Boston19: CometAdapter has problems with Temp files on Windows (with spaces in path?)

[jpfeuffer]

[jpfeuffer]

Confirmed:
If your tmp path has space (e.g. because it is in your user folder and your username has spaces)
Comet has problems reading the temporary param file since it does not handle spaces correctly.

C:\jenkins\ws\openms_nightly_packaging\c2e226b2\build\bin\Release>set "TMP=C:\foo bar baz"

C:\jenkins\ws\openms_nightly_packaging\c2e226b2\build\bin\Release>echo %TMP%
C:\foo bar baz

C:\jenkins\ws\openms_nightly_packaging\c2e226b2\build\bin\Release>CometAdapter.exe -in C:\jenkins\ws\openms_nightly_packaging\c2e226b2\source\share\OpenMS\examples\BSA\BSA1.mzML -out foo.idXML -comet_executable C:\jenkins\ws\openms_nightly_packaging\c2e226b2\thirdparties_flat\Comet\comet.exe -database C:\jenkins\ws\openms_nightly_packaging\c2e226b2\source\share\OpenMS\examples\TOPPAS\data\BSA_Identification\18Protein_SoCe_Tr_detergents_trace_target_decoy.fasta
File 'C:/Users/jpfeuffer/.OpenMS/OpenMS.ini' is deprecated.
Updating missing/wrong entries in 'C:/Users/jpfeuffer/.OpenMS/OpenMS.ini' with defaults!
Comet is writing the default parameter file...
Executing: C:\jenkins\ws\openms_nightly_packaging\c2e226b2\thirdparties_flat\Comet\comet.exe
Executed C:\jenkins\ws\openms_nightly_packaging\c2e226b2\thirdparties_flat\Comet\comet.exe successfully!
Progress of 'loading spectra list':
-- done [took 0.28 s (CPU), 0.28 s (Wall)] --
FATAL: External invocation of C:\jenkins\ws\openms_nightly_packaging\c2e226b2\thirdparties_flat\Comet\comet.exe failed. Standard output and error were:

<Executing: C:\jenkins\ws\openms_nightly_packaging\c2e226b2\thirdparties_flat\Comet\comet.exe> occurred 2 times

 Comet version 2016.01 rev. 3
 Error - cannot open parameter file "C:\foo".

[jpfeuffer]

Either try to fix the path before passing to Comet or write the Comet guys.

[cbielow]

on first sight, we pass the arguments quoted, i.e. "C:\Program Files\OpenMS-2.4.0\share\OpenMS\THIRDPARTY\Comet/comet.exe" -P"C:\TEMP\with space\20190528_093217_ukkonen_6624_2\param.txt" "-NC:\TEMP\with space\20190528_093217_ukkonen_6624_2\result" C:/dev/openmsqt5/src/tests/topp/THIRDPARTY/CometAdapter_3.mzML

still yields

 Comet version 2016.01 rev. 3

 Error - cannot open parameter file "C:\TEMP\with".

[cbielow]

ok, seems the comet guys should revisit their code:
at https://sourceforge.net/p/comet-ms/code/HEAD/tree/trunk/comet-ms/Comet.cpp#l124 the argument
"-PC:\TEMP\with space\20190528_093217_ukkonen_6624_2\param.txt" is parsed (as char* arg), and then a string is extracted via sscanf (which stops at the first whitespace).
Solution: just remove the first two characters, i.e. -P, and treat the remaining string as filename.
This also needs to be done for all other arguments, e.g. -N, which uses the same mechanism.

[cbielow]

all we can do is check the filenames and quit with a better error message... not sure its worth the trouble though, because we'd need to check the comet version and stop doing this when the bug is fixed on their side...

[cbielow]

posted as issue on the Comet ticket system: https://groups.google.com/forum/#!topic/comet-ms/lTGA76ul1pk