Versions Compared

Old Version 3

changes.mady.by.user Nicole Deflaux

Saved on

compared with

New Version 4

changes.mady.by.user Nicole Deflaux

Saved on

Key

  • This line was added.
  • This line was removed.
  • Formatting was changed.

...

In requests to the service, dates can be serialized either as long integers expressing epoch time or human readable dates in http://www.ietf.org/rfc/rfc3339.txt format such as '2011-01-31' or '2011-01-31T22:00:00'

Usage Examples

Get a Dataset

...

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.

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/agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYseQDDA/annotations",
   "id":"agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYseQDDA",
   "version":"0.0.1",
   "description":null,
   "status":"Available",
   "uri":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYseQDDA",
   "etag":"456728335",
   "creator":null,
   "creationDate":1296182238229,
   "releaseDate":null,
   "layers":[
      {
         "id":"agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw",
         "type":"C",
         "uri":"/datalayer/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw"
      },
      {
         "id":"agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYiaECDA",
         "type":"E",
         "uri":"agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYiaECDA"
      },
      {
         "id":"agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYmfIBDA",
         "type":"G",
         "uri":"/datalayer/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

{
   "id":"agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYseQDDA",
   "uri":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYseQDDA/annotations",
   "etag":"-1919132670",
   "creationDate":null,
   "stringAnnotations":{
      "Disease":[
         "Cancer"
      ],
      "Tumor / Tissue Type":[
         "Glioblastoma"
      ],
      "Species":[
         "Human"
      ],
      "Institution":[
         "TCGA"
      ],
      "Reference / PubMed ID":[
         "18772890"      ]
   },
   "floatAnnotations":{
      "Number of Samples":[
         465.0
      ]
   },
   "dateAnnotations":{

   }
}

Get Datasets

Optional Parameters

  • offset - integer - 1-based pagination offset
  • limit - integer - maximum number of results to return
  • sort - string - the name of the primary field upon which to sort
  • ascending - boolean - whether or not to sort ascending

Request

Code Block

curl -i -H Accept:application/json "http://deflaux-test.appspot.com/repo/v1/dataset?limit=3"

Response

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,
         "layers":[
            {
               "id":"agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw",
               "type":"C",
               "uri":"/datalayer/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw"
            },
            {
               "id":"agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYiaECDA",
               "type":"E",
               "uri":"agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYiaECDA"
            },
            {
               "id":"agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYseQDDAagxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYmfIBDA",
       "version":"0.0.1",    "description":null,    "statustype":"AvailableG",
   "uri":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYseQDDA",    "etag":"456728335",    "creator":null,    "creationDateuri":1296182238229,"/datalayer/agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYmfIBDA"
     "releaseDate":null,    "layers":[   }
   {      ]
   "id":"agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw",   },
      "type":"C",{
         "uriname":"/datalayer/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw"Flint HS Mice",
    },       {"annotations":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQY2q0DDA/annotations",
         "id":"agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYiaECDAagxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQY2q0DDA",
         "typeversion":"E0.0.1",
         "uridescription":"agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYiaECDA"null,
      },    "status":"Future",
  {          "iduri":"agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYmfIBDA/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQY2q0DDA",
         "typeetag":"G1025901212",
         "uricreator":"/datalayer/agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYmfIBDA"Jonathan Flint",
      }   "creationDate":1296182255070,
 ] }

Get Annotations for a Dataset

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

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

{ "releaseDate":null,
         "layers":[
            {
               "id":"agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYseQDDAagxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw",
   "uri            "type":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYseQDDA/annotationsC",
        "etag       "uri":"-1919132670",/datalayer/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw"
   "creationDate":null,    "stringAnnotations":{     },
 "Disease":[          "Cancer" {
     ],       "Tumor / Tissue Type"id":["agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYiaECDA",
         "Glioblastoma"       ],"type":"E",
        "Species":[       "uri":"agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYiaECDA"
  "Human"       ],   },
   "Institution":[         {
"TCGA"       ]    },    "floatAnnotationsid":{"agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYmfIBDA",
      "Number of Samples":[        "type":"G",
 465.0       ],       "Reference / PubMed ID":[uri":"/datalayer/agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYmfIBDA"
         1.877289E7   }
   ]    },  ]
 "dateAnnotations":{     },
 }

Get Datasets

Optional Parameters

  • offset - integer - 1-based pagination offset
  • limit - integer - maximum number of results to return
  • sort - string - the name of the primary field upon which to sort
  • ascending - boolean - whether or not to sort ascending
Code Block

curl -i -H Accept:application/json "http://deflaux-test.appspot.com/repo/v1/dataset?limit=3"

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":"Glioblastoma TCGA",
         "annotations":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYseQDDA/annotations",
         "id":"agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYseQDDA",
         "version":"0.0.1",
         {"description":null,
         "namestatus":"Pediatric AML TARGETAvailable",
         "annotationsuri":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYgvcCDA/annotationsagxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYseQDDA",
         "etag":"456728335",
         "idcreator":"agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYgvcCDA"null,
         "versioncreationDate":"0.0.1"1296182238229,
         "descriptionreleaseDate":null,
         "statuslayers":"In Transition",[
            {
     "uri":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYgvcCDA",          "etagid":"1703131409",agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw",
               "creatortype":"Soheil MeshinchiC",
         "creationDate":1296182253120,      "uri":"/datalayer/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw"
   "releaseDate":null,          "layers":[},
            {
               "id":"agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQwagxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYiaECDA",
               "type":"CE",
               "uri":"/datalayer/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQwagxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYiaECDA"
            },
            {
               "id":"agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYiaECDAagxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYmfIBDA",
               "type":"EG",
               "uri":"agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYiaECDA""/datalayer/agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYmfIBDA"
            }
     },    ]
      }
 {  ],
   "totalNumberOfResults":10,
   "paging":{
      "idnext":"agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYmfIBDA",/repo/v1/dataset?offset=4&limit=3"
   }
}

Create a Dataset

Request:

Code Block
curl -i        "type":"G",
               "uri":"/datalayer/agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYmfIBDA"
            }
         ]
      },
      {
         "name":"Flint HS Mice",
     -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/agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQY2q0DDAagxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw/annotations",
     
   "id":"agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQY2q0DDAagxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw",
         "version":"0.0.1",
     "creator":"fake creator",
   "description":null,
     "creationDate":1296595870715,
   "status":"Futurenot curated",
  
      "uri":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQY2q0DDAagxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw",
   "etag":"1309185941",
     "etagreleaseDate":"1025901212"1254355200000,
   "layers":[
     "creator":"Jonathan Flint", {
         "creationDateid":1296182255070"agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw",
         "type"releaseDate:"C":null,
         "layersuri":["/datalayer/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw"
      },
      {
               "id":"agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQwagxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYiaECDA",
               "type":"CE",
     
         "uri":"/datalayer/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw"
   agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYiaECDA"
        },
     
      {
               "id":"agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYiaECDAagxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYmfIBDA",
     
         "type":"EG",
     
         "uri":"agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYiaECDA/datalayer/agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYmfIBDA"
      }
    ]
},
            {

Add Annotations to a Dataset

Code Block
Update a Dataset
Note that 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 '{
   "idname":"agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYmfIBDAtest dataset",
           "annotations":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw/annotations",
   "typeid":"GagxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw",
 
             "uri"version":"/datalayer/agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYmfIBDA"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":[
     "name":"Glioblastoma TCGA", {
         "annotationsid":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYseQDDA/annotationsagxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw",
         "idtype":"agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYseQDDAC",
         "versionuri":"0.0.1",/datalayer/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw"
      },
      "description":null,{
         "statusid":"AvailableagxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYiaECDA",
         "uritype":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYseQDDAE",
         "etaguri":"456728335",agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYiaECDA"
      },
      "creator":null,{
         "creationDateid":1296182238229"agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYmfIBDA",
         "releaseDatetype":null"G",
         "layersuri":["/datalayer/agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYmfIBDA"
      }
   ]
}
' 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)

 {
   "idname":"agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQwtest dataset",
           "annotations":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw/annotations",
   "typeid":"CagxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw",
    
          "uri"version":"/datalayer/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw"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,
   "idlayers":"agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYiaECDA",[
      {
         "typeid":"EagxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw",
     
         "uritype":"agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYiaECDAC",
         "uri":"/datalayer/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw"
  },      },
      {
 
             "id":"agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYmfIBDAagxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYiaECDA",
     
         "type":"GE",
     
         "uri":"/datalayer/agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYmfIBDAagxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYiaECDA"
      },
     } {
        ]
     "id":"agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYmfIBDA",
 }    ],    "totalNumberOfResultstype":10"G",
   "paging":{
      "nexturi":"/repo/v1/dataset?offset=4&limit=3"datalayer/agxkZWZsYXV4LXRlc3RyFQsSDUdBRUpET0RhdGFzZXQYmfIBDA"
      }
   ]
}

Create a Dataset
...
Add Annotations to a Dataset
...
Update a Dataset
code
Delete a Dataset
 Code Block