bb1de08ea64e41b63cb861913f65712c29607e11 angie Fri Sep 22 15:51:49 2017 -0700 Updating urls for MGI ID. diff --git src/hg/hgc/hgc.c src/hg/hgc/hgc.c index f0c9bcf..2bba36b 100644 --- src/hg/hgc/hgc.c +++ src/hg/hgc/hgc.c @@ -11535,31 +11535,31 @@ rl->locusLinkId); printf("%d</A><BR>\n", rl->locusLinkId); if ( (strstr(database, "mm") != NULL) && hTableExists(database, "MGIid")) { char *mgiID; sqlSafef(query, sizeof(query), "select MGIid from MGIid where LLid = '%d';", rl->locusLinkId); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) { printf("<B>Mouse Genome Informatics:</B> "); mgiID = cloneString(row[0]); - printf("<A HREF=\"http://www.informatics.jax.org/searches/accession_report.cgi?id=%s\" TARGET=_BLANK>%s</A><BR>\n",mgiID, mgiID); + printf("<A HREF=\"http://www.informatics.jax.org/marker/%s\" TARGET=_BLANK>%s</A><BR>\n",mgiID, mgiID); } else { /* per Carol Bult from Jackson Lab 4/12/02, JAX do not always agree * with Locuslink on seq to gene association. * Thus, not finding a MGIid even if a LocusLink ID * exists is always a possibility. */ } sqlFreeResult(&sr); } } if (!startsWith("Worm", organism)) { if (startsWith("dm", database)) { @@ -11593,31 +11593,31 @@ { struct jaxOrtholog jo; char * sqlRlName = rl->name; /* Make sure to escape single quotes for DB parseability */ if (strchr(rl->name, '\'')) { sqlRlName = replaceChars(rl->name, "'", "''"); } sqlSafef(query, sizeof(query), "select * from jaxOrtholog where humanSymbol='%s'", sqlRlName); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { jaxOrthologStaticLoad(row, &jo); printf("<B>MGI Mouse Ortholog:</B> "); - printf("<A HREF=\"http://www.informatics.jax.org/searches/accession_report.cgi?id=%s\" target=_BLANK>", jo.mgiId); + printf("<A HREF=\"http://www.informatics.jax.org/marker/%s\" target=_BLANK>", jo.mgiId); printf("%s</A><BR>\n", jo.mouseSymbol); } sqlFreeResult(&sr); } if (startsWith("hg", database)) { printf("\n"); printf("<B>AceView:</B> "); printf("<A HREF = \"https://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi?db=human&l=%s\" TARGET=_blank>", rl->name); printf("%s</A><BR>\n", rl->name); } prGRShortRefGene(rl->name); } @@ -11672,31 +11672,31 @@ rl->locusLinkId); printf("%d</A><BR>\n", rl->locusLinkId); if ( (strstr(database, "mm") != NULL) && hTableExists(database, "MGIid")) { char *mgiID; sqlSafef(query, sizeof(query), "select MGIid from MGIid where LLid = '%d';", rl->locusLinkId); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) { printf("<B>Mouse Genome Informatics:</B> "); mgiID = cloneString(row[0]); - printf("<A HREF=\"http://www.informatics.jax.org/searches/accession_report.cgi?id=%s\" TARGET=_BLANK>%s</A><BR>\n",mgiID, mgiID); + printf("<A HREF=\"http://www.informatics.jax.org/marker/%s\" TARGET=_BLANK>%s</A><BR>\n",mgiID, mgiID); } else { /* per Carol Bult from Jackson Lab 4/12/02, JAX do not always agree * with Locuslink on seq to gene association. * Thus, not finding a MGIid even if a LocusLink ID * exists is always a possibility. */ } sqlFreeResult(&sr); } } } void doKnownGene(struct trackDb *tdb, char *rnaName) /* Process click on a known gene. */ @@ -14793,33 +14793,33 @@ sqlFreeResult(&sr); sqlSafef(query, sizeof query, "SELECT * FROM stsInfoMouse WHERE identNo = '%d'", stsRow.identNo); sr = sqlMustGetResult(conn, query); row = sqlNextRow(sr); if (row != NULL) { infoRow = stsInfoMouseLoad(row); printf("<TABLE>\n"); printf("<TR><TH ALIGN=left>Chromosome:</TH><TD>%s</TD></TR>\n", seqName); printf("<TR><TH ALIGN=left>Start:</TH><TD>%d</TD></TR>\n",start+1); printf("<TR><TH ALIGN=left>End:</TH><TD>%d</TD></TR>\n",end); printf("</TABLE>\n"); htmlHorizontalLine(); printf("<TABLE>\n"); printf("<TR><TH ALIGN=left>MGI Marker ID:</TH><TD><B>MGI:</B>"); - printf("<A HREF = \"http://www.informatics.jax.org/searches/accession_report.cgi?id=MGI:%d\" TARGET=_blank>%d</A></TD></TR>\n", infoRow->MGIMarkerID, infoRow->MGIMarkerID); + printf("<A HREF = \"http://www.informatics.jax.org/marker/MGI:%d\" TARGET=_blank>%d</A></TD></TR>\n", infoRow->MGIMarkerID, infoRow->MGIMarkerID); printf("<TR><TH ALIGN=left>MGI Probe ID:</TH><TD><B>MGI:</B>"); - printf("<A HREF = \"http://www.informatics.jax.org/searches/accession_report.cgi?id=MGI:%d\" TARGET=_blank>%d</A></TD></TR>\n", infoRow->MGIPrimerID, infoRow->MGIPrimerID); + printf("<A HREF = \"http://www.informatics.jax.org/marker/MGI:%d\" TARGET=_blank>%d</A></TD></TR>\n", infoRow->MGIPrimerID, infoRow->MGIPrimerID); printf("</TABLE>\n"); htmlHorizontalLine(); /* Print out primer information */ printf("<TABLE>\n"); printf("<TR><TH ALIGN=left>Left Primer:</TH><TD>%s</TD></TR>\n",infoRow->primer1); printf("<TR><TH ALIGN=left>Right Primer:</TH><TD>%s</TD></TR>\n",infoRow->primer2); printf("<TR><TH ALIGN=left>Distance:</TH><TD>%s bps</TD></TR>\n",infoRow->distance); printf("</TABLE>\n"); htmlHorizontalLine(); /* Print out information from genetic maps for this marker */ printf("<H3>Genetic Map Position</H3>\n"); printf("<TABLE>\n"); printf("<TH> </TH><TH ALIGN=left WIDTH=150>Name</TH><TH ALIGN=left WIDTH=150>Chromosome</TH><TH ALIGN=left WIDTH=150>Position</TH></TR>\n"); printf("<TH ALIGN=left> </TH><TD WIDTH=150>%s</TD><TD WIDTH=150>%s</TD><TD WIDTH=150>%.2f</TD></TR>\n", infoRow->stsMarkerName, infoRow->Chr, infoRow->geneticPos); @@ -18810,31 +18810,31 @@ struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char query[256]; char **row; int start = cartInt(cart, "o"); struct jaxQTL3 *jaxQTL; genericHeader(tdb, item); sqlSafef(query, sizeof query, "select * from jaxQTL3 where name = '%s' and chrom = '%s' and chromStart = %d", item, seqName, start); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) { jaxQTL = jaxQTL3Load(row); printf("<B>Jax/MGI Link: </B>"); - printf("<a TARGET=\"_blank\" href=\"http://www.informatics.jax.org/searches/accession_report.cgi?id=%s\">%s</a><BR>\n", + printf("<a TARGET=\"_blank\" href=\"http://www.informatics.jax.org/marker/%s\">%s</a><BR>\n", jaxQTL->mgiID, jaxQTL->mgiID); printf("<B>QTL:</B> %s<BR>\n", jaxQTL->name); printf("<B>Description:</B> %s <BR>\n", jaxQTL->description); if (!sameWord("", jaxQTL->flank1)) { printf("<B>Flank Marker 1: </B>"); printf("<a TARGET=\"_blank\" href=\"http://www.informatics.jax.org/javawi2/servlet/WIFetch?page=searchTool&query=%s", jaxQTL->flank1); printf("+&selectedQuery=Genes+and+Markers\">%s</a><BR>\n", jaxQTL->flank1); } if (!sameWord("", jaxQTL->marker)) { printf("<B>Peak Marker: </B>"); printf("<a TARGET=\"_blank\" href=\"http://www.informatics.jax.org/javawi2/servlet/WIFetch?page=searchTool&query=%s", jaxQTL->marker); printf("+&selectedQuery=Genes+and+Markers\">%s</a><BR>\n", jaxQTL->marker);