Package 'MsBackendMongoDb'

Description

Creates connections to required MongoDb collections used by the MsBackendMongoDb.

Usage

connectMsBackendMongoDb(
  db = "spectra_db",
  url = "mongodb://localhost",
  clean = FALSE
)

Arguments

Value

A named list() of mongo connection objects.

Author(s)

Ahlam Mentag

Description

MsBackendMongoDb is an implementation of the Spectra::MsBackend() class for Spectra::Spectra() objects, storing and retrieving MS data from a MongoDb database.

This backend allows read-only access to spectra and peaks stored in MongoDb, but supports temporary modifications of spectra variables via caching.

Usage

## S4 method for signature 'MsBackendMongoDb'
show(object)

## S4 method for signature 'MsBackendMongoDb'
backendInitialize(object, dbcon, data, ...)

## S4 method for signature 'MsBackendMongoDb'
dataStorage(object)

## S4 method for signature 'MsBackendMongoDb'
peaksData(object, columns = c("mz", "intensity"))

## S4 method for signature 'MsBackendMongoDb'
peaksVariables(object)

## S4 method for signature 'MsBackendMongoDb'
mz(object)

## S4 replacement method for signature 'MsBackendMongoDb'
mz(object) <- value

## S4 method for signature 'MsBackendMongoDb'
intensity(object)

## S4 replacement method for signature 'MsBackendMongoDb'
intensity(object) <- value

## S4 method for signature 'MsBackendMongoDb'
spectraNames(object)

## S4 replacement method for signature 'MsBackendMongoDb'
spectraNames(object) <- value

## S4 method for signature 'MsBackendMongoDb'
spectraData(object, columns = spectraVariables(object))

## S4 method for signature 'MsBackendMongoDb'
x[i, j, ..., drop = FALSE]

## S4 method for signature 'MsBackendMongoDb,ANY'
extractByIndex(object, i)

## S4 method for signature 'MsBackendMongoDb'
reset(object)

## S4 method for signature 'MsBackendMongoDb'
supportsSetBackend(object, ...)

Arguments

Value

Depends on the method. See individual function documentation.

Creation of backend objects

New backend objects can be created using:

con <- connectMsBackendMongoDb(db = <database name>, url = <db url>)
backend <- backendInitialize(MsBackendMongoDb(), dbcon = con)

• dbcon: A list of MongoDb collections (e.g. from mongolite::mongo()) as created by the connectMsBackendMongoDb().

• backendInitialize(): populates the object with spectrum IDs and caches metadata. If data is provided, it can insert data into the collection.

Accessing data

• peaksData(object, columns = c("mz", "intensity")): returns a list of matrices containing the peak data for each spectrum.

• peaksVariables(object): returns available columns for peaksData.

• intensity(object), mz(object): return SimpleList objects with numeric intensity or m/z values for each spectrum.

• spectraData(object, columns): returns a DataFrame with requested spectrum metadata columns.

• spectraNames(object): returns spectrum_id values as character.

Read-only data

• ⁠intensity<-⁠ and ⁠mz<-⁠ are not supported.

• ⁠spectraNames<-⁠ is not supported.

Subsetting and extraction

• ⁠[i]⁠ and extractByIndex(object, i) subset the backend by spectrum indices. Original data in the database is never changed.

• reset(object) restores the backend to its original state, removing subsetting and cached variables.

Miscellaneous

• dataStorage(object) returns a string describing the MongoDb collections used by the backend.

Implementation notes

Internally, the backend stores:

• spectraIds: integer vector of spectrum IDs

• dbcon: MongoDb connection(s)

• .collections: list of collection names

• peak_fun: function used to fetch peak data

• localData: cached spectrum variables

• nspectra: total number of spectra

Data access functions use peak_fun to fetch peaks on demand.

Note

MsBackendMongoDb keeps a connection to a MongoDb collection(s) and fetches spectra and peaks data on demand. By storing only the primary keys (spectrum_id) in memory, it ensures minimal memory usage, while peaks and metadata are fetched dynamically.

The backend inherits from Spectra::MsBackendCached() and supports temporary modification of spectra variables via the ⁠$<-⁠ operator. Original data in the database cannot be changed (intensities and m/z values are read-only).

Author(s)

Ahlam Mentag

Examples

## Start a MongoDB for the example; this requires the *mongod* binary of
## a MongoDB server installation to be present in the System's path.
## We use a specific temporary folder for the database that we can remove
## later safely
d <- file.path(tempdir(), "test_example")
start_mongodb()

## Loading test data files from MsDataHub
library(Spectra)
library(MsDataHub)
fls <- c(X20171016_POOL_POS_1_105.134.mzML(),
         X20171016_POOL_POS_3_105.134.mzML())

## Load the data as a `Spectra` object

s <- Spectra(fls)

## Connect to the MongoDB database
mcon <- connectMsBackendMongoDb(
   db = "ms_backend_mongodb",
   url = "mongodb://localhost:27017",
   clean = TRUE)

## Change the backend of the `Spectra` object to `MsBackendMongoDb`: store
## all MS data into the MongoDB
mng <- setBackend(s, backend = MsBackendMongoDb(), dbcon = mcon)
mng

## Get the *m/z* values from the data
mz(mng)

## Stopping the MongoDB and removing the directory
stop_mongodb()
unlink(d, recursive = TRUE)

Description

The start_mongodb() and stop_mongodb() functions start and stop a MongoDB database using the mongod system call. These functions require an installation of the MongoDB server and the mongod binary to be present in the System path.

Usage

start_mongodb(
  cmd = "mongod",
  dbpath = file.path(tempdir(), "mongo"),
  logpath = file.path(tempdir(), "mongo.log")
)

stop_mongodb(cmd = "mongod", dbpath = file.path(tempdir(), "mongo"))

Arguments

Value

start_mongodb() and stop_mongodb() don't return any value, but throw an error if the system2 call did not return 0.

Examples

## Start a MongoDB service with the database location in *test_mongo* in
## the System's temporary folder.
start_mongodb(dbpath = file.path(tempdir(), "test_mongo"))

## Stop the MongoDB
stop_mongodb(dbpath = file.path(tempdir(), "test_mongo"))

## Remove the database
unlink(file.path(tempdir(), "test_mongo"), recursive = TRUE)