[Swift-commit] r3090 - SwiftApps/SIDGrid/swift/projects/andric/ccf_emblem/NonParametric_lag_analy

[noreply at svn.ci.uchicago.edu]

Author: andric
Date: 2009-08-09 00:14:36 -0500 (Sun, 09 Aug 2009)
New Revision: 3090

Modified:
   SwiftApps/SIDGrid/swift/projects/andric/ccf_emblem/NonParametric_lag_analy/FriedmanPerm.swift
Log:
updated to map only Rscript and Rdata with a new type

Modified: SwiftApps/SIDGrid/swift/projects/andric/ccf_emblem/NonParametric_lag_analy/FriedmanPerm.swift
===================================================================
--- SwiftApps/SIDGrid/swift/projects/andric/ccf_emblem/NonParametric_lag_analy/FriedmanPerm.swift	2009-08-09 05:03:28 UTC (rev 3089)
+++ SwiftApps/SIDGrid/swift/projects/andric/ccf_emblem/NonParametric_lag_analy/FriedmanPerm.swift	2009-08-09 05:14:36 UTC (rev 3090)
@@ -1,17 +1,17 @@
 #---- coded 08.August.2009
 type file{}
 type Rscript;
-type AnalyConfig{
+type PermAnaly{
+    Rscript R;
     file Rdata;
-    file txt;
 }
 
-app (file rout) run_query (string allcatargs, file config, Rscript code, AnalyConfig permutationSetup){
-    Mediator allcatargs @filename(code);
+app (file rout) run_query (string allcatargs, file config, PermAnaly code){
+    Mediator allcatargs @code.R;
 }
 
 
-loop_query(int bvox, string user, string db, string host, string query_outline, Rscript code, file config, string id, string h, int perm, AnalyConfig permutationSetup, int batchstep){
+loop_query(int bvox, string user, string db, string host, string query_outline, PermAnaly code, file config, string id, string h, int perm, int batchstep){
     int evox = bvox+(batchstep-1);
     string outName = @strcat("permout",h,"/perm",perm,"_",h,bvox,"_",evox);
     string med_args = @strcat("--user ","andric",
@@ -19,7 +19,7 @@
         " --db ", db,
         " --host ", host,
         " --query ", query_outline,
-        " --r_script ", @filename(code),
+        " --r_script ", @filename(code.R),
         " --begin_vox ", bvox,
         " --end_vox ", evox,
         " --outprefix ", "TOLDJA",
@@ -27,7 +27,7 @@
         " --r_swift_args ", outName," ",perm,
         " --subject ", id);
     file r_result <single_file_mapper; file=@strcat(outName,".txt")>;
-    r_result = run_query(med_args, config, code, permutationSetup);
+    r_result = run_query(med_args, config, code);
 }
 
 string user = @arg("user");
@@ -35,8 +35,7 @@
 string host = "tp-neurodb.ci.uchicago.edu";
 file config<single_file_mapper; file="user.config">;
 
-Rscript code<single_file_mapper; file="PermScripts/FriedmanPerm.R">;
-AnalyConfig permutationSetup<simple_mapper; location="PermScripts", prefix="PermConfig.">;
+PermAnaly code<simple_mapper; location="PermScripts", prefix="FriedmanPerm.">;
 
 string hemilist[] = ["lh"];
 int batchstep = 7000;
@@ -50,7 +49,7 @@
     foreach perm in permbrains{
         foreach batch in mybatches{
             string query_outline = @strcat("SELECT subject, vertex, speech_lag, emblem_lag, embspeech_lag FROM interpCCF_",h," WHERE vertex BETWEEN BEGIN_BATCH and END_BATCH");
-            loop_query(batch, user, db, host, query_outline, code, config, id, h, perm, permutationSetup, batchstep);
+            loop_query(batch, user, db, host, query_outline, code, config, id, h, perm, batchstep);
         }
     }
 }