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AI-assisted user comments model updates #199

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88788e2
docs: design spec for AI provenance in gene-page User Comments table
bobular Jun 24, 2026
3e6c457
docs: implementation plan for AI provenance in gene-page comments table
bobular Jun 24, 2026
5c0a4a7
feat: AI provenance + source PMID in GeneComments query
bobular Jun 24, 2026
e346068
feat: show AI-assisted pill in gene-page User Comments Made-by column
bobular Jun 24, 2026
59e0e61
add title-based tooltips for pills
bobular Jun 24, 2026
83df28a
Better linkage to full comment page
bobular Jun 25, 2026
3c6ef31
remove the html from the link and try again
bobular Jun 25, 2026
df4ea02
go with right-Guillemet in the end
bobular Jun 25, 2026
9abbc30
hide comment ID column
bobular Jun 25, 2026
885aa79
put AI-assisted pill on a new line
bobular Jun 25, 2026
66546ea
add ai_source_kind column for downloads
bobular Jun 25, 2026
3c2037f
modernise the Community Annotations comments table too
bobular Jun 25, 2026
8fa799c
feat(comments): union upload-path PMID into GeneComments pmids
bobular Jun 25, 2026
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48 changes: 45 additions & 3 deletions Model/lib/wdk/model/records/commentTableQueries.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -64,6 +64,8 @@
<column name="stable_id"/>
<column name="headline"/>
<column name="user_name_org"/>
<column name="user_name_org_display"/>
<column name="ai_source_kind"/>
<column name="comment_date"/>
<column name="comment_target_id"/>
<column name="comment_status"/>
Expand Down Expand Up @@ -94,7 +96,28 @@
END AS pmids_link,
gene_counts.geneCount,
&&selectReviewed&&
CONCAT(u.first_name , ' ' , u.last_name , ', ' , u.organization ) as user_name_org
CONCAT(u.first_name , ' ' , u.last_name , ', ' , u.organization ,
CASE
WHEN aiprov.comment_id IS NULL THEN ''
WHEN aiprov.is_edited THEN ' · AI-assisted (edited)'
ELSE ' · AI-assisted (as-is)'
END) as user_name_org,
CASE
WHEN aiprov.comment_id IS NULL
THEN CONCAT(u.first_name , ' ' , u.last_name , ', ' , u.organization )
ELSE CONCAT(u.first_name , ' ' , u.last_name , ', ' , u.organization ,
'<br/><span title="',
CASE
WHEN aiprov.is_edited
THEN 'AI-generated summary of a publication, edited by the author before publishing.'
ELSE 'AI-generated summary of a publication, published unedited after author review.'
END,
'" style="display:inline-block;margin-top:3px;padding:1px 6px;border-radius:8px;background-color:#0a7c8a;color:#fff;font-size:0.85em;font-weight:500;white-space:nowrap;">AI-assisted &middot; ',
CASE WHEN aiprov.is_edited THEN 'edited' ELSE 'as-is' END,
'</span>')
END as user_name_org_display,
-- download-only AI provenance source: 'pubmed' | 'upload' | 'N/A'
COALESCE(car2.source_kind, 'N/A') as ai_source_kind
FROM
@REMOTE_COMMENT_SCHEMA@MappedComment c
INNER JOIN webready.GeneAttributes_p ga ON c.project_name = ga.project_id AND c.stable_id = ga.source_id
Expand All @@ -107,8 +130,23 @@
) files ON c.comment_id = files.comment_id
LEFT JOIN (
SELECT comment_id, string_agg(source_id,',') as pmids
FROM @REMOTE_COMMENT_SCHEMA@CommentReference
WHERE database_name='pubmed'
FROM (
SELECT comment_id, source_id
FROM @REMOTE_COMMENT_SCHEMA@CommentReference
WHERE database_name='pubmed'
UNION
SELECT cap.comment_id, car.pubmed_id AS source_id
FROM @REMOTE_COMMENT_SCHEMA@comment_ai_provenance cap
JOIN @REMOTE_COMMENT_SCHEMA@comment_ai_run car ON cap.run_job_id = car.job_id
WHERE car.source_kind = 'pubmed' AND car.pubmed_id IS NOT NULL
UNION
SELECT cap.comment_id, car.external_ref AS source_id
FROM @REMOTE_COMMENT_SCHEMA@comment_ai_provenance cap
JOIN @REMOTE_COMMENT_SCHEMA@comment_ai_run car ON cap.run_job_id = car.job_id
WHERE car.source_kind = 'upload'
AND car.external_ref_kind = 'pubmed'
AND car.external_ref IS NOT NULL
) merged
GROUP BY comment_id
) refs ON c.comment_id = refs.comment_id
LEFT JOIN (
Expand All @@ -117,6 +155,10 @@
WHERE stable_id IN (SELECT source_id FROM webready.GeneAttributes_p where org_abbrev IN (%%PARTITION_KEYS%%))
GROUP BY comment_id
) gene_counts ON c.comment_id = gene_counts.comment_id
LEFT JOIN @REMOTE_COMMENT_SCHEMA@comment_ai_provenance aiprov
ON c.comment_id = aiprov.comment_id
LEFT JOIN @REMOTE_COMMENT_SCHEMA@comment_ai_run car2
ON aiprov.run_job_id = car2.job_id
LEFT JOIN (
SELECT dr.primary_identifier AS comment_id , ta.gene_source_id
FROM sres.dbref dr
Expand Down
58 changes: 35 additions & 23 deletions Model/lib/wdk/model/records/geneRecord.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -1679,22 +1679,26 @@ name" internal="true"/>
displayName="User Comments"
inReportMaker="true"
queryRef="CommentTables.GeneComments">
<!-- opaque primary key: kept internal for the headline link's #fragment and
downloads, but no longer shown as its own column (the headline is the
click-through to the show page) -->
<columnAttribute name="comment_id" internal="true" displayName="Comment ID"/>
<linkAttribute name="comment_id_link"
displayName="Comment ID">
<displayText>
<![CDATA[
$$comment_id$$
]]>
</displayText>
<columnAttribute internal="true" displayName="project_id" name="project_id"/>
<columnAttribute name="stable_id" internal="true"/>
<columnAttribute name="comment_target_id" internal="true"/>
<!-- plain text: hidden on screen, used by report maker / downloads + sorting -->
<columnAttribute name="headline" displayName="Headline" internal="true"/>
<!-- headline as a link (with a trailing » arrow cue) to the modernised show
page; whole cell is clickable and scrolls to this comment.
NB: linkAttribute displayText is HTML-escaped, so no inline markup here -
the arrow must be a literal glyph, not an &#xxxx; entity.
-->
<linkAttribute name="headline_link" displayName="Headline" inReportMaker="false">
<displayText><![CDATA[$$headline$$ »]]></displayText>
<url>
<![CDATA[@WEBAPP_BASE_URL@/user-comments/show?projectId=$$project_id$$&stableId=$$stable_id$$&commentTargetId=$$comment_target_id$$#$$comment_id$$]]>
</url>
</linkAttribute>
<columnAttribute internal="true" displayName="project_id" name="project_id"/>
<columnAttribute name="stable_id" internal="true"/>
<columnAttribute name="comment_target_id" internal="true"/>
<columnAttribute name="headline" displayName="Headline"/>
<columnAttribute name="pmids" internal="true" displayName="PubMed ID(s)"/>
<linkAttribute name="pmids_link"
displayName="PubMed ID(s)">
Expand All @@ -1710,7 +1714,12 @@ name" internal="true"/>
<columnAttribute name="genecount" displayName="# Related Genes"/>
<columnAttribute name="comment_status" displayName="Status"/>
<columnAttribute name="filecount" displayName="# Uploaded Files"/>
<columnAttribute name="user_name_org" displayName="Made by"/>
<!-- plain text: hidden on screen, used by report maker / downloads + sorting -->
<columnAttribute name="user_name_org" displayName="Made by" internal="true"/>
<!-- name + styled AI-assisted pill: shown on screen as "Made by", excluded from downloads -->
<columnAttribute name="user_name_org_display" displayName="Made by" inReportMaker="false"/>
<!-- download-only: AI provenance source kind ('pubmed' | 'upload' | 'N/A') -->
<columnAttribute name="ai_source_kind" displayName="AI Source Type" internal="true"/>
<columnAttribute name="comment_date" displayName="Date"/>

</table>
Expand All @@ -1723,22 +1732,25 @@ name" internal="true"/>
inReportMaker="false"
displayName="Community Annotations"
queryRef="CommentTables.CommunityComments">
<!-- opaque primary key: kept internal for the headline link's #fragment and
downloads, but no longer shown as its own column (the headline is the
click-through to the show page) -->
<columnAttribute name="comment_id" internal="true" displayName="Comment ID"/>
<linkAttribute name="comment_id_link"
displayName="Comment ID">
<displayText>
<![CDATA[
$$comment_id$$
]]>
</displayText>
<columnAttribute internal="true" displayName="project_id" name="project_id"/>
<columnAttribute name="stable_id" internal="true"/>
<columnAttribute name="comment_target_id" internal="true"/>
<!-- plain text: hidden on screen, used by report maker / downloads + sorting -->
<columnAttribute name="headline" displayName="Proposed Product" internal="true"/>
<!-- headline as a link (with a trailing » cue) to the modernised show page;
whole cell is clickable and scrolls to this comment.
NB: linkAttribute displayText is HTML-escaped, so the cue must be a
literal glyph, not an &#xxxx; entity. -->
<linkAttribute name="headline_link" displayName="Proposed Product" inReportMaker="false">
<displayText><![CDATA[$$headline$$ »]]></displayText>
<url>
<![CDATA[@WEBAPP_BASE_URL@/user-comments/show?projectId=$$project_id$$&stableId=$$stable_id$$&commentTargetId=$$comment_target_id$$#$$comment_id$$]]>
</url>
</linkAttribute>
<columnAttribute internal="true" displayName="project_id" name="project_id"/>
<columnAttribute name="stable_id" internal="true"/>
<columnAttribute name="comment_target_id" internal="true"/>
<columnAttribute name="headline" displayName="Proposed Product"/>
<columnAttribute name="pmids" internal="true" displayName="PubMed ID(s)"/>
<linkAttribute name="pmids_link"
displayName="PubMed ID(s)">
Expand Down
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