Mercurial > hg > orthanc-databases

annotate PostgreSQL/Plugins/PostgreSQLIndex.cpp @ 403:91124cc8a8c7 db-protobuf

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database plugins are informed about the identifier tags
author Sebastien Jodogne <s.jodogne@gmail.com>
date Tue, 11 Apr 2023 11:10:19 +0200
parents 7b3acfa95bd8
children a7f0f27fe33c d700c8f9fc24
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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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5 * Copyright (C) 2017-2023 Osimis S.A., Belgium
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6 * Copyright (C) 2021-2023 Sebastien Jodogne, ICTEAM UCLouvain, Belgium
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7 *
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8 * This program is free software: you can redistribute it and/or
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9 * modify it under the terms of the GNU Affero General Public License
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10 * as published by the Free Software Foundation, either version 3 of
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11 * the License, or (at your option) any later version.
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12 *
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13 * This program is distributed in the hope that it will be useful, but
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14 * WITHOUT ANY WARRANTY; without even the implied warranty of
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15 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
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16 * Affero General Public License for more details.
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17 *
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18 * You should have received a copy of the GNU Affero General Public License
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19 * along with this program. If not, see <http://www.gnu.org/licenses/>.
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20 **/
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22
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23 #include "PostgreSQLIndex.h"
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25 #include "../../Framework/Plugins/GlobalProperties.h"
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26 #include "../../Framework/PostgreSQL/PostgreSQLDatabase.h"
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27 #include "../../Framework/PostgreSQL/PostgreSQLTransaction.h"
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28 #include "PostgreSQLDefinitions.h"
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30 #include <EmbeddedResources.h> // Auto-generated file
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31
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32 #include <Compatibility.h> // For std::unique_ptr<>
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33 #include <Logging.h>
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34 #include <OrthancException.h>
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37 namespace Orthanc
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38 {
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39 // Some aliases for internal properties
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40 static const GlobalProperty GlobalProperty_HasTrigramIndex = GlobalProperty_DatabaseInternal0;
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41 static const GlobalProperty GlobalProperty_HasCreateInstance = GlobalProperty_DatabaseInternal1;
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42 static const GlobalProperty GlobalProperty_HasFastCountResources = GlobalProperty_DatabaseInternal2;
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43 static const GlobalProperty GlobalProperty_GetLastChangeIndex = GlobalProperty_DatabaseInternal3;
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44 }
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47 namespace OrthancDatabases
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48 {
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49 PostgreSQLIndex::PostgreSQLIndex(OrthancPluginContext* context,
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50 const PostgreSQLParameters& parameters) :
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51 IndexBackend(context),
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52 parameters_(parameters),
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53 clearAll_(false)
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54 {
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55 }
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58 IDatabaseFactory* PostgreSQLIndex::CreateDatabaseFactory()
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59 {
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60 return PostgreSQLDatabase::CreateDatabaseFactory(parameters_);
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61 }
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63
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64 void PostgreSQLIndex::ConfigureDatabase(DatabaseManager& manager,
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65 bool hasIdentifierTags,
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66 const std::list<IdentifierTag>& identifierTags)
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67 {
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68 uint32_t expectedVersion = 6;
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69
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70 if (GetContext()) // "GetContext()" can possibly be NULL in the unit tests
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71 {
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72 expectedVersion = OrthancPluginGetExpectedDatabaseVersion(GetContext());
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73 }
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74
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75 // Check the expected version of the database
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76 if (expectedVersion != 6)
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77 {
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78 LOG(ERROR) << "This database plugin is incompatible with your version of Orthanc "
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79 << "expecting the DB schema version " << expectedVersion
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80 << ", but this plugin is only compatible with version 6";
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81 throw Orthanc::OrthancException(Orthanc::ErrorCode_Plugin);
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82 }
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83
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84 PostgreSQLDatabase& db = dynamic_cast<PostgreSQLDatabase&>(manager.GetDatabase());
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85
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86 if (parameters_.HasLock())
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87 {
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88 db.AdvisoryLock(POSTGRESQL_LOCK_INDEX);
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89 }
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91 {
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92 PostgreSQLDatabase::TransientAdvisoryLock lock(db, POSTGRESQL_LOCK_DATABASE_SETUP);
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94 if (clearAll_)
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95 {
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96 db.ClearAll();
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97 }
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98
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99 {
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100 DatabaseManager::Transaction t(manager, TransactionType_ReadWrite);
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101
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102 if (!t.GetDatabaseTransaction().DoesTableExist("Resources"))
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103 {
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104 std::string query;
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105
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106 Orthanc::EmbeddedResources::GetFileResource
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107 (query, Orthanc::EmbeddedResources::POSTGRESQL_PREPARE_INDEX);
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108 t.GetDatabaseTransaction().ExecuteMultiLines(query);
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109
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110 SetGlobalIntegerProperty(manager, MISSING_SERVER_IDENTIFIER, Orthanc::GlobalProperty_DatabaseSchemaVersion, expectedVersion);
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111 SetGlobalIntegerProperty(manager, MISSING_SERVER_IDENTIFIER, Orthanc::GlobalProperty_DatabasePatchLevel, 1);
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112 SetGlobalIntegerProperty(manager, MISSING_SERVER_IDENTIFIER, Orthanc::GlobalProperty_HasTrigramIndex, 0);
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113 }
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114
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115 if (!t.GetDatabaseTransaction().DoesTableExist("Resources"))
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116 {
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117 LOG(ERROR) << "Corrupted PostgreSQL database";
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118 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError);
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119 }
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120
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121 int version = 0;
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122 if (!LookupGlobalIntegerProperty(version, manager, MISSING_SERVER_IDENTIFIER, Orthanc::GlobalProperty_DatabaseSchemaVersion) ||
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123 version != 6)
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124 {
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125 LOG(ERROR) << "PostgreSQL plugin is incompatible with database schema version: " << version;
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126 throw Orthanc::OrthancException(Orthanc::ErrorCode_Database);
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127 }
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128
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129 int revision;
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130 if (!LookupGlobalIntegerProperty(revision, manager, MISSING_SERVER_IDENTIFIER, Orthanc::GlobalProperty_DatabasePatchLevel))
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131 {
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132 revision = 1;
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133 SetGlobalIntegerProperty(manager, MISSING_SERVER_IDENTIFIER, Orthanc::GlobalProperty_DatabasePatchLevel, revision);
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134 }
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136 if (revision != 1)
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137 {
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138 LOG(ERROR) << "PostgreSQL plugin is incompatible with database schema revision: " << revision;
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139 throw Orthanc::OrthancException(Orthanc::ErrorCode_Database);
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140 }
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141
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142 t.Commit();
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143 }
0
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144
136
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145 {
237
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146 DatabaseManager::Transaction t(manager, TransactionType_ReadWrite);
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147
136
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148 int hasTrigram = 0;
237
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149 if (!LookupGlobalIntegerProperty(hasTrigram, manager, MISSING_SERVER_IDENTIFIER,
136
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150 Orthanc::GlobalProperty_HasTrigramIndex) ||
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151 hasTrigram != 1)
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152 {
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153 /**
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154 * Apply fix for performance issue (speed up wildcard search
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155 * by using GIN trigrams). This implements the patch suggested
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156 * in issue #47, BUT we also keep the original
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157 * "DicomIdentifiersIndexValues", as it leads to better
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158 * performance for "strict" searches (i.e. searches involving
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159 * no wildcard).
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160 * https://www.postgresql.org/docs/current/static/pgtrgm.html
336
c0c12b3974b2 fix URLs to the old repositories
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161 * https://bugs.orthanc-server.com/show_bug.cgi?id=47
136
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162 **/
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163 try
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164 {
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165 // We've observed 9 minutes on DB with 100000 studies
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166 LOG(WARNING) << "Trying to enable trigram matching on the PostgreSQL database "
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167 << "to speed up wildcard searches. This may take several minutes";
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168
241
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169 t.GetDatabaseTransaction().ExecuteMultiLines(
136
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170 "CREATE EXTENSION IF NOT EXISTS pg_trgm; "
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171 "CREATE INDEX DicomIdentifiersIndexValues2 ON DicomIdentifiers USING gin(value gin_trgm_ops);");
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172
237
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173 SetGlobalIntegerProperty(manager, MISSING_SERVER_IDENTIFIER, Orthanc::GlobalProperty_HasTrigramIndex, 1);
136
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174 LOG(WARNING) << "Trigram index has been created";
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175
136
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176 t.Commit();
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177 }
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178 catch (Orthanc::OrthancException&)
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179 {
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180 LOG(WARNING) << "Performance warning: Your PostgreSQL server does "
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181 << "not support trigram matching";
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182 LOG(WARNING) << "-> Consider installing the \"pg_trgm\" extension on the "
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183 << "PostgreSQL server, e.g. on Debian: sudo apt install postgresql-contrib";
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184 }
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185 }
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186 else
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187 {
136
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188 t.Commit();
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189 }
136
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190 }
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191
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192 {
237
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193 DatabaseManager::Transaction t(manager, TransactionType_ReadWrite);
136
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194
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195 int property = 0;
237
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196 if (!LookupGlobalIntegerProperty(property, manager, MISSING_SERVER_IDENTIFIER,
136
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197 Orthanc::GlobalProperty_HasCreateInstance) ||
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198 property != 2)
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199 {
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200 LOG(INFO) << "Installing the CreateInstance extension";
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201
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202 if (property == 1)
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203 {
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204 // Drop older, experimental versions of this extension
241
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205 t.GetDatabaseTransaction().ExecuteMultiLines("DROP FUNCTION CreateInstance("
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206 "IN patient TEXT, IN study TEXT, IN series TEXT, in instance TEXT)");
136
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207 }
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208
136
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209 std::string query;
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210 Orthanc::EmbeddedResources::GetFileResource
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211 (query, Orthanc::EmbeddedResources::POSTGRESQL_CREATE_INSTANCE);
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212 t.GetDatabaseTransaction().ExecuteMultiLines(query);
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213
237
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214 SetGlobalIntegerProperty(manager, MISSING_SERVER_IDENTIFIER, Orthanc::GlobalProperty_HasCreateInstance, 2);
136
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215 }
71
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216
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217
237
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218 if (!LookupGlobalIntegerProperty(property, manager, MISSING_SERVER_IDENTIFIER,
136
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219 Orthanc::GlobalProperty_GetTotalSizeIsFast) ||
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220 property != 1)
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221 {
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222 LOG(INFO) << "Installing the FastTotalSize extension";
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223
136
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224 std::string query;
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225 Orthanc::EmbeddedResources::GetFileResource
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226 (query, Orthanc::EmbeddedResources::POSTGRESQL_FAST_TOTAL_SIZE);
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227 t.GetDatabaseTransaction().ExecuteMultiLines(query);
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228
237
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229 SetGlobalIntegerProperty(manager, MISSING_SERVER_IDENTIFIER, Orthanc::GlobalProperty_GetTotalSizeIsFast, 1);
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230 }
72
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231
79
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232
136
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233 // Installing this extension requires the "GlobalIntegers" table
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234 // created by the "FastTotalSize" extension
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235 property = 0;
237
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236 if (!LookupGlobalIntegerProperty(property, manager, MISSING_SERVER_IDENTIFIER,
136
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237 Orthanc::GlobalProperty_HasFastCountResources) ||
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238 property != 1)
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239 {
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240 LOG(INFO) << "Installing the FastCountResources extension";
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241
136
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242 std::string query;
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243 Orthanc::EmbeddedResources::GetFileResource
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244 (query, Orthanc::EmbeddedResources::POSTGRESQL_FAST_COUNT_RESOURCES);
241
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245 t.GetDatabaseTransaction().ExecuteMultiLines(query);
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246
237
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247 SetGlobalIntegerProperty(manager, MISSING_SERVER_IDENTIFIER, Orthanc::GlobalProperty_HasFastCountResources, 1);
136
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248 }
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249
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250
136
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251 // Installing this extension requires the "GlobalIntegers" table
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252 // created by the "GetLastChangeIndex" extension
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253 property = 0;
237
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254 if (!LookupGlobalIntegerProperty(property, manager, MISSING_SERVER_IDENTIFIER,
136
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255 Orthanc::GlobalProperty_GetLastChangeIndex) ||
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256 property != 1)
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257 {
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258 LOG(INFO) << "Installing the GetLastChangeIndex extension";
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259
136
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260 std::string query;
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261 Orthanc::EmbeddedResources::GetFileResource
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262 (query, Orthanc::EmbeddedResources::POSTGRESQL_GET_LAST_CHANGE_INDEX);
241
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263 t.GetDatabaseTransaction().ExecuteMultiLines(query);
237
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264
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265 SetGlobalIntegerProperty(manager, MISSING_SERVER_IDENTIFIER, Orthanc::GlobalProperty_GetLastChangeIndex, 1);
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266 }
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267
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268 t.Commit();
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269 }
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270
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271
237
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272 {
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273 // New in release 4.0 to deal with multiple writers
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274 DatabaseManager::Transaction t(manager, TransactionType_ReadWrite);
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275
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276 if (!t.GetDatabaseTransaction().DoesTableExist("ServerProperties"))
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277 {
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278 t.GetDatabaseTransaction().ExecuteMultiLines("CREATE TABLE ServerProperties(server VARCHAR(64) NOT NULL, "
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279 "property INTEGER, value TEXT, PRIMARY KEY(server, property))");
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280 }
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281
266
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282 /**
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283 * PostgreSQL 9.5: "Adding a column with a default requires
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284 * updating each row of the table (to store the new column
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285 * value). However, if no default is specified, PostgreSQL is
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286 * able to avoid the physical update." => We set no default
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287 * for performance (older entries will be NULL)
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288 * https://www.postgresql.org/docs/9.5/ddl-alter.html
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289 **/
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290 if (!db.DoesColumnExist("Metadata", "revision"))
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291 {
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292 t.GetDatabaseTransaction().ExecuteMultiLines("ALTER TABLE Metadata ADD COLUMN revision INTEGER");
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293 }
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294
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295 if (!db.DoesColumnExist("AttachedFiles", "revision"))
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296 {
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297 t.GetDatabaseTransaction().ExecuteMultiLines("ALTER TABLE AttachedFiles ADD COLUMN revision INTEGER");
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298 }
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299
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300 t.Commit();
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301 }
396
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302
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303
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304 {
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305 // New in release 5.0 to deal with labels
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306 DatabaseManager::Transaction t(manager, TransactionType_ReadWrite);
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307
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308 if (!t.GetDatabaseTransaction().DoesTableExist("Labels"))
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309 {
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310 t.GetDatabaseTransaction().ExecuteMultiLines(
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311 "CREATE TABLE Labels("
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312 "id BIGINT REFERENCES Resources(internalId) ON DELETE CASCADE,"
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313 "label TEXT, PRIMARY KEY(id, label));"
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314 "CREATE INDEX LabelsIndex1 ON LABELS(id);"
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315 "CREATE INDEX LabelsIndex2 ON LABELS(label);");
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316 }
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317
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318 t.Commit();
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319 }
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320 }
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321 }
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322
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323
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324 int64_t PostgreSQLIndex::CreateResource(DatabaseManager& manager,
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325 const char* publicId,
0
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326 OrthancPluginResourceType type)
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327 {
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328 DatabaseManager::CachedStatement statement(
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329 STATEMENT_FROM_HERE, manager,
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330 "INSERT INTO Resources VALUES(DEFAULT, ${type}, ${id}, NULL) RETURNING internalId");
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331
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332 statement.SetParameterType("id", ValueType_Utf8String);
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333 statement.SetParameterType("type", ValueType_Integer64);
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334
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335 Dictionary args;
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336 args.SetUtf8Value("id", publicId);
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337 args.SetIntegerValue("type", static_cast<int>(type));
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338
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339 statement.Execute(args);
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340
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341 return statement.ReadInteger64(0);
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342 }
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343
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344
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345 uint64_t PostgreSQLIndex::GetTotalCompressedSize(DatabaseManager& manager)
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346 {
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347 // Fast version if extension "./FastTotalSize.sql" is installed
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348 uint64_t result;
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349
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350 {
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351 DatabaseManager::CachedStatement statement(
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352 STATEMENT_FROM_HERE, manager,
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353 "SELECT value FROM GlobalIntegers WHERE key = 0");
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354
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355 statement.SetReadOnly(true);
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356 statement.Execute();
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357
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358 result = static_cast<uint64_t>(statement.ReadInteger64(0));
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359 }
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360
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361 assert(result == IndexBackend::GetTotalCompressedSize(manager));
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362 return result;
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363 }
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364
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365
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366 uint64_t PostgreSQLIndex::GetTotalUncompressedSize(DatabaseManager& manager)
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367 {
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368 // Fast version if extension "./FastTotalSize.sql" is installed
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369 uint64_t result;
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370
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371 {
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372 DatabaseManager::CachedStatement statement(
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373 STATEMENT_FROM_HERE, manager,
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374 "SELECT value FROM GlobalIntegers WHERE key = 1");
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375
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376 statement.SetReadOnly(true);
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377 statement.Execute();
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378
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379 result = static_cast<uint64_t>(statement.ReadInteger64(0));
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380 }
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381
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382 assert(result == IndexBackend::GetTotalUncompressedSize(manager));
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383 return result;
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384 }
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385
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386
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387 #if ORTHANC_PLUGINS_HAS_DATABASE_CONSTRAINT == 1
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388 void PostgreSQLIndex::CreateInstance(OrthancPluginCreateInstanceResult& result,
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389 DatabaseManager& manager,
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390 const char* hashPatient,
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391 const char* hashStudy,
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392 const char* hashSeries,
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393 const char* hashInstance)
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394 {
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395 DatabaseManager::CachedStatement statement(
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396 STATEMENT_FROM_HERE, manager,
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397 "SELECT * FROM CreateInstance(${patient}, ${study}, ${series}, ${instance})");
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398
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399 statement.SetParameterType("patient", ValueType_Utf8String);
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400 statement.SetParameterType("study", ValueType_Utf8String);
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401 statement.SetParameterType("series", ValueType_Utf8String);
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402 statement.SetParameterType("instance", ValueType_Utf8String);
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403
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404 Dictionary args;
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405 args.SetUtf8Value("patient", hashPatient);
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406 args.SetUtf8Value("study", hashStudy);
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407 args.SetUtf8Value("series", hashSeries);
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408 args.SetUtf8Value("instance", hashInstance);
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409
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410 statement.Execute(args);
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411
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412 if (statement.IsDone() ||
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413 statement.GetResultFieldsCount() != 8)
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414 {
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415 throw Orthanc::OrthancException(Orthanc::ErrorCode_Database);
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416 }
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417
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418 for (size_t i = 0; i < 8; i++)
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419 {
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420 statement.SetResultFieldType(i, ValueType_Integer64);
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421 }
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422
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423 result.isNewInstance = (statement.ReadInteger64(3) == 1);
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424 result.instanceId = statement.ReadInteger64(7);
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425
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426 if (result.isNewInstance)
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427 {
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428 result.isNewPatient = (statement.ReadInteger64(0) == 1);
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429 result.isNewStudy = (statement.ReadInteger64(1) == 1);
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430 result.isNewSeries = (statement.ReadInteger64(2) == 1);
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431 result.patientId = statement.ReadInteger64(4);
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432 result.studyId = statement.ReadInteger64(5);
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433 result.seriesId = statement.ReadInteger64(6);
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434 }
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435 }
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436 #endif
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437
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438
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439 uint64_t PostgreSQLIndex::GetResourcesCount(DatabaseManager& manager,
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440 OrthancPluginResourceType resourceType)
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441 {
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442 // Optimized version thanks to the "FastCountResources.sql" extension
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443
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444 assert(OrthancPluginResourceType_Patient == 0 &&
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445 OrthancPluginResourceType_Study == 1 &&
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446 OrthancPluginResourceType_Series == 2 &&
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447 OrthancPluginResourceType_Instance == 3);
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448
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449 uint64_t result;
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450
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451 {
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452 DatabaseManager::CachedStatement statement(
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453 STATEMENT_FROM_HERE, manager,
79
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454 "SELECT value FROM GlobalIntegers WHERE key = ${key}");
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455
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456 statement.SetParameterType("key", ValueType_Integer64);
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457
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458 Dictionary args;
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459
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460 // For an explanation of the "+ 2" below, check out "FastCountResources.sql"
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461 args.SetIntegerValue("key", static_cast<int>(resourceType + 2));
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462
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463 statement.SetReadOnly(true);
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464 statement.Execute(args);
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465
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466 result = static_cast<uint64_t>(statement.ReadInteger64(0));
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467 }
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468
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469 assert(result == IndexBackend::GetResourcesCount(manager, resourceType));
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470 return result;
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471 }
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472
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473
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474 int64_t PostgreSQLIndex::GetLastChangeIndex(DatabaseManager& manager)
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475 {
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476 DatabaseManager::CachedStatement statement(
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477 STATEMENT_FROM_HERE, manager,
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478 "SELECT value FROM GlobalIntegers WHERE key = 6");
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479
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480 statement.SetReadOnly(true);
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481 statement.Execute();
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482
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483 return statement.ReadInteger64(0);
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484 }
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485
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486
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487 void PostgreSQLIndex::TagMostRecentPatient(DatabaseManager& manager,
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488 int64_t patient)
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489 {
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490 // This behavior is implemented in "CreateInstance()", and no
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491 // backward compatibility is necessary
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492 throw Orthanc::OrthancException(Orthanc::ErrorCode_Database);
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493 }
0
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494 }