# Editing Case-Attributes

## Tags

* type: document
* keywords: case-attribute, editing
* assigned: fredm, zachs, acenteno, bonfacem
* status: requirements gathering

## 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:

=> https://github.com/genenetwork/genenetwork1/blob/0f170f0b748a4e10eaf8538f6bcbf88b573ce8e7/web/webqtl/showTrait/DataEditingPage.py 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)
```

=> https://github.com/genenetwork/genenetwork3/blob/dd0b29c07017ec398c447ca683dd4b4be18d73b7/scripts/update-case-attribute-tables-20230818 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.

## See Also

=> https://matrix.to/#/!EhYjlMbZHbGPjmAFbh:matrix.org/$myIoafLp_dIONnyNvEI0k2xf3Y8-LyiI_mkP2vBN08o?via=matrix.org Discussion on Case-Attributes Editing in Matrix
=> https://matrix.to/#/!EhYjlMbZHbGPjmAFbh:matrix.org/$P6SNnpY-nAZsDr3VZlRi05m6MT32lXBsCl-BYLh-YLM?via=matrix.org More Discussion on Matrix
=> /issues/case-attr-edit-error Case Attribute Edting Problems
=> /issues/fix-case-attribute-work Fix Case Attribute Work (Same Columns)
=> /issues/fix-case-attribute-editing Editing Case Attribute
=> /issues/consecutive-crud-applications-when-uploading-data Fix Case Attribute Work (Consecutive CRUD applications)
=> /issues/edit-metadata-bugs Cannot Edit Metadata of BXD Traits Effectively
=> /topics/data-uploads/datasets Some Historical Context