This package is an implementation of the Unipept API that's being used by the Unipept Web Application and Desktop application to succesfully perform analysis of metaproteomics samples.

Overview of existing endpoints

This is an exhaustive list of all endpoints that are exposed by this API

Public endpoints

API v1

• /api/v1/pept2taxa
• /api/v1/pept2lca
• /api/v1/taxa2lca
• /api/v1/pept2prot
• /api/v1/pept2funct
• /api/v1/pept2ec
• /api/v1/pept2go
• /api/v1/pept2interpro
• /api/v1/taxa2tree
• /api/v1/peptinfo
• /api/v1/taxonomy
• /api/v1/messages

API v2

• /api/v2/pept2taxa
• /api/v2/pept2lca
• /api/v2/taxa2lca
• /api/v2/pept2prot
• /api/v2/pept2funct
• /api/v2/pept2ec
• /api/v2/pept2go
• /api/v2/pept2interpro
• /api/v2/taxa2tree
• /api/v2/peptinfo
• /api/v2/taxonomy
• /api/v2/messages

Private endpoints

• /private_api/goterms
• /private_api/ecnumbers
• /private_api/interpros
• /private_api/taxa
• /private_api/proteins
• /private_api/metadata
• /mpa/pept2data
• /datasets/sampledata

Developing the Unipept API

You can use the included devcontainer in order to start working on this API. The devcontainer will automatically download the most recent version of the Unipept Index built from SwissProt. Follow these steps in order to easily work on the Unipept API in the devcontainer:

• You first have to build the binaries by running cargo build --release.
• Then, you should start the OpenSearch server: /usr/share/opensearch/bin/opensearch
• Sometimes, a previous invocation of OpenSearch crashed or didn't shut down properly. If you see errors, try and clear the file locks: rm /var/lib/opensearch/nodes/0/node.lock /var/lib/opensearch/nodes/0/_state/write.lock
• Make the directory where we can store the logfiles for a running instance of the Unipept API: mkdir -p /var/log/unipept-api.
• Finally, the Unipept API can be started with this command: ./target/release/unipept-api -i "/unipept-index-data" -d "http://localhost:9200" -p 80 > /var/log/unipept-api/api.log 2> /var/log/unipept-api/api_error.log.

Running OpenSearch as non-root user in devcontainer

• sudo groupadd --system opensearch
• sudo useradd --system --gid opensearch --home /usr/share/opensearch --shell /usr/sbin/nologin opensearch
• sudo chown -R opensearch:opensearch /usr/share/opensearch /etc/opensearch /var/lib/opensearch /var/log/opensearch && sudo chmod -R 750 /var/lib/opensearch /var/log/opensearch
• sudo -u opensearch /usr/share/opensearch/bin/opensearch