Editing Case-Attributes

Introduction

Case-attributes metadata for samples. They are include: sex, age, etc of the various individuals and exist separately from "normal" traits mainly because they're non-numeric. From the GN2 traits page, they are shown as extra columns under the "Reviews and Edit Data" section.

Case-attributes are determined at the group-level. E.g. for BXD, case attributes would apply at the level of each sample, across all BXD data. Every strain has a unique attribute and it's fixed, not variable.

We need to differentiate these two things:

Case-Attribute labels/names/categories (e.g. Sex, Height, Cage-handler, etc)
Case-Attribute values (e.g. Male/Female, 20cm, Frederick, etc.)

Currently, both labels and values are set at the group level:

Case-Attributes on GeneNetwork1

is a good starting point to help with understanding how case-attributes were implemented and how they worked.

Critical bug existed where editing one case-attribute affected all case-attributes defined for a group.

Case attributes can have the following data-types:

Free-form text (no constraints) - see the `Status` column
Enumerations - textual data, but where the user can only pick from specific values
Links - The value displayed also acts as a link - e.g. the 'JAX:*' values in the `RRID` column

HOWTO

Example SQL query to fetch case-attribute data:

SELECT
	caxrn.*, ca.Name AS CaseAttributeName,
	ca.Description AS CaseAttributeDescription,
	iset.InbredSetId AS OrigInbredSetId
FROM
	CaseAttribute AS ca INNER JOIN CaseAttributeXRefNew AS caxrn
	ON ca.Id=caxrn.CaseAttributeId
INNER JOIN
      StrainXRef AS sxr
      ON caxrn.StrainId=sxr.StrainId
INNER JOIN
      InbredSet AS iset
      ON sxr.InbredSetId=iset.InbredSetId
WHERE
	caxrn.value != 'x'
	AND caxrn.value IS NOT NULL;

CaseAttributeXRefNew differs from CaseAttributeXRef:

mysql> describe CaseAttributeXRef;
+------------------+----------------------+------+-----+---------+-------+
| Field            | Type                 | Null | Key | Default | Extra |
+------------------+----------------------+------+-----+---------+-------+
| ProbeSetFreezeId | smallint(5) unsigned | NO   | PRI | 0       |       |
| StrainId         | smallint(5) unsigned | NO   | PRI | 0       |       |
| CaseAttributeId  | smallint(5)          | NO   | PRI | 0       |       |
| Value            | varchar(100)         | NO   |     |         |       |
+------------------+----------------------+------+-----+---------+-------+
4 rows in set (0.01 sec)

mysql> describe CaseAttributeXRefNew;
+-----------------+------------------+------+-----+---------+-------+
| Field           | Type             | Null | Key | Default | Extra |
+-----------------+------------------+------+-----+---------+-------+
| InbredSetId     | int(5) unsigned  | NO   | PRI | NULL    |       |
| StrainId        | int(20) unsigned | NO   | PRI | NULL    |       |
| CaseAttributeId | int(5) unsigned  | NO   | PRI | NULL    |       |
| Value           | varchar(100)     | NO   |     | NULL    |       |
+-----------------+------------------+------+-----+---------+-------+
4 rows in set (0.01 sec)

Script to update CaseAttribute and CaseAttributeXRefNew table

Tasks

@bmunyoki: Model case-attributes correctly in RDF.
@bmunyoki, @zachs: Implement case-attributes editing in GN3 that correctly models case-attributes at the group-level. CRUD operations with the correct authorization. People who can edit sample data should not be able to edit case-attributes because case-attributes are defined at the group level; and editing case-attributes at the group-level will affect other samples.
@rob: Confirm to team whether "N" and "SE" are case-attributes. @bmunyoki AFAICT, no.

Possible set of privileges subject to discussion:

group:resource:add-case-attributes - Allows user to add a completely new case attribute
group:resource:edit-case-attributes - Allows user to edit an existing case attribute
group:resource:delete-case-attributes - Allows user to delete an existing case attribute
group:resource:view-case-attributes - Allows user to view case attributes and their value

Given groups are not directly linked to any auth resource, we may introduce some level of indirection. Addy a new resource type that handles groups may solve this.

Editing Case-Attributes

Tags

Introduction

HOWTO

Tasks

See Also