Code Integration: Operations and Scenarios
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, printing out the needed svn command(s). [Alt.: Could do svn 'add', 'commit' on the user's behalf.]
Creates or updates metadata in Synapse, including code version.
returns
nothing
downloadEntity(codeId, localPath)
parameters
codeId: id of metadata object in Synapse
localPath: directory on machine which is running the R session
side effects
Checks that Version in Code object matches repository, and revises the Code object if not.
Checks that local files are in sync with repository and, if not, prints the svn command needed to sync. [Alt: Could do svn 'checkout' or 'update' on user's behalf.]
returns
Code object
loadEntity(codeObj)
parameters
codeObj
side effects
If (codeId!=null)
- 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 (printing the svn command needed to sync). [Alt: Could do svn 'checkout' or 'update' on user's behalf.]
- Get current Step.
- Adds codeId, revision into Step.
'sources' code into memory
(i.e. if 'codeObj' is just a local variable, this is a utility to source a collection of files.)
returns
nothing
deleteEntity(codeId)
parameters
codeId: ID of the object in Synapse
side effects
Delete metadata from Synapse.
Print out delete command that user should execute.[Alt: Delete from the code repository.]
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
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.)
Retrieve existing code, modify and save.
Develop new code, then save.
(Per Matt F., this is an important use case for data curators.)
Run code and capture provenance info.