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FileSystemLike #222

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labkey-matthewb wants to merge 3 commits into from
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FileSystemLike #222

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5dcca2b
ModuleLoader interface change
labkey-matthewb Sep 11, 2024
b000cbf
Merge remote-tracking branch 'origin/develop' into fb_authorizedfiles…
labkey-matthewb Sep 25, 2024
dc911ce
FileSystemLike and FileLike interfaces
labkey-matthewb Sep 26, 2024
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7 changes: 4 additions & 3 deletions tcrdb/src/org/labkey/tcrdb/pipeline/MiXCRWrapper.java
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Original file line number Diff line number Diff line change
Expand Up @@ -7,6 +7,8 @@
import org.labkey.api.reader.Readers;
import org.labkey.api.sequenceanalysis.pipeline.SequencePipelineService;
import org.labkey.api.sequenceanalysis.run.AbstractCommandWrapper;
import org.labkey.api.util.Path;
import org.labkey.vfs.FileLike;

import java.io.BufferedReader;
import java.io.File;
Expand Down Expand Up @@ -353,11 +355,10 @@ private List<String> getBaseArgs()

private File getJAR()
{
File jar = new File(ModuleLoader.getInstance().getWebappDir(), "WEB-INF/lib");
jar = new File(jar, "mixcr.jar");
FileLike jar = ModuleLoader.getInstance().getWebappDir().resolveFile(new Path("WEB-INF","lib","mixcr.jar"));
if (jar.exists())
{
return jar;
return jar.toNioPathForRead().toFile();
}

return SequencePipelineService.get().getExeForPackage("mixcr", "mixcr.jar");
Expand Down