Frequently Asked Questions

Below please find our most commonly asked questions regarding configuring the InterMine webapp. If you still don't find what you need, please contact us.

How can I …

1. How can I …
   1. Make templates and lists show up on the templates/lists page?
   2. Make a public template or list show up on the homepage?
   3. Set which fields are links on the results page?
   4. Set which fields are used to create lists on the results page?
   5. Customise how data is displayed on the report page?
   6. Add my own logo and change the colour scheme?
   7. Save user data and port over to a newly rebuilt mine?
   8. Set the list of default templates?
   9. Change how the quick search works?
   10. Customise the data categories on the main page?
   11. Customise the data categories on the report page?
   12. Set the password for the superuser.account?

See WebappConfig for the complete list of configuration files

Make templates and lists show up on the templates/lists page?

1. Log into your site's super user account.
2. Tag the template or list as "im:public".

See: Tagging

Make a public template or list show up on the homepage?

1. Log into your site's super user account.
2. Tag the template or list as "im:frontpage".

See: Tagging

Set which fields are links on the results page?

Add them to the class_keys file.

See: WebappConfig

Set which fields are used to create lists on the results page?

Add them to the class_keys file.

See: WebappConfig

Customise how data is displayed on the report page?

Make a custom jsp page.

See: LongDisplayers

Add my own logo and change the colour scheme?

See: WebappAppearance?

Save user data and port over to a newly rebuilt mine?

No, all the data will be saved unless you do ant build-db-userprofile in the webapp directory. However, saved lists work with internal ids which change when a new build of the mine is done. To solve this you write the userprofile to XML first and re-import it.

1. While you still have your old build do ant write-userprofile-xml in webapp and copy the userprofile.xml file somewhere.
2. When the new build is ready copy userprofile.xml back into the build directory.
3. Run ant read-userprofile-xml to read it back in, this should do queries to update the lists to new ids.

I would check this works before you risk losing a userprofile database. Of course, if you only have a couple of lists you can just re-import them from the webapp.

Set the list of default templates?

Update the default-template-queries.xml file.

See: User Profile

Change how the quick search works?

At the moment the quick search is configured to run a particular template query. We use a query called A_IdentifierSynonym_Object this is configured in webapp/resources/web.properties.

All biological feature classes in the model have a collection of Synonyms objects to represent alternative identifiers. We also create synonyms for each object identifier, e.g for a Gene with identifier 'eve' we also create a Synonym with value 'eve'. This means we can just search through the synonym table to find any feature type.

Customise the data categories on the main page?

1. Customise your categories in aspects.xml
2. Run ant default remove-webapp release-webapp to update the customized categories. The "default" target makes forces a re-build of the WAR file before releasing.

See: DataCategories

Customise the data categories on the report page?

1. Fields
   • Tag classes with the im:aspect:Genomics tag. When this class appears on a report page, it will be displayed underneath the Genomics data category.
2. Templates
   • Tag templates with the im:public and im:aspect:Genomics tags.
   • Update the identifier template constraint to be the correct field.

See: DataCategories

Set the password for the superuser.account?

There is a property for setting an initial password, along with the property for setting the superuser's email address:

superuser.account=some@email.address
superuser.initialPassword=somepassword

This should only be used to set an initial password - obviously the fact that the password is stored in a properties file makes it insecure, so you should change the password as soon as possible. If you don't set that property, then a random password will be generated (but since it is stored in hashed form and the original is thrown away, there is no way to find out what that is).

If you do not know the superuser's password, then you can as with any other account use the "Forgotten password" facility on the login page. This will send you an email containing a link that you can follow to your webapp to change the password.