Code Integration: Operations and Scenarios
R Convenience Functions
"Level 1" functions
saveCode(localFolder, codeRepo)
...
localFolder: folder or file on the local file system
codeRepo short, easily remembered 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 that/ those be made part of the codeRepo object?
...
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
Checks Check out code from code repository, if not already checked out. Otherwise, updates local copy from code repository.
"SourcesSource" code into R session.
returns
...
TODO: What if not all steps are successful?
saveAndExecute(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.
TODO: Should the convenience function do something to run the code, or can we say it's the code's responsibility to run when it's sourced?
returns
ID of the object created in Synapse
Note: Code version is not recorded in the code metadata.
delete(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?
Web Services
These manipulation only the metadata, stored in Synapse.
Note: It is assumed that code versions are represented by refererences.
...