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