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diff --git a/topics/editing/case-attributes.gmi b/topics/editing/case-attributes.gmi new file mode 100644 index 0000000..1a86131 --- /dev/null +++ b/topics/editing/case-attributes.gmi @@ -0,0 +1,110 @@ +# 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 |