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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

519

Version

1.5.2

License

GPL-3

Maintainer

Yannick Marcon

Last Published

January 21st, 2021

Functions in opalr (1.5.2)

.aclsToDataFrame

Permsissions (ACLs) into a data frame.
dictionary.annotate

Set variable annotation with a taxonomy term
dictionary.annotations

List the annotations
dictionary.apply

Apply the dictionary to a tibble
dsadmin.install_package

Install a DataSHIELD package
dsadmin.install_local_package

Install a DataSHIELD package from a local archive file
.extractJsonField

Extract JSON
.getSessions

Get all R session in Opal.
.handleError

Handle error response
.authorizationHeader

Constructs the value for the Authorization header
.extractLabel

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

Remove a Opal session (logout)
dsadmin.set_option

Set DataSHIELD option
.opal.login

Create the opal object
.verbose

Verbose flag
dictionary.annotate.harmo_status

Set variable annotation with Harmonization Status term
.deparse

Turn expression into character strings.
.url

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

Set DataSHIELD package methods
.handleResponseOrCallback

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

Remove DataSHIELD package methods
dsadmin.set_method

Set DataSHIELD method
.tickProgress

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

Default request response handler.
.newProgress

Create a new progress instance with default settings.
.is.verbose

Verbose option
.tokenHeader

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

Create a new R session in Opal.
.handleResponseLocation

Default request response Location handler.
.select

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

Remove a R session from Opal.
oadmin.install_package

Install package
oadmin.installed_package

Check package is installed
oadmin.installed_packages

List installed packages
dsadmin.rm_option

Remove a DataSHIELD option
dsadmin.rm_methods

Remove DataSHIELD methods.
.getRSessionId

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

Get the annotations of a Opal table
opal.as_md_table

Array to Markdown
.getPEMFilePath

Extract absolute path to the pem file
oadmin.installed_devtools

Check devtools package
opal.assign.data

Data assignment
opal.assign

Data or expression assignment
opal.commands

List the asynchronous commands
.listToJson

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

Check if response content is empty.
dsadmin.installed_package

Check DataSHIELD package
dsadmin.install_github_package

Install a DataSHIELD package from GitHub
dsadmin.perm

Get the DataSHIELD permissions
harmo.annotations

List the annotations (deprecated)
dsadmin.get_options

Get the DataSHIELD options
dsadmin.package_descriptions

Get DataSHIELD package descriptions
dsadmin.package_description

Get DataSHIELD package description
harmo.dictionary_apply

Apply the dictionary to a tibble (deprecated)
oadmin.package_description

Get package description
opal.attribute_values

Get a vector of values
oadmin.install_devtools

Install devtools package
harmo.table_save

Save a local tibble as a Opal table (deprecated)
oadmin.install_github

Install a package from GitHub (deprecated)
oadmin.install_bioconductor_package

Install a package from Bioconductor
opal.assign.resource

Resource assignment
dsadmin.get_methods

Get DataSHIELD methods
opal.file_ls

List content of a folder
opal.command

Get an asynchronous command
dsadmin.get_method

Get a DataSHIELD method
opal.assign.script

R script assignment
dsadmin.perm_add

Add or update a DataSHIELD permission
opal.file_read

Read a file
opal.commands_rm

Remove all asynchronous commands
opal.file_mkdir

Make a folder
opal.resource_delete

Delete a resource reference
opal.file_rm

Remove a file
opal.project_create

Create a project
opal.project_delete

Delete a project
oadmin.perm

Get the R permissions
opal.get

Generic REST resource getter.
opal.execute.source

Execute a R file script
dsadmin.perm_delete

Delete a DataSHIELD permission
opal.file

Get file content
opal.resources

Get the resource references of a project
opal.load_package

Load package
opal.symbols

List R symbols
opal.resource_exists

Check a resource reference exists
opal.table

Get a table of a datasource
harmo.dictionary_update

Update the dictionary of a Opal table (deprecated)
oadmin.remove_package

Remove package
opal.annotate

Apply the annotations to a Opal table
opal.project_exists

Check a project exists
opal.resource_get

Get the resource object of a project
opal.project_perm

Get the permissions on a project
opal.resource_perm

Get the permissions on a resource
harmo.table_get

Get a Opal table as a tibble (deprecated)
opal.resources_perm_add

Add or update a permission on any resource
dsadmin.rm_method

Remove DataSHIELD method
dsadmin.remove_package

Remove DataSHIELD package
opal.rm

Remove a R symbol (deprecated)
opal.resources_perm

Get the permissions on any resource
opal.assign.table

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

Data assignment to a tibble
harmo.annotate.status

Set variable annotation with Harmonization Status term (deprecated)
harmo.annotate

Set variable annotation with a taxonomy term (deprecated)
opal.symbol_import

Import a tibble
oadmin.install_github_package

Install a package from GitHub
oadmin.install_local_package

Install a package from a local archive file
opal.task_wait

Wait for a task to complete.
opal.task_cancel

Cancel a task
opal.command_result

Get result of an asynchronous command
oadmin.perm_add

Add or update a R permission
opal.file_mkdir_tmp

Make a temporary folder
opal.command_rm

Remove an asynchronous command
oadmin.perm_delete

Delete a R permission
opal.table_dictionary_get

Get the dictionary of a Opal table
opal.delete

Generic REST resource deletion.
opal.workspaces

Get the R workspaces from a opal.
opal.unload_package

Unload package
opal.terms

Get the terms of a vocabulary
opal.table_dictionary_update

Update the dictionary of a Opal table
opal.datasource

Get a datasource
opal.file_cp

Copy a file
opal.datasources

Get datasources
opal.file_download

Download a file
opal.post

Generic REST resource creation.
opal.file_mv

Move and/or rename a file
opal.project

Get a project
opal.projects

Get projects
opal.put

Generic REST resource update.
opal.execute

Execute a R script
opal.vocabularies

Get the vocabularies of a taxonomy
opal.resources_perm_delete

Delete a permission from any resource
opal.report

Opal report
opal.logout

Logout from Opal(s)
opal.login

Opal login
opal.report_md

Turn a R markdown file to html.
opal.vocabulary

Get a taxonomy vocabulary
opal.table_perm_delete

Delete a permission from a table
opal.resource_perm_add

Add or update a permission on a resource
opal.resource

Get a resource reference of a project
opal.file_upload

Upload a file
opal.project_perm_add

Add or update a permission on a project
opal.file_write

Write a file
opal.project_perm_delete

Delete a permission from a project
opal.table_perm

Get the permissions on a table
opal.resource_create

Create a resource reference in a project
opal.table_create

Create a Opal table or view
opal.table_perm_add

Add or update a permission on a table
opal.resource_perm_delete

Delete a permission from a resource
opal.table_save

Save a local tibble as a Opal table
opal.taxonomy_download

Download a taxonomy file
opal.taxonomy_delete

Delete a taxonomy
opal.taxonomy

Get a taxonomy
opal.symbol_save

Save a tibble
opal.tasks

Get the tasks
opal.symbol_rm

Remove a R symbol
opal.variables

Get variables of a table
opal.taxonomies

Get taxonomies
opal.version_compare

Compare
opal.table_delete

Delete a Opal table
opal.table_truncate

Truncate a Opal table
opal.table_get

Get a Opal table as a tibble
opal.table_exists

Check a Opal table exists
opal.task

Get a task
opal.tables_perm_delete

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

Upload a taxonomy file
opal.tables

Get tables of a datasource
opal.tables_perm

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

Get the values of an entity
opal.variable

Get a variable of a table
opal.tables_perm_add

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

Remove a R workspace from a opal.
opal.workspace_save

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

Wrapper of httr::content()
.extractOpalSessionId

Extract opalsid from cookie data frame.
.as.zeroOne

Turns a value into 0/1 numeric.