Introduction
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.
Encoding
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'
Security
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
Query API Examples
'Select *' Query
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: Wed, 30 Mar 2011 17:51:53 GMT
Server: Apache-Coyote/1.1
Content-Length: 3481
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": 1301505581000,
"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": "1",
"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": 1301505582000,
"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": "2",
"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": 1301505584000,
"dataset.creator": "Soheil Meshinchi/ Bob Arceci",
"dataset.db_id": [3],
"dataset.description": null,
"dataset.hasClinicalData": false,
"dataset.hasExpressionData": false,
"dataset.hasGeneticData": false,
"dataset.id": "3",
"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
}
'Order By' Query
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: Wed, 30 Mar 2011 17:51:54 GMT
Server: Apache-Coyote/1.1
Content-Length: 3414
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": 1301505626000,
"dataset.creator": "Dan Levy",
"dataset.db_id": [31],
"dataset.description": null,
"dataset.hasClinicalData": false,
"dataset.hasExpressionData": false,
"dataset.hasGeneticData": false,
"dataset.id": "31",
"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": 1301505581000,
"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": "1",
"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": 1301505582000,
"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": "2",
"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
}
'Where Equal To' Query
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: Wed, 30 Mar 2011 17:51:54 GMT
Server: Apache-Coyote/1.1
Content-Length: 1200
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": 1301505623000,
"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": "29",
"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": 1
}
'Where Equal To' Query with a Limit
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: Wed, 30 Mar 2011 17:51:56 GMT
Server: Apache-Coyote/1.1
Content-Length: 3480
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": 1301505581000,
"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": "1",
"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": 1301505582000,
"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": "2",
"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": 1301505584000,
"dataset.creator": "Soheil Meshinchi/ Bob Arceci",
"dataset.db_id": [3],
"dataset.description": null,
"dataset.hasClinicalData": false,
"dataset.hasExpressionData": false,
"dataset.hasGeneticData": false,
"dataset.id": "3",
"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": 92
}
'Select *' Query for the Layers of a Dataset
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+==+"29"'
Response
HTTP/1.1 200 OK
Content-Type: application/json
Date: Wed, 30 Mar 2011 17:51:56 GMT
Server: Apache-Coyote/1.1
transfer-encoding:chunked
Connection: keep-alive
{
"results": [
{
"layer.creationDate": 1301505753000,
"layer.description": null,
"layer.id": "4",
"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": 1301505754000,
"layer.description": null,
"layer.id": "5",
"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
}
'Order By' Query for the Layers of a Dataset
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+==+"29"+ORDER+BY+type'
Response
HTTP/1.1 200 OK
Content-Type: application/json
Date: Wed, 30 Mar 2011 17:51:58 GMT
Server: Apache-Coyote/1.1
transfer-encoding:chunked
Connection: keep-alive
{
"results": [
{
"layer.creationDate": 1301505753000,
"layer.description": null,
"layer.id": "4",
"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": 1301505754000,
"layer.description": null,
"layer.id": "5",
"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
}
REST API Examples (Read Only)
Sanity check request
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: Wed, 30 Mar 2011 17:51:58 GMT
Expires: Thu, 01 Jan 1970 00:00:00 GMT
Pragma: no-cache
Server: Apache-Coyote/1.1
transfer-encoding:chunked
Connection: keep-alive
{"hello": "REST for Datasets rocks"}
Get All Datasets
Optional Parameters
- offset - integer - 1-based pagination offset
- limit - integer - maximum number of results to return
- sort - string - the name of the field upon which to sort
- ascending - boolean - whether or not to sort ascending
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: Wed, 30 Mar 2011 17:51:58 GMT
Server: Apache-Coyote/1.1
Content-Length: 1242
Connection: keep-alive
{
"paging": {"next": "/repo/v1/dataset?offset=4&limit=3&sort=name&ascending=true"},
"results": [
{
"annotations": "/repo/v1/dataset/74/annotations",
"creationDate": 1301505688000,
"creator": "Stephen Friend",
"description": null,
"etag": "1841477848",
"hasClinicalData": false,
"hasExpressionData": false,
"hasGeneticData": false,
"id": "74",
"layer": "/repo/v1/dataset/74/layer",
"name": "AML Nonresponders Cohort",
"releaseDate": null,
"status": "Future",
"uri": "/repo/v1/dataset/74",
"version": "0.0.1"
},
{
"annotations": "/repo/v1/dataset/96/annotations",
"creationDate": 1301505719000,
"creator": "TCGA",
"description": null,
"etag": "867915198",
"hasClinicalData": false,
"hasExpressionData": false,
"hasGeneticData": false,
"id": "96",
"layer": "/repo/v1/dataset/96/layer",
"name": "AML TCGA",
"releaseDate": null,
"status": "Future",
"uri": "/repo/v1/dataset/96",
"version": "0.0.1"
},
{
"annotations": "/repo/v1/dataset/25/annotations",
"creationDate": 1301505618000,
"creator": "Cookson",
"description": null,
"etag": "-619027979",
"hasClinicalData": false,
"hasExpressionData": false,
"hasGeneticData": false,
"id": "25",
"layer": "/repo/v1/dataset/25/layer",
"name": "Asthma Human Lymphoblastoid Cell Lines",
"releaseDate": null,
"status": "Future",
"uri": "/repo/v1/dataset/25",
"version": "0.0.1"
}
],
"totalNumberOfResults": 114
}
Get a Dataset
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/29'
Response
HTTP/1.1 200 OK
Content-Type: application/json
Date: Wed, 30 Mar 2011 17:51:58 GMT
ETag: 1251978675
Server: Apache-Coyote/1.1
Content-Length: 399
Connection: keep-alive
{
"annotations": "/repo/v1/dataset/29/annotations",
"creationDate": 1301505623000,
"creator": "Fred Guengrich/Steve Strom/ Erin Schuetz",
"description": null,
"etag": "1251978675",
"hasClinicalData": true,
"hasExpressionData": true,
"hasGeneticData": false,
"id": "29",
"layer": "/repo/v1/dataset/29/layer",
"name": "Human Liver Cohort",
"releaseDate": null,
"status": "Current",
"uri": "/repo/v1/dataset/29",
"version": "0.0.1"
}
Get Annotations for a Dataset
This returns the annotations for a dataset.
Request
curl -i -H Accept:application/json 'http://repositoryservice.sagebase.org/repo/v1/dataset/29/annotations'
Response
HTTP/1.1 200 OK
Content-Type: application/json
Date: Wed, 30 Mar 2011 17:51:59 GMT
ETag: 759752322
Server: Apache-Coyote/1.1
Content-Length: 878
Connection: keep-alive
{
"creationDate": null,
"dateAnnotations": {},
"doubleAnnotations": {},
"etag": "759752322",
"id": "29",
"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/29/annotations"
}
Get all the Layers for a Dataset
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/29/layer'
Response
HTTP/1.1 200 OK
Content-Type: application/json
Date: Wed, 30 Mar 2011 17:52:01 GMT
Server: Apache-Coyote/1.1
Content-Length: 1225
Connection: keep-alive
{
"paging": {},
"results": [
{
"annotations": "/repo/v1/dataset/29/layer/4/annotations",
"creationDate": 1301505753000,
"description": null,
"etag": "-1961017803",
"id": "4",
"locations": [
"/repo/v1/dataset/29/layer/4/awsEBSLocation",
"/repo/v1/dataset/29/layer/4/locations",
"/repo/v1/dataset/29/layer/4/sageLocation",
"/repo/v1/dataset/29/layer/4/awsS3Location"
],
"name": "clinical data",
"platform": null,
"preview": "/repo/v1/dataset/29/layer/4/preview",
"processingFacility": null,
"publicationDate": null,
"qcBy": null,
"qcDate": null,
"releaseNotes": null,
"tissueType": null,
"type": "C",
"uri": "/repo/v1/dataset/29/layer/4",
"version": "0.0.1"
},
{
"annotations": "/repo/v1/dataset/29/layer/5/annotations",
"creationDate": 1301505754000,
"description": null,
"etag": "1442309632",
"id": "5",
"locations": [
"/repo/v1/dataset/29/layer/5/sageLocation",
"/repo/v1/dataset/29/layer/5/awsEBSLocation",
"/repo/v1/dataset/29/layer/5/awsS3Location",
"/repo/v1/dataset/29/layer/5/locations"
],
"name": "expression data",
"platform": null,
"preview": "/repo/v1/dataset/29/layer/5/preview",
"processingFacility": null,
"publicationDate": null,
"qcBy": null,
"qcDate": null,
"releaseNotes": null,
"tissueType": null,
"type": "E",
"uri": "/repo/v1/dataset/29/layer/5",
"version": "0.0.1"
}
],
"totalNumberOfResults": 2
}
Get a Clinical Dataset Layer
This returns the metadata for a dataset layer.
Request
curl -i -H Accept:application/json 'http://repositoryservice.sagebase.org/repo/v1/dataset/29/layer/4'
Response
HTTP/1.1 200 OK
Content-Type: application/json
Date: Wed, 30 Mar 2011 17:52:01 GMT
ETag: -1961017803
Server: Apache-Coyote/1.1
Content-Length: 586
Connection: keep-alive
{
"annotations": "/repo/v1/dataset/29/layer/4/annotations",
"creationDate": 1301505753000,
"description": null,
"etag": "-1961017803",
"id": "4",
"locations": [
"/repo/v1/dataset/29/layer/4/awsEBSLocation",
"/repo/v1/dataset/29/layer/4/locations",
"/repo/v1/dataset/29/layer/4/sageLocation",
"/repo/v1/dataset/29/layer/4/awsS3Location"
],
"name": "clinical data",
"platform": null,
"preview": "/repo/v1/dataset/29/layer/4/preview",
"processingFacility": null,
"publicationDate": null,
"qcBy": null,
"qcDate": null,
"releaseNotes": null,
"tissueType": null,
"type": "C",
"uri": "/repo/v1/dataset/29/layer/4",
"version": "0.0.1"
}
Get Annotations for a Clinical Dataset Layer
This returns the annotations for a dataset layer.
Request
curl -i -H Accept:application/json 'http://repositoryservice.sagebase.org/repo/v1/dataset/29/layer/4/annotations'
Response
HTTP/1.1 200 OK
Content-Type: application/json
Date: Wed, 30 Mar 2011 17:52:01 GMT
ETag: 923521
Server: Apache-Coyote/1.1
Content-Length: 182
Connection: keep-alive
{
"creationDate": null,
"dateAnnotations": {},
"doubleAnnotations": {},
"etag": "923521",
"id": "4",
"longAnnotations": {},
"stringAnnotations": {},
"uri": "/repo/v1/dataset/29/layer/4/annotations"
}
Get preview data for a Clinical Dataset Layer
This returns the preview data for a dataset layer.
Request
curl -i -H Accept:application/json 'http://repositoryservice.sagebase.org/repo/v1/dataset/29/layer/4/preview'
Response
HTTP/1.1 200 OK
Content-Type: application/json
Date: Wed, 30 Mar 2011 17:52:01 GMT
ETag: -397819108
Server: Apache-Coyote/1.1
Content-Length: 1331
Connection: keep-alive
{
"etag": "-397819108",
"id": "4",
"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/29/layer/4/preview"
}
Get preview data as a map for a Clinical Dataset Layer
This returns the preview data for a dataset layer.
Request
curl -i -H Accept:application/json 'http://repositoryservice.sagebase.org/repo/v1/dataset/29/layer/4/previewAsMap'
Response
HTTP/1.1 200 OK
Content-Type: application/json
Date: Wed, 30 Mar 2011 17:52:02 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
}
Get the awsEBSLocation for a Clinical Dataset Layer
This returns the location data for a dataset layer.
Request
curl -i -H Accept:application/json 'http://repositoryservice.sagebase.org/repo/v1/dataset/29/layer/4/awsEBSLocation'
Response
HTTP/1.1 200 OK
Content-Type: application/json
Date: Wed, 30 Mar 2011 17:52:02 GMT
Server: Apache-Coyote/1.1
Content-Length: 50
Connection: keep-alive
{
"path": "snap-29d33a42 (US West)",
"type": "awsebs"
}
Get the sageLocation for a Clinical Dataset Layer
This returns the location data for a dataset layer.
Request
curl -i -H Accept:application/json 'http://repositoryservice.sagebase.org/repo/v1/dataset/29/layer/4/sageLocation'
Response
HTTP/1.1 200 OK
Content-Type: application/json
Date: Wed, 30 Mar 2011 17:52:02 GMT
Server: Apache-Coyote/1.1
Content-Length: 74
Connection: keep-alive
{
"path": "/Shares/external-data/DAT_030__human_liver_cohort",
"type": "sage"
}
Get the awsS3Location for a Clinical Dataset Layer
This returns the location data for a dataset layer.
Request
curl -i -H Accept:application/json 'http://repositoryservice.sagebase.org/repo/v1/dataset/29/layer/4/awsS3Location'
Response
HTTP/1.1 200 OK
Content-Type: application/json
Date: Wed, 30 Mar 2011 17:52:03 GMT
Server: Apache-Coyote/1.1
Content-Length: 206
Connection: keep-alive
{
"path": "https://data01.sagebase.org.s3.amazonaws.com/human_liver_cohort.phenotype.tar.gz?Expires=1301508123&AWSAccessKeyId=thisIsAFakeAWSAccessId&Signature=Hpz6XVOOsgu%2FOAVeBTSlfqptVic%3D",
"type": "awss3"
}
Get a Expression Dataset Layer
This returns the metadata for a dataset layer.
Request
curl -i -H Accept:application/json 'http://repositoryservice.sagebase.org/repo/v1/dataset/29/layer/5'
Response
HTTP/1.1 200 OK
Content-Type: application/json
Date: Wed, 30 Mar 2011 17:52:03 GMT
ETag: 1442309632
Server: Apache-Coyote/1.1
Content-Length: 587
Connection: keep-alive
{
"annotations": "/repo/v1/dataset/29/layer/5/annotations",
"creationDate": 1301505754000,
"description": null,
"etag": "1442309632",
"id": "5",
"locations": [
"/repo/v1/dataset/29/layer/5/sageLocation",
"/repo/v1/dataset/29/layer/5/awsEBSLocation",
"/repo/v1/dataset/29/layer/5/awsS3Location",
"/repo/v1/dataset/29/layer/5/locations"
],
"name": "expression data",
"platform": null,
"preview": "/repo/v1/dataset/29/layer/5/preview",
"processingFacility": null,
"publicationDate": null,
"qcBy": null,
"qcDate": null,
"releaseNotes": null,
"tissueType": null,
"type": "E",
"uri": "/repo/v1/dataset/29/layer/5",
"version": "0.0.1"
}
Get Annotations for a Expression Dataset Layer
This returns the annotations for a dataset layer.
Request
curl -i -H Accept:application/json 'http://repositoryservice.sagebase.org/repo/v1/dataset/29/layer/5/annotations'
Response
HTTP/1.1 200 OK
Content-Type: application/json
Date: Wed, 30 Mar 2011 17:52:03 GMT
ETag: 923521
Server: Apache-Coyote/1.1
transfer-encoding:chunked
Connection: keep-alive
{
"creationDate": null,
"dateAnnotations": {},
"doubleAnnotations": {},
"etag": "923521",
"id": "5",
"longAnnotations": {},
"stringAnnotations": {},
"uri": "/repo/v1/dataset/29/layer/5/annotations"
}
Get preview data for a Expression Dataset Layer
This returns the preview data for a dataset layer.
Request
curl -i -H Accept:application/json 'http://repositoryservice.sagebase.org/repo/v1/dataset/29/layer/5/preview'
Response
HTTP/1.1 200 OK
Content-Type: application/json
Date: Wed, 30 Mar 2011 17:52:03 GMT
ETag: 158504117
Server: Apache-Coyote/1.1
transfer-encoding:chunked
Connection: keep-alive
{
"etag": "158504117",
"id": "5",
"preview": 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"uri": "/repo/v1/dataset/29/layer/5/preview"
}
Get preview data as a map for a Expression Dataset Layer
This returns the preview data for a dataset layer.
Request
curl -i -H Accept:application/json 'http://repositoryservice.sagebase.org/repo/v1/dataset/29/layer/5/previewAsMap'
Response
HTTP/1.1 200 OK
Content-Type: application/json
Date: Wed, 30 Mar 2011 17:52:04 GMT
Server: Apache-Coyote/1.1
transfer-encoding:chunked
Connection: keep-alive
{
"results": [
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"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
}
Get the sageLocation for a Expression Dataset Layer
This returns the location data for a dataset layer.
Request
curl -i -H Accept:application/json 'http://repositoryservice.sagebase.org/repo/v1/dataset/29/layer/5/sageLocation'
Response
HTTP/1.1 200 OK
Content-Type: application/json
Date: Wed, 30 Mar 2011 17:52:04 GMT
Server: Apache-Coyote/1.1
transfer-encoding:chunked
Connection: keep-alive
{
"path": "/Shares/external-data/DAT_030__human_liver_cohort",
"type": "sage"
}
Get the awsEBSLocation for a Expression Dataset Layer
This returns the location data for a dataset layer.
Request
curl -i -H Accept:application/json 'http://repositoryservice.sagebase.org/repo/v1/dataset/29/layer/5/awsEBSLocation'
Response
HTTP/1.1 200 OK
Content-Type: application/json
Date: Wed, 30 Mar 2011 17:52:04 GMT
Server: Apache-Coyote/1.1
Content-Length: 50
Connection: keep-alive
{
"path": "snap-29d33a42 (US West)",
"type": "awsebs"
}
Get the awsS3Location for a Expression Dataset Layer
This returns the location data for a dataset layer.
Request
curl -i -H Accept:application/json 'http://repositoryservice.sagebase.org/repo/v1/dataset/29/layer/5/awsS3Location'
Response
HTTP/1.1 200 OK
Content-Type: application/json
Date: Wed, 30 Mar 2011 17:52:04 GMT
Server: Apache-Coyote/1.1
transfer-encoding:chunked
Connection: keep-alive
{
"path": "https://data01.sagebase.org.s3.amazonaws.com/human_liver_cohort.expression.tar.gz?Expires=1301508125&AWSAccessKeyId=thisIsAFakeAWSAccessId&Signature=18%2FZnvDfpkOoGbLRuTIga3SXZUs%3D",
"type": "awss3"
}
Query API Schema
Query Response Schema
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: Wed, 30 Mar 2011 17:52:05 GMT
Server: Apache-Coyote/1.1
transfer-encoding:chunked
Connection: keep-alive
{
"optional": true,
"properties": {
"results": {
"items": {
"optional": true,
"type": "object"
},
"optional": true,
"type": "array"
},
"totalNumberOfResults": {
"optional": true,
"type": "integer"
}
},
"type": "object"
}
REST API Schemas
Datasets List Schema
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: Wed, 30 Mar 2011 17:52:05 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"
}
Dataset Schema
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/29/schema'
Response
HTTP/1.1 200 OK
Content-Type: application/json
Date: Wed, 30 Mar 2011 17:52:05 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"
}
Dataset Annotations Schema
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/29/annotations/schema'
Response
HTTP/1.1 200 OK
Content-Type: application/json
Date: Wed, 30 Mar 2011 17:52:05 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"
}
Dataset Layers List Schema
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/29/layer/schema'
Response
HTTP/1.1 200 OK
Content-Type: application/json
Date: Wed, 30 Mar 2011 17:52:05 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"
}
Layer Schema
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/29/layer/5/schema'
Response
HTTP/1.1 200 OK
Content-Type: application/json
Date: Wed, 30 Mar 2011 17:52:05 GMT
Server: Apache-Coyote/1.1
transfer-encoding:chunked
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"
}
Layer Preview Schema
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/29/layer/5/preview/schema'
Response
HTTP/1.1 200 OK
Content-Type: application/json
Date: Wed, 30 Mar 2011 17:52:05 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"
}
Layer Preview as Map Schema
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/29/layer/5/previewAsMap/schema'
Response
HTTP/1.1 200 OK
Content-Type: application/json
Date: Wed, 30 Mar 2011 17:52:05 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"
}
Layer Locations Schema
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/29/layer/5/locations/schema'
Response
HTTP/1.1 200 OK
Content-Type: application/json
Date: Wed, 30 Mar 2011 17:52:05 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"
},
"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"
}
Get the sageLocation for a Dataset Layer
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/29/layer/5/sageLocation/schema'
Response
HTTP/1.1 200 OK
Content-Type: application/json
Date: Wed, 30 Mar 2011 17:52:05 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"
}
Get the awsEBSLocation for a Dataset Layer
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/29/layer/5/awsEBSLocation/schema'
Response
HTTP/1.1 200 OK
Content-Type: application/json
Date: Wed, 30 Mar 2011 17:52:05 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"
}
Get the awsS3Location for a Dataset Layer
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/29/layer/5/awsS3Location/schema'
Response
HTTP/1.1 200 OK
Content-Type: application/json
Date: Wed, 30 Mar 2011 17:52:05 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"
}
REST API Usage Examples (Read/Write and slightly out of date)
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.
Create a Dataset
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":[]
}
Update a Dataset
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":[]
}
Add Annotations to a Dataset
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
]
}
}
Delete a Dataset
Request
curl -i -X DELETE http://localhost:8080/repo/v1/dataset/agxkZWZsYXV4LXRlc3RyEwsSDUdBRUpET0RhdGFzZXQYAQw
Response
HTTP/1.1 204 No Content Server: Jetty(6.1.x)
Get a Layers for a Dataset
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":{
}
}
Get a Layer
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
}
Get annotations for a layer
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":{
}
}
Create a layer
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"
}
]
}
Update a 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
}
Delete a layer
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)
Add annotations to a layer
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":{
}
}