...
Code Block |
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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 |
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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 |
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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 |
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curl -i -k -H sessionToken:YourSessionToken -H Accept:application/json 'https://repo-stagingprod.sagebase.org/repo/v1/datasetentity/17336syn1151499/annotations' |
Response
Code Block |
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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 |
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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 |
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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:
- Add header
Content-Type: <location.contentType>
- Add header
Content-MD5: <the base64 encoded md5 checksum>
- Add header
x-amz-acl: bucket-owner-full-control
Here is an example with curl:
Code Block |
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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 |
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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 |
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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 |
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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:
- Add header
Content-Type: <location.contentType>
- Add header
Content-MD5: <the base64 encoded md5 checksum>
- 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
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