src/hg/makeDb/metaTblUpdate/metaTblPrint.c 1.5
1.5 2010/03/30 23:45:15 tdreszer
Better handling of RA style files and extension to select by 'vars'.
Index: src/hg/makeDb/metaTblUpdate/metaTblPrint.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/metaTblUpdate/metaTblPrint.c,v
retrieving revision 1.4
retrieving revision 1.5
diff -b -B -U 1000000 -r1.4 -r1.5
--- src/hg/makeDb/metaTblUpdate/metaTblPrint.c 25 Mar 2010 21:56:41 -0000 1.4
+++ src/hg/makeDb/metaTblUpdate/metaTblPrint.c 30 Mar 2010 23:45:15 -0000 1.5
@@ -1,200 +1,190 @@
/* metaTblPrint - Prints 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 OBJTYPE_DEFAULT "table"
void usage()
/* Explain usage and exit. */
{
errAbort(
"metaTblPrint - Prints metadata objects and variables from the metaTbl.\n\n"
"There are two basic views of the data: by objects and by variables. Unless a single variable "
"and no object is requested the default view is by object. Each line of output will contain "
- "object and all it's var=val pairs as 'formatted metadata' line. In var view, a single line "
- "per var=val and then a space seprated list of each obj(type) follows. Long view will place "
- "each object and var=val on a separate line with tab indentation. Alternatively, count will "
+ "object and all it's var=val pairs as 'formatted metadata' line. In 'byVar' view, a single line "
+ "per var=val and then a space seperated list of each obj(type) follows. RA style will place "
+ "each object and var val on a separate line with indentation. Alternatively, count will "
"return a count of unique obj var=val combinations. It is also possible to select a "
"combination of vars by entering a string of var=val pairs.\n\n"
"usage:\n"
- " metaTblPrint -db= [-table=] [-long/-countObjs/-countVarss/-countVals]\n"
- " [-all [-byVar]]\n"
- " [-obj=] [-var= [-val=]]]\n"
+ " metaTblPrint -db= [-table=] [-byVar] [-ra/-countObjs/-countVarss/-countVals]\n"
+ " [-all]\n"
+ " [-obj= [-var= [-val=]]]\n"
" [-var= [-val=]]\n"
- " [-vars=\"var1=val1 var2=val2...\" [-byVar]]\n\n"
+ " [-vars=\"var1=val1 var2=val2...]\n\n"
"Options:\n"
" -db Database to query. This argument is required.\n"
" -table Table to query. Default is '" METATBL_DEFAULT_NAME "'.\n"
- " -long Print each obj, var=val as separate line.\n"
+ " -byVar Print each var and val, then all objects that match,\n"
+ " as opposed to printing objects and all the var=val pairs that match.\n"
+ " -ra Print each obj with a set of indented var val pairs on separate lines.\n"
+ " With -byVar prints pseudo-RA style with 2 levels of indentation (not val obj pairs).\n"
" -countObjs Just print count of objects returned in the query.\n"
" -countVars Just print count of variables returned in the query.\n"
" -countVals Just print count of values returned in the query.\n"
" Four alternate ways to select metadata:\n"
" -all Will print entire table (this could be huge).\n"
- " -byVar Print which objects belong to which var=val pairs.\n"
" -obj={objName} Request a single object. The request can be further narrowed by var and val.\n"
" -var={varName} Request a single variable. The request can be further narrowed by val.\n"
" -vars={var=val...} Request a combination of var=val pairs.\n"
"Examples:\n"
" metaTblPrint -vars=\"grant=Snyder cell=GM12878 antibody=CTCF\"\n"
" Return all objs that satify ALL of the constraints.\n"
" metaTblPrint -byVar -vars=\"grant=Snyder cell=GM12878 antibody=CTCF\"\n"
" Return each var=val pair and ANY objects that have any constraint.\n"
" metaTblPrint -db=hg18 -obj=wgEncodeUncFAIREseqPeaksPanislets\n"
" Return the formatted metadata line for the one object.\n"
" metaTblPrint -countObjs -var=treatment\n"
" Return the count of objects which have a declared treatment.\n"
);
}
static struct optionSpec optionSpecs[] = {
{"db", OPTION_STRING}, // default "hg19"
{"table", OPTION_STRING}, // default "metaTbl"
- {"long", OPTION_BOOLEAN},// long format
+ {"ra", OPTION_BOOLEAN},// ra format
{"countObjs",OPTION_BOOLEAN},// returns only count of objects
{"countVars",OPTION_BOOLEAN},// returns only count of variables
{"countVals",OPTION_BOOLEAN},// returns only count of values
{"all", OPTION_BOOLEAN},// query entire table
{"byVar", OPTION_BOOLEAN},// With -all prints from var perspective
{"obj", OPTION_STRING}, // objName or objId
{"var", OPTION_STRING}, // variable
{"val", OPTION_STRING}, // value
{"vars", OPTION_STRING},// var1=val1 var2=val2...
{NULL, 0}
};
int main(int argc, char *argv[])
// Process command line.
{
struct metaObj * metaObjs = NULL;
struct metaByVar * metaByVars = NULL;
int objsCnt=0, varsCnt=0,valsCnt=0;
optionInit(&argc, argv, optionSpecs);
if(!optionExists("db"))
+ {
+ verbose(1, "REQUIRED -db argument is missing.\n");
usage();
+ }
char *db = optionVal("db",NULL);
char *table = optionVal("table",METATBL_DEFAULT_NAME);
-boolean printLong = optionExists("long");
+boolean raStyle = optionExists("ra");
boolean cntObjs = optionExists("countObjs");
boolean cntVars = optionExists("countVars");
boolean cntVals = optionExists("countVals");
-boolean byVar = FALSE;
+boolean byVar = optionExists("byVar");
-if(printLong && (cntObjs || cntVars || cntVals))
+if(raStyle && (cntObjs || cntVars || cntVals))
usage();
boolean all = optionExists("all");
if(all)
{
if(optionExists("obj")
|| optionExists("var") || optionExists("val") || optionExists("vars"))
usage();
-
- byVar = optionExists("byVar");
}
else if(optionExists("obj"))
{
- byVar = FALSE;
metaObjs = metaObjCreate(optionVal("obj", NULL),NULL,optionVal("var", NULL), NULL,optionVal("val", NULL));
}
else if(optionExists("var"))
{
- byVar = TRUE;
metaByVars = metaByVarCreate(optionVal("var", NULL),NULL,optionVal("val", NULL));
}
else if(optionExists("vars"))
{
- byVar = optionExists("byVar");
metaByVars = metaByVarsLineParse(optionVal("vars", NULL));
}
else
usage();
struct sqlConnection *conn = sqlConnect(db);
if(byVar)
{
if(!all && metaByVars == NULL) // assertable
usage();
// Requested a single var
struct metaByVar * queryResults = metaByVarsQuery(conn,table,metaByVars);
if(queryResults == NULL)
verbose(1, "No metadata met your selection criteria\n");
else
{
objsCnt=metaByVarCount(queryResults,FALSE,FALSE);
varsCnt=metaByVarCount(queryResults,TRUE ,FALSE);
valsCnt=metaByVarCount(queryResults,FALSE,TRUE );
if(!cntObjs && !cntVars && !cntVals)
- metaByVarPrint(queryResults,printLong);
+ metaByVarPrint(queryResults,raStyle);
metaByVarsFree(&queryResults);
}
}
else
{
struct metaObj * queryResults = NULL;
if(metaByVars != NULL)
{
// Requested a set of var=val pairs and looking for the unique list of objects that have all of them!
queryResults = metaObjsQueryByVars(conn,table,metaByVars);
}
else
{
// Requested a single obj
queryResults = metaObjQuery(conn,table,metaObjs);
}
if(queryResults == NULL)
verbose(1, "No metadata met your selection criteria\n");
else
{
objsCnt=metaObjCount(queryResults,TRUE);
varsCnt=metaObjCount(queryResults,FALSE);
valsCnt=varsCnt;
if(!cntObjs && !cntVars && !cntVals)
- metaObjPrint(queryResults,printLong);
+ metaObjPrint(queryResults,raStyle);
metaObjsFree(&queryResults);
}
}
sqlDisconnect(&conn);
if(cntObjs || cntVars || cntVals)
{
if(cntObjs)
printf("%d objects\n",objsCnt);
if(cntVars)
printf("%d variable\n",varsCnt);
if(cntVals)
printf("%d values\n",valsCnt);
}
else if( varsCnt>0 || valsCnt>0 || objsCnt>0 )
{
if(byVar)
verbose(1,"vars:%d vals:%d objects:%d\n",varsCnt,valsCnt,objsCnt);
else
verbose(1,"objects:%d vars:%d\n",objsCnt,varsCnt);
}
if(metaObjs)
metaObjsFree(&metaObjs);
if(metaByVars)
metaByVarsFree(&metaByVars);
return 0;
}