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Opal R

Opal R Client for the Opal data warehouse. Most of the web services of Opal can be reached by an opalr function: import/export, data dictionaries, projects, tables, resources, permissions, users, DataSHIELD profiles etc.

See opalr documentation.

Installation:

# install from CRAN
install.packages("opalr")

# or install latest development version
remotes::install_github("obiba/opalr")

Basic usage:

library(opalr)
o <- opal.login('administrator', 'password', url = 'https://opal-demo.obiba.org')

# assign a table (as a data.frame) to a R symbol
opal.assign(o, 'D', 'CNSIM.CNSIM1')

# perform R operations on the server side
opal.execute(o, 'summary(D$GENDER)')
opal.execute(o, 'summary(D$LAB_GLUC)')

opal.logout(o)

Cookbooks

How to perform DataSHIELD Administration
How to manage Opal Files
How to manage Opal Projects
How to interact with an Opal R Session

DataSHIELD Client

See the DSOpal documentation.

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Version

Install

install.packages('opalr')

Monthly Downloads

1,014

Version

3.4.0

License

GPL-3

Issues

Pull Requests

Stars

Forks

Repository

https://github.com/obiba/opalr/

Homepage

https://www.obiba.org/opalr/

Maintainer

Yannick Marcon

Last Published

October 6th, 2023

Functions in opalr (3.4.0)

.handleResponseOrCallback

Process response with default handler or the provided one

Handle error response

Remove a R session from Opal.

Get all R session in Opal.

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

Remove a Opal session (logout)

dsadmin.activity

Get DataSHIELD activity

dsadmin.get_options

Get the DataSHIELD options

dsadmin.get_methods

Get DataSHIELD methods

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

.handleResponse

Default request response handler.

Create a new progress instance with default settings.

Wrapper of httr::content()

Create the opal object

.getPEMFilePath

Extract absolute path to the pem file

Constructs the value for the X-Opal-Auth header

Create a new R session in Opal.

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

dsadmin.package_descriptions

Get DataSHIELD package descriptions

Get the DataSHIELD permissions

dsadmin.profile_rparser

Set or remove the R parser version of a DataSHIELD profile

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

dsadmin.profile_init

Initialize a DataSHIELD profile

dsadmin.profile_perm

Get the permissions of a DataSHIELD profile

dsadmin.profile

Get a DataSHIELD profile

dsadmin.profile_access

Restrict or open access to a DataSHIELD profile

dsadmin.profiles

Get DataSHIELD profiles

dsadmin.activity_summary

Get DataSHIELD activity summary

dsadmin.perm_add

Add or update a DataSHIELD permission

dsadmin.get_method

Get a DataSHIELD method

dsadmin.perm_delete

Delete a DataSHIELD permission

dsadmin.install_github_package

Install a DataSHIELD package from GitHub

dsadmin.profile_delete

Delete a DataSHIELD profile

dsadmin.profile_create

Create a DataSHIELD profile

.isContentEmpty

Check if response content is empty.

oadmin.install_bioconductor_package

Install a package from Bioconductor

dsadmin.remove_package

Remove DataSHIELD package

oadmin.activity_summary

Get R activity summary

dsadmin.publish_package

Publish DataSHIELD package settings

dsadmin.profile_perm_add

Add or update a permission on a DataSHIELD profile

dsadmin.profile_perm_delete

Delete a permission from a DataSHIELD profile

dsadmin.rm_method

Remove DataSHIELD method

dsadmin.rm_methods

Remove DataSHIELD methods.

dsadmin.rm_option

Remove a DataSHIELD option

Get Opal SQL API logs

oadmin.installed_package

Check package is installed

oadmin.system_perm_add

Add or update a System permission

oadmin.installed_packages

List installed packages

oadmin.system_perm

Get the System permissions

dsadmin.install_local_package

Install a DataSHIELD package from a local archive file

dsadmin.install_package

Install a DataSHIELD package

dsadmin.set_option

Set DataSHIELD option

oadmin.install_cran_package

Install a package from CRAN

dsadmin.installed_package

Check DataSHIELD package

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

dsadmin.set_package_methods

Set DataSHIELD package methods

opal.annotations

Get the annotations of a Opal table

Get DataSHIELD logs

oadmin.install_package

Install CRAN package

dsadmin.profile_exists

Check a DataSHIELD profile exists

dsadmin.set_method

Set DataSHIELD method

dsadmin.profile_enable

Enable or disable a DataSHIELD profile

dsadmin.rm_package_methods

Remove DataSHIELD package methods

oadmin.install_devtools

Install devtools package

oadmin.install_github_package

Install a package from GitHub

dsadmin.package_description

Get DataSHIELD package description

Get the R permissions

oadmin.perm_delete

Delete a R permission (deprecated)

opal.as_md_table

Array to Markdown

opal.datasource

Get a datasource

List the asynchronous commands

opal.datasources

Get datasources

opal.commands_rm

Remove all asynchronous commands

oadmin.package_description

Get package description

oadmin.system_perm_delete

Delete a System permission

oadmin.user_add

oadmin.installed_devtools

Check devtools package

oadmin.r_perm_add

Add or update a R permission

opal.file_download

Download a file

opal.attribute_values

Get a vector of attribute values

oadmin.user_exists

Check user exists

oadmin.user_profile_delete

Delete a user profile

Get an asynchronous command

Get Opal main logs

oadmin.user_profiles

Get user profiles

oadmin.r_perm_delete

Delete a R permission

opal.load_package

opal.project_delete

Delete a project

Generic REST resource creation.

List content of a folder

List R profiles

opal.assign.script

R script assignment

oadmin.user_reset_password

Reset user password

opal.assign.resource

Resource assignment

opal.file_mkdir

opal.file_mkdir_tmp

Make a temporary folder

oadmin.log_rest

Get Opal REST API logs

opal.project_exists

Check a project exists

Move and/or rename a file

opal.assign.table

Data assignment to a data.frame

Apply the annotations to a Opal table

opal.assign.table.tibble

Data assignment to a tibble

opal.execute.source

Execute a R file script

Get file content

oadmin.activity

dsadmin.rm_options

Remove all DataSHIELD options

Generic REST resource update.

dsadmin.unpublish_package

Unpublish DataSHIELD package settings

oadmin.remove_package

Get the permissions of a subject

oadmin.system_metrics

Get system metrics

Logout from Opal(s)

Generic REST resource deletion.

Execute a R script

Get the R permissions (deprecated)

oadmin.install_local_package

Install a package from a local archive file

opal.project_perm_delete

Delete a permission from a project

oadmin.perm_add

Add or update a R permission (deprecated)

opal.project_restore

Restore a project

opal.sql_history

SQL query execution history

opal.symbol_import

Import a tibble

opal.file_unzip

Unzip a zip archive file

opal.table_create

Create an Opal table or view

opal.resource_create

Create a resource reference in a project

Get the resource references of a project

opal.table_delete

Delete a Opal table

opal.resource_delete

Delete a resource reference

opal.resources_perm

Get the permissions on any resource

opal.resource_extension_create

Create an extended resource reference in a project

opal.file_upload

Upload a file or a folder

opal.resource_exists

Check a resource reference exists

opal.project_command

Get project task

opal.projects_databases

Get projects databases

opal.table_dictionary_get

Get the dictionary of a Opal table

opal.resource_perm

Get the permissions on a resource

opal.resources_perm_delete

Delete a permission from any resource

opal.resource_get

Get the resource object of a project

opal.resources_perm_add

Add or update a permission on any resource

opal.project_create

Create a project

Remove a R symbol

opal.project_perm

Get the permissions on a project

opal.table_perm

Get the permissions on a table

opal.table_dictionary_update

Update the dictionary of a Opal table

opal.symbol_save

opal.table_export

Export a table as a file

opal.table_exists

Check a Opal table exists

opal.table_truncate

Truncate a Opal table

opal.taxonomy_delete

Delete a taxonomy

opal.table_view_create

Create an Opal view over tables

opal.tables_perm

Get the permissions on any table of a project

opal.assign.data

Data assignment

opal.tables_perm_add

Add or update a permission on any table of a project

opal.task_cancel

Generic REST resource getter.

Data or expression assignment

opal.command_rm

Remove an asynchronous command

oadmin.user_enable

opal.command_result

Get result of an asynchronous command

oadmin.user_delete

opal.file_write

opal.project_perm_add

Add or update a permission on a project

opal.token_sql_create

Create a personal access token for SQL usage

opal.resource_perm_add

Add or update a permission on a resource

Wait for a task to complete.

Get the personal access tokens

opal.table_perm_add

Add or update a permission on a table

opal.variable_summary

Get summary statistics of a variable of a table

opal.token_datashield_create

Create a personal access token for Datashield usage

Get a variable of a table

opal.token_renew

Renew an inactive personal access token

opal.token_r_create

Create a personal access token for R usage

opal.workspace_rm

Remove a R workspace from a opal.

opal.token_delete

Delete a personal access token

opal.workspace_restore

Restore a R workspace from a opal.

opal.workspaces

Get the R workspaces from a opal.

opal.workspace_save

Save the current session in a opal R workspace.

opalr: 'Opal' Data Repository Client and 'DataSHIELD' Utils

opal.table_view_update

Update the table references and the entity filter of an Opal view

Get tables of a datasource

opal.taxonomy_download

Download a taxonomy file

opal.taxonomy_upload

Upload a taxonomy file

opal.project_backup

Backup a project

opal.resource_perm_delete

Delete a permission from a resource

Turn a R markdown file to html.

Remove a R symbol (deprecated)

Execute a SQL query on tables

Get a table of a datasource

Get a resource reference of a project

opal.tables_perm_delete

Delete a permission from any table of a project

Get a personal access token

Get the terms of a vocabulary

opal.resource_view_create

Create an Opal view over a resource reference

Get a Opal table as a tibble

opal.resource_view_reconnect

Reconnect an Opal view to its underlying resource

opal.table_perm_delete

Delete a permission from a table

opal.table_import

Import a file as table

opal.taxonomies

opal.table_save

Save a local tibble as a Opal table

opal.unload_package

opal.version_compare

Get variables of a table

Get the values of an entity

opal.vocabularies

Get the vocabularies of a taxonomy

opal.vocabulary

Get a taxonomy vocabulary

Turns a value into 0/1 numeric.

dictionary.annotate.harmo_status

Set variable annotation with Harmonization Status term

dictionary.annotations

List the annotations

dictionary.annotate

Set variable annotation with a taxonomy term

dictionary.inspect

Inspect the dictionary of a tibble

dictionary.apply

Apply the dictionary to a tibble

.extractJsonField

.handleResponseLocation

Default request response Location handler.

.authorizationHeader

Constructs the value for the Authorization header

Turn expression into character strings.

.aclsToDataFrame

Permsissions (ACLs) into a data frame.

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

.extractOpalSessionId

Extract opalsid from cookie data frame.