Merge remote-tracking branch 'origin/develop' into fb_migrate_ss_to_pg

labkey-adam · labkey-adam · commit c41b783db99a · 2025-07-30T23:01:37.000-07:00
diff --git 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<String> getSchemaNames()
     {
         return Collections.singleton(QueryExtensionsSchema.NAME);
     }
-}
+}
diff --git 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
@@ -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());
         }
     }
-}
+}
diff --git 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
@@ -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<String, Pair<String, Integer>> getNameTranslationMap(List<RefNtSequenceModel> refNtSequenceModels) throws PipelineJobException
diff --git 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;
     }
-}
+}
diff --git 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<String, Pair<File, String>> 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
@@ -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
@@ -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<Integer> trackIds, List<Integer> 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)

Original file line number	Diff line number	Diff line change
`@@ -40,7 +40,7 @@ public String getName()`
`40`	`40`	`@Override`
`41`	`41`	`public @Nullable Double getSchemaVersion()`
`42`	`42`	`{`
`43`		`- return 23.000;`
	`43`	`+ return 25.000;`
`44`	`44`	`}`
`45`	`45`
`46`	`46`	`@Override`
`@@ -81,4 +81,4 @@ public Set<String> getSchemaNames()`
`81`	`81`	`{`
`82`	`82`	`return Collections.singleton(QueryExtensionsSchema.NAME);`
`83`	`83`	`}`
`84`		`-}`
	`84`	`+}`
Original file line number	Diff line number	Diff line change
`@@ -2151,7 +2151,7 @@ protected File getTargetFile(String filename) throws IOException`
`2151`	`2151`
`2152`	`2152`	`File targetDirectory = root.getRootPath();`
`2153`	`2153`
`2154`		`- return AssayFileWriter.findUniqueFileName(filename, targetDirectory);`
	`2154`	`+ return FileUtil.findUniqueFileName(filename, targetDirectory);`
`2155`	`2155`	`}`
`2156`	`2156`
`2157`	`2157`	`@Override`
`@@ -2449,7 +2449,7 @@ protected File getTargetFile(String filename) throws IOException`
`2449`	`2449`	`try`
`2450`	`2450`	`{`
`2451`	`2451`	`FileLike targetDirectory = AssayFileWriter.ensureUploadDirectory(getContainer(), "sequenceOutputs");`
`2452`		`- return AssayFileWriter.findUniqueFileName(filename, targetDirectory).toNioPathForWrite().toFile();`
	`2452`	`+ return FileUtil.findUniqueFileName(filename, targetDirectory).toNioPathForWrite().toFile();`
`2453`	`2453`	`}`
`2454`	`2454`	`catch (ExperimentException e)`
`2455`	`2455`	`{`
`@@ -2582,7 +2582,7 @@ protected File getTargetFile(String filename) throws IOException`
`2582`	`2582`	`try`
`2583`	`2583`	`{`
`2584`	`2584`	`FileLike targetDirectory = AssayFileWriter.ensureUploadDirectory(getContainer());`
`2585`		`- return AssayFileWriter.findUniqueFileName(filename, targetDirectory).toNioPathForWrite().toFile();`
	`2585`	`+ return FileUtil.findUniqueFileName(filename, targetDirectory).toNioPathForWrite().toFile();`
`2586`	`2586`	`}`
`2587`	`2587`	`catch (ExperimentException e)`
`2588`	`2588`	`{`
`@@ -2747,7 +2747,7 @@ protected File getTargetFile(String filename) throws IOException`
`2747`	`2747`	`try`
`2748`	`2748`	`{`
`2749`	`2749`	`FileLike targetDirectory = AssayFileWriter.ensureUploadDirectory(getContainer());`
`2750`		`- return AssayFileWriter.findUniqueFileName(filename, targetDirectory).toNioPathForWrite().toFile();`
	`2750`	`+ return FileUtil.findUniqueFileName(filename, targetDirectory).toNioPathForWrite().toFile();`
`2751`	`2751`	`}`
`2752`	`2752`	`catch (ExperimentException e)`
`2753`	`2753`	`{`
`@@ -4089,7 +4089,7 @@ public ApiResponse execute(ImportOutputFilesForm form, BindException errors) thr`
`4089`	`4089`
`4090`	`4090`	`for (File file : toCreate.keySet())`
`4091`	`4091`	`{`
`4092`		`- FileLike target = AssayFileWriter.findUniqueFileName(file.getName(), targetDirectory);`
	`4092`	`+ FileLike target = FileUtil.findUniqueFileName(file.getName(), targetDirectory);`
`4093`	`4093`	`FileUtils.moveFile(file, target.toNioPathForWrite().toFile());`
`4094`	`4094`
`4095`	`4095`	`ExpData data = ExperimentService.get().createData(getContainer(), new DataType("Sequence Output"));`
Original file line number	Diff line number	Diff line change
`@@ -69,7 +69,7 @@ public static File createLocalDirectory(PipeRoot pipeRoot) throws IOException`
`69`	`69`
`70`	`70`	`AssayFileWriter writer = new AssayFileWriter();`
`71`	`71`	`String folderName = "SequenceImport_" + FileUtil.getTimestamp();`
`72`		`- webserverOutDir = AssayFileWriter.findUniqueFileName(folderName, webserverOutDir);`
	`72`	`+ webserverOutDir = FileUtil.findUniqueFileName(folderName, webserverOutDir);`
`73`	`73`	`if (!webserverOutDir.exists())`
`74`	`74`	`{`
`75`	`75`	`webserverOutDir.mkdirs();`
Original file line number	Diff line number	Diff line change
`@@ -10,7 +10,6 @@`
`10`	`10`	`import org.json.JSONObject;`
`11`	`11`	`import org.junit.Assert;`
`12`	`12`	`import org.junit.Test;`
`13`		`-import org.labkey.api.assay.AssayFileWriter;`
`14`	`13`	`import org.labkey.api.data.Container;`
`15`	`14`	`import org.labkey.api.data.ContainerManager;`
`16`	`15`	`import org.labkey.api.exp.api.DataType;`
`@@ -164,7 +163,7 @@ protected void addCustomParams(JSONObject params)`
`164`	`163`
`165`	`164`	`private Path _getLogFile()`
`166`	`165`	`{`
`167`		`- var file = AssayFileWriter.findUniqueFileName((FileUtil.makeLegalName(_jobName) + ".log"), getDataDirectoryFileObject());`
	`166`	`+ var file = FileUtil.findUniqueFileName((FileUtil.makeLegalName(_jobName) + ".log"), getDataDirectoryFileObject());`
`168`	`167`	`return file.toNioPathForWrite();`
`169`	`168`	`}`
`170`	`169`
`@@ -228,7 +227,7 @@ protected FileLike createLocalDirectory(PipeRoot pipeRoot) throws IOException`
`228`	`227`	`}`
`229`	`228`
`230`	`229`	`String folderName = FileUtil.makeLegalName(StringUtils.capitalize(_folderPrefix) + "_" + FileUtil.getTimestamp());`
`231`		`- webserverOutDir = AssayFileWriter.findUniqueFileName(folderName, webserverOutDir);`
	`230`	`+ webserverOutDir = FileUtil.findUniqueFileName(folderName, webserverOutDir);`
`232`	`231`	`if (!webserverOutDir.exists())`
`233`	`232`	`{`
`234`	`233`	`webserverOutDir.mkdir();`
`@@ -681,4 +680,4 @@ public File getLocationForCachedInputs(WorkDirectory wd, boolean createIfDoesntE`
`681`	`680`
`682`	`681`	`return ret;`
`683`	`682`	`}`
`684`		`-}`
	`683`	`+}`
Original file line number	Diff line number	Diff line change
`@@ -50,6 +50,7 @@`
`50`	`50`	`import org.labkey.api.security.permissions.ReadPermission;`
`51`	`51`	`import org.labkey.api.security.permissions.UpdatePermission;`
`52`	`52`	`import org.labkey.api.util.ExceptionUtil;`
	`53`	`+import org.labkey.api.util.FileUtil;`
`53`	`54`	`import org.labkey.api.util.PageFlowUtil;`
`54`	`55`	`import org.labkey.api.util.Pair;`
`55`	`56`	`import org.labkey.api.util.StringUtilsLabKey;`
`@@ -217,7 +218,7 @@ protected File getTargetFile(String filename) throws IOException`
`217`	`218`	`try`
`218`	`219`	`{`
`219`	`220`	`FileLike targetDirectory = AssayFileWriter.ensureUploadDirectory(getContainer());`
`220`		`- return AssayFileWriter.findUniqueFileName(filename, targetDirectory).toNioPathForWrite().toFile();`
	`221`	`+ return FileUtil.findUniqueFileName(filename, targetDirectory).toNioPathForWrite().toFile();`
`221`	`222`	`}`
`222`	`223`	`catch (ExperimentException e)`
`223`	`224`	`{`
`@@ -265,7 +266,7 @@ public String getResponse(RunBlastForm form, Map<String, Pair<File, String>> fil`
`265`	`266`	`try`
`266`	`267`	`{`
`267`	`268`	`FileLike targetDirectory = AssayFileWriter.ensureUploadDirectory(getContainer());`
`268`		`- FileLike input = AssayFileWriter.findUniqueFileName("blast", targetDirectory);`
	`269`	`+ FileLike input = FileUtil.findUniqueFileName("blast", targetDirectory);`
`269`	`270`	`input.createFile();`
`270`	`271`	`try (PrintWriter fw = PrintWriters.getPrintWriter(input.openOutputStream()))`
`271`	`272`	`{`