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Merged
github-actions merged 5 commits into from
Aug 12, 2026
Merged

[bot] Merge 26.8 to develop #23

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2dc043f
Use shared treatment link display column factory (#10)
labkey-martyp Aug 6, 2026
93d4c77
Add animal group assignment tracking and recode pairing formation typ…
labkey-martyp Aug 10, 2026
dabb1a6
Projects, protocols and investigators (#18)
labkey-martyp Aug 10, 2026
30cef7e
Merge 26.7 to 26.8
labkey-teamcity Aug 11, 2026
909c226
Merge 26.8 to develop
labkey-teamcity Aug 12, 2026
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18 changes: 11 additions & 7 deletions nbri_ehr/resources/data/pairing_formation_types.tsv
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value
Full Contact Pair
Group Formation
Introduction
Limited Contact Pair
Pair Formation
Other
value title date_disabled
C Compatible 2026-08-06
CF CF
CP Continuous pair
F Fought 2026-08-06
FC Full Contact
IC Intermittent Contact
IG Indoor Group Housing
PC Protected Contact
S Single Housing
U Unsuccessful
106 changes: 3 additions & 103 deletions nbri_ehr/resources/domain-templates/ehr.template.xml
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<template xsi:type="EHRTemplateType">
<table tableName="protocol" tableDbType="TABLE">
<dat:columns>
<dat:column columnName="departmentId">
<dat:rangeURI>string</dat:rangeURI>
</dat:column>
<dat:column columnName="authorId">
<dat:rangeURI>int</dat:rangeURI>
</dat:column>
<dat:column columnName="prefix">
<dat:rangeURI>string</dat:rangeURI>
</dat:column>
<dat:column columnName="suffix">
<dat:rangeURI>string</dat:rangeURI>
</dat:column>
<dat:column columnName="shortDescription">
<dat:rangeURI>string</dat:rangeURI>
</dat:column>
<dat:column columnName="expirationDate">
<dat:rangeURI>dateTime</dat:rangeURI>
</dat:column>
<dat:column columnName="renewalDate">
<dat:rangeURI>dateTime</dat:rangeURI>
</dat:column>
<dat:column columnName="nextReviewDate">
<dat:rangeURI>dateTime</dat:rangeURI>
</dat:column>
<dat:column columnName="inactiveDate">
<dat:rangeURI>dateTime</dat:rangeURI>
</dat:column>
<dat:column columnName="requestedEffectiveDate">
<dat:rangeURI>dateTime</dat:rangeURI>
</dat:column>
<dat:column columnName="submissionDate">
<dat:rangeURI>dateTime</dat:rangeURI>
</dat:column>
<dat:column columnName="reviewCompletionDate">
<dat:rangeURI>dateTime</dat:rangeURI>
</dat:column>
<dat:column columnName="effectiveDate">
<dat:rangeURI>dateTime</dat:rangeURI>
</dat:column>
<dat:column columnName="emergencyPhoneNumber">
<dat:rangeURI>string</dat:rangeURI>
</dat:column>
<dat:column columnName="currentState">
<dat:rangeURI>string</dat:rangeURI>
</dat:column>
<dat:column columnName="ownerId">
<dat:rangeURI>int</dat:rangeURI>
</dat:column>
<dat:column columnName="userReferenceNumber">
<dat:rangeURI>string</dat:rangeURI>
</dat:column>
<dat:column columnName="isUnrestrictedView">
<dat:rangeURI>boolean</dat:rangeURI>
</dat:column>
<dat:column columnName="isAudit">
<dat:column columnName="exemptFood">
<dat:rangeURI>boolean</dat:rangeURI>
</dat:column>
<dat:column columnName="isAuditModified">
<dat:column columnName="exemptHousing">
<dat:rangeURI>boolean</dat:rangeURI>
</dat:column>
<dat:column columnName="protocolTypeId">
<dat:rangeURI>string</dat:rangeURI>
</dat:column>
<dat:column columnName="parentProtocolId">
<dat:rangeURI>string</dat:rangeURI>
</dat:column>
<dat:column columnName="questionnaireId">
<dat:rangeURI>string</dat:rangeURI>
</dat:column>
<dat:column columnName="amendmentReason">
<dat:rangeURI>string</dat:rangeURI>
</dat:column>
<dat:column columnName="protocolCategoryId">
<dat:rangeURI>string</dat:rangeURI>
</dat:column>
<dat:column columnName="objective">
<dat:rangeURI>string</dat:rangeURI>
</dat:column>
<dat:column columnName="rationale">
<dat:rangeURI>string</dat:rangeURI>
</dat:column>
<dat:column columnName="isTissueHarvest">
<dat:rangeURI>boolean</dat:rangeURI>
</dat:column>
<dat:column columnName="isOrderTracking">
<dat:rangeURI>boolean</dat:rangeURI>
</dat:column>
<dat:column columnName="isLongTerm">
<dat:rangeURI>boolean</dat:rangeURI>
</dat:column>
<dat:column columnName="isInVivo">
<dat:column columnName="exemptPairing">
<dat:rangeURI>boolean</dat:rangeURI>
</dat:column>
<dat:column columnName="isStock">
<dat:rangeURI>boolean</dat:rangeURI>
</dat:column>
<dat:column columnName="isHonorReset">
<dat:rangeURI>boolean</dat:rangeURI>
</dat:column>
<dat:column columnName="area">
<dat:rangeURI>string</dat:rangeURI>
</dat:column>
</dat:columns>
</table>
</template>

<template xsi:type="EHRTemplateType">
<table tableName="protocol_counts" tableDbType="TABLE">
<dat:columns>
<dat:column columnName="Euthanasia">
<dat:rangeURI>int</dat:rangeURI>
</dat:column>
</dat:columns>
</table>
</template>
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26 changes: 26 additions & 0 deletions nbri_ehr/resources/queries/ehr/investigators.query.xml
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<query xmlns="http://labkey.org/data/xml/query">
<metadata>
<tables xmlns="http://labkey.org/data/xml">
<table tableName="investigators" tableDbType="TABLE">
<tableTitle>Investigators</tableTitle>
<insertUrl />
<importUrl />
<updateUrl />
<deleteUrl />
<columns>
<column columnName="lastName">
<columnTitle>Last Name</columnTitle>
<required>true</required>
</column>
<column columnName="firstName">
<columnTitle>First Name</columnTitle>
</column>
<column columnName="userid">
<columnTitle>User</columnTitle>
<conceptURI>http://www.labkey.org/types#userId</conceptURI>
</column>
</columns>
</table>
</tables>
</metadata>
</query>
8 changes: 4 additions & 4 deletions nbri_ehr/resources/queries/ehr/project.query.xml
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<isHidden>true</isHidden>
<!-- lookup needed even though the column is hidden: EHR's project field selects investigatorId/lastName -->
<fk>
<fkDbSchema>core</fkDbSchema>
<fkTable>Users</fkTable>
<fkColumnName>UserId</fkColumnName>
<fkDisplayColumnName>DisplayName</fkDisplayColumnName>
<fkDbSchema>ehr</fkDbSchema>
<fkTable>investigators</fkTable>
<fkColumnName>rowid</fkColumnName>
<fkDisplayColumnName>lastName</fkDisplayColumnName>
</fk>
</column>
<column columnName="inves2">
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73 changes: 5 additions & 68 deletions nbri_ehr/resources/queries/ehr/protocol.query.xml
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<columnTitle>PI</columnTitle>
<isHidden>false</isHidden>
<fk>
<fkDbSchema>core</fkDbSchema>
<fkTable>Users</fkTable>
<fkColumnName>UserId</fkColumnName>
<fkDisplayColumnName>DisplayName</fkDisplayColumnName>
<fkDbSchema>ehr</fkDbSchema>
<fkTable>investigators</fkTable>
<fkColumnName>rowid</fkColumnName>
<fkDisplayColumnName>lastName</fkDisplayColumnName>
</fk>
</column>
<column columnName="inves">
<isHidden>true</isHidden>
</column>
<column columnName="AuthorId">
<columnTitle>Author</columnTitle>
<fk>
<fkDbSchema>core</fkDbSchema>
<fkTable>Users</fkTable>
<fkColumnName>UserId</fkColumnName>
<fkDisplayColumnName>DisplayName</fkDisplayColumnName>
</fk>
</column>
<column columnName="OwnerId">
<columnTitle>Owner</columnTitle>
<fk>
<fkDbSchema>core</fkDbSchema>
<fkTable>Users</fkTable>
<fkColumnName>UserId</fkColumnName>
<fkDisplayColumnName>DisplayName</fkDisplayColumnName>
</fk>
</column>
<column columnName="ProtocolTypeId">
<columnTitle>Protocol Type</columnTitle>
<fk>
<fkDbSchema>ehr_lookups</fkDbSchema>
<fkTable>protocol_type</fkTable>
<fkColumnName>value</fkColumnName>
<fkDisplayColumnName>title</fkDisplayColumnName>
</fk>
</column>
<column columnName="ProtocolCategoryId">
<columnTitle>Protocol Category</columnTitle>
<fk>
<fkDbSchema>ehr_lookups</fkDbSchema>
<fkTable>protocol_category</fkTable>
<fkColumnName>value</fkColumnName>
<fkDisplayColumnName>title</fkDisplayColumnName>
</fk>
</column>
<column columnName="CurrentState">
<columnTitle>Current State</columnTitle>
<fk>
<fkDbSchema>ehr_lookups</fkDbSchema>
<fkTable>protocol_state</fkTable>
<fkColumnName>value</fkColumnName>
<fkDisplayColumnName>title</fkDisplayColumnName>
</fk>
</column>
<column columnName="ParentProtocolId">
<columnTitle>Parent Protocol</columnTitle>
<fk>
<fkDbSchema>ehr</fkDbSchema>
<fkTable>protocol</fkTable>
<fkColumnName>protocol</fkColumnName>
<fkDisplayColumnName>displayName</fkDisplayColumnName>
</fk>
</column>
<column columnName="QuestionnaireId">
<columnTitle>Questionnaire</columnTitle>
<fk>
<fkDbSchema>ehr_lookups</fkDbSchema>
<fkTable>questionnaire</fkTable>
<fkColumnName>value</fkColumnName>
<fkDisplayColumnName>title</fkDisplayColumnName>
</fk>
</column>
<column columnName="Approve">
<columnTitle>Approval Date</columnTitle>
</column>
</columns>
</table>
</tables>
</metadata>
</query>
</query>
34 changes: 4 additions & 30 deletions nbri_ehr/resources/queries/ehr/protocol/.qview.xml
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<columns>
<column name="protocol"/>
<column name="title"/>
<column name="shortDescription"/>
<column name="description"/>
<column name="prefix"/>
<column name="suffix"/>
<column name="investigatorId"/>
<column name="authorId"/>
<column name="ownerId"/>
<column name="approve"/>
<column name="endDate"/>
<column name="renewalDate"/>
<column name="nextReviewDate"/>
<column name="inactiveDate"/>
<column name="requestedEffectiveDate"/>
<column name="submissionDate"/>
<column name="reviewCompletionDate"/>
<column name="effectiveDate"/>
<column name="currentState"/>
<column name="protocolTypeId"/>
<column name="protocolCategory"/>
<column name="parentProtocolId"/>
<column name="departmentId"/>
<column name="emergencyPhoneNumber"/>
<column name="userReferenceNumber"/>
<column name="questionnaire"/>
<column name="amendmentReason"/>
<column name="objective"/>
<column name="rationale"/>
<column name="isTissueHarvest"/>
<column name="isOrderTracking"/>
<column name="isLongTerm"/>
<column name="isInVivo"/>
<column name="isStock"/>
<column name="isHonorReset"/>
<column name="exemptFood"/>
<column name="exemptHousing"/>
<column name="exemptPairing"/>
<column name="displayName"/>
<column name="isActive"/>
</columns>
</customView>
</customView>
9 changes: 0 additions & 9 deletions nbri_ehr/resources/queries/ehr/protocol_counts.query.xml
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<fkDisplayColumnName>scientific_name</fkDisplayColumnName>
</fk>
</column>
<column columnName="euthanasia">
<columnTitle>Euthanasia</columnTitle>
<fk>
<fkDbSchema>ehr_lookups</fkDbSchema>
<fkTable>euthanasia_type</fkTable>
<fkColumnName>value</fkColumnName>
<fkDisplayColumnName>title</fkDisplayColumnName>
</fk>
</column>
</columns>
</table>
</tables>
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2 changes: 1 addition & 1 deletion nbri_ehr/resources/queries/study/activeAssignments.sql
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SELECT pa.Id,
pa.protocol.title AS protocolTitle,
pa.protocol.InvestigatorId AS investigatorId,
pa.protocol.InvestigatorId.DisplayName AS investigatorName,
initcap(pa.protocol.InvestigatorId.FirstName) || ' ' || initcap(pa.protocol.InvestigatorId.LastName) AS investigatorName,
pa.protocol.InvestigatorId.LastName AS investigatorLastName,
a.project.name AS project,
a.isActive AS isActiveAssignment,
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15 changes: 15 additions & 0 deletions nbri_ehr/resources/queries/study/animalGroupHousingSummary.query.xml
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<query xmlns="http://labkey.org/data/xml/query">
<metadata>
<tables xmlns="http://labkey.org/data/xml">
<table tableName="animalGroupHousingSummary" tableDbType="TABLE">
<tableTitle>Animal Groups Housing Summary</tableTitle>
<columns>
<column columnName="totalAnimals">
<columnTitle>Total Animals</columnTitle>
<url>/query/executeQuery.view?schemaName=study&amp;query.queryName=demographics&amp;query.id/curLocation/room~eq=${room}&amp;query.id/activeAnimalGroups/groups~contains=${groupId/title}</url>
</column>
</columns>
</table>
</tables>
</metadata>
</query>
13 changes: 13 additions & 0 deletions nbri_ehr/resources/queries/study/animalGroupHousingSummary.sql
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/*
* Copyright (c) 2026 LabKey Corporation
*
* Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0
*/
SELECT
m.groupId,
m.id.curLocation.room,
count(distinct m.id) as totalAnimals

FROM study.animal_group_members m
WHERE m.isActive = true
GROUP BY m.groupId, m.id.curLocation.room
22 changes: 22 additions & 0 deletions nbri_ehr/resources/queries/study/animalGroupOverlapSummary.query.xml
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<query xmlns="http://labkey.org/data/xml/query">
<metadata>
<tables xmlns="http://labkey.org/data/xml">
<table tableName="animalGroupOverlapSummary" tableDbType="TABLE">
<tableTitle>Animal Group Member Summary</tableTitle>
<description>This query identifies the total distinct animals that were part of a group over the provided date range</description>
<columns>
<column columnName="totalAnimals">
<url>/query/executeQuery.view?schemaName=study&amp;query.queryName=animalGroupOverlaps&amp;query.param.StartDate=${StartDate}&amp;query.param.EndDate=${EndDate}&amp;query.groupId/title~eq=${groupId/title}</url>
<columnTitle>Total Animals</columnTitle>
</column>
<column columnName="startDate">
<isHidden>true</isHidden>
</column>
<column columnName="endDate">
<isHidden>true</isHidden>
</column>
</columns>
</table>
</tables>
</metadata>
</query>
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