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Merge discvr-23.11 to discvr-24.3 #155

Merged
merged 6 commits into from
Apr 9, 2024
Merged

Merge discvr-23.11 to discvr-24.3 #155

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ac404d9
Update npm packages
bbimber Apr 5, 2024
bd76fe8
Update the logic used for mGAP variant pie chart
bbimber Apr 5, 2024
ebb2106
Allows views to be overridden
bbimber Apr 8, 2024
537f81d
Switch from ETLHelper to DataIntegrationHelper
bbimber Apr 8, 2024
8d3aed5
Merge pull request #154 from bimberlabinternal/23.11_fb_etlhelper
bbimber Apr 9, 2024
d3ea673
Merge discvr-23.11 to discvr-24.3
bbimber Apr 9, 2024
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2 changes: 1 addition & 1 deletion LabPurchasing/resources/queries/labpurchasing/purchases/.qview.xml
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
<customView xmlns="http://labkey.org/data/xml/queryCustomView" label="All Items">
<customView xmlns="http://labkey.org/data/xml/queryCustomView" label="All Items" canOverride="true">
<columns>
<column name="purchaseId"/>
<column name="requestor"/>
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2 changes: 1 addition & 1 deletion LabPurchasing/resources/queries/labpurchasing/purchases/Items To Order.qview.xml
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
<customView xmlns="http://labkey.org/data/xml/queryCustomView">
<customView xmlns="http://labkey.org/data/xml/queryCustomView" canOverride="true">
<columns>
<column name="purchaseId"/>
<column name="requestor"/>
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2 changes: 1 addition & 1 deletion LabPurchasing/resources/queries/labpurchasing/purchases/Waiting for Item.qview.xml
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
<customView xmlns="http://labkey.org/data/xml/queryCustomView">
<customView xmlns="http://labkey.org/data/xml/queryCustomView" canOverride="true">
<columns>
<column name="purchaseId"/>
<column name="requestor"/>
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2 changes: 1 addition & 1 deletion LabPurchasing/resources/queries/labpurchasing/referenceItems/.qview.xml
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
<customView xmlns="http://labkey.org/data/xml/queryCustomView">
<customView xmlns="http://labkey.org/data/xml/queryCustomView" canOverride="true">
<columns>
<column name="rowId"/>
<column name="vendorId"/>
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14 changes: 3 additions & 11 deletions PMR/test/src/org/labkey/test/tests/pmr/PMRTest.java
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Expand Up @@ -17,38 +17,30 @@
package org.labkey.test.tests.pmr;

import au.com.bytecode.opencsv.CSVReader;
import org.apache.hc.client5.http.classic.methods.HttpUriRequest;
import org.junit.Assert;
import org.junit.Before;
import org.junit.BeforeClass;
import org.junit.Test;
import org.junit.experimental.categories.Category;
import org.labkey.remoteapi.Command;
import org.labkey.remoteapi.CommandResponse;
import org.labkey.remoteapi.PostCommand;
import org.labkey.remoteapi.query.SelectRowsCommand;
import org.labkey.remoteapi.query.TruncateTableCommand;
import org.labkey.serverapi.reader.Readers;
import org.labkey.test.BaseWebDriverTest;
import org.labkey.test.Locator;
import org.labkey.test.Locators;
import org.labkey.test.ModulePropertyValue;
import org.labkey.test.TestFileUtils;
import org.labkey.test.TestTimeoutException;
import org.labkey.test.WebTestHelper;
import org.labkey.test.categories.External;
import org.labkey.test.categories.LabModule;
import org.labkey.test.tests.di.ETLHelper;
import org.labkey.test.util.Ext4Helper;
import org.labkey.test.util.PipelineStatusTable;
import org.labkey.test.util.RReportHelper;
import org.labkey.test.util.RemoteConnectionHelper;
import org.labkey.test.util.SqlserverOnlyTest;
import org.labkey.test.util.di.DataIntegrationHelper;
import org.labkey.test.util.ehr.EHRClientAPIHelper;
import org.labkey.test.util.ehr.EHRTestHelper;

import java.io.File;
import java.net.URI;
import java.util.Arrays;
import java.util.Collections;
import java.util.Date;
Expand All @@ -60,7 +52,7 @@
@Category({External.class, LabModule.class})
public class PMRTest extends BaseWebDriverTest implements SqlserverOnlyTest
{
private final ETLHelper _etlHelper = new ETLHelper(this, getProjectName());
private final DataIntegrationHelper _etlHelper = new DataIntegrationHelper(getProjectName());

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

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

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46 changes: 14 additions & 32 deletions mGAP/resources/web/mGAP/Utils.js
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Expand Up @@ -55,43 +55,25 @@ mGAP.Utils = (function($){
var metricNames = values.split(';');
var targets = [];

//filter:
if (metricNames.length > 1 && metricNames.indexOf('intron_variant') > -1) {
metricNames.remove('downstream_gene_variant');
metricNames.remove('upstream_gene_variant');
// Then accept each of these categories in priority order:
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) {
targets.push('Exonic');
}

if (metricNames.indexOf('downstream_gene_variant') > -1) {
else if ($(metricNames).filter(['intron_variant', 'splice_acceptor_variant', 'splice_region_variant', 'splice_donor_variant']).length) {
targets.push('Intronic/<br>Non-coding');
}
else if ($(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) {
targets.push('Intronic/<br>Non-coding');
}
else if (metricNames.indexOf('downstream_gene_variant') > -1) {
targets.push('Downstream<br>Gene');
}
if (metricNames.indexOf('upstream_gene_variant') > -1) {
else if (metricNames.indexOf('upstream_gene_variant') > -1) {
targets.push('Upstream<br>Gene');
}

$.each(metricNames, function(idx, val) {
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) {
targets.push('Exonic');
return false;
}
else if (['downstream_gene_variant'].indexOf(val) > -1) {

}
else if (['upstream_gene_variant'].indexOf(val) > -1) {

}
else if (['intron_variant', 'splice_acceptor_variant', 'splice_region_variant', 'splice_donor_variant'].indexOf(val) > -1) {
targets.push('Intronic/<br>Non-coding');
return false;
}
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) {
targets.push('Intronic/<br>Non-coding');
return false;
}
else if (['intergenic_region'].indexOf(val) > -1) {
targets.push('Intergenic');
return false;
}
}, this);
else if (metricNames.indexOf('intergenic_region') > -1) {
targets.push('Intergenic');
}

if (!targets.length){
targets.push(values);
Expand Down
32 changes: 16 additions & 16 deletions mcc/package-lock.json
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