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annotate PostgreSQL/Plugins/PostgreSQLIndex.cpp @ 134:cc3dc759c989

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Added an advisory lock to avoid race conditions during database setup
author Sebastien Jodogne <s.jodogne@gmail.com>
date Wed, 08 May 2019 20:21:13 +0200
parents e61587582cef
children 3266785d5627
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1 /**
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2 * Orthanc - A Lightweight, RESTful DICOM Store
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3 * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics
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4 * Department, University Hospital of Liege, Belgium
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714c5d2bee76 preparing for 2019
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5 * Copyright (C) 2017-2019 Osimis S.A., Belgium
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6 *
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7 * This program is free software: you can redistribute it and/or
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8 * modify it under the terms of the GNU Affero General Public License
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9 * as published by the Free Software Foundation, either version 3 of
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10 * the License, or (at your option) any later version.
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11 *
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12 * This program is distributed in the hope that it will be useful, but
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13 * WITHOUT ANY WARRANTY; without even the implied warranty of
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14 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
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15 * Affero General Public License for more details.
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16 *
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17 * You should have received a copy of the GNU Affero General Public License
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18 * along with this program. If not, see <http://www.gnu.org/licenses/>.
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19 **/
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20
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21
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22 #include "PostgreSQLIndex.h"
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23
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24 #include "../../Framework/Plugins/GlobalProperties.h"
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25 #include "../../Framework/PostgreSQL/PostgreSQLDatabase.h"
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26 #include "../../Framework/PostgreSQL/PostgreSQLTransaction.h"
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27
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28 #include <EmbeddedResources.h> // Auto-generated file
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29
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30 #include <Core/Logging.h>
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31 #include <Core/OrthancException.h>
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32
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33
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34 namespace Orthanc
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35 {
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36 // Some aliases for internal properties
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37 static const GlobalProperty GlobalProperty_HasTrigramIndex = GlobalProperty_DatabaseInternal0;
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38 static const GlobalProperty GlobalProperty_HasCreateInstance = GlobalProperty_DatabaseInternal1;
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39 static const GlobalProperty GlobalProperty_HasFastCountResources = GlobalProperty_DatabaseInternal2;
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40 static const GlobalProperty GlobalProperty_GetLastChangeIndex = GlobalProperty_DatabaseInternal3;
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41 }
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42
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44 namespace OrthancDatabases
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45 {
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46 IDatabase* PostgreSQLIndex::OpenInternal()
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47 {
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48 uint32_t expectedVersion = 6;
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49 if (context_)
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50 {
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51 expectedVersion = OrthancPluginGetExpectedDatabaseVersion(context_);
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52 }
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53 else
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54 {
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55 // This case only occurs during unit testing
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56 expectedVersion = 6;
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57 }
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58
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59 // Check the expected version of the database
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60 if (expectedVersion != 6)
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61 {
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62 LOG(ERROR) << "This database plugin is incompatible with your version of Orthanc "
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63 << "expecting the DB schema version " << expectedVersion
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64 << ", but this plugin is only compatible with version 6";
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65 throw Orthanc::OrthancException(Orthanc::ErrorCode_Plugin);
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66 }
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67
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68 std::auto_ptr<PostgreSQLDatabase> db(new PostgreSQLDatabase(parameters_));
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70 db->Open();
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72 if (parameters_.HasLock())
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73 {
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74 db->AdvisoryLock(42 /* some arbitrary constant */);
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75 }
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77 /**
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78 * Try and acquire a transient advisory lock to protect the setup
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79 * of the database, because concurrent statements like "CREATE
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80 * TABLE" are not protected by transactions.
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81 * https://groups.google.com/d/msg/orthanc-users/yV3LSTh_TjI/h3PRApJFBAAJ
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82 **/
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83 PostgreSQLDatabase::TransientAdvisoryLock lock(*db, 44 /* some arbitrary constant */);
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84
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85 if (clearAll_)
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86 {
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87 db->ClearAll();
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88 }
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89
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90 {
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91 PostgreSQLTransaction t(*db);
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92
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93 if (!db->DoesTableExist("Resources"))
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94 {
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95 std::string query;
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96
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97 Orthanc::EmbeddedResources::GetFileResource
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98 (query, Orthanc::EmbeddedResources::POSTGRESQL_PREPARE_INDEX);
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99 db->Execute(query);
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100
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101 SetGlobalIntegerProperty(*db, t, Orthanc::GlobalProperty_DatabaseSchemaVersion, expectedVersion);
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102 SetGlobalIntegerProperty(*db, t, Orthanc::GlobalProperty_DatabasePatchLevel, 1);
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103 SetGlobalIntegerProperty(*db, t, Orthanc::GlobalProperty_HasTrigramIndex, 0);
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104 }
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105
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106 if (!db->DoesTableExist("Resources"))
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107 {
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108 LOG(ERROR) << "Corrupted PostgreSQL database";
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109 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError);
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110 }
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111
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112 int version = 0;
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113 if (!LookupGlobalIntegerProperty(version, *db, t, Orthanc::GlobalProperty_DatabaseSchemaVersion) ||
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114 version != 6)
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115 {
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116 LOG(ERROR) << "PostgreSQL plugin is incompatible with database schema version: " << version;
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117 throw Orthanc::OrthancException(Orthanc::ErrorCode_Database);
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118 }
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119
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120 int revision;
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121 if (!LookupGlobalIntegerProperty(revision, *db, t, Orthanc::GlobalProperty_DatabasePatchLevel))
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122 {
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123 revision = 1;
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124 SetGlobalIntegerProperty(*db, t, Orthanc::GlobalProperty_DatabasePatchLevel, revision);
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125 }
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126
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127 if (revision != 1)
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128 {
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129 LOG(ERROR) << "PostgreSQL plugin is incompatible with database schema revision: " << revision;
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130 throw Orthanc::OrthancException(Orthanc::ErrorCode_Database);
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131 }
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132
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133 t.Commit();
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134 }
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135
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136 {
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137 PostgreSQLTransaction t(*db);
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138
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139 int hasTrigram = 0;
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140 if (!LookupGlobalIntegerProperty(hasTrigram, *db, t,
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141 Orthanc::GlobalProperty_HasTrigramIndex) ||
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142 hasTrigram != 1)
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143 {
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144 /**
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145 * Apply fix for performance issue (speed up wildcard search
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146 * by using GIN trigrams). This implements the patch suggested
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147 * in issue #47, BUT we also keep the original
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148 * "DicomIdentifiersIndexValues", as it leads to better
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149 * performance for "strict" searches (i.e. searches involving
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150 * no wildcard).
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151 * https://www.postgresql.org/docs/current/static/pgtrgm.html
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152 * https://bitbucket.org/sjodogne/orthanc/issues/47/index-improvements-for-pg-plugin
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153 **/
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154 try
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155 {
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156 // We've observed 9 minutes on DB with 100000 studies
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157 LOG(WARNING) << "Trying to enable trigram matching on the PostgreSQL database "
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158 << "to speed up wildcard searches. This may take several minutes";
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159
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160 db->Execute(
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161 "CREATE EXTENSION IF NOT EXISTS pg_trgm; "
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162 "CREATE INDEX DicomIdentifiersIndexValues2 ON DicomIdentifiers USING gin(value gin_trgm_ops);");
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163
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164 SetGlobalIntegerProperty(*db, t, Orthanc::GlobalProperty_HasTrigramIndex, 1);
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165 LOG(WARNING) << "Trigram index has been created";
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166
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167 t.Commit();
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168 }
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169 catch (Orthanc::OrthancException&)
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170 {
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171 LOG(WARNING) << "Performance warning: Your PostgreSQL server does "
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172 << "not support trigram matching";
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173 LOG(WARNING) << "-> Consider installing the \"pg_trgm\" extension on the "
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174 << "PostgreSQL server, e.g. on Debian: sudo apt install postgresql-contrib";
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175 }
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176 }
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177 else
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178 {
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179 t.Commit();
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180 }
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181 }
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182
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183 {
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184 PostgreSQLTransaction t(*db);
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185
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186 int property = 0;
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187 if (!LookupGlobalIntegerProperty(property, *db, t,
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188 Orthanc::GlobalProperty_HasCreateInstance) ||
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189 property != 2)
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190 {
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191 LOG(INFO) << "Installing the CreateInstance extension";
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192
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193 if (property == 1)
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194 {
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195 // Drop older, experimental versions of this extension
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196 db->Execute("DROP FUNCTION CreateInstance("
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197 "IN patient TEXT, IN study TEXT, IN series TEXT, in instance TEXT)");
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198 }
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199
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200 std::string query;
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201 Orthanc::EmbeddedResources::GetFileResource
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202 (query, Orthanc::EmbeddedResources::POSTGRESQL_CREATE_INSTANCE);
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203 db->Execute(query);
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204
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205 SetGlobalIntegerProperty(*db, t, Orthanc::GlobalProperty_HasCreateInstance, 2);
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206 }
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207
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208
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209 if (!LookupGlobalIntegerProperty(property, *db, t,
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210 Orthanc::GlobalProperty_GetTotalSizeIsFast) ||
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211 property != 1)
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212 {
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213 LOG(INFO) << "Installing the FastTotalSize extension";
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214
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215 std::string query;
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216 Orthanc::EmbeddedResources::GetFileResource
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217 (query, Orthanc::EmbeddedResources::POSTGRESQL_FAST_TOTAL_SIZE);
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218 db->Execute(query);
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219
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220 SetGlobalIntegerProperty(*db, t, Orthanc::GlobalProperty_GetTotalSizeIsFast, 1);
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221 }
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222
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223
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224 // Installing this extension requires the "GlobalIntegers" table
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225 // created by the "FastTotalSize" extension
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226 property = 0;
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227 if (!LookupGlobalIntegerProperty(property, *db, t,
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228 Orthanc::GlobalProperty_HasFastCountResources) ||
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229 property != 1)
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230 {
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231 LOG(INFO) << "Installing the FastCountResources extension";
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232
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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_COUNT_RESOURCES);
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236 db->Execute(query);
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237
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238 SetGlobalIntegerProperty(*db, t, Orthanc::GlobalProperty_HasFastCountResources, 1);
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239 }
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240
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241
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242 // Installing this extension requires the "GlobalIntegers" table
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243 // created by the "GetLastChangeIndex" extension
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244 property = 0;
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245 if (!LookupGlobalIntegerProperty(property, *db, t,
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246 Orthanc::GlobalProperty_GetLastChangeIndex) ||
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247 property != 1)
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248 {
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249 LOG(INFO) << "Installing the GetLastChangeIndex extension";
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250
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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_GET_LAST_CHANGE_INDEX);
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254 db->Execute(query);
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255
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256 SetGlobalIntegerProperty(*db, t, Orthanc::GlobalProperty_GetLastChangeIndex, 1);
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257 }
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258
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259 t.Commit();
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260 }
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261
0
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262 return db.release();
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263 }
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264
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265
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266 PostgreSQLIndex::PostgreSQLIndex(const PostgreSQLParameters& parameters) :
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267 IndexBackend(new Factory(*this)),
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268 context_(NULL),
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269 parameters_(parameters),
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270 clearAll_(false)
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271 {
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272 }
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273
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274
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275 int64_t PostgreSQLIndex::CreateResource(const char* publicId,
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276 OrthancPluginResourceType type)
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277 {
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278 DatabaseManager::CachedStatement statement(
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279 STATEMENT_FROM_HERE, GetManager(),
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280 "INSERT INTO Resources VALUES(${}, ${type}, ${id}, NULL) RETURNING internalId");
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281
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282 statement.SetParameterType("id", ValueType_Utf8String);
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283 statement.SetParameterType("type", ValueType_Integer64);
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284
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285 Dictionary args;
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286 args.SetUtf8Value("id", publicId);
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287 args.SetIntegerValue("type", static_cast<int>(type));
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288
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289 statement.Execute(args);
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290
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291 return ReadInteger64(statement, 0);
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292 }
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293
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294
72
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295 uint64_t PostgreSQLIndex::GetTotalCompressedSize()
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296 {
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297 // Fast version if extension "./FastTotalSize.sql" is installed
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298 uint64_t result;
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299
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300 {
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301 DatabaseManager::CachedStatement statement(
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302 STATEMENT_FROM_HERE, GetManager(),
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303 "SELECT value FROM GlobalIntegers WHERE key = 0");
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304
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305 statement.SetReadOnly(true);
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306 statement.Execute();
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307
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308 result = static_cast<uint64_t>(ReadInteger64(statement, 0));
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309 }
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310
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311 assert(result == IndexBackend::GetTotalCompressedSize());
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312 return result;
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313 }
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314
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315
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316 uint64_t PostgreSQLIndex::GetTotalUncompressedSize()
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317 {
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318 // Fast version if extension "./FastTotalSize.sql" is installed
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319 uint64_t result;
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320
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321 {
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322 DatabaseManager::CachedStatement statement(
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323 STATEMENT_FROM_HERE, GetManager(),
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324 "SELECT value FROM GlobalIntegers WHERE key = 1");
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325
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326 statement.SetReadOnly(true);
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327 statement.Execute();
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328
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329 result = static_cast<uint64_t>(ReadInteger64(statement, 0));
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330 }
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331
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332 assert(result == IndexBackend::GetTotalUncompressedSize());
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333 return result;
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334 }
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335
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336
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337 #if ORTHANC_PLUGINS_HAS_DATABASE_CONSTRAINT == 1
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338 void PostgreSQLIndex::CreateInstance(OrthancPluginCreateInstanceResult& result,
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339 const char* hashPatient,
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340 const char* hashStudy,
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341 const char* hashSeries,
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342 const char* hashInstance)
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343 {
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344 DatabaseManager::CachedStatement statement(
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345 STATEMENT_FROM_HERE, GetManager(),
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346 "SELECT * FROM CreateInstance(${patient}, ${study}, ${series}, ${instance})");
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347
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348 statement.SetParameterType("patient", ValueType_Utf8String);
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349 statement.SetParameterType("study", ValueType_Utf8String);
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350 statement.SetParameterType("series", ValueType_Utf8String);
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351 statement.SetParameterType("instance", ValueType_Utf8String);
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352
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353 Dictionary args;
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354 args.SetUtf8Value("patient", hashPatient);
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355 args.SetUtf8Value("study", hashStudy);
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356 args.SetUtf8Value("series", hashSeries);
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357 args.SetUtf8Value("instance", hashInstance);
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358
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359 statement.Execute(args);
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360
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361 if (statement.IsDone() ||
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362 statement.GetResultFieldsCount() != 8)
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363 {
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364 throw Orthanc::OrthancException(Orthanc::ErrorCode_Database);
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365 }
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366
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367 for (size_t i = 0; i < 8; i++)
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368 {
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369 statement.SetResultFieldType(i, ValueType_Integer64);
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370 }
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371
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372 result.isNewInstance = (ReadInteger64(statement, 3) == 1);
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373 result.instanceId = ReadInteger64(statement, 7);
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374
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375 if (result.isNewInstance)
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376 {
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377 result.isNewPatient = (ReadInteger64(statement, 0) == 1);
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378 result.isNewStudy = (ReadInteger64(statement, 1) == 1);
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379 result.isNewSeries = (ReadInteger64(statement, 2) == 1);
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380 result.patientId = ReadInteger64(statement, 4);
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381 result.studyId = ReadInteger64(statement, 5);
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382 result.seriesId = ReadInteger64(statement, 6);
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383 }
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384 }
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385 #endif
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386
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387
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388 uint64_t PostgreSQLIndex::GetResourceCount(OrthancPluginResourceType resourceType)
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389 {
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390 // Optimized version thanks to the "FastCountResources.sql" extension
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391
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392 assert(OrthancPluginResourceType_Patient == 0 &&
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393 OrthancPluginResourceType_Study == 1 &&
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394 OrthancPluginResourceType_Series == 2 &&
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395 OrthancPluginResourceType_Instance == 3);
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396
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397 uint64_t result;
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398
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399 {
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400 DatabaseManager::CachedStatement statement(
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401 STATEMENT_FROM_HERE, GetManager(),
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402 "SELECT value FROM GlobalIntegers WHERE key = ${key}");
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403
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404 statement.SetParameterType("key", ValueType_Integer64);
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405
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406 Dictionary args;
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407
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408 // For an explanation of the "+ 2" below, check out "FastCountResources.sql"
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409 args.SetIntegerValue("key", static_cast<int>(resourceType + 2));
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410
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411 statement.SetReadOnly(true);
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412 statement.Execute(args);
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413
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414 result = static_cast<uint64_t>(ReadInteger64(statement, 0));
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415 }
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416
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417 assert(result == IndexBackend::GetResourceCount(resourceType));
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418 return result;
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419 }
85
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420
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421
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422 int64_t PostgreSQLIndex::GetLastChangeIndex()
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423 {
1012fe77241c new extension implemented for PostgreSQL and SQLite: GetLastChangeIndex
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424 DatabaseManager::CachedStatement statement(
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425 STATEMENT_FROM_HERE, GetManager(),
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426 "SELECT value FROM GlobalIntegers WHERE key = 6");
1012fe77241c new extension implemented for PostgreSQL and SQLite: GetLastChangeIndex
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427
1012fe77241c new extension implemented for PostgreSQL and SQLite: GetLastChangeIndex
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428 statement.SetReadOnly(true);
1012fe77241c new extension implemented for PostgreSQL and SQLite: GetLastChangeIndex
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429 statement.Execute();
1012fe77241c new extension implemented for PostgreSQL and SQLite: GetLastChangeIndex
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430
1012fe77241c new extension implemented for PostgreSQL and SQLite: GetLastChangeIndex
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431 return ReadInteger64(statement, 0);
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432 }
90
e61587582cef moved extension TagMostRecentPatient into stored procedure CreateInstance
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433
e61587582cef moved extension TagMostRecentPatient into stored procedure CreateInstance
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434
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435 void PostgreSQLIndex::TagMostRecentPatient(int64_t patient)
e61587582cef moved extension TagMostRecentPatient into stored procedure CreateInstance
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436 {
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437 // This behavior is implemented in "CreateInstance()", and no
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438 // backward compatibility is necessary
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439 throw Orthanc::OrthancException(Orthanc::ErrorCode_Database);
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440 }
0
7cea966b6829 initial commit
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441 }