-
Notifications
You must be signed in to change notification settings - Fork 1
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
- Loading branch information
Showing
2 changed files
with
91 additions
and
158 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -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'[email protected]', | ||
| '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 | ||
|
|
||