Lev,

Can provide a little more information about the problem you are having? Are you seeing an error message of some sort?

Also,can you provide alittle more information about the files you are attempting to import. Are they just the search engine output files? Or have you also run Protein Prophet and Peptide Prophet on the results.

Lastly what is the naming format for your files that you want to import (if you just cut and paste the name of one of your files that would be great).

-Brian

Hi Lev,

If you have files that are already in PepXML or ProtXML format (from the Trans Proteomic Pipeline), the issue may be that they don't have the file extension that LabKey Server is expecting.

For PepXML, we expect the extension to be either .pep.xml or .pepxml.

For ProtXML, we expect the extension to be .prot.xml, .protxml, or .pep-prot.xml.

If you rename or copy the files, does the import succeed?

If you have another file type, what format is it in?

Thanks,
Josh

The sorcerer runs TPP and generates interact.prot and interact.pep files that I am trying to import. These files are of the xml type but do not show the .xml extension. The error message that I am running into is that CPAS cannot locate the fasta file (also stored on the sorcerer). To summarize I can upload the files but cannot import them.

Do I have to setup a pipeline override in order to tell cpas where to find the fasta file?

We are looking into setting up a enterprise pipeline, do you think this would help?

Thanks a lot for the support!

I forgot to include the error message....

17 Nov 2011 14:43:37,286 INFO : Starting to load ProteinProphet file C:\Program Files\LabKey Server\files\test2\@files\.\interact.prot.xml
17 Nov 2011 14:43:37,290 INFO : Resolved referenced PepXML file to C:\Program Files\LabKey Server\files\test2\@files\.\interact.pep.xml
17 Nov 2011 14:43:37,291 INFO : Starting import from interact.pep.xml
17 Nov 2011 14:43:37,295 INFO : Starting to clear out any previously imported data for interact.pep.xml
17 Nov 2011 14:43:37,383 INFO : 0.09 seconds to clear out any previously imported data for interact.pep.xml
17 Nov 2011 14:43:37,383 INFO : Starting to import FASTA file /home/sorcerer/fasta/swissprot.fasta
17 Nov 2011 14:43:37,386 ERROR: MS2 import failed due to a missing file.
java.io.FileNotFoundException: /home/sorcerer/fasta/swissprot.fasta

Hi Lev,

As you've probably guessed, the problem is that the location that the pepXML file gives for the FASTA file isn't available to the LabKey Server installation.

If you set up the Enterprise pipeline, it's possible to give configuration that tells the the server how to translate the location from the pepXML file to something that's available on the server.

However, you should be able to get things moving by just copying the FASTA file to the same directory that holds the pepXML/protXML files. The server will look there if it can't find it elsewhere.

Thanks,
Josh

Thanks for all of your help!

I tried copying the fasta file into the folder as you suggested and the same error appeared as before.

Lev

I was able to fix this problem by changing the extension to the fasta file in the pep.xml and prot.xml files to the local folder in CPAS.

Does anyone know if there is a way to circumvent this problem without having to manually change the file extensions?

Thanks

Hi Lev,

I'm glad to hear you got the data imported.

I know the original path was "/home/sorcerer/fasta/swissprot.fasta" - what did you end up changing it to?

Thanks,
Josh

Josh,

I copied the fasta file into the root CPAS folder and then changed the path to simply read "swissprot.fasta". Although this worked for uploading data this time, it will be difficult to repeat this setup in a production setting. Do you have any suggestions?

I am looking into installing CPAS locally on the Sorcerer server so that the files would be accessed locally. Seems like CPAS has trouble accessing files that are not local. I could not even point to a folder that is attached to the computer via USB.

Lev

Lev,
I am sorry for the late reply to your messages. I wonder if there might be a configuration problem of some sort on your CPAS server. CPAS should be able to support reading files from your USB drive. And you should not have to install CPAS directly on the Sorcerer server to get this working.
 
If you are interested, we can setup a web conference to review your servers configuration and figure out what might be wrong.

- Brian

Brian,

Thank you for your response. I would love to get some help via web conference. Perhaps we schedule schedule something after the long week end. Enjoy your Thanksgiving!

Lev

Lev,
I will send you a private email to schedule a web conference.

- Brian