Package 'biodb'

Description

The biodb package provides access to standard remote chemical and biological databases (ChEBI, KEGG, HMDB, ...), as well as to in-house local database files (CSV, SQLite), with easy retrieval of entries, access to web services, search of compounds by mass and/or name, and mass spectra matching for LCMS and MSMS. Its architecture as a development framework facilitates the development of new database connectors for local projects or inside separate published packages.

Details

To get a presentation of the biodb package and get started with it, please see the "biodb" vignette.

vignette('biodb', package='biodb')

Author(s)

Maintainer: Pierrick Roger [email protected] (ORCID)

Other contributors:

• Alexis Delabrière [email protected] (ORCID) [contributor]

See Also

BiodbMain, BiodbConfig, BiodbFactory, BiodbDbsInfo, BiodbEntryFields.

Description

Forbids instantiation of an abstract class. This method must be called from within a constructor of an abstract class. It will throw an error if a direct call is made to this constructor.

Usage

abstractClass(cls, obj)

Arguments

Value

Nothing.

Description

This method must be called from within the abstract method.

Usage

abstractMethod(obj)

Arguments

Value

Nothing.

Description

A class for storing configuration values.

A class for storing configuration values.

Details

This class is responsible for storing configuration. You must go through the single instance of this class to create and set and get configuration values. To get the single instance of this class, call the getConfig() method of class BiodbMain.

Methods

Public methods

• BiodbConfig$new()

• BiodbConfig$getKeys()

• BiodbConfig$getTitle()

• BiodbConfig$getDescription()

• BiodbConfig$getDefaultValue()

• BiodbConfig$hasKey()

• BiodbConfig$isDefined()

• BiodbConfig$isEnabled()

• BiodbConfig$get()

• BiodbConfig$set()

• BiodbConfig$reset()

• BiodbConfig$enable()

• BiodbConfig$disable()

• BiodbConfig$print()

• BiodbConfig$listKeys()

• BiodbConfig$getAssocEnvVar()

• BiodbConfig$define()

• BiodbConfig$notifyNewObservers()

• BiodbConfig$terminate()

• BiodbConfig$clone()

Method new()

New instance initializer. No BiodbConfig object must not be created directly. Instead, access the config instance through the BiodbMain instance using the getConfig() method.

Usage

BiodbConfig$new(parent)

Arguments

Returns

Nothing.

Method getKeys()

Get the list of available keys.

Usage

BiodbConfig$getKeys(deprecated = FALSE)

Arguments

Returns

A character vector containing the config key names.

Method getTitle()

Get the title of a key.

Usage

BiodbConfig$getTitle(key)

Arguments

Returns

The title of the key as a character value.

Method getDescription()

Get the description of a key.

Usage

BiodbConfig$getDescription(key)

Arguments

Returns

The description of the key as a character value.

Method getDefaultValue()

Get the default value of a key.

Usage

BiodbConfig$getDefaultValue(key, as.chr = FALSE)

Arguments

Returns

The default value for that key.

Method hasKey()

Test if a key exists.

Usage

BiodbConfig$hasKey(key)

Arguments

Returns

TRUE if a key with this name exists, FALSE otherwise.

Method isDefined()

Test if a key is defined (i.e.: if a value exists for this key).

Usage

BiodbConfig$isDefined(key, fail = TRUE)

Arguments

Returns

TRUE if the key has a value, FALSE otherwise.

Method isEnabled()

Test if a boolean key is set to TRUE. This method will raise an error if the key is not a boolean key.

Usage

BiodbConfig$isEnabled(key)

Arguments

Returns

TRUE if the boolean key has a value set to TRUE, FALSE otherwise.

Method get()

Get the value of a key.

Usage

BiodbConfig$get(key)

Arguments

Returns

The value associated with the key.

Method set()

Set the value of a key.

Usage

BiodbConfig$set(key, value)

Arguments

Returns

Nothing.

Method reset()

Reset the value of a key.

Usage

BiodbConfig$reset(key = NULL)

Arguments

Returns

Nothing.

Method enable()

Set a boolean key to TRUE.

Usage

BiodbConfig$enable(key)

Arguments

Returns

Nothing.

Method disable()

Set a boolean key to FALSE.

Usage

BiodbConfig$disable(key)

Arguments

Returns

Nothing.

Method print()

Print list of configuration keys and their values.

Usage

BiodbConfig$print()

Returns

Nothing.

Method listKeys()

Get the full list of keys as a data frame.

Usage

BiodbConfig$listKeys()

Returns

A data frame containing keys, titles, types, and default values.

Method getAssocEnvVar()

Returns the environment variable associated with this configuration key.

Usage

BiodbConfig$getAssocEnvVar(key)

Arguments

Returns

The environment variable's value.

Method define()

Defines config properties from a structured object, normally loaded from a YAML file.

Usage

BiodbConfig$define(def)

Arguments

Returns

Nothing.

Method notifyNewObservers()

Called by BiodbMain when a new observer is registered.

Usage

BiodbConfig$notifyNewObservers(obs)

Arguments

Returns

Nothing.

Method terminate()

Terminates the instance. This method will be called automatically by the BiodbMain instance when you call

Usage

BiodbConfig$terminate()

Arguments

Returns

Nothing.

Method clone()

The objects of this class are cloneable with this method.

Usage

BiodbConfig$clone(deep = FALSE)

Arguments

See Also

BiodbMain.

Examples

# Create an instance with default settings:
mybiodb <- biodb::newInst()

# Get the config instance:
config <- mybiodb$getConfig()

# Print all available keys
config$getKeys()

# Get a configuration value:
value <- config$get('cache.directory')

# Set a configuration value:
config$set('dwnld.timeout', 600)

# For boolean values, you can use boolean methods:
config$get('offline')
config$enable('offline')    # set to TRUE
config$disable('offline')   # set to FALSE
config$isEnabled('offline')

# Terminate instance.
mybiodb$terminate()

Description

The mother abstract class of all database connectors.

The mother abstract class of all database connectors.

Details

This is the super class of all connector classes. All methods defined here are thus common to all connector classes. All connector classes inherit from this abstract class.

See section Fields for a list of the constructor's parameters. Concrete classes may have direct web services methods or other specific methods implemented, in which case they will be described inside the documentation of the concrete class. Please refer to the documentation of each concrete class for more information. The database direct web services methods will be named "ws.*".

The constructor has the following arguments:

id: The identifier of the connector.

cache.id: The identifier used in the disk cache.

Super class

biodb::BiodbConnBase -> BiodbConn

Methods

Public methods

• BiodbConn$new()

• BiodbConn$getBiodb()

• BiodbConn$getId()

• BiodbConn$print()

• BiodbConn$correctIds()

• BiodbConn$getEntry()

• BiodbConn$getCacheFile()

• BiodbConn$getEntryContent()

• BiodbConn$getEntryContentFromDb()

• BiodbConn$getEntryContentRequest()

• BiodbConn$getEntryIds()

• BiodbConn$getNbEntries()

• BiodbConn$isEditable()

• BiodbConn$editingIsAllowed()

• BiodbConn$allowEditing()

• BiodbConn$disallowEditing()

• BiodbConn$setEditingAllowed()

• BiodbConn$addNewEntry()

• BiodbConn$isWritable()

• BiodbConn$allowWriting()

• BiodbConn$disallowWriting()

• BiodbConn$setWritingAllowed()

• BiodbConn$writingIsAllowed()

• BiodbConn$write()

• BiodbConn$isSearchableByField()

• BiodbConn$getSearchableFields()

• BiodbConn$searchForEntries()

• BiodbConn$searchByName()

• BiodbConn$isDownloadable()

• BiodbConn$isDownloaded()

• BiodbConn$requiresDownload()

• BiodbConn$getDownloadPath()

• BiodbConn$setDownloadedFile()

• BiodbConn$isExtracted()

• BiodbConn$download()

• BiodbConn$isRemotedb()

• BiodbConn$isCompounddb()

• BiodbConn$searchCompound()

• BiodbConn$annotateMzValues()

• BiodbConn$isMassdb()

• BiodbConn$checkDb()

• BiodbConn$getAllVolatileCacheEntries()

• BiodbConn$getAllCacheEntries()

• BiodbConn$deleteAllEntriesFromVolatileCache()

• BiodbConn$deleteAllEntriesFromPersistentCache()

• BiodbConn$deleteWholePersistentCache()

• BiodbConn$deleteAllCacheEntries()

• BiodbConn$getCacheId()

• BiodbConn$makesRefToEntry()

• BiodbConn$makeRequest()

• BiodbConn$getEntryImageUrl()

• BiodbConn$getEntryPageUrl()

• BiodbConn$getChromCol()

• BiodbConn$getMatchingMzField()

• BiodbConn$setMatchingMzField()

• BiodbConn$getMzValues()

• BiodbConn$getNbPeaks()

• BiodbConn$filterEntriesOnRt()

• BiodbConn$searchForMassSpectra()

• BiodbConn$searchMsEntries()

• BiodbConn$searchMsPeaks()

• BiodbConn$msmsSearch()

• BiodbConn$collapseResultsDataFrame()

• BiodbConn$searchMzRange()

• BiodbConn$searchMzTol()

• BiodbConn$clone()

Method new()

New instance initializer. Connector objects must not be created directly. Instead, you create new connector instances through the BiodbFactory instance.

Usage

BiodbConn$new(id = NA_character_, cache.id = NA_character_, bdb, ...)

Arguments

Returns

Nothing.

Method getBiodb()

Returns the biodb main class instance to which this object is attached.

Usage

BiodbConn$getBiodb()

Returns

The main biodb instance.

Method getId()

Get the identifier of this connector.

Usage

BiodbConn$getId()

Returns

The identifier of this connector.

Method print()

Prints a description of this connector.

Usage

BiodbConn$print()

Returns

Nothing.

Method correctIds()

Correct a vector of IDs by formatting them to the database official format, if required and possible.

Usage

BiodbConn$correctIds(ids)

Arguments

Returns

The vector of IDs corrected.

Method getEntry()

Return the entry corresponding to this ID. You can pass a vector of IDs, and you will get a list of entries.

Usage

BiodbConn$getEntry(id, drop = TRUE, nulls = TRUE)

Arguments

Returns

A list of BiodbEntry objects, the same size of the vector of IDs. The list will contain NULL values for invalid IDs. If drop is set to TRUE and only one etrny was requested then a single BiodbEntry is returned instead of a list.

Method getCacheFile()

Get the path to the persistent cache file.

Usage

BiodbConn$getCacheFile(entry.id)

Arguments

Returns

A character vector, the same length as the vector of IDs, containing the paths to the cache files corresponding to the requested entry IDs.

Method getEntryContent()

Get the contents of database entries from IDs (accession numbers).

Usage

BiodbConn$getEntryContent(id)

Arguments

Returns

A character vector containing the contents of the requested IDs. If no content is available for an entry ID, then NA will be used.

Method getEntryContentFromDb()

Get the contents of entries directly from the database. A direct request or an access to the database will be made in order to retrieve the contents. No access to the biodb cache system will be made.

Usage

BiodbConn$getEntryContentFromDb(entry.id)

Arguments

Returns

A character vector, the same size of entry.id, with contents of the requested entries. An NA value will be set for the content of each entry for which the retrieval failed.

Method getEntryContentRequest()

Gets the URL to use in order to get the contents of the specified entries.

Usage

BiodbConn$getEntryContentRequest(entry.id, concatenate = TRUE, max.length = 0)

Arguments

Returns

A vector of URL strings.

Method getEntryIds()

Get entry identifiers from the database. More arguments can be given, depending on implementation in specific databases. For mass databases the ms.level argument can also be set.

Usage

BiodbConn$getEntryIds(max.results = 0, ...)

Arguments

Returns

A character vector containing entry IDs from the database. An empty vector for a remote database may mean that the database does not support requesting for entry accessions.

Method getNbEntries()

Get the number of entries contained in this database.

Usage

BiodbConn$getNbEntries(count = FALSE)

Arguments

Returns

The number of entries in the database, as an integer.

Method isEditable()

Tests if this connector is able to edit the database (i.e.: the connector class implements the interface BiodbEditable). If this connector is editable, then you can call allowEditing() to enable editing.

Usage

BiodbConn$isEditable()

Returns

Returns TRUE if the database is editable.

Method editingIsAllowed()

Tests if editing is allowed.

Usage

BiodbConn$editingIsAllowed()

Returns

TRUE if editing is allowed for this database, FALSE otherwise.

Method allowEditing()

Allows editing for this database.

Usage

BiodbConn$allowEditing()

Returns

Nothing.

Method disallowEditing()

Disallows editing for this database.

Usage

BiodbConn$disallowEditing()

Returns

Nothing.

Method setEditingAllowed()

Allow or disallow editing for this database.

Usage

BiodbConn$setEditingAllowed(allow)

Arguments

Returns

Nothing.

Method addNewEntry()

Adds a new entry to the database. The passed entry must have been previously created from scratch using BiodbFactory :createNewEntry() or cloned from an existing entry using BiodbEntry :clone().

Usage

BiodbConn$addNewEntry(entry)

Arguments

Returns

Nothing.

Method isWritable()

Tests if this connector is able to write into the database. If this connector is writable, then you can call allowWriting() to enable writing.

Usage

BiodbConn$isWritable()

Returns

Returns TRUE if the database is writable.

Method allowWriting()

Allows the connector to write into this database.

Usage

BiodbConn$allowWriting()

Returns

Nothing.

Method disallowWriting()

Disallows the connector to write into this database.

Usage

BiodbConn$disallowWriting()

Returns

Nothing.

Method setWritingAllowed()

Allows or disallows writing for this database.

Usage

BiodbConn$setWritingAllowed(allow)

Arguments

Returns

Nothing.

Method writingIsAllowed()

Tests if the connector has access right to the database.

Usage

BiodbConn$writingIsAllowed()

Returns

TRUE if writing is allowed for this database, FALSE otherwise.

Method write()

Writes into the database. All modifications made to the database since the last time write() was called will be saved.

Usage

BiodbConn$write()

Returns

Nothing.

Method isSearchableByField()

Tests if a field can be used to search entries when using method searchForEntries().

Usage

BiodbConn$isSearchableByField(field = NULL, field.type = NULL)

Arguments

Returns

Returns TRUE if the database is searchable using the specified field or searchable by any field of the specified type, FALSE otherwise.

Method getSearchableFields()

Get the list of all searchable fields.

Usage

BiodbConn$getSearchableFields()

Returns

A character vector containing all searchable fields for this connector.

Method searchForEntries()

Searches the database for entries whose name matches the specified name. Returns a character vector of entry IDs.

Usage

BiodbConn$searchForEntries(fields = NULL, max.results = 0)

Arguments

Returns

A character vector of entry IDs whose name matches the requested name.

Method searchByName()

DEPRECATED. Use searchForEntries() instead.

Usage

BiodbConn$searchByName(name, max.results = 0)

Arguments

Returns

A character vector of entry IDs whose name matches the requested name.

Method isDownloadable()

Tests if the connector can download the database.

Usage

BiodbConn$isDownloadable()

Returns

Returns TRUE if the database is downloadable.

Method isDownloaded()

Tests if the database has been downloaded.

Usage

BiodbConn$isDownloaded()

Returns

TRUE if the database content has already been downloaded.

Method requiresDownload()

Tests if the connector requires the download of the database.

Usage

BiodbConn$requiresDownload()

Returns

TRUE if the connector requires download of the database.

Method getDownloadPath()

Gets the path where the downloaded content is written.

Usage

BiodbConn$getDownloadPath()

Returns

The path where the downloaded database is written.

Method setDownloadedFile()

Set the downloaded file into the cache.

Usage

BiodbConn$setDownloadedFile(src, action = c("copy", "move"))

Arguments

Returns

Nothing.

Method isExtracted()

Tests if the downloaded database has been extracted (in case the database needs extraction).

Usage

BiodbConn$isExtracted()

Returns

TRUE if the downloaded database content has been extracted, FALSE otherwise.

Method download()

Downloads the database content locally.

Usage

BiodbConn$download()

Returns

Nothing.

Method isRemotedb()

Tests if the connector is connected to a remote database.

Usage

BiodbConn$isRemotedb()

Returns

Returns TRUE if the database is a remote database."

Method isCompounddb()

Tests if the connector's database is a compound database.

Usage

BiodbConn$isCompounddb()

Returns

Returns TRUE if the database is a compound database.

Method searchCompound()

This method is deprecated. Use searchForEntries() instead. Searches for compounds by name and/or by mass. At least one of name or mass must be set.

Usage

BiodbConn$searchCompound(
  name = NULL,
  mass = NULL,
  mass.field = NULL,
  mass.tol = 0.01,
  mass.tol.unit = "plain",
  max.results = 0
)

Arguments

Returns

A character vector of entry IDs."

Method annotateMzValues()

Annotates a mass spectrum with the database. For each matching entry the entry field values will be set inside columns appended to the data frame. Names of these columns will use a common prefix in order to distinguish them from other data from the input data frame.

Usage

BiodbConn$annotateMzValues(
  x,
  mz.tol,
  ms.mode,
  mz.tol.unit = c("plain", "ppm"),
  mass.field = "monoisotopic.mass",
  max.results = 3,
  mz.col = "mz",
  fields = NULL,
  prefix = NULL,
  insert.input.values = TRUE,
  fieldsLimit = 0
)

Arguments

Returns

A data frame containing the input values, and annotation columns appended at the end. The first annotation column contains the IDs of the matched entries. The following columns contain the fields you have requested through the fields parameter.

Method isMassdb()

Tests if the connector's database is a mass spectra database.

Usage

BiodbConn$isMassdb()

Returns

Returns TRUE if the database is a mass database.

Method checkDb()

Checks that the database is correct by trying to retrieve all its entries.

Usage

BiodbConn$checkDb()

Returns

Nothing.

Method getAllVolatileCacheEntries()

Get all entries stored in the memory cache (volatile cache).

Usage

BiodbConn$getAllVolatileCacheEntries()

Returns

A list of BiodbEntry instances.

Method getAllCacheEntries()

This method is deprecated. Use getAllVolatileCacheEntries() instead.

Usage

BiodbConn$getAllCacheEntries()

Returns

All entries cached in memory.

Method deleteAllEntriesFromVolatileCache()

Delete all entries from the volatile cache (memory cache).

Usage

BiodbConn$deleteAllEntriesFromVolatileCache()

Returns

Nothing.

Method deleteAllEntriesFromPersistentCache()

Delete all entries from the persistent cache (disk cache).

Usage

BiodbConn$deleteAllEntriesFromPersistentCache(deleteVolatile = TRUE)

Arguments

Returns

Nothing.

Method deleteWholePersistentCache()

Delete all files associated with this connector from the persistent cache (disk cache).

Usage

BiodbConn$deleteWholePersistentCache(deleteVolatile = TRUE)

Arguments

Returns

Nothing.

Method deleteAllCacheEntries()

Delete all entries from the memory cache. This method is deprecated, please use deleteAllEntriesFromVolatileCache() instead.

Usage

BiodbConn$deleteAllCacheEntries()

Returns

Nothing.

Method getCacheId()

Gets the ID used by this connector in the disk cache.

Usage

BiodbConn$getCacheId()

Returns

The cache ID of this connector.

Method makesRefToEntry()

Tests if some entry of this database makes reference to another entry of another database.

Usage

BiodbConn$makesRefToEntry(id, db, oid, any = FALSE, recurse = FALSE)

Arguments

Returns

A logical vector, the same size as id, with TRUE for each entry making reference to oid, and FALSE otherwise.

Method makeRequest()

Makes a sched::Request instance using the passed parameters.

Usage

BiodbConn$makeRequest(...)

Arguments

Returns

The sched::Request instance.

Method getEntryImageUrl()

Gets the URL to a picture of the entry (e.g.: a picture of the molecule in case of a compound entry).

Usage

BiodbConn$getEntryImageUrl(entry.id)

Arguments

Returns

A character vector, the same length as entry.id, containing for each entry ID either a URL or NA if no URL exists.

Method getEntryPageUrl()

Gets the URL to the page of the entry on the database web site.

Usage

BiodbConn$getEntryPageUrl(entry.id)

Arguments

Returns

A list of sched::URL objects, the same length as entry.id.

Method getChromCol()

Gets a list of chromatographic columns contained in this database.

Usage

BiodbConn$getChromCol(ids = NULL)

Arguments

Returns

A data.frame with two columns, one for the ID 'id' and another one for the title 'title'.

Method getMatchingMzField()

Gets the field to use for M/Z matching.

Usage

BiodbConn$getMatchingMzField()

Returns

The name of the field (one of peak.mztheo or peak.mzexp).

Method setMatchingMzField()

Sets the field to use for M/Z matching.

Usage

BiodbConn$setMatchingMzField(field = c("peak.mztheo", "peak.mzexp"))

Arguments

Returns

Nothing.

Method getMzValues()

Gets a list of M/Z values contained inside the database.

Usage

BiodbConn$getMzValues(
  ms.mode = NULL,
  max.results = 0,
  precursor = FALSE,
  ms.level = 0
)

Arguments

Returns

A numeric vector containing M/Z values.

Method getNbPeaks()

Gets the number of peaks contained in the database.

Usage

BiodbConn$getNbPeaks(mode = NULL, ids = NULL)

Arguments

Returns

The number of peaks, as an integer.

Method filterEntriesOnRt()

Filters a list of entries on retention time values.

Usage

BiodbConn$filterEntriesOnRt(
  entry.ids,
  rt,
  rt.unit,
  rt.tol,
  rt.tol.exp,
  chrom.col.ids,
  match.rt
)

Arguments

Returns

A character vector containing entry IDs after filtering.

Method searchForMassSpectra()

Searches for entries (i.e.: spectra) that contain a peak around the given M/Z value. Entries can also be filtered on RT values. You can input either a list of M/Z values through mz argument and set a tolerance with mz.tol argument, or two lists of minimum and maximum M/Z values through mz.min and mz.max arguments.

Usage

BiodbConn$searchForMassSpectra(
  mz.min = NULL,
  mz.max = NULL,
  mz = NULL,
  mz.tol = NULL,
  mz.tol.unit = c("plain", "ppm"),
  rt = NULL,
  rt.unit = c("s", "min"),
  rt.tol = NULL,
  rt.tol.exp = NULL,
  chrom.col.ids = NULL,
  precursor = FALSE,
  min.rel.int = 0,
  ms.mode = NULL,
  max.results = 0,
  ms.level = 0,
  include.ids = NULL
)

Arguments

Returns

A character vector of spectra IDs.

Method searchMsEntries()

DEPRECATED. Use searchForMassSpectra() instead.

Usage

BiodbConn$searchMsEntries(
  mz.min = NULL,
  mz.max = NULL,
  mz = NULL,
  mz.tol = NULL,
  mz.tol.unit = c("plain", "ppm"),
  rt = NULL,
  rt.unit = c("s", "min"),
  rt.tol = NULL,
  rt.tol.exp = NULL,
  chrom.col.ids = NULL,
  precursor = FALSE,
  min.rel.int = 0,
  ms.mode = NULL,
  max.results = 0,
  ms.level = 0
)

Arguments

Returns

A character vector of spectra IDs.

Method searchMsPeaks()

For each M/Z value, searches for matching MS spectra and returns the matching peaks.

Usage

BiodbConn$searchMsPeaks(
  input.df = NULL,
  mz = NULL,
  mz.tol = NULL,
  mz.tol.unit = c("plain", "ppm"),
  min.rel.int = 0,
  ms.mode = NULL,
  ms.level = 0,
  max.results = 0,
  chrom.col.ids = NULL,
  rt = NULL,
  rt.unit = c("s", "min"),
  rt.tol = NULL,
  rt.tol.exp = NULL,
  precursor = FALSE,
  precursor.rt.tol = NULL,
  insert.input.values = TRUE,
  prefix = NULL,
  compute = TRUE,
  fields = NULL,
  fieldsLimit = 0,
  input.df.colnames = c(mz = "mz", rt = "rt"),
  match.rt = FALSE
)

Arguments

Returns

A data frame with at least input MZ and RT columns, and annotation columns prefixed with prefix if set. For each matching found a row is output. Thus if n matchings are found for M/Z value x, then there will be n rows for x, each for a different match. The number of matching found for each M/Z value is limited to max.results.

Method msmsSearch()

Searches MSMS spectra matching a template spectrum. The mz.tol parameter is applied on the precursor search.

Usage

BiodbConn$msmsSearch(
  spectrum,
  precursor.mz,
  mz.tol,
  mz.tol.unit = c("plain", "ppm"),
  ms.mode,
  npmin = 2,
  dist.fun = c("wcosine", "cosine", "pkernel", "pbachtttarya"),
  msms.mz.tol = 3,
  msms.mz.tol.min = 0.005,
  max.results = 0
)

Arguments

Returns

A data frame with columns id, score and ⁠peak.*⁠. Each ⁠peak.*⁠ column corresponds to a peak in the input spectrum, in the same order and gives the number of the peak that was matched with it inside the matched spectrum whose ID is inside the id column.

Method collapseResultsDataFrame()

Collapse rows of a results data frame, by outputing a data frame with only one row for each MZ/RT value.

Usage

BiodbConn$collapseResultsDataFrame(
  results.df,
  mz.col = "mz",
  rt.col = "rt",
  sep = "|"
)

Arguments

Returns

A data frame with rows collapsed."

Method searchMzRange()

Find spectra in the given M/Z range. Returns a list of spectra IDs.

Usage

BiodbConn$searchMzRange(
  mz.min,
  mz.max,
  min.rel.int = 0,
  ms.mode = NULL,
  max.results = 0,
  precursor = FALSE,
  ms.level = 0
)

Arguments

Returns

A character vector of spectra IDs.

Method searchMzTol()

Find spectra containg a peak around the given M/Z value. Returns a character vector of spectra IDs.

Usage

BiodbConn$searchMzTol(
  mz,
  mz.tol,
  mz.tol.unit = "plain",
  min.rel.int = 0,
  ms.mode = NULL,
  max.results = 0,
  precursor = FALSE,
  ms.level = 0
)

Arguments

Returns

A character vector of spectra IDs.

Method clone()

The objects of this class are cloneable with this method.

Usage

BiodbConn$clone(deep = FALSE)

Arguments

See Also

Super class BiodbConnBase, and BiodbFactory class.

Examples

# Create an instance with default settings:
mybiodb <- biodb::newInst()

# Get a compound CSV file database
chebi.tsv <- system.file("extdata", "chebi_extract.tsv", package='biodb')

# Create a connector
conn <- mybiodb$getFactory()$createConn('comp.csv.file', url=chebi.tsv)

# Get 10 identifiers from the database:
ids <- conn$getEntryIds(10)

# Get number of entries contained in the database:
n <- conn$getNbEntries()

# Terminate instance.
mybiodb$terminate()

Description

Base class of BiodbConn for encapsulating all needed information for database access.

Base class of BiodbConn for encapsulating all needed information for database access.

Details

This is the base class for BiodbConn and BiodbDbInfo. When defining a new connector class, your class must not inherit from BiodbBaseConn but at least from BiodbConn (or BiodbRemoteConn or any subclass of BiodbConn). Its main purpose is to store property values. Those values are initialized from YAML files. The default definition file is located inside the package in "inst/definitions.yml" and is loaded at Biodb startup. However you can define your own files and load them using the BiodbMain::loadDefinitions() method.

Arguments to the contructor are:

other: Another object inheriting from BiodbBaseConn, and from which property values will be copied.

db.class: The class of the database ("mass.csv.file", "comp.csv.file", ...).

properties: Some properties to set at initialization.

Methods

Public methods

• BiodbConnBase$new()

• BiodbConnBase$print()

• BiodbConnBase$hasProp()

• BiodbConnBase$getPropSlots()

• BiodbConnBase$hasPropSlot()

• BiodbConnBase$propExists()

• BiodbConnBase$isSlotProp()

• BiodbConnBase$getPropValSlot()

• BiodbConnBase$updatePropertiesDefinition()

• BiodbConnBase$getEntryFileExt()

• BiodbConnBase$getDbClass()

• BiodbConnBase$getConnClassName()

• BiodbConnBase$getConnClass()

• BiodbConnBase$getEntryClassName()

• BiodbConnBase$getEntryClass()

• BiodbConnBase$getEntryIdField()

• BiodbConnBase$getPropertyValue()

• BiodbConnBase$setPropertyValue()

• BiodbConnBase$setPropValSlot()

• BiodbConnBase$getBaseUrl()

• BiodbConnBase$setBaseUrl()

• BiodbConnBase$getWsUrl()

• BiodbConnBase$setWsUrl()

• BiodbConnBase$getToken()

• BiodbConnBase$setToken()

• BiodbConnBase$getName()

• BiodbConnBase$getEntryContentType()

• BiodbConnBase$getSchedulerNParam()

• BiodbConnBase$setSchedulerNParam()

• BiodbConnBase$getSchedulerTParam()

• BiodbConnBase$setSchedulerTParam()

• BiodbConnBase$getUrls()

• BiodbConnBase$getUrl()

• BiodbConnBase$setUrl()

• BiodbConnBase$getXmlNs()

• BiodbConnBase$clone()

Method new()

New instance initializer. Connector objects must not be created directly. Instead, you create new connector instances through the BiodbFactory instance.

Usage

BiodbConnBase$new(other = NULL, db.class = NULL, properties = NULL, cfg = NULL)

Arguments

Returns

Nothing.

Method print()

Prints a description of this connector.

Usage

BiodbConnBase$print()

Returns

Nothing.

Method hasProp()

Tests if this connector has a property.

Usage

BiodbConnBase$hasProp(name)

Arguments

Returns

Returns true if the property name exists.

Method getPropSlots()

Gets the slot fields of a property.

Usage

BiodbConnBase$getPropSlots(name)

Arguments

Returns

Returns a character vector containing all slot names defined.

Method hasPropSlot()

Tests if a slot property has a specific slot.

Usage

BiodbConnBase$hasPropSlot(name, slot)

Arguments

Returns

Returns TRUE if the property name exists and has the slot slot defined, and FALSE otherwise."

Method propExists()

Checks if property exists.

Usage

BiodbConnBase$propExists(name)

Arguments

Returns

Returns TRUE if the property name exists, and FALSE otherwise.

Method isSlotProp()

Tests if a property is a slot property.

Usage

BiodbConnBase$isSlotProp(name)

Arguments

Returns

Returns TRUE if the property is a slot propert, FALSE otherwise.

Method getPropValSlot()

Retrieve the value of a slot of a property.

Usage

BiodbConnBase$getPropValSlot(name, slot, hook = TRUE)

Arguments

Returns

The value of the slot slot of the property name.

Method updatePropertiesDefinition()

Update the definition of properties.

Usage

BiodbConnBase$updatePropertiesDefinition(def)

Arguments

Returns

Nothing.

Method getEntryFileExt()

Returns the entry file extension used by this connector.

Usage

BiodbConnBase$getEntryFileExt()

Returns

A character value containing the file extension.

Method getDbClass()

Gets the Biodb name of the database associated with this connector.

Usage

BiodbConnBase$getDbClass()

Returns

A character value containing the Biodb database name.

Method getConnClassName()

Gets the name of the associated connector OOP class.

Usage

BiodbConnBase$getConnClassName()

Returns

Returns the connector OOP class name.

Method getConnClass()

Gets the associated connector OOP class.

Usage

BiodbConnBase$getConnClass()

Returns

Returns the connector OOP class.

Method getEntryClassName()

Gets the name of the associated entry class.

Usage

BiodbConnBase$getEntryClassName()

Returns

Returns the name of the associated entry class.

Method getEntryClass()

Gets the associated entry class.

Usage

BiodbConnBase$getEntryClass()

Returns

Returns the associated entry class.

Method getEntryIdField()

Gets the name of the corresponding database ID field in entries.

Usage

BiodbConnBase$getEntryIdField()

Returns

Returns the name of the database ID field.

Method getPropertyValue()

Gets a property value.

Usage

BiodbConnBase$getPropertyValue(name, hook = TRUE)

Arguments

Returns

The value of the property.

Method setPropertyValue()

Sets the value of a property.

Usage

BiodbConnBase$setPropertyValue(name, value)

Arguments

Returns

Nothing.

Method setPropValSlot()

Set the value of the slot of a property.

Usage

BiodbConnBase$setPropValSlot(name, slot, value, hook = TRUE)

Arguments

Returns

Nothing.

Method getBaseUrl()

Returns the base URL.

Usage

BiodbConnBase$getBaseUrl()

Returns

THe baae URL.

Method setBaseUrl()

Sets the base URL.

Usage

BiodbConnBase$setBaseUrl(url)

Arguments

Returns

Nothing.

Method getWsUrl()

Returns the web sevices URL.

Usage

BiodbConnBase$getWsUrl()

Method setWsUrl()

Sets the web sevices URL.

Usage

BiodbConnBase$setWsUrl(ws.url)

Arguments

Returns

Nothing.

Method getToken()

Returns the access token.

Usage

BiodbConnBase$getToken()

Method setToken()

Sets the access token.

Usage

BiodbConnBase$setToken(token)

Arguments

Returns

Nothing.

Method getName()

Returns the full database name.

Usage

BiodbConnBase$getName()

Method getEntryContentType()

Returns the entry content type.

Usage

BiodbConnBase$getEntryContentType()

Method getSchedulerNParam()

Returns the N parameter for the scheduler.

Usage

BiodbConnBase$getSchedulerNParam()

Method setSchedulerNParam()

Sets the N parameter for the scheduler.

Usage

BiodbConnBase$setSchedulerNParam(n)

Arguments

Returns

Nothing.

Method getSchedulerTParam()

Returns the T parameter for the scheduler.

Usage

BiodbConnBase$getSchedulerTParam()

Method setSchedulerTParam()

Sets the T parameter for the scheduler.

Usage

BiodbConnBase$setSchedulerTParam(t)

Arguments

Returns

Nothing.

Method getUrls()

Returns the URLs.

Usage

BiodbConnBase$getUrls()

Method getUrl()

Returns a URL.

Usage

BiodbConnBase$getUrl(name)

Arguments

Returns

The URL as a character value.

Method setUrl()

Sets a URL.

Usage

BiodbConnBase$setUrl(name, url)

Arguments

Returns

Nothing.

Method getXmlNs()

Returns the XML namespace.

Usage

BiodbConnBase$getXmlNs()

Method clone()

The objects of this class are cloneable with this method.

Usage

BiodbConnBase$clone(deep = FALSE)

Arguments

See Also

Sub-classes BiodbDbInfo and BiodbConn.

Examples

# Create an instance with default settings:
mybiodb <- biodb::newInst()

# Accessing BiodbConnBase methods when using a BiodbDbInfo object
dbinf <- mybiodb$getDbsInfo()$get('comp.csv.file')

# Test if a property exists
dbinf$hasProp('name')

# Get a property value
dbinf$getPropertyValue('name')

# Get a property value slot
dbinf$getPropValSlot('urls', 'base.url')

# Terminate instance.
mybiodb$terminate()

Description

Entry class for content in CSV format.

Entry class for content in CSV format.

Details

This is an abstract class for handling database entries whose content is in CSV format.

Super class

biodb::BiodbEntry -> BiodbCsvEntry

Methods

Public methods

• BiodbCsvEntry$new()

• BiodbCsvEntry$clone()

Method new()

New instance initializer. Entry objects must not be created directly. Instead, they are retrieved through the connector instances.

Usage

BiodbCsvEntry$new(sep = ",", na.strings = "NA", quotes = "", ...)

Arguments

Returns

Nothing.

Method clone()

The objects of this class are cloneable with this method.

Usage

BiodbCsvEntry$clone(deep = FALSE)

Arguments

See Also

Super class BiodbEntry.

Examples

# Create a concrete entry class inheriting from CSV class:
MyEntry <- R6::R6Class("MyEntry", inherit=biodb::BiodbCsvEntry)

Description

This class is used by BiodbDbsInfo for storing database characteristics, and returning them through the get() method. This class inherits from BiodbConnBase.

Super class

biodb::BiodbConnBase -> BiodbDbInfo

Methods

Public methods

• BiodbDbInfo$clone()

Method clone()

The objects of this class are cloneable with this method.

Usage

BiodbDbInfo$clone(deep = FALSE)

Arguments

See Also

Parent class BiodbDbsInfo and super class BiodbConnBase.

Examples

# Create an instance with default settings:
mybiodb <- biodb::newInst()

# Get a BiodbDbInfo object for a database:
mybiodb$getDbsInfo()$get('comp.csv.file')

# Terminate instance.
mybiodb$terminate()

Description

A class for describing the available databases.

A class for describing the available databases.

Details

The unique instance of this class is handle by the BiodbMain class and accessed through the getDbsInfo() method.

Methods

Public methods

• BiodbDbsInfo$new()

• BiodbDbsInfo$define()

• BiodbDbsInfo$getIds()

• BiodbDbsInfo$isDefined()

• BiodbDbsInfo$checkIsDefined()

• BiodbDbsInfo$get()

• BiodbDbsInfo$getAll()

• BiodbDbsInfo$print()

• BiodbDbsInfo$clone()

Method new()

New instance initializer. The class must not be instantiated directly. Instead, access the BiodbDbsInfo instance through the BiodbMain instance using the getDbsInfo() method.

Usage

BiodbDbsInfo$new(cfg)

Arguments

Returns

Nothing.

Method define()

Define databases from a structured object, normally loaded from a YAML file.

Usage

BiodbDbsInfo$define(def, package = "biodb")

Arguments

Returns

Nothing.

Method getIds()

Gets the database IDs.

Usage

BiodbDbsInfo$getIds()

Returns

A character vector containing all the IDs of the defined databases.

Method isDefined()

Tests if a database is defined.

Usage

BiodbDbsInfo$isDefined(db.id)

Arguments

Returns

TRUE if the specified id corresponds to a defined database, FALSE otherwise.

Method checkIsDefined()

Checks if a database is defined. Throws an error if the specified id does not correspond to a defined database.

Usage

BiodbDbsInfo$checkIsDefined(db.id)

Arguments

Returns

Nothing.

Method get()

Gets information on a database.

Usage

BiodbDbsInfo$get(db.id = NULL, drop = TRUE)

Arguments

Returns

A list of BiodbDbInfo instances corresponding to the specified database IDs.

Method getAll()

Gets informations on all databases.

Usage

BiodbDbsInfo$getAll()

Returns

A list of all BiodbDbInfo instances."

Method print()

Prints informations about this instance, listing also all databases defined.

Usage

BiodbDbsInfo$print()

Returns

Nothing.

Method clone()

The objects of this class are cloneable with this method.

Usage

BiodbDbsInfo$clone(deep = FALSE)

Arguments

See Also

BiodbMain and child class BiodbDbInfo.

Examples

# Create an instance with default settings:
mybiodb <- biodb::newInst()

# Getting the entry content type of a database:
db.inf <- mybiodb$getDbsInfo()$get('comp.csv.file')
cont.type <- db.inf$getPropertyValue('entry.content.type')

# Terminate instance.
mybiodb$terminate()

Description

The mother abstract class of all database entry classes.

The mother abstract class of all database entry classes.

Details

An entry is an element of a database, identifiable by its accession number. Each contains a list of fields defined by a name and a value. The details of all fields that can be set into an entry are defined inside the class BiodbEntryFields. From this class are derived other abstract classes for different types of entry contents: BiodbTxtEntry, BiodbXmlEntry, BiodbCsvEntry, BiodbJsonEntry and BiodbHtmlEntry. Then concrete classes are derived for each database: CompCsvEntry, MassCsvEntry, etc. For biodb users, there is no need to know this hierarchy; the knowledge of this class and its methods is sufficient.

Methods

Public methods

• BiodbEntry$new()

• BiodbEntry$parentIsAConnector()

• BiodbEntry$getParent()

• BiodbEntry$getBiodb()

• BiodbEntry$cloneInstance()

• BiodbEntry$getId()

• BiodbEntry$isNew()

• BiodbEntry$getDbClass()

• BiodbEntry$setFieldValue()

• BiodbEntry$appendFieldValue()

• BiodbEntry$getFieldNames()

• BiodbEntry$hasField()

• BiodbEntry$removeField()

• BiodbEntry$getFieldValue()

• BiodbEntry$getFieldsByType()

• BiodbEntry$getFieldsAsDataframe()

• BiodbEntry$getFieldsAsJson()

• BiodbEntry$parseContent()

• BiodbEntry$computeFields()

• BiodbEntry$print()

• BiodbEntry$getName()

• BiodbEntry$makesRefToEntry()

• BiodbEntry$getField()

• BiodbEntry$setField()

• BiodbEntry$getFieldClass()

• BiodbEntry$getFieldDef()

• BiodbEntry$getFieldCardinality()

• BiodbEntry$fieldHasBasicClass()

• BiodbEntry$clone()

Method new()

New instance initializer. Entry objects must not be created directly. Instead, they are retrieved through the connector instances.

Usage

BiodbEntry$new(parent)

Arguments

Returns

Nothing.

Method parentIsAConnector()

Tests if the parent of this entry is a connector instance.

Usage

BiodbEntry$parentIsAConnector()

Returns

TRUE if this entry belongs to a connector, FALSE otherwise.

Method getParent()

Returns the parent instance (A BiodbConn or BiodbFactory object) to which this object is attached.

Usage

BiodbEntry$getParent()

Returns

A BiodbConn instance or a BiodbFactory object.

Method getBiodb()

Returns the biodb main class instance to which this object is attached.

Usage

BiodbEntry$getBiodb()

Returns

The main biodb instance.

Method cloneInstance()

Clones this entry.

Usage

BiodbEntry$cloneInstance(db.class = NULL)

Arguments

Returns

The clone, as a new BiodbEntry instance.

Method getId()

Gets the entry ID.

Usage

BiodbEntry$getId()

Returns

the entry ID, which is the value if the accession field.

Method isNew()

Tests if this entry is new.

Usage

BiodbEntry$isNew()

Returns

TRUE if this entry was newly created, FALSE otherwise.

Method getDbClass()

Gets the ID of the database associated with this entry.

Usage

BiodbEntry$getDbClass()

Returns

The name of the database class associated with this entry.

Method setFieldValue()

Sets the value of a field. If the field is not already set for this entry, then the field will be created. See BiodbEntryFields for a list of possible fields in biodb.

Usage

BiodbEntry$setFieldValue(field, value)

Arguments

Returns

Nothing.

Method appendFieldValue()

Appends a value to an existing field. If the field is not defined for this entry, then the field will be created and set to this value. Only fields with a cardinality greater than one can accept multiple values.

Usage

BiodbEntry$appendFieldValue(field, value)

Arguments

Returns

Nothing.

Method getFieldNames()

Gets a list of all fields defined for this entry.

Usage

BiodbEntry$getFieldNames()

Returns

A character vector containing all field names defined in this entry.

Method hasField()

Tests if a field is defined in this entry.

Usage

BiodbEntry$hasField(field)

Arguments

Returns

TRUE if the specified field is defined in this entry, FALSE otherwise.

Method removeField()

Removes the specified field from this entry.

Usage

BiodbEntry$removeField(field)

Arguments

Returns

Nothing.

Method getFieldValue()

Gets the value of the specified field.

Usage

BiodbEntry$getFieldValue(
  field,
  compute = TRUE,
  flatten = FALSE,
  last = FALSE,
  limit = 0,
  withNa = TRUE,
  duplicatedValues = TRUE
)

Arguments

Returns

The value of the field.

Method getFieldsByType()

Gets the fields of this entry that have the specified type.

Usage

BiodbEntry$getFieldsByType(type)

Arguments

Returns

A character vector containing the field names.

Method getFieldsAsDataframe()

Converts this entry into a data frame.

Usage

BiodbEntry$getFieldsAsDataframe(
  only.atomic = TRUE,
  compute = TRUE,
  fields = NULL,
  fields.type = NULL,
  flatten = TRUE,
  limit = 0,
  only.card.one = FALSE,
  own.id = TRUE,
  duplicate.rows = TRUE,
  sort = FALSE,
  virtualFields = FALSE
)

Arguments

Returns

A data frame containg the values of the fields.

Method getFieldsAsJson()

Converts this entry into a JSON string.

Usage

BiodbEntry$getFieldsAsJson(compute = TRUE)

Arguments

Returns

A JSON object from jsonlite package.

Method parseContent()

Parses content string and set values accordingly for this entry's fields. This method is called automatically and should be run directly by users.

Usage

BiodbEntry$parseContent(content)

Arguments

Returns

Nothing.

Method computeFields()

Computes fields. Look at all missing fields, and try to compute them using references to other databases, if a rule exists.

Usage

BiodbEntry$computeFields(fields = NULL)

Arguments

Returns

TRUE if at least one field was computed successfully, FALSE otherwise.

Method print()

Displays short information about this instance.

Usage

BiodbEntry$print()

Returns

Nothing.

Method getName()

Gets a short text describing this entry instance.

Usage

BiodbEntry$getName()

Returns

A character value concatenating the connector name with the entry accession.

Method makesRefToEntry()

Tests if this entry makes reference to another entry.

Usage

BiodbEntry$makesRefToEntry(db, oid, recurse = FALSE)

Arguments

Returns

TRUE if this entry makes reference to the entry oid from database db, FALSE otherwise.

Method getField()

DEPRECATED. Gets the value of a field.

Usage

BiodbEntry$getField(field)

Arguments

Returns

The value of the field.

Method setField()

DEPRECATED. Sets the value of a field.

Usage

BiodbEntry$setField(field, value)

Arguments

Returns

Nothing.

Method getFieldClass()

Gets the class of a field.

Usage

BiodbEntry$getFieldClass(field)

Arguments

Returns

The class of the field.

Method getFieldDef()

Gets the definition of an entry field.

Usage

BiodbEntry$getFieldDef(field)

Arguments

Returns

An object BiodbEntryField which defines the field.

Method getFieldCardinality()

Gets the cardinality of the field.

Usage

BiodbEntry$getFieldCardinality(field)

Arguments

Returns

The cardinality of the field.

Method fieldHasBasicClass()

DEPRECATED. Use BiodbEntryField::isVector() instead.

Usage

BiodbEntry$fieldHasBasicClass(field)

Arguments

Returns

TRUE if the field as a basic type (logical, numeric, character, ...).

Method clone()

The objects of this class are cloneable with this method.

Usage

BiodbEntry$clone(deep = FALSE)

Arguments

See Also

BiodbFactory, BiodbConn, BiodbEntryFields.

Examples

# Create an instance with default settings:
mybiodb <- biodb::newInst()

# Get a compound CSV file database
chebi.tsv <- system.file("extdata", "chebi_extract.tsv", package='biodb')

# Get the connector of a compound database
conn <- mybiodb$getFactory()$createConn('comp.csv.file', url=chebi.tsv)

# Get an entry:
entry <- conn$getEntry(conn$getEntryIds(1))

# Get all defined fields:
entry$getFieldNames()

# Get a field value:
accession <- entry$getFieldValue('accession')

# Test if a field is defined:
if (entry$hasField('name'))
  print(paste("The entry's name is ", entry$getFieldValue('name'),
  '.', sep=''))

# Export an entry as a data frame:
df <- entry$getFieldsAsDataframe()

# You can set or reset a field's value:
entry$setFieldValue('mass', 1893.1883)

# Terminate instance.
mybiodb$terminate()

Description

A class for describing an entry field.

A class for describing an entry field.

Details

This class is used by BiodbEntryFields for storing field characteristics, and returning them through the get() method. The constructor is not meant to be used, but for development purposes the constructor's parameters are nevertheless described in the Fields section.

The constructor accepts the following arguments:

name: The name of the field.

alias: A character vector containing zero or more aliases for the field.

type: A type describing the field. One of: "mass", "name" or "id". Optional.

class: The class of the field. One of: "character", "integer", "double", "logical", "object", "data.frame".

card: The cardinality of the field: either "1" or "*".

forbids.duplicates: If set to TRUE, the field forbids duplicated values.

description: A description of the field.

allowed.values: The values authorized for the field.

lower.case: Set to TRUE if you want all values set to the field to be forced to lower case.

case.insensitive: Set to TRUE of you want the field to ignore case when checking a value.

computable.from: The Biodb ID of a database, from which this field can be computed.

virtual: If set to TRUE, the field is computed from other fields, and thus cannot be modified.

virtual.group.by.type: For a virtual field of class data.frame, this indicates to gather all fields of the specified type to build a data frame.

Methods

Public methods

• BiodbEntryField$new()

• BiodbEntryField$getName()

• BiodbEntryField$getType()

• BiodbEntryField$isOfType()

• BiodbEntryField$getDescription()

• BiodbEntryField$hasAliases()

• BiodbEntryField$getAliases()

• BiodbEntryField$addAlias()

• BiodbEntryField$removeAlias()

• BiodbEntryField$getAllNames()

• BiodbEntryField$isComputable()

• BiodbEntryField$getComputableFrom()

• BiodbEntryField$getDataFrameGroup()

• BiodbEntryField$isComputableFrom()

• BiodbEntryField$addComputableFrom()

• BiodbEntryField$removeComputableFrom()

• BiodbEntryField$correctValue()

• BiodbEntryField$isEnumerate()

• BiodbEntryField$isVirtual()

• BiodbEntryField$getVirtualGroupByType()

• BiodbEntryField$getAllowedValues()

• BiodbEntryField$addAllowedValue()

• BiodbEntryField$checkValue()

• BiodbEntryField$hasCardOne()

• BiodbEntryField$hasCardMany()

• BiodbEntryField$forbidsDuplicates()

• BiodbEntryField$isCaseInsensitive()

• BiodbEntryField$getClass()

• BiodbEntryField$isObject()

• BiodbEntryField$isDataFrame()

• BiodbEntryField$isAtomic()

• BiodbEntryField$isVector()

• BiodbEntryField$equals()

• BiodbEntryField$updateWithValuesFrom()

• BiodbEntryField$print()

• BiodbEntryField$getCardinality()

• BiodbEntryField$check()

• BiodbEntryField$clone()

Method new()

New instance initializer. This class must not be instantiated directly. Instead, you access the instances of this class through the BiodbEntryFields instance that you get from the BiodbMain instance.

Usage

BiodbEntryField$new(
  parent,
  name,
  alias = NA_character_,
  type = NA_character_,
  class = c("character", "integer", "double", "logical", "object", "data.frame"),
  card = c("one", "many"),
  forbids.duplicates = FALSE,
  description = NA_character_,
  allowed.values = NULL,
  lower.case = FALSE,
  case.insensitive = FALSE,
  computable.from = NULL,
  virtual = FALSE,
  virtual.group.by.type = NULL,
  dataFrameGroup = NA_character_
)

Arguments

Returns

Nothing.

Method getName()

Gets the name.

Usage

BiodbEntryField$getName()

Returns

The name of this field.

Method getType()

Gets field's type.

Usage

BiodbEntryField$getType()

Returns

The type of this field.

Method isOfType()

Tests if this field is of the specified type.

Usage

BiodbEntryField$isOfType(type)

Arguments

Returns

TRUE if this field is of the specified type, FALSE otherwise.

Method getDescription()

Get field's description.

Usage

BiodbEntryField$getDescription()

Returns

The description of this field.

Method hasAliases()

Tests if this field has aliases.

Usage

BiodbEntryField$hasAliases()

Returns

TRUE if this entry field defines aliases, FALSE otherwise.

Method getAliases()

Get aliases.

Usage

BiodbEntryField$getAliases()

Returns

The list of aliases if some are defined, otherwise returns NULL."

Method addAlias()

Adds an alias to the list of aliases.

Usage

BiodbEntryField$addAlias(alias)

Arguments

Returns

Nothing.

Method removeAlias()

Removes an alias from the list of aliases.

Usage

BiodbEntryField$removeAlias(alias)

Arguments

Returns

Nothing.

Method getAllNames()

Gets all names.

Usage

BiodbEntryField$getAllNames()

Returns

The list of all names (main name and aliases).

Method isComputable()

Tests if this field is computable from another field or another database.

Usage

BiodbEntryField$isComputable()

Returns

TRUE if the field is computable, FALSE otherwise.

Method getComputableFrom()

Get the list of connectors that can be used to compute this field.

Usage

BiodbEntryField$getComputableFrom()

Returns

A list of list objects. Each list object contains the name of the database from which the field is computable.

Method getDataFrameGroup()

Gets the defined data frame group, if any.

Usage

BiodbEntryField$getDataFrameGroup()

Returns

The data frame group, as a character value.

Method isComputableFrom()

Gets the ID of the database from which this field can be computed.

Usage

BiodbEntryField$isComputableFrom()

Returns

The list of databases where to find this field's value.

Method addComputableFrom()

Adds a directive from the list of computableFrom.

Usage

BiodbEntryField$addComputableFrom(directive)

Arguments

Returns

Nothing.

Method removeComputableFrom()

Removes a directive from the list of computableFrom.

Usage

BiodbEntryField$removeComputableFrom(directive)

Arguments

Returns

Nothing.

Method correctValue()

Corrects a value so it is compatible with this field.

Usage

BiodbEntryField$correctValue(value)

Arguments

Returns

The corrected value.

Method isEnumerate()

Tests if this field is an enumerate type (i.e.: it defines allowed values).

Usage

BiodbEntryField$isEnumerate()

Returns

TRUE if this field defines some allowed values, FALSE otherwise.

Method isVirtual()

Tests if this field is a virtual field.

Usage

BiodbEntryField$isVirtual()

Returns

TRUE if this field is virtual, FALSE otherwise.

Method getVirtualGroupByType()

Gets type for grouping field values when building a virtual data frame.

Usage

BiodbEntryField$getVirtualGroupByType()

Returns

The type, as a character value.

Method getAllowedValues()

Gets allowed values.

Usage

BiodbEntryField$getAllowedValues(value = NULL)

Arguments

Returns

A character vector containing all allowed values.

Method addAllowedValue()

Adds an allowed value, as a synonym to already an existing value. Note that not all enumerate fields accept synonyms.

Usage

BiodbEntryField$addAllowedValue(key, value)

Arguments

Returns

Nothing.

Method checkValue()

Checks if a value is correct. Fails if value is incorrect.

Usage

BiodbEntryField$checkValue(value)

Arguments

Returns

Nothing.

Method hasCardOne()

Tests if this field has a cardinality of one.

Usage

BiodbEntryField$hasCardOne()

Returns

TRUE if the cardinality of this field is one, FALSE otherwise.

Method hasCardMany()

Tests if this field has a cardinality greater than one.

Usage

BiodbEntryField$hasCardMany()

Returns

TRUE if the cardinality of this field is many, FALSE otherwise.

Method forbidsDuplicates()

Tests if this field forbids duplicates.

Usage

BiodbEntryField$forbidsDuplicates()

Returns

TRUE if this field forbids duplicated values, FALSE otherwise.

Method isCaseInsensitive()

Tests if this field is case sensitive.

Usage

BiodbEntryField$isCaseInsensitive()

Returns

TRUE if this field is case insensitive, FALSE otherwise.

Method getClass()

Gets the class of this field's value.

Usage

BiodbEntryField$getClass()

Returns

class) of this field.

Method isObject()

Tests if this field's type is a class.

Usage

BiodbEntryField$isObject()

Returns

TRUE if field's type is a class, FALSE otherwise.

Method isDataFrame()

Tests if this field's type is data.frame.

Usage

BiodbEntryField$isDataFrame()

Returns

TRUE if field's type is data frame, FALSE otherwise."

Method isAtomic()

Tests if this field's type is an atomic type.

Usage

BiodbEntryField$isAtomic()

Returns

character, integer, double or logical), FALSE otherwise.

Method isVector()

Tests if this field's type is a basic vector type.

Usage

BiodbEntryField$isVector()

Returns

character, integer, double or logical), FALSE otherwise.

Method equals()

Compares this instance with another, and tests if they are equal.

Usage

BiodbEntryField$equals(other, fail = FALSE)

Arguments

Returns

TRUE if they are equal, FALSE otherwise.

Method updateWithValuesFrom()

Updates fields using values from other instance. The updated fields

Usage

BiodbEntryField$updateWithValuesFrom(other)

Arguments

Returns

Nothing.

Method print()

Print informations about this entry.

Usage

BiodbEntryField$print()

Returns

Nothing.

Method getCardinality()

Gets the field's cardinality.

Usage

BiodbEntryField$getCardinality()

Returns

The cardinality: "one" or "many".

Method check()

Checks if essential values are defined.

Usage

BiodbEntryField$check()

Returns

Nothing.

Method clone()

The objects of this class are cloneable with this method.

Usage

BiodbEntryField$clone(deep = FALSE)

Arguments

See Also

Parent class BiodbEntryFields.

Examples

# Get the class of the InChI field.
mybiodb <- biodb::newInst()
inchi.field.class <- mybiodb$getEntryFields()$get('inchi')$getClass()

# Test the cardinality of a field
card.one <- mybiodb$getEntryFields()$get('name')$hasCardOne()
card.many <- mybiodb$getEntryFields()$get('name')$hasCardMany()

# Get the description of a field
desc <- mybiodb$getEntryFields()$get('inchi')$getDescription()

# Terminate instance.
mybiodb$terminate()

Description

A class for handling description of all entry fields.

A class for handling description of all entry fields.

Details

The unique instance of this class is handle by the BiodbMain class and accessed through the getEntryFields() method.

Methods

Public methods

• BiodbEntryFields$new()

• BiodbEntryFields$notifyCfgUpdate()

• BiodbEntryFields$isAlias()

• BiodbEntryFields$formatName()

• BiodbEntryFields$isDefined()

• BiodbEntryFields$checkIsDefined()

• BiodbEntryFields$getRealName()

• BiodbEntryFields$get()

• BiodbEntryFields$getFieldNames()

• BiodbEntryFields$getDatabaseIdField()

• BiodbEntryFields$print()

• BiodbEntryFields$define()

• BiodbEntryFields$terminate()

• BiodbEntryFields$clone()

Method new()

New instance initializer. No BiodbEntryFields instance must be created directly. Instead, call the getEntryFields() method of BiodbMain.

Usage

BiodbEntryFields$new(parent)

Arguments

Returns

Nothing.

Method notifyCfgUpdate()

Call back method called when a value is modified inside the configuration.

Usage

BiodbEntryFields$notifyCfgUpdate(k, v)

Arguments

Returns

Nothing.

Method isAlias()

Tests if names are aliases.

Usage

BiodbEntryFields$isAlias(name)

Arguments

Returns

A logical vector, the same length as name, with TRUE for name values that are an alias of a field, and FALSE otherwise."

Method formatName()

Format field name(s) for biodb format: set to lower case and remove dot or underscore characters depending on configuration.

Usage

BiodbEntryFields$formatName(name)

Arguments

Returns

A character vector of formatted names.

Method isDefined()

Tests if names are defined fields.

Usage

BiodbEntryFields$isDefined(name)

Arguments

Returns

A logical vector, the same length as name, with TRUE for name values that corresponds to a defined field.

Method checkIsDefined()

Tests if names are valid defined fields. Throws an error if any name does not correspond to a defined field.

Usage

BiodbEntryFields$checkIsDefined(name)

Arguments

Returns

Nothing.

Method getRealName()

Gets the real names (main names) of fields. If some name is not found neither in aliases nor in real names, an error is thrown.

Usage

BiodbEntryFields$getRealName(name, fail = TRUE)

Arguments

Returns

A character vector, the same length as name, with the real field name for each name given (i.e. each alias is replaced with the real name).

Method get()

Gets a BiodbEntryField instance.

Usage

BiodbEntryFields$get(name, drop = TRUE)

Arguments

Returns

A named list of BiodbEntryField instances. The names of the list are the real names of the entry fields, thus they may be different from the one provided inside the name argument.

Method getFieldNames()

Gets the main names of all fields.

Usage

BiodbEntryFields$getFieldNames(type = NULL, computable = NULL)

Arguments

Returns

A character vector containing all selected field names.

Method getDatabaseIdField()

Gets a database ID field.

Usage

BiodbEntryFields$getDatabaseIdField(database)

Arguments

Returns

accession numbers) for this database.

Method print()

Prints information about the instance.

Usage

BiodbEntryFields$print()

Returns

Nothing.

Method define()

Defines fields.

Usage

BiodbEntryFields$define(def)

Arguments

Returns

Nothing.

Method terminate()

Terminates the instance. This method will be called automatically by the BiodbMain instance when you call

Usage

BiodbEntryFields$terminate()

Arguments

Returns

Nothing.

Method clone()

The objects of this class are cloneable with this method.

Usage

BiodbEntryFields$clone(deep = FALSE)

Arguments

See Also

BiodbMain and child class BiodbEntryField.

Examples

# Getting information about the accession field:
mybiodb <- biodb::newInst()
entry.field <- mybiodb$getEntryFields()$get('accession')

# Test if a name is an alias of a field
mybiodb$getEntryFields()$isAlias('genesymbols')

# Test if a name is associated with a defined field
mybiodb$getEntryFields()$isDefined('name')

# Terminate instance.
mybiodb$terminate()

Description

A class for constructing biodb objects.

A class for constructing biodb objects.

Details

This class is responsible for the creation of database connectors and database entries. You must go through the single instance of this class to create and get connectors, as well as instantiate entries. To get the single instance of this class, call the getFactory() method of class BiodbMain.

Methods

Public methods

• BiodbFactory$new()

• BiodbFactory$getBiodb()

• BiodbFactory$createConn()

• BiodbFactory$connExists()

• BiodbFactory$deleteConn()

• BiodbFactory$deleteConnByClass()

• BiodbFactory$getAllConnectors()

• BiodbFactory$deleteAllConnectors()

• BiodbFactory$getConn()

• BiodbFactory$getEntry()

• BiodbFactory$createNewEntry()

• BiodbFactory$createEntryFromContent()

• BiodbFactory$getAllCacheEntries()

• BiodbFactory$deleteAllEntriesFromVolatileCache()

• BiodbFactory$deleteAllCacheEntries()

• BiodbFactory$print()

• BiodbFactory$clone()

Method new()

New instance initializer. The BiodbFactory class must not be instantiated directly. Instead, call the getFactory() method from the BiodbMain instance.

Usage

BiodbFactory$new(bdb)

Arguments

Returns

Nothing.

Method getBiodb()

Returns the biodb main class instance to which this object is attached.

Usage

BiodbFactory$getBiodb()

Returns

The main biodb instance.

Method createConn()

Creates a connector to a database.

Usage

BiodbFactory$createConn(
  db.class,
  url = NULL,
  token = NA_character_,
  fail.if.exists = TRUE,
  get.existing.conn = TRUE,
  conn.id = NULL,
  cache.id = NULL
)

Arguments

Returns

An instance of the requested connector class.

Method connExists()

Tests if a connector exists.

Usage

BiodbFactory$connExists(conn.id)

Arguments

Returns

TRUE if a connector with this ID exists, FALSE otherwise.

Method deleteConn()

Deletes an existing connector.

Usage

BiodbFactory$deleteConn(conn)

Arguments

Returns

Nothing.

Method deleteConnByClass()

Deletes all existing connectors from a same class.

Usage

BiodbFactory$deleteConnByClass(db.class)

Arguments

Returns

Nothing.

Method getAllConnectors()

Gets all connectors.

Usage

BiodbFactory$getAllConnectors()

Returns

A list of all created connectors.

Method deleteAllConnectors()

Deletes all connectors.

Usage

BiodbFactory$deleteAllConnectors()

Returns

Nothing.

Method getConn()

Gets an instantiated connector instance, or create a new one.

Usage

BiodbFactory$getConn(conn.id, class = TRUE, create = TRUE)

Arguments

Returns

The connector instance corresponding to the connector ID or to the database ID submitted (if class \"parameter\" is set to TRUE).

Method getEntry()

Retrieves database entry objects from IDs (accession numbers), for the specified connector.

Usage

BiodbFactory$getEntry(conn.id, id, drop = TRUE, no.null = FALSE, limit = 0)

Arguments

Returns

A list of BiodbEntry objects, the same length as id. A NULL value is put into the list for each invalid ID of id.

Method createNewEntry()

Creates a new empty entry object from scratch. This entry is not stored in cache, and is directly attached to the factory instance instead of a particular connector.

Usage

BiodbFactory$createNewEntry(db.class)

Arguments

Returns

A new BiodbEntry object.

Method createEntryFromContent()

Creates an entry instance from a content.

Usage

BiodbFactory$createEntryFromContent(conn.id, content, drop = TRUE)

Arguments

Returns

A list of new BiodbEntry objects.

Method getAllCacheEntries()

For a connector, gets all entries stored in the cache.

Usage

BiodbFactory$getAllCacheEntries(conn.id)

Arguments

Returns

A list of BiodbEntry objects.

Method deleteAllEntriesFromVolatileCache()

Deletes all entries stored in the cache of the given connector. This method is deprecated, please use deleteAllEntriesFromVolatileCache() instead.

Usage

BiodbFactory$deleteAllEntriesFromVolatileCache(conn.id)

Arguments

Returns

Nothing.

Method deleteAllCacheEntries()

Deletes all entries stored in the cache of the given connector.

Usage

BiodbFactory$deleteAllCacheEntries(conn.id)

Arguments

Returns

Nothing.

Method print()

Prints information about this instance.

Usage

BiodbFactory$print()

Returns

Nothing.

Method clone()

The objects of this class are cloneable with this method.

Usage

BiodbFactory$clone(deep = FALSE)

Arguments

See Also

BiodbMain, BiodbConn and BiodbEntry.

Examples

# Create a BiodbMain instance with default settings:
mybiodb <- biodb::newInst()

# Obtain the factory instance:
factory <- mybiodb$getFactory()

# Get a compound CSV file database
chebi.tsv <- system.file("extdata", "chebi_extract.tsv", package='biodb')

# Create a connector:
conn <- mybiodb$getFactory()$createConn('comp.csv.file', url=chebi.tsv)

# Get a database entry:
entry <- conn$getEntry(conn$getEntryIds(1))

# Terminate instance.
mybiodb$terminate()

Description

Entry class for content in HTML format.

Entry class for content in HTML format.

Details

This is an abstract class for handling database entries whose content is in HTML format.

Super classes

biodb::BiodbEntry -> biodb::BiodbXmlEntry -> BiodbHtmlEntry

Methods

Public methods

• BiodbHtmlEntry$new()

• BiodbHtmlEntry$clone()

Method new()

New instance initializer. Entry objects must not be created directly. Instead, they are retrieved through the connector instances.

Usage

BiodbHtmlEntry$new(...)

Arguments

Returns

Nothing.

Method clone()

The objects of this class are cloneable with this method.

Usage

BiodbHtmlEntry$clone(deep = FALSE)

Arguments

See Also

Super class BiodbXmlEntry.

Examples

# Create a concrete entry class inheriting from this class:
MyEntry <- R6::R6Class("MyEntry", inherit=biodb::BiodbHtmlEntry)

Description

This is an abstract class for handling database entries whose content is in JSON format.

Super class

biodb::BiodbEntry -> BiodbJsonEntry

Methods

Public methods

• BiodbJsonEntry$clone()

Method clone()

The objects of this class are cloneable with this method.

Usage

BiodbJsonEntry$clone(deep = FALSE)

Arguments

See Also

Super class BiodbEntry.

Examples

# Create a concrete entry class inheriting from CSV class:
MyEntry <- R6::R6Class("MyEntry", inherit=biodb::BiodbJsonEntry)

Description

This is an abstract class for handling database entries whose content is in list format.

Super class

biodb::BiodbEntry -> BiodbListEntry

Methods

Public methods

• BiodbListEntry$clone()

Method clone()

The objects of this class are cloneable with this method.

Usage

BiodbListEntry$clone(deep = FALSE)

Arguments

See Also

Super class BiodbEntry.

Examples

# Create a concrete entry class inheriting from CSV class:
MyEntry <- R6::R6Class("MyEntry", inherit=biodb::BiodbListEntry)

Description

The central class of the biodb package.

The central class of the biodb package.

Details

The main class of the biodb package. In order to use the biodb package, you need first to create an instance of this class.

The constructor takes a single argument, autoloadExtraPkgs, to enable (TRUE or default) or disable (FALSE) autoloading of extra biodb packages.

Once the instance is created, some other important classes (BiodbFactory, BiodbConfig, ...) are instantiated (just once) and their instances are later accessible through get*() methods.

Methods

Public methods

• BiodbMain$new()

• BiodbMain$terminate()

• BiodbMain$loadDefinitions()

• BiodbMain$getConfig()

• BiodbMain$getPersistentCache()

• BiodbMain$getDbsInfo()

• BiodbMain$getEntryFields()

• BiodbMain$getFactory()

• BiodbMain$getRequestScheduler()

• BiodbMain$addObservers()

• BiodbMain$getObservers()

• BiodbMain$convertEntryIdFieldToDbClass()

• BiodbMain$entriesFieldToVctOrLst()

• BiodbMain$entriesToDataframe()

• BiodbMain$entryIdsToDataframe()

• BiodbMain$addColsToDataframe()

• BiodbMain$entriesToJson()

• BiodbMain$collapseRows()

• BiodbMain$entriesToSingleFieldValues()

• BiodbMain$entryIdsToSingleFieldValues()

• BiodbMain$computeFields()

• BiodbMain$saveEntriesAsJson()

• BiodbMain$copyDb()

• BiodbMain$print()

• BiodbMain$fieldIsAtomic()

• BiodbMain$getFieldClass()

• BiodbMain$clone()

Method new()

New instance initializer. The BiodbMain must not be instantiated directly. Instead use the newInst() global method.

Usage

BiodbMain$new(autoloadExtraPkgs = NULL)

Arguments

Returns

Nothing.

Method terminate()

Closes BiodbMain instance. Call this method when you are done with your BiodbMain instance.

Usage

BiodbMain$terminate()

Returns

Nothing.

Method loadDefinitions()

Loads databases and entry fields definitions from YAML file.

Usage

BiodbMain$loadDefinitions(file, package = "biodb")

Arguments

Returns

Nothing.

Method getConfig()

Returns the single instance of the BiodbConfig class.

Usage

BiodbMain$getConfig()

Returns

The instance of the BiodbConfig class attached to this BiodbMain instance.

Method getPersistentCache()

Returns the single instance of the BiodbPersistentCache class.

Usage

BiodbMain$getPersistentCache()

Returns

The instance of the BiodbPersistentCache class attached to this BiodbMain instance.

Method getDbsInfo()

Returns the single instance of the BiodbDbsInfo class.

Usage

BiodbMain$getDbsInfo()

Returns

The instance of the BiodbDbsInfo class attached to this BiodbMain instance.

Method getEntryFields()

Returns the single instance of the BiodbEntryFields class.

Usage

BiodbMain$getEntryFields()

Returns

The instance of the BiodbEntryFields class attached to this BiodbMain instance.

Method getFactory()

Returns the single instance of the BiodbFactory class.

Usage

BiodbMain$getFactory()

Returns

The instance of the BiodbFactory class attached to this BiodbMain instance.

Method getRequestScheduler()

Returns the single instance of the Scheduler class.

Usage

BiodbMain$getRequestScheduler()

Returns

The instance of the Scheduler class attached to this BiodbMain instance.

Method addObservers()

Adds new observers. Observers will be called each time an event occurs. This is the way used in biodb to get feedback about what is going inside biodb code.

Usage

BiodbMain$addObservers(observers)

Arguments

Returns

Nothing.

Method getObservers()

Gets the list of registered observers.

Usage

BiodbMain$getObservers()

Returns

The list or registered observers.

Method convertEntryIdFieldToDbClass()

Gets the database class name corresponding to an entry ID field.

Usage

BiodbMain$convertEntryIdFieldToDbClass(entry.id.field)

Arguments

Method entriesFieldToVctOrLst()

Extracts the value of a field from a list of entries. Returns either a vector or a list depending on the type of the field.

Usage

BiodbMain$entriesFieldToVctOrLst(
  entries,
  field,
  flatten = FALSE,
  compute = TRUE,
  limit = 0,
  withNa = TRUE
)

Arguments

Returns

A vector if the field is atomic or flatten is set to TRUE, otherwise a list.

Method entriesToDataframe()

Converts a list of entries or a list of list of entries (BiodbEntry objects) into a data frame.

Usage

BiodbMain$entriesToDataframe(
  entries,
  only.atomic = TRUE,
  null.to.na = TRUE,
  compute = TRUE,
  fields = NULL,
  limit = 0,
  drop = FALSE,
  sort.cols = FALSE,
  flatten = TRUE,
  only.card.one = FALSE,
  own.id = TRUE,
  prefix = ""
)

Arguments

Returns

A data frame containing the entries. Columns are named according to field names.

Method entryIdsToDataframe()

Construct a data frame using entry IDs and field values of the corresponding entries.

Usage

BiodbMain$entryIdsToDataframe(
  ids,
  db,
  fields = NULL,
  limit = 3,
  prefix = "",
  own.id = FALSE
)

Arguments

Method addColsToDataframe()

Add values from a database to an existing data frame using a column containing entry identifiers.

Usage

BiodbMain$addColsToDataframe(x, id.col, db, fields, limit = 3, prefix = "")

Arguments

Returns

A data frame containing x and new columns appended for the fields requested.

Method entriesToJson()

Converts a list of BiodbEntry objects into JSON. Returns a vector of characters.

Usage

BiodbMain$entriesToJson(entries, compute = TRUE)

Arguments

Returns

A list of JSON strings, the same length as entries list.

Method collapseRows()

Collapses rows of a data frame, by looking for duplicated values in the reference columns (parameter cols). The values contained in the reference columns are supposed to be ordered inside the data frame, in the sens that all duplicated values are supposed to directly follow the original values. For all rows containing duplicated values, we look at values in all other columns and concatenate values in each column containing different values.

Usage

BiodbMain$collapseRows(x, sep = "|", cols = 1L)

Arguments

Returns

A data frame, with rows collapsed."

Method entriesToSingleFieldValues()

Extract all values of a field from a list of entries.

Usage

BiodbMain$entriesToSingleFieldValues(
  entries,
  field,
  sortOutput = FALSE,
  uniq = TRUE
)

Arguments

Returns

The values of the field as a vector.

Method entryIdsToSingleFieldValues()

Extract all values of a field from a list of entries.

Usage

BiodbMain$entryIdsToSingleFieldValues(
  ids,
  db,
  field,
  sortOutput = FALSE,
  uniq = TRUE
)

Arguments

Returns

The values of the field as a vector.

Method computeFields()

Computes missing fields in entries, for those fields that are comptable.

Usage

BiodbMain$computeFields(entries)

Arguments

Returns

Nothing.

Method saveEntriesAsJson()

Saves a list of entries in JSON format. Each entry will be saved in a separate file.

Usage

BiodbMain$saveEntriesAsJson(entries, files, compute = TRUE)

Arguments

Returns

Nothing.

Method copyDb()

Copies all entries of a database into another database. The connector of the destination database must be editable.

Usage

BiodbMain$copyDb(conn.from, conn.to, limit = 0)

Arguments

Returns

Nothing.

Method print()

Prints object information.

Usage

BiodbMain$print()

Returns

Nothing.

Method fieldIsAtomic()

DEPRECATED method to test if a field is an atomic field. The new method is BiodbEntryField :isVector()."

Usage

BiodbMain$fieldIsAtomic(field)

Arguments

Returns

TRUE if the field's value is atomic.

Method getFieldClass()

DEPRECATED method to get the class of a field. The new method is BiodbMain :getEntryFields()$get(field)$getClass().

Usage

BiodbMain$getFieldClass(field)

Arguments

Returns

The class of the field.

Method clone()

The objects of this class are cloneable with this method.

Usage

BiodbMain$clone(deep = FALSE)

Arguments

See Also

BiodbFactory, BiodbConfig, BiodbEntryFields, BiodbDbsInfo.

Examples

# Create an instance:
mybiodb <- biodb::newInst()

# Get the factory instance
fact <- mybiodb$getFactory()

# Terminate instance.
mybiodb$terminate()
mybiodb <- NULL

Description

Entry class for content in SDF format.

Entry class for content in SDF format.

Details

This is an abstract class for handling database entries whose content is in SDF format.

Super classes

biodb::BiodbEntry -> biodb::BiodbTxtEntry -> BiodbSdfEntry

Methods

Public methods

• BiodbSdfEntry$new()

• BiodbSdfEntry$clone()

Method new()

New instance initializer. Entry objects must not be created directly. Instead, they are retrieved through the connector instances.

Usage

BiodbSdfEntry$new(...)

Arguments

Returns

Nothing.

Method clone()

The objects of this class are cloneable with this method.

Usage

BiodbSdfEntry$clone(deep = FALSE)

Arguments

See Also

Super class BiodbTxtEntry.

Examples

# Create a concrete entry class inheriting from CSV class:
MyEntry <- R6::R6Class("MyEntry", inherit=biodb::BiodbSdfEntry)

Description

A class for acknowledging messages during tests.

A class for acknowledging messages during tests.

Details

This observer is used to call a testthat::expect_*() method each time a message is received. This is used when running tests on Travis-CI, so Travis does not stop tests because no change is detected in output.

Methods

Public methods

• BiodbTestMsgAck$new()

• BiodbTestMsgAck$notifyProgress()

• BiodbTestMsgAck$clone()

Method new()

New instance initializer.

Usage

BiodbTestMsgAck$new()

Returns

Nothing.

Method notifyProgress()

Call back method used to get progress advancement of a long process.

Usage

BiodbTestMsgAck$notifyProgress(what, index, total)

Arguments

Returns

Nothing.

Method clone()

The objects of this class are cloneable with this method.

Usage

BiodbTestMsgAck$clone(deep = FALSE)

Arguments

Examples

# To use the acknowledger, set ack=TRUE when creating the Biodb test
# instance:
biodb <- biodb::createBiodbTestInstance(ack=TRUE)

# Terminate the BiodbMain instance
biodb$terminate()

Description

Entry class for content in text format.

Entry class for content in text format.

Details

This is an abstract class for handling database entries whose content is in text format.

Super class

biodb::BiodbEntry -> BiodbTxtEntry

Methods

Public methods

• BiodbTxtEntry$new()

• BiodbTxtEntry$clone()