Continue adopting FileLike instead of File or Path (#584)

labkey-jeckels · web-flow · commit 60efaa5c222e · 2025-12-03T14:30:14.000-08:00
diff --git a/SkylineToolsStore/src/org/labkey/skylinetoolsstore/SkylineToolsStoreController.java b/SkylineToolsStore/src/org/labkey/skylinetoolsstore/SkylineToolsStoreController.java
@@ -1180,7 +1180,7 @@ public ModelAndView getView(DownloadFileForm form, BindException errors) throws
                 }
                 else
                 {
-                    PageFlowUtil.streamFile(getViewContext().getResponse(), downloadFile, true);
+                    PageFlowUtil.streamFile(getViewContext().getResponse(), downloadFile.toPath(), true);
                     return null;
                 }
             }
diff --git a/lincs/src/org/labkey/lincs/LincsController.java b/lincs/src/org/labkey/lincs/LincsController.java
@@ -87,6 +87,7 @@
 import org.labkey.lincs.psp.LincsPspUtil;
 import org.labkey.lincs.psp.PspEndpoint;
 import org.labkey.lincs.view.GctUtils;
+import org.labkey.vfs.FileLike;
 import org.springframework.beans.MutablePropertyValues;
 import org.springframework.validation.BindException;
 import org.springframework.validation.Errors;
@@ -144,35 +145,32 @@ public void addNavTrail(NavTree root)
         }
     }
 
-    private void copyFiles(Path gctDir, String outputFileBaseName, Path gct, File reportDir) throws IOException
+    private void copyFiles(Path gctDir, String outputFileBaseName, Path gct, FileLike reportDir) throws IOException
     {
         // reportDir is a local directory under tomcat's temp directory
-        File[] reportDirFiles = reportDir.listFiles(new FilenameFilter()
+        List<FileLike> reportDirFiles = reportDir.getChildren((f) ->
         {
-            @Override
-            public boolean accept(File dir, String name)
-            {
-                return name.toLowerCase().endsWith(".txt")
+            String name = f.getName();
+            return name.toLowerCase().endsWith(".txt")
                         || name.toLowerCase().endsWith(".gct")
                         || name.equals("script.Rout");
-            }
         });
 
         // The report should create two files: lincs.gct and lincs.processed.gct
         // Copy both to the GCT folder
-        for(File file: reportDirFiles)
+        for(FileLike file: reportDirFiles)
         {
             if(file.getName().equalsIgnoreCase("lincs.gct"))
             {
-                Files.copy(file.toPath(), gct, StandardCopyOption.REPLACE_EXISTING);
+                Files.copy(file.toNioPathForRead(), gct, StandardCopyOption.REPLACE_EXISTING);
             }
             else if(file.getName().equalsIgnoreCase("console.txt"))
             {
-                Files.copy(file.toPath(), gctDir.resolve(outputFileBaseName + ".console.txt" ), StandardCopyOption.REPLACE_EXISTING);
+                Files.copy(file.toNioPathForRead(), gctDir.resolve(outputFileBaseName + ".console.txt" ), StandardCopyOption.REPLACE_EXISTING);
             }
             else if(file.getName().equals("script.Rout"))
             {
-                Files.copy(file.toPath(), gctDir.resolve(outputFileBaseName + ".script.Rout" ), StandardCopyOption.REPLACE_EXISTING);
+                Files.copy(file.toNioPathForRead(), gctDir.resolve(outputFileBaseName + ".script.Rout" ), StandardCopyOption.REPLACE_EXISTING);
             }
         }
     }
@@ -306,11 +304,11 @@ public ApiResponse execute(GCTReportForm form, BindException errors) throws Exce
             }
             catch(Exception e)
             {
-                copyFiles(gctDir, outputFileBaseName, downloadFile, rreport.getReportDir(getContainer().getId()));
+                copyFiles(gctDir, outputFileBaseName, downloadFile, rreport.getReportDirFileLike(getContainer().getId()));
                 throw new ApiUsageException("There was an error running the GCT R script.", e);
             }
 
-            copyFiles(gctDir, outputFileBaseName, downloadFile, rreport.getReportDir(getContainer().getId()));
+            copyFiles(gctDir, outputFileBaseName, downloadFile, rreport.getReportDirFileLike(getContainer().getId()));
 
             if(!Files.exists(downloadFile))
             {
diff --git a/lincs/src/org/labkey/lincs/psp/LincsPspPipelineJob.java b/lincs/src/org/labkey/lincs/psp/LincsPspPipelineJob.java
@@ -43,7 +43,7 @@ public LincsPspPipelineJob(ViewBackgroundInfo info, PipeRoot root, ITargetedMSRu
         String baseLogFileName = FileUtil.makeFileNameWithTimestamp("LincsPSP_" + (_oldPspJob != null ? "rerun_" : "") + run.getBaseName().replace(" ", "_"));
 
         LocalDirectory localDirectory = LocalDirectory.create(root, baseLogFileName,
-                !root.isCloudRoot() ? root.getRootPath().getAbsolutePath() : FileUtil.getTempDirectory().getPath());
+                !root.isCloudRoot() ? root.getRootFileLike() : FileUtil.getTempDirectoryFileLike());
         setLocalDirectory(localDirectory);
         setLogFile(localDirectory.determineLogFile());
 
diff --git a/nextflow/src/org/labkey/nextflow/pipeline/NextFlowPipelineJob.java b/nextflow/src/org/labkey/nextflow/pipeline/NextFlowPipelineJob.java
@@ -25,7 +25,6 @@
 import org.labkey.vfs.FileLike;
 
 import java.io.BufferedWriter;
-import java.io.File;
 import java.io.IOException;
 import java.io.InputStream;
 import java.nio.file.Files;
@@ -117,7 +116,7 @@ private static FileLike createConfig(Path configTemplate, FileLike parentDir, Fi
     @Override
     public String getDescription()
     {
-        return "NextFlow analysis of " + StringUtilsLabKey.pluralize(getInputFilePaths().size(), "file") + " using config: " + config.getName();
+        return "NextFlow analysis of " + StringUtilsLabKey.pluralize(getInputFiles().size(), "file") + " using config: " + config.getName();
     }
 
     @Override
@@ -139,13 +138,13 @@ public AbstractFileAnalysisJob createSingleFileJob(FileLike file)
     }
 
     @Override
-    public File findInputFile(String name)
+    public FileLike findInputFile(String name)
     {
         throw new UnsupportedOperationException();
     }
 
     @Override
-    public File findOutputFile(String name)
+    public FileLike findOutputFile(String name)
     {
         return null;
     }
diff --git a/nextflow/src/org/labkey/nextflow/pipeline/NextFlowRunTask.java b/nextflow/src/org/labkey/nextflow/pipeline/NextFlowRunTask.java
@@ -19,7 +19,6 @@
 import org.labkey.vfs.FileLike;
 
 import java.io.BufferedReader;
-import java.io.File;
 import java.io.IOException;
 import java.io.InputStream;
 import java.io.InputStreamReader;
@@ -76,7 +75,7 @@ public NextFlowRunTask(Factory factory, PipelineJob job)
             // Need to pass to the main process directly in the future to allow concurrent execution for different users
             ProcessBuilder secretsPB = new ProcessBuilder("nextflow", "secrets", "set", "PANORAMA_API_KEY", apiKey);
             log.info("Setting secrets");
-            File dir = getJob().getLogFile().getParentFile();
+            FileLike dir = getJob().getLogFileLike().getParent();
             getJob().runSubProcess(secretsPB, dir);
 
             ProcessBuilder executionPB = new ProcessBuilder(getArgs());
@@ -85,9 +84,9 @@ public NextFlowRunTask(Factory factory, PipelineJob job)
             NextFlowPipelineJob.LOG.info("Finished executing NextFlow: {}", getJob().getJsonJobInfo(true));
 
             RecordedAction action = new RecordedAction(ACTION_NAME);
-            for (Path inputFile : getJob().getInputFilePaths())
+            for (FileLike inputFile : getJob().getInputFiles())
             {
-                action.addInput(inputFile.toFile(), SPECTRA_INPUT_ROLE);
+                action.addInput(inputFile, SPECTRA_INPUT_ROLE);
             }
             addOutputs(action, getJob().getLogFilePath().getParent().resolve("reports"), log);
             addOutputs(action, getJob().getLogFilePath().getParent().resolve("results"), log);
diff --git a/panoramapublic/src/org/labkey/panoramapublic/PanoramaPublicController.java b/panoramapublic/src/org/labkey/panoramapublic/PanoramaPublicController.java
@@ -139,6 +139,7 @@
 import org.labkey.api.view.template.ClientDependency;
 import org.labkey.api.wiki.WikiRendererType;
 import org.labkey.api.wiki.WikiRenderingService;
+import org.labkey.api.writer.PrintWriters;
 import org.labkey.panoramapublic.bluesky.BlueskyApiClient;
 import org.labkey.panoramapublic.bluesky.BlueskyException;
 import org.labkey.panoramapublic.bluesky.BlueskySettingsManager;
@@ -4617,11 +4618,11 @@ private PxXml createPxXml(ExperimentAnnotations expAnnot, JournalExperiment je,
             }
         }
 
-        private File writePxXmlFile(String xmlString) throws PxException
+        private FileLike writePxXmlFile(String xmlString) throws PxException
         {
-            File xml = getLocalFile(getContainer(), "px.xml"); // TODO: Add date time stamp
+            FileLike xml = getLocalFile(getContainer(), "px.xml"); // TODO: Add date time stamp
 
-            try (PrintWriter out = new PrintWriter(new FileWriter(xml, StandardCharsets.UTF_8)))
+            try (PrintWriter out = PrintWriters.getPrintWriter(xml.openOutputStream()))
             {
                 out.write(xmlString);
             }
@@ -4656,7 +4657,7 @@ public void assignPxId(boolean useTestDb, boolean testMode, String pxUser, Strin
 
         private void validatePxXml(boolean useTestDb, String pxChangeLog, String pxUser, String pxPassword, BindException errors) throws PxException, ProteomeXchangeServiceException
         {
-            File xmlFile = writePxXmlFile(createPxXml(_expAnnot, _journalExperiment, _submission, _validationStatus, pxChangeLog, true).getXml());
+            FileLike xmlFile = writePxXmlFile(createPxXml(_expAnnot, _journalExperiment, _submission, _validationStatus, pxChangeLog, true).getXml());
             _pxResponse = ProteomeXchangeService.validatePxXml(xmlFile, useTestDb, pxUser, pxPassword);
             if(ProteomeXchangeService.responseHasErrors(_pxResponse))
             {
@@ -4677,7 +4678,7 @@ private void submitPxXml(boolean useTestDb, boolean testMode, String pxChangeLog
                 return;
             }
             PxXml pxXml = createPxXml(_expAnnot, _journalExperiment, _submission, _validationStatus, pxChangeLog, true);
-            File xmlFile = writePxXmlFile(pxXml.getXml());
+            FileLike xmlFile = writePxXmlFile(pxXml.getXml());
             _pxResponse = ProteomeXchangeService.submitPxXml(xmlFile, useTestDb, pxUser, pxPassword);
             if(ProteomeXchangeService.responseHasErrors(_pxResponse))
             {
@@ -4699,7 +4700,7 @@ private void updatePxXml(boolean useTestDb, boolean testMode, String pxChangeLog
             submitPxXml(useTestDb, testMode, pxChangeLog, pxUser, pxPassword, errors);
         }
 
-        private static File getLocalFile(Container container, String fileName) throws PxException
+        private static FileLike getLocalFile(Container container, String fileName) throws PxException
         {
             // File.createTempFile()
             java.nio.file.Path fileRoot = FileContentService.get().getFileRootPath(container, FileContentService.ContentType.files);
@@ -4713,7 +4714,7 @@ private static File getLocalFile(Container container, String fileName) throws Px
                 if (root != null)
                 {
                     LocalDirectory localDirectory = LocalDirectory.create(root);
-                    return new File(localDirectory.getLocalDirectoryFile(), fileName);
+                    return localDirectory.getLocalDirectoryFile().resolveChild(fileName);
                 }
                 else
                 {
@@ -4722,7 +4723,7 @@ private static File getLocalFile(Container container, String fileName) throws Px
             }
             else
             {
-                return fileRoot.resolve(fileName).toFile();
+                return FileSystemLike.wrapFile(fileRoot).resolveChild(fileName);
             }
         }
     }
diff --git a/panoramapublic/src/org/labkey/panoramapublic/pipeline/CopyExperimentPipelineJob.java b/panoramapublic/src/org/labkey/panoramapublic/pipeline/CopyExperimentPipelineJob.java
@@ -34,9 +34,6 @@
 import org.labkey.panoramapublic.model.Journal;
 import org.labkey.vfs.FileLike;
 
-import java.io.File;
-import java.io.IOException;
-
 /**
  * User: vsharma
  * Date: 8/21/2014
@@ -118,7 +115,7 @@ public String getDescription()
     }
 
     @Override
-    public TaskPipeline getTaskPipeline()
+    public TaskPipeline<?> getTaskPipeline()
     {
         return PipelineJobService.get().getTaskPipeline(new TaskId(CopyExperimentPipelineJob.class));
     }
@@ -133,19 +130,6 @@ protected void finallyCleanUpLocalDirectory()
        }
    }
 
-    public static File getLogFileFor(PipeRoot root, ExperimentAnnotations experimentAnnotations) throws IOException
-    {
-        File rootDir = root.getLogDirectory();
-        if (!rootDir.exists())
-        {
-            throw new IOException("Pipeline root directory " + rootDir.getAbsolutePath() + " does not exist.");
-        }
-
-        String logFileName = "Experiment_" + experimentAnnotations.getExperimentId() + ".log";
-
-        return new File(rootDir, logFileName);
-    }
-
     @Override
     public ExperimentAnnotations getExpAnnotations()
     {
diff --git a/panoramapublic/src/org/labkey/panoramapublic/pipeline/PxDataValidationPipelineJob.java b/panoramapublic/src/org/labkey/panoramapublic/pipeline/PxDataValidationPipelineJob.java
@@ -14,8 +14,6 @@
 import org.labkey.api.view.ViewBackgroundInfo;
 import org.labkey.panoramapublic.model.ExperimentAnnotations;
 
-import java.io.File;
-
 public class PxDataValidationPipelineJob extends PipelineJob implements PxDataValidationJobSupport
 {
     private final ExperimentAnnotations _experimentAnnotations;
@@ -41,7 +39,7 @@ public PxDataValidationPipelineJob(ViewBackgroundInfo info, PipeRoot root, Exper
         _description = String.format("Validating data for experiment Id: %d, validation Id: %d", experiment.getId(), validationId);
 
         String baseLogFileName = FileUtil.makeFileNameWithTimestamp("Experiment_Validation_" + experiment.getExperimentId(), "log");
-        setLogFile(new File(root.getLogDirectory(), baseLogFileName));
+        setLogFile(root.getLogDirectory(true).resolveChild(baseLogFileName));
 
         header("Validating data for a ProteomeXchange submission.");
     }
diff --git a/panoramapublic/src/org/labkey/panoramapublic/proteomexchange/ProteomeXchangeService.java b/panoramapublic/src/org/labkey/panoramapublic/proteomexchange/ProteomeXchangeService.java
@@ -17,17 +17,20 @@
 
 import org.apache.hc.client5.http.classic.methods.HttpPost;
 import org.apache.hc.client5.http.entity.mime.FileBody;
+import org.apache.hc.client5.http.entity.mime.InputStreamBody;
 import org.apache.hc.client5.http.entity.mime.MultipartEntityBuilder;
 import org.apache.hc.client5.http.impl.classic.CloseableHttpClient;
 import org.apache.hc.client5.http.impl.classic.CloseableHttpResponse;
 import org.apache.hc.client5.http.impl.classic.HttpClientBuilder;
+import org.apache.hc.core5.http.ContentType;
 import org.apache.hc.core5.http.HttpEntity;
 import org.apache.hc.core5.http.ParseException;
 import org.apache.hc.core5.http.io.entity.EntityUtils;
 import org.apache.logging.log4j.Logger;
 import org.jetbrains.annotations.NotNull;
 import org.labkey.api.util.PageFlowUtil;
 import org.labkey.api.util.logging.LogHelper;
+import org.labkey.vfs.FileLike;
 
 import java.io.File;
 import java.io.IOException;
@@ -49,17 +52,17 @@ private enum METHOD {submitDataset, validateXML, requestID}
 
     private static final Logger LOG = LogHelper.getLogger(ProteomeXchangeService.class, "Handles requests to the ProteomeXchange server");
 
-    public static String validatePxXml(File pxxmlFile, boolean testDatabase, String user, String pass) throws ProteomeXchangeServiceException
+    public static String validatePxXml(FileLike pxxmlFile, boolean testDatabase, String user, String pass) throws ProteomeXchangeServiceException
     {
         return postPxXml(pxxmlFile, testDatabase, user, pass, METHOD.validateXML);
     }
 
-    public static String submitPxXml(File pxxmlFile, boolean testDatabase, String user, String pass) throws ProteomeXchangeServiceException
+    public static String submitPxXml(FileLike pxxmlFile, boolean testDatabase, String user, String pass) throws ProteomeXchangeServiceException
     {
         return postPxXml(pxxmlFile, testDatabase, user, pass, METHOD.submitDataset);
     }
 
-    private static String postPxXml(File pxxmlFile, boolean testDatabase, String user, String pass, METHOD method) throws ProteomeXchangeServiceException
+    private static String postPxXml(FileLike pxxmlFile, boolean testDatabase, String user, String pass, METHOD method) throws ProteomeXchangeServiceException
     {
         String responseMessage;
         try {
@@ -118,12 +121,12 @@ public static String getPxId(boolean testDatabase, String user, String pass) thr
     }
 
     @NotNull
-    private static MultipartEntityBuilder getMultipartEntityBuilder(File pxxmlFile, boolean testDatabase, METHOD method, String user, String pass)
+    private static MultipartEntityBuilder getMultipartEntityBuilder(FileLike pxxmlFile, boolean testDatabase, METHOD method, String user, String pass) throws IOException
     {
         MultipartEntityBuilder builder = MultipartEntityBuilder.create();
         if(pxxmlFile != null)
         {
-            builder.addPart("ProteomeXchangeXML", new FileBody(pxxmlFile));
+            builder.addPart("ProteomeXchangeXML", new InputStreamBody(pxxmlFile.openInputStream(), ContentType.TEXT_XML, pxxmlFile.getName()));
         }
         builder.addTextBody("PXPartner", user);
         builder.addTextBody("authentication", pass);
@@ -140,7 +143,7 @@ private static MultipartEntityBuilder getMultipartEntityBuilder(File pxxmlFile,
         return builder;
     }
 
-    private static MultipartEntityBuilder getMultipartEntityBuilder(boolean testDatabase, METHOD method, String user, String pass)
+    private static MultipartEntityBuilder getMultipartEntityBuilder(boolean testDatabase, METHOD method, String user, String pass) throws IOException
     {
         return getMultipartEntityBuilder(null, testDatabase, method, user, pass);
     }

Original file line number	Diff line number	Diff line change
`@@ -1180,7 +1180,7 @@ public ModelAndView getView(DownloadFileForm form, BindException errors) throws`
`1180`	`1180`	`}`
`1181`	`1181`	`else`
`1182`	`1182`	`{`
`1183`		`- PageFlowUtil.streamFile(getViewContext().getResponse(), downloadFile, true);`
	`1183`	`+ PageFlowUtil.streamFile(getViewContext().getResponse(), downloadFile.toPath(), true);`
`1184`	`1184`	`return null;`
`1185`	`1185`	`}`
`1186`	`1186`	`}`
Original file line number	Diff line number	Diff line change
`@@ -87,6 +87,7 @@`
`87`	`87`	`import org.labkey.lincs.psp.LincsPspUtil;`
`88`	`88`	`import org.labkey.lincs.psp.PspEndpoint;`
`89`	`89`	`import org.labkey.lincs.view.GctUtils;`
	`90`	`+import org.labkey.vfs.FileLike;`
`90`	`91`	`import org.springframework.beans.MutablePropertyValues;`
`91`	`92`	`import org.springframework.validation.BindException;`
`92`	`93`	`import org.springframework.validation.Errors;`
`@@ -144,35 +145,32 @@ public void addNavTrail(NavTree root)`
`144`	`145`	`}`
`145`	`146`	`}`
`146`	`147`
`147`		`- private void copyFiles(Path gctDir, String outputFileBaseName, Path gct, File reportDir) throws IOException`
	`148`	`+ private void copyFiles(Path gctDir, String outputFileBaseName, Path gct, FileLike reportDir) throws IOException`
`148`	`149`	`{`
`149`	`150`	`// reportDir is a local directory under tomcat's temp directory`
`150`		`- File[] reportDirFiles = reportDir.listFiles(new FilenameFilter()`
	`151`	`+ List<FileLike> reportDirFiles = reportDir.getChildren((f) ->`
`151`	`152`	`{`
`152`		`- @Override`
`153`		`- public boolean accept(File dir, String name)`
`154`		`- {`
`155`		`- return name.toLowerCase().endsWith(".txt")`
	`153`	`+ String name = f.getName();`
	`154`	`+ return name.toLowerCase().endsWith(".txt")`
`156`	`155`	`\|\| name.toLowerCase().endsWith(".gct")`
`157`	`156`	`\|\| name.equals("script.Rout");`
`158`		`- }`
`159`	`157`	`});`
`160`	`158`
`161`	`159`	`// The report should create two files: lincs.gct and lincs.processed.gct`
`162`	`160`	`// Copy both to the GCT folder`
`163`		`- for(File file: reportDirFiles)`
	`161`	`+ for(FileLike file: reportDirFiles)`
`164`	`162`	`{`
`165`	`163`	`if(file.getName().equalsIgnoreCase("lincs.gct"))`
`166`	`164`	`{`
`167`		`- Files.copy(file.toPath(), gct, StandardCopyOption.REPLACE_EXISTING);`
	`165`	`+ Files.copy(file.toNioPathForRead(), gct, StandardCopyOption.REPLACE_EXISTING);`
`168`	`166`	`}`
`169`	`167`	`else if(file.getName().equalsIgnoreCase("console.txt"))`
`170`	`168`	`{`
`171`		`- Files.copy(file.toPath(), gctDir.resolve(outputFileBaseName + ".console.txt" ), StandardCopyOption.REPLACE_EXISTING);`
	`169`	`+ Files.copy(file.toNioPathForRead(), gctDir.resolve(outputFileBaseName + ".console.txt" ), StandardCopyOption.REPLACE_EXISTING);`
`172`	`170`	`}`
`173`	`171`	`else if(file.getName().equals("script.Rout"))`
`174`	`172`	`{`
`175`		`- Files.copy(file.toPath(), gctDir.resolve(outputFileBaseName + ".script.Rout" ), StandardCopyOption.REPLACE_EXISTING);`
	`173`	`+ Files.copy(file.toNioPathForRead(), gctDir.resolve(outputFileBaseName + ".script.Rout" ), StandardCopyOption.REPLACE_EXISTING);`
`176`	`174`	`}`
`177`	`175`	`}`
`178`	`176`	`}`
`@@ -306,11 +304,11 @@ public ApiResponse execute(GCTReportForm form, BindException errors) throws Exce`
`306`	`304`	`}`
`307`	`305`	`catch(Exception e)`
`308`	`306`	`{`
`309`		`- copyFiles(gctDir, outputFileBaseName, downloadFile, rreport.getReportDir(getContainer().getId()));`
	`307`	`+ copyFiles(gctDir, outputFileBaseName, downloadFile, rreport.getReportDirFileLike(getContainer().getId()));`
`310`	`308`	`throw new ApiUsageException("There was an error running the GCT R script.", e);`
`311`	`309`	`}`
`312`	`310`
`313`		`- copyFiles(gctDir, outputFileBaseName, downloadFile, rreport.getReportDir(getContainer().getId()));`
	`311`	`+ copyFiles(gctDir, outputFileBaseName, downloadFile, rreport.getReportDirFileLike(getContainer().getId()));`
`314`	`312`
`315`	`313`	`if(!Files.exists(downloadFile))`
`316`	`314`	`{`
Original file line number	Diff line number	Diff line change
`@@ -25,7 +25,6 @@`
`25`	`25`	`import org.labkey.vfs.FileLike;`
`26`	`26`
`27`	`27`	`import java.io.BufferedWriter;`
`28`		`-import java.io.File;`
`29`	`28`	`import java.io.IOException;`
`30`	`29`	`import java.io.InputStream;`
`31`	`30`	`import java.nio.file.Files;`
`@@ -117,7 +116,7 @@ private static FileLike createConfig(Path configTemplate, FileLike parentDir, Fi`
`117`	`116`	`@Override`
`118`	`117`	`public String getDescription()`
`119`	`118`	`{`
`120`		`- return "NextFlow analysis of " + StringUtilsLabKey.pluralize(getInputFilePaths().size(), "file") + " using config: " + config.getName();`
	`119`	`+ return "NextFlow analysis of " + StringUtilsLabKey.pluralize(getInputFiles().size(), "file") + " using config: " + config.getName();`
`121`	`120`	`}`
`122`	`121`
`123`	`122`	`@Override`
`@@ -139,13 +138,13 @@ public AbstractFileAnalysisJob createSingleFileJob(FileLike file)`
`139`	`138`	`}`
`140`	`139`
`141`	`140`	`@Override`
`142`		`- public File findInputFile(String name)`
	`141`	`+ public FileLike findInputFile(String name)`
`143`	`142`	`{`
`144`	`143`	`throw new UnsupportedOperationException();`
`145`	`144`	`}`
`146`	`145`
`147`	`146`	`@Override`
`148`		`- public File findOutputFile(String name)`
	`147`	`+ public FileLike findOutputFile(String name)`
`149`	`148`	`{`
`150`	`149`	`return null;`
`151`	`150`	`}`
Original file line number	Diff line number	Diff line change
`@@ -139,6 +139,7 @@`
`139`	`139`	`import org.labkey.api.view.template.ClientDependency;`
`140`	`140`	`import org.labkey.api.wiki.WikiRendererType;`
`141`	`141`	`import org.labkey.api.wiki.WikiRenderingService;`
	`142`	`+import org.labkey.api.writer.PrintWriters;`
`142`	`143`	`import org.labkey.panoramapublic.bluesky.BlueskyApiClient;`
`143`	`144`	`import org.labkey.panoramapublic.bluesky.BlueskyException;`
`144`	`145`	`import org.labkey.panoramapublic.bluesky.BlueskySettingsManager;`
`@@ -4617,11 +4618,11 @@ private PxXml createPxXml(ExperimentAnnotations expAnnot, JournalExperiment je,`
`4617`	`4618`	`}`
`4618`	`4619`	`}`
`4619`	`4620`
`4620`		`- private File writePxXmlFile(String xmlString) throws PxException`
	`4621`	`+ private FileLike writePxXmlFile(String xmlString) throws PxException`
`4621`	`4622`	`{`
`4622`		`- File xml = getLocalFile(getContainer(), "px.xml"); // TODO: Add date time stamp`
	`4623`	`+ FileLike xml = getLocalFile(getContainer(), "px.xml"); // TODO: Add date time stamp`
`4623`	`4624`
`4624`		`- try (PrintWriter out = new PrintWriter(new FileWriter(xml, StandardCharsets.UTF_8)))`
	`4625`	`+ try (PrintWriter out = PrintWriters.getPrintWriter(xml.openOutputStream()))`
`4625`	`4626`	`{`
`4626`	`4627`	`out.write(xmlString);`
`4627`	`4628`	`}`
`@@ -4656,7 +4657,7 @@ public void assignPxId(boolean useTestDb, boolean testMode, String pxUser, Strin`
`4656`	`4657`
`4657`	`4658`	`private void validatePxXml(boolean useTestDb, String pxChangeLog, String pxUser, String pxPassword, BindException errors) throws PxException, ProteomeXchangeServiceException`
`4658`	`4659`	`{`
`4659`		`- File xmlFile = writePxXmlFile(createPxXml(_expAnnot, _journalExperiment, _submission, _validationStatus, pxChangeLog, true).getXml());`
	`4660`	`+ FileLike xmlFile = writePxXmlFile(createPxXml(_expAnnot, _journalExperiment, _submission, _validationStatus, pxChangeLog, true).getXml());`
`4660`	`4661`	`_pxResponse = ProteomeXchangeService.validatePxXml(xmlFile, useTestDb, pxUser, pxPassword);`
`4661`	`4662`	`if(ProteomeXchangeService.responseHasErrors(_pxResponse))`
`4662`	`4663`	`{`
`@@ -4677,7 +4678,7 @@ private void submitPxXml(boolean useTestDb, boolean testMode, String pxChangeLog`
`4677`	`4678`	`return;`
`4678`	`4679`	`}`
`4679`	`4680`	`PxXml pxXml = createPxXml(_expAnnot, _journalExperiment, _submission, _validationStatus, pxChangeLog, true);`
`4680`		`- File xmlFile = writePxXmlFile(pxXml.getXml());`
	`4681`	`+ FileLike xmlFile = writePxXmlFile(pxXml.getXml());`
`4681`	`4682`	`_pxResponse = ProteomeXchangeService.submitPxXml(xmlFile, useTestDb, pxUser, pxPassword);`
`4682`	`4683`	`if(ProteomeXchangeService.responseHasErrors(_pxResponse))`
`4683`	`4684`	`{`
`@@ -4699,7 +4700,7 @@ private void updatePxXml(boolean useTestDb, boolean testMode, String pxChangeLog`
`4699`	`4700`	`submitPxXml(useTestDb, testMode, pxChangeLog, pxUser, pxPassword, errors);`
`4700`	`4701`	`}`
`4701`	`4702`
`4702`		`- private static File getLocalFile(Container container, String fileName) throws PxException`
	`4703`	`+ private static FileLike getLocalFile(Container container, String fileName) throws PxException`
`4703`	`4704`	`{`
`4704`	`4705`	`// File.createTempFile()`
`4705`	`4706`	`java.nio.file.Path fileRoot = FileContentService.get().getFileRootPath(container, FileContentService.ContentType.files);`
`@@ -4713,7 +4714,7 @@ private static File getLocalFile(Container container, String fileName) throws Px`
`4713`	`4714`	`if (root != null)`
`4714`	`4715`	`{`
`4715`	`4716`	`LocalDirectory localDirectory = LocalDirectory.create(root);`
`4716`		`- return new File(localDirectory.getLocalDirectoryFile(), fileName);`
	`4717`	`+ return localDirectory.getLocalDirectoryFile().resolveChild(fileName);`
`4717`	`4718`	`}`
`4718`	`4719`	`else`
`4719`	`4720`	`{`
`@@ -4722,7 +4723,7 @@ private static File getLocalFile(Container container, String fileName) throws Px`
`4722`	`4723`	`}`
`4723`	`4724`	`else`
`4724`	`4725`	`{`
`4725`		`- return fileRoot.resolve(fileName).toFile();`
	`4726`	`+ return FileSystemLike.wrapFile(fileRoot).resolveChild(fileName);`
`4726`	`4727`	`}`
`4727`	`4728`	`}`
`4728`	`4729`	`}`
Original file line number	Diff line number	Diff line change
`@@ -34,9 +34,6 @@`
`34`	`34`	`import org.labkey.panoramapublic.model.Journal;`
`35`	`35`	`import org.labkey.vfs.FileLike;`
`36`	`36`
`37`		`-import java.io.File;`
`38`		`-import java.io.IOException;`
`39`		`-`
`40`	`37`	`/**`
`41`	`38`	`* User: vsharma`
`42`	`39`	`* Date: 8/21/2014`
`@@ -118,7 +115,7 @@ public String getDescription()`
`118`	`115`	`}`
`119`	`116`
`120`	`117`	`@Override`
`121`		`- public TaskPipeline getTaskPipeline()`
	`118`	`+ public TaskPipeline<?> getTaskPipeline()`
`122`	`119`	`{`
`123`	`120`	`return PipelineJobService.get().getTaskPipeline(new TaskId(CopyExperimentPipelineJob.class));`
`124`	`121`	`}`
`@@ -133,19 +130,6 @@ protected void finallyCleanUpLocalDirectory()`
`133`	`130`	`}`
`134`	`131`	`}`
`135`	`132`
`136`		`- public static File getLogFileFor(PipeRoot root, ExperimentAnnotations experimentAnnotations) throws IOException`
`137`		`- {`
`138`		`- File rootDir = root.getLogDirectory();`
`139`		`- if (!rootDir.exists())`
`140`		`- {`
`141`		`- throw new IOException("Pipeline root directory " + rootDir.getAbsolutePath() + " does not exist.");`
`142`		`- }`
`143`		`-`
`144`		`- String logFileName = "Experiment_" + experimentAnnotations.getExperimentId() + ".log";`
`145`		`-`
`146`		`- return new File(rootDir, logFileName);`
`147`		`- }`
`148`		`-`
`149`	`133`	`@Override`
`150`	`134`	`public ExperimentAnnotations getExpAnnotations()`
`151`	`135`	`{`
Original file line number	Diff line number	Diff line change
`@@ -14,8 +14,6 @@`
`14`	`14`	`import org.labkey.api.view.ViewBackgroundInfo;`
`15`	`15`	`import org.labkey.panoramapublic.model.ExperimentAnnotations;`
`16`	`16`
`17`		`-import java.io.File;`
`18`		`-`
`19`	`17`	`public class PxDataValidationPipelineJob extends PipelineJob implements PxDataValidationJobSupport`
`20`	`18`	`{`
`21`	`19`	`private final ExperimentAnnotations _experimentAnnotations;`
`@@ -41,7 +39,7 @@ public PxDataValidationPipelineJob(ViewBackgroundInfo info, PipeRoot root, Exper`
`41`	`39`	`_description = String.format("Validating data for experiment Id: %d, validation Id: %d", experiment.getId(), validationId);`
`42`	`40`
`43`	`41`	`String baseLogFileName = FileUtil.makeFileNameWithTimestamp("Experiment_Validation_" + experiment.getExperimentId(), "log");`
`44`		`- setLogFile(new File(root.getLogDirectory(), baseLogFileName));`
	`42`	`+ setLogFile(root.getLogDirectory(true).resolveChild(baseLogFileName));`
`45`	`43`
`46`	`44`	`header("Validating data for a ProteomeXchange submission.");`
`47`	`45`	`}`
Original file line number	Diff line number	Diff line change
`@@ -17,17 +17,20 @@`
`17`	`17`
`18`	`18`	`import org.apache.hc.client5.http.classic.methods.HttpPost;`
`19`	`19`	`import org.apache.hc.client5.http.entity.mime.FileBody;`
	`20`	`+import org.apache.hc.client5.http.entity.mime.InputStreamBody;`
`20`	`21`	`import org.apache.hc.client5.http.entity.mime.MultipartEntityBuilder;`
`21`	`22`	`import org.apache.hc.client5.http.impl.classic.CloseableHttpClient;`
`22`	`23`	`import org.apache.hc.client5.http.impl.classic.CloseableHttpResponse;`
`23`	`24`	`import org.apache.hc.client5.http.impl.classic.HttpClientBuilder;`
	`25`	`+import org.apache.hc.core5.http.ContentType;`
`24`	`26`	`import org.apache.hc.core5.http.HttpEntity;`
`25`	`27`	`import org.apache.hc.core5.http.ParseException;`
`26`	`28`	`import org.apache.hc.core5.http.io.entity.EntityUtils;`
`27`	`29`	`import org.apache.logging.log4j.Logger;`
`28`	`30`	`import org.jetbrains.annotations.NotNull;`
`29`	`31`	`import org.labkey.api.util.PageFlowUtil;`
`30`	`32`	`import org.labkey.api.util.logging.LogHelper;`
	`33`	`+import org.labkey.vfs.FileLike;`
`31`	`34`
`32`	`35`	`import java.io.File;`
`33`	`36`	`import java.io.IOException;`
`@@ -49,17 +52,17 @@ private enum METHOD {submitDataset, validateXML, requestID}`
`49`	`52`
`50`	`53`	`private static final Logger LOG = LogHelper.getLogger(ProteomeXchangeService.class, "Handles requests to the ProteomeXchange server");`
`51`	`54`
`52`		`- public static String validatePxXml(File pxxmlFile, boolean testDatabase, String user, String pass) throws ProteomeXchangeServiceException`
	`55`	`+ public static String validatePxXml(FileLike pxxmlFile, boolean testDatabase, String user, String pass) throws ProteomeXchangeServiceException`
`53`	`56`	`{`
`54`	`57`	`return postPxXml(pxxmlFile, testDatabase, user, pass, METHOD.validateXML);`
`55`	`58`	`}`
`56`	`59`
`57`		`- public static String submitPxXml(File pxxmlFile, boolean testDatabase, String user, String pass) throws ProteomeXchangeServiceException`
	`60`	`+ public static String submitPxXml(FileLike pxxmlFile, boolean testDatabase, String user, String pass) throws ProteomeXchangeServiceException`
`58`	`61`	`{`
`59`	`62`	`return postPxXml(pxxmlFile, testDatabase, user, pass, METHOD.submitDataset);`
`60`	`63`	`}`
`61`	`64`
`62`		`- private static String postPxXml(File pxxmlFile, boolean testDatabase, String user, String pass, METHOD method) throws ProteomeXchangeServiceException`
	`65`	`+ private static String postPxXml(FileLike pxxmlFile, boolean testDatabase, String user, String pass, METHOD method) throws ProteomeXchangeServiceException`
`63`	`66`	`{`
`64`	`67`	`String responseMessage;`
`65`	`68`	`try {`
`@@ -118,12 +121,12 @@ public static String getPxId(boolean testDatabase, String user, String pass) thr`
`118`	`121`	`}`
`119`	`122`
`120`	`123`	`@NotNull`
`121`		`- private static MultipartEntityBuilder getMultipartEntityBuilder(File pxxmlFile, boolean testDatabase, METHOD method, String user, String pass)`
	`124`	`+ private static MultipartEntityBuilder getMultipartEntityBuilder(FileLike pxxmlFile, boolean testDatabase, METHOD method, String user, String pass) throws IOException`
`122`	`125`	`{`
`123`	`126`	`MultipartEntityBuilder builder = MultipartEntityBuilder.create();`
`124`	`127`	`if(pxxmlFile != null)`
`125`	`128`	`{`
`126`		`- builder.addPart("ProteomeXchangeXML", new FileBody(pxxmlFile));`
	`129`	`+ builder.addPart("ProteomeXchangeXML", new InputStreamBody(pxxmlFile.openInputStream(), ContentType.TEXT_XML, pxxmlFile.getName()));`
`127`	`130`	`}`
`128`	`131`	`builder.addTextBody("PXPartner", user);`
`129`	`132`	`builder.addTextBody("authentication", pass);`
`@@ -140,7 +143,7 @@ private static MultipartEntityBuilder getMultipartEntityBuilder(File pxxmlFile,`
`140`	`143`	`return builder;`
`141`	`144`	`}`
`142`	`145`
`143`		`- private static MultipartEntityBuilder getMultipartEntityBuilder(boolean testDatabase, METHOD method, String user, String pass)`
	`146`	`+ private static MultipartEntityBuilder getMultipartEntityBuilder(boolean testDatabase, METHOD method, String user, String pass) throws IOException`
`144`	`147`	`{`
`145`	`148`	`return getMultipartEntityBuilder(null, testDatabase, method, user, pass);`
`146`	`149`	`}`