'Opal' Data Repository Client and 'DataSHIELD' Utils
Set variable annotation with Harmonization Status term
Set variable annotation with a taxonomy term
List the annotations
Apply the dictionary to a tibble
Inspect the dictionary of a tibble
Permsissions (ACLs) into a data frame.
Turns a value into 0/1 numeric.
Constructs the value for the Authorization header
Turn expression into character strings.
Extract JSON
Extract label for locale. If not found, fallback to undefined language...
Extract CSRF token from cookie data frame.
Extract opalsid from cookie data frame.
Wrapper of httr::content()
Extract absolute path to the pem file
Get all R session in Opal.
Handle error response
Default request response handler.
Default request response Location handler.
Process response with default handler or the provided one
Verbose option
Check if response content is empty.
Simple transformation function of a list into a JSON object/array.
Create a new progress instance with default settings.
Create a new R session in Opal.
Create the opal object
Remove a Opal session (logout)
Remove a R session from Opal.
Returns a list r such that r[[i]] == l[[i]][field] for all i:length(l)
Output the progress status if option "datashield.progress" is allows t...
Constructs the value for the X-Opal-Auth header
Utility method to build urls. Concatenates all arguments and adds a '/...
Verbose flag
Get DataSHIELD activity summary
Get DataSHIELD activity
Get a DataSHIELD method
Get DataSHIELD methods
Get the DataSHIELD options
Install a DataSHIELD package from GitHub
Install a DataSHIELD package from a local archive file
Install a DataSHIELD package
Check DataSHIELD package
Get DataSHIELD logs
Get DataSHIELD package description
Get DataSHIELD package descriptions
Add or update a DataSHIELD permission
Delete a DataSHIELD permission
Get the DataSHIELD permissions
Restrict or open access to a DataSHIELD profile
Create a DataSHIELD profile
Delete a DataSHIELD profile
Enable or disable a DataSHIELD profile
Check a DataSHIELD profile exists
Initialize a DataSHIELD profile
Add or update a permission on a DataSHIELD profile
Delete a permission from a DataSHIELD profile
Get the permissions of a DataSHIELD profile
Set or remove the R parser version of a DataSHIELD profile
Get a DataSHIELD profile
Get DataSHIELD profiles
Publish DataSHIELD package settings
Remove DataSHIELD package
Remove DataSHIELD method
Remove DataSHIELD methods.
Remove a DataSHIELD option
Remove all DataSHIELD options
Remove DataSHIELD package methods
Set DataSHIELD method
Set DataSHIELD option
Set DataSHIELD package methods
Unpublish DataSHIELD package settings
Get R activity summary
Get R activity
Install a package from Bioconductor
Install a package from CRAN
Install devtools package
Install a package from GitHub
Install a package from a local archive file
Install CRAN package
Check devtools package
Check package is installed
List installed packages
Get Opal REST API logs
Get Opal SQL API logs
Get Opal main logs
Get package description
Add or update a R permission (deprecated)
Delete a R permission (deprecated)
Get the R permissions (deprecated)
Add or update a R permission
Delete a R permission
Get the R permissions
Remove package
Get system metrics
Add or update a System permission
Delete a System permission
Get the System permissions
Add a user
Delete a user
Enable a user
Check user exists
Delete a user profile
Get user profiles
Reset user password
Get the users
Apply the annotations to a Opal table
Get the annotations of a Opal table
Array to Markdown
Data assignment
Data or expression assignment
Resource assignment
R script assignment
Data assignment to a data.frame
Data assignment to a tibble
Get a vector of attribute values
Get result of an asynchronous command
Remove an asynchronous command
Get an asynchronous command
Remove all asynchronous commands
List the asynchronous commands
Get a datasource
Get datasources
Generic REST resource deletion.
Execute a R script
Execute a R file script
Copy a file
Download a file
List content of a folder
Make a temporary folder
Make a folder
Move and/or rename a file
Read a file
Remove a file
Unzip a zip archive file
Upload a file or a folder
Write a file
Get file content
Generic REST resource getter.
Load package
Opal login
Logout from Opal(s)
Get the permissions of a subject
Generic REST resource creation.
List R profiles
Backup a project
Get project task
Create a project
Delete a project
Check a project exists
Add or update a permission on a project
Delete a permission from a project
Get the permissions on a project
Restore a project
Get a project
Get projects databases
Get projects
Generic REST resource update.
Turn a R markdown file to html.
Opal report
Create a resource reference in a project
Delete a resource reference
Check a resource reference exists
Create an extended resource reference in a project
Get the resource object of a project
Add or update a permission on a resource
Delete a permission from a resource
Get the permissions on a resource
Create an Opal view over a resource reference
Reconnect an Opal view to its underlying resource
Get a resource reference of a project
Add or update a permission on any resource
Delete a permission from any resource
Get the permissions on any resource
Get the resource references of a project
Remove a R symbol (deprecated)
Delete the R session
Get the events associated to the R session
Check if the R session exists
Get the R session
Check if the R session is running
Create the R session
SQL query execution history
Execute a SQL query on tables
Import a tibble
Remove a R symbol
Save a tibble
List R symbols
Create an Opal table or view
Delete a Opal table
Get the dictionary of a Opal table
Update the dictionary of a Opal table
Check a Opal table exists
Export a table as a file
Get a Opal table as a tibble
Import a file as table
Add or update a permission on a table
Delete a permission from a table
Get the permissions on a table
Save a local tibble as a Opal table
Truncate a Opal table
Create an Opal view over tables
Update the table references and the entity filter of an Opal view
Get a table of a datasource
Add or update a permission on any table of a project
Delete a permission from any table of a project
Get the permissions on any table of a project
Get tables of a datasource
Cancel a task
Wait for a task to complete.
Get a task
Get the tasks
Get taxonomies
Delete a taxonomy
Download a taxonomy file
Upload a taxonomy file
Get a taxonomy
Get the terms of a vocabulary
Create a personal access token for Datashield usage
Delete a personal access token
Create a personal access token for R usage
Renew an inactive personal access token
Create a personal access token for SQL usage
Get a personal access token
Get the personal access tokens
Unload package
Get the values of an entity
Get summary statistics of a variable of a table
Get a variable of a table
Get variables of a table
Compare
Get the vocabularies of a taxonomy
Get a taxonomy vocabulary
Restore a R workspace from a opal.
Remove a R workspace from a opal.
Save the current session in a opal R workspace.
Get the R workspaces from a opal.
opalr: '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.
Useful links