src/hg/makeDb/metaTblUpdate/metaTblUpdate.c 1.8
1.8 2010/03/31 23:39:38 tdreszer
Oops. Changed objName to obj.
Index: src/hg/makeDb/metaTblUpdate/metaTblUpdate.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/metaTblUpdate/metaTblUpdate.c,v
retrieving revision 1.7
retrieving revision 1.8
diff -b -B -U 1000000 -r1.7 -r1.8
--- src/hg/makeDb/metaTblUpdate/metaTblUpdate.c 31 Mar 2010 23:36:08 -0000 1.7
+++ src/hg/makeDb/metaTblUpdate/metaTblUpdate.c 31 Mar 2010 23:39:38 -0000 1.8
@@ -1,261 +1,261 @@
/* metaTblUpdate - Adds, updates or removes metadata objects and variables from the metaTbl. */
#include "common.h"
#include "linefile.h"
#include "options.h"
#include "metaTbl.h"
#include "hash.h"
static char const rcsid[] = "$Id$";
#define OBJTYPE_DEFAULT "table"
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"
"NOTE: Updates to the shared '" METATBL_DEFAULT_NAME "' can only be done by a file written\n"
" directly from metaTblPrint. Update sandbox first, then move updates to shared table.\n\n"
"usage:\n"
" metaTblUpdate -db= [-table= [-force]] [-recreate] [-test [-verbose=2]]\n"
" [-obj= [-type=] [-delete] [-var=] [-binary] [-val=]]\n"
" [-vars=\"var1=val1 var2=val2... [-delete] [-var=] [-binary] [-val=]]\n"
" [fileName] [-replace]\n\n"
"Options:\n"
" -db Database to load metadata to. This argument is required.\n"
" -table Table to load metadata to. Default is the sandbox version of '" METATBL_DEFAULT_NAME "'.\n"
" -recreate Creates new or recreates the table. With this flag, no further arguemts are needed.\n"
" -force Overrides restrictions placed on shared '" METATBL_DEFAULT_NAME "'. Use caution.\n"
" -test Does not update but only reports results. Use with -verbose=2 to see each SQL statement.\n"
" if file not provided, then -obj or -vars must be provided\n"
" -obj={objName} Means Load from command line:\n"
" -type={objType} Used if adding new obj, otherwise ignored. Default is '" OBJTYPE_DEFAULT "'.\n"
" -vars={var=val...} An alternate way of requesting a group of objects to apply an update to.\n"
" It is recommended you use the selection criteria in metaTblPrint to verify\n"
" which objects meat your selection criteria first.\n"
" These options work with -obj or -vars:\n"
" -delete Remove 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 objects)\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 each 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
{"vars", OPTION_STRING}, // Select set of object by vars
{"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
{"recreate",OPTION_BOOLEAN},// creates or recreates the table
{"force", OPTION_BOOLEAN},// override restrictions on shared table
{"test", OPTION_BOOLEAN},// give it a test, will ya?
{NULL, 0}
};
int main(int argc, char *argv[])
// Process command line.
{
struct metaObj * metaObjs = NULL;
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",NULL);
boolean deleteIt = optionExists("delete");
boolean testIt = optionExists("test");
boolean recreate = optionExists("recreate");
boolean force = optionExists("force");
boolean replace = FALSE;
char *var = optionVal("var",NULL);
char *val = optionVal("val",NULL);
struct sqlConnection *conn = sqlConnect(db);
// Find the table if necessary
if(table == NULL)
{
table = metaTblName((recreate?NULL:conn),TRUE); // Look for sandBox name first
if(table == NULL)
{
table = metaTblName((recreate?NULL:conn),FALSE); // Okay, default then
if(table == NULL) // Now you are just getting me angry!
{
sqlDisconnect(&conn);
if(!recreate) // assertable
errAbort("No '%s.%s' found. Consider using -recreate flag.\n",db,METATBL_DEFAULT_NAME);
else
errAbort("No '%s.%s' found.\n",db,METATBL_DEFAULT_NAME);
}
}
verbose(1, "Using table named '%s.%s'.\n",db,table);
}
boolean sharedTbl = sameWord(table,METATBL_DEFAULT_NAME); // Special restrictions apply
// Recreate the table
if(recreate)
{
if(sharedTbl && ! force)
{
sqlDisconnect(&conn);
verbose(1, "NOT SUPPORTED for shared table '%s'.\n",METATBL_DEFAULT_NAME);
}
boolean recreated = sqlTableExists(conn,table);
metaTblReCreate(conn,table,testIt);
if(testIt)
{
verbose(1, "Would %screate table named '%s'.\n",
(recreated?"re":""),table);
if(!recreated)
{
sqlDisconnect(&conn);
if(optionExists("obj") || optionExists("vars") || argc > 1)
verbose(1, "Can't test further commands. Consider '-db= [-table=] -recreate' as the only arguments.\n");
return 0; // Don't test any update if we haven't actually created the table!
}
}
else
verbose(1, "%s table named '%s'.\n",(recreated?"Recreated":"Created"),table);
}
if(argc > 1 && (deleteIt || var != NULL || val != NULL))
{
verbose(1, "INCONSISTENT REQUEST: can't combine supplied file with -delete -var or -val arguments.\n");
usage();
}
if(deleteIt && var != NULL && val != NULL)
{
verbose(1, "INCONSISTENT REQUEST: cant combine -delete with -var and -val.\n");
usage();
}
if (argc != 2 && !deleteIt && (var == NULL || val == NULL))
{
if(recreate) // no problem
return 0;
verbose(1, "INCONSISTENT REQUEST: need both -var and -val.\n");
usage();
}
// Now get the object list
if(optionExists("obj"))
{
if(sharedTbl && !force)
{
sqlDisconnect(&conn);
verbose(1, "NOT SUPPORTED for shared table '%s'.\n",METATBL_DEFAULT_NAME);
usage(); // Must not have submitted formatted file also
}
if(argc > 1 || optionExists("vars"))
{
sqlDisconnect(&conn);
verbose(1, "INCONSISTENT REQUEST: can't combine -obj with -vars or a supplied file.\n");
usage(); // Must not have submitted formatted file also
}
metaObjs = metaObjCreate(optionVal("obj", NULL),
optionVal("type", OBJTYPE_DEFAULT),
var,
(optionExists("binary") ? "binary" : "txt"), // FIXME: don't know how to deal with binary yet
val);
metaObjs->deleteThis = deleteIt;
verbose(2, "metadata %s %s %s%s%s%s\n",
- metaObjs->objName,metaObjTypeEnumToString(metaObjs->objType),
+ metaObjs->obj,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 if(optionExists("vars"))
{
if(sharedTbl && !force)
{
sqlDisconnect(&conn);
verbose(1, "NOT SUPPORTED for shared table '%s'.\n",METATBL_DEFAULT_NAME);
usage(); // Must not have submitted formatted file also
}
if(argc > 1)
{
sqlDisconnect(&conn);
verbose(1, "INCONSISTENT REQUEST: can't combine -vars with a supplied file.\n");
usage(); // Must not have submitted formatted file also
}
struct metaByVar * metaByVars = metaByVarsLineParse(optionVal("vars", NULL));
metaObjs = metaObjsQueryByVars(conn,table,metaByVars);
metaObjTransformToUpdate(metaObjs,var,
(optionExists("binary") ? "binary" : "txt"), // FIXME: don't know how to deal with binary yet
val,deleteIt);
}
else // Must be submitting formatted file
{
if(argc != 2)
{
sqlDisconnect(&conn);
if(recreate) // no problem
return 0;
verbose(1, "REQUIRED: must declare -obj, -vars or supply a file.\n");
usage(); // Must not have submitted formatted file also
}
replace = optionExists("replace");
boolean validated = FALSE;
metaObjs = metaObjsLoadFromFormattedFile(argv[1],&validated);
if(sharedTbl && !force && !validated)
{
sqlDisconnect(&conn);
errAbort("Update to shared table '%s' requires file directly written by metTblPrint from sandbox file.\n", table);
}
if(metaObjs != NULL)
verbose(1, "Read %d metadata objects from %s\n", slCount(metaObjs),argv[1]);
}
int count = 0;
if(metaObjs != NULL)
{
if(testIt && verboseLevel() > 2)
metaObjPrint(metaObjs,FALSE);
count = metaObjsSetToDb(conn,table,metaObjs,replace,testIt);
}
if(testIt)
verbose(1, "Command would affected %d row(s) in %s.%s\n", count,db,table);
else
verbose(1, "Affected %d row(s) in %s.%s\n", count,db,table);
sqlDisconnect(&conn);
metaObjsFree(&metaObjs);
return 0;
// TODO:
// 1) make hgc use metaTbl
// 2) Diagram flow: (a) update/add "metaTbl_tdreszer" (b) Test in sandbox (c) print to RA file. (d) check in RA file (e) load RA file to "metaTbl"
// 3) expId table?
}