1 | ###########################################################################
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2 | #
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3 | # GreenstoneSQLPlugin.pm -- reads into doc_obj from SQL db and docsql.xml
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4 | # Metadata and/or fulltext are stored in SQL db, the rest may be stored in
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5 | # the docsql .xml files.
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6 | # A component of the Greenstone digital library software
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7 | # from the New Zealand Digital Library Project at the
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8 | # University of Waikato, New Zealand.
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9 | #
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10 | # Copyright (C) 2001 New Zealand Digital Library Project
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11 | #
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12 | # This program is free software; you can redistribute it and/or modify
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13 | # it under the terms of the GNU General Public License as published by
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14 | # the Free Software Foundation; either version 2 of the License, or
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15 | # (at your option) any later version.
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16 | #
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17 | # This program is distributed in the hope that it will be useful,
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18 | # but WITHOUT ANY WARRANTY; without even the implied warranty of
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19 | # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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20 | # GNU General Public License for more details.
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21 | #
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22 | # You should have received a copy of the GNU General Public License
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23 | # along with this program; if not, write to the Free Software
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24 | # Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA.
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25 | #
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26 | ###########################################################################
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27 |
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28 | package GreenstoneSQLPlugin;
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29 |
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30 |
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31 | use strict;
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32 | no strict 'refs'; # allow filehandles to be variables and viceversa
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33 |
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34 | use DBI;
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35 | use docprint; # for new unescape_text() subroutine
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36 | use GreenstoneXMLPlugin;
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37 | use gssql;
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38 |
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39 |
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40 | # TODO:
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41 | # - Run TODOs here, in Plugout and in gssql.pm by Dr Bainbridge.
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42 | # - Have not yet tested writing out just meta or just fulltxt to sql db and reading just that
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43 | # back in from the sql db while the remainder is to be read back in from the docsql .xml files.
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44 |
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45 | # TODO: deal with incremental vs removeold. If docs removed from import folder, then import step
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46 | # won't delete it from archives but buildcol step will. Need to implement this with this database plugin or wherever the actual flow is
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47 |
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48 | # TODO Q: is "reindex" = del from db + add to db?
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49 | # - is this okay for reindexing, or will it need to modify existing values (update table)
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50 | # - if it's okay, what does reindex need to accomplish (and how) if the OID changes because hash id produced is different?
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51 | # - delete is accomplished in GS SQL Plugin, during buildcol.pl. When should reindexing take place?
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52 | # during SQL plugout/import.pl or during plugin? If adding is done by GSSQLPlugout, does it need to
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53 | # be reimplemented in GSSQLPlugin to support the adding portion of reindexing.
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54 |
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55 | # TODO: Add public instructions on using this plugin and its plugout: start with installing mysql binary, changing pwd, running the server (and the client against it for checking: basic cmds like create and drop). Then discuss db name, table names (per coll), db cols and col types, and how the plugout and plugin work.
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56 | # Discuss the plugin/plugout parameters.
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57 |
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58 |
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59 | # DONE:
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60 | # + TODO: Incremental delete can't work until GSSQLPlugout has implemented build_mode = incremental
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61 | # (instead of tossing away db on every build)
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62 | # + Ask about docsql naming convention adopted to identify OID. Better way?
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63 | # collection names -> table names: it seems hyphens not allowed. Changed to underscores.
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64 | # + Startup parameters (except removeold/build_mode)
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65 | # + how do we detect we're to do removeold during plugout in import.pl phase
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66 | # + incremental building: where do we need to add code to delete rows from our sql table after
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67 | # incrementally importing a coll with fewer docs (for instance)? What about deleted/modified meta?
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68 | # + Ask if I can assume that all SQL dbs (not just MySQL) will preserve the order of inserted nodes
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69 | # (sections) which in this case had made it easy to reconstruct the doc_obj in memory in the correct order.
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70 | # YES: Otherwise for later db types (drivers), can set order by primary key column and then order by did column
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71 | # + NOTTODO: when db is not running GLI is paralyzed -> can we set timeout on DBI connection attempt?
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72 | # NOT A PROBLEM: Tested to find DBI connection attempt fails immediately when MySQL server not
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73 | # running. The GLI "paralyzing" incident last time was not because of the gs sql connection code,
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74 | # but because my computer was freezing on-and-off.
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75 | # + "Courier" demo documents in lucene-sql collection: character (degree symbol) not preserved in title. Is this because we encode in utf8 when putting into db and reading back in?
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76 | # Test doc with meta and text like macron in Maori text.
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77 | # + TODO Q: During import, the GS SQL Plugin is called before the GS SQL Plugout with undesirable side
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78 | # effect that if the db doesn't exist, gssql::use_db() fails, as it won't create db.
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79 | # This got fixed when GSSQLPlugin stopped connecting on init().
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80 |
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81 |
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82 | ########################################################################################
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83 |
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84 | # GreenstoneSQLPlugin inherits from GreenstoneXMLPlugin so that it if meta or fulltext
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85 | # is still written out to doc.xml (docsql .xml), that will be processed as usual,
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86 | # whereas GreenstoneSQLPlugin will process all the rest (full text and/or meta, whichever
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87 | # is written out by GreenstoneSQLPlugout into the SQL db).
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88 |
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89 |
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90 | sub BEGIN {
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91 | @GreenstoneSQLPlugin::ISA = ('GreenstoneXMLPlugin');
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92 | }
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93 |
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94 | # This plugin must be in the document plugins pipeline IN PLACE OF GreenstoneXMLPlugin
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95 | # So we won't have a process exp conflict here.
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96 | # The structure of docsql.xml files is identical to doc.xml and the contents are similar except:
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97 | # - since metadata and/or fulltxt are stored in mysql db instead, just XML comments indicating
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98 | # this are left inside docsql.xml within the <Description> (for meta) and/or <Content> (for txt)
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99 | # - the root element Archive now has a docoid attribute: <Archive docoid="OID">
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100 | sub get_default_process_exp {
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101 | my $self = shift (@_);
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102 |
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103 | return q^(?i)docsql(-\d+)?\.xml$^; # regex based on this method in GreenstoneXMLPlugin
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104 | #return q^(?i)docsql(-.+)?\.xml$^; # no longer storing the OID embedded in docsql .xml filename
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105 | }
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106 |
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107 | my $process_mode_list =
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108 | [ { 'name' => "meta_only",
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109 | 'desc' => "{GreenstoneSQLPlug.process_mode.meta_only}" },
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110 | { 'name' => "text_only",
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111 | 'desc' => "{GreenstoneSQLPlug.process_mode.text_only}" },
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112 | { 'name' => "all",
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113 | 'desc' => "{GreenstoneSQLPlug.process_mode.all}" } ];
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114 |
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115 | my $arguments =
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116 | [ { 'name' => "process_exp",
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117 | 'desc' => "{BaseImporter.process_exp}",
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118 | 'type' => "regexp",
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119 | 'deft' => &get_default_process_exp(),
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120 | 'reqd' => "no" },
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121 | { 'name' => "process_mode",
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122 | 'desc' => "{GreenstoneSQLPlug.process_mode}",
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123 | 'type' => "enum",
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124 | 'list' => $process_mode_list,
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125 | 'deft' => "all",
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126 | 'reqd' => "no"},
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127 | { 'name' => "db_driver",
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128 | 'desc' => "{GreenstoneSQLPlug.db_driver}",
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129 | 'type' => "string",
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130 | 'deft' => "mysql",
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131 | 'reqd' => "yes"},
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132 | { 'name' => "db_client_user",
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133 | 'desc' => "{GreenstoneSQLPlug.db_client_user}",
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134 | 'type' => "string",
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135 | 'deft' => "root",
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136 | 'reqd' => "yes"},
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137 | { 'name' => "db_client_pwd",
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138 | 'desc' => "{GreenstoneSQLPlug.db_client_pwd}",
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139 | 'type' => "string",
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140 | 'deft' => "",
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141 | 'reqd' => "yes"}, # pwd required?
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142 | { 'name' => "db_host",
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143 | 'desc' => "{GreenstoneSQLPlug.db_host}",
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144 | 'type' => "string",
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145 | 'deft' => "127.0.0.1",
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146 | 'reqd' => "yes"},
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147 | ];
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148 |
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149 | my $options = { 'name' => "GreenstoneSQLPlugin",
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150 | 'desc' => "{GreenstoneSQLPlugin.desc}",
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151 | 'abstract' => "no",
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152 | 'inherits' => "yes",
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153 | 'args' => $arguments };
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154 |
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155 |
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156 | # TODO: For on cancel, add a SIGTERM handler or so to call end()
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157 | # or to explicitly call gs_sql->close_connection if $gs_sql def
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158 |
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159 | sub new {
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160 | my ($class) = shift (@_);
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161 | my ($pluginlist,$inputargs,$hashArgOptLists) = @_;
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162 | push(@$pluginlist, $class);
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163 |
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164 | push(@{$hashArgOptLists->{"ArgList"}},@{$arguments});
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165 | push(@{$hashArgOptLists->{"OptList"}},$options);
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166 |
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167 | my $self = new GreenstoneXMLPlugin($pluginlist, $inputargs, $hashArgOptLists);
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168 |
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169 |
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170 | #return bless $self, $class;
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171 | $self = bless $self, $class;
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172 | if ($self->{'info_only'}) {
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173 | # If running pluginfo, we don't need to go further.
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174 | return $self;
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175 | }
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176 |
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177 | # do anything else that needs to be done here when not pluginfo
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178 |
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179 | return $self;
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180 | }
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181 |
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182 | # This is called once if removeold is set with import.pl. Most plugins will do
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183 | # nothing but if a plugin does any stuff outside of creating doc obj, then
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184 | # it may need to clear something.
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185 | # In the case of GreenstoneSQL plugs: this is the first time we have a chance
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186 | # to purge the tables of the current collection from the current site's database
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187 | sub remove_all {
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188 | my $self = shift (@_);
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189 | my ($pluginfo, $base_dir, $processor, $maxdocs) = @_;
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190 |
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191 | print STDERR " Building with removeold option set, so deleting current collection's tables if they exist\n" if($self->{'verbosity'});
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192 |
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193 | # if we're in here, we'd already have run 'use database <site_name>;' during sub init()
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194 | # so we can go ahead and delete the collection's tables
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195 | my $gs_sql = $self->{'gs_sql'};
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196 | $gs_sql->delete_collection_tables(); # will delete them if they exist
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197 |
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198 | # and recreate tables? No. Tables' existence is ensured in GreenstoneSQLPlugout::begin()
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199 | my $proc_mode = $self->{'process_mode'};
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200 | if($proc_mode ne "text_only") {
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201 | $gs_sql->ensure_meta_table_exists();
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202 | }
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203 | if($proc_mode ne "meta_only") {
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204 | $gs_sql->ensure_fulltxt_table_exists();
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205 | }
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206 | }
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207 |
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208 | # This is called per document for docs that have been deleted from the
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209 | # collection. Most plugins will do nothing
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210 | # but if a plugin does any stuff outside of creating doc obj, then it may need
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211 | # to clear something.
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212 | # remove the doc(s) denoted by oids from GS SQL db
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213 | # This takes care of incremental deletes (docs marked D by ArchivesInfPlugin when building
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214 | # incrementally) as well as cases of "Non-icremental Delete", see ArchivesInfPlugin.pm
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215 | sub remove_one {
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216 | my $self = shift (@_);
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217 |
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218 | my ($file, $oids, $archivedir) = @_;
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219 |
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220 | print STDERR "@@@ IN SQLPLUG::REMOVE_ONE: $file\n";
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221 |
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222 | #return undef unless $self->can_process_this_file($file); # NO, DON'T DO THIS:
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223 | # WE DON'T CARE IF IT'S AN IMAGE FILE THAT WAS DELETED.
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224 | # WE CARE ABOUT REMOVING THE DOCOID OF THAT IMAGE FILE FROM THE DB
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225 |
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226 | print STDERR "*****************************\nAsked to remove_one oid\n***********************\n";
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227 |
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228 | my $gs_sql = $self->{'gs_sql'} || return 0; # couldn't make the connection or no db etc
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229 | if(scalar @$oids > 1) {
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230 | print STDERR "TODO: We now have reason to optimise GreenstoneSQLPlugin::remove_one() by using prepare and execute.\n";
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231 | }
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232 |
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233 | my $proc_mode = $self->{'process_mode'};
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234 | foreach my $oid (@$oids) {
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235 | if($proc_mode eq "all" || $proc_mode eq "meta_only") {
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236 | print STDERR "@@@@@@@@ Deleting $oid from meta table\n" if $self->{'verbosity'} > 2;
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237 | $gs_sql->delete_recs_from_metatable_with_docid($oid);
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238 | }
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239 | if($proc_mode eq "all" || $proc_mode eq "text_only") {
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240 | print STDERR "@@@@@@@@ Deleting $oid from fulltxt table\n" if $self->{'verbosity'} > 2;
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241 | $gs_sql->delete_recs_from_texttable_with_docid($oid);
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242 | }
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243 | }
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244 | return 1;
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245 | }
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246 |
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247 |
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248 | sub xml_start_tag {
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249 | my $self = shift(@_);
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250 | my ($expat, $element) = @_;
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251 |
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252 | my $outhandle = $self->{'outhandle'};
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253 |
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254 | $self->{'element'} = $element;
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255 | if ($element eq "Archive") { # docsql.xml files contain a OID attribute on Archive element
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256 | # the element's attributes are in %_ as per ReadXMLFile::xml_start_tag() (while $_
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257 | # contains the tag)
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258 |
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259 | # Don't access %_{'docoid'} directly: keep getting a warning message to
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260 | # use $_{'docoid'} for scalar contexts, but %_ is the element's attr hashmap
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261 | # whereas $_ has the tag info. So we don't want to do $_{'docoid'}.
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262 | my %attr_hash = %_; # right way, see OAIPlugin.pm
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263 | $self->{'doc_oid'} = $attr_hash{'docoid'};
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264 | ##print STDERR "XXXXXXXXXXXXXX in SQLPlugin::xml_start_tag()\n";
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265 | print $outhandle "Extracted OID from docsql.xml: ".$self->{'doc_oid'}."\n"
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266 | if $self->{'verbosity'} > 2;
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267 |
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268 | }
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269 | else { # let superclass GreenstoneXMLPlugin continue to process <Section> and <Metadata> elements
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270 | $self->SUPER::xml_start_tag(@_);
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271 | }
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272 | }
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273 |
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274 | # TODO Q: Why are there 4 passes when we're only indexing at doc and section level (2 passes)? What's the dummy pass, why is there a pass for infodb?
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275 |
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276 | # We should only ever get here during the buildcol.pl phase
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277 | # At the end of superclass GreenstoneXMLPlugin.pm's close_document() method,
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278 | # the doc_obj in memory is processed (indexed) and then made undef.
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279 | # So we have to work with doc_obj before superclass close_document() is finished.
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280 | sub close_document {
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281 | my $self = shift(@_);
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282 |
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283 | ##print STDERR "XXXXXXXXX in SQLPlugin::close_doc()\n";
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284 |
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285 | my $gs_sql = $self->{'gs_sql'};
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286 |
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287 | my $outhandle = $self->{'outhandle'};
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288 | my $doc_obj = $self->{'doc_obj'};
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289 |
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290 | my $oid = $self->{'doc_oid'}; # we stored current doc's OID during sub xml_start_tag()
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291 | my $proc_mode = $self->{'process_mode'};
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292 |
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293 | # For now, we have access to doc_obj (until just before super::close_document() terminates)
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294 |
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295 | # no need to call $self->{'doc_obj'}->set_OID($oid);
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296 | # because either the OID is stored in the SQL db as meta 'Identifier' alongside other metadata
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297 | # or it's stored in the doc.xml as metadata 'Identifier' alongside other metadata
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298 | # Either way, Identifier meta will be read into the docobj automatically with other meta.
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299 |
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300 | print STDERR " GreenstoneSQLPlugin processing doc $oid (reading into docobj from SQL db)\n"
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301 | if $self->{'verbosity'} > 0;
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302 |
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303 | if($proc_mode eq "all" || $proc_mode eq "meta_only") {
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304 | # read in meta for the collection (i.e. select * from <col>_metadata table
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305 |
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306 | my $sth = $gs_sql->select_from_metatable_matching_docid($oid);
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307 | print $outhandle "### SQL select stmt: ".$sth->{'Statement'}."\n"
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308 | if $self->{'verbosity'} > 2;
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309 |
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310 | print $outhandle "----------SQL DB contains meta-----------\n" if $self->{'verbosity'} > 2;
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311 | # https://www.effectiveperlprogramming.com/2010/07/set-custom-dbi-error-handlers/
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312 | while( my @row = $sth->fetchrow_array() ) {
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313 | #print $outhandle "row: @row\n";
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314 | my ($primary_key, $did, $sid, $metaname, $metaval) = @row;
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315 |
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316 | # get rid of the artificial "root" introduced in section id when saving to sql db
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317 | $sid =~ s@^root@@;
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318 | $sid = $doc_obj->get_top_section() unless $sid;
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319 | print $outhandle "### did: $did, sid: |$sid|, meta: $metaname, val: $metaval\n"
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320 | if $self->{'verbosity'} > 2;
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321 |
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322 | # TODO: we accessed the db in utf8 mode, so, we can call doc_obj->add_utf8_meta directly:
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323 | $doc_obj->add_utf8_metadata($sid, $metaname, &docprint::unescape_text($metaval));
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324 | }
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325 | print $outhandle "----------FIN READING DOC's META FROM SQL DB------------\n"
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326 | if $self->{'verbosity'} > 2;
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327 | }
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328 |
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329 | if($proc_mode eq "all" || $proc_mode eq "text_only") {
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330 | # read in fulltxt for the collection (i.e. select * from <col>_fulltxt table
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331 |
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332 | my $fulltxt_table = $gs_sql->get_fulltext_table_name();
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333 |
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334 |
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335 | my $sth = $gs_sql->select_from_texttable_matching_docid($oid);
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336 | print $outhandle "### stmt: ".$sth->{'Statement'}."\n" if $self->{'verbosity'} > 2;
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337 |
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338 | print $outhandle "----------\nSQL DB contains txt entries for-----------\n"
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339 | if $self->{'verbosity'} > 2;
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340 | while( my ($primary_key, $did, $sid, $text) = $sth->fetchrow_array() ) {
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341 |
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342 | # get rid of the artificial "root" introduced in section id when saving to sql db
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343 | #$sid =~ s@^root@@;
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344 | $sid = $doc_obj->get_top_section() if ($sid eq "root");
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345 | print $outhandle "### did: $did, sid: |$sid|, fulltext: <TXT>\n"
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346 | if $self->{'verbosity'} > 2;
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347 |
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348 | # TODO - pass by ref?
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349 | # TODO: we accessed the db in utf8 mode, so, we can call doc_obj->add_utf8_text directly:
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350 | $doc_obj->add_utf8_text($sid, &docprint::unescape_text($text));
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351 | }
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352 | print $outhandle "----------FIN READING DOC's TXT FROM SQL DB------------\n"
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353 | if $self->{'verbosity'} > 2;
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354 | }
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355 |
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356 | # done reading into docobj from SQL db
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357 |
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358 | # don't forget to clean up on close() in superclass
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359 | # It will get the doc_obj indexed then make it undef
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360 | $self->SUPER::close_document(@_);
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361 | }
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362 |
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363 |
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364 | # TODO: only want to work with sql db if buildcol.pl. Unfortunately, also runs on import.pl.
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365 | # During import, the GS SQL Plugin is called before the GS SQL Plugout with undesirable side
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366 | # effect that if the db doesn't exist, gssql::use_db() fails, as it won't create db.
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367 |
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368 | # GS SQL Plugin::init() (and deinit()) is called by import.pl and also by buildcol.pl
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369 | # This means it connects and deconnects during import.pl as well. This is okay
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370 | # as removeold, which should drop the collection tables, happens during the import phase
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371 | # and therefore also requires a db connection.
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372 | # TODO: Eventually can try moving get_gssql_instance into gssql.pm? That way both GS SQL Plugin
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373 | # and Plugout would be using one connection during import.pl phase when both plugs exist.
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374 |
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375 | # Call init() not begin() because there can be multiple plugin passes and begin() called for
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376 | # each pass (one for doc level and another for section level indexing), whereas init() should
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377 | # be called before any and all passes.
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378 | # This way, we can connect to the SQL database once per buildcol run.
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379 | sub init {
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380 | my ($self) = shift (@_);
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381 | ##print STDERR "@@@@@@@@@@ INIT CALLED\n";
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382 |
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383 | $self->SUPER::init(@_); # super (GreenstoneXMLPlugin) will not yet be trying to read from doc.xml (docsql .xml) files in init().
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384 |
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385 | ####################
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386 | # print "@@@ SITE NAME: ". $self->{'site_name'} . "\n" if defined $self->{'site_name'};
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387 | # print "@@@ COLL NAME: ". $ENV{'GSDLCOLLECTION'} . "\n";
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388 |
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389 | # print STDERR "@@@@ db_pwd: " . $self->{'db_client_pwd'} . "\n";
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390 | # print STDERR "@@@@ user: " . $self->{'db_client_user'} . "\n";
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391 | # print STDERR "@@@@ db_host: " . $self->{'db_host'} . "\n";
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392 | # print STDERR "@@@@ db_driver: " . $self->{'db_driver'} . "\n";
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393 | ####################
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394 |
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395 | # create gssql object.
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396 | # collection name will be used for naming tables (site name will be used for naming database)
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397 | my $gs_sql = new gssql({
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398 | 'collection_name' => $ENV{'GSDLCOLLECTION'},
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399 | 'verbosity' => $self->{'verbosity'}
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400 | });
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401 |
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402 | # try connecting to the mysql db, if that fails it will die
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403 | if(!$gs_sql->connect_to_db({
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404 | 'db_driver' => $self->{'db_driver'},
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405 | 'db_client_user' => $self->{'db_client_user'},
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406 | 'db_client_pwd' => $self->{'db_client_pwd'},
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407 | 'db_host' => $self->{'db_host'}
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408 | })
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409 | )
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410 | {
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411 | # This is fatal for the plugout, let's terminate here
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412 | # PrintError would already have displayed the warning message on connection fail
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413 | die("Could not connect to db. Can't proceed.\n");
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414 | }
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415 |
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416 | my $db_name = $self->{'site_name'} || "greenstone2"; # one database per GS3 site, for GS2 the db is called greenstone2
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417 |
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418 | # Attempt to use the db, create it if it doesn't exist (but don't create the tables yet)
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419 | # Bail if we can't use the database
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420 | if(!$gs_sql->use_db($db_name)) {
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421 |
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422 | # This is fatal for the plugout, let's terminate here after disconnecting again
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423 | # PrintError would already have displayed the warning message on load fail
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424 | $gs_sql->disconnect_from_db()
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425 | || warn("Unable to disconnect from database.\n");
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426 | die("Could not use db $db_name. Can't proceed.\n");
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427 | }
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428 |
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429 |
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430 | # store db handle now that we're connected
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431 | $self->{'gs_sql'} = $gs_sql;
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432 | }
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433 |
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434 |
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435 | # This method also runs on import.pl if gs_sql has a value. But we just want to run it on buildcol
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436 | # Call deinit() not end() because there can be multiple plugin passes:
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437 | # one for doc level and another for section level indexing
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438 | # and deinit() should be called before all passes
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439 | # This way, we can close the SQL database once per buildcol run.
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440 | sub deinit {
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441 | my ($self) = shift (@_);
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442 |
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443 | ##print STDERR "@@@@@@@@@@ GreenstoneSQLPlugin::DEINIT CALLED\n";
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444 |
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445 | if($self->{'gs_sql'}) { # only want to work with sql db if buildcol.pl, gs_sql won't have
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446 | # a value except during buildcol, so when processor =~ m/buildproc$/.
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447 | $self->{'gs_sql'}->disconnect_from_db()
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448 | || warn("Unable to disconnect from database " . $self->{'site_name'} . "\n");
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449 |
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450 | # explicitly delete gs_sql key (setting key to undef has a different meaning from deleting)
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451 | # so all future use has to make the connection again
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452 | delete $self->{'gs_sql'};
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453 | }
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454 |
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455 | $self->SUPER::deinit(@_);
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456 | }
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457 |
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458 |
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459 |
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460 |
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