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Deployment instructions

Prerequisites

You should have installed:

Installation

All of the commands should be executed from the deploy directory.

cd deploy

Light up the database

Up the DB

docker-compose up -d db
docker-compose up -d mongo-express

With mongo-express we can see the contents of the database at http://localhost:8081.

Load the data

To load the database we execute the following commands:

mongoimport --jsonArray --uri "mongodb://root:[email protected]:27017/beacon?authSource=admin" --file data/analyses*.json --collection analyses
mongoimport --jsonArray --uri "mongodb://root:[email protected]:27017/beacon?authSource=admin" --file data/biosamples*.json --collection biosamples
mongoimport --jsonArray --uri "mongodb://root:[email protected]:27017/beacon?authSource=admin" --file data/cohorts*.json --collection cohorts
mongoimport --jsonArray --uri "mongodb://root:[email protected]:27017/beacon?authSource=admin" --file data/datasets*.json --collection datasets
mongoimport --jsonArray --uri "mongodb://root:[email protected]:27017/beacon?authSource=admin" --file data/individuals*.json --collection individuals
mongoimport --jsonArray --uri "mongodb://root:[email protected]:27017/beacon?authSource=admin" --file data/runs*.json --collection runs
mongoimport --jsonArray --uri "mongodb://root:[email protected]:27017/beacon?authSource=admin" --file data/genomicVariations*.json --collection genomicVariations

This loads the JSON files inside of the data folder into the MongoDB database.

You can also use make load as a convenience alias.

Create the indexes

You can create the necessary indexes running the following Python script:

# Install the dependencies
pip3 install pymongo

python3 reindex.py

Automatically fetch the ontologies

This step might require a bit of tinkering since some ontologies used in the dummy data will fail to loaded. We recommend skipping this step unless you know what you are doing.

You can automatically fetch the ontologies that the database is using with the following script:

# Install the dependencies
pip3 install pymongo tqdm

python3 fetch_ontologies.py

Extract the filtering terms

If you have the ontologies loaded, you can automatically extract the filtering terms from the data in the database using the following utility script:

# Install the dependencies
pip3 install pymongo tqdm owlready2 progressbar

python3 extract_filtering_terms.py

Light up the beacon

Up the beacon

Once the database is setup, you can up the beacon with the following command:

docker-compose up -d beacon

Check the logs

Check the logs until the beacon is ready to be queried:

docker-compose logs -f beacon

Usage

You can query the beacon using GET or POST. Below, you can find some examples of usage:

For simplicity (and readability), we will be using HTTPie.

Using GET

Querying this endpoit it should return the 13 variants of the beacon (paginated):

http GET http://localhost:5050/api/g_variants/

You can also add request parameters to the query, like so:

http GET http://localhost:5050/api/g_variants/?start=9411499,9411644&end=9411609

This should return 3 genomic variants.

Using POST

You can use POST to make the previous query. With a request.json file like this one:

{
    "meta": {
        "apiVersion": "2.0"
    },
    "query": {
        "requestParameters": {
            "start": [ 9411499, 9411644 ],
            "end": [ 9411609 ]
        },
        "filters": [],
        "includeResultsetResponses": "HIT",
        "pagination": {
            "skip": 0,
            "limit": 10
        },
        "testMode": false,
        "requestedGranularity": "count"
    }
}

You can execute:

http POST http://localhost:5050/api/g_variants/ --json < request.json

But you can also use complex filters:

{
    "meta": {
        "apiVersion": "2.0"
    },
    "query": {
        "filters": [
            {
                "id": "UBERON:0001256",
                "scope": "biosamples",
                "includeDescendantTerms": false
            }
        ],
        "includeResultsetResponses": "HIT",
        "pagination": {
            "skip": 0,
            "limit": 10
        },
        "testMode": false,
        "requestedGranularity": "count"
    }
}

You can execute:

http POST http://localhost:5050/api/biosamples/ --json < request.json

And it will use the ontology filter to filter the results.