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Merge pull request #155 from bimberlabinternal/24.3_fb_merge
Merge discvr-23.11 to discvr-24.3
2 parents 218e52b + d3ea673 commit 03d0129

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-63
lines changed

7 files changed

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-63
lines changed

‎LabPurchasing/resources/queries/labpurchasing/purchases/.qview.xml‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
1-
<customView xmlns="http://labkey.org/data/xml/queryCustomView" label="All Items">
1+
<customView xmlns="http://labkey.org/data/xml/queryCustomView" label="All Items" canOverride="true">
22
<columns>
33
<column name="purchaseId"/>
44
<column name="requestor"/>

‎LabPurchasing/resources/queries/labpurchasing/purchases/Items To Order.qview.xml‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
1-
<customView xmlns="http://labkey.org/data/xml/queryCustomView">
1+
<customView xmlns="http://labkey.org/data/xml/queryCustomView" canOverride="true">
22
<columns>
33
<column name="purchaseId"/>
44
<column name="requestor"/>

‎LabPurchasing/resources/queries/labpurchasing/purchases/Waiting for Item.qview.xml‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
1-
<customView xmlns="http://labkey.org/data/xml/queryCustomView">
1+
<customView xmlns="http://labkey.org/data/xml/queryCustomView" canOverride="true">
22
<columns>
33
<column name="purchaseId"/>
44
<column name="requestor"/>

‎LabPurchasing/resources/queries/labpurchasing/referenceItems/.qview.xml‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
1-
<customView xmlns="http://labkey.org/data/xml/queryCustomView">
1+
<customView xmlns="http://labkey.org/data/xml/queryCustomView" canOverride="true">
22
<columns>
33
<column name="rowId"/>
44
<column name="vendorId"/>

‎PMR/test/src/org/labkey/test/tests/pmr/PMRTest.java‎

Lines changed: 3 additions & 11 deletions
Original file line numberDiff line numberDiff line change
@@ -17,38 +17,30 @@
1717
package org.labkey.test.tests.pmr;
1818

1919
import au.com.bytecode.opencsv.CSVReader;
20-
import org.apache.hc.client5.http.classic.methods.HttpUriRequest;
2120
import org.junit.Assert;
2221
import org.junit.Before;
2322
import org.junit.BeforeClass;
2423
import org.junit.Test;
2524
import org.junit.experimental.categories.Category;
26-
import org.labkey.remoteapi.Command;
27-
import org.labkey.remoteapi.CommandResponse;
28-
import org.labkey.remoteapi.PostCommand;
2925
import org.labkey.remoteapi.query.SelectRowsCommand;
3026
import org.labkey.remoteapi.query.TruncateTableCommand;
3127
import org.labkey.serverapi.reader.Readers;
3228
import org.labkey.test.BaseWebDriverTest;
3329
import org.labkey.test.Locator;
34-
import org.labkey.test.Locators;
3530
import org.labkey.test.ModulePropertyValue;
3631
import org.labkey.test.TestFileUtils;
3732
import org.labkey.test.TestTimeoutException;
3833
import org.labkey.test.WebTestHelper;
3934
import org.labkey.test.categories.External;
4035
import org.labkey.test.categories.LabModule;
41-
import org.labkey.test.tests.di.ETLHelper;
4236
import org.labkey.test.util.Ext4Helper;
43-
import org.labkey.test.util.PipelineStatusTable;
4437
import org.labkey.test.util.RReportHelper;
4538
import org.labkey.test.util.RemoteConnectionHelper;
4639
import org.labkey.test.util.SqlserverOnlyTest;
40+
import org.labkey.test.util.di.DataIntegrationHelper;
4741
import org.labkey.test.util.ehr.EHRClientAPIHelper;
48-
import org.labkey.test.util.ehr.EHRTestHelper;
4942

5043
import java.io.File;
51-
import java.net.URI;
5244
import java.util.Arrays;
5345
import java.util.Collections;
5446
import java.util.Date;
@@ -60,7 +52,7 @@
6052
@Category({External.class, LabModule.class})
6153
public class PMRTest extends BaseWebDriverTest implements SqlserverOnlyTest
6254
{
63-
private final ETLHelper _etlHelper = new ETLHelper(this, getProjectName());
55+
private final DataIntegrationHelper _etlHelper = new DataIntegrationHelper(getProjectName());
6456

6557
@Override
6658
protected void doCleanup(boolean afterTest) throws TestTimeoutException
@@ -158,7 +150,7 @@ private void testKinshipEtl() throws Exception
158150
Assert.assertEquals("Incorrect number of kinship rows", 0, select1.execute(getApiHelper().getConnection(), getProjectName()).getRowCount().intValue());
159151

160152
// Kick off ETL to stage data. This should also kick off a separate pipeline job to import, using geneticscore-importGeneticsData.view
161-
_etlHelper.runETL("{PMR}/KinshipDataStaging");
153+
_etlHelper.runTransform("{PMR}/KinshipDataStaging");
162154
goToDataPipeline();
163155
waitForPipelineJobsToComplete(4, "ETL Job: Import PRIMe-seq Kinship Data", false);
164156

‎mGAP/resources/web/mGAP/Utils.js‎

Lines changed: 14 additions & 32 deletions
Original file line numberDiff line numberDiff line change
@@ -55,43 +55,25 @@ mGAP.Utils = (function($){
5555
var metricNames = values.split(';');
5656
var targets = [];
5757

58-
//filter:
59-
if (metricNames.length > 1 && metricNames.indexOf('intron_variant') > -1) {
60-
metricNames.remove('downstream_gene_variant');
61-
metricNames.remove('upstream_gene_variant');
58+
// Then accept each of these categories in priority order:
59+
if ($(metricNames).filter(['missense_variant', 'synonymous_variant', 'stop_lost', 'stop_retained_variant', 'stop_gained', 'initiator_codon_variant', 'start_lost', 'non_canonical_start_codon', 'exon_loss_variant', 'frameshift_variant', 'conservative_inframe_insertion', 'disruptive_inframe_insertion', 'conservative_inframe_deletion', 'disruptive_inframe_deletion']).length) {
60+
targets.push('Exonic');
6261
}
63-
64-
if (metricNames.indexOf('downstream_gene_variant') > -1) {
62+
else if ($(metricNames).filter(['intron_variant', 'splice_acceptor_variant', 'splice_region_variant', 'splice_donor_variant']).length) {
63+
targets.push('Intronic/<br>Non-coding');
64+
}
65+
else if ($(metricNames).filter(['intragenic_variant', 'non_coding_transcript_variant', 'non_coding_transcript_exon_variant', '3_prime_UTR_variant', '5_prime_UTR_premature_start_codon_gain_variant', '5_prime_UTR_variant']).length) {
66+
targets.push('Intronic/<br>Non-coding');
67+
}
68+
else if (metricNames.indexOf('downstream_gene_variant') > -1) {
6569
targets.push('Downstream<br>Gene');
6670
}
67-
if (metricNames.indexOf('upstream_gene_variant') > -1) {
71+
else if (metricNames.indexOf('upstream_gene_variant') > -1) {
6872
targets.push('Upstream<br>Gene');
6973
}
70-
71-
$.each(metricNames, function(idx, val) {
72-
if (['missense_variant', 'synonymous_variant', 'stop_lost', 'stop_retained_variant', 'stop_gained', 'initiator_codon_variant', 'start_lost', 'non_canonical_start_codon', 'exon_loss_variant', 'frameshift_variant', 'conservative_inframe_insertion', 'disruptive_inframe_insertion', 'conservative_inframe_deletion', 'disruptive_inframe_deletion'].indexOf(val) > -1) {
73-
targets.push('Exonic');
74-
return false;
75-
}
76-
else if (['downstream_gene_variant'].indexOf(val) > -1) {
77-
78-
}
79-
else if (['upstream_gene_variant'].indexOf(val) > -1) {
80-
81-
}
82-
else if (['intron_variant', 'splice_acceptor_variant', 'splice_region_variant', 'splice_donor_variant'].indexOf(val) > -1) {
83-
targets.push('Intronic/<br>Non-coding');
84-
return false;
85-
}
86-
else if (['intragenic_variant', 'non_coding_transcript_variant', 'non_coding_transcript_exon_variant', '3_prime_UTR_variant', '5_prime_UTR_premature_start_codon_gain_variant', '5_prime_UTR_variant'].indexOf(val) > -1) {
87-
targets.push('Intronic/<br>Non-coding');
88-
return false;
89-
}
90-
else if (['intergenic_region'].indexOf(val) > -1) {
91-
targets.push('Intergenic');
92-
return false;
93-
}
94-
}, this);
74+
else if (metricNames.indexOf('intergenic_region') > -1) {
75+
targets.push('Intergenic');
76+
}
9577

9678
if (!targets.length){
9779
targets.push(values);

‎mcc/package-lock.json‎

Lines changed: 16 additions & 16 deletions
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