Searching RIN Indices

Introduction to searching the RIN indices

Introduction

The Resources Information Network (RIN) APIs are provided via an ElasticSearch endpoint. Simple URL based searches are available via the GET method. More complex queries can be supplied via the POST method.

Access to the RIN APIs

Access to the RIN API is provided via an Elasticsearch pass-through.

Elasticsearch Pass-Through

POST https://api.scicrunch.io/elastic/v1/{index}/_search

The pass-through is accessible at https://scicrunch.org/api/1/elastic. Similar to standard Elasticsearch APIs you must then supply an index and an action. In this case the index, the type and the search command (_search). Documentation on the Elasticsearch Search API is available at https://www.elastic.co/guide/en/elasticsearch/reference/6.8/search.html

Path Parameters

Name	Type	Description
index*	String	Production RIN index

Headers

Name	Type	Description
apikey*	String	Your API key to access the services

Request Body

Name	Type	Description
data	String	JSON query body

200: OK Successful request

{
    "took": 23,
    "timed_out": false,
    "_shards": {
        "total": 2,
        "successful": 2,
        "skipped": 0,
        "failed": 0
    },
    "hits": {...}
}

401: Unauthorized No API key supplied

{
    "error": {
        "root_cause": [
            {
                "type": "security_exception",
                "reason": "action [indices:data/read/search] requires authentication",
                "header": {
                    "WWW-Authenticate": [
                        "Bearer realm=\"security\"",
                        "ApiKey",
                        "Basic realm=\"security\" charset=\"UTF-8\""
                    ]
                }
            }
        ],
        "type": "security_exception",
        "reason": "action [indices:data/read/search] requires authentication",
        "header": {
            "WWW-Authenticate": [
                "Bearer realm=\"security\"",
                "ApiKey",
                "Basic realm=\"security\" charset=\"UTF-8\""
            ]
        }
    },
    "status": 401
}

400: Bad Request API request is malformed

{
    "error": {
        "root_cause": [
            {
                "type": "illegal_argument_exception",
                "reason": "request [/RIN_Addgene_pr/rin/_search] contains unrecognized parameter: [api_key]"
            }
        ],
        "type": "illegal_argument_exception",
        "reason": "request [/RIN_Addgene_pr/rin/_search] contains unrecognized parameter: [api_key]"
    },
    "status": 400
}

404: Not Found The index or the uri is incorrect

{
    "error": {
        "root_cause": [
            {
                "type": "index_not_found_exception",
                "reason": "no such index",
                "resource.type": "index_or_alias",
                "resource.id": "RIN_Addgene",
                "index_uuid": "_na_",
                "index": "RIN_Addgene"
            }
        ],
        "type": "index_not_found_exception",
        "reason": "no such index",
        "resource.type": "index_or_alias",
        "resource.id": "RIN_Addgene",
        "index_uuid": "_na_",
        "index": "RIN_Addgene"
    },
    "status": 404
}

500: Internal Server Error The query is incorrect

{
    "error": {
        "root_cause": [
            {
                "type": "json_parse_exception",
                "reason": "Unexpected character ('=' (code 61)): was expecting a colon to separate field name and value\n at [Source: org.elasticsearch.transport.netty4.ByteBufStreamInput@4eccf1fd; line: 5, column: 25]"
            }
        ],
        "type": "json_parse_exception",
        "reason": "Unexpected character ('=' (code 61)): was expecting a colon to separate field name and value\n at [Source: org.elasticsearch.transport.netty4.ByteBufStreamInput@4eccf1fd; line: 5, column: 25]"
    },
    "status": 500
}

403: Forbidden Invalid API key

Elasticsearch Pass-Through

GET https://api.scicrunch.io/elastic/v1/{index}/_search

The pass-through is accessible at https://scicrunch.org/api/1/elastic. Similar to standard Elasticsearch APIs you must then supply an index and an action. In this case the index, the type and the URL search query paramter.

Documentation on the Elasticsearch Search API is available at https://www.elastic.co/guide/en/elasticsearch/reference/6.8/search.html

Path Parameters

Name	Type	Description
index*	String	Production RIN index

Query Parameters

Name	Type	Description
q	String	Search String

Headers

Name	Type	Description
apikey*	String	Your API key to access the services

200: OK Successful request

400: Bad Request API request is malformed

401: Unauthorized No API key supplied

403: Forbidden Invalid API key

404: Not Found The index or the uri is incorrect

500: Internal Server Error The query is incorrect

RIN Index Aliases

Management of indices is accomplished via Elasticsearch aliases. The index aliases are provided:

Index Alias	Description
RIN_Tool_pr	Production tools index
RIN_Antibody_pr	Production antibodies index
RIN_CellLine_pr	Production cell lines index
RIN_Organism_pr	Production organisms index
RIN_Addgene_pr,RIN_DGRC_*_pr	Production plasmids (AddGene & DGRC) indices
RIN_BioSample_pr	Production biosamples index
RIN_Protocols_pr	Production protocols index
*_pr	Production all indices

Using aliases will allow for testing on updates and enhancements to the index structure. If needed additional aliases can be constructed for specialized testing.