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Merge discvr-23.11 to develop
2 parents 5471ce7 + 90fd733 commit 5a27b81

7 files changed

Lines changed: 49 additions & 108 deletions

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‎GenotypeAssays/src/org/labkey/genotypeassays/AlignmentDisplayColumn.java‎

Lines changed: 0 additions & 95 deletions
This file was deleted.

‎mGAP/resources/web/mGAP/DownloadWindow.js‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -2,7 +2,7 @@ Ext4.define('mGAP.window.DownloadWindow', {
22
extend: 'Ext.window.Window',
33

44
statics: {
5-
buttonHandler: function(releaseId, el){
5+
buttonHandler: function(releaseId){
66
Ext4.create('mGAP.window.DownloadWindow', {
77
releaseId: releaseId
88
});

‎mGAP/src/org/labkey/mgap/query/VariantReleaseDisplayColumnFactory.java‎

Lines changed: 11 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -10,11 +10,11 @@
1010
import org.labkey.api.query.DetailsURL;
1111
import org.labkey.api.query.FieldKey;
1212
import org.labkey.api.util.PageFlowUtil;
13+
import org.labkey.api.view.HttpView;
1314
import org.labkey.api.view.template.ClientDependency;
1415

1516
import java.io.IOException;
1617
import java.io.Writer;
17-
import java.util.Collections;
1818
import java.util.Set;
1919

2020
/**
@@ -45,13 +45,22 @@ private FieldKey getBoundKey(String colName)
4545
return new FieldKey(getBoundColumn().getFieldKey().getParent(), colName);
4646
}
4747

48+
private boolean _clickHandlerRegistered = false;
49+
4850
@Override
4951
public void renderGridCellContents(RenderContext ctx, Writer out) throws IOException
5052
{
5153
Integer rowId = ctx.get(getBoundKey("rowid"), Integer.class);
5254
if (rowId != null)
5355
{
54-
out.write("<a class=\"labkey-text-link\" href=\"javascript:void(0);\" onclick=\"mGAP.window.DownloadWindow.buttonHandler(" + PageFlowUtil.jsString(rowId.toString()) + ", this);\">Download</a>");
56+
out.write("<a class=\"labkey-text-link vrdc-row\" data-rowid=" + PageFlowUtil.jsString(rowId.toString()) + ">Download</a>");
57+
58+
if (!_clickHandlerRegistered)
59+
{
60+
HttpView.currentPageConfig().addHandlerForQuerySelector("a.vrdc-row", "click", "mGAP.window.DownloadWindow.buttonHandler(this.attributes.getNamedItem('data-rowid').value); return false;");
61+
62+
_clickHandlerRegistered = true;
63+
}
5564
}
5665

5766
String jbrowseId = ctx.get(getBoundKey("jbrowseId"), String.class);

‎mcc/package-lock.json‎

Lines changed: 3 additions & 3 deletions
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‎mcc/src/org/labkey/mcc/query/RequestScoreActionsDisplayColumnFactory.java‎

Lines changed: 11 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -13,6 +13,7 @@
1313
import org.labkey.api.security.User;
1414
import org.labkey.api.security.UserManager;
1515
import org.labkey.api.util.PageFlowUtil;
16+
import org.labkey.api.view.HttpView;
1617
import org.labkey.api.view.template.ClientDependency;
1718
import org.labkey.mcc.MccManager;
1819
import org.labkey.mcc.security.MccFinalReviewPermission;
@@ -32,6 +33,8 @@ public DisplayColumn createRenderer(ColumnInfo colInfo)
3233
{
3334
return new AbstractMccDisplayColumn(colInfo)
3435
{
36+
private boolean _hasRegisteredApprovedHandler = false;
37+
3538
@Override
3639
public void renderGridCellContents(RenderContext ctx, Writer out) throws IOException
3740
{
@@ -94,7 +97,14 @@ else if (st == MccManager.RequestStatus.PendingDecision)
9497
}
9598
else if (st == MccManager.RequestStatus.Approved)
9699
{
97-
out.write("<br><a class=\"labkey-text-link\" onclick=\"MCC.window.ChangeStatusWindow.buttonHandler(" + PageFlowUtil.jsString(ctx.getCurrentRegion().getName()) + "," + requestRowId + ", 'Fulfilled')\">Mark Fulfilled</a>");
100+
out.write("<br><a class=\"labkey-text-link rsadc-approved\" data-requestrowid=" + PageFlowUtil.jsString(String.valueOf(requestRowId)) + ">Mark Fulfilled</a>");
101+
102+
if (!_hasRegisteredApprovedHandler)
103+
{
104+
HttpView.currentPageConfig().addHandlerForQuerySelector("a.rsadc-approved", "click", "MCC.window.ChangeStatusWindow.buttonHandler(" + PageFlowUtil.jsString(ctx.getCurrentRegion().getName()) + ", this.attributes.getNamedItem('data-requestrowid').value, 'Fulfilled'); return false;");
105+
106+
_hasRegisteredApprovedHandler = true;
107+
}
98108
}
99109
}
100110
catch (IllegalArgumentException e)
@@ -128,9 +138,4 @@ public void addQueryFieldKeys(Set<FieldKey> keys)
128138
}
129139
};
130140
}
131-
132-
private String getWithdrawnLine(RenderContext ctx, int requestRowId)
133-
{
134-
return "<br><a class=\"labkey-text-link\" onclick=\"MCC.window.ChangeStatusWindow.buttonHandler(" + PageFlowUtil.jsString(ctx.getCurrentRegion().getName()) + "," + requestRowId + ", 'Withdrawn')\">Withdraw Request</a>";
135-
}
136141
}

‎primeseq/src/org/labkey/primeseq/pipeline/SequenceJobResourceAllocator.java‎

Lines changed: 14 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -43,7 +43,8 @@ public Integer getPriority(TaskId taskId)
4343
{
4444
return (taskId.getNamespaceClass() != null && (
4545
(taskId.getNamespaceClass().getName().startsWith("org.labkey.sequenceanalysis.pipeline") ||
46-
taskId.getNamespaceClass().getName().startsWith("org.labkey.jbrowse.pipeline"))
46+
taskId.getNamespaceClass().getName().startsWith("org.labkey.jbrowse.pipeline") ||
47+
taskId.getNamespaceClass().getName().endsWith("GeneticCalculationsRTask"))
4748
)) ? 50 : null;
4849
}
4950
}
@@ -53,6 +54,11 @@ private boolean isSequenceNormalizationTask(PipelineJob job)
5354
return (job.getActiveTaskId() != null && job.getActiveTaskId().getNamespaceClass().getName().endsWith("SequenceNormalizationTask"));
5455
}
5556

57+
private boolean isGeneticsTask(PipelineJob job)
58+
{
59+
return (job.getActiveTaskId() != null && job.getActiveTaskId().getNamespaceClass().getName().endsWith("GeneticCalculationsRTask"));
60+
}
61+
5662
private boolean isLuceneIndexJob(PipelineJob job)
5763
{
5864
return (job.getActiveTaskId() != null && job.getActiveTaskId().getNamespaceClass().getName().endsWith("JBrowseLuceneTask"));
@@ -95,6 +101,7 @@ public Integer getMaxRequestCpus(PipelineJob job)
95101
job.getLogger().debug("setting max CPUs to 8");
96102
return 8;
97103
}
104+
98105
if (isLuceneIndexJob(job))
99106
{
100107
job.getLogger().debug("setting max CPUs to 24");
@@ -152,6 +159,12 @@ public Integer getMaxRequestMemory(PipelineJob job)
152159
return 48;
153160
}
154161

162+
if (isGeneticsTask(job))
163+
{
164+
job.getLogger().debug("setting memory to 72");
165+
return 72;
166+
}
167+
155168
if (isCacheAlignerIndexesTask(job))
156169
{
157170
job.getLogger().debug("setting memory to 48");

‎tcrdb/src/org/labkey/tcrdb/pipeline/CellRangerVDJUtils.java‎

Lines changed: 9 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -53,6 +53,7 @@
5353
import java.util.List;
5454
import java.util.Map;
5555
import java.util.Set;
56+
import java.util.TreeMap;
5657

5758
public class CellRangerVDJUtils
5859
{
@@ -296,6 +297,8 @@ else if ("Low Counts".equals(hto))
296297
int fullLengthNoClonotype = 0;
297298
int multiChainConverted = 0;
298299
int discordantLoci = 0;
300+
Map<String, Integer> chainMap = new TreeMap<>();
301+
299302
Set<String> knownBarcodes = new HashSet<>();
300303

301304
Map<HEADER_FIELD, Integer> headerToIdx = null;
@@ -398,6 +401,8 @@ else if (discordantBarcodes.contains(barcode))
398401
discordantLoci++;
399402
}
400403

404+
chainMap.put(locus, chainMap.getOrDefault(locus, 0) + 1);
405+
401406
// Aggregate by: cDNA_ID, cdr3, chain, raw_clonotype_id, coalescedContigName, vHit, dHit, jHit, cHit, cdr3_nt
402407
String key = StringUtils.join(new String[]{cDNA.toString(), line[headerToIdx.get(HEADER_FIELD.CDR3)], locus, rawClonotypeId, coalescedContigName, removeNone(line[headerToIdx.get(HEADER_FIELD.V_GENE)]), removeNone(line[headerToIdx.get(HEADER_FIELD.D_GENE)]), removeNone(line[headerToIdx.get(HEADER_FIELD.J_GENE)]), cGene, removeNone(line[headerToIdx.get(HEADER_FIELD.CDR3_NT)])}, "<>");
403408
AssayModel am;
@@ -447,6 +452,10 @@ else if (discordantBarcodes.contains(barcode))
447452
_log.info("total rows lacking clonotype, but marked full-length: " + fullLengthNoClonotype);
448453
_log.info("total rows converted from Multi to TRA: " + multiChainConverted);
449454
_log.info("total rows with discordant chain/c-gene calls: " + discordantLoci);
455+
for (String chain : chainMap.keySet())
456+
{
457+
_log.info("total rows for " + chain + ":" + chainMap.get(chain));
458+
}
450459

451460
}
452461
catch (IOException e)

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