From 95d3df6b29d7f286d261fd3d3c15b679f3d25f5c Mon Sep 17 00:00:00 2001 From: Sabela Date: Wed, 30 Jan 2019 15:31:23 +0100 Subject: [PATCH] Update examples --- beacon.md | 88 +++++++++++++++++++++++++++---------------------------- 1 file changed, 43 insertions(+), 45 deletions(-) diff --git a/beacon.md b/beacon.md index f0059622..13d34982 100644 --- a/beacon.md +++ b/beacon.md @@ -57,7 +57,7 @@ The response body SHOULD be a JSON object (`Content-Type: application/json`) pro [ { "beaconId": "some-beacon", - "apiVersion": "v1.0.1", + "apiVersion": "v1.1.1", "exists": null, "alleleRequest": { "referenceName": "1", @@ -92,7 +92,7 @@ which means that at least one of the datasets in this Beacon has a different ass [ { "beaconId": "some-beacon", - "apiVersion": "v1.0.1", + "apiVersion": "v1.1.1", "exists": true, "alleleRequest": { "referenceName": "1", @@ -192,7 +192,7 @@ Beacon API SHOULD support cross-origin resource sharing (CORS) and follow [GA4GH |---|---|:---:|---| |*id* *|Unique identifier of the beacon. Use reverse domain name notation.|string|org.ga4gh.beacon| |*name* *|Human readable name of the beacon|string|EGA Beacon| -|*apiVersion* *|Version of the API provided by the beacon.|string|v1.0.0| +|*apiVersion* *|Version of the API provided by the beacon.|string|v1.1.1| |*organisation* *|Organisation providing the Beacon|object|Beacon Organisation object (see below)| |*datasets* *|Datasets served by the beacon. Any beacon should specify at least one dataset.|array|Array of Beacon Dataset objects (see below)| |description|Description of the beacon.|string|"This sample set comprises cases of schizophrenia with additional cognitive measurements, collected in Aberdeen, Scotland."| @@ -272,7 +272,7 @@ An example `GET` request and response to the info endpoint: < { "alternativeUrl": "https://ega-archive.org/beacon_web/", - "apiVersion": "0.4", + "apiVersion": "1.1.1", "createDateTime": "2015-06-15T00:00.000Z", "dataset": [ { @@ -285,7 +285,7 @@ An example `GET` request and response to the info endpoint: "variantCount": 74, } ], - "description": "This Beacon is based on the GA4GH Beacon API 0.4", + "description" : "This Beacon is based on the GA4GH Beacon ", "id": "ega-beacon", "info": { "size": "60270153" @@ -333,7 +333,7 @@ An example `GET` request and response to the info endpoint: "start": 866510 } ], - "version": "v04", + "version": "v1.1.1", "welcomeUrl": "https://ega-archive.org/beacon_web/" } * Closing connection 0 @@ -414,11 +414,11 @@ Example of how to use the GET method in the `/query` endpoint: < Content-Type: application/json < Content-Length: 1078 < Server: Werkzeug/0.14.1 Python/3.6.5 - < Date: Mon, 11 Jun 2018 07:29:26 GMT + < Date: Wed, 30 Jan 2018 07:29:26 GMT < { "beaconId": "ega-beacon", - "apiVersion": "0.4", + "apiVersion": "1.1.1", "exists": true, "error": { "errorCode": 200 @@ -459,7 +459,7 @@ Example of how to use the GET method in the `/query` endpoint: * Closing connection 0 ``` -Example of how to use the POST method in the "/query" path: +Example of how to use the POST method in the `/query` path: `curl -v -d "referenceName=1&start=14929&referenceBases=A&alternateBases=G&assemblyId=GRCh37&datasetIds=EGAD00000000028&includeDatsetResponses=ALL" https://localhost:5000/query` @@ -477,11 +477,11 @@ Example of how to use the POST method in the "/query" path: < Content-Type: application/json < Content-Length: 1056 < Server: Werkzeug/0.14.1 Python/3.6.5 - < Date: Mon, 11 Jun 2018 07:15:48 GMT + < Date: Wed, 30 Jan 2018 07:15:48 GMT < { "beaconId": "ega-beacon", - "apiVersion": "0.4", + "apiVersion": "1.1.1", "exists": true, "error": { "errorCode": 200 @@ -522,53 +522,51 @@ Example of how to use the POST method in the "/query" path: * Closing connection 0 ``` -`curl -v 'https://localhost:5000/query?&start=0&end=0&startMin=28000000&startMax=29000000&endMin=28000000&endMax=29000000&referenceBases=A&alternateBases=T&assemblyId=GRCh37&datasetIds=EGAD00000000028&includeDatasetResponses=ALL'` +Example of error: +`curl -v 'https://localhost:5000/query?&start=0&end=0&startMin=28000000&startMax=29000000&endMin=28000000&endMax=29000000&referenceBases=A&alternateBases=T&assemblyId=GRCh37&datasetIds=EGAD00000000028&includeDatasetResponses=ALL'` ``` -* Trying 127.0.0.1... -* TCP_NODELAY set -* Connected to localhost (127.0.0.1) port 5000 (#0) -> GET /query?&start=0&end=0&startMin=28000000&startMax=29000000&endMin=28000000&endMax=29000000&referenceBases=A&alternateBases=T&assemblyId=GRCh37&datasetIds=EGAD00000000028&includeDatasetResponses=ALL HTTP/1.1 -> Host: localhost:5000 -> User-Agent: curl/7.54.0 -> Accept: */* -> -* HTTP 1.0, assume close after body -< HTTP/1.0 400 BAD REQUEST -< Content-Type: application/json -< Content-Length: 791 -< Server: Werkzeug/0.14.1 Python/3.6.5 -< Date: Fri, 06 Jul 2018 09:15:39 GMT -< -{ - "message": { + > POST /query HTTP/1.1 + > Host: localhost:5000 + > User-Agent: curl/7.54.0 + > Accept: */* + > Content-Length: 133 + > Content-Type: application/x-www-form-urlencoded + > + * upload completely sent off: 133 out of 133 bytes + * HTTP 1.0, assume close after body + < HTTP/1.0 200 OK + < Content-Type: application/json + < Content-Length: 1056 + < Server: Werkzeug/0.14.1 Python/3.6.5 + < Date: Wed, 30 Jan 2018 07:15:48 GMT + < + { "beaconId": "ega-beacon", - "apiVersion": "0.4", - "exists": null, + "apiVersion": "1.1.1", + "exists": true, "error": { "errorCode": 400, - "errorMessage": "Missing mandatory parameter referenceName" + "errorMessage" : "User provided assemblyId (GRCh38) does not match with dataset assembly (GRCh37)" }, - "allelRequest": { - "referenceName": "0", - "start": 0, - "startMin": 28000000, - "startMax": 29000000, + "alleleRequest": { + "referenceName": "1", + "start": 14929, + "startMin": 0, + "startMax": 0, "end": 0, - "endMin": 28000000, - "endMax": 29000000, + "endMin": 0, + "endMax": 0, "referenceBases": "A", - "alternateBases": "T", - "variantType": "0", + "alternateBases": "G", "assemblyId": "GRCh37", "datasetIds": [ "EGAD00000000028" ], - "includeDatasetResponses": "ALL" + "includeDatasetResponses": "NONE" }, - "datasetAlleleResponses": [] + "datasetAlleleResponses": null } -} -* Closing connection 0 + * Closing connection 0 ```