bioprotocol-service

bioprotocol-service is an application that receives requests from the eLife journal for Bioprotocol data and keeps Bioprotocol updated with newly published articles.

It is a Python and Django application.

API

bioprotocol-service can be accessed directly at https://prod--bp.elifesciences.org/, and content is available at /bioprotocol/article/{msid}, for example, Homo Naledi:

{
    "total": 19,
    "items": [
        {
            "sectionId": "s5-1-1",
            "title": "Australopithecus afarensis",
            "status": false,
            "uri": "https://bio-protocol.org/eLIFErap09560?item=s5-1-1"
        },
        {
            "sectionId": "s5-1-2",
            "title": "Australopithecus africanus",
            "status": false,
            "uri": "https://bio-protocol.org/eLIFErap09560?item=s5-1-2"
        },
        {
            "sectionId": "s5-1-3",
            "title": "Australopithecus garhi",
            "status": false,
            "uri": "https://bio-protocol.org/eLIFErap09560?item=s5-1-3"
        },
        
        [...]
        
        {
            "sectionId": "s5-6",
            "title": "Stature estimation methods",
            "status": false,
            "uri": "https://bio-protocol.org/eLIFErap09560?item=s5-6"
        }
    ]
}

bioprotocol-service is available through the eLife API gateway at: https://api.elifesciences.org/bioprotocol/

The availability of the API can be tested with /ping

The status of the API can be tested with /status

eLife updates of Bioprotocol data

bioprotocol-service will monitor an AWS SQS queue for article publication notifications, download the article, convert it to a Bioprotocol-preferred data structure and then HTTP POST the results to the Bioprotocol servers. This ensures Bioprotocol has the most recent set of published articles and relieves them of polling eLife infrastructure for new articles.

Articles that fail to send to Bioprotocol can be re-sent with:

./resend-elife-article-to-bp.sh {msid}

Bioprotocol updates of article data

Bioprotocol data is sent to eLife's bioprotocol-service as it becomes available via a HTTP POST request.

Bioprotocol data that fails to be ingested can be reloaded with:

./reload-article-data-from-bp.sh {msid}

Installation

./install.sh

Testing

./test.sh

Maintenance

./update-dependencies.sh
./update-fixtures.sh

Copyright & Licence

Copyright 2019 eLife Sciences.

The bioprotocol-service project is MIT licenced.