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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

648

Version

3.3.1

License

GPL-3

Issues

Pull Requests

Stars

Forks

Repository

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

Homepage

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

Maintainer

Last Published

February 28th, 2023

Functions in opalr (3.3.1)

dictionary.annotate

Set variable annotation with a taxonomy term

dictionary.apply

Apply the dictionary to a tibble

Turns a value into 0/1 numeric.

.extractJsonField

.extractOpalSessionId

Extract opalsid from cookie data frame.

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

Turn expression into character strings.

Get all R session in Opal.

Wrapper of httr::content()

Handle error response

.handleResponseLocation

Default request response Location handler.

.handleResponse

Default request response handler.

Create the opal object

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

.getPEMFilePath

Extract absolute path to the pem file

.handleResponseOrCallback

Process response with default handler or the provided one

Create a new R session in Opal.

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

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

.isContentEmpty

Check if response content is empty.

Remove a Opal session (logout)

Remove a R session from Opal.

dsadmin.install_local_package

Install a DataSHIELD package from a local archive file

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

dsadmin.install_github_package

Install a DataSHIELD package from GitHub

Create a new progress instance with default settings.

dsadmin.profile

Get a DataSHIELD profile

dsadmin.perm_delete

Delete a DataSHIELD permission

dsadmin.get_method

Get a DataSHIELD method

dsadmin.profile_create

Create a DataSHIELD profile

dsadmin.profile_access

Restrict or open access to a DataSHIELD profile

dsadmin.perm_add

Add or update a DataSHIELD permission

Get the DataSHIELD permissions

Constructs the value for the X-Opal-Auth header

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

dsadmin.get_options

Get the DataSHIELD options

dsadmin.get_methods

Get DataSHIELD methods

dsadmin.profile_delete

Delete a DataSHIELD profile

dsadmin.remove_package

Remove DataSHIELD package

dsadmin.rm_method

Remove DataSHIELD method

dsadmin.profiles

Get DataSHIELD profiles

dsadmin.profile_init

Initialize a DataSHIELD profile

dsadmin.profile_exists

Check a DataSHIELD profile exists

dsadmin.rm_methods

Remove DataSHIELD methods.

dsadmin.profile_perm_delete

Delete a permission from a DataSHIELD profile

dsadmin.profile_rparser

Set or remove the R parser version of a DataSHIELD profile

dsadmin.rm_option

Remove a DataSHIELD option

dsadmin.install_package

Install a DataSHIELD package

dsadmin.set_method

Set DataSHIELD method

dsadmin.package_descriptions

Get DataSHIELD package descriptions

dsadmin.package_description

Get DataSHIELD package description

dsadmin.installed_package

Check DataSHIELD package

dsadmin.profile_perm

Get the permissions of a DataSHIELD profile

oadmin.install_cran_package

Install a package from CRAN

oadmin.install_bioconductor_package

Install a package from Bioconductor

dsadmin.publish_package

Publish DataSHIELD package settings

oadmin.install_package

Install CRAN package

oadmin.install_local_package

Install a package from a local archive file

oadmin.install_github_package

Install a package from GitHub

oadmin.install_devtools

Install devtools package

dsadmin.unpublish_package

Unpublish DataSHIELD package settings

oadmin.installed_devtools

Check devtools package

dsadmin.profile_enable

Enable or disable a DataSHIELD profile

dsadmin.set_package_methods

Set DataSHIELD package methods

oadmin.installed_package

Check package is installed

dsadmin.rm_package_methods

Remove DataSHIELD package methods

dsadmin.rm_options

Remove all DataSHIELD options

oadmin.installed_packages

List installed packages

oadmin.perm_delete

Delete a R permission (deprecated)

oadmin.system_perm

Get the System permissions

oadmin.remove_package

oadmin.system_metrics

Get system metrics

oadmin.package_description

Get package description

oadmin.r_perm_delete

Delete a R permission

opal.assign.table.tibble

Data assignment to a tibble

oadmin.user_delete

Data or expression assignment

opal.assign.data

Data assignment

Apply the annotations to a Opal table

oadmin.r_perm_add

Add or update a R permission

oadmin.user_enable

oadmin.system_perm_add

Add or update a System permission

opal.assign.table

Data assignment to a data.frame

oadmin.system_perm_delete

Delete a System permission

oadmin.user_profile_delete

Delete a user profile

opal.attribute_values

Get a vector of attribute values

Get an asynchronous command

Execute a R script

oadmin.user_exists

Check user exists

oadmin.user_add

Generic REST resource deletion.

opal.command_result

Get result of an asynchronous command

opal.command_rm

Remove an asynchronous command

opal.execute.source

Execute a R file script

Get file content

Get the R permissions

List content of a folder

opal.as_md_table

Array to Markdown

opal.datasource

Get a datasource

opal.annotations

Get the annotations of a Opal table

List R profiles

opal.datasources

Get datasources

opal.file_mkdir

opal.load_package

opal.file_download

Download a file

opal.file_unzip

Unzip a zip archive file

opal.file_upload

Upload a file or a folder

List the asynchronous commands

opal.project_backup

Backup a project

opal.project_command

Get project task

Generic REST resource creation.

Generic REST resource update.

opal.resource_perm

Get the permissions on a resource

opal.projects_databases

Get projects databases

opal.resource_perm_add

Add or update a permission on a resource

opal.project_perm

Get the permissions on a project

opal.resource_perm_delete

Delete a permission from a resource

opal.project_exists

Check a project exists

Logout from Opal(s)

opal.resource_view_create

Create an Opal view over a resource reference

opal.commands_rm

Remove all asynchronous commands

opal.resource_view_reconnect

Reconnect an Opal view to its underlying resource

Get a resource reference of a project

Get the resource references of a project

Turn a R markdown file to html.

opal.resource_create

Create a resource reference in a project

dsadmin.profile_perm_add

Add or update a permission on a DataSHIELD profile

opal.resources_perm_add

Add or update a permission on any resource

opal.resources_perm

Get the permissions on any resource

opal.project_perm_add

Add or update a permission on a project

dsadmin.set_option

Set DataSHIELD option

opal.symbol_import

Import a tibble

Get the R permissions (deprecated)

Execute a SQL query on tables

opal.sql_history

SQL query execution history

opal.table_delete

Delete a Opal table

Remove a R symbol (deprecated)

opal.table_dictionary_get

Get the dictionary of a Opal table

opal.table_perm_add

Add or update a permission on a table

opal.table_save

Save a local tibble as a Opal table

opal.table_perm_delete

Delete a permission from a table

opal.table_truncate

Truncate a Opal table

opal.taxonomies

opal.table_perm

Get the permissions on a table

oadmin.user_reset_password

Reset user password

opal.assign.script

R script assignment

Wait for a task to complete.

opal.table_export

Export a table as a file

Get a Opal table as a tibble

oadmin.perm_add

Add or update a R permission (deprecated)

opal.file_mkdir_tmp

Make a temporary folder

oadmin.user_profiles

Get user profiles

opal.table_import

Import a file as table

opal.file_write

opal.tables_perm_add

Add or update a permission on any table of a project

opal.tables_perm_delete

Delete a permission from any table of a project

Get the personal access tokens

opal.vocabulary

Get a taxonomy vocabulary

opal.unload_package

opal.variable_summary

Get summary statistics of a variable of a table

opal.token_delete

Delete a personal access token

opal.token_renew

Renew an inactive personal access token

Get variables of a table

opal.assign.resource

Resource assignment

opal.symbol_save

opal.workspace_restore

Restore a R workspace from a opal.

opal.token_r_create

Create a personal access token for R usage

opal.token_datashield_create

Create a personal access token for Datashield usage

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

opal.task_cancel

opal.workspaces

Get the R workspaces from a opal.

Get a personal access token

Get tables of a datasource

opal.version_compare

Generic REST resource getter.

opal.vocabularies

Get the vocabularies of a taxonomy

Get a table of a datasource

opal.project_perm_delete

Delete a permission from a project

Move and/or rename a file

opal.resource_delete

Delete a resource reference

opal.taxonomy_delete

Delete a taxonomy

Remove a R symbol

opal.taxonomy_download

Download a taxonomy file

opal.tables_perm

Get the permissions on any table of a project

opal.table_create

Create an Opal table or view

opal.resource_exists

Check a resource reference exists

opal.workspace_rm

Remove a R workspace from a opal.

opal.table_dictionary_update

Update the dictionary of a Opal table

opal.project_create

Create a project

opal.resource_get

Get the resource object of a project

opal.project_restore

Restore a project

opal.table_exists

Check a Opal table exists

opal.project_delete

Delete a project

opal.workspace_save

Save the current session in a opal R workspace.

opal.resource_extension_create

Create an extended resource reference in a project

opal.token_sql_create

Create a personal access token for SQL usage

Get the values of an entity

opal.table_view_create

Create an Opal view over tables

opal.resources_perm_delete

Delete a permission from any resource

opal.taxonomy_upload

Upload a taxonomy file

opal.table_view_update

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

Get the terms of a vocabulary

Get a variable of a table

.authorizationHeader

Constructs the value for the Authorization header

dictionary.annotations

List the annotations

dictionary.inspect

Inspect the dictionary of a tibble

dictionary.annotate.harmo_status

Set variable annotation with Harmonization Status term

.aclsToDataFrame

Permsissions (ACLs) into a data frame.