Code Integration: Operations and Scenarios
R Convenience Functions
saveCode(localFolder, codeRepo)
parameters
localFolder: folder or file on the local file system
codeRepo short, easily remembered 'nickname' of code repository system. If omitted, user's default is used.
TODO: Do we need additional repository parameters (e.g. a folder within the repository) or can those be made part of the codeRepo object?
side effects
Register folder with code repository, if not already registered.
Commit code.
Create metadata in Synapse, if not already created.
TODO: What if not all steps are successful?
returns
ID of the object created in Synapse
Note: Code version is not recorded in the code metadata.
saveAndRun(localFolder, codeRepo)
parameters
localFolder: folder or file on the local file system
codeRepo short, easily remembered 'nickname' of code repository system. If omitted, user's default is used.
side effects
Register folder with code repository, if not already registered.
Commit code, retaining the version information.
Set a global "code.version" variable to the current version.
Create metadata in Synapse, if not already created.
"Source" code into R session.
Call "run()".
TODO: Check if code has changed before committing, to avoid making new version each time code is run.
returns
ID of the object created in Synapse
Note: Code version is not recorded in the code metadata.
loadCode(id, localFolder)
parameters
id: ID of the object in Synapse
localFolder: location for local copy of code. If omitted, then a default location is used.
side effects
Check out code from code repository, if not already checked out. Otherwise, updates local copy from code repository.
"Source" code into R session.
returns
location of local copy of code
TODO: What if not all steps are successful?
deleteCode(id)
parameters
ID of the object in Synapse
side effects
Delete from the code repository.
Delete metadata from Synapse.
returns
Nothing.
TODO: What if not all steps are successful?
TODO: Should we delete from the local disk? From the R session?
TODO: Can we defer the convenience function for loading a specific code version?
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", "codeRepoId":"4567", "codeRepoLoc":"/trunk/analysisProject/R"}
Note: "parentId" is the ID of a Synapse Project; "codeRepoId" is the ID of a Code Repository object.
Successful Response:
HTTP/1.1 201 Created
{"id":"8901", "parentId":"1234", "codeRepoId":"4567", "codeRepoLoc":"/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", "codeRepoId":"4567", "codeRepoLoc":"/trunk/analysisProject/R"}
Update Code
PUT https://repo-staging.sagebase.org/repo/v1/code/8901
{"id":"8901", "parentId":"5432", "codeRepoId":"4567", "codeRepoLoc":"/trunk/analysisProject/R"}
Successful Response:
HTTP/1.1 200 OK
{"id":"8901", "parentId":"5432", "codeRepoId":"4567", "codeRepoLoc":"/trunk/analysisProject/R"}
Delete Code
DELETE https://repo-staging.sagebase.org/repo/v1/code/8901
Successful Response:
HTTP/1.1 204 No Content
Create Code Repository
POST https://repo-staging.sagebase.org/repo/v1/codeRepo
{"codeRepoType":"svn", "nickname":"sageSvn", "codeRepoURL":"https://sagebionetworks.jira.com/svn"}
Successful Response:
HTTP/1.1 201 Created
{id:"9876", "codeRepoType":"svn", "codeRepoURL":https://sagebionetworks.jira.com/svn}
TODO: Error response if 'nickname' is already used.
TODO: GET, PUT, DELETE
Create Code Repo Credentials
POST https://repo-staging.sagebase.org/repo/v1/codeRepoCredentials
{"codeRepoId:"9876", "username":"foo": "password":"bar"}
Note: This request must be authenticated and the credentials are created for the authenticated user. The given "username" need not be the same as the user's Synapse username.
Successful Response:
HTTP/1.1 201 Created
{"id":"5432", "codeRepoId:"9876", "username":"foo": "password":"bar"}
TODO: Should the password not be 'echoed'?
TODO: GET, PUT, DELETE
Scenarios
Discover, retrieve and load code into R session.
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:
# Load in Synapse R Client:
entity.3733 <- loadCode(3733)
and begins by executing this in R.
(Note: "Repo" is the code repository client. The interaction between the repository client and server is not shown.)