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changes.mady.by.user John Hill

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...

Code Block
curl -i -k -H sessionToken:XXXXXXXXXXXXXYourSessionToken -H ETag:0 -H Accept:application/json -H Content-Type:application/json -X PUT -d '{
   "createdOn":"2012-08-29T03:34:00.967Z",
   "id":"syn1058078",
   "parentId":"syn4489",
   "modifiedOn":"2012-08-29T03:34:00.967Z",
   "createdBy":"John Hill",
   "accessControlList":"/repo/v1/entity/syn1058078/acl",
   "etag":"0",
   "modifiedBy":"John Hill",
   "name":"Example Project",
   "annotations":"/repo/v1/entity/syn1058078/annotations",
   "entityType":"org.sagebionetworks.repo.model.Project",
   "uri":"/repo/v1/entity/syn1058078"
}' https://repo-prod.sagebase.org/repo/v1/entity/syn1058078

...

Code Block
curl -i -k -H sessionToken:YourSessionToken -H Accept:application/json -H Content-Type:application/json -d '{"entityType": "org.sagebionetworks.repo.model.FolderData", "parentId":"syn1058078", "name":"Sample FolderData"}' https://repo-prod.sagebase.org/repo/v1/entity

...

Code Block
HTTP/1.1 201 Created
Content-Type: application/json
Date: Thu, 13 Sep 2012 0002:4633:1006 GMT
ETag: b6c9ab19c5dc66a6-c5edc864-43ef4886-9fa2a8f1-ae72a8d63bab25c4c84ba48b
Location: /repo/v1/entity/syn1144716syn1151499
Server: Apache-Coyote/1.1
Content-Length: 436620
Connection: keep-alive
{
   "createdOns3Token":"2012-09-13T00:46:11.700Z/repo/v1/entity/syn1151499/s3Token",
   "versionLabel":"0.0.0",
   "idetag":"syn1144716c5dc66a6-c864-4886-a8f1-25c4c84ba48b",
   "parentIdaccessControlList":"syn1058078/repo/v1/entity/syn1151499/acl",
   "modifiedOnversionUrl":"2012-09-13T00:46:11.700Z/repo/v1/entity/syn1151499/version/1",
   "createdBymodifiedBy":"John Hill",
   "entityType":"org.sagebionetworks.repo.model.Data",
   "accessControlListuri":"/repo/v1/entity/syn1144716/aclsyn1151499",
   "id":"syn1151499",
   "etagcreatedOn":"b6c9ab192012-c5ed-43ef-9fa2-ae72a8d63bab09-13T02:33:06.314Z",
   "modifiedBymodifiedOn":"John Hill2012-09-13T02:33:06.314Z",
   "nameparentId":"Sample Foldersyn1058078",
   "annotationsversions":"/repo/v1/entity/syn1144716/annotationssyn1151499/version",
   "createdBy":"John Hill",
   "entityTypename":"org.sagebionetworks.repo.model.FolderSample Data",
   "uriannotations":"/repo/v1/entity/syn1144716"/syn1151499/annotations",
   "versionNumber":1
}

 

 

...

Entity Annotations

Get

...

Annotations

First get the current annotations for your newly created datasetdata entity.

Request

Code Block
curl -i -k -H sessionToken:YourSessionToken -H Accept:application/json 'https://repo-stagingprod.sagebase.org/repo/v1/datasetentity/17336syn1151499/annotations'

Response

Code Block
HTTP/1.1 200 OK
Content-Type: application/json
Date: WedThu, 0513 OctSep 20112012 1602:3438:4603 GMT
ETag: 1c5dc66a6-c864-4886-a8f1-25c4c84ba48b
Server: Apache-Coyote/1.1
transferContent-encodingLength: chunked244
Connection: keep-alive
{
{   "blobAnnotationsid": {},"syn1151499",
   "creationDate":"1347503586314",
1317832486693,   "dateAnnotationsstringAnnotations":{
  { },
   "doubleAnnotationsdateAnnotations":{
   {},
   "etag": "1"c5dc66a6-c864-4886-8f1-25c4c84ba48b",
   "iddoubleAnnotations": "17336"{
   },
   "longAnnotations":{
   {},
   "stringAnnotationsblobAnnotations":{
   {},
   "uri": "/repoentity/v1syn1151499/dataset/17336/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.

Request

Code Block
curl -i -k -H sessionToken:YourSessionTokenEHtmrVNnzOkyrZTqQTyycw00 -H ETag:1843bddfc-d6f8-45d2-b88e-09b4aa27a1cf -H Accept:application/json -H Content-Type:application/json -X PUT -d '
{
   "blobAnnotationsid": {},"syn1151499",
   "creationDate":"1347503586314",
1317832486693,   "dateAnnotationsstringAnnotations": {"last_modified_date": ["2009-03-06"]},{
      "doubleAnnotationsstringExampleA":[
{},    "etag": "1",   "id": "17336one",
   "longAnnotations": {     "Number_of_Samplestwo":
[218],     "number_of_downloads": [32],
    "number_of_followers  "stringExampleB": [7],[
         "pubmed_id": [2.0579941E7]cat",
      },   "stringAnnotationsdog":
{     "Disease": ["Cancer"],
    "Institution": ["Memorial Sloan Kettering Cancer Center"],},
   "dateAnnotations":{
      "dateExample":[
       "Internal_Name": ["Prostate cancer-MSKCC"] 1347519600000,
    "Posting_Restriction": ["unspecified"],     1347606000000
     "Species": ["Human"]]
   },
    "Tissue_Tumoretag": ["Prostate"],
"843bddfc-d6f8-45d2-b88e-09b4aa27a1cf",
   "TypedoubleAnnotations": ["GCD"],{
      "citationfloatExample": ["Integrative genomic profiling of human prostate cancer. Taylor BS, Schultz N, Hieronymus H, Gopalan A, Xiao Y, Carver BS, Arora VK, Kaushik P, Cerami E, Reva B, Antipin Y, Mitsiades N, Landers T, Dolgalev I, Major JE, Wilson M, Socci ND, Lash AE, Heguy A, Eastham JA, Scher HI, Reuter VE, Scardino PT, Sander C, Sawyers CL, Gerald WL. Cancer Cell. 2010 Jul 13;18(1):11-22.  "]
  },[
         1.234,
         99.789
      ]
   },
   "longAnnotations":{
      "longExample":[
         123,
         456879
      ]
   },
   "blobAnnotations":{

   },
   "uri": "/repoentity/v1syn1151499/dataset/17336/annotations"
}' https://repo-stagingprod.sagebase.org/repo/v1/datasetentity/17336syn1151499/annotations

Response

Code Block
HTTP/1.1 200 OK
Content-Type: application/json
Date: WedThu, 0513 OctSep 20112012 1602:3451:4754 GMT
ETag: 22526dd09-565e-4989-b8c4-a82e724672c6
Server: Apache-Coyote/1.1
transferContent-encodingLength: chunked403
Connection: keep-alive
{
{   "blobAnnotationsid": {},"syn1151499",
   "creationDate":"1347503586314",
1317832486693,   "dateAnnotationsstringAnnotations":{
      {"last_modified_datestringEampleB":[
 [1236297600000]},   "doubleAnnotations": {},   "etag": "2cat",
     "id": "17336",   "longAnnotationsdog":
{     "Number_of_Samples": [218],
    "number_of_downloads  "stringExampleA": [32],[
         "number_of_followers": [7],one",
         "pubmed_id": [20579941]two"
      ]
   },
   "stringAnnotationsdateAnnotations":{
{      "DiseasedateEample": ["Cancer"],
    "Institution": ["Memorial Sloan Kettering Cancer Center"]1347519600000,
      "Internal_Name": ["Prostate cancer-MSKCC"], 1347606000000
   "Posting_Restriction": ["unspecified"],  ]
  "Species": ["Human"],
 },
   "Tissue_Tumoretag": ["Prostate"]"2526dd09-565e-4989-b8c4-a82e72467c6",
    "TypedoubleAnnotations": ["GCD"],{
      "citationfloatExample": ["Integrative
genomic profiling of human prostate cancer. Taylor BS, Schultz N, Hieronymus H, Gopalan A, Xiao Y, Carver BS, Arora VK, Kaushik P, Cerami E, Reva B, Antipin Y, Mitsiades N, Landers T, Dolgalev I, Major JE, Wilson M, Socci ND, Lash AE, Heguy A, Eastham JA, Scher HI, Reuter VE, Scardino PT, Sander C, Sawyers CL, Gerald WL. Cancer Cell. 2010 Jul 13;18(1):11-22.  "]
  },1.234,
         99.789
      ]
   },
   "longAnnotations":{
      "longExample":[
         123,
         456879
      ]
   },
   "blobAnnotations":{

   },
   "uri": "/repoentity/v1/datasetsyn1151499/17336/annotations"
}

Add a Layer to a Dataset

Create a new layer object and set its parentId to be that of the dataset

Request

...

The PUT the data to S3

Then PUT the data to S3 via an HTTP Client that supports multipart upload. Note that you must:

  1. Add header Content-Type: <location.contentType>
  2. Add header Content-MD5: <the base64 encoded md5 checksum>
  3. Add header x-amz-acl: bucket-owner-full-control

Here is an example with curl:

Code Block
curl -v -X PUT -H Content-MD5:tROiP8VLew1lMS4akAr1pg== -H x-amz-acl:bucket-owner-full-control \
 -H Content-Type:application/jsonzip --data-dbinary '{
  "name": "phenotypes",
  "numSamples": "261",
  "parentId": "17336",
  "platform": "",
  "status": "curated",
  "type": "C",
  "version": "1.0.0"
}' https://repo-staging@<localFilepath> \
'https://s3.amazonaws.com/stagingdata.sagebase.org/repo/v1/layer

Response

Code Block
HTTP/1.1 201 Created
Content-Type: application/json
Date: Wed, 05 Oct 2011 16:34:47 GMT
ETag: 0
Location: /repo/v1/layer/17337
Server: Apache-Coyote/1.1
transfer-encoding: chunked
Connection: keep-alive

{
  "accessControlList": "/repo/v1/layer/17337/acl",
  "annotations": "/repo/v1/layer/17337/annotations",
  "creationDate": 1317832487612,
  "description": null,
  "etag": "0",
  "id": "17337",
  "locations": "/repo/v1/layer/17337/location",
  "name": "phenotypes",
  "numSamples": 261,
  "parentId": "17336",
  "platform": "",
  "previews": "/repo/v1/layer/17337/preview",
  "processingFacility": null,
  "publicationDate": null,
  "qcBy": null,
  "qcDate": null,
  "releaseNotes": null,
  "status": "curated",
  "tissueType": null,
  "type": "C",
  "uri": "/repo/v1/layer/17337",
  "version": "1.0.0"
}

Add a Location to a Layer

First create the location to which to PUT your data.

First get the presigned S3 URL to use for the upload. You must specify the parentId of the Layer (or Dataset) to which this location belongs.

Request

Code Block
curl -i  -H sessionToken:YourSessionToken -H Accept:application/json -H Content-Type:application/json -d '{
  "md5sum": "b513a23fc54b7b0d65312e1a900af5a6",
  "parentId": "17337",
  "path": "mskcc_prostate_cancer.phenotype.zip",
  "type": "awss3"
}' https://repo-staging.sagebase.org/repo/v1/location

Response

Code Block
HTTP/1.1 201 Created
Content-Type: application/json
Date: Wed, 05 Oct 2011 16:34:47 GMT
ETag: 0
Location: /repo/v1/location/17338
Server: Apache-Coyote/1.1
transfer-encoding: chunked
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=1317918888&AWSAccessKeyId=AKIAJQBSYCAUPIYF5WTA&Signature=LVIZSORj5o%2BHy%2BPZ4T6aOC%2BjMlM%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"
}

The PUT the data to S3

Then PUT the data to S3 via an HTTP Client that supports multipart upload. Note that you must:

  1. Add header Content-Type: <location.contentType>
  2. Add header Content-MD5: <the base64 encoded md5 checksum>
  3. Add header x-amz-acl: bucket-owner-full-control

Here is an example with curl:

Code Block
curl -v -X PUT -H Content-MD5:tROiP8VLew1lMS4akAr1pg== -H x-amz-acl:bucket-owner-full-control \
 -H Content-Type:application/zip --data-binary @<localFilepath> \
'https://s3.amazonaws.com/stagingdata.sagebase.org/17338/0.0.0/mskcc_prostate_cancer.phenotype.zip?Expires=1317918888&AWSAccessKeyId=AKIAJQBSYCAUPIYF5WTA&Signature=LVIZSORj5o%2BHy%2BPZ4T6aOC%2BjMlM%3D'

Add a Preview to a Layer

Create a new preview object and set its parentId to be that of the layer

Request

Code Block
curl -i  -H sessionToken:YourSessionToken -H Accept:application/json -H Content-Type:application/json -d '{
  "parentId": "17337",
  "previewString": "phenotype_id\tsample_type\tmetastatic_site\tethnicity\tpredxbxpsa\tage\tclinical_primary_gleason\tclinical_secondary_gleason\tclinical_gleason_score\tpre_treatment_psa\tclinical_tnm_stage_t\tneoadjradtx\tchemotx\thormtx\tradtxtype\trp_type\tsms\textra_capsular_extension\tseminal_vesicle_invasion\ttnm_stage_n\tnumber_nodes_removed\tnumber_nodes_positive\tpathologic_tnm_stage_t\tpathologic_primary_gleason\tpathologic_secondary_gleason\tpathologic_gleason_score\tbcr_freetime\tbcr_event\tmetsevent\tsurvtime\tevent\tnomogram_pfp_postrp\tnomogram_nomopred_extra_capsular_extension\tnomogram_nomopred_lni\tnomogram_nomopred_ocd\tnomogram_nomopred_seminal_vesicle_invasion\tcopy_number_cluster\texpression_array_tissue_source\r\nPCA0004\tPRIMARY\tNA\tWhite Non Hispanic\t27.5\t68.93\t3\t2\t5\t11.8\tT2B\tNA\tNA\tNA\tNA\tRP\tNegative\tESTABLISHED\tNegative\tNormal_N0\t13\t0\tT3A\t3\t4\t7\t152.55\tNO\tNO\t152.55\tNO\tNA\t37.937846\t3.593974\t55.082939\tNA\t1\tNA\r\nPCA0006\tPRIMARY\tNA\tWhite Non Hispanic\t15.7\t56.64\t3\t3\t6\t8.2\tT2B\tNA\tNA\tNeoadjuvant HORM\tNA\tRP\tNegative\tNONE\tNegative\tNormal_N0\t4\t0\tT2C\t3\t3\t6\t160.96\tNO\tNO\t160.96\tNO\tNA\tNA\tNA\tNA\tNA\t4\tNA\r\nPCA0016\tPRIMARY\tNA\tWhite Non Hispanic\t12\t67.36\t3\t3\t6\t12\tT2B\tNA\tNA\tNeoadjuvant HORM\tNA\tRP\tNegative\tNONE\tNegative\tNormal_N0\t2\t0\tT2C\t4\t4\t8\t74.22\tNO\tNO\t74.22\tNO\t99\tNA\tNA\tNA\t97.11015465\t2\tNA\r\nPCA0019\tPRIMARY\tNA\tWhite Non Hispanic\t6.6\t68.12\t3\t4\t7\t6.6\tT1C\tNA\tNA\tNA\tNA\tRP\tNegative\tNONE\tNegative\tNormal_N0\t1\t0\tT2C\t3\t3\t6\t110.33\tBCR_Algorithm\tNO\t123.67\tNO\tNA\tNA\tNA\tNA\t79.85545652\t2\tNA\r\nPCA0023\tPRIMARY\tNA\tBlack Non Hispanic\t4.3\t60.57\t4\t3\t7\t3.88\tT1C\tNA\tNA\tPostHORM\tNA\tRP\tPositive\tNONE\tNegative\tNormal_N0\t2\t0\tT2C\t4\t5\t9\t10.61\tBCR_Algorithm\tNO\t72.84\tDEATH FROM OTHER CANCER\t79.85546\t19.190208\t2.138938\t77.240045\t99\t4\tNA\r\n"
}' https://repo-staging.sagebase.org/repo/v1/preview

Response

Code Block
HTTP/1.1 201 Created
Content-Type: application/json
Date: Wed, 05 Oct 2011 16:34:48 GMT
ETag: 0
Location: /repo/v1/preview/17339
Server: Apache-Coyote/1.1
transfer-encoding: chunked
Connection: keep-alive

{
  "accessControlList": "/repo/v1/preview/17339/acl",
  "annotations": "/repo/v1/preview/17339/annotations",
  "creationDate": 1317832488413,
  "etag": "0",
  "headers": [
    "phenotype_id",
    "sample_type",
    "metastatic_site",
    "ethnicity",
    "predxbxpsa",
    "age",
    "clinical_primary_gleason",
    "clinical_secondary_gleason",
    "clinical_gleason_score",
    "pre_treatment_psa",
    "clinical_tnm_stage_t",
    "neoadjradtx",
    "chemotx",
    "hormtx",
    "radtxtype",
    "rp_type",
    "sms",
    "extra_capsular_extension",
    "seminal_vesicle_invasion",
    "tnm_stage_n",
    "number_nodes_removed",
    "number_nodes_positive",
    "pathologic_tnm_stage_t",
    "pathologic_primary_gleason",
    "pathologic_secondary_gleason",
    "pathologic_gleason_score",
    "bcr_freetime",
    "bcr_event",
    "metsevent",
    "survtime",
    "event",
    "nomogram_pfp_postrp",
    "nomogram_nomopred_extra_capsular_extension",
    "nomogram_nomopred_lni",
    "nomogram_nomopred_ocd",
    "nomogram_nomopred_seminal_vesicle_invasion",
    "copy_number_cluster",
    "expression_array_tissue_source\r"
  ],
  "id": "17339",
  "name": "17339",
  "parentId": "17337",
  "previewBlob": null,
  "previewString": "phenotype_id\tsample_type\tmetastatic_site\tethnicity\tpredxbxpsa\tage\tclinical_primary_gleason\tclinical_secondary_gleason\tclinical_gleason_score\tpre_treatment_psa\tclinical_tnm_stage_t\tneoadjradtx\tchemotx\thormtx\tradtxtype\trp_type\tsms\textra_capsular_extension\tseminal_vesicle_invasion\ttnm_stage_n\tnumber_nodes_removed\tnumber_nodes_positive\tpathologic_tnm_stage_t\tpathologic_primary_gleason\tpathologic_secondary_gleason\tpathologic_gleason_score\tbcr_freetime\tbcr_event\tmetsevent\tsurvtime\tevent\tnomogram_pfp_postrp\tnomogram_nomopred_extra_capsular_extension\tnomogram_nomopred_lni\tnomogram_nomopred_ocd\tnomogram_nomopred_seminal_vesicle_invasion\tcopy_number_cluster\texpression_array_tissue_source\r\nPCA0004\tPRIMARY\tNA\tWhite Non Hispanic\t27.5\t68.93\t3\t2\t5\t11.8\tT2B\tNA\tNA\tNA\tNA\tRP\tNegative\tESTABLISHED\tNegative\tNormal_N0\t13\t0\tT3A\t3\t4\t7\t152.55\tNO\tNO\t152.55\tNO\tNA\t37.937846\t3.593974\t55.082939\tNA\t1\tNA\r\nPCA0006\tPRIMARY\tNA\tWhite Non Hispanic\t15.7\t56.64\t3\t3\t6\t8.2\tT2B\tNA\tNA\tNeoadjuvant HORM\tNA\tRP\tNegative\tNONE\tNegative\tNormal_N0\t4\t0\tT2C\t3\t3\t6\t160.96\tNO\tNO\t160.96\tNO\tNA\tNA\tNA\tNA\tNA\t4\tNA\r\nPCA0016\tPRIMARY\tNA\tWhite Non Hispanic\t12\t67.36\t3\t3\t6\t12\tT2B\tNA\tNA\tNeoadjuvant HORM\tNA\tRP\tNegative\tNONE\tNegative\tNormal_N0\t2\t0\tT2C\t4\t4\t8\t74.22\tNO\tNO\t74.22\tNO\t99\tNA\tNA\tNA\t97.11015465\t2\tNA\r\nPCA0019\tPRIMARY\tNA\tWhite Non Hispanic\t6.6\t68.12\t3\t4\t7\t6.6\tT1C\tNA\tNA\tNA\tNA\tRP\tNegative\tNONE\tNegative\tNormal_N0\t1\t0\tT2C\t3\t3\t6\t110.33\tBCR_Algorithm\tNO\t123.67\tNO\tNA\tNA\tNA\tNA\t79.85545652\t2\tNA\r\nPCA0023\tPRIMARY\tNA\tBlack Non Hispanic\t4.3\t60.57\t4\t3\t7\t3.88\tT1C\tNA\tNA\tPostHORM\tNA\tRP\tPositive\tNONE\tNegative\tNormal_N0\t2\t0\tT2C\t4\t5\t9\t10.61\tBCR_Algorithm\tNO\t72.84\tDEATH FROM OTHER CANCER\t79.85546\t19.190208\t2.138938\t77.240045\t99\t4\tNA\r\n",
  "rows": [
    {
      "age": "68.93",
      "bcr_event": "NO",
      "bcr_freetime": "152.55",
      "chemotx": "NA",
      "clinical_gleason_score": "5",
      "clinical_primary_gleason": "3",
      "clinical_secondary_gleason": "2",
      "clinical_tnm_stage_t": "T2B",
      "copy_number_cluster": "1",
      "ethnicity": "White Non Hispanic",
      "event": "NO",
      "expression_array_tissue_source\r": "NA\r",
      "extra_capsular_extension": "ESTABLISHED",
      "hormtx": "NA",
      "metastatic_site": "NA",
      "metsevent": "NO",
      "neoadjradtx": "NA",
      "nomogram_nomopred_extra_capsular_extension": "37.937846",
      "nomogram_nomopred_lni": "3.593974",
      "nomogram_nomopred_ocd": "55.082939",
      "nomogram_nomopred_seminal_vesicle_invasion": "NA",
      "nomogram_pfp_postrp": "NA",
      "number_nodes_positive": "0",
      "number_nodes_removed": "13",
      "pathologic_gleason_score": "7",
      "pathologic_primary_gleason": "3",
      "pathologic_secondary_gleason": "4",
      "pathologic_tnm_stage_t": "T3A",
      "phenotype_id": "PCA0004",
      "pre_treatment_psa": "11.8",
      "predxbxpsa": "27.5",
      "radtxtype": "NA",
      "rp_type": "RP",
      "sample_type": "PRIMARY",
      "seminal_vesicle_invasion": "Negative",
      "sms": "Negative",
      "survtime": "152.55",
      "tnm_stage_n": "Normal_N0"
    },
    {
      "age": "56.64",
      "bcr_event": "NO",
      "bcr_freetime": "160.96",
      "chemotx": "NA",
      "clinical_gleason_score": "6",
      "clinical_primary_gleason": "3",
      "clinical_secondary_gleason": "3",
      "clinical_tnm_stage_t": "T2B",
      "copy_number_cluster": "4",
      "ethnicity": "White Non Hispanic",
      "event": "NO",
      "expression_array_tissue_source\r": "NA\r",
      "extra_capsular_extension": "NONE",
      "hormtx": "Neoadjuvant HORM",
      "metastatic_site": "NA",
      "metsevent": "NO",
      "neoadjradtx": "NA",
      "nomogram_nomopred_extra_capsular_extension": "NA",
      "nomogram_nomopred_lni": "NA",
      "nomogram_nomopred_ocd": "NA",
      "nomogram_nomopred_seminal_vesicle_invasion": "NA",
      "nomogram_pfp_postrp": "NA",
      "number_nodes_positive": "0",
      "number_nodes_removed": "4",
      "pathologic_gleason_score": "6",
      "pathologic_primary_gleason": "3",
      "pathologic_secondary_gleason": "3",
      "pathologic_tnm_stage_t": "T2C",
      "phenotype_id": "PCA0006",
      "pre_treatment_psa": "8.2",
      "predxbxpsa": "15.7",
      "radtxtype": "NA",
      "rp_type": "RP",
      "sample_type": "PRIMARY",
      "seminal_vesicle_invasion": "Negative",
      "sms": "Negative",
      "survtime": "160.96",
      "tnm_stage_n": "Normal_N0"
    },
    {
      "age": "67.36",
      "bcr_event": "NO",
      "bcr_freetime": "74.22",
      "chemotx": "NA",
      "clinical_gleason_score": "6",
      "clinical_primary_gleason": "3",
      "clinical_secondary_gleason": "3",
      "clinical_tnm_stage_t": "T2B",
      "copy_number_cluster": "2",
      "ethnicity": "White Non Hispanic",
      "event": "NO",
      "expression_array_tissue_source\r": "NA\r",
      "extra_capsular_extension": "NONE",
      "hormtx": "Neoadjuvant HORM",
      "metastatic_site": "NA",
      "metsevent": "NO",
      "neoadjradtx": "NA",
      "nomogram_nomopred_extra_capsular_extension": "NA",
      "nomogram_nomopred_lni": "NA",
      "nomogram_nomopred_ocd": "NA",
      "nomogram_nomopred_seminal_vesicle_invasion": "97.11015465",
      "nomogram_pfp_postrp": "99",
      "number_nodes_positive": "0",
      "number_nodes_removed": "2",
      "pathologic_gleason_score": "8",
      "pathologic_primary_gleason": "4",
      "pathologic_secondary_gleason": "4",
      "pathologic_tnm_stage_t": "T2C",
      "phenotype_id": "PCA0016",
      "pre_treatment_psa": "12",
      "predxbxpsa": "12",
      "radtxtype": "NA",
      "rp_type": "RP",
      "sample_type": "PRIMARY",
      "seminal_vesicle_invasion": "Negative",
      "sms": "Negative",
      "survtime": "74.22",
      "tnm_stage_n": "Normal_N0"
    },
    {
      "age": "68.12",
      "bcr_event": "BCR_Algorithm",
      "bcr_freetime": "110.33",
      "chemotx": "NA",
      "clinical_gleason_score": "7",
      "clinical_primary_gleason": "3",
      "clinical_secondary_gleason": "4",
      "clinical_tnm_stage_t": "T1C",
      "copy_number_cluster": "2",
      "ethnicity": "White Non Hispanic",
      "event": "NO",
      "expression_array_tissue_source\r": "NA\r",
      "extra_capsular_extension": "NONE",
      "hormtx": "NA",
      "metastatic_site": "NA",
      "metsevent": "NO",
      "neoadjradtx": "NA",
      "nomogram_nomopred_extra_capsular_extension": "NA",
      "nomogram_nomopred_lni": "NA",
      "nomogram_nomopred_ocd": "NA",
      "nomogram_nomopred_seminal_vesicle_invasion": "79.85545652",
      "nomogram_pfp_postrp": "NA",
      "number_nodes_positive": "0",
      "number_nodes_removed": "1",
      "pathologic_gleason_score": "6",
      "pathologic_primary_gleason": "3",
      "pathologic_secondary_gleason": "3",
      "pathologic_tnm_stage_t": "T2C",
      "phenotype_id": "PCA0019",
      "pre_treatment_psa": "6.6",
      "predxbxpsa": "6.6",
      "radtxtype": "NA",
      "rp_type": "RP",
      "sample_type": "PRIMARY",
      "seminal_vesicle_invasion": "Negative",
      "sms": "Negative",
      "survtime": "123.67",
      "tnm_stage_n": "Normal_N0"
    },
    {
      "age": "60.57",
      "bcr_event": "BCR_Algorithm",
      "bcr_freetime": "10.61",
      "chemotx": "NA",
      "clinical_gleason_score": "7",
      "clinical_primary_gleason": "4",
      "clinical_secondary_gleason": "3",
      "clinical_tnm_stage_t": "T1C",
      "copy_number_cluster": "4",
      "ethnicity": "Black Non Hispanic",
      "event": "DEATH FROM OTHER CANCER",
      "expression_array_tissue_source\r": "NA\r",
      "extra_capsular_extension": "NONE",
      "hormtx": "PostHORM",
      "metastatic_site": "NA",
      "metsevent": "NO",
      "neoadjradtx": "NA",
      "nomogram_nomopred_extra_capsular_extension": "19.190208",
      "nomogram_nomopred_lni": "2.138938",
      "nomogram_nomopred_ocd": "77.240045",
      "nomogram_nomopred_seminal_vesicle_invasion": "99",
      "nomogram_pfp_postrp": "79.85546",
      "number_nodes_positive": "0",
      "number_nodes_removed": "2",
      "pathologic_gleason_score": "9",
      "pathologic_primary_gleason": "4",
      "pathologic_secondary_gleason": "5",
      "pathologic_tnm_stage_t": "T2C",
      "phenotype_id": "PCA0023",
      "pre_treatment_psa": "3.88",
      "predxbxpsa": "4.3",
      "radtxtype": "NA",
      "rp_type": "RP",
      "sample_type": "PRIMARY",
      "seminal_vesicle_invasion": "Negative",
      "sms": "Positive",
      "survtime": "72.84",
      "tnm_stage_n": "Normal_N0"
    }
  ],
  "uri": "/repo/v1/preview/17339"
}

Create an agreement between a user and the End-User Licence Agreement for a particular dataset

Note that the userId is determined from the sessionToken

Request

Code Block
curl -i  -H sessionToken:YourSessionToken -H Accept:application/json -H Content-Type:application/json -d '{
  "datasetId": "17336",
  "eulaId": "17335"
}' https://repo-staging.sagebase.org/repo/v1/agreement

Response

Code Block
HTTP/1.1 201 Created
Content-Type: application/json
Date: Wed, 05 Oct 2011 16:34:48 GMT
ETag: 0
Location: /repo/v1/agreement/17340
Server: Apache-Coyote/1.1
transfer-encoding: chunked
Connection: keep-alive

{
  "accessControlList": "/repo/v1/agreement/17340/acl",
  "annotations": "/repo/v1/agreement/17340/annotations",
  "createdBy": "nicole.deflaux@sagebase.org",
  "creationDate": 1317832488685,
  "datasetId": "17336",
  "datasetVersionNumber": -1,
  "etag": "0",
  "eulaId": "17335",
  "eulaVersionNumber": -1,
  "id": "17340",
  "name": "17340",
  "parentId": "3729",
  "uri": "/repo/v1/agreement/17340"
}17338/0.0.0/mskcc_prostate_cancer.phenotype.zip?Expires=1317918888&AWSAccessKeyId=AKIAJQBSYCAUPIYF5WTA&Signature=LVIZSORj5o%2BHy%2BPZ4T6aOC%2BjMlM%3D'

Versions Create/Read/Update/Delete

...