BiodbPersistentCache {biodb} | R Documentation

## 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

- `BiodbPersistentCache$new()`

- `BiodbPersistentCache$isReadable()`

- `BiodbPersistentCache$isWritable()`

- `BiodbPersistentCache$getDir()`

- `BiodbPersistentCache$getFolderPath()`

- `BiodbPersistentCache$folderExists()`

- `BiodbPersistentCache$getFilePath()`

- `BiodbPersistentCache$filesExist()`

- `BiodbPersistentCache$fileExist()`

- `BiodbPersistentCache$fileExists()`

- `BiodbPersistentCache$markerExist()`

- `BiodbPersistentCache$markerExists()`

- `BiodbPersistentCache$setMarker()`

- `BiodbPersistentCache$getTmpFolderPath()`

- `BiodbPersistentCache$getUsedCacheIds()`

- `BiodbPersistentCache$loadFileContent()`

- `BiodbPersistentCache$saveContentToFile()`

- `BiodbPersistentCache$addFilesToCache()`

- `BiodbPersistentCache$copyFilesIntoCache()`

- `BiodbPersistentCache$moveFilesIntoCache()`

- `BiodbPersistentCache$erase()`

- `BiodbPersistentCache$deleteFile()`

- `BiodbPersistentCache$deleteAllFiles()`

- `BiodbPersistentCache$deleteFiles()`

- `BiodbPersistentCache$listFiles()`

- `BiodbPersistentCache$print()`

- `BiodbPersistentCache$enabled()`

- `BiodbPersistentCache$enable()`

- `BiodbPersistentCache$disable()`

- `BiodbPersistentCache$clone()`

#### 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()

[Package biodb version 1.2.2 Index]