src/hg/makeDb/metaTblUpdate/metaTblUpdate.c 1.7
1.7 2010/03/31 23:36:08 tdreszer
Tightening screws. Don't allow shared metaTbl update except from protected file.
Index: src/hg/makeDb/metaTblUpdate/metaTblUpdate.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/metaTblUpdate/metaTblUpdate.c,v
retrieving revision 1.6
retrieving revision 1.7
diff -b -B -U 4 -r1.6 -r1.7
--- src/hg/makeDb/metaTblUpdate/metaTblUpdate.c 30 Mar 2010 23:45:27 -0000 1.6
+++ src/hg/makeDb/metaTblUpdate/metaTblUpdate.c 31 Mar 2010 23:36:08 -0000 1.7
@@ -25,17 +25,21 @@
" 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"
+ " 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=] [-test [-verbose=2]]\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 '" METATBL_DEFAULT_NAME "'.\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"
@@ -62,8 +66,10 @@
{"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}
};
@@ -80,15 +85,66 @@
usage();
}
char *db = optionVal("db",NULL);
-char *table = optionVal("table",METATBL_DEFAULT_NAME);
+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();
@@ -99,16 +155,23 @@
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();
}
-struct sqlConnection *conn = sqlConnect(db);
-
+// 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");
@@ -131,8 +194,14 @@
(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");
@@ -148,14 +217,22 @@
{
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");
- metaObjs = metaObjsLoadFromFormattedFile(argv[1]);
+ 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]);
}
@@ -178,9 +255,7 @@
return 0;
// TODO:
// 1) make hgc use metaTbl
-// 2) support for metaTbl_tdreszer in sandbox. Auto-create table when requsting.
-// 3) Restrict updates to metaTbl to ONLY support checked in files. No command line, no single line
-// 4) 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"
-// 5) expId table?
+// 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?
}