########################################################################### # # GreenstoneXMLPlugout.pm -- the plugout module for Greenstone Archives # A component of the Greenstone digital library software # from the New Zealand Digital Library Project at the # University of Waikato, New Zealand. # # Copyright (C) 2006 New Zealand Digital Library Project # # This program is free software; you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by # the Free Software Foundation; either version 2 of the License, or # (at your option) any later version. # # This program is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # GNU General Public License for more details. # # You should have received a copy of the GNU General Public License # along with this program; if not, write to the Free Software # Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA. # ########################################################################### package MySQLPlugout; use strict; no strict 'refs'; no strict 'subs'; use util; use FileUtils; use GreenstoneXMLPlugout; use docprint; use IPC::Open2; use POSIX ":sys_wait_h"; # for waitpid, http://perldoc.perl.org/functions/waitpid.html # TODO: SIGTERM rollback and disconnect? # this plugout does not output xml to a file, but outputs rows into a mysql table sub BEGIN { @MySQLPlugout::ISA = ('GreenstoneXMLPlugout'); } # TODO: deal with -removeold and everything? Or type out instructions for user # TODO Q: what is "group" in GreenstoneXMLPlugout? # TODO Q: site_name only exists for GS3. What about GS2? my $process_mode_list = [ { 'name' => "meta_only", 'desc' => "{MySQLPlugout.process_mode.meta_only}" }, { 'name' => "text_only", 'desc' => "{MySQLPlugout.process_mode.text_only}" }, { 'name' => "all", 'desc' => "{MySQLPlugout.process_mode.all}" } ]; my $arguments = [ { 'name' => "process_mode", 'desc' => "{MySQLPlugout.process_mode}", 'type' => "enum", 'list' => $process_mode_list, 'deft' => "all", 'reqd' => "no", 'hiddengli' => "no"} ]; my $options = { 'name' => "MySQLPlugout", 'desc' => "{MySQLPlugout.desc}", 'abstract' => "no", 'inherits' => "yes", 'args' => $arguments }; sub new { my ($class) = shift (@_); my ($plugoutlist, $inputargs,$hashArgOptLists) = @_; push(@$plugoutlist, $class); push(@{$hashArgOptLists->{"ArgList"}},@{$arguments}); push(@{$hashArgOptLists->{"OptList"}},$options); my $self = new GreenstoneXMLPlugout($plugoutlist,$inputargs,$hashArgOptLists); if ($self->{'info_only'}) { # don't worry about any options etc return bless $self, $class; } print STDERR "***** MySQLPlugout process mode = \"", $self->{'process_mode'}, "\"\n"; return bless $self, $class; } # connect here and ensure all tables and databases exist sub begin { my $self= shift (@_); ########### TODO: these should be set from cmdline/GLI options to plugout ######### $self->{'db_driver'} = "mysql"; $self->{'site_name'} = "localsite"; $self->{'db_client_user'} = "root"; $self->{'db_client_pwd'} = "6reenstone3"; #$self->{'db_host'} = "127.0.0.1"; #$self->{'db_encoding'} = "utf8"; #TODO: proc_mode is also a saveas option ############ LOAD NECESSARY OPTIONS ########### print STDERR "########## COLLECTION: ". $ENV{'GSDLCOLLECTION'}."\n"; $self->{'collection_name'} = $ENV{'GSDLCOLLECTION'}; if(!$self->connect_to_db()) { # This is fatal for the plugout, let's terminate here # PrintError would already have displayed the warning message on connection fail die("Could not connect to db. Can't proceed.\n"); } if(!$self->load_db_and_tables()) { # This is fatal for the plugout, let's terminate here # PrintError would already have displayed the warning message on connection fail die("Could not use db or prepare its tables. Can't proceed.\n"); } # prepare the shared/common HANDLES to SQL insert statements that contain placeholders # and which we will reuse repeatedly when actually executing the insert statements my $proc_mode = $self->{'process_mode'}; if($proc_mode eq "all" || $proc_mode eq "meta_only" ) { $self->{'metadata_prepared_insert_statement_handle'} = $self->prepare_insert_metadata_row_stmthandle(); } if($proc_mode eq "all" || $proc_mode eq "text_only" ) { $self->{'fulltxt_prepared_insert_statement_handle'} = $self->prepare_insert_fulltxt_row_stmthandle(); } # if setting up to work with sql db failed, we'd have terminated and wouldn't come up to here: # won't bother preparing GreenstoneXMLPlugout by calling superclass' begin() # finally, can call begin on super - important as doc.xml is opened as a group etc $self->GreenstoneXMLPlugout::begin(@_); } # disconnect from database here, see inexport.pm sub end { my $self = shift(@_); # do the superclass stuff first, as any sql db failures should not prevent superclass cleanup $self->GreenstoneXMLPlugout::end(@_); $self->disconnect_from_db() || warn("Unable to disconnect from database " . $self->{'site_name'} . "\n"); # disconnect_from_db() will also issue a warning, but this may be clearer } # TODO: check arc-inf.db for whether each entry is to be deleted/indexed/reindexed/been indexed sub saveas { my $self = shift (@_); my ($doc_obj, $doc_dir) = @_; my $proc_mode = $self->{'process_mode'}; # 1. pre save out and saving debug handle # must call superclass (pre/post) saveas methods, as they handle assoc_files too my ($docxml_outhandler, $output_file) = $self->GreenstoneXMLPlugout::pre_saveas(@_); $self->{'debug_outhandle'} = $docxml_outhandler if ($self->{'debug'}); # STDOUT if debug # TODO: also set debugging in begin()? Then stmts creating db and tables also sent to debug out and not executed # TODO: remove unused old_unused_saveas from GreenstoneXMLPlugout # 2. overriding saving behaviour to do what the superclass does PLUS saving to sql db #NOTE: if proc_mode == all, then "breadcrumbs" go into both meta and txt elements of doc.xml: # statements pointing viewer to the sql db for contents # write the INVERSE into doc.xml as to what is written to the db my $docxml_output_options = { 'output' => docprint::OUTPUT_NONE }; if($proc_mode eq "meta_only" ) { # since only meta to go into MySQL db, text will go into docxml $docxml_output_options->{'output'} = docprint::OUTPUT_TEXT_ONLY; } elsif($proc_mode eq "text_only" ) { # since only full text to go into MySQL db, meta will go into docxml $docxml_output_options->{'output'} = docprint::OUTPUT_META_ONLY; } # now we've prepared to write out whatever is meant to go into docxml # and can do actual the steps superclass GreenstoneXMLPlugout carries out to write out docxml # So: write out the doc xml file for the current document my $section_text = &docprint::get_section_xml($doc_obj, $docxml_output_options); print $docxml_outhandler $section_text; # We also write out whatever needs to go into the MySQL database $self->write_meta_and_text($doc_obj); # 3. post save out #$self->GreenstoneXMLPlugout::post_saveas(@_); $self->GreenstoneXMLPlugout::post_saveas($doc_obj, $doc_dir, $docxml_outhandler, $output_file); # database connection is closed in end() method # so we don't open and close over and over for each doc during a single build } # write meta and/or text PER DOC out to DB sub write_meta_and_text { my $self = shift (@_); my ($doc_obj) = @_; my $root_section = $doc_obj->get_top_section(); my $doc_oid = $doc_obj->get_OID(); # we're processing a single doc at a time, so single OID # load the prepared INSERT statement handles for both tables (can be undef for any table depending on whether meta_only or txt_only are set) my $metadata_table_sth = $self->{'metadata_prepared_insert_statement_handle'}; my $fulltxt_table_sth = $self->{'fulltxt_prepared_insert_statement_handle'}; $self->recursive_write_meta_and_text($doc_obj, $root_section, $metadata_table_sth, $fulltxt_table_sth); } # Perl: Reading or Writing to Another Program # https://nnc3.com/mags/Perl3/cookbook/ch16_05.htm sub recursive_write_meta_and_text { my $self = shift (@_); my ($doc_obj, $doc_oid, $section, $metadata_table_sth, $fulltxt_table_sth) = @_; # If section=ROOT, write "root" as section name into table # doc->get_top_section() is the name of the doc root section, which is "" my $section_name = ($section eq "") ? "root" : $section; my $section_ptr = $doc_obj->_lookup_section ($section); return "" unless defined $section_ptr; my $debug_out = $self->{'debug_outhandle'}; #my $proc_mode = $self->{'process_mode'}; #if($proc_mode eq "all" || $proc_mode eq "meta_only" ) { if($metadata_table_sth) { # meta insert statement handle will be undef if not writing meta foreach my $data (@{$section_ptr->{'metadata'}}) { my $meta_name = $data->[0]; my $escaped_meta_value = &escape_text($data->[1]); # Write out the current section's meta to collection db's METADATA table # for each set of values to write to meta table, execute the prepared statement, filling in the values if($self->{'debug'}) { # just print the statement we were going to execute print $debug_out $metadata_table_sth->Statement . "($doc_oid, $section_name, $meta_name, $escaped_meta_value)\n"; } else { $metadata_table_sth->execute($doc_oid, $section_name, $meta_name, $escaped_meta_value); #|| warn ("Unable to write metadata row to db:\n\tOID $doc_oid, section $section_name,\n\tmeta name: $meta_name, val: $escaped_meta_value"); # Execution failure will print out info anyway: since db connection sets PrintError } } } #if($proc_mode eq "all" || $proc_mode eq "text_only" ) { if($fulltxt_table_sth) { # fulltxt insert statement handle will be undef if not writing fulltxt if($self->{'debug'}) { # just print the statement we were going to execute, minus the fulltxt value my $txt_repr = $section_ptr->{'text'} ? "" : "NULL"; print $debug_out $fulltxt_table_sth->Statement . "($doc_oid, $section_name, $txt_repr)\n"; } else { my $section_text = &escape_text($section_ptr->{'text'}); # fulltxt column can be SQL NULL. undef value gets written out as NULL: # https://stackoverflow.com/questions/12708633/which-one-represents-null-undef-or-empty-string # Write out the current section's text to collection db's FULLTeXT table $fulltxt_table_sth->execute($doc_oid, $section_name, $section_text); #|| warn ("Unable to write fulltxt row to db for row:\n\tOID $doc_oid, section $section_name"); # Execution failure will print out info anyway: since db connection sets PrintError } } # output all subsections: RECURSIVE CALL foreach my $subsection (@{$section_ptr->{'subsection_order'}}) { &recursive_write_meta_and_text($doc_obj, $doc_oid, "$section.$subsection", $metadata_table_sth, $fulltxt_table_sth); } } ################################# # Database access related functions # http://g2pc1.bu.edu/~qzpeng/manual/MySQL%20Commands.htm # https://www.guru99.com/insert-into.html # TODO Q: What on cancelling a build: delete table? But what if it was a rebuild and the rebuild is cancelled (not the original build)? # Do we create a copy of the orig database as backup, then start populating current db, and if cancelled, delete current db and RENAME backup table to current? # https://stackoverflow.com/questions/3280006/duplicating-a-mysql-table-indexes-and-data # BUT what if the table is HUGE? (Think of a collection with millions of docs.) Huge overhead in copying? # The alternative is we just quit on cancel, but then: cancel could leave the table in a partial committed state, with no way of rolling back. # Unless they do a full rebuild, which will recreate the table from scratch? # SOLUTION-> rollback transaction on error, see https://www.effectiveperlprogramming.com/2010/07/set-custom-dbi-error-handlers/ # But then should set AutoCommit to off on connection, and remember to commit every time ################# # Database functions that use the perl DBI module (with the DBD driver module for mysql) ################# # THE NEW DB FUNCTIONS # NOTE: FULLTEXT is a reserved keyword in (My)SQL. So we can't name a table or any of its columns "fulltext". # https://dev.mysql.com/doc/refman/5.5/en/keywords.html # TODO: Consider AutoCommit status (and Autocommit off allowing commit or rollback for GS coll build cancel) later sub connect_to_db { my $self= shift (@_); my $db_driver = $self->{'db_driver'}; my $db_user = $self->{'db_client_user'} || "root"; my $db_pwd = $self->{'db_client_pwd'}; my $db_host = $self->{'db_host'} || "127.0.0.1"; my $db_enc = $self->{'db_encoding'} || "utf8"; #my $db_name = $self->{'site_name'}; # try connecting to the mysql db, if that fails it will die # so don't bother preparing GreenstoneXMLPlugout by calling superclass' begin() # localhost doesn't work for us, but 127.0.0.1 works # https://metacpan.org/pod/DBD::mysql # "The hostname, if not specified or specified as '' or 'localhost', will default to a MySQL server # running on the local machine using the default for the UNIX socket. To connect to a MySQL server # on the local machine via TCP, you must specify the loopback IP address (127.0.0.1) as the host." #my $connect_str = "dbi:$db_driver:database=$db_name;host=$db_host"; my $connect_str = "dbi:$db_driver:host=$db_host"; # don't provide db, so we can check the db is there my $dbh = DBI->connect("$connect_str", $db_user, $db_pwd, { ShowErrorStatement => 1, # more informative as DBI will append failed SQL stmt to error message PrintError => 1, # on by default, but being explicit RaiseError => 0, # off by default, but being explicit AutoCommit => 1, # on by default, but being explicit }); if(!$dbh) { # NOTE, despite handle dbh being undefined, error code will be in DBI->err return 0; } # set encoding https://metacpan.org/pod/DBD::mysql # https://dev.mysql.com/doc/refman/5.7/en/charset.html # https://dev.mysql.com/doc/refman/5.7/en/charset-conversion.html # Setting the encoding at db server level. # Not sure if this command is mysql specific: my $stmt = "set NAMES '" . $db_enc . "'"; $dbh->do($stmt) || warn("Unable to set charset encoding at db server level to: " . $db_enc . "\n"); # if we're here, then connection succeeded, store handle $self->{'db_handle'} = $dbh; return 1; } sub load_db_and_tables { my $self= shift (@_); my $db_name = $self->{'site_name'}; # one database per GS3 site my $dbh = $self->{'db_handle'}; # perl DBI switch database: https://www.perlmonks.org/?node_id=995434 # do() returns undef on error. # connection succeeded, try to load our database. If that didn't work, attempt to create db my $success = $dbh->do("use $db_name"); if(!$success && $dbh->err == 1049) { # "Unknown database" error has code 1049 (mysql only?) meaning db doesn't exist yet # attempt to create the db and its tables $self->create_db($db_name) || return 0; # once more attempt to use db, now that it exists $dbh->do("use $db_name") || return 0; #$dbh->do("use localsite") or die "Error (code" . $dbh->err ."): " . $dbh->errstr . "\n"; # attempt to create tables in current db $self->create_metadata_table() || return 0; $self->create_fulltext_table() || return 0; $success = 1; } elsif($success) { # database existed and loaded successfully, but # before proceeding check that the current collection's tables exist # attempt to create tables in current db if(!$self->table_exists($self->{'collection_name'} . "metadata")) { $self->create_metadata_table() || return 0; } if(!$self->table_exists($self->{'collection_name'} . "fulltxt")) { $self->create_fulltext_table() || return 0; } } return $success; # could still return 0, if database failed to load with an error code != 1049 } # disconnect from db - https://metacpan.org/pod/DBI#disconnect # TODO: make sure to have committed or rolled back before disconnect # and that you've call finish() on statement handles if any fetch remnants remain sub disconnect_from_db { my $self= shift (@_); my $dbh = $self->{'db_handle'}; # make sure any active stmt handles are finished # NO: "When all the data has been fetched from a SELECT statement, the driver will automatically call finish for you. So you should not call it explicitly except when you know that you've not fetched all the data from a statement handle and the handle won't be destroyed soon." #$meta_sth = $self->{'metadata_prepared_insert_statement_handle'}; #$txt_sth = $self->{'fulltxt_prepared_insert_statement_handle'}; #$meta_sth->finish() if($meta_sth); #$txt_sth->finish() if($txt_sth); my $rc = $dbh->disconnect or warn $dbh->errstr; # The handle is of little use after disconnecting. Possibly PrintError already prints a warning and this duplicates it? return $rc; } sub create_db { my $self= shift (@_); my $db_name = $self->{'site_name'}; my $dbh = $self->{'db_handle'}; # https://stackoverflow.com/questions/5025768/how-can-i-create-a-mysql-database-from-a-perl-script return $dbh->do("create database $db_name"); # do() will return undef on fail, https://metacpan.org/pod/DBI#do } sub create_metadata_table { my $self= shift (@_); my $dbh = $self->{'db_handle'}; my $table_name = $self->{'collection_name'} . "metadata"; # If using an auto incremented primary key: my $stmt = "CREATE TABLE $table_name (id INT NOT NULL AUTO_INCREMENT, did VARCHAR(63) NOT NULL, sid VARCHAR(63) NOT NULL, metaname VARCHAR(127) NOT NULL, metavalue VARCHAR(1023) NOT NULL, PRIMARY KEY(id));"; return $dbh->do($stmt); } # TODO: Investigate: https://dev.mysql.com/doc/search/?d=10&p=1&q=FULLTEXT # 12.9.1 Natural Language Full-Text Searches # to see whether we have to index the 'fulltxt' column of the 'fulltext' tables # or let user edit this file, or add it as another option sub create_fulltext_table { my $self= shift (@_); my $dbh = $self->{'db_handle'}; my $table_name = $self->{'collection_name'} . "fulltxt"; # If using an auto incremented primary key: my $stmt = "CREATE TABLE $table_name (id INT NOT NULL AUTO_INCREMENT, did VARCHAR(63) NOT NULL, sid VARCHAR(63) NOT NULL, fulltxt LONGTEXT, PRIMARY KEY(id));"; return $dbh->do($stmt); } # USEFUL: https://metacpan.org/pod/DBI # "Many methods have an optional \%attr parameter which can be used to pass information to the driver implementing the method. Except where specifically documented, the \%attr parameter can only be used to pass driver specific hints. In general, you can ignore \%attr parameters or pass it as undef." # https://www.guru99.com/insert-into.html # and https://dev.mysql.com/doc/refman/8.0/en/example-auto-increment.html # for inserting multiple rows at once # https://www.perlmonks.org/bare/?node_id=316183 # https://metacpan.org/pod/DBI#do # https://www.quora.com/What-is-the-difference-between-prepare-and-do-statements-in-Perl-while-we-make-a-connection-to-the-database-for-executing-the-query # https://docstore.mik.ua/orelly/linux/dbi/ch05_05.htm # https://metacpan.org/pod/DBI#performance # 'The q{...} style quoting used in this example avoids clashing with quotes that may be used in the SQL statement. Use the double-quote like qq{...} operator if you want to interpolate variables into the string. See "Quote and Quote-like Operators" in perlop for more details.' sub prepare_insert_metadata_row_stmthandle { my $self = shift (@_); my ($did, $sid, $metaname, $metavalue) = @_; my $dbh = $self->{'db_handle'}; my $tablename = $self->{'colname'}."_metadata"; #my $stmt = "INSERT INTO $tablename (did, sid, metaname, metavalue) VALUES ('$did', '$sid', '$metaname', '$metavalue');"; # ?, ?, ?, ? # using qq{} since we want $tablename placeholder to be filled in # returns Statement Handle object! my $sth = $dbh->prepare(qq{INSERT INTO $tablename (did, sid, metaname, metavalue) VALUES (?, ?, ?, ?)"}) || warn("Could not prepare insert statement for metadata table\n"); return $sth; } sub prepare_insert_fulltxt_row_stmthandle { my $self = shift (@_); my ($did, $sid, $fulltext) = @_; my $dbh = $self->{'db_handle'}; my $tablename = $self->{'colname'}."_fulltxt"; #my $stmt = "INSERT INTO $tablename (did, sid, fulltxt) VALUES ('$did', '$sid', '$fulltext');"; ?, ?, ? # using qq{} since we want $tablename placeholder to be filled in # returns Statement Handle object! my $sth = $dbh->prepare(qq{INSERT INTO $tablename (did, sid, fulltxt) VALUES (?, ?, ?)"}) || warn("Could not prepare insert statement for fulltxt table\n"); return $sth; } # I can get my version of table_exists to work, but it's not so ideal # Interesting that MySQL has non-standard command to CREATE TABLE IF NOT EXISTS and DROP TABLE IF EXISTS, # see https://www.perlmonks.org/bare/?node=DBI%20Recipes # The page further has a table_exists function that could work with proper comparison # Couldn't get the first solution at https://www.perlmonks.org/bare/?node_id=500050 to work though sub table_exists { my ($dbh,$table_name) = @_; my @table_list = $dbh->tables; #my $tables_str = @table_list[0]; foreach my $table (@table_list) { return 1 if ($table =~ m/$table_name/); } return 0; } 1;