4898794edd81be5285ea6e544acbedeaeb31bf78 max Tue Nov 23 08:10:57 2021 -0800 Fixing pointers to README file for license in all source code files. refs #27614 diff --git src/hg/utils/mdbQuery/mdbQuery.c src/hg/utils/mdbQuery/mdbQuery.c index b936061..4fed8ac 100644 --- src/hg/utils/mdbQuery/mdbQuery.c +++ src/hg/utils/mdbQuery/mdbQuery.c @@ -1,272 +1,272 @@ /* mdbQuery - Select objects from metaDb table. Print all or selected fields in a variety * of formats. */ /* Copyright (C) 2011 The Regents of the University of California - * See README in this or parent directory for licensing information. */ + * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */ #include "common.h" #include "linefile.h" #include "localmem.h" #include "hash.h" #include "options.h" #include "jksql.h" #include "rql.h" #include "mdb.h" /* Variables that can be set from command line. */ char *clOut = "line"; char *clTable = "metaDb"; void usage() /* Explain usage and exit. */ { errAbort( "mdbQuery - Select objects from metaDb table. Print all or selected fields in a variety\n" "of formats\n" "usage:\n" " mdbQuery sqlStatement\n" "Where the SQL statement is enclosed in quotations to avoid the shell interpreting it.\n" "Only a very restricted subset of a single SQL statement (select) is supported. Examples:\n" " mdbQuery \"select count(*) from hg18\"\n" "counts all of the metaDb objects in the hg18 database and prints the results to stdout\n" " mdbQuery \"select obj,cell,antibody from hg18 where antibody like 'pol%%'\"\n" "print the obj, cell, and antibody fields from all objects where there is an antibody fields\n" "and that field starts with pol. Note obj is treated differently from other fields a bit\n" "since it comes from the obj column rather than the var/val columns in the database table.\n" "You can use metaObject as a synonym for obj.\n" "OPTIONS:\n" " -out=type output one of the following types. Default is %s\n" " line - a line full of this=that; pairs\n" " 3col - 3 column obj/var/val format like in metaDb table\n" " tab - tab-separated format.\n" " ra - two column ra format with objs as stanzas\n" " -table=name - use the given table. Default is metaDb\n" , clOut ); } static struct optionSpec options[] = { {"table", OPTION_STRING}, {"out", OPTION_STRING}, {NULL, 0}, }; static char *lookupField(void *record, char *key) /* Lookup a field in a mdbObj. */ { struct mdbObj *mdb = record; if (sameString(key, "obj")) { return mdb->obj; } else { struct mdbVar *var = hashFindVal(mdb->varHash, key); if (var == NULL) return NULL; else return var->val; } } static boolean rqlStatementMatch(struct rqlStatement *rql, struct mdbObj *mdb, struct lm *lm) /* Return TRUE if where clause and tableList in statement evaluates true for tdb. */ { struct rqlParse *whereClause = rql->whereClause; if (whereClause == NULL) return TRUE; else { struct rqlEval res = rqlEvalOnRecord(whereClause, mdb, lookupField, lm); res = rqlEvalCoerceToBoolean(res); return res.val.b; } } static boolean stringMatch(char *a, char *b, boolean wild) /* Return true if strings a and b are the same. If wild is true, do comparision * expanding wildcards in a. */ { if (wild) return wildMatch(a,b); else return strcmp(a,b) == 0; } static void raOutput(struct rqlStatement *rql, struct mdbObj *mdb, FILE *out) /* Output fields from mdb to file in ra format. */ { struct slName *fieldList = rql->fieldList, *field; for (field = fieldList; field != NULL; field = field->next) { struct mdbVar *var; boolean doWild = anyWild(field->name); if (stringMatch(field->name, "obj", doWild) || stringMatch(field->name, "metaObject", doWild)) fprintf(out, "%s %s\n", "metaObject", mdb->obj); for (var = mdb->vars; var != NULL; var = var->next) { if (stringMatch(field->name, var->var, doWild)) fprintf(out, "%s %s\n", var->var, var->val); } } fprintf(out, "\n"); } static void fourColOutput(struct rqlStatement *rql, struct mdbObj *mdb, FILE *out) /* Output fields from mdb to file in four column obj/var/val format. */ { struct slName *fieldList = rql->fieldList, *field; for (field = fieldList; field != NULL; field = field->next) { struct mdbVar *var; boolean doWild = anyWild(field->name); for (var = mdb->vars; var != NULL; var = var->next) { if (stringMatch(field->name, var->var, doWild)) fprintf(out, "%s\t%s\t%s\n", mdb->obj, var->var, var->val); } } } static void lineOutput(struct rqlStatement *rql, struct mdbObj *mdb, FILE *out) /* Output fields from mdb to file in this=that; line format. */ { struct slName *fieldList = rql->fieldList, *field; fprintf(out, "%s", mdb->obj); for (field = fieldList; field != NULL; field = field->next) { struct mdbVar *var; boolean doWild = anyWild(field->name); for (var = mdb->vars; var != NULL; var = var->next) { if (stringMatch(field->name, var->var, doWild)) fprintf(out, " %s=%s;", var->var, var->val); } } fprintf(out, "\n"); } static void tabOutput(struct rqlStatement *rql, struct mdbObj *mdb, FILE *out) /* Output fields from mdb to file in tab-separated format. */ { /* First make sure no wildcards in field name */ struct slName *fieldList = rql->fieldList, *field; for (field = fieldList; field != NULL; field = field->next) { if (anyWild(field->name)) errAbort("No wildcards in field names with out=tab option"); } for (field = fieldList; field != NULL; field = field->next) { char *val = NULL; if (sameString(field->name, "obj") || sameString(field->name, "metaObject")) val = mdb->obj; else { struct mdbVar *var; for (var = mdb->vars; var != NULL; var = var->next) { if (sameString(field->name, var->var)) { val = var->val; break; } } } fprintf(out, "%s", naForNull(val)); if (field->next == NULL) fprintf(out, "\n"); else fprintf(out, "\t"); } } void mdbQuery(char *statement) /* mdbQuery - Select things from metaDb table.. */ { /* Parse out sql statement. */ struct lineFile *lf = lineFileOnString("query", TRUE, cloneString(statement)); struct rqlStatement *rql = rqlStatementParse(lf); lineFileClose(&lf); /* Figure out list of databases to work on. */ struct slName *db, *dbList = sqlListOfDatabases(); struct slRef *dbOrderList = NULL; struct slName *t; for (t = rql->tableList; t != NULL; t = t->next) { for (db = dbList; db!= NULL; db = db->next) { if (wildMatch(t->name, db->name)) refAdd(&dbOrderList, db); } } verbose(2, "%d databases in from clause\n", slCount(dbOrderList)); /* Make sure we actually only have one valid database, and point database variable * to it's name. */ if (slCount(dbOrderList) != 1) { if (dbOrderList == NULL) { if (rql->tableList == NULL) errAbort("Missing from clause in sql statement"); else errAbort("No database %s", rql->tableList->name); } else errAbort("Too many matching databases"); } db = dbOrderList->val; char *database = db->name; /* Grab list of all metaDb obj. */ struct sqlConnection *conn = sqlConnect(database); struct mdbObj *mdb, *mdbList = mdbObjsQueryAll(conn, clTable); verbose(2, "%d objects in %s.%s\n", slCount(mdbList), database, clTable); sqlDisconnect(&conn); /* Loop through all objects, evaluating the RQL on them. */ struct lm *lm = lmInit(0); int matchCount = 0; boolean doSelect = sameString(rql->command, "select"); for (mdb = mdbList; mdb != NULL; mdb = mdb->next) { if (rqlStatementMatch(rql, mdb, lm)) { matchCount += 1; if (doSelect) { if (sameString(clOut, "ra")) raOutput(rql, mdb, stdout); else if (sameString(clOut, "line")) lineOutput(rql, mdb, stdout); else if (sameString(clOut, "3col")) fourColOutput(rql, mdb, stdout); else if (sameString(clOut, "tab")) tabOutput(rql, mdb, stdout); else errAbort("Unknown out type %s", clOut); } if (rql->limit >= 0 && matchCount >= rql->limit) break; } } if (sameString(rql->command, "count")) printf("%d\n", matchCount); } int main(int argc, char *argv[]) /* Process command line. */ { optionInit(&argc, argv, options); if (argc != 2) usage(); clTable = optionVal("table", clTable); clOut = optionVal("out", clOut); mdbQuery(argv[1]); return 0; }