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

Index: src/hg/makeDb/metaTblUpdate/metaTblUpdate.c
===================================================================
RCS file: src/hg/makeDb/metaTblUpdate/metaTblUpdate.c
diff -N src/hg/makeDb/metaTblUpdate/metaTblUpdate.c
--- /dev/null	1 Jan 1970 00:00:00 -0000
+++ src/hg/makeDb/metaTblUpdate/metaTblUpdate.c	18 Mar 2010 01:56:26 -0000	1.1
@@ -0,0 +1,141 @@
+/* metaTblUpdate - Adds, updates or removes metadata obkjects 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[] = "$Id$";
+
+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 'hg19'.\n"
+  "    -table table to load metadata to.  Default is 'metaTbl'.\n"
+  "  if file not provided, then -obj must be provided\n"
+  "    -obj={objName}     means Load from command line:\n"
+  "       -type={objType} needed if adding new obj, otherwise ignored\n"
+  "       -delete         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}
+};
+
+#define DB_DEFAULT      "hg19"
+#define TBL_DEFAULT     "metaTbl"
+#define OBJTYPE_DEFAULT "table"
+
+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",TBL_DEFAULT);
+boolean replace = FALSE;
+
+if(optionExists("obj"))
+    {
+    if(argc > 1)
+        usage(); // Must not have submitted formatted file also
+
+    AllocVar(metaObjs);
+
+    metaObjs->objName = cloneString(optionVal("obj",  NULL));
+    metaObjs->objType = metaObjTypeStringToEnum(optionVal("type", OBJTYPE_DEFAULT));
+
+    metaObjs->deleteThis = optionExists("delete");
+
+    if(optionExists("var"))
+        {
+        struct metaVar * metaVar;
+        AllocVar(metaVar);
+
+        metaVar->var     = cloneString(optionVal("var", NULL));
+        metaVar->varType = (optionExists("binary") ? vtBinary : vtTxt);
+        metaVar->val     = cloneString(optionVal("val", NULL));
+        metaObjs->vars = metaVar; // Only one
+
+        if (!metaObjs->deleteThis && metaVar->val == NULL)
+            usage();
+        }
+    else if (!metaObjs->deleteThis)
+            usage();
+
+    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);
+
+verbose(1, "Affected %d row(s) in %s.%s\n", count,db,table);
+
+metaObjsFree(&metaObjs);
+sqlDisconnect(&conn);
+return 0;
+}