e8499e560e60e115ca15069b9eadb36f01a7614d
markd
  Sat Apr 13 09:45:15 2024 -0700
delete dead links for MGC/ORFeome

diff --git src/hg/hgc/mgcClick.c src/hg/hgc/mgcClick.c
index 14db3b2..b017776 100644
--- src/hg/hgc/mgcClick.c
+++ src/hg/hgc/mgcClick.c
@@ -92,111 +92,74 @@
 return mgcDb;
 }
 
 char *mgcDbName()
 /* get just the MGC collection name for the current ucsc database */
 {
 return getMgcDb().name;
 }
 
 void printMgcHomeUrl(struct mgcDb *mgcDb)
 /* print out an URL to link to the MGC site */
 {
 printf("http://%s.nci.nih.gov/", mgcDb->server);
 }
 
-void printMgcUrl(int imageId)
-/* print out an URL to link to the MGC site for a full-length MGC clone */
-{
-struct mgcDb mgcDb = getMgcDb();
-printf("http://%s.nci.nih.gov/Reagents/CloneInfo?ORG=%s&IMAGE=%d",
-       mgcDb.server, mgcDb.organism, imageId);
-}
-
 static void printOrderUrl(int gi)
 /* print out an URL to link to the NCBI order CGI for a full-length MGC clone */
 {
 printf("https://www.ncbi.nlm.nih.gov/genome/clone/orderclone.cgi?db=nucleotide&uid=%d", gi);
 }
 
-static void printImageUrl(int imageId)
-/* print out an URL to link to IMAGE database for a clone */
-{
-printf("http://www.imageconsortium.org/IQ/bin/singleCloneQuery?clone_id=%d", imageId);
-}
-
 void printMgcDetailsUrl(char *acc, int start)
 /* print out an URL to link to MGC details pages from another details page in
  * the browser.*/
 {
 // pass zero coordiates for window to indicate this isn't a browser click
 printf("../cgi-bin/hgc?%s&g=mgcGenes&o=%d&i=%s&l=0&r=0&db=%s",
        cartSidUrlString(cart), start, acc, database);
 }
 
-static void printMBLabValidDbUrl(char *acc)
-/* print out an URL to link to Brent lab validation database */
-{
-printf("http://mblab.wustl.edu/cgi-bin/mgc.cgi?acc=%s&action=cloneRpt&alignment=Submit", acc);
-}
-
 struct cloneInfo
 /* Information on a MGC or ORFeome clone collected from various tables */
 {
     boolean isMgc;    // is this MGC or ORFeome
     char *acc;
     int start;
     char *pslTbl;     // psl-format table
     char *gpTbl;      // genePred format table
     char *desc;       // genbank info
     char *organism;
     char *tissue;
     char *library;
     char *development;
     char *geneName;
     char *productName;
     char *moddate;
     char *clone;
     char *cds;
     char *keyword;
     int version;
     int imageId;
     int mgcId;
     int gi;
     char *refSeqAccv;     // best RefSeq acc.version, or NULL
     char *refSeqSum;      // RefSeq from best matching RefSeq with summary, or NULL.
     char *refSeqSumAccv;  // accv for summary, maybe different than best match
     struct geneSimilarities *refSeqs;  // most similar RefSeqs, with name set to acc.version
 };
 
-static boolean isInMBLabValidDb(char *acc)
-/* check if an accession is in the Brent lab validation database */
-{
-boolean inMBLabValidDb = FALSE;
-struct sqlConnection *fconn = sqlMayConnect("hgFixed");
-if ((fconn != NULL) && sqlTableExists(fconn, "mgcMBLabValid"))
-    {
-    char query[64], buf[32];
-    sqlSafef(query, sizeof(query), "select acc from mgcMBLabValid where acc=\"%s\"",
-          acc);
-    if (sqlQuickQuery(fconn, query, buf, sizeof(buf)) != NULL)
-        inMBLabValidDb = TRUE;
-    sqlDisconnect(&fconn);
-    }
-return inMBLabValidDb;
-}
-
 static void cdnaInfoLoad(struct cloneInfo *ci, struct sqlConnection *conn)
 /* Loading clone information from gbCdnaInfoTable relational tables. */
 {
 // data from gbCdnaInfoTable and friends
 char query[1024];
 sqlSafef(query, sizeof(query),
       "select "
       "des.name, o.name, t.name, l.name,"
       "dev.name, gene.name, p.name, m.name,"
       "c.name,k.name,g.moddate,g.version,"
       "g.gi"
       " from "
       "%s g,%s des,%s o,%s t,%s l,%s dev,"
       "%s gene,%s p,%s m,%s c,%s k"
       " where "
@@ -597,41 +560,30 @@
 printf("Click <A HREF=\"%s&g=htcTrackHtml&table=%s&c=%s&l=%d&r=%d\">here</A> for details",
        hgcPathAndSettings(), track, seqName, winStart, winEnd);
 }
 
 static void prOrderLink(char *name, struct cloneInfo *ci)
 /* create link to NCBI clone order CGI */
 {
 webPrintLinkTableNewRow();
 webPrintLinkCellStart();
 printf("<a href=\"");
 printOrderUrl(ci->gi);
 printf("\" TARGET=_blank>Order %s clone</a>", name);
 webPrintLinkCellEnd();
 }
 
-static void prImageLink(struct cloneInfo *ci)
-/* create link to IMAGE database */
-{
-webPrintLinkTableNewRow();
-webPrintLinkCellStart();
-printf("<a href=\"");
-printImageUrl(ci->imageId);
-printf("\" TARGET=_blank>IMAGE clone %d</a>", ci->imageId);
-webPrintLinkCellEnd();
-}
-
 static void prGenbankLink(struct cloneInfo *ci)
 /* create link to Genbank database */
 {
 webPrintLinkTableNewRow();
 webPrintLinkCellStart();
 printf("<a href=\"");
 printEntrezNucleotideUrl(stdout, ci->acc);
 printf("\" TARGET=_blank>Genbank %s</a>", ci->acc);
 webPrintLinkCellEnd();
 }
 
 static void prRefSeqLinks(struct cloneInfo *ci)
 /* print link to RefSeq */
 {
 webPrintLinkTableNewRow();
@@ -677,57 +629,38 @@
     printf("<A href=\"../cgi-bin/hgGene?%s&db=%s&hgg_gene=%s&hgg_chrom=%s&hgg_start=%d&hgg_end=%d&hgg_type=knownGene\">UCSC Gene %s</A>",
            cartSidUrlString(cart), database, gene->name, seqName, gene->txStart, gene->txEnd, gene->name);
     webPrintLinkCellEnd();
     }
 geneSimilaritiesFree(&ucscGenes);
 }
 
 static void prMgcCloneLinks(struct sqlConnection *conn, struct mgcDb *mgcDb, struct cloneInfo *ci)
 /* print table of clone links */
 {
 webPrintLinkTableStart();
 webPrintLabelCell("Links");
 if (ci->gi > 0)
     prOrderLink(mgcDb->name, ci);
 
-// link to MGC database
-webPrintLinkTableNewRow();
-webPrintLinkCellStart();
-printf("<a href=\"");
-printMgcUrl(ci->imageId);
-printf("\" TARGET=_blank>%s clone database</a>", mgcDb->name);
-webPrintLinkCellEnd();
-
-prImageLink(ci);
 prGenbankLink(ci);
 if (ci->refSeqAccv != NULL)
     prRefSeqLinks(ci);
 if (sqlTableExists(conn, "ccdsGene"))
     prCcdsLinks(conn, ci);
 if (sqlTableExists(conn, "knownGene"))
     prUcscGenesLinks(conn, ci);
 
-// Brent lab validation database
-if (isInMBLabValidDb(ci->acc))
-    {
-    webPrintLinkTableNewRow();
-    webPrintLinkCellStart();
-    printf("<a href=\"");
-    printMBLabValidDbUrl(ci->acc);
-    printf("\" TARGET=_blank>Brent Lab Clone Validation</a>");
-    webPrintLinkCellEnd();
-    }
 webPrintLinkTableEnd();
 }
 
 static void prMgcInfoLinks(struct sqlConnection *conn, char *acc, struct mgcDb *mgcDb,
                            struct cloneInfo *ci)
 /* print clone info and links */
 {
 webNewSection("%s Clone Information and Links", mgcDb->name);
 printf("<table border=0><tr valign=top><td>\n");
 prCloneInfo(ci);
 printf("<td>\n");
 prMgcCloneLinks(conn, mgcDb, ci);
 printf("</tr></table>\n");
 }
 
@@ -803,32 +736,30 @@
 static void prOrfeomeCloneLinks(struct sqlConnection *conn, char *acc, struct cloneInfo *ci)
 /* print table of clone links */
 {
 webPrintLinkTableStart();
 webPrintLabelCell("Links");
 webPrintLinkTableNewRow();
 if (ci->gi > 0)
     prOrderLink("ORFeome", ci);
 
 #if 0
 // link to ORFeome database
 // FIXME: this doesn't appear to work, need to ask Christa
 // http://www.orfeomecollaboration.org/bin/cloneStatus.pl
 #endif
 
-if (ci->imageId > 0)
-    prImageLink(ci);
 prGenbankLink(ci);
 if (ci->refSeqAccv != NULL)
     prRefSeqLinks(ci);
 if (sqlTableExists(conn, "ccdsGene"))
     prCcdsLinks(conn, ci);
 if (sqlTableExists(conn, "knownGene"))
     prUcscGenesLinks(conn, ci);
 
 webPrintLinkTableEnd();
 }
 
 static void prOrfeomeInfoLinks(struct sqlConnection *conn, char *acc, struct cloneInfo *ci)
 /* print clone info and links */
 {
 webNewSection("ORFeome Clone Information and Links");