Type: Package
Title: Resource Resolver
Version: 1.4.0
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, RPostgreSQL, sparklyr, RPresto (≥ 1.4.0), nodbi, rmarkdown
BugReports: https://github.com/obiba/resourcer
RoxygenNote: 7.2.3
VignetteBuilder: knitr
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2023-04-25 08:09:08 UTC; yannick
Author: Yannick Marcon ORCID iD [aut, cre], OBiBa group [cph]
Maintainer: Yannick Marcon <yannick.marcon@obiba.org>
Repository: CRAN
Date/Publication: 2023-04-25 09:40:02 UTC

Command resource client

Description

Command resource client

Command resource client

Format

A R6 object of class CommandResourceClient

Details

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

Super class

resourcer::ResourceClient -> CommandResourceClient

Methods

Public methods

Inherited methods

Method new()

Creates a new CommandResourceClient instance

Usage
CommandResourceClient$new(resource)
Arguments
resource

A valid resource object.

Returns

A CommandResourceClient object.

Method 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

DBI resource connector

DBI resource connector

Format

A R6 object of class DBIResourceConnector

Details

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

Methods

Public methods

Method new()

Creates a new DBIResourceConnector instance

Usage
DBIResourceConnector$new()
Returns

A DBIResourceConnector object.

Method isFor()

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

Usage
DBIResourceConnector$isFor(resource)
Arguments
resource

The resource object to validate.

Returns

A logical.

Method 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.

Method 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.

Method 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.

Method 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.

Method closeDBIConnection()

Disconnect the DBI connection.

Usage
DBIResourceConnector$closeDBIConnection(conn)
Arguments
conn

A DBI connection object.

Method 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

File resource client

File resource client

Format

A R6 object of class FileResourceClient

Details

Base class that connects to a file using a FileResourceGetter.

Super class

resourcer::ResourceClient -> FileResourceClient

Methods

Public methods

Inherited methods

Method 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.

Method downloadFile()

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

Usage
FileResourceClient$downloadFile()
Returns

The local path to the downloaded file.

Method close()

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

Usage
FileResourceClient$close()

Method 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

File resource getter

File resource getter

Format

A R6 object of class FileResourceGetter

Details

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.

Methods

Public methods

Method new()

Creates a new FileResourceGetter instance.

Usage
FileResourceGetter$new()
Returns

A FileResourceGetter object.

Method 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.

Method 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.

Method 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.

Method 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.

Method 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

GridFS file resource getter

GridFS file resource getter

Format

A R6 object of class GridFsFileResourceGetter

Details

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

Super class

resourcer::FileResourceGetter -> GridFsFileResourceGetter

Methods

Public methods

Inherited methods

Method new()

Creates a new GridFsFileResourceGetter instance.

Usage
GridFsFileResourceGetter$new()
Returns

A GridFsFileResourceGetter object.

Method 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.

Method 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.

Method 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

HTTP file resource getter

HTTP file resource getter

Format

A R6 object of class HttpFileResourceGetter

Details

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

Super class

resourcer::FileResourceGetter -> HttpFileResourceGetter

Methods

Public methods

Inherited methods

Method new()

Creates a new HttpFileResourceGetter instance.

Usage
HttpFileResourceGetter$new()
Returns

A HttpFileResourceGetter object.

Method 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.

Method 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.

Method 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

Local file resource getter

Local file resource getter

Format

A R6 object of class LocalFileResourceGetter

Details

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

Super class

resourcer::FileResourceGetter -> LocalFileResourceGetter

Methods

Public methods

Inherited methods

Method new()

Creates a new LocalFileResourceGetter instance.

Usage
LocalFileResourceGetter$new()
Returns

A LocalFileResourceGetter object.

Method 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.

Method 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.

Method 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

MariaDB DBI resource connector

MariaDB DBI resource connector

Format

A R6 object of class MariaDBResourceConnector

Details

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

Super class

resourcer::DBIResourceConnector -> MariaDBResourceConnector

Methods

Public methods

Inherited methods

Method new()

Creates a new MariaDBResourceConnector instance.

Usage
MariaDBResourceConnector$new()
Returns

A MariaDBResourceConnector object.

Method 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.

Method createDBIConnection()

Creates a DBI connection object from a resource.

Usage
MariaDBResourceConnector$createDBIConnection(resource)
Arguments
resource

A valid resource object.

Returns

A DBI connection object.

Method 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

NoSQL database resource client

NoSQL database resource client

Format

A R6 object of class NoSQLResourceClient

Details

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

Super class

resourcer::ResourceClient -> NoSQLResourceClient

Methods

Public methods

Inherited methods

Method new()

Creates a new NoSQLResourceClient instance.

Usage
NoSQLResourceClient$new(resource)
Arguments
resource

A valid resource object.

Returns

A NoSQLResourceClient object.

Method getConnection()

Creates the nodbi connection object if it does not exist.

Usage
NoSQLResourceClient$getConnection()
Returns

The nodbi connection object.

Method asDataFrame()

Makes a data.frame from the remote database table.

Usage
NoSQLResourceClient$asDataFrame()
Returns

A tibble.

Method getDatabaseName()

Extract the database name from the resource URL.

Usage
NoSQLResourceClient$getDatabaseName()
Returns

The database name.

Method getTableName()

Extract the database table name from the resource URL.

Usage
NoSQLResourceClient$getTableName()
Returns

The database table name.

Method close()

Close the nodbi connection.

Usage
NoSQLResourceClient$close()

Method 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

NoSQL Database Resource resolver

NoSQL Database Resource resolver

Format

A R6 object of class NoSQLResourceResolver

Details

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

Super class

resourcer::ResourceResolver -> NoSQLResourceResolver

Methods

Public methods

Inherited methods

Method 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.

Method newClient()

Creates a NoSQLResourceClient instance from provided resource.

Usage
NoSQLResourceResolver$newClient(x)
Arguments
x

A valid resource object.

Returns

A NoSQLResourceClient object.

Method 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

Opal file resource getter

Opal file resource getter

Format

A R6 object of class OpalFileResourceGetter

Details

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.

Super class

resourcer::FileResourceGetter -> OpalFileResourceGetter

Methods

Public methods

Inherited methods

Method new()

Creates a new OpalFileResourceGetter instance.

Usage
OpalFileResourceGetter$new()
Returns

A OpalFileResourceGetter object.

Method 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.

Method 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.

Method 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

Postgres DBI resource connector

Postgres DBI resource connector

Format

A R6 object of class PostgresResourceConnector

Details

Makes a Postgres DBI connection from a resource description.

Super class

resourcer::DBIResourceConnector -> PostgresResourceConnector

Methods

Public methods

Inherited methods

Method new()

Creates a new PostgresResourceConnector instance.

Usage
PostgresResourceConnector$new()
Returns

A PostgresResourceConnector object.

Method 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.

Method createDBIConnection()

Creates a DBI connection object from a resource.

Usage
PostgresResourceConnector$createDBIConnection(resource)
Arguments
resource

A valid resource object.

Returns

A DBI connection object.

Method 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

Presto DBI resource connector

Presto DBI resource connector

Format

A R6 object of class PrestoResourceConnector

Details

Makes a Presto DBI connection from a resource description.

Super class

resourcer::DBIResourceConnector -> PrestoResourceConnector

Methods

Public methods

Inherited methods

Method new()

Creates a new PrestoResourceConnector instance.

Usage
PrestoResourceConnector$new()
Returns

A PrestoResourceConnector object.

Method 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.

Method createDBIConnection()

Creates a DBI connection object from a resource.

Usage
PrestoResourceConnector$createDBIConnection(resource)
Arguments
resource

A valid resource object.

Returns

A DBI connection object.

Method 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

R object file resource client

R object file resource client

Format

A R6 object of class RDSFileResourceClient

Details

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.

Super classes

resourcer::ResourceClient -> resourcer::FileResourceClient -> RDSFileResourceClient

Methods

Public methods

Inherited methods

Method new()

Creates a new RDSFileResourceClient instance.

Usage
RDSFileResourceClient$new(resource)
Arguments
resource

A valid resource object.

Returns

A RDSFileResourceClient object.

Method 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.

Method 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.

Method 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

R object file Resource resolver

R object file Resource resolver

Format

A R6 object of class RDSFileResourceResolver

Details

The resource is a RDS file.

Super class

resourcer::ResourceResolver -> RDSFileResourceResolver

Methods

Public methods

Inherited methods

Method 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.

Method newClient()

Creates a RDSFileResourceClient instance from provided resource.

Usage
RDSFileResourceResolver$newClient(x)
Arguments
x

A valid resource object.

Returns

A RDSFileResourceClient object.

Method 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

R data file resource client

R data file resource client

Format

A R6 object of class RDSFileResourceClient

Details

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

Super classes

resourcer::ResourceClient -> resourcer::FileResourceClient -> RDataFileResourceClient

Methods

Public methods

Inherited methods

Method new()

Creates a new RDataFileResourceClient instance.

Usage
RDataFileResourceClient$new(resource)
Arguments
resource

A valid resource object.

Returns

A RDataFileResourceClient object.

Method 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.

Method 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.

Method 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

R data file Resource resolver

R data file Resource resolver

Format

A R6 object of class RDataFileResourceResolver

Details

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

Super class

resourcer::ResourceResolver -> RDataFileResourceResolver

Methods

Public methods

Inherited methods

Method 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.

Method newClient()

Creates a RDataFileResourceClient instance from provided resource.

Usage
RDataFileResourceResolver$newClient(x)
Arguments
x

A valid resource object.

Returns

A RDataFileResourceClient object.

Method 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

Resource client

Resource client

Format

A R6 object of class ResourceClient

Details

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

Methods

Public methods

Method new()

Creates a ResourceClient instance.

Usage
ResourceClient$new(resource)
Arguments
resource

The resource object to be interprated.

Returns

A ResourceClient object.

Method getResource()

Get the resource object.

Usage
ResourceClient$getResource()
Returns

The resource object.

Method getConnection()

Get the implementation-specific object that connects to the resource

Usage
ResourceClient$getConnection()
Returns

The connection object.

Method 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.

Method 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).

Method 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.

Method 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.

Method close()

Silently closes the connection to the resource

Usage
ResourceClient$close()

Method 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

Resource resolver

Resource resolver

Format

A R6 object of class ResourceResolver

Details

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

Methods

Public methods

Method new()

Creates a new ResourceResolver instance.

Usage
ResourceResolver$new()
Returns

A ResourceResolver object.

Method isFor()

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

Usage
ResourceResolver$isFor(x)
Arguments
x

The resource object to evaluate.

Returns

A logical.

Method 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.

Method 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

SQL database resource client

SQL database resource client

Format

A R6 object of class SQLResourceClient

Details

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

Super class

resourcer::ResourceClient -> SQLResourceClient

Methods

Public methods

Inherited methods

Method 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.

Method getConnection()

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

Usage
SQLResourceClient$getConnection()
Returns

The DBI connection object.

Method 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).

Method asTbl()

Get the SQL table as a dplyr's tbl.

Usage
SQLResourceClient$asTbl()
Returns

A dplyr's tbl object.

Method close()

Silently close the DBI connection.

Usage
SQLResourceClient$close()

Method 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

SQL Database Resource resolver

SQL Database Resource resolver

Format

A R6 object of class SQLResourceResolver

Details

The resource is SQL database.

Super class

resourcer::ResourceResolver -> SQLResourceResolver

Methods

Public methods

Inherited methods

Method isFor()

Check that the provided resource has a registered DBIResourceConnector.

Usage
SQLResourceResolver$isFor(x)
Arguments
x

The resource object to evaluate.

Returns

A logical.

Method newClient()

Creates a SQLResourceClient instance from provided resource.

Usage
SQLResourceResolver$newClient(x)
Arguments
x

A valid resource object.

Returns

A SQLResourceClient object.

Method 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

SCP file resource getter

SCP file resource getter

Format

A R6 object of class ScpFileResourceGetter

Details

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

Super class

resourcer::FileResourceGetter -> ScpFileResourceGetter

Methods

Public methods

Inherited methods

Method new()

Creates a ScpFileResourceGetter instance.

Usage
ScpFileResourceGetter$new()
Returns

The ScpFileResourceGetter object.

Method 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.

Method 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.

Method 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

Shell resource client

Shell resource client

Format

A R6 object of class ShellResourceClient

Details

Executes local system shell commands.

Super classes

resourcer::ResourceClient -> resourcer::CommandResourceClient -> ShellResourceClient

Methods

Public methods

Inherited methods

Method 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.

Method getAllowedCommands()

Get the command names that can be executed.

Usage
ShellResourceClient$getAllowedCommands()
Returns

A character vector

Method 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.

Method 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.

Method 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

Shell Resource resolver

Shell Resource resolver

Format

A R6 object of class ShellResourceResolver

Details

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

Super class

resourcer::ResourceResolver -> ShellResourceResolver

Methods

Public methods

Inherited methods

Method 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.

Method newClient()

Create a ShellResourceClient instance from the provided resource.

Usage
ShellResourceResolver$newClient(x)
Arguments
x

A valid resource object.

Returns

A ShellResourceClient object.

Method 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

Apache Spark DBI resource connector

Apache Spark DBI resource connector

Format

A R6 object of class SparkResourceConnector

Details

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

Super class

resourcer::DBIResourceConnector -> SparkResourceConnector

Methods

Public methods

Inherited methods

Method new()

Create a SparkResourceConnector instance.

Usage
SparkResourceConnector$new()
Returns

A SparkResourceConnector object.

Method 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.

Method 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.

Method closeDBIConnection()

Close the DBI connection to Apache Spark.

Usage
SparkResourceConnector$closeDBIConnection(conn)
Arguments
conn

A DBI connection object.

Method 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

SSH resource client

SSH resource client

Format

A R6 object of class SshResourceClient

Details

Connects to a SSH server.

Super classes

resourcer::ResourceClient -> resourcer::CommandResourceClient -> SshResourceClient

Methods

Public methods

Inherited methods

Method 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.

Method getAllowedCommands()

Get the command names that can be executed.

Usage
SshResourceClient$getAllowedCommands()
Returns

A character vector

Method getConnection()

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

Usage
SshResourceClient$getConnection()
Returns

The SSH connection object.

Method 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.

Method 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.

Method 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.

Method removeTempDir()

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

Usage
SshResourceClient$removeTempDir()

Method 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.

Method close()

Close the SSH connection.

Usage
SshResourceClient$close()

Method 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

SSH Resource resolver

SSH Resource resolver

Format

A R6 object of class SshResourceResolver

Details

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

Super class

resourcer::ResourceResolver -> SshResourceResolver

Methods

Public methods

Inherited methods

Method 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.

Method newClient()

Create a SshResourceClient instance from the provided resource.

Usage
SshResourceResolver$newClient(x)
Arguments
x

A valid resource object.

Returns

A SshResourceClient object.

Method 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

Tidy file resource client

Tidy file resource client

Format

A R6 object of class TidyFileResourceClient

Details

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

Super classes

resourcer::ResourceClient -> resourcer::FileResourceClient -> TidyFileResourceClient

Methods

Public methods

Inherited methods

Method new()

Create a TidyFileResourceClient instance.

Usage
TidyFileResourceClient$new(resource)
Arguments
resource

A valid resource object.

Returns

A TidyFileResourceClient object.

Method 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).

Method 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

Tidy file Resource resolver

Tidy file Resource resolver

Format

A R6 object of class TidyFileResourceResolver

Details

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.

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

resourcer::ResourceResolver -> TidyFileResourceResolver

Methods

Public methods

Inherited methods

Method 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.

Method newClient()

Creates a TidyFileResourceClient instance from provided resource.

Usage
TidyFileResourceResolver$newClient(x)
Arguments
x

A valid resource object.

Returns

A TidyFileResourceClient object.

Method 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)