diff --git a/snprc_ehr/src/org/labkey/snprc_ehr/controllers/FeeScheduleController.java b/snprc_ehr/src/org/labkey/snprc_ehr/controllers/FeeScheduleController.java
index cd8512f6f..dc85e57c2 100644
--- a/snprc_ehr/src/org/labkey/snprc_ehr/controllers/FeeScheduleController.java
+++ b/snprc_ehr/src/org/labkey/snprc_ehr/controllers/FeeScheduleController.java
@@ -29,18 +29,24 @@
 import org.labkey.api.security.RequiresPermission;
 import org.labkey.api.security.permissions.AdminPermission;
 import org.labkey.api.util.PageFlowUtil;
+import org.labkey.api.util.Path;
+import org.labkey.api.util.URIUtil;
 import org.labkey.api.util.URLHelper;
 import org.labkey.api.view.ActionURL;
 import org.labkey.api.view.JspView;
 import org.labkey.api.view.NavTree;
+import org.labkey.api.view.NotFoundException;
 import org.labkey.snprc_ehr.pipeline.FeeScheduleExcelParser;
 import org.labkey.snprc_ehr.pipeline.FeeScheduleImportForm;
 import org.labkey.snprc_ehr.pipeline.FeeSchedulePipelineJob;
+import org.labkey.vfs.FileLike;
+import org.labkey.vfs.FileSystemLike;
 import org.springframework.validation.BindException;
 import org.springframework.validation.Errors;
 import org.springframework.web.servlet.ModelAndView;
 
 import java.io.File;
+import java.net.URI;
 import java.text.SimpleDateFormat;
 import java.util.Date;
 import java.util.List;
@@ -108,7 +114,8 @@ public ModelAndView getView(FeeScheduleImportForm form, boolean reshow, BindExce
             FeeScheduleExcelParser fsep;
             if (form.getFilePath() != null)
             {
-                file = new File(form.getFilePath());
+                //file path here is constructed from the pipeline, and contains pipeline root + file.
+                file = getVerifiedFile(form.getFilePath());
             }
             if (file != null && file.exists())
             {
@@ -146,16 +153,45 @@ public ModelAndView getView(FeeScheduleImportForm form, boolean reshow, BindExce
             return new JspView<>("/org/labkey/snprc_ehr/pipeline/FeeScheduleImport.jsp", form, errors);
         }
 
+        private File getVerifiedFile(String filePath)
+        {
+            File fileToVerify = new File(filePath);
+
+            PipeRoot pipeRoot = PipelineService.get().findPipelineRoot(getContainer());
+            if (pipeRoot == null)
+            {
+                throw new NotFoundException("Could not find a pipeline root for '" + getContainer().getPath() + "'");
+            }
+
+            FileLike allowedRoot = pipeRoot.getRootFileLike();
+            URI relativeURI = URIUtil.relativize(allowedRoot.toURI(), fileToVerify.toURI()); // if root = /a/b/c/ and file = /a/b/c/d/e/f.xlsx, relativeURI = d/e/f.xlsx
+
+            if (relativeURI == null)
+            {
+                throw new IllegalArgumentException("File '" + fileToVerify.toURI().getPath() + "' is outside the allowed root '" + allowedRoot.toURI().getPath() + "'");
+            }
+
+            if (allowedRoot.isDescendant(fileToVerify.toURI())) // if root = /a/b/c/ and file = /a/b/c/d/e/f.xlsx - among other things, this essentially checks if '/a/b/c/d/e/f.xlsx' starts with '/a/b/c/'
+            {
+                return FileSystemLike.toFile(allowedRoot.resolveFile(new Path(relativeURI.getPath())));
+            }
+            else
+            {
+                throw new IllegalArgumentException("File '" + relativeURI.getPath() + "' is not a descendent of '" + allowedRoot.toURI().getPath() + "'");
+            }
+        }
+
         @Override
         public void validateCommand(FeeScheduleImportForm form, Errors errors)
         {
-            _fsFile = new File(form.getFilePath());
+            _fsFile = getVerifiedFile(form.getFilePath());
             // Be sure that the referenced file exists
-            if (_fsFile == null || !_fsFile.exists())
+            if (!_fsFile.exists())
             {
                 errors.reject(ERROR_MSG, "Could not find file at path: " + form.getFilePath());
             }
         }
+
         @Override
         public boolean handlePost(FeeScheduleImportForm form, BindException errors)
         {
@@ -163,7 +199,7 @@ public boolean handlePost(FeeScheduleImportForm form, BindException errors)
             try
             {
                 PipeRoot pipelineRoot = PipelineService.get().findPipelineRoot(getContainer());
-                PipelineService.get().queueJob(new FeeSchedulePipelineJob(getContainer(), getUser(), getViewContext().getActionURL(), pipelineRoot, _fsFile, form));
+                PipelineService.get().queueJob(new FeeSchedulePipelineJob(getContainer(), getUser(), getViewContext().getActionURL(), pipelineRoot, getVerifiedFile(_fsFile.getAbsolutePath()), form));
 
                 _url = PageFlowUtil.urlProvider(PipelineStatusUrls.class).urlBegin(getContainer().getProject());
                 _url.addParameter("StatusFiles.containerFilterName", ContainerFilter.Type.CurrentAndSubfolders.name());
diff --git a/snprc_ehr/src/org/labkey/snprc_ehr/pipeline/FeeSchedulePipelineJob.java b/snprc_ehr/src/org/labkey/snprc_ehr/pipeline/FeeSchedulePipelineJob.java
index 57b3d79e0..ef08d2c19 100644
--- a/snprc_ehr/src/org/labkey/snprc_ehr/pipeline/FeeSchedulePipelineJob.java
+++ b/snprc_ehr/src/org/labkey/snprc_ehr/pipeline/FeeSchedulePipelineJob.java
@@ -22,9 +22,12 @@
 import org.labkey.api.pipeline.PipelineJobException;
 import org.labkey.api.security.User;
 import org.labkey.api.util.FileUtil;
+import org.labkey.api.util.Path;
 import org.labkey.api.util.URLHelper;
 import org.labkey.api.view.ActionURL;
 import org.labkey.api.view.ViewBackgroundInfo;
+import org.labkey.vfs.FileLike;
+import org.labkey.vfs.FileSystemLike;
 
 import java.io.File;
 
@@ -47,7 +50,8 @@ public FeeSchedulePipelineJob(Container c, User user, ActionURL url, PipeRoot pi
     {
         super(null, new ViewBackgroundInfo(c, user, url), pipeRoot);
         _importFile = importFile;
-        setLogFile(new File(pipeRoot.getRootPath(), FileUtil.makeFileNameWithTimestamp("FeeSchedulePipeline", "log")));
+        FileLike logFile = pipeRoot.getLogDirectoryFileLike(true).resolveChild(FileUtil.makeFileNameWithTimestamp("FeeSchedulePipeline", "log"));
+        setLogFile(logFile.toNioPathForWrite());
         _form = form;
         _container = c;
         _user = user;