add metrics pivot column to analyses table

Author: bbimber

SequenceAnalysis/resources/queries/sequenceanalysis/quality_metrics_analyses_pivoted.query.xml

@@ -0,0 +1,14 @@
+<query xmlns="http://labkey.org/data/xml/query">
+    <metadata>
+        <tables xmlns="http://labkey.org/data/xml">
+            <table tableName="quality_metrics_analyses_pivoted" tableDbType="TABLE">
+                <tableTitle>Quality Metrics By Analysis</tableTitle>
+                <columns>
+                    <column columnName="analysis_id">
+                        <isKeyField>true</isKeyField>
+                    </column>
+                </columns>
+            </table>
+        </tables>
+    </metadata>
+</query>

SequenceAnalysis/resources/queries/sequenceanalysis/quality_metrics_analyses_pivoted.sql

@@ -0,0 +1,13 @@
+select
+  analysis_id,
+  max(readset) as readset,
+  --container,
+  max(category) as category,
+  count(*) as records,
+  metricName,
+  avg(metricValue) as metricValue
+
+from sequenceanalysis.quality_metrics q
+where (category is null or category not in ('FIRST_OF_PAIR', 'SECOND_OF_PAIR'))
+group by analysis_id, metricName
+pivot metricValue by metricName

SequenceAnalysis/resources/queries/sequenceanalysis/quality_metrics_pivoted.query.xml

@@ -2,7 +2,7 @@
     <metadata>
         <tables xmlns="http://labkey.org/data/xml">
             <table tableName="quality_metrics_pivoted" tableDbType="TABLE">
-                <tableTitle>Quality Metrics</tableTitle>
+                <tableTitle>Quality Metrics By File</tableTitle>
                 <columns>
                     <column columnName="dataId">
                         <isKeyField>true</isKeyField>

SequenceAnalysis/resources/schemas/sequenceanalysis.xml

@@ -484,6 +484,15 @@
                 <columnTitle>SRA Run</columnTitle>
                 <url>https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=${sra_accession}</url>
             </column>
+            <column columnName="metrics" wrappedColumnName="rowid">
+                <columnTitle>Quality Metrics</columnTitle>
+                <isUnselectable>true</isUnselectable>
+                <fk>
+                    <fkDbSchema>sequenceanalysis</fkDbSchema>
+                    <fkTable>quality_metrics_analyses_pivoted</fkTable>
+                    <fkColumnName>analysis_id</fkColumnName>
+                </fk>
+            </column>
         </columns>
         <buttonBarOptions includeStandardButtons="false">
             <includeScript>laboratory.context</includeScript>