Page Comparison

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HTTP/1.1 201 Created
Content-Type: application/json
Date: Thu, 13 Sep 2012 02:33:06 GMT
ETag: c5dc66a6-c864-4886-a8f1-25c4c84ba48b
Location: /repo/v1/entity/syn1151499
Server: Apache-Coyote/1.1
Content-Length: 620
Connection: keep-alive
{
   "s3Token":"/repo/v1/entity/syn1151499/s3Token",
   "versionLabel":"0.0.0",
   "etag":"c5dc66a6-c864-4886-a8f1-25c4c84ba48b",
   "accessControlList":"/repo/v1/entity/syn1151499/acl",
   "versionUrl":"/repo/v1/entity/syn1151499/version/1",
   "modifiedBy":"John Hill",
   "entityType":"org.sagebionetworks.repo.model.Data",
   "uri":"/repo/v1/entity/syn1151499",
   "id":"syn1151499",
   "createdOn":"2012-09-13T02:33:06.314Z",
   "modifiedOn":"2012-09-13T02:33:06.314Z",
   "parentId":"syn1058078",
   "versions":"/repo/v1/entity/syn1151499/version",
   "createdBy":"John Hill",
   "name":"Sample Data",
   "annotations":"/repo/v1/entity/syn1151499/annotations",
   "versionNumber":1
}

Entity Annotations

Get Annotations

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HTTP/1.1 200 OK
Content-Type: application/json
Date: Thu, 13 Sep 2012 02:38:03 GMT
ETag: c5dc66a6-c864-4886-a8f1-25c4c84ba48b
Server: Apache-Coyote/1.1
Content-Length: 244
Connection: keep-alive
{
   "id":"syn1151499",
   "creationDate":"1347503586314",
   "stringAnnotations":{
   },
   "dateAnnotations":{
   },
   "etag":"c5dc66a6-c864-4886-8f1-25c4c84ba48b",
   "doubleAnnotations":{
   },
   "longAnnotations":{
   },
   "blobAnnotations":{
   },
   "uri":"/entity/syn1151499/annotations"
}

Update Annotations

Then you add new annotations to the existing annotations, or modify the existing annotations, and do a PUT. Note that annotation values must always be arrays even if the array is only of length one.

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1. Create an S3 Token.  We will use this token to upload the file to Amazon's S3.
   

   1. Request

      Code Block
      curl -i -k -H sessionToken:YourSessionToken -H Accept:application/json -H Content-Type:application/json -d '{"path": "SampleTextFile.txt", "md5":"6b65ca38d3596e0e0e6e1ed3cfa981eb"}' https://repo-prod.sagebase.org/repo/v1/entity/syn1151499/s3Token

      Response

      Expand
      title [Click to show]
      Code Block { "sessionToken":"AQoDYXdzEG4asAKFXWZXVmnAG7q1zyUzRjVz6rnN6wIRT0msXgSRBC3suTAItfuQjJRv9YOAw3Fr4nlJL2HAnRbNvF1NC4xnW5+j6VUNnJYGtZUj+wii+bTGYncNrruXLxqqLM8Kg/dmGQGWluVZkYy7rLDbofrWcWunRjSYBb7uEe74EURM1jg1ae3qMnNgwBUHWJvJb1AjOojpNujh0N5KX0C3ux6VCDcFrgHR6K+siyfiPqSW25XmabA5jGAnV6EGXn1iazywrl2ZW8z+fYAZB1kgsoTCQgCZMsPxpXxh/BdQi7cc7rwflCr/P1wD51N9PGFakFhJkbm8glGhE+YQDYEOpvRmOF0+S2+xrstIzsEAoZ5NXmMg97pqOWx1sBQVvKp8NXgdkXn422CFJLFPW8u+Vd/HzO6EILnQxYIF", "secretAccessKey":"XXXXXXXXXXXXXXXXX", "bucket":"proddata.sagebase.org", "path":"/1151499/1159148/SampleTextFile.txt", "accessKeyId":"XXXXXXXXXXXXXXXXXXXX", "md5":"6b65ca38d3596e0e0e6e1ed3cfa981eb", "contentType":"text/plain", "presignedUrl":"https://s3.amazonaws.com/proddata.sagebase.org/1151499/1159148/SampleTextFile.txt?Expires=1347598777&x-amz-security-token=AQoDYXdzEG4asAKFXWZXVmnAG7q1zyUzRjVz6rnN6wIRT0msXgSRBC3suTAItfuQjJRv9YOAw3Fr4nlJL2HAnRbNvF1NC4xnW5%2Bj6VUNnJYGtZUj%2Bwii%2BbTGYncNrruXLxqqLM8Kg%2FdmGQGWluVZkYy7rLDbofrWcWunRjSYBb7uEe74EURM1jg1ae3qMnNgwBUHWJvJb1AjOojpNujh0N5KX0C3ux6VCDcFrgHR6K%2BsiyfiPqSW25XmabA5jGAnV6EGXn1iazywrl2ZW8z%2BfYAZB1kgsoTCQgCZMsPxpXxh%2FBdQi7cc7rwflCr%2FP1wD51N9PGFakFhJkbm8glGhE%2BYQDYEOpvRmOF0%2BS2%2BxrstIzsEAoZ5NXmMg97pqOWx1sBQVvKp8NXgdkXn422CFJLFPW8u%2BVd%2FHzO6EILnQxYIF&AWSAccessKeyId=ASIAIGRZMDNEEK777KGA&Signature=c%2BC0HOBQ2MOzS4L89ev4OPbzD1w%3D" }

2. Use the "presignedUrl" from the previous step to upload the file to Amazon S3:  Note: For more information on uploading files to S3 see: http://docs.amazonwebservices.com/AmazonS3/latest/API/RESTObjectPUT.html
   
   1. Request 
      
      

      Code Block

      curl -v -k -X PUT -H Content-MD5:a2XKONNZbg4Obh7Tz6mB6w== -H x-amz-acl:bucket-owner-full-control -H Content-Type:text/plain --data-ascii SampleTextFile.txt https://s3.amazonaws.com/proddata.sagebase.org/1151499/1159148/SampleTextFile.txt?Expires=1347598777&x-amz-security-token=AQoDYXdzEG4asAKFXWZXVmnAG7q1zyUzRjVz6rnN6wIRT0msXgSRBC3suTAItfuQjJRv9YOAw3Fr4nlJL2HAnRbNvF1NC4xnW5%2Bj6VUNnJYGtZUj%2Bwii%2BbTGYncNrruXLxqqLM8Kg%2FdmGQGWluVZkYy7rLDbofrWcWunRjSYBb7uEe74EURM1jg1ae3qMnNgwBUHWJvJb1AjOojpNujh0N5KX0C3ux6VCDcFrgHR6K%2BsiyfiPqSW25XmabA5jGAnV6EGXn1iazywrl2ZW8z%2BfYAZB1kgsoTCQgCZMsPxpXxh%2FBdQi7cc7rwflCr%2FP1wD51N9PGFakFhJkbm8glGhE%2BYQDYEOpvRmOF0%2BS2%2BxrstIzsEAoZ5NXmMg97pqOWx1sBQVvKp8NXgdkXn422CFJLFPW8u%2BVd%2FHzO6EILnQxYIF&AWSAccessKeyId=ASIAIGRZMDNEEK777KGA&Signature=c%2BC0HOBQ2MOzS4L89ev4OPbzD1w%3D

3. Once the file has been successfully uploaded to S3 update the Entity using the S3 Token:
   

   1. Request

      Code Block

      curl -i -k -H sessionToken:YourSessionToken -H ETag:2526dd09-565e-4989-b8c4-a82e724672c6 -H Accept:application/json -H Content-Type:application/json -X PUT -d '{ "s3Token":"/repo/v1/entity/syn1151499/s3Token", "versionLabel":"0.0.0", "etag":"2526dd09-565e-4989-b8c4-a82e724672c6", "accessControlList":"/repo/v1/entity/syn1151499/acl", "versionUrl":"/repo/v1/entity/syn1151499/version/1", "modifiedBy":"John Hill", "contentType":"text/plain", "entityType":"org.sagebionetworks.repo.model.Data", "uri":"/repo/v1/entity/syn1151499", "id":"syn1151499", "createdOn":"2012-09-12T19:33:06.314-07:00", "modifiedOn":"2012-09-12T19:44:39.544-07:00", "parentId":"syn1058078", "versions":"/repo/v1/entity/syn1151499/version", "createdBy":"John Hill", "locations":[ { "path":"/1151499/1158826/SampleTextFile.txt", "type":"awss3" } ], "name":"Sample Data", "md5":"6b65ca38d3596e0e0e6e1ed3cfa981eb", "annotations":"/repo/v1/entity/syn1151499/annotations", "versionNumber":1 }' https://repo-prod.sagebase.org/repo/v1/entity/syn1151499

      Response

       

      Expand
      title [Click to show]
      Code Block HTTP/1.1 200 OK Content-Type: application/json Date: Thu, 13 Sep 2012 05:10:20 GMT ETag: 0bf4af7b-0dc9-4c5c-9454-3931bcf08a17 Server: Apache-Coyote/1.1 Content-Length: 1382 Connection: keep-alive { "s3Token":"/repo/v1/entity/syn1151499/s3Token", "versionLabel":"0.0.0", "etag":"0bf4af7b-0dc9-4c5c-9454-3931bcf08a17", "accessControlList":"/repo/v1/entity/syn1151499/acl", "versionUrl":"/repo/v1/entity/syn1151499/version/1", "modifiedBy":"John Hill", "contentType":"text/plain", "entityType":"org.sagebionetworks.repo.model.Data", "uri":"/repo/v1/entity/syn1151499", "id":"syn1151499", "createdOn":"2012-09-13T02:33:06.314Z", "modifiedOn":"2012-09-13T05:12:26.121Z", "parentId":"syn1058078", "versions":"/repo/v1/entity/syn1151499/version", "createdBy":"John Hill", "locations":[ { "path":"https://s3.amazonaws.com/proddata.sagebase.org/1151499/1158826/SampleTextFile.txt?Expires=1347599546&x-amz-security-token=AQoDYXdzEG4asAKml38O7Ej08SS50xD7p84phJD9YjcylB6FmjsrDCyGKdb7rpC8GsZloCFT3jd5pVdLDMo58SgDFYNPZjGzg%2BpA6AWk0HTIirwdJvQCdq2KnImv3NMWmvnULs%2B%2Fbbkl6V6C0EPK5W8EhZsCtH55zuOofEpVnNk9BrhhU0VcmStaCevCv6eaCHJw5DsmIsnOlKswGnoibuEAh7WA2JTTU4sg6aDrzYCnDL6MgGxxtnNw7%2B5N9GPmrfLRk7NdqqF2NulYpv%2BH5ZmALdW1YjRAB8C9o9SGPX8nQci1e2r5cGIJyNc6kuw1Fzs0vhRKBH3Jz%2FMR3hdqE7zQmMp5x%2F4eAtgm09GKhPC1kH%2BJdrMFP0i6N%2BmPsQVF4lNx0yhVCwIbC%2BRxYFAIzmiredqAKbvhsOKeILrWxYIF&AWSAccessKeyId=ASIAJNRHQYY4PXQAD3YA&Signature=jtY54hJMHqhWoBiHEsbVIUWipuQ%3D", "type":"awss3" } ], "name":"Sample Data", "md5":"6b65ca38d3596e0e0e6e1ed3cfa981eb", "annotations":"/repo/v1/entity/syn1151499/annotations", "versionNumber":1 }

Versions Create/Read/Update/Delete

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HTTP/1.1 200 OK
Content-Type: application/json
Date: Wed, 05 Oct 2011 16:34:48 GMT
ETag: 0
Server: Apache-Coyote/1.1
Content-Length: 675
Connection: keep-alive

{
  "accessControlList": "/repo/v1/location/17338/acl",
  "annotations": "/repo/v1/location/17338/annotations",
  "contentType": "application/zip",
  "creationDate": 1317832487819,
  "etag": "0",
  "id": "17338",
  "md5sum": "b513a23fc54b7b0d65312e1a900af5a6",
  "name": "17338",
  "parentId": "17337",
  "path": "https://s3.amazonaws.com/stagingdata.sagebase.org/17338/0.0.0/mskcc_prostate_cancer.phenotype.zip?Expires=1317918889&AWSAccessKeyId=AKIAJQBSYCAUPIYF5WTA&Signature=2vTczuWgJ88Z0tiau1%2BPse4L2NA%3D",
  "type": "awss3",
  "uri": "/repo/v1/location/17338",
  "versionComment": null,
  "versionLabel": "0.0.0",
  "versionNumber": 1,
  "versionUrl": "/repo/v1/location/17338/version/1",
  "versions": "/repo/v1/location/17338/version"
}

Create New Version

To create a new version of a location, we set the version comment and label. We also want to set a new path for this version:

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