diff --git a/nirc_ehr/resources/data/editable_lookups.tsv b/nirc_ehr/resources/data/editable_lookups.tsv index 23c7d2ac..7f3ba907 100644 --- a/nirc_ehr/resources/data/editable_lookups.tsv +++ b/nirc_ehr/resources/data/editable_lookups.tsv @@ -73,8 +73,7 @@ ehr_lookups mens_score Clinical Menses Types Clinical observation fixed values. ehr_lookups mucous_membranes Clinical Mucous Membranes Used in clinical observations. ehr_lookups musculoskeletal_observations Clinical Musculoskeletal Observations Used in clinical observations. ehr_lookups necropsy_disposition_codes Colony Management Necropsy Disposition Codes -ehr_lookups necropsy_exam_reason Colony Management Necropsy Exam Reason -ehr_lookups necropsy_organ_appearance Colony Management Necropsy Organ Appearance +ehr_lookups necropsy_organ_appearance Colony Management Necropsy Organ Appearance ehr_lookups necropsy_organ_systems Colony Management Necropsy Organ Systems ehr_lookups necropsy_physical_condition Colony Management Necropsy Physical Condition ehr_lookups necropsy_specimen_condition Colony Management Necropsy Specimen Condition diff --git a/nirc_ehr/resources/data/lookup_sets.tsv b/nirc_ehr/resources/data/lookup_sets.tsv index 749d16c0..cea86af6 100644 --- a/nirc_ehr/resources/data/lookup_sets.tsv +++ b/nirc_ehr/resources/data/lookup_sets.tsv @@ -61,7 +61,6 @@ mens_score Menses value mucous_membranes Mucous Membranes value musculoskeletal_observations Musculoskeletal Observations value necropsy_disposition_codes Tissue Disposition Codes value title -necropsy_exam_reason Necropsy Reason value title necropsy_organ_appearance Appearance value title necropsy_organ_systems Organ Systems value title necropsy_physical_condition Physical Condition value title diff --git a/nirc_ehr/resources/data/lookupsManifest.tsv b/nirc_ehr/resources/data/lookupsManifest.tsv index ebf0d0c3..936ec52a 100644 --- a/nirc_ehr/resources/data/lookupsManifest.tsv +++ b/nirc_ehr/resources/data/lookupsManifest.tsv @@ -68,7 +68,6 @@ mens_score mucous_membranes musculoskeletal_observations necropsy_disposition_codes -necropsy_exam_reason necropsy_organ_appearance necropsy_organ_systems necropsy_physical_condition diff --git a/nirc_ehr/resources/data/lookupsManifestTest.tsv b/nirc_ehr/resources/data/lookupsManifestTest.tsv index 8784b08b..fde39961 100644 --- a/nirc_ehr/resources/data/lookupsManifestTest.tsv +++ b/nirc_ehr/resources/data/lookupsManifestTest.tsv @@ -67,7 +67,6 @@ mens_score mucous_membranes musculoskeletal_observations necropsy_disposition_codes -necropsy_exam_reason necropsy_organ_appearance necropsy_organ_systems necropsy_physical_condition diff --git a/nirc_ehr/resources/queries/study/cases.js b/nirc_ehr/resources/queries/study/cases.js index 02dc3b8b..a8e3b6c3 100644 --- a/nirc_ehr/resources/queries/study/cases.js +++ b/nirc_ehr/resources/queries/study/cases.js @@ -33,7 +33,7 @@ EHR.Server.TriggerManager.registerHandlerForQuery(EHR.Server.TriggerManager.Even error = true; } - if (!helper.isValidateOnly() && row.caseid && row.enddate && (row.enddate != oldRow.enddate)) { + if (!helper.isValidateOnly() && row.caseid && row.enddate && oldRow && (row.enddate != oldRow.enddate)) { triggerHelper.closeDailyClinicalObs(row.caseid, row.enddate); } @@ -57,7 +57,7 @@ EHR.Server.TriggerManager.registerHandlerForQuery(EHR.Server.TriggerManager.Even if (oldQc.Label != 'In Progress') { EHR.Server.Utils.addError(errors, null, 'Cannot save a draft copy of a case already opened or in review.', 'ERROR'); } - } else if (row.category == 'Clinical' && (qc.Label == 'Completed' || qc.Label == 'Review Required') && row.caseid && row.Id && row.performedby && row.taskid) { + } else if (row.category == 'Clinical' && (qc.Label == 'Completed' || qc.Label == 'Review Required') && row.caseid && row.Id && row.performedby && row.taskid && !row.enddate) { var ordersInTransaction = helper.getProperty('ordersInTransaction'); var oit = []; if (ordersInTransaction && ordersInTransaction.length) { diff --git a/nirc_ehr/resources/queries/study/deaths.js b/nirc_ehr/resources/queries/study/deaths.js index c6a89eea..03b9d2df 100644 --- a/nirc_ehr/resources/queries/study/deaths.js +++ b/nirc_ehr/resources/queries/study/deaths.js @@ -122,6 +122,21 @@ function onUpsert(helper, scriptErrors, row, oldRow) { console.log(row.id + " is not a valid animal id"); } } + + if(row.QCStateLabel && EHR.Server.Security.getQCStateByLabel(row.QCStateLabel).PublicData) { + var qcstate = helper.getJavaHelper().getQCStateForLabel(row.QCStateLabel).getRowId(); + + //add/update weight record + var weightRecord = { + Id: row.Id, + date: row.date, + weight: row.deathWeight, + taskid: row.taskid, + qcstate: qcstate, + performedby: row.performedby + }; + triggerHelper.upsertWeightRecord(weightRecord); + } } } } diff --git a/nirc_ehr/resources/queries/study/deaths.query.xml b/nirc_ehr/resources/queries/study/deaths.query.xml index f16eebcd..35c2e6ae 100644 --- a/nirc_ehr/resources/queries/study/deaths.query.xml +++ b/nirc_ehr/resources/queries/study/deaths.query.xml @@ -7,7 +7,6 @@ Death Date - Disposition @@ -17,6 +16,9 @@ title + + Death Weight (kg) + diff --git a/nirc_ehr/resources/queries/study/deaths/.qview.xml b/nirc_ehr/resources/queries/study/deaths/.qview.xml index d04d768b..fdc063c2 100644 --- a/nirc_ehr/resources/queries/study/deaths/.qview.xml +++ b/nirc_ehr/resources/queries/study/deaths/.qview.xml @@ -7,6 +7,7 @@ + diff --git a/nirc_ehr/resources/queries/study/necropsy.js b/nirc_ehr/resources/queries/study/necropsy.js index 05522f36..bbfa3878 100644 --- a/nirc_ehr/resources/queries/study/necropsy.js +++ b/nirc_ehr/resources/queries/study/necropsy.js @@ -35,29 +35,16 @@ function onUpsert(helper, scriptErrors, row, oldRow) { (deathIdMap[row.Id].QCStateLabel.toUpperCase() === 'REQUEST: PENDING' || deathIdMap[row.Id].QCStateLabel.toUpperCase() === 'REVIEW REQUIRED')) { - if (!row.examReason) - EHR.Server.Utils.addError(scriptErrors, 'examReason', "'Reason for Examination' is required", 'ERROR'); if (!row.specimenCondition) EHR.Server.Utils.addError(scriptErrors, 'specimenCondition', "'Condition of Specimen' is required", 'ERROR'); if (!row.physicalCondition) EHR.Server.Utils.addError(scriptErrors, 'physicalCondition', "'Physical Condition' is required", 'ERROR'); if (!row.diagnosis) EHR.Server.Utils.addError(scriptErrors, 'diagnosis', "'Diagnosis' is required", 'ERROR'); - } - - if(row.QCStateLabel && EHR.Server.Security.getQCStateByLabel(row.QCStateLabel).PublicData) { - var qcstate = helper.getJavaHelper().getQCStateForLabel(row.QCStateLabel).getRowId(); - - //add/update weight record - var weightRecord = { - Id: row.Id, - date: row.date, - weight: row.necropsyWeight, - taskid: row.taskid, - qcstate: qcstate, - performedby: row.performedby - }; - triggerHelper.upsertWeightRecord(weightRecord); + if (!row.grossAbnormalities) + EHR.Server.Utils.addError(scriptErrors, 'grossAbnormalities', "'Gross Abnormalities' is required", 'ERROR'); + if (!row.accessionNumber) + EHR.Server.Utils.addError(scriptErrors, 'accessionNumber', "'Accession Number' is required", 'ERROR'); } } } diff --git a/nirc_ehr/resources/queries/study/necropsy.query.xml b/nirc_ehr/resources/queries/study/necropsy.query.xml index 73cd38fd..35290a87 100644 --- a/nirc_ehr/resources/queries/study/necropsy.query.xml +++ b/nirc_ehr/resources/queries/study/necropsy.query.xml @@ -6,20 +6,12 @@ Exam Date - Category Diagnosis - - - ehr_lookups - necropsy_exam_reason - value - - ehr_lookups @@ -34,9 +26,6 @@ value - - Weight - true diff --git a/nirc_ehr/resources/queries/study/necropsy/.qview.xml b/nirc_ehr/resources/queries/study/necropsy/.qview.xml index b1af3175..2a4be61a 100644 --- a/nirc_ehr/resources/queries/study/necropsy/.qview.xml +++ b/nirc_ehr/resources/queries/study/necropsy/.qview.xml @@ -7,10 +7,8 @@ - - diff --git a/nirc_ehr/resources/referenceStudy/study/datasets/datasets_metadata.xml b/nirc_ehr/resources/referenceStudy/study/datasets/datasets_metadata.xml index 91ac8907..bc4e8f73 100644 --- a/nirc_ehr/resources/referenceStudy/study/datasets/datasets_metadata.xml +++ b/nirc_ehr/resources/referenceStudy/study/datasets/datasets_metadata.xml @@ -33,6 +33,7 @@ Alias + Records alternative identifiers and aliases assigned to individual primates within the facility. varchar @@ -59,6 +60,7 @@
Arrival + Tracks the arrival of primates into the research facility, including source, acquisition type, and associated documentation. entityid @@ -110,6 +112,7 @@
Project Assignments + Records project assignments for individual primates, linking animals to specific research projects with start and end dates. varchar @@ -134,6 +137,7 @@
Biopsy + Documents biopsy procedures performed on primates, including tissue type and associated pathology reports. varchar @@ -160,6 +164,7 @@
Protocol Assignments + Tracks the assignment of primates to IACUC-approved research protocols with effective date ranges. varchar @@ -183,6 +188,7 @@
Birth + Records birth events for primates born within the facility, including location and associated protocols. entityid @@ -216,6 +222,7 @@
Blood Draws + Tracks blood draw procedures performed on primates, including volume, sample type, tube type, and purpose. varchar @@ -262,6 +269,7 @@
Breeder + Records breeding evaluations and reproductive assessments for primates in the colony breeding program. varchar @@ -292,6 +300,7 @@
Clinical/Behavior Observations + Documents clinical and behavioral observations recorded during routine monitoring and veterinary assessments of primates. varchar @@ -332,6 +341,7 @@
Clinical Remarks + Stores veterinary clinical remarks and SOAP notes associated with primate health assessments and case management. varchar @@ -388,6 +398,7 @@
Demographics + Contains core demographic information for each primate, including species, sex, parentage, birth and death dates, and colony status. entityid @@ -462,6 +473,7 @@
Departure + Records the departure of primates from the research facility, including destination information. entityid @@ -487,6 +499,7 @@
Deaths + Documents primate deaths, including date, cause of death, and terminal body weight. entityid @@ -508,10 +521,14 @@ varchar + + double +
Exemptions + Tracks approved exemptions from standard care or procedural requirements for individual primates. varchar @@ -560,9 +577,11 @@ Animal Record Flags + Stores active record flags and status indicators applied to individual primates for colony management purposes.
Histopathology + Records histopathology findings from tissue examinations performed on primates, including diagnoses and associated reports. varchar @@ -614,9 +633,11 @@ Historical Other + Captures miscellaneous historical health and research records for primates that do not fit other specific categories.
Housing + Tracks housing assignments and location transfers for primates within the research facility. varchar @@ -677,9 +698,11 @@ Inbreeding Coefficients + Records calculated inbreeding coefficients for primates to support genetic management of the colony.
Necropsy + Documents necropsy (postmortem) examination findings for primates, including gross and histological observations, diagnoses, and reports. varchar @@ -693,9 +716,6 @@ http://cpas.labkey.com/Study#VisitDate http://cpas.labkey.com/Study#VisitDate - - double - Category varchar @@ -704,10 +724,6 @@ Accession Number varchar - - Reason for Examination - varchar - Condition of Specimen varchar @@ -744,6 +760,7 @@
Gross Pathology + Records gross pathology findings observed during necropsy examinations of primates. varchar @@ -768,6 +785,7 @@
Tissue Disposition + Tracks the disposition of tissue samples collected during necropsy of primates. varchar @@ -791,6 +809,7 @@
Pairings + Records social pairing and group housing arrangements for primates, including formation type, compatibility observations, and separation details. varchar @@ -843,6 +862,7 @@
Physical Exam + Documents physical examination findings and measurements recorded during veterinary assessments of primates. varchar @@ -878,6 +898,7 @@
Procedures + Records research and veterinary procedures performed on primates, including procedure type, category, and associated case information. varchar @@ -918,6 +939,7 @@
Procedure Orders + Tracks scheduled procedure orders for primates, including ordering veterinarian and scheduling windows. varchar @@ -957,6 +979,7 @@
Serology + Records serological test results for primates, used for infectious disease screening and colony health monitoring. varchar @@ -980,6 +1003,7 @@
Problem List + Maintains the active and historical problem list for individual primates, supporting ongoing veterinary case management. varchar @@ -1006,6 +1030,7 @@
Drug Administration + Records drug and medication administrations for primates, including dosage, route, concentration, and ordering clinician. varchar @@ -1080,6 +1105,7 @@
Treatment Cases + Tracks veterinary treatment cases for primates, supporting clinical case management from opening through resolution. varchar @@ -1145,6 +1171,7 @@
Treatment Orders + Stores standing treatment orders for primates, including medication details, dosing frequency, and prescribing veterinarian. varchar @@ -1268,9 +1295,11 @@ Vital Signs + Records vital sign measurements for primates, including temperature, heart rate, respiration rate, blood pressure, and pulse oximetry.
Weight + Tracks body weight measurements for primates, used for health monitoring and drug dosage calculations. varchar diff --git a/nirc_ehr/resources/views/necropsy.html b/nirc_ehr/resources/views/necropsy.html index 5b51a70d..2d62d51b 100644 --- a/nirc_ehr/resources/views/necropsy.html +++ b/nirc_ehr/resources/views/necropsy.html @@ -59,7 +59,7 @@ schemaName: 'study', queryName: 'deaths', filterArray: filterArray, - columns: 'Id,Id/demographics/species,date,reason,Id/lastProtocol/protocol,Id/lastProject/project', + columns: 'Id,Id/demographics/species,date,reason,deathWeight,Id/lastProtocol/protocol,Id/lastProject/project', }, title: 'Death', renderTo: 'animalDeath', diff --git a/nirc_ehr/resources/web/nirc_ehr/model/sources/DeathNecropsy.js b/nirc_ehr/resources/web/nirc_ehr/model/sources/DeathNecropsy.js index 4be79f4c..1db8b70c 100644 --- a/nirc_ehr/resources/web/nirc_ehr/model/sources/DeathNecropsy.js +++ b/nirc_ehr/resources/web/nirc_ehr/model/sources/DeathNecropsy.js @@ -12,12 +12,18 @@ EHR.model.DataModelManager.registerMetadata('DeathNecropsy', { dateFormat: 'Y-m-d', timeFormat: 'H:i' }, + }, + deathWeight: { + label: 'Weight (kg)', + allowBlank: false, + nullable: false, + }, + reason: { + allowBlank: false, + nullable: false, } }, 'study.necropsy': { - necropsyWeight: { - label: 'Weight (kg)' - }, date: { label: 'Exam Date', xtype: 'xdatetime', diff --git a/nirc_ehr/resources/web/nirc_ehr/panel/SnapshotPanel.js b/nirc_ehr/resources/web/nirc_ehr/panel/SnapshotPanel.js index 708d6b57..16bc553c 100644 --- a/nirc_ehr/resources/web/nirc_ehr/panel/SnapshotPanel.js +++ b/nirc_ehr/resources/web/nirc_ehr/panel/SnapshotPanel.js @@ -291,7 +291,7 @@ Ext4.define('NIRC_EHR.panel.SnapshotPanel', { var html = ''; var sep = ''; Ext4.each(animals, function(id) { - html += sep + '' + LABKEY.Utils.encodeHtml(id) + ''; + html += sep + '' + encodeURIComponent(id) + ''; sep = ', '; }); toSet['cagemates'] = html; @@ -346,4 +346,44 @@ Ext4.define('NIRC_EHR.panel.SnapshotPanel', { } }]); }, + + appendParentageResults: function(toSet, results){ + if (results){ + var parentMap = {}; + Ext4.each(results, function(row){ + var parent = row.parent; + var relationship = row.relationship; + + if (parent && relationship){ + var text = LABKEY.Utils.encodeHtml(relationship + ' - ' + parent); + + if (!parentMap[text]) + parentMap[text] = []; + + var method = row.method; + if (method){ + parentMap[text].push(LABKEY.Utils.encodeHtml(method)); + } + } + }, this); + + var values = []; + Ext4.Array.forEach(Ext4.Object.getKeys(parentMap).sort(), function(text){ + parentMap[text] = Ext4.unique(parentMap[text]); + var subject = text; + var textParts = text.split(' - '); + if (textParts.length > 1){ + subject = textParts[1]; + } + + values.push('' + encodeURIComponent(subject) + ''); + }, this); + + if (values.length) + toSet['parents'] = values.join('
'); + } + else { + toSet['parents'] = 'No data'; + } + }, }); \ No newline at end of file diff --git a/nirc_ehr/test/src/org.labkey.test/tests.nirc_ehr/NIRC_EHRTest.java b/nirc_ehr/test/src/org.labkey.test/tests.nirc_ehr/NIRC_EHRTest.java index 8e57226e..68e770dd 100644 --- a/nirc_ehr/test/src/org.labkey.test/tests.nirc_ehr/NIRC_EHRTest.java +++ b/nirc_ehr/test/src/org.labkey.test/tests.nirc_ehr/NIRC_EHRTest.java @@ -837,7 +837,8 @@ public void testDeathNecropsyForm() throws IOException, CommandException setFormElement(Locator.name("Id"), aliveAnimalId); _ext4Helper.selectComboBoxItem("Disposition:", "Euthaniasia (project)"); - + waitForElement(Locator.name("deathWeight")); + setFormElement(Locator.name("deathWeight"), "23"); Assert.assertFalse(isElementPresent(Locator.linkWithText("Submit Necropsy for Review"))); Assert.assertFalse(isElementPresent(Locator.linkWithText("Submit Final"))); submitForm("Submit Death", "Confirm"); @@ -861,13 +862,11 @@ public void testDeathNecropsyForm() throws IOException, CommandException beginAt(url); Ext4GridRef necropsy = _helper.getExt4GridForFormSection("Necropsy"); necropsy.expand(); - waitForElement(Locator.name("necropsyWeight")); - setFormElement(Locator.name("necropsyWeight"), "23"); scrollIntoView(Locator.linkContainingText("More Actions")); _ext4Helper.selectComboBoxItem("Physical Condition:", "Excellent"); - _ext4Helper.selectComboBoxItem("Reason for Examination:", "Natural Death"); _ext4Helper.selectComboBoxItem("Condition of Specimen:", "Fresh"); scrollIntoView(Locator.name("diagnosis")); + _helper.setDataEntryField("accessionNumber", "123"); _helper.setDataEntryField("identification", "Extra information"); _helper.setDataEntryField("grossAbnormalities", "Extra leg"); _helper.setDataEntryField("diagnosis", "Dead");