It looks like you didn't include the .xml in the file name. Please give it a try with C:\CPASDemo\databases\yeast_a.xml as the full file name.

Thanks,
Josh

The file was extracted with the yeast_a file name without any extension. I have tried all iterations of the file name for "load new anot file" and it fails. Here is the output for when I have renamed the file yeast_a.xml

ERROR ionUploadManager 2007-10-01 16:20:30,187 AnnotLoader1 : Failed to parse file C:\CPASDemo\databases\yeast_a.xml
org.xml.sax.SAXException: Can't open file 'C:\CPASDemo\databases\yeast_a.xml'
    at org.labkey.ms2.protein.XMLProteinLoader.parseFile(XMLProteinLoader.java:105)
    at org.labkey.ms2.protein.AnnotationUploadManager$AnnotationLoadJob.run(AnnotationUploadManager.java:132)
    at java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)
    at java.util.concurrent.FutureTask$Sync.innerRun(Unknown Source)
    at java.util.concurrent.FutureTask.run(Unknown Source)
    at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$301(Unknown Source)
    at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(Unknown Source)
    at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(Unknown Source)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
    at java.lang.Thread.run(Unknown Source)

That error message happens after the server checks to see that the file exists.

Can you verify that the account that was used to start the Tomcat process has permission to read that file? For example, if you set up a Data Pipeline that's pointed at C:\CPASDemo and click on the Process and Upload Files button can you browse the file system?

Thanks,
Josh