Skip to content

Commit 70058a9

Browse files
bbimberbbimber
committed
Bugfix to serialization of Map<Long, Long>
1 parent 265ad09 commit 70058a9

File tree

1 file changed

+20
-19
lines changed

1 file changed

+20
-19
lines changed

‎singlecell/src/org/labkey/singlecell/CellHashingServiceImpl.java‎

Lines changed: 20 additions & 19 deletions
Original file line numberDiff line numberDiff line change
@@ -48,6 +48,7 @@
4848
import org.labkey.api.singlecell.model.Sample;
4949
import org.labkey.api.singlecell.model.Sort;
5050
import org.labkey.api.singlecell.pipeline.SeuratToolParameter;
51+
import org.labkey.api.util.FileUtil;
5152
import org.labkey.api.util.PageFlowUtil;
5253
import org.labkey.api.writer.PrintWriters;
5354
import org.labkey.singlecell.run.CellRangerFeatureBarcodeHandler;
@@ -518,12 +519,12 @@ else if (genomeIds.size() > 1)
518519

519520
public File getValidCiteSeqBarcodeFile(File sourceDir, long gexReadsetId)
520521
{
521-
return new File(sourceDir, "validADTS." + gexReadsetId + ".csv");
522+
return FileUtil.appendName(sourceDir, "validADTS." + gexReadsetId + ".csv");
522523
}
523524

524525
public File getValidCiteSeqBarcodeMetadataFile(File sourceDir, long gexReadsetId)
525526
{
526-
return new File(sourceDir, "validADTS." + gexReadsetId + ".metadata.txt");
527+
return FileUtil.appendName(sourceDir, "validADTS." + gexReadsetId + ".metadata.txt");
527528
}
528529

529530
private void writeCiteSeqBarcodes(PipelineJob job, Map<Long, Set<String>> gexToPanels, File outputDir) throws PipelineJobException
@@ -585,7 +586,7 @@ private void writeCiteSeqBarcodes(PipelineJob job, Map<Long, Set<String>> gexToP
585586

586587
public File getValidHashingBarcodeFile(File sourceDir)
587588
{
588-
return new File(sourceDir, "validHashingBarcodes.csv");
589+
return FileUtil.appendName(sourceDir, "validHashingBarcodes.csv");
589590
}
590591

591592
@Override
@@ -725,7 +726,7 @@ public File generateHashingCallsForRawMatrix(Readset parentReadset, PipelineOutp
725726

726727
private Map<Long, Long> getCachedCiteSeqReadsetMap(SequenceAnalysisJobSupport support) throws PipelineJobException
727728
{
728-
return support.getCachedObject(READSET_TO_CITESEQ_MAP, PipelineJob.createObjectMapper().getTypeFactory().constructParametricType(Map.class, Integer.class, Integer.class));
729+
return support.getCachedObject(READSET_TO_CITESEQ_MAP, LongHashMap.class);
729730
}
730731

731732
@Override
@@ -784,7 +785,7 @@ public File getH5FileForGexReadset(SequenceAnalysisJobSupport support, long read
784785
throw new PipelineJobException("Unable to find loupe file: " + loupe.getPath());
785786
}
786787

787-
File h5 = new File(loupe.getParentFile(), "raw_feature_bc_matrix.h5");
788+
File h5 = FileUtil.appendName(loupe.getParentFile(), "raw_feature_bc_matrix.h5");
788789
if (!h5.exists())
789790
{
790791
throw new PipelineJobException("Unable to find h5 file: " + h5.getPath());
@@ -796,12 +797,12 @@ public File getH5FileForGexReadset(SequenceAnalysisJobSupport support, long read
796797
@Override
797798
public File getCDNAInfoFile(File sourceDir)
798799
{
799-
return new File(sourceDir, "cDNAInfo.txt");
800+
return FileUtil.appendName(sourceDir, "cDNAInfo.txt");
800801
}
801802

802803
public Map<Long, Long> getCachedHashingReadsetMap(SequenceAnalysisJobSupport support) throws PipelineJobException
803804
{
804-
return support.getCachedObject(READSET_TO_HASHING_MAP, PipelineJob.createObjectMapper().getTypeFactory().constructParametricType(Map.class, Integer.class, Integer.class));
805+
return support.getCachedObject(READSET_TO_HASHING_MAP, LongHashMap.class);
805806
}
806807

807808
public File getCachedReadsetToCountMatrix(SequenceAnalysisJobSupport support, long readsetId, CellHashingService.BARCODE_TYPE type) throws PipelineJobException
@@ -1033,7 +1034,7 @@ public List<ToolParameterDescriptor> getHashingCallingParams(boolean allowMethod
10331034

10341035
public File getAllHashingBarcodesFile(File webserverDir)
10351036
{
1036-
return new File(webserverDir, BARCODE_TYPE.hashing.getAllBarcodeFileName());
1037+
return FileUtil.appendName(webserverDir, BARCODE_TYPE.hashing.getAllBarcodeFileName());
10371038
}
10381039

10391040
private void writeAllHashingBarcodes(Collection<String> groupNames, User u, Container c, File webserverDir) throws PipelineJobException
@@ -1154,12 +1155,12 @@ else if ("Negative".equals(line[htoClassIdx]))
11541155

11551156
private File getExpectedCallsFile(File outputDir, String basename)
11561157
{
1157-
return new File(outputDir, basename + CALL_EXTENSION);
1158+
return FileUtil.appendName(outputDir, basename + CALL_EXTENSION);
11581159
}
11591160

11601161
private File getMolInfoFileFromCounts(File citeSeqCountOutDir)
11611162
{
1162-
return new File(citeSeqCountOutDir.getParentFile(), "molecule_info.h5");
1163+
return FileUtil.appendName(citeSeqCountOutDir.getParentFile(), "molecule_info.h5");
11631164
}
11641165

11651166
public File generateCellHashingCalls(File citeSeqCountOutDir, File outputDir, String basename, Logger log, File localPipelineDir, CellHashingService.CellHashingParameters parameters, PipelineContext ctx) throws PipelineJobException
@@ -1195,11 +1196,11 @@ public File generateCellHashingCalls(File citeSeqCountOutDir, File outputDir, St
11951196
File cellBarcodeWhitelistFile = parameters.cellBarcodeWhitelistFile;
11961197
inputFiles.add(cellBarcodeWhitelistFile);
11971198

1198-
File htmlFile = new File(outputDir, basename + ".html");
1199-
File localHtml = new File(localPipelineDir, htmlFile.getName());
1199+
File htmlFile = FileUtil.appendName(outputDir, basename + ".html");
1200+
File localHtml = FileUtil.appendName(localPipelineDir, htmlFile.getName());
12001201

1201-
File countFile = new File(outputDir, basename + ".rawCounts.rds");
1202-
File localCounts = new File(localPipelineDir, countFile.getName());
1202+
File countFile = FileUtil.appendName(outputDir, basename + ".rawCounts.rds");
1203+
File localCounts = FileUtil.appendName(localPipelineDir, countFile.getName());
12031204

12041205
// Note: if this job fails and then is resumed, having that pre-existing copy of the HTML can pose a problem
12051206
if (localHtml.exists())
@@ -1219,7 +1220,7 @@ public File generateCellHashingCalls(File citeSeqCountOutDir, File outputDir, St
12191220
metricsFile.delete();
12201221
}
12211222

1222-
File localRScript = new File(outputDir, "generateCallsWrapper.R");
1223+
File localRScript = FileUtil.appendName(outputDir, "generateCallsWrapper.R");
12231224
try (PrintWriter writer = PrintWriters.getPrintWriter(localRScript))
12241225
{
12251226
String cellbarcodeWhitelist = cellBarcodeWhitelistFile != null ? "'" + cellBarcodeWhitelistFile.getPath() + "'" : "NULL";
@@ -1394,7 +1395,7 @@ public void copyHtmlLocally(SequenceOutputHandler.JobContext ctx) throws Pipelin
13941395
if (f.getName().endsWith(".hashing.html"))
13951396
{
13961397
ctx.getLogger().info("Copying hashing HTML locally for debugging: " + f.getName());
1397-
File target = new File(ctx.getSourceDirectory(), f.getName());
1398+
File target = FileUtil.appendName(ctx.getSourceDirectory(), f.getName());
13981399
if (target.exists())
13991400
{
14001401
target.delete();
@@ -1461,7 +1462,7 @@ public Set<String> getHtosForReadset(Long hashingReadsetId, File webserverJobDir
14611462
public File subsetBarcodes(File allCellBarcodes, @Nullable String barcodePrefix) throws PipelineJobException
14621463
{
14631464
//Subset barcodes by dataset:
1464-
File output = new File(allCellBarcodes.getParentFile(), "cellBarcodeWhitelist." + (barcodePrefix == null ? "all" : barcodePrefix ) + ".txt");
1465+
File output = FileUtil.appendName(allCellBarcodes.getParentFile(), "cellBarcodeWhitelist." + (barcodePrefix == null ? "all" : barcodePrefix ) + ".txt");
14651466
try (CSVReader reader = new CSVReader(Readers.getReader(allCellBarcodes), '\t'); CSVWriter writer = new CSVWriter(PrintWriters.getPrintWriter(output), '\t', CSVWriter.NO_QUOTE_CHARACTER))
14661467
{
14671468
String[] line;
@@ -1490,7 +1491,7 @@ public File getCellBarcodesFromSeurat(File seuratObj)
14901491

14911492
public File getCellBarcodesFromSeurat(File seuratObj, boolean throwIfNotFound)
14921493
{
1493-
File barcodes = new File(seuratObj.getParentFile(), seuratObj.getName().replaceAll("seurat.rds$", "cellBarcodes.csv"));
1494+
File barcodes = FileUtil.appendName(seuratObj.getParentFile(), seuratObj.getName().replaceAll("seurat.rds$", "cellBarcodes.csv"));
14941495
if (throwIfNotFound && !barcodes.exists())
14951496
{
14961497
throw new IllegalArgumentException("Unable to find expected cell barcodes file. This might indicate the seurat object was created with an older version of the pipeline. Expected: " + barcodes.getPath());
@@ -1506,7 +1507,7 @@ public File getMetaTableFromSeurat(File seuratObj)
15061507

15071508
public File getMetaTableFromSeurat(File seuratObj, boolean throwIfNotFound)
15081509
{
1509-
File barcodes = new File(seuratObj.getParentFile(), seuratObj.getName().replaceAll("seurat.rds$", "seurat.meta.txt.gz"));
1510+
File barcodes = FileUtil.appendName(seuratObj.getParentFile(), seuratObj.getName().replaceAll("seurat.rds$", "seurat.meta.txt.gz"));
15101511
if (throwIfNotFound && !barcodes.exists())
15111512
{
15121513
throw new IllegalArgumentException("Unable to find expected metadata file. This might indicate the seurat object was created with an older version of the pipeline. Expected: " + barcodes.getPath());

0 commit comments

Comments
 (0)