In rformassspectrometry/MsBackendHSDS: Mass spectrometry data backend

Data and server setup

Here we first create the test data that we will use later in combination with an h5serv instance.

Data preparation

We will use the two sciex test files from the msdata package.

library(Spectra)
library(msdata)

fls <- dir(system.file("sciex", package = "msdata"), full.names = TRUE)

sps <- Spectra(fls, backend = MsBackendHdf5Peaks(),
               source = MsBackendMzR(), hdf5path = normalizePath("."))

Server setup

To use the h5serv we install first the according docker image with docker pull hdfgroup/h5serv. The server can then be started with docker run -p 5000:5000 -d -v <mydata>:/data hdfgroup/h5serv where <mydata> is the folder path that contains any HDF5 files we want to serve. Use the browser to connect to port 5000 to see if the server has started.

Tests with the `hdf5client` package

Assuming we have started the above server we try to access files on it. Note that there might be some problems if R is running within a docker too.

library(rhdf5client)
s <- HSDSSource("http://host.docker.internal:5000", type = "h5serv")
f <- HSDSFile(s, "20171016_POOL_POS_1_105-134.hdfgroup.org")
f <- HSDSFile(s, "sciex")

s <- HSDSSource("http://localhost:5000", type = "h5serv")
f <- HSDSFile(s, "20171016_POOL_POS_1_105-134.h5")
d <- HSDSDataset(f, "/spectra")

HSDSArray("http://host.docker.internal:5000", "h5serv", "20171016_POOL_POS_1_105-134.hdfgroup.org",
          "spectra/1")

s <- H5S_source("http://host.docker.internal:5000", "hdfgroup.org")