See Service API Design for the rationale and design details for this api.
See Developer Bootstrap#DeveloperBootstrap-ServiceDevelopment for instructions on how to run a local instance of this service.
The primary request and response encoding for the service is JSON. Here's a handy tool to make a blob of JSON more readable: http://jsonformatter.curiousconcept.com/
In responses from the service, dates are serialized as long integers expressing epoch time - the number of seconds elapsed since midnight Coordinated Universal Time (UTC) of January 1, 1970, not counting leap seconds. Here's a handy tool to convert from epoch time to human readable dates: http://www.epochconverter.com/
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'
Eventually these services will be HTTPS only and disallow HTTP. Users will pass something like ?access_token=... as a query parameter for every request to the service
Right now only a subset of query functionality is supported
SELECT * FROM <data type> [LIMIT <#>] [OFFSET <#>] |
Request
curl -i -H Accept:application/json 'http://repositoryservice.sagebase.org/repo/v1/query?query=select+*+from+dataset+limit+3+offset+1' |
Response
HTTP/1.1 200 OK Content-Type: application/json Date: Thu, 24 Mar 2011 19:03:03 GMT Server: Apache-Coyote/1.1 Content-Length: 3483 Connection: keep-alive { "results": [ { "dataset.Disease": ["Cancer"], "dataset.Institution": ["Asian Cancer Research Group, Inc., (ACRG)"], "dataset.Internal_Name": ["ACRG_gastric"], "dataset.Number_of_Samples": [2000], "dataset.Posting_Restriction": ["unspecified"], "dataset.Species": ["Human"], "dataset.Tissue/Tumor": ["Stomach"], "dataset.Type": ["GCD"], "dataset.abstract_file_path": ["/srv/www/htdocs/Foswiki/downloads/data/v2/abstract_files/gastric_cancer_acrg.txt"], "dataset.citation_file_path": ["/srv/www/htdocs/Foswiki/downloads/data/v2/citation_files/gastric_cancer_acrg.txt"], "dataset.creationDate": 1300992846641, "dataset.creator": "Asian Cancer Research Group, Inc., (ACRG)", "dataset.db_id": [1], "dataset.description": null, "dataset.hasClinicalData": false, "dataset.hasExpressionData": false, "dataset.hasGeneticData": false, "dataset.id": "0", "dataset.name": "Gastric Cancer ACRG", "dataset.readme_file_path": ["/srv/www/htdocs/Foswiki/downloads/data/v2/readme_files/gastric_cancer_acrg.txt"], "dataset.releaseDate": null, "dataset.status": "Future", "dataset.user_agreement_file_path": ["/srv/www/htdocs/Foswiki/downloads/data/v2/user_agreement_files/gastric_cancer_acrg.txt"], "dataset.version": "0.0.1" }, { "dataset.Disease": ["Cancer"], "dataset.Institution": ["Asian Cancer Research Group, Inc., (ACRG)"], "dataset.Internal_Name": ["ACRG_lung"], "dataset.Number_of_Samples": [2000], "dataset.Posting_Restriction": ["unspecified"], "dataset.Species": ["Human"], "dataset.Tissue/Tumor": ["Lung"], "dataset.Type": ["GCD"], "dataset.abstract_file_path": ["/srv/www/htdocs/Foswiki/downloads/data/v2/abstract_files/lung_cancer_acrg.txt"], "dataset.citation_file_path": ["/srv/www/htdocs/Foswiki/downloads/data/v2/citation_files/lung_cancer_acrg.txt"], "dataset.creationDate": 1300992847445, "dataset.creator": "Asian Cancer Research Group, Inc., (ACRG)", "dataset.db_id": [2], "dataset.description": null, "dataset.hasClinicalData": false, "dataset.hasExpressionData": false, "dataset.hasGeneticData": false, "dataset.id": "23", "dataset.name": "Lung Cancer ACRG", "dataset.readme_file_path": ["/srv/www/htdocs/Foswiki/downloads/data/v2/readme_files/lung_cancer_acrg.txt"], "dataset.releaseDate": null, "dataset.status": "Future", "dataset.user_agreement_file_path": ["/srv/www/htdocs/Foswiki/downloads/data/v2/user_agreement_files/lung_cancer_acrg.txt"], "dataset.version": "0.0.1" }, { "dataset.Disease": ["Cancer"], "dataset.Institution": ["Fred Hutchinson Cancer Research Center /SKCCC at Johns Hopkins"], "dataset.Internal_Name": ["AML-Ped_TARGET"], "dataset.Number_of_Samples": [200], "dataset.Posting_Restriction": ["Link to data source"], "dataset.Species": ["Human"], "dataset.Tissue/Tumor": ["Blood"], "dataset.Type": ["GCD"], "dataset.abstract_file_path": ["/srv/www/htdocs/Foswiki/downloads/data/v2/abstract_files/pediatric_aml_target.txt"], "dataset.citation_file_path": ["/srv/www/htdocs/Foswiki/downloads/data/v2/citation_files/pediatric_aml_target.txt"], "dataset.creationDate": 1300992848002, "dataset.creator": "Soheil Meshinchi/ Bob Arceci", "dataset.db_id": [3], "dataset.description": null, "dataset.hasClinicalData": false, "dataset.hasExpressionData": false, "dataset.hasGeneticData": false, "dataset.id": "42", "dataset.name": "Pediatric AML TARGET", "dataset.readme_file_path": ["/srv/www/htdocs/Foswiki/downloads/data/v2/readme_files/pediatric_aml_target.txt"], "dataset.releaseDate": null, "dataset.status": "Pending", "dataset.user_agreement_file_path": ["/srv/www/htdocs/Foswiki/downloads/data/v2/user_agreement_files/pediatric_aml_target.txt"], "dataset.version": "0.0.1" } ], "totalNumberOfResults": 114 } |
Right now only a subset of query functionality is supported
SELECT * FROM <data type> ORDER BY <field name> [ASC|DESC] [LIMIT <#>] [OFFSET #] |
Request
curl -i -H Accept:application/json 'http://repositoryservice.sagebase.org/repo/v1/query?query=select+*+from+dataset+order+by+Number_of_Samples+DESC+limit+3+offset+1' |
Response
HTTP/1.1 200 OK Content-Type: application/json Date: Thu, 24 Mar 2011 19:03:03 GMT Server: Apache-Coyote/1.1 Content-Length: 3416 Connection: keep-alive { "results": [ { "dataset.Disease": ["Multiple"], "dataset.Institution": ["NHLBI"], "dataset.Internal_Name": ["Framingham"], "dataset.Number_of_Samples": [5000], "dataset.Posting_Restriction": ["Link to data source"], "dataset.Species": ["Human"], "dataset.Tissue/Tumor": ["Blood"], "dataset.Type": ["GCD"], "dataset.abstract_file_path": ["/srv/www/htdocs/Foswiki/downloads/data/v2/abstract_files/framingham_heart_study.txt"], "dataset.citation_file_path": ["/srv/www/htdocs/Foswiki/downloads/data/v2/citation_files/framingham_heart_study.txt"], "dataset.creationDate": 1300992862351, "dataset.creator": "Dan Levy", "dataset.db_id": [31], "dataset.description": null, "dataset.hasClinicalData": false, "dataset.hasExpressionData": false, "dataset.hasGeneticData": false, "dataset.id": "603", "dataset.name": "Framingham Heart Study", "dataset.readme_file_path": ["/srv/www/htdocs/Foswiki/downloads/data/v2/readme_files/framingham_heart_study.txt"], "dataset.releaseDate": null, "dataset.status": "Future", "dataset.user_agreement_file_path": ["/srv/www/htdocs/Foswiki/downloads/data/v2/user_agreement_files/framingham_heart_study.txt"], "dataset.version": "0.0.1" }, { "dataset.Disease": ["Cancer"], "dataset.Institution": ["Asian Cancer Research Group, Inc., (ACRG)"], "dataset.Internal_Name": ["ACRG_gastric"], "dataset.Number_of_Samples": [2000], "dataset.Posting_Restriction": ["unspecified"], "dataset.Species": ["Human"], "dataset.Tissue/Tumor": ["Stomach"], "dataset.Type": ["GCD"], "dataset.abstract_file_path": ["/srv/www/htdocs/Foswiki/downloads/data/v2/abstract_files/gastric_cancer_acrg.txt"], "dataset.citation_file_path": ["/srv/www/htdocs/Foswiki/downloads/data/v2/citation_files/gastric_cancer_acrg.txt"], "dataset.creationDate": 1300992846641, "dataset.creator": "Asian Cancer Research Group, Inc., (ACRG)", "dataset.db_id": [1], "dataset.description": null, "dataset.hasClinicalData": false, "dataset.hasExpressionData": false, "dataset.hasGeneticData": false, "dataset.id": "0", "dataset.name": "Gastric Cancer ACRG", "dataset.readme_file_path": ["/srv/www/htdocs/Foswiki/downloads/data/v2/readme_files/gastric_cancer_acrg.txt"], "dataset.releaseDate": null, "dataset.status": "Future", "dataset.user_agreement_file_path": ["/srv/www/htdocs/Foswiki/downloads/data/v2/user_agreement_files/gastric_cancer_acrg.txt"], "dataset.version": "0.0.1" }, { "dataset.Disease": ["Cancer"], "dataset.Institution": ["Asian Cancer Research Group, Inc., (ACRG)"], "dataset.Internal_Name": ["ACRG_lung"], "dataset.Number_of_Samples": [2000], "dataset.Posting_Restriction": ["unspecified"], "dataset.Species": ["Human"], "dataset.Tissue/Tumor": ["Lung"], "dataset.Type": ["GCD"], "dataset.abstract_file_path": ["/srv/www/htdocs/Foswiki/downloads/data/v2/abstract_files/lung_cancer_acrg.txt"], "dataset.citation_file_path": ["/srv/www/htdocs/Foswiki/downloads/data/v2/citation_files/lung_cancer_acrg.txt"], "dataset.creationDate": 1300992847445, "dataset.creator": "Asian Cancer Research Group, Inc., (ACRG)", "dataset.db_id": [2], "dataset.description": null, "dataset.hasClinicalData": false, "dataset.hasExpressionData": false, "dataset.hasGeneticData": false, "dataset.id": "23", "dataset.name": "Lung Cancer ACRG", "dataset.readme_file_path": ["/srv/www/htdocs/Foswiki/downloads/data/v2/readme_files/lung_cancer_acrg.txt"], "dataset.releaseDate": null, "dataset.status": "Future", "dataset.user_agreement_file_path": ["/srv/www/htdocs/Foswiki/downloads/data/v2/user_agreement_files/lung_cancer_acrg.txt"], "dataset.version": "0.0.1" } ], "totalNumberOfResults": 114 } |
Right now only a subset of query functionality is supported
SELECT * FROM <data type> WHERE <field name> == "<value>" [LIMIT <#>] [OFFSET #] |
Request
curl -i -H Accept:application/json 'http://repositoryservice.sagebase.org/repo/v1/query?query=select+*+from+dataset+where+name+==+"Human+Liver+Cohort"' |
Response
HTTP/1.1 200 OK Content-Type: application/json Date: Thu, 24 Mar 2011 19:03:03 GMT Server: Apache-Coyote/1.1 Content-Length: 1203 Connection: keep-alive { "results": [{ "dataset.Disease": ["CVD"], "dataset.Institution": ["Vanderbilt University/ University of Pittsburg/ StJudes Hospital"], "dataset.Internal_Name": ["Deliver"], "dataset.Number_of_Samples": [517], "dataset.Posting_Restriction": ["Link to data source"], "dataset.Species": ["Human"], "dataset.Tissue/Tumor": ["Liver"], "dataset.Type": ["GCD"], "dataset.abstract_file_path": ["/srv/www/htdocs/Foswiki/downloads/data/v2/abstract_files/human_liver_cohort.txt"], "dataset.citation_file_path": ["/srv/www/htdocs/Foswiki/downloads/data/v2/citation_files/human_liver_cohort.txt"], "dataset.creationDate": 1300992860514, "dataset.creator": "Fred Guengrich/Steve Strom/ Erin Schuetz", "dataset.db_id": [29], "dataset.description": null, "dataset.hasClinicalData": true, "dataset.hasExpressionData": true, "dataset.hasGeneticData": false, "dataset.id": "563", "dataset.name": "Human Liver Cohort", "dataset.readme_file_path": ["/srv/www/htdocs/Foswiki/downloads/data/v2/readme_files/human_liver_cohort.txt"], "dataset.releaseDate": null, "dataset.status": "Current", "dataset.user_agreement_file_path": ["/srv/www/htdocs/Foswiki/downloads/data/v2/user_agreement_files/human_liver_cohort.txt"], "dataset.version": "0.0.1" }], "totalNumberOfResults": 114 } |
Right now only a subset of query functionality is supported
SELECT * FROM <data type> WHERE <field name> == "<value>" [LIMIT <#>] [OFFSET #] |
Request
curl -i -H Accept:application/json 'http://repositoryservice.sagebase.org/repo/v1/query?query=select+*+from+dataset+where+Species+==+"Human"+limit+3+offset+1' |
Response
HTTP/1.1 200 OK Content-Type: application/json Date: Thu, 24 Mar 2011 19:03:04 GMT Server: Apache-Coyote/1.1 Content-Length: 3483 Connection: keep-alive { "results": [ { "dataset.Disease": ["Cancer"], "dataset.Institution": ["Asian Cancer Research Group, Inc., (ACRG)"], "dataset.Internal_Name": ["ACRG_gastric"], "dataset.Number_of_Samples": [2000], "dataset.Posting_Restriction": ["unspecified"], "dataset.Species": ["Human"], "dataset.Tissue/Tumor": ["Stomach"], "dataset.Type": ["GCD"], "dataset.abstract_file_path": ["/srv/www/htdocs/Foswiki/downloads/data/v2/abstract_files/gastric_cancer_acrg.txt"], "dataset.citation_file_path": ["/srv/www/htdocs/Foswiki/downloads/data/v2/citation_files/gastric_cancer_acrg.txt"], "dataset.creationDate": 1300992846641, "dataset.creator": "Asian Cancer Research Group, Inc., (ACRG)", "dataset.db_id": [1], "dataset.description": null, "dataset.hasClinicalData": false, "dataset.hasExpressionData": false, "dataset.hasGeneticData": false, "dataset.id": "0", "dataset.name": "Gastric Cancer ACRG", "dataset.readme_file_path": ["/srv/www/htdocs/Foswiki/downloads/data/v2/readme_files/gastric_cancer_acrg.txt"], "dataset.releaseDate": null, "dataset.status": "Future", "dataset.user_agreement_file_path": ["/srv/www/htdocs/Foswiki/downloads/data/v2/user_agreement_files/gastric_cancer_acrg.txt"], "dataset.version": "0.0.1" }, { "dataset.Disease": ["Cancer"], "dataset.Institution": ["Asian Cancer Research Group, Inc., (ACRG)"], "dataset.Internal_Name": ["ACRG_lung"], "dataset.Number_of_Samples": [2000], "dataset.Posting_Restriction": ["unspecified"], "dataset.Species": ["Human"], "dataset.Tissue/Tumor": ["Lung"], "dataset.Type": ["GCD"], "dataset.abstract_file_path": ["/srv/www/htdocs/Foswiki/downloads/data/v2/abstract_files/lung_cancer_acrg.txt"], "dataset.citation_file_path": ["/srv/www/htdocs/Foswiki/downloads/data/v2/citation_files/lung_cancer_acrg.txt"], "dataset.creationDate": 1300992847445, "dataset.creator": "Asian Cancer Research Group, Inc., (ACRG)", "dataset.db_id": [2], "dataset.description": null, "dataset.hasClinicalData": false, "dataset.hasExpressionData": false, "dataset.hasGeneticData": false, "dataset.id": "23", "dataset.name": "Lung Cancer ACRG", "dataset.readme_file_path": ["/srv/www/htdocs/Foswiki/downloads/data/v2/readme_files/lung_cancer_acrg.txt"], "dataset.releaseDate": null, "dataset.status": "Future", "dataset.user_agreement_file_path": ["/srv/www/htdocs/Foswiki/downloads/data/v2/user_agreement_files/lung_cancer_acrg.txt"], "dataset.version": "0.0.1" }, { "dataset.Disease": ["Cancer"], "dataset.Institution": ["Fred Hutchinson Cancer Research Center /SKCCC at Johns Hopkins"], "dataset.Internal_Name": ["AML-Ped_TARGET"], "dataset.Number_of_Samples": [200], "dataset.Posting_Restriction": ["Link to data source"], "dataset.Species": ["Human"], "dataset.Tissue/Tumor": ["Blood"], "dataset.Type": ["GCD"], "dataset.abstract_file_path": ["/srv/www/htdocs/Foswiki/downloads/data/v2/abstract_files/pediatric_aml_target.txt"], "dataset.citation_file_path": ["/srv/www/htdocs/Foswiki/downloads/data/v2/citation_files/pediatric_aml_target.txt"], "dataset.creationDate": 1300992848002, "dataset.creator": "Soheil Meshinchi/ Bob Arceci", "dataset.db_id": [3], "dataset.description": null, "dataset.hasClinicalData": false, "dataset.hasExpressionData": false, "dataset.hasGeneticData": false, "dataset.id": "42", "dataset.name": "Pediatric AML TARGET", "dataset.readme_file_path": ["/srv/www/htdocs/Foswiki/downloads/data/v2/readme_files/pediatric_aml_target.txt"], "dataset.releaseDate": null, "dataset.status": "Pending", "dataset.user_agreement_file_path": ["/srv/www/htdocs/Foswiki/downloads/data/v2/user_agreement_files/pediatric_aml_target.txt"], "dataset.version": "0.0.1" } ], "totalNumberOfResults": 114 } |
Right now only a subset of query functionality is supported
SELECT * FROM layer WHERE dataset.id == <datasetId> [LIMIT <#>] [OFFSET <#>] |
Request
curl -i -H Accept:application/json 'http://repositoryservice.sagebase.org/repo/v1/query?query=select+*+from+layer+where+dataset.id+==+"563"' |
Response
HTTP/1.1 200 OK Content-Type: application/json Date: Thu, 24 Mar 2011 19:03:04 GMT Server: Apache-Coyote/1.1 Content-Length: 770 Connection: keep-alive { "results": [ { "layer.creationDate": 1300992903392, "layer.description": null, "layer.id": "2268", "layer.locations": null, "layer.name": "expression data", "layer.platform": null, "layer.preview": null, "layer.processingFacility": null, "layer.publicationDate": null, "layer.qcBy": null, "layer.qcDate": null, "layer.releaseNotes": null, "layer.tissueType": null, "layer.type": "E", "layer.version": "0.0.1" }, { "layer.creationDate": 1300992902719, "layer.description": null, "layer.id": "2258", "layer.locations": null, "layer.name": "clinical data", "layer.platform": null, "layer.preview": null, "layer.processingFacility": null, "layer.publicationDate": null, "layer.qcBy": null, "layer.qcDate": null, "layer.releaseNotes": null, "layer.tissueType": null, "layer.type": "C", "layer.version": "0.0.1" } ], "totalNumberOfResults": 2 } |
Right now only a subset of query functionality is supported
SELECT * FROM layer WHERE dataset.id == <datasetId> ORDER BY <field name> [ASC|DESC] [LIMIT <#>] [OFFSET <#>] |
Request
curl -i -H Accept:application/json 'http://repositoryservice.sagebase.org/repo/v1/query?query=select+*+from+layer+where+dataset.id+==+"563"+ORDER+BY+type' |
Response
HTTP/1.1 200 OK Content-Type: application/json Date: Thu, 24 Mar 2011 19:03:04 GMT Server: Apache-Coyote/1.1 transfer-encoding:chunked Connection: keep-alive { "results": [ { "layer.creationDate": 1300992902719, "layer.description": null, "layer.id": "2258", "layer.locations": null, "layer.name": "clinical data", "layer.platform": null, "layer.preview": null, "layer.processingFacility": null, "layer.publicationDate": null, "layer.qcBy": null, "layer.qcDate": null, "layer.releaseNotes": null, "layer.tissueType": null, "layer.type": "C", "layer.version": "0.0.1" }, { "layer.creationDate": 1300992903392, "layer.description": null, "layer.id": "2268", "layer.locations": null, "layer.name": "expression data", "layer.platform": null, "layer.preview": null, "layer.processingFacility": null, "layer.publicationDate": null, "layer.qcBy": null, "layer.qcDate": null, "layer.releaseNotes": null, "layer.tissueType": null, "layer.type": "E", "layer.version": "0.0.1" } ], "totalNumberOfResults": 2 } |
This is just a 'hello world' type request that you can make to ensure that the service is running.
Request
curl -i -H Accept:application/json 'http://repositoryservice.sagebase.org/repo/v1/dataset/test' |
Response
HTTP/1.1 200 OK Cache-Control: no-cache, no-store, max-age=0 Content-Language: en-US Content-Type: application/json;charset=UTF-8 Date: Thu, 24 Mar 2011 19:03:04 GMT Expires: Thu, 01 Jan 1970 00:00:00 GMT Pragma: no-cache Server: Apache-Coyote/1.1 Content-Length: 35 Connection: keep-alive {"hello": "REST for Datasets rocks"} |
Optional Parameters
Request
curl -i -H Accept:application/json 'http://repositoryservice.sagebase.org/repo/v1/dataset?sort=name&limit=3' |
Response
HTTP/1.1 200 OK Content-Type: application/json Date: Thu, 24 Mar 2011 19:03:04 GMT Server: Apache-Coyote/1.1 transfer-encoding:chunked Connection: keep-alive { "paging": {"next": "/repo/v1/dataset?offset=4&limit=3&sort=name&ascending=true"}, "results": [ { "annotations": "/repo/v1/dataset/1439/annotations", "creationDate": 1300992881670, "creator": "Stephen Friend", "description": null, "etag": "-973247299", "hasClinicalData": false, "hasExpressionData": false, "hasGeneticData": false, "id": "1439", "layer": "/repo/v1/dataset/1439/layer", "name": "AML Nonresponders Cohort", "releaseDate": null, "status": "Future", "uri": "/repo/v1/dataset/1439", "version": "0.0.1" }, { "annotations": "/repo/v1/dataset/1867/annotations", "creationDate": 1300992891575, "creator": "TCGA", "description": null, "etag": "-2088850069", "hasClinicalData": false, "hasExpressionData": false, "hasGeneticData": false, "id": "1867", "layer": "/repo/v1/dataset/1867/layer", "name": "AML TCGA", "releaseDate": null, "status": "Future", "uri": "/repo/v1/dataset/1867", "version": "0.0.1" }, { "annotations": "/repo/v1/dataset/484/annotations", "creationDate": 1300992858639, "creator": "Cookson", "description": null, "etag": "640102020", "hasClinicalData": false, "hasExpressionData": false, "hasGeneticData": false, "id": "484", "layer": "/repo/v1/dataset/484/layer", "name": "Asthma Human Lymphoblastoid Cell Lines", "releaseDate": null, "status": "Future", "uri": "/repo/v1/dataset/484", "version": "0.0.1" } ], "totalNumberOfResults": 114 } |
This returns the primary fields of a dataset and links to get additional info.
Request
curl -i -H Accept:application/json 'http://repositoryservice.sagebase.org/repo/v1/dataset/563' |
Response
HTTP/1.1 200 OK Content-Type: application/json Date: Thu, 24 Mar 2011 19:03:04 GMT ETag: 1169669811 Server: Apache-Coyote/1.1 transfer-encoding:chunked Connection: keep-alive { "annotations": "/repo/v1/dataset/563/annotations", "creationDate": 1300992860514, "creator": "Fred Guengrich/Steve Strom/ Erin Schuetz", "description": null, "etag": "1169669811", "hasClinicalData": true, "hasExpressionData": true, "hasGeneticData": false, "id": "563", "layer": "/repo/v1/dataset/563/layer", "name": "Human Liver Cohort", "releaseDate": null, "status": "Current", "uri": "/repo/v1/dataset/563", "version": "0.0.1" } |
This returns the annotations for a dataset.
Request
curl -i -H Accept:application/json 'http://repositoryservice.sagebase.org/repo/v1/dataset/563/annotations' |
Response
HTTP/1.1 200 OK Content-Type: application/json Date: Thu, 24 Mar 2011 19:03:04 GMT ETag: -614496206 Server: Apache-Coyote/1.1 Content-Length: 881 Connection: keep-alive { "creationDate": null, "dateAnnotations": {}, "doubleAnnotations": {}, "etag": "-614496206", "id": "563", "longAnnotations": { "Number_of_Samples": [517], "db_id": [29] }, "stringAnnotations": { "Disease": ["CVD"], "Institution": ["Vanderbilt University/ University of Pittsburg/ StJudes Hospital"], "Internal_Name": ["Deliver"], "Posting_Restriction": ["Link to data source"], "Species": ["Human"], "Tissue/Tumor": ["Liver"], "Type": ["GCD"], "abstract_file_path": ["/srv/www/htdocs/Foswiki/downloads/data/v2/abstract_files/human_liver_cohort.txt"], "citation_file_path": ["/srv/www/htdocs/Foswiki/downloads/data/v2/citation_files/human_liver_cohort.txt"], "readme_file_path": ["/srv/www/htdocs/Foswiki/downloads/data/v2/readme_files/human_liver_cohort.txt"], "user_agreement_file_path": ["/srv/www/htdocs/Foswiki/downloads/data/v2/user_agreement_files/human_liver_cohort.txt"] }, "uri": "/repo/v1/dataset/563/annotations" } |
This returns the primary fields for all the layers of a dataset.
Request
curl -i -H Accept:application/json 'http://repositoryservice.sagebase.org/repo/v1/dataset/563/layer' |
Response
HTTP/1.1 200 OK Content-Type: application/json Date: Thu, 24 Mar 2011 19:03:04 GMT Server: Apache-Coyote/1.1 Content-Length: 1285 Connection: keep-alive { "paging": {}, "results": [ { "annotations": "/repo/v1/dataset/563/layer/2268/annotations", "creationDate": 1300992903392, "description": null, "etag": "90681233", "id": "2268", "locations": [ "/repo/v1/dataset/563/layer/2268/awsS3Location", "/repo/v1/dataset/563/layer/2268/sageLocation", "/repo/v1/dataset/563/layer/2268/awsEBSLocation", "/repo/v1/dataset/563/layer/2268/locations" ], "name": "expression data", "platform": null, "preview": "/repo/v1/dataset/563/layer/2268/preview", "processingFacility": null, "publicationDate": null, "qcBy": null, "qcDate": null, "releaseNotes": null, "tissueType": null, "type": "E", "uri": "/repo/v1/dataset/563/layer/2268", "version": "0.0.1" }, { "annotations": "/repo/v1/dataset/563/layer/2258/annotations", "creationDate": 1300992902719, "description": null, "etag": "-1634935957", "id": "2258", "locations": [ "/repo/v1/dataset/563/layer/2258/awsEBSLocation", "/repo/v1/dataset/563/layer/2258/sageLocation", "/repo/v1/dataset/563/layer/2258/awsS3Location", "/repo/v1/dataset/563/layer/2258/locations" ], "name": "clinical data", "platform": null, "preview": "/repo/v1/dataset/563/layer/2258/preview", "processingFacility": null, "publicationDate": null, "qcBy": null, "qcDate": null, "releaseNotes": null, "tissueType": null, "type": "C", "uri": "/repo/v1/dataset/563/layer/2258", "version": "0.0.1" } ], "totalNumberOfResults": 2 } |
This returns the metadata for a dataset layer.
Request
curl -i -H Accept:application/json 'http://repositoryservice.sagebase.org/repo/v1/dataset/563/layer/2268' |
Response
HTTP/1.1 200 OK Content-Type: application/json Date: Thu, 24 Mar 2011 19:03:04 GMT ETag: 90681233 Server: Apache-Coyote/1.1 Content-Length: 616 Connection: keep-alive { "annotations": "/repo/v1/dataset/563/layer/2268/annotations", "creationDate": 1300992903392, "description": null, "etag": "90681233", "id": "2268", "locations": [ "/repo/v1/dataset/563/layer/2268/awsS3Location", "/repo/v1/dataset/563/layer/2268/sageLocation", "/repo/v1/dataset/563/layer/2268/awsEBSLocation", "/repo/v1/dataset/563/layer/2268/locations" ], "name": "expression data", "platform": null, "preview": "/repo/v1/dataset/563/layer/2268/preview", "processingFacility": null, "publicationDate": null, "qcBy": null, "qcDate": null, "releaseNotes": null, "tissueType": null, "type": "E", "uri": "/repo/v1/dataset/563/layer/2268", "version": "0.0.1" } |
This returns the annotations for a dataset layer.
Request
curl -i -H Accept:application/json 'http://repositoryservice.sagebase.org/repo/v1/dataset/563/layer/2268/annotations' |
Response
HTTP/1.1 200 OK Content-Type: application/json Date: Thu, 24 Mar 2011 19:03:04 GMT ETag: 923521 Server: Apache-Coyote/1.1 transfer-encoding:chunked Connection: keep-alive { "creationDate": null, "dateAnnotations": {}, "doubleAnnotations": {}, "etag": "923521", "id": "2268", "longAnnotations": {}, "stringAnnotations": {}, "uri": "/repo/v1/dataset/563/layer/2268/annotations" } |
This returns the preview data for a dataset layer.
Request
curl -i -H Accept:application/json 'http://repositoryservice.sagebase.org/repo/v1/dataset/563/layer/2268/preview' |
Response
HTTP/1.1 200 OK Content-Type: application/json Date: Thu, 24 Mar 2011 19:03:04 GMT ETag: 158504117 Server: Apache-Coyote/1.1 transfer-encoding:chunked Connection: keep-alive { "etag": "158504117", "id": "2268", "preview": 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"uri": "/repo/v1/dataset/563/layer/2268/preview" } |
This returns the preview data for a dataset layer.
Request
curl -i -H Accept:application/json 'http://repositoryservice.sagebase.org/repo/v1/dataset/563/layer/2268/previewAsMap' |
Response
HTTP/1.1 200 OK Content-Type: application/json Date: Thu, 24 Mar 2011 19:03:05 GMT Server: Apache-Coyote/1.1 transfer-encoding:chunked Connection: keep-alive { "results": [ { "1110001": "0.235562", "1110005": "0.218965", "1110006": "0.300516", "1110008": "0.16009", "1110009": "0.233883", "1110010": "0.139364", "1110011": "0.260499", "1110023": "0.13199", "1110025": "0.11855", "1110033": "0.270383", "1110035": "0.268439", "1110043": "0.190762", "1110044": "0.274975", "1110063": "0.125049", "1110066": "0.156258", "1110070": "0.129942", "1110071": "0.236298", "1110072": "0.415599", "1110073": "0.108745", "1110075": "0.586675", "1110076": "0.215099", "1110077": "0.119742", "1110081": "0.127944", "1110082": "0.190528", "1110083": "0.324113", "1110085": "0.056604", "1110086": "0.229058", "1110087": "0.171396", "1110088": "0.239457", "1110090": "0.185605", "1110094": "0.28129", "1110095": "0.434382", "1110096": "0.106157", "1110097": "0.209314", "1110099": "0.148762", "1110102": "0.384891", "1110103": "0.083221", "1110105": "0.061347", "1110106": "0.213321", "1110107": "0.394484", "1110109": "0.331495", "1110110": "0.375077", "1110111": "0.189593", "1110112": "0.210103", "1110113": "0.288722", "1110114": "0.290022", "1110115": "0.441432", "1110117": "0.176891", "1110119": "0.211516", "1110121": "0.114255", "1110122": "0.15486", "1110123": "0.226049", "1110125": "0.323837", "1110126": "0.323438", "1110128": "0.245062", "1110129": "0.158348", "1110130": "0.157438", "1110131": "0.245658", "1110132": "0.045379", "1110133": "0.148622", "1110134": "0.088179", "1110135": "0.135844", "1110137": "0.097061", "1110138": "0.13629", "1110139": "0.01557", "1110140": "0.148356", "1110143": "0.106346", "1110144": "0.290704", "1110145": "0.452654", "1110146": "0.140398", "1110147": "0.072526", "1110149": "0.143955", "1110150": "0.340495", "1110164": "0.191651", "1110165": "0.17374", "1110166": "0.060613", "1110180": "0.197906", "1110181": "0.107014", "1110184": "0.011581", "1110185": 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"0.190833", "1110147": "0.134194", "1110149": "0.210924", "1110150": "0.381192", "1110164": "0.230237", "1110165": "0.223845", "1110166": "0.116504", "1110180": "0.235338", "1110181": "0.180056", "1110184": "0.078236", "1110185": "0.112041", "1110187": "0.060627", "1110188": "0.504429", "1110189": "0.25131", "1110191": "0.175482", "1110192": "0.098991", "1110193": "0.212537", "1110194": "0.134445", "1110195": "0.261663", "1110196": "0.397394", "1110197": "0.126125", "1110200": "0.112724", "1110201": "0.28142", "1110202": "0.27781", "1110203": "0.227873", "1110204": "0.291229", "1110205": "0.293653", "1110206": "0.117806", "1110208": "0.253446", "1110210": "0.32851", "1110212": "0.058817", "1110214": "0.076524", "1110215": "0.281525", "1110217": "0.233975", "1110218": "0.246489", "1110219": "0.153788", "1110220": "0.232106", "1110221": "0.106666", "1110222": "0.135263", "1110223": "0.165314", "1110227": "0.117171", "1110228": "0.179668", "1110229": "0.077517", "1110230": "0.234853", "1110232": "0.199454", "1110234": "0.320408", "1110236": "0.237605", "1110237": "0.526592", "1110238": "0.304669", "1110239": "0.155639", "1110241": "0.239662", "1110242": "0.027807", "1110243": "-0.019492", "1110245": "0.138768", "1110246": "0.346082", "1110251": "0.181678", "1110252": "0.192582", "1110255": "0.258808", "1110256": "0.253503", "1110257": "0.25205", "1110258": "0.307398", "1110259": "0.389188", "1110260": "0.092683", "1110261": "0.200276", "1110262": "0.189049", "1110263": "0.105281", "1110264": "0.17734", "1110265": "0.208413", "1110267": "0.240623", "1110268": "0.375138", "1110272": "0.334906", "1110273": "0.367642", "1110274": "0.296458", "1110275": "0.17776", "1110279": "0.392046", "1110291": "0.220998", "1110292": "0.052679", "1110293": "0.25831", "1110294": "0.174249", "1110299": "0.232972", "1110300": "0.19171", "1110310": "0.192448", "1110319": "0.129079", "1110320": "0.147145", "1110321": "0.120522", "1110322": "0.180569", "1110334": "0.183015", "1110335": "0.265182", "1110336": "0.208698", "1110337": "0.401779", "1110338": "0.192857", "1110339": "0.190793", "1110340": "0.017854", "1110341": "-0.002501", "1110344": "0.241949", "1110345": "0.250874", "1110349": "0.201896", "1110350": "0.325308", "1110351": "0.156997", "1110353": "0.179924", "1110356": "0.244661", "1110357": "0.263107", "1110360": "0.299801", "1110361": "0.277458", "1110363": "0.464374", "1110366": "0.177457", "1110367": "0.174146", "1110368": "0.299532", "1110372": "0.396401", "1110373": "0.480128", "1110377": "0.275576", "1110378": "0.208331", "1110385": "0.220092", "1110386": "0.101479", "1110387": "0.217751", "1110389": "0.103696", "1110393": "0.183871", "1110394": "0.187703", "1110395": "0.135226", "1110396": "0.153838", "1110397": "0.070062", "1110398": "0.057413", "1110400": "0.152186", "1110403": "0.1224", "1110404": "0.056733", "1110405": "0.18442", "1110406": "0.126033", "1110411": "0.125111", "1110412": "0.19033", "1110413": "0.022608", "1110418": "0.079295", "1110420": "0.105933", "1110421": "0.02368", "1110422": "-0.078739", "1110427": "0.198813", "1110428": "0.197968", "1110429": "0.276692", "1110430": "0.07682", "1110433": "0.112384", "1110436": "0.256792", "1110437": "0.161083", "1110438": "0.080685", "1110439": "0.092393", "1110440": "0.174021", "1110441": "0.071764", "1110443": "0.024021", "1110447": "0.090689", "1110448": "0.072015", "1110449": "0.286602", "1110450": "0.427668", "1110451": "0.427492", "1110453": "0.293875", "1110454": "0.411796", "1110455": "0.338124", "1110456": "0.272089", "1110457": "0.153146", "1110458": "0.251674", "1110459": "0.193905", "1110460": "0.19251", "1110461": "0.12911", "1110463": "0.134593", "1110473": "0.325273", "1110474": "0.197258", "1110476": "0.196374", "1110477": "0.245164", "1110478": "0.138556", "1110480": "0.094767", "1110482": "0.021671", "1110485": "0.200722", "1110488": "0.180922", "1110497": "0.264828", "1110499": "0.422095", "1110500": "0.320859", "1110502": "0.094586", "1110503": "0.09897", "1110504": "0.280238", "2220001": "0.229985", "2220004": "0.274772", "2220008": "0.186658", "2220011": "0.156253", "2220012": "0.33949", "2220015": "0.174408", "2220017": "0.361175", "2220018": "0.233708", "2220019": "0.356785", "2220021": "0.222286", "2220025": "0.245433", "2220026": "0.146346", "2220029": "0.113412", "2220040": "0.190627", "2220041": "0.151848", "2220043": "0.305029", "2220046": "0.107891", "2220048": "0.144022", "2220049": "0.011899", "2220051": "0.05256", "2220052": "0.129226", "2220053": "0.22367", "2220055": "0.136944", "2220056": "0.111048", "2220057": "0.183696", "2220058": "0.159517", "2220061": "0.026261", "2220062": "0.180307", "2220063": "0.006662", "2220067": "-0.011621", "2220068": "0.150914", "2220070": "0.106121", "2220071": "0.293525", "2220072": "0.281548", "2220073": "0.018772", "2220074": "0.194204", "2220075": "0.366349", "2220076": "0.26721", "2220077": "0.074769", "2220079": "0.225061", "2220083": "0.017441", "2220084": "0.132791", "2220086": "0.064267", "2220087": "0.016096", "2220088": "0.205966", "2220089": "0.178169", "2220091": "0.152823", "2220092": "0.360118", "2220093": "0.133203", "2220094": "0.327367", "2220095": "0.128382", "2220097": "0.162597", "2220098": "0.12093", "2220099": "0.246529", "2220100": "-0.026199", "2220101": "-0.061679", "2220102": "0.055915", "2220104": "0.202533", "2220106": "0.206885", "2220107": "0.15291", "2220108": "0.360705", "2220109": "0.105715", "2220112": "0.100716", "2220116": "0.183118", "2220117": "0.316459", "2220121": "0.148413", "2220122": "0.342686", "2220125": "0.242741", "2220126": "0.4495", "2220129": "0.079091", "2220131": "0.344276", "2220132": "0.630635", "2220133": "0.152315", "2220134": "0.178607", "2220135": "0.105609", "2220137": "0.364888", "2220138": "0.546607", "2220139": "0.079847", "2220140": "0.137605", "2220141": "0.203415", "2220143": "0.200999", "2220144": "0.298101", "2220145": "0.280048", "2220146": "0.307746", "2220147": "0.324096", "2220148": "0.052015", "2220149": "0.027345", "2220150": "0.446968", "2220151": "0.153178", "2220152": "0.228421", "2220153": "0.299219", "2220154": "0.249392", "2220155": "0.174299", "2220157": "0.333741", "2220158": "0.076501", "2220159": "0.122121", "2220160": "0.391236", "2220162": "0.190459", "2220163": "0.226404", "2220165": "0.330293", "2220166": "0.073217", "2220167": "0.326581", "2220169": "0.081702", "2220171": "0.150719", "2220172": "0.160544", "2220173": "0.35913", "2220174": "0.404611", "2220175": "0.159918", "2220176": "0.321622", "2220177": "0.167614", "2220178": "0.146613", "2220180": "0.115655", "2220181": "0.165564", "2220182": "0.267642", "2220183": "0.170034", "2220184": "0.280724", "2220185": "0.14266", "2220186": "0.214699", "2220187": "-0.001975", "2220188": "0.116087", "2220189": "0.215859", "2220190": "0.092078", "2220191": "0.183574", "2220192": "0.035345", "2220194": "0.25222", "2220196": "0.064413", "2220197": "0.259857", "2220198": "0.311587", "2220199": "0.126711", "2220200": "0.240151", "2220201": "0.16711", "2220202": "0.1066", "2220203": "0.194742", "2220204": "0.148556", "2220205": "0.051356", "2220206": "0.201368", "2220209": "0.1615", "2220219": "0.131901", "2220220": "0.227001", "2220221": "0.138792", "2220222": "0.172675", "2220225": "0.417415", "2220226": "0.195586", "2220233": "0.000931", "2220234": "0.132476", "2220235": "0.400392", "2220236": "0.079754", "2220238": "0.145346", "2220239": "0.092109", "2220241": "0.360001", "2220242": "0.033625", "2220243": "0.175429", "2220248": "0.156852", "2220249": "0.211229", "2220250": "0.209847", "2220251": "0.091778", "2220252": "0.081436", "2220253": "0.294029", "2220254": "0.141466", "2220256": "0.12975", "2220257": "0.46631", "2220260": "0.11142", "2220261": "0.082951", "2220262": "0.168436", "2220263": "-0.030086", "2220264": "0.089947", "2220265": "0.248787", "2220266": "0.121247", "2220268": "0.095001", "2220269": "0.134048", "2220270": "0.074181", "2220271": "0.045499", "2220274": "0.295274", "2220275": "0.134652", "2220276": "0.174626", "2220277": "0.05751", "2220279": "0.156141", "2220280": "0.199478", "2220281": "0.137635", "2220282": "0.120329", "2220283": "0.198103", "2220285": "0.225398", "2220286": "0.156343", "2220287\r": "0.351209\r", "3330053": "-0.112587", "3330055": "0.077331", "3330056": "-0.109552", "3330057": "-0.149806", "3330059": "-0.02538", "3330062": "-0.090189", "3330063": "-0.119141", "3330064": "-0.12093", "3330065": "-0.216322", "3330066": "-0.172308", "3330067": "-0.271969", "3330071": "-0.310695", "3330074": "-0.062768", "3330075": "-0.011025", "3330079": "-0.077482", "3330085": "0.058062", "3330089": "-0.165972", "3330092": "-0.069364", "3330093": "-0.180868", "3330094": "-0.00629", "3330105": "-0.301962", "3330106": "-0.222758", "3330108": "-0.12886", "3330110": "-0.066225", "3330112": "0.017932", "3330114": "-0.14038", "3330115": "-0.164887", "3330117": "-0.07982", "3330118": "-0.081687", "3330119": "-0.086826", "3330121": "-0.206353", "3330124": "-0.182005", "3330125": "0.006138", "3330127": "-0.031197", "3330130": "0.083787", "3330131": "-0.232442", "3330143": "-0.190241", "accessioncode": "Pro25G", "genesymbol": "Pro25G", "genesymbol_more": "Pro25G", "reporterid": "10005619496" } ], "totalNumberOfResults": 5 } |
This returns the location data for a dataset layer.
Request
curl -i -H Accept:application/json 'http://repositoryservice.sagebase.org/repo/v1/dataset/563/layer/2268/awsS3Location' |
Response
HTTP/1.1 200 OK Content-Type: application/json Date: Thu, 24 Mar 2011 19:03:05 GMT Server: Apache-Coyote/1.1 Content-Length: 203 Connection: keep-alive { "path": "https://data01.sagebase.org.s3.amazonaws.com/human_liver_cohort.expression.tar.gz?Expires=1300993985&AWSAccessKeyId=AKIAJJJU3OSM6GUDICNQ&Signature=RQlMCp5uS6gXD7XcMwV1GdVZYas%3D", "type": "awss3" } |
This returns the location data for a dataset layer.
Request
curl -i -H Accept:application/json 'http://repositoryservice.sagebase.org/repo/v1/dataset/563/layer/2268/sageLocation' |
Response
HTTP/1.1 200 OK Content-Type: application/json Date: Thu, 24 Mar 2011 19:03:05 GMT Server: Apache-Coyote/1.1 Content-Length: 74 Connection: keep-alive { "path": "/Shares/external-data/DAT_030__human_liver_cohort", "type": "sage" } |
This returns the location data for a dataset layer.
Request
curl -i -H Accept:application/json 'http://repositoryservice.sagebase.org/repo/v1/dataset/563/layer/2268/awsEBSLocation' |
Response
HTTP/1.1 200 OK Content-Type: application/json Date: Thu, 24 Mar 2011 19:03:05 GMT Server: Apache-Coyote/1.1 Content-Length: 50 Connection: keep-alive { "path": "snap-29d33a42 (US West)", "type": "awsebs" } |
This returns the metadata for a dataset layer.
Request
curl -i -H Accept:application/json 'http://repositoryservice.sagebase.org/repo/v1/dataset/563/layer/2258' |
Response
HTTP/1.1 200 OK Content-Type: application/json Date: Thu, 24 Mar 2011 19:03:05 GMT ETag: -1634935957 Server: Apache-Coyote/1.1 transfer-encoding:chunked Connection: keep-alive { "annotations": "/repo/v1/dataset/563/layer/2258/annotations", "creationDate": 1300992902719, "description": null, "etag": "-1634935957", "id": "2258", "locations": [ "/repo/v1/dataset/563/layer/2258/awsEBSLocation", "/repo/v1/dataset/563/layer/2258/sageLocation", "/repo/v1/dataset/563/layer/2258/awsS3Location", "/repo/v1/dataset/563/layer/2258/locations" ], "name": "clinical data", "platform": null, "preview": "/repo/v1/dataset/563/layer/2258/preview", "processingFacility": null, "publicationDate": null, "qcBy": null, "qcDate": null, "releaseNotes": null, "tissueType": null, "type": "C", "uri": "/repo/v1/dataset/563/layer/2258", "version": "0.0.1" } |
This returns the annotations for a dataset layer.
Request
curl -i -H Accept:application/json 'http://repositoryservice.sagebase.org/repo/v1/dataset/563/layer/2258/annotations' |
Response
HTTP/1.1 200 OK Content-Type: application/json Date: Thu, 24 Mar 2011 19:03:05 GMT ETag: 923521 Server: Apache-Coyote/1.1 transfer-encoding:chunked Connection: keep-alive { "creationDate": null, "dateAnnotations": {}, "doubleAnnotations": {}, "etag": "923521", "id": "2258", "longAnnotations": {}, "stringAnnotations": {}, "uri": "/repo/v1/dataset/563/layer/2258/annotations" } |
This returns the preview data for a dataset layer.
Request
curl -i -H Accept:application/json 'http://repositoryservice.sagebase.org/repo/v1/dataset/563/layer/2258/preview' |
Response
HTTP/1.1 200 OK Content-Type: application/json Date: Thu, 24 Mar 2011 19:03:05 GMT ETag: -397819108 Server: Apache-Coyote/1.1 Content-Length: 1338 Connection: keep-alive { "etag": "-397819108", "id": "2258", "preview": "Patient_ID\tAGE_(YRS)\tGENDER\tself_reported_ethnicity\tinferred_population\tWEIGHT_(KG)\taldehyde_oxydase\tLiver_Triglyceride_(mg_per_dL)\tBMI\tCYP3A4M_activity\tCYP3A4T_activity\tCYP2D6_activity\tCYP2C9_activity\tCYP2C19_activity\tCYP1A2_activity\tCYP2E1_activity\tCYP2C8_activity\tCYP2B6_activity\tCYP2A6_activity\r\n2220047\t28\tMale\tW\t\t81.6466266\t0\t39.549496\t24.41213818\t243.0098852\t2140\t106.3893066\t192.1470848\t33.9\t214.121382\t1463.340565\t25.41287049\t136.3497127\t372.2884775\r\n2220125\t53\tMale\tW\tCauc\t90.718474\t301.1994652\t38.043172\t26.38654831\t998.1112015\t1090\t217.9309594\t153.6023179\t2.29\t85.25288801\t604.1760022\t14.38833099\t90.72594827\t1190\r\n2220074\t13\tMale\tW\tCauc\t79.83225712\t270.6021297\t35.197126\t32.19049064\t1280\t8290\t190.0967695\t118.1938134\t4\t165.948579\t1150.957744\t35.81644051\t597.7469548\t1090\r\n2220061\t67\tMale\tW\tCauc\t80.73944186\t207.2369312\t34.77267\t24.82570624\t578.5124238\t3820\t98.84809931\t139.3941994\t4.31\t107.5039309\t614.2210811\t9.422549075\t87.0766129\t562.6816642\r\n2220035\t7\tFemale\tW\t\t24.94758035\t482.0762739\t34.677976\t13.26091457\t2180\t13400\t121.2930083\t405.9352223\t45.4\t378.584658\t1372.071808\t82.5516209\t212.8191764\t283.4658954\r\n", "uri": "/repo/v1/dataset/563/layer/2258/preview" } |
This returns the preview data for a dataset layer.
Request
curl -i -H Accept:application/json 'http://repositoryservice.sagebase.org/repo/v1/dataset/563/layer/2258/previewAsMap' |
Response
HTTP/1.1 200 OK Content-Type: application/json Date: Thu, 24 Mar 2011 19:03:05 GMT Server: Apache-Coyote/1.1 Content-Length: 2762 Connection: keep-alive { "results": [ { "AGE_(YRS)": "28", "BMI": "24.41213818", "CYP1A2_activity": "214.121382", "CYP2A6_activity\r": "372.2884775\r", "CYP2B6_activity": "136.3497127", "CYP2C19_activity": "33.9", "CYP2C8_activity": "25.41287049", "CYP2C9_activity": "192.1470848", "CYP2D6_activity": "106.3893066", "CYP2E1_activity": "1463.340565", "CYP3A4M_activity": "243.0098852", "CYP3A4T_activity": "2140", "GENDER": "Male", "Liver_Triglyceride_(mg_per_dL)": "39.549496", "Patient_ID": "2220047", "WEIGHT_(KG)": "81.6466266", "aldehyde_oxydase": "0", "inferred_population": "", "self_reported_ethnicity": "W" }, { "AGE_(YRS)": "53", "BMI": "26.38654831", "CYP1A2_activity": "85.25288801", "CYP2A6_activity\r": "1190\r", "CYP2B6_activity": "90.72594827", "CYP2C19_activity": "2.29", "CYP2C8_activity": "14.38833099", "CYP2C9_activity": "153.6023179", "CYP2D6_activity": "217.9309594", "CYP2E1_activity": "604.1760022", "CYP3A4M_activity": "998.1112015", "CYP3A4T_activity": "1090", "GENDER": "Male", "Liver_Triglyceride_(mg_per_dL)": "38.043172", "Patient_ID": "2220125", "WEIGHT_(KG)": "90.718474", "aldehyde_oxydase": "301.1994652", "inferred_population": "Cauc", "self_reported_ethnicity": "W" }, { "AGE_(YRS)": "13", "BMI": "32.19049064", "CYP1A2_activity": "165.948579", "CYP2A6_activity\r": "1090\r", "CYP2B6_activity": "597.7469548", "CYP2C19_activity": "4", "CYP2C8_activity": "35.81644051", "CYP2C9_activity": "118.1938134", "CYP2D6_activity": "190.0967695", "CYP2E1_activity": "1150.957744", "CYP3A4M_activity": "1280", "CYP3A4T_activity": "8290", "GENDER": "Male", "Liver_Triglyceride_(mg_per_dL)": "35.197126", "Patient_ID": "2220074", "WEIGHT_(KG)": "79.83225712", "aldehyde_oxydase": "270.6021297", "inferred_population": "Cauc", "self_reported_ethnicity": "W" }, { "AGE_(YRS)": "67", "BMI": "24.82570624", "CYP1A2_activity": "107.5039309", "CYP2A6_activity\r": "562.6816642\r", "CYP2B6_activity": "87.0766129", "CYP2C19_activity": "4.31", "CYP2C8_activity": "9.422549075", "CYP2C9_activity": "139.3941994", "CYP2D6_activity": "98.84809931", "CYP2E1_activity": "614.2210811", "CYP3A4M_activity": "578.5124238", "CYP3A4T_activity": "3820", "GENDER": "Male", "Liver_Triglyceride_(mg_per_dL)": "34.77267", "Patient_ID": "2220061", "WEIGHT_(KG)": "80.73944186", "aldehyde_oxydase": "207.2369312", "inferred_population": "Cauc", "self_reported_ethnicity": "W" }, { "AGE_(YRS)": "7", "BMI": "13.26091457", "CYP1A2_activity": "378.584658", "CYP2A6_activity\r": "283.4658954\r", "CYP2B6_activity": "212.8191764", "CYP2C19_activity": "45.4", "CYP2C8_activity": "82.5516209", "CYP2C9_activity": "405.9352223", "CYP2D6_activity": "121.2930083", "CYP2E1_activity": "1372.071808", "CYP3A4M_activity": "2180", "CYP3A4T_activity": "13400", "GENDER": "Female", "Liver_Triglyceride_(mg_per_dL)": "34.677976", "Patient_ID": "2220035", "WEIGHT_(KG)": "24.94758035", "aldehyde_oxydase": "482.0762739", "inferred_population": "", "self_reported_ethnicity": "W" } ], "totalNumberOfResults": 5 } |
This returns the location data for a dataset layer.
Request
curl -i -H Accept:application/json 'http://repositoryservice.sagebase.org/repo/v1/dataset/563/layer/2258/awsEBSLocation' |
Response
HTTP/1.1 200 OK Content-Type: application/json Date: Thu, 24 Mar 2011 19:03:05 GMT Server: Apache-Coyote/1.1 transfer-encoding:chunked Connection: keep-alive { "path": "snap-29d33a42 (US West)", "type": "awsebs" } |
This returns the location data for a dataset layer.
Request
curl -i -H Accept:application/json 'http://repositoryservice.sagebase.org/repo/v1/dataset/563/layer/2258/sageLocation' |
Response
HTTP/1.1 200 OK Content-Type: application/json Date: Thu, 24 Mar 2011 19:03:06 GMT Server: Apache-Coyote/1.1 Content-Length: 74 Connection: keep-alive { "path": "/Shares/external-data/DAT_030__human_liver_cohort", "type": "sage" } |
This returns the location data for a dataset layer.
Request
curl -i -H Accept:application/json 'http://repositoryservice.sagebase.org/repo/v1/dataset/563/layer/2258/awsS3Location' |
Response
HTTP/1.1 200 OK Content-Type: application/json Date: Thu, 24 Mar 2011 19:03:06 GMT Server: Apache-Coyote/1.1 Content-Length: 208 Connection: keep-alive { "path": "https://data01.sagebase.org.s3.amazonaws.com/human_liver_cohort.phenotype.tar.gz?Expires=1300993986&AWSAccessKeyId=AKIAJJJU3OSM6GUDICNQ&Signature=u%2F%2F5aGvEz%2FimR4AwFZSI8uyFIAE%3D", "type": "awss3" } |
The JsonSchema is an emerging standard similar to DTDs for XML.
Request
curl -i -H Accept:application/json 'http://repositoryservice.sagebase.org/repo/v1/query/schema' |
Response
HTTP/1.1 200 OK Content-Type: application/json Date: Thu, 24 Mar 2011 19:03:06 GMT Server: Apache-Coyote/1.1 Content-Length: 191 Connection: keep-alive { "optional": true, "properties": { "results": { "items": { "optional": true, "type": "object" }, "optional": true, "type": "array" }, "totalNumberOfResults": { "optional": true, "type": "integer" } }, "type": "object" } |
The JsonSchema is an emerging standard similar to DTDs for XML.
Request
curl -i -H Accept:application/json 'http://repositoryservice.sagebase.org/repo/v1/dataset/schema' |
Response
HTTP/1.1 200 OK Content-Type: application/json Date: Thu, 24 Mar 2011 19:03:06 GMT Server: Apache-Coyote/1.1 transfer-encoding:chunked Connection: keep-alive { "optional": true, "properties": { "paging": { "optional": true, "type": "object" }, "results": { "items": { "optional": true, "type": "any" }, "optional": true, "type": "array" }, "totalNumberOfResults": { "optional": true, "type": "integer" } }, "type": "object" } |
The JsonSchema is an emerging standard similar to DTDs for XML.
Request
curl -i -H Accept:application/json 'http://repositoryservice.sagebase.org/repo/v1/dataset/563/schema' |
Response
HTTP/1.1 200 OK Content-Type: application/json Date: Thu, 24 Mar 2011 19:03:06 GMT Server: Apache-Coyote/1.1 Content-Length: 735 Connection: keep-alive { "optional": true, "properties": { "annotations": { "optional": true, "type": "string" }, "creationDate": { "optional": true, "type": "number" }, "creator": { "optional": true, "type": "string" }, "description": { "optional": true, "type": "string" }, "etag": { "optional": true, "type": "string" }, "hasClinicalData": { "optional": true, "type": "boolean" }, "hasExpressionData": { "optional": true, "type": "boolean" }, "hasGeneticData": { "optional": true, "type": "boolean" }, "id": { "optional": true, "type": "string" }, "layer": { "optional": true, "type": "string" }, "name": { "optional": true, "type": "string" }, "releaseDate": { "optional": true, "type": "number" }, "status": { "optional": true, "type": "string" }, "uri": { "optional": true, "type": "string" }, "version": { "optional": true, "type": "string" } }, "type": "object" } |
The JsonSchema is an emerging standard similar to DTDs for XML.
Request
curl -i -H Accept:application/json 'http://repositoryservice.sagebase.org/repo/v1/dataset/563/annotations/schema' |
Response
HTTP/1.1 200 OK Content-Type: application/json Date: Thu, 24 Mar 2011 19:03:06 GMT Server: Apache-Coyote/1.1 Content-Length: 429 Connection: keep-alive { "optional": true, "properties": { "creationDate": { "optional": true, "type": "number" }, "dateAnnotations": { "optional": true, "type": "object" }, "doubleAnnotations": { "optional": true, "type": "object" }, "etag": { "optional": true, "type": "string" }, "id": { "optional": true, "type": "string" }, "longAnnotations": { "optional": true, "type": "object" }, "stringAnnotations": { "optional": true, "type": "object" }, "uri": { "optional": true, "type": "string" } }, "type": "object" } |
The JsonSchema is an emerging standard similar to DTDs for XML.
Request
curl -i -H Accept:application/json 'http://repositoryservice.sagebase.org/repo/v1/dataset/563/layer/schema' |
Response
HTTP/1.1 200 OK Content-Type: application/json Date: Thu, 24 Mar 2011 19:03:06 GMT Server: Apache-Coyote/1.1 Content-Length: 231 Connection: keep-alive { "optional": true, "properties": { "paging": { "optional": true, "type": "object" }, "results": { "items": { "optional": true, "type": "any" }, "optional": true, "type": "array" }, "totalNumberOfResults": { "optional": true, "type": "integer" } }, "type": "object" } |
The JsonSchema is an emerging standard similar to DTDs for XML.
Request
curl -i -H Accept:application/json 'http://repositoryservice.sagebase.org/repo/v1/dataset/563/layer/2258/schema' |
Response
HTTP/1.1 200 OK Content-Type: application/json Date: Thu, 24 Mar 2011 19:03:06 GMT Server: Apache-Coyote/1.1 Content-Length: 902 Connection: keep-alive { "optional": true, "properties": { "annotations": { "optional": true, "type": "string" }, "creationDate": { "optional": true, "type": "number" }, "description": { "optional": true, "type": "string" }, "etag": { "optional": true, "type": "string" }, "id": { "optional": true, "type": "string" }, "locations": { "items": { "optional": true, "type": "string" }, "optional": true, "type": "array" }, "name": { "optional": true, "type": "string" }, "platform": { "optional": true, "type": "string" }, "preview": { "optional": true, "type": "string" }, "processingFacility": { "optional": true, "type": "string" }, "publicationDate": { "optional": true, "type": "number" }, "qcBy": { "optional": true, "type": "string" }, "qcDate": { "optional": true, "type": "number" }, "releaseNotes": { "optional": true, "type": "string" }, "tissueType": { "optional": true, "type": "string" }, "type": { "optional": true, "type": "string" }, "uri": { "optional": true, "type": "string" }, "version": { "optional": true, "type": "string" } }, "type": "object" } |
The JsonSchema is an emerging standard similar to DTDs for XML.
Request
curl -i -H Accept:application/json 'http://repositoryservice.sagebase.org/repo/v1/dataset/563/layer/2258/preview/schema' |
Response
HTTP/1.1 200 OK Content-Type: application/json Date: Thu, 24 Mar 2011 19:03:06 GMT Server: Apache-Coyote/1.1 transfer-encoding:chunked Connection: keep-alive { "optional": true, "properties": { "etag": { "optional": true, "type": "string" }, "id": { "optional": true, "type": "string" }, "preview": { "optional": true, "type": "string" }, "uri": { "optional": true, "type": "string" } }, "type": "object" } |
The JsonSchema is an emerging standard similar to DTDs for XML.
Request
curl -i -H Accept:application/json 'http://repositoryservice.sagebase.org/repo/v1/dataset/563/layer/2258/previewAsMap/schema' |
Response
HTTP/1.1 200 OK Content-Type: application/json Date: Thu, 24 Mar 2011 19:03:06 GMT Server: Apache-Coyote/1.1 Content-Length: 191 Connection: keep-alive { "optional": true, "properties": { "results": { "items": { "optional": true, "type": "object" }, "optional": true, "type": "array" }, "totalNumberOfResults": { "optional": true, "type": "integer" } }, "type": "object" } |
The JsonSchema is an emerging standard similar to DTDs for XML.
Request
curl -i -H Accept:application/json 'http://repositoryservice.sagebase.org/repo/v1/dataset/563/layer/2258/locations/schema' |
Response
HTTP/1.1 200 OK Content-Type: application/json Date: Thu, 24 Mar 2011 19:03:06 GMT Server: Apache-Coyote/1.1 Content-Length: 352 Connection: keep-alive { "optional": true, "properties": { "etag": { "optional": true, "type": "string" }, "id": { "optional": true, "type": "string" }, "locations": { "items": { "optional": true, "properties": { "path": { "optional": true, "type": "string" }, "type": { "optional": true, "type": "string" } }, "type": "object" }, "optional": true, "type": "array" }, "uri": { "optional": true, "type": "string" } }, "type": "object" } |
The JsonSchema is an emerging standard similar to DTDs for XML.
Request
curl -i -H Accept:application/json 'http://repositoryservice.sagebase.org/repo/v1/dataset/563/layer/2258/awsEBSLocation/schema' |
Response
HTTP/1.1 200 OK Content-Type: application/json Date: Thu, 24 Mar 2011 19:03:06 GMT Server: Apache-Coyote/1.1 Content-Length: 130 Connection: keep-alive { "optional": true, "properties": { "path": { "optional": true, "type": "string" }, "type": { "optional": true, "type": "string" } }, "type": "object" } |
The JsonSchema is an emerging standard similar to DTDs for XML.
Request
curl -i -H Accept:application/json 'http://repositoryservice.sagebase.org/repo/v1/dataset/563/layer/2258/sageLocation/schema' |
Response
HTTP/1.1 200 OK Content-Type: application/json Date: Thu, 24 Mar 2011 19:03:06 GMT Server: Apache-Coyote/1.1 transfer-encoding:chunked Connection: keep-alive { "optional": true, "properties": { "path": { "optional": true, "type": "string" }, "type": { "optional": true, "type": "string" } }, "type": "object" } |
The JsonSchema is an emerging standard similar to DTDs for XML.
Request
curl -i -H Accept:application/json 'http://repositoryservice.sagebase.org/repo/v1/dataset/563/layer/2258/awsS3Location/schema' |
Response
HTTP/1.1 200 OK Content-Type: application/json Date: Thu, 24 Mar 2011 19:03:07 GMT Server: Apache-Coyote/1.1 transfer-encoding:chunked Connection: keep-alive { "optional": true, "properties": { "path": { "optional": true, "type": "string" }, "type": { "optional": true, "type": "string" } }, "type": "object" } |
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.
Request:
curl -i -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
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/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw/annotations", "id":"agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw", "version":"0.0.1", "creator":"fake creator", "description":null, "creationDate":1296595870715, "status":"not curated", "uri":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw", "etag":"1309185941", "releaseDate":1254355200000, "layers":[] } |
Note that in the example below the creator and description fields have been changed but all others remain the same.
Request:
curl -i -H Accept:application/json -H Content-Type:application/json -X PUT -H ETag:1309185941 -d '{ "name":"test dataset", "annotations":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw/annotations", "id":"agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw", "version":"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":[] } ' http://localhost:8080/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw |
Response
HTTP/1.1 200 OK ETag: -852418664 Content-Type: application/json Transfer-Encoding: chunked Server: Jetty(6.1.x) { "name":"test dataset", "annotations":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw/annotations", "id":"agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw", "version":"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, "layers":[] } |
First get the empty annotations container for your newly created dataset
Request
curl -i -H Accept:application/json http://localhost:8080/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw/annotations |
Response
HTTP/1.1 200 OK ETag: 923521 Content-Type: application/json Transfer-Encoding: chunked Server: Jetty(6.1.x) { "id":"agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw", "creationDate":null, "uri":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw/annotations", "etag":"923521", "stringAnnotations":{ }, "floatAnnotations":{ }, "dateAnnotations":{ } } |
Then you add/modify the annotations of interest and do a PUT. Note that annotation values must always be list values even if the list is only of length one.
Request
curl -i -H Accept:application/json -H Content-Type:application/json -X PUT -H ETag:923521 -d '{ "id":"agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw", "creationDate":null, "uri":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw/annotations", "etag":"923521", "stringAnnotations":{ "Experimental Design Templates":["exp-122887", "exp-97765"] }, "floatAnnotations":{ "Number of Samples":[500] }, "dateAnnotations":{ "Publication Date":["2011-01-15"] } }' http://localhost:8080/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw/annotations |
Response
HTTP/1.1 200 OK ETag: -1638393853 Content-Type: application/json Transfer-Encoding: chunked Server: Jetty(6.1.x) { "id":"agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYBww", "creationDate":null, "uri":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYBww/annotations", "etag":"-1638393853", "stringAnnotations":{ "Experimental Design Templates":[ "exp-122887", "exp-97765" ] }, "floatAnnotations":{ "Number of Samples":[ 500.0 ] }, "dateAnnotations":{ "Publication Date":[ 1295049600000 ] } } |
Request
curl -i -X DELETE http://localhost:8080/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw |
Response
HTTP/1.1 204 No Content Server: Jetty(6.1.x) |
Request
curl -i -H Accept:application/json http://localhost:8080/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer |
Response
HTTP/1.1 200 OK Content-Type: application/json Transfer-Encoding: chunked Server: Jetty(6.1.x) { "results":[ { "name":"Flint HS Mice Affy", "annotations":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww/annotations", "id":"agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww", "type":"E", "version":"0.0.1", "description":"this is a description", "creationDate":1296690778880, "uri":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww", "etag":"1424771925", "publicationDate":null, "releaseNotes":"this is a release note", "tissueType":"liver", "platform":null, "processingFacility":null, "qcBy":null, "qcDate":null }, { "name":"Flint HS Mice Phenotypes", "annotations":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjpBww/annotations", "id":"agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjpBww", "type":"C", "version":"0.0.1", "description":"this is a description", "creationDate":1296693007167, "uri":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjpBww", "etag":"1445062754", "publicationDate":null, "releaseNotes":"this is a release note", "tissueType":null, "platform":null, "processingFacility":null, "qcBy":null, "qcDate":null } ], "totalNumberOfResults":2, "paging":{ } } |
Request
curl -i -H Accept:application/json http://localhost:8080/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww |
Response
HTTP/1.1 200 OK ETag: 1240467407 Content-Type: application/json Transfer-Encoding: chunked Server: Jetty(6.1.x) { "name":"Flint HS Mice Affy", "annotations":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww/annotations", "id":"agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww", "type":"E", "version":"0.0.1", "description":"this is a description", "creationDate":1296690778880, "uri":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww", "etag":"1240467407", "publicationDate":null, "releaseNotes":"this is a release note", "tissueType":null, "platform":null, "processingFacility":null, "qcBy":null, "qcDate":null } |
Request
curl -i -H Accept:application/json http://localhost:8080/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww/annotations |
Response
HTTP/1.1 200 OK ETag: 923521 Content-Type: application/json Transfer-Encoding: chunked Server: Jetty(6.1.x) { "id":"agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww", "creationDate":null, "uri":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww/annotations", "etag":"923521", "stringAnnotations":{ }, "floatAnnotations":{ }, "dateAnnotations":{ } } |
Request
curl -i -H Accept:application/json -H Content-Type:application/json -d '{"name":"Flint HS Mice Affy", "type":"E", "description":"this is a description", "releaseNotes":"this is a release note"}' http://localhost:8080/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer |
Response
HTTP/1.1 201 Created ETag: 1240467407 Location: /repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww Content-Type: application/json Transfer-Encoding: chunked Server: Jetty(6.1.x) { "name":"Flint HS Mice Affy", "annotations":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww/annotations", "id":"agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww", "type":"E", "version":"0.0.1", "description":"this is a description", "creationDate":1296690778880, "uri":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww", "etag":"1240467407", "publicationDate":null, "releaseNotes":"this is a release note", "tissueType":null, "platform":null, "processingFacility":null, "qcBy":null, "qcDate":null } |
Now ask for the owning dataset and you can see the preview of the layer
Request
curl -i -H Accept:application/json http://localhost:8080/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww |
Response
HTTP/1.1 200 OK ETag: -801135512 Content-Type: application/json Transfer-Encoding: chunked Server: Jetty(6.1.x) { "name":"Flint HS Mice", "annotations":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/annotations", "id":"agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww", "version":"0.0.1", "creator":"Jonathan Flint", "description":null, "creationDate":1296690549675, "status":"Future", "uri":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww", "etag":"-801135512", "releaseDate":null, "layers":[ { "id":"agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww", "type":"E", "uri":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww" },{ "id":"use this uri to make a new layer", "type":"hack", "uri":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer" } ] } |
In the example below we updated the tissue type.
Request
curl -i -H Accept:application/json -H Content-Type:application/json -X PUT -H ETag:1240467407 -d ' { "name":"Flint HS Mice Affy", "annotations":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww/annotations", "id":"agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww", "type":"E", "version":"0.0.1", "description":"this is a description", "creationDate":1296690778880, "uri":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww", "etag":"1240467407", "publicationDate":null, "releaseNotes":"this is a release note", "tissueType":"liver", "platform":null, "processingFacility":null, "qcBy":null, "qcDate":null }' http://localhost:8080/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww |
Response
HTTP/1.1 200 OK ETag: 1424771925 Content-Type: application/json Transfer-Encoding: chunked Server: Jetty(6.1.x) { "name":"Flint HS Mice Affy", "annotations":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww/annotations", "id":"agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww", "type":"E", "version":"0.0.1", "description":"this is a description", "creationDate":1296690778880, "uri":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww", "etag":"1424771925", "publicationDate":null, "releaseNotes":"this is a release note", "tissueType":"liver", "platform":null, "processingFacility":null, "qcBy":null, "qcDate":null } |
Request
curl -i -X DELETE http://localhost:8080/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww |
Response
HTTP/1.1 204 No Content Server: Jetty(6.1.x) |
Request
curl -i -H Accept:application/json -H Content-Type:application/json -X PUT -H ETag:923521 -d ' { "id":"agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww", "creationDate":null, "uri":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww/annotations", "etag":"923521", "stringAnnotations":{ "notes":["I threw away 6 samples during the curation process due to gender chromosome mismatches"] }, "floatAnnotations":{ }, "dateAnnotations":{ } }' http://localhost:8080/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww/annotations |
Response
HTTP/1.1 200 OK ETag: -1897035229 Content-Type: application/json Transfer-Encoding: chunked Server: Jetty(6.1.x) { "id":"agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww", "creationDate":null, "uri":"/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYUww/layer/agxkZWZsYXV4LXRlc3RyLgsSDUdBRUpET0RhdGFzZXQYUwwLEhRHQUVKRE9JbnB1dERhdGFMYXllchjoBww/annotations", "etag":"-1897035229", "stringAnnotations":{ "notes":[ "I threw away 6 samples during the curation process due to gender chromosome mismatches" ] }, "floatAnnotations":{ }, "dateAnnotations":{ } } |