Mercurial > hg > orthanc-databases

annotate PostgreSQL/Plugins/PostgreSQLIndex.cpp @ 77:a2134531473c db-changes

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avoid warnings "An active PostgreSQL transaction was dismissed"
author Sebastien Jodogne <s.jodogne@gmail.com>
date Sun, 06 Jan 2019 12:35:29 +0100
parents a4e440e65c68
children 2ee166f77501
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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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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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28 #include <EmbeddedResources.h> // Auto-generated file
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30 #include <Core/Logging.h>
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31 #include <Core/OrthancException.h>
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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 }
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42 namespace OrthancDatabases
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43 {
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44 IDatabase* PostgreSQLIndex::OpenInternal()
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45 {
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46 uint32_t expectedVersion = 6;
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47 if (context_)
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48 {
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49 expectedVersion = OrthancPluginGetExpectedDatabaseVersion(context_);
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50 }
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51 else
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52 {
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53 // This case only occurs during unit testing
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54 expectedVersion = 6;
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55 }
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57 // Check the expected version of the database
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58 if (expectedVersion != 6)
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59 {
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60 LOG(ERROR) << "This database plugin is incompatible with your version of Orthanc "
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61 << "expecting the DB schema version " << expectedVersion
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62 << ", but this plugin is only compatible with version 6";
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63 throw Orthanc::OrthancException(Orthanc::ErrorCode_Plugin);
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64 }
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65
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66 std::auto_ptr<PostgreSQLDatabase> db(new PostgreSQLDatabase(parameters_));
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67
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68 db->Open();
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69
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70 if (parameters_.HasLock())
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71 {
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72 db->AdvisoryLock(42 /* some arbitrary constant */);
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73 }
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75 if (clearAll_)
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76 {
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77 db->ClearAll();
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78 }
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80 {
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81 PostgreSQLTransaction t(*db);
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83 if (!db->DoesTableExist("Resources"))
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84 {
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85 std::string query;
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86
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87 Orthanc::EmbeddedResources::GetFileResource
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88 (query, Orthanc::EmbeddedResources::POSTGRESQL_PREPARE_INDEX);
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89 db->Execute(query);
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90
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91 SetGlobalIntegerProperty(*db, t, Orthanc::GlobalProperty_DatabaseSchemaVersion, expectedVersion);
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92 SetGlobalIntegerProperty(*db, t, Orthanc::GlobalProperty_DatabasePatchLevel, 1);
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93 SetGlobalIntegerProperty(*db, t, Orthanc::GlobalProperty_HasTrigramIndex, 0);
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94 }
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95
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96 if (!db->DoesTableExist("Resources"))
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97 {
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98 LOG(ERROR) << "Corrupted PostgreSQL database";
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99 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError);
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100 }
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101
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102 int version = 0;
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103 if (!LookupGlobalIntegerProperty(version, *db, t, Orthanc::GlobalProperty_DatabaseSchemaVersion) ||
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104 version != 6)
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105 {
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106 LOG(ERROR) << "PostgreSQL plugin is incompatible with database schema version: " << version;
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107 throw Orthanc::OrthancException(Orthanc::ErrorCode_Database);
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108 }
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109
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110 int revision;
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111 if (!LookupGlobalIntegerProperty(revision, *db, t, Orthanc::GlobalProperty_DatabasePatchLevel))
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112 {
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113 revision = 1;
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114 SetGlobalIntegerProperty(*db, t, Orthanc::GlobalProperty_DatabasePatchLevel, revision);
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115 }
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116
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117 if (revision != 1)
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118 {
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119 LOG(ERROR) << "PostgreSQL plugin is incompatible with database schema revision: " << revision;
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120 throw Orthanc::OrthancException(Orthanc::ErrorCode_Database);
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121 }
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122
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123 t.Commit();
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124 }
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125
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126 {
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127 PostgreSQLTransaction t(*db);
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128
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129 int hasTrigram = 0;
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130 if (!LookupGlobalIntegerProperty(hasTrigram, *db, t,
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131 Orthanc::GlobalProperty_HasTrigramIndex) ||
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132 hasTrigram != 1)
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133 {
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134 /**
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135 * Apply fix for performance issue (speed up wildcard search
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136 * by using GIN trigrams). This implements the patch suggested
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137 * in issue #47, BUT we also keep the original
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138 * "DicomIdentifiersIndexValues", as it leads to better
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139 * performance for "strict" searches (i.e. searches involving
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140 * no wildcard).
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141 * https://www.postgresql.org/docs/current/static/pgtrgm.html
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142 * https://bitbucket.org/sjodogne/orthanc/issues/47/index-improvements-for-pg-plugin
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143 **/
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144 try
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145 {
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146 // We've observed 9 minutes on DB with 100000 studies
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147 LOG(WARNING) << "Trying to enable trigram matching on the PostgreSQL database "
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148 << "to speed up wildcard searches. This may take several minutes";
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149
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150 db->Execute(
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151 "CREATE EXTENSION IF NOT EXISTS pg_trgm; "
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152 "CREATE INDEX DicomIdentifiersIndexValues2 ON DicomIdentifiers USING gin(value gin_trgm_ops);");
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153
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154 SetGlobalIntegerProperty(*db, t, Orthanc::GlobalProperty_HasTrigramIndex, 1);
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155 LOG(WARNING) << "Trigram index has been created";
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156
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157 t.Commit();
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158 }
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159 catch (Orthanc::OrthancException&)
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160 {
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161 LOG(WARNING) << "Performance warning: Your PostgreSQL server does "
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162 << "not support trigram matching";
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163 LOG(WARNING) << "-> Consider installing the \"pg_trgm\" extension on the "
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164 << "PostgreSQL server, e.g. on Debian: sudo apt install postgresql-contrib";
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165 }
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166 }
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167 else
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168 {
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169 t.Commit();
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170 }
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171 }
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172
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173 {
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174 PostgreSQLTransaction t(*db);
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175
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176 int hasCreateInstance = 0;
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177 if (!LookupGlobalIntegerProperty(hasCreateInstance, *db, t,
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178 Orthanc::GlobalProperty_HasCreateInstance) ||
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179 hasCreateInstance != 1)
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180 {
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181 LOG(INFO) << "Installing the CreateInstance extension";
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182
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183 std::string query;
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184 Orthanc::EmbeddedResources::GetFileResource
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185 (query, Orthanc::EmbeddedResources::POSTGRESQL_CREATE_INSTANCE);
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186 db->Execute(query);
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187
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188 SetGlobalIntegerProperty(*db, t, Orthanc::GlobalProperty_HasCreateInstance, 1);
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189 }
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190
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191 t.Commit();
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192 }
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193
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194 {
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195 PostgreSQLTransaction t(*db);
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196
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197 int hasFastTotalSize = 0;
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198 if (!LookupGlobalIntegerProperty(hasFastTotalSize, *db, t,
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199 Orthanc::GlobalProperty_GetTotalSizeIsFast) ||
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200 hasFastTotalSize != 1)
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201 {
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202 LOG(INFO) << "Installing the FastTotalSize extension";
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203
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204 std::string query;
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205 Orthanc::EmbeddedResources::GetFileResource
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206 (query, Orthanc::EmbeddedResources::POSTGRESQL_FAST_TOTAL_SIZE);
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207 db->Execute(query);
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208
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209 SetGlobalIntegerProperty(*db, t, Orthanc::GlobalProperty_GetTotalSizeIsFast, 1);
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210 }
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211
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212 t.Commit();
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213 }
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214
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215 return db.release();
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216 }
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217
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218
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219 PostgreSQLIndex::PostgreSQLIndex(const PostgreSQLParameters& parameters) :
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220 IndexBackend(new Factory(*this)),
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221 context_(NULL),
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222 parameters_(parameters),
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223 clearAll_(false)
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224 {
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225 }
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226
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227
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228 int64_t PostgreSQLIndex::CreateResource(const char* publicId,
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229 OrthancPluginResourceType type)
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230 {
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231 DatabaseManager::CachedStatement statement(
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232 STATEMENT_FROM_HERE, GetManager(),
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233 "INSERT INTO Resources VALUES(${}, ${type}, ${id}, NULL) RETURNING internalId");
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234
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235 statement.SetParameterType("id", ValueType_Utf8String);
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236 statement.SetParameterType("type", ValueType_Integer64);
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237
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238 Dictionary args;
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239 args.SetUtf8Value("id", publicId);
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240 args.SetIntegerValue("type", static_cast<int>(type));
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241
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242 statement.Execute(args);
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243
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244 return ReadInteger64(statement, 0);
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245 }
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246
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247
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248 uint64_t PostgreSQLIndex::GetTotalCompressedSize()
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249 {
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250 // Fast version if extension "./FastTotalSize.sql" is installed
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251 DatabaseManager::CachedStatement statement(
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252 STATEMENT_FROM_HERE, GetManager(),
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253 "SELECT value FROM GlobalIntegers WHERE key = 0");
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254
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255 statement.SetReadOnly(true);
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256 statement.Execute();
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257
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258 return static_cast<uint64_t>(ReadInteger64(statement, 0));
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259 }
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260
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261
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262 uint64_t PostgreSQLIndex::GetTotalUncompressedSize()
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263 {
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264 // Fast version if extension "./FastTotalSize.sql" is installed
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265 DatabaseManager::CachedStatement statement(
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266 STATEMENT_FROM_HERE, GetManager(),
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267 "SELECT value FROM GlobalIntegers WHERE key = 1");
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268
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269 statement.SetReadOnly(true);
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270 statement.Execute();
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271
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272 return static_cast<uint64_t>(ReadInteger64(statement, 0));
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273 }
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274
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275
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276 #if ORTHANC_PLUGINS_HAS_DATABASE_OPTIMIZATIONS_1 == 1
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277 void PostgreSQLIndex::CreateInstance(OrthancPluginCreateInstanceResult& result,
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278 const char* hashPatient,
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279 const char* hashStudy,
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280 const char* hashSeries,
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281 const char* hashInstance)
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282 {
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283 DatabaseManager::CachedStatement statement(
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284 STATEMENT_FROM_HERE, GetManager(),
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285 "SELECT * FROM CreateInstance(${patient}, ${study}, ${series}, ${instance})");
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286
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287 statement.SetParameterType("patient", ValueType_Utf8String);
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288 statement.SetParameterType("study", ValueType_Utf8String);
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289 statement.SetParameterType("series", ValueType_Utf8String);
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290 statement.SetParameterType("instance", ValueType_Utf8String);
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291
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292 Dictionary args;
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293 args.SetUtf8Value("patient", hashPatient);
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294 args.SetUtf8Value("study", hashStudy);
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295 args.SetUtf8Value("series", hashSeries);
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296 args.SetUtf8Value("instance", hashInstance);
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297
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298 statement.Execute(args);
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299
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300 if (statement.IsDone() ||
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301 statement.GetResultFieldsCount() != 8)
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302 {
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303 throw Orthanc::OrthancException(Orthanc::ErrorCode_Database);
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304 }
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305
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306 for (size_t i = 0; i < 8; i++)
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307 {
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308 statement.SetResultFieldType(i, ValueType_Integer64);
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309 }
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310
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311 result.isNewInstance = (ReadInteger64(statement, 3) == 1);
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312 result.instanceId = ReadInteger64(statement, 7);
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313
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314 if (result.isNewInstance)
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315 {
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316 result.isNewPatient = (ReadInteger64(statement, 0) == 1);
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317 result.isNewStudy = (ReadInteger64(statement, 1) == 1);
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318 result.isNewSeries = (ReadInteger64(statement, 2) == 1);
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319 result.patientId = ReadInteger64(statement, 4);
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320 result.studyId = ReadInteger64(statement, 5);
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321 result.seriesId = ReadInteger64(statement, 6);
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322 }
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323 }
73
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324 #endif
0
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325 }