Update to utility method name

OpenLdapSync/resources/views/ldapSettings.view.xml

@@ -1,7 +1,7 @@
 <view xmlns="http://labkey.org/data/xml/view" title="LDAP Sync Settings">
-    <permissions>
-        <permission name="admin"/>
-    </permissions>
+    <permissionClasses>
+        <permissionClass name="org.labkey.api.security.permissions.AdminPermission"/>
+    </permissionClasses>
     <dependencies>
         <dependency path="clientapi"/>
         <dependency path="clientapi_core"/>

OpenLdapSync/src/org/labkey/openldapsync/ldap/LdapSettings.java

@@ -3,6 +3,7 @@
 import org.apache.commons.lang3.StringUtils;
 import org.apache.directory.api.ldap.model.exception.LdapException;
 import org.labkey.api.data.PropertyManager;
+import org.labkey.api.data.PropertyManager.WritablePropertyMap;
 import org.labkey.api.security.User;
 import org.labkey.api.security.UserManager;
 import org.labkey.api.security.ValidEmail;
@@ -112,13 +113,13 @@ public static void setLdapSettings(Map<String, String> props, Map<String, String
             }
         }
 
-        PropertyManager.PropertyMap writableProps = PropertyManager.getWritableProperties(PROPERTY_CATEGORY, true);
+        WritablePropertyMap writableProps = PropertyManager.getWritableProperties(PROPERTY_CATEGORY, true);
         writableProps.clear();
 
         writableProps.putAll(props);
         writableProps.save();
 
-        PropertyManager.PropertyMap encryptedWritableProps = PropertyManager.getEncryptedStore().getWritableProperties(PROPERTY_CATEGORY_ENCRYPTED, true);
+        WritablePropertyMap encryptedWritableProps = PropertyManager.getEncryptedStore().getWritableProperties(PROPERTY_CATEGORY_ENCRYPTED, true);
         encryptedWritableProps.clear();
 
         encryptedWritableProps.putAll(encryptedProps);

SequenceAnalysis/build.gradle

@@ -163,7 +163,7 @@ dependencies {
 if (project.findProject(BuildUtils.getTestProjectPath(project.gradle)) != null && project.hasProperty("teamcity"))
 {
     project.evaluationDependsOn(BuildUtils.getTestProjectPath(project.gradle))
-    def configDir = new File(ServerDeployExtension.getServerDeployDirectory(project), "config")
+    def configDir = new File(ServerDeployExtension.getServerDeployDirectoryPath(project), "config")
     def testProject = project.findProject(BuildUtils.getTestProjectPath(project.gradle))
     def createPipelineConfigTask = project.tasks.register("createPipelineConfig", Copy) {
         Copy task ->
@@ -185,19 +185,15 @@ if (project.findProject(BuildUtils.getTestProjectPath(project.gradle)) != null &
             })
             task.destinationDir = configDir
 
-            if (BuildUtils.useEmbeddedTomcat(project)) {
-                rootProject.allprojects {
-                    task.mustRunAfter tasks.withType(DoThenSetup)
-                }
+            rootProject.allprojects {
+                task.mustRunAfter tasks.withType(DoThenSetup)
             }
     }
     testProject.tasks.named("startTomcat").configure {
         dependsOn(createPipelineConfigTask)
-        if (BuildUtils.useEmbeddedTomcat(project)) {
-            it.doFirst {
-                new File(new File(BuildUtils.getEmbeddedConfigPath(project)), "application.properties")
-                        << "\ncontext.pipelineConfig=${configDir.getAbsolutePath().replace("\\", "\\\\")}"
-            }
+        it.doFirst {
+            new File(new File(BuildUtils.getEmbeddedConfigPath(project)), "application.properties")
+                    << "\ncontext.pipelineConfig=${configDir.getAbsolutePath().replace("\\", "\\\\")}"
         }
     }
 }

SequenceAnalysis/pipeline_code/sequence_tools_install.sh

@@ -818,9 +818,9 @@ then
       install ./cutadapt-1.8.1/bin/_preamble.py ${LKTOOLS_DIR}/_preamble.py
       cp -R ./cutadapt-1.8.1/cutadapt ${LKTOOLS_DIR}/cutadapt
     else
-      $PIP_EXE install --user cutadapt==4.2
+      $PIP_EXE install --user --break-system-packages cutadapt==4.2
       $PIP_EXE show cutadapt
-      $PIP_EXE install --user pyinstaller
+      $PIP_EXE install --user --break-system-packages pyinstaller
       $PIP_EXE show pyinstaller
       ~/.local/bin/pyinstaller --onefile --clean ~/.local/bin/cutadapt
       cp ./dist/cutadapt ${LKTOOLS_DIR}/cutadapt

SequenceAnalysis/resources/views/importFasta.view.xml

@@ -1,7 +1,7 @@
 <view xmlns="http://labkey.org/data/xml/view" title="Import Sequence Data">
-    <permissions>
-        <permission name="insert"/>
-    </permissions>
+    <permissionClasses>
+        <permissionClass name="org.labkey.api.security.permissions.InsertPermission"/>
+    </permissionClasses>
     <dependencies>
         <dependency path="laboratory.context"/>
         <dependency path="SequenceAnalysis/sequenceAnalysis"/>

SequenceAnalysis/resources/views/importTracks.view.xml

@@ -1,7 +1,7 @@
 <view xmlns="http://labkey.org/data/xml/view" title="Import Tracks">
-    <permissions>
-        <permission name="insert"/>
-    </permissions>
+    <permissionClasses>
+        <permissionClass name="org.labkey.api.security.permissions.InsertPermission"/>
+    </permissionClasses>
     <dependencies>
         <dependency path="laboratory.context"/>
         <dependency path="SequenceAnalysis/sequenceAnalysis"/>

SequenceAnalysis/resources/views/sequenceDefaults.view.xml

@@ -1,7 +1,7 @@
 <view xmlns="http://labkey.org/data/xml/view" title="DISCVR-Seq Settings">
-    <permissions>
-        <permission name="admin"/>
-    </permissions>
+    <permissionClasses>
+        <permissionClass name="org.labkey.api.security.permissions.AdminPermission"/>
+    </permissionClasses>
     <dependencies>
         <dependency path="laboratory.context"/>
         <dependency path="SequenceAnalysis/sequenceAnalysis"/>

SequenceAnalysis/resources/views/siteAdmin.view.xml

@@ -1,7 +1,7 @@
 <view xmlns="http://labkey.org/data/xml/view" title="DISCVR-Seq Site Settings">
-    <permissions>
-        <permission name="admin"/>
-    </permissions>
+    <permissionClasses>
+        <permissionClass name="org.labkey.api.security.permissions.AdminPermission"/>
+    </permissionClasses>
     <dependencies>
         <dependency path="laboratory.context"/>
         <dependency path="SequenceAnalysis/sequenceAnalysis"/>

SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisController.java

@@ -19,6 +19,8 @@
 import htsjdk.tribble.TribbleException;
 import htsjdk.variant.vcf.VCFFileReader;
 import htsjdk.variant.vcf.VCFHeader;
+import jakarta.servlet.http.HttpServletRequest;
+import jakarta.servlet.http.HttpServletResponse;
 import org.apache.commons.io.FileUtils;
 import org.apache.commons.io.IOUtils;
 import org.apache.commons.lang3.ArrayUtils;
@@ -59,6 +61,7 @@
 import org.labkey.api.data.ConvertHelper;
 import org.labkey.api.data.DataRegionSelection;
 import org.labkey.api.data.PropertyManager;
+import org.labkey.api.data.PropertyManager.WritablePropertyMap;
 import org.labkey.api.data.Results;
 import org.labkey.api.data.ResultsImpl;
 import org.labkey.api.data.SQLFragment;
@@ -167,14 +170,13 @@
 import org.labkey.sequenceanalysis.util.ChainFileValidator;
 import org.labkey.sequenceanalysis.util.FastqUtils;
 import org.labkey.sequenceanalysis.util.SequenceUtil;
+import org.labkey.vfs.FileLike;
 import org.springframework.beans.PropertyValues;
 import org.springframework.validation.BindException;
 import org.springframework.validation.Errors;
 import org.springframework.web.bind.ServletRequestParameterPropertyValues;
 import org.springframework.web.servlet.ModelAndView;
 
-import jakarta.servlet.http.HttpServletRequest;
-import jakarta.servlet.http.HttpServletResponse;
 import java.io.File;
 import java.io.FileInputStream;
 import java.io.FileNotFoundException;
@@ -2015,30 +2017,30 @@ else if (!d.getFile().exists())
                 }
                 else if (o.has("relPath") || o.has("fileName"))
                 {
-                    File f;
+                    FileLike f;
                     if (o.opt("relPath") == null)
                     {
                         if (path != null)
                         {
-                            f = pr.resolvePath(path);
-                            f = new File(f, o.getString("fileName"));
+                            f = pr.resolvePathToFileLike(path);
+                            f = f.resolveFile(Path.parse(o.getString("fileName")));
                         }
                         else
                         {
-                            f = pr.resolvePath(o.getString("fileName"));
+                            f = pr.resolvePathToFileLike(o.getString("fileName"));
                         }
                     }
                     else
                     {
-                        f = pr.resolvePath(o.getString("relPath"));
+                        f = pr.resolvePathToFileLike(o.getString("relPath"));
                     }
 
                     if (f == null || !f.exists())
                     {
                         throw new PipelineValidationException("Unknown file: " + o.getString("relPath") + " / " + o.getString("fileName"));
                     }
 
-                    ret.add(f);
+                    ret.add(f.toNioPathForRead().toFile());
                 }
                 else if (o.opt("filePath") != null)
                 {
@@ -2554,8 +2556,8 @@ protected File getTargetFile(String filename) throws IOException
 
             try
             {
-                File targetDirectory = AssayFileWriter.ensureUploadDirectory(getContainer(), "sequenceOutputs");
-                return AssayFileWriter.findUniqueFileName(filename, targetDirectory);
+                FileLike targetDirectory = AssayFileWriter.ensureUploadDirectory(getContainer(), "sequenceOutputs");
+                return AssayFileWriter.findUniqueFileName(filename, targetDirectory).toNioPathForWrite().toFile();
             }
             catch (ExperimentException e)
             {
@@ -2687,8 +2689,8 @@ protected File getTargetFile(String filename) throws IOException
 
             try
             {
-                File targetDirectory = AssayFileWriter.ensureUploadDirectory(getContainer());
-                return AssayFileWriter.findUniqueFileName(filename, targetDirectory);
+                FileLike targetDirectory = AssayFileWriter.ensureUploadDirectory(getContainer());
+                return AssayFileWriter.findUniqueFileName(filename, targetDirectory).toNioPathForWrite().toFile();
             }
             catch (ExperimentException e)
             {
@@ -2852,8 +2854,8 @@ protected File getTargetFile(String filename) throws IOException
 
             try
             {
-                File targetDirectory = AssayFileWriter.ensureUploadDirectory(getContainer());
-                return AssayFileWriter.findUniqueFileName(filename, targetDirectory);
+                FileLike targetDirectory = AssayFileWriter.ensureUploadDirectory(getContainer());
+                return AssayFileWriter.findUniqueFileName(filename, targetDirectory).toNioPathForWrite().toFile();
             }
             catch (ExperimentException e)
             {
@@ -3642,7 +3644,7 @@ else if (fastaFileType.isType(data.getFile()))
                         }
                     }
 
-                    File dict = new File(data.getFile().getParentFile(), FileUtil.getBaseName(data.getFile()) + ".dict");
+                    File dict = FileUtil.appendName(data.getFile().getParentFile(), FileUtil.getBaseName(data.getFile()) + ".dict");
                     if (dict.exists())
                     {
                         files.add(dict);
@@ -4141,10 +4143,10 @@ public ApiResponse execute(ImportOutputFilesForm form, BindException errors) thr
                 return null;
             }
 
-            File targetDirectory = AssayFileWriter.ensureUploadDirectory(getContainer(), "sequenceOutputs");
+            FileLike targetDirectory = AssayFileWriter.ensureUploadDirectory(getContainer(), "sequenceOutputs");
             if (!targetDirectory.exists())
             {
-                targetDirectory.mkdirs();
+                targetDirectory.mkdir();
             }
 
             if (form.getRecords() != null)
@@ -4154,7 +4156,7 @@ public ApiResponse execute(ImportOutputFilesForm form, BindException errors) thr
                 Map<File, Map<String, Object>> toCreate = new HashMap<>();
                 for (JSONObject o : JsonUtil.toJSONObjectList(arr))
                 {
-                    File file = new File(dirData, o.getString("fileName"));
+                    File file = FileUtil.appendName(dirData, o.getString("fileName"));
                     if (!file.exists())
                     {
                         errors.reject(ERROR_MSG, "Unknown file: " + file.getPath());
@@ -4195,8 +4197,8 @@ public ApiResponse execute(ImportOutputFilesForm form, BindException errors) thr
 
                 for (File file : toCreate.keySet())
                 {
-                    File target = AssayFileWriter.findUniqueFileName(file.getName(), targetDirectory);
-                    FileUtils.moveFile(file, target);
+                    FileLike target = AssayFileWriter.findUniqueFileName(file.getName(), targetDirectory);
+                    FileUtils.moveFile(file, target.toNioPathForWrite().toFile());
 
                     ExpData data = ExperimentService.get().createData(getContainer(), new DataType("Sequence Output"));
                     data.setName(file.getName());
@@ -4235,14 +4237,14 @@ public ApiResponse execute(ImportOutputFilesForm form, BindException errors) thr
                             }
 
                             _log.info("moving associated file: " + idx.getPath() + ", to: " + idxTargetName);
-                            File idxTarget = new File(targetDirectory, idxTargetName);
+                            FileLike idxTarget = targetDirectory.resolveChild(idxTargetName);
                             if (idxTarget.exists())
                             {
                                 _log.error("target already exists, skipping: " + idxTargetName);
                             }
                             else
                             {
-                                FileUtils.moveFile(idx, idxTarget);
+                                FileUtils.moveFile(idx, idxTarget.toNioPathForWrite().toFile());
 
                                 ExpData idxData = ExperimentService.get().createData(getContainer(), new DataType("Sequence Output"));
                                 idxData.setName(idxTarget.getName());
@@ -4971,7 +4973,7 @@ public static class SetSequenceImportDefaultsAction extends MutatingApiAction<Se
         public ApiResponse execute(SetSequenceImportDefaultsForm form, BindException errors) throws Exception
         {
             Container target = getContainer().isWorkbook() ? getContainer().getParent() : getContainer();
-            PropertyManager.PropertyMap configMap = PropertyManager.getWritableProperties(target, CONFIG_PROPERTY_DOMAIN_IMPORT, true);
+            WritablePropertyMap configMap = PropertyManager.getWritableProperties(target, CONFIG_PROPERTY_DOMAIN_IMPORT, true);
             configMap.put(INPUT_FILE_TREATMENT, form.getInputFileTreatment());
 
             configMap.save();