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starter-kit-storage-and-interfaces

There exist two compose files at the root of the repo. Details on how to use them are provided below.

Note: Before deploying the stack, please make sure that all configuration files are in place. The following files need to be created from their respective examples:

cp ./config/config.yaml.example ./config/config.yaml
cp ./config/iss.json.example ./config/iss.json
cp ./.env.example ./.env

no further editing to the above files is required for running the stack locally.

Starting the full stack with LS-AAI-mock

To bootstrap the full stack of storage-and-interfaces services use the file docker-compose.yml. Note that this requires a running LS-AAI-mock service. To configure the LS-AAI-mock service follow the instructions below.

First clone the startet-kit-lsaai-mock repo.

Add the sda-auth client by creating a file configuration/aai-mock/clients/client1.yaml with the following contents:

client-name: "auth"
client-id: "XC56EL11xx"
client-secret: "wHPVQaYXmdDHg"
redirect-uris: ["http://localhost:8085/oidc/login"]
token-endpoint-auth-method: "client_secret_basic"
scope: ["openid", "profile", "email", "ga4gh_passport_v1", "eduperson_entitlement"]
grant-types: ["authorization_code"]
post-logout-redirect-uris: ["http://localhost:8085/oidc/login"]

Starting storage-and-interfaces with LS-AAI-mock

From the root of the starter-kit-storage-and-interfaces folder and run:

docker compose up -d

and then from the root folder of the starter-kit-lsaai-mock run:

docker compose up -d

Starting the stack in standalone demo mode

The file docker-compose-demo.yml is used to start the storage-and-interfaces services in demo mode with an example dataset preloaded and ingested to the sensitive data archive when the deployment is done. This comes with its own python implementation of a mock-oidc in place of LS-AAI and can be run as standalone for demonstration purposes.

The files imported by the data loading script come from here:

To deploy use the following command:

docker compose -f docker-compose-demo.yml up -d

After deployment is done, follow the instructions below to test that the demo worked as expected.

Download unencrypted files directly

Get token for downloading data

For the purpose of the demo stack, tokens can be issued by the included oidc service and be used to authorize calls to the download service's API. The oidc is a simple Python implementation that mimics the basic OIDC functionality of LS-AAI. It does not require user authentication and serves a valid token through its /token endpoint:

token=$(curl -s -k https://localhost:8080/tokens | jq -r '.[0]')

This token is created upon deployment. See scripts/make_credentials.sh for more details. Note that the API returns a list of tokens where the first element is the token of interest, and the rest are tokens for testing sda-download.

List datasets

curl -s -H "Authorization: Bearer $token" http://localhost:8443/metadata/datasets | jq .

List files in a dataset

datasetID=$(curl -s -H "Authorization: Bearer $token" http://localhost:8443/metadata/datasets | jq -r .'[0]')
curl -s -H "Authorization: Bearer $token" "http://localhost:8443/metadata/datasets/$datasetID/files" | jq .

Download a specific file

The sda-download service offers multiple methods for downloading files through the API, with options for both encrypted and unencrypted results. Below, you will find an example illustrating each of these methods.

To download the file htsnexus_test_NA12878.bam, first obtain the respective fileID using the following command. The datasetID, which is DATASET0001, can be obtained by following the instructions at List datasets

filename="htsnexus_test_NA12878.bam"
fileID=$(curl -s -H "Authorization: Bearer $token" "http://localhost:8443/metadata/datasets/$datasetID/files" | jq -r --arg filename "$filename".c4gh '.[] | select(.displayFileName==$filename) | .fileId')

1. Download unencrypted file from the /files endpoint

curl -s -H "Authorization: Bearer $token" http://localhost:8443/files/$fileID -o "$filename"

After successful execution, the BAM file htsnexus_test_NA12878.bam will be downloaded to your current folder.

2. Download unencrypted file from the /s3 endpoint

curl -s -H "Authorization: Bearer $token" http://localhost:8443/s3/$datasetID/$filename -o "$filename"

3. Download encrypted file from the /s3-encrypted endpoint

To download an encrypted file that is re-encrypted with a custom Crypt4GH public key, you need to first create a key pair by the sda-cli tool, instructions can be found here.

# create a crypt4gh key pair
sda-cli createKey c4gh
pubkey=$(base64 -w0 c4gh.pub.pem) 
curl -s -H "Authorization: Bearer $token" -H "Client-Public-Key: $pubkey" http://localhost:8443/s3-encrypted/$datasetID/$filename -o "$filename.c4gh"

After successful execution, the Crypt4GH encrypted BAM file htsnexus_test_NA12878.bam.c4gh will be downloaded to your current folder. This file can be decrypted using the private key of the key pair you have created by

sda-cli decrypt -key c4gh.sec.pem htsnexus_test_NA12878.bam.c4gh