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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

836

Version

1.4.0

License

GPL-3

Maintainer

Yannick Marcon

Last Published

May 18th, 2020

Functions in opalr (1.4.0)

.handleResponse

Default request response handler.
.handleResponseLocation

Default request response Location handler.
.getPEMFilePath

Extract absolute path to the pem file
.handleError

Handle error response
dsadmin.installed_package

Check DataSHIELD package
.getRSessionId

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

Constructs the value for the X-Opal-Auth header
.getSessions

Get all R session in Opal.
.extractJsonField

Extract JSON
.is.verbose

Verbose option
dsadmin.set_method

Set DataSHIELD method
.tickProgress

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

Process response with default handler or the provided one
dsadmin.set_option

Set DataSHIELD option
.isContentEmpty

Check if response content is empty.
dsadmin.package_description

Get DataSHIELD package description
.opal.login

Create the opal object
dsadmin.rm_option

Remove a DataSHIELD option
oadmin.install_devtools

Install devtools package
.url

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

Remove a R session from Opal.
.select

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

Install a package form GitHub
dsadmin.set_package_methods

Set DataSHIELD package methods
harmo.annotate

Set variable annotation with a taxonomy term
dsadmin.get_options

Get the DataSHIELD options
.listToJson

Simple transformation function of a list into a JSON object/array.
opal.assign.table.tibble

Data assignment to a tibble
.rmOpalSession

Remove a Opal session (logout)
opal.attribute_values

Get a vector of values
dsadmin.rm_method

Remove DataSHIELD method
.verbose

Verbose flag
.extractLabel

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

Remove DataSHIELD methods.
harmo.annotate.status

Set variable annotation with Harmonization Status term
dsadmin.rm_package_methods

Remove DataSHIELD package methods
opal.as_md_table

Array to Markdown
opal.assign

Data or expression assignment
dsadmin.install_package

Install a DataSHIELD package
harmo.dictionary_apply

Apply the dictionary to a tibble
harmo.dictionary_update

Update the dictionary of a Opal table
harmo.annotations

List the annotations
opal.annotate

Apply the annotations to a Opal table
opal.datasources

Get datasources
opal.assign.data

Data assignment
opal.assign.resource

Resource assignment
opal.command_rm

Remove an asynchronous command
opal.commands

List the asynchronous commands
opal.execute

Execute a R script
opal.annotations

Get the annotations of a Opal table
dsadmin.package_descriptions

Get DataSHIELD package descriptions
oadmin.package_description

Get package description
opal.delete

Generic REST resource deletion.
opal.file

Get file content
dsadmin.remove_package

Remove DataSHIELD package
oadmin.remove_package

Remove package
opal.logout

Logout from Opal(s)
opal.file_write

Write a file
opal.post

Generic REST resource creation.
opal.file_cp

Copy a file
opal.file_download

Download a file
opal.resource

Get a resource of a project
opal.report_md

Turn a R markdown file to html.
opal.put

Generic REST resource update.
opal.get

Generic REST resource getter.
opal.table

Get a table of a datasource
opal.tables

Get tables of a datasource
opal.file_mv

Move and/or rename a file
opal.symbol_save

Save a tibble
opal.symbol_rm

Remove a R symbol
opal.file_upload

Upload a file
opal.symbols

List R symbols
opal.file_rm

Remove a file
opal.symbol_import

Import a tibble
opal.vocabularies

Get the vocabularies of a taxonomy
oadmin.installed_package

Check package is installed
harmo.table_get

Get a Opal table as a tibble
oadmin.installed_packages

List installed packages
opal.vocabulary

Get a taxonomy vocabulary
opal.workspaces

Get the R workspaces from a opal.
opal.workspace_save

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

Remove a R workspace from a opal.
opal.command_result

Get result of an asynchronous command
opal.load_package

Load package
opal.command

Get an asynchronous command
opal.datasource

Get a datasource
opal.commands_rm

Remove all asynchronous commands
opal.report

Opal report
harmo.table_save

Save a local tibble as a Opal table
opal.login

Opal login
oadmin.install_package

Install package
oadmin.installed_devtools

Check devtools package
opal.assign.table

Data assignment to a data.frame
opal.file_ls

List content of a folder
opal.task_wait

Wait for a task to complete.
opal.file_read

Read a file
opal.assign.script

R script assignment
opal.resources

Get the resource references of a project
opal.task

Get a task
opal.tasks

Get the tasks
opal.rm

Remove a R symbol (deprecated)
opal.variables

Get variables of a table
opal.task_cancel

Cancel a task
opal.version_compare

Compare
opal.variable

Get a variable of a table
opal.projects

Get projects
opal.project

Get a project
opal.file_mkdir

Make a folder
opal.taxonomy

Get a taxonomy
opal.terms

Get the terms of a vocabulary
opal.valueset

Get the values of an entity
opal.taxonomies

Get taxonomies
opal.unload_package

Unload package
.authorizationHeader

Constructs the value for the Authorization header
.extractOpalSessionId

Extract opalsid from cookie data frame.
.getContent

Wrapper of httr::content()
.deparse

Turn expression into character strings.
.newProgress

Create a new progress instance with default settings.
.newSession

Create a new R session in Opal.
dsadmin.get_method

Get a DataSHIELD method
dsadmin.get_methods

Get DataSHIELD methods