uid); return ''; } /************************************************************************* * */ function tripal_core_install_chado ($dummy = NULL, $job = NULL){ $schema_file = drupal_get_path('module', 'tripal_core').'/default_schema.sql'; $init_file = drupal_get_path('module', 'tripal_core').'/initialize.sql'; tripal_core_reset_chado_schema(); tripal_core_install_sql($schema_file); tripal_core_install_sql($init_file); } /************************************************************************* * */ function tripal_core_reset_chado_schema (){ global $active_db; // iterate through the lines of the schema file and rebuild the SQL pg_query($active_db,"drop schema chado cascade"); pg_query($active_db,"drop schema genetic_code cascade"); pg_query($active_db,"drop schema so cascade"); pg_query($active_db,"drop schema frange cascade"); pg_query($active_db,"create schema chado"); pg_query($active_db,"create language plpgsql"); } /************************************************************************* * */ function tripal_core_install_sql ($sql_file){ global $active_db; pg_query($active_db,"set search_path to chado,public"); print "Loading $sql_file...\n"; $lines = file($sql_file,FILE_SKIP_EMPTY_LINES); if(!$lines){ return 'Cannot open $schema_file'; } $stack = array(); $in_string = 0; $query = ''; $i = 0; foreach ($lines as $line_num => $line) { $i++; $type = ''; // find and remove comments except when inside of strings if(preg_match('/--/',$line) and !$in_string and !preg_match("/'.*?--.*?'/",$line)){ $line = preg_replace('/--.*$/','',$line); // remove comments } if(preg_match('/\/\*.*?\*\//',$line)){ $line = preg_replace('/\/\*.*?\*\//','',$line); // remove comments } // skip empty lines if(preg_match('/^\s*$/',$line) or strcmp($line,'')==0){ continue; } // Find SQL for new objects if(preg_match('/^\s*CREATE\s+TABLE/i',$line) and !$in_string){ $stack[] = 'table'; $line = preg_replace("/public./","chado.",$line); } if(preg_match('/^\s*ALTER\s+TABLE/i',$line) and !$in_string){ $stack[] = 'alter table'; $line = preg_replace("/public./","chado.",$line); } if(preg_match('/^\s*SET/i',$line) and !$in_string){ $stack[] = 'set'; } if(preg_match('/^\s*CREATE\s+SCHEMA/i',$line) and !$in_string){ $stack[] = 'schema'; } if(preg_match('/^\s*CREATE\s+SEQUENCE/i',$line) and !$in_string){ $stack[] = 'sequence'; $line = preg_replace("/public./","chado.",$line); } if(preg_match('/^\s*CREATE\s+(?:OR\s+REPLACE\s+)*VIEW/i',$line) and !$in_string){ $stack[] = 'view'; $line = preg_replace("/public./","chado.",$line); } if(preg_match('/^\s*COMMENT/i',$line) and !$in_string and sizeof($stack)==0){ $stack[] = 'comment'; $line = preg_replace("/public./","chado.",$line); } if(preg_match('/^\s*CREATE\s+(?:OR\s+REPLACE\s+)*FUNCTION/i',$line) and !$in_string){ $stack[] = 'function'; $line = preg_replace("/public./","chado.",$line); } if(preg_match('/^\s*CREATE\s+INDEX/i',$line) and !$in_string){ $stack[] = 'index'; } if(preg_match('/^\s*INSERT\s+INTO/i',$line) and !$in_string){ $stack[] = 'insert'; $line = preg_replace("/public./","chado.",$line); } if(preg_match('/^\s*CREATE\s+TYPE/i',$line) and !$in_string){ $stack[] = 'type'; } if(preg_match('/^\s*GRANT/i',$line) and !$in_string){ $stack[] = 'grant'; } if(preg_match('/^\s*CREATE\s+AGGREGATE/i',$line) and !$in_string){ $stack[] = 'aggregate'; } // determine if we are in a string that spans a line $matches = preg_match_all("/[']/i",$line,$temp); $in_string = $in_string - ($matches % 2); $in_string = abs($in_string); // if we've reached the end of an object the pop the stack if(strcmp($stack[sizeof($stack)-1],'table') == 0 and preg_match('/\);\s*$/',$line)){ $type = array_pop($stack); } if(strcmp($stack[sizeof($stack)-1],'alter table') == 0 and preg_match('/;\s*$/',$line) and !$in_string){ $type = array_pop($stack); } if(strcmp($stack[sizeof($stack)-1],'set') == 0 and preg_match('/;\s*$/',$line) and !$in_string){ $type = array_pop($stack); } if(strcmp($stack[sizeof($stack)-1],'schema') == 0 and preg_match('/;\s*$/',$line) and !$in_string){ $type = array_pop($stack); } if(strcmp($stack[sizeof($stack)-1],'sequence') == 0 and preg_match('/;\s*$/',$line) and !$in_string){ $type = array_pop($stack); } if(strcmp($stack[sizeof($stack)-1],'view') == 0 and preg_match('/;\s*$/',$line) and !$in_string){ $type = array_pop($stack); } if(strcmp($stack[sizeof($stack)-1],'comment') == 0 and preg_match('/;\s*$/',$line) and !$in_string){ $type = array_pop($stack); } if(strcmp($stack[sizeof($stack)-1],'function') == 0 and preg_match("/LANGUAGE.*?;\s+$/i",$line)){ $type = array_pop($stack); } if(strcmp($stack[sizeof($stack)-1],'index') == 0 and preg_match('/;\s*$/',$line) and !$in_string){ $type = array_pop($stack); } if(strcmp($stack[sizeof($stack)-1],'insert') == 0 and preg_match('/\);\s*$/',$line)){ $type = array_pop($stack); } if(strcmp($stack[sizeof($stack)-1],'type') == 0 and preg_match('/\);\s*$/',$line)){ $type = array_pop($stack); } if(strcmp($stack[sizeof($stack)-1],'grant') == 0 and preg_match('/;\s*$/',$line) and !$in_string){ $type = array_pop($stack); } if(strcmp($stack[sizeof($stack)-1],'aggregate') == 0 and preg_match('/\);\s*$/',$line)){ $type = array_pop($stack); } // if we're in a recognized SQL statement then let's keep track of lines if($type or sizeof($stack) > 0){ $query .= "$line"; } else { print "UNHANDLED $i, $in_string: $line"; return tripal_core_chado_install_done(); } if(preg_match_all("/\n/",$query,$temp) > 100){ print "SQL query is too long. Terminating:\n$query\n"; return tripal_core_chado_install_done(); } if($type and sizeof($stack) == 0){ print "Adding $type: line $i\n"; // rewrite the set serach_path to make 'public' be 'chado' if(strcmp($type,'set')==0){ $query = preg_replace("/public/m","chado",$query); } $result = pg_query($active_db, $query); if(!$result){ $error = pg_last_error(); print "Installation failed:\nSQL $i, $in_string: $query\n$error\n"; pg_query($active_db,"set search_path to public,chado"); return tripal_core_chado_install_done(); } $query = ''; } } print "Installation Complete!\n"; tripal_core_chado_install_done(); } /************************************************************************* * */ function tripal_core_chado_install_done (){ // return the search path to normal global $active_db; pg_query($active_db,"set search_path to public,chado"); }