src/hg/instinct/bioInt2/grabData.c 1.4

Index: src/hg/instinct/bioInt2/grabData.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/instinct/bioInt2/grabData.c,v
retrieving revision 1.3
retrieving revision 1.4
diff -b -B -U 4 -r1.3 -r1.4
--- src/hg/instinct/bioInt2/grabData.c	7 Apr 2009 03:41:09 -0000	1.3
+++ src/hg/instinct/bioInt2/grabData.c	29 Apr 2009 18:22:08 -0000	1.4
@@ -255,33 +255,8 @@
 
 spHashListPrint(spList, slList, clinTableName);
 }
 
-
-struct hash *probeIdToGene(struct sqlConnection *conn, struct datasets *da)
-{
-char query[512];
-
-safef(query, sizeof(query), 
-      "select DISTINCT %s.id,geneSymbol from %s join %s on id=probe_id "
-      "join %s on gene_id=%s.id join %s on %s.kgId=%s.kgId;", 
-      da->probe_table, da->probe_table, da->probe_to_gene_table, GL_TABLE, 
-      GL_TABLE, KX_TABLE, GL_TABLE, KX_TABLE);
-
-struct sqlResult *sr = sqlGetResult(conn, query);
-char **row = NULL;
-
-struct hash *hash = hashNew(0);
-while ((row = sqlNextRow(sr)) != NULL)
-    {
-    char *id = row[0];
-    char *gene = cloneString(row[1]);
-    hashAdd(hash, id, gene);
-    }
-sqlFreeResult(&sr);
-return hash;
-}
-
 void medianSpHashList(struct slPair *spList, struct slName *slList)
 {
 struct hashEl *el;
 struct slPair *sp;
@@ -304,79 +279,8 @@
 	}
     }
 }
 
-void grabRawData(struct sqlConnection *conn, char *tableName)
-{
-struct datasets *da = findDataset(conn, tableName);
-if (!da)
-    errAbort("No dataset by name of %s in db\n", tableName);
-
-struct samples *sa, *saList = getSamples(conn, da);
-struct hash *idGeneHash = probeIdToGene(conn, da);
-
-char query[256];
-safef(query, sizeof(query), "select * from %s", tableName);
-
-struct hash *featureData = hashNew(0);
-struct slPair *sp, *spList = NULL;
-
-struct sqlResult *sr = sqlGetResult(conn, query);
-char **row = NULL;
-while ((row = sqlNextRow(sr)) != NULL)
-    {
-    char *probe_id = row[0];
-    struct probeVals *pv = probeValsLoad(row);
-    
-    struct hashEl *el = hashLookup(idGeneHash, probe_id);
-    if (!el)
-	continue;
-    char *gene = el->val;
-
-    struct hash *sampleData;
-    el = hashLookup(featureData, gene);
-    if (!el)
-	{
-	sampleData = hashNew(0);
-	hashAdd(featureData, gene, sampleData);
-	AllocVar(sp);
-	sp->name = cloneString(gene);
-	sp->val = sampleData;
-	slAddHead(&spList, sp);
-	}
-    else
-	sampleData = el->val;
-
-    for (sa = saList; sa; sa = sa->next)
-	{
-	double val = pv->sample_data[sa->exp_id];
-	struct slDouble *sd = slDoubleNew(val);
-
-	el = hashLookup(sampleData, sa->name);
-	if (!el)
-	    hashAdd(sampleData, sa->name, sd);
-	else
-	    {
-	    struct slDouble *sdList = el->val;
-	    slAddTail(&sdList, sd);
-	    }
-	}
-    }
-sqlFreeResult(&sr);
-hashFree(&featureData);
-
-struct slName *slList = NULL;
-for (sa = saList; sa; sa = sa->next)
-    slNameAddHead(&slList, sa->name);
-
-slReverse(&spList);
-slReverse(&slList);
-
-medianSpHashList(spList, slList);
-
-spHashListPrint(spList, slList, tableName);
-}
-
 void grabAnalysisData(struct sqlConnection *conn, char *tableName)
 {
 struct hash *sampleIdHash = createHash(conn, SA_TABLE, "id", "name");
 struct hash *featureIdHash = createHash(conn, AF_TABLE, "id", "feature_name");
@@ -452,17 +356,12 @@
 struct sqlConnection *conn = hAllocConnProfile(localDb, db);
 if (!sqlTableExists(conn, tableName))
     errAbort("%s doesn't exist in %s db.\n", tableName, db);
 
-if (isAnalysisTable(conn, tableName))
-    grabAnalysisData(conn, tableName);
-else
-    {
-    if (getClinical)
+if (getClinical)
 	grabClinicalData(conn, tableName);
-    else
-	grabRawData(conn, tableName);
-    }
+else
+    grabAnalysisData(conn, tableName);
 }
 
 
 int main(int argc, char *argv[])