Version: 4.0.0

Website Admin

The SuperUser is the administrator of your InterMine webapp. The SuperUser can use tagging to configure the appearance and functionality of the webapp.

The SuperUser account is created when the UserProfile database is built using the properties specified in the Intermine properties file.

Templates#

All logged in users can create template queries, but the SuperUser can make them available to all users by tagging them as public templates. Making a template query is an easy way to get users of your webapp to the data they want very quickly.

Tagging#

Template queries and lists#

The SuperUser can change where templates and lists appear by adding tags via the templates and lists pages in the MyMine section of the webapp. Only the administrator can apply/view/edit tags starting at im: . The tag data is stored in the user-profile database.

tag	purpose
im:public [1]	make list/template viewable by all users
im:frontpage	put list on home page
im:converter	template used in generating links in the ‘Convert’ section on the list analysis page
im:aspect:CategoryName	template appears underneath specified category. For instance, template with im:aspect:Genomics tag will be displayed in Genomics category on the report page and on the home page
im:report	allows template to be displayed on report or list analysis page
im:order:n	specify the order lists should go in (on homepage only currently). If two lists have the same Integer “n” value, natural ordering on the list name will be applied as a decisive criterion

[1] Editable by all admins

Fields and collections#

The SuperUser can change how fields are displayed by adding tags via the report page.

tag	purpose
im:hidden	hides the field/collection
im:summary	adds collection to ‘Summary’ section of report page
im:aspect:CategoryName	collection appears underneath category

Classes#

The SuperUser can change how classes are displayed by adding tags via the model browser.

tag	purpose
im:aspect:CategoryName	class appears on aspect page
im:preferredBagType	class appears first in the class selection

tag#

If a template is tagged with im:converter, it is:

Used by the list analysis page, in the "Convert" section.
Used by the list upload page to convert between types.

E.g., the user pastes in a protein identifier, but chooses "Gene" from the type dropdown menu. A converter template can be used to look up the Gene corresponding to the given Protein.

To work as a converter, the template must follow the following pattern:

the top-level class in the query must be the class we wish to convert from (eg. Gene)
there must be exactly one editable constraint - the id field of the top level class (eg. Gene.id)
the fields selected for output must be Gene.id and the id field of the class to convert to

Normally the id field isn't shown in the query builder and probably isn't useful in other queries. Only the administrator user can create queries using the id field. Here is an example converter template:

<template name="Gene_To_Protein_Type_Converter" title="Gene to protein type converter" longDescription="" comment="">
    <query name="Gene_To_Protein_Type_Converter" model="genomic" view="Gene.id Gene.proteins.id" longDescription="" sortOrder="Gene.id asc">
        <node path="Gene" type="Gene"></node>
        <node path="Gene.id" type="Integer">
            <constraint op="=" value="0" description="Gene.id" identifier="Gene.id" editable="true" code="A"></constraint>
        </node>
    </query>
</template>