Add possibility to change the file path for a `MsBackendMzR`
Closed this issue · 2 comments
We have some use cases in which we run some part of the analysis (e.g. the preprocessing using xcms
) on our cluster, save then the results (which include a Spectra
) to an RData to then continue the analysis (more interactively) on a local computer. This works only if we use a MsBackendMemory
as a backend, but e.g. with a MsBackendMzR
we would have different file paths locally and on the cluster.
Maybe we could add a method backendFilePath,MsBackend
and backendFilePath<-,MsBackend
that allows to get/change the directory where the data is stored - for backends that support this.
A method could be implemented for MsBackendMzR
, MsBackendHdf5Peaks
and eventually the MsBackendOfflineSql
, if a SQLite database is used. Other backends would throw an error as this method would not be supported/needed for them.
Open for discussions or alternative ideas/thoughts.
Pinging @philouail
Maybe dataStorageBasePath
would make more sense as a name - so, essentially, the common (base) path for the dataStorage
. For in-memory backends or backends where the dataStorage
is not defined or used it could/should return NA_character_
, while for backends that keep a reference to the (on-disk stored) data it should return the base file path common to all spectra in Spectra
(as determined with MsCoreUtils::common_path()
).