Use query parameters in alignment_summary queries

Author: bbimber

SequenceAnalysis/resources/queries/sequenceanalysis/alignment_summary_by_lineage.sql

@@ -1,20 +1,7 @@
-/*
- * Copyright (c) 2012 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.
- */
+PARAMETERS(AnalysisId INTEGER)
+
 select
-  (CAST(a.analysis_id as varchar) || '<>' || a.lineages) as key,
+  (CAST(AnalysisId as varchar) || '<>' || a.lineages) as key,
   a.analysis_id,
   a.lineages,
   max(a.totalLineages) as totalLineages,
@@ -25,13 +12,13 @@ select
   round(100 * (cast(sum(a.total) as float) / cast(max(a.total_reads) as float)), 2) as percent,
   group_concat(distinct a.haplotypesWithAllele) as haplotypesWithAllele,
 
-  CAST((select sum(s.total) as total FROM sequenceanalysis.alignment_summary s WHERE s.analysis_id = a.analysis_id AND s.rowid IN (
-      SELECT distinct asj.alignment_id from sequenceanalysis.alignment_summary_junction asj WHERE asj.ref_nt_id.locus = a.loci and asj.status = true
+  CAST((select sum(s.total) as total FROM sequenceanalysis.alignment_summary s WHERE s.analysis_id = AnalysisId AND s.rowid IN (
+      SELECT distinct asj.alignment_id from sequenceanalysis.alignment_summary_junction asj WHERE asj.analysis_id = AnalysisId AND asj.ref_nt_id.locus = a.loci and asj.status = true
     )
   ) as integer) as total_reads_from_locus,
 
-  round(100 * (cast(sum(a.total) as float) / cast((select sum(s.total) as total FROM sequenceanalysis.alignment_summary s WHERE s.analysis_id = a.analysis_id AND s.rowid IN (
-      SELECT distinct asj.alignment_id from sequenceanalysis.alignment_summary_junction asj WHERE asj.ref_nt_id.locus = a.loci and asj.status = true
+  round(100 * (cast(sum(a.total) as float) / cast((select sum(s.total) as total FROM sequenceanalysis.alignment_summary s WHERE s.analysis_id = AnalysisId AND s.rowid IN (
+      SELECT distinct asj.alignment_id from sequenceanalysis.alignment_summary_junction asj WHERE asj.analysis_id = AnalysisId AND asj.ref_nt_id.locus = a.loci and asj.status = true
     )
   ) as float)), 2) as percent_from_locus,
   group_concat(distinct a.rowid, ',') as rowids
@@ -47,15 +34,16 @@ FROM (
     group_concat(distinct coalesce(j.ref_nt_id.locus, j.ref_nt_id.name), chr(10)) as loci,
 
     total,
-    cast((select sum(total) as total FROM sequenceanalysis.alignment_summary s WHERE s.analysis_id = a.analysis_id) as integer) as total_reads,
+    cast((select sum(total) as total FROM sequenceanalysis.alignment_summary s WHERE s.analysis_id = AnalysisId) as integer) as total_reads,
     group_concat(distinct hs.haplotype, chr(10)) as haplotypesWithAllele
 
   from sequenceanalysis.alignment_summary a
-  join sequenceanalysis.alignment_summary_junction j ON (j.alignment_id = a.rowid and j.status = true)
+  join sequenceanalysis.alignment_summary_junction j ON (j.analysis_id = AnalysisId AND j.alignment_id = a.rowid and j.status = true)
   left join sequenceanalysis.haplotype_sequences hs ON ((
     (hs.name = j.ref_nt_id.lineage AND hs.type = 'Lineage') OR
     (hs.name = j.ref_nt_id.name AND hs.type = 'Allele')
   ) AND hs.haplotype.datedisabled IS NULL)
+  WHERE a.analysis_id = AnalysisId
   group by a.analysis_id, a.rowid, a.total
 
 ) a

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

@@ -1,18 +1,5 @@
-/*
- * Copyright (c) 2012 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.
- */
+PARAMETERS(AnalysisId INTEGER)
+
 select
   a.analysis_id,
   a.alleles,
@@ -36,13 +23,13 @@ select
   group_concat(a.rowid, ',') as rowids,
   group_concat(distinct a.haplotypesWithAllele) as haplotypesWithAllele,
 
-  CAST((select sum(s.total) as total FROM sequenceanalysis.alignment_summary s WHERE s.analysis_id = a.analysis_id AND s.rowid IN (
-      SELECT distinct asj.alignment_id from sequenceanalysis.alignment_summary_junction asj WHERE asj.ref_nt_id.locus = a.loci and asj.status = true
+  CAST((select sum(s.total) as total FROM sequenceanalysis.alignment_summary s WHERE s.analysis_id = AnalysisId AND s.rowid IN (
+      SELECT distinct asj.alignment_id from sequenceanalysis.alignment_summary_junction asj WHERE asj.analysis_id = AnalysisId AND asj.ref_nt_id.locus = a.loci and asj.status = true
     )
   ) as INTEGER) as total_reads_from_locus,
 
-  round(100 * (cast(sum(a.total) as float) / CASE WHEN count(a.lineages) = 0 THEN max(a.total_reads) ELSE cast((select sum(s.total) as total FROM sequenceanalysis.alignment_summary s WHERE s.analysis_id = a.analysis_id AND s.rowid IN (
-      SELECT distinct asj.alignment_id from sequenceanalysis.alignment_summary_junction asj WHERE asj.ref_nt_id.locus = a.loci and asj.status = true
+  round(100 * (cast(sum(a.total) as float) / CASE WHEN count(a.lineages) = 0 THEN max(a.total_reads) ELSE cast((select sum(s.total) as total FROM sequenceanalysis.alignment_summary s WHERE s.analysis_id = AnalysisId AND s.rowid IN (
+      SELECT distinct asj.alignment_id from sequenceanalysis.alignment_summary_junction asj WHERE asj.analysis_id = AnalysisId AND asj.ref_nt_id.locus = a.loci and asj.status = true
     )
   ) as float) END), 2) as percent_from_locus,
   max(lastModified) as lastModified,
@@ -67,14 +54,15 @@ FROM (
     total_forward,
     total_reverse,
     valid_pairs,
-    (select sum(total) as total FROM sequenceanalysis.alignment_summary s WHERE s.analysis_id = a.analysis_id) as total_reads,
+    (select sum(total) as total FROM sequenceanalysis.alignment_summary s WHERE s.analysis_id = AnalysisId) as total_reads,
     max(j.modified) as lastModified
   from sequenceanalysis.alignment_summary a
-  left join sequenceanalysis.alignment_summary_junction j ON (j.alignment_id = a.rowid and j.status = true)
+  left join sequenceanalysis.alignment_summary_junction j ON (j.analysis_id = AnalysisId AND j.alignment_id = a.rowid and j.status = true)
   left join sequenceanalysis.haplotype_sequences hs ON ((
     (hs.name = j.ref_nt_id.lineage AND hs.type = 'Lineage') OR
     (hs.name = j.ref_nt_id.name AND hs.type = 'Allele')
   ) AND hs.haplotype.datedisabled IS NULL)
+  WHERE a.analysis_id = AnalysisId
   group by a.analysis_id, a.rowid, a.total, total_forward, total_reverse, valid_pairs
 
 ) a

SequenceAnalysis/resources/queries/sequenceanalysis/alignment_summary_by_lineage_pivoted.sql

@@ -523,15 +523,7 @@
                     <onClick>SequenceAnalysis.window.RunExportWindow.downloadFilesForAnalysis(dataRegionName);</onClick>
                 </item>
                 <item text="Alignment Reports">
-                    <item text="Alignment Summary">
-                        <onClick>SequenceAnalysis.Buttons.viewQuery(dataRegionName, {queryName: 'alignment_summary_grouped'})</onClick>
-                    </item>
-                    <item text="Alignment Summary, By Lineage">
-                        <onClick>SequenceAnalysis.Buttons.viewQuery(dataRegionName, {queryName: 'alignment_summary_by_lineage'})</onClick>
-                    </item>
-                    <item text="Alignment Summary, Pivoted By Lineage">
-                        <onClick>SequenceAnalysis.Buttons.viewAlignmentsPivoted(dataRegionName)</onClick>
-                    </item>
+<!--                    TODO: use analysisId-->
                     <item text="Matching Haplotypes">
                         <onClick>SequenceAnalysis.Buttons.viewQuery(dataRegionName, {queryName: 'haplotypeMatches'})</onClick>
                     </item>