Dotmatics Platform Integration plugin description
This plugin enables integration with Dotmatics Bioregister. Note that this requires Geneious Prime version 2022.0.0 or later and Bioregister 2022.2 or later.
The plugin launches the registration workflow for creating or updating Bioregister records based on the selected sequences in Geneious Prime. Single and bulk registration scenarios are supported.
Download the latest plugin version from here.
Install the plugin by downloading the gplugin file and dragging it into Geneious Prime or using the plugin manager in Geneious Prime (Tools > Plugins).
Once installed, enter the URL of the Dotmatics server in Preferences > Dotmatics Integration and click on the Apply or OK button to save or Cancel to close the Preferences dialogue. Please refer to the example below for the URL format.
Enterprise admins can configure a default Bioregister server as described in the "Pre-configure Bioregister server in the plugin settings" chapter so that the plugin can be pre-configured and users do not need to change it.
Authenticate in Dotmatics Bioregister
Select one or multiple sequences in Geneious Prime and click on the File > Register button. Alternatively, click on the Register button on the main application toolbar or use the context menu after right click on the entity.
Authenticate in Bioregister by entering your Username and Password or by following a single sign-on procedure according to your enterprise policy.
⚠️ Geneious Prime is not intended for password reset or the first login attempt. We recommend making it in the Bioregister web application to avoid any unexpected behaviour.
Single entity registration
Select Entity Type and Subtype and click Create to continue registration or Cancel to abort the registration.
If the Keep me logged in checkbox remains selected, the system does not ask to provide the credentials during the next registration (unless the session has expired).
Fill in the meta-data details as a next step as requested by Bioregister:
The Bioregister ID is also stored on the Properties > Info tab of the file.
Additional meta-data may be lost if the file will be saved to a non-native format.
Standard (out-of-the-box subtypes)
Select Entity Type, Subtype and Project (if the out-of-the-box Project field is made optional in Bioregister, then the system does not ask to select a project on this dialogue):
If Project is set as “From Meta-Data”, it means that every selected entity will be registered against its project selected on the Info > Properties tab (Bioregister Fields section). All the selected sequences shall have an associated Project to proceed with this option.
If the Bioregister section is missing, it can be added by clicking on Add Meta-Data and selecting Bioregister Fields group.
Meta data can be changed for an individual record or in bulk.
If Project is set as “Select a project for all items”, then select one Project for all sequences and click on Create button to proceed. All the sequences will be registered to the selected Bioregister project.
Check the registration confirmation for more details about the registered entities. Click Close to complete the workflow or Show details link to explore registration details.
Bulk registration of custom subtypes
If custom fields were added in Bioregister for the entity type or subtype, they need to be also set in Geneious Prime for bulk registration (at least required fields).
In order to add a custom field in Geneious Prime, select entities to register and click on Edit Meta-Data Types on Info > Properties tab:
For example, let’s say your Bioregister type requires you to enter the “Host disease” field when registering a sequence in the web application:
Update the Bioregister meta-data
As a part of the bulk registration workflow
Update sequence meta-data in the Excel template, save the file, click on Select a file and select its location.
Click on Update in Bioregister to upload and update the meta-data in Bioregister according to the selected file.
Select previously registered entities and click on Export > Update metadata in Bioregister
Then update the meta-data in the same way as described above (in the "As a part of the bulk registration workflow" section).
Pre-configure Bioregister server URL in the plugin settings
BioregisterIntegratinonPlugin.gplugin contains a file
plugin.properties (unzip the plugin to see the file).
bioregister.urlproperty that predefines the Dotmatics Bioregister server URL by default.
In case of empty properties in the plugin Preferences (with first installation or with Reset All Preferences), opening/restarting the application will set settings from