SqliteConn {biodb} | R Documentation

## 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

- `SqliteConn$new()`

- `SqliteConn$isSearchableByField()`

- `SqliteConn$hasField()`

- `SqliteConn$getQuery()`

- `SqliteConn$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$print()`

- `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

    SqliteConn$new(...)

##### Arguments

`...`

  All parameters are passed to the super class initializer.

##### Returns

Nothing.

#### Method `isSearchableByField()`

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

##### Usage

    SqliteConn$isSearchableByField(field)

##### Arguments

`field`

  The name of the field.

##### Returns

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

#### 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()

[Package biodb version 1.2.2 Index]