Mercurial > hg > orthanc-databases

annotate PostgreSQL/Plugins/PostgreSQLIndex.cpp @ 359:16aac0287485

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copyright upgraded to 2022
author Sebastien Jodogne <s.jodogne@gmail.com>
date Mon, 21 Feb 2022 09:32:46 +0100
parents c0c12b3974b2
children 3d6886f3e5b3
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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) 2017-2022 Osimis S.A., Belgium
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6 * Copyright (C) 2021-2022 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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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 {
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66 uint32_t expectedVersion = 6;
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67
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68 if (GetContext()) // "GetContext()" can possibly be NULL in the unit tests
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69 {
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70 expectedVersion = OrthancPluginGetExpectedDatabaseVersion(GetContext());
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71 }
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72
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73 // Check the expected version of the database
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74 if (expectedVersion != 6)
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75 {
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76 LOG(ERROR) << "This database plugin is incompatible with your version of Orthanc "
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77 << "expecting the DB schema version " << expectedVersion
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78 << ", but this plugin is only compatible with version 6";
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79 throw Orthanc::OrthancException(Orthanc::ErrorCode_Plugin);
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80 }
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81
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82 PostgreSQLDatabase& db = dynamic_cast<PostgreSQLDatabase&>(manager.GetDatabase());
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83
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84 if (parameters_.HasLock())
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85 {
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86 db.AdvisoryLock(POSTGRESQL_LOCK_INDEX);
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87 }
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89 {
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90 PostgreSQLDatabase::TransientAdvisoryLock lock(db, POSTGRESQL_LOCK_DATABASE_SETUP);
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92 if (clearAll_)
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93 {
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94 db.ClearAll();
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95 }
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96
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97 {
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98 DatabaseManager::Transaction t(manager, TransactionType_ReadWrite);
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99
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100 if (!t.GetDatabaseTransaction().DoesTableExist("Resources"))
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101 {
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102 std::string query;
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103
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104 Orthanc::EmbeddedResources::GetFileResource
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105 (query, Orthanc::EmbeddedResources::POSTGRESQL_PREPARE_INDEX);
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106 t.GetDatabaseTransaction().ExecuteMultiLines(query);
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107
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108 SetGlobalIntegerProperty(manager, MISSING_SERVER_IDENTIFIER, Orthanc::GlobalProperty_DatabaseSchemaVersion, expectedVersion);
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109 SetGlobalIntegerProperty(manager, MISSING_SERVER_IDENTIFIER, Orthanc::GlobalProperty_DatabasePatchLevel, 1);
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110 SetGlobalIntegerProperty(manager, MISSING_SERVER_IDENTIFIER, Orthanc::GlobalProperty_HasTrigramIndex, 0);
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111 }
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112
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113 if (!t.GetDatabaseTransaction().DoesTableExist("Resources"))
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114 {
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115 LOG(ERROR) << "Corrupted PostgreSQL database";
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116 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError);
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117 }
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118
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119 int version = 0;
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120 if (!LookupGlobalIntegerProperty(version, manager, MISSING_SERVER_IDENTIFIER, Orthanc::GlobalProperty_DatabaseSchemaVersion) ||
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121 version != 6)
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122 {
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123 LOG(ERROR) << "PostgreSQL plugin is incompatible with database schema version: " << version;
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124 throw Orthanc::OrthancException(Orthanc::ErrorCode_Database);
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125 }
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126
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127 int revision;
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128 if (!LookupGlobalIntegerProperty(revision, manager, MISSING_SERVER_IDENTIFIER, Orthanc::GlobalProperty_DatabasePatchLevel))
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129 {
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130 revision = 1;
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131 SetGlobalIntegerProperty(manager, MISSING_SERVER_IDENTIFIER, Orthanc::GlobalProperty_DatabasePatchLevel, revision);
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132 }
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133
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134 if (revision != 1)
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135 {
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136 LOG(ERROR) << "PostgreSQL plugin is incompatible with database schema revision: " << revision;
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137 throw Orthanc::OrthancException(Orthanc::ErrorCode_Database);
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138 }
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139
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140 t.Commit();
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141 }
0
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142
136
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143 {
237
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144 DatabaseManager::Transaction t(manager, TransactionType_ReadWrite);
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145
136
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146 int hasTrigram = 0;
237
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147 if (!LookupGlobalIntegerProperty(hasTrigram, manager, MISSING_SERVER_IDENTIFIER,
136
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148 Orthanc::GlobalProperty_HasTrigramIndex) ||
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149 hasTrigram != 1)
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150 {
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151 /**
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152 * Apply fix for performance issue (speed up wildcard search
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153 * by using GIN trigrams). This implements the patch suggested
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154 * in issue #47, BUT we also keep the original
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155 * "DicomIdentifiersIndexValues", as it leads to better
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156 * performance for "strict" searches (i.e. searches involving
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157 * no wildcard).
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158 * https://www.postgresql.org/docs/current/static/pgtrgm.html
336
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159 * https://bugs.orthanc-server.com/show_bug.cgi?id=47
136
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160 **/
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161 try
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162 {
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163 // We've observed 9 minutes on DB with 100000 studies
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164 LOG(WARNING) << "Trying to enable trigram matching on the PostgreSQL database "
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165 << "to speed up wildcard searches. This may take several minutes";
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166
241
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167 t.GetDatabaseTransaction().ExecuteMultiLines(
136
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168 "CREATE EXTENSION IF NOT EXISTS pg_trgm; "
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169 "CREATE INDEX DicomIdentifiersIndexValues2 ON DicomIdentifiers USING gin(value gin_trgm_ops);");
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170
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171 SetGlobalIntegerProperty(manager, MISSING_SERVER_IDENTIFIER, Orthanc::GlobalProperty_HasTrigramIndex, 1);
136
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172 LOG(WARNING) << "Trigram index has been created";
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173
136
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174 t.Commit();
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175 }
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176 catch (Orthanc::OrthancException&)
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177 {
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178 LOG(WARNING) << "Performance warning: Your PostgreSQL server does "
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179 << "not support trigram matching";
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180 LOG(WARNING) << "-> Consider installing the \"pg_trgm\" extension on the "
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181 << "PostgreSQL server, e.g. on Debian: sudo apt install postgresql-contrib";
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182 }
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183 }
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184 else
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185 {
136
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186 t.Commit();
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187 }
136
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188 }
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189
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190 {
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191 DatabaseManager::Transaction t(manager, TransactionType_ReadWrite);
136
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192
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193 int property = 0;
237
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194 if (!LookupGlobalIntegerProperty(property, manager, MISSING_SERVER_IDENTIFIER,
136
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195 Orthanc::GlobalProperty_HasCreateInstance) ||
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196 property != 2)
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197 {
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198 LOG(INFO) << "Installing the CreateInstance extension";
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199
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200 if (property == 1)
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201 {
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202 // Drop older, experimental versions of this extension
241
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203 t.GetDatabaseTransaction().ExecuteMultiLines("DROP FUNCTION CreateInstance("
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204 "IN patient TEXT, IN study TEXT, IN series TEXT, in instance TEXT)");
136
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205 }
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206
136
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207 std::string query;
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208 Orthanc::EmbeddedResources::GetFileResource
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209 (query, Orthanc::EmbeddedResources::POSTGRESQL_CREATE_INSTANCE);
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210 t.GetDatabaseTransaction().ExecuteMultiLines(query);
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211
237
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212 SetGlobalIntegerProperty(manager, MISSING_SERVER_IDENTIFIER, Orthanc::GlobalProperty_HasCreateInstance, 2);
136
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213 }
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214
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215
237
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216 if (!LookupGlobalIntegerProperty(property, manager, MISSING_SERVER_IDENTIFIER,
136
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217 Orthanc::GlobalProperty_GetTotalSizeIsFast) ||
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218 property != 1)
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219 {
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220 LOG(INFO) << "Installing the FastTotalSize extension";
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221
136
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222 std::string query;
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223 Orthanc::EmbeddedResources::GetFileResource
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224 (query, Orthanc::EmbeddedResources::POSTGRESQL_FAST_TOTAL_SIZE);
241
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225 t.GetDatabaseTransaction().ExecuteMultiLines(query);
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226
237
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227 SetGlobalIntegerProperty(manager, MISSING_SERVER_IDENTIFIER, Orthanc::GlobalProperty_GetTotalSizeIsFast, 1);
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228 }
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229
79
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230
136
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231 // Installing this extension requires the "GlobalIntegers" table
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232 // created by the "FastTotalSize" extension
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233 property = 0;
237
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234 if (!LookupGlobalIntegerProperty(property, manager, MISSING_SERVER_IDENTIFIER,
136
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235 Orthanc::GlobalProperty_HasFastCountResources) ||
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236 property != 1)
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237 {
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238 LOG(INFO) << "Installing the FastCountResources extension";
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239
136
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240 std::string query;
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241 Orthanc::EmbeddedResources::GetFileResource
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242 (query, Orthanc::EmbeddedResources::POSTGRESQL_FAST_COUNT_RESOURCES);
241
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243 t.GetDatabaseTransaction().ExecuteMultiLines(query);
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244
237
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245 SetGlobalIntegerProperty(manager, MISSING_SERVER_IDENTIFIER, Orthanc::GlobalProperty_HasFastCountResources, 1);
136
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246 }
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247
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248
136
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249 // Installing this extension requires the "GlobalIntegers" table
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250 // created by the "GetLastChangeIndex" extension
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251 property = 0;
237
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252 if (!LookupGlobalIntegerProperty(property, manager, MISSING_SERVER_IDENTIFIER,
136
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253 Orthanc::GlobalProperty_GetLastChangeIndex) ||
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254 property != 1)
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255 {
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256 LOG(INFO) << "Installing the GetLastChangeIndex extension";
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257
136
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258 std::string query;
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259 Orthanc::EmbeddedResources::GetFileResource
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260 (query, Orthanc::EmbeddedResources::POSTGRESQL_GET_LAST_CHANGE_INDEX);
241
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261 t.GetDatabaseTransaction().ExecuteMultiLines(query);
237
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262
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263 SetGlobalIntegerProperty(manager, MISSING_SERVER_IDENTIFIER, Orthanc::GlobalProperty_GetLastChangeIndex, 1);
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264 }
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265
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266 t.Commit();
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267 }
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268
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269
237
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270 {
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271 // New in release 4.0 to deal with multiple writers
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272 DatabaseManager::Transaction t(manager, TransactionType_ReadWrite);
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273
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274 if (!t.GetDatabaseTransaction().DoesTableExist("ServerProperties"))
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275 {
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276 t.GetDatabaseTransaction().ExecuteMultiLines("CREATE TABLE ServerProperties(server VARCHAR(64) NOT NULL, "
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277 "property INTEGER, value TEXT, PRIMARY KEY(server, property))");
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278 }
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279
266
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280 /**
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281 * PostgreSQL 9.5: "Adding a column with a default requires
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282 * updating each row of the table (to store the new column
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283 * value). However, if no default is specified, PostgreSQL is
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284 * able to avoid the physical update." => We set no default
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285 * for performance (older entries will be NULL)
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286 * https://www.postgresql.org/docs/9.5/ddl-alter.html
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287 **/
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288 if (!db.DoesColumnExist("Metadata", "revision"))
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289 {
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290 t.GetDatabaseTransaction().ExecuteMultiLines("ALTER TABLE Metadata ADD COLUMN revision INTEGER");
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291 }
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292
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293 if (!db.DoesColumnExist("AttachedFiles", "revision"))
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294 {
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295 t.GetDatabaseTransaction().ExecuteMultiLines("ALTER TABLE AttachedFiles ADD COLUMN revision INTEGER");
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296 }
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297
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298 t.Commit();
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299 }
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300 }
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301 }
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302
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303
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304 int64_t PostgreSQLIndex::CreateResource(DatabaseManager& manager,
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305 const char* publicId,
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306 OrthancPluginResourceType type)
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307 {
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308 DatabaseManager::CachedStatement statement(
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309 STATEMENT_FROM_HERE, manager,
302
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310 "INSERT INTO Resources VALUES(DEFAULT, ${type}, ${id}, NULL) RETURNING internalId");
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311
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312 statement.SetParameterType("id", ValueType_Utf8String);
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313 statement.SetParameterType("type", ValueType_Integer64);
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314
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315 Dictionary args;
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316 args.SetUtf8Value("id", publicId);
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317 args.SetIntegerValue("type", static_cast<int>(type));
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318
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319 statement.Execute(args);
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320
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321 return statement.ReadInteger64(0);
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322 }
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323
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324
225
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325 uint64_t PostgreSQLIndex::GetTotalCompressedSize(DatabaseManager& manager)
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326 {
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327 // Fast version if extension "./FastTotalSize.sql" is installed
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328 uint64_t result;
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329
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330 {
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331 DatabaseManager::CachedStatement statement(
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332 STATEMENT_FROM_HERE, manager,
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333 "SELECT value FROM GlobalIntegers WHERE key = 0");
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334
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335 statement.SetReadOnly(true);
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336 statement.Execute();
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337
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338 result = static_cast<uint64_t>(statement.ReadInteger64(0));
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339 }
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340
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341 assert(result == IndexBackend::GetTotalCompressedSize(manager));
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342 return result;
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343 }
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344
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345
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346 uint64_t PostgreSQLIndex::GetTotalUncompressedSize(DatabaseManager& manager)
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347 {
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348 // Fast version if extension "./FastTotalSize.sql" is installed
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349 uint64_t result;
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350
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351 {
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352 DatabaseManager::CachedStatement statement(
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353 STATEMENT_FROM_HERE, manager,
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354 "SELECT value FROM GlobalIntegers WHERE key = 1");
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355
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356 statement.SetReadOnly(true);
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357 statement.Execute();
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358
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359 result = static_cast<uint64_t>(statement.ReadInteger64(0));
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360 }
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361
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362 assert(result == IndexBackend::GetTotalUncompressedSize(manager));
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363 return result;
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364 }
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365
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366
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367 #if ORTHANC_PLUGINS_HAS_DATABASE_CONSTRAINT == 1
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368 void PostgreSQLIndex::CreateInstance(OrthancPluginCreateInstanceResult& result,
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369 DatabaseManager& manager,
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370 const char* hashPatient,
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371 const char* hashStudy,
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372 const char* hashSeries,
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373 const char* hashInstance)
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374 {
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375 DatabaseManager::CachedStatement statement(
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376 STATEMENT_FROM_HERE, manager,
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377 "SELECT * FROM CreateInstance(${patient}, ${study}, ${series}, ${instance})");
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378
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379 statement.SetParameterType("patient", ValueType_Utf8String);
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380 statement.SetParameterType("study", ValueType_Utf8String);
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381 statement.SetParameterType("series", ValueType_Utf8String);
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382 statement.SetParameterType("instance", ValueType_Utf8String);
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383
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384 Dictionary args;
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385 args.SetUtf8Value("patient", hashPatient);
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386 args.SetUtf8Value("study", hashStudy);
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387 args.SetUtf8Value("series", hashSeries);
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388 args.SetUtf8Value("instance", hashInstance);
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389
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390 statement.Execute(args);
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391
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392 if (statement.IsDone() ||
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393 statement.GetResultFieldsCount() != 8)
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394 {
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395 throw Orthanc::OrthancException(Orthanc::ErrorCode_Database);
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396 }
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397
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398 for (size_t i = 0; i < 8; i++)
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399 {
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400 statement.SetResultFieldType(i, ValueType_Integer64);
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401 }
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402
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403 result.isNewInstance = (statement.ReadInteger64(3) == 1);
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404 result.instanceId = statement.ReadInteger64(7);
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405
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406 if (result.isNewInstance)
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407 {
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408 result.isNewPatient = (statement.ReadInteger64(0) == 1);
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409 result.isNewStudy = (statement.ReadInteger64(1) == 1);
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410 result.isNewSeries = (statement.ReadInteger64(2) == 1);
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411 result.patientId = statement.ReadInteger64(4);
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412 result.studyId = statement.ReadInteger64(5);
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413 result.seriesId = statement.ReadInteger64(6);
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414 }
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415 }
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416 #endif
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417
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418
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419 uint64_t PostgreSQLIndex::GetResourcesCount(DatabaseManager& manager,
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420 OrthancPluginResourceType resourceType)
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421 {
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422 // Optimized version thanks to the "FastCountResources.sql" extension
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423
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424 assert(OrthancPluginResourceType_Patient == 0 &&
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425 OrthancPluginResourceType_Study == 1 &&
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426 OrthancPluginResourceType_Series == 2 &&
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427 OrthancPluginResourceType_Instance == 3);
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428
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429 uint64_t result;
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430
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431 {
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432 DatabaseManager::CachedStatement statement(
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433 STATEMENT_FROM_HERE, manager,
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434 "SELECT value FROM GlobalIntegers WHERE key = ${key}");
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435
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436 statement.SetParameterType("key", ValueType_Integer64);
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437
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438 Dictionary args;
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439
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440 // For an explanation of the "+ 2" below, check out "FastCountResources.sql"
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441 args.SetIntegerValue("key", static_cast<int>(resourceType + 2));
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442
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443 statement.SetReadOnly(true);
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444 statement.Execute(args);
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445
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446 result = static_cast<uint64_t>(statement.ReadInteger64(0));
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447 }
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448
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449 assert(result == IndexBackend::GetResourcesCount(manager, resourceType));
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450 return result;
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451 }
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452
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453
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454 int64_t PostgreSQLIndex::GetLastChangeIndex(DatabaseManager& manager)
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455 {
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456 DatabaseManager::CachedStatement statement(
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457 STATEMENT_FROM_HERE, manager,
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458 "SELECT value FROM GlobalIntegers WHERE key = 6");
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459
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460 statement.SetReadOnly(true);
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461 statement.Execute();
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462
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463 return statement.ReadInteger64(0);
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464 }
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465
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466
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467 void PostgreSQLIndex::TagMostRecentPatient(DatabaseManager& manager,
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468 int64_t patient)
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469 {
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470 // This behavior is implemented in "CreateInstance()", and no
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471 // backward compatibility is necessary
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472 throw Orthanc::OrthancException(Orthanc::ErrorCode_Database);
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473 }
0
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474 }