e4ebd36df9ba24360fa4d77a015d8b0cff911f62
chinhli
Wed Sep 21 08:49:27 2011 -0700
Finished up the bigBed update approach for geneReviews track
diff --git src/hg/hgc/hgc.c src/hg/hgc/hgc.c
index 856d18d..6405f4d 100644
--- src/hg/hgc/hgc.c
+++ src/hg/hgc/hgc.c
@@ -9724,69 +9724,70 @@
printedCnt = 0;
while ((row = sqlNextRow(sr)) != NULL)
{
if (printedCnt < 1)
printf("RefSeq Gene(s): ");
else
printf(", ");
printf("", "../cgi-bin/hgc?g=refGene&i=", row[0], chromStart, chromEnd);
printf("%s", row[0]);
printedCnt++;
}
if (printedCnt >= 1) printf("
\n");
}
sqlFreeResult(&sr);
- // show GeneReviews link(s)
- if (sqlTablesExist(conn, "geneReviews"))
- {
- safef(query, sizeof(query),
- "select distinct r.name2 from refLink l, mim2gene g, refGene r where l.omimId=%s and g.geneId=l.locusLinkId and g.entryType='gene' and chrom='%s' and txStart = %s and txEnd= %s",
- itemName, chrom, chromStart, chromEnd);
- sr = sqlMustGetResult(conn, query);
- if (sr != NULL)
- {
- while ((row = sqlNextRow(sr)) != NULL)
- {
- prGRShortRefGene(row[0]);
- }
- }
- sqlFreeResult(&sr);
- }
-
// show Related UCSC Gene links
safef(query, sizeof(query),
"select distinct kgId from kgXref x, refLink l, omim2gene g where x.refseq = mrnaAcc and l.omimId=%s and g.omimId=l.omimId and g.entryType='gene'",
itemName);
sr = sqlMustGetResult(conn, query);
if (sr != NULL)
{
int printedCnt;
printedCnt = 0;
while ((row = sqlNextRow(sr)) != NULL)
{
if (printedCnt < 1)
printf("Related UCSC Gene(s): ");
else
printf(", ");
printf("", "../cgi-bin/hgGene?hgg_gene=", row[0]);
printf("%s", row[0]);
printedCnt++;
}
if (printedCnt >= 1) printf("
\n");
}
sqlFreeResult(&sr);
+
+ // show GeneReviews link(s)
+ if (sqlTablesExist(conn, "geneReviewsRefGene"))
+ {
+ safef(query, sizeof(query),
+ "select distinct r.name2 from refLink l, mim2gene g, refGene r where l.omimId=%s and g.geneId=l.locusLinkId and g.entryType='gene' and chrom='%s' and txStart = %s and txEnd= %s",
+ itemName, chrom, chromStart, chromEnd);
+ sr = sqlMustGetResult(conn, query);
+ if (sr != NULL)
+ {
+ while ((row = sqlNextRow(sr)) != NULL)
+ {
+ prGRShortRefGene(row[0]);
+ }
+ }
+ sqlFreeResult(&sr);
+ }
+
}
printf("
");
printPosOnChrom(chrom, atoi(chromStart), atoi(chromEnd), NULL, FALSE, itemName);
}
void printOmimLocationDetails(struct trackDb *tdb, char *itemName, boolean encode)
/* Print details of an OMIM Class 3 Gene entry. */
{
struct sqlConnection *conn = hAllocConn(database);
struct sqlConnection *conn2 = hAllocConn(database);
char query[256];
struct sqlResult *sr;
char **row;
char *url = tdb->url;
@@ -23859,78 +23860,90 @@
int i;
char *clickMsg = "Click 'Short name' link below to search GeneReviews";
boolean firstTime = TRUE;
safef(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("
GeneReview available for %s: (%s)
",itemName,clickMsg);
+ printf("
GeneReview(s) available for %s: (%s)
",itemName,clickMsg);
firstTime = FALSE;
printf("");
// #1234567890123456789012345678901234567890
printf("Short name Disease ID GeneTests disease name
");
printf("-----------------------------------------------------------");
printf("-----------------------------------------------------------");
printf("----------------------------------
");
}
printf("%s", grShort, grShort);
if (strlen(grShort) <= 15) {
for (i = 0; i < 15-strlen(grShort); i ++ )
{
printf("%s", " " );
}
}
- printf("%-10s %s
", diseaseID, diseaseName);
+ printf("%-10s ", diseaseID);
+ printf("%s
", diseaseName, diseaseName);
+
} /* end while */
printf("");
//printf("
");
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;
safef(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(" GeneReviews: ");
+ printf("Related GeneReview(s) and GeneTests disease(s): ");
firstTime = FALSE;
printf("%s", grShort, grShort);
- printf(" (%s) ", diseaseName);
+ printf(" (");
+ printf("%s", diseaseName, diseaseName);
+ printf(")");
+
+// printf("%s", grShort, grShort);
+// printf(" (%s) ", diseaseName);
} else {
printf(", ");
printf("%s", grShort, grShort);
- printf(" (%s) ", diseaseName);
+ printf(" (");
+ printf("%s", diseaseName, diseaseName);
+ printf(")");
+
+// printf("%s", grShort, grShort);
+// printf(" (%s) ", diseaseName);
}
}
printf("
");
sqlFreeResult(&sr);
} /* end of prGRShortRefGene */
void doMiddle()
/* Generate body of HTML. */
{
char *track = cartString(cart, "g");
char *item = cartOptionalString(cart, "i");
char *parentWigMaf = cartOptionalString(cart, "parentWigMaf");
struct trackDb *tdb = NULL;