src/hg/instinct/bioInt2/bioIntUI.c 1.8

Index: src/hg/instinct/bioInt2/bioIntUI.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/instinct/bioInt2/bioIntUI.c,v
retrieving revision 1.7
retrieving revision 1.8
diff -b -B -U 4 -r1.7 -r1.8
--- src/hg/instinct/bioInt2/bioIntUI.c	31 Mar 2009 05:06:38 -0000	1.7
+++ src/hg/instinct/bioInt2/bioIntUI.c	31 Mar 2009 20:36:50 -0000	1.8
@@ -139,8 +139,18 @@
 
 return sqlQuickString(conn, query);
 }
 
+struct pathways *getPathwayByName(struct sqlConnection *conn, char *name)
+{
+char query[256];
+safef(query, sizeof(query), 
+      "select * from %s where name = \"%s\" ",
+      PA_TABLE, name);
+
+return pathwaysLoadByQuery(conn, query);
+}
+
 void setAnalysisFeatureDesc(struct sqlConnection *conn, struct json *js, 
 			    struct analysisFeatures *af)
 {
 char *desc = getFieldFromKgXref(conn, af->feature_name, "description");
@@ -157,11 +167,23 @@
 
 void setAnalysisFeatureLink(struct sqlConnection *conn, struct json *js,
 			    struct analysisFeatures *af)
 {
-char *kgId = getFieldFromKgXref(conn, af->feature_name, "kgId");
-if (kgId)
-    jsonAddString(js, "hgg_gene", kgId);
+char *name, *source;
+name = getFieldFromKgXref(conn, af->feature_name, "kgId");
+if (name)
+    source = "UCSC";
+else
+    {
+    struct pathways *pa = getPathwayByName(conn, af->feature_name);
+    if (!pa)
+	return;
+    name = pa->name;
+    source = pa->source;
+    }
+
+jsonAddString(js, "name", name);
+jsonAddString(js, "source", source);
 }
 
 /****** END HELPER FUNCTIONS *******/
 
@@ -382,8 +404,35 @@
     cohort_id = 1;  // hard code for first analysis during testing!
 
 /* feature source = gene,geneset,clinical... */
 char *source = cartOptionalString(cart, bioIntSourceName);
+char *feature_name = cartOptionalString(cart, bioIntFeatureName);
+if (!feature_name || !source)
+    errAbort("%s and %s must be set for mode=getFeatureData\n", bioIntFeature, bioIntSourceName);
+
+struct sqlConnection *conn = hAllocConnProfile(localDb, db);
+
+struct datasets *daList = getDatasetsByCohortId(conn, cohort_id);
+if (!daList)
+    errAbort("No datasets matching cohort_id = %d", cohort_id);
+
+struct json *js = newJson();
+sendUniqueMatch(conn, js, cohort_id, feature_name, source, daList);
+
+if (js)
+    hPrintf("%s\n", js->print(js));
+
+hFreeConn(&conn);
+}
+
+void getSuggestions()
+{
+int cohort_id = cartUsualInt(cart, bioIntCohortId, -1);
+if (cohort_id == -1)
+    cohort_id = 1;  // hard code for first analysis during testing!
+
+/* feature source = gene,geneset,clinical... */
+//char *source = cartOptionalString(cart, bioIntSourceName);
 
 char *feature_name = cartOptionalString(cart, bioIntFeatureName);
 if (!feature_name)
     errAbort("%s or %s must be set for mode=getFeatureData\n", bioIntFeature, bioIntFeatureId);
@@ -394,25 +443,14 @@
 if (!daList)
     errAbort("No datasets matching cohort_id = %d", cohort_id);
 
 struct json *js = newJson();
-if (source)
-    sendUniqueMatch(conn, js, cohort_id, feature_name, source, daList);
-else
-    {
-    struct slPair *spList = searchForFeatures(conn, cohort_id, daList, feature_name);
-    
-    int numMatched = slCount(spList);
-    if (numMatched == 0)
+struct slPair *spList = searchForFeatures(conn, cohort_id, daList, feature_name);
+int numMatched = slCount(spList);
+if (numMatched == 0)
 	sendNoMatch(js);
-    else if (numMatched == 1)
-	{
-	source = spList->val;
-	sendUniqueMatch(conn, js, cohort_id, spList->name, source, daList);
-	}
-    else
+else
 	sendAmbiguities(js, spList);
-    }
 
 if (js)
     hPrintf("%s\n", js->print(js));
 
@@ -644,8 +682,10 @@
 if (sameString(mode, "getAnalyses"))
     getAnalyses();
 else if (sameString(mode, "getFeatureData"))
     getFeatureData();
+else if (sameString(mode, "getSuggestions"))
+    getSuggestions();
 else if (sameString(mode, "getClinicalData"))
     getClinicalData();
 else if (sameString(mode, "getClinicalFeatures"))
     getClinicalFeatures();