src/hg/makeDb/metaTblUpdate/metaTblUpdate.c 1.4

Index: src/hg/makeDb/metaTblUpdate/metaTblUpdate.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/metaTblUpdate/metaTblUpdate.c,v
retrieving revision 1.3
retrieving revision 1.4
diff -b -B -U 1000000 -r1.3 -r1.4
--- src/hg/makeDb/metaTblUpdate/metaTblUpdate.c	19 Mar 2010 17:36:50 -0000	1.3
+++ src/hg/makeDb/metaTblUpdate/metaTblUpdate.c	19 Mar 2010 21:25:15 -0000	1.4
@@ -1,132 +1,129 @@
 /* metaTblUpdate - Adds, updates or removes metadata objects and variables from the metaTbl. */
 #include "common.h"
 #include "linefile.h"
 #include "hash.h"
 #include "options.h"
 #include "sqlList.h"
 #include "jksql.h"
 #include "trackDb.h"
 #include "hui.h"
 #include "hdb.h"
 #include "hVarSubst.h"
 #include "obscure.h"
 #include "portable.h"
 #include "dystring.h"
 #include "metaTbl.h"
 
 static char const rcsid[] = "$Id$";
 
 #define DB_DEFAULT      "hg19"
 #define OBJTYPE_DEFAULT "table"
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "metaTblUpdate - Adds, updates or removes metadata objects and variables from the metaTbl.\n\n"
   "There are two ways to call this.  A single object/variable can be declared on the command "
   "line, or a file of formatted metadata lines can be provided.  The lines in the file can "
   "have the following formats:\n"
   "  metadata objName objType var1=val1 var2=\"val2 with spaces\" var3=...\n"
   "    Adds or updates the specific object and variables\n"
   "  metadata objName delete\n"
   "    delete all metadata for objName\n"
   "  metadata objName delete var=val var2=val2\n"
   "     deletes specifically named variables for objName. Must provide val but value is ignored.\n"
   "Special ENCODE format:"
   "  metadata var=val var2=\"val2 with spaces\" tableName=someTable fileName=someTable.narrowPeak.gz\n"
   "    if tableName and fileName and tableName=fileName.* then objName=someTable and objType=table.\n"
   "    else if tableName or fileName load as table or file\n\n"
   "usage:\n"
   "   metaTblUpdate [-db=] [-table=] [-obj= [-type=] [-delete] [-var=] [-binary] [-val=]]\n"
   "                       [-replace] [fileName]\n\n"
   "Options:\n"
   "    -db      Database to load metadata to.  Default is '" DB_DEFAULT "'.\n"
   "    -table   Table to load metadata to.  Default is '" METATBL_DEFAULT_NAME "'.\n"
   "  if file not provided, then -obj must be provided\n"
   "    -obj={objName}     Means Load from command line:\n"
   "       -type={objType} Used if adding new obj, otherwise ignored.  Default is '" OBJTYPE_DEFAULT "'.\n"
   "       -delete         Remove a specific var or entire obj (if -var not provided) otherwise add or update\n"
   "       -var={varName}  Provide variable name (if no -var then must be -remove to remove obj)\n"
   "       -binary         NOT YET IMPLEMENTED.  This var has a binary val and -val={file}\n"
   "       -val={value}    (Enclosed in \"quotes if necessary\".) If -var and no -val then must be -remove\n"
   "    [file]       File containing formatted metadata lines.  Ignored if -obj param provided:\n"
   "      -replace   Means remove all old variables for an object before adding new variables\n"
   );
 }
 
 static struct optionSpec optionSpecs[] = {
     {"db",      OPTION_STRING}, // default "hg19"
     {"table",   OPTION_STRING}, // default "metaTbl"
     {"obj",     OPTION_STRING}, // objName or objId
     {"type",    OPTION_STRING}, // object type: table or file
     {"var",     OPTION_STRING}, // variable
     {"val",     OPTION_STRING}, // value
     {"delete",  OPTION_BOOLEAN},// delete one obj or obj/var
     {"binary",  OPTION_BOOLEAN},// val is binary (NOT YET IMPLEMENTED) implies -val={file}
     {"replace", OPTION_BOOLEAN},// replace entire obj when loading from file
     {NULL,      0}
 };
 
 
 int main(int argc, char *argv[])
 // Process command line.
 {
 struct metaObj * metaObjs = NULL;
 
 optionInit(&argc, argv, optionSpecs);
 char *db    = optionVal("db",   DB_DEFAULT);
 char *table = optionVal("table",METATBL_DEFAULT_NAME);
 boolean replace = FALSE;
 
 if(optionExists("obj"))
     {
     if(argc > 1)
         usage(); // Must not have submitted formatted file also
 
     if(optionExists("delete") && optionExists("var") && optionExists("val"))
         usage();
 
     if (!optionExists("delete") && (!optionExists("var") || !optionExists("val")))
         usage();
 
     metaObjs = metaObjCreate(optionVal("obj",  NULL),
                              optionVal("type", OBJTYPE_DEFAULT),
                              optionVal("var", NULL),
                             (optionExists("binary") ? "binary" : "txt"), // FIXME: don't know how to deal with binary yet
                              optionVal("val", NULL));
 
     metaObjs->deleteThis = optionExists("delete");
 
     verbose(2, "metadata %s %s %s%s%s%s\n",
         metaObjs->objName,metaObjTypeEnumToString(metaObjs->objType),
         (metaObjs->deleteThis ? "delete ":""),
         (metaObjs->vars && metaObjs->vars->var!=NULL?metaObjs->vars->var:""),
         (metaObjs->vars && metaObjs->vars->val!=NULL?"=":""),
         (metaObjs->vars && metaObjs->vars->val!=NULL?metaObjs->vars->val:""));
     }
 else // Must be submitting formatted file
     {
     if(argc != 2)
         usage();
 
     replace = optionExists("replace");
 
     metaObjs = metaObjsLoadFromFormattedFile(argv[1]);
     if(metaObjs != NULL)
         verbose(1, "Read %d metadata lines from %s\n", slCount(metaObjs),argv[1]);
     }
 
 if(metaObjs == NULL)
     usage();
 
-struct sqlConnection *conn = sqlConnect(db);
-
-int count = metaObjsSetToDb(conn,table,metaObjs,replace);
+int count = metaObjsSetToDb(db,table,metaObjs,replace);
 
 verbose(1, "Affected %d row(s) in %s.%s\n", count,db,table);
 
 metaObjsFree(&metaObjs);
-sqlDisconnect(&conn);
 return 0;
 }