Mercurial > hg > orthanc-databases

annotate PostgreSQL/Plugins/PostgreSQLIndex.cpp @ 427:3cdea26ece73 pg-transactions

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merge default -> pg-transactions
author Alain Mazy <am@osimis.io>
date Wed, 29 Nov 2023 10:24:18 +0100
parents a7f0f27fe33c d700c8f9fc24
children 4d0bacbd0fba
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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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135
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136 if (revision == 1)
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137 {
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138 LOG(WARNING) << "PostgreSQL plugin: adding UNIQUE(publicId) constraint to the 'Resources' table ";
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139 t.GetDatabaseTransaction().ExecuteMultiLines("ALTER TABLE Resources ADD UNIQUE (publicId);");
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140
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141 revision = 2;
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142 SetGlobalIntegerProperty(manager, MISSING_SERVER_IDENTIFIER, Orthanc::GlobalProperty_DatabasePatchLevel, revision);
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143 }
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144
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145 if (revision != 2)
136
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146 {
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147 LOG(ERROR) << "PostgreSQL plugin is incompatible with database schema revision: " << revision;
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148 throw Orthanc::OrthancException(Orthanc::ErrorCode_Database);
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149 }
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150
77
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151 t.Commit();
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152 }
0
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153
136
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154 {
237
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155 DatabaseManager::Transaction t(manager, TransactionType_ReadWrite);
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156
136
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157 int hasTrigram = 0;
237
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158 if (!LookupGlobalIntegerProperty(hasTrigram, manager, MISSING_SERVER_IDENTIFIER,
136
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159 Orthanc::GlobalProperty_HasTrigramIndex) ||
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160 hasTrigram != 1)
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161 {
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162 /**
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163 * Apply fix for performance issue (speed up wildcard search
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164 * by using GIN trigrams). This implements the patch suggested
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165 * in issue #47, BUT we also keep the original
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166 * "DicomIdentifiersIndexValues", as it leads to better
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167 * performance for "strict" searches (i.e. searches involving
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168 * no wildcard).
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169 * https://www.postgresql.org/docs/current/static/pgtrgm.html
426
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170 * https://orthanc.uclouvain.be/bugs/show_bug.cgi?id=47
136
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171 **/
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172 try
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173 {
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174 // We've observed 9 minutes on DB with 100000 studies
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175 LOG(WARNING) << "Trying to enable trigram matching on the PostgreSQL database "
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176 << "to speed up wildcard searches. This may take several minutes";
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177
241
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178 t.GetDatabaseTransaction().ExecuteMultiLines(
136
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179 "CREATE EXTENSION IF NOT EXISTS pg_trgm; "
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180 "CREATE INDEX DicomIdentifiersIndexValues2 ON DicomIdentifiers USING gin(value gin_trgm_ops);");
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181
237
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182 SetGlobalIntegerProperty(manager, MISSING_SERVER_IDENTIFIER, Orthanc::GlobalProperty_HasTrigramIndex, 1);
136
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183 LOG(WARNING) << "Trigram index has been created";
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184
136
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185 t.Commit();
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186 }
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187 catch (Orthanc::OrthancException&)
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188 {
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189 LOG(WARNING) << "Performance warning: Your PostgreSQL server does "
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190 << "not support trigram matching";
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191 LOG(WARNING) << "-> Consider installing the \"pg_trgm\" extension on the "
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192 << "PostgreSQL server, e.g. on Debian: sudo apt install postgresql-contrib";
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193 }
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194 }
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195 else
90
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196 {
136
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197 t.Commit();
90
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198 }
136
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199 }
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200
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201 {
237
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202 DatabaseManager::Transaction t(manager, TransactionType_ReadWrite);
136
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203
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204 int property = 0;
237
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205 if (!LookupGlobalIntegerProperty(property, manager, MISSING_SERVER_IDENTIFIER,
136
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206 Orthanc::GlobalProperty_HasCreateInstance) ||
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207 property != 2)
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208 {
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209 LOG(INFO) << "Installing the CreateInstance extension";
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210
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211 if (property == 1)
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212 {
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213 // Drop older, experimental versions of this extension
241
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214 t.GetDatabaseTransaction().ExecuteMultiLines("DROP FUNCTION CreateInstance("
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215 "IN patient TEXT, IN study TEXT, IN series TEXT, in instance TEXT)");
136
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216 }
90
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217
136
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218 std::string query;
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219 Orthanc::EmbeddedResources::GetFileResource
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220 (query, Orthanc::EmbeddedResources::POSTGRESQL_CREATE_INSTANCE);
241
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221 t.GetDatabaseTransaction().ExecuteMultiLines(query);
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222
237
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223 SetGlobalIntegerProperty(manager, MISSING_SERVER_IDENTIFIER, Orthanc::GlobalProperty_HasCreateInstance, 2);
136
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224 }
71
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225
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226
237
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227 if (!LookupGlobalIntegerProperty(property, manager, MISSING_SERVER_IDENTIFIER,
136
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228 Orthanc::GlobalProperty_GetTotalSizeIsFast) ||
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229 property != 1)
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230 {
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231 LOG(INFO) << "Installing the FastTotalSize extension";
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diff changeset
232
136
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233 std::string query;
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234 Orthanc::EmbeddedResources::GetFileResource
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235 (query, Orthanc::EmbeddedResources::POSTGRESQL_FAST_TOTAL_SIZE);
241
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236 t.GetDatabaseTransaction().ExecuteMultiLines(query);
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237
237
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238 SetGlobalIntegerProperty(manager, MISSING_SERVER_IDENTIFIER, Orthanc::GlobalProperty_GetTotalSizeIsFast, 1);
136
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239 }
72
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240
79
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241
136
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242 // Installing this extension requires the "GlobalIntegers" table
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243 // created by the "FastTotalSize" extension
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244 property = 0;
237
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245 if (!LookupGlobalIntegerProperty(property, manager, MISSING_SERVER_IDENTIFIER,
136
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246 Orthanc::GlobalProperty_HasFastCountResources) ||
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247 property != 1)
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248 {
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249 LOG(INFO) << "Installing the FastCountResources extension";
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diff changeset
250
136
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251 std::string query;
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252 Orthanc::EmbeddedResources::GetFileResource
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253 (query, Orthanc::EmbeddedResources::POSTGRESQL_FAST_COUNT_RESOURCES);
241
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254 t.GetDatabaseTransaction().ExecuteMultiLines(query);
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255
237
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256 SetGlobalIntegerProperty(manager, MISSING_SERVER_IDENTIFIER, Orthanc::GlobalProperty_HasFastCountResources, 1);
136
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257 }
79
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258
85
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diff changeset
259
136
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260 // Installing this extension requires the "GlobalIntegers" table
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261 // created by the "GetLastChangeIndex" extension
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262 property = 0;
237
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263 if (!LookupGlobalIntegerProperty(property, manager, MISSING_SERVER_IDENTIFIER,
136
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264 Orthanc::GlobalProperty_GetLastChangeIndex) ||
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265 property != 1)
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266 {
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267 LOG(INFO) << "Installing the GetLastChangeIndex extension";
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268
136
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diff changeset
269 std::string query;
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270 Orthanc::EmbeddedResources::GetFileResource
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271 (query, Orthanc::EmbeddedResources::POSTGRESQL_GET_LAST_CHANGE_INDEX);
241
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272 t.GetDatabaseTransaction().ExecuteMultiLines(query);
237
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273
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274 SetGlobalIntegerProperty(manager, MISSING_SERVER_IDENTIFIER, Orthanc::GlobalProperty_GetLastChangeIndex, 1);
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275 }
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276
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277 t.Commit();
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278 }
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279
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280
237
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281 {
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282 // New in release 4.0 to deal with multiple writers
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283 DatabaseManager::Transaction t(manager, TransactionType_ReadWrite);
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284
241
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285 if (!t.GetDatabaseTransaction().DoesTableExist("ServerProperties"))
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286 {
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287 t.GetDatabaseTransaction().ExecuteMultiLines("CREATE TABLE ServerProperties(server VARCHAR(64) NOT NULL, "
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288 "property INTEGER, value TEXT, PRIMARY KEY(server, property))");
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289 }
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290
266
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291 /**
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292 * PostgreSQL 9.5: "Adding a column with a default requires
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293 * updating each row of the table (to store the new column
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294 * value). However, if no default is specified, PostgreSQL is
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295 * able to avoid the physical update." => We set no default
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296 * for performance (older entries will be NULL)
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297 * https://www.postgresql.org/docs/9.5/ddl-alter.html
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298 **/
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299 if (!db.DoesColumnExist("Metadata", "revision"))
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300 {
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301 t.GetDatabaseTransaction().ExecuteMultiLines("ALTER TABLE Metadata ADD COLUMN revision INTEGER");
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302 }
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303
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304 if (!db.DoesColumnExist("AttachedFiles", "revision"))
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305 {
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306 t.GetDatabaseTransaction().ExecuteMultiLines("ALTER TABLE AttachedFiles ADD COLUMN revision INTEGER");
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307 }
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308
136
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309 t.Commit();
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310 }
396
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311
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312
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313 {
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314 // New in release 5.0 to deal with labels
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315 DatabaseManager::Transaction t(manager, TransactionType_ReadWrite);
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316
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317 if (!t.GetDatabaseTransaction().DoesTableExist("Labels"))
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318 {
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319 t.GetDatabaseTransaction().ExecuteMultiLines(
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320 "CREATE TABLE Labels("
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321 "id BIGINT REFERENCES Resources(internalId) ON DELETE CASCADE,"
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322 "label TEXT, PRIMARY KEY(id, label));"
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323 "CREATE INDEX LabelsIndex1 ON LABELS(id);"
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324 "CREATE INDEX LabelsIndex2 ON LABELS(label);");
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325 }
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326
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327 t.Commit();
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328 }
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329 }
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330 }
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331
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332
225
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333 int64_t PostgreSQLIndex::CreateResource(DatabaseManager& manager,
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334 const char* publicId,
0
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335 OrthancPluginResourceType type)
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336 {
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337 DatabaseManager::CachedStatement statement(
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338 STATEMENT_FROM_HERE, manager,
302
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339 "INSERT INTO Resources VALUES(DEFAULT, ${type}, ${id}, NULL) RETURNING internalId");
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340
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341 statement.SetParameterType("id", ValueType_Utf8String);
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342 statement.SetParameterType("type", ValueType_Integer64);
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343
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344 Dictionary args;
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345 args.SetUtf8Value("id", publicId);
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346 args.SetIntegerValue("type", static_cast<int>(type));
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347
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348 statement.Execute(args);
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349
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350 return statement.ReadInteger64(0);
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351 }
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352
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353
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354 uint64_t PostgreSQLIndex::GetTotalCompressedSize(DatabaseManager& manager)
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355 {
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356 // Fast version if extension "./FastTotalSize.sql" is installed
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357 uint64_t result;
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358
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359 {
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360 DatabaseManager::CachedStatement statement(
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361 STATEMENT_FROM_HERE, manager,
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362 "SELECT value FROM GlobalIntegers WHERE key = 0");
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363
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364 statement.SetReadOnly(true);
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365 statement.Execute();
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366
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367 result = static_cast<uint64_t>(statement.ReadInteger64(0));
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368 }
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369
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370 assert(result == IndexBackend::GetTotalCompressedSize(manager));
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371 return result;
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372 }
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373
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374
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375 uint64_t PostgreSQLIndex::GetTotalUncompressedSize(DatabaseManager& manager)
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376 {
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377 // Fast version if extension "./FastTotalSize.sql" is installed
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378 uint64_t result;
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379
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380 {
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381 DatabaseManager::CachedStatement statement(
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382 STATEMENT_FROM_HERE, manager,
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383 "SELECT value FROM GlobalIntegers WHERE key = 1");
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384
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385 statement.SetReadOnly(true);
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386 statement.Execute();
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387
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388 result = static_cast<uint64_t>(statement.ReadInteger64(0));
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389 }
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diff changeset
390
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391 assert(result == IndexBackend::GetTotalUncompressedSize(manager));
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392 return result;
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393 }
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394
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395
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396 #if ORTHANC_PLUGINS_HAS_DATABASE_CONSTRAINT == 1
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397 void PostgreSQLIndex::CreateInstance(OrthancPluginCreateInstanceResult& result,
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398 DatabaseManager& manager,
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diff changeset
399 const char* hashPatient,
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400 const char* hashStudy,
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diff changeset
401 const char* hashSeries,
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diff changeset
402 const char* hashInstance)
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403 {
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404 DatabaseManager::CachedStatement statement(
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405 STATEMENT_FROM_HERE, manager,
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406 "SELECT * FROM CreateInstance(${patient}, ${study}, ${series}, ${instance})");
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407
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408 statement.SetParameterType("patient", ValueType_Utf8String);
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409 statement.SetParameterType("study", ValueType_Utf8String);
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410 statement.SetParameterType("series", ValueType_Utf8String);
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411 statement.SetParameterType("instance", ValueType_Utf8String);
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412
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413 Dictionary args;
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414 args.SetUtf8Value("patient", hashPatient);
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415 args.SetUtf8Value("study", hashStudy);
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416 args.SetUtf8Value("series", hashSeries);
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417 args.SetUtf8Value("instance", hashInstance);
418
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418
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419 { // The CreateInstance procedure is not 100% safe in highly concurrent environments when the
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420 // transaction isolation is set to "READ COMMITED": (e.g, with 10 clients
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421 // anonymizing studies in parallel with the "ResourceModification" config set to 8, we have observed
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422 // the same series being created twice). Therefore, we protect the whole CreateInstance procedure
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423 // with an advisory lock
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424 PostgreSQLDatabase& db = dynamic_cast<PostgreSQLDatabase&>(manager.GetDatabase());
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425 PostgreSQLDatabase::TransientAdvisoryLock lock(db, POSTGRESQL_LOCK_CREATE_INSTANCE, 100, 1);
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426
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427 statement.Execute(args);
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428 }
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429
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430 if (statement.IsDone() ||
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431 statement.GetResultFieldsCount() != 8)
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432 {
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433 throw Orthanc::OrthancException(Orthanc::ErrorCode_Database);
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434 }
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435
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436 for (size_t i = 0; i < 8; i++)
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437 {
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438 statement.SetResultFieldType(i, ValueType_Integer64);
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439 }
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440
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441 result.isNewInstance = (statement.ReadInteger64(3) == 1);
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442 result.instanceId = statement.ReadInteger64(7);
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443
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444 if (result.isNewInstance)
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445 {
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446 result.isNewPatient = (statement.ReadInteger64(0) == 1);
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447 result.isNewStudy = (statement.ReadInteger64(1) == 1);
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448 result.isNewSeries = (statement.ReadInteger64(2) == 1);
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449 result.patientId = statement.ReadInteger64(4);
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450 result.studyId = statement.ReadInteger64(5);
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451 result.seriesId = statement.ReadInteger64(6);
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452 }
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453 }
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454 #endif
79
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455
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456
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457 uint64_t PostgreSQLIndex::GetResourcesCount(DatabaseManager& manager,
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458 OrthancPluginResourceType resourceType)
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459 {
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460 // Optimized version thanks to the "FastCountResources.sql" extension
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461
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462 assert(OrthancPluginResourceType_Patient == 0 &&
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463 OrthancPluginResourceType_Study == 1 &&
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464 OrthancPluginResourceType_Series == 2 &&
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465 OrthancPluginResourceType_Instance == 3);
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466
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467 uint64_t result;
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468
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469 {
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470 DatabaseManager::CachedStatement statement(
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471 STATEMENT_FROM_HERE, manager,
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472 "SELECT value FROM GlobalIntegers WHERE key = ${key}");
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473
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474 statement.SetParameterType("key", ValueType_Integer64);
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475
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476 Dictionary args;
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477
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478 // For an explanation of the "+ 2" below, check out "FastCountResources.sql"
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479 args.SetIntegerValue("key", static_cast<int>(resourceType + 2));
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480
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481 statement.SetReadOnly(true);
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482 statement.Execute(args);
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483
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484 result = static_cast<uint64_t>(statement.ReadInteger64(0));
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485 }
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486
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487 assert(result == IndexBackend::GetResourcesCount(manager, resourceType));
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488 return result;
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489 }
85
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490
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491
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492 int64_t PostgreSQLIndex::GetLastChangeIndex(DatabaseManager& manager)
85
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493 {
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494 DatabaseManager::CachedStatement statement(
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495 STATEMENT_FROM_HERE, manager,
85
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496 "SELECT value FROM GlobalIntegers WHERE key = 6");
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497
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498 statement.SetReadOnly(true);
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499 statement.Execute();
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500
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501 return statement.ReadInteger64(0);
85
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502 }
90
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503
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504
225
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505 void PostgreSQLIndex::TagMostRecentPatient(DatabaseManager& manager,
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506 int64_t patient)
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diff changeset
507 {
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508 // This behavior is implemented in "CreateInstance()", and no
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509 // backward compatibility is necessary
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510 throw Orthanc::OrthancException(Orthanc::ErrorCode_Database);
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511 }
0
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512 }