diff --git a/nbri_ehr/resources/data/pairing_formation_types.tsv b/nbri_ehr/resources/data/pairing_formation_types.tsv index 64101aa..ed90dde 100644 --- a/nbri_ehr/resources/data/pairing_formation_types.tsv +++ b/nbri_ehr/resources/data/pairing_formation_types.tsv @@ -1,7 +1,11 @@ -value -Full Contact Pair -Group Formation -Introduction -Limited Contact Pair -Pair Formation -Other \ No newline at end of file +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 \ No newline at end of file diff --git a/nbri_ehr/resources/domain-templates/ehr.template.xml b/nbri_ehr/resources/domain-templates/ehr.template.xml index 281f4bd..a29a278 100644 --- a/nbri_ehr/resources/domain-templates/ehr.template.xml +++ b/nbri_ehr/resources/domain-templates/ehr.template.xml @@ -6,118 +6,18 @@ - - diff --git a/nbri_ehr/resources/queries/ehr/investigators.query.xml b/nbri_ehr/resources/queries/ehr/investigators.query.xml new file mode 100644 index 0000000..13d4973 --- /dev/null +++ b/nbri_ehr/resources/queries/ehr/investigators.query.xml @@ -0,0 +1,26 @@ + + + + + Investigators + + + + + + + Last Name + true + + + First Name + + + User + http://www.labkey.org/types#userId + + +
+ + + diff --git a/nbri_ehr/resources/queries/ehr/project.query.xml b/nbri_ehr/resources/queries/ehr/project.query.xml index 5b72f21..8ce9715 100644 --- a/nbri_ehr/resources/queries/ehr/project.query.xml +++ b/nbri_ehr/resources/queries/ehr/project.query.xml @@ -49,10 +49,10 @@ true - core - Users - UserId - DisplayName + ehr + investigators + rowid + lastName diff --git a/nbri_ehr/resources/queries/ehr/protocol.query.xml b/nbri_ehr/resources/queries/ehr/protocol.query.xml index 82667e7..edf95db 100644 --- a/nbri_ehr/resources/queries/ehr/protocol.query.xml +++ b/nbri_ehr/resources/queries/ehr/protocol.query.xml @@ -9,78 +9,15 @@ PI false - core - Users - UserId - DisplayName + ehr + investigators + rowid + lastName true - - Author - - core - Users - UserId - DisplayName - - - - Owner - - core - Users - UserId - DisplayName - - - - Protocol Type - - ehr_lookups - protocol_type - value - title - - - - Protocol Category - - ehr_lookups - protocol_category - value - title - - - - Current State - - ehr_lookups - protocol_state - value - title - - - - Parent Protocol - - ehr - protocol - protocol - displayName - - - - Questionnaire - - ehr_lookups - questionnaire - value - title - - Approval Date @@ -88,4 +25,4 @@ - \ No newline at end of file + diff --git a/nbri_ehr/resources/queries/ehr/protocol/.qview.xml b/nbri_ehr/resources/queries/ehr/protocol/.qview.xml index e2e125f..62dfd8e 100644 --- a/nbri_ehr/resources/queries/ehr/protocol/.qview.xml +++ b/nbri_ehr/resources/queries/ehr/protocol/.qview.xml @@ -2,40 +2,14 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + - - \ No newline at end of file + diff --git a/nbri_ehr/resources/queries/ehr/protocol_counts.query.xml b/nbri_ehr/resources/queries/ehr/protocol_counts.query.xml index 6586f91..82b9060 100644 --- a/nbri_ehr/resources/queries/ehr/protocol_counts.query.xml +++ b/nbri_ehr/resources/queries/ehr/protocol_counts.query.xml @@ -14,15 +14,6 @@ scientific_name - - Euthanasia - - ehr_lookups - euthanasia_type - value - title - - diff --git a/nbri_ehr/resources/queries/study/activeAssignments.sql b/nbri_ehr/resources/queries/study/activeAssignments.sql index 990598c..9cd67a4 100644 --- a/nbri_ehr/resources/queries/study/activeAssignments.sql +++ b/nbri_ehr/resources/queries/study/activeAssignments.sql @@ -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, diff --git a/nbri_ehr/resources/queries/study/animalGroupHousingSummary.query.xml b/nbri_ehr/resources/queries/study/animalGroupHousingSummary.query.xml new file mode 100644 index 0000000..95ce7a9 --- /dev/null +++ b/nbri_ehr/resources/queries/study/animalGroupHousingSummary.query.xml @@ -0,0 +1,15 @@ + + + + + Animal Groups Housing Summary + + + Total Animals + /query/executeQuery.view?schemaName=study&query.queryName=demographics&query.id/curLocation/room~eq=${room}&query.id/activeAnimalGroups/groups~contains=${groupId/title} + + +
+ + + diff --git a/nbri_ehr/resources/queries/study/animalGroupHousingSummary.sql b/nbri_ehr/resources/queries/study/animalGroupHousingSummary.sql new file mode 100644 index 0000000..5ca3a32 --- /dev/null +++ b/nbri_ehr/resources/queries/study/animalGroupHousingSummary.sql @@ -0,0 +1,13 @@ +/* + * 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 diff --git a/nbri_ehr/resources/queries/study/animalGroupOverlapSummary.query.xml b/nbri_ehr/resources/queries/study/animalGroupOverlapSummary.query.xml new file mode 100644 index 0000000..0db6a6c --- /dev/null +++ b/nbri_ehr/resources/queries/study/animalGroupOverlapSummary.query.xml @@ -0,0 +1,22 @@ + + + + + Animal Group Member Summary + This query identifies the total distinct animals that were part of a group over the provided date range + + + /query/executeQuery.view?schemaName=study&query.queryName=animalGroupOverlaps&query.param.StartDate=${StartDate}&query.param.EndDate=${EndDate}&query.groupId/title~eq=${groupId/title} + Total Animals + + + true + + + true + + +
+ + + diff --git a/nbri_ehr/resources/queries/study/animalGroupOverlapSummary.sql b/nbri_ehr/resources/queries/study/animalGroupOverlapSummary.sql new file mode 100644 index 0000000..c855540 --- /dev/null +++ b/nbri_ehr/resources/queries/study/animalGroupOverlapSummary.sql @@ -0,0 +1,15 @@ +/* + * Copyright (c) 2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT + o.groupId, + count(distinct o.id) as totalAnimals, + + max(o.StartDate) as StartDate, + max(o.EndDate) as EndDate + +FROM study.animalGroupOverlaps o + +GROUP BY o.groupId diff --git a/nbri_ehr/resources/queries/study/animalGroupOverlaps.query.xml b/nbri_ehr/resources/queries/study/animalGroupOverlaps.query.xml new file mode 100644 index 0000000..92106fe --- /dev/null +++ b/nbri_ehr/resources/queries/study/animalGroupOverlaps.query.xml @@ -0,0 +1,18 @@ + + + + + Animal Group Overlaps + This query identifies distinct animals that were part of a group over the provided date range + + + true + + + true + + +
+ + + diff --git a/nbri_ehr/resources/queries/study/animalGroupOverlaps.sql b/nbri_ehr/resources/queries/study/animalGroupOverlaps.sql new file mode 100644 index 0000000..c5a2e62 --- /dev/null +++ b/nbri_ehr/resources/queries/study/animalGroupOverlaps.sql @@ -0,0 +1,34 @@ +/* + * Copyright (c) 2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ + +/** + * This query is designed to find distinct animals that were part of a group at a given point in time + */ +PARAMETERS(StartDate TIMESTAMP, EndDate TIMESTAMP) + +SELECT + m.Id, + m.groupId, + + max(StartDate) as StartDate, + max(EndDate) as EndDate +FROM study.animal_group_members m + +WHERE ( + /* entered startdate must be <= entered enddate */ + coalesce( StartDate , cast('1900-01-01 00:00:00.0' as timestamp)) <= coalesce(EndDate, now()) + AND + + /* entered startdate must be less than record's enddate */ + cast(coalesce( StartDate , cast('1900-01-01 00:00:00.0' as DATE)) AS DATE) <= m.enddateCoalesced + + and + + /* entered enddate must be greater than record's startdate */ + cast(coalesce(EndDate, curdate()) AS DATE) >= m.dateOnly + ) + +GROUP BY m.groupId, m.id diff --git a/nbri_ehr/resources/queries/study/animalGroupsPivoted.query.xml b/nbri_ehr/resources/queries/study/animalGroupsPivoted.query.xml new file mode 100644 index 0000000..3ff39fc --- /dev/null +++ b/nbri_ehr/resources/queries/study/animalGroupsPivoted.query.xml @@ -0,0 +1,9 @@ + + + + + Active Groups +
+ + + diff --git a/nbri_ehr/resources/queries/study/animalGroupsPivoted.sql b/nbri_ehr/resources/queries/study/animalGroupsPivoted.sql new file mode 100644 index 0000000..5c5c53b --- /dev/null +++ b/nbri_ehr/resources/queries/study/animalGroupsPivoted.sql @@ -0,0 +1,17 @@ +/* + * Copyright (c) 2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT +g.id, +g.groupId.title as name, +cast('yes' as varchar) as valueField + +FROM study.animal_group_members g + +WHERE (g.enddate IS NULL OR COALESCE(g.enddate, curdate()) >= curdate()) + +GROUP BY g.id, g.groupId.title + +PIVOT valueField by name IN (select title FROM ehr_lookups.breeding_type) diff --git a/nbri_ehr/resources/queries/study/animal_group_members.query.xml b/nbri_ehr/resources/queries/study/animal_group_members.query.xml new file mode 100644 index 0000000..4cf726e --- /dev/null +++ b/nbri_ehr/resources/queries/study/animal_group_members.query.xml @@ -0,0 +1,42 @@ + + + + + Animal Group Members + + + + Date Added + + + Date Removed + false + + + Group + + ehr_lookups + breeding_type + value + title + + + + + core + qcstate + rowid + + + + true + + + false + false + + +
+ + + diff --git a/nbri_ehr/resources/queries/study/demographicsActiveAnimalGroups.query.xml b/nbri_ehr/resources/queries/study/demographicsActiveAnimalGroups.query.xml new file mode 100644 index 0000000..f12d8e0 --- /dev/null +++ b/nbri_ehr/resources/queries/study/demographicsActiveAnimalGroups.query.xml @@ -0,0 +1,19 @@ + + + + + Active Animal Groups + + + + ALWAYS_OFF + Total Groups + + + Groups + + +
+ + + diff --git a/nbri_ehr/resources/queries/study/demographicsActiveAnimalGroups.sql b/nbri_ehr/resources/queries/study/demographicsActiveAnimalGroups.sql new file mode 100644 index 0000000..435a4b4 --- /dev/null +++ b/nbri_ehr/resources/queries/study/demographicsActiveAnimalGroups.sql @@ -0,0 +1,16 @@ +/* + * Copyright (c) 2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +SELECT + m.Id, + count(distinct m.objectid) as totalGroups, + group_concat(distinct m.name, chr(10)) as groups + +FROM (SELECT Id, + objectid, + groupId.title as name + FROM study.animal_group_members + WHERE enddate is NULL AND qcstate.publicdata = true) m +GROUP BY m.Id diff --git a/nbri_ehr/resources/queries/study/pairings.query.xml b/nbri_ehr/resources/queries/study/pairings.query.xml index 727a724..d75ab6a 100644 --- a/nbri_ehr/resources/queries/study/pairings.query.xml +++ b/nbri_ehr/resources/queries/study/pairings.query.xml @@ -45,6 +45,7 @@ ehr_lookups pairing_formation_types value + title diff --git a/nbri_ehr/resources/referenceStudy/study/datasets/datasets_manifest.xml b/nbri_ehr/resources/referenceStudy/study/datasets/datasets_manifest.xml index a4cd2a4..fbc9052 100644 --- a/nbri_ehr/resources/referenceStudy/study/datasets/datasets_manifest.xml +++ b/nbri_ehr/resources/referenceStudy/study/datasets/datasets_manifest.xml @@ -2,6 +2,7 @@ + diff --git a/nbri_ehr/resources/referenceStudy/study/datasets/datasets_metadata.xml b/nbri_ehr/resources/referenceStudy/study/datasets/datasets_metadata.xml index 2ae212d..aa2bd6a 100644 --- a/nbri_ehr/resources/referenceStudy/study/datasets/datasets_metadata.xml +++ b/nbri_ehr/resources/referenceStudy/study/datasets/datasets_metadata.xml @@ -58,6 +58,32 @@ + + Animal Group Members + Records membership of individual primates in named animal groups, with the date the animal joined and the date it was removed. + + + varchar + http://cpas.labkey.com/Study#ParticipantId + + ptid + + + + timestamp + http://cpas.labkey.com/Study#VisitDate + http://cpas.labkey.com/Study#VisitDate + + + timestamp + urn:ehr.labkey.org/#EndDate + + + Group + varchar + + +
ArrivalTracks the arrival of primates into the research facility, including source, acquisition type, and associated documentation. diff --git a/nbri_ehr/resources/scripts/nbri_triggers.js b/nbri_ehr/resources/scripts/nbri_triggers.js index 16b2ddc..320c63f 100644 --- a/nbri_ehr/resources/scripts/nbri_triggers.js +++ b/nbri_ehr/resources/scripts/nbri_triggers.js @@ -27,7 +27,7 @@ exports.init = function (EHR) { EHR.Server.TriggerManager.unregisterAllHandlersForQueryNameAndEvent('study', 'cases', EHR.Server.TriggerManager.Events.AFTER_DELETE); helper.setScriptOptions({ - datasetsToClose: ['assignment', 'protocolAssignment' , 'housing', 'treatment_order', 'observation_order', 'cases', 'pairings', 'exemptions', 'flags'] + datasetsToClose: ['assignment', 'protocolAssignment' , 'housing', 'treatment_order', 'observation_order', 'cases', 'pairings', 'exemptions', 'flags', 'animal_group_members'] }); }); @@ -54,6 +54,14 @@ exports.init = function (EHR) { }); }); + EHR.Server.TriggerManager.registerHandlerForQuery(EHR.Server.TriggerManager.Events.INIT, 'study', 'animal_group_members', function(event, helper) { + // group memberships are routinely backdated, so historical dates must not raise a warning + helper.setScriptOptions({ + requiresStatusRecalc: false, + allowDatesInDistantPast: true + }); + }); + EHR.Server.TriggerManager.registerHandlerForQuery(EHR.Server.TriggerManager.Events.INIT, 'study', 'assignment', function(event, helper) { helper.setScriptOptions({ allowAnyId: isAllowAnyIdRequested(helper), @@ -136,7 +144,7 @@ exports.init = function (EHR) { EHR.Server.TriggerManager.registerHandlerForQuery(EHR.Server.TriggerManager.Events.INIT, 'study', 'deaths', function(event, helper) { helper.setScriptOptions({ - datasetsToClose: ['assignment', 'protocolAssignment' , 'housing', 'treatment_order', 'observation_order', 'cases', 'pairings', 'exemptions', 'flags'], + datasetsToClose: ['assignment', 'protocolAssignment' , 'housing', 'treatment_order', 'observation_order', 'cases', 'pairings', 'exemptions', 'flags', 'animal_group_members'], allowShippedIds: false, allowDeadIds: false, requiresStatusRecalc: true, diff --git a/nbri_ehr/resources/web/nbri_ehr/data/AllowAnyIdClientStore.js b/nbri_ehr/resources/web/nbri_ehr/data/AllowAnyIdClientStore.js new file mode 100644 index 0000000..49ecfdb --- /dev/null +++ b/nbri_ehr/resources/web/nbri_ehr/data/AllowAnyIdClientStore.js @@ -0,0 +1,16 @@ +/* + * Copyright (c) 2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +Ext4.define('NBRI_EHR.data.AllowAnyIdClientStore', { + extend: 'EHR.data.DataEntryClientStore', + + getExtraContext: function () { + var ret = this.callParent(arguments) || {}; + + // Tell the trigger scripts to allow any Id. Requires handling in trigger script to fully enable. + ret['allowAnyId'] = true; + return ret; + } +}); diff --git a/nbri_ehr/resources/web/nbri_ehr/model/sources/AnimalGroupMembers.js b/nbri_ehr/resources/web/nbri_ehr/model/sources/AnimalGroupMembers.js new file mode 100644 index 0000000..3678d54 --- /dev/null +++ b/nbri_ehr/resources/web/nbri_ehr/model/sources/AnimalGroupMembers.js @@ -0,0 +1,52 @@ +/* + * Copyright (c) 2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ +EHR.model.DataModelManager.registerMetadata('AnimalGroupMembers', { + byQuery: { + 'study.animal_group_members': { + Id: { + xtype: 'ehr-animalIdUpperField', + dataIndex: 'Id', + nullable: false, + allowBlank: false, + lookups: false, + noSaveInTemplateByDefault: true, + columnConfig: { + width: 95, + showLink: false + }, + editorConfig: { + allowAnyId: true + } + }, + date: { + allowBlank: false, + nullable: false, + noSaveInTemplateByDefault: true, + hidden: false, + getInitialValue: function(v, rec){ + if (v) + return v; + + let curDate = new Date(); + curDate.setHours(0, 0, 0, 0); + return curDate; + } + }, + groupId: { + allowBlank: false, + nullable: false, + lookup: { + // the shared default filters on a date column that the breeding type lookup does not have + filterArray: [] + } + }, + performedBy: { + shownInGrid: false, + hidden: true + } + } + } +}); diff --git a/nbri_ehr/resources/web/nbri_ehr/model/sources/Assignment.js b/nbri_ehr/resources/web/nbri_ehr/model/sources/Assignment.js index 4d38d3c..b055afb 100644 --- a/nbri_ehr/resources/web/nbri_ehr/model/sources/Assignment.js +++ b/nbri_ehr/resources/web/nbri_ehr/model/sources/Assignment.js @@ -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, @@ -27,6 +26,9 @@ EHR.model.DataModelManager.registerMetadata('Assignment', { } }, 'study.protocolAssignment': { + 'enddate': { + hidden: true + }, 'project': { hidden: true }, diff --git a/nbri_ehr/src/org/labkey/nbri_ehr/NBRI_EHRModule.java b/nbri_ehr/src/org/labkey/nbri_ehr/NBRI_EHRModule.java index aa76225..b76fdbb 100644 --- a/nbri_ehr/src/org/labkey/nbri_ehr/NBRI_EHRModule.java +++ b/nbri_ehr/src/org/labkey/nbri_ehr/NBRI_EHRModule.java @@ -136,6 +136,8 @@ protected void doStartupAfterSpringConfig(ModuleContext moduleContext) ehrService.registerDemographicsProvider(new SourceDemographicsProvider(this)); ehrService.registerDemographicsProvider(new NecropsyStatusDemographicsProvider(this)); + EHRService.get().registerHistoryDataSource(new AnimalGroupsDataSource(this)); + EHRService.get().registerHistoryDataSource(new AnimalGroupsEndDataSource(this)); EHRService.get().registerHistoryDataSource(new ArrivalDataSource(this)); EHRService.get().registerHistoryDataSource(new BiopsyDataSource(this)); EHRService.get().registerHistoryDataSource(new BirthDataSource(this)); @@ -177,7 +179,7 @@ protected void doStartupAfterSpringConfig(ModuleContext moduleContext) ehrService.registerActionOverride("participantView", this, "views/participantView.html"); ehrService.registerActionOverride("enterData", this, "views/enterData.html"); - ehrService.registerTriggerScriptOption("datasetsToCloseOnNewEntry", List.of("assignment", "protocolAssignment")); + ehrService.registerTriggerScriptOption("datasetsToCloseOnNewEntry", List.of("assignment", "protocolAssignment", "animal_group_members")); RoleManager.registerRole(new NBRIEHRVetTechRole()); EHRService.get().registerMoreActionsButton(new ShowEditUIButton(this, "ehr", "observation_types", EHRDataAdminPermission.class), "ehr", "observation_types"); @@ -207,6 +209,7 @@ private void registerDataEntry() { EHRService.get().registerFormType(new DefaultDataEntryFormFactory(NBRIAliasFormType.class, this)); EHRService.get().registerFormType(new DefaultDataEntryFormFactory(NBRIAssignmentFormType.class, this)); + EHRService.get().registerFormType(new DefaultDataEntryFormFactory(NBRIGroupAssignmentFormType.class, this)); EHRService.get().registerFormType(new DefaultDataEntryFormFactory(NBRIArrivalFormType.class, this)); EHRService.get().registerFormType(new DefaultDataEntryFormFactory(NBRIBirthFormType.class, this)); EHRService.get().registerFormType(new DefaultDataEntryFormFactory(NBRIBulkClinicalFormType.class, this)); @@ -217,6 +220,7 @@ 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)); diff --git a/nbri_ehr/src/org/labkey/nbri_ehr/dataentry/form/NBRIGroupAssignmentFormType.java b/nbri_ehr/src/org/labkey/nbri_ehr/dataentry/form/NBRIGroupAssignmentFormType.java new file mode 100644 index 0000000..5ebea19 --- /dev/null +++ b/nbri_ehr/src/org/labkey/nbri_ehr/dataentry/form/NBRIGroupAssignmentFormType.java @@ -0,0 +1,48 @@ +/* + * Copyright (c) 2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ +package org.labkey.nbri_ehr.dataentry.form; + +import org.labkey.api.ehr.dataentry.DataEntryFormContext; +import org.labkey.api.ehr.dataentry.FormSection; +import org.labkey.api.module.Module; +import org.labkey.api.view.template.ClientDependency; +import org.labkey.nbri_ehr.dataentry.section.NBRIAnimalDetailsFormSection; +import org.labkey.nbri_ehr.dataentry.section.NBRIGroupAssignmentFormSection; +import org.labkey.nbri_ehr.dataentry.section.NBRITaskFormSection; + +import java.util.List; + +public class NBRIGroupAssignmentFormType extends NBRIBaseTaskFormType +{ + public static final String NAME = "animalGroupAssignment"; + public static final String LABEL = "Animal Group Assignment"; + + public NBRIGroupAssignmentFormType(DataEntryFormContext ctx, Module owner) + { + super(ctx, owner, NAME, LABEL, "Colony Management", List.of( + new NBRITaskFormSection(), + new NBRIAnimalDetailsFormSection(), + new NBRIGroupAssignmentFormSection(false, true, false) + )); + + addClientDependency(ClientDependency.supplierFromPath("nbri_ehr/model/sources/AnimalGroupMembers.js")); + + for (FormSection s : getFormSections()) + { + s.addConfigSource("AnimalGroupMembers"); + } + } +} diff --git a/nbri_ehr/src/org/labkey/nbri_ehr/dataentry/form/NBRIInvestigatorsFormType.java b/nbri_ehr/src/org/labkey/nbri_ehr/dataentry/form/NBRIInvestigatorsFormType.java new file mode 100644 index 0000000..14055b2 --- /dev/null +++ b/nbri_ehr/src/org/labkey/nbri_ehr/dataentry/form/NBRIInvestigatorsFormType.java @@ -0,0 +1,48 @@ +/* + * Copyright (c) 2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ +package org.labkey.nbri_ehr.dataentry.form; + +import org.labkey.api.ehr.dataentry.DataEntryFormContext; +import org.labkey.api.ehr.dataentry.forms.AdminLinksFormType; +import org.labkey.api.ehr.security.EHRDataAdminPermission; +import org.labkey.api.module.Module; +import org.labkey.api.view.ActionURL; + +import java.util.ArrayList; + +public class NBRIInvestigatorsFormType extends AdminLinksFormType +{ + public NBRIInvestigatorsFormType(DataEntryFormContext ctx, Module owner) + { + super(ctx, owner, "Investigators", "Investigators", "Admin", new ArrayList<>()); + } + + @Override + protected ActionURL dataEntryLink() + { + ActionURL url = new ActionURL("ldk", "updateQuery", getCtx().getContainer()); + url.addParameter("schemaName", "ehr"); + url.addParameter("query.queryName", "investigators"); + url.addParameter("showImport", "true"); + return url; + } + + @Override + public boolean isAvailable() + { + return (super.isAvailable() || getCtx().getContainer().hasPermission(getCtx().getUser(), EHRDataAdminPermission.class)); + } +} diff --git a/nbri_ehr/src/org/labkey/nbri_ehr/dataentry/section/NBRIGroupAssignmentFormSection.java b/nbri_ehr/src/org/labkey/nbri_ehr/dataentry/section/NBRIGroupAssignmentFormSection.java new file mode 100644 index 0000000..3ef5297 --- /dev/null +++ b/nbri_ehr/src/org/labkey/nbri_ehr/dataentry/section/NBRIGroupAssignmentFormSection.java @@ -0,0 +1,32 @@ +/* + * Copyright (c) 2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ +package org.labkey.nbri_ehr.dataentry.section; + +import org.labkey.api.view.template.ClientDependency; + +public class NBRIGroupAssignmentFormSection extends BaseFormSection +{ + public NBRIGroupAssignmentFormSection(boolean allowAnyId, boolean collapsible, boolean initCollapsed) + { + super("study", "animal_group_members", "Group Assignments", "ehr-gridpanel", collapsible, initCollapsed, true); + + if (allowAnyId) + { + setClientStoreClass("NBRI_EHR.data.AllowAnyIdClientStore"); + addClientDependency(ClientDependency.supplierFromPath("nbri_ehr/data/AllowAnyIdClientStore.js")); + } + } +} diff --git a/nbri_ehr/src/org/labkey/nbri_ehr/history/AnimalGroupsDataSource.java b/nbri_ehr/src/org/labkey/nbri_ehr/history/AnimalGroupsDataSource.java new file mode 100644 index 0000000..69f1ace --- /dev/null +++ b/nbri_ehr/src/org/labkey/nbri_ehr/history/AnimalGroupsDataSource.java @@ -0,0 +1,52 @@ +/* + * Copyright (c) 2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ +package org.labkey.nbri_ehr.history; + +import org.labkey.api.data.Container; +import org.labkey.api.data.Results; +import org.labkey.api.ehr.history.AbstractDataSource; +import org.labkey.api.module.Module; +import org.labkey.api.query.FieldKey; +import org.labkey.api.util.PageFlowUtil; + +import java.sql.SQLException; +import java.util.Set; + +public class AnimalGroupsDataSource extends AbstractDataSource +{ + public AnimalGroupsDataSource(Module module) + { + super("study", "animal_group_members", "Added To Group", "Animal Groups", module); + } + + @Override + protected Set getColumnNames() + { + return PageFlowUtil.set("Id", "date", "enddate", "groupId", "groupId/title"); + } + + @Override + protected String getHtml(Container c, Results rs, boolean redacted) throws SQLException + { + StringBuilder sb = new StringBuilder(); + + FieldKey title = FieldKey.fromString("groupId/title"); + if (rs.hasColumn(title) && rs.getObject(title) != null) + sb.append("Added to group: ").append(rs.getString(title)).append("\n"); + + return sb.toString(); + } +} diff --git a/nbri_ehr/src/org/labkey/nbri_ehr/history/AnimalGroupsEndDataSource.java b/nbri_ehr/src/org/labkey/nbri_ehr/history/AnimalGroupsEndDataSource.java new file mode 100644 index 0000000..dfdf187 --- /dev/null +++ b/nbri_ehr/src/org/labkey/nbri_ehr/history/AnimalGroupsEndDataSource.java @@ -0,0 +1,71 @@ +/* + * Copyright (c) 2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ +package org.labkey.nbri_ehr.history; + +import org.jetbrains.annotations.NotNull; +import org.labkey.api.data.CompareType; +import org.labkey.api.data.Container; +import org.labkey.api.data.Results; +import org.labkey.api.data.SimpleFilter; +import org.labkey.api.ehr.history.AbstractDataSource; +import org.labkey.api.ehr.history.HistoryRow; +import org.labkey.api.module.Module; +import org.labkey.api.query.FieldKey; +import org.labkey.api.security.User; +import org.labkey.api.util.PageFlowUtil; + +import java.sql.SQLException; +import java.util.List; +import java.util.Set; + +public class AnimalGroupsEndDataSource extends AbstractDataSource +{ + public AnimalGroupsEndDataSource(Module module) + { + super("study", "animal_group_members", "Removed From Group", "Animal Groups", module); + } + + @Override + protected String getDateField() + { + return "enddate"; + } + + @Override + protected @NotNull List getRows(Container c, User u, SimpleFilter filter, boolean redacted) + { + filter.addCondition(FieldKey.fromString(getDateField()), null, CompareType.NONBLANK); + return super.getRows(c, u, filter, redacted); + } + + @Override + protected Set getColumnNames() + { + return PageFlowUtil.set("Id", "date", "enddate", "groupId", "groupId/title"); + } + + @Override + protected String getHtml(Container c, Results rs, boolean redacted) throws SQLException + { + StringBuilder sb = new StringBuilder(); + + FieldKey title = FieldKey.fromString("groupId/title"); + if (rs.hasColumn(title) && rs.getObject(title) != null) + sb.append("Removed from group: ").append(rs.getString(title)).append("\n"); + + return sb.toString(); + } +} diff --git a/nbri_ehr/src/org/labkey/nbri_ehr/table/NBRI_EHRCustomizer.java b/nbri_ehr/src/org/labkey/nbri_ehr/table/NBRI_EHRCustomizer.java index b365680..7f4406b 100644 --- a/nbri_ehr/src/org/labkey/nbri_ehr/table/NBRI_EHRCustomizer.java +++ b/nbri_ehr/src/org/labkey/nbri_ehr/table/NBRI_EHRCustomizer.java @@ -36,6 +36,8 @@ import org.labkey.api.ehr.security.EHRDataEntryPermission; import org.labkey.api.ehr.security.EHRVeterinarianPermission; import org.labkey.api.ehr.table.FixedWidthDisplayColumn; +import org.labkey.api.ehr.table.TreatmentLinkConfig; +import org.labkey.api.ehr.table.TreatmentLinkDisplayColumnFactory; import org.labkey.api.exp.api.StorageProvisioner; import org.labkey.api.exp.property.Domain; import org.labkey.api.gwt.client.FacetingBehaviorType; @@ -67,6 +69,10 @@ public class NBRI_EHRCustomizer extends AbstractTableCustomizer { + private static final TreatmentLinkConfig RECORD_TREATMENT = TreatmentLinkConfig.builder() + .formTypes("Behavior", "Behavioral Rounds", "Bulk Behavior Entry") + .build(); + public UserSchema getEHRUserSchema(AbstractTableInfo ds, String name) { Container ehrContainer = EHRService.get().getEHRStudyContainer(ds.getUserSchema().getContainer()); @@ -926,6 +932,21 @@ private void customizeAnimalTable(AbstractTableInfo ds) prjAssignment.setDescription("Shows all project to which the animal is actively assigned on the current date"); ds.addColumn(prjAssignment); } + if (ds.getColumn("activeAnimalGroups") == null) + { + var activeGroups = getWrappedCol(us, ds, "activeAnimalGroups", "demographicsActiveAnimalGroups", "Id", "Id"); + activeGroups.setLabel("Animal Groups - Active"); + activeGroups.setDescription("Displays the animal groups to which this animal currently belongs"); + ds.addColumn(activeGroups); + } + if (ds.getColumn("animalGroupsPivoted") == null) + { + var groupsPivoted = getWrappedCol(us, ds, "animalGroupsPivoted", "animalGroupsPivoted", "Id", "Id"); + groupsPivoted.setLabel("Active Group Summary"); + groupsPivoted.setHidden(true); + groupsPivoted.setDescription("Displays the active groups for each animal"); + ds.addColumn(groupsPivoted); + } if (ds.getColumn("alias") == null) { var col = getWrappedCol(us, ds, "alias", "demographicsAliases", "Id", "Id"); @@ -1008,7 +1029,7 @@ private void customizeTreatmentOrder(AbstractTableInfo ti) { WrappedColumn col = new WrappedColumn(ti.getColumn("objectid"), "treatmentRecord"); col.setLabel("Record Treatment"); - col.setDisplayColumnFactory(new TreatmentDisplayColumnFactory(false)); + col.setDisplayColumnFactory(TreatmentLinkDisplayColumnFactory.forOrder(RECORD_TREATMENT)); ti.addColumn(col); } } @@ -1019,7 +1040,7 @@ private void customizeTreatmentSchedule(AbstractTableInfo ti) { WrappedColumn col = new WrappedColumn(ti.getColumn("objectid"), "treatmentRecord"); col.setLabel("Record Treatment"); - col.setDisplayColumnFactory(new TreatmentDisplayColumnFactory(true)); + col.setDisplayColumnFactory(TreatmentLinkDisplayColumnFactory.forSchedule(RECORD_TREATMENT)); ti.addColumn(col); } } diff --git a/nbri_ehr/src/org/labkey/nbri_ehr/table/TreatmentDisplayColumnFactory.java b/nbri_ehr/src/org/labkey/nbri_ehr/table/TreatmentDisplayColumnFactory.java deleted file mode 100644 index 83db906..0000000 --- a/nbri_ehr/src/org/labkey/nbri_ehr/table/TreatmentDisplayColumnFactory.java +++ /dev/null @@ -1,130 +0,0 @@ -/* - * Copyright (c) 2026 LabKey Corporation - * - * Licensed under the Apache License, Version 2.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, software - * distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. - */ -package org.labkey.nbri_ehr.table; - -import org.labkey.api.data.ColumnInfo; -import org.labkey.api.data.DataColumn; -import org.labkey.api.data.DisplayColumn; -import org.labkey.api.data.DisplayColumnFactory; -import org.labkey.api.data.RenderContext; -import org.labkey.api.ehr.security.EHRClinicalEntryPermission; -import org.labkey.api.query.FieldKey; -import org.labkey.api.util.DateUtil; -import org.labkey.api.util.LinkBuilder; -import org.labkey.api.view.ActionURL; -import org.labkey.api.writer.HtmlWriter; - -import java.util.Date; -import java.util.Set; - -/** - * Display column factory for creating Record Treatment links. When includeScheduledDate is set, the row's date is - * passed as the scheduledDate URL parameter, so it should only be set on tables whose date column is the scheduled - * slot being recorded (e.g. treatmentSchedule), not the treatment order's start date. - */ -public class TreatmentDisplayColumnFactory implements DisplayColumnFactory -{ - private final boolean _includeScheduledDate; - - public TreatmentDisplayColumnFactory(boolean includeScheduledDate) - { - _includeScheduledDate = includeScheduledDate; - } - - @Override - public DisplayColumn createRenderer(final ColumnInfo colInfo) - { - return new DataColumn(colInfo){ - - @Override - public void renderGridCellContents(RenderContext ctx, HtmlWriter out) - { - String objectid = (String)getBoundColumn().getValue(ctx); - Date date = (Date)ctx.get("date"); - String caseid = (String)ctx.get("caseid"); - String category = (String)ctx.get("category"); - ActionURL url = new ActionURL("ehr", "dataEntryForm", colInfo.getParentTable().getUserSchema().getContainer()); - if (!colInfo.getParentTable().getUserSchema().getContainer().hasPermission(colInfo.getParentTable().getUserSchema().getUser(), EHRClinicalEntryPermission.class)) - return; - - if (category == null) - return; - - if (category.equals("Behavior")) - { - if (caseid != null) - { - url.addParameter("formType", "Behavioral Rounds"); - url.addParameter("caseid", caseid); - } - else - { - url.addParameter("formType", "Bulk Behavior Entry"); - } - } - else - { - if (caseid != null) - { - url.addParameter("formType", "Clinical Rounds"); - url.addParameter("caseid", caseid); - } - else - { - url.addParameter("formType", "medicationTreatment"); - } - } - - url.addParameter("treatmentid", objectid); - if (_includeScheduledDate && date != null) - url.addParameter("scheduledDate", DateUtil.formatIsoDateShortTime(date)); - - String returnUrl = new ActionURL("ehr", "animalHistory", colInfo.getParentTable().getUserSchema().getContainer()) + "#inputType:none&showReport:0&activeReport:clinMedicationSchedule"; - url.addParameter("returnUrl", returnUrl); - - out.write(LinkBuilder.labkeyLink("Record Treatment", url).target("_blank")); - } - - @Override - public void addQueryFieldKeys(Set keys) - { - super.addQueryFieldKeys(keys); - keys.add(getBoundColumn().getFieldKey()); - keys.add(FieldKey.fromString("date")); - keys.add(FieldKey.fromString("caseid")); - keys.add(FieldKey.fromString("category")); - } - - @Override - public boolean isSortable() - { - return false; - } - - @Override - public boolean isFilterable() - { - return false; - } - - @Override - public boolean isEditable() - { - return false; - } - }; - } -}