6d140e6f65c1491b7f6ae406bc4f0acf82cc41d1
kent
  Wed Feb 15 12:07:25 2017 -0800
Making it accept wildcards in field list.

diff --git src/utils/tabQuery/tabQuery.c src/utils/tabQuery/tabQuery.c
index 3899f10..4aed2d0 100644
--- src/utils/tabQuery/tabQuery.c
+++ src/utils/tabQuery/tabQuery.c
@@ -1,141 +1,157 @@
 /* tabQuery - Run sql-like query on a tab separated file.. */
 #include "common.h"
 #include "linefile.h"
 #include "hash.h"
 #include "localmem.h"
 #include "dystring.h"
 #include "fieldedTable.h"
 #include "rql.h"
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "tabQuery - Run sql-like query on a tab separated file.\n"
   "usage:\n"
   "   tabQuery rqlStatement\n"
   "where rqlStatement is much like a SQL statement, but with no joins and no commands\n"
   "other than select allowed.  The input file name is taken from the 'from' clause.\n"
   "examples\n"
   "    tabQuery select file,date from manifest.tsv\n"
   "This will output the file and date fields from the manifest.tsv file\n"
   "    tabQuery select file,date,lab from manifest.tsv where lab like 'myLab%%'\n"
   "This will output the selected three fields from the file where the lab starts with myLab\n"
   "    tabQuery select file,data from manifest.tsv where lab='myLab'\n"
   "This will output the selected two fields where the lab field is exactly myLab.\n"
-  "This will output the file and date fields from the manifest.tsv file\n"
+  "    tabQuery select * from manifest.tsv where lab='myLab'\n"
+  "This will output all fields where the lab field is exactly myLab.\n"
+  "    tabQuery select a*,b* from manifest.tsv where lab='myLab'\n"
+  "This will output all fields starting with a or b where the lab field is exactly myLab.\n"
   "    tabQuery select count(*) from manifest.tsv where type='fastq' and size < 1000\n"
   "This will count the number of records where type is fastq and size less than 1000\n"
   );
 }
 
 struct fieldedTable *gTable;
 struct hash *gFieldHash;
 
 char *lookup(void *record, char *key)
 /* Lookup key in record */
 {
 struct fieldedRow *row = record;
 int fieldIx = hashIntValDefault(gFieldHash, key, -1);
 if (fieldIx < 0)
     errAbort("Field %s isn't found in %s", key, gTable->name);
 return row->row[fieldIx];
 }
 
 void tabQuery(char *query)
 /* tabQuery - Run sql-like query on a tab separated file.. */
 {
 /* Parse statement and make sure that it just references one table */
 struct rqlStatement *rql = rqlStatementParseString(query);
 int tableCount = slCount(rql->tableList);
 if (tableCount != 1)
     errAbort("One and only one file allowed in the from clause\n");
 
 boolean doCount = FALSE;
 if (sameWord(rql->command, "count"))
     doCount = TRUE;
 else if (sameWord(rql->command, "select"))
     doCount = FALSE;
 else
     errAbort("Unrecognized rql command %s", rql->command);
 
 /* Read in tab separated value file */
 char *tabFile = rql->tableList->name;
 gTable = fieldedTableFromTabFile(tabFile, tabFile, NULL, 0);
 
 /* Make an integer valued hash of field indexes */
 gFieldHash = hashNew(0);
 int i;
 for (i=0; i<gTable->fieldCount; ++i)
     hashAddInt(gFieldHash, gTable->fields[i], i);
 
 /* Make sure all fields in query exist */
 struct slName *field;
 for (field = rql->fieldList; field != NULL; field = field->next)
     if (!hashLookup(gFieldHash, field->name))
+	{
+	if (!anyWild(field->name))
 	    errAbort("field %s doesn't exist in %s", field->name, tabFile);
+	}
+
+/* Make list of fields as opposed to array  */
+struct slName *allFieldList = NULL;
+for (i=0; i<gTable->fieldCount; ++i)
+    slNameAddHead(&allFieldList, gTable->fields[i]);
+slReverse(&allFieldList);
+
+/* Expand any field names with wildcards. */
+rql->fieldList = wildExpandList(allFieldList, rql->fieldList, TRUE);
+
 
 /* Print out label row. */
 if (!doCount)
     {
     printf("#");
     char *sep = "";
     for (field = rql->fieldList; field != NULL; field = field->next)
 	{
 	printf("%s%s", sep, field->name);
 	sep = "\t";
 	}
     printf("\n");
     }
 
 /* Print out or just count selected fields that match query */
 int matchCount = 0;
 struct lm *lm = lmInit(0);
 struct fieldedRow *row;
 for (row = gTable->rowList; row != NULL; row = row->next)
     {
     boolean pass = TRUE;
     if (rql->whereClause != NULL)
         {
 	struct rqlEval res = rqlEvalOnRecord(rql->whereClause, row, lookup, lm);
 	res = rqlEvalCoerceToBoolean(res);
 	pass = res.val.b;
 	}
     if (pass)
         {
 	if (doCount)
 	    ++matchCount;
 	else
 	    {
 	    char *sep = "";
 	    for (field = rql->fieldList; field != NULL; field = field->next)
 		{
 		int fieldIx = hashIntVal(gFieldHash, field->name);
 		printf("%s%s", sep, row->row[fieldIx]);
 		sep = "\t";
 		}
 	    printf("\n");
 	    }
 	}
     }
 
 if (doCount)
     printf("%d\n", matchCount);
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 if (argc < 2)
     usage();
 struct dyString *query = dyStringNew(0);
 int i;
 for (i=1; i<argc; ++i)
     {
     if (i != 1)
         dyStringAppendC(query, ' ');
     dyStringAppend(query, argv[i]);
     }
 tabQuery(query->string);
 return 0;
 }