Convert File usages to use FileLike or the comparable class

genotyping/src/org/labkey/genotyping/GenotypingController.java

@@ -18,7 +18,6 @@
 
 import jakarta.servlet.http.HttpServletResponse;
 import org.apache.commons.io.IOUtils;
-import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
 import org.jetbrains.annotations.NotNull;
 import org.jetbrains.annotations.Nullable;
@@ -86,10 +85,12 @@
 import org.labkey.api.security.permissions.ReadPermission;
 import org.labkey.api.security.permissions.UpdatePermission;
 import org.labkey.api.util.DateUtil;
+import org.labkey.api.util.FileUtil;
 import org.labkey.api.util.MinorConfigurationException;
 import org.labkey.api.util.PageFlowUtil;
 import org.labkey.api.util.Pair;
 import org.labkey.api.util.URLHelper;
+import org.labkey.api.util.logging.LogHelper;
 import org.labkey.api.view.ActionURL;
 import org.labkey.api.view.DataView;
 import org.labkey.api.view.DetailsView;
@@ -110,6 +111,8 @@
 import org.labkey.genotyping.sequences.FastqGenerator;
 import org.labkey.genotyping.sequences.FastqWriter;
 import org.labkey.genotyping.sequences.SequenceManager;
+import org.labkey.vfs.FileLike;
+import org.labkey.vfs.FileSystemLike;
 import org.springframework.validation.BindException;
 import org.springframework.validation.Errors;
 import org.springframework.web.servlet.ModelAndView;
@@ -122,6 +125,8 @@
 import java.math.BigInteger;
 import java.net.MalformedURLException;
 import java.net.URL;
+import java.nio.file.Path;
+import java.nio.file.Paths;
 import java.sql.ResultSet;
 import java.sql.SQLException;
 import java.util.Collection;
@@ -139,7 +144,7 @@
 
 public class GenotypingController extends SpringActionController
 {
-    private static final Logger LOG = LogManager.getLogger(GenotypingController.class);
+    private static final Logger LOG = LogHelper.getLogger(GenotypingController.class, "Logger for Genotyping Controller");
     @SuppressWarnings({"unchecked"})
     private static final DefaultActionResolver _actionResolver = new DefaultActionResolver(GenotypingController.class);
 
@@ -1005,9 +1010,13 @@ private String importReads(ImportReadsForm form) throws Exception
             if (null == form.getPlatform())
                 return "You must specify a sequence platform";
 
+            PipeRoot root = PipelineService.get().getPipelineRootSetting(getContainer());
+            if (!root.getRootFileLike().isDescendant(FileUtil.createUri(form.getReadsPath())))
+                return "File must be a descendant of a pipeline";
+
             try
             {
-                File readsFile = new File(form.getReadsPath());
+                FileLike readsFile = root.resolvePathToFileLike(root.relativePath(Paths.get(form.getReadsPath())));
                 GenotypingRun run;
 
                 try
@@ -1023,7 +1032,6 @@ private String importReads(ImportReadsForm form) throws Exception
                 }
 
                 ViewBackgroundInfo vbi = new ViewBackgroundInfo(getContainer(), getUser(), getViewContext().getActionURL());
-                PipeRoot root = PipelineService.get().findPipelineRoot(getContainer());
                 ImportReadsForm.Platforms platform = ImportReadsForm.Platforms.valueOf(form.getPlatform());
 
                 platform.prepareAndQueueRunJob(vbi, root, new File(form.getReadsPath()), run, form.getPrefix());
@@ -1178,10 +1186,17 @@ private ColumnInfo getColumnInfo(Map<FieldKey, ColumnInfo> fieldMap, String colu
         public boolean handlePost(AnalyzeForm form, BindException errors) throws Exception
         {
             GenotypingRun run = GenotypingManager.get().getRun(getContainer(), form.getRun());
-            File readsPath = new File(run.getPath(), run.getFileName());
-            ViewBackgroundInfo vbi = new ViewBackgroundInfo(getContainer(), getUser(), getViewContext().getActionURL());
+            if (run == null)
+            {
+                errors.rejectValue("run", ERROR_MSG, "No run found");
+                return false;
+            }
+
             PipeRoot root = PipelineService.get().findPipelineRoot(getContainer());
 
+            FileLike readsFile = run.getWorkingDir().resolveChild(run.getFileName());
+            ViewBackgroundInfo vbi = new ViewBackgroundInfo(getContainer(), getUser(), getViewContext().getActionURL());
+
             String sequencesViewName = form.getSequencesView();
             String description = form.getDescription();
             String sequencesView = DEFAULT_VIEW_PLACEHOLDER.equals(sequencesViewName) ? null : sequencesViewName;
@@ -1202,7 +1217,7 @@ public boolean handlePost(AnalyzeForm form, BindException errors) throws Excepti
             GenotypingAnalysis analysis = GenotypingManager.get().createAnalysis(getContainer(), getUser(), run, description, sequencesView);
             try
             {
-                PipelineJob analysisJob = new SubmitAnalysisJob(vbi, root, readsPath, analysis, sampleKeys);
+                PipelineJob analysisJob = new SubmitAnalysisJob(vbi, root, readsFile, analysis, sampleKeys);
                 PipelineService.get().queueJob(analysisJob);
             }
             catch (MinorConfigurationException e)
@@ -1292,10 +1307,10 @@ public Object execute(ImportAnalysisForm form, BindException errors) throws Exce
 
             try
             {
+                FileLike analysisDir = FileSystemLike.getVerifiedFileLike(getContainer(), form.getPath());
                 int analysisId = form.getAnalysis();
-                File analysisDir = new File(form.getPath());
-                User user = getUser();
 
+                User user = getUser();
                 if (user.isGuest())
                 {
                     Properties props = GenotypingManager.get().readProperties(analysisDir);
@@ -1378,16 +1393,26 @@ public void validateCommand(PipelinePathForm target, Errors errors)
         @Override
         public boolean handlePost(PipelinePathForm form, BindException errors) throws IOException, PipelineValidationException
         {
+            Container container = getContainer();
             // Manual upload of genotyping analysis; pipeline provider posts to this action with matches file.
-            File matches = form.getValidatedSingleFile(getContainer());
-            File analysisDir = matches.getParentFile();
+            Path singleFile = form.getValidatedSinglePath(container);
+
+            if (form.getPipeRoot(container).getRootFileLike().isDescendant(singleFile.toUri()))
+            {
 
-            // Load properties to determine the run.
-            Properties props = GenotypingManager.get().readProperties(analysisDir);
-            int analysisId = Integer.parseInt((String)props.get("analysis"));
-            importAnalysis(analysisId, analysisDir, getUser());
+                FileLike matches = form.getPipeRoot(container).resolvePathToFileLike(singleFile.toString());
+                FileLike analysisDir = matches.getParent();
 
-            return true;
+                // Load properties to determine the run.
+                Properties props = GenotypingManager.get().readProperties(analysisDir);
+                int analysisId = Integer.parseInt((String) props.get("analysis"));
+                importAnalysis(analysisId, analysisDir, getUser());
+
+                return true;
+            }
+
+            errors.reject(ERROR_MSG, "File was not found under the pipeline root");
+            return false;
         }
 
         @Override
@@ -1398,13 +1423,13 @@ public URLHelper getSuccessURL(PipelinePathForm pipelinePathForm)
     }
 
 
-    private void importAnalysis(int analysisId, File pipelineDir, User user) throws IOException, PipelineValidationException
+    private void importAnalysis(int analysisId, FileLike pipelineDir, User user) throws IOException, PipelineValidationException
     {
         GenotypingAnalysis analysis = GenotypingManager.get().getAnalysis(getContainer(), analysisId);
-        File analysisDir = new File(analysis.getPath());
+        FileLike analysisDir = new FileSystemLike.Builder(Paths.get(analysis.getPath())).readwrite().root();
 
-        String pipelinePath = pipelineDir.getCanonicalPath();
-        String analysisPath = analysisDir.getCanonicalPath();
+        String pipelinePath = FileUtil.getAbsoluteCaseSensitiveFile(pipelineDir.toNioPathForRead().toFile()).getAbsolutePath();
+        String analysisPath = FileUtil.getAbsoluteCaseSensitiveFile(analysisDir.toNioPathForRead().toFile()).getAbsolutePath();
 
         if (!pipelinePath.equals(analysisPath))
             throw new FileNotFoundException("Analysis path (\"" + analysisPath +

genotyping/src/org/labkey/genotyping/GenotypingManager.java

@@ -32,13 +32,12 @@
 import org.labkey.api.query.FieldKey;
 import org.labkey.api.query.QueryHelper;
 import org.labkey.api.security.User;
+import org.labkey.api.util.FileUtil;
 import org.labkey.api.util.SafeToRenderEnum;
 import org.labkey.api.view.NotFoundException;
+import org.labkey.vfs.FileLike;
 
-import java.io.File;
-import java.io.FileInputStream;
 import java.io.FileNotFoundException;
-import java.io.FileOutputStream;
 import java.io.IOException;
 import java.io.InputStream;
 import java.io.OutputStream;
@@ -124,14 +123,14 @@ public void saveSettings(Container c, GenotypingFolderSettings settings)
         map.save();
     }
 
-    public GenotypingRun createRun(Container c, User user, Integer metaDataId, File readsFile, String platform)
+    public GenotypingRun createRun(Container c, User user, Integer metaDataId, FileLike readsFile, String platform)
     {
         MetaDataRun mdRun = null;
 
         if (null != metaDataId)
             mdRun = getMetaDataRun(c, user, metaDataId, "importing reads");
 
-        GenotypingRun run = new GenotypingRun(c, readsFile, mdRun, platform);
+        GenotypingRun run = new GenotypingRun(c, readsFile.toNioPathForWrite().toFile(), mdRun, platform);
         return Table.insert(user, GenotypingSchema.get().getRunsTable(), run);
     }
 
@@ -281,39 +280,31 @@ private void deleteAnalyses(CharSequence analysisFilter, Object... params)
     }
 
 
-    public void writeProperties(Properties props, File directory) throws IOException
+    public void writeProperties(Properties props, FileLike directory) throws IOException
     {
-        File propXml = new File(directory, PROPERTIES_FILE_NAME);
-        OutputStream os = null;
-        try
+        try (OutputStream os = directory.resolveChild(PROPERTIES_FILE_NAME).openOutputStream())
         {
-            os = new FileOutputStream(propXml);
             props.storeToXML(os, null);
         }
-        finally
-        {
-            if (null != os)
-                os.close();
-        }
     }
 
-    public Properties readProperties(File directory) throws IOException
+    public Properties readProperties(FileLike directory) throws IOException
     {
         if (!directory.exists())
-            throw new FileNotFoundException(directory.getAbsolutePath() + " does not exist");
+            throw new FileNotFoundException(FileUtil.getAbsolutePath(directory.toNioPathForRead()) + " does not exist");
 
         if (!directory.isDirectory())
-            throw new FileNotFoundException(directory.getAbsolutePath() + " is not a directory");
+            throw new FileNotFoundException(FileUtil.getAbsolutePath(directory.toNioPathForRead()) + " is not a directory");
 
-        File properties = new File(directory, PROPERTIES_FILE_NAME);
+        FileLike properties = directory.resolveChild(PROPERTIES_FILE_NAME);
 
         // Load properties to determine the run.
         Properties props = new Properties();
         InputStream is = null;
 
         try
         {
-            is = new FileInputStream(properties);
+            is = properties.openInputStream();
             props.loadFromXML(is);
         }
         finally

genotyping/src/org/labkey/genotyping/GenotypingRun.java

@@ -15,13 +15,17 @@
  */
 package org.labkey.genotyping;
 
+import com.fasterxml.jackson.annotation.JsonIgnore;
 import org.jetbrains.annotations.Nullable;
 import org.labkey.api.data.Container;
+import org.labkey.api.pipeline.PipelineService;
 import org.labkey.api.security.User;
 import org.labkey.api.util.FileUtil;
 import org.labkey.api.util.MemTracker;
+import org.labkey.vfs.FileLike;
 
 import java.io.File;
+import java.nio.file.Paths;
 import java.util.Date;
 
 /**
@@ -167,4 +171,10 @@ public void setStatusEnum(Status statusEnum)
     {
         _status = statusEnum.getStatusId();
     }
+
+    @JsonIgnore
+    public FileLike getWorkingDir()
+    {
+        return PipelineService.get().findPipelineRoot(getContainer()).resolvePathToFileLike(PipelineService.get().findPipelineRoot(getContainer()).relativePath(Paths.get(getPath())));
+    }
 }

genotyping/src/org/labkey/genotyping/Import454ReadsJob.java

@@ -30,6 +30,8 @@
 import org.labkey.api.util.FileUtil;
 import org.labkey.api.util.Formats;
 import org.labkey.api.view.ViewBackgroundInfo;
+import org.labkey.vfs.FileLike;
+import org.labkey.vfs.FileSystemLike;
 
 import java.io.File;
 import java.io.IOException;
@@ -65,8 +67,9 @@ protected Import454ReadsJob(@JsonProperty("_reads") File reads)
     public Import454ReadsJob(ViewBackgroundInfo info, PipeRoot root, File reads, GenotypingRun run)
     {
         super(Import454ReadsPipelineProvider.NAME, info, root, run);
-        _reads = reads;
-        setLogFile(new File(_reads.getParentFile(), FileUtil.makeFileNameWithTimestamp("import_reads", "log")));
+        FileLike verifiedFileLike = FileSystemLike.getVerifiedFileLike(root.getContainer(), reads.getAbsolutePath());
+        _reads = FileSystemLike.toFile(verifiedFileLike);
+        setLogFile(verifiedFileLike.getParent().resolveChild(FileUtil.makeFileNameWithTimestamp("import_reads", "log")).toNioPathForWrite());
     }
 
     @Override

genotyping/src/org/labkey/genotyping/ImportAnalysisJob.java

@@ -36,8 +36,8 @@
 import org.labkey.api.view.ViewBackgroundInfo;
 import org.labkey.genotyping.sequences.SequenceDictionary;
 import org.labkey.genotyping.sequences.SequenceManager;
+import org.labkey.vfs.FileLike;
 
-import java.io.File;
 import java.io.IOException;
 import java.sql.SQLException;
 import java.util.Map;
@@ -50,21 +50,21 @@
  */
 public class ImportAnalysisJob extends PipelineJob
 {
-    private File _dir;
+    private FileLike _dir;
     private GenotypingAnalysis _analysis;
 
     // For serialization
     protected ImportAnalysisJob() {}
 
-    public ImportAnalysisJob(ViewBackgroundInfo info, PipeRoot root, File pipelineDir, GenotypingAnalysis analysis)
+    public ImportAnalysisJob(ViewBackgroundInfo info, PipeRoot root, FileLike pipelineDir, GenotypingAnalysis analysis)
     {
         super("Import Analysis", info, root);
         _dir = pipelineDir;
         _analysis = analysis;
-        setLogFile(new File(_dir, FileUtil.makeFileNameWithTimestamp("import_analysis", "log")));
+        setLogFile(_dir.resolveChild(FileUtil.makeFileNameWithTimestamp("import_analysis", "log")).toNioPathForWrite());
 
         if (!_dir.exists())
-            throw new IllegalArgumentException("Pipeline directory does not exist: " + _dir.getAbsolutePath());
+            throw new IllegalArgumentException("Pipeline directory does not exist: " + _dir.toNioPathForRead().toAbsolutePath());
 
         if (null == _analysis)
             throw new IllegalArgumentException("Analysis was not specified");
@@ -92,7 +92,7 @@ public void run()
 
         try
         {
-            File sourceMatches = new File(_dir, GenotypingManager.MATCHES_FILE_NAME);
+            FileLike sourceMatches = _dir.resolveChild(GenotypingManager.MATCHES_FILE_NAME);
             GenotypingSchema gs = GenotypingSchema.get();
             DbSchema schema = gs.getSchema();
             TempTableInfo matches = null;
@@ -180,9 +180,9 @@ public void run()
 
 
     // columnNames: comma-separated list of column names to include; null means include all columns
-    private TempTableInfo createTempTable(File file, @Nullable String columnNames) throws IOException, SQLException
+    private TempTableInfo createTempTable(FileLike file, @Nullable String columnNames) throws IOException, SQLException
     {
-        try (TabLoader loader = new TabLoader(file, true))
+        try (TabLoader loader = new TabLoader(file.toNioPathForRead().toFile(), true))
         {
             // Load only the specified columns
             if (null != columnNames)

genotyping/src/org/labkey/genotyping/ImportIlluminaReadsJob.java

@@ -34,6 +34,8 @@
 import org.labkey.api.util.FileUtil;
 import org.labkey.api.util.Pair;
 import org.labkey.api.view.ViewBackgroundInfo;
+import org.labkey.vfs.FileLike;
+import org.labkey.vfs.FileSystemLike;
 
 import java.io.File;
 import java.io.IOException;
@@ -71,9 +73,10 @@ protected ImportIlluminaReadsJob(@JsonProperty("_sampleFile") File sampleFile, @
     public ImportIlluminaReadsJob(ViewBackgroundInfo info, PipeRoot root, File sampleFile, GenotypingRun run, @Nullable String fastqPrefix)
     {
         super(ImportIlluminaReadsPipelineProvider.NAME, info, root, run);
-        _sampleFile = sampleFile;
+        FileLike verifiedFileLike = FileSystemLike.getVerifiedFileLike(root.getContainer(), sampleFile.getAbsolutePath());
+        _sampleFile = FileSystemLike.toFile(verifiedFileLike);
         _fastqPrefix = fastqPrefix;
-        setLogFile(new File(_sampleFile.getParentFile(), FileUtil.makeFileNameWithTimestamp("import_reads", "log")));
+        setLogFile(verifiedFileLike.getParent().resolveChild(FileUtil.makeFileNameWithTimestamp("import_reads", "log")).toNioPathForWrite());
     }
 
     @Override