Learn R Programming

⚠️There's a newer version (3.4.2) of this package.Take me there.

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.

Copy Link

Version

Install

install.packages('opalr')

Monthly Downloads

519

Version

1.4.1

License

GPL-3

Maintainer

Yannick Marcon

Last Published

June 8th, 2020

Functions in opalr (1.4.1)

.handleError

Handle error response
dsadmin.install_package

Install a DataSHIELD package
.handleResponseLocation

Default request response Location handler.
dsadmin.get_options

Get the DataSHIELD options
dsadmin.get_method

Get a DataSHIELD method
dsadmin.rm_option

Remove a DataSHIELD option
dsadmin.get_methods

Get DataSHIELD methods
dsadmin.rm_method

Remove DataSHIELD method
.is.verbose

Verbose option
.handleResponse

Default request response handler.
.handleResponseOrCallback

Process response with default handler or the provided one
.isContentEmpty

Check if response content is empty.
dsadmin.set_package_methods

Set DataSHIELD package methods
opal.as_md_table

Array to Markdown
harmo.annotate

Set variable annotation with a taxonomy term
opal.assign

Data or expression assignment
dsadmin.rm_methods

Remove DataSHIELD methods.
.newProgress

Create a new progress instance with default settings.
dsadmin.set_method

Set DataSHIELD method
.rmOpalSession

Remove a Opal session (logout)
.opal.login

Create the opal object
dsadmin.rm_package_methods

Remove DataSHIELD package methods
opal.command_rm

Remove an asynchronous command
opal.execute

Execute a R script
.tickProgress

Output the progress status if option "datashield.progress" is allows to.
opal.commands

List the asynchronous commands
dsadmin.installed_package

Check DataSHIELD package
.listToJson

Simple transformation function of a list into a JSON object/array.
dsadmin.package_description

Get DataSHIELD package description
harmo.table_get

Get a Opal table as a tibble
harmo.dictionary_apply

Apply the dictionary to a tibble
oadmin.install_package

Install package
.tokenHeader

Constructs the value for the X-Opal-Auth header
harmo.dictionary_update

Update the dictionary of a Opal table
oadmin.installed_package

Check package is installed
dsadmin.set_option

Set DataSHIELD option
.rmRSession

Remove a R session from Opal.
opal.execute.source

Execute a R file script
opal.annotate

Apply the annotations to a Opal table
opal.annotations

Get the annotations of a Opal table
.select

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

Save a local tibble as a Opal table
harmo.annotate.status

Set variable annotation with Harmonization Status term
opal.login

Opal login
oadmin.installed_packages

List installed packages
.newSession

Create a new R session in Opal.
oadmin.installed_devtools

Check devtools package
opal.assign.data

Data assignment
harmo.annotations

List the annotations
oadmin.package_description

Get package description
oadmin.remove_package

Remove package
opal.file_download

Download a file
opal.command

Get an asynchronous command
opal.assign.script

R script assignment
.url

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

Remove DataSHIELD package
dsadmin.package_descriptions

Get DataSHIELD package descriptions
opal.assign.table

Data assignment to a data.frame
opal.assign.table.tibble

Data assignment to a tibble
opal.attribute_values

Get a vector of values
.verbose

Verbose flag
oadmin.install_devtools

Install devtools package
opal.file_read

Read a file
opal.command_result

Get result of an asynchronous command
opal.datasources

Get datasources
opal.file_rm

Remove a file
opal.delete

Generic REST resource deletion.
opal.report

Opal report
opal.logout

Logout from Opal(s)
opal.commands_rm

Remove all asynchronous commands
opal.report_md

Turn a R markdown file to html.
opal.tasks

Get the tasks
oadmin.install_github

Install a package form GitHub
opal.taxonomies

Get taxonomies
opal.file_upload

Upload a file
opal.file_write

Write a file
opal.datasource

Get a datasource
opal.resource

Get a resource of a project
opal.assign.resource

Resource assignment
opal.file_cp

Copy a file
opal.file

Get file content
opal.task_cancel

Cancel a task
opal.resources

Get the resource references of a project
opal.tables

Get tables of a datasource
opal.file_ls

List content of a folder
opal.task

Get a task
opal.file_mv

Move and/or rename a file
opal.file_mkdir

Make a folder
opal.symbols

List R symbols
opal.rm

Remove a R symbol (deprecated)
opal.symbol_import

Import a tibble
opal.variable

Get a variable of a table
opal.table

Get a table of a datasource
opal.post

Generic REST resource creation.
opal.get

Generic REST resource getter.
opal.load_package

Load package
opal.task_wait

Wait for a task to complete.
opal.projects

Get projects
opal.symbol_rm

Remove a R symbol
opal.put

Generic REST resource update.
opal.variables

Get variables of a table
opal.vocabularies

Get the vocabularies of a taxonomy
opal.version_compare

Compare
opal.vocabulary

Get a taxonomy vocabulary
opal.project

Get a project
opal.workspace_rm

Remove a R workspace from a opal.
opal.symbol_save

Save a tibble
opal.taxonomy

Get a taxonomy
opal.workspaces

Get the R workspaces from a opal.
opal.workspace_save

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

Get the terms of a vocabulary
opal.valueset

Get the values of an entity
opal.unload_package

Unload package
.getContent

Wrapper of httr::content()
.getSessions

Get all R session in Opal.
.getPEMFilePath

Extract absolute path to the pem file
.getRSessionId

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

Extract JSON
.authorizationHeader

Constructs the value for the Authorization header
.extractOpalSessionId

Extract opalsid from cookie data frame.
.deparse

Turn expression into character strings.
.extractLabel

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