From ebe5165782d735a454b7e1cdea253c001e5dba71 Mon Sep 17 00:00:00 2001 From: XingY Date: Tue, 15 Jul 2025 16:01:17 -0700 Subject: [PATCH 1/3] Issue 53419: Aliquot parent with number like names that starts with leading zeroes aren't resolved during import --- .../api/query/AbstractQueryImportAction.java | 2 ++ .../test/integration/SampleTypeCrud.ispec.ts | 16 +++++++++++----- 2 files changed, 13 insertions(+), 5 deletions(-) diff --git a/api/src/org/labkey/api/query/AbstractQueryImportAction.java b/api/src/org/labkey/api/query/AbstractQueryImportAction.java index e5ada4d6baa..5a4e3d0df97 100644 --- a/api/src/org/labkey/api/query/AbstractQueryImportAction.java +++ b/api/src/org/labkey/api/query/AbstractQueryImportAction.java @@ -40,6 +40,7 @@ import org.labkey.api.dataiterator.DataIterator; import org.labkey.api.dataiterator.DataIteratorContext; import org.labkey.api.dataiterator.DetailedAuditLogDataIterator; +import org.labkey.api.exp.api.ExpMaterial; import org.labkey.api.exp.api.ExperimentService; import org.labkey.api.gwt.client.AuditBehaviorType; import org.labkey.api.module.Module; @@ -702,6 +703,7 @@ public static void configureLoader(DataLoader loader, @Nullable TableInfo target String name = col.name.toLowerCase(); if (ExperimentService.isInputOutputColumn(col.name) || name.equalsIgnoreCase("Name") || /* Issue 50710: Treat "Name" column as a string value for sample or data class import */ + name.equalsIgnoreCase(ExpMaterial.ALIQUOTED_FROM_INPUT) || /* Issue 53419: Aliquot parent with number like names that starts with leading zeroes aren't resolved during import */ (lineageAliasNames != null && lineageAliasNames.contains(name)) ) { col.clazz = String.class; diff --git a/experiment/src/client/test/integration/SampleTypeCrud.ispec.ts b/experiment/src/client/test/integration/SampleTypeCrud.ispec.ts index fc216383297..b070697b182 100644 --- a/experiment/src/client/test/integration/SampleTypeCrud.ispec.ts +++ b/experiment/src/client/test/integration/SampleTypeCrud.ispec.ts @@ -1,4 +1,4 @@ -import { ExperimentCRUDUtils, hookServer, RequestOptions, successfulResponse } from '@labkey/test'; +import { ExperimentCRUDUtils, hookServer, RequestOptions, selectRandomN, successfulResponse } from '@labkey/test'; import mock from 'mock-fs'; import { checkDomainName, @@ -394,6 +394,7 @@ describe('Aliquot crud', () => { const aliquotQueryCols = 'name, rowid, lsid, description, str, int, isAliquot, AliquotedFromLsid/name, rootmaterialrowid, Myparentcol, Myaliquotcol, Myindependentcol'; async function verifyImportingWithNameValue(parentSampleName: string, sampleType: string) { + console.log('Selected parentSampleName: ' + parentSampleName); const parentInsertRow = { name: parentSampleName, description: 'testImportingWithNameValue parent' @@ -559,14 +560,19 @@ describe('Aliquot crud', () => { *
  • An aliquot with the name formatted as an aliquot (SAI_1-101).
    • *
  • And have an aliquot w/o a name set.
    • *
  • Validate that the names are as expected.
    • + *
  • Issue 53419: Aliquot parent with number like names that starts with leading zeroes aren't resolved during import
    • * * Because importing is batched the imported aliquot without an explicit name set it should have the next * index (default behavior). *

    */ - it('testImportingWithNameValue - with naming patten', async () => { + + const parentSampleName = ['S-1', '123', '0001', '0002', 'With Space', '+ -_.&)(:']; + + + it('(Fuzz Test) testImportingWithNameValue - with naming patten ', async () => { // also include scenarios from testImportWithUpdate - await verifyImportingWithNameValue('withNameValueParent', SAMPLE_ALIQUOT_IMPORT_TYPE_NAME); + await verifyImportingWithNameValue(selectRandomN(parentSampleName, 1)[0], SAMPLE_ALIQUOT_IMPORT_TYPE_NAME); }); /** @@ -583,8 +589,8 @@ describe('Aliquot crud', () => { * *

    */ - it('testImportingWithNameValue - without naming patten', async () => { - await verifyImportingWithNameValue('withNameValueParentNoPattern', SAMPLE_ALIQUOT_IMPORT_NO_NAME_PATTERN_NAME); + it('(Fuzz Test) testImportingWithNameValue - without naming patten', async () => { + await verifyImportingWithNameValue(selectRandomN(parentSampleName, 1)[0], SAMPLE_ALIQUOT_IMPORT_NO_NAME_PATTERN_NAME); }); async function verifyMultipleRootsAndAliquots(parentSampleName1: string, parentSampleName2: string, sampleType: string) { From 00d4e819d65b50ad11f0704ec59e36fa82591a3f Mon Sep 17 00:00:00 2001 From: XingY Date: Wed, 16 Jul 2025 12:36:23 -0700 Subject: [PATCH 2/3] limit change to sample import only --- .../labkey/api/query/AbstractQueryImportAction.java | 1 - .../controllers/exp/ExperimentController.java | 10 +++++----- 2 files changed, 5 insertions(+), 6 deletions(-) diff --git a/api/src/org/labkey/api/query/AbstractQueryImportAction.java b/api/src/org/labkey/api/query/AbstractQueryImportAction.java index 5a4e3d0df97..a01610f199d 100644 --- a/api/src/org/labkey/api/query/AbstractQueryImportAction.java +++ b/api/src/org/labkey/api/query/AbstractQueryImportAction.java @@ -703,7 +703,6 @@ public static void configureLoader(DataLoader loader, @Nullable TableInfo target String name = col.name.toLowerCase(); if (ExperimentService.isInputOutputColumn(col.name) || name.equalsIgnoreCase("Name") || /* Issue 50710: Treat "Name" column as a string value for sample or data class import */ - name.equalsIgnoreCase(ExpMaterial.ALIQUOTED_FROM_INPUT) || /* Issue 53419: Aliquot parent with number like names that starts with leading zeroes aren't resolved during import */ (lineageAliasNames != null && lineageAliasNames.contains(name)) ) { col.clazz = String.class; diff --git a/experiment/src/org/labkey/experiment/controllers/exp/ExperimentController.java b/experiment/src/org/labkey/experiment/controllers/exp/ExperimentController.java index 0086c905888..710cb334ff2 100644 --- a/experiment/src/org/labkey/experiment/controllers/exp/ExperimentController.java +++ b/experiment/src/org/labkey/experiment/controllers/exp/ExperimentController.java @@ -4413,6 +4413,9 @@ protected Map getRenamedColumns() @Override protected @Nullable Set getLineageImportAliases() throws IOException { + Set aliases = new CaseInsensitiveHashSet(); + // Issue 53419: Aliquot parent with number like names that starts with leading zeroes aren't resolved during import + aliases.add(ExpMaterial.ALIQUOTED_FROM_INPUT); boolean crossTypeImport = getOptionParamValue(AbstractQueryImportAction.Params.crossTypeImport); // Issue 51894: We need to stop conversion to numbers for alias fields for all type // If there are aliases defined for one type that are number fields in another type, this will prevent @@ -4421,18 +4424,15 @@ protected Map getRenamedColumns() if (crossTypeImport) { List sampleTypes = SampleTypeServiceImpl.get().getSampleTypes(getContainer(), getUser(), true); - Set aliases = new CaseInsensitiveHashSet(); for (ExpSampleTypeImpl sampleType : sampleTypes) - { aliases.addAll(sampleType.getImportAliases().keySet()); - } - return aliases; } else { ExpSampleTypeImpl sampleType = SampleTypeServiceImpl.get().getSampleType(getContainer(), getUser(), _form.getQueryName()); - return new CaseInsensitiveHashSet(sampleType.getImportAliases().keySet()); + aliases.addAll(sampleType.getImportAliases().keySet()); } + return aliases; } @Override From 6aee0471d531424e6e216893abaee780804657ba Mon Sep 17 00:00:00 2001 From: XingY Date: Wed, 16 Jul 2025 12:54:26 -0700 Subject: [PATCH 3/3] clean --- api/src/org/labkey/api/query/AbstractQueryImportAction.java | 1 - 1 file changed, 1 deletion(-) diff --git a/api/src/org/labkey/api/query/AbstractQueryImportAction.java b/api/src/org/labkey/api/query/AbstractQueryImportAction.java index a01610f199d..e5ada4d6baa 100644 --- a/api/src/org/labkey/api/query/AbstractQueryImportAction.java +++ b/api/src/org/labkey/api/query/AbstractQueryImportAction.java @@ -40,7 +40,6 @@ import org.labkey.api.dataiterator.DataIterator; import org.labkey.api.dataiterator.DataIteratorContext; import org.labkey.api.dataiterator.DetailedAuditLogDataIterator; -import org.labkey.api.exp.api.ExpMaterial; import org.labkey.api.exp.api.ExperimentService; import org.labkey.api.gwt.client.AuditBehaviorType; import org.labkey.api.module.Module;