Raw mode is meant to deal with large collections of PEPs (like
hundreds of thousands). In this case, problems may arise while
trying to convert GEPs by loading all of them in memory at
once. Raw mode is meant to be used with HDF5 format, which allows
to load subsets of GEPs from the disk.
buildPEPs, when used
in raw mode, can create the corresponding subsets of PEPs, so that
the job can be distributed on a computer
importFromRawMode is meant to join the chunks into
HDF5 matrices, which are than stored into the repository. The
.loadPEPs function can seamlessly load PEPs stored in normal
(RDS) or HDF5 format.
A repository created by
Path were raw PEPs are stored (default is a "raw" directory under the repository root folder).
A subset of the collection names returned by
PEPs are expect to be found at the specified
and follow the naming convention as generated by
buildPEPs. According to such convention, each file is
named usign the format
category_subcategory#chunknumber.RDS. All non-alphanumeric
characters from the original category and subcategory names are
replace with an underscore (in rare cases this could create
ambiguity that should be manually prevented). All chunks for
the same subcategory are joined together following the chunk
numbers into a single HDF5 matrix and stored in the repository
as an "attachment" (see
Note that raw PEPs (by default everything at repository_root/raw) can be safly removed once they have been imported.
Nothing, used for side effects.
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db <- loadSamplePWS() repo_path <- file.path(tempdir(), "gep2pepTemp") rp <- createRepository(repo_path, db) ## The following will create PEPs in 2 separate files geps <- loadSampleGEP() buildPEPs(rp, geps[,1:2], progress_bar=FALSE, rawmode_id=1) buildPEPs(rp, geps[,3:5], progress_bar=FALSE, rawmode_id=2) ## The separate files are then merged into one (possibly big) file ## in HDF5 format importFromRawMode(rp) ## Now most operations (excluding the addition of new PEPs to ## existing collections) will be available as usual. unlink(repo_path, TRUE)
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