diff --git a/README.md b/README.md index 70b77d8..f6e02b5 100644 --- a/README.md +++ b/README.md @@ -9,12 +9,12 @@ * [Technologies](#technologies) ##What it is -This project contains BDK (beacon development kit) for Python developers. It provides a skeleton of a simple beacon allowing the developers to plug in their own data/functionality. The API makes sure the response produced is compatible with what the Beacon of Beacons can consume. +This project contains BDK (beacon development kit) for Python developers. It provides a skeleton of a simple beacon allowing the developers to plug in their own data/functionality. The API makes sure the response produced is compatible with the [Beacon API](https://github.com/ga4gh/beacon-team/). ##System requirements -All you need to build this project is Python and Flask web framework. If you're running Linux, OS X or Windows with cygwin support, the following commands should be enough to set up Flask (the process is a bit different with the native version of Python on Windows): +All you need to build this project is Python 2 and Flask web framework. If you're running Linux, OS X or Windows with cygwin support, the following commands should be enough to set up Flask (the process is a bit different with the native version of Python on Windows): - $ cd todo-api + $ pip install virtualenv $ virtualenv flask $ flask/bin/pip install flask @@ -31,12 +31,12 @@ In order to implement a beacon, simply override beacon details and query functio The API takes care of the rest and provides the following endpoints when you start your beacon: - http://127.0.0.1:5000/beacon-python/info - information about your beacon + http://127.0.0.1:5000/beacon-python - information about your beacon http://127.0.0.1:5000/beacon-python/query - access to query service Query example: - GET http://127.0.0.1:5000/beacon-python/query?chrom=15&pos=41087870&allele=A&ref=hg19 + GET http://127.0.0.1:5000/beacon-python/query?referenceName=1&start=1000&referenceBases=A&alternateBases=T&assemblyId=GRCh37&datasetIds=&includeDatasetResponses=true ##Technologies -Python, Flask. +Python 2, Flask. diff --git a/beacon.py b/beacon.py index 3033f4c..2c36091 100755 --- a/beacon.py +++ b/beacon.py @@ -1,6 +1,6 @@ #!flask/bin/python -''' +""" The MIT License Copyright 2014 DNAstack. @@ -22,185 +22,118 @@ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. -''' +""" from flask import Flask, jsonify, request - -class IncompleteQuery(Exception): - status_code = 400 - - def __init__(self, message, status_code=None, payload=None, ErrorResource=None, query=None, beacon_id=None): - Exception.__init__(self) - self.message = message - if status_code is not None: - self.status_code = status_code - self.payload = payload - self.ErrorResource = ErrorResource - self.query = query - self.beacon_id = beacon_id - - def to_dict(self): - rv = dict(self.payload or ()) - rv["beacon"] = self.beacon_id - rv["query"] = self.query - rv['error'] = self.ErrorResource - return rv - - app = Flask(__name__) -# --------------- Information endpont (start) --------------------# - -# TODO: override with the details of your beacon - -########### DataSetResource for beacon details ############ - -# required field(s): name -DataUseRequirementResource = { - 'name': u'example name', - 'description': u'example description' +BeaconAlleleRequest = { + 'referenceName': u'', # required + 'start': 0, # required + 'referenceBases': u'', # required + 'alternateBases': u'', # required + 'assemblyId': '', # required + 'datasetIds': [], # optional + 'includeDatasetResponses': False, # optional } -# required field(s): variants -DataSizeResource = { - 'variants': 1, # integer - 'samples': 1 # integer +BeaconDataset = { + 'id': u'', # required + 'name': u'', # required + 'description': u'', # optional + 'assemblyId': u'', # required + 'createDateTime': u'', # required + 'updateDateTime': u'', # required + 'version': u'', # optional + 'variantCount': 1, # optional + 'callCount': 1, # optional + 'sampleCount': 1, # optional + 'externalUrl': u'', # optional + 'info': {} # optional } -# required field(s): category -DataUseResource = { - 'category': u'example use category', - 'description': u'example description', - 'requirements': [ - DataUseRequirementResource - ] +BeaconOrganization = { + 'id': u'', # required + 'name': u'', # required + 'description': u'', # optional + 'address': u'', # optional + 'welcomeUrl': u'', # optional + 'contactUrl': u'', # optional + 'logoUrl': u'', # optional + 'info': {} # optional } -# required field(s): id -DataSetResource = { - 'id': u'example Id', - 'description': u'dataset description', - 'reference': u'reference genome', - 'size': DataSizeResource, # Dimensions of the data set (required if the beacon reports allele frequencies) - 'data_uses': [ - DataUseResource # Data use limitations - ] +Beacon = { + 'id': u'', # required + 'name': u'', # required + 'apiVersion': u'0.3', # required + 'organization': BeaconOrganization, # required + 'description': u'', # optional + 'version': u'', # optional + 'welconeUrl': u'', # optional + 'alternativeUrl': u'', # optional + 'createDateTime': u'', # optional + 'updateDateTime': u'', # optional + 'datasets': [ # optional + BeaconDataset + ], + 'sampleAlleleRequests': [ # optional + BeaconAlleleRequest # Examples of interesting queries + ], + 'info': {} } -########### QueryResource for beacon details ############### +BeaconError = { + 'errorCode': 400, # required + 'message': u'' # optional +} -# required field(s): allele, chromosome, position, reference -QueryResource = { - 'allele': u'allele string', - 'chromosome': u'chromosome Id', - 'position': 1, # integer - 'reference': u'genome Id', - 'dataset_id': u'dataset Id' +BeaconDatasetAlleleResponse = { + 'datasetId': u'', # required + 'exists': True, # optional (required in no-error cases) + 'error': None, # optional (required in case of an error) + 'frequency': u'', # optional + 'variantCount': 1, # optional + 'callCount': 1, # optional + 'sampleCount': 1, # optional + 'note': u'', # optional + 'externalUrl': u'', # optional + 'info': {} # optional } -################### Beacon details ######################### - -# required field(s): id, name, organization, api -beacon = { - 'id': u'foo', - 'name': u'bar', - 'organization': u'org', - 'api': u'0.1/0.2', - 'description': u'beacon description', - 'datasets': [ - DataSetResource # Datasets served by the beacon - ], - 'homepage': u'http://dnastack.com/ga4gh/bob/', - 'email': u'beacon@dnastack.com', - 'auth': u'oauth2', # OAUTH2, defaults to none - 'queries': [ - QueryResource # Examples of interesting queries +BeaconAlleleResponse = { + 'beaconId': u'', # required + 'exists': True, # optional (required in no-error cases) + 'error': None, # optional (required in case of an error) + 'alleleRequest': BeaconAlleleRequest, # optional + 'datasetAlleleResponses': [ # optional + BeaconDatasetAlleleResponse ] } -# --------------- Information endpoint (end) ----------------------# - # info function -@app.route('/beacon-python/info', methods=['GET']) +# TODO: override with the details of your beacon (see https://github.com/ga4gh/beacon-team/ for more details) +@app.route('/beacon-python/', methods=['GET']) def info(): - return jsonify(beacon) + return jsonify(Beacon) # query function -# TODO: plug in the functionality of your beacon +# TODO: plug in the functionality of your beacon (see https://github.com/ga4gh/beacon-team/ for more details) @app.route('/beacon-python/query', methods=['GET']) def query(): # parse query - chromosome = request.args.get('chrom') - position = long(request.args.get('pos')) - allele = request.args.get('allele') - reference = request.args.get('ref') - dataset = request.args.get('dataset') if 'dataset' in request.args else beacon['datasets'][0]['id'] - - # ---- TODO: override with the necessary response details ----# - - ############## AlleleResource for response ############### - - # required field(s): allele - AlleleResource = { - 'allele': allele, - 'frequency': 0.5 # double between 0 & 1 - } - - ############# ErrorResource for response ################# - - # required field(s): name - ErrorResource = { - 'name': u'error name/code', - 'description': u'error message' - } - - ################### Response object ######################### - - # generate response - # required field(s): exists - response = { - 'exists': True, - 'observed': 0, # integer, min 0 - 'alleles': [ - AlleleResource - ], - 'info': u'response information', - } - - query = { - 'chromosome': chromosome, - 'position': position, - 'allele': allele, - 'reference': reference, - 'dataset_id': dataset - } - - if query['chromosome'] is None or query['position'] is None or query['allele'] is None or query[ - 'reference'] is None: - ErrorResource['description'] = 'Required parameters are missing' - ErrorResource['name'] = 'Incomplete Query' - raise IncompleteQuery('IncompleteQuery', status_code=410, ErrorResource=ErrorResource, query=query, - beacon_id=beacon["id"]) - - # --------------------------------------------------------------# - - return jsonify({"beacon": beacon['id'], "query": query, "response": response}) - - -# info function -@app.route('/beacon-python/', methods=['GET']) -def welcome(): - return 'WELCOME!!! Beacon of Beacons Project (BoB) provides a unified REST API to publicly available GA4GH Beacons. BoB standardizes the way beacons are accessed and aggregates their results, thus addressing one of the missing parts of the Beacon project itself. BoB was designed with ease of programmatic access in mind. It provides XML, JSON and plaintext responses to accommodate needs of all the clients across all the programming languages. The API to use is determined using the header supplied by the client in its GET request, e.g.: "Accept: application/json".' - - -# required parameters missing -@app.errorhandler(IncompleteQuery) -def handle_invalid_usage(error): - response = jsonify(error.to_dict()) - return response + BeaconAlleleRequest['referenceName'] = request.args.get('referenceName') + BeaconAlleleRequest['start'] = int(request.args.get('start')) + BeaconAlleleRequest['referenceBases'] = request.args.get('referenceBases') + BeaconAlleleRequest['alternateBases'] = request.args.get('alternateBases') + BeaconAlleleRequest['assemblyId'] = request.args.get('assemblyId') + BeaconAlleleRequest['datasetIds'] = request.args.getlist('datasetIds') + BeaconAlleleRequest['includeDatasetResponses'] = bool(request.args.get('includeDatasetResponses')) + + return jsonify(BeaconAlleleResponse) # page not found