Adopt FileLike for more pipeline APIs

flow/src/org/labkey/flow/controllers/executescript/AnalysisScriptController.java

@@ -291,7 +291,7 @@ else if (form.getFile() == null || form.getFile().length == 0)
         }
         else
         {
-            files.addAll(form.getValidatedFiles(getContainer()));
+            files.addAll(form.getValidatedFiles(getContainer()).stream().map(FileLike::toNioPathForRead).map(Path::toFile).toList());
         }
 
         Set<File> usedPaths = new HashSet<>();
@@ -390,7 +390,7 @@ protected ModelAndView uploadRuns(ImportRunsForm form, BindException errors) thr
             if (form.isCurrent())
                 files = Collections.singletonList(pr.resolvePath(form.getPath()));
             else
-                files = form.getValidatedFiles(form.getContainer());
+                files = form.getValidatedFiles(form.getContainer()).stream().map(FileLike::toNioPathForRead).map(Path::toFile).toList();
 
             // validate target study
             Container targetStudy = getTargetStudy(form.getTargetStudy(), errors);
@@ -544,7 +544,7 @@ public class ImportAnalysisFromPipelineAction extends SimpleViewAction<PipelineP
         @Override
         public ModelAndView getView(PipelinePathForm form, BindException errors)
         {
-            Path f = form.getValidatedSinglePath(getContainer());
+            FileLike f = form.getValidatedSingleFile(getContainer());
             PipeRoot root = Objects.requireNonNull(PipelineService.get().findPipelineRoot(getContainer()));
             String workspacePath = "/" + root.relativePath(f).replace('\\', '/');
 

flow/src/org/labkey/flow/controllers/run/RunController.java

@@ -86,6 +86,7 @@
 import org.labkey.flow.query.FlowTableType;
 import org.labkey.flow.view.ExportAnalysisForm;
 import org.labkey.flow.view.ExportAnalysisManifest;
+import org.labkey.vfs.FileLike;
 import org.springframework.validation.BindException;
 import org.springframework.validation.Errors;
 import org.springframework.web.servlet.ModelAndView;
@@ -604,13 +605,13 @@ else if (_wells != null && !_wells.isEmpty())
             return _success = true;
         }
 
-        private void writeManifest(String manifestJson, String dir) throws IOException
+        private void writeManifest(String manifestJson, File dir) throws IOException
         {
             if (manifestJson == null || manifestJson.isEmpty())
                 return;
 
 
-            File file = new File(dir,MANIFEST_FILENAME);
+            File file = FileUtil.appendName(dir, MANIFEST_FILENAME);
             FileOutputStream statisticsFile = new FileOutputStream(file);
 
             try (PrintWriter pw = PrintWriters.getPrintWriter(statisticsFile))
@@ -694,7 +695,7 @@ URLHelper onExportComplete(ExportAnalysisForm form, VirtualFile vf, SampleIdMap<
                     ViewBackgroundInfo vbi = new ViewBackgroundInfo(getContainer(), getUser(), null);
 
                     ExportAnalysisManifest analysisManifest = buildExportAnalysisManifest(form, files);
-                    writeManifest(analysisManifest.toJSON(), vf.getLocation());
+                    writeManifest(analysisManifest.toJSON(), location);
 
                     PipelineJob job = new ExportToScriptJob(_guid, _exportToScriptPath, _exportToScriptCommandLine, _exportToScriptFormat, form.getLabel(), location, _exportToScriptTimeout, _exportToScriptDeleteOnComplete, vbi, root);
                     String jobGuid = null;
@@ -780,7 +781,7 @@ public ExportToScriptJob(String guid, String exportToScriptPath, String exportTo
             _deleteOnComplete = deleteOnComplete;
 
             // setup the log file
-            File logFile = FileUtil.appendName(root.getLogDirectory(), FileUtil.makeFileNameWithTimestamp("export-to-script", "log"));
+            FileLike logFile = root.getLogDirectoryFileLike(true).resolveChild(FileUtil.makeFileNameWithTimestamp("export-to-script", "log"));
             setLogFile(logFile);
         }
 

flow/src/org/labkey/flow/data/FlowAssayProvider.java

@@ -27,10 +27,8 @@
 import org.labkey.api.exp.OntologyManager;
 import org.labkey.api.exp.XarContext;
 import org.labkey.api.exp.api.ExpData;
-import org.labkey.api.exp.api.ExpExperiment;
 import org.labkey.api.exp.api.ExpProtocol;
 import org.labkey.api.exp.api.ExpRun;
-import org.labkey.api.exp.api.IAssayDomainType;
 import org.labkey.api.exp.property.Domain;
 import org.labkey.api.exp.property.DomainProperty;
 import org.labkey.api.gwt.client.DefaultValueType;
@@ -68,7 +66,6 @@
 import org.labkey.flow.script.FlowPipelineProvider;
 import org.labkey.flow.view.FlowQueryView;
 import org.labkey.flow.webparts.AnalysesWebPart;
-import org.springframework.validation.BindException;
 import org.springframework.web.servlet.ModelAndView;
 import org.springframework.web.servlet.mvc.Controller;
 
@@ -214,7 +211,7 @@ public Domain getResultsDomain(ExpProtocol protocol, boolean forUpdate)
     }
 
     @Override
-    public AssayRunCreator getRunCreator()
+    public AssayRunCreator<?> getRunCreator()
     {
         throw new UnsupportedOperationException();
     }
@@ -399,18 +396,6 @@ public DefaultValueType getDefaultValueDefault(Domain domain)
         throw new UnsupportedOperationException();
     }
 
-    @Override
-    public boolean hasCustomView(IAssayDomainType domainType, boolean details)
-    {
-        return false;
-    }
-
-    @Override
-    public ModelAndView createBeginView(ViewContext context, ExpProtocol protocol)
-    {
-        return null;
-    }
-
     @Override
     public ModelAndView createBatchesView(ViewContext context, ExpProtocol protocol)
     {
@@ -423,12 +408,6 @@ public ModelAndView createBatchesView(ViewContext context, ExpProtocol protocol)
         return view;
     }
 
-    @Override
-    public ModelAndView createBatchDetailsView(ViewContext context, ExpProtocol protocol, ExpExperiment batch)
-    {
-        return null;
-    }
-
     @Override
     public ModelAndView createRunsView(ViewContext context, ExpProtocol protocol)
     {
@@ -437,18 +416,6 @@ public ModelAndView createRunsView(ViewContext context, ExpProtocol protocol)
         return new FlowQueryView(form);
     }
 
-    @Override
-    public ModelAndView createRunDetailsView(ViewContext context, ExpProtocol protocol, ExpRun run)
-    {
-        return null;
-    }
-
-    @Override
-    public ModelAndView createResultsView(ViewContext context, ExpProtocol protocol, BindException errors)
-    {
-        return null;
-    }
-
     @Override
     public ModelAndView createResultDetailsView(ViewContext context, ExpProtocol protocol, ExpData data, Object dataRowId)
     {

flow/src/org/labkey/flow/script/AbstractExternalAnalysisJob.java

@@ -36,6 +36,7 @@
 import org.labkey.api.pipeline.PipelineService;
 import org.labkey.api.query.FieldKey;
 import org.labkey.api.security.User;
+import org.labkey.api.util.FileUtil;
 import org.labkey.api.util.Pair;
 import org.labkey.api.view.ActionURL;
 import org.labkey.api.view.ViewBackgroundInfo;
@@ -383,7 +384,7 @@ protected FlowRun saveAnalysis(User user, Container container, FlowExperiment ex
                                    MultiValuedMap<String, String> sampleIdToNameMap) throws Exception
     {
         // Fake file URI set on the FCSFile/FCSAnalsyis ExpData to ensure it's recognized by the FlowDataHandler.
-        URI dataFileURI = new File(externalAnalysisFile.getParent(), "attributes.flowdata.xml").toURI();
+        URI dataFileURI = FileUtil.appendName(externalAnalysisFile.getParentFile(), "attributes.flowdata.xml").toURI();
 
         // Prepare comp matrices for saving
         Map<CompensationMatrix, AttributeSet> compMatrixMap = new HashMap<>();

flow/src/org/labkey/flow/script/FlowJob.java

@@ -202,7 +202,7 @@ protected void runPostAnalysisJobs()
             info("Running post-analysis jobs...");
         for (FlowReportJob job : jobs)
         {
-            job.setLogFile(getLogFile());
+            job.setLogFile(getLogFileLike());
             job.setLogLevel(getLogLevel());
             job.setSubmitted();
             job.run();

flow/src/org/labkey/flow/script/ScriptXarSource.java

@@ -22,6 +22,8 @@
 import org.labkey.api.exp.XarSource;
 import org.labkey.api.pipeline.PipelineJob;
 import org.labkey.api.util.FileUtil;
+import org.labkey.vfs.FileLike;
+import org.labkey.vfs.FileSystemLike;
 
 import java.io.File;
 import java.io.FileWriter;
@@ -85,8 +87,8 @@ public ExperimentArchiveDocument getDocument()
 
 
     @Override
-    public Path getLogFilePath()
+    public FileLike getLogFilePath()
     {
-        return _logFile.toPath();
+        return FileSystemLike.wrapFile(_logFile);
     }
 }

luminex/src/org/labkey/luminex/LuminexAssayProvider.java

@@ -51,7 +51,6 @@
 import org.labkey.api.assay.AssayDataType;
 import org.labkey.api.assay.AssayPipelineProvider;
 import org.labkey.api.assay.AssayProtocolSchema;
-import org.labkey.api.assay.AssayRunCreator;
 import org.labkey.api.assay.AssayRunDatabaseContext;
 import org.labkey.api.assay.AssayRunUploadContext;
 import org.labkey.api.assay.AssayTableMetadata;
@@ -113,7 +112,7 @@ public LuminexProtocolSchema createProtocolSchema(User user, Container container
     public void registerLsidHandler()
     {
         super.registerLsidHandler();
-        LsidManager.get().registerHandler(LUMINEX_DATA_ROW_LSID_PREFIX, new LsidManager.ExpObjectLsidHandler()
+        LsidManager.get().registerHandler(LUMINEX_DATA_ROW_LSID_PREFIX, new LsidManager.ExpObjectLsidHandler<>()
         {
             @Override
             public ExpData getObject(Lsid lsid)
@@ -454,7 +453,7 @@ public void deleteProtocol(ExpProtocol protocol, User user, @Nullable final Stri
     }
 
     @Override
-    public AssayRunDatabaseContext createRunDatabaseContext(ExpRun run, User user, HttpServletRequest request)
+    public AssayRunDatabaseContext<?> createRunDatabaseContext(ExpRun run, User user, HttpServletRequest request)
     {
         return new LuminexRunDatabaseContext(run, user, request);
     }
@@ -466,7 +465,7 @@ public AssayRunAsyncContext<?> createRunAsyncContext(AssayRunUploadContext<?> co
     }
 
     @Override
-    public AssayRunCreator getRunCreator()
+    public LuminexRunCreator getRunCreator()
     {
         return new LuminexRunCreator(this);
     }

luminex/src/org/labkey/luminex/LuminexExclusionPipelineJob.java

@@ -44,7 +44,7 @@ public LuminexExclusionPipelineJob(ViewBackgroundInfo info, PipeRoot root, Lumin
     {
         super(LuminexAssayProvider.NAME, info, root);
 
-        setLogFile(root.getLogDirectoryFileLike(true).resolveChild(FileUtil.makeFileNameWithTimestamp("luminex_exclusion", "log")).toNioPathForWrite());
+        setLogFile(root.getLogDirectoryFileLike(true).resolveChild(FileUtil.makeFileNameWithTimestamp("luminex_exclusion", "log")));
 
         _form = form;
         _exclusionType = LuminexManager.ExclusionType.valueOf(form.getTableName());

luminex/src/org/labkey/luminex/query/WellExclusionTable.java

@@ -73,18 +73,18 @@ public WellExclusionTable(LuminexProtocolSchema schema, ContainerFilter cf, bool
     {
         super(LuminexProtocolSchema.getTableInfoWellExclusion(), schema, cf, filter);
 
-        getMutableColumn("DataId").setLabel("Data File");
-        getMutableColumn("DataId").setFk(new ExpSchema(schema.getUser(), schema.getContainer()).getDataIdForeignKey(cf));
+        getMutableColumnOrThrow("DataId").setLabel("Data File");
+        getMutableColumnOrThrow("DataId").setFk(new ExpSchema(schema.getUser(), schema.getContainer()).getDataIdForeignKey(cf));
 
-        getMutableColumn("Analytes").setFk(new MultiValuedForeignKey(new LookupForeignKey(cf, "WellExclusionId", null)
+        getMutableColumnOrThrow("Analytes").setFk(new MultiValuedForeignKey(new LookupForeignKey(cf, "WellExclusionId", null)
         {
             @Override
             public TableInfo getLookupTableInfo()
             {
                 return _userSchema.createWellExclusionAnalyteTable(getLookupContainerFilter());
             }
         }, "AnalyteId"));
-        getMutableColumn("Analytes").setUserEditable(false);
+        getMutableColumnOrThrow("Analytes").setUserEditable(false);
 
         SQLFragment joinSQL = new SQLFragment(" FROM ");
         joinSQL.append(LuminexProtocolSchema.getTableInfoDataRow(), "dr");
@@ -123,8 +123,7 @@ public Object getDisplayValue(RenderContext ctx)
                 if (null != result)
                 {
                     // get the list of unique wells (by splitting the concatenated string)
-                    TreeSet<String> uniqueWells = new TreeSet<>();
-                    uniqueWells.addAll(Arrays.asList(result.toString().split(MultiValuedRenderContext.VALUE_DELIMITER_REGEX)));
+                    TreeSet<String> uniqueWells = new TreeSet<>(Arrays.asList(result.toString().split(MultiValuedRenderContext.VALUE_DELIMITER_REGEX)));
 
                     // put the unique wells back into a comma separated string
                     StringBuilder sb = new StringBuilder();
@@ -332,7 +331,7 @@ private void rerunTransformScripts(BatchValidationException errors) throws Query
                     for (ExpRun run : _runsToRefresh)
                     {
                         AssayProvider provider = AssayService.get().getProvider(run);
-                        AssayRunDatabaseContext context = provider.createRunDatabaseContext(run, _userSchema.getUser(), null);
+                        AssayRunDatabaseContext<?> context = provider.createRunDatabaseContext(run, _userSchema.getUser(), null);
                         provider.getRunCreator().saveExperimentRun(context, AssayService.get().findBatch(run), run, false, null);
                     }
                 }

luminex/test/src/org/labkey/test/tests/luminex/LuminexPositivityTest.java

@@ -19,6 +19,7 @@
 import org.junit.BeforeClass;
 import org.junit.Test;
 import org.junit.experimental.categories.Category;
+import org.labkey.api.util.FileUtil;
 import org.labkey.test.BaseWebDriverTest;
 import org.labkey.test.Locator;
 import org.labkey.test.TestFileUtils;
@@ -57,7 +58,7 @@ public final class LuminexPositivityTest extends LuminexTest
     private Boolean _expectedNegativeControlValue = false;
     private Boolean _newNegativeControlValue = false;
     private static final String _negControlAnalyte = _analyteNames.get(1);
-    private static final File POSITIVITY_RTRANSFORM_SCRIPT_FILE =  new File(TestFileUtils.getLabKeyRoot(), "server/modules/commonAssays/luminex/resources/transformscripts/description_parsing_example.pl");
+    private static final File POSITIVITY_RTRANSFORM_SCRIPT_FILE = FileUtil.appendPath(TestFileUtils.getLabKeyRoot(), org.labkey.api.util.Path.parse("server/modules/commonAssays/luminex/resources/transformscripts/description_parsing_example.pl"));
     private static final String RUN_ID_BASE = "Positivity";
 
     @BeforeClass

luminex/test/src/org/labkey/test/tests/luminex/LuminexTest.java

@@ -19,6 +19,7 @@
 import org.apache.commons.lang3.StringUtils;
 import org.junit.BeforeClass;
 import org.labkey.api.query.QueryKey;
+import org.labkey.api.util.FileUtil;
 import org.labkey.remoteapi.CommandException;
 import org.labkey.remoteapi.Connection;
 import org.labkey.remoteapi.assay.GetProtocolCommand;
@@ -101,8 +102,8 @@ public abstract class LuminexTest extends BaseWebDriverTest
     public static final File TEST_ASSAY_MULTIPLE_STANDARDS_3 = TestFileUtils.getSampleData("luminex/plate 3_IgA-Biot (Standard1).xls");
     public static final File TEST_ASSAY_MULTIPLE_STANDARDS_3_XLSX = TestFileUtils.getSampleData("luminex/plate 3_IgA-Biot (Standard1).xls");
 
-    public static final File RTRANSFORM_SCRIPT_FILE_LABKEY = new File(TestFileUtils.getLabKeyRoot(), "server/modules/commonAssays/luminex/resources/transformscripts/labkey_luminex_transform.R");
-    public static final File RTRANSFORM_SCRIPT_FILE_LAB =  new File(TestFileUtils.getLabKeyRoot(), "server/modules/commonAssays/luminex/resources/transformscripts/tomaras_luminex_transform.R");
+    public static final File RTRANSFORM_SCRIPT_FILE_LABKEY = FileUtil.appendPath(TestFileUtils.getLabKeyRoot(), org.labkey.api.util.Path.parse("server/modules/commonAssays/luminex/resources/transformscripts/labkey_luminex_transform.R"));
+    public static final File RTRANSFORM_SCRIPT_FILE_LAB = FileUtil.appendPath(TestFileUtils.getLabKeyRoot(), org.labkey.api.util.Path.parse("server/modules/commonAssays/luminex/resources/transformscripts/tomaras_luminex_transform.R"));
 
     public static final String ASSAY_DATA_FILE_LOCATION_MULTIPLE_FIELD = "__primaryFile__";
 

microarray/src/org/labkey/microarray/matrix/ExpressionMatrixAssayProvider.java

@@ -26,7 +26,6 @@
 import org.labkey.api.assay.AssayDataType;
 import org.labkey.api.assay.AssayPipelineProvider;
 import org.labkey.api.assay.AssayProtocolSchema;
-import org.labkey.api.assay.AssayRunCreator;
 import org.labkey.api.assay.AssayTableMetadata;
 import org.labkey.api.assay.actions.AssayRunUploadForm;
 import org.labkey.api.assay.matrix.ColumnMappingProperty;
@@ -93,7 +92,7 @@ public AssayTableMetadata getTableMetadata(@NotNull ExpProtocol protocol)
     }
 
     @Override
-    public AssayRunCreator getRunCreator()
+    public ExpressionMatrixRunCreator getRunCreator()
     {
         return new ExpressionMatrixRunCreator(this);
     }