Adopt FileLike for more pipeline APIs (#1061)

labkey-jeckels · web-flow · commit 7a49d3a97823 · 2025-11-04T17:48:01.000-08:00
diff --git a/ehr/api-src/org/labkey/api/ehr/EHRService.java b/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);
diff --git a/ehr/resources/web/ehr/panel/ManageTreatmentsPanel.js b/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;
diff --git a/ehr/src/org/labkey/ehr/EHRServiceImpl.java b/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);
     }
diff --git a/ehr/src/org/labkey/ehr/pipeline/GeneticCalculationsImportTask.java b/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)
                     {
diff --git a/ehr/src/org/labkey/ehr/pipeline/GeneticCalculationsRunnable.java b/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)
         {
diff --git a/ehr/test/src/org/labkey/test/tests/ehr/AbstractEHRTest.java b/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);
diff --git a/ehr/test/src/org/labkey/test/tests/ehr/ComplianceTrainingTest.java b/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()
diff --git a/ehr/test/src/org/labkey/test/tests/ehr/EHRBillingHelper.java b/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());
             }
diff --git a/ehr_billing/src/org/labkey/ehr_billing/pipeline/BillingTask.java b/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);
         }
 

Original file line number	Diff line number	Diff line change
`@@ -276,7 +276,7 @@ Ext4.define('EHR.panel.ManageTreatmentsPanel', {`
`276`	`276`	`dataIndex: 'amountAndVolume',`
`277`	`277`	`renderer: function(value, cellMetaData, record){`
`278`	`278`	`if (value){`
`279`		`- return value.replace(/\n/, '<br>');`
	`279`	`+ return value.replace(/\n/g, '<br>');`
`280`	`280`	`}`
`281`	`281`
`282`	`282`	`return value;`
Original file line number	Diff line number	Diff line change
`@@ -83,8 +83,8 @@`
`83`	`83`	`import org.labkey.ehr.security.EHRSecurityManager;`
`84`	`84`	`import org.labkey.ehr.table.DefaultEHRCustomizer;`
`85`	`85`	`import org.labkey.ehr.table.SNOMEDCodesDisplayColumn;`
	`86`	`+import org.labkey.vfs.FileLike;`
`86`	`87`
`87`		`-import java.io.File;`
`88`	`88`	`import java.io.FileNotFoundException;`
`89`	`89`	`import java.io.IOException;`
`90`	`90`	`import java.io.InputStream;`
`@@ -923,28 +923,28 @@ public void importFolderDefinition(Container container, User user, Module m, Pat`
`923`	`923`	`{`
`924`	`924`	`Resource root = m.getModuleResource(sourceFolderDirPath);`
`925`	`925`	`PipeRoot pipeRoot = PipelineService.get().findPipelineRoot(container);`
`926`		`- java.nio.file.Path pipeRootPath = pipeRoot.getRootNioPath();`
	`926`	`+ FileLike pipeRootPath = pipeRoot.getRootFileLike();`
`927`	`927`
`928`		`- java.nio.file.Path folderXmlPath;`
	`928`	`+ FileLike folderXmlPath;`
`929`	`929`
`930`		`- if (root instanceof DirectoryResource && ((DirectoryResource)root).getDir().equals(pipeRootPath.toFile()))`
	`930`	`+ if (root instanceof DirectoryResource dir && dir.getDir().equals(pipeRootPath.toNioPathForRead().toFile()))`
`931`	`931`	`{`
`932`	`932`	`// The pipeline root is already pointed at the folder definition, like it might be on a dev machine.`
`933`	`933`	`// No need to copy, especially since copying can cause infinite recursion when the paths are nested`
`934`		`- folderXmlPath = pipeRootPath.resolve("folder.xml");`
	`934`	`+ folderXmlPath = pipeRootPath.resolveChild("folder.xml");`
`935`	`935`	`}`
`936`	`936`	`else`
`937`	`937`	`{`
`938`		`- java.nio.file.Path folderPath = pipeRootPath.resolve("moduleFolderImport");`
`939`		`- folderXmlPath = folderPath.resolve("folder.xml");`
`940`		`- if (Files.exists(folderPath))`
	`938`	`+ FileLike folderPath = pipeRootPath.resolveChild("moduleFolderImport");`
	`939`	`+ folderXmlPath = folderPath.resolveChild("folder.xml");`
	`940`	`+ if (folderPath.exists())`
`941`	`941`	`{`
`942`	`942`	`FileUtil.deleteDir(folderPath);`
`943`	`943`	`}`
`944`	`944`	`copyResourceToPath(root, folderPath);`
`945`	`945`	`}`
`946`	`946`
`947`		`- if (!Files.exists(folderXmlPath))`
	`947`	`+ if (!folderXmlPath.exists())`
`948`	`948`	`{`
`949`	`949`	`throw new FileNotFoundException("Couldn't find an extracted " + folderXmlPath);`
`950`	`950`	`}`
`@@ -954,21 +954,21 @@ public void importFolderDefinition(Container container, User user, Module m, Pat`
`954`	`954`	`PipelineService.get().runFolderImportJob(container, user, null, folderXmlPath, "folder.xml", pipeRoot, options);`
`955`	`955`	`}`
`956`	`956`
`957`		`- private void copyResourceToPath(Resource resource, java.nio.file.Path target) throws IOException`
	`957`	`+ private void copyResourceToPath(Resource resource, FileLike target) throws IOException`
`958`	`958`	`{`
`959`	`959`	`if (resource.isCollection())`
`960`	`960`	`{`
`961`		`- Files.createDirectory(target);`
	`961`	`+ FileUtil.createDirectory(target);`
`962`	`962`	`for (Resource child : resource.list())`
`963`	`963`	`{`
`964`		`- java.nio.file.Path childTarget = target.resolve(child.getName());`
	`964`	`+ FileLike childTarget = target.resolveChild(child.getName());`
`965`	`965`	`copyResourceToPath(child, childTarget);`
`966`	`966`	`}`
`967`	`967`	`}`
`968`	`968`	`else`
`969`	`969`	`{`
`970`	`970`	`try (InputStream in = resource.getInputStream();`
`971`		`- OutputStream out = Files.newOutputStream(target))`
	`971`	`+ OutputStream out = target.openOutputStream())`
`972`	`972`	`{`
`973`	`973`	`FileUtil.copyData(in, out);`
`974`	`974`	`}`
`@@ -1069,7 +1069,7 @@ public void appendSNOMEDCols(AbstractTableInfo ti, String displayColumnName, Str`
`1069`	`1069`	`}`
`1070`	`1070`
`1071`	`1071`	`@Override`
`1072`		`- public void standaloneProcessKinshipAndInbreeding(Container c, User u, File pipelineDir, Logger log) throws PipelineJobException`
	`1072`	`+ public void standaloneProcessKinshipAndInbreeding(Container c, User u, FileLike pipelineDir, Logger log) throws PipelineJobException`
`1073`	`1073`	`{`
`1074`	`1074`	`GeneticCalculationsImportTask.standaloneProcessKinshipAndInbreeding(c, u, pipelineDir, log);`
`1075`	`1075`	`}`
Original file line number	Diff line number	Diff line change
`@@ -57,6 +57,7 @@`
`57`	`57`	`import org.labkey.api.util.FileType;`
`58`	`58`	`import org.labkey.api.util.PageFlowUtil;`
`59`	`59`	`import org.labkey.ehr.EHRSchema;`
	`60`	`+import org.labkey.vfs.FileLike;`
`60`	`61`
`61`	`62`	`import java.io.BufferedReader;`
`62`	`63`	`import java.io.File;`
`@@ -151,8 +152,8 @@ public RecordedActionSet run() throws PipelineJobException`
`151`	`152`	`PipelineJob job = getJob();`
`152`	`153`	`FileAnalysisJobSupport support = (FileAnalysisJobSupport) job;`
`153`	`154`
`154`		`- processInbreeding(job.getContainer(), job.getUser(), support.getAnalysisDirectoryPath().toFile(), job.getLogger());`
`155`		`- processKinship(job.getContainer(), job.getUser(), support.getAnalysisDirectoryPath().toFile(), job.getLogger(), job);`
	`155`	`+ processInbreeding(job.getContainer(), job.getUser(), support.getAnalysisDirectoryFileLike(), job.getLogger());`
	`156`	`+ processKinship(job.getContainer(), job.getUser(), support.getAnalysisDirectoryFileLike(), job.getLogger(), job);`
`156`	`157`
`157`	`158`	`if (GeneticCalculationsJob.isKinshipValidation())`
`158`	`159`	`{`
`@@ -170,15 +171,15 @@ public RecordedActionSet run() throws PipelineJobException`
`170`	`171`	`return new RecordedActionSet(actions);`
`171`	`172`	`}`
`172`	`173`
`173`		`- public static void standaloneProcessKinshipAndInbreeding(Container c, User u, File pipelineDir, Logger log) throws PipelineJobException`
	`174`	`+ public static void standaloneProcessKinshipAndInbreeding(Container c, User u, FileLike pipelineDir, Logger log) throws PipelineJobException`
`174`	`175`	`{`
`175`	`176`	`processInbreeding(c, u, pipelineDir, log);`
`176`	`177`	`processKinship(c, u, pipelineDir, log, null);`
`177`	`178`	`}`
`178`	`179`
`179`		`- private static void processKinship(Container c, User u, File pipelineDir, Logger log, @Nullable PipelineJob job) throws PipelineJobException`
	`180`	`+ private static void processKinship(Container c, User u, FileLike pipelineDir, Logger log, @Nullable PipelineJob job) throws PipelineJobException`
`180`	`181`	`{`
`181`		`- File output = new File(pipelineDir, KINSHIP_FILE);`
	`182`	`+ FileLike output = pipelineDir.resolveChild(KINSHIP_FILE);`
`182`	`183`	`if (!output.exists())`
`183`	`184`	`throw new PipelineJobException("Unable to find file: " + output.getPath());`
`184`	`185`
`@@ -190,7 +191,7 @@ private static void processKinship(Container c, User u, File pipelineDir, Logger`
`190`	`191`	`try`
`191`	`192`	`{`
`192`	`193`	`try (DbScope.Transaction transaction = ExperimentService.get().ensureTransaction();`
`193`		`- LineNumberReader lnr = new LineNumberReader(Readers.getReader(output)))`
	`194`	`+ LineNumberReader lnr = new LineNumberReader(Readers.getReader(output.openInputStream())))`
`194`	`195`	`{`
`195`	`196`	`while (lnr.readLine() != null)`
`196`	`197`	`{`
`@@ -248,7 +249,7 @@ else if (kinshipTable.getSqlDialect().isPostgreSQL())`
`248`	`249`	`}`
`249`	`250`
`250`	`251`	`try (DbScope.Transaction transaction = ExperimentService.get().ensureTransaction();`
`251`		`- BufferedReader reader = Readers.getReader(output);`
	`252`	`+ BufferedReader reader = Readers.getReader(output.openInputStream());`
`252`	`253`	`PreparedStatement stmt = transaction.getConnection().prepareStatement(`
`253`	`254`	`"INSERT INTO " + EHRSchema.EHR_SCHEMANAME + ".kinship\n" +`
`254`	`255`	`"\t(Id, Id2, coefficient, container, created, createdby, modified, modifiedby)\n" +`
`@@ -619,9 +620,9 @@ private static TableInfo getRealTable(TableInfo ti)`
`619`	`620`	`return null;`
`620`	`621`	`}`
`621`	`622`
`622`		`- private static void processInbreeding(Container c, User u, File pipelineDir, Logger log) throws PipelineJobException`
	`623`	`+ private static void processInbreeding(Container c, User u, FileLike pipelineDir, Logger log) throws PipelineJobException`
`623`	`624`	`{`
`624`		`- File output = new File(pipelineDir, INBREEDING_FILE);`
	`625`	`+ FileLike output = pipelineDir.resolveChild(INBREEDING_FILE);`
`625`	`626`	`if (!output.exists())`
`626`	`627`	`throw new PipelineJobException("Unable to find file: " + output.getPath());`
`627`	`628`
`@@ -636,12 +637,12 @@ private static void processInbreeding(Container c, User u, File pipelineDir, Log`
`636`	`637`	`QueryUpdateService qus = ti.getUpdateService();`
`637`	`638`	`qus.setBulkLoad(true);`
`638`	`639`
`639`		`- try (BufferedReader reader = Readers.getReader(output))`
	`640`	`+ try (BufferedReader reader = Readers.getReader(output.openInputStream()))`
`640`	`641`	`{`
`641`	`642`	`try (DbScope.Transaction transaction = ExperimentService.get().ensureTransaction())`
`642`	`643`	`{`
`643`	`644`	`log.info("Inspecting file length: " + output.getPath());`
`644`		`- try (LineNumberReader lnr = new LineNumberReader(Readers.getReader(output)))`
	`645`	`+ try (LineNumberReader lnr = new LineNumberReader(Readers.getReader(output.openInputStream())))`
`645`	`646`	`{`
`646`	`647`	`while (lnr.readLine() != null)`
`647`	`648`	`{`
Original file line number	Diff line number	Diff line change
`@@ -50,7 +50,7 @@`
`50`	`50`	`@BaseWebDriverTest.ClassTimeout(minutes = 5)`
`51`	`51`	`public abstract class ComplianceTrainingTest extends BaseWebDriverTest implements AdvancedSqlTest`
`52`	`52`	`{`
`53`		`- private final String listZIP = TestFileUtils.getLabKeyRoot() + "/server/modules/ehrModules/EHR_ComplianceDB/tools/SOP_Lists.zip";`
	`53`	`+ private final String listZIP = new File(TestFileUtils.getLabKeyRoot(), "server/modules/ehrModules/EHR_ComplianceDB/tools/SOP_Lists.zip").getPath();`
`54`	`54`
`55`	`55`	`@Override`
`56`	`56`	`protected String getProjectName()`
Original file line number	Diff line number	Diff line change
`@@ -45,9 +45,6 @@ public class EHRBillingHelper`
`45`	`45`	`{`
`46`	`46`	`private final BaseWebDriverTest _test;`
`47`	`47`	`private final String _projectName;`
`48`		`- private String _folderName;`
`49`		`- private String _modulePath;`
`50`		`- private String _containerPath;`
`51`	`48`	`private String _billingFolder;`
`52`	`49`	`public Ext4Helper _ext4Helper;`
`53`	`50`
`@@ -58,12 +55,9 @@ public EHRBillingHelper(BaseWebDriverTest test, String projectName)`
`58`	`55`	`_ext4Helper = new Ext4Helper(_test);`
`59`	`56`	`}`
`60`	`57`
`61`		`- public EHRBillingHelper(BaseWebDriverTest test, String projectName, String folderName, String modulePath, String containerPath, String billingFolder)`
	`58`	`+ public EHRBillingHelper(BaseWebDriverTest test, String projectName, String billingFolder)`
`62`	`59`	`{`
`63`	`60`	`this(test, projectName);`
`64`		`- _folderName = folderName;`
`65`		`- _modulePath = modulePath;`
`66`		`- _containerPath = containerPath;`
`67`	`61`	`_billingFolder = billingFolder;`
`68`	`62`	`}`
`69`	`63`
`@@ -88,7 +82,7 @@ public void performBillingRun(String startDate, String endDate, String comment,`
`88`	`82`
`89`	`83`	`public void checkMessageWindow(String title, @Nullable String bodyText, String buttonText)`
`90`	`84`	`{`
`91`		`- Window msgWindow = new Window.WindowFinder(_test.getDriver()).withTitle(title).waitFor();`
	`85`	`+ Window<?> msgWindow = new Window.WindowFinder(_test.getDriver()).withTitle(title).waitFor();`
`92`	`86`	`assertEquals("Message window Title mismatch", title, msgWindow.getTitle());`
`93`	`87`
`94`	`88`	`if (null != bodyText)`
`@@ -149,7 +143,7 @@ public void verifyBillingInvoicedItemsUsingAPI(String InvoicedId, List<InvoicedI`
`149`	`143`	`int sumQuantity = 0;`
`150`	`144`	`for (Map<String, Object> row : resp.getRows())`
`151`	`145`	`if (row.get("quantity") != null)`
`152`		`- sumQuantity += (double) row.get("quantity");`
	`146`	`+ sumQuantity += ((Number) row.get("quantity")).intValue();`
`153`	`147`
`154`	`148`	`assertEquals("Total quantity is not as expected", String.valueOf(sumQuantity), item.getTotalQuantity());`
`155`	`149`	`}`
Original file line number	Diff line number	Diff line change
`@@ -111,9 +111,8 @@ public List<String> getProtocolActionNames()`
`111`	`111`	`}`
`112`	`112`
`113`	`113`	`@Override`
`114`		`- public PipelineJob.Task createTask(PipelineJob job)`
	`114`	`+ public BillingTask createTask(PipelineJob job)`
`115`	`115`	`{`
`116`		`-`
`117`	`116`	`return new BillingTask(this, job);`
`118`	`117`	`}`
`119`	`118`