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Eventually these services will be HTTPS only and disallow HTTP. Users will pass something like ?access_token=... as a query parameter for every request to the service

REST API Usage Examples

This is a REST api (see Service API Design for more details as to what this means). You can create entities, updated entities, read entities, and delete entities. More advanced querying will be implemented as a separate API. Partial updates (e.g., just updating two fields in a dataset) are not supported. In a nutshell, when you update something like a dataset, you GET the dataset first, modify the properties you want to change, and then send the entire object back to the service so that this revised entity overwrites the previously stored entity.

The layer preview info in the dataset examples is out of date. It will be updated soon. Just use curl against the live service to see the current format.

Get Datasets

Optional Parameters

...

Code Block
HTTP/1.1 200 OK
ETag: 22610276
Content-Type: application/json
Date: Tue, 01 Feb 2011 18:07:45 GMT
Server: Google Frontend
Cache-Control: private, x-gzip-ok=""
Transfer-Encoding: chunked
{
   "results":[
      {
         "name":"Pediatric AML TARGET",
         "annotations":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYgvcCDA/annotations",
         "id":"agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYgvcCDA",
         "version":"0.0.1",
         "description":null,
         "status":"In Transition",
         "uri":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYgvcCDA",
         "etag":"1703131409",
         "creator":"Soheil Meshinchi",
         "creationDate":1296182253120,
         "releaseDate":null,
         "layerslayer":["/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYgvcCDA/layer",
         "hasExpressionData":true,
   {      "hasGeneticData":false,
         "idhasClinicalData":"agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw"false
      },
      {
         "typename":"CFlint HS Mice",
               "uri"annotations":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYgvcCDAagxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQY2q0DDA/layer/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQwannotations",
            }"id":"agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQY2q0DDA",
         "version":"0.0.1",
  {
               "id"description":"agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYiaECDA",
     null,
         "typestatus":"EFuture",
 
             "uri":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYgvcCDA/layer/agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYiaECDAagxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQY2q0DDA",
         "etag":"1025901212",
  },       "creator":"Jonathan Flint",
    {      "creationDate":1296182255070,
         "idreleaseDate":"agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYmfIBDA"null,
               "type":"G"layer":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQY2q0DDA/layer",
               "uri":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYgvcCDA/layer/agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYmfIBDA""hasExpressionData":true,
         "hasGeneticData":true,
  }       "hasClinicalData":true
  ]       },
      {
         "name":"FlintGlioblastoma HS MiceTCGA",
         "annotations":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQY2q0DDAagxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYseQDDA/annotations",
         "id":"agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQY2q0DDAagxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYseQDDA",
         "version":"0.0.1",
         "description":null,
         "status":"FutureAvailable",
         "uri":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQY2q0DDAagxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYseQDDA",
         "etag":"1025901212456728335",
         "creator":"Jonathan Flint"null,
         "creationDate":12961822550701296182238229,
         "releaseDate":null,
         "layerslayer":["/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYseQDDA/layer",
          "hasExpressionData":false,
 {        "hasGeneticData":false,
         "idhasClinicalData":"agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw",false
      }
    ],
   "typetotalNumberOfResults":"C"10,
     "paging":{
         "urinext":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQY2q0DDA/layer/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw?offset=4&limit=3"
            },
            {
               "id":"agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYiaECDA",
               "type":"E",
               "uri}
}

Get a Dataset

Request

Code Block

curl -i -H Accept:application/json "http://deflaux-test.appspot.com/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYseQDDA"

Response

Code Block

HTTP/1.1 200 OK
ETag: 456728335
Content-Type: application/json
Date: Tue, 01 Feb 2011 18:22:24 GMT
Server: Google Frontend
Cache-Control: private, x-gzip-ok=""
Transfer-Encoding: chunked

{
   "name":"Glioblastoma TCGA",
   "annotations":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQY2q0DDAagxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYseQDDA/layer/agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYiaECDAannotations",
   "id":"agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYseQDDA",
   "version":"0.0.1",
    }"description":null,
   "status":"Available",
   "uri":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYseQDDA",
    {"etag":"456728335",
   "creator":null,
   "creationDate":1296182238229,
   "releaseDate":null,
    "idlayers":"agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYmfIBDA",[
      {
         "typeid":"GagxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw",
          "type":"C",
         "uri":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQY2q0DDAagxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYseQDDA/layer/agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYmfIBDAagxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw"

           },
      {
  ]       }"id":"agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYiaECDA",
      {          "name"type":"Glioblastoma TCGAE",
         "annotationsuri":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYseQDDA/layer/annotationsagxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYiaECDA",
         "id":"agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYseQDDA"},
         "version":"0.0.1",{
         "descriptionid":null"agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYmfIBDA",
         "statustype":"AvailableG",
         "uri":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYseQDDA",/layer/agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYmfIBDA"
      }
    "etag":"456728335",
         "creator":null,
         "creationDate":1296182238229,
         "releaseDate":null,
         "layers":[
            {
     ]
}

Get Annotations for a Dataset

Request

Code Block

curl -i -H Accept:application/json "http://deflaux-test.appspot.com/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYseQDDA/annotations"

Response

Code Block

HTTP/1.1 200 OK
ETag: -1919132670
Content-Type: application/json
Date: Tue, 01 Feb 2011 18:24:15 GMT
Server: Google Frontend
Cache-Control: private, x-gzip-ok=""
Transfer-Encoding: chunked

{
   "id":"agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYseQDDA",
   "uri":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYseQDDA/annotations",
   "etag":"-1919132670",
   "creationDate":null,
   "stringAnnotations":{
      "Disease":[
         "id":"agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw",Cancer"
      ],
      "Tumor / Tissue Type"type":"C",:[
         "Glioblastoma"
      "uri":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYseQDDA/layer/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw"],
      "Species":[
     },    "Human"
      ],
 {      "Institution":[
         "id":"agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYiaECDA",TCGA"
      ],
      "Reference / PubMed "typeID":"E",[
         "18772890"      "uri":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYseQDDA/layer/agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYiaECDA"]
   },
   "floatAnnotations":{
    },  "Number of Samples":[
        { 465.0
      ]
   },
   "iddateAnnotations":"agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYmfIBDA",{

   }
}

Create a Dataset

Request:

Code Block
curl -i -H Accept:application/json -H Content-Type:application/json
-d  '{"typename":"Gtest dataset", "creator":"fake               "uri":"creator", "releaseDate":"2009-10-01", "status":"not curated"}'
http://localhost:8080/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYseQDDA/layer/agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYmfIBDA"
            }
         ]
      }
   ]

Response

Code Block

HTTP/1.1 201 Created
ETag: 1736839268
Location: /repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYBAw
Content-Type: application/json
Transfer-Encoding: chunked
Server: Jetty(6.1.x)

{
   "name":"test dataset",
   "annotations":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw/annotations",
   "totalNumberOfResultsid":10"agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw",
   "pagingversion":{"0.0.1",
   "creator":"fake creator",
   "nextdescription":"/repo/v1/dataset?offset=4&limit=3"null,
   "creationDate":1296595870715,
   }
}

Get a Dataset

Request

Code Block

curl -i -H Accept:application/json "http://deflaux-test.appspot.com/"status":"not curated",
   "uri":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYseQDDAagxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw",

Response

Code Block
 HTTP/1.1 200 OK
ETag: 456728335
Content-Type: application/json
Date: Tue, 01 Feb 2011 18:22:24 GMT
Server: Google Frontend
Cache-Control: private, x-gzip-ok=""
Transfer-Encoding: chunked

{ "etag":"1309185941",
   "releaseDate":1254355200000,
   "layers":[]
}

Update a Dataset

Note that in the example below the creator and description fields have been changed but all others remain the same.

Request:

Code Block

curl -i -H Accept:application/json -H Content-Type:application/json -X PUT -H ETag:1309185941 -d '{
   "name":"test dataset",
   "annotations":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw/annotations",
   "id":"agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw",
   "version":"0.0.1",
   "creator":"updated creator",
   "description":"I just added a description",
   "creationDate":1296595870715,
   "status":"not curated",
   "uri":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw",
   "etag":"1309185941",
   "releaseDate":1254355200000,
   "layers":[]
}
' http://localhost:8080/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw

Response

Code Block

HTTP/1.1 200 OK
ETag: -852418664
Content-Type: application/json
Transfer-Encoding: chunked
Server: Jetty(6.1.x)

{
   "name":"test dataset",
   "annotations":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw/annotations",
   "id":"agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw",
   "version":"0.0.1",
   "creator":"updated creator",
   "description":"I just added a description",
   "creationDate":1296595870715,
   "status":"not curated",
   "uri":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw",
   "etag":"-852418664",
   "releaseDate":1254355200000,
   "layers":[]
}

Add Annotations to a Dataset

First get the empty annotations container for your newly created dataset

Request

Code Block

curl -i -H Accept:application/json http://localhost:8080/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw/annotations

Response

Code Block

HTTP/1.1 200 OK
ETag: 923521
Content-Type: application/json
Transfer-Encoding: chunked
Server: Jetty(6.1.x)

{
   "id":"agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw",
   "creationDate":null,
   "uri":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw/annotations",
   "etag":"923521",
   "stringAnnotations":{

   },
   "floatAnnotations":{

   },
   "dateAnnotations":{

   }
}

Then you add/modify the annotations of interest and do a PUT. Note that annotation values must always be list values even if the list is only of length one.

Request

Code Block

curl -i -H Accept:application/json -H Content-Type:application/json -X PUT -H ETag:923521 -d '{
   "id":"agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw",
   "creationDate":null,
   "uri":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw/annotations",
   "etag":"923521",
   "stringAnnotations":{
        "Experimental Design Templates":["exp-122887", "exp-97765"]
   },
   "floatAnnotations":{
        "Number of Samples":[500]
   },
   "dateAnnotations":{
        "Publication Date":["2011-01-15"]
   }
}' http://localhost:8080/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw/annotations

Response

Code Block

HTTP/1.1 200 OK
ETag: -1638393853
Content-Type: application/json
Transfer-Encoding: chunked
Server: Jetty(6.1.x)

{
   "id":"agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYBww",
   "creationDate":null,
   "uri":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYBww/annotations",
   "etag":"-1638393853",
   "stringAnnotations":{
      "Experimental Design Templates":[
         "exp-122887",
         "exp-97765"
      ]
   },
   "floatAnnotations":{
      "Number of Samples":[
         500.0
      ]
   },
   "dateAnnotations":{
      "Publication Date":[
         1295049600000
      ]
   }
}

Delete a Dataset

Request

Code Block

curl -i -X DELETE http://localhost:8080/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw

Response

Code Block

HTTP/1.1 204 No Content
Server: Jetty(6.1.x)

Get a Layers for a Dataset

Request

Code Block

curl -i -H Accept:application/json http://localhost:8080/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer

Response

Code Block

HTTP/1.1 200 OK
Content-Type: application/json
Transfer-Encoding: chunked
Server: Jetty(6.1.x)

{
   "results":[
      {
         "name":"Flint HS Mice Affy",
         "annotations":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww/annotations",
         "id":"agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww",
         "type":"E",
         "version":"0.0.1",
         "description":"this is a description",
         "creationDate":1296690778880,
         "uri":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww",
         "etag":"1424771925",
         "publicationDate":null,
         "releaseNotes":"this is a release note",
         "tissueType":"liver",
         "platform":null,
         "processingFacility":null,
         "qcBy":null,
         "qcDate":null
      },
      {
         "name":"Flint HS Mice Phenotypes",
         "annotations":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjpBww/annotations",
         "id":"agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjpBww",
         "type":"C",
         "version":"0.0.1",
         "description":"this is a description",
         "creationDate":1296693007167,
         "uri":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjpBww",
         "etag":"1445062754",
         "publicationDate":null,
         "releaseNotes":"this is a release note",
         "tissueType":null,
         "platform":null,
         "processingFacility":null,
         "qcBy":null,
         "qcDate":null
      }
   ],
   "totalNumberOfResults":2,
   "paging":{

   }
}

Get a Layer

Request

Code Block

curl -i -H Accept:application/json http://localhost:8080/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww

Response

Code Block

HTTP/1.1 200 OK
ETag: 1240467407
Content-Type: application/json
Transfer-Encoding: chunked
Server: Jetty(6.1.x)

{
   "name":"Flint HS Mice Affy",
   "annotations":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww/annotations",
   "id":"agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww",
   "type":"E",
   "version":"0.0.1",
   "description":"this is a description",
   "creationDate":1296690778880,
   "uri":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww",
   "etag":"1240467407",
   "publicationDate":null,
   "releaseNotes":"this is a release note",
   "tissueType":null,
   "platform":null,
   "processingFacility":null,
   "qcBy":null,
   "qcDate":null
}

Get annotations for a layer

Request

Code Block
curl -i -H Accept:application/json http://localhost:8080/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww/annotations

Response

Code Block

HTTP/1.1 200 OK
ETag: 923521
Content-Type: application/json
Transfer-Encoding: chunked
Server: Jetty(6.1.x)

{
   "id":"agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww",
   "creationDate":null,
   "uri":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww/annotations",
   "etag":"923521",
   "stringAnnotations":{

   },
   "floatAnnotations":{

   },
   "dateAnnotations":{

   }
}

Create a layer

Request

Code Block

curl -i -H Accept:application/json -H Content-Type:application/json -d '{"name":"Flint HS Mice Affy", "type":"E", "description":"this is a description", "releaseNotes":"this is a release note"}' http://localhost:8080/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer

Response

Code Block

HTTP/1.1 201 Created
ETag: 1240467407
Location: /repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww
Content-Type: application/json
Transfer-Encoding: chunked
Server: Jetty(6.1.x)

{
   "name":"Flint HS Mice Affy",
   "annotations":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww/annotations",
   "id":"agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww",
   "type":"E",
   "version":"0.0.1",
   "description":"this is a description",
   "creationDate":1296690778880,
   "uri":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww",
   "etag":"1240467407",
   "publicationDate":null,
   "releaseNotes":"this is a release note",
   "tissueType":null,
   "platform":null,
   "processingFacility":null,
   "qcBy":null,
   "qcDate":null
}

Now ask for the owning dataset and you can see the preview of the layer

Request

Code Block

curl -i -H Accept:application/json http://localhost:8080/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww

Response

Code Block

HTTP/1.1 200 OK
ETag: -801135512
Content-Type: application/json
Transfer-Encoding: chunked
Server: Jetty(6.1.x)

{
"name":"Flint HS Mice",
"annotations":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/annotations",
"id":"agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww",
"version":"0.0.1",
"creator":"Jonathan Flint",
"description":null,
"creationDate":1296690549675,
"status":"Future",
"uri":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww",
"etag":"-801135512",
"releaseDate":null,
"layers":[
{
         "id":"agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww",
         "type":"E",
         "uri":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww"
      },{
         "id":"use this uri to make a new layer",
         "type":"hack",
         "uri":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer"
      }
]
}

Update a Layer

In the example below we updated the tissue type.

Request

Code Block

curl -i -H Accept:application/json -H Content-Type:application/json -X PUT -H ETag:1240467407 -d '
{
   "name":"Flint HS Mice Affy",
   "annotations":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww/annotations",
   "id":"agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww",
   "type":"E",
   "version":"0.0.1",
   "description":"this is a description",
   "creationDate":1296690778880,
   "uri":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww",
   "etag":"1240467407",
   "publicationDate":null,
   "releaseNotes":"this is a release note",
   "tissueType":"liver",
   "platform":null,
   "processingFacility":null,
   "qcBy":null,
   "qcDate":null
}' http://localhost:8080/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww

Response

Code Block

HTTP/1.1 200 OK
ETag: 1424771925
Content-Type: application/json
Transfer-Encoding: chunked
Server: Jetty(6.1.x)

{
   "name":"Flint HS Mice Affy",
   "annotations":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww/annotations",
   "id":"agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww",
   "type":"E",
   "version":"0.0.1",
   "description":"this is a description",
   "creationDate":1296690778880,
   "uri":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww",
   "etag":"1424771925",
   "publicationDate":null,
   "releaseNotes":"this is a release note",
   "tissueType":"liver",
   "platform":null,
   "processingFacility":null,
   "qcBy":null,
   "qcDate":null
}

Delete a layer

Request

Code Block

curl -i -X DELETE http://localhost:8080/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww

Response

Code Block

HTTP/1.1 204 No Content
Server: Jetty(6.1.x)

Add annotations to a layer

Request

Code Block

curl -i -H Accept:application/json -H Content-Type:application/json -X PUT -H ETag:923521 -d '
{
   "id":"agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww",
   "creationDate":null,
   "uri":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww/annotations",
   "etag":"923521",
   "stringAnnotations":{
      "notes":["I threw away 6 samples during the curation process due to gender chromosome mismatches"]
   },
   "floatAnnotations":{

   },
   "dateAnnotations":{

   }
}' http://localhost:8080/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww/annotations

Response

Code Block

HTTP/1.1 200 OK
ETag: -1897035229
Content-Type: application/json
Transfer-Encoding: chunked
Server: Jetty(6.1.x)

{
   "id":"agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww",
   "creationDate":null,
   "uri":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww/annotations",
   "etag":"-1897035229",
   "stringAnnotations":{
      "notes":[
         "I threw away 6 samples during the curation process due to gender chromosome mismatches"
      ]
   },
   "floatAnnotations":{

   },
   "dateAnnotations":{

   }
}

Query API Usage Examples

Sort clause

Request

Code Block

curl -H Accept:application/json -i 'http://deflaux-test.appspot.com/repo/v1/query?query=select+*+from+dataset+order+by+"name"+limit+3+offset+1'

Response

Code Block

{
   "totalNumberOfResults":10,
   "results":[
      {
         "name":"Flint HS Mice",
         "id":"agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQY2q0DDA",
         "version":"0.0.1",
         "description":null,
         "status":"Future",
         "creator":"Jonathan Flint",
         "creationDate":1296182255070,
         "releaseDate":null,
         "hasExpressionData":true,
         "hasGeneticData":false,
         "hasClinicalData":false,
         "Disease":[
            "Normal Phenotypes"
         ],
         "Species":[
            "Mouse"
         ],
         "Number of Samples":[
            1027.0
         ]
      },
      {
         "name":"Glioblastoma TCGA",
         "id":"agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYseQDDA",
         "version":"0.0.1",
         "description":null,
         "status":"Available",
         "creator":null,
         "creationDate":1296182238229,
         "releaseDate":null,
         "hasExpressionData":true,
         "hasGeneticData":false,
         "hasClinicalData":false,
         "Disease":[
            "Cancer"
         ],
         "Tumor / Tissue Type":[
            "Glioblastoma"
         ],
         "Institution":[
            "TCGA"
         ],
         "Species":[
            "Human"
         ],
         "Reference / PubMed ID":[
            1.877289E7
         ],
         "Number of Samples":[
            465.0
         ]
      },
      {
         "name":"Glioblastoma TCGAHarvard Brain Tissue Resource Center",
   "annotations":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYseQDDA/annotations",      "id":"agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYseQDDAagxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYiZsEDA",
         "version":"0.0.1",
         "description":null,
         "status":"AvailableIn Transition",
         "uricreator":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYseQDDAFrancine Benes",
   "etag":"456728335",      "creatorcreationDate":null1296182251551,
     "creationDate":1296182238229,    "releaseDate":null,
   "layers":[       {"hasExpressionData":true,
         "idhasGeneticData":"agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw"false,
         "typehasClinicalData":"C"false,
         "uriDisease":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYseQDDA/layer/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw"[
      },      "Neuro-degenerative"
{          "id":"agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYiaECDA"],
         "type":"E",Tumor / Tissue Type":[
            "uri":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYseQDDA/layer/agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYiaECDA" Visual Cortex",
         },   "Prefrontal cortex",
  {          "id":"agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYmfIBDA", Cerbellum"
         "type":"G"],
         "uriSpecies":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYseQDDA/layer/agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYmfIBDA"[
      }    ] }

Get Annotations for a Dataset

Request

Code Block

curl -i -H Accept:application/json "http://deflaux-test.appspot.com/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYseQDDA/annotations"

Response

Code Block

HTTP/1.1 200 OK
ETag: -1919132670
Content-Type: application/json
Date: Tue, 01 Feb 2011 18:24:15 GMT
Server: Google Frontend
Cache-Control: private, x-gzip-ok=""
Transfer-Encoding: chunked

{"Human"
         ],
         "Institution":[
            "id":"agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYseQDDA",HBTRC"
     "uri":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYseQDDA/annotations",    "etag":"-1919132670",],
     "creationDate":null,    "stringAnnotationsNumber of Samples":{
[
     "Disease":[       700.0
  "Cancer"       ],
      "Tumor}
/ Tissue Type":[ ]
}

Where clause

Currently only '==' is supported on either primary fields or annotations

Request

Code Block
curl -H Accept:application/json    "Glioblastoma"
      ],
      "Species":[
         "Human"
      ],
      "Institution-i 'http://deflaux-test.appspot.com/repo/v1/query?query=select+*+from+dataset+where+Species+==+"Human"'

Response

Code Block

{
   "totalNumberOfResults":10,
   "results":[
      {
  "TCGA"       ],
      "Reference / PubMed ID":[
         "18772890"      ]
   },
   "floatAnnotations":{"name":"Pediatric AML TARGET",
         "Number of Samplesid":["agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYgvcCDA",
         465"version":"0.0.1",
      ]    },"description":null,
     "dateAnnotations":{     }
}

Create a Dataset

Request:

Code Block

curl -i -H Accept:application/json -H Content-Type:application/json
-d '{"name":"test dataset", "creator":"fake creator", "releaseDate":"2009-10-01", "status":"not curated"}'
http://localhost:8080/repo/v1/dataset

Response

Code Block

HTTP/1.1 201 Created
ETag: 1736839268
Location: /repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYBAw
Content-Type: application/json
Transfer-Encoding: chunked
Server: Jetty(6.1.x)

{
   "name":"test dataset",
   "annotations":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw/annotations",
   "id":"agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw",
   "version":"0.0.1",
   "creator":"fake creator",
   "description":null,
   "creationDate":1296595870715,
   "status":"not curated",
   "uri":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw",
   "etag":"1309185941",
   "releaseDate":1254355200000,
   "layers":[]
}

Update a Dataset

Note that in the example below the creator and description fields have been changed but all others remain the same.

Request:

Code Block

curl -i -H Accept:application/json -H Content-Type:application/json -X PUT -H ETag:1309185941 -d '{
   "name":"test dataset",
   "annotations":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw/annotations",
   "id":"agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw",
   "version":"0.0.1",
   "creator":"updated creator",
   "description":"I just added a description",
   "creationDate":1296595870715,
   "status":"not curated",
   "uri":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw",
   "etag":"1309185941",
   "releaseDate":1254355200000,
   "layers":[]
}
' http://localhost:8080/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw

Response

Code Block

HTTP/1.1 200 OK
ETag: -852418664
Content-Type: application/json
Transfer-Encoding: chunked
Server: Jetty(6.1.x)

{"status":"In Transition",
         "creator":"Soheil Meshinchi",
         "creationDate":1296182253120,
         "releaseDate":null,
         "hasExpressionData":true,
         "hasGeneticData":false,
         "hasClinicalData":false,
         "Disease":[
            "Cancer"
         ],
         "Tumor / Tissue Type":[
            "AML (pediatric)"
         ],
         "Institution":[
            "FHCRC"
         ],
         "Species":[
            "Human"
         ],
         "Number of Samples":[
            200.0
         ]
      },
      {
         "name":"testGlioblastoma datasetTCGA",
    "annotations":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw/annotations",     "id":"agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQwagxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYseQDDA",
         "version":"0.0.1",
   "creator":"updated creator",      "description":"I just added a description",null,
         "creationDatestatus":1296595870715"Available",
    "status":"not curated",    "uri":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw",creator":null,
         "etagcreationDate":"-852418664"1296182238229,
         "releaseDate":1254355200000null,
         "layershasExpressionData":[]
}

Add Annotations to a Dataset

First get the empty annotations container for your newly created dataset

Request

Code Block

curl -i -H Accept:application/json http://localhost:8080/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw/annotations

Response

Code Block

HTTP/1.1 200 OK
ETag: 923521
Content-Type: application/json
Transfer-Encoding: chunked
Server: Jetty(6.1.x)

{true,
         "hasGeneticData":false,
         "hasClinicalData":false,
         "idDisease":"agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw",[
            "Cancer"
         ],
         "creationDateTumor / Tissue Type":null,[
       "uri":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw/annotations",     "etag":"923521",Glioblastoma"
    "stringAnnotations":{     }],
   "floatAnnotations      "Institution":{[
     },    "dateAnnotations":{   "TCGA"
 } }

Then you add/modify the annotations of interest and do a PUT. Note that annotation values must always be list values even if the list is only of length one.

Request

Code Block
 curl -i -H Accept:application/json -H Content-Type:application/json -X PUT -H ETag:923521 -d '{ ],
         "idSpecies":"agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw",[
            "Human"
         "creationDate":null,],
     "uri":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw/annotations",    "etagReference / PubMed ID":"923521",[
   "stringAnnotations":{         "Experimental1.877289E7
Design Templates":["exp-122887", "exp-97765"]    },   ],
"floatAnnotations":{         "Number of Samples":[500]
        },    "dateAnnotations":{465.0
        "Publication Date":["2011-01-15"]
   } }' http://localhost:8080/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw/annotations

Response

Code Block

HTTP/1.1 200 OK
ETag: -1638393853
Content-Type: application/json
Transfer-Encoding: chunked
Server: Jetty(6.1.x)

{ },
      {
         "idname":"agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYBwwTCGA Curation Package",
     "creationDate":null,    "uriid":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYBww/annotationsagxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYgfQDDA",
   "etag      "version":"-16383938530.0.1",
   "stringAnnotations":{
      "Experimental Design Templatesdescription":[null,
         "exp-122887status":"Available",
         "exp-97765"
creator":null,
     ]    },
   "floatAnnotations":{
      "Number of Samples":["creationDate":1296182242619,
         "releaseDate":null,
   500.0      "hasExpressionData":true,
 ]    },    "dateAnnotationshasGeneticData":{false,
         "Publication DatehasClinicalData":[false,
         1295049600000"Disease":[
      ]    } }

Delete a Dataset

Request

Code Block

curl -i -X DELETE http://localhost:8080/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw

Response

Code Block

HTTP/1.1 204 No Content
Server: Jetty(6.1.x)

Get a Layers for a Dataset

Request

Code Block

curl -i -H Accept:application/json http://localhost:8080/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer

Response

Code Block

HTTP/1.1 200 OK
Content-Type: application/json
Transfer-Encoding: chunked
Server: Jetty(6.1.x)

{
   "results":["Cancer"
         ],
         "Tumor / Tissue Type":[
            "Multiple"
         {],
         "nameInstitution":"Flint[
HS Mice Affy",          "annotations":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww/annotations",TCGA"
         "id":"agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww"],
         "typeSpecies":"E",[
         "version":"0.0.1",   "Human"
      "description":"this is a description"],
         "creationDate":1296690778880,Number of Samples":[
            2400.0
   "uri":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww",      ]
   "etag":"1424771925",   },
      "publicationDate":null,{
         "releaseNotesname":"thisHepatocellular is a release noteCarcinoma HongKong",
         "tissueTypeid":"liveragxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQY0YMEDA",
         "platformversion":null"0.0.1",
         "processingFacilitydescription":null,
         "qcBystatus":null"Available",
         "qcDatecreator":null"John Luk",
     },       {"creationDate":1296182245850,
         "namereleaseDate":"Flint HS Mice Phenotypes"null,
         "annotations":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjpBww/annotations"hasExpressionData":true,
         "idhasGeneticData":"agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjpBww"false,
         "typehasClinicalData":"C"false,
         "versionDisease":"0.0.1",[
            "description":"this is a description"Cancer"
         ],
         "creationDateTumor / Tissue Type":1296693007167,[
            "uri":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjpBww",HCC"
         "etag":"1445062754"],
         "publicationDateSpecies":null,
[
        "releaseNotes":"this is a release note"Human",
         "tissueType":null],
         "platformInstitution":null,[
            "processingFacilityHKU":null,
         "qcBy":null],
         "qcDateNumber of Samples":null[
            }250.0
   ],    "totalNumberOfResults":2,  ]
 "paging":{     },
}

Get a Layer

Request

Code Block

curl -i -H Accept:application/json http://localhost:8080/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww

Response

Code Block

HTTP/1.1 200 OK
ETag: 1240467407
Content-Type: application/json
Transfer-Encoding: chunked
Server: Jetty(6.1.x)

{      {
         "name":"Human Liver Cohort",
         "nameid":"Flint HS Mice Affy","agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYuYsEDA",
         "version":"0.0.1",
         "annotationsdescription":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww/annotations",null,
         "idstatus":"agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBwwAvailable",
         "typecreator":"EGuengrich, Strom, Schuetz",
         "versioncreationDate":"0.0.1",1296182248134,
         "descriptionreleaseDate":"this is a description",null,
         "creationDatehasExpressionData":1296690778880,true,
         "urihasGeneticData":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww",false,
         "etaghasClinicalData":"1240467407"false,
     "publicationDate":null,    "releaseNotesDisease":"this[
 is a release note",    "tissueType":null,    "platform":null,Cardiovascular Disease"
   "processingFacility":null,    "qcBy":null,  ],
 "qcDate":null }

Get annotations for a layer

Request

Code Block
curl -i -H Accept:application/json http://localhost:8080/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww/annotations

Response

Code Block
 HTTP/1.1 200 OK"Tumor ETag:/ 923521Tissue Content-Type":[
application/json
Transfer-Encoding: chunked
Server: Jetty(6.1.x)

{            "id":"agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww",Liver"
     "creationDate":null,    "uri":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww/annotations",],
     "etag":"923521",    "stringAnnotationsSpecies":{[
     },    "floatAnnotations":{   "Human"
 },    "dateAnnotations":{    ],
} }

Create a layer

Request

Code Block
 curl -i -H Accept:application/json -H Content-Type:application/json -d '{"nameInstitution":"Flint[
HS Mice Affy", "type":"E", "description":"this is a description", "releaseNotes":"this is a release note"}' http://localhost:8080/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer

Response

Code Block

HTTP/1.1 201 Created
ETag: 1240467407
Location: /repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww
Content-Type: application/json
Transfer-Encoding: chunked
Server: Jetty(6.1.x)

{" Pittsburg",
            " St. Judes",
            "name":"Flint HS Mice Affy",Vanderbilt"
         "annotations":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww/annotations"],
   "id":"agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww",      "typeReference / PubMed ID":"E",[
   "version":"0.0.1",    "description":"this is a description",  1.8462016E7
 "creationDate":1296690778880,    "uri":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww",    "etag":"1240467407",],
     "publicationDate":null,    "releaseNotesNumber of Samples":"this[
 is a release note",    "tissueType":null,    "platform":null,517.0
   "processingFacility":null,    "qcBy":null,  ]
 "qcDate":null }

Now ask for the owning dataset and you can see the preview of the layer

Request

Code Block
 curl -i -H Accept:application/json http://localhost:8080/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww

Response

Code Block

HTTP/1.1 200 OK
ETag: -801135512
Content-Type: application/json
Transfer-Encoding: chunked
Server: Jetty(6.1.x)

{},
      {
         "name":"FlintMETABRIC HSBreast MiceCancer",
"annotations":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/annotations",
         "id":"agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUwwagxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYoZMEDA",
         "version":"0.0.1",
"creator":"Jonathan Flint",
         "description":null,
"creationDate":1296690549675,         "status":"FutureIn Transition",
         "uricreator":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww"Aparicio, Caldas"etag":"-801135512",
"releaseDate         "creationDate":null1296182250209,
"layers":[ {
         "idreleaseDate":"agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww"null,
         "typehasExpressionData":"E"true,
         "uri":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww"hasGeneticData":false,
         }"hasClinicalData":false,{
         "idDisease":"use this uri to make a new layer",[
            "Cancer"
         "type":"hack"],
         "uri":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer"Tumor / Tissue Type":[
      } ] }

Update a Layer

In the example below we updated the tissue type.

Request

Code Block
 curl -i -H Accept:application/json -H Content-Type:application/json -X PUT -H ETag:1240467407 -d '
{
   "name":"Flint HS Mice Affy", "Breast"
         ],
         "annotationsInstitution":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww/annotations",[
    "id":"agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww",    "type":"E",    "version":"0.0.1",BCCA Cambridge"
    "description":"this is a description",  ],
 "creationDate":1296690778880,    "uri":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww",    "etagSpecies":"1240467407",[
            "publicationDate":null,Human"
     "releaseNotes":"this is a release note"],
    "tissueType":"liver",     "Number of Samples":[
       "platform":null,    "processingFacility":null,
 1500.0
  "qcBy":null,    "qcDate":null }' http://localhost:8080/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww

Response

Code Block

HTTP/1.1 200 OK
ETag: 1424771925
Content-Type: application/json
Transfer-Encoding: chunked
Server: Jetty(6.1.x)

{
     ]
      },
      {
         "name":"FlintHarvard Brain HSTissue MiceResource AffyCenter",
     "annotations":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww/annotations",    "id":"agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBwwagxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYiZsEDA",
     "type":"E",    "version":"0.0.1",,
         "description":"thisnull,
is a description",    "creationDate":1296690778880,    "uristatus":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBwwIn Transition",
         "etagcreator":"1424771925Francine Benes",
         "publicationDatecreationDate":null1296182251551,
   "releaseNotes":"this is a release note",      "releaseDate":null,
         "tissueTypehasExpressionData":"liver"true,
   "platform":null,      "processingFacilityhasGeneticData":nullfalse,
    "qcBy":null,     "qcDatehasClinicalData":nullfalse,
}

Delete a layer

Request

Code Block
 curl -i -X DELETE http://localhost:8080/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww

Response

Code Block
 HTTP/1.1 204 No Content
Server: Jetty(6.1.x)

Add annotations to a layer

Request

Code Block

curl -i -H Accept:application/json -H Content-Type:application/json -X PUT -H ETag:923521 -d '
{
   "id":"agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww",
   "creationDate":null,
   "uri":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww/annotations",
   "etag":"923521",
   "stringAnnotations":{ "Disease":[
            "Neuro-degenerative"
         ],
         "Tumor / Tissue Type":[
            "notes":["I threw away 6 samples during the curation process due to gender chromosome mismatches"] Visual Cortex",
            "Prefrontal cortex",
        },    "floatAnnotations Cerbellum":{
    },    "dateAnnotations":{ ],
   } }' http://localhost:8080/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww/annotations

Response

Code Block
 HTTP/1.1 200 OK
ETag: -1897035229
Content-Type: application/json
Transfer-Encoding: chunked
Server: Jetty(6.1.x)

{ "Species":[
            "id":"agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww",Human"
         "creationDate":null],
    "uri":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww/annotations",     "etagInstitution":"-1897035229",[
     "stringAnnotations":{       "notesHBTRC":[
         "I],
threw away 6 samples during the curation process due to"Number gender chromosome mismatches"of Samples":[
       ]    }, 700.0
  "floatAnnotations":{     },  ]
 "dateAnnotations":{     }
   ]
}