Package {resourcer}

Type: Package
Title: Resource Resolver
Version: 1.5.2
Description: A resource represents some data or a computation unit. It is described by a URL and credentials. This package proposes a Resource model with "resolver" and "client" classes to facilitate the access and the usage of the resources.
License: LGPL-2.1 | LGPL-3 [expanded from: LGPL (≥ 2.1)]
Depends: R (≥ 3.5.0), R6, httr
Suggests: testthat, knitr, haven, readr, readxl, ssh, sys, mongolite, dplyr, dbplyr, DBI, RMariaDB, RPostgres, sparklyr, nodbi, rmarkdown
URL: https://www.obiba.org/resourcer/
BugReports: https://github.com/obiba/resourcer/issues
VignetteBuilder: knitr
Encoding: UTF-8
Config/roxygen2/version: 8.1.0
NeedsCompilation: no
Packaged: 2026-11-07 12:46:10 UTC; yannick
Author: Yannick Marcon ORCID iD [aut, cre], OBiBa group [cph]
Maintainer: Yannick Marcon <yannick.marcon@obiba.org>
Repository: CRAN
Date/Publication: 2026-11-07 13:10:02 UTC

Command resource client

Description

Base class for resource clients issuing commands and get a result with the status of the execution, the output and the error messages.

Format

A R6 object of class CommandResourceClient

Super class

ResourceClient -> CommandResourceClient

Methods

Public methods

Inherited methods

CommandResourceClient$new()

Creates a new CommandResourceClient instance

Usage
CommandResourceClient$new(resource)
Arguments
resource

A valid resource object.

Returns

A CommandResourceClient object.

CommandResourceClient$clone()

The objects of this class are cloneable with this method.

Usage
CommandResourceClient$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

DBI resource connector

Description

Makes a DBI connection from a resource description, used in SQLResourceClient that is based on DBI.

Format

A R6 object of class DBIResourceConnector

Methods

Public methods

DBIResourceConnector$new()

Creates a new DBIResourceConnector instance

Usage
DBIResourceConnector$new()
Returns

A DBIResourceConnector object.

DBIResourceConnector$isFor()

Check that the provided parameter is of class "resource".

Usage
DBIResourceConnector$isFor(resource)
Arguments
resource

The resource object to validate.

Returns

A logical.

DBIResourceConnector$createDBIConnection()

Stub function which subclasses will implement to create a DBI connection object from a resource.

Usage
DBIResourceConnector$createDBIConnection(resource)
Arguments
resource

A valid resource object.

DBIResourceConnector$getTableName()

Get the SQL table name from the resource URL.

Usage
DBIResourceConnector$getTableName(resource)
Arguments
resource

A valid resource object.

Returns

The SQL table name.

DBIResourceConnector$readDBTable()

Read a table as a vanilla tibble using DBI connection object.

Usage
DBIResourceConnector$readDBTable(conn, resource)
Arguments
conn

A DBI connection object.

resource

A valid resource object.

Returns

A vanilla tibble.

DBIResourceConnector$readDBTibble()

Read a table as a SQL tibble using DBI connection object.

Usage
DBIResourceConnector$readDBTibble(conn, resource)
Arguments
conn

A DBI connection object.

resource

A valid resource object.

Returns

A SQL tibble.

DBIResourceConnector$closeDBIConnection()

Disconnect the DBI connection.

Usage
DBIResourceConnector$closeDBIConnection(conn)
Arguments
conn

A DBI connection object.

DBIResourceConnector$clone()

The objects of this class are cloneable with this method.

Usage
DBIResourceConnector$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

File resource client

Description

Base class that connects to a file using a FileResourceGetter.

Format

A R6 object of class FileResourceClient

Super class

ResourceClient -> FileResourceClient

Methods

Public methods

Inherited methods

FileResourceClient$new()

Creates a new FileResourceClient instance.

Usage
FileResourceClient$new(resource, file.getter = NULL)
Arguments
resource

A valid resource object.

file.getter

A FileResourceGetter object, optional. If not provided, it will be looked up in the FileResourceGetters registry. The operation will fail if none can be found.

Returns

A FileResourceClient object.

FileResourceClient$downloadFile()

Performs the file download, if it does not already exists locally.

Usage
FileResourceClient$downloadFile()
Returns

The local path to the downloaded file.

FileResourceClient$close()

Removes the file if it was downloaded. A local file resource will remain untouched.

Usage
FileResourceClient$close()

FileResourceClient$clone()

The objects of this class are cloneable with this method.

Usage
FileResourceClient$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

File resource getter

Description

Helper base class for getting the file described by the resource object. ResourceClient class implementations can use this utility to retrieve files from any locations before processing them according to the declared data format.

Format

A R6 object of class FileResourceGetter

Methods

Public methods

FileResourceGetter$new()

Creates a new FileResourceGetter instance.

Usage
FileResourceGetter$new()
Returns

A FileResourceGetter object.

FileResourceGetter$isFor()

Check that the provided parameter is of class "resource" and has a format defined.

Usage
FileResourceGetter$isFor(resource)
Arguments
resource

The resource object to validate.

Returns

A logical.

FileResourceGetter$downloadFile()

Stub function which subclasses will implement to make a "resource.file" object from a resource.

Usage
FileResourceGetter$downloadFile(resource, ...)
Arguments
resource

A valid resource object.

...

Additional parameters that may be relevant for FileResourceGetter subclasses.

Returns

A "resource.file" object.

FileResourceGetter$extractFileName()

Utility to get the base name from the file path.

Usage
FileResourceGetter$extractFileName(resource)
Arguments
resource

A valid resource object.

Returns

The file base name.

FileResourceGetter$makeDownloadDir()

Creates a directory where to download file in the R session's temporary directory. This directory will be flushed when the R session ends.

Usage
FileResourceGetter$makeDownloadDir()
Returns

The path to the download directory.

FileResourceGetter$clone()

The objects of this class are cloneable with this method.

Usage
FileResourceGetter$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

GridFS file resource getter

Description

Access a file that is in the MongoDB file store (GridFS). Credentials may apply.

Format

A R6 object of class GridFsFileResourceGetter

Super class

FileResourceGetter -> GridFsFileResourceGetter

Methods

Public methods

Inherited methods

GridFsFileResourceGetter$new()

Creates a new GridFsFileResourceGetter instance.

Usage
GridFsFileResourceGetter$new()
Returns

A GridFsFileResourceGetter object.

GridFsFileResourceGetter$isFor()

Check that the provided resource has a URL that locates a GridFS object: either the URL scheme is "gridfs" or it is "mongodb"/"mongodb+srv" with a query parameter "prefix=fs" (that identifies GridFS collection names).

Usage
GridFsFileResourceGetter$isFor(resource)
Arguments
resource

The resource object to validate.

Returns

A logical.

GridFsFileResourceGetter$downloadFile()

Download the file from the MongoDB file store in a temporary location.

Usage
GridFsFileResourceGetter$downloadFile(resource, ...)
Arguments
resource

A valid resource object.

...

Unused additional parameters.

Returns

The "resource.file" object.

GridFsFileResourceGetter$clone()

The objects of this class are cloneable with this method.

Usage
GridFsFileResourceGetter$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

HTTP file resource getter

Description

Access a file that is stored at a HTTP(S) address. Use Basic authentication header if both resource's identity and secret are defined.

Format

A R6 object of class HttpFileResourceGetter

Super class

FileResourceGetter -> HttpFileResourceGetter

Methods

Public methods

Inherited methods

HttpFileResourceGetter$new()

Creates a new HttpFileResourceGetter instance.

Usage
HttpFileResourceGetter$new()
Returns

A HttpFileResourceGetter object.

HttpFileResourceGetter$isFor()

Check that the provided resource has a URL that locates a file accessible through "http" or "https".

Usage
HttpFileResourceGetter$isFor(resource)
Arguments
resource

The resource object to validate.

Returns

A logical.

HttpFileResourceGetter$downloadFile()

Download the file from the remote address in a temporary location. Applies Basic authentication if credentials are provided in the resource.

Usage
HttpFileResourceGetter$downloadFile(resource, ...)
Arguments
resource

A valid resource object.

...

Unused additional parameters.

Returns

The "resource.file" object.

HttpFileResourceGetter$clone()

The objects of this class are cloneable with this method.

Usage
HttpFileResourceGetter$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Local file resource getter

Description

Access a file that is stored in the local file system. No credentials apply.

Format

A R6 object of class LocalFileResourceGetter

Super class

FileResourceGetter -> LocalFileResourceGetter

Methods

Public methods

Inherited methods

LocalFileResourceGetter$new()

Creates a new LocalFileResourceGetter instance.

Usage
LocalFileResourceGetter$new()
Returns

A LocalFileResourceGetter object.

LocalFileResourceGetter$isFor()

Check that the provided resource has a URL that locates a file stored in the local file system.

Usage
LocalFileResourceGetter$isFor(resource)
Arguments
resource

The resource object to validate.

Returns

A logical.

LocalFileResourceGetter$downloadFile()

Make a "resource.file" object from a local file resource.

Usage
LocalFileResourceGetter$downloadFile(resource, ...)
Arguments
resource

A valid resource object.

...

Unused additional parameters.

Returns

The "resource.file" object.

LocalFileResourceGetter$clone()

The objects of this class are cloneable with this method.

Usage
LocalFileResourceGetter$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

MariaDB DBI resource connector

Description

Makes a MariaDB/MySQL DBI connection from a resource description.

Format

A R6 object of class MariaDBResourceConnector

Super class

DBIResourceConnector -> MariaDBResourceConnector

Methods

Public methods

Inherited methods

MariaDBResourceConnector$new()

Creates a new MariaDBResourceConnector instance.

Usage
MariaDBResourceConnector$new()
Returns

A MariaDBResourceConnector object.

MariaDBResourceConnector$isFor()

Check that the provided resource has a URL that locates a MySQL or MariaDB object: the URL scheme must be "mysql" or "mariadb".

Usage
MariaDBResourceConnector$isFor(resource)
Arguments
resource

The resource object to validate.

Returns

A logical.

MariaDBResourceConnector$createDBIConnection()

Creates a DBI connection object from a resource.

Usage
MariaDBResourceConnector$createDBIConnection(resource)
Arguments
resource

A valid resource object.

Returns

A DBI connection object.

MariaDBResourceConnector$clone()

The objects of this class are cloneable with this method.

Usage
MariaDBResourceConnector$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

NoSQL database resource client

Description

Resource client that connects to a NoSQL database supported by nodbi.

Format

A R6 object of class NoSQLResourceClient

Super class

ResourceClient -> NoSQLResourceClient

Methods

Public methods

Inherited methods

NoSQLResourceClient$new()

Creates a new NoSQLResourceClient instance.

Usage
NoSQLResourceClient$new(resource)
Arguments
resource

A valid resource object.

Returns

A NoSQLResourceClient object.

NoSQLResourceClient$getConnection()

Creates the nodbi connection object if it does not exist.

Usage
NoSQLResourceClient$getConnection()
Returns

The nodbi connection object.

NoSQLResourceClient$asDataFrame()

Makes a data.frame from the remote database table.

Usage
NoSQLResourceClient$asDataFrame()
Returns

A tibble.

NoSQLResourceClient$getDatabaseName()

Extract the database name from the resource URL.

Usage
NoSQLResourceClient$getDatabaseName()
Returns

The database name.

NoSQLResourceClient$getTableName()

Extract the database table name from the resource URL.

Usage
NoSQLResourceClient$getTableName()
Returns

The database table name.

NoSQLResourceClient$close()

Close the nodbi connection.

Usage
NoSQLResourceClient$close()

NoSQLResourceClient$clone()

The objects of this class are cloneable with this method.

Usage
NoSQLResourceClient$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

NoSQL Database Resource resolver

Description

The resource is NoSQL database such as mongodb (elasticsearch, redis, couchdb, sqlite are not supported yet).

Format

A R6 object of class NoSQLResourceResolver

Super class

ResourceResolver -> NoSQLResourceResolver

Methods

Public methods

Inherited methods

NoSQLResourceResolver$isFor()

Check that the provided resource has a URL that locates a nodbi object: the URL scheme must be one of "mongodb", "mongodb+srv". Other NoSQL databases "elasticsearch", "redis", "couchdb", "sqlite" are not supported yet.

Usage
NoSQLResourceResolver$isFor(x)
Arguments
x

The resource object to validate.

Returns

A logical.

NoSQLResourceResolver$newClient()

Creates a NoSQLResourceClient instance from provided resource.

Usage
NoSQLResourceResolver$newClient(x)
Arguments
x

A valid resource object.

Returns

A NoSQLResourceClient object.

NoSQLResourceResolver$clone()

The objects of this class are cloneable with this method.

Usage
NoSQLResourceResolver$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Opal file resource getter

Description

Access a file that is stored in a Opal server. Use Basic authentication header if both resource's identity and secret are defined, token authentication if secret only is defined.

Format

A R6 object of class OpalFileResourceGetter

Super class

FileResourceGetter -> OpalFileResourceGetter

Methods

Public methods

Inherited methods

OpalFileResourceGetter$new()

Creates a new OpalFileResourceGetter instance.

Usage
OpalFileResourceGetter$new()
Returns

A OpalFileResourceGetter object.

OpalFileResourceGetter$isFor()

Check that the provided resource has a URL that locates a Opal file: the URL scheme must be "opal+http" or "opal+https" and the path must designate a file web service entry point (i.e. starts with "ws/files/").

Usage
OpalFileResourceGetter$isFor(resource)
Arguments
resource

The resource object to validate.

Returns

A logical.

OpalFileResourceGetter$downloadFile()

Download the file from the Opal file system in a temporary location.

Usage
OpalFileResourceGetter$downloadFile(resource, ...)
Arguments
resource

A valid resource object.

...

Unused additional parameters.

Returns

The "resource.file" object.

OpalFileResourceGetter$clone()

The objects of this class are cloneable with this method.

Usage
OpalFileResourceGetter$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Postgres DBI resource connector

Description

Makes a Postgres DBI connection from a resource description.

Format

A R6 object of class PostgresResourceConnector

Super class

DBIResourceConnector -> PostgresResourceConnector

Methods

Public methods

Inherited methods

PostgresResourceConnector$new()

Creates a new PostgresResourceConnector instance.

Usage
PostgresResourceConnector$new()
Returns

A PostgresResourceConnector object.

PostgresResourceConnector$isFor()

Check that the provided resource has a URL that locates a Postgres object: the URL scheme must be "postgres" or "postgresql".

Usage
PostgresResourceConnector$isFor(resource)
Arguments
resource

The resource object to validate.

Returns

A logical.

PostgresResourceConnector$createDBIConnection()

Creates a DBI connection object from a resource.

Usage
PostgresResourceConnector$createDBIConnection(resource)
Arguments
resource

A valid resource object.

Returns

A DBI connection object.

PostgresResourceConnector$clone()

The objects of this class are cloneable with this method.

Usage
PostgresResourceConnector$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Presto DBI resource connector

Description

Makes a Presto DBI connection from a resource description.

Format

A R6 object of class PrestoResourceConnector

Super class

DBIResourceConnector -> PrestoResourceConnector

Methods

Public methods

Inherited methods

PrestoResourceConnector$new()

Creates a new PrestoResourceConnector instance.

Usage
PrestoResourceConnector$new()
Returns

A PrestoResourceConnector object.

PrestoResourceConnector$isFor()

Check that the provided resource has a URL that locates a Presto object: the URL scheme must be "presto", "presto+http" or "presto+https".

Usage
PrestoResourceConnector$isFor(resource)
Arguments
resource

The resource object to validate.

Returns

A logical.

PrestoResourceConnector$createDBIConnection()

Creates a DBI connection object from a resource.

Usage
PrestoResourceConnector$createDBIConnection(resource)
Arguments
resource

A valid resource object.

Returns

A DBI connection object.

PrestoResourceConnector$clone()

The objects of this class are cloneable with this method.

Usage
PrestoResourceConnector$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

R object file resource client

Description

Connects to a RDS file and loads the serialized object. Similar to the R data file resource, except that the RDS format stores a single R object.

Format

A R6 object of class RDSFileResourceClient

Super classes

ResourceClient -> FileResourceClient -> RDSFileResourceClient

Methods

Public methods

Inherited methods

RDSFileResourceClient$new()

Creates a new RDSFileResourceClient instance.

Usage
RDSFileResourceClient$new(resource)
Arguments
resource

A valid resource object.

Returns

A RDSFileResourceClient object.

RDSFileResourceClient$asDataFrame()

Coerce the resource value extracted from the R object file to a data.frame.

Usage
RDSFileResourceClient$asDataFrame(...)
Arguments
...

Additional parameters to as.data.frame (not used yet).

Returns

A data.frame.

RDSFileResourceClient$getValue()

Get the resource value extracted from the R object file.

Usage
RDSFileResourceClient$getValue(...)
Arguments
...

Additional parameters to get the value object (not used yet).

Returns

The resource value.

RDSFileResourceClient$clone()

The objects of this class are cloneable with this method.

Usage
RDSFileResourceClient$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

R object file Resource resolver

Description

The resource is a RDS file.

Format

A R6 object of class RDSFileResourceResolver

Super class

ResourceResolver -> RDSFileResourceResolver

Methods

Public methods

Inherited methods

RDSFileResourceResolver$isFor()

Check that the provided resource has a URL that locates a R object file: the resource can be accessed as a file and the resource URL path ends with ".rds" (case ignored), or the resource format is prefixed with "rds:" (a kind of namespace to qualify the R object class).

Usage
RDSFileResourceResolver$isFor(x)
Arguments
x

The resource object to validate.

Returns

A logical.

RDSFileResourceResolver$newClient()

Creates a RDSFileResourceClient instance from provided resource.

Usage
RDSFileResourceResolver$newClient(x)
Arguments
x

A valid resource object.

Returns

A RDSFileResourceClient object.

RDSFileResourceResolver$clone()

The objects of this class are cloneable with this method.

Usage
RDSFileResourceResolver$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

R data file resource client

Description

Connects to a R data file and loads it in a controlled environment.

Format

A R6 object of class RDSFileResourceClient

Super classes

ResourceClient -> FileResourceClient -> RDataFileResourceClient

Methods

Public methods

Inherited methods

RDataFileResourceClient$new()

Creates a new RDataFileResourceClient instance.

Usage
RDataFileResourceClient$new(resource)
Arguments
resource

A valid resource object.

Returns

A RDataFileResourceClient object.

RDataFileResourceClient$asDataFrame()

Coerce the resource value extracted from the R data file to a data.frame.

Usage
RDataFileResourceClient$asDataFrame(...)
Arguments
...

Additional parameters to as.data.frame (not used yet).

Returns

A data.frame.

RDataFileResourceClient$getValue()

Get the resource value extracted from the R data file.

Usage
RDataFileResourceClient$getValue(...)
Arguments
...

Additional parameters to get the value object (not used yet).

Returns

The resource value.

RDataFileResourceClient$clone()

The objects of this class are cloneable with this method.

Usage
RDataFileResourceClient$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

R data file Resource resolver

Description

The resource is a R data file and data format is the class of the symbol that will be loaded.

Format

A R6 object of class RDataFileResourceResolver

Super class

ResourceResolver -> RDataFileResourceResolver

Methods

Public methods

Inherited methods

RDataFileResourceResolver$isFor()

Check that the provided resource has a URL that locates a R data file: the resource can be accessed as a file and the resource URL path ends with ".rda" or ".rdata" (case ignored), or the resource format is prefixed with "r:" or "rda:" (a kind of namespace to qualify the R object class).

Usage
RDataFileResourceResolver$isFor(x)
Arguments
x

The resource object to validate.

Returns

A logical.

RDataFileResourceResolver$newClient()

Creates a RDataFileResourceClient instance from provided resource.

Usage
RDataFileResourceResolver$newClient(x)
Arguments
x

A valid resource object.

Returns

A RDataFileResourceClient object.

RDataFileResourceResolver$clone()

The objects of this class are cloneable with this method.

Usage
RDataFileResourceResolver$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Resource client

Description

Helper class for connecting to a resource data store or a computation unit.

Format

A R6 object of class ResourceClient

Methods

Public methods

ResourceClient$new()

Creates a ResourceClient instance.

Usage
ResourceClient$new(resource)
Arguments
resource

The resource object to be interprated.

Returns

A ResourceClient object.

ResourceClient$getResource()

Get the resource object.

Usage
ResourceClient$getResource()
Returns

The resource object.

ResourceClient$getConnection()

Get the implementation-specific object that connects to the resource

Usage
ResourceClient$getConnection()
Returns

The connection object.

ResourceClient$downloadFile()

Stub function to be implemented by subclasses if relevant. Get the resource as a local file.

Usage
ResourceClient$downloadFile(...)
Arguments
...

Additional parameters.

Returns

The path to the local file.

ResourceClient$asDataFrame()

Stub function to be implemented by subclasses if relevant. Coerce the resource as a data.frame.

Usage
ResourceClient$asDataFrame(...)
Arguments
...

Additional parameters.

Returns

A data.frame object (can also be a tibble).

ResourceClient$asTbl()

Stub function to be implemented by subclasses if relevant. Coerce the resource as a dplyr's tbl.

Usage
ResourceClient$asTbl(...)
Arguments
...

Additional parameters.

Returns

A dplyr's tbl object.

ResourceClient$exec()

Stub function to be implemented by subclasses if relevant. Executes a command on a computation resource.

Usage
ResourceClient$exec(...)
Arguments
...

Additional parameters that will represent the command to execute.

Returns

A command execution result object.

ResourceClient$close()

Silently closes the connection to the resource

Usage
ResourceClient$close()

ResourceClient$clone()

The objects of this class are cloneable with this method.

Usage
ResourceClient$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Resource resolver

Description

Helper class for building a Client that implements the access to the data or the computation unit.

Format

A R6 object of class ResourceResolver

Methods

Public methods

ResourceResolver$new()

Creates a new ResourceResolver instance.

Usage
ResourceResolver$new()
Returns

A ResourceResolver object.

ResourceResolver$isFor()

Check that the provided object is of class "resource".

Usage
ResourceResolver$isFor(x)
Arguments
x

The resource object to evaluate.

Returns

A logical.

ResourceResolver$newClient()

Stub function to be implemented by subclasses. Makes an object which class inherits from ResourceClient.

Usage
ResourceResolver$newClient(x)
Arguments
x

The resource object to evaluate.

Returns

The ResourceClient object that will access the provided resource.

ResourceResolver$clone()

The objects of this class are cloneable with this method.

Usage
ResourceResolver$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

SQL database resource client

Description

Resource client that connects to a SQL database supported by DBI.

Format

A R6 object of class SQLResourceClient

Super class

ResourceClient -> SQLResourceClient

Methods

Public methods

Inherited methods

SQLResourceClient$new()

Creates a SQLResourceClient from a resource.

Usage
SQLResourceClient$new(resource, dbi.connector = NULL)
Arguments
resource

The resource object.

dbi.connector

An optional DBIResourceConnector object. If not provided, it will be looked up in the DBIResourceConnector registry.

Returns

The SQLResourceClient object.

SQLResourceClient$getConnection()

Get or create the DBI connection object that will access the resource.

Usage
SQLResourceClient$getConnection()
Returns

The DBI connection object.

SQLResourceClient$asDataFrame()

Coerce the SQL table to a data.frame.

Usage
SQLResourceClient$asDataFrame(...)
Arguments
...

Additional parameters (not used).

Returns

A data.frame (more specifically a tibble).

SQLResourceClient$asTbl()

Get the SQL table as a dplyr's tbl.

Usage
SQLResourceClient$asTbl()
Returns

A dplyr's tbl object.

SQLResourceClient$close()

Silently close the DBI connection.

Usage
SQLResourceClient$close()

SQLResourceClient$clone()

The objects of this class are cloneable with this method.

Usage
SQLResourceClient$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

SQL Database Resource resolver

Description

The resource is SQL database.

Format

A R6 object of class SQLResourceResolver

Super class

ResourceResolver -> SQLResourceResolver

Methods

Public methods

Inherited methods

SQLResourceResolver$isFor()

Check that the provided resource has a registered DBIResourceConnector.

Usage
SQLResourceResolver$isFor(x)
Arguments
x

The resource object to evaluate.

Returns

A logical.

SQLResourceResolver$newClient()

Creates a SQLResourceClient instance from provided resource.

Usage
SQLResourceResolver$newClient(x)
Arguments
x

A valid resource object.

Returns

A SQLResourceClient object.

SQLResourceResolver$clone()

The objects of this class are cloneable with this method.

Usage
SQLResourceResolver$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

SCP file resource getter

Description

Access a file that is stored on a server accessible through SSH. Credentials apply.

Format

A R6 object of class ScpFileResourceGetter

Super class

FileResourceGetter -> ScpFileResourceGetter

Methods

Public methods

Inherited methods

ScpFileResourceGetter$new()

Creates a ScpFileResourceGetter instance.

Usage
ScpFileResourceGetter$new()
Returns

The ScpFileResourceGetter object.

ScpFileResourceGetter$isFor()

Check that the provided resource is a file accessible by SCP: the resource URL scheme must be "scp".

Usage
ScpFileResourceGetter$isFor(resource)
Arguments
resource

The resource object to evaluate.

Returns

A logical.

ScpFileResourceGetter$downloadFile()

Download the file described by the resource over an SSH connection.

Usage
ScpFileResourceGetter$downloadFile(resource, ...)
Arguments
resource

The resource that identifies the file.

...

Additional parameters (not used).

Returns

The "resource.file" object.

ScpFileResourceGetter$clone()

The objects of this class are cloneable with this method.

Usage
ScpFileResourceGetter$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Shell resource client

Description

Executes local system shell commands.

Format

A R6 object of class ShellResourceClient

Super classes

ResourceClient -> CommandResourceClient -> ShellResourceClient

Methods

Public methods

Inherited methods

ShellResourceClient$new()

Create a ShellResourceClient instance. This client will interact wtih a computation resource using shell commands.

Usage
ShellResourceClient$new(resource)
Arguments
resource

The computation resource.

Returns

The ShellResourceClient object.

ShellResourceClient$getAllowedCommands()

Get the command names that can be executed.

Usage
ShellResourceClient$getAllowedCommands()
Returns

A character vector

ShellResourceClient$copyFile()

Copy one or more files (wilcard * is supported in the file name (which can be a directory))

Usage
ShellResourceClient$copyFile(file, to = ".", verbose = FALSE)
Arguments
file

The file to copy.

to

The copy destination.

verbose

If TRUE, details the file operations on the console output.

Returns

The path to the files having been copied.

ShellResourceClient$exec()

Executes a shell command in the working directory specified in the resource's URL.

Usage
ShellResourceClient$exec(command, params = NULL, test = FALSE)
Arguments
command

The command name.

params

A character vector of arguments to pass.

test

If TRUE, the command is printed but not executed (for debugging).

Returns

The command execution result object.

ShellResourceClient$clone()

The objects of this class are cloneable with this method.

Usage
ShellResourceClient$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Shell Resource resolver

Description

The resource is a computation unit, accessible by issuing local system commands, i.e. which URL scheme is "sh".

Format

A R6 object of class ShellResourceResolver

Super class

ResourceResolver -> ShellResourceResolver

Methods

Public methods

Inherited methods

ShellResourceResolver$isFor()

Check that the provided resource is a computation resource accessible by shell commands. The resource URL scheme must be "sh" or "shell".

Usage
ShellResourceResolver$isFor(x)
Arguments
x

The resource object.

Returns

A logical.

ShellResourceResolver$newClient()

Create a ShellResourceClient instance from the provided resource.

Usage
ShellResourceResolver$newClient(x)
Arguments
x

A valid resource object.

Returns

A ShellResourceClient object.

ShellResourceResolver$clone()

The objects of this class are cloneable with this method.

Usage
ShellResourceResolver$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Apache Spark DBI resource connector

Description

Makes a Apache Spark connection object, that is also a DBI connection object, from a resource description.

Format

A R6 object of class SparkResourceConnector

Super class

DBIResourceConnector -> SparkResourceConnector

Methods

Public methods

Inherited methods

SparkResourceConnector$new()

Create a SparkResourceConnector instance.

Usage
SparkResourceConnector$new()
Returns

A SparkResourceConnector object.

SparkResourceConnector$isFor()

Check if the provided resource applies to a Apache Spark server. The resource URL scheme must be one of "spark", "spark+http" or "spark+https".

Usage
SparkResourceConnector$isFor(resource)
Arguments
resource

The resource object to validate.

Returns

A logical.

SparkResourceConnector$createDBIConnection()

Creates a DBI connection object from a Apache Spark resource.

Usage
SparkResourceConnector$createDBIConnection(resource)
Arguments
resource

A valid resource object.

Returns

A DBI connection object.

SparkResourceConnector$closeDBIConnection()

Close the DBI connection to Apache Spark.

Usage
SparkResourceConnector$closeDBIConnection(conn)
Arguments
conn

A DBI connection object.

SparkResourceConnector$clone()

The objects of this class are cloneable with this method.

Usage
SparkResourceConnector$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

SSH resource client

Description

Connects to a SSH server.

Format

A R6 object of class SshResourceClient

Super classes

ResourceClient -> CommandResourceClient -> SshResourceClient

Methods

Public methods

Inherited methods

SshResourceClient$new()

Create a SshResourceClient instance. This client will interact wtih a computation resource using ssh commands.

Usage
SshResourceClient$new(resource)
Arguments
resource

The computation resource.

Returns

The SshResourceClient object.

SshResourceClient$getAllowedCommands()

Get the command names that can be executed.

Usage
SshResourceClient$getAllowedCommands()
Returns

A character vector

SshResourceClient$getConnection()

Get or create the SSH connection object, for raw interaction.

Usage
SshResourceClient$getConnection()
Returns

The SSH connection object.

SshResourceClient$downloadFile()

Download one or more files (wilcard * is supported in the file name (which can be a directory))

Usage
SshResourceClient$downloadFile(file, to = ".", verbose = FALSE)
Arguments
file

The file path(s) to download, either absolute or relative to the working directory.

to

The download destination.

verbose

If TRUE, details the file operations on the console output.

Returns

The paths of the files having been downloaded.

SshResourceClient$uploadFile()

Upload one or more files

Usage
SshResourceClient$uploadFile(file, to = ".", verbose = FALSE)
Arguments
file

The file or vector of files to upload.

to

The upload destination, either absolute or relative to working directory.

verbose

If TRUE, details the file operations on the console output.

Returns

The paths of the files having been uploaded.

SshResourceClient$tempDir()

Get connection's temporary directory in the remote server, create it if it does not exists.

Usage
SshResourceClient$tempDir()
Returns

The path to the temporary directory.

SshResourceClient$removeTempDir()

Remove the connection's temporary directory from the remote server, if it was defined.

Usage
SshResourceClient$removeTempDir()

SshResourceClient$exec()

Executes a ssh command.

Usage
SshResourceClient$exec(command, params = NULL, test = FALSE)
Arguments
command

The command name.

params

A character vector of arguments to pass.

test

If TRUE, the command is printed but not executed (for debugging).

Returns

The command execution result object.

SshResourceClient$close()

Close the SSH connection.

Usage
SshResourceClient$close()

SshResourceClient$clone()

The objects of this class are cloneable with this method.

Usage
SshResourceClient$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

SSH Resource resolver

Description

The resource is a computation unit, accessible through SSH, i.e. which URL scheme is "ssh".

Format

A R6 object of class SshResourceResolver

Super class

ResourceResolver -> SshResourceResolver

Methods

Public methods

Inherited methods

SshResourceResolver$isFor()

Check that the provided resource is a computation resource accessible by ssh commands. The resource URL scheme is expected to be "ssh".

Usage
SshResourceResolver$isFor(x)
Arguments
x

The resource object.

Returns

A logical.

SshResourceResolver$newClient()

Create a SshResourceClient instance from the provided resource.

Usage
SshResourceResolver$newClient(x)
Arguments
x

A valid resource object.

Returns

A SshResourceClient object.

SshResourceResolver$clone()

The objects of this class are cloneable with this method.

Usage
SshResourceResolver$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Tidy file resource client

Description

Connects to a file and use one of the tidyverse reader.

Format

A R6 object of class TidyFileResourceClient

Super classes

ResourceClient -> FileResourceClient -> TidyFileResourceClient

Methods

Public methods

Inherited methods

TidyFileResourceClient$new()

Create a TidyFileResourceClient instance.

Usage
TidyFileResourceClient$new(resource)
Arguments
resource

A valid resource object.

Returns

A TidyFileResourceClient object.

TidyFileResourceClient$asDataFrame()

Coerce the resource value extracted from the file in tidy format to a data.frame.

Usage
TidyFileResourceClient$asDataFrame(...)
Arguments
...

Additional parameters to as.data.frame (not used yet).

Returns

A data.frame (more specifically a tibble).

TidyFileResourceClient$clone()

The objects of this class are cloneable with this method.

Usage
TidyFileResourceClient$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Tidy file Resource resolver

Description

The resource is a file and data format is handled by a reader from tidyverse. The data format is one of: csv (comma delimiter), csv2 (semicolon delimiter), tsv (tab delimiter), ssv (space delimiter), delim (delim parameter to be specified in the URL, default is space char), spss, sav, por, stata, dta, sas, xpt, excel, xls, xlsx.

Format

A R6 object of class TidyFileResourceResolver

Methods

$new() Create new TidyFileResourceResolver instance. $isFor(x) Get a logical that indicates that the resolver is applicable to the provided resource object. $newClient() Make a client for the provided resource.

Super class

ResourceResolver -> TidyFileResourceResolver

Methods

Public methods

Inherited methods

TidyFileResourceResolver$isFor()

Check that the provided resource has a URL that locates a tidy data file: the resource can be accessed as a file and the resource format is one of "csv", "csv2", "tsv", "delim", "ssv", "spss", "sav", "por", "stata", "dta", "sas", "xpt", "excel", "xls" or "xlsx" (case is ignored).

Usage
TidyFileResourceResolver$isFor(x)
Arguments
x

The resource object to validate.

Returns

A logical.

TidyFileResourceResolver$newClient()

Creates a TidyFileResourceClient instance from provided resource.

Usage
TidyFileResourceResolver$newClient(x)
Arguments
x

A valid resource object.

Returns

A TidyFileResourceClient object.

TidyFileResourceResolver$clone()

The objects of this class are cloneable with this method.

Usage
TidyFileResourceResolver$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Coerce a ResourceClient object to a data.frame

Description

Attempt to coerce a resource object to a data.frame: find a ResourceResolver and get the ResourceClient that will connect to the described dataset and make a data.frame of it.

Usage

## S3 method for class 'ResourceClient'
as.data.frame(x, ...)

Arguments

x

a ResourceClient object

...

additional parameters, that may be used (or ignored) by the resource client.

Value

a data.frame (or a tibble)

Coerce a resource to a data.frame

Description

Attempt to coerce a resource object to a data.frame: find a ResourceResolver and get the ResourceClient that will connect to the described dataset and make a data.frame of it.

Usage

## S3 method for class 'resource'
as.data.frame(x, ...)

Arguments

x

a resource object.

...

additional parameters, that may be used (or ignored) by the resource client.

Value

a data.frame (or a tibble)

Coerce resource client to a data.frame

Description

Coerce a ResourceClient object to a data.frame.

Usage

as.resource.data.frame(x, strict = FALSE, ...)

Arguments

x

The ResourceClient object to coerce to a data.frame.

strict

logical whether the resulting object must be strictly of class data.frame or if it can be a tibble.

...

Additional parameters, that may be used (or ignored) by the resource client.

Value

a data.frame (or a tibble)

Coerce resource client to the internal data object

Description

Coerce a ResourceClient object to internal data object: depending on the implementation of the ResourceClient, it can be a data connection object (like a DBI connection to a SQL database), or the actual data structure (when a resource is a R object extracted from a R data file for instance).

Usage

as.resource.object(x, ...)

Arguments

x

The ResourceClient object to coerce to a data.frame.

...

Additional parameters, that may be used (or ignored) by the resource client.

Value

the internal data object.

Coerce resource client to a tbl

Description

Coerce a ResourceClient object to a dplyr's tbl.

Usage

as.resource.tbl(x, ...)

Arguments

x

The ResourceClient object to coerce to a data.frame

...

Additional parameters, that may be used (or ignored) by the resource client.

Value

a dplyr's tbl

Find a DBI resource connector

Description

Find the DBI resource connector that will download the DBI from the provided resource object.

Usage

findDBIResourceConnector(x)

Arguments

x

The resource object which corresponding DBI connector is to be found.

Value

The corresponding DBIResourceConnector object or NULL if none applies.

Find a file resource getter

Description

Find the file resource getter that will download the file from the provided resource object.

Usage

findFileResourceGetter(x)

Arguments

x

The resource object which corresponding file getter is to be found.

Value

The corresponding FileResourceGetter object or NULL if none applies.

Get DBI resource connectors registry

Description

Get the DBIResourceConnectors registry, create it if it does not exist.

Usage

getDBIResourceConnectors()

Get file resource getters registry

Description

Get the FileResourceGetters registry, create it if it does not exist.

Usage

getFileResourceGetters()

Get resource resolvers registry

Description

Get the resource resolvers registry, create it if it does not exist.

Usage

getResourceResolvers()

Examples

{
resourcer::getResourceResolvers()
}

Create a Resource

Description

Creates a new Resource structure.

Usage

newResource(name = "", url, identity = NULL, secret = NULL, format = NULL)

Arguments

name

Otpional human friendly name that identifies the resource.

url

URL to access the resource whether it is data or computation capability.

identity

User name or account ID (if credentials are applicable).

secret

User password or token (if credentials are applicable).

format

Data format, to help resource resolver identification and coercing to other formats, optional.

Examples

{
# make a SPSS file resource
res <- resourcer::newResource(
  name = "CNSIM1",
  url = "file:///data/CNSIM1.sav",
  format = "spss"
)
}

Creates a resource client

Description

From a resource object, find the corresponding resolver in the resolver registry and create a new resource client.

Usage

newResourceClient(x)

Arguments

x

The resource object which corresponding resolver is to be found.

Value

The corresponding ResourceClient object or NULL if none applies.

Examples


library(resourcer)
res <- newResource(
  name = "CNSIM1",
  url = "file:///data/CNSIM1.sav",
  format = "spss"
)
client <- newResourceClient(res)

Register a DBI resource connector

Description

Maintain an list of DBIResourceConnectors that will be called when a new DBI resource connector is to be found.

Usage

registerDBIResourceConnector(x)

Arguments

x

The DBI resource connector object to register.

Register a file resource getter

Description

Maintain an list of FileResourceGetters that will be called when a new file resource getter is to be found.

Usage

registerFileResourceGetter(x)

Arguments

x

The file resource getter object to register.

Register a resource resolver

Description

Maintain an list of resource resolvers that will be called when a new resource is to be resolved.

Usage

registerResourceResolver(x)

Arguments

x

The resource resolver object to register.

Examples

## Not run: 
resourcer::registerResourceResolver(MyFileFormatResourceResolver$new())

## End(Not run)

Find a resource resolver

Description

Find the resolver that will make a client from the provided resource object.

Usage

resolveResource(x)

Arguments

x

The resource object which corresponding resolver is to be found.

Value

The corresponding ResourceResolver object or NULL if none applies.

Examples


library(resourcer)
res <- newResource(
  name = "CNSIM1",
  url = "file:///data/CNSIM1.sav",
  format = "spss"
)
resolver <- resolveResource(res)

Remove a DBI resource connector from the registry

Description

Remove any DBI resource connectors with the provided class name.

Usage

unregisterDBIResourceConnector(x)

Arguments

x

The DBI resource connector class name to unregister.

Remove a file resource getter from the registry

Description

Remove any file resource getters with the provided class name.

Usage

unregisterFileResourceGetter(x)

Arguments

x

The file resource getter class name to unregister.

Remove a resource resolver from the registry

Description

Remove any resolvers with the provided class name.

Usage

unregisterResourceResolver(x)

Arguments

x

The resource resolver class name to unregister.

Examples

## Not run: 
resourcer::unregisterResourceResolver("MyFileFormatResourceResolver")

## End(Not run)