Create data validation report for animal parentage

ehr/resources/queries/study/parentsBothDamAndSire.sql

@@ -0,0 +1,30 @@
+SELECT t.Id as Parent, GROUP_CONCAT(t.DamChildren, ',') as DamChildren, GROUP_CONCAT(t.SireChildren, ',') as SireChildren FROM
+(
+
+SELECT d.Id, d.DamChildren, s.SireChildren FROM (
+
+SELECT Id as DamChildren,
+dam as Id
+FROM demographics
+WHERE dam IN (
+SELECT Distinct dam as Id 
+FROM demographics
+WHERE dam IN (SELECT Distinct sire FROM demographics))
+) d   
+
+JOIN
+
+(SELECT * FROM (
+
+SELECT Id as SireChildren,
+sire as Id
+FROM demographics
+WHERE sire IN (
+SELECT Distinct dam as Id 
+FROM demographics
+WHERE dam IN (SELECT Distinct sire FROM demographics))
+) si ) s   
+
+ON s.Id = d.Id   
+) t
+GROUP BY t.Id

ehr/resources/queries/study/parentsDifferentSpecies.sql

@@ -0,0 +1,15 @@
+SELECT * FROM (
+SELECT d1.Id,
+d1.Dataset.Demographics.gender,
+d1.Dataset.Demographics.species,
+d1.Parents.dam,
+d1.Parents.dam.Demographics.species as damSpecies,
+d1.Parents.sire,
+d1.Parents.sire.Demographics.species as sireSpecies,
+CASE WHEN (d1.Parents.dam.Demographics.species IS NOT NULL AND d1.Parents.dam.Demographics.species != d1.Dataset.Demographics.species) OR (d1.Parents.sire.Demographics.species IS NOT NULL AND d1.Parents.sire.Demographics.species != d1.Dataset.Demographics.species)
+THEN TRUE
+ELSE FALSE
+END as parentSpeciesMismatch
+FROM study.Animal d1
+) d2
+WHERE d2.parentSpeciesMismatch = TRUE

ehr/resources/queries/study/parentsWrongGender.sql

@@ -0,0 +1,15 @@
+SELECT * FROM (
+SELECT d1.Id,
+d1.Dataset.Demographics.gender,
+d1.Dataset.Demographics.species,
+d1.Parents.dam,
+d1.Parents.dam.Demographics.gender as damSex,
+d1.Parents.sire,
+d1.Parents.sire.Demographics.gender as sireSex,
+CASE WHEN (d1.Parents.dam.Demographics.gender.code IS NOT NULL AND d1.Parents.dam.Demographics.gender.code != 'f') OR (d1.Parents.sire.Demographics.gender.code IS NOT NULL AND d1.Parents.sire.Demographics.gender.code != 'm')
+THEN TRUE
+ELSE FALSE
+END as parentSexMismatch
+FROM study.Animal d1
+) d2
+WHERE d2.parentSexMismatch = TRUE

ehr/resources/queries/study/parentsYoungerThanOffspring.sql

@@ -0,0 +1,15 @@
+SELECT * FROM (
+SELECT 
+dem.Id,
+dem.gender,
+dem.species,
+dem.birth,
+dem.dam,
+damDem.birth as damBirth,
+dem.sire,
+sireDem.birth as sireBirth
+FROM demographics dem
+LEFT JOIN demographics damDem ON dem.dam = damDem.Id
+LEFT JOIN demographics sireDem ON dem.sire = sireDem.Id
+   ) t
+WHERE (t.birth <= t.damBirth OR t.birth <= t.sireBirth)

ehr/resources/views/begin.html

@@ -86,6 +86,7 @@
             {header: 'Misc',
             items: [
                 {name: 'About the EHR Project', url: '<%=contextPath%>/project' + ctx['EHRStudyContainer'] + '/About The EHR/begin.view?'},
+                {name: 'Data Validation', url: '<%=contextPath%>/ehr' + ctx['EHRStudyContainer'] + '/dataValidationReport.view?'},
                 {name: 'Compare Lists of Animals', url: '<%=contextPath%>/ehr' + ctx['EHRStudyContainer'] + '/utilities.view?'},
                 {name: 'Run SQL Directly', url: '<%=contextPath%>/ehr' + ctx['EHRStudyContainer'] + '/executeSql.view?'},
                 {name: 'Search Center SNOMED Codes', url: '<%=contextPath%>/query' + ctx['EHRStudyContainer'] + '/executeQuery.view?schemaName=ehr_lookups&query.queryName=snomed'},
@@ -120,4 +121,4 @@
 
 }
 
-</script>
+</script>

ehr/resources/views/dataValidationReport.html

@@ -0,0 +1,71 @@
+<p>
+    Each of the below data grids identifies issues present in the animal colony data that would prevent the pedigree plots from working correctly.<br>
+    To correct any data consistency issues, use this report as a reference for identifying the data issues, and then correct them on the demographics dataset, which can be access with the below button.<br>
+</p>
+<button onclick = "linkBrowseData()">
+    Correct Data
+</button>
+<p><br></p>
+<table>
+    <tr>
+        <td>
+            <div name="webpart" id='parentsDifferentSpeciesReport' />
+        </td>
+        <td>
+            <div name="webpart" id='parentsBothDamAndSireReport' />
+        </td>
+    </tr>
+    <tr>
+        <td>
+            <div name="webpart" id='parentsWrongGenderReport' />
+        </td>
+        <td>
+            <div name="webpart" id='parentsYoungerThanOffspringReport' />
+        </td>
+    </tr>
+</table>
+
+<script>
+
+function linkBrowseData() {
+    window.location = LABKEY.ActionURL.buildURL(
+        "ehr",
+        "updateQuery",
+        LABKEY.ActionURL.getContainer(),
+        {
+            schemaName: "study",
+            queryName: "demographics",
+            returnUrl: window.location
+        }
+        );
+}
+
+new LABKEY.QueryWebPart({
+            renderTo: 'parentsDifferentSpeciesReport',
+            title: 'Parents that are wrong species',
+            schemaName: 'study',
+            queryName: 'parentsDifferentSpecies'
+});
+
+new LABKEY.QueryWebPart({
+            renderTo: 'parentsBothDamAndSireReport',
+            title: 'Parents that are listed as both dam and sire',
+            schemaName: 'study',
+            queryName: 'parentsBothDamAndSire'
+});
+
+new LABKEY.QueryWebPart({
+            renderTo: 'parentsWrongGenderReport',
+            title: 'Parents that are listed as both dam and sire',
+            schemaName: 'study',
+            queryName: 'parentsWrongGender'
+});
+
+new LABKEY.QueryWebPart({
+            renderTo: 'parentsYoungerThanOffspringReport',
+            title: 'Parents that are listed as both dam and sire',
+            schemaName: 'study',
+            queryName: 'parentsYoungerThanOffspring'
+});
+
+</script>

ehr/resources/views/dataValidationReport.view.xml

@@ -0,0 +1,5 @@
+<view xmlns="http://labkey.org/data/xml/view" frame="none" title="Data Validation Report">
+    <dependencies>
+        <dependency path="ehr.context" />
+    </dependencies>
+</view>