[Swift-commit] r3066 - SwiftApps/SIDGrid/swift/projects/andric/peakfit_pilots/PK2/wholebrain

[noreply at svn.ci.uchicago.edu]

Author: andric
Date: 2009-08-06 10:59:18 -0500 (Thu, 06 Aug 2009)
New Revision: 3066

Modified:
   SwiftApps/SIDGrid/swift/projects/andric/peakfit_pilots/PK2/wholebrain/PK2mediator.swift
Log:
now Mediator using a 'VOX' arg. also switched 'r_script' back into Mediator call

Modified: SwiftApps/SIDGrid/swift/projects/andric/peakfit_pilots/PK2/wholebrain/PK2mediator.swift
===================================================================
--- SwiftApps/SIDGrid/swift/projects/andric/peakfit_pilots/PK2/wholebrain/PK2mediator.swift	2009-08-06 15:56:09 UTC (rev 3065)
+++ SwiftApps/SIDGrid/swift/projects/andric/peakfit_pilots/PK2/wholebrain/PK2mediator.swift	2009-08-06 15:59:18 UTC (rev 3066)
@@ -17,18 +17,17 @@
 
 ## Mediator app declaration:
 app (file q_result, PeakResult outObj) run_query (string med_args, file config, PeakfitR code){
-    Mediator med_args stdout=@filename(q_result) @filename(code.ShellpeakMediatorPK2);
+    Mediator med_args stdout=@filename(q_result) "--r_script" @filename(code.ShellpeakMediatorPK2);
 }
 
 ## this process sets parameters and calls Mediator:
 loop_query(int vert, string user, string db, string host, string query_outline, PeakfitR code, file config, string subject, string h){
-    int evox = vert;
     string theoutprefix = "FAH_Q";
-    PeakResult outObj<simple_mapper; location="results", prefix=@strcat(subject,"_",h,"vert",vert,".out.")>;
-    file q_result<single_file_mapper; file=@strcat("Qresults/",subject,"_",h,"vert",vert,".qresult")>;
+    PeakResult outObj<simple_mapper; location="results", prefix=@strcat(subject,"_",h,"vert",vert,".result.")>;
+    file q_result <single_file_mapper; file=@strcat("Qresults/",subject,"_",h,"vert",vert,".qresult")>;
     string med_args = @strcat("--user ","andric"," --conf ", @filename(config)," --db ", db," --host ", host,
-        " --subject ", subject,
-        " --query ", query_outline," --r_swift_args ", @filename(outObj)," --outprefix ", theoutprefix, " --r_script Rscripts/ShellpeakMediatorPK2.R");
+        " --vox ", vert," --subject ", subject,
+        " --query ", query_outline," --r_swift_args ", @filename(outObj)," --outprefix ", theoutprefix);
     trace(med_args);
     (q_result, outObj) = run_query(med_args, config, code);
 }
@@ -45,12 +44,12 @@
 ## variables to move across in the foreach loops:
 string declarelist[] = ["PK2smth"];
 string hemilist[] = ["lh"];
-int vertices[] = [3:4:1];
+int vertices[] = [1:2:1];
 
 ## nest the loop_query process in foreach loops to move across variable sets
 foreach subject in declarelist{
     foreach h in hemilist{
-        string query_outline = @strcat("SELECT * FROM peakTS_data",h," WHERE subject = '",subject,"' AND vertex between BEGIN_BATCH and END_BATCH");
+        string query_outline = @strcat("SELECT * FROM peakTS_data",h," WHERE subject = '",subject,"' AND vertex=VOX");
         trace(query_outline);
         foreach vert in vertices{
             loop_query(vert, user, db, host, query_outline, code, config, subject, h);