functions which deal with configuring routes are exposed in the public API.
This crate has the following features:
* s3-storage: used to enable AwsS3Storage functionality.
Benchmarks for this crate written using Criterion.rs, and aim to compare the performance of this crate with the htsget Reference Server. There are a set of light benchmarks, and one heavy benchmark. Light benchmarks can be performed by executing:
cargo bench -p htsget-actix -- LIGHT
To run the heavy benchmark, an additional vcf file needs to be downloaded, and placed in the data/vcf directory:
curl ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000_genomes_project/release/20190312_biallelic_SNV_and_INDEL/ALL.chr14.shapeit2_integrated_snvindels_v2a_27022019.GRCh38.phased.vcf.gz > data/vcf/internationalgenomesample.vcf.gz
Then to run the heavy benchmark:
cargo bench -p htsget-actix -- HEAVY
This project is licensed under the MIT license.