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Proposed Changes to Location API

Proposed Changes to Location API

Aug 30, 2011

Add a Location to a Layer

First create the presigned a S3 URL to use for upload.

Request

curl -i -H sessionToken:YourSessionToken -H Accept:application/json -H Content-Type:application/json -d '{ "md5sum": "b513a23fc54b7b0d65312e1a900af5a6", "fileName": "mskcc_prostate_cancer.phenotype.zip", }' https://repo-staging.sagebase.org/repo/v1/createNewS3Url

Response

HTTP/1.1 201 Created Content-Type: application/json Date: Mon, 29 Aug 2011 23:55:11 GMT ETag: 0 Location: /repo/v1/location/8237 Server: Apache-Coyote/1.1 transfer-encoding: chunked Connection: keep-alive { "presignedUrl": "https://s3.amazonaws.com/stagingdata.sagebase.org/8237/mskcc_prostate_cancer.phenotype.zip?Expires=1314748511&AWSAccessKeyId=AKIAJO2DMB3LTOB6IJOA&Signature=%2BryKGGJujZxtliiynGDZHyzqETU%3D", }

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: application/binary

  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:

curl -v -X PUT -H Content-MD5:tROiP8VLew1lMS4akAr1pg== -H x-amz-acl:bucket-owner-full-control \ -H Content-Type:application/binary --data-binary @<localFilepath> \ 'https://s3.amazonaws.com/stagingdata.sagebase.org/8237/mskcc_prostate_cancer.phenotype.zip?Expires=1314748511&AWSAccessKeyId=AKIAJO2DMB3LTOB6IJOA&Signature=%2BryKGGJujZxtliiynGDZHyzqETU%3D'

Create the location using the URL as the path

Request

curl -i -H sessionToken:YourSessionToken -H Accept:application/json -H Content-Type:application/json -d '{ "md5sum": "b513a23fc54b7b0d65312e1a900af5a6", "parentId": "8236", "path": "https://s3.amazonaws.com/stagingdata.sagebase.org/8237/mskcc_prostate_cancer.phenotype.zip?Expires=1314748511&AWSAccessKeyId=AKIAJO2DMB3LTOB6IJOA&Signature=%2BryKGGJujZxtliiynGDZHyzqETU%3D", "type": "awss3" }' https://repo-staging.sagebase.org/repo/v1/location

Response

HTTP/1.1 201 Created Content-Type: application/json Date: Mon, 29 Aug 2011 23:55:11 GMT ETag: 0 Location: /repo/v1/location/8237 Server: Apache-Coyote/1.1 transfer-encoding: chunked Connection: keep-alive { "accessControlList": "/repo/v1/location/8237/acl", "annotations": "/repo/v1/location/8237/annotations", "contentType": "application/zip", "creationDate": 1314662110686, "etag": "0", "id": "8237", "md5sum": "b513a23fc54b7b0d65312e1a900af5a6", "name": "8237", "parentId": "8236", "path": "https://s3.amazonaws.com/stagingdata.sagebase.org/8237/mskcc_prostate_cancer.phenotype.zip?Expires=1314748511&AWSAccessKeyId=AKIAJO2DMB3LTOB6IJOA&Signature=%2BryKGGJujZxtliiynGDZHyzqETU%3D", "type": "awss3", "uri": "/repo/v1/location/8237", "versionComment": null, "versionLabel": "0.0.0", "versionNumber": 1, "versionUrl": "/repo/v1/location/8237/version/1", "versions": "/repo/v1/location/8237/version" }

Update an existing location

First create a new presigned S3 URL to use for upload.

Request

curl -i -H sessionToken:YourSessionToken -H Accept:application/json -H Content-Type:application/json -d '{ "md5sum": "b513a23fc54b7b0d65312e1a900af5a6", "fileName": "mskcc_prostate_cancer.phenotype2.zip", }' https://repo-staging.sagebase.org/repo/v1/createS3Url

Response

HTTP/1.1 201 Created Content-Type: application/json Date: Mon, 29 Aug 2011 23:55:11 GMT ETag: 0 Location: /repo/v1/location/8237 Server: Apache-Coyote/1.1 transfer-encoding: chunked Connection: keep-alive { "presignedUrl": "https://s3.amazonaws.com/stagingdata.sagebase.org/8238/mskcc_prostate_cancer.phenotype2.zip?Expires=1314748511&AWSAccessKeyId=AKIAJO2DMB3LTOB6IJOA&Signature=%2BryKGGJujZxtliiynGDZHyzqETU%3D", }

Upload the file to S3, the same as above.

See: above

Update the location with the new URL

Request

curl -i -H sessionToken:YourSessionToken -H Accept:application/json -H Content-Type:application/json -d '{ "accessControlList": "/repo/v1/location/8237/acl", "annotations": "/repo/v1/location/8237/annotations", "contentType": "application/zip", "creationDate": 1314662110686, "etag": "0", "id": "8237", "md5sum": "b513a23fc54b7b0d65312e1a900af5a6", "name": "8237", "parentId": "8236", "path": "https://s3.amazonaws.com/stagingdata.sagebase.org/8238/mskcc_prostate_cancer.phenotype2.zip?Expires=1314748511&AWSAccessKeyId=AKIAJO2DMB3LTOB6IJOA&Signature=%2BryKGGJujZxtliiynGDZHyzqETU%3D", "type": "awss3", "uri": "/repo/v1/location/8237", "versionComment": null, "versionLabel": "0.0.0", "versionNumber": 1, "versionUrl": "/repo/v1/location/8237/version/1", "versions": "/repo/v1/location/8237/version" }' https://repo-staging.sagebase.org/repo/v1/location

Response

HTTP/1.1 201 Created Content-Type: application/json Date: Mon, 29 Aug 2011 23:55:11 GMT ETag: 0 Location: /repo/v1/location/8237 Server: Apache-Coyote/1.1 transfer-encoding: chunked Connection: keep-alive { "accessControlList": "/repo/v1/location/8237/acl", "annotations": "/repo/v1/location/8237/annotations", "contentType": "application/zip", "creationDate": 1314662110686, "etag": "0", "id": "8237", "md5sum": b513a23fc54b7b0d65312e1a900af5a6", "name": "8237", "parentId": "8236", "path": "https://s3.amazonaws.com/stagingdata.sagebase.org/8238/mskcc_prostate_cancer.phenotype2.zip?Expires=1314748511&AWSAccessKeyId=AKIAJO2DMB3LTOB6IJOA&Signature=%2BryKGGJujZxtliiynGDZHyzqETU%3D", "type": "awss3", "uri": "/repo/v1/location/8237", "versionComment": null, "versionLabel": "0.0.0", "versionNumber": 1, "versionUrl": "/repo/v1/location/8237/version/1", "versions": "/repo/v1/location/8237/version" }