Tagging

The SuperUser can use tags to change the display of lists, template queries and data.

Template queries and lists

The administrator 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	make lists and templates available and visible to all users
im:frontpage	put list/template on home page make templates and lists visible on the front page. NOTE: templates must also be tagged as im:public to appear on the front 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
im:noreport	prevents template from being displayed on report or list analysis page

Fields and collections

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

tag	purpose
im:hidden	hides the field/collection
im:summary	add collection to 'Summary' section of report page
im:aspect:CategoryName	collection appears underneath specified category. For instance collection with im:aspect:Genomics tag will be displayed in Genomics category.

Classes

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

tag	purpose
im:aspect:CategoryName	class appears as starting point on the specified category page
im:preferredBagType	class to show up first and in bold on the class chooser page

Tagging template queries

Log in to the webapp with the administrator account and navigate to the "Saved template queries" tab in MyMine.

Enter the tag im:aspect:CategoryName and click the "Add" button. This will associate the template with the given category so that the template appears on the category's page and in that section of the report page.

Note that the category title is case sensitive.

Tagging classes

You can associate a class with an category with an im:aspect:CategoryName tag. Apply tags to classes from the "Browse model" page.

Log in as the administrator.

Go to New Query -> Browse model.

Enter the tag, hit the Return/Enter key or the "Add" button.

Refresh category pages to see changes.

Tagging collections and references

Log in as the administrator user.

You can assign references and collections to one or more categories. They will then display under a sub-section for that category on report pages along with template queries assigned to that category.

Choose the class for which you want to tag collections and references. Go to a report page for an instance that class. Find the collection or reference. It will be listed under the "Miscellaneous" section at the bottom of the page if it has not been tagged.

Remember to refresh the page to see the changes applied.

im:converter tag details

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

1. Used by the list analysis page, in the "Convert" section.
2. Used by the list upload page to converter between types.
   • Eg, the user pastes in a protein identifier, but chooses "Gene" from the type drop down 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

Note that 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>