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Projects, protocols and investigators #18

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786959f
Track investigators as EHR data instead of server accounts
labkey-martyp Aug 5, 2026
9a4ae62
Drop unused protocol columns and the counts table template
labkey-martyp Aug 5, 2026
50ac6f0
Add food, housing, and pairing exemption flags to protocols
labkey-martyp Aug 5, 2026
dc8151b
Prune protocol metadata to columns that still exist
labkey-martyp Aug 5, 2026
921293a
Update end date visibility
labkey-martyp Aug 7, 2026
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106 changes: 3 additions & 103 deletions nbri_ehr/resources/domain-templates/ehr.template.xml
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Expand Up @@ -6,118 +6,18 @@
<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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@@ -0,0 +1,26 @@
<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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Expand Up @@ -49,10 +49,10 @@
<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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Expand Up @@ -9,83 +9,20 @@
<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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Expand Up @@ -2,40 +2,14 @@
<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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Expand Up @@ -14,15 +14,6 @@
<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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Expand Up @@ -6,7 +6,7 @@
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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12 changes: 7 additions & 5 deletions nbri_ehr/resources/web/nbri_ehr/model/sources/Assignment.js
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Expand Up @@ -5,13 +5,12 @@
*/

EHR.model.DataModelManager.registerMetadata('Assignment', {
allQueries: {
endDate: {
hidden: true
}
},
byQuery: {
'study.assignment': {
// the dataset column is hidden by default; project assignments are ended by entering an end date
'enddate': {
hidden: false
},
'project': {
xtype: 'combo',
nullable: false,
Expand All @@ -27,6 +26,9 @@ EHR.model.DataModelManager.registerMetadata('Assignment', {
}
},
'study.protocolAssignment': {
'enddate': {
hidden: true
},
'project': {
hidden: true
},
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1 change: 1 addition & 0 deletions nbri_ehr/src/org/labkey/nbri_ehr/NBRI_EHRModule.java
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Expand Up @@ -217,6 +217,7 @@ private void registerDataEntry()
EHRService.get().registerFormType(new DefaultDataEntryFormFactory(NBRIMedicationTreatmentFormType.class, this));
EHRService.get().registerFormType(new DefaultDataEntryFormFactory(NBRIProjectFormType.class, this));
EHRService.get().registerFormType(new DefaultDataEntryFormFactory(NBRIProtocolFormType.class, this));
EHRService.get().registerFormType(new DefaultDataEntryFormFactory(NBRIInvestigatorsFormType.class, this));
EHRService.get().registerFormType(new DefaultDataEntryFormFactory(NBRIPregnancyFormType.class, this));
EHRService.get().registerFormType(new DefaultDataEntryFormFactory(NBRIWeightFormType.class, this));
EHRService.get().registerFormType(new DefaultDataEntryFormFactory(NBRIFlagsFormType.class, this));
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