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rformassspectrometry / Spectra

Low level infrastructure to handle MS spectra
https://rformassspectrometry.github.io/Spectra/
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Add possibility to change the file path for a `MsBackendMzR` #321

Closed jorainer closed 1 month ago

jorainer commented 1 month ago

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.

jorainer commented 1 month ago

Pinging @philouail

jorainer commented 1 month ago

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()).