The Query API is loosely modeled after Facebook's Query Language.
The REST API took inspiration from several successful REST APIs:
See Service API Design for more information regarding the rationale and design details.
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. For all requests requiring authentication, users will pass a special header sessionToken with
each request to the service.
You must have an account with permission to create entities in Synapse.
Request
curl -i -k -H Accept:application/json -H Content-Type:application/json -d '{
"email": "me@myEmail.com",
"password": "thisIsAFakePassword"
}' https://auth-prod.sagebase.org/auth/v1/session |
Response
|
You can create entities, update entities, read entities, and delete entities. More advanced querying is 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. Conflicting updates are detected and rejected through the use of the ETag header.
An entity is created with a POST where the entity body is passed with a content type of application/json. The only required property for any entity is the 'entityType' which indicates the type of entity you wish to create. See the following table for common entity types:
| entityType | Alias (for query) | Description |
|---|---|---|
| org.sagebionetworks.repo.model.Project | project | A project entity serves as the root for collaboration. It is a common practices to place all other entities within a project. |
| org.sagebionetworks.repo.model.Folder | folder | A simple tool for organizing entities. This is similar to a file folder. |
| org.sagebionetworks.repo.model.Link | link | An entity that points to another entity, similar to a Window's Short Cut or a Linux/Mac Link. |
| org.sagebionetworks.repo.model.Code | code | An entity where the location is composed of source code. |
| org.sagebionetworks.repo.model.PhenotypeData | phenotypedata | Used for phenotypic data. |
| org.sagebionetworks.repo.model.GenotypeData | genotypedata | Used for genotypic data. |
| org.sagebionetworks.repo.model.ExpressionData | expressiondata | Used for expression data. |
| org.sagebionetworks.repo.model.RObject | robject | Language specific 'R' object. |
| org.sagebionetworks.repo.model.Study | study | Used for a study. |
| org.sagebionetworks.repo.model.Data | data | Generic data. |
For more information on entity types see: Synapse Entity Types.
Note that the request is a POST and the content type of the data we are sending to the service is json
In the following example we are going to create a project entity:
Request
curl -i -k -H sessionToken:YourSessionToken -H Accept:application/json -H Content-Type:application/json -d '{"entityType": "org.sagebionetworks.repo.model.Project"}' https://repo-prod.sagebase.org/repo/v1/entity |
Response
|
In the above example, we created an entity with only the 'entityType' but the returned entity had many more fields set. In the next section we will cover the basic fields of an entity.
The following are fields that are common to all entities and entity types:
| Field Name | Type | Description | Editable | Default Value |
|---|---|---|---|---|
| id | String | The ID issued to this entity by Synapse to unique identify it. This ID is immutable and guaranteed to be unique within Synapse. Once an ID is issue to entity the ID will never be issued to another entity even if the original entity is deleted. | false | auto-generated |
parentId | String | This is the ID of this entity's parent. This is used to build a hierarchy of entities. | true | Root folder |
createdOn | ISO 8601 date-time | The date and time when the entity was original created. | false | auto-generated |
modifiedOn | ISO 8601 date-time | The date and time when the entity was last modified. | false | auto-generated |
createdBy | String | The name of the user that originally created the entity. | false | auto-generated |
modifiedBy | String | The name of the user that last modified the entity. | false | auto-generated |
name | String | The name of the entity. This is the most prominent fields of the entity and will show up everywhere. Just like a file must have a unique name within a folder, an Entity must have a unique name within its parent. | true | entity id |
| description | String | The description provides more details about an Entity. This field is very prominent on the Synapse web site. | true | null |
etag | String | Used to concurrency and change detection. | false | auto-generated |
uri | String | Relative URI of the entity. | false | auto-generated |
annotations | String | The relative URL for the entity annotations. | false | auto-generated |
accessControlList | String | The relative URL for the entity Access Control List ACL. | false | auto-generated |
Any editable field can be set at creation time or updated.
In this example we want to give our project entity from the previous example a more meaningful name (the default name is the same as the entity's id) .
Note that the request is a PUT. Also note that we add a header 'ETag' with a value that is the same as current etag of the entity. If the entity has been modified since we last fetched it the etag will not match and we will receive a concurrent modification error.
Request
curl -i -k -H sessionToken:YourSessionToken -H ETag:0 -H Accept:application/json -H Content-Type:application/json -X PUT -d '{
"createdOn":"2012-08-29T03:34:00.967Z",
"id":"syn1058078",
"parentId":"syn4489",
"modifiedOn":"2012-08-29T03:34:00.967Z",
"createdBy":"John Hill",
"accessControlList":"/repo/v1/entity/syn1058078/acl",
"etag":"0",
"modifiedBy":"John Hill",
"name":"Example Project",
"annotations":"/repo/v1/entity/syn1058078/annotations",
"entityType":"org.sagebionetworks.repo.model.Project",
"uri":"/repo/v1/entity/syn1058078"
}' https://repo-prod.sagebase.org/repo/v1/entity/syn1058078 |
Response
|
Hierarchy is created in Synapse by setting the "parentId" field of an entity. In this example we are going to create a new folder entity as a child to our project:
Request
curl -i -k -H sessionToken:YourSessionToken -H Accept:application/json -H Content-Type:application/json -d '{"entityType": "org.sagebionetworks.repo.model.Data", "parentId":"syn1058078", "name":"Sample Data"}' https://repo-prod.sagebase.org/repo/v1/entity |
Response
|
First get the current annotations for your newly created data entity.
Request
curl -i -k -H sessionToken:YourSessionToken -H Accept:application/json https://repo-prod.sagebase.org/repo/v1/entity/syn1151499/annotations |
Response
|
Then you add new annotations to the existing annotations, or modify the existing annotations, and do a PUT. Note that annotation values must always be arrays even if the array is only of length one.
Request
curl -i -k -H sessionToken:YourSessionToken -H ETag:843bddfc-d6f8-45d2-b88e-09b4aa27a1cf -H Accept:application/json -H Content-Type:application/json -X PUT -d '
{
"id":"syn1151499",
"creationDate":"1347503586314",
"stringAnnotations":{
"stringExampleA":[
"one",
"two"
],
"stringExampleB":[
"cat",
"dog"
]
},
"dateAnnotations":{
"dateExample":[
1347519600000,
1347606000000
]
},
"etag":"843bddfc-d6f8-45d2-b88e-09b4aa27a1cf",
"doubleAnnotations":{
"floatExample":[
1.234,
99.789
]
},
"longAnnotations":{
"longExample":[
123,
456879
]
},
"blobAnnotations":{
},
"uri":"/entity/syn1151499/annotations"
}' https://repo-prod.sagebase.org/repo/v1/entity/syn1151499/annotations |
Response
|
In this example we will be uploading a simple text file with the following content:
Some simple text! |
We will need to know the md5 of our file before we start. For this example the text the MD5 is:
6b65ca38d3596e0e0e6e1ed3cfa981eb |
There are three steps required to set an Entity's location data:
Request
curl -i -k -H sessionToken:YourSessionToken -H Accept:application/json -H Content-Type:application/json -d '{"path": "SampleTextFile.txt", "md5":"6b65ca38d3596e0e0e6e1ed3cfa981eb"}' https://repo-prod.sagebase.org/repo/v1/entity/syn1151499/s3Token |
Response
|
Request
curl -v -k -X PUT -H Content-MD5:a2XKONNZbg4Obh7Tz6mB6w== -H x-amz-acl:bucket-owner-full-control -H Content-Type:text/plain --data-ascii SampleTextFile.txt https://s3.amazonaws.com/proddata.sagebase.org/1151499/1159148/SampleTextFile.txt?Expires=1347598777&x-amz-security-token=AQoDYXdzEG4asAKFXWZXVmnAG7q1zyUzRjVz6rnN6wIRT0msXgSRBC3suTAItfuQjJRv9YOAw3Fr4nlJL2HAnRbNvF1NC4xnW5%2Bj6VUNnJYGtZUj%2Bwii%2BbTGYncNrruXLxqqLM8Kg%2FdmGQGWluVZkYy7rLDbofrWcWunRjSYBb7uEe74EURM1jg1ae3qMnNgwBUHWJvJb1AjOojpNujh0N5KX0C3ux6VCDcFrgHR6K%2BsiyfiPqSW25XmabA5jGAnV6EGXn1iazywrl2ZW8z%2BfYAZB1kgsoTCQgCZMsPxpXxh%2FBdQi7cc7rwflCr%2FP1wD51N9PGFakFhJkbm8glGhE%2BYQDYEOpvRmOF0%2BS2%2BxrstIzsEAoZ5NXmMg97pqOWx1sBQVvKp8NXgdkXn422CFJLFPW8u%2BVd%2FHzO6EILnQxYIF&AWSAccessKeyId=ASIAIGRZMDNEEK777KGA&Signature=c%2BC0HOBQ2MOzS4L89ev4OPbzD1w%3D |
Request
curl -i -k -H sessionToken:YourSessionToken -H ETag:2526dd09-565e-4989-b8c4-a82e724672c6 -H Accept:application/json -H Content-Type:application/json -X PUT -d '{
"s3Token":"/repo/v1/entity/syn1151499/s3Token",
"versionLabel":"0.0.0",
"etag":"2526dd09-565e-4989-b8c4-a82e724672c6",
"accessControlList":"/repo/v1/entity/syn1151499/acl",
"versionUrl":"/repo/v1/entity/syn1151499/version/1",
"modifiedBy":"John Hill",
"contentType":"text/plain",
"entityType":"org.sagebionetworks.repo.model.Data",
"uri":"/repo/v1/entity/syn1151499",
"id":"syn1151499",
"createdOn":"2012-09-12T19:33:06.314-07:00",
"modifiedOn":"2012-09-12T19:44:39.544-07:00",
"parentId":"syn1058078",
"versions":"/repo/v1/entity/syn1151499/version",
"createdBy":"John Hill",
"locations":[
{
"path":"/1151499/1158826/SampleTextFile.txt",
"type":"awss3"
}
],
"name":"Sample Data",
"md5":"6b65ca38d3596e0e0e6e1ed3cfa981eb",
"annotations":"/repo/v1/entity/syn1151499/annotations",
"versionNumber":1
}' https://repo-prod.sagebase.org/repo/v1/entity/syn1151499 |
Response
|
Any leaf entity that is version-able will have additional metada. Here is the JSON schema for these additional fields:
{
"properties": {
"versionLabel": {"type": "string"},
"versionNumber": {"type": "number"},
"versionUrl": {"type": "string"},
"versions": {"type": "string"},
"versionComment" {"type": "string"},
},
"type": "object"
}
|
Field Name | User Provided / Auto-generated | Description |
|---|---|---|
versionLabel | User Provided | The user visible label for this revision. It is up to the user to provide a meaningful label |
versionComment | User Provided | The user provided comment for this version. For example, what is this version, and why was it created? |
versionNumber | Auto-generate | The contiguous number representing this version. The first version will be '1', followed by '2'...'n' |
versionUrl | Auto-generated | The URL that can be used to fetch this version of the entity |
versions | Auto-generated | The URL to list all versions of this entity |
For version-able Entities, some metadata applies to the root object and is therefore version independent, while other metadata applies to the version and is therefore, version dependent. For example, the Access Control List (ACL) of an entity is version independent. This means it is not possible to apply different permissions to different versions of an entity. While the Annotations of an entity are version dependent. This means each version of the same entity can have different Annotations. The following table lists the various entity metadata and whether it is version dependent or independent.
Metadata | Version Dependent /Independent | Implications |
|---|---|---|
Access Control List | Independent | Access to all versions is controlled with a single ACL |
Name | Independent | One name applies to all versions of an entity |
Description | Independent | One description applies to all versions of an entity |
Created-On | Independent | An entity can only be created once |
Created-By | Independent | An entity can only be created once |
Parent-Id | Independent | All version of an entity must have the same parent |
Annotations | Dependent | Each version of an entity can have its own annotations |
Modified-By | Dependent | First set when a new version is created, and updated every time its version is change. Once a new version is created the Modified-By fields of older versions will remain static as older versions are immutable |
Modified-On | Dependent | First set when a new version is created, and updated every time its version is change. Once a new version is created the Modified-On fields of older versions will remain static as older versions are immutable |
All Entity specific matadata | Dependent | Each version of an entity can have its own values for all entity specific metadata. For example, the Location.path can have a unique value for each version. |
The following table describes how versioning effects the current entity CRUD API:
URL | HTTP Type | Description |
|---|---|---|
/{entityType} | POST | Creates a new entity of the given {entityType}. For version-able entities, this will create the first version of this entity. This entity will have a versionNumber=1 |
/{entityType} | GET | Get a list of all entities of the given type: {entityType}. For version-able entity types, this will list the current version of each entity of that type. |
/{entityType}/{id} | GET | Get an entity using its type and id. For version-able entities this will return the current version of the entity. |
/{entityType}/{id} | PUT | Update the entity identified by type and id. For a version-able entity this will update the current version of the entity. |
/{entityType}/{id} | DELETE | Delete the entity identified by type and id. For a version-able entity this will delete the entity and all versions of the entity. |
/{entityType}/{id}/annotations | GET | Get the annotations for the entity identified by type and id. For a version-able entity this will return the annotations of the current entity. |
/{entityType}/{id}/annotations | PUT | Update the annotations for the entity identified by type and id. For a version-able entity this will update the annotations of the current entity. |
The following table describes the new methods for manipulating the versions of a version-able entity.
URL | HTTP Type | Description |
|---|---|---|
/{versionable-entityType}/{entityId}/version | PUT | Create a new version of a given version-able entity. The user should provide a versionLabel and Synapse will auto-generate a new versionNumber. When this called on a version-able entity, the annotations of the current entity will be copied and applied to the newly created version. |
/{versionable-entityType}/{entityId}/version | GET | Returns a list of all versions of this entity. This will be a paginated list with a default sort on versionNumber descending |
/{versionable-entityType}/{entityId}/version/{versionNumber} | GET | Get a particular version of a version-able entity using the given id and version number. Note that the specific version fetched cannot be used to update the current version. Instead, promote it to the current version. |
/{versionable-entityType}/{entityId}/version/{versionNumber} | PUT | Not supported! Only the current version of an entity can be updated using the existing API. |
/{versionable-entityType}/{entityId}/version/{versionNumber} | DELETE | Delete a particular version of a version-able entity using the given id and version number. |
/{versionable-entityType}/{entityId}/version/{versionNumber}/annotations | GET | Get the annotations of a particular version of a version-able entity using the given id and version number. |
/{versionable-entityType}/{entityId}/version/{versionNumber}/annotations | PUT | Not Supported! You can only change the annotations of the current version. |
| /{versionable-entityType}/{entityId}/promoteVersion/{versionNumber} | POST | Promote the specified versionNumber to be the current version. Effectively, this just changes the number of that version to be current + 1. |
Get the location object we created earlier:
Request
curl -i -H sessionToken:YourSessionToken -H Accept:application/json 'https://repo-staging.sagebase.org/repo/v1/location/17338' |
Response
|
To create a new version of a location, we set the version comment and label. We also want to set a new path for this version:
Request
curl -i -H sessionToken:YourSessionToken -H ETag:0 -H Accept:application/json -H Content-Type:application/json -X PUT -d '{
"contentType": "application/zip",
"etag": "0",
"id": "17338",
"md5sum": "b513a23fc54b7b0d65312e1a900af5a6",
"name": "17338",
"parentId": "17337",
"path": "https://s3.amazonaws.com/stagingdata.sagebase.org/17338/0.0.2/mskcc_prostate_cancer.phenotype.zip?Expires=1317918889&AWSAccessKeyId=AKIAJQBSYCAUPIYF5WTA&Signature=2vTczuWgJ88Z0tiau1%2BPse4L2NA%3D",
"type": "awss3",
"uri": "/repo/v1/location/17338",
"versionComment": "The second version of this location.",
"versionLabel": "0.0.2"
}' https://repo-staging.sagebase.org/repo/v1/location/17338/version |
Response
|
List all of the version of this location. The current version will be the first in the list:
Request
curl -i -H sessionToken:YourSessionToken -H Accept:application/json 'https://repo-staging.sagebase.org/repo/v1/location/17338/version' |
Response
|
To get a previous version we must provide the version number we would like to fetch:
Request
curl -i -H sessionToken:YourSessionToken -H Accept:application/json 'https://repo-staging.sagebase.org/repo/v1/location/17338/version/1' |
Response
|
To get the annotations of a previous version we must provide the version number we would like to fetch:
Request
curl -i -H sessionToken:YourSessionToken -H Accept:application/json 'https://repo-staging.sagebase.org/repo/v1/location/17338/version/1/annotations' |
Response
|
To delete a specific versoin we must provide the version number. Note: You cannot delete the last version of an entity.
Request
curl -i -H sessionToken:YourSessionToken -H Accept:application/json -X DELETE https://repo-staging.sagebase.org/repo/v1/location/17338/version/1 |
Response
|
To promote a specific version we must provide the version number. Note: you can promote the current version of an entity, but it is a no-op
Request
curl -i -H sessionToken:YourSessionToken -H Accept:application/json -X DELETE https://repo-staging.sagebase.org/repo/v1/location/17338/promoteVersion/1 |
Response
|
List all of the version of this location. Since we deleted the first version, only the second remains:
Request
curl -i -H sessionToken:YourSessionToken -H Accept:application/json 'https://repo-staging.sagebase.org/repo/v1/location/17338/version' |
Response
|
Note that the request is a DELETE and no content is returned. Also note that this will delete all of the datasets layers, etc.
Request
curl -i -H sessionToken:YourSessionToken -H Accept:application/json -X DELETE https://repo-staging.sagebase.org/repo/v1/project/17334 |
Response
|
The Query API is loosely modeled after Facebook's Query Language.
These queries are generally of the form:
SELECT * FROM <data type> [LIMIT <#>] [OFFSET <#>] |
Currently supported data types:
| <data type> |
|---|
| project |
| folder |
file entity |
Request
curl -i -H sessionToken:YourSessionToken -H Accept:application/json 'https://repo-staging.sagebase.org/repo/v1/query?query=select+*+from+dataset+limit+3+offset+1' |
Response
|
These queries are generally of the form:
SELECT * FROM <data type> ORDER BY <field name> [ASC|DESC] [LIMIT <#>] [OFFSET #] |
Request
curl -i -H sessionToken:YourSessionToken -H Accept:application/json 'https://repo-staging.sagebase.org/repo/v1/query?query=select+*+from+dataset+order+by+Number_of_Samples+DESC+limit+3+offset+1' |
Response
|
These queries are generally of the form:
SELECT * FROM <data type> WHERE <expression> (AND <expression>)* [LIMIT <#>] [OFFSET #] <expresssion> := <field name> <operator> <value> |
<value> should be in quotes for strings, but not numbers (i.e. name == "Smith" AND size > 10)
Curently supported <operators> with their required URL escape codes:
Operator | Value | URL Escape Code |
|---|---|---|
Equal | == | %3D%3D |
Does Not equal | != | !%3D |
Greater Than | > | %3E |
Less than | < | %3C |
Greater than or equals | >= | %3E%3D |
Less than or equals | <= | %3C%3D |
Request
curl -i -H sessionToken:YourSessionToken -H Accept:application/json 'https://repo-staging.sagebase.org/repo/v1/query?query=select+*+from+dataset+where+name+==+%22MSKCC+Prostate+Cancer%22' |
Response
|
These queries are generally of the form:
SELECT * FROM <data type> WHERE <expression> (AND <expression>)* [LIMIT <#>] [OFFSET #] <expresssion> := <field name> <operator> <value> |
<value> should be in quotes for strings, but not numbers (i.e. name == "Smith" AND size > 10)
Curently supported <operators> with their required URL escape codes:
Operator | Value | URL Escape Code |
|---|---|---|
Equal | == | %3D%3D |
Does Not equal | != | !%3D |
Greater Than | > | %3E |
Less than | < | %3C |
Greater than or equals | >= | %3E%3D |
Less than or equals | <= | %3C%3D |
Request
curl -i -H sessionToken:YourSessionToken -H Accept:application/json 'https://repo-staging.sagebase.org/repo/v1/query?query=select+*+from+dataset+where+dataset.Species+==+%22Human%22+and+dataset.Number_of_Samples+%3E+100+limit+3+offset+1' |
Response
|
These queries are generally of the form:
SELECT * FROM layer WHERE parentId == <parentId> [LIMIT <#>] [OFFSET <#>] |
Request
curl -i -H sessionToken:YourSessionToken -H Accept:application/json 'https://repo-staging.sagebase.org/repo/v1/query?query=select+*+from+layer+where+layer.parentId+==+%223733%22' |
Response
|
These queries are generally of the form:
SELECT * FROM layer WHERE parentId == <parentId> ORDER BY <field name> [ASC|DESC] [LIMIT <#>] [OFFSET <#>] |
Request
curl -i -H sessionToken:YourSessionToken -H Accept:application/json 'https://repo-staging.sagebase.org/repo/v1/query?query=select+*+from+layer+where+layer.parentId+==+%223733%22+ORDER+BY+type' |
Response
|
These queries are generally of the form:
SELECT * FROM <data type> WHERE <expression> (AND <expression>)* [LIMIT <#>] [OFFSET #] <expresssion> := <field name> <operator> <value> |
<value> should be in quotes for strings, but not numbers (i.e. name == "Smith" AND size > 10)
Curently supported <operators> with their required URL escape codes:
Operator | Value | URL Escape Code |
|---|---|---|
Equal | == | %3D%3D |
Does Not equal | != | !%3D |
Greater Than | > | %3E |
Less than | < | %3C |
Greater than or equals | >= | %3E%3D |
Less than or equals | <= | %3C%3D |
Request
curl -i -H sessionToken:YourSessionToken -H Accept:application/json 'https://repo-staging.sagebase.org/repo/v1/query?query=select+*+from+agreement+where+agreement.datasetId+==+%223733%22' |
Response
|
The JsonSchema is an emerging standard similar to DTDs for XML.
Request
curl -i -H sessionToken:YourSessionToken -H Accept:application/json 'https://repo-staging.sagebase.org/repo/v1/query/schema' |
Response
|
The REST API took inspiration from several successful REST APIs:
Optional Parameters
Request
curl -i -H sessionToken:YourSessionToken -H Accept:application/json 'https://repo-staging.sagebase.org/repo/v1/dataset?sort=name&limit=3' |
Response
|
This returns the primary fields of a dataset and links to get additional info.
Request
curl -i -H sessionToken:YourSessionToken -H Accept:application/json 'https://repo-staging.sagebase.org/repo/v1/dataset/3733' |
Response
|
This returns the annotations for a dataset.
Request
curl -i -H sessionToken:YourSessionToken -H Accept:application/json 'https://repo-staging.sagebase.org/repo/v1/dataset/3733/annotations' |
Response
|
This returns the primary fields for all the layers of a dataset.
Request
curl -i -H sessionToken:YourSessionToken -H Accept:application/json 'https://repo-staging.sagebase.org/repo/v1/dataset/3733/layer' |
Response
|
This returns the metadata for a dataset layer.
Request
curl -i -H sessionToken:YourSessionToken -H Accept:application/json 'https://repo-staging.sagebase.org/repo/v1/layer/3874' |
Response
|
This returns the annotations for a dataset layer.
Request
curl -i -H sessionToken:YourSessionToken -H Accept:application/json 'https://repo-staging.sagebase.org/repo/v1/layer/3874/annotations' |
Response
|
This returns the eula for a dataset.
Request
curl -i -H sessionToken:YourSessionToken -H Accept:application/json 'https://repo-staging.sagebase.org/repo/v1/eula/3732' |
Response
|
This returns the preview data for a dataset layer.
Request
curl -i -H sessionToken:YourSessionToken -H Accept:application/json 'https://repo-staging.sagebase.org/repo/v1/layer/3874/preview' |
Response
|
This returns the preview data for a dataset layer.
Request
curl -i -H sessionToken:YourSessionToken -H Accept:application/json 'https://repo-staging.sagebase.org/repo/v1/layer/3874/preview' |
Response
|
This returns all the locations metadata for a dataset layer.
Request
curl -i -H sessionToken:YourSessionToken -H Accept:application/json 'https://repo-staging.sagebase.org/repo/v1/layer/3874/location' |
Response
|
This returns the location data for a dataset layer.
Request
curl -i -H sessionToken:YourSessionToken -H Accept:application/json 'https://repo-staging.sagebase.org/repo/v1/location/3875' |
Response
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An example to fetch the file using curl:
curl -o local/path/to/file.zip 'https://s3.amazonaws.com/stagingdata.sagebase.org/3875/0.0.0/mskcc_prostate_cancer.phenotype.zip?Expires=1317918906&AWSAccessKeyId=AKIAJQBSYCAUPIYF5WTA&Signature=Rb%2BXDamGfltAbWKGZsifuo0qdgA%3D' |
An example to conditionally fetch the file using curl:
curl -i -H If-None-Match:b513a23fc54b7b0d65312e1a900af5a6 'https://s3.amazonaws.com/stagingdata.sagebase.org/3875/0.0.0/mskcc_prostate_cancer.phenotype.zip?Expires=1317918906&AWSAccessKeyId=AKIAJQBSYCAUPIYF5WTA&Signature=Rb%2BXDamGfltAbWKGZsifuo0qdgA%3D' HTTP/1.1 304 Not Modified x-amz-id-2: h3qt9NfdRw7utcyVMCZF/dNRto9ZpmKY56w69HNpuMkNsaDv9MgduGY9L3zBQWl x-amz-request-id: 3AADDC9EF832ADD2 Date: Tue, 07 Jun 2011 18:40:15 GMT Last-Modified: Tue, 05 Apr 2011 00:42:50 GMT ETag: "b513a23fc54b7b0d65312e1a900af5a6" Server: AmazonS3 |
This returns the location data for a dataset layer with the S3 URL presigned for a HEAD request instead of the default GET.
Request
curl -i -H sessionToken:YourSessionToken -H Accept:application/json 'https://repo-staging.sagebase.org/repo/v1/location/3875?method=HEAD' |
Response
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An example double check that Synapse's MD5 matches the one in S3 using curl:
curl -I -H If-Match:b513a23fc54b7b0d65312e1a900af5a6 'https://s3.amazonaws.com/stagingdata.sagebase.org/3875/0.0.0/mskcc_prostate_cancer.phenotype.zip?Expires=1317918907&AWSAccessKeyId=AKIAJQBSYCAUPIYF5WTA&Signature=UO%2FtfA18HQxed317Nq4YU7ZjPnQ%3D' HTTP/1.1 200 OK x-amz-id-2: h3qt9NfdRw7utcyVMCZF/dNRto9ZpmKY56w69HNpuMkNsaDv9MgduGY9L3zBQWl x-amz-request-id: 3AADDC9EF832ADD2 Date: Tue, 07 Jun 2011 18:40:15 GMT Last-Modified: Tue, 05 Apr 2011 00:42:50 GMT ETag: "b513a23fc54b7b0d65312e1a900af5a6" Accept-Ranges: bytes Content-Type: application/binary Content-Length: 30681 Server: AmazonS3 |
Login required to get the storage usage associated with the current user.
Gets aggregated totals over a list of aggregation dimensions. The list of aggregation dimensions are concatenated by comma and assigned to the query parameter 'aggregation'. The list of valid aggregating dimensions are defined in StorageUsageDimension (See Synapse Entity Types). Except for USER_ID and ENTITY_ID, which are reserved for administrators, any combination of aggregations is accepted. The following example aggregates over STORAGE_PROVIDER and CONTENT_TYPE.
Request
curl -i -H sessionToken:<yourSessionToken> -H Accept:application/json https://repo-staging.sagebase.org/repo/v1/storageSummary?aggregation=STORAGE_PROVIDER,CONTENT_TYPE |
Response
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To see details, the following URL fetches the list of storage items for the current user.
Request
curl -i -H sessionToken:<yourSessionToken> -H Accept:application/json https://repo-staging.sagebase.org/repo/v1/storageDetails |
Response
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Note that the results are paginated.
To see the list of storage items for a particular entity, use the following URL.
Request
curl -i -H sessionToken:<yourSessionToken> -H Accept:application/json https://repo-staging.sagebase.org/repo/v1/storageDetails/entity/<entityID> |
Response
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Note that the query for descendants is based on secondary indices which are eventually consistent. You may not be able to see the complete list of descendants immediately.
Get all the descendants of an entity. The results are paginated. Use the optional query parameter limit to set the maximum page size. The default page size is 20. To fetch the next page, find the last entity (descendant) on the current page and use its ID to set the query parameter lastEntityId. Here is an example:
curl -i -H sessionToken:<yourToken> -H Accept:application/json 'https://repo.prod.sagebase.org/repo/v1/entity/<entityID>/descendants&limit=2' |
{
"idList": [
{
"id": "syn111"
},
{
"id": "syn112"
}
]
}
|
curl -i -H sessionToken:<yourToken> -H Accept:application/json 'https://repo.prod.sagebase.org/repo/v1/entity/<entityID>/descendants?limit=20&lastEntityId=syn112' |
{
"idList": [
{
"id": "syn113"
},
{
"id": "syn114"
},
{
"id": "syn115"
}
]
}
|
Get all the descendants that are exactly n generations away. The children is generation 1. Children's children are generation 2. So on and so forth. The results are paginated in the same manner. To fetch the next page, find the last entity (descendant) on the current page and use its ID to set the query parameter lastEntityId. Here is an example:
curl -i -H sessionToken:<yourToken> -H Accept:application/json 'https://repo.prod.sagebase.org/repo/v1/entity/<entityID>/descendants/2' |
{
"idList": [
{
"id": "syn114"
},
{
"id": "syn115"
}
]
} |
Request
curl -i -H sessionToken:YourSessionToken -H Accept:application/json 'https://repo-staging.sagebase.org/repo/v1/entity/6/referencedby' |
Response
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Request
curl -i -H sessionToken:YourSessionToken -H Accept:application/json 'https://repo-staging.sagebase.org/repo/v1/entity/6/version/1/referencedby' |
Response
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The JsonSchema is an emerging standard similar to DTDs for XML.
Request
curl -i -H sessionToken:YourSessionToken -H Accept:application/json 'https://repo-staging.sagebase.org/repo/v1/query/schema' |
Response
|
The JsonSchema is an emerging standard similar to DTDs for XML.
Request
curl -i -H sessionToken:YourSessionToken -H Accept:application/json 'https://repo-staging.sagebase.org/repo/v1/project/schema' |
Response
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The JsonSchema is an emerging standard similar to DTDs for XML.
Request
curl -i -H sessionToken:YourSessionToken -H Accept:application/json 'https://repo-staging.sagebase.org/repo/v1/eula/schema' |
Response
|
The JsonSchema is an emerging standard similar to DTDs for XML.
Request
curl -i -H sessionToken:YourSessionToken -H Accept:application/json 'https://repo-staging.sagebase.org/repo/v1/agreement/schema' |
Response
|
The JsonSchema is an emerging standard similar to DTDs for XML.
Request
curl -i -H sessionToken:YourSessionToken -H Accept:application/json 'https://repo-staging.sagebase.org/repo/v1/dataset/schema' |
Response
|
The JsonSchema is an emerging standard similar to DTDs for XML.
Request
curl -i -H sessionToken:YourSessionToken -H Accept:application/json 'https://repo-staging.sagebase.org/repo/v1/layer/schema' |
Response
|
The JsonSchema is an emerging standard similar to DTDs for XML.
Request
curl -i -H sessionToken:YourSessionToken -H Accept:application/json 'https://repo-staging.sagebase.org/repo/v1/preview/schema' |
Response
|
The JsonSchema is an emerging standard similar to DTDs for XML.
Request
curl -i -H sessionToken:YourSessionToken -H Accept:application/json 'https://repo-staging.sagebase.org/repo/v1/location/schema' |
Response
|
The JsonSchema is an emerging standard similar to DTDs for XML.
Request
curl -i -H sessionToken:YourSessionToken -H Accept:application/json 'https://repo-staging.sagebase.org/repo/v1/annotations/schema' |
Response
|
The JsonSchema is an emerging standard similar to DTDs for XML.
Request
curl -i -H sessionToken:YourSessionToken -H Accept:application/json 'https://repo-staging.sagebase.org/repo/v1/acl/schema' |
Response
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