HMDB XML data loading

[gmhhope]

Hi Johannes,

You see I am your fans now. I am testing your docker container for doing MS/MS search. However, I encountered issues with loading the hmdb spectra XML data.

In brief, I have downloaded the All Spectra Files (XML) from https://hmdb.ca/downloads. And then I put into a local folder and then I run your docker container by:

docker run -e PASSWORD=bioc -p 8787:8787 -v /Users/gongm/Documents/projects/test/SpectraTutorials/SpectraTutorials/data/:/home/rstudio/external jorainer/spectra_tutorials:latest

So that I can also access the spectra data in ../external/hmdb_all_spectra/. However, when I run the below r script, the fls did not load correctly. And thus it gives me character(0).

library(MsBackendHmdb)

#' Get all MS2 spectra xml files and import data
fls <- dir("../external/hmdb_all_spectra/", full.names = TRUE, pattern = "ms_ms")
hmdb <- Spectra(fls, source = MsBackendHmdbXml(), nonStop = TRUE)

fls
character(0)

Do you know what is going wrong? And the loading did take at least 6 minutes before it ends.

Thanks very much always for your continuos help!

Thanks,
Minghao Gong

[gmhhope]

Later today, I did notice you have precompiled hmdb from your package:

#' Load the pre-generated Spectra object with spectra from HMDB.
library(MsBackendHmdb)
data("hmdb", package = "SpectraTutorials")

However, it will be great if you could still guide me through the previous question, as the database will continue to update.

But again I love to see your youtube video: https://www.youtube.com/watch?v=W6JISCrAtk0! It was fascinating for putting all these. Thanks very much!

Best,
Minghao

[jorainer]

Thanks Minghao!

hm, this is strange. I guess this has to do with the paths not being correct. Could you check what you get if you do dir("/home/rstudio/external/hmdb_all_spectra/", full.names = TRUE, pattern = "ms_ms") - maybe by defining the absolute path it works - I have no idea where the R workspace within docker is by default.

[gmhhope]

hm, this is strange. I guess this has to do with the paths not being correct. Could you check what you get if you do dir("/home/rstudio/external/hmdb_all_spectra/", full.names = TRUE, pattern = "ms_ms") - maybe by defining the absolute path it works - I have no idea where the R workspace within docker is by default.

You are right. I guess there is something wrong with the path maybe in docker. It sometimes works, sometimes not (not because of the path I entered is wrong). I am not sure what are the issues but I will check myself.

#' Load the pre-generated Spectra object with spectra from HMDB.
library(MsBackendHmdb)
data("hmdb", package = "SpectraTutorials")

But your precompiled HMDB Rdata is great! Could I check what version of HMDB spectra Xml you used to convert to the Rdata? At least I know whether is enough to use your precompiled HMDB Rdata?

Thanks,
Minghao

[jorainer]

I downloaded the spectra data on 2021-01-01 from HMDB.