Skip to content

Use query parameters in alignment_summary queries #371

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
bbimber merged 3 commits into from
Jan 17, 2026
Merged

Use query parameters in alignment_summary queries #371

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
ec71a72
Use query parameters in alignment_summary queries
bbimber Jan 16, 2026
35e3d2c
Remove TODOs
bbimber Jan 16, 2026
0dbaa41
Bugfix
bbimber Jan 16, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
32 changes: 10 additions & 22 deletions SequenceAnalysis/resources/queries/sequenceanalysis/alignment_summary_by_lineage.sql
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -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,
Expand All @@ -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
Expand All @@ -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
Expand Down
9 changes: 0 additions & 9 deletions ...nalysis/resources/queries/sequenceanalysis/alignment_summary_by_lineage_pivoted.query.xml
View file
Open in desktop

This file was deleted.

9 changes: 0 additions & 9 deletions SequenceAnalysis/resources/queries/sequenceanalysis/alignment_summary_by_lineage_pivoted.sql
View file
Open in desktop

This file was deleted.

30 changes: 9 additions & 21 deletions SequenceAnalysis/resources/queries/sequenceanalysis/alignment_summary_grouped.sql
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -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,
Expand All @@ -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,
Expand All @@ -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
Expand Down
11 changes: 1 addition & 10 deletions SequenceAnalysis/resources/schemas/sequenceanalysis.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -523,17 +523,8 @@
<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>
<item text="Matching Haplotypes">
<onClick>SequenceAnalysis.Buttons.viewQuery(dataRegionName, {queryName: 'haplotypeMatches'})</onClick>
<onClick>SequenceAnalysis.Buttons.viewMatchingHaplotypes(dataRegionName)</onClick>
</item>
<item text="View Coverage">
<onClick>SequenceAnalysis.Buttons.viewQuery(dataRegionName, {queryName: 'sequence_coverage'})</onClick>
Expand Down
Loading