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Opal R

Opal R Client

Usage:

library(opalr)
o <- opal.login('username', 'passwd', 'http://localhost:8080')
# Assign one variable to a R symbol
opal.assign(o, 'VAR1', 'datasource.table:VAR1')
opal.execute(o, 'summary(VAR1)')
# Assign some variables as a data.frame to a R symbol
opal.assign(o, 'TABLE', 'datasource.table', variables=list('VAR1','VAR2'))
opal.execute(o, 'summary(TABLE$VAR1)')
opal.execute(o, 'summary(TABLE$VAR2)')
opal.logout(o)

DataSHIELD Client

See DSOpal.

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Version

Install

install.packages('opalr')

Monthly Downloads

894

Version

1.2.0

License

GPL-3

Maintainer

Yannick Marcon

Last Published

August 19th, 2019

Functions in opalr (1.2.0)

.newSession

Create a new R session in Opal.
.url

Utility method to build urls. Concatenates all arguments and adds a '/' separator between each element
dsadmin.install_package

Install a DataSHIELD package
dsadmin.get_options

Get the DataSHIELD options
.verbose

Verbose flag
.opal.login

Create the opal object
dsadmin.get_method

Get a DataSHIELD method
dsadmin.get_methods

Get DataSHIELD methods
.handleResponseOrCallback

Process response with default handler or the provided one
.is.verbose

Verbose option
.handleError

Handle error response
.handleResponse

Default request response handler.
oadmin.install_devtools

Install devtools package
dsadmin.set_package_methods

Set DataSHIELD package methods
oadmin.installed_devtools

Check devtools package
oadmin.installed_package

Check package is installed
.rmOpalSession

Remove a Opal session (logout)
.select

Returns a list r such that r[[i]] == l[[i]][field] for all i:length(l)
dsadmin.package_descriptions

Get DataSHIELD package descriptions
.rmRSession

Remove a R session from Opal.
.tokenHeader

Constructs the value for the X-Opal-Auth header
dsadmin.rm_option

Remove a DataSHIELD option
dsadmin.rm_package_methods

Remove DataSHIELD package methods
opal.command_rm

Remove an asynchronous command
dsadmin.installed_package

Check DataSHIELD package
dsadmin.set_method

Set DataSHIELD method
opal.execute

Execute a R script
dsadmin.package_description

Get DataSHIELD package description
dsadmin.set_option

Set DataSHIELD option
opal.commands

List the asynchronous commands
.handleResponseLocation

Default request response Location handler.
.isContentEmpty

Check if response content is empty.
dsadmin.remove_package

Remove DataSHIELD package
opal.assign.table.tibble

Data assignment to a tibble
opal.terms

Get the terms of a vocabulary
opal.project

Get a project
opal.vocabularies

Get the vocabularies of a taxonomy
opal.load_package

Load package
opal.vocabulary

Get a taxonomy vocabulary
opal.unload_package

Unload package
opal.file

Get file content
opal.projects

Get projects
opal.login

Opal login
oadmin.remove_package

Remove package
opal.annotations

Get the annotations of a Opal table
opal.file_ls

List content of a folder
opal.taxonomies

Get taxonomies
opal.command

Get an asynchronous command
opal.annotate

Apply the annotations to a Opal table
opal.command_result

Get result of an asynchronous command
opal.taxonomy

Get a taxonomy
opal.file_mkdir

Make a folder
opal.as_md_table

Array to Markdown
opal.attribute_values

Get a vector of values
oadmin.install_package

Install package
opal.assign.data

Data assignment
opal.assign

Data or expression assignment
oadmin.install_github

Install a package form GitHub
opal.file_download

Download a file
opal.assign.table

Data assignment to a data.frame
opal.assign.script

R script assignment
opal.file_cp

Copy a file
opal.logout

Logout from Opal(s)
opal.datasources

Get datasources
opal.report

Opal report
opal.put

Generic REST resource update.
opal.file_mv

Move and/or rename a file
opal.file_read

Read a file
opal.post

Generic REST resource creation.
opal.file_write

Write a file
opal.workspaces

Get the R workspaces from a opal.
opal.table

Get a table of a datasource
opal.symbol_import

Import a tibble
opal.delete

Generic REST resource deletion.
opal.symbol_rm

Remove a R symbol
opal.tables

Get tables of a datasource
opal.get

Generic REST resource getter.
opal.task

Get a task
opal.task_cancel

Cancel a task
.listToJson

Simple transformation function of a list into a JSON object/array.
opal.tasks

Get the tasks
opal.workspace_rm

Remove a R workspace from a opal.
opal.rm

Remove a R symbol (deprecated)
opal.report_md

Turn a R markdown file to html.
opal.task_wait

Wait for a task to complete.
opal.workspace_save

Save the current session in a opal R workspace.
opal.version_compare

Compare
opal.variables

Get variables of a table
dsadmin.rm_method

Remove DataSHIELD method
opal.commands_rm

Remove all asynchronous commands
oadmin.installed_packages

List installed packages
oadmin.package_description

Get package description
dsadmin.rm_methods

Remove DataSHIELD methods.
opal.datasource

Get a datasource
opal.file_upload

Upload a file
opal.file_rm

Remove a file
opal.symbol_save

Save a tibble
opal.symbols

List R symbols
opal.valueset

Get the values of an entity
opal.variable

Get a variable of a table
.getPEMFilePath

Extract absolute path to the pem file
.authorizationHeader

Constructs the value for the Authorization header
.extractJsonField

Extract JSON
.getSessions

Get all R session in Opal.
.extractLabel

Extract label for locale. If not found, fallback to undefined language label (if any).
.deparse

Turn expression into character strings.
.extractOpalSessionId

Extract opalsid from cookie data frame.
.getRSessionId

Extract R session Id from opal object, create a new R session if not found.
.getContent

Wrapper of httr::content()