New Statistical Algorithms for the Analysis of Mass - FU Berlin, FB MI ...

6.2. CASE STUDIES 161
first entry in “params” contains the filename of the user-defined script, the
remaining array entries contain the parameters. Line 10-16 show how the
calling string “c” is built and that the first two parameters mentioned above
are the “MCP” string and the object reference (line 10). Line 18 shows how the
QAD Grid worker object can be used to communicate directly with the QAD
Grid: here, the state string of the worker is changed, which will automatically
be updated in the QAD Grid database. The Matlab built-in function “eval”
is then used with the start string “c” as parameter to start the actual userdefined
Matlab script.
Binaries The QAD Grid worker concept offers another far more general
approach to enable non-Grid applications in the case where no source code is
available. Using a wrapper worker almost any binary application can use the
power of distributed computing. To achieve this, a standard base worker is
available that offers the following:
� Authenticate at and integrate into the proteomics.net platform
� Request new tasks (and respective parameters) for the configured purpose
� Perform any system call or run any binary application
� Process results and transmit them to the proteomics.net platform
To give a concrete example listing 6.3 shows how we use a wrapper worker
to start a binary (“tophat”, line 47-51), and process the results (copy to some
destination, line 57).
Listing 6.3: Core of wrapper worker to start tophat filter binary.
1 public s t a t i c void main ( S t r i n g [ ] a r g s ) throws Exception {
2
3 . . .
4
5 % i n i t i a l i z e o b j e c t
6
7 PROTEOMICSWORKER apply tophat
8 myPROTEOMICSWORKER apply tophat =
9 new PROTEOMICSWORKER apply tophat(
10 ”PROTEOMICSWORKER apply tophat . java ” , ” a p p l i c a t i o n t o p h a t ” ,
11 ”” , false , ”” , ”” , a r g s [ 0 ] ) ;
12
13 % run main method
14
15 myPROTEOMICSWORKER apply tophat . do work ( ) ;
16 }
17
18 . . .
19
20 // −−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−
21 public void do work ( ) {
22
23 . . .
24
25 params = g e t n e x t t a s k ( ) ;
26
27 i f ( ( params != null ) && ( ! params . e q u a l s ( ( ”” ) ) ) ) {
28 t a sk h a n d l e d = true ;