Code Integration
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R Convenience Functions
codeObj <- Code(name, parent, codeRepo)
parameters
name
parent: a Project ID
codeRepo: the (brief and easily remembered) name of the code repository. If omitted, a default is used.
side effects
none
returns
new Code object
addFile(codeObj, localPath, repoPath)
parameters
codeObj
localPath: path to file or directory on machine running the R session
repoPath: path relative to repository. If omitted then a default path is generated.
side effects
none
returns
nothing
storeEntity(codeObj)
parameters
codeObj
side effects
Checks that code is committed to svn, stops if not. [Alt.: Could do svn 'add', 'commit' on the user's behalf.]
Creates or updates metadata in Synapse, including code version.
returns
nothing
loadEntity(codeId, localPath)
parameters
codeId: id of metadata object in Synapse
localPath: directory on machine which is running the R session
repoSync:
side effects
Checks that Version in Code object is up-to-date with repository, and revises the Code object if not.
Checks that local files are in sync with repository, and throws exception if not. [Alt: Could do svn 'checkout' or 'update' on user's behalf.]
Get current Step.
Gets code version, adds codeId and version into Step.
'sources' code into memory
returns
Code object
deleteEntity(codeId)
parameters
codeId: ID of the object in Synapse
side effects
Delete metadata from Synapse.
Delete from the code repository. [Alt: Print out delete command that user should execute.]
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?
Scenarios
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Scenarios
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.
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:# Load in Synapse R Client:
entity.3733 <- loadCodedownloadEntity(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.)
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Develop new code, then
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(Per Matt F., this is an important use case for data curators.)
Run code and capture provenance info.
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Store