7e5c73375ec879890233ed77f22a52fb2f82d9ba
angie
  Wed Jan 27 13:48:51 2016 -0800
Adding taxId column to dbDb.{as,c,h,sql} -- the column seems to have been
in our dbDb tables for years, just not in these files.

diff --git src/hg/lib/dbDb.c src/hg/lib/dbDb.c
index e437aac..3e512ec 100644
--- src/hg/lib/dbDb.c
+++ src/hg/lib/dbDb.c
@@ -1,202 +1,210 @@
 /* dbDb.c was originally generated by the autoSql program, which also 
  * generated dbDb.h and dbDb.sql.  This module links the database and
  * the RAM representation of objects. */
 
-/* Copyright (C) 2014 The Regents of the University of California 
+/* Copyright (C) 2004, 2016 The Regents of the University of California
  * See README in this or parent directory for licensing information. */
 
 #include "common.h"
 #include "linefile.h"
 #include "dystring.h"
 #include "jksql.h"
 #include "dbDb.h"
 
 
+
+char *dbDbCommaSepFieldNames = "name,description,nibPath,organism,defaultPos,active,orderKey,genome,scientificName,htmlPath,hgNearOk,hgPbOk,sourceName,taxId";
+
 void dbDbStaticLoad(char **row, struct dbDb *ret)
 /* Load a row from dbDb table into ret.  The contents of ret will
  * be replaced at the next call to this function. */
 {
 
 ret->name = row[0];
 ret->description = row[1];
 ret->nibPath = row[2];
 ret->organism = row[3];
 ret->defaultPos = row[4];
 ret->active = sqlSigned(row[5]);
 ret->orderKey = sqlSigned(row[6]);
 ret->genome = row[7];
 ret->scientificName = row[8];
 ret->htmlPath = row[9];
 ret->hgNearOk = sqlSigned(row[10]);
 ret->hgPbOk = sqlSigned(row[11]);
 ret->sourceName = row[12];
+ret->taxId = sqlSigned(row[13]);
 }
 
 struct dbDb *dbDbLoad(char **row)
 /* Load a dbDb from row fetched with select * from dbDb
  * from database.  Dispose of this with dbDbFree(). */
 {
 struct dbDb *ret;
 
 AllocVar(ret);
 ret->name = cloneString(row[0]);
 ret->description = cloneString(row[1]);
 ret->nibPath = cloneString(row[2]);
 ret->organism = cloneString(row[3]);
 ret->defaultPos = cloneString(row[4]);
 ret->active = sqlSigned(row[5]);
 ret->orderKey = sqlSigned(row[6]);
 ret->genome = cloneString(row[7]);
 ret->scientificName = cloneString(row[8]);
 ret->htmlPath = cloneString(row[9]);
 ret->hgNearOk = sqlSigned(row[10]);
 ret->hgPbOk = sqlSigned(row[11]);
 ret->sourceName = cloneString(row[12]);
+ret->taxId = sqlSigned(row[13]);
 return ret;
 }
 
 struct dbDb *dbDbLoadAll(char *fileName) 
 /* Load all dbDb from a whitespace-separated file.
  * Dispose of this with dbDbFreeList(). */
 {
 struct dbDb *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
-char *row[13];
+char *row[14];
 
 while (lineFileRow(lf, row))
     {
     el = dbDbLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct dbDb *dbDbLoadAllByChar(char *fileName, char chopper) 
 /* Load all dbDb from a chopper separated file.
  * Dispose of this with dbDbFreeList(). */
 {
 struct dbDb *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
-char *row[13];
+char *row[14];
 
 while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
     {
     el = dbDbLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct dbDb *dbDbCommaIn(char **pS, struct dbDb *ret)
 /* Create a dbDb out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new dbDb */
 {
 char *s = *pS;
 
 if (ret == NULL)
     AllocVar(ret);
 ret->name = sqlStringComma(&s);
 ret->description = sqlStringComma(&s);
 ret->nibPath = sqlStringComma(&s);
 ret->organism = sqlStringComma(&s);
 ret->defaultPos = sqlStringComma(&s);
 ret->active = sqlSignedComma(&s);
 ret->orderKey = sqlSignedComma(&s);
 ret->genome = sqlStringComma(&s);
 ret->scientificName = sqlStringComma(&s);
 ret->htmlPath = sqlStringComma(&s);
 ret->hgNearOk = sqlSignedComma(&s);
 ret->hgPbOk = sqlSignedComma(&s);
 ret->sourceName = sqlStringComma(&s);
+ret->taxId = sqlSignedComma(&s);
 *pS = s;
 return ret;
 }
 
 void dbDbFree(struct dbDb **pEl)
 /* Free a single dynamically allocated dbDb such as created
  * with dbDbLoad(). */
 {
 struct dbDb *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->name);
 freeMem(el->description);
 freeMem(el->nibPath);
 freeMem(el->organism);
 freeMem(el->defaultPos);
 freeMem(el->genome);
 freeMem(el->scientificName);
 freeMem(el->htmlPath);
 freeMem(el->sourceName);
 freez(pEl);
 }
 
 void dbDbFreeList(struct dbDb **pList)
 /* Free a list of dynamically allocated dbDb's */
 {
 struct dbDb *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     dbDbFree(&el);
     }
 *pList = NULL;
 }
 
 void dbDbOutput(struct dbDb *el, FILE *f, char sep, char lastSep) 
 /* Print out dbDb.  Separate fields with sep. Follow last field with lastSep. */
 {
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->name);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->description);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->nibPath);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->organism);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->defaultPos);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%d", el->active);
 fputc(sep,f);
 fprintf(f, "%d", el->orderKey);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->genome);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->scientificName);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->htmlPath);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%d", el->hgNearOk);
 fputc(sep,f);
 fprintf(f, "%d", el->hgPbOk);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->sourceName);
 if (sep == ',') fputc('"',f);
+fputc(sep,f);
+fprintf(f, "%d", el->taxId);
 fputc(lastSep,f);
 }
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */