Package 'MolgenisArmadillo'

Title: Armadillo Client for the Armadillo Service
Description: A set of functions to manage data shared on a 'MOLGENIS Armadillo' server.
Authors: Mariska Slofstra [aut, cre] , Sido Haakma [aut] , Tommy de Boer [aut] , Fleur Kelpin [aut] , Morris Swertz [aut] , Tim Cadman [aut]
Maintainer: Mariska Slofstra <[email protected]>
License: LGPL (>= 2.1)
Version: 2.9.0
Built: 2025-03-30 07:13:12 UTC
Source: https://github.com/molgenis/molgenis-r-armadillo

Help Index

Add a Slash to a URL if Missing

Description

This function ensures that a given URL string ends with a slash ('/'). If the URL does not end with a slash, it appends one.

Usage

.add_slash_if_missing(url)

Arguments

url

A character string representing the URL.

Value

A character string with a trailing slash if it was missing.

Helper function for compressing to an RDS file

Description

Helper function for compressing to an RDS file

Usage

.compress_resource(resource, file)

Arguments

resource

the resource to write to file
file

the name of the file (without extension)

Value

the extension of the file

Helper function for compressing to a parquet file

Description

Helper function for compressing to a parquet file

Usage

.compress_table(table, file)

Arguments

table

the table to write to file
file

the name of the file (without extension)

Value

the extension of the file

Formats API posts based on subset definition

Description

Formats API posts based on subset definition

Usage

.format_api_posts(posts, subset_def)

Arguments

posts

A list of API posts
subset_def

A tibble containing subset definition

Value

A tibble consisting of original subset_def with columns 'posts' and 'status' appended.

Helper function to get the contents of a linkfile

Description

Helper function to get the contents of a linkfile

Usage

.get_linkfile_content(project, object_name)

Arguments

project

projectname where the linkfile is stored
object_name

folder/name of linkfile

Value

the contents of the linkfile

Helper function to extract the source parquet file in a linkfile

Description

Helper function to extract the source parquet file in a linkfile

Usage

.load_linked_table(file, columns)

Arguments

file

source table parquet file
columns

character list of columns to select from source file

Value

the contents of the file, as data frame

Helper function to extract an RDS file

Description

Helper function to extract an RDS file

Usage

.load_resource(file)

Arguments

file

file to extract

Value

the contents of the file

Helper function to extract a parquet file

Description

Helper function to extract a parquet file

Usage

.load_table(file)

Arguments

file

file to extract

Value

the contents of the file, as data frame

Copy resource

Description

Copy resource

Usage

armadillo.copy_resource(
  project,
  folder,
  name,
  new_folder = folder,
  new_name = name
)

Arguments

project

study or other variable collection
folder

the folder containing the resource
name

specific resource for copy action
new_folder

name of the folder in which to place the copy, defaults to folder
new_name

name of the copy, defaults to name

Value

the response from the server

Examples

## Not run: 
armadillo.copy_resource(
  project = "gecko",
  folder = "core_all",
  name = "table1",
  new_folder = "core_all_v2",
)

## End(Not run)

Copy table

Description

Copy table

Usage

armadillo.copy_table(
  project,
  folder,
  name,
  new_folder = folder,
  new_name = name
)

Arguments

project

study or other variable collection
folder

the folder containing the table
name

specific table for copy action
new_folder

name of the folder in which to place the copy, defaults to folder
new_name

name of the copy, defaults to name

Value

the response from the server

Examples

## Not run: 
armadillo.copy_table(
  project = "gecko",
  folder = "core_all",
  name = "table1",
  new_folder = "core_all_v2",
)

## End(Not run)

Create a project for a variable collection

Description

Create a project for a variable collection

Usage

armadillo.create_project(
  project_name = NULL,
  users = NULL,
  overwrite_existing = "choose"
)

Arguments

project_name

The name of the project to create. The project name

  • cannot be empty.

  • must be no more than 56 characters.

  • cannot end with a -.

  • must consist of lowercase letters and numbers.

users

A list collection of the users that should have access to the project
overwrite_existing

Character, specifying action to take if project still exists: 'choose' (default) displays a menu giving the option to overwrite or not, 'yes' overwrites the existing project and 'no' exists the function with a message.

Examples

## Not run: 
armadillo.create_project("gecko")

## End(Not run)

Delete project

Description

A project represents usually a study or collection of variables

Usage

armadillo.delete_project(project_name)

Arguments

project_name

the name of the study or collection of variables name

Examples

## Not run: 
armadillo.delete_project(project_name = "gecko")

## End(Not run)

Delete project folder

Description

Delete project folder

Usage

armadillo.delete_project_folder(project, folder)

Arguments

project

project to delete the object from
folder

folder to delete the object from

Delete resource

Description

Delete resource

Usage

armadillo.delete_resource(project, folder, name)

Arguments

project

project to delete the resource from
folder

folder to delete the resource from
name

resource name

Examples

## Not run: 
armadillo.delete_resource(
  project = "gecko",
  folder = "core_all",
  name = "table1"
)

## End(Not run)

Delete table

Description

Delete table

Usage

armadillo.delete_table(project, folder, name)

Arguments

project

project to delete the table from
folder

folder to delete the table from
name

table name

Examples

## Not run: 
armadillo.delete_table(
  project = "gecko",
  folder = "core_all",
  name = "table1"
)

## End(Not run)

Gets the users of an given project name

Description

Gets the users of an given project name

Usage

armadillo.get_project_users(project_name)

Arguments

project_name

the name of the project to extract the users from

Value

List of all users within "project_name"

Examples

## Not run: 
armadillo.get_project_users("some-project")

## End(Not run)

Gets the Projects information

Description

Gets the Projects information

Usage

armadillo.get_projects_info()

Value

the projects and their information

Examples

## Not run: 
armadillo.get_projects_info()

## End(Not run)

Install package

Description

Installs a user defined package into the provided profile. The package is automatically whitelisted after installation. Only available during development.

Usage

armadillo.install_packages(paths, profile = "default")

Arguments

paths

the path(s) to the package(s), can be a vector or a string
profile

the selected profile

List the projects

Description

List the projects

Usage

armadillo.list_projects()

Value

the projects

Examples

## Not run: 
armadillo.list_projects()

## End(Not run)

List the resources in a project

Description

List the resources in a project

Usage

armadillo.list_resources(project)

Arguments

project

the shared project in which the resources are located

Value

the resources in the project

Examples

## Not run: 
armadillo.list_resources("gecko")

## End(Not run)

List the tables in a project

Description

List the tables in a project

Usage

armadillo.list_tables(project)

Arguments

project

the shared project in which the tables are located

Value

the table names, without the extension

Examples

## Not run: 
armadillo.list_tables("gecko")

## End(Not run)

Load a resource from a project

Description

Load a resource from a project

Usage

armadillo.load_resource(project, folder, name)

Arguments

project

study or collection variables
folder

the folder containing the resource
name

name of the resource

Value

the loaded resource

Examples

## Not run: 
armadillo.load_resource(
  project = "gecko",
  folder = "core_all",
  name = "lc_core_1"
)

## End(Not run)

Load a table from a project

Description

Load a table from a project

Usage

armadillo.load_table(project, folder, name)

Arguments

project

study or collection variables
folder

the folder containing the table
name

name of the table

Value

the contents of the table file, as data frame

Examples

## Not run: 
armadillo.load_table(
  project = "gecko",
  folder = "core_all",
  name = "lc_core_1"
)

## End(Not run)

Login

Description

Interactively obtains an id token and uses it to create a session token for an Armadillo Service

Usage

armadillo.login(armadillo)

Arguments

armadillo

URL of the Armadillo server,

Value

the id token

Examples

## Not run: 
armadillo.login(
  "https://armadillo.dev.molgenis.org"
)
armadillo.login("http://localhost:8080")

## End(Not run)

Login with username / password (meant for dev and test environments)

Description

Login with username / password (meant for dev and test environments)

Usage

armadillo.login_basic(armadillo, username, password)

Arguments

armadillo

URL of the Armadillo server
username

the username
password

the password

Examples

## Not run: 
armadillo.login(
  "https://armadillo.dev.molgenis.org", "admin", "admin"
)
armadillo.login("http://localhost:8080", "admin", "admin")

## End(Not run)

Move the resource

Description

Move the resource

Usage

armadillo.move_resource(
  project,
  folder,
  name,
  new_folder = folder,
  new_name = name
)

Arguments

project

a study or collection of variables
folder

the folder containing the resource to move
name

a resource to move
new_folder

the folder to move the resource to, defaults to folder
new_name

use to rename the file, defaults to name

Value

NULL, invisibly

Examples

## Not run: 
armadillo.move_resource(
  project = "gecko",
  folder = "core_all",
  name = "table1",
  new_folder = "core_all_v2",
)

## End(Not run)

Move the table

Description

Move the table

Usage

armadillo.move_table(
  project,
  folder,
  name,
  new_folder = folder,
  new_name = name
)

Arguments

project

a study or collection of variables
folder

the folder containing the table to move
name

a table to move
new_folder

the folder to move the table to, defaults to folder
new_name

use to rename the file, defaults to name

Value

NULL, invisibly

Examples

## Not run: 
armadillo.move_table(
  project = "gecko",
  folder = "core_all",
  name = "table1",
  new_folder = "core_all_v2",
)

## End(Not run)

Describes data available to subset and makes subset

Description

This automates the process of:

  1. Checking what data is available to create subsets

  2. Make the subset

Usage

armadillo.subset(
  input_source = NULL,
  subset_def = NULL,
  source_project = NULL,
  source_folder = NULL,
  source_table = NULL,
  target_project = NULL,
  target_folder = NULL,
  target_table = NULL,
  target_vars = NULL,
  new_project = NULL,
  dry_run = NULL,
  strict = FALSE
)

Arguments

input_source

Character specifying how information about the target view is provided: choose 'subset_def' if providing a subset definition object, or 'arguments' if providing information directly.
subset_def

R object containing subset definition created by armadillo.subset_definition(). Compulsory if input_source = 'subset_def'
source_project

project from which to subset data
source_folder

folder from which to subset data. Compulsory if input_source = 'arguments'.
source_table

table from which to subset data. Compulsory if input_source = 'arguments'.
target_project

project to upload subset to. Will be created if it doesn't exist.
target_folder

folder to upload subset to. Will be created if it doesn't exist. Compulsory if input_source = 'arguments'.
target_table

table to upload subset to. Compulsory if input_source = 'arguments'.
target_vars

variables from 'source_table' to include in the view. Compulsory if input_source = 'arguments'.
new_project

Deprecated: use target_project instead
dry_run

Defunct: previously enabgled dry-run to check which variables are missing
strict

Boolean specifying whether to create subset if one or more target variables do not exist in the target data. Option FALSE will throw and error, option TRUE (default) creates subset and return a warning

Value

missing variables provided in the subset definition

Examples

## Not run: 
armadillo.subset(
  source_project = "gecko",
  target_project = "study1",
  subset_def = local_subset
)

## End(Not run)

Builds an R object containing info required to make subsets

Description

Builds an R object containing info required to make subsets

Usage

armadillo.subset_definition(reference_csv = NULL, vars = NULL)

Arguments

reference_csv

.csv file containing details of the variable to subset. Must contain 5 columns: 'source_folder' specifying the folder from which to subset, 'souce_table' specifying the table from which to subset, 'target_folder' specifying the folder in which to create the subset 'target_table' specifying the name of the subset and 'variable' specifying the variable(s) to include in the subset. Note that 'source_project' and 'target_project' are specified as arguments to 'armadillo.subset'.
vars

Deprecated: use reference_csv instead

Value

A dataframe containing variables that is used for input in the armadillo.subset() method

Examples

## Not run: 
armadillo.subset_definition(
  reference_csv = "C:/tmp/vars.csv"
)

## End(Not run)

Uploads a resource to a folder in a project

Description

Uploads a resource to a folder in a project

Usage

armadillo.upload_resource(project, folder, resource, name = NULL)

Arguments

project

the project to upload to
folder

the folder to upload to
resource

the resource to upload
name

name of the resource (optional)

Examples

## Not run: 
armadillo.upload_table(
  project = "gecko",
  folder = "core_all",
  table1
)

## End(Not run)

Uploads a table to a folder in a project

Description

Uploads a table to a folder in a project

Usage

armadillo.upload_table(project, folder, table, name = NULL)

Arguments

project

the project to upload to
folder

the folder to upload to
table

the table to upload
name

name of the table (optional)

Examples

## Not run: 
armadillo.upload_table(
  project = "gecko",
  folder = "core_all",
  table1
)

## End(Not run)