Code Integration Scenarios

R Convenience Functions

"Level 1" functions

"Level 2" functions

Web Services

These manipulation only the metadata, stored in Synapse.
Note: It is assumed that code versions are represented by refererences.

Create Code

POST https://repo-staging.sagebase.org/repo/v1/code
{"parentId":"1234", "srcRepoId":"4567", "srcRepoLoc":"/trunk/analysisProject/R"}

Note: "parentId" is the ID of a Synapse Project; "srcRepoId" is the ID of a Source Repository object.

Successful Response:

HTTP/1.1 201 Created
{"id":"8901", "parentId":"1234", "srcRepoId":"4567", "srcRepoLoc":"/trunk/analysisProject/R"}

Get Code

GET https://repo-staging.sagebase.org/repo/v1/code/8901

Successful Response:

HTTP/1.1 200 OK
{"id":"8901", "parentId":"1234", "srcRepoId":"4567", "srcRepoLoc":"/trunk/analysisProject/R"}

Update Code

PUT https://repo-staging.sagebase.org/repo/v1/code/8901
{"id":"8901", "parentId":"5432", "srcRepoId":"4567", "srcRepoLoc":"/trunk/analysisProject/R"}

Successful Response:

HTTP/1.1 200 OK
{"id":"8901", "parentId":"5432", "srcRepoId":"4567", "srcRepoLoc":"/trunk/analysisProject/R"}

Delete Code

DELETE https://repo-staging.sagebase.org/repo/v1/code/8901

Successful Response:

HTTP/1.1 204 No Content

...

The development cycle for preexisting code:  The code is Downloaded from Synapse, and Loaded into the R session.  The user repeatedly Runs, Edits and reLoads the code.  When satisfied, she may Store the code back to Synapse.  To help capture provenance, the Load and Store functions put the Code's ID and version into the current Step.  For the provenance record to be accurate, the user must Store prior to running.

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Discover, retrieve, load and run code

A user, browsing Synapse, sees a piece of code of interest (mentioned in a discussion or used in an analysis), and clicks on it.  She sees:

entity.3733 <- downloadEntity(3733)

and begins by executing this in R.

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Develop new code, then Store

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