Body condition scores

snprc_ehr/resources/data/reports.tsv

@@ -69,4 +69,5 @@ Exposure History	Exposures	query	Exposure History	true		study	ExpExposureHistory
 Procedure History	Exposures	query	Procedure History	true		study	ExpProcedureHistory			Date	false	false		qcstate/publicdata	Exposure procedures data
 Research Treatments	Exposures	query	Research Treatments	true		study	ExpResearchTreatments			Date	false	false		qcstate/publicdata	Research Treatments data
 Abnormal Behavior	Behavior	query	Abnormal Behavior	true		study	BehaviorAbnormalSummary			Date	false	false		qcstate/publicdata	Abnormal behavoir detail data
-Vaccines	Exposures	query	Vaccines	true		study	ExpVaccines			Date	false	false		qcstate/publicdata	Exposure vaccines data
+Vaccines	Exposures	query	Vaccines	true		study	ExpVaccines			Date	false	false		qcstate/publicdata	Exposure vaccines data
+Body Condition Score	Clinical	query	Body Condition Score	true		study	BodyConditionScores	

snprc_ehr/resources/queries/study/BodyConditionScores.query.xml

@@ -0,0 +1,50 @@
+<query xmlns="http://labkey.org/data/xml/query">
+    <metadata>
+        <tables xmlns="http://labkey.org/data/xml">
+            <table tableName="BodyConditionScores" tableDbType="NOT_IN_DB">
+                <tableTitle>Body Condition Scores</tableTitle>
+                <columns>
+                    <column columnName="Id">
+                        <isKeyField>true</isKeyField>
+                        <fk>
+                            <fkDbSchema>study</fkDbSchema>
+                            <fkTable>animal</fkTable>
+                            <fkColumnName>Id</fkColumnName>
+                        </fk>
+                    </column>
+                    <column columnName="BcsDate">
+                        <columnTitle>BCS Date</columnTitle>
+                    </column>
+                    <column columnName="BCS">
+                        <columnTitle>Body Condition Score</columnTitle>
+                    </column>
+                    <column columnName="BCSValue">
+                        <columnTitle>Numeric BCS Value</columnTitle>
+                    </column>
+                    <column columnName="Created">
+                        <isHidden>true</isHidden>
+                    </column>
+                    <column columnName="CreatedBy">
+                        <isHidden>true</isHidden>
+                        <fk>
+                            <fkColumnName>UserId</fkColumnName>
+                            <fkTable>Users</fkTable>
+                            <fkDbSchema>core</fkDbSchema>
+                        </fk>
+                    </column>
+                    <column columnName="Modified">
+                        <isHidden>true</isHidden>
+                    </column>
+                    <column columnName="ModifiedBy">
+                        <isHidden>true</isHidden>
+                        <fk>
+                            <fkColumnName>UserId</fkColumnName>
+                            <fkTable>Users</fkTable>
+                            <fkDbSchema>core</fkDbSchema>
+                        </fk>
+                    </column>
+                </columns>
+            </table>
+        </tables>
+    </metadata>
+</query>

snprc_ehr/resources/queries/study/BodyConditionScores.sql

@@ -0,0 +1,17 @@
+
+SELECT
+    p.id as Id,
+    p.date as BcsDate,
+    p.procNarrative as BCS,
+    case when substring(p.procNarrative, 7, 1) = ' ' then  cast(substring (p.procNarrative, 6,1) as float)
+         else cast( substring (p.procNarrative, 6,3) as float )
+         end as BCSValue,
+    p.Created,
+    p.CreatedBy,
+    p.Modified,
+    p.ModifiedBy
+
+FROM study.procedure AS p
+WHERE p.qcstate.publicdata = true
+  AND p.pkgId.categories like '%BCS%'
+  AND p.procNarrative <> 'BCS: error'

snprc_ehr/resources/queries/study/BrowseDataSets.sql

@@ -60,3 +60,5 @@ UNION
 select 'study' as schema, 'Misc' as CategoryId,'Animals with Genetic data' as Label, 'GenDemohasData' as Name,  true as ShowByDefault, true as isAnimal
 UNION
 select 'study' as schema, 'Behavior' as CategoryId,'Abnormal Behavior' as Label, 'BehaviorAbnormalAll' as Name,  true as ShowByDefault, true as isAnimal
+UNION
+select 'study' as schema, 'Clinical' as CategoryId,'Body Condition Scores' as Label, 'BodyConditionScores' as Name,  true as ShowByDefault, true as isAnimal

snprc_ehr/resources/queries/study/demographicsLastBCS.sql

@@ -0,0 +1,12 @@
+
+SELECT
+    p.id as Id,
+    p.date as BcsDate,
+    p.procNarrative as LastBCS,
+    p.QCState
+
+FROM study.procedure AS p
+WHERE p.qcstate.publicdata = true
+AND p.pkgId.categories like '%BCS%'
+and p.date = (select max(p2.date) from study.procedure as p2
+                where p2.id = p.id and p2.pkgId.categories like '%BCS%')

snprc_ehr/resources/web/snprc_ehr/DemographicsRecord.js

@@ -201,6 +201,10 @@ EHR.DemographicsRecord = function(data){
 
         getSourceRecord: function(){
             return data.source;
-        }
+        },
+
+        getLastBcs: function() {
+            return data['LastBCS'];
+        },
     }
-}
+}

snprc_ehr/resources/web/snprc_ehr/snprcOverrides.js

@@ -110,6 +110,27 @@ Ext4.override(EHR.panel.SnapshotPanel, {
         toSet['idHistories'] = text.length ? '<table>' + text.join('') + '</table>' : null;
     },
 
+    appendLastBcs: function (toSet, results) {
+        var text = [];
+        if (results) {
+            var rows = [];
+            Ext4.each(results, function (row) {
+                var d = LDK.ConvertUtils.parseDate(row['BcsDate'], LABKEY.extDefaultDateFormat);
+                var newRow = {
+                    BcsDate: d.format(LABKEY.extDefaultDateFormat),
+                    LastBCS: row['LastBCS']
+                };
+                rows.push(newRow);
+            }, this);
+
+            Ext4.each(rows, function (r) {
+                text.push('<tr><td nowrap>' + r.BcsDate + ':' + '</td><td style="padding-left: 5px;" nowrap>' + r.LastBCS + '</td></tr>');
+            }, this);
+        }
+
+        toSet['LastBCS'] = text.length ? '<table>' + text.join('') + '</table>' : null;
+    },
+
 
     appendCurrentAccountsResults: function (toSet, results) {
         var text = [];
@@ -337,7 +358,11 @@ Ext4.override(EHR.panel.SnapshotPanel, {
                         xtype: 'displayfield',
                         fieldLabel: 'Id History',
                         name: 'idHistories'
-                    }]
+                    },{
+                        xtype: 'displayfield',
+                        fieldLabel: 'Last BCS',
+                        name: 'LastBCS'
+                    },]
                 }]
             }]
         }];
@@ -499,6 +524,7 @@ Ext4.override(EHR.panel.SnapshotPanel, {
 
         this.appendFlags(toSet, results.getActiveFlags());
         this.appendTBResults(toSet, results.getTBRecord());
+        this.appendLastBcs(toSet, results.getLastBcs());
 
         if (this.showExtendedInformation) {
             this.appendBirthResults(toSet, results.getBirthInfo(), results.getBirth());
@@ -533,4 +559,4 @@ Ext4.override(EHR.panel.SnapshotPanel, {
 //             }]
 //         }]
 //     }
-// });
+// });

snprc_ehr/src/org/labkey/snprc_ehr/SNPRC_EHRModule.java

@@ -64,6 +64,7 @@
 import org.labkey.snprc_ehr.demographics.ActiveFlagsDemographicsProvider;
 import org.labkey.snprc_ehr.demographics.BirthDemographicsProvider;
 import org.labkey.snprc_ehr.demographics.CurrentAccountsDemographicsProvider;
+import org.labkey.snprc_ehr.demographics.LastBcsDemographicsProvider;
 import org.labkey.snprc_ehr.demographics.CurrentDietDemographicsProvider;
 import org.labkey.snprc_ehr.demographics.CurrentPedigreeDemographicsProvider;
 import org.labkey.snprc_ehr.demographics.DeathsDemographicsProvider;
@@ -199,6 +200,7 @@ protected void doStartupAfterSpringConfig(ModuleContext moduleContext)
         EHRService.get().registerDemographicsProvider(new ActiveFlagsDemographicsProvider(this));
         EHRService.get().registerDemographicsProvider(new MhcSummaryDemographicsProvider(this));
         EHRService.get().registerDemographicsProvider(new LastHousingDemographicsProvider(this));
+        EHRService.get().registerDemographicsProvider(new LastBcsDemographicsProvider(this));
 
         EHRService.get().registerReportLink(EHRService.REPORT_LINK_TYPE.housing, "Find Animals Housed In A Given Room/Cage At A Specific Time", this, DetailsURL.fromString("/ehr/housingOverlaps.view?groupById=1"), "Commonly Used Queries");
         EHRService.get().registerReportLink(EHRService.REPORT_LINK_TYPE.animalSearch, "Population Summary By Species, Gender and Age", this, DetailsURL.fromString("/query/executeQuery.view?schemaName=study&query.queryName=colonyPopulationByAge"), "Other Searches");
@@ -370,4 +372,4 @@ public WebPartView getWebPartView(@NotNull ViewContext portalCtx, @NotNull Porta
 
         return webPartFactories;
     }
-}
+}

snprc_ehr/src/org/labkey/snprc_ehr/demographics/LastBcsDemographicsProvider.java

@@ -0,0 +1,53 @@
+package org.labkey.snprc_ehr.demographics;
+
+
+import org.labkey.api.data.CompareType;
+import org.labkey.api.data.SimpleFilter;
+import org.labkey.api.data.Sort;
+import org.labkey.api.ehr.demographics.AbstractListDemographicsProvider;
+import org.labkey.api.module.Module;
+import org.labkey.api.query.FieldKey;
+
+import java.util.Collection;
+import java.util.HashSet;
+import java.util.Set;
+
+/**
+ * Created by thawkins on 7/6/2020.
+ */
+
+public class LastBcsDemographicsProvider extends AbstractListDemographicsProvider
+{
+
+    public LastBcsDemographicsProvider(Module owner)
+    {
+        super(owner, "study", "demographicsLastBCS", "LastBCS");
+        _supportsQCState = false;
+    }
+
+    @Override
+    protected Set<FieldKey> getFieldKeys()
+    {
+        Set<FieldKey> keys = new HashSet<>();
+        keys.add(FieldKey.fromString("Id"));
+        keys.add(FieldKey.fromString("BcsDate"));
+        keys.add(FieldKey.fromString("LastBCS"));
+
+        return keys;
+    }
+
+    @Override
+    protected Sort getSort()
+    {
+        return new Sort("-Id");
+    }
+
+    @Override
+    protected SimpleFilter getFilter(Collection<String> ids)
+    {
+        SimpleFilter filter = super.getFilter(ids);
+        filter.addCondition(FieldKey.fromString("qcstate/publicData"), true, CompareType.EQUAL);
+
+        return filter;
+    }
+}

snprc_ehr/src/org/labkey/snprc_ehr/table/SNPRC_EHRCustomizer.java

@@ -460,6 +460,13 @@ private void customizeAnimalTable(AbstractTableInfo ds)
             col.setDescription("Queries the most recent TB date for the animal.");
             ds.addColumn(col);
         }
+        if (ds.getColumn("LastBCS") == null)
+        {
+            var col = getWrappedCol(us, ds, "LastBCS", "demographicsLastBCS", "Id", "Id");
+            col.setLabel("Most Recent BCS");
+            col.setDescription("Queries the most recent BCS value for the animal.");
+            ds.addColumn(col);
+        }
 
         // Change label and description 8/31/2017 tjh
         if (ds.getColumn("MostRecentArrival") != null)
@@ -480,6 +487,7 @@ private void customizeAnimalTable(AbstractTableInfo ds)
             col.setDescription("Calculates the earliest and most recent departure per animal, if applicable, and most recent acquisition.");
             ds.addColumn(col);
         }
+
         // Because of performance, changed to study based dataset ETLed from genetics folder 10/14/19 srr
         if (genetics != null)
         {
@@ -533,4 +541,4 @@ else if (targetTable.getSchema() != null)
         }
         return realTable;
     }
-}
+}