CsvFileConn-class {biodb}R Documentation

CSV File connector class.

Description

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

Methods

addField(field, value)

:

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.

field: A valid Biodb entry field name.

value: The value to set for this field.

Returned value: None.

getCsvQuote()

:

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

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

getCsvSep()

:

Gets the current CSV separator used for the database file.

Returned value: The CSV separator as a character value.

getEntryContentFromDb(entry.id)

:

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.

entry.id: A character vector with the IDs of entries to retrieve.

Returned value: 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.

getFieldColName(field)

:

Get the column name corresponding to a Biodb field.

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

Returned value: The column name from the CSV file.

getFieldNames()

:

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

Returned value: A character vector of the biodb field names.

getNbEntries(count = FALSE)

:

Get the number of entries contained in this database.

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

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

hasField(field)

:

Tests if a field is defined for this database instance.

field: A valid Biodb entry field name.

Returned value: TRUE of the field is defined, FALSE otherwise.

isSearchableByField(field)

:

Tests if a field can be used to search entries when using methods searchByName() and searchCompound().

field: The name of the field.

Returned value: Returns TRUE if the database is searchable using the specified field, FALSE otherwise.

setCsvQuote(quote)

:

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

quote: The characters used to delimit quotes as a single character value. You may specify several characters. Example: "\"'".

Returned value: None.

setCsvSep(sep)

:

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.

sep: The CSV separator as a character value.

Returned value: None.

setDb(db)

:

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

db: A data frame containing your database.

Returned value: None.

setField(field, colname, ignore.if.missing = FALSE)

:

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

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.

Returned value: None.

show()

:

Prints a description of this connector.

Returned value: None.

See Also

Super classes BiodbConn, BiodbWritable, BiodbEditable, 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()


[Package biodb version 1.0.4 Index]