Adopt FileLike for more pipeline APIs

api/src/org/labkey/api/admin/FolderImportContext.java

@@ -29,11 +29,10 @@
 import org.labkey.api.util.XmlValidationException;
 import org.labkey.api.writer.VirtualFile;
 import org.labkey.folder.xml.FolderDocument;
+import org.labkey.vfs.FileLike;
 
 import java.io.IOException;
 import java.io.InputStream;
-import java.nio.file.Files;
-import java.nio.file.Path;
 import java.util.HashMap;
 import java.util.HashSet;
 import java.util.Map;
@@ -47,7 +46,7 @@
  */
 public class FolderImportContext extends AbstractFolderContext
 {
-    private Path _folderXml;
+    private FileLike _folderXml;
 
     private String _xarJobId;
 
@@ -66,7 +65,7 @@ public FolderImportContext()
         super(null, null, null, null, null, null);
     }
 
-    public FolderImportContext(User user, Container c, Path folderXml, Set<String> dataTypes, LoggerGetter logger, VirtualFile root)
+    public FolderImportContext(User user, Container c, FileLike folderXml, Set<String> dataTypes, LoggerGetter logger, VirtualFile root)
     {
         super(user, c, null, dataTypes, logger, root);
         _folderXml = folderXml;
@@ -112,17 +111,17 @@ public synchronized FolderDocument getDocument() throws ImportException
         return folderDoc;
     }
 
-    private FolderDocument readFolderDocument(Path folderXml) throws ImportException, IOException
+    private FolderDocument readFolderDocument(FileLike folderXml) throws ImportException, IOException
     {
-        if (!Files.exists(folderXml))
-            throw new ImportException(folderXml.getFileName() + " file does not exist.");
+        if (!folderXml.exists())
+            throw new ImportException(folderXml.getName() + " file does not exist.");
 
         FolderDocument folderDoc;
 
-        try (InputStream inputStream = Files.newInputStream(folderXml))
+        try (InputStream inputStream = folderXml.openInputStream())
         {
             folderDoc = FolderDocument.Factory.parse(inputStream, XmlBeansUtil.getDefaultParseOptions());
-            XmlBeansUtil.validateXmlDocument(folderDoc, folderXml.getFileName().toString());
+            XmlBeansUtil.validateXmlDocument(folderDoc, folderXml.getName());
         }
         catch (XmlException | XmlValidationException e)
         {

api/src/org/labkey/api/admin/ImportOptions.java

@@ -19,6 +19,7 @@
 import org.labkey.api.data.Activity;
 import org.labkey.api.security.User;
 import org.labkey.api.security.UserManager;
+import org.labkey.vfs.FileLike;
 
 import java.nio.file.Path;
 import java.util.Collection;
@@ -41,7 +42,7 @@ public class ImportOptions
     private final Collection<String> _messages = new LinkedList<>();
     private Set<String> _dataTypes;
     private Activity _activity;
-    private Path _analysisDir;
+    private FileLike _analysisDir;
     private String _folderArchiveSourceName = null;
 
     private boolean _isNewFolderImport; // if we know the target folder is empty, can skip certain merge logic
@@ -142,12 +143,12 @@ public void setActivity(Activity activity)
         _activity = activity;
     }
 
-    public Path getAnalysisDir()
+    public FileLike getAnalysisDir()
     {
         return _analysisDir;
     }
 
-    public void setAnalysisDir(Path analysisDir)
+    public void setAnalysisDir(FileLike analysisDir)
     {
         _analysisDir = analysisDir;
     }

api/src/org/labkey/api/admin/InvalidFileException.java

@@ -20,18 +20,19 @@
 import org.apache.xmlbeans.XmlException;
 import org.labkey.api.util.XmlValidationException;
 import org.labkey.api.writer.VirtualFile;
+import org.labkey.vfs.FileLike;
 
 import java.io.File;
 import java.nio.file.Path;
 
 public class InvalidFileException extends ImportException
 {
-    @Deprecated // prefer the Path version
-    public InvalidFileException(File root, File file, Throwable t)
+    public InvalidFileException(FileLike root, FileLike file, Throwable t)
     {
-        this(root.toPath(), file.toPath(), t);
+        this(root.toNioPathForRead(), file.toNioPathForRead(), t);
     }
 
+    @Deprecated // prefer the FileLike version
     public InvalidFileException(Path root, Path file, Throwable t)
     {
         super(getErrorString(root, file, t.getMessage()));
@@ -42,21 +43,11 @@ public InvalidFileException(VirtualFile root, File file, Throwable t)
         super(getErrorString(root.getRelativePath(file.getName()), t.getMessage()));
     }    
 
-    public InvalidFileException(File root, File file, XmlException e)
-    {
-        super(getErrorString(root, file, e));
-    }
-
     public InvalidFileException(VirtualFile root, File file, XmlException e)
     {
         super(getErrorString(root, file, e));
     }
 
-    public InvalidFileException(File root, File file, XmlValidationException e)
-    {
-        super(getErrorString(root, file, (String)null), e);
-    }
-
     public InvalidFileException(VirtualFile root, File file, XmlValidationException e)
     {
         super(getErrorString(root.getRelativePath(file.getName()), null), e);

api/src/org/labkey/api/assay/AbstractAssayProvider.java

@@ -116,7 +116,6 @@
 import org.labkey.api.view.NotFoundException;
 import org.labkey.api.view.ViewContext;
 import org.labkey.vfs.FileLike;
-import org.labkey.vfs.FileSystemLike;
 import org.springframework.validation.BindException;
 import org.springframework.web.servlet.ModelAndView;
 import org.springframework.web.servlet.mvc.Controller;
@@ -285,12 +284,7 @@ public ActionURL linkToStudy(User user, Container assayDataContainer, ExpProtoco
                     dataMap.put(StudyPublishService.TARGET_STUDY_PROPERTY_NAME, targetStudyContainer);
 
                     // Remember which rows we're planning to link, partitioned by the target study
-                    Set<Long> rowIds = rowIdsByTargetContainer.get(targetStudyContainer);
-                    if (rowIds == null)
-                    {
-                        rowIds = new HashSet<>();
-                        rowIdsByTargetContainer.put(targetStudyContainer, rowIds);
-                    }
+                    Set<Long> rowIds = rowIdsByTargetContainer.computeIfAbsent(targetStudyContainer, k -> new HashSet<>());
                     rowIds.add(publishKey.getDataId());
 
                     dataMaps.add(dataMap);
@@ -732,7 +726,7 @@ private void addReusableData(Map<String, org.labkey.vfs.FileLike> reusableFiles,
     }
 
     @Override
-    public AssayRunCreator getRunCreator()
+    public AssayRunCreator<?> getRunCreator()
     {
         return new DefaultAssayRunCreator<>(this);
     }
@@ -1459,13 +1453,13 @@ public AssaySaveHandler getSaveHandler()
     }
 
     @Override
-    public AssayRunUploadContext.Factory<? extends AbstractAssayProvider, ? extends AssayRunUploadContext.Factory> createRunUploadFactory(ExpProtocol protocol, ViewContext context)
+    public AssayRunUploadContext.Factory<? extends AbstractAssayProvider, ? extends AssayRunUploadContext.Factory<?, ?>> createRunUploadFactory(ExpProtocol protocol, ViewContext context)
     {
         return new AssayRunUploadContextImpl.Factory<>(protocol, this, context);
     }
 
     @Override
-    public AssayRunUploadContext.Factory<? extends AbstractAssayProvider, ? extends AssayRunUploadContext.Factory> createRunUploadFactory(ExpProtocol protocol, User user, Container c)
+    public AssayRunUploadContext.Factory<? extends AbstractAssayProvider, ? extends AssayRunUploadContext.Factory<?, ?>> createRunUploadFactory(ExpProtocol protocol, User user, Container c)
     {
         return new AssayRunUploadContextImpl.Factory<>(protocol, this, user, c);
     }
@@ -1518,15 +1512,15 @@ public DataExchangeHandler createDataExchangeHandler()
     }
 
     @Override
-    public AssayRunDatabaseContext createRunDatabaseContext(ExpRun run, User user, HttpServletRequest request)
+    public AssayRunDatabaseContext<?> createRunDatabaseContext(ExpRun run, User user, HttpServletRequest request)
     {
-        return new AssayRunDatabaseContext(run, user, request);
+        return new AssayRunDatabaseContext<>(run, user, request);
     }
 
     @Override
     public AssayRunAsyncContext<?> createRunAsyncContext(AssayRunUploadContext<?> context) throws IOException, ExperimentException
     {
-        return new AssayRunAsyncContext(context);
+        return new AssayRunAsyncContext<>(context);
     }
 
     @Override
@@ -1698,16 +1692,6 @@ public Pair<ExpProtocol, Integer> getAssayResultRowIdFromLsid(Container containe
         return Pair.of(protocol, rowId);
     }
 
-    @Override
-    public @Nullable ActionURL getResultRowURL(Container container, Lsid lsid)
-    {
-        var pair = getAssayResultRowIdFromLsid(container, lsid);
-        if (pair == null)
-            return null;
-
-        return PageFlowUtil.urlProvider(AssayUrls.class).getAssayResultRowURL(this, container, pair.first, pair.second);
-    }
-
     @Override
     public boolean supportsFlagColumnType(ExpProtocol.AssayDomainTypes type)
     {
@@ -2141,18 +2125,15 @@ private void updateDataFileUrl(List<ExpRun> runs, Container sourceContainer, Con
                     AuditLogService.get().addEvent(user, event);
                 }
             }
-            catch (Exception e)
-            {
-
-            }
+            catch (Exception ignored) {}
         }
     }
 
     protected void moveAssayResults(List<ExpRun> runs, ExpProtocol protocol, Container sourceContainer, Container targetContainer, User user, AssayMoveData assayMoveData) throws ExperimentException
     {
         String tableName = AssayProtocolSchema.DATA_TABLE_NAME;
         AssaySchema schema = createProtocolSchema(user, targetContainer, protocol, null);
-        FilteredTable assayResultTable = (FilteredTable) schema.getTable(tableName);
+        FilteredTable<?> assayResultTable = (FilteredTable<?>) schema.getTable(tableName);
         if (assayResultTable == null)
             return;
 
@@ -2161,7 +2142,7 @@ protected void moveAssayResults(List<ExpRun> runs, ExpProtocol protocol, Contain
 
     record AssayFileMoveReference(String sourceFilePath, File updatedFile, String runName, String fieldName) {}
 
-    private void updateResultFiles(FilteredTable assayResultTable, List<ExpRun> runs, ExpProtocol assayProtocol, Container sourceContainer, Container targetContainer, User user, AssayMoveData assayMoveData) throws ExperimentException
+    private void updateResultFiles(FilteredTable<?> assayResultTable, List<ExpRun> runs, ExpProtocol assayProtocol, Container sourceContainer, Container targetContainer, User user, AssayMoveData assayMoveData) throws ExperimentException
     {
         FileContentService fileContentService = FileContentService.get();
         if (fileContentService == null)

api/src/org/labkey/api/assay/AssayProvider.java

@@ -297,7 +297,7 @@ enum Scope
      */
     DataExchangeHandler createDataExchangeHandler();
     /** Make a context that knows how to update a run that's already been stored in the database */
-    AssayRunDatabaseContext createRunDatabaseContext(ExpRun run, User user, HttpServletRequest request);
+    AssayRunDatabaseContext<?> createRunDatabaseContext(ExpRun run, User user, HttpServletRequest request);
     /**
      * Make a context that knows how to do the import in the background, on a separate thread
      * (and therefore detached from the HTTP request that might have spawned it)
@@ -322,11 +322,6 @@ enum Scope
     @Nullable
     Pair<ExpProtocol, Integer> getAssayResultRowIdFromLsid(Container container, Lsid assayResultRowLsid);
 
-    /**
-     * Get the URL for an assay result row's LSID.
-     */
-    @Nullable ActionURL getResultRowURL(Container container, Lsid lsid);
-
     /**
      * Return a SQL pattern that can be used to match a protocol's LSID to this AssayProvider.
      * The pattern must match a protocol's LSID in the same manner as

api/src/org/labkey/api/assay/AssayService.java

@@ -249,6 +249,8 @@ ParticipantVisitResolver createResolver(User user, ExpRun run, @Nullable ExpProt
     /** Returns the lineage "role" for an assay run/result property. */
     @NotNull String getPropertyInputLineageRole(@NotNull DomainProperty dp);
 
+    AssayDomainService createAssayDomainService(User user, Container container);
+
     interface ResultsCheckHelper
     {
         @NotNull Logger getLogger();

api/src/org/labkey/api/assay/DefaultAssayRunCreator.java

@@ -221,9 +221,9 @@ private ExpExperiment saveExperimentRunAsync(AssayRunUploadContext<ProviderType>
                 // Choose another file as the primary
                 primaryFile = context.getUploadedData().entrySet().iterator().next().getValue();
             }
-            primaryFile = Objects.requireNonNull(primaryFile);
+            Objects.requireNonNull(primaryFile);
             AssayRunAsyncContext asyncContext = context.getProvider().createRunAsyncContext(context);
-            final AssayUploadPipelineJob<ProviderType> pipelineJob = new AssayUploadPipelineJob<ProviderType>(
+            final AssayUploadPipelineJob<ProviderType> pipelineJob = new AssayUploadPipelineJob<>(
                 asyncContext,
                 info,
                 batch,

api/src/org/labkey/api/assay/transform/AnalysisScript.java

@@ -40,13 +40,13 @@ private AnalysisScript(File script, List<String> operations)
 
     private AnalysisScript(File script)
     {
-        try
+        if (!script.exists())
         {
-            _script = FileSystemLike.wrapFile(script.getParentFile(), script);
+            _script = new FileSystemLike.Builder(script).build().getRoot();
         }
-        catch (IOException e)
+        else
         {
-            throw UnexpectedException.wrap(e);
+            _script = FileSystemLike.wrapFile(script);
         }
     }
 

api/src/org/labkey/api/cloud/CloudArchiveImporterSupport.java

@@ -26,7 +26,7 @@ public interface CloudArchiveImporterSupport
     default void downloadCloudArchive(@NotNull PipelineJob job, @NotNull Path studyXml, BindException errors) throws UnsupportedOperationException
     {
         //check if cloud based pipeline root, and study xml hasn't been downloaded already
-        if (!studyXml.startsWith(job.getPipeRoot().getImportDirectory().toPath().toAbsolutePath()))
+        if (!studyXml.startsWith(job.getPipeRoot().getImportDirectory().toNioPathForRead().toAbsolutePath()))
         {
             if (CloudStoreService.get() != null)   //proxy of is Cloud Module enabled for the current job/container
             {

api/src/org/labkey/api/cloud/CloudStoreService.java

@@ -23,6 +23,8 @@
 import org.labkey.api.services.ServiceRegistry;
 import org.labkey.api.util.Pair;
 import org.labkey.api.webdav.WebdavResource;
+import org.labkey.vfs.FileLike;
+import org.labkey.vfs.FileSystemLike;
 
 import java.nio.file.Path;
 import java.util.Collection;
@@ -141,6 +143,17 @@ default Collection<String> getEnabledCloudStores(Container container, boolean ex
     @Nullable
     Path getPath(Container container, String storeName, org.labkey.api.util.Path path);
 
+    /**
+     * Return nio.Path to cloud file/directory
+     */
+    @Nullable
+    FileLike getFileLike(Container container, String storeName, org.labkey.api.util.Path path);
+
+    /**
+     * Return FileSystem for cloud root
+     */
+    public @Nullable FileSystemLike getFileSystemLike(Container container, String configName);
+
     /**
      * Return path relative to cloud store
      */

api/src/org/labkey/api/data/TSVGridWriter.java

@@ -22,10 +22,9 @@
 import org.jetbrains.annotations.Nullable;
 import org.labkey.api.collections.ResultSetRowMapFactory;
 import org.labkey.api.query.FieldKey;
-import org.labkey.api.util.FileUtil;
 import org.labkey.api.view.HttpView;
+import org.labkey.vfs.FileLike;
 
-import java.io.File;
 import java.io.IOException;
 import java.sql.SQLException;
 import java.util.ArrayList;
@@ -198,7 +197,7 @@ private int writeBody(Results results)
      * @return List of the output Files.
      */
     @NotNull
-    public List<File> writeBatchFiles(@NotNull File outputDir, @NotNull String baseName, @Nullable String extension, int batchSize, @Nullable FieldKey batchColumn)
+    public List<FileLike> writeBatchFiles(@NotNull FileLike outputDir, @NotNull String baseName, @Nullable String extension, int batchSize, @Nullable FieldKey batchColumn)
     {
         extension = StringUtils.trimToEmpty(extension);
         String ext = "".equals(extension) || extension.startsWith(".") ? extension : "." + extension;
@@ -211,13 +210,13 @@ public List<File> writeBatchFiles(@NotNull File outputDir, @NotNull String baseN
     }
 
     @NotNull
-    private List<File> writeResultSetBatches(Results results, File outputDir, String baseName, String extension, int batchSize, @Nullable FieldKey batchColumn) throws IOException
+    private List<FileLike> writeResultSetBatches(Results results, FileLike outputDir, String baseName, String extension, int batchSize, @Nullable FieldKey batchColumn) throws IOException
     {
         int currentBatchSize = 0;
         int totalBatches = 1;
         Object previousBatchColumnValue = null;
         Object newBatchColumnValue;
-        List<File> outputFiles = new ArrayList<>();
+        List<FileLike> outputFiles = new ArrayList<>();
         outputFiles.add(startBatchFile(outputDir, baseName, extension, batchSize, totalBatches));
         RenderContext ctx = getRenderContext();
         ctx.setResults(results);
@@ -264,11 +263,11 @@ private List<File> writeResultSetBatches(Results results, File outputDir, String
     }
 
     @NotNull
-    private File startBatchFile(File outputDir, String baseName, String extension, int batchSize, int totalBatches) throws IOException
+    private FileLike startBatchFile(FileLike outputDir, String baseName, String extension, int batchSize, int totalBatches) throws IOException
     {
         String batchId = batchSize == 0 ? "" : "-" + totalBatches;
-        File file = FileUtil.appendName(outputDir, baseName + batchId + extension);
-        prepare(file);
+        FileLike file = outputDir.resolveChild(baseName + batchId + extension);
+        prepare(file.openOutputStream());
         writeFileHeader();
         if (isHeaderRowVisible())
             writeColumnHeaders();