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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

533

Version

2.1.0

License

GPL-3

Issues

Pull Requests

Stars

Forks

Maintainer

Yannick Marcon

Last Published

April 29th, 2021

Functions in opalr (2.1.0)

dictionary.annotations

List the annotations
dictionary.inspect

Inspect the dictionary of a tibble
dictionary.annotate

Set variable annotation with a taxonomy term
.extractJsonField

Extract JSON
dictionary.annotate.harmo_status

Set variable annotation with Harmonization Status term
dictionary.apply

Apply the dictionary to a tibble
.deparse

Turn expression into character strings.
.aclsToDataFrame

Permsissions (ACLs) into a data frame.
.as.zeroOne

Turns a value into 0/1 numeric.
.extractLabel

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

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

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

Install a DataSHIELD package
.handleResponseLocation

Default request response Location handler.
.isContentEmpty

Check if response content is empty.
.is.verbose

Verbose option
.authorizationHeader

Constructs the value for the Authorization header
.getContent

Wrapper of httr::content()
.getPEMFilePath

Extract absolute path to the pem file
.newSession

Create a new R session in Opal.
.tokenHeader

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

Handle error response
oadmin.install_local_package

Install a package from a local archive file
oadmin.install_package

Install package
dsadmin.installed_package

Check DataSHIELD package
dsadmin.perm

Get the DataSHIELD permissions
dsadmin.set_method

Set DataSHIELD method
dsadmin.perm_add

Add or update a DataSHIELD permission
.url

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

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

Default request response handler.
.opal.login

Create the opal object
dsadmin.get_methods

Get DataSHIELD methods
.getSessions

Get all R session in Opal.
.rmRSession

Remove a R session from Opal.
dsadmin.get_method

Get a DataSHIELD method
dsadmin.package_description

Get DataSHIELD package description
opal.assign.script

R script assignment
opal.as_md_table

Array to Markdown
.rmOpalSession

Remove a Opal session (logout)
.verbose

Verbose flag
opal.assign

Data or expression assignment
dsadmin.set_option

Set DataSHIELD option
oadmin.installed_packages

List installed packages
.extractOpalSessionId

Extract opalsid from cookie data frame.
.select

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

Get the DataSHIELD options
dsadmin.package_descriptions

Get DataSHIELD package descriptions
oadmin.perm_delete

Delete a R permission
dsadmin.install_github_package

Install a DataSHIELD package from GitHub
dsadmin.perm_delete

Delete a DataSHIELD permission
dsadmin.remove_package

Remove DataSHIELD package
.newProgress

Create a new progress instance with default settings.
oadmin.remove_package

Remove package
dsadmin.install_local_package

Install a DataSHIELD package from a local archive file
opal.logout

Logout from Opal(s)
opal.assign.table

Data assignment to a data.frame
.tickProgress

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

Remove DataSHIELD method
opal.annotations

Get the annotations of a Opal table
opal.delete

Generic REST resource deletion.
opal.assign.resource

Resource assignment
oadmin.install_github_package

Install a package from GitHub
opal.annotate

Apply the annotations to a Opal table
opal.file_rm

Remove a file
oadmin.install_devtools

Install devtools package
opal.assign.data

Data assignment
opal.datasources

Get datasources
opal.command

Get an asynchronous command
opal.post

Generic REST resource creation.
opal.file_mkdir

Make a folder
opal.file

Get file content
opal.assign.table.tibble

Data assignment to a tibble
opal.attribute_values

Get a vector of values
opal.file_cp

Copy a file
oadmin.package_description

Get package description
dsadmin.rm_option

Remove a DataSHIELD option
oadmin.installed_devtools

Check devtools package
dsadmin.rm_package_methods

Remove DataSHIELD package methods
opal.file_mkdir_tmp

Make a temporary folder
dsadmin.rm_methods

Remove DataSHIELD methods.
dsadmin.set_package_methods

Set DataSHIELD package methods
oadmin.perm

Get the R permissions
opal.command_rm

Remove an asynchronous command
oadmin.install_bioconductor_package

Install a package from Bioconductor
oadmin.perm_add

Add or update a R permission
opal.commands

List the asynchronous commands
opal.resource_create

Create a resource reference in a project
opal.resource_delete

Delete a resource reference
opal.file_upload

Upload a file
opal.table_dictionary_update

Update the dictionary of a Opal table
opal.sql

Execute a SQL query on tables
opal.resource_extension_create

Create an extended resource reference in a project
opal.table_get

Get a Opal table as a tibble
opal.table_dictionary_get

Get the dictionary of a Opal table
opal.rm

Remove a R symbol (deprecated)
opal.resource_exists

Check a resource reference exists
opal.table_import

Import a file as table
opal.execute

Execute a R script
opal.command_result

Get result of an asynchronous command
opal.project_perm

Get the permissions on a project
opal.file_mv

Move and/or rename a file
opal.execute.source

Execute a R file script
opal.file_read

Read a file
opal.report

Opal report
opal.project_perm_delete

Delete a permission from a project
opal.projects

Get projects
opal.put

Generic REST resource update.
opal.resources

Get the resource references of a project
opal.resources_perm

Get the permissions on any resource
opal.project_perm_add

Add or update a permission on a project
opal.report_md

Turn a R markdown file to html.
opal.symbol_rm

Remove a R symbol
opal.resources_perm_add

Add or update a permission on any resource
opal.table_create

Create a Opal table or view
opal.table_delete

Delete a Opal table
opal.resources_perm_delete

Delete a permission from any resource
opal.task_wait

Wait for a task to complete.
opal.token

Get a personal access token
opal.variables

Get variables of a table
opal.terms

Get the terms of a vocabulary
opal.task_cancel

Cancel a task
oadmin.installed_package

Check package is installed
opal.resource

Get a resource reference of a project
opal.symbol_save

Save a tibble
opal.commands_rm

Remove all asynchronous commands
opal.load_package

Load package
opal.datasource

Get a datasource
opal.version_compare

Compare
opal.get

Generic REST resource getter.
opal.file_ls

List content of a folder
opal.project_exists

Check a project exists
opal.file_write

Write a file
opal.project_delete

Delete a project
opal.symbols

List R symbols
opal.file_download

Download a file
opal.symbol_import

Import a tibble
opal.sql_history

SQL query execution history
opal.table

Get a table of a datasource
opal.tables_perm_delete

Delete a permission from any table of a project
opal.table_perm

Get the permissions on a table
opal.table_perm_delete

Delete a permission from a table
opal.valueset

Get the values of an entity
opal.vocabularies

Get the vocabularies of a taxonomy
opal.variable

Get a variable of a table
opal.table_perm_add

Add or update a permission on a table
opal.vocabulary

Get a taxonomy vocabulary
opal.token_r_create

Create a personal access token for R usage
opal.taxonomy_download

Download a taxonomy file
opal.table_save

Save a local tibble as a Opal table
opal.taxonomy_upload

Upload a taxonomy file
opal.login

Opal login
opal.table_truncate

Truncate a Opal table
opal.project

Get a project
opal.token_datashield_create

Create a personal access token for Datashield usage
opal.token_delete

Delete a personal access token
opal.task

Get a task
opal.token_sql_create

Create a personal access token for SQL usage
opal.workspaces

Get the R workspaces from a opal.
opal.tasks

Get the tasks
opal.workspace_rm

Remove a R workspace from a opal.
opal.tokens

Get the personal access tokens
opal.tables

Get tables of a datasource
opal.unload_package

Unload package
opal.taxonomies

Get taxonomies
opal.workspace_save

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

Get the resource object of a project
opal.project_create

Create a project
opal.resource_perm

Get the permissions on a resource
opal.resource_perm_add

Add or update a permission on a resource
opal.resource_perm_delete

Delete a permission from a resource
opal.table_export

Export a table as a file
opal.taxonomy_delete

Delete a taxonomy
opal.tables_perm_add

Add or update a permission on any table of a project
opal.tables_perm

Get the permissions on any table of a project
opal.taxonomy

Get a taxonomy
opal.table_exists

Check a Opal table exists