Unable to store spectrum data

[GoogleCodeExporter]

For our group I am trying to setup MSLIMS as a proof-of-concept to see if the 
product caters to all our needs. After setting up a new project in the DB I am 
trying to store a set of spectra files.

- After selecting the Thermo FT-ICR instrument, I browse to a (mapped network) 
folder containing a set of Thermo RAW files with accompanying mzXML and 
mgf-files.
- Clicking OK shows the 'Loading LC run folders' popup which stays at 0% 
indefinitely.
- Closing the popup shows the 'Spectrum storage' window stating that '0 new LC 
runs loaded' with an empty LC run list.

I have tried:
- putting only mgf files in a local directory
- making sure that the only extension is '.mgf'
- changing file access permissions / running MSLIMS as forced admin user
- converted the RAW files with two different converters to mgf format
.. with no success.

Also, when deselecting the 'Mascot Distiller' option (could not find 
documentation regarding the effects of this setting) shows the error which is 
attached (are there some bogus paths hardcoded since this system never had an 
F: drive mounted?).

This is using MSLIMS version 7.7.5 (the 'About' window says version 7.6.7!) on 
Windows 7 Pro 64-bit with a view-only version of Macot Distiller. The MySQL DB 
is running on a remote Linux system.

Original issue reported on code.google.com by MarcelKe...@gmail.com on 9 Aug 2012 at 2:37

Attachments:

• issue_store_spectra.png

[GoogleCodeExporter]

Hello Marcel

The difference between the Mascot Distiller option on and off, is what kind of 
storage class we use. If it is on, MSLIMS will look for .mgf files. Turned off, 
it will look for the .dta files your FT-ICR machine normally outputs.

The f:/temp/MGF_test is only used if a path has never before been selected on 
the computer for that instrument. This will be something to look at in a future 
release, as it is confusing. For now you can ignore the error message saying 
that the path has not been found, and navigate to the folder containing the 
.dta files (should you choose to store the data this way).

You say you tried - putting only mgf files in a local directory, is that on the 
local computer where you ran MSLIMS from? 
Could you also upload the errorlog? (should be 
C:/Users/yourusername/.compomics/mslims/mslims-log4j).

Kind regards

Original comment by davy.mad...@gmail.com on 13 Aug 2012 at 11:19

[GoogleCodeExporter]

Hello,

Thanks for your response. I have tried loading in data from other instruments 
from multiple locations as well as manually changing device types in the mgf 
file with no luck. Something seems to be blocking the loading of the data and 
nothing happens when trying (the java process is only reading a few bytes 
before stalling. Pointing MSLIMS to an empty mgf file (0 bytes) does succeed 
and shows the file in the 'LC run list'.

The attached logfile is from a clean install up until the point of error while 
trying to import mgf files (I think the first error shown is because I selected 
the wrong database).

Kind regards,

Marcel

Original comment by MarcelKe...@gmail.com on 21 Aug 2012 at 11:50

Attachments:

• mslims-log4j.log