Armadillo UI
Relevant for:
Armadillo features a user interface, or UI for short.
Login
To login to the UI, select the Institute account (oath2) button and login using the institute or organisation login screen you will be redirected to.
Superuser
You need to have admin or superuser permissions if you want to add projects, users or profiles. This means you need to be granted permission in order to be able to use the UI. If you don't have correct permissions, you will receive the following error:
If you receive this error, contact someone in your institute that is already able to login without an error, or contact MOLGENIS Support.
To grant a user superuser permissions simply search for that user in the Users tab of the UI, and tick the admin checkbox for that user:
Projects
Once you're logged in, you will be redirected to the Projects page. On this page you can add and edit projects.
You can add users to projects and navigate to the "project-editor"-view and search through the projects using the search bar on the top right.
Editing projects
To edit your project, click on the edit button in front of the project you want to edit: 
.
The row will be opened in edit mode:
The edit mode can be recognized by its blue background color and you have the option to add new users to your project by clicking on the + button 
of the users column. Then, you can either select an existing user from the dropdown, or add the email address of a new user.
In case of adding a user in this screen, a warning will be shown to prevent email addresses with typographical errors from being added to your system. For example, if you have the address j.doe@example.com in your users table but attempt to add j.die@example.com a warning message will be displayed asking if you want to add a new user.
It is not possible to edit the name of your project; this is intentional in order to ensure tables, resources, users, and permissions are transferred to the new project name correctly.
Click on the checkmark 
to save the edited row and the X 
to cancel.
Be careful, if you do cancel your changes will be lost.
Adding projects
To add a new project, click on the + button 
on top of the table. If you click this button, an empty row will be opened in edit mode.
Click on the checkmark to save the edited row and the X to cancel.
Be careful, if you do cancel your changes will be lost.
Project explorer
If you click on the icon 
next to the project name, you will be directed to the project editor. In this screen you can upload and preview data in projects. To go back to your projects page,
press the back button 
.
If you click on a folder, it will open.
Here you can upload files to that folder, or click on the tables (files) to preview their contents.
To upload files, either drag a file from your file browser to the file upload area, or click the area and select the file.
After selecting the file, click on upload to upload it. This usually only takes a few seconds but will take longer in your uploading a large file.
It is also possible to create new folders. To do so, click the "add folder" button 
just below the project name. An input dialog will be presented:
Fill in the name you want to use and click on the checkmark button . Please keep in mind that the folder will only be saved if you put data into it. Select the new folder to select files to upload.
Resources
All file types can be uploaded into Armadillo, however previews will only be available for .parquet files. Other files that can be uploaded are treated as resources. Resource filetypes usually are .rda files or .Rdata files.
To be able to use these resources as a researcher, first an .rds file must be generated. How to create these files, is described here.
The URL of your resources should consist of:
Here is an example, with some example parameters:
url = "https://armadillo3.demo.molgenis.net"
project = "omics"
folder = "ewas"
file = "gse66351_1.rda"
Which results in the following url:
Users
The Users page works just as the Projects page. You can search users by entering (a part of) the email address or name of the user into the search box:
Editing users
Users can be edited, except for their email addresses. This is because when user's email address changes, that user is possibly no longer working for the same institution and therefore might not be allowed to access the data anymore.
In edit mode, the row will turn blue. Projects can be added by clicking on the + icon in the projects column.
You can add a new project by typing it and clicking the checkmark button . You will be prompted with a warning message, asking you to confirm if you want to add a new project.
Alternatively, you can select an existing project by using the search box or scrolling through the presented list.
Adding users
By clicking on the plus button on the top of the table, a new user can be added. The row with the new user will turn blue in edit mode.
Users can be added before they have logged in previously. These users can be added to projects, which will grant them permission to use the data from those projects upon their first login. Researchers should not be set as admin.
Analysis Profiles
Since the release of Armadillo 3.0.0, it is possible to create and manage analysis profiles in the user interface, rather than asking system administrators to manage these profiles. You can start 
and stop 
profiles.
When you start a profile for the first time, it will take a bit longer to load because the profile needs to be downloaded and installed before it can be started.
If you switch to another screen whilst either starting or stopping a profile, the profiles page will no longer show the loading information. It is however still loading, and when it's done, if you reload the page, you will see that your profile started or stopped successfully.
As in the other screens, you can add profiles with the add-button .
By default, some fields will be set. Please update them to install the correct profile.
Possible images can be found on dockerhub. We recommend selecting one of the DataSHIELD standard profiles. The image name of those profiles can be found on the dockerhub link above.
Although the default port setting should find an available port, please keep in mind that the port has to be unique, otherwise you cannot start your profile and will receive an error message.
R packages can be whitelisted by adding them to the package whitelist column so researchers can use them. 'Whitelisting' a package allows analysts to use it. If you want to whitelist a package, you need to make sure it is installed on the image you selected. Additionally, it is possible to blacklist certain R functions in the blacklist function column. This can be useful if certain functions are not allowed to be used on certain data or within certain cohorts.