e5d963606c378c0f08cb946c3a9393847dd6ce22
kate
  Wed Oct 7 15:23:41 2020 -0700
Add bigBed to GeneReviews to support mouseOver with diseases. refs #19841

diff --git src/hg/hgc/geneReviewsClick.c src/hg/hgc/geneReviewsClick.c
index 3e06283..97021f1 100644
--- src/hg/hgc/geneReviewsClick.c
+++ src/hg/hgc/geneReviewsClick.c
@@ -1,132 +1,118 @@
 /* geneReviewsClick - hgc code to display geneReviews track item detail page */
 
 /* Copyright (C) 2014 The Regents of the University of California 
  * See README in this or parent directory for licensing information. */
 #include "common.h"
 #include "hgc.h"
 #include "geneReviewsClick.h"
 
 void doGeneReviews(struct trackDb *tdb, char *itemName)
 /* generate the detail page for geneReviews */
 {
-struct sqlConnection *conn = hAllocConn(database);
-char *table = tdb->table;
-int start = cartInt(cart, "o");
-int num = 4;
-
 genericHeader(tdb, itemName);
 
- char query[512];
- char **row;
- struct bed *bed;
- boolean hasBin = TRUE;
- struct sqlResult *sr;
-
- sqlSafef(query, sizeof query, "select * from %s where name = '%s' and chrom = '%s' and chromStart = %d",
-	    table, itemName, seqName, start);
- sr = sqlGetResult(conn, query);
- while ((row = sqlNextRow(sr)) != NULL)
-    {
-    bed = bedLoadN(row+hasBin, num);
-    printf("<B>Link to Gene Reviews:</B> <a href='https://www.ncbi.nlm.nih.gov/books/NBK1116/?term=%s' target=_blank>%s</a><BR>\n", bed->name, bed->name);
-    printPos(bed->chrom, bed->chromStart, bed->chromEnd, NULL, TRUE, bed->name);
-    }
+struct sqlConnection *conn = hAllocConn(database);
+int start = cartInt(cart, "o");
+int end = cartInt(cart, "t");
+printf("<B>Link to Gene Reviews:</B> "
+       "<a href='https://www.ncbi.nlm.nih.gov/books/NBK1116/?term=%s' target=_blank>%s</a><BR>\n",
+         itemName, itemName); printPos(seqName, start, end, NULL, TRUE, itemName);
 prGeneReviews(conn, itemName);
 printf("<BR>");
 printTrackHtml(tdb);
 hFreeConn(&conn);
 }
 
 void prGeneReviews(struct sqlConnection *conn, char *itemName)
 /* print GeneReviews associated to this item
    Note: this print function has been replaced by addGeneReviewToBed.pl
          which print the same information to the field 5 of bigBed file
 */
 {
 struct sqlResult *sr;
 char **row;
 char query[512];
 int i;
 char *clickMsg = "Click GR short name link to find the GeneReviews article on NCBI Bookshelf.";
 char *spacer = "   ";
 boolean firstTime = TRUE;
 
 if (!sqlTableExists(conn, "geneReviewsDetail")) return;
 
 
 sqlSafef(query, sizeof(query), "select  grShort, NBKid, grTitle from geneReviewsDetail where geneSymbol='%s'", itemName);
 
 sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
         char *grShort = *row++;
         char *NBKid  = *row++;
         char *grTitle = *row++;
 
 
         if (firstTime)
         {
           printf("<BR><B> GeneReviews available for %s:</B> (%s)<BR>",itemName,clickMsg);
           firstTime = FALSE;
           printf("<PRE><TT>");
               // #123456789-123456789-123456789-123456789-123456789-123456789-
           printf("GR short name          Disease name<BR>");
 
           printf("---------------------------------------------------------");
           printf("--------------------<BR>");
         }
         printf("<A HREF=\"https://www.ncbi.nlm.nih.gov/books/%s\" TARGET=_blank><B>%s</B></A>", NBKid, grShort);
         if (strlen(grShort) <= 20) {
           for (i = 0; i <  20-strlen(grShort); i ++ )
              {
                 printf("%s", " " );
              }
            }
        printf("%s%s<BR>", spacer, grTitle);
 
 //        printf("<A HREF=\"https://www.ncbi.nlm.nih.gov/books/%s\" TARGET=_blank><B>%s</B></A>%s%s<BR>", NBKid, NBKid, spacer, grTitle);
     }  /* end while */
  printf("</TT></PRE>");
  sqlFreeResult(&sr);
 } /* end of prGeneReviews */
 
 void prGRShortRefGene(char *itemName)
 /* print GeneReviews short label associated to this refGene item */
 {
 struct sqlConnection *conn  = hAllocConn(database);
 struct sqlResult *sr;
 char **row;
 char query[512];
 boolean firstTime = TRUE;
 
 if (!sqlTableExists(conn, "geneReviewsDetail")) return;
 
 sqlSafef(query, sizeof(query), "select grShort, NBKid, grTitle from geneReviewsDetail where geneSymbol='%s'", itemName);
 
 sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
         char *grShort = *row++;
 	char *NBKid = *row++;
         char *grTitle = *row++;
         if (firstTime)
         {
           printf("<B>Related GeneReviews disease(s): </B>");
           firstTime = FALSE;
        printf("<A HREF=\"https://www.ncbi.nlm.nih.gov/books/%s\" TARGET=_blank><B>%s</B></A>", NBKid, grShort);
         printf(" (");
        printf("%s", grTitle);
        printf(")");
         } else {
           printf(", ");
        printf("<A HREF=\"https://www.ncbi.nlm.nih.gov/books/n/gene/%s\" TARGET=_blank><B>%s</B></A>", grShort, grShort);
        printf(" (");
        printf("%s", grTitle);
        printf(")");
         }
      }
      printf("<BR>");
      sqlFreeResult(&sr);
 } /* end of prGRShortRefGene */