Adopt FileLike for more pipeline APIs

ehr/api-src/org/labkey/api/ehr/EHRService.java

@@ -44,8 +44,8 @@
 import org.labkey.api.util.URLHelper;
 import org.labkey.api.view.ActionURL;
 import org.labkey.api.view.template.ClientDependency;
+import org.labkey.vfs.FileLike;
 
-import java.io.File;
 import java.io.IOException;
 import java.util.Collection;
 import java.util.Date;
@@ -339,7 +339,7 @@ public EHRQCState getQCState(@NotNull Container c)
      * A use case is a separate pipeline server that performs the R computation on a cluster, and then triggers the main webserver to import
      * those results.
      */
-    abstract public void standaloneProcessKinshipAndInbreeding(Container c, User u, File pipelineDir, Logger log) throws PipelineJobException;
+    abstract public void standaloneProcessKinshipAndInbreeding(Container c, User u, FileLike pipelineDir, Logger log) throws PipelineJobException;
 
     /** Applicable for centers who use the model that projects have a reference to a protocol. Caches a protocol for a given project. **/
     abstract public void updateCachedProtocol(Container c, Integer project, String protocol);

ehr/resources/web/ehr/panel/ManageTreatmentsPanel.js

@@ -276,7 +276,7 @@ Ext4.define('EHR.panel.ManageTreatmentsPanel', {
                 dataIndex: 'amountAndVolume',
                 renderer: function(value, cellMetaData, record){
                     if (value){
-                        return value.replace(/\n/, '<br>');
+                        return value.replace(/\n/g, '<br>');
                     }
 
                     return value;

ehr/src/org/labkey/ehr/EHRServiceImpl.java

@@ -83,8 +83,8 @@
 import org.labkey.ehr.security.EHRSecurityManager;
 import org.labkey.ehr.table.DefaultEHRCustomizer;
 import org.labkey.ehr.table.SNOMEDCodesDisplayColumn;
+import org.labkey.vfs.FileLike;
 
-import java.io.File;
 import java.io.FileNotFoundException;
 import java.io.IOException;
 import java.io.InputStream;
@@ -923,28 +923,28 @@ public void importFolderDefinition(Container container, User user, Module m, Pat
     {
         Resource root = m.getModuleResource(sourceFolderDirPath);
         PipeRoot pipeRoot = PipelineService.get().findPipelineRoot(container);
-        java.nio.file.Path pipeRootPath = pipeRoot.getRootNioPath();
+        FileLike pipeRootPath = pipeRoot.getRootFileLike();
 
-        java.nio.file.Path folderXmlPath;
+        FileLike folderXmlPath;
 
-        if (root instanceof DirectoryResource && ((DirectoryResource)root).getDir().equals(pipeRootPath.toFile()))
+        if (root instanceof DirectoryResource dir && dir.getDir().equals(pipeRootPath.toNioPathForRead().toFile()))
         {
             // The pipeline root is already pointed at the folder definition, like it might be on a dev machine.
             // No need to copy, especially since copying can cause infinite recursion when the paths are nested
-            folderXmlPath = pipeRootPath.resolve("folder.xml");
+            folderXmlPath = pipeRootPath.resolveChild("folder.xml");
         }
         else
         {
-            java.nio.file.Path folderPath = pipeRootPath.resolve("moduleFolderImport");
-            folderXmlPath = folderPath.resolve("folder.xml");
-            if (Files.exists(folderPath))
+            FileLike folderPath = pipeRootPath.resolveChild("moduleFolderImport");
+            folderXmlPath = folderPath.resolveChild("folder.xml");
+            if (folderPath.exists())
             {
                 FileUtil.deleteDir(folderPath);
             }
             copyResourceToPath(root, folderPath);
         }
 
-        if (!Files.exists(folderXmlPath))
+        if (!folderXmlPath.exists())
         {
             throw new FileNotFoundException("Couldn't find an extracted " + folderXmlPath);
         }
@@ -954,21 +954,21 @@ public void importFolderDefinition(Container container, User user, Module m, Pat
         PipelineService.get().runFolderImportJob(container, user, null, folderXmlPath, "folder.xml", pipeRoot, options);
     }
 
-    private void copyResourceToPath(Resource resource, java.nio.file.Path target) throws IOException
+    private void copyResourceToPath(Resource resource, FileLike target) throws IOException
     {
         if (resource.isCollection())
         {
-            Files.createDirectory(target);
+            FileUtil.createDirectory(target);
             for (Resource child : resource.list())
             {
-                java.nio.file.Path childTarget = target.resolve(child.getName());
+                FileLike childTarget = target.resolveChild(child.getName());
                 copyResourceToPath(child, childTarget);
             }
         }
         else
         {
             try (InputStream in = resource.getInputStream();
-                OutputStream out = Files.newOutputStream(target))
+                OutputStream out = target.openOutputStream())
             {
                 FileUtil.copyData(in, out);
             }
@@ -1069,7 +1069,7 @@ public void appendSNOMEDCols(AbstractTableInfo ti, String displayColumnName, Str
     }
 
     @Override
-    public void standaloneProcessKinshipAndInbreeding(Container c, User u, File pipelineDir, Logger log) throws PipelineJobException
+    public void standaloneProcessKinshipAndInbreeding(Container c, User u, FileLike pipelineDir, Logger log) throws PipelineJobException
     {
         GeneticCalculationsImportTask.standaloneProcessKinshipAndInbreeding(c, u, pipelineDir, log);
     }

ehr/src/org/labkey/ehr/pipeline/GeneticCalculationsImportTask.java

@@ -57,6 +57,7 @@
 import org.labkey.api.util.FileType;
 import org.labkey.api.util.PageFlowUtil;
 import org.labkey.ehr.EHRSchema;
+import org.labkey.vfs.FileLike;
 
 import java.io.BufferedReader;
 import java.io.File;
@@ -151,8 +152,8 @@ public RecordedActionSet run() throws PipelineJobException
             PipelineJob job = getJob();
             FileAnalysisJobSupport support = (FileAnalysisJobSupport) job;
 
-            processInbreeding(job.getContainer(), job.getUser(), support.getAnalysisDirectoryPath().toFile(), job.getLogger());
-            processKinship(job.getContainer(), job.getUser(), support.getAnalysisDirectoryPath().toFile(), job.getLogger(), job);
+            processInbreeding(job.getContainer(), job.getUser(), support.getAnalysisDirectoryFileLike(), job.getLogger());
+            processKinship(job.getContainer(), job.getUser(), support.getAnalysisDirectoryFileLike(), job.getLogger(), job);
 
             if (GeneticCalculationsJob.isKinshipValidation())
             {
@@ -170,15 +171,15 @@ public RecordedActionSet run() throws PipelineJobException
         return new RecordedActionSet(actions);
     }
 
-    public static void standaloneProcessKinshipAndInbreeding(Container c, User u, File pipelineDir, Logger log) throws PipelineJobException
+    public static void standaloneProcessKinshipAndInbreeding(Container c, User u, FileLike pipelineDir, Logger log) throws PipelineJobException
     {
         processInbreeding(c, u, pipelineDir, log);
         processKinship(c, u, pipelineDir, log, null);
     }
 
-    private static void processKinship(Container c, User u, File pipelineDir, Logger log, @Nullable PipelineJob job) throws PipelineJobException
+    private static void processKinship(Container c, User u, FileLike pipelineDir, Logger log, @Nullable PipelineJob job) throws PipelineJobException
     {
-        File output = new File(pipelineDir, KINSHIP_FILE);
+        FileLike output = pipelineDir.resolveChild(KINSHIP_FILE);
         if (!output.exists())
             throw new PipelineJobException("Unable to find file: " + output.getPath());
 
@@ -190,7 +191,7 @@ private static void processKinship(Container c, User u, File pipelineDir, Logger
         try
         {
             try (DbScope.Transaction transaction = ExperimentService.get().ensureTransaction();
-                 LineNumberReader lnr = new LineNumberReader(Readers.getReader(output)))
+                 LineNumberReader lnr = new LineNumberReader(Readers.getReader(output.openInputStream())))
             {
                 while (lnr.readLine() != null)
                 {
@@ -248,7 +249,7 @@ else if (kinshipTable.getSqlDialect().isPostgreSQL())
             }
 
             try (DbScope.Transaction transaction = ExperimentService.get().ensureTransaction();
-                 BufferedReader reader = Readers.getReader(output);
+                 BufferedReader reader = Readers.getReader(output.openInputStream());
                  PreparedStatement stmt = transaction.getConnection().prepareStatement(
                     "INSERT INTO " + EHRSchema.EHR_SCHEMANAME + ".kinship\n" +
                             "\t(Id, Id2, coefficient, container, created, createdby, modified, modifiedby)\n" +
@@ -619,9 +620,9 @@ private static TableInfo getRealTable(TableInfo ti)
         return null;
     }
 
-    private static void processInbreeding(Container c, User u, File pipelineDir, Logger log) throws PipelineJobException
+    private static void processInbreeding(Container c, User u, FileLike pipelineDir, Logger log) throws PipelineJobException
     {
-        File output = new File(pipelineDir, INBREEDING_FILE);
+        FileLike output = pipelineDir.resolveChild(INBREEDING_FILE);
         if (!output.exists())
             throw new PipelineJobException("Unable to find file: " + output.getPath());
 
@@ -636,12 +637,12 @@ private static void processInbreeding(Container c, User u, File pipelineDir, Log
         QueryUpdateService qus = ti.getUpdateService();
         qus.setBulkLoad(true);
 
-        try (BufferedReader reader = Readers.getReader(output))
+        try (BufferedReader reader = Readers.getReader(output.openInputStream()))
         {
             try (DbScope.Transaction transaction = ExperimentService.get().ensureTransaction())
             {
                 log.info("Inspecting file length: " + output.getPath());
-                try (LineNumberReader lnr = new LineNumberReader(Readers.getReader(output)))
+                try (LineNumberReader lnr = new LineNumberReader(Readers.getReader(output.openInputStream())))
                 {
                     while (lnr.readLine() != null)
                     {

ehr/src/org/labkey/ehr/pipeline/GeneticCalculationsRunnable.java

@@ -31,11 +31,13 @@
 import org.labkey.api.pipeline.file.FileAnalysisTaskPipeline;
 import org.labkey.api.security.User;
 import org.labkey.api.util.ConfigurationException;
+import org.labkey.api.util.FileUtil;
 import org.labkey.api.util.StringUtilsLabKey;
 import org.labkey.api.util.logging.LogHelper;
 import org.labkey.api.view.ActionURL;
 import org.labkey.api.view.ViewBackgroundInfo;
 import org.labkey.ehr.EHRManager;
+import org.labkey.vfs.FileLike;
 
 import java.io.File;
 import java.io.FileWriter;
@@ -97,11 +99,11 @@ private void startCalculation(User u, Container c, boolean allowRunningDuringDay
 
             protocol.setTimestampLog(true);
 
-            File fileParameters = protocol.getParametersFile(root.getRootPath(), root);
+            FileLike fileParameters = protocol.getParametersFile(root.getRootFileLike(), root);
             if (!fileParameters.exists())
             {
-                fileParameters.getParentFile().mkdirs();
-                fileParameters.createNewFile();
+                fileParameters.getParent().mkdirs();
+                FileUtil.createNewFile(fileParameters, true);
             }
             protocol.saveInstance(fileParameters, c);
 
@@ -118,11 +120,11 @@ private void startCalculation(User u, Container c, boolean allowRunningDuringDay
                 w.write(xml);
             }
 
-            File inputFile = new File(root.getRootPath(), "kinship.txt");
+            FileLike inputFile = root.resolvePathToFileLike("kinship.txt");
             if (!inputFile.exists())
-                inputFile.createNewFile();
+                FileUtil.createNewFile(inputFile, true);
 
-            AbstractFileAnalysisJob job = protocol.createPipelineJob(bg, root, Collections.singletonList(inputFile.toPath()), fileParameters.toPath(), null);
+            AbstractFileAnalysisJob job = protocol.createPipelineJob(bg, root, Collections.singletonList(inputFile), fileParameters, null);
             PipelineService.get().queueJob(job);
 
             String dateFormat = "yyyy_MM_dd_hh_mm_ss";
@@ -131,7 +133,7 @@ private void startCalculation(User u, Container c, boolean allowRunningDuringDay
             Date now = cal.getTime();
             String timestamp = formatter.format(now);
 
-            job.setLogFile(new File(job.getLogFile().getParent() + "/kinship_" + timestamp + ".txt.log"));
+            job.setLogFile(job.getLogFileLike().getParent().resolveChild("kinship_" + timestamp + ".txt.log"));
         }
         catch (ClassNotFoundException e)
         {

ehr/test/src/org/labkey/test/tests/ehr/AbstractEHRTest.java

@@ -18,6 +18,8 @@
 import org.apache.commons.lang3.StringUtils;
 import org.json.JSONObject;
 import org.junit.Assert;
+import org.labkey.api.util.FileUtil;
+import org.labkey.api.util.Path;
 import org.labkey.remoteapi.CommandException;
 import org.labkey.remoteapi.Connection;
 import org.labkey.remoteapi.SimplePostCommand;
@@ -59,7 +61,6 @@
 import java.util.List;
 import java.util.Map;
 import java.util.UUID;
-import java.util.regex.Pattern;
 
 import static org.junit.Assert.assertNull;
 import static org.junit.Assert.fail;
@@ -144,7 +145,7 @@ abstract public class AbstractEHRTest extends BaseWebDriverTest implements Advan
     protected List<Long> _saveRowsTimes;
 
     protected abstract String getModuleDirectory();
-    protected EHRBillingHelper _billingHelper = new EHRBillingHelper(this, getProjectName(), FOLDER_NAME, getModulePath(), getContainerPath(),BILLING_FOLDER);
+    protected EHRBillingHelper _billingHelper = new EHRBillingHelper(this, getProjectName(), BILLING_FOLDER);
 
     //xpath fragment
     public static final String VISIBLE = "not(ancestor-or-self::*[contains(@style,'visibility: hidden') or contains(@class, 'x-hide-display')])";
@@ -203,14 +204,6 @@ public void validateQueries(boolean validateSubfolders)
         }
     }
 
-    protected Pattern[] getIgnoredElements()
-    {
-        return new Pattern[] {
-                Pattern.compile("qcstate", Pattern.CASE_INSENSITIVE),//qcstate IDs aren't predictable
-                Pattern.compile("stacktrace", Pattern.CASE_INSENSITIVE)
-        };
-    }
-
     protected String getMale() {
         return "m";
     }
@@ -365,8 +358,8 @@ public void doCleanup(boolean afterTest) throws TestTimeoutException
 
     protected void importFolderFromPath(int jobCount)
     {
-        File path = new File(TestFileUtils.getLabKeyRoot(), getModulePath() + "/resources/referenceStudy");
-        setPipelineRoot(path.getPath());
+        File path = FileUtil.appendPath(TestFileUtils.getLabKeyRoot(), Path.parse(getModulePath() + "/resources/referenceStudy"));
+        setPipelineRoot(path.getPath(), false);
 
         beginAt(WebTestHelper.getBaseURL() + "/" + getContainerPath() + "/pipeline-status-begin.view");
         clickButton("Process and Import Data", defaultWaitForPage);

ehr/test/src/org/labkey/test/tests/ehr/ComplianceTrainingTest.java

@@ -50,7 +50,7 @@
 @BaseWebDriverTest.ClassTimeout(minutes = 5)
 public abstract class ComplianceTrainingTest extends BaseWebDriverTest implements AdvancedSqlTest
 {
-    private final String listZIP = TestFileUtils.getLabKeyRoot() + "/server/modules/ehrModules/EHR_ComplianceDB/tools/SOP_Lists.zip";
+    private final String listZIP = new File(TestFileUtils.getLabKeyRoot(), "server/modules/ehrModules/EHR_ComplianceDB/tools/SOP_Lists.zip").getPath();
 
     @Override
     protected String getProjectName()

ehr/test/src/org/labkey/test/tests/ehr/EHRBillingHelper.java

@@ -45,9 +45,6 @@ public class EHRBillingHelper
 {
     private final BaseWebDriverTest _test;
     private final String _projectName;
-    private String _folderName;
-    private String _modulePath;
-    private String _containerPath;
     private String _billingFolder;
     public Ext4Helper _ext4Helper;
 
@@ -58,12 +55,9 @@ public EHRBillingHelper(BaseWebDriverTest test, String projectName)
         _ext4Helper = new Ext4Helper(_test);
     }
 
-    public EHRBillingHelper(BaseWebDriverTest test, String projectName, String folderName, String modulePath, String containerPath, String billingFolder)
+    public EHRBillingHelper(BaseWebDriverTest test, String projectName, String billingFolder)
     {
         this(test, projectName);
-        _folderName = folderName;
-        _modulePath = modulePath;
-        _containerPath = containerPath;
         _billingFolder = billingFolder;
     }
 
@@ -88,7 +82,7 @@ public void performBillingRun(String startDate, String endDate, String comment,
 
     public void checkMessageWindow(String title, @Nullable String bodyText, String buttonText)
     {
-        Window msgWindow = new Window.WindowFinder(_test.getDriver()).withTitle(title).waitFor();
+        Window<?> msgWindow = new Window.WindowFinder(_test.getDriver()).withTitle(title).waitFor();
         assertEquals("Message window Title mismatch", title, msgWindow.getTitle());
 
         if (null != bodyText)
@@ -149,7 +143,7 @@ public void verifyBillingInvoicedItemsUsingAPI(String InvoicedId, List<InvoicedI
                 int sumQuantity = 0;
                 for (Map<String, Object> row : resp.getRows())
                     if (row.get("quantity") != null)
-                        sumQuantity += (double) row.get("quantity");
+                        sumQuantity += ((Number) row.get("quantity")).intValue();
 
                 assertEquals("Total quantity is not as expected", String.valueOf(sumQuantity), item.getTotalQuantity());
             }

ehr_billing/src/org/labkey/ehr_billing/pipeline/BillingTask.java

@@ -111,9 +111,8 @@ public List<String> getProtocolActionNames()
         }
 
         @Override
-        public PipelineJob.Task createTask(PipelineJob job)
+        public BillingTask createTask(PipelineJob job)
         {
-
             return new BillingTask(this, job);
         }