b3bbb2830441deb68f6645938db234d0ce7f170d
kate
  Thu Apr 28 13:17:13 2016 -0700
Cleanup for readability.

diff --git src/hg/hgc/gtexClick.c src/hg/hgc/gtexClick.c
index 1a73b20..7cd11df 100644
--- src/hg/hgc/gtexClick.c
+++ src/hg/hgc/gtexClick.c
@@ -33,60 +33,63 @@
     return "#FE0000";
 return unknown;
 }
 
 
 static struct gtexGeneBed *getGtexGene(char *item, char *chrom, int start, int end, char *table)
 /* Retrieve gene info for this item from the main track table */
 {
 struct gtexGeneBed *gtexGene = NULL;
 struct sqlConnection *conn = hAllocConn(database);
 char **row;
 char query[512];
 struct sqlResult *sr;
 if (sqlTableExists(conn, table))
     {
-    sqlSafef(query, sizeof query, "select * from %s where name = '%s' and chrom = '%s' "
+    sqlSafef(query, sizeof query, "SELECT * FROM %s WHERE name = '%s' AND chrom = '%s' "
                                   " and chromStart = %d and chromEnd = %d", 
                                         table, item, chrom, start, end);
     sr = sqlGetResult(conn, query);
     row = sqlNextRow(sr);
     if (row != NULL)
         {
         gtexGene = gtexGeneBedLoad(row);
         }
     sqlFreeResult(&sr);
     }
 hFreeConn(&conn);
 return gtexGene;
 }
 
 char *getGeneDescription(struct gtexGeneBed *gtexGene)
 /* Get description for gene. Needed because knownGene table semantics have changed in hg38 */
 {
 char query[256];
 if (sameString(database, "hg38"))
     {
     char *geneId = cloneString(gtexGene->geneId);
     chopSuffix(geneId);
     sqlSafef(query, sizeof(query), 
-        "select kgXref.description from kgXref, knownCanonical where knownCanonical.protein like '%%%s%%' and knownCanonical.transcript=kgXref.kgID", geneId);
+        "SELECT kgXref.description FROM kgXref, knownCanonical WHERE "
+                "knownCanonical.protein LIKE '%%%s%%' AND "
+                "knownCanonical.transcript=kgXref.kgID", geneId);
     }
 else
     {
     sqlSafef(query, sizeof(query), 
-                "select kgXref.description from kgXref where geneSymbol='%s'", gtexGene->name);
+                "SELECT kgXref.description FROM kgXref WHERE geneSymbol='%s'", 
+                        gtexGene->name);
     }
 struct sqlConnection *conn = hAllocConn(database);
 char *desc = sqlQuickString(conn, query);
 hFreeConn(&conn);
 return desc;
 }
 
 void doGtexGeneExpr(struct trackDb *tdb, char *item)
 /* Details of GTEx gene expression item */
 {
 int start = cartInt(cart, "o");
 int end = cartInt(cart, "t");
 struct gtexGeneBed *gtexGene = getGtexGene(item, seqName, start, end, tdb->table);
 if (gtexGene == NULL)
     errAbort("Can't find gene %s in GTEx gene table %s\n", item, tdb->table);
@@ -99,34 +102,35 @@
 else
     {
     printf("<a target='_blank' href='%s?db=%s&hgg_gene=%s'>%s</a><br>\n", 
                         hgGeneName(), database, gtexGene->name, gtexGene->name);
     printf("<b>Description:</b> %s<br>\n", desc);
     }
 printf("<b>Ensembl gene ID:</b> %s<br>\n", gtexGene->geneId);
 // The actual transcript model is a union, so this identification is approximate
 // (used just to find a transcript class)
 char *geneClass = gtexGeneClass(gtexGene);
 printf("<b>GENCODE biotype: </b> %s<br>\n", gtexGene->geneType); 
 printf("<b>Gene class: </b><span style='color: %s'>%s</span><br>\n", 
             geneClassColorCode(geneClass), geneClass);
 printf("<b>Total median expression: </b> %0.2f RPKM<br>\n", gtexGeneTotalMedianExpression(gtexGene));
 printf("<b>Score: </b> %d<br>\n", gtexGene->score); 
-printf("<b>Genomic position: </b>%s <a href='%s&db=%s&position=%s%%3A%d-%d'>%s:%d-%d</a><br>\n", 
+printf("<b>Genomic position: "
+                "</b>%s <a href='%s&db=%s&position=%s%%3A%d-%d'>%s:%d-%d</a><br>\n", 
                     database, hgTracksPathAndSettings(), database, 
                     gtexGene->chrom, gtexGene->chromStart+1, gtexGene->chromEnd,
                     gtexGene->chrom, gtexGene->chromStart+1, gtexGene->chromEnd);
 puts("<p>");
 
 // set gtexDetails (e.g. to 'log') to show log transformed details page 
 //      if hgTracks is log-transformed
-boolean doLogTransform = (trackDbSetting(tdb, "gtexDetails") &&
+boolean doLogTransform = 
+        (trackDbSetting(tdb, "gtexDetails") &&
             cartUsualBooleanClosestToHome(cart, tdb, FALSE, GTEX_LOG_TRANSFORM,
                                                 GTEX_LOG_TRANSFORM_DEFAULT));
 char *version = gtexVersion(tdb->table);
 struct tempName pngTn;
 if (gtexGeneBoxplot(gtexGene->geneId, gtexGene->name, version, doLogTransform, &pngTn))
     printf("<IMG SRC = \"%s\" BORDER=1><BR>\n", pngTn.forHtml);
 gtexPortalLink(gtexGene->geneId);
-
 printTrackHtml(tdb);
 }