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BioSamples Search

BioSamples search is a Spring Boot application leveraging ElasticSearch for full-text search, filtering and faceting.

Project Structure

The project contains 2 modules: proto and server. The following list shows important directories in the project.

  • proto - protobuf definitions and generated code
  • server - server application exposing search endpoints ..
    • model - core biosamples model
    • filter - filtering related code
    • facet - faceting related code
  • helm - cicd, k8s deployment
  • k8s - other related deployment files (ES, PV, ..)
  • docs - further documentation

API

Three main APIs are exposed by the application.

  1. Search samples (POST, GRPC)
  2. Search samples streaming (GRPC)
  3. Get facets for search (POST, GRPC)

BioSamples core services uses GRPC to communicate with biosamples-search. The RESTfull services are implemented mainly for the testing and development purposes.

Build

Requirements

  • Java 24
./gradlew build
# build without unit and integration tests
./gradlew build -x test -x check
# build only proto module
./gradlew :proto:build

Search samples

POST

curl --location 'http://localhost:8080/search' \
--header 'Content-Type: application/json' \
--data '{
    "text": "soil",
    "filters": [
      {
        "type": "attr",
        "field": "env_medium",
        "values": ["Soil"]
      },
      {
        "type": "attr",
        "field": "locus_tag_prefix",
        "values": ["SM2"]
      },
      {
        "type": "acc",
        "accession": "SAMD00000364"
      },
      {
        "type": "dt",
        "field": "create",
        "from": "2014-04-21T00:00:00Z",
        "to": "2014-04-22T05:00:00Z"
      }
    ],
    "page": 0,
    "size": 3,
    "sort": [
      {
        "direction": "DESC",
        "field": "create"
      }
    ]
}'

Get facets for search

POST

curl --location 'http://localhost:8080/facet' \
--header 'Content-Type: application/json' \
--data '{
    "text": "live",
    "filters": [
    ]
}'

Facets

Currently, there are two faceting strategies implemented. The default implementation RegularFacetingStratey could be slow due to large number of attributes in BioSamples database. The SamplingFacetingStrategy uses sampling method to get facets from all shards faster, but is not providing the exact facet count. It is possible to limit the set of attributes to be faceted for even faster results. This is left as a future enhancement.