Configuration tab allows privileged users to configure global parameters of a MINERVA instance. Particular categories of configuration items are grouped in separate tabs (see image below).

General configuration#

MINERVA configuration categories are listed below:

• Email notification details

  • E-mail address - e-mail address used for sending notifications about the activity of a MINERVA instance - project uploads, comments, sign up, etc.

  • Email content used for requesting an account - the Info and Overlay tabs in the user interface allow to a Request for an account action, which will auto-compose an email with the message defined in Email content used for requesting an account to addressed to the e-mail, or e-mails (separated by a semicolon) provided in the field Email used for requesting an account.

  • E-mail server login, E-mail server password, IMAP server, SMTP port and SMTP server - configuration of your mail server for notification sending.

• Server configuration

  • Allow users to create accounts - if enabled, this allows users to sign up on their own.

  • Authentication token in minerva-net - allows to register instance in MINERVA-Net, token is “password” and root url of instance is login, both necessary for registration.

  • Default project Id - the project that will be displayed by default under the root address of the platform (your.url/MapViewer/).

  • Domain allowed to connect via x-frame technology - the address of a website allowed to embed a MINERVA instance via x-frame technology.

  • Disable CORS - when selected the response will allow for Cross-Origin Resource Sharing when authenticated (for instance when JS code on other site would like to connect to the API of this specific minerva instance). However, to make it work properly CORS request must have ‘ORIGIN’ header set properly.

  • Domain allowed to connect via x-frame technology - the address of a website allowed to embed a MINERVA instance via x-frame technology.

  • Google Analytics tracking ID used for statistics - provide here a valid Google Analytics ID to track user activity of a MINERVA instance.

    • Max session inactivity time (in seconds) set the time after inactive session is expired.

  • Minerva net host - MINERVA-NET URL.

  • Minerva root url - MINERVA instance URL.

  • Path to store big files - location in the directory structure of a MINERVA instance to store big files.

  • Privacy policy (url) - URL of the cookie policy.

  • Require admin approval for auto-registered accounts - specifies whether a user’s account is activated immediately after signing up or requires an administrator’s review and approval.

• Legend and logo

  • Custom CSS - path to user’s own stylesheet.

  • Left logo description - the popup text that will be displayed upon mouse hover your left logo.

  • Left logo icon - the filename of your left logo icon, displayed in the bottom-left corner of the main view; path in the directory or URL.

  • Left logo link (after click) - the website to which you will be redirected after clicking on the left logo.

  • Legend 1-4 image files - path in the directory structure of a MINERVA instance for displayed legend images.

  • Right logo description - the popup text that will be displayed upon mouse hover your right logo.

  • Right logo icon - the filename of your right logo icon, displayed in the bottom-right corner of the main view; path in the directory or URL.

  • Right logo link (after click) - the website to which you will be redirected after clicking on the left logo.

  • URL of platform Terms of Service - path in the directory or URL.

  • User manual file - location in the directory structure of a MINERVA instance for the user manual file.

• Point and click

  • Max distance for clicking on element (px) - the content visualized by MINERVA is interactive, and clicked elements or interactions are recognized by the vicinity of the click event. This parameter controls how close to an element or interaction, in pixels, you need to click to select them.

  • Max number of map zoom levels - sets the max size (of canvas) of the map, that can be uploaded to MINERVA.

  • Max number of results - sets the max number of search results, (similar elements are grouped into a single search result).

• Overlays

  • Opacity used when drawing data overlays (value between 0.0-1.0)

  • Overlay color for negative/positive values - sets the colors should be used for positive and negative values in basic overlays. Values close to zero have the lowest color saturation, values close to -1/1 have the highest color saturation.

  • Overlay color for value=0

  • Overlay color when no values are defined - sets the color to use for coloring list of elements overlays; see section User manual - Upload user-provided overlay data

• Default user privileges Sets default user privileges to manage comments, overlays and view projects for any project on a MINERVA instance.

• Search panel options Defines which search results in the left panel will be expandable via plus/minus icon.

LDAP configuration#

LDAP allows to log in to MINERVA with user’s global credentials. Note that: A user can log in to MINERVA via LDAP authentication without creating account on MINERVA instance. Such users is granted by default with the privileges of the public user (anonymous). To set non-default privileges for a user (who have not logged in yet) it is necessary to create MINERVA account for him. Then set the custom privileges and choose LDAP authentication in Users section.

Please find below description and examples of LDAP configuration for MINERVA:

• LDAP address - address of the machine where LDAP server is located; e.g. lums2.uni.lu

• LDAP base DN - definition of the point from where a server will search for users; e.g. cn=users,cn=accounts,dc=uni,dc=lu

• LDAP bind DN - Distinguished Name of the user account that should be used for LDAP connection (this user should be able to search/list accounts on LDAP server); e.g. uid=ldap-reader-minerva,cn=users,cn=accounts,dc=uni,dc=lu

• LDAP email attribute - which attribute in LDAP directory corresponds to the user email address; e.g. mail

• LDAP filter - when there are many accounts in LDAP administrators create groups of users that have access to specific systems, this filter allows to define LDAP filter that will limit set of accounts that can access minerva, empty string disable filtering; e.g. (memberof=cn=minerva,cn=groups,cn=accounts,dc=uni,dc=lu)

• LDAP filter objectClass - this parameter allows to filter by objectClass type of LDAP entry; value * skips the filtering

• LDAP first name attribute - which attribute in LDAP directory corresponds to “First name” of the user; e.g. givenName

• LDAP last name attribute - which attribute in LDAP directory corresponds to “Last name” of the user; e.g sn

• LDAP login (user id); e.g. uid

• LDAP password - password for the LDAP bind DN

• LDAP port - port on which LDAP is listening (by default it’s 389, for SSL connections usually it’s 636)

• LDAP uses SSL - check to use SSL for LDAP connection

Data-API configuration#

Data-API (DAPI) is a data endpoint used by MINERVA for bioinformatics databases, to provide their content in bulk download files, instead of an open API endpoint. The manual covers DAPI configuration and usage in the MINERVA Platform. More details about the DAPI as a service can be found here.

MINERVA Data-API configuration tab in is displayed below:

You can log in to DAPI using your LDAP global credentials. If you do not have a DAPI account, you will have to create a new one. This way we can store your agreement to use datasets provided by DAPI according to their original license.

If you create an account, a popup will appear (see below), informing about the need to confirm an account creation via received email.

After successful login, you see your username in the DAPI connection validity field (see image below). The following rows list all datasets available in DAPI. You can view the dataset license by clicking the hyperlink next to its name. In the Value column you can see the dataset connection status:

• Connect the license is not accepted yet, the dataset is not available
• Accepted the license is accepted, the dataset is available

Logging out (button next to username) disconnects the MINERVA Platform from the datasets. A given user cannot revoke his agreement to the license, and this agreement is preserved between logins. Only one user can be logged in to DAPI at the same time on a given instance of the MINERVA Platform.

In case there is no user logged in to DAPI, the connections to datasets are not available. The corresponding warning icon is displayed next to the drugs/chemicals search box in the User View (see image below).

ORCID configuration#

This configuration item allows you to link your MINERVA Platform to ORCID system. In effect, the users will be able to log in to your MINERVA instance using their ORCID credentials.

• Create an account in ORCID: https://orcid.org/ or use an existing one
• After signing in to ORCID go to developers page: https://orcid.org/developer-tools
• Generate Client ID and Client secret
• Fill in Application details.
• Add a Redirect URI to your instance of the MINERVA Platform.
  • The Redirect URI must look like: “https://{domain_name}/minerva/login/oauth2/code/orcid” where {domain_name} is domain where the minerva instance is hosted
  • Example: if the MINERVA Platform is hosted at https://minerva-dev.lcsb.uni.lu/minerva/ then a Redirect URI will be: https://minerva-dev.lcsb.uni.lu/minerva/login/oauth2/code/orcid
• Go to your instance of the MINERVA Platform and login to admin panel.
• Go to CONFIGURATION > Oauth configuration page and enter your Orcid Client ID and Orcid Client Secret in respective fields.