0c4c7028a43e7434f9e01bca2c8794ecd8e5c6ae
chinhli
  Wed Jul 3 12:14:41 2013 -0700
RM To Do 10993 path for the files necessary to compute the links has changed.
diff --git src/hg/hgc/hgc.c src/hg/hgc/hgc.c
index 6f53033..d55851b 100644
--- src/hg/hgc/hgc.c
+++ src/hg/hgc/hgc.c
@@ -227,30 +227,31 @@
 #include "itemConf.h"
 #include "chromInfo.h"
 #include "gbWarn.h"
 #include "lsSnpPdbChimera.h"
 #include "mammalPsg.h"
 #include "net.h"
 #include "jsHelper.h"
 #include "virusClick.h"
 #include "gwasCatalog.h"
 #include "parClick.h"
 #include "mdb.h"
 #include "yaleGencodeAssoc.h"
 #include "itemDetailsHtml.h"
 #include "trackVersion.h"
 #include "numtsClick.h"
+#include "geneReviewsClick.h"
 
 static char *rootDir = "hgcData";
 
 #define LINESIZE 70  /* size of lines in comp seq feature */
 
 struct cart *cart;	/* User's settings. */
 char *seqName;		/* Name of sequence we're working on. */
 int winStart, winEnd;   /* Bounds of sequence. */
 char *database;		/* Name of mySQL database. */
 char *organism;		/* Colloquial name of organism. */
 char *genome;		/* common name, e.g. Mouse, Human */
 char *scientificName;	/* Scientific name of organism. */
 
 struct hash *trackHash;	/* A hash of all tracks - trackDb valued */
 
@@ -23899,132 +23900,30 @@
 
 bedDetailFree(&r);
 hFreeConn(&conn);
 }
 
 struct trackDb *tdbForTableArg()
 /* get trackDb for track passed in table arg */
 {
 char *table = cartString(cart, "table");
 struct trackDb *tdb = hashFindVal(trackHash, table);
 if (tdb == NULL)
     errAbort("no trackDb entry for %s", table);
 return tdb;
 }
 
-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);
- genericBedClick(conn, tdb, itemName, start, num);
- 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-   Note: this print function has been replaced by addGeneReviewToBed.pl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 link(s) below to search GeneReviews and GeneTests";
-boolean firstTime = TRUE;
-
-if (!sqlTableExists(conn, "geneReviewsRefGene")) return;
-
-sqlSafef(query, sizeof(query), "select  grShort, diseaseID, diseaseName from geneReviewsRefGene where geneSymbol='%s'", itemName);
-sr = sqlGetResult(conn, query);
-while ((row = sqlNextRow(sr)) != NULL)
-    {
-        char *grShort = *row++;
-        char *diseaseID = *row++;
-        char *diseaseName = *row++;
-
-
-        if (firstTime)
-        {
-          printf("<BR><B> GeneReview(s) available for %s:</B> (%s)<BR>",itemName,clickMsg);
-          firstTime = FALSE;
-          printf("<PRE><TT>");
-              // #123456789-123456789-123456789-123456789-123456789-123456789-
-          printf("Short name    Disease ID     GeneTests disease name<BR>");
-          printf("------------------------------------------------------------");
-          printf("--------------------<BR>");
-        }
-        printf("<A HREF=\"http://www.ncbi.nlm.nih.gov/books/n/gene/%s\" TARGET=_blank><B>%s</B></A>", grShort, grShort);
-        if (strlen(grShort) <= 15) {
-          for (i = 0; i <  15-strlen(grShort); i ++ )
-             {
-                printf("%s", " " );
-             }
-           }
-         printf("%-10s    ", diseaseID);
-        printf("<A HREF=\"http://www.ncbi.nlm.nih.gov/sites/GeneTests/review/disease/%s?db=genetests&search_param=contains\" TARGET=_blank><B>%s</B></A><BR>", diseaseName, diseaseName);
-
-    }  /* 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, "geneReviewsRefGene")) return;
-
-sqlSafef(query, sizeof(query), "select grShort, diseaseName from geneReviewsRefGene where geneSymbol='%s'", itemName);
-sr = sqlGetResult(conn, query);
-while ((row = sqlNextRow(sr)) != NULL)
-    {
-        char *grShort = *row++;
-        char *diseaseName = *row++;
-        if (firstTime)
-        {
-          printf("<B>Related GeneReview(s) and GeneTests disease(s): </B>");
-          firstTime = FALSE;
-       printf("<A HREF=\"http://www.ncbi.nlm.nih.gov/books/n/gene/%s\" TARGET=_blank><B>%s</B></A>", grShort, grShort);
-        printf(" (");
-       printf("<A HREF=\"http://www.ncbi.nlm.nih.gov/sites/GeneTests/review/disease/%s?db=genetests&search_param=contains\" TARGET=_blank>%s</A>", diseaseName, diseaseName);
-       printf(")");
-        } else {
-          printf(", ");
-       printf("<A HREF=\"http://www.ncbi.nlm.nih.gov/books/n/gene/%s\" TARGET=_blank><B>%s</B></A>", grShort, grShort);
-       printf(" (");
-       printf("<A HREF=\"http://www.ncbi.nlm.nih.gov/sites/GeneTests/review/disease/%s?db=genetests&search_param=contains\" TARGET=_blank>%s</A>", diseaseName, diseaseName);
-       printf(")");
-        }
-     }
-     printf("<BR>");
-     sqlFreeResult(&sr);
-} /* end of prGRShortRefGene */
-
 void doQPCRPrimers(struct trackDb *tdb, char *itemName)
 /* Put up page for QPCRPrimers. */
 {
 genericHeader(tdb, itemName);
 doBedDetail(tdb, NULL, itemName);
 } /* end of doQPCRPrimers */
 
 void doSnakeClick(struct trackDb *tdb, char *itemName)
 /* Put up page for snakes. */
 {
 genericHeader(tdb, itemName);
 char *otherSpecies = trackHubSkipHubName(tdb->table) + strlen("snake");
 char *hubName = cloneString(database);
 char *ptr = strchr(hubName + 4, '_');
 *ptr = 0;