TestRefEntries {biodb} | R Documentation

## 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

- `TestRefEntries$new()`

- `TestRefEntries$getAllIds()`

- `TestRefEntries$getContents()`

- `TestRefEntries$getRealEntries()`

- `TestRefEntries$saveEntriesAsJson()`

- `TestRefEntries$getRealEntry()`

- `TestRefEntries$getRefEntry()`

- `TestRefEntries$getAllRefEntriesDf()`

- `TestRefEntries$clone()`

#### 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()

[Package biodb version 1.2.2 Index]