diff --git a/LabPurchasing/resources/queries/labpurchasing/purchases/.qview.xml b/LabPurchasing/resources/queries/labpurchasing/purchases/.qview.xml index 34b409cfc..963d35ba4 100644 --- a/LabPurchasing/resources/queries/labpurchasing/purchases/.qview.xml +++ b/LabPurchasing/resources/queries/labpurchasing/purchases/.qview.xml @@ -1,4 +1,4 @@ - + diff --git a/LabPurchasing/resources/queries/labpurchasing/purchases/Items To Order.qview.xml b/LabPurchasing/resources/queries/labpurchasing/purchases/Items To Order.qview.xml index 9d7deee43..31c56032a 100644 --- a/LabPurchasing/resources/queries/labpurchasing/purchases/Items To Order.qview.xml +++ b/LabPurchasing/resources/queries/labpurchasing/purchases/Items To Order.qview.xml @@ -1,4 +1,4 @@ - + diff --git a/LabPurchasing/resources/queries/labpurchasing/purchases/Waiting for Item.qview.xml b/LabPurchasing/resources/queries/labpurchasing/purchases/Waiting for Item.qview.xml index f4736de93..68e15235e 100644 --- a/LabPurchasing/resources/queries/labpurchasing/purchases/Waiting for Item.qview.xml +++ b/LabPurchasing/resources/queries/labpurchasing/purchases/Waiting for Item.qview.xml @@ -1,4 +1,4 @@ - + diff --git a/LabPurchasing/resources/queries/labpurchasing/referenceItems/.qview.xml b/LabPurchasing/resources/queries/labpurchasing/referenceItems/.qview.xml index 62c4822f9..17c6c0344 100644 --- a/LabPurchasing/resources/queries/labpurchasing/referenceItems/.qview.xml +++ b/LabPurchasing/resources/queries/labpurchasing/referenceItems/.qview.xml @@ -1,4 +1,4 @@ - + diff --git a/PMR/test/src/org/labkey/test/tests/pmr/PMRTest.java b/PMR/test/src/org/labkey/test/tests/pmr/PMRTest.java index 6dd2d5746..650b7ffd8 100644 --- a/PMR/test/src/org/labkey/test/tests/pmr/PMRTest.java +++ b/PMR/test/src/org/labkey/test/tests/pmr/PMRTest.java @@ -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; @@ -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 @@ -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); diff --git a/mGAP/resources/web/mGAP/Utils.js b/mGAP/resources/web/mGAP/Utils.js index 2a44a72d4..340473ccb 100644 --- a/mGAP/resources/web/mGAP/Utils.js +++ b/mGAP/resources/web/mGAP/Utils.js @@ -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 ($(metricNames).filter(['intron_variant', 'splice_acceptor_variant', 'splice_region_variant', 'splice_donor_variant']).length) { + targets.push('Intronic/
Non-coding'); + } + else if ($(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/
Non-coding'); + } + else if (metricNames.indexOf('downstream_gene_variant') > -1) { targets.push('Downstream
Gene'); } - if (metricNames.indexOf('upstream_gene_variant') > -1) { + else if (metricNames.indexOf('upstream_gene_variant') > -1) { targets.push('Upstream
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/
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/
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); diff --git a/mcc/package-lock.json b/mcc/package-lock.json index 68e5f5e0e..fa19fb024 100644 --- a/mcc/package-lock.json +++ b/mcc/package-lock.json @@ -4757,13 +4757,13 @@ } }, "node_modules/body-parser": { - "version": "1.20.1", - "resolved": "https://registry.npmjs.org/body-parser/-/body-parser-1.20.1.tgz", - "integrity": "sha512-jWi7abTbYwajOytWCQc37VulmWiRae5RyTpaCyDcS5/lMdtwSz5lOpDE67srw/HYe35f1z3fDQw+3txg7gNtWw==", + "version": "1.20.2", + "resolved": "https://registry.npmjs.org/body-parser/-/body-parser-1.20.2.tgz", + "integrity": "sha512-ml9pReCu3M61kGlqoTm2umSXTlRTuGTx0bfYj+uIUKKYycG5NtSbeetV3faSU6R7ajOPw0g/J1PvK4qNy7s5bA==", "dev": true, "dependencies": { "bytes": "3.1.2", - "content-type": "~1.0.4", + "content-type": "~1.0.5", "debug": "2.6.9", "depd": "2.0.0", "destroy": "1.2.0", @@ -4771,7 +4771,7 @@ "iconv-lite": "0.4.24", "on-finished": "2.4.1", "qs": "6.11.0", - "raw-body": "2.5.1", + "raw-body": "2.5.2", "type-is": "~1.6.18", "unpipe": "1.0.0" }, @@ -5389,9 +5389,9 @@ "integrity": "sha512-ASFBup0Mz1uyiIjANan1jzLQami9z1PoYSZCiiYW2FczPbenXc45FZdBZLzOT+r6+iciuEModtmCti+hjaAk0A==" }, "node_modules/cookie": { - "version": "0.5.0", - "resolved": "https://registry.npmjs.org/cookie/-/cookie-0.5.0.tgz", - "integrity": "sha512-YZ3GUyn/o8gfKJlnlX7g7xq4gyO6OSuhGPKaaGssGB2qgDUS0gPgtTvoyZLTt9Ab6dC4hfc9dV5arkvc/OCmrw==", + "version": "0.6.0", + "resolved": "https://registry.npmjs.org/cookie/-/cookie-0.6.0.tgz", + "integrity": "sha512-U71cyTamuh1CRNCfpGY6to28lxvNwPG4Guz/EVjgf3Jmzv0vlDp1atT9eS5dDjMYHucpHbWns6Lwf3BKz6svdw==", "dev": true, "engines": { "node": ">= 0.6" @@ -6362,17 +6362,17 @@ } }, "node_modules/express": { - "version": "4.18.2", - "resolved": "https://registry.npmjs.org/express/-/express-4.18.2.tgz", - "integrity": "sha512-5/PsL6iGPdfQ/lKM1UuielYgv3BUoJfz1aUwU9vHZ+J7gyvwdQXFEBIEIaxeGf0GIcreATNyBExtalisDbuMqQ==", + "version": "4.19.2", + "resolved": "https://registry.npmjs.org/express/-/express-4.19.2.tgz", + "integrity": "sha512-5T6nhjsT+EOMzuck8JjBHARTHfMht0POzlA60WV2pMD3gyXw2LZnZ+ueGdNxG+0calOJcWKbpFcuzLZ91YWq9Q==", "dev": true, "dependencies": { "accepts": "~1.3.8", "array-flatten": "1.1.1", - "body-parser": "1.20.1", + "body-parser": "1.20.2", "content-disposition": "0.5.4", "content-type": "~1.0.4", - "cookie": "0.5.0", + "cookie": "0.6.0", "cookie-signature": "1.0.6", "debug": "2.6.9", "depd": "2.0.0", @@ -11661,9 +11661,9 @@ } }, "node_modules/raw-body": { - "version": "2.5.1", - "resolved": "https://registry.npmjs.org/raw-body/-/raw-body-2.5.1.tgz", - "integrity": "sha512-qqJBtEyVgS0ZmPGdCFPWJ3FreoqvG4MVQln/kCgF7Olq95IbOp0/BWyMwbdtn4VTvkM8Y7khCQ2Xgk/tcrCXig==", + "version": "2.5.2", + "resolved": "https://registry.npmjs.org/raw-body/-/raw-body-2.5.2.tgz", + "integrity": "sha512-8zGqypfENjCIqGhgXToC8aB2r7YrBX+AQAfIPs/Mlk+BtPTztOvTS01NRW/3Eh60J+a48lt8qsCzirQ6loCVfA==", "dev": true, "dependencies": { "bytes": "3.1.2",