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Merged
labkey-jeckels merged 1 commit into from
Dec 3, 2025
Merged

Continue adopting FileLike instead of File or Path #186

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53 changes: 0 additions & 53 deletions genotyping/src/org/labkey/genotyping/sequences/AlleleFastaLoader.java
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3 changes: 2 additions & 1 deletion genotyping/test/src/org/labkey/test/tests/GenotypingTest.java
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Original file line numberDiff line numberDiff line change
Expand Up@@ -19,6 +19,7 @@
import org.junit.BeforeClass;
import org.junit.Test;
import org.junit.experimental.categories.Category;
import org.labkey.api.util.FileUtil;
import org.labkey.test.BaseWebDriverTest;
import org.labkey.test.Locator;
import org.labkey.test.categories.CustomModules;
Expand DownExpand Up@@ -118,7 +119,7 @@ private void receiveDataFromGalaxyServer()
String analysisFolder = "analysis_" + getRunNumber();
for (String file: filesToCopy)
{
copyFile(new File(getPipelineLoc(), file), new File(getPipelineLoc(), analysisFolder + "/" + file));
copyFile(FileUtil.appendName(getPipelineLoc(), file), FileUtil.appendName(FileUtil.appendName(getPipelineLoc(), analysisFolder), file));
}
refresh();
waitForPipelineJobsToComplete(++pipelineJobCount, "Import genotyping analysis", false);
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3 changes: 2 additions & 1 deletion genotyping/test/src/org/labkey/test/tests/IlluminaTest.java
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Original file line numberDiff line numberDiff line change
Expand Up@@ -19,6 +19,7 @@
import org.junit.BeforeClass;
import org.junit.Test;
import org.junit.experimental.categories.Category;
import org.labkey.api.util.FileUtil;
import org.labkey.serverapi.reader.Readers;
import org.labkey.test.BaseWebDriverTest;
import org.labkey.test.Locator;
Expand DownExpand Up@@ -90,7 +91,7 @@ public void testSteps() throws Exception
//https://docs.google.com/a/labkey.com/file/d/0B45Fm0-0-NLtdmpDR1hKaW5jSWc/edit
private void verifyCleanIlluminaSampleSheets()
{
importFolderFromZip(new File(getPipelineLoc(), "genoCleanSamples.folder.zip"), true, 2);
importFolderFromZip(FileUtil.appendName(getPipelineLoc(), "genoCleanSamples.folder.zip"), true, 2);
goToProjectHome();
click(Locator.linkWithText("Samples"));
waitForText("SIVkcol2");
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