src/hg/makeDb/metaTblUpdate/metaTblPrint.c 1.6
1.6 2010/03/31 23:47:03 tdreszer
Discover metaTbl name if not provided. Prefer sandBox version.
Index: src/hg/makeDb/metaTblUpdate/metaTblPrint.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/metaTblUpdate/metaTblPrint.c,v
retrieving revision 1.5
retrieving revision 1.6
diff -b -B -U 1000000 -r1.5 -r1.6
--- src/hg/makeDb/metaTblUpdate/metaTblPrint.c 30 Mar 2010 23:45:15 -0000 1.5
+++ src/hg/makeDb/metaTblUpdate/metaTblPrint.c 31 Mar 2010 23:47:03 -0000 1.6
@@ -1,190 +1,200 @@
/* metaTblPrint - Prints metadata objects and variables from the metaTbl. */
#include "common.h"
#include "linefile.h"
#include "options.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 '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=] [-byVar] [-ra/-countObjs/-countVarss/-countVals]\n"
" [-all]\n"
" [-obj= [-var= [-val=]]]\n"
" [-var= [-val=]]\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"
" -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"
" -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"
{"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);
+char *table = optionVal("table",NULL);
boolean raStyle = optionExists("ra");
boolean cntObjs = optionExists("countObjs");
boolean cntVars = optionExists("countVars");
boolean cntVals = optionExists("countVals");
boolean byVar = optionExists("byVar");
if(raStyle && (cntObjs || cntVars || cntVals))
usage();
boolean all = optionExists("all");
if(all)
{
if(optionExists("obj")
|| optionExists("var") || optionExists("val") || optionExists("vars"))
usage();
}
else if(optionExists("obj"))
{
metaObjs = metaObjCreate(optionVal("obj", NULL),NULL,optionVal("var", NULL), NULL,optionVal("val", NULL));
}
else if(optionExists("var"))
{
metaByVars = metaByVarCreate(optionVal("var", NULL),NULL,optionVal("val", NULL));
}
else if(optionExists("vars"))
{
metaByVars = metaByVarsLineParse(optionVal("vars", NULL));
}
else
usage();
struct sqlConnection *conn = sqlConnect(db);
+
+// Find the table if necessary
+if(table == NULL)
+ {
+ table = metaTblName(conn,TRUE); // Look for sandBox name first
+ if(table == NULL)
+ errAbort("TABLE NOT FOUND: '%s.%s'.\n",db,METATBL_DEFAULT_NAME);
+ verbose(1, "Using table named '%s.%s'.\n",db,table);
+ }
+
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,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,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;
}