a9c9cf2828c124535a1562f709bd4437b1bf60a2
braney
  Mon Jun 22 16:41:31 2020 -0700
starting on making hgGene use and external database for the know* tables

diff --git src/hg/hgGene/links.c src/hg/hgGene/links.c
index ed58ea2..5c7d19c 100644
--- src/hg/hgGene/links.c
+++ src/hg/hgGene/links.c
@@ -1,266 +1,266 @@
 /* links.c - Handle links section. */
 
 /* Copyright (C) 2013 The Regents of the University of California 
  * See README in this or parent directory for licensing information. */
 
 #include "common.h"
 #include "hash.h"
 #include "linefile.h"
 #include "dystring.h"
 #include "web.h"
 #include "hui.h"
 #include "hdb.h"
 #include "hgGene.h"
 #include "wikiTrack.h"
 
 
 struct link
 /* A link to another web site. */
     {
     struct link *next;	/* Next in list. */
     double priority;	/* Order to print in. */
     char *name;		/* Symbolic name. */
     char *shortLabel;	/* Short human-readable label. */
     char *idSql;	/* SQL to create ID. */
     char *nameSql;	/* SQL to create name. */
     char *nameFormat;	/* Text formatting for name. */
     char *url;		/* URL of link. */
     boolean useHgsid;	/* If true add hgsid to link. */
     boolean useDb;	/* If true add db= to link. */
     char *preCutAt;	/* String to chop at before sql. */
     char *postCutAt;	/* String to chop at after sql. */
     };
 
 static int linkCmpPriority(const void *va, const void *vb)
 /* Compare to sort links based on priority. */
 {
 const struct link *a = *((struct link **)va);
 const struct link *b = *((struct link **)vb);
 float dif = a->priority - b->priority;
 if (dif < 0)
     return -1;
 else if (dif > 0)
     return 1;
 else
     {
     return differentWord(b->shortLabel, a->shortLabel);
     }
 }
 
 static char *linkRequiredField(struct hash *hash, char *name)
 /* Return required field in link hash.  Squawk and die if it doesn't exist. */
 {
 char *s = hashFindVal(hash,name);
 if (s == NULL)
     errAbort("Couldn't find %s field in %s in links.ra", name, 
 	     (char *)hashFindVal(hash, "name"));
 return s;
 }
 
 static char *linkOptionalField(struct hash *hash, char *name)
 /* Return field in hash if it exists or NULL otherwise. */
 {
 return hashFindVal(hash, name);
 }
 
 static struct link *getLinkList(struct sqlConnection *conn,
 	char *raFile)
 /* Get list of links - starting with everything in .ra file,
  * and making sure any associated tables and databases exist. */
 {
 struct hash *ra, *raList = readRa(raFile, NULL);
 struct link *linkList = NULL, *link;
 for (ra = raList; ra != NULL; ra = ra->next)
     {
     if (linkOptionalField(ra, "hide") == NULL)
 	{
 	if (checkDatabases(linkOptionalField(ra, "databases")) 
 	    && sqlTablesExist(conn, linkOptionalField(ra, "tables")))
 	    {
 	    /* only include the wikiTrack if it is enabled */
 	    if (sameWord(linkRequiredField(ra, "name"), "wikiTrack") &&
 		! wikiTrackEnabled(database, NULL))
 		continue;
 	    AllocVar(link);
 	    link->priority = atof(linkRequiredField(ra, "priority"));
 	    link->name = linkRequiredField(ra, "name");
 	    link->shortLabel = linkRequiredField(ra, "shortLabel");
 	    link->idSql = linkRequiredField(ra, "idSql");
 	    link->nameSql = linkOptionalField(ra, "nameSql");
 	    link->nameFormat = linkOptionalField(ra, "nameFormat");
 	    link->url = linkRequiredField(ra, "url");
 	    link->useHgsid = (linkOptionalField(ra, "hgsid") != NULL);
 	    link->useDb = (linkOptionalField(ra, "dbInUrl") != NULL);
 	    link->preCutAt = linkOptionalField(ra, "preCutAt");
 	    link->postCutAt = linkOptionalField(ra, "postCutAt");
 	    slAddHead(&linkList, link);
 	    }
 	}
     }
 slSort(&linkList, linkCmpPriority);
 return linkList;
 }
 
 static char *cloneAndCut(char *s, char *cutAt)
 /* Return copy of string that may have stuff cut off end. */
 {
 char *clone = cloneString(s);
 if (cutAt != NULL)
     {
     char *end = stringIn(cutAt, clone);
     if (end != NULL)
 	*end = 0;
     }
 return clone;
 }
 
 static void addLinkExtras(struct link *link, struct dyString *dy)
 /* Add extra identifiers if specified in the .ra. */
 {
 if (link->useHgsid)
     dyStringPrintf(dy, "&%s", cartSidUrlString(cart));
 if (link->useDb)
     dyStringPrintf(dy, "&db=%s", database);
 }
 
 char *linkGetUrl(struct link *link, struct sqlConnection *conn,
 	char *geneId)
 /* Return URL string if possible or NULL if not.  FreeMem this when done. */
 {
 char query[512];
 struct sqlResult *sr;
 char **row;
 char *url = NULL;
 
 /* Some special case code here for things that need to
  * do more than check a table. */
 if (sameString(link->name, "family"))
     {
     if (!hgNearOk(database))
         return NULL;
     }
 if (sameString(link->name, "tbSchema"))
     {
     char *geneTable = genomeSetting("knownGene");
-    struct trackDb *tdb = hTrackDbForTrack(sqlGetDatabase(conn), geneTable);
+    struct trackDb *tdb = hTrackDbForTrack(database, geneTable);
     struct dyString *dy = NULL;
     if (tdb == NULL)
 	return NULL;
     dy = newDyString(256);
     dyStringPrintf(dy, link->url, tdb->grp, geneTable, geneTable);
     trackDbFree(&tdb);
     addLinkExtras(link, dy);
     return dyStringCannibalize(&dy);
     }
 geneId = cloneAndCut(geneId, link->preCutAt);
 sqlSafef(query, sizeof(query), link->idSql, geneId);
 
 sr = sqlGetResult(conn, query);
 row = sqlNextRow(sr);
 if (row != NULL && row[0][0] != 0) /* If not null or empty */
     {
     struct dyString *dy = newDyString(0);
     char *name = cloneAndCut(row[0], link->postCutAt);
     dyStringPrintf(dy, link->url, name, row[1], row[2], row[3]);
     addLinkExtras(link, dy);
     url = dyStringCannibalize(&dy);
     freez(&name);
     }
 sqlFreeResult(&sr);
 freeMem(geneId);
 return url;
 }
 
 char *linkGetName(struct link *link, struct sqlConnection *conn,
 	char *geneId)
 /* Return name string if possible or NULL if not. */
 {
 char *nameSql = link->nameSql;
 char *format = link->nameFormat;
 char query[512];
 struct sqlResult *sr;
 char **row;
 char *name = NULL;
 
 if (nameSql == NULL)
      nameSql = link->idSql;
 if (format == NULL)
      format = "%s";
 sqlSafef(query, sizeof(query), nameSql, geneId);
 sr = sqlGetResult(conn, query);
 row = sqlNextRow(sr);
 if (row != NULL)
     {
     char buf[256];
     safef(buf, sizeof(buf), format, row[0], row[1], row[2]);
     name = cloneString(buf);
     }
 sqlFreeResult(&sr);
 return name;
 }
 
 static boolean linksExists(struct section *section, 
 	struct sqlConnection *conn, char *geneId)
 /* Return TRUE if necessary database exists and has something
  * on this one. */
 {
 section->items = getLinkList(conn, section->raFile);
 return TRUE;
 }
 
 
 static void linksPrint(struct section *section, struct sqlConnection *conn,
 	char *geneId)
 /* Print the links section. */
 {
 int maxPerRow = 6, itemPos = 0;
 int rowIx = 0;
 struct link *link, *linkList = section->items;
 
 webPrintLinkTableStart();
 printGenomicSeqLink(conn, geneId, curGeneChrom, curGeneStart, curGeneEnd);
 printMrnaSeqLink(conn,geneId);
 printProteinSeqLink(conn,geneId);
 hPrintf("</TR>\n<TR>");
 ++rowIx;
 
 for (link = linkList; link != NULL; link = link->next)
     {
     char *url = linkGetUrl(link, conn, geneId);
     if (url != NULL)
 	{
 	boolean fakeOut = link->useHgsid &&
 		differentWord(link->name,"wikiTrack");
 	char *target = (fakeOut ? "" : " TARGET=_blank");
 	if (++itemPos > maxPerRow)
 	    {
 	    hPrintf("</TR>\n<TR>");
 	    itemPos = 1;
 	    ++rowIx;
 	    }
 	if (fakeOut)
 	    webPrintLinkCellStart();
 	else
 	    webPrintLinkOutCellStart();
 	hPrintf("<A HREF=\"%s\"%s class=\"toc\">", url, target);
 	hPrintf("%s", link->shortLabel);
 	hPrintf("</A>");
 	webPrintLinkCellEnd();
 	freez(&url);
 	}
     }
 webFinishPartialLinkOutTable(rowIx, itemPos, maxPerRow);
 webPrintLinkTableEnd();
 }
 
 struct section *linksSection(struct sqlConnection *conn,
 	struct hash *sectionRa)
 /* Create links section. */
 {
 struct section *section = sectionNew(sectionRa, "links");
 section->exists = linksExists;
 section->print = linksPrint;
 section->raFile = "links.ra";
 return section;
 }