Mercurial > hg > orthanc-databases

annotate PostgreSQL/Plugins/PostgreSQLIndex.cpp @ 302:3a52e27a2d80

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in GenericFormatter, replaced ${} by ${AUTOINCREMENT}
author Sebastien Jodogne <s.jodogne@gmail.com>
date Fri, 09 Jul 2021 16:25:08 +0200
parents cc7af42d4f23
children c0c12b3974b2
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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) 2017-2021 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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20
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21
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22 #include "PostgreSQLIndex.h"
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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 #include "PostgreSQLDefinitions.h"
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29 #include <EmbeddedResources.h> // Auto-generated file
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31 #include <Compatibility.h> // For std::unique_ptr<>
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32 #include <Logging.h>
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33 #include <OrthancException.h>
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35
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36 namespace Orthanc
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37 {
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38 // Some aliases for internal properties
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39 static const GlobalProperty GlobalProperty_HasTrigramIndex = GlobalProperty_DatabaseInternal0;
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40 static const GlobalProperty GlobalProperty_HasCreateInstance = GlobalProperty_DatabaseInternal1;
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41 static const GlobalProperty GlobalProperty_HasFastCountResources = GlobalProperty_DatabaseInternal2;
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42 static const GlobalProperty GlobalProperty_GetLastChangeIndex = GlobalProperty_DatabaseInternal3;
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43 }
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44
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46 namespace OrthancDatabases
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47 {
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48 PostgreSQLIndex::PostgreSQLIndex(OrthancPluginContext* context,
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49 const PostgreSQLParameters& parameters) :
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50 IndexBackend(context),
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51 parameters_(parameters),
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52 clearAll_(false)
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53 {
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54 }
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57 IDatabaseFactory* PostgreSQLIndex::CreateDatabaseFactory()
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58 {
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59 return PostgreSQLDatabase::CreateDatabaseFactory(parameters_);
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60 }
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62
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63 void PostgreSQLIndex::ConfigureDatabase(DatabaseManager& manager)
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64 {
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65 uint32_t expectedVersion = 6;
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66
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67 if (GetContext()) // "GetContext()" can possibly be NULL in the unit tests
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68 {
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69 expectedVersion = OrthancPluginGetExpectedDatabaseVersion(GetContext());
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70 }
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71
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72 // Check the expected version of the database
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73 if (expectedVersion != 6)
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74 {
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75 LOG(ERROR) << "This database plugin is incompatible with your version of Orthanc "
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76 << "expecting the DB schema version " << expectedVersion
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77 << ", but this plugin is only compatible with version 6";
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78 throw Orthanc::OrthancException(Orthanc::ErrorCode_Plugin);
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79 }
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80
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81 PostgreSQLDatabase& db = dynamic_cast<PostgreSQLDatabase&>(manager.GetDatabase());
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83 if (parameters_.HasLock())
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84 {
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85 db.AdvisoryLock(POSTGRESQL_LOCK_INDEX);
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86 }
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88 {
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89 PostgreSQLDatabase::TransientAdvisoryLock lock(db, POSTGRESQL_LOCK_DATABASE_SETUP);
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91 if (clearAll_)
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92 {
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93 db.ClearAll();
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94 }
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95
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96 {
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97 DatabaseManager::Transaction t(manager, TransactionType_ReadWrite);
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98
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99 if (!t.GetDatabaseTransaction().DoesTableExist("Resources"))
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100 {
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101 std::string query;
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102
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103 Orthanc::EmbeddedResources::GetFileResource
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104 (query, Orthanc::EmbeddedResources::POSTGRESQL_PREPARE_INDEX);
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105 t.GetDatabaseTransaction().ExecuteMultiLines(query);
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107 SetGlobalIntegerProperty(manager, MISSING_SERVER_IDENTIFIER, Orthanc::GlobalProperty_DatabaseSchemaVersion, expectedVersion);
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108 SetGlobalIntegerProperty(manager, MISSING_SERVER_IDENTIFIER, Orthanc::GlobalProperty_DatabasePatchLevel, 1);
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109 SetGlobalIntegerProperty(manager, MISSING_SERVER_IDENTIFIER, Orthanc::GlobalProperty_HasTrigramIndex, 0);
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110 }
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111
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112 if (!t.GetDatabaseTransaction().DoesTableExist("Resources"))
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113 {
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114 LOG(ERROR) << "Corrupted PostgreSQL database";
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115 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError);
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116 }
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117
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118 int version = 0;
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119 if (!LookupGlobalIntegerProperty(version, manager, MISSING_SERVER_IDENTIFIER, Orthanc::GlobalProperty_DatabaseSchemaVersion) ||
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120 version != 6)
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121 {
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122 LOG(ERROR) << "PostgreSQL plugin is incompatible with database schema version: " << version;
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123 throw Orthanc::OrthancException(Orthanc::ErrorCode_Database);
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124 }
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125
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126 int revision;
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127 if (!LookupGlobalIntegerProperty(revision, manager, MISSING_SERVER_IDENTIFIER, Orthanc::GlobalProperty_DatabasePatchLevel))
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128 {
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129 revision = 1;
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130 SetGlobalIntegerProperty(manager, MISSING_SERVER_IDENTIFIER, Orthanc::GlobalProperty_DatabasePatchLevel, revision);
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131 }
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133 if (revision != 1)
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134 {
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135 LOG(ERROR) << "PostgreSQL plugin is incompatible with database schema revision: " << revision;
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136 throw Orthanc::OrthancException(Orthanc::ErrorCode_Database);
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137 }
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138
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139 t.Commit();
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140 }
0
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141
136
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142 {
237
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143 DatabaseManager::Transaction t(manager, TransactionType_ReadWrite);
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144
136
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145 int hasTrigram = 0;
237
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146 if (!LookupGlobalIntegerProperty(hasTrigram, manager, MISSING_SERVER_IDENTIFIER,
136
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147 Orthanc::GlobalProperty_HasTrigramIndex) ||
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148 hasTrigram != 1)
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149 {
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150 /**
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151 * Apply fix for performance issue (speed up wildcard search
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152 * by using GIN trigrams). This implements the patch suggested
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153 * in issue #47, BUT we also keep the original
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154 * "DicomIdentifiersIndexValues", as it leads to better
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155 * performance for "strict" searches (i.e. searches involving
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156 * no wildcard).
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157 * https://www.postgresql.org/docs/current/static/pgtrgm.html
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158 * https://bitbucket.org/sjodogne/orthanc/issues/47/index-improvements-for-pg-plugin
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159 **/
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160 try
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161 {
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162 // We've observed 9 minutes on DB with 100000 studies
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163 LOG(WARNING) << "Trying to enable trigram matching on the PostgreSQL database "
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164 << "to speed up wildcard searches. This may take several minutes";
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165
241
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166 t.GetDatabaseTransaction().ExecuteMultiLines(
136
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167 "CREATE EXTENSION IF NOT EXISTS pg_trgm; "
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168 "CREATE INDEX DicomIdentifiersIndexValues2 ON DicomIdentifiers USING gin(value gin_trgm_ops);");
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169
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170 SetGlobalIntegerProperty(manager, MISSING_SERVER_IDENTIFIER, Orthanc::GlobalProperty_HasTrigramIndex, 1);
136
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171 LOG(WARNING) << "Trigram index has been created";
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172
136
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173 t.Commit();
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174 }
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175 catch (Orthanc::OrthancException&)
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176 {
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177 LOG(WARNING) << "Performance warning: Your PostgreSQL server does "
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178 << "not support trigram matching";
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179 LOG(WARNING) << "-> Consider installing the \"pg_trgm\" extension on the "
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180 << "PostgreSQL server, e.g. on Debian: sudo apt install postgresql-contrib";
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181 }
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182 }
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183 else
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184 {
136
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185 t.Commit();
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186 }
136
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187 }
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188
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189 {
237
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190 DatabaseManager::Transaction t(manager, TransactionType_ReadWrite);
136
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191
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192 int property = 0;
237
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193 if (!LookupGlobalIntegerProperty(property, manager, MISSING_SERVER_IDENTIFIER,
136
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194 Orthanc::GlobalProperty_HasCreateInstance) ||
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195 property != 2)
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196 {
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197 LOG(INFO) << "Installing the CreateInstance extension";
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198
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199 if (property == 1)
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200 {
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201 // Drop older, experimental versions of this extension
241
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202 t.GetDatabaseTransaction().ExecuteMultiLines("DROP FUNCTION CreateInstance("
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203 "IN patient TEXT, IN study TEXT, IN series TEXT, in instance TEXT)");
136
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204 }
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205
136
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206 std::string query;
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207 Orthanc::EmbeddedResources::GetFileResource
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208 (query, Orthanc::EmbeddedResources::POSTGRESQL_CREATE_INSTANCE);
241
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209 t.GetDatabaseTransaction().ExecuteMultiLines(query);
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210
237
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211 SetGlobalIntegerProperty(manager, MISSING_SERVER_IDENTIFIER, Orthanc::GlobalProperty_HasCreateInstance, 2);
136
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212 }
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213
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214
237
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215 if (!LookupGlobalIntegerProperty(property, manager, MISSING_SERVER_IDENTIFIER,
136
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216 Orthanc::GlobalProperty_GetTotalSizeIsFast) ||
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217 property != 1)
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218 {
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219 LOG(INFO) << "Installing the FastTotalSize extension";
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220
136
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221 std::string query;
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222 Orthanc::EmbeddedResources::GetFileResource
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223 (query, Orthanc::EmbeddedResources::POSTGRESQL_FAST_TOTAL_SIZE);
241
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224 t.GetDatabaseTransaction().ExecuteMultiLines(query);
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225
237
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226 SetGlobalIntegerProperty(manager, MISSING_SERVER_IDENTIFIER, Orthanc::GlobalProperty_GetTotalSizeIsFast, 1);
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227 }
72
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228
79
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229
136
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230 // Installing this extension requires the "GlobalIntegers" table
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231 // created by the "FastTotalSize" extension
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232 property = 0;
237
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233 if (!LookupGlobalIntegerProperty(property, manager, MISSING_SERVER_IDENTIFIER,
136
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234 Orthanc::GlobalProperty_HasFastCountResources) ||
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235 property != 1)
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236 {
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237 LOG(INFO) << "Installing the FastCountResources extension";
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238
136
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239 std::string query;
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240 Orthanc::EmbeddedResources::GetFileResource
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241 (query, Orthanc::EmbeddedResources::POSTGRESQL_FAST_COUNT_RESOURCES);
241
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242 t.GetDatabaseTransaction().ExecuteMultiLines(query);
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243
237
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244 SetGlobalIntegerProperty(manager, MISSING_SERVER_IDENTIFIER, Orthanc::GlobalProperty_HasFastCountResources, 1);
136
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245 }
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246
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247
136
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248 // Installing this extension requires the "GlobalIntegers" table
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249 // created by the "GetLastChangeIndex" extension
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250 property = 0;
237
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251 if (!LookupGlobalIntegerProperty(property, manager, MISSING_SERVER_IDENTIFIER,
136
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252 Orthanc::GlobalProperty_GetLastChangeIndex) ||
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253 property != 1)
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254 {
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255 LOG(INFO) << "Installing the GetLastChangeIndex extension";
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256
136
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257 std::string query;
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258 Orthanc::EmbeddedResources::GetFileResource
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259 (query, Orthanc::EmbeddedResources::POSTGRESQL_GET_LAST_CHANGE_INDEX);
241
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260 t.GetDatabaseTransaction().ExecuteMultiLines(query);
237
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261
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262 SetGlobalIntegerProperty(manager, MISSING_SERVER_IDENTIFIER, Orthanc::GlobalProperty_GetLastChangeIndex, 1);
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263 }
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264
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265 t.Commit();
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266 }
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267
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268
237
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269 {
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270 // New in release 4.0 to deal with multiple writers
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271 DatabaseManager::Transaction t(manager, TransactionType_ReadWrite);
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272
241
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273 if (!t.GetDatabaseTransaction().DoesTableExist("ServerProperties"))
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274 {
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275 t.GetDatabaseTransaction().ExecuteMultiLines("CREATE TABLE ServerProperties(server VARCHAR(64) NOT NULL, "
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276 "property INTEGER, value TEXT, PRIMARY KEY(server, property))");
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277 }
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278
266
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279 /**
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280 * PostgreSQL 9.5: "Adding a column with a default requires
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281 * updating each row of the table (to store the new column
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282 * value). However, if no default is specified, PostgreSQL is
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283 * able to avoid the physical update." => We set no default
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284 * for performance (older entries will be NULL)
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285 * https://www.postgresql.org/docs/9.5/ddl-alter.html
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286 **/
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287 if (!db.DoesColumnExist("Metadata", "revision"))
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288 {
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289 t.GetDatabaseTransaction().ExecuteMultiLines("ALTER TABLE Metadata ADD COLUMN revision INTEGER");
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290 }
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291
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292 if (!db.DoesColumnExist("AttachedFiles", "revision"))
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293 {
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294 t.GetDatabaseTransaction().ExecuteMultiLines("ALTER TABLE AttachedFiles ADD COLUMN revision INTEGER");
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295 }
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296
136
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297 t.Commit();
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298 }
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299 }
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300 }
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301
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302
225
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303 int64_t PostgreSQLIndex::CreateResource(DatabaseManager& manager,
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304 const char* publicId,
0
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305 OrthancPluginResourceType type)
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306 {
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307 DatabaseManager::CachedStatement statement(
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308 STATEMENT_FROM_HERE, manager,
302
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309 "INSERT INTO Resources VALUES(DEFAULT, ${type}, ${id}, NULL) RETURNING internalId");
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310
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311 statement.SetParameterType("id", ValueType_Utf8String);
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312 statement.SetParameterType("type", ValueType_Integer64);
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313
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314 Dictionary args;
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315 args.SetUtf8Value("id", publicId);
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316 args.SetIntegerValue("type", static_cast<int>(type));
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317
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318 statement.Execute(args);
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319
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320 return statement.ReadInteger64(0);
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321 }
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322
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323
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324 uint64_t PostgreSQLIndex::GetTotalCompressedSize(DatabaseManager& manager)
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325 {
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326 // Fast version if extension "./FastTotalSize.sql" is installed
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327 uint64_t result;
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328
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329 {
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330 DatabaseManager::CachedStatement statement(
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331 STATEMENT_FROM_HERE, manager,
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332 "SELECT value FROM GlobalIntegers WHERE key = 0");
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333
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334 statement.SetReadOnly(true);
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335 statement.Execute();
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336
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337 result = static_cast<uint64_t>(statement.ReadInteger64(0));
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338 }
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339
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340 assert(result == IndexBackend::GetTotalCompressedSize(manager));
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341 return result;
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342 }
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343
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344
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345 uint64_t PostgreSQLIndex::GetTotalUncompressedSize(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 = 1");
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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
225
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361 assert(result == IndexBackend::GetTotalUncompressedSize(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 #if ORTHANC_PLUGINS_HAS_DATABASE_CONSTRAINT == 1
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367 void PostgreSQLIndex::CreateInstance(OrthancPluginCreateInstanceResult& result,
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368 DatabaseManager& manager,
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369 const char* hashPatient,
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370 const char* hashStudy,
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371 const char* hashSeries,
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372 const char* hashInstance)
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373 {
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374 DatabaseManager::CachedStatement statement(
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375 STATEMENT_FROM_HERE, manager,
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376 "SELECT * FROM CreateInstance(${patient}, ${study}, ${series}, ${instance})");
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377
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378 statement.SetParameterType("patient", ValueType_Utf8String);
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379 statement.SetParameterType("study", ValueType_Utf8String);
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380 statement.SetParameterType("series", ValueType_Utf8String);
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381 statement.SetParameterType("instance", ValueType_Utf8String);
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382
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383 Dictionary args;
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384 args.SetUtf8Value("patient", hashPatient);
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385 args.SetUtf8Value("study", hashStudy);
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386 args.SetUtf8Value("series", hashSeries);
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387 args.SetUtf8Value("instance", hashInstance);
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388
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389 statement.Execute(args);
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390
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391 if (statement.IsDone() ||
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392 statement.GetResultFieldsCount() != 8)
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393 {
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394 throw Orthanc::OrthancException(Orthanc::ErrorCode_Database);
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395 }
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396
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397 for (size_t i = 0; i < 8; i++)
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398 {
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399 statement.SetResultFieldType(i, ValueType_Integer64);
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400 }
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401
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402 result.isNewInstance = (statement.ReadInteger64(3) == 1);
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403 result.instanceId = statement.ReadInteger64(7);
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404
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405 if (result.isNewInstance)
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406 {
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407 result.isNewPatient = (statement.ReadInteger64(0) == 1);
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408 result.isNewStudy = (statement.ReadInteger64(1) == 1);
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409 result.isNewSeries = (statement.ReadInteger64(2) == 1);
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410 result.patientId = statement.ReadInteger64(4);
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411 result.studyId = statement.ReadInteger64(5);
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412 result.seriesId = statement.ReadInteger64(6);
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413 }
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414 }
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415 #endif
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416
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417
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418 uint64_t PostgreSQLIndex::GetResourcesCount(DatabaseManager& manager,
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419 OrthancPluginResourceType resourceType)
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420 {
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421 // Optimized version thanks to the "FastCountResources.sql" extension
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422
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423 assert(OrthancPluginResourceType_Patient == 0 &&
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424 OrthancPluginResourceType_Study == 1 &&
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425 OrthancPluginResourceType_Series == 2 &&
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426 OrthancPluginResourceType_Instance == 3);
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427
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428 uint64_t result;
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429
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430 {
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431 DatabaseManager::CachedStatement statement(
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432 STATEMENT_FROM_HERE, manager,
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433 "SELECT value FROM GlobalIntegers WHERE key = ${key}");
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434
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435 statement.SetParameterType("key", ValueType_Integer64);
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436
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437 Dictionary args;
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438
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439 // For an explanation of the "+ 2" below, check out "FastCountResources.sql"
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440 args.SetIntegerValue("key", static_cast<int>(resourceType + 2));
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441
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442 statement.SetReadOnly(true);
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443 statement.Execute(args);
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444
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445 result = static_cast<uint64_t>(statement.ReadInteger64(0));
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446 }
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447
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448 assert(result == IndexBackend::GetResourcesCount(manager, resourceType));
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449 return result;
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450 }
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451
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452
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453 int64_t PostgreSQLIndex::GetLastChangeIndex(DatabaseManager& manager)
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454 {
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455 DatabaseManager::CachedStatement statement(
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456 STATEMENT_FROM_HERE, manager,
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457 "SELECT value FROM GlobalIntegers WHERE key = 6");
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458
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459 statement.SetReadOnly(true);
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460 statement.Execute();
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461
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462 return statement.ReadInteger64(0);
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463 }
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464
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465
225
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466 void PostgreSQLIndex::TagMostRecentPatient(DatabaseManager& manager,
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467 int64_t patient)
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468 {
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469 // This behavior is implemented in "CreateInstance()", and no
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470 // backward compatibility is necessary
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471 throw Orthanc::OrthancException(Orthanc::ErrorCode_Database);
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472 }
0
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473 }