Package 'biodb'

Title: biodb, a library and a development framework for connecting to chemical and biological databases
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.
Authors: Pierrick Roger [aut, cre] , Alexis Delabrière [ctb]
Maintainer: Pierrick Roger <[email protected]>
License: AGPL-3
Version: 1.15.0
Built: 2024-11-19 03:11:42 UTC
Source: https://github.com/bioc/biodb

Help Index

biodb: biodb, a library and a development framework for connecting to chemical and biological databases

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:

See Also

BiodbMain, BiodbConfig, BiodbFactory, BiodbPersistentCache, BiodbDbsInfo, BiodbEntryFields.

Declares a class as abstract.

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

cls

The name of the abstract class to check.
obj

The object being instantiated.

Value

Nothing.

Declares a method as abstract

Description

This method must be called from within the abstract method.

Usage

abstractMethod(obj)

Arguments

obj

The object on which the abstract method is called.

Value

Nothing.

A persistent cache implementation that uses BiocCache package.

Description

A persistent cache implementation that uses BiocCache package.

A persistent cache implementation that uses BiocCache package.

Super class

biodb::BiodbPersistentCache -> BiodbBiocPersistentCache

Methods

Public methods

Inherited methods

Method new()

New instance initializer. Cache objects must not be created directly. Instead, access the cache instance through the BiodbMain instance using the getPersistentCache() method.

Usage
BiodbBiocPersistentCache$new(...)
Arguments
...

See the constructor of ExtGenerator for the parameters.

Returns

Nothing.

Method clone()

The objects of this class are cloneable with this method.

Usage
BiodbBiocPersistentCache$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

See Also

BiodbPersistentCache, BiodbBiocPersistentCache.

A class for storing configuration values.

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

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
parent

The BiodbMain instance.

Returns

Nothing.

Method getKeys()

Get the list of available keys.

Usage
BiodbConfig$getKeys(deprecated = FALSE)
Arguments
deprecated

If set to TRUE returns also the deprecated keys.

Returns

A character vector containing the config key names.

Method getTitle()

Get the title of a key.

Usage
BiodbConfig$getTitle(key)
Arguments
key

The name of a configuration key.

Returns

The title of the key as a character value.

Method getDescription()

Get the description of a key.

Usage
BiodbConfig$getDescription(key)
Arguments
key

The name of a configuration key.

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
key

The name of a configuration key.

as.chr

If set to TRUE, returns the value as character.

Returns

The default value for that key.

Method hasKey()

Test if a key exists.

Usage
BiodbConfig$hasKey(key)
Arguments
key

The name of a configuration key.

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
key

The name of a configuration key.

fail

If set to TRUE and the configuration key does not exist, then an error will be raised.

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
key

The name of a configuration key.

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
key

The name of a configuration key.

Returns

The value associated with the key.

Method set()

Set the value of a key.

Usage
BiodbConfig$set(key, value)
Arguments
key

The name of a configuration key.

value

A value to associate with the key.

Returns

Nothing.

Method reset()

Reset the value of a key.

Usage
BiodbConfig$reset(key = NULL)
Arguments
key

The name of a configuration key. If NULL, all keys will be reset.

Returns

Nothing.

Method enable()

Set a boolean key to TRUE.

Usage
BiodbConfig$enable(key)
Arguments
key

The name of a configuration key.

Returns

Nothing.

Method disable()

Set a boolean key to FALSE.

Usage
BiodbConfig$disable(key)
Arguments
key

The name of a configuration key.

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
key

The name of a configuration key.

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
def

The list of key definitions.

Returns

Nothing.

Method notifyNewObservers()

Called by BiodbMain when a new observer is registered.

Usage
BiodbConfig$notifyNewObservers(obs)
Arguments
obs

The new observers registered by the BiodbMain instance.

Returns

Nothing.

Method terminate()

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

Usage
BiodbConfig$terminate()
Arguments
BiodbMain

:terminate().

Returns

Nothing.

Method clone()

The objects of this class are cloneable with this method.

Usage
BiodbConfig$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

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()

The mother abstract class of all database connectors.

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

Inherited methods

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
id

The ID of the connector instance.

cache.id

The Cache ID of the connector instance.

bdb

The BiodbMain instance.

...

Remaining arguments will be passed to the constructor of the super class.

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
ids

A character vector of IDs.

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
id

A character vector containing entry identifiers.

drop

If set to TRUE and only one entry is requrested, then the returned value will be a single BiodbEntry object, otherwise it will be a list of BiodbEntry objects.

nulls

If set to TRUE, NULL entries are preserved. This ensures that the output list has the same length than the input vector id. Otherwise they are removed from the final list.

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
entry.id

The identifiers (e.g.: accession numbers) as a character vector of the database entries.

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
id

A character vector of entry IDs.

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
entry.id

A character vector with the IDs of entries to retrieve.

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
entry.id

A character vector with the IDs of entries to retrieve.

concatenate

If set to TRUE, then try to build as few URLs as possible, sending requests with several identifiers at once.

max.length

The maximum length of the URLs to return, in number of characters.

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
max.results

The maximum of elements to return from the method.

...

Arguments specific to connectors.

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
count

If set to TRUE and no straightforward way exists to get number of entries, count the output of getEntryIds().

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
allow

A logical value.

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
entry

The new entry to add. It must be a valid BiodbEntry object.

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
allow

If set to TRUE, allows writing.

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
field

The name of the field.

field.type

The field type.

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
fields

A list of fields on which to filter entries. To get a match, all fields must be matched (i.e. logical AND). The keys of the list are the entry field names on which to filter, and the values are the filtering parameters. For character fields, the filter parameter is a character vector in which all strings must be found inside the field's value. For numeric fields, the filter parameter is either a list specifying a min-max range (list(min=1.0, max=2.5)) or a value with a tolerance in delta (list(value=2.0, delta=0.1)) or ppm (list(value=2.0, ppm=1.0)).

max.results

If set, the number of returned IDs is limited to this number.

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
name

A character value to search inside name fields.

max.results

If set, the number of returned IDs is limited to this number.

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
src

Path to the downloaded file.

action

Specifies if files have to be moved or copied into the cache.

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
name

The name of a compound to search for.

mass

The searched mass.

mass.field

For searching by mass, you must indicate a mass field to use ('monoisotopic.mass', 'molecular.mass', 'average.mass' or 'nominal.mass').

mass.tol

The tolerance value on the molecular mass.

mass.tol.unit

The type of mass tolerance. Either 'plain' or 'ppm'.

max.results

The maximum number of matches to return.

description

A character vector of words or expressions to search for inside description field. The words will be searched in order. A match will be made only if all words are inside the description field.

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
x

Either a data frame or a numeric vector containing the M/Z values.

mz.tol

The tolerance on the M/Z values.

ms.mode

The MS mode. Set it to either 'neg' or 'pos'.

mz.tol.unit

The type of the M/Z tolerance. Set it to either to 'ppm' or 'plain'.

mass.field

The mass field to use for matching M/Z values. One of: 'monoisotopic.mass', 'molecular.mass', 'average.mass', 'nominal.mass'.

max.results

If set, it is used to limit the number of matches found for each M/Z value. To get all the matches, set this parameter to NA_integer_. Default value is 3.

mz.col

The name of the column where to find M/Z values in case x is a data frame.

fields

A character vector containing the additional entry fields you would like to get for each matched entry. Each field will be output in a different column.

prefix

A prefix that will be inserted before the name of each added column in the output. By default it will be set to the name of the database followed by a dot.

insert.input.values

Insert input values at the beginning of the result data frame.

fieldsLimit

The maximum of values to output for fields with multiple values. Set it to 0 to get all values.

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
deleteVolatile

If TRUE deletes also all entries from the volatile cache (memory cache).

Returns

Nothing.

Method deleteWholePersistentCache()

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

Usage
BiodbConn$deleteWholePersistentCache(deleteVolatile = TRUE)
Arguments
deleteVolatile

If TRUE deletes also all entries from the volatile cache (memory cache).

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
id

A character vector of entry IDs from the connector's database.

db

Another database connector.

oid

A entry ID from database db.

any

If set to TRUE, returns a single logical value: TRUE if any entry contains a reference to oid, FALSE otherwise.

recurse

If set to TRUE, the algorithm will follow all references to entries from other databases, to see if it can establish an indirect link to oid.

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 BiodbRequest instance using the passed parameters, and set ifself as the associated connector.

Usage
BiodbConn$makeRequest(...)
Arguments
...

Those parameters are passed to the initializer of BiodbRequest.

Returns

The BiodbRequest 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
entry.id

A character vector containing entry IDs.

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
entry.id

A character vector with the IDs of entries to retrieve.

Returns

A list of BiodbUrl 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
ids

A character vector of entry identifiers (i.e.: accession numbers). Used to restrict the set of entries on which to run the algorithm.

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
field

The field to use for matching.

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
ms.mode

The MS mode. Set it to either 'neg' or 'pos' to limit the output to one mode.

max.results

If set, it is used to limit the size of the output.

precursor

If set to TRUE, then restrict the search to precursor peaks.

ms.level

The MS level to which you want to restrict your search. 0 means that you want to search in all levels.

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
mode

The MS mode. Set it to either 'neg' or 'pos' to limit the counting to one mode.

ids

A character vector of entry identifiers (i.e.: accession numbers). Used to restrict the set of entries on which to run the algorithm.

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
entry.ids

A character vector of entry IDs.

rt

A vector of retention times to match. Used if input.df is not set. Unit is specified by rt.unit parameter.

rt.unit

The unit for submitted retention times. Either 's' or 'min'.

rt.tol

The plain tolerance (in seconds) for retention times: input.rt

  • rt.tol <= database.rt <= input.rt + rt.tol.

rt.tol.exp

A special exponent tolerance for retention times: input.rt

  • input.rt ** rt.tol.exp <= database.rt <= input.rt + input.rt ** rt.tol.exp. This exponent is applied on the RT value in seconds. If both rt.tol and rt.tol.exp are set, the inequality expression becomes input.rt - rt.tol - input.rt ** rt.tol.exp <= database.rt <= input.rt + rt.tol + input.rt ** rt.tol.exp.

chrom.col.ids

IDs of chromatographic columns on which to match the retention time.

match.rt

If set to TRUE, filters on RT values, otherwise does not do any filtering.

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
mz.min

A vector of minimum M/Z values.

mz.max

A vector of maximum M/Z values. Its length must be the same as mz.min.

mz

A vector of M/Z values.

mz.tol

The M/Z tolerance, whose unit is defined by mz.tol.unit.

mz.tol.unit

The type of the M/Z tolerance. Set it to either to 'ppm' or 'plain'.

rt

A vector of retention times to match. Used if input.df is not set. Unit is specified by rt.unit parameter.

rt.unit

The unit for submitted retention times. Either 's' or 'min'.

rt.tol

The plain tolerance (in seconds) for retention times: input.rt

  • rt.tol <= database.rt <= input.rt + rt.tol.

rt.tol.exp

A special exponent tolerance for retention times: input.rt

  • input.rt ** rt.tol.exp <= database.rt <= input.rt + input.rt ** rt.tol.exp. This exponent is applied on the RT value in seconds. If both rt.tol and rt.tol.exp are set, the inequality expression becomes input.rt - rt.tol - input.rt ** rt.tol.exp <= database.rt <= input.rt + rt.tol + input.rt ** rt.tol.exp.

chrom.col.ids

IDs of chromatographic columns on which to match the retention time.

precursor

If set to TRUE, then restrict the search to precursor peaks.

min.rel.int

The minimum relative intensity, in percentage (i.e.: float number between 0 and 100).

ms.mode

The MS mode. Set it to either 'neg' or 'pos'.

max.results

If set, it is used to limit the number of matches found for each M/Z value.

ms.level

The MS level to which you want to restrict your search. 0 means that you want to search in all levels.

include.ids

A list of IDs to which to restrict the final results. All IDs that are not in this list will be excluded.

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
mz.min

A vector of minimum M/Z values.

mz.max

A vector of maximum M/Z values. Its length must be the same as mz.min.

mz

A vector of M/Z values.

mz.tol

The M/Z tolerance, whose unit is defined by mz.tol.unit.

mz.tol.unit

The type of the M/Z tolerance. Set it to either to 'ppm' or 'plain'.

rt

A vector of retention times to match. Used if input.df is not set. Unit is specified by rt.unit parameter.

rt.unit

The unit for submitted retention times. Either 's' or 'min'.

rt.tol

The plain tolerance (in seconds) for retention times: input.rt

  • rt.tol <= database.rt <= input.rt + rt.tol.

rt.tol.exp

A special exponent tolerance for retention times: input.rt

  • input.rt ** rt.tol.exp <= database.rt <= input.rt + input.rt ** rt.tol.exp. This exponent is applied on the RT value in seconds. If both rt.tol and rt.tol.exp are set, the inequality expression becomes input.rt - rt.tol - input.rt ** rt.tol.exp <= database.rt <= input.rt + rt.tol + input.rt ** rt.tol.exp.

chrom.col.ids

IDs of chromatographic columns on which to match the retention time.

precursor

If set to TRUE, then restrict the search to precursor peaks.

min.rel.int

The minimum relative intensity, in percentage (i.e.: float number between 0 and 100).

ms.mode

The MS mode. Set it to either 'neg' or 'pos'.

max.results

If set, it is used to limit the number of matches found for each M/Z value.

ms.level

The MS level to which you want to restrict your search. 0 means that you want to search in all levels.

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
input.df

A data frame taken as input for searchMsPeaks(). It must contain a columns 'mz', and optionaly an 'rt' column.

mz

A vector of M/Z values to match. Used if input.df is not set.

mz.tol

The M/Z tolerance, whose unit is defined by mz.tol.unit.

mz.tol.unit

The type of the M/Z tolerance. Set it to either to 'ppm' or 'plain'.

min.rel.int

The minimum relative intensity, in percentage (i.e.: float number between 0 and 100).

ms.mode

The MS mode. Set it to either 'neg' or 'pos'.

ms.level

The MS level to which you want to restrict your search. 0 means that you want to search in all levels.

max.results

If set, it is used to limit the number of matches found for each M/Z value.

chrom.col.ids

IDs of chromatographic columns on which to match the retention time.

rt

A vector of retention times to match. Used if input.df is not set. Unit is specified by rt.unit parameter.

rt.unit

The unit for submitted retention times. Either 's' or 'min'.

rt.tol

The plain tolerance (in seconds) for retention times: input.rt

  • rt.tol <= database.rt <= input.rt + rt.tol.

rt.tol.exp

A special exponent tolerance for retention times: input.rt

  • input.rt ** rt.tol.exp <= database.rt <= input.rt + input.rt ** rt.tol.exp. This exponent is applied on the RT value in seconds. If both rt.tol and rt.tol.exp are set, the inequality expression becomes input.rt - rt.tol - input.rt ** rt.tol.exp <= database.rt <= input.rt + rt.tol + input.rt ** rt.tol.exp.

precursor

If set to TRUE, then restrict the search to precursor peaks.

precursor.rt.tol

The RT tolerance used when matching the precursor.

insert.input.values

Insert input values at the beginning of the result data frame.

prefix

Add prefix on column names of result data frame.

compute

If set to TRUE, use the computed values when converting found entries to data frame.

fields

A character vector of field names to output. The data frame output will be restricted to this list of fields.

fieldsLimit

The maximum of values to output for fields with multiple values. Set it to 0 to get all values.

input.df.colnames

Names of the columns in the input data frame.

match.rt

If set to TRUE, match also RT values.

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
spectrum

A template spectrum to match inside the database.

precursor.mz

The M/Z value of the precursor peak of the mass spectrum.

mz.tol

The M/Z tolerance, whose unit is defined by mz.tol.unit.

mz.tol.unit

The type of the M/Z tolerance. Set it to either to 'ppm' or 'plain'.

ms.mode

The MS mode. Set it to either 'neg' or 'pos'.

npmin

The minimum number of peak to detect a match (2 is recommended).

dist.fun

The distance function used to compute the distance betweem two mass spectra.

msms.mz.tol

M/Z tolerance to apply while matching MSMS spectra. In PPM.

msms.mz.tol.min

Minimum of the M/Z tolerance (plain unit). If the M/Z tolerance computed with msms.mz.tol is lower than msms.mz.tol.min, then msms.mz.tol.min will be used.

max.results

If set, it is used to limit the number of matches found for each M/Z value.

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
results.df

Results data frame.

mz.col

The name of the M/Z column in the results data frame.

rt.col

The name of the RT column in the results data frame.

sep

The separator used to concatenate values, when collapsing results data frame.

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
mz.min

A vector of minimum M/Z values.

mz.max

A vector of maximum M/Z values. Its length must be the same as mz.min.

min.rel.int

The minimum relative intensity, in percentage (i.e.: float number between 0 and 100).

ms.mode

The MS mode. Set it to either 'neg' or 'pos'.

max.results

If set, it is used to limit the number of matches found for each M/Z value.

precursor

If set to TRUE, then restrict the search to precursor peaks.

ms.level

The MS level to which you want to restrict your search. 0 means that you want to search in all levels.

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
mz

A vector of M/Z values.

mz.tol

The M/Z tolerance, whose unit is defined by mz.tol.unit.

mz.tol.unit

The type of the M/Z tolerance. Set it to either to 'ppm' or 'plain'.

min.rel.int

The minimum relative intensity, in percentage (i.e.: float number between 0 and 100).

ms.mode

The MS mode. Set it to either 'neg' or 'pos'.

max.results

If set, it is used to limit the number of matches found for each M/Z value.

precursor

If set to TRUE, then restrict the search to precursor peaks.

ms.level

The MS level to which you want to restrict your search. 0 means that you want to search in all levels.

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
deep

Whether to make a deep clone.

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()

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

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

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
other

Another BiodbConnBase instance as a model from which to copy property values.

db.class

The class of the connector (i.e.: "mass.csv.file").

properties

Some new values for the properties.

cfg

The BiodbConfig instance from which will be taken some property values.

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
name

The name of the property to check.

Returns

Returns true if the property name exists.

Method getPropSlots()

Gets the slot fields of a property.

Usage
BiodbConnBase$getPropSlots(name)
Arguments
name

The name of a property.

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
name

The name of a property.

slot

The slot name to check.

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
name

The name of a property.

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
name

The name of a property.

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
name

The name of a property.

slot

The slot name inside the property.

hook

If set to TRUE, enables the calls to hook methods associated with the property. Otherwise, all calls to hook methods are disabled.

Returns

The value of the slot slot of the property name.

Method updatePropertiesDefinition()

Update the definition of properties.

Usage
BiodbConnBase$updatePropertiesDefinition(def)
Arguments
def

A named list of property definitions. The names of the list must be the property names.

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
name

The name of the property.

hook

If set to TRUE, enables the calls to hook methods associated with the property. Otherwise, all calls to hook methods are disabled.

Returns

The value of the property.

Method setPropertyValue()

Sets the value of a property.

Usage
BiodbConnBase$setPropertyValue(name, value)
Arguments
name

The name of the property.

value

The new value to set the property to.

Returns

Nothing.

Method setPropValSlot()

Set the value of the slot of a property.

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

The name of the property.

slot

The name of the property's slot.

value

The new value to set the property's slot to.

hook

If set to TRUE, enables the calls to hook methods associated with the property. Otherwise, all calls to hook methods are disabled.

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
url

A URL as a character value.

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
ws.url

A URL as a character value.

Returns

Nothing.

Method getToken()

Returns the access token.

Usage
BiodbConnBase$getToken()

Method setToken()

Sets the access token.

Usage
BiodbConnBase$setToken(token)
Arguments
token

The token to use to access the database, as a character value.

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
n

The N parameter as a whole number.

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
t

The T parameter as a whole number.

Returns

Nothing.

Method getUrls()

Returns the URLs.

Usage
BiodbConnBase$getUrls()

Method getUrl()

Returns a URL.

Usage
BiodbConnBase$getUrl(name)
Arguments
name

The name of the URL to retrieve.

Returns

The URL as a character value.

Method setUrl()

Sets a URL.

Usage
BiodbConnBase$setUrl(name, url)
Arguments
name

The name of the URL to set.

url

The URL value.

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
deep

Whether to make a deep clone.

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()

Entry class for content in CSV format.

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

Inherited methods

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
sep

The separator to use in CSV files.

na.strings

The strings to recognize as NA values. This is a character vector.

quotes

The characters to recognize as quotes. This is a single character value.

...

The remaining arguments will be passed to the super class initializer.

Returns

Nothing.

Method clone()

The objects of this class are cloneable with this method.

Usage
BiodbCsvEntry$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

See Also

Super class BiodbEntry.

Examples

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

A biodb custom persistent cache implementation.

Description

Inside the cache folder, one folder is created for each cache ID (each remote database has one single cache ID, always the same ,except if you change its URL). In each of theses folders are stored the cache files for this database.

Super class

biodb::BiodbPersistentCache -> BiodbCustomPersistentCache

Methods

Public methods

Inherited methods

Method clone()

The objects of this class are cloneable with this method.

Usage
BiodbCustomPersistentCache$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

See Also

BiodbPersistentCache, BiodbBiocPersistentCache.

A class for describing the characteristics of a database.

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

Inherited methods

Method clone()

The objects of this class are cloneable with this method.

Usage
BiodbDbInfo$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

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()

A class for describing the available databases.

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

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
cfg

The BiodbConfig instance.

Returns

Nothing.

Method define()

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

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

A named list of database definitions. The names of the list will be the IDs of the databases.

package

The package to which belong the new definitions.

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
db.id

A database ID, as a character string.

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
db.id

A character vector of database IDs.

Returns

Nothing.

Method get()

Gets information on a database.

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

Database IDs, as a character vector. If set to NULL, informations on all databases will be returned.

drop

If TRUE and only one database ID has been submitted, returns a single BiodbDbInfo instance instead of a list.

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
deep

Whether to make a deep clone.

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()

The mother abstract class of all database entry classes.

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

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
parent

A valid BiodbConn instance.

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
db.class

The database class (the Biodb database ID) of the clone. By setting this parameter, you can specify a different database for the clone, so you may clone an entry into another database if you wish. By default the class of the clone will be the same as the original entry.

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
field

The name of a field.

value

The value to set.

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
field

The name of a field.

value

The value to append.

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
field

The name of a field.

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
field

The name of a field.

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
field

The name of a field.

compute

If set to TRUE and a field is not defined, try to compute it using internal defined computing rules. If set to FALSE, let the field undefined.

flatten

If set to TRUE and a field's value is a vector of more than one element, then export the field's value as a single string composed of the field's value concatenated and separated by the character defined in the 'multival.field.sep' config key. If set to FALSE or the field contains only one value, changes nothing.

last

If set to TRUE and a field's value is a vector of more than one element, then export only the last value. If set to FALSE, changes nothing.

limit

The maximum number of values to get in case the field contains more than one value.

withNa

If set to TRUE, keep NA values. Otherwise filter out NAs values in vectors.

duplicatedValues

If set to TRUE, keeps duplicated values.

Returns

The value of the field.

Method getFieldsByType()

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

Usage
BiodbEntry$getFieldsByType(type)
Arguments
type

The type of fields to retrieve.

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
only.atomic

If set to TRUE, only export field's values that are atomic

compute

If set to TRUE and a field is not defined, try to compute it using internal defined computing rules. If set to FALSE, let the field undefined.

fields

Set to character vector of field names in order to restrict execution to this set of fields.

fields.type

If set, output all the fields of the specified type.

flatten

If set to TRUE and a field's value is a vector of more than one element, then export the field's value as a single string composed of the field's value concatenated and separated by the character defined in the 'multival.field.sep' config key. If set to FALSE or the field contains only one value, changes nothing.

limit

The maximum number of field values to write into new columns. Used for fields that can contain more than one value.

only.card.one

If set to TRUE, only fields with a cardinality of one will be extracted.

own.id

If set to TRUE includes the database id field named ⁠<database_name>.id⁠ whose values are the same as the accession field.

duplicate.rows

If set to TRUE and merging field values with cardinality greater than one, values will be duplicated.

sort

If set to TRUE sort the order of columns alphabetically, otherwise do not sort.

virtualFields

If set to TRUE includes also virtual fields, otherwise excludes them.

(i.e.

of type vector).

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
compute

If set to TRUE and a field is not defined, try to compute it using internal defined computing rules. If set to FALSE, let the field undefined.

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
content

A character string containing definition for an entry and

obtained

from a database. The format can be CSV, HTML, JSON, XML, or just text.

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
fields

A list of fields to review for computing. By default all fields will be reviewed.

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
db

Another database connector.

oid

A entry ID from database db.

recurse

If set to TRUE, the algorithm will follow all references to entries from other databases, to see if it can establish an indirect link to oid.

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
field

The name of the field.

Returns

The value of the field.

Method setField()

DEPRECATED. Sets the value of a field.

Usage
BiodbEntry$setField(field, value)
Arguments
field

The name of the field.

value

The new value of the field.

Returns

Nothing.

Method getFieldClass()

Gets the class of a field.

Usage
BiodbEntry$getFieldClass(field)
Arguments
field

The name of the field.

Returns

The class of the field.

Method getFieldDef()

Gets the definition of an entry field.

Usage
BiodbEntry$getFieldDef(field)
Arguments
field

The name of the field.

Returns

An object BiodbEntryField which defines the field.

Method getFieldCardinality()

Gets the cardinality of the field.

Usage
BiodbEntry$getFieldCardinality(field)
Arguments
field

The name of the field.

Returns

The cardinality of the field.

Method fieldHasBasicClass()

DEPRECATED. Use BiodbEntryField::isVector() instead.

Usage
BiodbEntry$fieldHasBasicClass(field)
Arguments
field

The name of the field.

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
deep

Whether to make a deep clone.

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()

A class for describing an entry field.

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

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
parent

The BiodbEntryFields parent instance.

name

The field name.

alias

The field aliases as a character vector.

type

The field type.

class

The field class.

card

The field cardinality.

forbids.duplicates

Set to TRUE to forbid duplicated values.

description

The field description.

allowed.values

Restrict possible values to a set of allowed values.

lower.case

All values will be converted to lower case.

case.insensitive

Comparison will be made case insensitive for this field.

computable.from

A list of databases from which to compute automatically the value of this field.

virtual

Set to TRUE if this field is virtual.

virtual.group.by.type

In case of a virtual field, set the type of fields to group together into a data frame.

dataFrameGroup

The data frame group.

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
type

The type.

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
alias

The name of a valid alias.

Returns

Nothing.

Method removeAlias()

Removes an alias from the list of aliases.

Usage
BiodbEntryField$removeAlias(alias)
Arguments
alias

The name of a valid alias.

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
directive

A valid \"computable from\" directive.

Returns

Nothing.

Method removeComputableFrom()

Removes a directive from the list of computableFrom.

Usage
BiodbEntryField$removeComputableFrom(directive)
Arguments
directive

A valid \"computable from\" directive.

Returns

Nothing.

Method correctValue()

Corrects a value so it is compatible with this field.

Usage
BiodbEntryField$correctValue(value)
Arguments
value

A value.

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
value

If this parameter is set to particular allowed values, then the method returns a list of synonyms for this value (if any).

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
key

The key associated with the value (i.e.: the key is the main name of an allowed value).

value

The new value to add.

Returns

Nothing.

Method checkValue()

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

Usage
BiodbEntryField$checkValue(value)
Arguments
value

The value to check.

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
other

Another BiodbEntryField instance.

fail

If set to TRUE, then throws error instead of returning FALSE.

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
other

Another BiodbEntryField instance.

are

'alias' and 'computable.from'. No values will be removed from those vectors. The new values will only be appended. This allows to extend an existing field inside a new connector definition.

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
deep

Whether to make a deep clone.

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()

A class for handling description of all entry fields.

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

Method new()

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

Usage
BiodbEntryFields$new(parent)
Arguments
parent

The BiodbMain instance.

Returns

Nothing.

Method notifyCfgUpdate()

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

Usage
BiodbEntryFields$notifyCfgUpdate(k, v)
Arguments
k

The config key name.

v

The value associated with the key.

Returns

Nothing.

Method isAlias()

Tests if names are aliases.

Usage
BiodbEntryFields$isAlias(name)
Arguments
name

A character vector of names or aliases to test.

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
name

A character vector of names or aliases to test.

Returns

A character vector of formatted names.

Method isDefined()

Tests if names are defined fields.

Usage
BiodbEntryFields$isDefined(name)
Arguments
name

A character vector of names or aliases to test.

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
name

A character vector of names or aliases to test.

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
name

A character vector of names or aliases.

fail

Fails if name is unknown.

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
name

A character vector of names or aliases.

drop

If TRUE and only one name has been submitted, returns a single BiodbEntryField instance instead of a list.

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
type

Set this parameter to a character vector in order to return only the names of the fields corresponding to the types specified.

computable

If set to TRUE, returns only the names of computable fields. If set to FALSE, returns only the names of fields that are not computable.

Returns

A character vector containing all selected field names.

Method getDatabaseIdField()

Gets a database ID field.

Usage
BiodbEntryFields$getDatabaseIdField(database)
Arguments
database

The name (i.e.: Biodb ID) of a database.

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
def

A named list of field definitions. The names of the list are the main names of the fields.

Returns

Nothing.

Method terminate()

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

Usage
BiodbEntryFields$terminate()
Arguments
BiodbMain

:terminate().

Returns

Nothing.

Method clone()

The objects of this class are cloneable with this method.

Usage
BiodbEntryFields$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

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()

A class for constructing biodb objects.

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

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
bdb

The BiodbMain instance.

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
db.class

The type of a database. The list of types can be obtained from the class BiodbDbsInfo.

url

An URL to the database for which to create a connection. Each database connector is configured with a default URL, but some allow you to change it.

token

A security access token for the database. Some database require such a token for all or some of their webservices. Usually you obtain the token through your account on the database website.

fail.if.exists

If set to TRUE, the method will fail if a connector for

get.existing.conn

This argument will be used only if fail.if.exists is set to FALSE and an identical connector already exists. If it set to TRUE, the existing connector instance will be returned, otherwise NULL will be returned.

conn.id

If set, this identifier will be used for the new connector. An error will be raised in case another connector already exists with this identifier.

cache.id

If set, this ID will be used as the cache ID for the new connector. An error will be raised in case another connector already exists with this cache identifier.

Returns

An instance of the requested connector class.

Method connExists()

Tests if a connector exists.

Usage
BiodbFactory$connExists(conn.id)
Arguments
conn.id

A connector ID.

Returns

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

Method deleteConn()

Deletes an existing connector.

Usage
BiodbFactory$deleteConn(conn)
Arguments
conn

A connector instance or a connector ID.

Returns

Nothing.

Method deleteConnByClass()

Deletes all existing connectors from a same class.

Usage
BiodbFactory$deleteConnByClass(db.class)
Arguments
db.class

The type of a database. All connectors of this database type will be deleted.

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
conn.id

An existing connector ID.

class

If set to TRUE, and \"conn.id\" does not correspond to any instantiated connector, then interpret \"conn.id\" as a database class and looks for the first instantiated connector of that class.

create

If set to TRUE, and \"class\" is also set to TRUE, and no suitable instantiated connector was found, then creates a new connector instance of the class specified by \"conn.id\".

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
conn.id

An existing connector ID.

id

A character vector containing database entry IDs (accession numbers).

drop

If set to TRUE and the list of entries contains only one element, then returns this element instead of the list. If set to FALSE, then returns always a list.

no.null

Set to TRUE to remove NULL entries.

limit

Set to a positive value to limit the number of entries returned.

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
db.class

A database ID.

Returns

A new BiodbEntry object.

Method createEntryFromContent()

Creates an entry instance from a content.

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

A valid BiodbConn identifier.

content

A list or character vector of contents to parse to create the entries.

drop

If set to TRUE

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
conn.id

A connector ID.

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
conn.id

A connector ID.

Returns

Nothing.

Method deleteAllCacheEntries()

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

Usage
BiodbFactory$deleteAllCacheEntries(conn.id)
Arguments
conn.id

A connector ID.

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
deep

Whether to make a deep clone.

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()

Entry class for content in HTML format.

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

Inherited methods

Method new()

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

Usage
BiodbHtmlEntry$new(...)
Arguments
...

All parameters are passed to the super class initializer.

Returns

Nothing.

Method clone()

The objects of this class are cloneable with this method.

Usage
BiodbHtmlEntry$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

See Also

Super class BiodbXmlEntry.

Examples

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

Entry class for content in JSON format.

Description

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

Super class

biodb::BiodbEntry -> BiodbJsonEntry

Methods

Public methods

Inherited methods

Method clone()

The objects of this class are cloneable with this method.

Usage
BiodbJsonEntry$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

See Also

Super class BiodbEntry.

Examples

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

Entry class for content in list format.

Description

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

Super class

biodb::BiodbEntry -> BiodbListEntry

Methods

Public methods

Inherited methods

Method clone()

The objects of this class are cloneable with this method.

Usage
BiodbListEntry$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

See Also

Super class BiodbEntry.

Examples

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

The central class of the biodb package.

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, BiodbPersistentCache, BiodbConfig, ...) are instantiated (just once) and their instances are later accessible through get*() methods.

Methods

Public methods

Method new()

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

Usage
BiodbMain$new(autoloadExtraPkgs = NULL)
Arguments
autoloadExtraPkgs

Set to TRUE to allow automatic loading of extension packages. Set to FALSE to forbid it. If left to NULL, the default, autoload.extra.pkgs configuration value will be used.

Returns

Nothing.

Method terminate()

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

Usage
BiodbMain$terminate()
Returns

Nothing.

Method loadDefinitions()

Loads databases and entry fields definitions from YAML file.

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

The path to a YAML file containing definitions for \codeBiodbMain (databases, fields or configuration keys).

package

The package to which belong the new definitions.

Returns

Nothing.

Method getConfig()

Returns the single instance of the \codeBiodbConfig class.

Usage
BiodbMain$getConfig()
Returns

The instance of the \codeBiodbConfig 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 \codeBiodbDbsInfo class.

Usage
BiodbMain$getDbsInfo()
Returns

The instance of the \codeBiodbDbsInfo class attached to this BiodbMain instance.

Method getEntryFields()

Returns the single instance of the \codeBiodbEntryFields class.

Usage
BiodbMain$getEntryFields()
Returns

The instance of the \codeBiodbEntryFields class attached to this BiodbMain instance.

Method getFactory()

Returns the single instance of the \codeBiodbFactory class.

Usage
BiodbMain$getFactory()
Returns

The instance of the \codeBiodbFactory class attached to this BiodbMain instance.

Method getRequestScheduler()

Returns the single instance of the \codeBiodbRequestScheduler class.

Usage
BiodbMain$getRequestScheduler()
Returns

The instance of the \codeBiodbRequestScheduler 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
observers

Either an object or a list of objects.

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
entry.id.field

The name of an ID field. It must end with \".id\".

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
entries

A list of \codeBiodbEntry instances.

field

The name of a field.

flatten

If set to \codeTRUE and the field has a cardinality greater than one, then values be converted into a vector of class character in which each entry values are collapsed.

compute

If set to \codeTRUE, computable fields will be output.

limit

The maximum number of values to retrieve for each entry. Set to 0 to get all values.

withNa

If set to TRUE, keep NA values. Otherwise filter out NAs values in vectors.

Returns

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

Method entriesToDataframe()

Converts a list of entries or a list of list of entries (\codeBiodbEntry 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
entries

A list of \codeBiodbEntry instances or a list of list of \codeBiodbEntry instances.

only.atomic

If set to \codeTRUE, output only atomic fields, i.e.: the fields whose value type is one of integer, numeric, logical or character.

null.to.na

If set to \codeTRUE, each \codeNULL entry in the list is converted into a row of NA values.

compute

If set to \codeTRUE, computable fields will be output.

fields

A character vector of field names to output. The data frame output will be restricted to this list of fields.

limit

The maximum number of field values to write into new columns. Used for fields that can contain more than one value. Set it to 0 to get all values.

drop

If set to \codeTRUE and the resulting data frame has only one column, a vector will be output instead of data frame.

sort.cols

Sort columns in alphabetical order.

flatten

If set to \codeTRUE, then each field with a cardinality greater than one, will be converted into a vector of class character whose values are collapsed.

only.card.one

Output only fields whose cardinality is one.

own.id

If set to TRUE includes the database id field named ⁠<database_name>.id⁠ whose values are the same as the accession field.

prefix

Insert a prefix at the start of all field names.

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
ids

A character vector of entry IDs or a list of character vectors of entry IDs.

db

The biodb database name for the entry IDs, or a connector ID, as a sinle character value.

fields

A character vector containing entry fields to add.

limit

The maximum number of field values to write into new columns. Used for fields that can contain more than one value. Set it to 0 to get all values.

prefix

Insert a prefix at the start of all field names.

own.id

If set to TRUE includes the database id field named ⁠<database_name>.id⁠ whose values are the same as the accession field.

A

data frame containing in columns the requested field values, with one entry per line, in the same order than in ids vector.

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
x

A data frame containing at least one column with Biodb entry IDs identified by the parameter id.col.

id.col

The name of the column containing IDs inside the input data frame.

db

The biodb database name for the entry IDs, or a connector ID, as a single character value.

fields

A character vector containing entry fields to add.

limit

The maximum number of field values to write into new columns. Used for fields that can contain more than one value. Set it to 0 to get all values.

prefix

Insert a prefix at the start of all field names.

Returns

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

Method entriesToJson()

Converts a list of \codeBiodbEntry objects into JSON. Returns a vector of characters.

Usage
BiodbMain$entriesToJson(entries, compute = TRUE)
Arguments
entries

A list of \codeBiodbEntry instances. It may contain NULL elements.

compute

If set to \codeTRUE, computable fields will added to JSON too.

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
x

A data frame.

sep

The separator to use when concatenating values in collapsed rows.

cols

The indices or the names of the columns used as reference.

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
entries

A list of BiodbEntry objects.

field

The field for which to extract values.

sortOutput

Set to TRUE to sort the values.

uniq

Set to TRUE to remove duplicates.

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
ids

A list of entry identifiers.

db

The database ID or connector ID where to find the entries.

field

The field for which to extract values.

sortOutput

Set to TRUE to sort the values.

uniq

Set to TRUE to remove duplicates.

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
entries

A list of \codeBiodbEntry instances. It may contain NULL elements.

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
entries

A list of \codeBiodbEntry instances. It may contain NULL elements.

files

A character vector of file paths, the same length as entries list.

compute

If set to \codeTRUE, computable fields will be saved too.

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
conn.from

The connector of the source datababase to copy.

conn.to

The connector of the destination database.

limit

The number of entries of the source database to copy. If set to \codeNULL, copy the whole database.

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 \codeBiodbEntryField :isVector()."

Usage
BiodbMain$fieldIsAtomic(field)
Arguments
field

The name of the field.

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
field

The name of the field.

Returns

The class of the field.

Method clone()

The objects of this class are cloneable with this method.

Usage
BiodbMain$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

See Also

BiodbFactory, BiodbPersistentCache, BiodbConfig, BiodbEntryFields, BiodbDbsInfo.

Examples

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

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

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

The abstract class for handling file caching.

Description

The abstract class for handling file caching.

The abstract class for handling file caching.

Details

This abstract class is the mother class of concrete classes that manage cache systems for saving downloaded files and request results.

It is designed for internal use, but you can still access some of the read-only methods if you wish.

Methods

Public methods

Method new()

New instance initializer. Persistent cache objects must not be created directly. Instead, access the cache instance through the BiodbMain instance using the getPersistentCache() method.

Usage
BiodbPersistentCache$new(cfg, bdb = NULL)
Arguments
cfg

An instance of the BiodbConfig class.

bdb

An instance of the BiodbMain class.

Returns

Nothing.

Method isReadable()

Checks if the cache system is readable.

Usage
BiodbPersistentCache$isReadable(conn = NULL)
Arguments
conn

If not \codeNULL, checks if the cache system is readable for this particular connector.

Returns

\codeTRUE if the cache system is readable, \codeFALSE otherwise.

Method isWritable()

Checks if the cache system is writable.

Usage
BiodbPersistentCache$isWritable(conn = NULL)
Arguments
conn

If not \codeNULL, checks if the cache system is writable for this particular connector.

Returns

\codeTRUE if the cache system is writable, \codeFALSE otherwise.

Method getDir()

Gets the path to the persistent cache folder.

Usage
BiodbPersistentCache$getDir()
Returns

The path to the cache folder as a character value.

Method getFolderPath()

Gets path to the cache system sub-folder dedicated to this cache ID.

Usage
BiodbPersistentCache$getFolderPath(cache.id, create = TRUE, fail = FALSE)
Arguments
cache.id

The cache ID to use.

create

If set to TRUE and the folder does not exist, creates it.

fail

If set to TRUE, throws a warning if the folder does not exist.

Returns

A string containing the path to the folder.

Method folderExists()

Tests if a cache folder exists for this cache ID.

Usage
BiodbPersistentCache$folderExists(cache.id)
Arguments
cache.id

The cache ID to use.

Returns

TRUE if a cache folder exists.

Method getFilePath()

Gets path of file in cache system.

Usage
BiodbPersistentCache$getFilePath(cache.id, name, ext)
Arguments
cache.id

The cache ID to use.

name

A character vector containing file names.

ext

The extension of the files.

Returns

A character vector, the same size as \codenames, containing the paths to the files.

Method filesExist()

Tests if at least one cache file exist for the specified cache ID.

Usage
BiodbPersistentCache$filesExist(cache.id)
Arguments
cache.id

The cache ID to use.

Returns

A single boolean value.

Method fileExist()

DEPRECATED. Use fileExists().

Usage
BiodbPersistentCache$fileExist(cache.id, name, ext)
Arguments
cache.id

The cache ID to use.

name

A character vector containing file names.

ext

The extension of the files, without the dot (\"html\", \"xml\", etc).

Returns

A logical vector, the same size as \codename, with \codeTRUE value if the file exists in the cache, or \codeFALSE otherwise.

Method fileExists()

Tests if a particular file exist in the cache.

Usage
BiodbPersistentCache$fileExists(cache.id, name, ext)
Arguments
cache.id

The cache ID to use.

name

A character vector containing file names.

ext

The extension of the files, without the dot (\"html\", \"xml\", etc).

Returns

A logical vector, the same size as \codename, with \codeTRUE value if the file exists in the cache, or \codeFALSE otherwise.

Method markerExist()

DEPRECATED. Use markerExists().

Usage
BiodbPersistentCache$markerExist(cache.id, name)
Arguments
cache.id

The cache ID to use.

name

A character vector containing marker names.

Returns

A logical vector, the same size as \codename, with \codeTRUE value if the marker file exists in the cache, or \codeFALSE otherwise.

Method markerExists()

Tests if markers exist in the cache. Markers are used, for instance, by biodb to remember that a downloaded zip file from a database has been extracted correctly.

Usage
BiodbPersistentCache$markerExists(cache.id, name)
Arguments
cache.id

The cache ID to use.

name

A character vector containing marker names.

Returns

A logical vector, the same size as \codename, with \codeTRUE value if the marker file exists in the cache, or \codeFALSE otherwise.

Method setMarker()

Sets a marker.

Usage
BiodbPersistentCache$setMarker(cache.id, name)
Arguments
cache.id

The cache ID to use.

name

A character vector containing marker names.

Returns

Nothing.

Method getTmpFolderPath()

Gets path to the cache system temporary folder.

Usage
BiodbPersistentCache$getTmpFolderPath()
Returns

A string containing the path to the folder.

Method getUsedCacheIds()

Returns a list of cache IDs actually used to store cache files.

Usage
BiodbPersistentCache$getUsedCacheIds()
Returns

A character vector containing all the cache IDs actually used inside the cache system.

Method loadFileContent()

Loads content of files from the cache.

Usage
BiodbPersistentCache$loadFileContent(
  cache.id,
  name,
  ext,
  output.vector = FALSE
)
Arguments
cache.id

The cache ID to use.

name

A character vector containing file names.

ext

The extension of the files.

output.vector

If set to \codeTRUE, force output to be a \codevector instead of a \codelist. Where the list contains a \codeNULL, the \codevector will contain an \codeNA value.

Returns

A list (or a vector if \codeoutput.vector is set to \codeTRUE), the same size as \codename, containing the contents of the files. If some file does not exist, a \codeNULL value is inserted inside the list.

Method saveContentToFile()

Saves content to files into the cache.

Usage
BiodbPersistentCache$saveContentToFile(content, cache.id, name, ext)
Arguments
content

A list or a character vector containing the contents of the files. It must have the same length as \codename.

cache.id

The cache ID to use.

name

A character vector containing file names.

ext

The extension of the files.

Returns

Nothing.

Method addFilesToCache()

Adds exisiting files into the cache.

Usage
BiodbPersistentCache$addFilesToCache(
  src.file.paths,
  cache.id,
  name,
  ext,
  action = c("copy", "move")
)
Arguments
src.file.paths

The current paths of the source files, as a character vector.

cache.id

The cache ID to use.

name

A character vector containing file names.

ext

The extension of the files.

action

Specifies if files have to be moved or copied into the cache.

Returns

Nothing.

Method copyFilesIntoCache()

Copies exisiting files into the cache.

Usage
BiodbPersistentCache$copyFilesIntoCache(src.file.paths, cache.id, name, ext)
Arguments
src.file.paths

The current paths of the source files, as a character vector.

cache.id

The cache ID to use.

name

A character vector containing file names.

ext

The extension of the files.

Returns

Nothing.

Method moveFilesIntoCache()

Moves exisiting files into the cache.

Usage
BiodbPersistentCache$moveFilesIntoCache(src.file.paths, cache.id, name, ext)
Arguments
src.file.paths

The current paths of the source files, as a character vector.

cache.id

The cache ID to use.

name

A character vector containing file names.

ext

The extension of the files.

Returns

Nothing.

Method erase()

Erases the whole cache.

Usage
BiodbPersistentCache$erase()
Returns

Nothing.

Method deleteFile()

Deletes a list of files inside the cache system.

Usage
BiodbPersistentCache$deleteFile(cache.id, name, ext)
Arguments
cache.id

The cache ID to use.

name

A character vector containing file names.

ext

The extension of the files, without the dot (\"html\", \"xml\", etc).

Returns

Nothing.

Method deleteAllFiles()

Deletes, in the cache system, all files associated with this cache ID.

Usage
BiodbPersistentCache$deleteAllFiles(cache.id, fail = FALSE, prefix = FALSE)
Arguments
cache.id

The cache ID to use.

fail

If set to TRUE, a warning will be emitted if no cache files exist for this cache ID.

prefix

DEPRECATED If set to TRUE, use cache.id as a prefix, deleting all files whose cache.id starts with this prefix.

Returns

Nothing.

Method deleteFiles()

Deletes all files with the specific extension of the cache ID in the cache system.

Usage
BiodbPersistentCache$deleteFiles(cache.id, ext)
Arguments
cache.id

The cache ID to use.

ext

The extension of the files, without the dot (\"html\", \"xml\", etc). Only files having this extension will be deleted.

Returns

Nothing.

Method listFiles()

Lists files present in the cache system.

Usage
BiodbPersistentCache$listFiles(
  cache.id,
  ext = NULL,
  extract.name = FALSE,
  full.path = FALSE
)
Arguments
cache.id

The cache ID to use.

ext

The extension of the files, without the dot (\"html\", \"xml\", etc).

extract.name

If set to \codeTRUE, instead of returning the file paths, returns the list of names used to construct the file name: [cache_folder]/[cache.id]/[name].[ext].

full.path

If set to \codeTRUE, returns full path for files.

Returns

The files of found files, or the names of the files if \codeextract.name is set to \codeTRUE.

Method print()

Displays information about this object.

Usage
BiodbPersistentCache$print()

Method enabled()

DEPRECATED method. Use now \codeBiodbConfig :isEnabled('cache.system').

Usage
BiodbPersistentCache$enabled()

Method enable()

DEPRECATED method. Use now \codeBiodbConfig :enable('cache.system').

Usage
BiodbPersistentCache$enable()

Method disable()

DEPRECATED method. Use now \codeBiodbConfig :disable('cache.system').

Usage
BiodbPersistentCache$disable()

Method clone()

The objects of this class are cloneable with this method.

Usage
BiodbPersistentCache$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

See Also

BiodbMain, BiodbBiocPersistentCache, BiodbBiocPersistentCache.

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

# Get all entries
entries <- conn$getEntry(conn$getEntryIds())

# Get the cache instance:
cache <- mybiodb$getPersistentCache()

# Get list of files inside the cache:
files <- cache$listFiles(conn$getCacheId())

# Delete files inside the cache:
cache$deleteAllFiles(conn$getCacheId())

# Terminate instance.
mybiodb$terminate()

Class Request.

Description

Class Request.

Class Request.

Details

This class represents a Request object that can be used with the Request Scheduler.

Methods

Public methods

Method new()

Initializer.

Usage
BiodbRequest$new(
  url,
  method = c("get", "post"),
  header = character(),
  body = character(),
  encoding = integer(),
  conn = NULL
)
Arguments
url

A BiodbUrl object.

method

HTTP method. Either "get" or "post".

header

The header.

body

The body.

encoding

The encoding to use.

conn

A valid BiodbConn instance for which this request is built.

Returns

Nothing.

Method setConn()

Sets the associated connector (usually the connector that created this request).

Usage
BiodbRequest$setConn(conn)
Arguments
conn

A valid BiodbConn object.

Returns

Nothing.

Method getConn()

gets the associated connector (usually the connector that created this request).

Usage
BiodbRequest$getConn()
Returns

The associated connector as a BiodbConn object.

Method getUrl()

Gets the URL.

Usage
BiodbRequest$getUrl()
Returns

The URL as a BiodbUrl object.

Method getMethod()

Gets the method.

Usage
BiodbRequest$getMethod()
Returns

The method as a character value.

Method getEncoding()

Gets the encoding.

Usage
BiodbRequest$getEncoding()
Returns

The encoding.

Method getCurlOptions()

Gets the options object to pass to cURL library.

Usage
BiodbRequest$getCurlOptions(useragent)
Arguments
useragent

The user agent as a character value.

Returns

An RCurl options object.

Method getUniqueKey()

Gets a unique key to identify this request. The key is an MD5 sum computed from the string representation of this request.

Usage
BiodbRequest$getUniqueKey()
Returns

A unique key as an MD5 sum.

Method getHeaderAsSingleString()

Gets the HTTP header as a string, concatenating all its information into a single string.

Usage
BiodbRequest$getHeaderAsSingleString()
Returns

The header as a single character value.

Method getBody()

Gets the body.

Usage
BiodbRequest$getBody()
Returns

The body as a character value.

Method print()

Displays information about this instance.

Usage
BiodbRequest$print()
Returns

self as invisible.

Method toString()

Gets a string representation of this instance.

Usage
BiodbRequest$toString()
Returns

A single string giving a representation of this instance.

Method clone()

The objects of this class are cloneable with this method.

Usage
BiodbRequest$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

See Also

BiodbRequestScheduler, BiodbUrl.

Examples

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

# Create a request object
u <- 'https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity'
url <- BiodbUrl$new(url=u)
url$setParam('chebiId', 15440)
request <- BiodbRequest$new(method='get', url=url)

# Send request
mybiodb$getRequestScheduler()$sendRequest(request)

# Terminate instance.
mybiodb$terminate()

Class for handling requests.

Description

Class for handling requests.

Class for handling requests.

Details

This class handles GET and POST requests, as well as file downloading. Each remote database connection instance creates an instance of BiodbRequestScheduler for handling database connection. A timer is used to schedule connections, and avoid sending too much requests to the database. This class is not meant to be used directly by the library user. See section Fields for a list of the constructor's parameters.

Methods

Public methods

Method new()

New instance initializer. BiodbRequestScheduler class must not be instantiated direrctly. Instead, use the getRequestScheduler() method from BiodbMain.

Usage
BiodbRequestScheduler$new(bdb)
Arguments
bdb

The BiodbMain instance.

Returns

Nothing.

Method sendSoapRequest()

Sends a SOAP request to a URL. Returns the string result.

Usage
BiodbRequestScheduler$sendSoapRequest(
  url,
  soap.request,
  soap.action = NA_character_,
  encoding = integer()
)
Arguments
url

The URL to access, as a character string.

soap.request

The XML SOAP request to send, as a character string.

soap.action

The SOAP action to contact, as a character string.

encoding

The encoding to use.

Returns

The results returned by the contacted server, as a single string value.

Method sendRequest()

Sends a request, and returns content result.

Usage
BiodbRequestScheduler$sendRequest(request, cache.read = TRUE)
Arguments
request

A BiodbRequest instance.

cache.read

If set to TRUE, the cache system will be used. In case the same request has already been run and its results saved into the cache, then the request is not run again, the targeted server not contacted, and the results are directly loaded from the cache system.

Returns

The results returned by the contacted server, as a single string value.

Method downloadFile()

Downloads the content of a URL and save it into the specified destination file.

Usage
BiodbRequestScheduler$downloadFile(url, dest.file)
Arguments
url

The URL to access, as a BiodbUrl object.

dest.file

A path to a destination file.

Returns

Nothing.

Method notifyConnUrlsUpdated()

Call back function called when connector URLs are changed.

Usage
BiodbRequestScheduler$notifyConnUrlsUpdated(conn)
Arguments
conn

The connector instance for which the URLs were changed.

Returns

Nothing.

Method notifyConnSchedulerFrequencyUpdated()

Call back function called when connector T and N parameters (frequency) are changed.

Usage
BiodbRequestScheduler$notifyConnSchedulerFrequencyUpdated(conn)
Arguments
conn

The connector instance for which the frequency were changed.

Returns

Nothing.

Method getUrlString()

Builds a URL object, using a base URL and parameters to be passed.

Usage
BiodbRequestScheduler$getUrlString(url, params = list())
Arguments
url

A URL string.

params

A list of URL parameters.

Returns

A BiodUrl object.

Method getUrl()

Sends a request and get the result.

Usage
BiodbRequestScheduler$getUrl(
  url,
  params = list(),
  method = c("get", "post"),
  header = character(),
  body = character(),
  encoding = integer()
)
Arguments
url

A URL string.

params

A list of URL parameters.

method

The method to use. Either 'get' or 'post'.

header

The header to send.

body

The body to send.

encoding

The encoding to use.

Returns

The results of the request.

Method findRule()

Searches for a rule by host name.

Usage
BiodbRequestScheduler$findRule(url, create = TRUE)
Arguments
url

The host URL.

create

Sets to TRUE to create a rule when none exists.

Returns

A BiodbRequestSchedulerRule object.

Method getConnectorRules()

Gets the rules associates with a connector.

Usage
BiodbRequestScheduler$getConnectorRules(conn)
Arguments
conn

A valid connector object.

Returns

A list of rules.

Method registerConnector()

Registers a new connector with the scheduler.

Usage
BiodbRequestScheduler$registerConnector(conn)
Arguments
conn

A valid connector object.

Returns

Nothing.

Method unregisterConnector()

Unregisters a connector from this scheduler.

Usage
BiodbRequestScheduler$unregisterConnector(conn)
Arguments
conn

A valid connector object.

Returns

Nothing.

Method getAllRules()

Gets all defined rules.

Usage
BiodbRequestScheduler$getAllRules()
Returns

The list of all rules.

Method clone()

The objects of this class are cloneable with this method.

Usage
BiodbRequestScheduler$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

See Also

BiodbRequestSchedulerRule.

Examples

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

# Get the scheduler
sched <- mybiodb$getRequestScheduler()

# Create a request object
u <- 'https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity'
url <- BiodbUrl$new(url=u)
url$setParam('chebiId', 15440)
request <- BiodbRequest$new(method='get', url=url)

# Send request
sched$sendRequest(request)

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

Scheduler rule class.

Description

Scheduler rule class.

Scheduler rule class.

Details

This class represents a rule for the request scheduler.

Methods

Public methods

Method new()

Initializer.

Usage
BiodbRequestSchedulerRule$new(host, conn = NULL)
Arguments
host

The web host for which this rules is applicable.

conn

The connector instance that is concerned by this rule.

Returns

Nothing.

Method getHost()

Gets host.

Usage
BiodbRequestSchedulerRule$getHost()
Returns

Returns the host.

Method getN()

Gets N value. The number of connections allowed during a period of T seconds.

Usage
BiodbRequestSchedulerRule$getN()
Returns

Returns N as an integer.

Method getT()

Gets T value. The number of seconds during which N connections are allowed.

Usage
BiodbRequestSchedulerRule$getT()
Returns

Returns T as a numeric.

Method setFrequency()

Sets both N and T.

Usage
BiodbRequestSchedulerRule$setFrequency(n, t)
Arguments
n

The number of connections allowed during a period of t seconds, as an integer.

t

The number of seconds during which n connections are allowed, as a numeric value.

Returns

Nothing.

Method getConnectors()

Gets connectors associaated with this rule.

Usage
BiodbRequestSchedulerRule$getConnectors()
Returns

A list of BiodbConn objects.

Method addConnector()

Associate a connector with this rule.

Usage
BiodbRequestSchedulerRule$addConnector(conn)
Arguments
conn

A BiodbConn object.

Returns

Nothing.

Method removeConnector()

Disassociate a connector from this rule.

Usage
BiodbRequestSchedulerRule$removeConnector(conn)
Arguments
conn

A BiodbConn instance.

Returns

Nothing.

Method print()

Displays information about this instance.

Usage
BiodbRequestSchedulerRule$print()
Returns

Nothing.

Method waitAsNeeded()

Wait (sleep) until a new request is allowed.

Usage
BiodbRequestSchedulerRule$waitAsNeeded()
Returns

Nothing.

Method recomputeFrequency()

Recompute frequency from submitted N and T values.

Usage
BiodbRequestSchedulerRule$recomputeFrequency()
Returns

Nothing.

Method computeSleepTime()

Compute the needed sleep time to wait until a new request is allowed, starting from the submitted time.

Usage
BiodbRequestSchedulerRule$computeSleepTime(cur.time = Sys.time())
Arguments
cur.time

Time from which to compute needed sleep time.

Returns

The needed sleep time in seconds.

Method storeCurrentTime()

Stores the current time.

Usage
BiodbRequestSchedulerRule$storeCurrentTime(cur.time = Sys.time())
Arguments
cur.time

The current time.

Returns

Nothing.

Method clone()

The objects of this class are cloneable with this method.

Usage
BiodbRequestSchedulerRule$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

See Also

BiodbRequestScheduler.

Entry class for content in SDF format.

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

Inherited methods

Method new()

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

Usage
BiodbSdfEntry$new(...)
Arguments
...

All parameters are passed to the super class initializer.

Returns

Nothing.

Method clone()

The objects of this class are cloneable with this method.

Usage
BiodbSdfEntry$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

See Also

Super class BiodbTxtEntry.

Examples

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

This class represents an SQL binary operator.

Description

This class represents an SQL binary operator.

This class represents an SQL binary operator.

Super class

biodb::BiodbSqlExpr -> BiodbSqlBinaryOp

Methods

Public methods

Method new()

Initializer.

Usage
BiodbSqlBinaryOp$new(lexpr, op, rexpr)
Arguments
lexpr

A BiodbSqlExpr instance for the left part.

op

The binary operator, as a string.

rexpr

A BiodbSqlExpr instance for the right part.

Returns

Nothing.

Method toString()

Converts into a string.

Usage
BiodbSqlBinaryOp$toString()
Returns

A string containing the SQL expression.

Method clone()

The objects of this class are cloneable with this method.

Usage
BiodbSqlBinaryOp$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

The SQL Expression abstact class.

Description

The SQL Expression abstact class.

The SQL Expression abstact class.

Details

This abstract class represents an SQL expression.

Methods

Public methods

Method toString()

Converts into a string.

Usage
BiodbSqlExpr$toString()
Returns

A string containing the SQL expression.

Method clone()

The objects of this class are cloneable with this method.

Usage
BiodbSqlExpr$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

This class represents an SQL field.

Description

This class represents an SQL field.

This class represents an SQL field.

Super class

biodb::BiodbSqlExpr -> BiodbSqlField

Methods

Public methods

Method new()

Initializer.

Usage
BiodbSqlField$new(table = NA_character_, field)
Arguments
table

The table name.

field

The field name.

Returns

Nothing.

Method toString()

Converts into a string.

Usage
BiodbSqlField$toString()
Returns

A string containing the SQL expression.

Method clone()

The objects of this class are cloneable with this method.

Usage
BiodbSqlField$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

This class represents an SQL list.

Description

This class represents an SQL list.

This class represents an SQL list.

Super class

biodb::BiodbSqlExpr -> BiodbSqlList

Methods

Public methods

Method new()

Initializer.

Usage
BiodbSqlList$new(values)
Arguments
values

The values of the list.

Returns

Nothing.

Method toString()

Converts into a string.

Usage
BiodbSqlList$toString()
Returns

A string containing the SQL expression.

Method clone()

The objects of this class are cloneable with this method.

Usage
BiodbSqlList$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

This class represents an SQL logical operator.

Description

This class represents an SQL logical operator.

This class represents an SQL logical operator.

Super class

biodb::BiodbSqlExpr -> BiodbSqlLogicalOp

Methods

Public methods

Method new()

Initializer.

Usage
BiodbSqlLogicalOp$new(op)
Arguments
op

The logical operator, as a string.

Returns

Nothing.

Method addExpr()

Add an SQL expression to the logical operator.

Usage
BiodbSqlLogicalOp$addExpr(expr)
Arguments
expr

A BiodbSqlExpr instance.

Returns

Nothing.

Method toString()

Converts into a string.

Usage
BiodbSqlLogicalOp$toString()
Returns

A string containing the SQL expression.

Method clone()

The objects of this class are cloneable with this method.

Usage
BiodbSqlLogicalOp$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

This class handles an SQL Query.

Description

This class handles an SQL Query.

This class handles an SQL Query.

Details

This class represents an SQL query. It is used internally to generate an SQL query string.

Methods

Public methods

Method new()

Initializer.

Usage
BiodbSqlQuery$new()
Returns

Nothing.

Method setTable()

Set the table.

Usage
BiodbSqlQuery$setTable(table)
Arguments
table

The table name.

Returns

Nothing.

Method addField()

Set the fields.

Usage
BiodbSqlQuery$addField(table = NULL, field)
Arguments
table

The table name.

field

A field name.

Returns

Nothing.

Method setDistinct()

Set or unset distinct modifier.

Usage
BiodbSqlQuery$setDistinct(distinct)
Arguments
distinct

Either TRUE or FALSE for setting or unsetting the distinct flag.

Returns

Nothing.

Method setLimit()

Set results limit.

Usage
BiodbSqlQuery$setLimit(limit)
Arguments
limit

The limit to set, as an integer value.

Returns

Nothing.

Method addJoin()

Add a join.

Usage
BiodbSqlQuery$addJoin(table1, field1, table2, field2)
Arguments
table1

The first table.

field1

The field of the first table.

table2

The second table.

field2

The field of the second table.

Returns

Nothing.

Method setWhere()

Set the where clause.

Usage
BiodbSqlQuery$setWhere(expr)
Arguments
expr

A BiodbSqlExpr representing the "where" clause.

Returns

Nothing.

Method getJoin()

Builds and returns the join expression.

Usage
BiodbSqlQuery$getJoin()
Returns

A character vector representing the join expression.

Method getWhere()

Gets the where expression.

Usage
BiodbSqlQuery$getWhere()
Returns

The BiodbSqlExpr instance representing the "where" clause.

Method getFields()

Gets the fields to retrieve.

Usage
BiodbSqlQuery$getFields()
Returns

A string containing the list of fields to retrieve.

Method toString()

Generates the string representation of this query.

Usage
BiodbSqlQuery$toString()
Returns

A string containing the full SQL query.

Method clone()

The objects of this class are cloneable with this method.

Usage
BiodbSqlQuery$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

See Also

BiodbRequestScheduler, BiodbRequest.

This class represents an SQL value.

Description

This class represents an SQL value.

This class represents an SQL value.

Super class

biodb::BiodbSqlExpr -> BiodbSqlValue

Methods

Public methods

Method new()

Initializer.

Usage
BiodbSqlValue$new(value)
Arguments
value

The value.

Returns

Nothing.

Method toString()

Converts into a string.

Usage
BiodbSqlValue$toString()
Returns

A string containing the SQL expression.

Method clone()

The objects of this class are cloneable with this method.

Usage
BiodbSqlValue$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

A class for acknowledging messages during tests.

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

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
what

The reason as a character value.

index

The index number representing the progress.

total

The total number to reach for completing the process.

Returns

Nothing.

Method clone()

The objects of this class are cloneable with this method.

Usage
BiodbTestMsgAck$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

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()

Entry class for content in text format.

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

Inherited methods

Method new()

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

Usage
BiodbTxtEntry$new(...)
Arguments
...

All parameters are passed to the super class initializer.

Returns

Nothing.

Method clone()

The objects of this class are cloneable with this method.

Usage
BiodbTxtEntry$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

See Also

Super class BiodbEntry.

Examples

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

Class URL.

Description

Class URL.

Class URL.

Details

This class represents a URL object that can be used in requests.

Methods

Public methods

Method new()

Initializer.

Usage
BiodbUrl$new(url = character(), params = character(), chompExtraSlashes = TRUE)
Arguments
url

The URL to access, as a character vector.

params

The list of parameters to append to this URL.

chompExtraSlashes

If set to TRUE, then slashes at the end and the beginning of each element of the url vector parameter will be removed before proper concatenation.

Returns

Nothing.

Method getDomain()

Gets the domain.

Usage
BiodbUrl$getDomain()
Returns

The domain.

Method setUrl()

Sets the base URL string.

Usage
BiodbUrl$setUrl(url)
Arguments
url

The base URL string.

Returns

Nothing.

Method setParam()

Sets a parameter.

Usage
BiodbUrl$setParam(key, value)
Arguments
key

The parameter name.

value

The value of the parameter.

Returns

Nothing.

Method print()

Displays information about this instance.

Usage
BiodbUrl$print()
Returns

self as invisible.

Method toString()

Gets the URL as a string representation.

Usage
BiodbUrl$toString(encode = TRUE)
Arguments
encode

If set to TRUE, then encodes the URL.

Returns

The URL as a string, with all parameters and values set.

Method clone()

The objects of this class are cloneable with this method.

Usage
BiodbUrl$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

See Also

BiodbRequestScheduler, BiodbRequest.

Examples

# Create a URL object
u <- c("https://www.uniprot.org", "uniprot")
p <- c(query="reviewed:yes+AND+organism:9606",
       columns='id,entry name,protein names',
       format="tab")
url <- BiodbUrl$new(url=u, params=p)
url$toString()

Entry class for content in XML format.

Description

Entry class for content in XML format.

Entry class for content in XML format.

Details

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

Super class

biodb::BiodbEntry -> BiodbXmlEntry

Methods

Public methods

Inherited methods

Method new()

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

Usage
BiodbXmlEntry$new(...)
Arguments
...

All parameters are passed to the super class initializer.

Returns

Nothing.

Method clone()

The objects of this class are cloneable with this method.

Usage
BiodbXmlEntry$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

See Also

Super class BiodbEntry.

Examples

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

Check deprecated default cache folders.

Description

Searches for a deprecated location of the default cache folder, and moves files to the new location if possible. Otherwise raises a warning.

Usage

checkDeprecatedCacheFolders()

Value

Nothing.

Examples

biodb::checkDeprecatedCacheFolders()

Close match PPM

Description

Matches peaks between two spectra.

Usage

closeMatchPpm(x, y, xidx, yidx, xolength, dppm, dmz)

Arguments

x

sorted M/Z values (ascending order) of input spectrum (no NA).
y

sorted M/Z values (ascending order) of reference spectrum (no NA).
xidx

indices of the M/Z peaks of x, taken from the original spectrum ordered in decreasing intensity values.
yidx

indices of the M/Z peaks of y, taken from the original spectrum ordered in decreasing intensity values.
xolength

The length of the output.
dppm

The M/Z tolerance in PPM.
dmz

Minimum M/Z tolerance.

Value

A list of results.

Compound CSV File connector class.

Description

Compound CSV File connector class.

Compound CSV File connector class.

Details

This is the connector class for a Compound CSV file database.

Super classes

biodb::BiodbConnBase -> biodb::BiodbConn -> biodb::CsvFileConn -> CompCsvFileConn

Methods

Public methods

Inherited methods

Method new()

New instance initializer. Connector classes must not be instantiated directly. Instead, you must use the createConn() method of the factory class.

Usage
CompCsvFileConn$new(...)
Arguments
...

All parameters are passed to the super class initializer.

Returns

Nothing.

Method clone()

The objects of this class are cloneable with this method.

Usage
CompCsvFileConn$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

See Also

Super class CsvFileConn.

Examples

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

# Get a connector:
chebi_file <- system.file("extdata", "chebi_extract.tsv", package="biodb")
conn <- mybiodb$getFactory()$createConn('comp.csv.file', url=chebi_file)

# Get an entry
e <- conn$getEntry('')

# Terminate instance.
mybiodb$terminate()

Compound CSV File entry class.

Description

Compound CSV File entry class.

Compound CSV File entry class.

Details

This is the entry class for Compound CSV file databases.

Super classes

biodb::BiodbEntry -> biodb::BiodbCsvEntry -> CompCsvFileEntry

Methods

Public methods

Inherited methods

Method new()

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

Usage
CompCsvFileEntry$new(...)
Arguments
...

All parameters are passed to the super class initializer.

Returns

Nothing.

Method clone()

The objects of this class are cloneable with this method.

Usage
CompCsvFileEntry$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

See Also

Super class BiodbCsvEntry.

Examples

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

# Get a connector that inherits from CsvFileConn:
chebi_file <- system.file("extdata", "chebi_extract.tsv", package="biodb")
conn <- mybiodb$getFactory()$createConn('comp.csv.file', url=chebi_file)

# Get an entry
e <- conn$getEntry('')

# Terminate instance.
mybiodb$terminate()

Class for handling a Compound database in SQLite format.

Description

This is the connector class for a Compound database.

Super classes

biodb::BiodbConnBase -> biodb::BiodbConn -> biodb::SqliteConn -> CompSqliteConn

Methods

Public methods

Inherited methods

Method clone()

The objects of this class are cloneable with this method.

Usage
CompSqliteConn$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

See Also

Super class SqliteConn.

Examples

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

# Get a connector:
chebi_file <- system.file("extdata", "chebi_extract.sqlite", package="biodb")
conn <- mybiodb$getFactory()$createConn('comp.sqlite', url=chebi_file)

# Get an entry
e <- conn$getEntry('1018')

# Terminate instance.
mybiodb$terminate()

Compound SQLite entry class.

Description

This is the entry class for a Compound SQLite database.

Super classes

biodb::BiodbEntry -> biodb::BiodbListEntry -> CompSqliteEntry

Methods

Public methods

Inherited methods

Method clone()

The objects of this class are cloneable with this method.

Usage
CompSqliteEntry$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

See Also

Super class BiodbListEntry.

Examples

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

# Get path to LCMS database example file
lcmsdb <- system.file("extdata", "chebi_extract.sqlite", package="biodb")

# Create a connector
conn <- mybiodb$getFactory()$createConn('comp.sqlite', url=lcmsdb)

# Get an entry
e <- conn$getEntry('34.pos.col12.0.78')

# Terminate instance.
mybiodb$terminate()

Convert connector name into class prefix.

Description

Converts the connector name into the class prefix (e.g.: "mass.csv.file" –> "MassCsvFile").

Usage

connNameToClassPrefix(connName)

Arguments

connName

A connector name (e.g.: "mass.csv.file").

Value

The corresponding class prefix (e.g.: "MassCsvFile").

Creating a BiodbMain instance for tests.

Description

Creates a BiodbMain instance with options specially adapted for tests. You can request the logging of all messages into a log file. It is also possible to ask for the creation of a BiodbTestMsgAck observer, which will receive all messages and emit a testthat test for each message. This will allow the testthat output to not stall a long time while, for example, downloading or extracting a database. Do not forget to call terminate() on your instance at the end of your tests.

Usage

createBiodbTestInstance(ack = FALSE)

Arguments

ack

If set to TRUE, an instance of BiodbTestMsgAck will be attached to the BiodbMain instance.

Value

The created BiodbMain instance.

Examples

# Instantiate a BiodbMain instance for testing
biodb <- biodb::createBiodbTestInstance()

# Terminate the instance
biodb$terminate()

CSV File connector class.

Description

CSV File connector class.

CSV File connector class.

Details

This is the abstract connector class for all CSV file databases.

Super classes

biodb::BiodbConnBase -> biodb::BiodbConn -> CsvFileConn

Methods

Public methods

Inherited methods

Method new()

New instance initializer. Connector classes must not be instantiated directly. Instead, you must use the createConn() method of the factory class.

Usage
CsvFileConn$new(...)
Arguments
...

All parameters are passed to the super class initializer.

Returns

Nothing.

Method getCsvQuote()

Gets the characters used to delimit quotes in the CSV database file.

Usage
CsvFileConn$getCsvQuote()
Returns

The characters used to delimit quotes as a single character value.

Method setCsvQuote()

Sets the characters used to delimit quotes in the CSV database file.

Usage
CsvFileConn$setCsvQuote(quote)
Arguments
quote

The characters used to delimit quotes as a single character value.

You

may specify several characters. Example \"\\"'\".

Returns

Nothing.

Method getCsvSep()

Gets the current CSV separator used for the database file.

Usage
CsvFileConn$getCsvSep()
Returns

The CSV separator as a character value.

Method setCsvSep()

Sets the CSV separator to be used for the database file. If this method is called after the loading of the database, it will throw an error.

Usage
CsvFileConn$setCsvSep(sep)
Arguments
sep

The CSV separator as a character value.

Returns

Nothing.

Method getFieldNames()

Get the list of all biodb fields handled by this database.

Usage
CsvFileConn$getFieldNames()
Returns

A character vector of the biodb field names.

Method hasField()

Tests if a field is defined for this database instance.

Usage
CsvFileConn$hasField(field)
Arguments
field

A valid Biodb entry field name.

Returns

TRUE of the field is defined, FALSE otherwise.

Method addField()

Adds a new field to the database. The field must not already exist. The same single value will be set to all entries for this field. A new column will be written in the memory data frame, containing the value given.

Usage
CsvFileConn$addField(field, value)
Arguments
field

A valid Biodb entry field name.

value

The value to set for this field.

Returns

Nothing.

Method getFieldColName()

Get the column name corresponding to a Biodb field.

Usage
CsvFileConn$getFieldColName(field)
Arguments
field

A valid Biodb entry field name. This field must be defined for this database instance.

Returns

The column name from the CSV file.

Method setField()

Sets a field by making a correspondence between a Biodb field and one or more columns of the loaded data frame.

Usage
CsvFileConn$setField(field, colname, ignore.if.missing = FALSE)
Arguments
field

A valid Biodb entry field name. This field must not be already defined for this database instance.

colname

A character vector containing one or more column names from the CSV file.

ignore.if.missing

Deprecated parameter.

Returns

Nothing.

Method getFieldsAndColumnsAssociation()

Gets the association between biodb field names and CSV file column names.

Usage
CsvFileConn$getFieldsAndColumnsAssociation()
Returns

A list with names being the biodb field names and values being a character vector of column names from the CSV file.

Method getUnassociatedColumns()

Gets the list of unassociated column names from the CSV file.

Usage
CsvFileConn$getUnassociatedColumns()
Returns

A character vector containing column names.

Method print()

Prints a description of this connector.

Usage
CsvFileConn$print()
Returns

Nothing.

Method setDb()

Sets the database directly from a data frame. You must not have set the database previously with the URL parameter.

Usage
CsvFileConn$setDb(db)
Arguments
db

A data frame containing your database.

Returns

Nothing.

Method setIgnoreUnassignedColumns()

Tells the connector to ignore or not the columns found in the CSV file for which no assignment were found.

Usage
CsvFileConn$setIgnoreUnassignedColumns(ignore)
Arguments
ignore

Set to TRUE to ignore the unassigned columns, and to FALSE otherwise.

Returns

Nothing.

Method clone()

The objects of this class are cloneable with this method.

Usage
CsvFileConn$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

See Also

Super classes BiodbConn, and sub-classes CompCsvFileConn, MassCsvFileConn.

Examples

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

# Get a connector that inherits from CsvFileConn:
chebi_file <- system.file("extdata", "chebi_extract.tsv", package="biodb")
conn <- mybiodb$getFactory()$createConn('comp.csv.file', url=chebi_file)

# Get an entry
e <- conn$getEntry('1018')

# Terminate instance.
mybiodb$terminate()

Convert a data.frame into a string.

Description

Prints a data frame (partially if too big) into a string.

Usage

df2str(x, rowCut = 5, colCut = 5)

Arguments

x

The data frame object.
rowCut

The maximum of rows to print.
colCut

The maximum of columns to print.

Value

A string containing the data frame representation (or part of it).

Examples

# Converts the first 5 rows and first 6 columns of a data frame into a
# string:
x <- data.frame(matrix(1:160, nrow=10, byrow=TRUE))
s <- df2str(x, rowCut=5, colCut=6)

Test if a URL is valid according to RCurl

Description

Test if a URL is valid according to RCurl

Usage

doesRCurlRequestUrlExist(request, useragent = NULL)

Arguments

request

A BiodbRequest object, from which the URL will be gotten.
useragent

The user agent identification.

Value

Returns TRUE if the URL

Throw an error and log it too.

Description

Throws am error and logs it too with biodb logger.

Usage

error(...)

Arguments

...

Values to be passed to sprintf().

Value

Nothing.

Examples

# Throws an error:
tryCatch(biodb::error('Index is %d.', 10), error=function(e){e$message})

Throw an error and log it too.

Description

Throws an error and logs it too with biodb logger, using paste0().

Usage

error0(...)

Arguments

...

Values to be passed to paste0().

Value

Nothing.

Examples

# Throws an error:
tryCatch(biodb::error0('Index is ', 10, '.'), error=function(e){e$message})

Extension connector clas

Description

A class for generating a new connector class.

Details

This class generates a new connector class from given parameters. The new class inherits from BiodbConn. It can be defined as a compound or mass database connector, and made downloadable, editable and/or writable.

Super classes

biodb::ExtGenerator -> biodb::ExtFileGenerator -> ExtConnClass

Methods

Public methods

Inherited methods

Method new()

Initializer.

Usage
ExtConnClass$new(...)
Arguments
...

See the constructor of ExtFileGenerator for the parameters.

Returns

Nothing.

Method clone()

The objects of this class are cloneable with this method.

Usage
ExtConnClass$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Examples

# Generate a new connector class inside R folder:
pkgFolder <- file.path(tempfile(), 'biodbFoo')
dir.create(pkgFolder, recursive=TRUE)
biodb::ExtConnClass$new(path=pkgFolder, dbName='foo.db',
                        dbTitle='Foo database',
                        connType='mass', remote=TRUE)$generate()

Extension C++ code class

Description

A class for generating C++ example files (code & test).

Details

This class generates examples of an R function written in C++ using Rcpp, of a pure C++ function used to speed up computing, and of C++ code for testing the pure C++ function. As for the R function written with Rcpp, it is tested inside standard testthat R code.

Super class

biodb::ExtGenerator -> ExtCpp

Methods

Public methods

Inherited methods

Method new()

Initializer.

Usage
ExtCpp$new(...)
Arguments
...

See the constructor of ExtGenerator for the parameters.

Returns

Nothing.

Method clone()

The objects of this class are cloneable with this method.

Usage
ExtCpp$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Examples

# Generate C++ files
pkgFolder <- file.path(tempfile(), 'biodbFoo')
dir.create(pkgFolder, recursive=TRUE)
biodb::ExtCpp$new(path=pkgFolder)$generate()

Extension defintions file class

Description

A class for generating the definitions.yml file of a new extension package.

Details

This class generates the definitions.yml of a new extension package, needed for definining the new connector.

Super classes

biodb::ExtGenerator -> biodb::ExtFileGenerator -> ExtDefinitions

Methods

Public methods

Inherited methods

Method new()

Initializer.

Usage
ExtDefinitions$new(...)
Arguments
...

See the constructor of ExtFileGenerator for the parameters. offers this possiblity.

Returns

Nothing.

Method clone()

The objects of this class are cloneable with this method.

Usage
ExtDefinitions$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Examples

# Generate the biodb definitions.yml file inside "inst" folder:
pkgFolder <- file.path(tempfile(), 'biodbFoo')
dir.create(pkgFolder, recursive=TRUE)
biodb::ExtDefinitions$new(path=pkgFolder, dbName='foo.db',
                          dbTitle='Foo database')$generate()

Extension DESCRIPTION file

Description

A class for generating a DESCRIPTION file for an extension package.

Details

This class generates a DESCRIPTION for a biodb extension package.

Super classes

biodb::ExtGenerator -> biodb::ExtFileGenerator -> ExtDescriptionFile

Methods

Public methods

Inherited methods

Method new()

Initializer.

Usage
ExtDescriptionFile$new(...)
Arguments
...

See the constructor of ExtFileGenerator for the parameters.

Returns

Nothing.

Method clone()

The objects of this class are cloneable with this method.

Usage
ExtDescriptionFile$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Examples

# Generate the DESCRIPTION file:
pkgFolder <- file.path(tempfile(), 'biodbFoo')
dir.create(pkgFolder, recursive=TRUE)
biodb::ExtDescriptionFile$new(path=pkgFolder, dbName='foo.db',
                              dbTitle='Foo database', email='[email protected]',
                              firstname='John', lastname='Smith', rcpp=TRUE,
                              entryType='xml')$generate()

Extension entry class

Description

A class for generating a new entry class.

Details

This class generates a new entry class from given parameters. The new class can inherit directly from BiodbEntry or from one of its sub-classes: BiodbCsvEntry, BiodbHtmlEntry, ...

Super classes

biodb::ExtGenerator -> biodb::ExtFileGenerator -> ExtEntryClass

Methods

Public methods

Inherited methods

Method new()

Initializer.

Usage
ExtEntryClass$new(...)
Arguments
...

See the constructor of ExtFileGenerator for the parameters.

Returns

Nothing.

Method clone()

The objects of this class are cloneable with this method.

Usage
ExtEntryClass$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Examples

# Generate a new entry class inside R folder:
pkgFolder <- file.path(tempfile(), 'biodbFoo')
dir.create(pkgFolder, recursive=TRUE)
biodb::ExtEntryClass$new(path=pkgFolder, dbName='foo.db',
                         dbTitle='Foo database',
                         connType='mass', entryType='xml')$generate()

Extension file generator abstract class

Description

The mother class of all file generators for biodb extension packages.

Details

All file generator classes for biodb extensions must inherit from this class.

Super class

biodb::ExtGenerator -> ExtFileGenerator

Methods

Public methods

Inherited methods

Method new()

Initializer.

Usage
ExtFileGenerator$new(
  filename = NULL,
  overwrite = FALSE,
  folder = character(),
  template = NULL,
  upgrader = c("fullReplacer", "lineAdder"),
  ...
)
Arguments
filename

The name of the generated file.

overwrite

If set to TRUE, then overwrite existing destination file, even whatever the version of the template file. If set to FALSE, only overwrite if the version of the template file is strictly greater than the existing destination file.

folder

The destination subfolder inside the package directory, as a character vector of subfolders hierarchy.

template

The filename of the template to use.

upgrader

The type of upgrader to use. "fullReplacer" replaces the whole destination file by the template if it is newer (it compares version numbers). "lineAdder" only adds to the destination file the missing lines from the template file.

...

See the constructor of ExtGenerator for the parameters.

Returns

Nothing.

Method clone()

The objects of this class are cloneable with this method.

Usage
ExtFileGenerator$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Examples

pkgFolder <- file.path(tempfile(), 'biodbFoo')
dir.create(pkgFolder, recursive=TRUE)
biodb::ExtConnClass$new(path=pkgFolder, dbName='foo.db',
                        dbTitle='Foo database',
                        connType='mass', remote=TRUE)$generate()

Extension generator abstract class

Description

The mother class of all generators for biodb extension packages.

Details

All generator classes for biodb extensions must inherit from this class.

Methods

Public methods

Method new()

Initializer.

Usage
ExtGenerator$new(
  path,
  loadCfg = TRUE,
  saveCfg = TRUE,
  pkgName = getPkgName(path),
  email = "[email protected]",
  dbName = "foo.db",
  dbTitle = "Foo database",
  pkgLicense = getLicenses(),
  firstname = "Firstname of author",
  lastname = "Lastname of author",
  newPkg = FALSE,
  connType = getConnTypes(),
  entryType = getEntryTypes(),
  editable = FALSE,
  writable = FALSE,
  remote = FALSE,
  downloadable = FALSE,
  makefile = FALSE,
  travis = FALSE,
  rcpp = FALSE,
  vignetteName = getPkgName(path),
  githubRepos = getReposName(path, default = "myaccount/myrepos")
)
Arguments
path

The path to the package folder.

loadCfg

Set to FALSE to disable loading of tag values from config file "biodb_ext.yml".

saveCfg

Set to FALSE to disable saving of tag values into config file "biodb_ext.yml".

pkgName

The package name. If set to NULL, the folder name pointer by the "path" paramater will be used as the package name.

email

The email of the author.

dbName

The name of the database (in biodb format "my.db.name"), that will be used in "definitions.yml" file and for connector and entry classes.

dbTitle

The official name of the database (e.g.: HMDB, UniProtKB, KEGG).

pkgLicense

The license of the package.

firstname

The firstname of the author.

lastname

The lastname of the author.

newPkg

Set to TRUE if the package is not yet published on Bioconductor.

connType

The type of connector class to implement.

entryType

The type of entry class to implement.

editable

Set to TRUE to allow the generated connector to create new entries in memory.

writable

Set to TRUE to enable the generated connector to write into the database.

remote

Set to TRUE if the database to connect to is not local.

downloadable

Set to TRUE if the database needs to be downloaded or offers this possiblity.

makefile

Set to TRUE if you want a Makefile to be generated.

travis

Set to TRUE if you want a .travis.yml file to be generated.

rcpp

Set to TRUE to enable Rcpp C/C++ code inside the package.

vignetteName

Set to the name of the default/main vignette.

githubRepos

Set to the name of the associated GitHub repository. Example: myaccount/myrepos.

Returns

Nothing.

Method generate()

Generates the destination file(s).

Usage
ExtGenerator$generate(overwrite = FALSE, fail = TRUE)
Arguments
overwrite

If set to TRUE and destination files exist, overwrite the destination files.

fail

If set to FALSE, do not fail if destination files exist, just do nothing and return.

Examples
# Generate a new extension package:
pkgFolder <- file.path(tempfile(), 'biodbFoo')
biodb::ExtPackage$new(pkgFolder)$generate()

Method upgrade()

Upgrade the destination file(s).

Usage
ExtGenerator$upgrade(generate = TRUE)
Arguments
generate

If set to FALSE, and destination file(s) do not exist, then do not generate them.

Method clone()

The objects of this class are cloneable with this method.

Usage
ExtGenerator$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Examples

# Generate a new connector class inside the R folder:
pkgFolder <- file.path(tempfile(), 'biodbFoo')
dir.create(pkgFolder, recursive=TRUE)
biodb::ExtConnClass$new(path=pkgFolder, dbName='foo.db',
                        dbTitle='Foo database',
                        connType='mass', remote=TRUE)$generate()


## ------------------------------------------------
## Method `ExtGenerator$generate`
## ------------------------------------------------

# Generate a new extension package:
pkgFolder <- file.path(tempfile(), 'biodbFoo')
biodb::ExtPackage$new(pkgFolder)$generate()

Extension Gitignore file class

Description

A class for generating the .gitignore file of an extension package.

Details

This class can be used to generate a new .gitignore file or to keep one up to date.

Super classes

biodb::ExtGenerator -> biodb::ExtFileGenerator -> ExtGitignore

Methods

Public methods

Inherited methods

Method new()

Initializer.

Usage
ExtGitignore$new(...)
Arguments
...

See the constructor of ExtFileGenerator for the parameters.

Returns

Nothing.

Method clone()

The objects of this class are cloneable with this method.

Usage
ExtGitignore$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Examples

# Generate a new package:
pkgFolder <- file.path(tempfile(), 'biodbFoo')
dir.create(pkgFolder, recursive=TRUE)
biodb::ExtGitignore$new(path=pkgFolder)$generate()

Extension license

Description

A class for generating or upgrading the license of a biodb extension package.

Details

This class generates the license for a new extension package, or update the license of an existing one.

Super classes

biodb::ExtGenerator -> biodb::ExtFileGenerator -> ExtLicense

Methods

Public methods

Inherited methods

Method new()

Initializer.

Usage
ExtLicense$new(...)
Arguments
...

See the constructor of ExtFileGenerator for the parameters.

Returns

Nothing.

Method clone()

The objects of this class are cloneable with this method.

Usage
ExtLicense$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Examples

# Generate a new connector class inside R folder:
pkgFolder <- file.path(tempfile(), 'biodbFoo')
dir.create(pkgFolder, recursive=TRUE)
biodb::ExtLicense$new(path=pkgFolder)$generate()

Extension Makefile

Description

A class for generating a Makefile for an extension package.

Details

This class generates a Makefile, usable on UNIX-like platforms, for managing a biodb extension package. Targets are automatically generated for running CRAN check, Bioconductor check, testthat tests, compiling, generating documentation, cleaning, etc.

Super class

biodb::ExtGenerator -> ExtMakefile

Methods

Public methods

Inherited methods

Method new()

Initializer.

Usage
ExtMakefile$new(...)
Arguments
...

See the constructor of ExtGenerator for the parameters.

Returns

Nothing.

Method clone()

The objects of this class are cloneable with this method.

Usage
ExtMakefile$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Examples

# Generate a new connector class inside R folder:
pkgFolder <- file.path(tempfile(), 'biodbFoo')
dir.create(pkgFolder, recursive=TRUE)
biodb::ExtMakefile$new(path=pkgFolder)$generate()

Extension package class

Description

A class for generating the skeleton of a new extension package.

Details

This class manages the files of an extension package.

It can generate all the files of a new extension package: DESCRIPTION, NEWS, README.md, tests, definitons.yml, etc. Optionnaly it also generates other files like: a .travis.yml file for Travis-CI, a Makefile for easing development on UNIX-like platforms outside of Rstudio.

It can also upgrade files of an existing package like: definitions.yml, Makefile, .travis.yml, LICENSE, etc.

Super class

biodb::ExtGenerator -> ExtPackage

Methods

Public methods

Inherited methods

Method new()

Initializer.

Usage
ExtPackage$new(...)
Arguments
...

See the constructor of ExtGenerator for the parameters.

Returns

Nothing.

Method clone()

The objects of this class are cloneable with this method.

Usage
ExtPackage$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Examples

# Generate a new package:
pkgFolder <- file.path(tempfile(), 'biodbFoo')
dir.create(pkgFolder, recursive=TRUE)
biodb::ExtPackage$new(path=pkgFolder, dbName='foo.db',
                        dbTitle='Foo database', rcpp=TRUE,
                        connType='mass', entryType='txt', downloadable=TRUE,
                        remote=TRUE)$generate()

Extension package file class.

Description

A class for generating the package.R file for a biodb extension.

Details

This class generates the package.R file, writing a reference to the generated skeleton vignette, and possibly including directives for C++ code.

Super classes

biodb::ExtGenerator -> biodb::ExtFileGenerator -> ExtPackageFile

Methods

Public methods

Inherited methods

Method new()

Initializer.

Usage
ExtPackageFile$new(...)
Arguments
...

See the constructor of ExtFileGenerator for the parameters.

Returns

Nothing.

Method clone()

The objects of this class are cloneable with this method.

Usage
ExtPackageFile$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Examples

# Generate a new package:
pkgFolder <- file.path(tempfile(), 'biodbFoo')
dir.create(pkgFolder, recursive=TRUE)
biodb::ExtPackageFile$new(path=pkgFolder, dbName='foo.db')$generate()

Extension Rbuildignore file class

Description

A class for generating the .Rbuildignore file of an extension package.

Details

This class can be used to generate a new .Rbuildignore file or to keep one up to date.

Super classes

biodb::ExtGenerator -> biodb::ExtFileGenerator -> ExtRbuildignore

Methods

Public methods

Inherited methods

Method new()

Initializer.

Usage
ExtRbuildignore$new(...)
Arguments
...

See the constructor of ExtFileGenerator for the parameters.

Returns

Nothing.

Method clone()

The objects of this class are cloneable with this method.

Usage
ExtRbuildignore$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Examples

# Generate a new package:
pkgFolder <- file.path(tempfile(), 'biodbFoo')
dir.create(pkgFolder, recursive=TRUE)
biodb::ExtRbuildignore$new(path=pkgFolder)$generate()

Extension README file class

Description

A class for generating a README file for a new extension package.

Details

Write a README file inside package directory, using a template file.

Super classes

biodb::ExtGenerator -> biodb::ExtFileGenerator -> ExtReadme

Methods

Public methods

Inherited methods

Method new()

Initializer.

Usage
ExtReadme$new(...)
Arguments
...

See the constructor of ExtFileGenerator for the parameters.

Returns

Nothing.

Method clone()

The objects of this class are cloneable with this method.

Usage
ExtReadme$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Examples

# Generate a new package:
pkgFolder <- file.path(tempfile(), 'biodbFoo')
dir.create(pkgFolder, recursive=TRUE)
biodb::ExtReadme$new(path=pkgFolder, dbName='foo.db',
                     dbTitle='Foo database')$generate()

Extension tests class

Description

A class for generating test files.

Details

This class generates a test file for running biodb generic tests, and a test file containing an example of a custom test for this extension.

Super class

biodb::ExtGenerator -> ExtTests

Methods

Public methods

Inherited methods

Method new()

Initializer.

Usage
ExtTests$new(...)
Arguments
...

See the constructor of ExtGenerator for the parameters.

Returns

Nothing.

Method clone()

The objects of this class are cloneable with this method.

Usage
ExtTests$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Examples

# Generate a new package:
pkgFolder <- file.path(tempfile(), 'biodbFoo')
dir.create(pkgFolder, recursive=TRUE)
biodb::ExtTests$new(path=pkgFolder, dbName='foo.db', rcpp=TRUE,
                    remote=TRUE)$generate()

Extension Travis YAML file generator class

Description

A class for generating a .travis.yml file for a new extension package.

Details

Write a .travis.yml file inside the package directory, using a template file.

Super classes

biodb::ExtGenerator -> biodb::ExtFileGenerator -> ExtTravisFile

Methods

Public methods

Inherited methods

Method new()

Initializer.

Usage
ExtTravisFile$new(...)
Arguments
...

See the constructor of ExtFileGenerator for the parameters.

Returns

Nothing.

Method clone()

The objects of this class are cloneable with this method.

Usage
ExtTravisFile$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Examples

# Generate a new package:
pkgFolder <- file.path(tempfile(), 'biodbFoo')
dir.create(pkgFolder, recursive=TRUE)
biodb::ExtTravisFile$new(path=pkgFolder, email='[email protected]')$generate()

Extension vignette class

Description

A class for generating a vignette example for an extension package.

Details

This class generates a vignette file, serving as example to demonstrate the use of the extension package.

Super classes

biodb::ExtGenerator -> biodb::ExtFileGenerator -> ExtVignette

Methods

Public methods

Inherited methods

Method new()

Initializer.

Usage
ExtVignette$new(...)
Arguments
...

See the constructor of ExtFileGenerator for the parameters.

Returns

Nothing.

Method clone()

The objects of this class are cloneable with this method.

Usage
ExtVignette$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Examples

# Generate a new package:
pkgFolder <- file.path(tempfile(), 'biodbFoo')
dir.create(pkgFolder, recursive=TRUE)
biodb::ExtVignette$new(path=pkgFolder, dbName='foo.db',
                       dbTitle='Foo database', vignetteName='main', 
                       firstname='John', lastname='Smith',
                       remote=TRUE)$generate()

File template class.

Description

A class for reading a file template, replacing tags inside, and writing the results in an output file.

Methods

Public methods

Method new()

Initializer.

Usage
FileTemplate$new(path)
Arguments
path

The path to the template file.

Returns

Nothing.

Method replace()

Replace a tag by its value inside the template file.

Usage
FileTemplate$replace(tag, value)
Arguments
tag

The tag to replace.

value

The value to replace the tag with.

Returns

invisible(self) for chaining method calls.

Method choose()

Choose one case among a set of cases.

Usage
FileTemplate$choose(set, case)
Arguments
set

The name of the case set.

case

The name of case.

Returns

invisible(self) for chaining method calls.

Method select()

Select or remove sections that match a name.

Usage
FileTemplate$select(section, enable)
Arguments
section

The name of the section.

enable

Set to TRUE to select the section (and keep it), and FALSE to remove it.

Returns

invisible(self) for chaining method calls.

Method write()

Write template with replaced values to disk.

Usage
FileTemplate$write(path, overwrite = FALSE, checkRemainingTags = TRUE)
Arguments
path

Path to output file.

overwrite

If set to FALSE and the destination file already exists, a message is thrown. Otherwise writes into the destination.

checkRemainingTags

If set to TRUE, checks first, before writing, if there any remaining tags that have not been processed. A warning is thrown for each found tag.

Returns

Nothing.

Method getLines()

Get the lines of the templates.

Usage
FileTemplate$getLines()
Returns

A vector containing the lines of the templates.

Method clone()

The objects of this class are cloneable with this method.

Usage
FileTemplate$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Generate a new extension package for biodb.

Description

Generates all the necessary files for a new extension package.

Usage

genNewExtPkg(...)

Arguments

...

Parameters passed to ExtPackage constructor.

Value

Nothing.

See Also

ExtPackage.

Examples

# Generate a new package:
pkgFolder <- file.path(tempfile(), 'biodbFoo')
dir.create(pkgFolder, recursive=TRUE)
biodb::genNewExtPkg(path=pkgFolder, dbName='foo.db',
                    dbTitle='Foo database', rcpp=TRUE,
                    connType='mass', entryType='txt', downloadable=TRUE,
                    remote=TRUE)

Get URL content using base::url().

Description

Get URL content using base::url().

Usage

getBaseUrlContent(u, binary = FALSE)

Arguments

u

The URL as a character value.
binary

Set to TRUE if the content to be retrieved is binary.

Value

The URL content as a character single value.

Get URL request result using base::url().

Description

Get URL request result using base::url().

Usage

getBaseUrlRequestResult(request)

Arguments

request

A BiodbRequest object.

Value

A RequestResult object.

Get connector class name.

Description

Gets the name of the connector class corresponding to a connector.

Usage

getConnClassName(connName)

Arguments

connName

A connector name (e.g.: "mass.csv.file").

Value

The name of the corresponding connector class (e.g.: "MassCsvFileConn").

Examples

biodb::getConnClassName('foo.db')

Get connector types.

Description

Get the list of available connector types.

Usage

getConnTypes()

Value

A character vector containing the connector types.

Examples

biodb::getConnTypes()

Get default cache folder.

Description

Returns the path to the default cache folder.

Usage

getDefaultCacheDir()

Value

The path to the cache folder.

Examples

cacheFolderPath <- biodb::getDefaultCacheDir()

Get entry class name.

Description

Gets the name of the entry class corresponding to a connector.

Usage

getEntryClassName(connName)

Arguments

connName

A connector name (e.g.: "mass.csv.file").

Value

The name of the corresponding entry class (e.g.: "MassCsvFileEntry").

Examples

biodb::getEntryClassName('foo.db')

Get entry types.

Description

Get the list of available entry types.

Usage

getEntryTypes()

Value

A character vector containing the entry types.

Examples

biodb::getEntryTypes()

Get the available licenses for extension packages.

Description

Get the available licenses for extension packages.

Usage

getLicenses()

Value

A character vector containing license names.

Examples

biodb::getLicenses()

Get the main package logger.

Description

Gets the main package logger, parent of all loggers of this package.

Usage

getLogger()

Value

The main package logger (named "biodb") as a lgr::Logger object.

Examples

biodb::getLogger()

Get the package name from a package folder path.

Description

The package name is extracted from the path by taking the basename.

Usage

getPkgName(pkgRoot, check = TRUE)

Arguments

pkgRoot

The path to the root folder of the package.
check

If set to TRUE the extracted package name is checked against regular expression "^biodb[A-Z][A-Za-z0-9]+$", to ensure the format is respected.

Value

The package name of the biodb extension.

Examples

biodb::getPkgName('/my/path/to/my/extension/biodbFoo')

Get URL content using RCurl::getURL().

Description

Get URL content using RCurl::getURL().

Usage

getRCurlContent(
  u,
  opts = NULL,
  enc = integer(),
  header.fct = NULL,
  ssl.verifypeer = TRUE,
  method = c("get", "post"),
  binary = FALSE
)

Arguments

u

The URL as a character value.
opts

A valid RCurl options object.
enc

The encoding.
header.fct

An RCurl header gatherer function.
ssl.verifypeer

Set to TRUE to enable SSL verify peer.
method

The HTTP method to use, either 'get' or 'post'.
binary

Set to TRUE if the content to be retrieved is binary.

Value

The URL content as a character single value.

Get URL request result using RCurcl::getURL().

Description

Get URL request result using RCurcl::getURL().

Usage

getRCurlRequestResult(request, useragent = NULL, ssl.verifypeer = TRUE)

Arguments

request

A BiodbRequest object.
useragent

The user agent identification.
ssl.verifypeer

Set to TRUE to enable SSL verify peer.

Value

A RequestResult object.

Extract the repository name from a package folder.

Description

Given the root path of a package, returns the GitHub repository name.

Usage

getReposName(pkgRoot, default = NULL)

Arguments

pkgRoot

The path to the root folder of the package.
default

A default value to return in case git4r package is not available or the folder is not a Git repository.

Value

The repository name.

Examples

biodb::getReposName('/my/path/to/my/extension/biodbFoo')

Get the test output directory.

Description

Returns the path to the test output directory. The function creates this also this directory if it does not exist.

Usage

getTestOutputDir()

Value

The path to the test output directory, as a character value.

Examples

# Get the test output directory:
biodb::getTestOutputDir()

Get a URL content.

Description

Get a URL content.

Usage

getUrlContent(u, binary = FALSE)

Arguments

u

The URL as a single character value.
binary

Set to TRUE if the content to be retrieved is binary.

Value

The content, as a single character value.

Send a request and get results.

Description

Send a request and get results.

Usage

getUrlRequestResult(request, useragent = NULL, ssl.verifypeer = TRUE)

Arguments

request

A BiodbRequest object.
useragent

The user agent identification.
ssl.verifypeer

Set to TRUE to enable SSL verify peer.

Value

A RequestResult object.

List test reference entries.

Description

DEPRECATED. Use TestRefEntries class instead.

Usage

listTestRefEntries(conn.id, pkgName, limit = 0)

Arguments

conn.id

A valid Biodb connector ID.
pkgName

The name of the
limit

The maximum number of entries to retrieve.

Details

Lists the reference entries in the test folder for a specified connector. The test reference files must be in ⁠<pkg>/inst/testref/⁠ folder and their names must match ⁠entry-<database_name>-<entry_accession>.json⁠ (e.g.: ⁠entry-comp.csv.file-1018.json⁠).

Value

A list of entry IDs.

Examples

# List IDs of test reference entries:
biodb::listTestRefEntries('comp.csv.file', pkgName='biodb')

Loads the contents of files in memory.

Description

This function loads the contents of a list of files and returns the contents as a list, each element being the content of a single file, in the same order. If a file could not be opened, a NULL value is used as the content. NA values are interpreted by default, but this behaviour can be turned off.

Usage

loadFileContents(x, naValues = "NA", outVect = FALSE)

Arguments

x

A character vector containing the paths of the files.
naValues

A character vector listing the content values to convert into NA value. Set to NULL to disable the interpretation of NA values. set to a different set of values to be interpreted.
outVect

If set to TRUE outputs a character vector (converting any NULL value into NA), otherwise outputs a list.

Value

A list with the contents of the files.

Log debug message.

Description

Logs a debug level message with biodb logger.

Usage

logDebug(...)

Arguments

...

Values to be passed to sprintf().

Value

Nothing.

Examples

# Logs a debug message:
biodb::logDebug('Index is %d.', 10)

Log debug message.

Description

Logs a debug level message with biodb logger, using paste0().

Usage

logDebug0(...)

Arguments

...

Values to be passed to paste0()

Value

Nothing.

Examples

# Logs a debug message:
biodb::logDebug0('Index is ', 10, '.')

Log information message.

Description

Logs an information level message with biodb logger.

Usage

logInfo(...)

Arguments

...

Values to be passed to sprintf().

Value

Nothing.

Examples

# Logs an info message:
biodb::logInfo('Index is %d.', 10)

Log information message.

Description

Logs an information level message with biodb logger, using paste0().

Usage

logInfo0(...)

Arguments

...

Values to be passed to paste0().

Value

Nothing.

Examples

# Logs an info message:
biodb::logInfo0('Index is ', 10, '.')

Log trace message.

Description

Logs a trace level message with biodb logger.

Usage

logTrace(...)

Arguments

...

Values to be passed to sprintf().

Value

Nothing.

Examples

# Logs a trace message:
biodb::logTrace('Index is %d.', 10)

Log trace message.

Description

Logs a trace level message with biodb logger, using paste0().

Usage

logTrace0(...)

Arguments

...

Values to be passed to paste0()

Value

Nothing.

Examples

# Logs a trace message:
biodb::logTrace0('Index is ', 10, '.')

Convert a list into a string.

Description

Prints a string (partially if too big) into a string.

Usage

lst2str(x, nCut = 10)

Arguments

x

The list to convert into a string.
nCut

The maximum of elements to print.

Value

A string containing the list representation (or part of it).

Examples

# Converts the first 5 elements of a list into a string:
s <- lst2str(1:10, nCut=5)

Build an RCurl::CURLOptions object.

Description

Build an RCurl::CURLOptions object.

Usage

makeRCurlOptions(
  useragent = NULL,
  httpheader = NULL,
  postfields = NULL,
  timeout.ms = 60000,
  verbose = FALSE
)

Arguments

useragent

The user agent identification.
httpheader

The HTTP header to send.
postfields

POST fields, in case of a POST method.
timeout.ms

The timeout in milliseconds.
verbose

Set to TRUE to get verbose output in RCurl.

Value

An RCurl::CURLOptions object.

Mass CSV File connector class.

Description

Mass CSV File connector class.

Mass CSV File connector class.

Details

This is the connector class for a MASS CSV file database.

Super classes

biodb::BiodbConnBase -> biodb::BiodbConn -> biodb::CsvFileConn -> MassCsvFileConn

Methods

Public methods

Inherited methods

Method new()

New instance initializer. Connector classes must not be instantiated directly. Instead, you must use the createConn() method of the factory class.

Usage
MassCsvFileConn$new(...)
Arguments
...

All parameters are passed to the super class initializer.

Returns

Nothing.

Method getPrecursorFormulae()

Gets the list of formulae used to recognize precursors.

Usage
MassCsvFileConn$getPrecursorFormulae()
Returns

A character vector containing chemical formulae.

Method isAPrecursorFormula()

Tests if a formula is a precursor formula.

Usage
MassCsvFileConn$isAPrecursorFormula(formula)
Arguments
formula

A chemical formula, as a character value.

Returns

TRUE if the submitted formula is considered a precursor.

Method setPrecursorFormulae()

Sets the list precursor formulae.

Usage
MassCsvFileConn$setPrecursorFormulae(formulae)
Arguments
formulae

A character vector containing formulae.

Returns

Nothing.

Method addPrecursorFormulae()

Adds new formulae to the list of formulae used to recognize precursors.

Usage
MassCsvFileConn$addPrecursorFormulae(formulae)
Arguments
formulae

A character vector containing formulae.

Returns

Nothing.

Method clone()

The objects of this class are cloneable with this method.

Usage
MassCsvFileConn$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

See Also

Super class CsvFileConn.

Examples

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

# Get path to LCMS database example file
lcmsdb <- system.file("extdata",
                      "massbank_extract_lcms_2.tsv", package="biodb")

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

# Get an entry
e <- conn$getEntry('PR010001')

# Terminate instance.
mybiodb$terminate()

Mass CSV File entry class.

Description

Mass CSV File entry class.

Mass CSV File entry class.

Details

This is the entry class for Mass CSV file databases.

Super classes

biodb::BiodbEntry -> biodb::BiodbCsvEntry -> MassCsvFileEntry

Methods

Public methods

Inherited methods

Method new()

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

Usage
MassCsvFileEntry$new(...)
Arguments
...

All parameters are passed to the super class initializer.

Returns

Nothing.

Method clone()

The objects of this class are cloneable with this method.

Usage
MassCsvFileEntry$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

See Also

Super class BiodbCsvEntry.

Examples

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

# Get path to LCMS database example file
lcmsdb <- system.file("extdata",
                      "massbank_extract_lcms_2.tsv", package="biodb")

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

# Get an entry
e <- conn$getEntry('PR010001')

# Terminate instance.
mybiodb$terminate()

Class for handling a Mass spectrometry database in SQLite format.

Description

This is the connector class for a MASS SQLite database.

Super classes

biodb::BiodbConnBase -> biodb::BiodbConn -> biodb::SqliteConn -> MassSqliteConn

Methods

Public methods

Inherited methods

Method clone()

The objects of this class are cloneable with this method.

Usage
MassSqliteConn$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

See Also

Super class SqliteConn.

Examples

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

# Get path to LCMS database example file
lcmsdb <- system.file("extdata", "massbank_extract.sqlite", package="biodb")

# Create a connector
conn <- mybiodb$getFactory()$createConn('mass.sqlite', url=lcmsdb)

# Get an entry
e <- conn$getEntry('34.pos.col12.0.78')

# Terminate instance.
mybiodb$terminate()

Mass spectra SQLite entry class.

Description

This is the entry class for a Mass spectra SQLite database.

Super classes

biodb::BiodbEntry -> biodb::BiodbListEntry -> MassSqliteEntry

Methods

Public methods

Inherited methods

Method clone()

The objects of this class are cloneable with this method.

Usage
MassSqliteEntry$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

See Also

Super class BiodbListEntry.

Examples

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

# Get path to LCMS database example file
lcmsdb <- system.file("extdata", "massbank_extract.sqlite", package="biodb")

# Create a connector
conn <- mybiodb$getFactory()$createConn('mass.sqlite', url=lcmsdb)

# Get an entry
e <- conn$getEntry('34.pos.col12.0.78')

# Terminate instance.
mybiodb$terminate()

Create a new BiodbMain instance.

Description

Instantiates a new BiodbMain object by calling the constructor.

Usage

newInst(...)

Arguments

...

The parameters to pass to the BiodbMain constructor. See BiodbMain.

Value

A new BiodbMain instance.

See Also

BiodbMain.

Examples

# Create a new BiodbMain instance:
mybiodb <- biodb::newInst()

# Terminate the instance:
mybiodb$terminate()

Prepares file contents for saving.

Description

Prepares file contents for saving.

Usage

prepareFileContents(contents)

Arguments

contents

File contents, as a list or a character vector.

Value

File contents.

Progress class.

Description

A class for informing user about the progress of a process.

Details

This class displays progress of a process to user, and sends notifications of this progress to observers too.

Methods

Public methods

Method new()

Initializer.

Usage
Progress$new(biodb = NULL, msg, total = NA_integer_)
Arguments
biodb

A BiodbMain instance that will be used to notify observers of progress.

msg

The message to display to the user.

total

The total number of elements to process or NA if unknown.

Returns

Nothing.

Method increment()

Increment progress.

Usage
Progress$increment()
Returns

Nothing.

Method clone()

The objects of this class are cloneable with this method.

Usage
Progress$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Examples

# Create an instance
prg <- biodb::Progress$new(msg='Processing data.', total=10L)

# Processing
for (i in seq_len(10)) {
    print("Doing something.")
    prg$increment()
}

Range class.

Description

Range class.

Range class.

Details

A class for storing min/max range or value/tolerance.

Methods

Public methods

Method new()

Initializer.

Usage
Range$new(
  min = NULL,
  max = NULL,
  value = NULL,
  delta = NULL,
  ppm = NULL,
  tol = NULL,
  tolType = c("delta", "plain", "ppm")
)
Arguments
min

The minimum value of the range.

max

The maximum value of the range.

value

The value.

delta

The delta tolerance.

ppm

The PPM tolerance.

tol

The tolerance value, whose type (ppm or delta) is specified by the "tolType" parameter.

tolType

The type of the tolerance value specified by the "tol" parameter.

Returns

Nothing.

Examples
# Create an instance from min and max:
Range$new(min=1.2, max=1.5)

Method getValue()

Gets the middle value of the range.

Usage
Range$getValue()
Returns

The middle value.

Method getMin()

Gets the minimum value of the range.

Usage
Range$getMin()
Returns

The minimum value.

Method getMax()

Gets the maximum value of the range.

Usage
Range$getMax()
Returns

The maximum value.

Method getMinMax()

Get the min/max range.

Usage
Range$getMinMax()
Returns

A list containing two fields: "min" and "max.

Method getDelta()

Gets the delta tolerance of the range.

Usage
Range$getDelta()
Returns

The delta tolerance.

Method getPpm()

Gets the PPM tolerance of the range.

Usage
Range$getPpm()
Returns

The tolerance in PPM.

Method getTolExpr()

Gets the tolerance expression as a list.

Usage
Range$getTolExpr()
Returns

A list containing the tolerance range expression.

Method clone()

The objects of this class are cloneable with this method.

Usage
Range$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Examples

# Convert a min/max range into a value/ppm tolerance:
rng <- Range$new(min=0.4, max=0.401)
value <- rng$getValue()
ppm <- rng$getPpm()


## ------------------------------------------------
## Method `Range$new`
## ------------------------------------------------

# Create an instance from min and max:
Range$new(min=1.2, max=1.5)

Class RequestResult.

Description

Class RequestResult.

Class RequestResult.

Details

Represents the result of a request.

Methods

Public methods

Method new()

New instance initializer.

Usage
RequestResult$new(
  content = NULL,
  retry = FALSE,
  errMsg = NULL,
  status = 0,
  statusMessage = "",
  retryAfter = NULL,
  location = NULL
)
Arguments
content

The result content.

retry

If request should be resent.

errMsg

Error message.

status

HTTP status.

statusMessage

Status message.

retryAfter

Time after which to retry.

location

New location.

Returns

Nothing.

Method getContent()

Get content.

Usage
RequestResult$getContent()
Returns

The content as a character value or NULL.

Method getRetry()

Get the retry flag.

Usage
RequestResult$getRetry()
Returns

TRUE if the URL request should be sent again, FALSE otherwise.

Method getErrMsg()

Get the error message.

Usage
RequestResult$getErrMsg()
Returns

The error message as a character value or NULL.

Method getStatus()

Get the HTTP status of the response.

Usage
RequestResult$getStatus()
Returns

The status as an integer.

Method getRetryAfter()

Get the time to wait before retrying.

Usage
RequestResult$getRetryAfter()
Returns

The time.

Method getLocation()

Get the redirect location.

Usage
RequestResult$getLocation()
Returns

The redirect location as a character value or NULL.

Method processRequestErrors()

Process possible HTTP error.

Usage
RequestResult$processRequestErrors()
Returns

Nothing.

Method clone()

The objects of this class are cloneable with this method.

Usage
RequestResult$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Run generic tests.

Description

This function must be used in tests on all connector classes, before any specific tests.

Usage

runGenericTests(
  conn,
  pkgName,
  testRefFolder = NULL,
  opt = NULL,
  short = TRUE,
  long = FALSE,
  maxShortTestRefEntries = 1
)

Arguments

conn

A valid biodb connector.
pkgName

The name of your package.
testRefFolder

The folder where to find test reference files.
opt

A set of options to pass to the test functions.
short

Run short tests.
long

Run long tests.
maxShortTestRefEntries

The maximum number of reference entries to use in short tests.

Value

Nothing.

Examples

# Instantiate a Biodb instance for testing
biodb <- biodb::createBiodbTestInstance()

# Create a connector instance
lcmsdb <- system.file("extdata", "massbank_extract.tsv", package="biodb")
conn <- biodb$getFactory()$createConn('mass.csv.file', lcmsdb)

# Run generic tests

biodb::runGenericTests(conn)


# Terminate the instance
biodb$terminate()

Saves contents to files.

Description

Saves contents to files.

Usage

saveContentsToFiles(files, contents, prepareContents = FALSE)

Arguments

files

The file paths to use for saving contents.
contents

The contents to save, as a list or a character vector.
prepareContents

If set to TRUE, then calls prepareFileContents() on the contents before saving them.

Value

Nothing.

SQLite connector class.

Description

SQLite connector class.

SQLite connector class.

Details

This is the abstract connector class for all SQLite databases.

Super classes

biodb::BiodbConnBase -> biodb::BiodbConn -> SqliteConn

Methods

Public methods

Inherited methods

Method new()

New instance initializer. Connector classes must not be instantiated directly. Instead, you must use the createConn() method of the factory class.

Usage
SqliteConn$new(...)
Arguments
...

All parameters are passed to the super class initializer.

Returns

Nothing.

Method hasField()

Tests if a field is defined for this database instance.

Usage
SqliteConn$hasField(field)
Arguments
field

A valid Biodb entry field name.

Returns

TRUE of the field is defined, FALSE otherwise.

Method getQuery()

Run a query using a biodb SQL object.

Usage
SqliteConn$getQuery(query)
Arguments
query

A valid BiodbSqlQuery object.

Returns

The result returned by DBI::dbGetQuery() call.

Method clone()

The objects of this class are cloneable with this method.

Usage
SqliteConn$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

See Also

Super class BiodbConn and sub-classes CompSqliteConn, and MassSqliteConn.

Examples

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

# Get a connector that inherits from SqliteConn:
chebi_file <- system.file("extdata", "chebi_extract.sqlite", package="biodb")
conn <- mybiodb$getFactory()$createConn('comp.sqlite', url=chebi_file)

# Get an entry
e <- conn$getEntry('1018')

# Terminate instance.
mybiodb$terminate()

Set a test context.

Description

Define a context for tests using testthat framework. In addition to calling testthat::context().

Usage

testContext(text)

Arguments

text

The text to print as test context.

Value

No value returned.

Examples

# Define a context before running tests:
biodb::testContext("Test my database connector.")

# Instantiate a BiodbMain instance for testing
biodb <- biodb::createBiodbTestInstance()

# Terminate the instance
biodb$terminate()

A class for accessing the test reference entries.

Description

A class for accessing the test reference entries.

A class for accessing the test reference entries.

Details

The test reference entries are stored as JSON files inside inst/testref folder of each extension package.

Methods

Public methods

Method new()

New instance initializer.

Usage
TestRefEntries$new(db.class, pkgName, folder = NULL, bdb = NULL)
Arguments
db.class

Identifier of the database.

pkgName

Name of the package in which are stored the reference entry files.

folder

The folder where to find test reference files for the package. Usually it is "inst/testref".

bdb

A valid BiodbMain instance or NULL.

Returns

Nothing.

Method getAllIds()

Retrieve all identifiers.

Usage
TestRefEntries$getAllIds(limit = 0)
Arguments
limit

The maximum number of identifiers to return.

Returns

A character vector containing the IDs.

Method getContents()

Get the reference contents for the specfied IDs.

Usage
TestRefEntries$getContents(ids)
Arguments
ids

The reference IDs for which to get the contents.

Returns

A character vector.

Method getRealEntries()

Retrieve all real entries from database corresponding to the reference entris.

Usage
TestRefEntries$getRealEntries(ids = NULL)
Arguments
ids

A character vector of entry identifiers.

Returns

A list containing BiodbEntry instances.

Method saveEntriesAsJson()

Saves a list of entries into separate JSON files, inside the test output folder.

Usage
TestRefEntries$saveEntriesAsJson(ids, entries)
Arguments
ids

The IDs of the entries.

entries

A list of entries. It can contain NULL values.

Returns

Nothing.

Method getRealEntry()

Retrieves one real entry from database corresponding to one reference entry.

Usage
TestRefEntries$getRealEntry(id)
Arguments
id

The identifier of the entry.

Returns

A BiodbEntry instance.

Method getRefEntry()

Retrieves the content of a single reference entry.

Usage
TestRefEntries$getRefEntry(id)
Arguments
id

The identifier of the reference entry to retrieve.

Returns

The content of the reference entry as a list.

Method getAllRefEntriesDf()

Load all reference entries.

Usage
TestRefEntries$getAllRefEntriesDf()
Returns

A data frame containing all the reference entries with their values.

Method clone()

The objects of this class are cloneable with this method.

Usage
TestRefEntries$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Examples

# Creates an instance
refEntries <- TestRefEntries$new('comp.sqlite', pkgName='biodb')

# Gets identifiers of all reference entries
refEntries$getAllIds()

# Gets a data frame with the content of the reference entries
refEntries$getAllRefEntriesDf()

Run a test.

Description

Run a test function, using testthat framework. In addition to calling testthat::test_that().

Usage

testThat(msg, fct, biodb = NULL, conn = NULL, opt = NULL)

Arguments

msg

The test message.
fct

The function to test.
biodb

A valid BiodbMain instance to be passed to the test function.
conn

A connector instance to be passed to the test function.
opt

A set of options to pass to the test function.

Value

No value returned.

Examples

# Define a context before running tests:
biodb::testContext("Test my database connector.")

# Instantiate a BiodbMain instance for testing
biodb <- biodb::createBiodbTestInstance()

# Define a test function
my_test_function <- function(biodb) {
  # Do my tests...
}

# Run test
biodb::testThat("My test works", my_test_function, biodb=biodb)

# Terminate the instance
biodb$terminate()

Upgrading an existing extension package for biodb.

Description

Upgrades some of the files previously generated (.gitignore, .travis.yml, .Rbuildignore, Makefile, etc) to the latest versions.

Usage

upgradeExtPkg(...)

Arguments

...

Parameters passed to ExtPackage constructor.

Value

Nothing.

Examples

# Generate a new package:
pkgFolder <- file.path(tempfile(), 'biodbFoo')
dir.create(pkgFolder, recursive=TRUE)
biodb::genNewExtPkg(path=pkgFolder, dbName='foo.db',
                    dbTitle='Foo database', rcpp=TRUE,
                    connType='mass', entryType='txt', downloadable=TRUE,
                    remote=TRUE)

# Upgrade it later
biodb::upgradeExtPkg(path=pkgFolder)

Throw a warning and log it too.

Description

Throws a warning and logs it too with biodb logger.

Usage

warn(...)

Arguments

...

Values to be passed to sprintf().

Value

Nothing.

Examples

# Throws a warning:
tryCatch(biodb::warn('Index is %d.', 10), warning=function(w){w$message})

Throw a warning and log it too.

Description

Throws a warning and logs it too with biodb logger, using paste0().

Usage

warn0(...)

Arguments

...

Values to be passed to paste0().

Value

Nothing.

Examples

# Throws a warning:
tryCatch(biodb::warn0('Index is ', 10, '.'), warning=function(w){w$message})