CsvFileConn {biodb} | R Documentation

## 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

- `CsvFileConn$new()`

- `CsvFileConn$getCsvQuote()`

- `CsvFileConn$setCsvQuote()`

- `CsvFileConn$getCsvSep()`

- `CsvFileConn$setCsvSep()`

- `CsvFileConn$getFieldNames()`

- `CsvFileConn$hasField()`

- `CsvFileConn$isSearchableByField()`

- `CsvFileConn$addField()`

- `CsvFileConn$getFieldColName()`

- `CsvFileConn$setField()`

- `CsvFileConn$getFieldsAndColumnsAssociation()`

- `CsvFileConn$getUnassociatedColumns()`

- `CsvFileConn$print()`

- `CsvFileConn$setDb()`

- `CsvFileConn$setIgnoreUnassignedColumns()`

- `CsvFileConn$clone()`

Inherited methods

- `biodb::BiodbConnBase$getBaseUrl()`

- `biodb::BiodbConnBase$getConnClass()`

- `biodb::BiodbConnBase$getConnClassName()`

- `biodb::BiodbConnBase$getDbClass()`

- `biodb::BiodbConnBase$getEntryClass()`

- `biodb::BiodbConnBase$getEntryClassName()`

- `biodb::BiodbConnBase$getEntryContentType()`

- `biodb::BiodbConnBase$getEntryFileExt()`

- `biodb::BiodbConnBase$getEntryIdField()`

- `biodb::BiodbConnBase$getName()`

- `biodb::BiodbConnBase$getPropSlots()`

- `biodb::BiodbConnBase$getPropValSlot()`

- `biodb::BiodbConnBase$getPropertyValue()`

- `biodb::BiodbConnBase$getSchedulerNParam()`

- `biodb::BiodbConnBase$getSchedulerTParam()`

- `biodb::BiodbConnBase$getToken()`

- `biodb::BiodbConnBase$getUrl()`

- `biodb::BiodbConnBase$getUrls()`

- `biodb::BiodbConnBase$getWsUrl()`

- `biodb::BiodbConnBase$getXmlNs()`

- `biodb::BiodbConnBase$hasProp()`

- `biodb::BiodbConnBase$hasPropSlot()`

- `biodb::BiodbConnBase$isSlotProp()`

- `biodb::BiodbConnBase$propExists()`

- `biodb::BiodbConnBase$setBaseUrl()`

- `biodb::BiodbConnBase$setPropValSlot()`

- `biodb::BiodbConnBase$setPropertyValue()`

- `biodb::BiodbConnBase$setSchedulerNParam()`

- `biodb::BiodbConnBase$setSchedulerTParam()`

- `biodb::BiodbConnBase$setToken()`

- `biodb::BiodbConnBase$setUrl()`

- `biodb::BiodbConnBase$setWsUrl()`

- `biodb::BiodbConnBase$updatePropertiesDefinition()`

- `biodb::BiodbConn$addNewEntry()`

- `biodb::BiodbConn$allowEditing()`

- `biodb::BiodbConn$allowWriting()`

- `biodb::BiodbConn$annotateMzValues()`

- `biodb::BiodbConn$checkDb()`

- `biodb::BiodbConn$collapseResultsDataFrame()`

- `biodb::BiodbConn$correctIds()`

- `biodb::BiodbConn$deleteAllCacheEntries()`

- `biodb::BiodbConn$deleteAllEntriesFromPersistentCache()`

- `biodb::BiodbConn$deleteAllEntriesFromVolatileCache()`

- `biodb::BiodbConn$deleteWholePersistentCache()`

- `biodb::BiodbConn$disallowEditing()`

- `biodb::BiodbConn$disallowWriting()`

- `biodb::BiodbConn$download()`

- `biodb::BiodbConn$editingIsAllowed()`

- `biodb::BiodbConn$filterEntriesOnRt()`

- `biodb::BiodbConn$getAllCacheEntries()`

- `biodb::BiodbConn$getAllVolatileCacheEntries()`

- `biodb::BiodbConn$getBiodb()`

- `biodb::BiodbConn$getCacheFile()`

- `biodb::BiodbConn$getCacheId()`

- `biodb::BiodbConn$getChromCol()`

- `biodb::BiodbConn$getDownloadPath()`

- `biodb::BiodbConn$getEntry()`

- `biodb::BiodbConn$getEntryContent()`

- `biodb::BiodbConn$getEntryContentFromDb()`

- `biodb::BiodbConn$getEntryContentRequest()`

- `biodb::BiodbConn$getEntryIds()`

- `biodb::BiodbConn$getEntryImageUrl()`

- `biodb::BiodbConn$getEntryPageUrl()`

- `biodb::BiodbConn$getId()`

- `biodb::BiodbConn$getMatchingMzField()`

- `biodb::BiodbConn$getMzValues()`

- `biodb::BiodbConn$getNbEntries()`

- `biodb::BiodbConn$getNbPeaks()`

- `biodb::BiodbConn$getSearchableFields()`

- `biodb::BiodbConn$isCompounddb()`

- `biodb::BiodbConn$isDownloadable()`

- `biodb::BiodbConn$isDownloaded()`

- `biodb::BiodbConn$isEditable()`

- `biodb::BiodbConn$isExtracted()`

- `biodb::BiodbConn$isMassdb()`

- `biodb::BiodbConn$isRemotedb()`

- `biodb::BiodbConn$isWritable()`

- `biodb::BiodbConn$makeRequest()`

- `biodb::BiodbConn$makesRefToEntry()`

- `biodb::BiodbConn$msmsSearch()`

- `biodb::BiodbConn$requiresDownload()`

- `biodb::BiodbConn$searchByName()`

- `biodb::BiodbConn$searchCompound()`

- `biodb::BiodbConn$searchForEntries()`

- `biodb::BiodbConn$searchForMassSpectra()`

- `biodb::BiodbConn$searchMsEntries()`

- `biodb::BiodbConn$searchMsPeaks()`

- `biodb::BiodbConn$searchMzRange()`

- `biodb::BiodbConn$searchMzTol()`

- `biodb::BiodbConn$setDownloadedFile()`

- `biodb::BiodbConn$setEditingAllowed()`

- `biodb::BiodbConn$setMatchingMzField()`

- `biodb::BiodbConn$setWritingAllowed()`

- `biodb::BiodbConn$write()`

- `biodb::BiodbConn$writingIsAllowed()`

#### 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 `isSearchableByField()`

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

##### Usage

    CsvFileConn$isSearchableByField(field)

##### Arguments

`field`

  The name of the field.

##### Returns

Returns TRUE if the database is searchable using the specified field, 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()

[Package biodb version 1.2.2 Index]