opalr v1.4.1

'Opal' Data Repository Client and 'DataSHIELD' Utils

Data integration Web application for biobanks by 'OBiBa'. 'Opal' is the core database application for biobanks. Participant data, once collected from any data source, must be integrated and stored in a central data repository under a uniform model. 'Opal' is such a central repository. It can import, process, validate, query, analyze, report, and export data. 'Opal' is typically used in a research center to analyze the data acquired at assessment centres. Its ultimate purpose is to achieve seamless data-sharing among biobanks. This 'Opal' client allows to interact with 'Opal' web services and to perform operations on the R server side. 'DataSHIELD' administration tools are also provided.

Readme

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.

Functions in opalr

Name	Description
.handleError	Handle error response
dsadmin.install_package	Install a DataSHIELD package
.handleResponseLocation	Default request response Location handler.
dsadmin.get_options	Get the DataSHIELD options
dsadmin.get_method	Get a DataSHIELD method
dsadmin.rm_option	Remove a DataSHIELD option
dsadmin.get_methods	Get DataSHIELD methods
dsadmin.rm_method	Remove DataSHIELD method
.is.verbose	Verbose option
.handleResponse	Default request response handler.
.handleResponseOrCallback	Process response with default handler or the provided one
.isContentEmpty	Check if response content is empty.
dsadmin.set_package_methods	Set DataSHIELD package methods
opal.as_md_table	Array to Markdown
harmo.annotate	Set variable annotation with a taxonomy term
opal.assign	Data or expression assignment
dsadmin.rm_methods	Remove DataSHIELD methods.
.newProgress	Create a new progress instance with default settings.
dsadmin.set_method	Set DataSHIELD method
.rmOpalSession	Remove a Opal session (logout)
.opal.login	Create the opal object
dsadmin.rm_package_methods	Remove DataSHIELD package methods
opal.command_rm	Remove an asynchronous command
opal.execute	Execute a R script
.tickProgress	Output the progress status if option "datashield.progress" is allows to.
opal.commands	List the asynchronous commands
dsadmin.installed_package	Check DataSHIELD package
.listToJson	Simple transformation function of a list into a JSON object/array.
dsadmin.package_description	Get DataSHIELD package description
harmo.table_get	Get a Opal table as a tibble
harmo.dictionary_apply	Apply the dictionary to a tibble
oadmin.install_package	Install package
.tokenHeader	Constructs the value for the X-Opal-Auth header
harmo.dictionary_update	Update the dictionary of a Opal table
oadmin.installed_package	Check package is installed
dsadmin.set_option	Set DataSHIELD option
.rmRSession	Remove a R session from Opal.
opal.execute.source	Execute a R file script
opal.annotate	Apply the annotations to a Opal table
opal.annotations	Get the annotations of a Opal table
.select	Returns a list r such that r[[i]] == l[[i]][field] for all i:length(l)
harmo.table_save	Save a local tibble as a Opal table
harmo.annotate.status	Set variable annotation with Harmonization Status term
opal.login	Opal login
oadmin.installed_packages	List installed packages
.newSession	Create a new R session in Opal.
oadmin.installed_devtools	Check devtools package
opal.assign.data	Data assignment
harmo.annotations	List the annotations
oadmin.package_description	Get package description
oadmin.remove_package	Remove package
opal.file_download	Download a file
opal.command	Get an asynchronous command
opal.assign.script	R script assignment
.url	Utility method to build urls. Concatenates all arguments and adds a '/' separator between each element
dsadmin.remove_package	Remove DataSHIELD package
dsadmin.package_descriptions	Get DataSHIELD package descriptions
opal.assign.table	Data assignment to a data.frame
opal.assign.table.tibble	Data assignment to a tibble
opal.attribute_values	Get a vector of values
.verbose	Verbose flag
oadmin.install_devtools	Install devtools package
opal.file_read	Read a file
opal.command_result	Get result of an asynchronous command
opal.datasources	Get datasources
opal.file_rm	Remove a file
opal.delete	Generic REST resource deletion.
opal.report	Opal report
opal.logout	Logout from Opal(s)
opal.commands_rm	Remove all asynchronous commands
opal.report_md	Turn a R markdown file to html.
opal.tasks	Get the tasks
oadmin.install_github	Install a package form GitHub
opal.taxonomies	Get taxonomies
opal.file_upload	Upload a file
opal.file_write	Write a file
opal.datasource	Get a datasource
opal.resource	Get a resource of a project
opal.assign.resource	Resource assignment
opal.file_cp	Copy a file
opal.file	Get file content
opal.task_cancel	Cancel a task
opal.resources	Get the resource references of a project
opal.tables	Get tables of a datasource
opal.file_ls	List content of a folder
opal.task	Get a task
opal.file_mv	Move and/or rename a file
opal.file_mkdir	Make a folder
opal.symbols	List R symbols
opal.rm	Remove a R symbol (deprecated)
opal.symbol_import	Import a tibble
opal.variable	Get a variable of a table
opal.table	Get a table of a datasource
opal.post	Generic REST resource creation.
opal.get	Generic REST resource getter.
opal.load_package	Load package
opal.task_wait	Wait for a task to complete.
opal.projects	Get projects
opal.symbol_rm	Remove a R symbol
opal.put	Generic REST resource update.
opal.variables	Get variables of a table
opal.vocabularies	Get the vocabularies of a taxonomy
opal.version_compare	Compare
opal.vocabulary	Get a taxonomy vocabulary
opal.project	Get a project
opal.workspace_rm	Remove a R workspace from a opal.
opal.symbol_save	Save a tibble
opal.taxonomy	Get a taxonomy
opal.workspaces	Get the R workspaces from a opal.
opal.workspace_save	Save the current session in a opal R workspace.
opal.terms	Get the terms of a vocabulary
opal.valueset	Get the values of an entity
opal.unload_package	Unload package
.getContent	Wrapper of httr::content()
.getSessions	Get all R session in Opal.
.getPEMFilePath	Extract absolute path to the pem file
.getRSessionId	Extract R session Id from opal object, create a new R session if not found.
.extractJsonField	Extract JSON
.authorizationHeader	Constructs the value for the Authorization header
.extractOpalSessionId	Extract opalsid from cookie data frame.
.deparse	Turn expression into character strings.
.extractLabel	Extract label for locale. If not found, fallback to undefined language label (if any).
No Results!

Name

Description

.handleError

Handle error response

dsadmin.install_package

Install a DataSHIELD package

.handleResponseLocation

Default request response Location handler.

dsadmin.get_options

Get the DataSHIELD options

dsadmin.get_method

Get a DataSHIELD method

dsadmin.rm_option

Remove a DataSHIELD option

dsadmin.get_methods

Get DataSHIELD methods

dsadmin.rm_method

Remove DataSHIELD method

.is.verbose

Verbose option

.handleResponse

Default request response handler.

.handleResponseOrCallback

Process response with default handler or the provided one

.isContentEmpty

Check if response content is empty.

dsadmin.set_package_methods

Set DataSHIELD package methods

opal.as_md_table

Array to Markdown

harmo.annotate

Set variable annotation with a taxonomy term

opal.assign

Data or expression assignment

dsadmin.rm_methods

Remove DataSHIELD methods.

.newProgress

Create a new progress instance with default settings.

dsadmin.set_method

Set DataSHIELD method

.rmOpalSession

Remove a Opal session (logout)

.opal.login

Create the opal object

dsadmin.rm_package_methods

Remove DataSHIELD package methods

opal.command_rm

Remove an asynchronous command

opal.execute

Execute a R script

.tickProgress

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

opal.commands

List the asynchronous commands

dsadmin.installed_package

Check DataSHIELD package

.listToJson

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

dsadmin.package_description

Get DataSHIELD package description

harmo.table_get

Get a Opal table as a tibble

harmo.dictionary_apply

Apply the dictionary to a tibble

oadmin.install_package

Install package

.tokenHeader

Constructs the value for the X-Opal-Auth header

harmo.dictionary_update

Update the dictionary of a Opal table

oadmin.installed_package

Check package is installed

dsadmin.set_option

Set DataSHIELD option

.rmRSession

Remove a R session from Opal.

opal.execute.source

Execute a R file script

opal.annotate

Apply the annotations to a Opal table

opal.annotations

Get the annotations of a Opal table

.select

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

harmo.table_save

Save a local tibble as a Opal table

harmo.annotate.status

Set variable annotation with Harmonization Status term

opal.login

Opal login

oadmin.installed_packages

List installed packages

.newSession

Create a new R session in Opal.

oadmin.installed_devtools

Check devtools package

opal.assign.data

Data assignment

harmo.annotations

List the annotations

oadmin.package_description

Get package description

oadmin.remove_package

Remove package

opal.file_download

Download a file

opal.command

Get an asynchronous command

opal.assign.script

R script assignment

.url

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

dsadmin.remove_package

Remove DataSHIELD package

dsadmin.package_descriptions

Get DataSHIELD package descriptions

opal.assign.table

Data assignment to a data.frame

opal.assign.table.tibble

Data assignment to a tibble

opal.attribute_values

Get a vector of values

.verbose

Verbose flag

oadmin.install_devtools

Install devtools package

opal.file_read

Read a file

opal.command_result

Get result of an asynchronous command

opal.datasources

Get datasources

opal.file_rm

Remove a file

opal.delete

Generic REST resource deletion.

opal.report

Opal report

opal.logout

Logout from Opal(s)

opal.commands_rm

Remove all asynchronous commands

opal.report_md

Turn a R markdown file to html.

opal.tasks

Get the tasks

oadmin.install_github

Install a package form GitHub

Get taxonomies

Upload a file

Write a file

Get a datasource

Get a resource of a project

Resource assignment

Copy a file

Get file content

Cancel a task

Get the resource references of a project

opal.tables

Get tables of a datasource

opal.file_ls

List content of a folder

opal.task

Get a task

opal.file_mv

Move and/or rename a file

opal.file_mkdir

Make a folder

opal.symbols

List R symbols

opal.rm

Remove a R symbol (deprecated)

opal.symbol_import

Import a tibble

opal.variable

Get a variable of a table

opal.table

Get a table of a datasource

opal.post

Generic REST resource creation.

opal.get

Generic REST resource getter.

opal.load_package

Load package

opal.task_wait

Wait for a task to complete.

opal.projects

Get projects

opal.symbol_rm

Remove a R symbol

opal.put

Generic REST resource update.

opal.variables

Get variables of a table

opal.vocabularies

Get the vocabularies of a taxonomy

opal.version_compare

Compare

opal.vocabulary

Get a taxonomy vocabulary

opal.project

Get a project

opal.workspace_rm

Remove a R workspace from a opal.

opal.symbol_save

Save a tibble

opal.taxonomy

Get a taxonomy

opal.workspaces

Get the R workspaces from a opal.

opal.workspace_save

Save the current session in a opal R workspace.

opal.terms

Get the terms of a vocabulary

opal.valueset

Get the values of an entity

opal.unload_package

Unload package

.getContent

Wrapper of httr::content()

.getSessions

Get all R session in Opal.

.getPEMFilePath

Extract absolute path to the pem file

.getRSessionId

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

.extractJsonField

Extract JSON

.authorizationHeader

Constructs the value for the Authorization header

.extractOpalSessionId

Extract opalsid from cookie data frame.

.deparse

Turn expression into character strings.

.extractLabel

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

No Results!

Vignettes of opalr

Name
opal-files.Rmd
opal-projects.Rmd
opal-rsession.Rmd
No Results!

Name

opal-files.Rmd

opal-projects.Rmd

opal-rsession.Rmd