API

To access the PhenomeDB API on a local docker installation go to: http://localhost:5001/custom/.

The username and password will be the same as your $AIRFLOW_ADMIN_USER and $AIRFLOW_ADMIN_PASSWORD

To view the OpenAPI/Swagger documentation for the API, go to: http://localhost:5001/custom/swagger/v1

Implemented API Import endpoints:

• import/samplemanifest

• import/brukerivdrannotations

• import/peakpantherannotations

More can be implemented using these as examples.

Please note, the files must be accessible to the server, either on the same server or via a file-system mount.

To use the API with Python:

import json
import requests

data = {"username": "admin","password": "testpass",'refresh':True}

session = requests.session()

login_url = "http://localhost:5001/custom/api/v1/security/login"
refresh_url = "https://localhost:5001/custom/api/v1/security/refresh"

# Login and set the JWT tokens
r = session.post(login_url,json=data)
access_token = json.loads(r.content)['access_token']
refresh_token = json.loads(r.content)['refresh_token']

print(access_token)
print(refresh_token)

# Import a sample manifest -
data = {"project_name":"PipelineTesting",
        "sample_manifest_path": '/opt/phenomedb_app/phenomedb/data/test/DEVSET_sampleManifest.xlsx',
        "columns_to_ignore":[],
        "username": "admin"}

r = self.session.post('http://localhost:5001/custom/api/v1/import/samplemanifest',
                      json=data,
                      headers={'Authorization': 'Bearer '+ access_token})

# Import the peak panther data
data = {"project_name":"PipelineTesting",
        "feature_metadata_csv_path": '/opt/phenomedb_app/phenomedb/data/test/DEVSET P LPOS PeakPantheR_featureMetadata.csv',
        "sample_metadata_csv_path": '/opt/phenomedb_app/phenomedb/data/test/DEVSET P LPOS PeakPantheR_sampleMetadata_SMALL.csv',
        "intensity_data_csv_path": '/opt/phenomedb_app/phenomedb/data/test/DEVSET P LPOS PeakPantheR_intensityData.csv',
        "batch_corrected_data_csv_path": '/opt/phenomedb_app/phenomedb/data/test/DEVSET P LPOS PeakPantheR_intensityData_batchcorrected.csv',
        "ppr_annotation_parameters_csv_path": '/opt/phenomedb_app/phenomedb/data/test/DEVSET_P_LPOS_annotationParameters_summary.csv',
        "ppr_mz_csv_path": '/opt/phenomedb_app/phenomedb/data/test/DEVSET_P_LPOS_PPR_mz.csv',
        "ppr_rt_csv_path": '/opt/phenomedb_app/phenomedb/data/test/DEVSET_P_LPOS_PPR_rt_with_extra_paths.csv',
        "sample_matrix": "plasma",
        "assay_name": "LPOS",
        "run_batch_correction": False,
        "username": "admin"}

r = session.post('http://localhost:5001/custom/api/v1/import/peakpanther',
json=data,
headers={'Authorization': 'Bearer '+access_token})
print(r.content)

# Refresh the JWT token (if access token expires)
r = session.post(refresh_url,headers={"Authorization": "Bearer " + refresh_token})
access_token = json.loads(r.content)['access_token']
refresh_token = json.loads(r.content)['refresh_token']