Mercurial > hg > orthanc-databases

annotate PostgreSQL/Plugins/PostgreSQLIndex.cpp @ 79:cb0aac9bbada db-changes

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author Sebastien Jodogne <s.jodogne@gmail.com>
date Tue, 08 Jan 2019 14:37:41 +0100
parents 2ee166f77501
children 1012fe77241c
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1 /**
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2 * Orthanc - A Lightweight, RESTful DICOM Store
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3 * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics
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4 * Department, University Hospital of Liege, Belgium
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714c5d2bee76 preparing for 2019
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5 * Copyright (C) 2017-2019 Osimis S.A., Belgium
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6 *
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7 * This program is free software: you can redistribute it and/or
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8 * modify it under the terms of the GNU Affero General Public License
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9 * as published by the Free Software Foundation, either version 3 of
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10 * the License, or (at your option) any later version.
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11 *
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12 * This program is distributed in the hope that it will be useful, but
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13 * WITHOUT ANY WARRANTY; without even the implied warranty of
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14 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
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15 * Affero General Public License for more details.
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16 *
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17 * You should have received a copy of the GNU Affero General Public License
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18 * along with this program. If not, see <http://www.gnu.org/licenses/>.
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19 **/
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21
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22 #include "PostgreSQLIndex.h"
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23
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24 #include "../../Framework/Plugins/GlobalProperties.h"
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25 #include "../../Framework/PostgreSQL/PostgreSQLDatabase.h"
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26 #include "../../Framework/PostgreSQL/PostgreSQLTransaction.h"
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27
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28 #include <EmbeddedResources.h> // Auto-generated file
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30 #include <Core/Logging.h>
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31 #include <Core/OrthancException.h>
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34 namespace Orthanc
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35 {
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36 // Some aliases for internal properties
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37 static const GlobalProperty GlobalProperty_HasTrigramIndex = GlobalProperty_DatabaseInternal0;
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38 static const GlobalProperty GlobalProperty_HasCreateInstance = GlobalProperty_DatabaseInternal1;
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39 static const GlobalProperty GlobalProperty_HasFastCountResources = GlobalProperty_DatabaseInternal2;
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40 }
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41
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43 namespace OrthancDatabases
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44 {
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45 IDatabase* PostgreSQLIndex::OpenInternal()
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46 {
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47 uint32_t expectedVersion = 6;
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48 if (context_)
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49 {
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50 expectedVersion = OrthancPluginGetExpectedDatabaseVersion(context_);
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51 }
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52 else
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53 {
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54 // This case only occurs during unit testing
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55 expectedVersion = 6;
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56 }
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57
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58 // Check the expected version of the database
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59 if (expectedVersion != 6)
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60 {
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61 LOG(ERROR) << "This database plugin is incompatible with your version of Orthanc "
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62 << "expecting the DB schema version " << expectedVersion
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63 << ", but this plugin is only compatible with version 6";
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64 throw Orthanc::OrthancException(Orthanc::ErrorCode_Plugin);
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65 }
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66
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67 std::auto_ptr<PostgreSQLDatabase> db(new PostgreSQLDatabase(parameters_));
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68
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69 db->Open();
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71 if (parameters_.HasLock())
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72 {
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73 db->AdvisoryLock(42 /* some arbitrary constant */);
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74 }
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76 if (clearAll_)
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77 {
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78 db->ClearAll();
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79 }
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81 {
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82 PostgreSQLTransaction t(*db);
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83
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84 if (!db->DoesTableExist("Resources"))
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85 {
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86 std::string query;
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87
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88 Orthanc::EmbeddedResources::GetFileResource
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89 (query, Orthanc::EmbeddedResources::POSTGRESQL_PREPARE_INDEX);
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90 db->Execute(query);
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91
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92 SetGlobalIntegerProperty(*db, t, Orthanc::GlobalProperty_DatabaseSchemaVersion, expectedVersion);
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93 SetGlobalIntegerProperty(*db, t, Orthanc::GlobalProperty_DatabasePatchLevel, 1);
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94 SetGlobalIntegerProperty(*db, t, Orthanc::GlobalProperty_HasTrigramIndex, 0);
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95 }
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96
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97 if (!db->DoesTableExist("Resources"))
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98 {
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99 LOG(ERROR) << "Corrupted PostgreSQL database";
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100 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError);
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101 }
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102
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103 int version = 0;
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104 if (!LookupGlobalIntegerProperty(version, *db, t, Orthanc::GlobalProperty_DatabaseSchemaVersion) ||
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105 version != 6)
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106 {
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107 LOG(ERROR) << "PostgreSQL plugin is incompatible with database schema version: " << version;
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108 throw Orthanc::OrthancException(Orthanc::ErrorCode_Database);
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109 }
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110
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111 int revision;
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112 if (!LookupGlobalIntegerProperty(revision, *db, t, Orthanc::GlobalProperty_DatabasePatchLevel))
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113 {
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114 revision = 1;
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115 SetGlobalIntegerProperty(*db, t, Orthanc::GlobalProperty_DatabasePatchLevel, revision);
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116 }
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117
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118 if (revision != 1)
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119 {
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120 LOG(ERROR) << "PostgreSQL plugin is incompatible with database schema revision: " << revision;
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121 throw Orthanc::OrthancException(Orthanc::ErrorCode_Database);
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122 }
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123
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124 t.Commit();
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125 }
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126
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127 {
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128 PostgreSQLTransaction t(*db);
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129
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130 int hasTrigram = 0;
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131 if (!LookupGlobalIntegerProperty(hasTrigram, *db, t,
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132 Orthanc::GlobalProperty_HasTrigramIndex) ||
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133 hasTrigram != 1)
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134 {
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135 /**
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136 * Apply fix for performance issue (speed up wildcard search
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137 * by using GIN trigrams). This implements the patch suggested
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138 * in issue #47, BUT we also keep the original
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139 * "DicomIdentifiersIndexValues", as it leads to better
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140 * performance for "strict" searches (i.e. searches involving
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141 * no wildcard).
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142 * https://www.postgresql.org/docs/current/static/pgtrgm.html
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143 * https://bitbucket.org/sjodogne/orthanc/issues/47/index-improvements-for-pg-plugin
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144 **/
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145 try
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146 {
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147 // We've observed 9 minutes on DB with 100000 studies
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148 LOG(WARNING) << "Trying to enable trigram matching on the PostgreSQL database "
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149 << "to speed up wildcard searches. This may take several minutes";
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150
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151 db->Execute(
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152 "CREATE EXTENSION IF NOT EXISTS pg_trgm; "
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153 "CREATE INDEX DicomIdentifiersIndexValues2 ON DicomIdentifiers USING gin(value gin_trgm_ops);");
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154
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155 SetGlobalIntegerProperty(*db, t, Orthanc::GlobalProperty_HasTrigramIndex, 1);
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156 LOG(WARNING) << "Trigram index has been created";
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157
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158 t.Commit();
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159 }
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160 catch (Orthanc::OrthancException&)
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161 {
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162 LOG(WARNING) << "Performance warning: Your PostgreSQL server does "
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163 << "not support trigram matching";
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164 LOG(WARNING) << "-> Consider installing the \"pg_trgm\" extension on the "
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165 << "PostgreSQL server, e.g. on Debian: sudo apt install postgresql-contrib";
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166 }
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167 }
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168 else
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169 {
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170 t.Commit();
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171 }
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172 }
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173
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174 {
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175 PostgreSQLTransaction t(*db);
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176
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177 int hasCreateInstance = 0;
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178 if (!LookupGlobalIntegerProperty(hasCreateInstance, *db, t,
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179 Orthanc::GlobalProperty_HasCreateInstance) ||
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180 hasCreateInstance != 1)
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181 {
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182 LOG(INFO) << "Installing the CreateInstance extension";
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183
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184 std::string query;
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185 Orthanc::EmbeddedResources::GetFileResource
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186 (query, Orthanc::EmbeddedResources::POSTGRESQL_CREATE_INSTANCE);
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187 db->Execute(query);
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188
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189 SetGlobalIntegerProperty(*db, t, Orthanc::GlobalProperty_HasCreateInstance, 1);
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190 }
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191
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192 t.Commit();
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193 }
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194
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195 {
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196 PostgreSQLTransaction t(*db);
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197
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198 int hasFastTotalSize = 0;
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199 if (!LookupGlobalIntegerProperty(hasFastTotalSize, *db, t,
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200 Orthanc::GlobalProperty_GetTotalSizeIsFast) ||
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201 hasFastTotalSize != 1)
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202 {
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203 LOG(INFO) << "Installing the FastTotalSize extension";
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204
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205 std::string query;
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206 Orthanc::EmbeddedResources::GetFileResource
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207 (query, Orthanc::EmbeddedResources::POSTGRESQL_FAST_TOTAL_SIZE);
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208 db->Execute(query);
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209
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210 SetGlobalIntegerProperty(*db, t, Orthanc::GlobalProperty_GetTotalSizeIsFast, 1);
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211 }
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212
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213 t.Commit();
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214 }
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215
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216 {
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217 PostgreSQLTransaction t(*db);
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218
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219 // Installing this extension requires the "GlobalIntegers" table
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220 // created by the "FastTotalSize" extension
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221 int property = 0;
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222 if (!LookupGlobalIntegerProperty(property, *db, t,
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223 Orthanc::GlobalProperty_HasFastCountResources) ||
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224 property != 1)
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225 {
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226 LOG(INFO) << "Installing the FastCountResources extension";
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227
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228 std::string query;
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229 Orthanc::EmbeddedResources::GetFileResource
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230 (query, Orthanc::EmbeddedResources::POSTGRESQL_FAST_COUNT_RESOURCES);
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231 db->Execute(query);
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232
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233 SetGlobalIntegerProperty(*db, t, Orthanc::GlobalProperty_HasFastCountResources, 1);
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234 }
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235
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236 t.Commit();
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237 }
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238
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239 return db.release();
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240 }
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241
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242
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243 PostgreSQLIndex::PostgreSQLIndex(const PostgreSQLParameters& parameters) :
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244 IndexBackend(new Factory(*this)),
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245 context_(NULL),
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246 parameters_(parameters),
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247 clearAll_(false)
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248 {
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249 }
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250
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251
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252 int64_t PostgreSQLIndex::CreateResource(const char* publicId,
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253 OrthancPluginResourceType type)
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254 {
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255 DatabaseManager::CachedStatement statement(
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256 STATEMENT_FROM_HERE, GetManager(),
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257 "INSERT INTO Resources VALUES(${}, ${type}, ${id}, NULL) RETURNING internalId");
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258
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259 statement.SetParameterType("id", ValueType_Utf8String);
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260 statement.SetParameterType("type", ValueType_Integer64);
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261
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262 Dictionary args;
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263 args.SetUtf8Value("id", publicId);
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264 args.SetIntegerValue("type", static_cast<int>(type));
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265
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266 statement.Execute(args);
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267
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268 return ReadInteger64(statement, 0);
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269 }
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270
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271
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272 uint64_t PostgreSQLIndex::GetTotalCompressedSize()
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273 {
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274 // Fast version if extension "./FastTotalSize.sql" is installed
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275 uint64_t result;
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276
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277 {
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278 DatabaseManager::CachedStatement statement(
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279 STATEMENT_FROM_HERE, GetManager(),
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280 "SELECT value FROM GlobalIntegers WHERE key = 0");
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281
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282 statement.SetReadOnly(true);
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283 statement.Execute();
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284
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285 result = static_cast<uint64_t>(ReadInteger64(statement, 0));
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286 }
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287
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288 assert(result == IndexBackend::GetTotalCompressedSize());
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289 return result;
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290 }
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291
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292
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293 uint64_t PostgreSQLIndex::GetTotalUncompressedSize()
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294 {
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295 // Fast version if extension "./FastTotalSize.sql" is installed
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296 uint64_t result;
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297
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298 {
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299 DatabaseManager::CachedStatement statement(
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300 STATEMENT_FROM_HERE, GetManager(),
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301 "SELECT value FROM GlobalIntegers WHERE key = 1");
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302
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303 statement.SetReadOnly(true);
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304 statement.Execute();
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305
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306 result = static_cast<uint64_t>(ReadInteger64(statement, 0));
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307 }
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308
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309 assert(result == IndexBackend::GetTotalUncompressedSize());
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310 return result;
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311 }
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312
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313
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314 #if ORTHANC_PLUGINS_HAS_DATABASE_CONSTRAINT == 1
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315 void PostgreSQLIndex::CreateInstance(OrthancPluginCreateInstanceResult& result,
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316 const char* hashPatient,
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317 const char* hashStudy,
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318 const char* hashSeries,
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319 const char* hashInstance)
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320 {
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321 DatabaseManager::CachedStatement statement(
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322 STATEMENT_FROM_HERE, GetManager(),
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323 "SELECT * FROM CreateInstance(${patient}, ${study}, ${series}, ${instance})");
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324
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325 statement.SetParameterType("patient", ValueType_Utf8String);
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326 statement.SetParameterType("study", ValueType_Utf8String);
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327 statement.SetParameterType("series", ValueType_Utf8String);
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328 statement.SetParameterType("instance", ValueType_Utf8String);
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329
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330 Dictionary args;
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331 args.SetUtf8Value("patient", hashPatient);
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332 args.SetUtf8Value("study", hashStudy);
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333 args.SetUtf8Value("series", hashSeries);
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334 args.SetUtf8Value("instance", hashInstance);
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335
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336 statement.Execute(args);
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337
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338 if (statement.IsDone() ||
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339 statement.GetResultFieldsCount() != 8)
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340 {
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341 throw Orthanc::OrthancException(Orthanc::ErrorCode_Database);
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342 }
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343
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344 for (size_t i = 0; i < 8; i++)
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345 {
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346 statement.SetResultFieldType(i, ValueType_Integer64);
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347 }
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348
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349 result.isNewInstance = (ReadInteger64(statement, 3) == 1);
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350 result.instanceId = ReadInteger64(statement, 7);
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351
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352 if (result.isNewInstance)
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353 {
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354 result.isNewPatient = (ReadInteger64(statement, 0) == 1);
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355 result.isNewStudy = (ReadInteger64(statement, 1) == 1);
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356 result.isNewSeries = (ReadInteger64(statement, 2) == 1);
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357 result.patientId = ReadInteger64(statement, 4);
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358 result.studyId = ReadInteger64(statement, 5);
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359 result.seriesId = ReadInteger64(statement, 6);
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360 }
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361 }
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362 #endif
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363
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364
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365 uint64_t PostgreSQLIndex::GetResourceCount(OrthancPluginResourceType resourceType)
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366 {
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367 // Optimized version thanks to the "FastCountResources.sql" extension
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368
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369 assert(OrthancPluginResourceType_Patient == 0 &&
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370 OrthancPluginResourceType_Study == 1 &&
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371 OrthancPluginResourceType_Series == 2 &&
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372 OrthancPluginResourceType_Instance == 3);
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373
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374 uint64_t result;
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375
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376 {
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377 DatabaseManager::CachedStatement statement(
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378 STATEMENT_FROM_HERE, GetManager(),
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379 "SELECT value FROM GlobalIntegers WHERE key = ${key}");
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380
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381 statement.SetParameterType("key", ValueType_Integer64);
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382
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383 Dictionary args;
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384
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385 // For an explanation of the "+ 2" below, check out "FastCountResources.sql"
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386 args.SetIntegerValue("key", static_cast<int>(resourceType + 2));
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387
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388 statement.SetReadOnly(true);
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389 statement.Execute(args);
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390
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391 result = static_cast<uint64_t>(ReadInteger64(statement, 0));
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392 }
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393
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394 assert(result == IndexBackend::GetResourceCount(resourceType));
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395 return result;
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396 }
0
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397 }