BiodbRemotedbConn-class {biodb} | R Documentation

## The mother class of all remote database connectors.

### Description

This is the super class of remote database connectors. It thus defines methods related to remote connection, like the definition of a token, and URL definitions. As with `BiodbConn` class, you won't need to use the constructor. Nevertheless we provide in the Fields section information about the constructor parameters, for eventual developers.

### Methods

`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.

`getEntryContentRequest(entry.id, concatenate = TRUE, max.length = 0)`

  :

  Gets the URL to use in order to get the contents of the specified entries.

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

  concatenate: If set to TRUE, then try to build as few URLs as possible, sending requests with several identifiers at once.

  max.length: The maximum length of the URLs to return, in number of characters.

  Returned value: A list of BiodbUrl objects.

`getEntryImageUrl(entry.id)`

  :

  Gets the URL to a picture of the entry (e.g.: a picture of the molecule in case of a compound entry).

  entry.id: A character vector containing entry IDs.

  Returned value: A character vector, the same length as 'entry.id', containing for each entry ID either a URL or NA if no URL exists.

`getEntryPageUrl(entry.id)`

  :

  Gets the URL to the page of the entry on the database web site.

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

  Returned value: A list of BiodbUrl objects, the same length as 'entry.id'.

### See Also

Super class `BiodbConn` and `BiodbRequestScheduler`.

### Examples

    # Create an instance with default settings:
    mybiodb <- biodb::newInst()

    # Define ChEBI connector example
    defFile <- system.file("extdata", "chebi_ex.yml", package="biodb")
    connFile <- system.file("extdata", "ChebiExConn.R", package="biodb")
    entryFile <- system.file("extdata", "ChebiExEntry.R", package="biodb")
    mybiodb$loadDefinitions(defFile)
    source(connFile)
    source(entryFile)

    # Get connector
    conn <- mybiodb$getFactory()$createConn('chebi.ex')

    # Get the picture URL of an entry
    picture.url <- conn$getEntryImageUrl('15440')

    # Get the page URL of an entry
    page.url <- conn$getEntryPageUrl('15440')

    # Terminate instance.
    mybiodb$terminate()

[Package biodb version 1.0.4 Index]