src/hg/instinct/bioInt2/bioController.c 1.5

Index: src/hg/instinct/bioInt2/bioController.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/instinct/bioInt2/bioController.c,v
retrieving revision 1.4
retrieving revision 1.5
diff -b -B -U 4 -r1.4 -r1.5
--- src/hg/instinct/bioInt2/bioController.c	22 Mar 2009 01:07:28 -0000	1.4
+++ src/hg/instinct/bioInt2/bioController.c	23 Mar 2009 18:19:29 -0000	1.5
@@ -166,8 +166,9 @@
 }
 
 void createSetLevelAnalyses(struct sqlConnection *biConn, int cohort_id)
 {
+/* Get all gene-level analyses */
 char query[256];
 safef(query, sizeof(query),
       "select * from analyses "
       "join analysisModules on analyses.module_id = analysisModules.id "
@@ -214,11 +215,22 @@
 
 char *module = sqlQuickString(biConn, query);
 
 if (sameString(module, "meta"))
+    {
+    ba->pipeline = geneLevelPipeline;
     ba->analyze = metaGene;
+    }
+else if (sameString(module, "metaGeneset"))
+    {
+    ba->pipeline = genesetLevelPipeline;
+    ba->analyze = metaGeneset;
+    }
 else
+    {
+    ba->pipeline = NULL;
     ba->analyze = NULL;
+    }
 }
 
 struct biAnalysis *biAnalysisListForCohort(struct sqlConnection *biConn, 
 					   char *db, int cohort_id)
@@ -234,30 +246,23 @@
 
 if (!anList)
     errAbort("No analyses for cohort = %d", cohort_id);
 
-struct datasets *da, *daList = datasetsInCohort(biConn, cohort_id);
-
 for (an = anList; an; an = an->next)
     {
     AllocVar(ba);
     ba->db = cloneString(db);
     ba->tableName  = cloneString(an->result_table);
     ba->parameters = hashNew(0);
-
-    struct slName *slList = NULL;
-    for (da = daList; da; da = da->next)
-	slNameAddHead(&slList, da->data_table);
-    ba->inputTables = slList;
+    ba->inputTables = slNameListFromComma(an->input_tables);
     
     biAnalysisAddModule(biConn, ba, an->module_id);
 
     slAddHead(&baList, ba);
     }
 slReverse(&baList);
 
 analysesFreeList(&anList);
-datasetsFreeList(&daList);
 
 return baList;
 } 
 
@@ -300,9 +305,9 @@
 /* Meta-Gene module */
 storeAnalysisModule(biConn, "meta", "gene");
 
 /* Set up more modules below, similar to above */
-
+storeAnalysisModule(biConn, "metaGeneset", "set");
 }
 
 void prepareDatabase(struct sqlConnection *biConn)
 {