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Update examples
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@sdelatorrep
sdelatorrep committed Feb 7, 2019
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Showing 1 changed file with 43 additions and 45 deletions.
88 changes: 43 additions & 45 deletions beacon.md
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Original file line number Diff line number Diff line change
Expand Up @@ -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",
Expand Down Expand Up @@ -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",
Expand Down Expand Up @@ -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."|
Expand Down Expand Up @@ -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": [
{
Expand All @@ -285,7 +285,7 @@ An example `GET` request and response to the info endpoint:
"variantCount": 74,
}
],
"description": "This <a href=\"http://ga4gh.org/#/beacon\">Beacon</a> is based on the GA4GH Beacon <a href=\"https://github.com/ga4gh/beacon-team/blob/develop/src/main/resources/avro/beacon.avdl\">API 0.4</a>",
"description" : "This <a href=\"https://beacon-project.io/\">Beacon</a> is based on the GA4GH Beacon <a href=\"https://raw.githubusercontent.com/ga4gh-beacon/specification/v1.1.1/beacon.yaml\"></a>",
"id": "ega-beacon",
"info": {
"size": "60270153"
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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`

Expand All @@ -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
Expand Down Expand Up @@ -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
```

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