060ada2535fca719656219c1214a3e1c16490693
tdreszer
  Wed Nov 9 16:06:41 2011 -0800
Moved as code in hgTables down to lib and access it from hgc and hgTrackUi.  This is to remove 'extraFields' support as per Jim's request in redmine 5883 and 5582
diff --git src/hg/lib/makeItemsItem.c src/hg/lib/makeItemsItem.c
index ea9817e..3c1f7b3 100644
--- src/hg/lib/makeItemsItem.c
+++ src/hg/lib/makeItemsItem.c
@@ -1,262 +1,268 @@
 /* makeItemsItem.c was originally generated by the autoSql program, which also 
  * generated makeItemsItem.h and makeItemsItem.sql.  This module links the database and
  * the RAM representation of objects. */
 
 #include "common.h"
 #include "linefile.h"
 #include "dystring.h"
 #include "jksql.h"
 #include "makeItemsItem.h"
 
 static char const rcsid[] = "$Id: makeItemsItem.c,v 1.6 2010/04/11 21:54:51 kent Exp $";
 
 void makeItemsItemStaticLoad(char **row, struct makeItemsItem *ret)
 /* Load a row from makeItemsItem table into ret.  The contents of ret will
  * be replaced at the next call to this function. */
 {
 
 ret->bin = sqlUnsigned(row[0]);
 ret->chrom = row[1];
 ret->chromStart = sqlUnsigned(row[2]);
 ret->chromEnd = sqlUnsigned(row[3]);
 ret->name = row[4];
 ret->score = sqlUnsigned(row[5]);
 safecpy(ret->strand, sizeof(ret->strand), row[6]);
 ret->thickStart = sqlUnsigned(row[7]);
 ret->thickEnd = sqlUnsigned(row[8]);
 ret->itemRgb = sqlUnsigned(row[9]);
 ret->description = row[10];
 ret->id = sqlUnsigned(row[11]);
 }
 
 struct makeItemsItem *makeItemsItemLoadByQuery(struct sqlConnection *conn, char *query)
 /* Load all makeItemsItem from table that satisfy the query given.  
  * Where query is of the form 'select * from example where something=something'
  * or 'select example.* from example, anotherTable where example.something = 
  * anotherTable.something'.
  * Dispose of this with makeItemsItemFreeList(). */
 {
 struct makeItemsItem *list = NULL, *el;
 struct sqlResult *sr;
 char **row;
 
 sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     el = makeItemsItemLoad(row);
     slAddHead(&list, el);
     }
 slReverse(&list);
 sqlFreeResult(&sr);
 return list;
 }
 
 void makeItemsItemSaveToDb(struct sqlConnection *conn, struct makeItemsItem *el, char *tableName, int updateSize)
 /* Save makeItemsItem as a row to the table specified by tableName. 
  * As blob fields may be arbitrary size updateSize specifies the approx size
  * of a string that would contain the entire query. Arrays of native types are
  * converted to comma separated strings and loaded as such, User defined types are
  * inserted as NULL. Note that strings must be escaped to allow insertion into the database.
  * For example "autosql's features include" --> "autosql\'s features include" 
  * If worried about this use makeItemsItemSaveToDbEscaped() */
 {
 struct dyString *update = newDyString(updateSize);
 dyStringPrintf(update, "insert into %s values ( %u,'%s',%u,%u,'%s',%u,'%s',%u,%u,%u,%s,%u)", 
 	tableName,  el->bin,  el->chrom,  el->chromStart,  el->chromEnd,  el->name,  el->score,  el->strand,  el->thickStart,  el->thickEnd,  el->itemRgb,  el->description,  el->id);
 sqlUpdate(conn, update->string);
 freeDyString(&update);
 }
 
 void makeItemsItemSaveToDbEscaped(struct sqlConnection *conn, struct makeItemsItem *el, char *tableName, int updateSize)
 /* Save makeItemsItem as a row to the table specified by tableName. 
  * As blob fields may be arbitrary size updateSize specifies the approx size.
  * of a string that would contain the entire query. Automatically 
  * escapes all simple strings (not arrays of string) but may be slower than makeItemsItemSaveToDb().
  * For example automatically copies and converts: 
  * "autosql's features include" --> "autosql\'s features include" 
  * before inserting into database. */ 
 {
 struct dyString *update = newDyString(updateSize);
 char  *chrom, *name, *strand, *description;
 chrom = sqlEscapeString(el->chrom);
 name = sqlEscapeString(el->name);
 strand = sqlEscapeString(el->strand);
 description = sqlEscapeString(el->description);
 
 dyStringPrintf(update, "insert into %s values ( %u,'%s',%u,%u,'%s',%u,'%s',%u,%u,%u,'%s',%u)", 
 	tableName,  el->bin,  chrom,  el->chromStart,  el->chromEnd,  name,  el->score,  strand,  el->thickStart,  el->thickEnd,  el->itemRgb,  description,  el->id);
 sqlUpdate(conn, update->string);
 freeDyString(&update);
 freez(&chrom);
 freez(&name);
 freez(&strand);
 freez(&description);
 }
 
 struct makeItemsItem *makeItemsItemLoad(char **row)
 /* Load a makeItemsItem from row fetched with select * from makeItemsItem
  * from database.  Dispose of this with makeItemsItemFree(). */
 {
 struct makeItemsItem *ret;
 
 AllocVar(ret);
 ret->bin = sqlUnsigned(row[0]);
 ret->chrom = cloneString(row[1]);
 ret->chromStart = sqlUnsigned(row[2]);
 ret->chromEnd = sqlUnsigned(row[3]);
 ret->name = cloneString(row[4]);
 ret->score = sqlUnsigned(row[5]);
 safecpy(ret->strand, sizeof(ret->strand), row[6]);
 ret->thickStart = sqlUnsigned(row[7]);
 ret->thickEnd = sqlUnsigned(row[8]);
 ret->itemRgb = sqlUnsigned(row[9]);
 ret->description = cloneString(row[10]);
 ret->id = sqlUnsigned(row[11]);
 return ret;
 }
 
 struct makeItemsItem *makeItemsItemLoadAll(char *fileName) 
 /* Load all makeItemsItem from a whitespace-separated file.
  * Dispose of this with makeItemsItemFreeList(). */
 {
 struct makeItemsItem *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[12];
 
 while (lineFileRow(lf, row))
     {
     el = makeItemsItemLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct makeItemsItem *makeItemsItemLoadAllByChar(char *fileName, char chopper) 
 /* Load all makeItemsItem from a chopper separated file.
  * Dispose of this with makeItemsItemFreeList(). */
 {
 struct makeItemsItem *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[12];
 
 while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
     {
     el = makeItemsItemLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct makeItemsItem *makeItemsItemCommaIn(char **pS, struct makeItemsItem *ret)
 /* Create a makeItemsItem out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new makeItemsItem */
 {
 char *s = *pS;
 
 if (ret == NULL)
     AllocVar(ret);
 ret->bin = sqlUnsignedComma(&s);
 ret->chrom = sqlStringComma(&s);
 ret->chromStart = sqlUnsignedComma(&s);
 ret->chromEnd = sqlUnsignedComma(&s);
 ret->name = sqlStringComma(&s);
 ret->score = sqlUnsignedComma(&s);
 sqlFixedStringComma(&s, ret->strand, sizeof(ret->strand));
 ret->thickStart = sqlUnsignedComma(&s);
 ret->thickEnd = sqlUnsignedComma(&s);
 ret->itemRgb = sqlUnsignedComma(&s);
 ret->description = sqlStringComma(&s);
 ret->id = sqlUnsignedComma(&s);
 *pS = s;
 return ret;
 }
 
 void makeItemsItemFree(struct makeItemsItem **pEl)
 /* Free a single dynamically allocated makeItemsItem such as created
  * with makeItemsItemLoad(). */
 {
 struct makeItemsItem *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->chrom);
 freeMem(el->name);
 freeMem(el->description);
 freez(pEl);
 }
 
 void makeItemsItemFreeList(struct makeItemsItem **pList)
 /* Free a list of dynamically allocated makeItemsItem's */
 {
 struct makeItemsItem *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     makeItemsItemFree(&el);
     }
 *pList = NULL;
 }
 
 void makeItemsItemOutput(struct makeItemsItem *el, FILE *f, char sep, char lastSep) 
 /* Print out makeItemsItem.  Separate fields with sep. Follow last field with lastSep. */
 {
 fprintf(f, "%u", el->bin);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->chrom);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%u", el->chromStart);
 fputc(sep,f);
 fprintf(f, "%u", el->chromEnd);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->name);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%u", el->score);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->strand);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%u", el->thickStart);
 fputc(sep,f);
 fprintf(f, "%u", el->thickEnd);
 fputc(sep,f);
 fprintf(f, "%u", el->itemRgb);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->description);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%u", el->id);
 fputc(lastSep,f);
 }
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */
 
-char *makeItemsItemAutoSqlString = 
+static char *makeItemsItemAutoSqlString =
 "table makeItemsItem\n"
 "\"An item in a makeItems type track.\"\n"
 "    (\n"
 "    uint bin;	       \"Bin for range index\"\n"
 "    string chrom;      \"Reference sequence chromosome or scaffold\"\n"
 "    uint   chromStart; \"Start position in chromosome\"\n"
 "    uint   chromEnd;   \"End position in chromosome\"\n"
 "    string name;       \"Name of item - up to 16 chars\"\n"
 "    uint  score;	\"0-1000.  Higher numbers are darker.\"\n"
 "    char[1] strand;     \"+ or - for strand\"\n"
 "    uint   thickStart; \"Start of thick part\"\n"
 "    uint   thickEnd;   \"End position of thick part\"\n"
 "    uint itemRgb;	\"RGB 8 bits each as in bed\"\n"
 "    lstring description; \"Longer item description\"\n"
 "    uint id;		\"Unique ID for item\"\n"
 "    )\n"
    ;
 
+struct asObject *makeItemsItemAsObj()
+// Return asObject describing fields of makeItemsItem
+{
+return asParseText(makeItemsItemAutoSqlString);
+}
+