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Portal Data Model

Models

org.icgc.dcc.portal.model

This package contains the Model classes that represent our Data Model. These classes are populated with the information from the results of Elasticsearch queries. Furthermore, these classes are all serializable to JSON for use in creating responses in the Resource classes.

There are two main groups of classes here. Those that represent individual entities, and those that represent a collection of entites.

Paginated

The model classes representing collections of entites all extend from the Paginated class. This abstract class provides functionality for holding and setting information about the pagination of the results as well as the information about the facets (aggregations).

The facet information is stored in a Map.

 private Map<String, TermFacet> facets

The pagination information is stored in a Pagination object that holds information about the following:

  • count
  • total
  • size
  • from
  • sort
  • order
  • page
  • pages

Using donors as an example: donor-model

Elasticsearch Documents to Models

Entities

From a user's point of view, you can think of entities as the basic basic building block of the Portal's data model.

Things like donors and genes, and mutations are entities, and for the end user, each entity has a corresponding entity page. Some examples:

Each entity type has a corresponding model class and Elasticsearch document type.

For example the Donor Model, has a donor type in Elasticsearch: donor.json. The class org.icgc.dcc.portal.model.Donor is the model class for this entity.

Searching and Text Types

All entities that can be searched through the Keyword Search have a corresponding analyzed version of their Elasticsearch documents. This documents have the suffix -text.

Following the donor example from the previous section, there exists a donor-text document type. The schema is as follows: donor-text.json.

These -text types allows us to leverage Elasticsearch's text search capabilities to quickly retrieve matches based on user input.

Advanced Search, Centric Types, and the Type Model

In advanced search and a few other places where we need to perform queries that essentially perform joins on entities. The queries run through the PQL infrastructure and use the -centric document types. These documents are prejoined documents with the primary entity as the root.

For example donor-centric documents have the donor entity as the root document with gene and project as nested child documents.

Every -centric type must have a corresponding TypeModel class. For the donor-centric document type, we have DonorCentricTypeModel. All the TypeModel classes are in the package org.dcc.portal.pql.meta. For more information about the TypeModel refer to the PQL documentation.

The results of these centric queries are used to populate the model classes that extend Paginated. In the donors examples, the model class responsible is org.icgc.dcc.portal.model.Donors.

The Big Picture

For more information about the structure of the Elasticsearch documents, please refer to SCHEMAS from the ETL documentation.

Model Diagram

Additional Reading

Useful Links