diff --git a/QueryExtensions/src/org/labkey/queryextensions/QueryExtensionsModule.java b/QueryExtensions/src/org/labkey/queryextensions/QueryExtensionsModule.java index d383227e4..464f1f01c 100644 --- a/QueryExtensions/src/org/labkey/queryextensions/QueryExtensionsModule.java +++ b/QueryExtensions/src/org/labkey/queryextensions/QueryExtensionsModule.java @@ -40,7 +40,7 @@ public String getName() @Override public @Nullable Double getSchemaVersion() { - return 23.000; + return 25.000; } @Override @@ -81,4 +81,4 @@ public Set getSchemaNames() { return Collections.singleton(QueryExtensionsSchema.NAME); } -} \ No newline at end of file +} diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisController.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisController.java index a5a70b813..d0b60e255 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisController.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisController.java @@ -2151,7 +2151,7 @@ protected File getTargetFile(String filename) throws IOException File targetDirectory = root.getRootPath(); - return AssayFileWriter.findUniqueFileName(filename, targetDirectory); + return FileUtil.findUniqueFileName(filename, targetDirectory); } @Override @@ -2449,7 +2449,7 @@ protected File getTargetFile(String filename) throws IOException try { FileLike targetDirectory = AssayFileWriter.ensureUploadDirectory(getContainer(), "sequenceOutputs"); - return AssayFileWriter.findUniqueFileName(filename, targetDirectory).toNioPathForWrite().toFile(); + return FileUtil.findUniqueFileName(filename, targetDirectory).toNioPathForWrite().toFile(); } catch (ExperimentException e) { @@ -2582,7 +2582,7 @@ protected File getTargetFile(String filename) throws IOException try { FileLike targetDirectory = AssayFileWriter.ensureUploadDirectory(getContainer()); - return AssayFileWriter.findUniqueFileName(filename, targetDirectory).toNioPathForWrite().toFile(); + return FileUtil.findUniqueFileName(filename, targetDirectory).toNioPathForWrite().toFile(); } catch (ExperimentException e) { @@ -2747,7 +2747,7 @@ protected File getTargetFile(String filename) throws IOException try { FileLike targetDirectory = AssayFileWriter.ensureUploadDirectory(getContainer()); - return AssayFileWriter.findUniqueFileName(filename, targetDirectory).toNioPathForWrite().toFile(); + return FileUtil.findUniqueFileName(filename, targetDirectory).toNioPathForWrite().toFile(); } catch (ExperimentException e) { @@ -4089,7 +4089,7 @@ public ApiResponse execute(ImportOutputFilesForm form, BindException errors) thr for (File file : toCreate.keySet()) { - FileLike target = AssayFileWriter.findUniqueFileName(file.getName(), targetDirectory); + FileLike target = FileUtil.findUniqueFileName(file.getName(), targetDirectory); FileUtils.moveFile(file, target.toNioPathForWrite().toFile()); ExpData data = ExperimentService.get().createData(getContainer(), new DataType("Sequence Output")); diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisManager.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisManager.java index 930469cc7..006ac7031 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisManager.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisManager.java @@ -24,7 +24,6 @@ import org.jetbrains.annotations.Nullable; import org.junit.Assert; import org.junit.Test; -import org.labkey.api.assay.AssayFileWriter; import org.labkey.api.collections.CaseInsensitiveHashMap; import org.labkey.api.data.CompareType; import org.labkey.api.data.Container; @@ -67,6 +66,7 @@ import org.labkey.api.sequenceanalysis.RefNtSequenceModel; import org.labkey.api.sequenceanalysis.SequenceOutputFile; import org.labkey.api.sequenceanalysis.pipeline.SequenceOutputHandler; +import org.labkey.api.util.FileUtil; import org.labkey.api.util.Job; import org.labkey.api.util.JobRunner; import org.labkey.api.util.PageFlowUtil; @@ -827,7 +827,7 @@ public void addChainFile(Container c, User u, File file, int genomeId1, int geno //create file String expectedName = "chain-" + genomeId1 + "to" + genomeId2 + ".chain"; - File outputFile = AssayFileWriter.findUniqueFileName(expectedName, targetDir); + File outputFile = FileUtil.findUniqueFileName(expectedName, targetDir); FileUtils.moveFile(file, outputFile); ExpData chainFile = ExperimentService.get().createData(c, new DataType("Sequence Track")); @@ -939,4 +939,4 @@ public void testJars() assertTrue("fastqcDir dir does not exist: " + fastqcDir.getPath(), fastqcDir.exists()); } } -} \ No newline at end of file +} diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/ImportFastaSequencesPipelineJob.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/ImportFastaSequencesPipelineJob.java index 524f6822b..4b840766d 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/ImportFastaSequencesPipelineJob.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/ImportFastaSequencesPipelineJob.java @@ -69,7 +69,7 @@ public static File createLocalDirectory(PipeRoot pipeRoot) throws IOException AssayFileWriter writer = new AssayFileWriter(); String folderName = "SequenceImport_" + FileUtil.getTimestamp(); - webserverOutDir = AssayFileWriter.findUniqueFileName(folderName, webserverOutDir); + webserverOutDir = FileUtil.findUniqueFileName(folderName, webserverOutDir); if (!webserverOutDir.exists()) { webserverOutDir.mkdirs(); diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/ImportGenomeTrackTask.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/ImportGenomeTrackTask.java index 5c6498d0c..adfeeee4a 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/ImportGenomeTrackTask.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/ImportGenomeTrackTask.java @@ -33,7 +33,6 @@ import org.apache.commons.lang3.StringUtils; import org.apache.commons.lang3.SystemUtils; import org.jetbrains.annotations.Nullable; -import org.labkey.api.assay.AssayFileWriter; import org.labkey.api.collections.CaseInsensitiveHashMap; import org.labkey.api.data.CompareType; import org.labkey.api.data.Container; @@ -61,6 +60,7 @@ import org.labkey.api.sequenceanalysis.pipeline.ReferenceGenomeManager; import org.labkey.api.sequenceanalysis.pipeline.SequencePipelineService; import org.labkey.api.util.FileType; +import org.labkey.api.util.FileUtil; import org.labkey.api.util.Job; import org.labkey.api.util.JobRunner; import org.labkey.api.util.PageFlowUtil; @@ -354,7 +354,7 @@ private void sortGxf(File gxf) throws PipelineJobException } private File getOutputFile(File file, File tracksDir) { - return AssayFileWriter.findUniqueFileName(file.getName().replaceAll(" ", "_"), tracksDir); + return FileUtil.findUniqueFileName(file.getName().replaceAll(" ", "_"), tracksDir); } private Map> getNameTranslationMap(List refNtSequenceModels) throws PipelineJobException diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/SequenceJob.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/SequenceJob.java index 80fddbc7f..8bab610b5 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/SequenceJob.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/SequenceJob.java @@ -10,7 +10,6 @@ import org.json.JSONObject; import org.junit.Assert; import org.junit.Test; -import org.labkey.api.assay.AssayFileWriter; import org.labkey.api.data.Container; import org.labkey.api.data.ContainerManager; import org.labkey.api.exp.api.DataType; @@ -164,7 +163,7 @@ protected void addCustomParams(JSONObject params) private Path _getLogFile() { - var file = AssayFileWriter.findUniqueFileName((FileUtil.makeLegalName(_jobName) + ".log"), getDataDirectoryFileObject()); + var file = FileUtil.findUniqueFileName((FileUtil.makeLegalName(_jobName) + ".log"), getDataDirectoryFileObject()); return file.toNioPathForWrite(); } @@ -228,7 +227,7 @@ protected FileLike createLocalDirectory(PipeRoot pipeRoot) throws IOException } String folderName = FileUtil.makeLegalName(StringUtils.capitalize(_folderPrefix) + "_" + FileUtil.getTimestamp()); - webserverOutDir = AssayFileWriter.findUniqueFileName(folderName, webserverOutDir); + webserverOutDir = FileUtil.findUniqueFileName(folderName, webserverOutDir); if (!webserverOutDir.exists()) { webserverOutDir.mkdir(); @@ -681,4 +680,4 @@ public File getLocationForCachedInputs(WorkDirectory wd, boolean createIfDoesntE return ret; } -} \ No newline at end of file +} diff --git a/blast/src/org/labkey/blast/BLASTController.java b/blast/src/org/labkey/blast/BLASTController.java index 06ec27082..d93458b8a 100644 --- a/blast/src/org/labkey/blast/BLASTController.java +++ b/blast/src/org/labkey/blast/BLASTController.java @@ -50,6 +50,7 @@ import org.labkey.api.security.permissions.ReadPermission; import org.labkey.api.security.permissions.UpdatePermission; import org.labkey.api.util.ExceptionUtil; +import org.labkey.api.util.FileUtil; import org.labkey.api.util.PageFlowUtil; import org.labkey.api.util.Pair; import org.labkey.api.util.StringUtilsLabKey; @@ -217,7 +218,7 @@ protected File getTargetFile(String filename) throws IOException try { FileLike targetDirectory = AssayFileWriter.ensureUploadDirectory(getContainer()); - return AssayFileWriter.findUniqueFileName(filename, targetDirectory).toNioPathForWrite().toFile(); + return FileUtil.findUniqueFileName(filename, targetDirectory).toNioPathForWrite().toFile(); } catch (ExperimentException e) { @@ -265,7 +266,7 @@ public String getResponse(RunBlastForm form, Map> fil try { FileLike targetDirectory = AssayFileWriter.ensureUploadDirectory(getContainer()); - FileLike input = AssayFileWriter.findUniqueFileName("blast", targetDirectory); + FileLike input = FileUtil.findUniqueFileName("blast", targetDirectory); input.createFile(); try (PrintWriter fw = PrintWriters.getPrintWriter(input.openOutputStream())) { diff --git a/jbrowse/src/org/labkey/jbrowse/pipeline/JBrowseLucenePipelineJob.java b/jbrowse/src/org/labkey/jbrowse/pipeline/JBrowseLucenePipelineJob.java index 4ae81ac0f..f72f9cfe0 100644 --- a/jbrowse/src/org/labkey/jbrowse/pipeline/JBrowseLucenePipelineJob.java +++ b/jbrowse/src/org/labkey/jbrowse/pipeline/JBrowseLucenePipelineJob.java @@ -3,7 +3,6 @@ import org.apache.commons.io.FileUtils; import org.apache.commons.lang3.SystemUtils; import org.apache.logging.log4j.Logger; -import org.labkey.api.assay.AssayFileWriter; import org.labkey.api.data.Container; import org.labkey.api.files.FileUrls; import org.labkey.api.module.Module; @@ -59,7 +58,7 @@ public JBrowseLucenePipelineJob(Container c, User user, PipeRoot pipeRoot, Strin _infoFields = infoFields; _allowLenientLuceneProcessing = allowLenientLuceneProcessing; - setLogFile(AssayFileWriter.findUniqueFileName("jbrowse-lucene" + new GUID() + ".log", JBrowseManager.get().getBaseDir(c, true))); + setLogFile(FileUtil.findUniqueFileName("jbrowse-lucene" + new GUID() + ".log", JBrowseManager.get().getBaseDir(c, true))); } public static class JBrowseLucenePipelineProvider extends PipelineProvider diff --git a/jbrowse/src/org/labkey/jbrowse/pipeline/JBrowseSessionPipelineJob.java b/jbrowse/src/org/labkey/jbrowse/pipeline/JBrowseSessionPipelineJob.java index f008441e4..0ab53b118 100644 --- a/jbrowse/src/org/labkey/jbrowse/pipeline/JBrowseSessionPipelineJob.java +++ b/jbrowse/src/org/labkey/jbrowse/pipeline/JBrowseSessionPipelineJob.java @@ -1,7 +1,6 @@ package org.labkey.jbrowse.pipeline; import org.jetbrains.annotations.Nullable; -import org.labkey.api.assay.AssayFileWriter; import org.labkey.api.data.Container; import org.labkey.api.data.ContainerManager; import org.labkey.api.data.SimpleFilter; @@ -15,6 +14,7 @@ import org.labkey.api.query.DetailsURL; import org.labkey.api.query.FieldKey; import org.labkey.api.security.User; +import org.labkey.api.util.FileUtil; import org.labkey.api.util.GUID; import org.labkey.api.util.PageFlowUtil; import org.labkey.api.view.ActionURL; @@ -101,7 +101,7 @@ private JBrowseSessionPipelineJob(Container c, User user, PipeRoot pipeRoot, Lis _sourceContainerId = databaseGuid == null ? getContainerId() : getSourceContainerId(databaseGuid); _mode = mode; - setLogFile(AssayFileWriter.findUniqueFileName("jbrowse-" + new GUID() + ".log", JBrowseManager.get().getBaseDir(c, true))); + setLogFile(FileUtil.findUniqueFileName("jbrowse-" + new GUID() + ".log", JBrowseManager.get().getBaseDir(c, true))); } private JBrowseSessionPipelineJob(Container c, User user, PipeRoot pipeRoot, String name, String description, Integer libraryId, List trackIds, List outputFileIds, @Nullable String existingDatabaseGuid, boolean isTemporarySession) @@ -118,7 +118,7 @@ private JBrowseSessionPipelineJob(Container c, User user, PipeRoot pipeRoot, Str _sourceContainerId = existingDatabaseGuid == null ? getContainerId() : getSourceContainerId(existingDatabaseGuid); _isTemporarySession = isTemporarySession; - setLogFile(AssayFileWriter.findUniqueFileName("jbrowse-" + _databaseGuid + ".log", JBrowseManager.get().getBaseDir(c, true))); + setLogFile(FileUtil.findUniqueFileName("jbrowse-" + _databaseGuid + ".log", JBrowseManager.get().getBaseDir(c, true))); } private String getSourceContainerId(String databaseGuid)