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[bot] Fast-forward for 24.7.6 #398

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merged 5 commits into from
Sep 24, 2024
Merged

[bot] Fast-forward for 24.7.6 #398

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d6a56b6
Bulk medication treatment and performed by refactor (#381)
labkey-martyp Sep 12, 2024
622a3c0
Daily Clinical Observations (#385)
labkey-martyp Sep 14, 2024
f846312
New behavioral animal training data entry form and dataset (#387)
ankurjuneja Sep 15, 2024
465f628
Automation test for clinical case workflow updates (#386)
labkey-sweta Sep 16, 2024
3fa7391
Changing the link text to Today's Medication/Treatment Schedule (#394)
labkey-sweta Sep 23, 2024
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3 changes: 3 additions & 0 deletions nirc_ehr/resources/data/editable_lookups.tsv
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Expand Up @@ -67,6 +67,9 @@ necropsy_physical_condition Colony Management Necropsy Physical Condition
necropsy_specimen_condition Colony Management Necropsy Specimen Condition
necropsy_tissue Colony Management Necropsy Tissue
neurologic_types Clinical Neurologic Types Clinical observation fixed values.
nhp_training_reason Behavior NHP Training Reason Behavior training reason values
nhp_training_result Behavior NHP Training Result Behavior training result values
nhp_training_type Behavior NHP Training Type Behavior training type values
numeric_unit Colony Management Numeric Unit
observation_types Clinical Clin remarks observation types
observation_areas Clinical Observation Areas Clinical observation areas.
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3 changes: 3 additions & 0 deletions nirc_ehr/resources/data/lookup_sets.tsv
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Expand Up @@ -58,6 +58,9 @@ necropsy_physical_condition Physical Condition value title
necropsy_specimen_condition Specimen Condition value title
necropsy_tissue Tissues value title
neurologic_types Neurologic Types value title
nhp_training_reason NHP Training Reason value
nhp_training_result NHP Training Result value
nhp_training_type NHP Training Type value
numeric_unit Numeric Units value title
observation_areas Observation Areas value
ocular_problem Ocular Problem value
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3 changes: 3 additions & 0 deletions nirc_ehr/resources/data/lookupsManifest.tsv
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Expand Up @@ -64,6 +64,9 @@ necropsy_physical_condition
necropsy_specimen_condition
necropsy_tissue
neurologic_types
nhp_training_reason
nhp_training_result
nhp_training_type
numeric_unit
observation_areas
ocular_problem
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3 changes: 3 additions & 0 deletions nirc_ehr/resources/data/lookupsManifestTest.tsv
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Expand Up @@ -63,6 +63,9 @@ necropsy_physical_condition
necropsy_specimen_condition
necropsy_tissue
neurologic_types
nhp_training_reason
nhp_training_result
nhp_training_type
numeric_unit
observation_areas
ocular_problem
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6 changes: 6 additions & 0 deletions nirc_ehr/resources/data/nhp_training_reason.tsv
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@@ -0,0 +1,6 @@
value
PI Request
Behavioral Initiated
Clinic
Husbandry
Other
4 changes: 4 additions & 0 deletions nirc_ehr/resources/data/nhp_training_result.tsv
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@@ -0,0 +1,4 @@
value
In-Progress
Successful
Unsuccessful
5 changes: 5 additions & 0 deletions nirc_ehr/resources/data/nhp_training_type.tsv
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@@ -0,0 +1,5 @@
value
Chair
Present
Physical Therapy
Other
4 changes: 1 addition & 3 deletions nirc_ehr/resources/queries/study/assignment.query.xml
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Expand Up @@ -17,9 +17,7 @@
</fk>
</column>
<column columnName="remark"/>
<column columnName="performedBy">
<columnTitle>Performed By</columnTitle>
</column>
<column columnName="performedBy" />
<column columnName="taskid">
<isHidden>true</isHidden>
</column>
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26 changes: 26 additions & 0 deletions nirc_ehr/resources/queries/study/cases.js
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Expand Up @@ -4,6 +4,7 @@
* Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0
*/

const console = require("console");
require("ehr/triggers").initScript(this);

var triggerHelper = new org.labkey.nirc_ehr.query.NIRC_EHRTriggerHelper(LABKEY.Security.currentUser.id, LABKEY.Security.currentContainer.id);
Expand All @@ -15,3 +16,28 @@ EHR.Server.TriggerManager.registerHandlerForQuery(EHR.Server.TriggerManager.Even
}
}
});

EHR.Server.TriggerManager.registerHandlerForQuery(EHR.Server.TriggerManager.Events.COMPLETE, 'study', 'cases', function(event, errors, helper){
if (!helper.isETL()) {
var rows = helper.getRows();
if (helper.getEvent() == 'insert' && rows.length && !helper.isValidateOnly()) {
for (var i = 0; i < rows.length; i++) {
var row = rows[i].row;
var qc;
if (row.QCStateLabel) {
qc = EHR.Server.Security.getQCStateByLabel(row.QCStateLabel);
}
else if (row.QCState) {
qc = EHR.Server.Security.getQCStateByRowId(row.QCState);
}

if (!qc) {
console.error('Unable to find QCState: ' + row.QCState + '/' + row.QCStateLabel);
}
else if (qc.Label != 'COMPLETED' && row.caseid && row.Id && qc) {
triggerHelper.ensureDailyClinicalObservationOrders(row.Id, row.caseid, row.performedby, qc.RowId);
}
}
}
}
});
56 changes: 17 additions & 39 deletions nirc_ehr/resources/queries/study/clinical_observations.js
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Expand Up @@ -4,41 +4,12 @@
* Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0
*/

const console = require("console");
require("ehr/triggers").initScript(this);

var animalIdCasesMap = {};
var triggerHelper = new org.labkey.nirc_ehr.query.NIRC_EHRTriggerHelper(LABKEY.Security.currentUser.id, LABKEY.Security.currentContainer.id);

function onInit(event, helper){

LABKEY.Query.selectRows({
schemaName: 'study',
queryName: 'cases',
columns: ['Id', 'caseid', 'taskid', 'enddate'],
scope: this,
sort: 'Id',
success: function (results) {
if (!results || !results.rows || results.rows.length < 1)
return;

for(var i=0; i < results.rows.length; i++) {

// get all open cases associated with an animal
if (null === results.rows[i]["enddate"]) {
var animal = results.rows[i]["Id"];
if (!animalIdCasesMap[animal]) {
animalIdCasesMap[animal] = [];
}
animalIdCasesMap[animal].push(results.rows[i]);
}
}
// console.log("animalIdCasesMap: " + JSON.stringify(animalIdCasesMap));
},
failure: function (error) {
console.log("error getting death data in death trigger onInit()\n" + error);
}
});
}

function onUpsert(helper, scriptErrors, row, oldRow) {

Expand All @@ -53,14 +24,21 @@ function onUpsert(helper, scriptErrors, row, oldRow) {
EHR.Server.Utils.addError(scriptErrors, 'remark', "You selected 'No' for 'Verified Id?', please enter Remark", "WARN");
}

// if (!helper.isValidateOnly()) {
// if (row.Id) {
// if (animalIdCasesMap[row.Id] && animalIdCasesMap[row.Id].length > 0) {
//
//TODO:
// triggerHelper.addClinicalObsForCases(row, oldRow, animalIdCasesMap[row.Id]); //Add clinical obs for all open cases associated with an animal
// }
// }
// }
if (!helper.isValidateOnly()) {
var qc;
if (row.QCStateLabel) {
qc = EHR.Server.Security.getQCStateByLabel(row.QCStateLabel);
}
else if (row.QCState) {
qc = EHR.Server.Security.getQCStateByRowId(row.QCState);
}

if (!qc) {
console.error('Unable to find QCState: ' + row.QCState + '/' + row.QCStateLabel);
}
else {
triggerHelper.propagateClinicalObs(row, qc.RowId); //Add clinical obs for all open cases associated with an animal
}
}
}
}
7 changes: 7 additions & 0 deletions nirc_ehr/resources/queries/study/clinical_observations.query.xml
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Expand Up @@ -36,6 +36,13 @@
<columnTitle>Performed By</columnTitle>
<nullable>false</nullable>
</column>
<column columnName="scheduledDate">
<columnTitle>Scheduled Date</columnTitle>
</column>
<column columnName="type">
<columnTitle>Type</columnTitle>
<isHidden>true</isHidden>
</column>
</columns>
</table>
</tables>
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9 changes: 1 addition & 8 deletions nirc_ehr/resources/queries/study/deaths.query.xml
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Expand Up @@ -18,14 +18,7 @@
</fk>
</column>
<column columnName="remark"/>
<column columnName="performedby">
<fk>
<fkDbSchema>core</fkDbSchema>
<fkTable>Users</fkTable>
<fkColumnName>UserId</fkColumnName>
<fkDisplayColumnName>DisplayName</fkDisplayColumnName>
</fk>
</column>
<column columnName="performedby" />
<column columnName="description">
<isHidden>true</isHidden>
</column>
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5 changes: 2 additions & 3 deletions nirc_ehr/resources/queries/study/drug.query.xml
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Expand Up @@ -90,9 +90,8 @@
<fkDisplayColumnName useRawValue="true"/>
</fk>
</column>
<column columnName="performedby">
<columnTitle>Ordered By</columnTitle>
</column>
<column columnName="orderedby" />
<column columnName="performedby" />
<column columnName="scheduledDate">
<columnTitle>Scheduled Date</columnTitle>
</column>
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1 change: 1 addition & 0 deletions nirc_ehr/resources/queries/study/drug/.qview.xml
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Expand Up @@ -17,6 +17,7 @@
<column name="conc_units"/>
<column name="dosage"/>
<column name="dosage_units"/>
<column name="orderedby"/>
<column name="performedBy"/>
<column name="description"/>
<column name="remark"/>
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4 changes: 1 addition & 3 deletions nirc_ehr/resources/queries/study/flags.query.xml
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Expand Up @@ -32,9 +32,7 @@
<isHidden>true</isHidden>
</column>
<column columnName="remark"/>
<column columnName="performedby">
<columnTitle>Performed By</columnTitle>
</column>
<column columnName="performedby" />
<column columnName="project">
<isHidden>true</isHidden>
</column>
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4 changes: 1 addition & 3 deletions nirc_ehr/resources/queries/study/housing.query.xml
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Expand Up @@ -43,9 +43,7 @@
</fk>
</column>
<column columnName="remark"/>
<column columnName="performedBy">
<columnTitle>Performed By</columnTitle>
</column>
<column columnName="performedBy" />
</columns>
</table>
</tables>
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9 changes: 1 addition & 8 deletions nirc_ehr/resources/queries/study/necropsy.query.xml
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Expand Up @@ -43,14 +43,7 @@
<column columnName="remark">
<isHidden>true</isHidden>
</column>
<column columnName="performedby">
<fk>
<fkDbSchema>core</fkDbSchema>
<fkTable>Users</fkTable>
<fkColumnName>userId</fkColumnName>
<fkDisplayColumnName>DisplayName</fkDisplayColumnName>
</fk>
</column>
<column columnName="performedby" />
<column columnName="taskid">
<isHidden>true</isHidden>
</column>
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1 change: 1 addition & 0 deletions nirc_ehr/resources/queries/study/nhpTraining.js
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@@ -0,0 +1 @@
require("ehr/triggers").initScript(this);
41 changes: 41 additions & 0 deletions nirc_ehr/resources/queries/study/nhpTraining.query.xml
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@@ -0,0 +1,41 @@
<query xmlns="http://labkey.org/data/xml/query">
<metadata>
<tables xmlns="http://labkey.org/data/xml">
<table tableName="nhpTraining" tableDbType="TABLE" useColumnOrder="true">
<tableTitle>Animal Training</tableTitle>
<columns>
<column columnName="Id" />
<column columnName="date" />
<column columnName="trainingType">
<columnTitle>Training Type</columnTitle>
<fk>
<fkDbSchema>ehr_lookups</fkDbSchema>
<fkTable>nhp_training_type</fkTable>
<fkColumnName>value</fkColumnName>
</fk>
</column>
<column columnName="reason">
<columnTitle>Reason</columnTitle>
<fk>
<fkDbSchema>ehr_lookups</fkDbSchema>
<fkTable>nhp_training_reason</fkTable>
<fkColumnName>value</fkColumnName>
</fk>
</column>
<column columnName="result">
<columnTitle>Result</columnTitle>
<fk>
<fkDbSchema>ehr_lookups</fkDbSchema>
<fkTable>nhp_training_result</fkTable>
<fkColumnName>value</fkColumnName>
</fk>
</column>
<column columnName="trainingStaff" >
<columnTitle>Training Staff</columnTitle>
</column>

</columns>
</table>
</tables>
</metadata>
</query>
22 changes: 22 additions & 0 deletions nirc_ehr/resources/queries/study/observationSchedule.query.xml
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@@ -0,0 +1,22 @@
<query xmlns="http://labkey.org/data/xml/query">
<metadata>
<tables xmlns="http://labkey.org/data/xml">
<table tableName="observationSchedule" tableDbType="TABLE" useColumnOrder="true">
<javaCustomizer class="org.labkey.ehr.table.DefaultEHRCustomizer" />
<tableTitle>Observation Schedule</tableTitle>
<columns>
<column columnName="Id" />
<column columnName="scheduledDate">
<columnTitle>Scheduled Date/Time</columnTitle>
</column>
<column columnName="observations">
<columnTitle>Observations</columnTitle>
</column>
<column columnName="observationRecord">
<columnTitle></columnTitle>
</column>
</columns>
</table>
</tables>
</metadata>
</query>
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