src/hg/makeDb/metaTblUpdate/metaTblPrint.c 1.1

Index: src/hg/makeDb/metaTblUpdate/metaTblPrint.c
===================================================================
RCS file: src/hg/makeDb/metaTblUpdate/metaTblPrint.c
diff -N src/hg/makeDb/metaTblUpdate/metaTblPrint.c
--- /dev/null	1 Jan 1970 00:00:00 -0000
+++ src/hg/makeDb/metaTblUpdate/metaTblPrint.c	18 Mar 2010 23:37:51 -0000	1.1
@@ -0,0 +1,150 @@
+/* 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 DB_DEFAULT      "hg19"
+#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 variable but "
+  "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 "
+  "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/-count]\n"
+  "                [-all [-byVar]]\n"
+  "                [-obj=] [-var= [-val=]]]\n"
+  "                [-var= [-val=]]\n"
+  "                [-vars=\"var1=val1 var2=val2...\"]\n\n"
+  "Options:\n"
+  "    -db      Database to query.  Default is '" DB_DEFAULT "'.\n"
+  "    -table   Table to query.  Default is '" METATBL_DEFAULT_NAME "'.\n"
+  "    -long    Print each obj, var=val as separate line.\n"
+  "    -count   Just print count of unique obj var=val combinations.\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.  Example:\n"
+  "       -vars=\"grant=Snyder cell=GM12878 antibody=CTCF\" will return all objs\n"
+  "             that satify those constraints.\n"
+  );
+}
+
+static struct optionSpec optionSpecs[] = {
+    {"db",      OPTION_STRING}, // default "hg19"
+    {"table",   OPTION_STRING}, // default "metaTbl"
+    {"long",    OPTION_BOOLEAN},// long format
+    {"count",   OPTION_BOOLEAN},// returns only count of unique obj var=val combinations
+    {"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
+    {"vals",     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;
+
+optionInit(&argc, argv, optionSpecs);
+char *db    = optionVal("db",   DB_DEFAULT);
+char *table = optionVal("table",METATBL_DEFAULT_NAME);
+boolean printLong = optionExists("long");
+boolean printCount = optionExists("count");
+boolean byVar = FALSE;
+
+if(printLong && printCount)
+    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 = TRUE;
+    metaByVars = metaByVarsLineParse(optionVal("vars", NULL));
+    }
+else
+    usage();
+
+struct sqlConnection *conn = sqlConnect(db);
+if(byVar)
+    {
+    struct metaByVar * queryResults = metaByVarsQuery(conn,table,metaByVars);
+    if(queryResults == NULL)
+        verbose(1, "No metadata met your selection criteria\n");
+    else
+        {
+        if(printCount)
+            printf("%d\n",metaByVarCount(queryResults));
+        else
+            metaByVarPrint(queryResults,printLong); // FIXME: write
+        metaByVarsFree(&queryResults);
+        }
+    }
+else
+    {
+    struct metaObj * queryResults = metaObjQuery(conn,table,metaObjs);
+    if(queryResults == NULL)
+        verbose(1, "No metadata met your selection criteria\n");
+    else
+        {
+        if(printCount)
+            printf("%d\n",metaObjCount(queryResults));
+        else
+            metaObjPrint(queryResults,printLong); // FIXME: write
+        metaObjsFree(&queryResults);
+        }
+    }
+sqlDisconnect(&conn);
+
+if(metaObjs)
+    metaObjsFree(&metaObjs);
+if(metaByVars)
+    metaByVarsFree(&metaByVars);
+
+return 0;
+}