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

Use query parameters in alignment_summary queries #210

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3447205
Use query parameters in alignment_summary queries
bbimber Jan 16, 2026
38595b7
Remove TODO
bbimber Jan 16, 2026
d3eebb0
Remove TODOs
bbimber Jan 16, 2026
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8 changes: 4 additions & 4 deletions GenotypeAssays/resources/views/bulkHaplotype.html
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Original file line number Diff line number Diff line change
@@ -1,10 +1,10 @@
<script type="text/javascript" nonce="<%=scriptNonce%>">

Ext4.onReady(function () {
var analysisIds = LABKEY.ActionURL.getParameter('analysisIds');
var analysisId = LABKEY.ActionURL.getParameter('analysisId');

if (!analysisIds) {
alert('Must Provide At Least One Analysis Id');
if (!analysisId) {
alert('Must Provide An Analysis Id');
return;
}

Expand All @@ -15,7 +15,7 @@
title: 'Haplotype Matches',
items: [{
xtype: 'genotypeassays-haplotypepanel',
analysisIds: analysisIds.split(';'),
analysisIds: analysisId,
showCheckBoxes: true
}]
}).render(webpart.wrapperDivId);
Expand Down
14 changes: 9 additions & 5 deletions GenotypeAssays/resources/views/sbtReview.html
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Expand Up @@ -155,13 +155,15 @@
allowHeaderLock: false,
schemaName: 'sequenceanalysis',
queryName: 'alignment_summary_grouped',
//viewName: 'With Haplotype Matches',
viewName: 'With Haplotype Matches',
//sort: '-percent',
containerPath: Laboratory.Utils.getQueryContainerPath(),
filterArray: [LABKEY.Filter.create('analysis_id', analysisId, LABKEY.Filter.Types.EQUAL)],
removeableFilters: [
LABKEY.Filter.create('percent_from_locus', 0.25, LABKEY.Filter.Types.GTE)
],
parameters: {
AnalysisId: analysisId
},
scope: this,
success: this.onDataRegionLoad
})
Expand All @@ -173,15 +175,17 @@
allowHeaderLock: false,
schemaName: 'sequenceanalysis',
queryName: 'alignment_summary_by_lineage',
//viewName: 'With Haplotype Matches',
viewName: 'With Haplotype Matches',
sort: '-percent',
containerPath: Laboratory.Utils.getQueryContainerPath(),
filterArray: [LABKEY.Filter.create('analysis_id', analysisId, LABKEY.Filter.Types.EQUAL)],
removeableFilters: [
LABKEY.Filter.create('percent_from_locus', 0.25, LABKEY.Filter.Types.GTE),
LABKEY.Filter.create('total_reads', 5, LABKEY.Filter.Types.GT),
LABKEY.Filter.create('totalLineages', 1, LABKEY.Filter.Types.EQUAL)
],
parameters: {
AnalysisId: analysisId
},
scope: this,
success: this.onDataRegionLoad
})
Expand All @@ -191,7 +195,7 @@
title: 'Haplotype Matches',
items: [{
xtype: 'genotypeassays-haplotypepanel',
analysisIds: [analysisId]
analysisId: [analysisId]
}]
},{
xtype: 'ldk-querypanel',
Expand Down
7 changes: 6 additions & 1 deletion GenotypeAssays/resources/web/genotypeassays/buttons.js
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Expand Up @@ -21,9 +21,14 @@ GenotypeAssays.buttons = new function(){
return;
}

if (checked.length !== 1) {
alert('Only one row at a time can be selected');
return;
}

var newForm = Ext4.DomHelper.append(document.getElementsByTagName('body')[0],
'<form method="POST" action="' + LABKEY.ActionURL.buildURL("genotypeassays", "bulkHaplotype", null) + '">' +
'<input type="hidden" name="analysisIds" value="' + Ext4.htmlEncode(checked.join(';')) + '" />' +
'<input type="hidden" name="analysisId" value="' + Ext4.htmlEncode(checked[0]) + '" />' +
'</form>');
newForm.submit();
}
Expand Down
15 changes: 9 additions & 6 deletions GenotypeAssays/resources/web/genotypeassays/panel/HaplotypePanel.js
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
Ext4.define('GenotypeAssays.panel.HaplotypePanel', {
extend: 'Ext.panel.Panel',
alias: 'widget.genotypeassays-haplotypepanel',
analysisIds: null,
analysisId: null,
showCheckBoxes: false,

initComponent: function(){
Expand Down Expand Up @@ -266,10 +266,11 @@ Ext4.define('GenotypeAssays.panel.HaplotypePanel', {
}
}, this);

Ext4.Msg.confirm('Publish Selected?', 'You have chosen to published the following haplotypes:<br><br>' + (haplotypeNames.length > 8 ? 'Too many to display' : haplotypeNames.join('<br>')) + '<br><br>Continue?', function (val) {
Ext4.Msg.confirm('Publish Selected?', 'You have chosen to publish the following haplotypes:<br><br>' + (haplotypeNames.length > 8 ? 'Too many to display' : haplotypeNames.join('<br>')) + '<br><br>Continue?', function (val) {
if (val == 'yes') {
Ext4.create('GenotypeAssays.window.PublishResultsWindow', {
actionName: 'cacheHaplotypes',
analysisId: this.analysisId,
json: json
}).show();
}
Expand Down Expand Up @@ -460,10 +461,12 @@ Ext4.define('GenotypeAssays.panel.HaplotypePanel', {
schemaName: 'sequenceanalysis',
queryName: 'alignment_summary_by_lineage',
columns: 'analysis_id,analysis_id/readset,analysis_id/readset/subjectId,lineages,loci,total,total_reads,percent,total_reads_from_locus,percent_from_locus',
parameters: {
AnalysisId: this.analysisId
},
apiVersion: 13.2,
scope: this,
filterArray: [
LABKEY.Filter.create('analysis_id', this.analysisIds.join(';'), LABKEY.Filter.Types.IN),
LABKEY.Filter.create('percent_from_locus', minPct || 0, LABKEY.Filter.Types.GTE)
],
failure: LDK.Utils.getErrorCallback(),
Expand Down Expand Up @@ -502,9 +505,9 @@ Ext4.define('GenotypeAssays.panel.HaplotypePanel', {
sort: 'analysis_id',
apiVersion: 13.2,
scope: this,
filterArray: [
LABKEY.Filter.create('analysis_id', this.analysisIds.join(';'), LABKEY.Filter.Types.IN)
],
parameters: {
AnalysisId: this.analysisId
},
failure: LDK.Utils.getErrorCallback(),
success: function(results){
this.lineageToAlleleMap = {};
Expand Down
25 changes: 10 additions & 15 deletions GenotypeAssays/resources/web/genotypeassays/window/PublishResultsWindow.js
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Original file line number Diff line number Diff line change
Expand Up @@ -11,26 +11,20 @@ Ext4.define('GenotypeAssays.window.PublishResultsWindow', {
return;
}

const analysisId = dr.getParameters()?.AnalysisId;
if (!analysisId) {
Ext4.Msg.alert('Error', 'Error: unable to find analysisId. This should not occur.');
LDK.Assert.assertNotEmpty('Unable to find AnalysisId parameter from the DataRegion in PublishResultsWindow');

return;
}

Ext4.create('GenotypeAssays.window.PublishResultsWindow', {
dataRegionName: dataRegionName,
analysisId: analysisId,
actionName: 'cacheAnalyses'
}).show();
}

// haplotypeButtonHandler: function(dataRegionName){
// var dr = LABKEY.DataRegions[dataRegionName];
// LDK.Assert.assertNotEmpty('Unable to find dataregion in PublishResultsWindow', dr);
//
// if (!dr.getChecked().length) {
// Ext4.Msg.alert('Error', 'No rows selected');
// return;
// }
//
// Ext4.create('GenotypeAssays.window.PublishResultsWindow', {
// dataRegionName: dataRegionName,
// actionName: 'cacheHaplotypes'
// }).show();
// }
},

initComponent: function(){
Expand Down Expand Up @@ -122,6 +116,7 @@ Ext4.define('GenotypeAssays.window.PublishResultsWindow', {
scope: this,
jsonData: {
alleleNames: alleleNames,
analysisId: this.analysisId,
json: Ext4.encode(this.json),
protocolId: protocol
},
Expand Down
13 changes: 12 additions & 1 deletion GenotypeAssays/src/org/labkey/genotypeassays/GenotypeAssaysController.java
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Original file line number Diff line number Diff line change
Expand Up @@ -133,7 +133,7 @@ public ApiResponse execute(CacheAnalysesForm form, BindException errors)
}

String[] alleleNames = Arrays.stream(form.getAlleleNames()).map(StringEscapeUtils::unescapeHtml4).toArray(String[]::new);
Pair<List<Long>, List<Long>> ret = GenotypeAssaysManager.get().cacheAnalyses(getViewContext(), protocol, alleleNames);
Pair<List<Long>, List<Long>> ret = GenotypeAssaysManager.get().cacheAnalyses(getViewContext(), form.getAnalysisId(), protocol, alleleNames);
resultProperties.put("runsCreated", ret.first);
resultProperties.put("runsDeleted", ret.second);
}
Expand All @@ -159,6 +159,7 @@ public static class CacheAnalysesForm
{
private String[] _alleleNames;
private String _json;
private int _analysisId;
private int _protocolId;

public String[] getAlleleNames()
Expand Down Expand Up @@ -190,6 +191,16 @@ public void setJson(String json)
{
_json = json;
}

public int getAnalysisId()
{
return _analysisId;
}

public void setAnalysisId(int analysisId)
{
_analysisId = analysisId;
}
}

@RequiresPermission(UpdatePermission.class)
Expand Down
5 changes: 3 additions & 2 deletions GenotypeAssays/src/org/labkey/genotypeassays/GenotypeAssaysManager.java
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Original file line number Diff line number Diff line change
Expand Up @@ -90,8 +90,7 @@ public static GenotypeAssaysManager get()
return _instance;
}


public Pair<List<Long>, List<Long>> cacheAnalyses(final ViewContext ctx, final ExpProtocol protocol, String[] pks) throws IllegalArgumentException
public Pair<List<Long>, List<Long>> cacheAnalyses(final ViewContext ctx, final int analysisId, final ExpProtocol protocol, String[] pks) throws IllegalArgumentException
{
final User u = ctx.getUser();
final List<Long> runsCreated = new ArrayList<>();
Expand Down Expand Up @@ -126,6 +125,8 @@ public Pair<List<Long>, List<Long>> cacheAnalyses(final ViewContext ctx, final E

AtomicInteger records = new AtomicInteger();
TableSelector tsAlignments = new TableSelector(tableAlignments, cols.values(), new SimpleFilter(FieldKey.fromString("key"), Arrays.asList(pks), CompareType.IN), null);
tsAlignments.setNamedParameters(Map.of("AnalysisId", analysisId));

tsAlignments.forEach(new Selector.ForEachBlock<ResultSet>()
{
@Override
Expand Down
31 changes: 24 additions & 7 deletions primeseq/src/org/labkey/primeseq/pipeline/MhcCleanupPipelineJob.java
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Original file line number Diff line number Diff line change
Expand Up @@ -283,7 +283,11 @@ private void processAnalysis(int analysisId)
final Map<String, Double> existingData = new HashMap<>();
SimpleFilter dataFilter = new SimpleFilter(FieldKey.fromString("analysis_id"), analysisId, CompareType.EQUAL);
dataFilter.addCondition(FieldKey.fromString("percent_from_locus"), getPipelineJob().getLineageThreshold(), CompareType.GT);
new TableSelector(QueryService.get().getUserSchema(getJob().getUser(), getJob().getContainer(), "sequenceanalysis").getTable("alignment_summary_by_lineage"), PageFlowUtil.set("lineages", "percent_from_locus"), dataFilter, null).forEachResults(rs -> {

TableSelector ts = new TableSelector(QueryService.get().getUserSchema(getJob().getUser(), getJob().getContainer(), "sequenceanalysis").getTable("alignment_summary_by_lineage"), PageFlowUtil.set("lineages", "percent_from_locus"), dataFilter, null);
ts.setNamedParameters(Map.of("AnalysisId", analysisId));

ts.forEachResults(rs -> {
existingData.put(rs.getString(FieldKey.fromString("lineages")), rs.getDouble(FieldKey.fromString("percent_from_locus")));
});

Expand Down Expand Up @@ -311,7 +315,10 @@ private void processAnalysis(int analysisId)
SimpleFilter filter = new SimpleFilter(FieldKey.fromString("analysis_id"), analysisId, CompareType.EQUAL);
filter.addCondition(FieldKey.fromString("percent_from_locus"), getPipelineJob().getLineageThreshold(), CompareType.LT);

List<String> lowFreqRowIdList = new TableSelector(QueryService.get().getUserSchema(getJob().getUser(), getJob().getContainer(), "sequenceanalysis").getTable("alignment_summary_by_lineage"), PageFlowUtil.set("rowids"), filter, null).getArrayList(String.class);
ts = new TableSelector(QueryService.get().getUserSchema(getJob().getUser(), getJob().getContainer(), "sequenceanalysis").getTable("alignment_summary_by_lineage"), PageFlowUtil.set("rowids"), filter, null);
ts.setNamedParameters(Map.of("AnalysisId", analysisId));

List<String> lowFreqRowIdList = ts.getArrayList(String.class);
if (!lowFreqRowIdList.isEmpty())
{
getJob().getLogger().info("Analysis: " + analysisId + ", low freq lineages: " + lowFreqRowIdList.size());
Expand All @@ -329,7 +336,9 @@ private void processAnalysis(int analysisId)
SimpleFilter filter = new SimpleFilter(FieldKey.fromString("analysis_id"), analysisId, CompareType.EQUAL);
filter.addCondition(FieldKey.fromString("percent_from_locus"), getPipelineJob().getAlleleGroupThreshold(), CompareType.LT);

List<String> lowFreqRowIdList = new TableSelector(QueryService.get().getUserSchema(getJob().getUser(), getJob().getContainer(), "sequenceanalysis").getTable("alignment_summary_grouped"), PageFlowUtil.set("rowids"), filter, null).getArrayList(String.class);
ts = new TableSelector(QueryService.get().getUserSchema(getJob().getUser(), getJob().getContainer(), "sequenceanalysis").getTable("alignment_summary_grouped"), PageFlowUtil.set("rowids"), filter, null);
ts.setNamedParameters(Map.of("AnalysisId", analysisId));
List<String> lowFreqRowIdList = ts.getArrayList(String.class);
if (!lowFreqRowIdList.isEmpty())
{
getJob().getLogger().info("Analysis: " + analysisId + ", low freq allele groups: " + lowFreqRowIdList.size());
Expand Down Expand Up @@ -363,7 +372,9 @@ private void processAnalysis(int analysisId)
filter.addCondition(FieldKey.fromString("totalLineages"), 1, CompareType.GT);
filter.addCondition(FieldKey.fromString("loci"), "MHC", CompareType.CONTAINS);

List<String> rowIdList = new TableSelector(QueryService.get().getUserSchema(getJob().getUser(), getJob().getContainer(), "sequenceanalysis").getTable("alignment_summary_grouped"), PageFlowUtil.set("rowids"), filter, null).getArrayList(String.class);
ts = new TableSelector(QueryService.get().getUserSchema(getJob().getUser(), getJob().getContainer(), "sequenceanalysis").getTable("alignment_summary_grouped"), PageFlowUtil.set("rowids"), filter, null);
ts.setNamedParameters(Map.of("AnalysisId", analysisId));
List<String> rowIdList = ts.getArrayList(String.class);
if (!rowIdList.isEmpty())
{
getJob().getLogger().info("Analysis: " + analysisId + ", multi-lineage records: " + rowIdList.size());
Expand All @@ -380,7 +391,9 @@ private void processAnalysis(int analysisId)
{
SimpleFilter nAlignmentFilter = new SimpleFilter(FieldKey.fromString("analysis_id"), analysisId, CompareType.EQUAL);
nAlignmentFilter.addCondition(FieldKey.fromString("nAlignments"), 1, CompareType.GT);
List<String> redundantAlignmentSets = new TableSelector(QueryService.get().getUserSchema(getJob().getUser(), getJob().getContainer(), "sequenceanalysis").getTable("alignment_summary_grouped"), PageFlowUtil.set("rowids"), nAlignmentFilter, null).getArrayList(String.class);
ts = new TableSelector(QueryService.get().getUserSchema(getJob().getUser(), getJob().getContainer(), "sequenceanalysis").getTable("alignment_summary_grouped"), PageFlowUtil.set("rowids"), nAlignmentFilter, null);
ts.setNamedParameters(Map.of("AnalysisId", analysisId));
List<String> redundantAlignmentSets = ts.getArrayList(String.class);
if (!redundantAlignmentSets.isEmpty())
{
getJob().getLogger().info("Analysis: " + analysisId + ", redundant alignment sets: " + redundantAlignmentSets.size());
Expand Down Expand Up @@ -446,7 +459,9 @@ private void processAnalysis(int analysisId)

// verify ending data:
final Map<String, Double> endingData = new HashMap<>();
new TableSelector(QueryService.get().getUserSchema(getJob().getUser(), getJob().getContainer(), "sequenceanalysis").getTable("alignment_summary_by_lineage"), PageFlowUtil.set("lineages", "percent_from_locus"), dataFilter, null).forEachResults(rs -> {
ts = new TableSelector(QueryService.get().getUserSchema(getJob().getUser(), getJob().getContainer(), "sequenceanalysis").getTable("alignment_summary_by_lineage"), PageFlowUtil.set("lineages", "percent_from_locus"), dataFilter, null);
ts.setNamedParameters(Map.of("AnalysisId", analysisId));
ts.forEachResults(rs -> {
endingData.put(rs.getString(FieldKey.fromString("lineages")), rs.getDouble(FieldKey.fromString("percent_from_locus")));
});

Expand Down Expand Up @@ -515,7 +530,9 @@ public AlignmentGroupCompare(final int analysisId, Container c, User u)
{
this.analysisId = analysisId;

new TableSelector(QueryService.get().getUserSchema(u, c, "sequenceanalysis").getTable("alignment_summary_grouped"), PageFlowUtil.set("analysis_id", "alleles", "lineages", "totalLineages", "total_reads", "total_forward", "total_reverse", "valid_pairs", "rowids"), new SimpleFilter(FieldKey.fromString("analysis_id"), analysisId), null).forEachResults(rs -> {
TableSelector ts = new TableSelector(QueryService.get().getUserSchema(u, c, "sequenceanalysis").getTable("alignment_summary_grouped"), PageFlowUtil.set("analysis_id", "alleles", "lineages", "totalLineages", "total_reads", "total_forward", "total_reverse", "valid_pairs", "rowids"), new SimpleFilter(FieldKey.fromString("analysis_id"), analysisId), null);
ts.setNamedParameters(Map.of("AnalysisId", analysisId));
ts.forEachResults(rs -> {
if (rs.getString(FieldKey.fromString("alleles")) == null)
{
return;
Expand Down