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annotate PostgreSQL/Plugins/PostgreSQLIndex.cpp @ 152:063aa53b5917

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author Sebastien Jodogne <s.jodogne@gmail.com>
date Wed, 01 Jul 2020 08:54:32 +0200
parents 4cd7e45b671e
children 275e14f57f1e
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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) 2017-2020 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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22 #include "PostgreSQLIndex.h"
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24 #include "../../Framework/Plugins/GlobalProperties.h"
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25 #include "../../Framework/PostgreSQL/PostgreSQLDatabase.h"
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26 #include "../../Framework/PostgreSQL/PostgreSQLTransaction.h"
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27 #include "PostgreSQLDefinitions.h"
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29 #include <EmbeddedResources.h> // Auto-generated file
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30
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31 #include <Logging.h>
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32 #include <OrthancException.h>
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34
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35 namespace Orthanc
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36 {
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37 // Some aliases for internal properties
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38 static const GlobalProperty GlobalProperty_HasTrigramIndex = GlobalProperty_DatabaseInternal0;
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39 static const GlobalProperty GlobalProperty_HasCreateInstance = GlobalProperty_DatabaseInternal1;
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40 static const GlobalProperty GlobalProperty_HasFastCountResources = GlobalProperty_DatabaseInternal2;
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41 static const GlobalProperty GlobalProperty_GetLastChangeIndex = GlobalProperty_DatabaseInternal3;
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42 }
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45 namespace OrthancDatabases
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46 {
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47 IDatabase* PostgreSQLIndex::OpenInternal()
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48 {
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49 uint32_t expectedVersion = 6;
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50 if (context_)
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51 {
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52 expectedVersion = OrthancPluginGetExpectedDatabaseVersion(context_);
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53 }
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54 else
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55 {
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56 // This case only occurs during unit testing
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57 expectedVersion = 6;
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58 }
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59
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60 // Check the expected version of the database
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61 if (expectedVersion != 6)
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62 {
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63 LOG(ERROR) << "This database plugin is incompatible with your version of Orthanc "
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64 << "expecting the DB schema version " << expectedVersion
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65 << ", but this plugin is only compatible with version 6";
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66 throw Orthanc::OrthancException(Orthanc::ErrorCode_Plugin);
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67 }
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68
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69 std::auto_ptr<PostgreSQLDatabase> db(new PostgreSQLDatabase(parameters_));
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71 db->Open();
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72
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73 if (parameters_.HasLock())
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74 {
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75 db->AdvisoryLock(POSTGRESQL_LOCK_INDEX);
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76 }
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78 {
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79 PostgreSQLDatabase::TransientAdvisoryLock lock(*db, POSTGRESQL_LOCK_DATABASE_SETUP);
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81 if (clearAll_)
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82 {
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83 db->ClearAll();
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84 }
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86 {
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87 PostgreSQLTransaction t(*db);
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88
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89 if (!db->DoesTableExist("Resources"))
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90 {
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91 std::string query;
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92
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93 Orthanc::EmbeddedResources::GetFileResource
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94 (query, Orthanc::EmbeddedResources::POSTGRESQL_PREPARE_INDEX);
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95 db->Execute(query);
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96
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97 SetGlobalIntegerProperty(*db, t, Orthanc::GlobalProperty_DatabaseSchemaVersion, expectedVersion);
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98 SetGlobalIntegerProperty(*db, t, Orthanc::GlobalProperty_DatabasePatchLevel, 1);
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99 SetGlobalIntegerProperty(*db, t, Orthanc::GlobalProperty_HasTrigramIndex, 0);
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100 }
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101
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102 if (!db->DoesTableExist("Resources"))
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103 {
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104 LOG(ERROR) << "Corrupted PostgreSQL database";
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105 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError);
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106 }
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107
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108 int version = 0;
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109 if (!LookupGlobalIntegerProperty(version, *db, t, Orthanc::GlobalProperty_DatabaseSchemaVersion) ||
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110 version != 6)
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111 {
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112 LOG(ERROR) << "PostgreSQL plugin is incompatible with database schema version: " << version;
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113 throw Orthanc::OrthancException(Orthanc::ErrorCode_Database);
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114 }
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115
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116 int revision;
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117 if (!LookupGlobalIntegerProperty(revision, *db, t, Orthanc::GlobalProperty_DatabasePatchLevel))
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118 {
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119 revision = 1;
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120 SetGlobalIntegerProperty(*db, t, Orthanc::GlobalProperty_DatabasePatchLevel, revision);
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121 }
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122
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123 if (revision != 1)
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124 {
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125 LOG(ERROR) << "PostgreSQL plugin is incompatible with database schema revision: " << revision;
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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 t.Commit();
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130 }
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132 {
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133 PostgreSQLTransaction t(*db);
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134
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135 int hasTrigram = 0;
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136 if (!LookupGlobalIntegerProperty(hasTrigram, *db, t,
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137 Orthanc::GlobalProperty_HasTrigramIndex) ||
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138 hasTrigram != 1)
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139 {
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140 /**
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141 * Apply fix for performance issue (speed up wildcard search
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142 * by using GIN trigrams). This implements the patch suggested
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143 * in issue #47, BUT we also keep the original
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144 * "DicomIdentifiersIndexValues", as it leads to better
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145 * performance for "strict" searches (i.e. searches involving
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146 * no wildcard).
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147 * https://www.postgresql.org/docs/current/static/pgtrgm.html
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148 * https://bitbucket.org/sjodogne/orthanc/issues/47/index-improvements-for-pg-plugin
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149 **/
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150 try
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151 {
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152 // We've observed 9 minutes on DB with 100000 studies
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153 LOG(WARNING) << "Trying to enable trigram matching on the PostgreSQL database "
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154 << "to speed up wildcard searches. This may take several minutes";
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155
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156 db->Execute(
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157 "CREATE EXTENSION IF NOT EXISTS pg_trgm; "
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158 "CREATE INDEX DicomIdentifiersIndexValues2 ON DicomIdentifiers USING gin(value gin_trgm_ops);");
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159
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160 SetGlobalIntegerProperty(*db, t, Orthanc::GlobalProperty_HasTrigramIndex, 1);
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161 LOG(WARNING) << "Trigram index has been created";
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162
136
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163 t.Commit();
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164 }
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165 catch (Orthanc::OrthancException&)
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166 {
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167 LOG(WARNING) << "Performance warning: Your PostgreSQL server does "
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168 << "not support trigram matching";
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169 LOG(WARNING) << "-> Consider installing the \"pg_trgm\" extension on the "
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170 << "PostgreSQL server, e.g. on Debian: sudo apt install postgresql-contrib";
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171 }
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172 }
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173 else
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174 {
136
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175 t.Commit();
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176 }
136
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177 }
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178
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179 {
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180 PostgreSQLTransaction t(*db);
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181
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182 int property = 0;
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183 if (!LookupGlobalIntegerProperty(property, *db, t,
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184 Orthanc::GlobalProperty_HasCreateInstance) ||
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185 property != 2)
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186 {
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187 LOG(INFO) << "Installing the CreateInstance extension";
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188
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189 if (property == 1)
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190 {
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191 // Drop older, experimental versions of this extension
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192 db->Execute("DROP FUNCTION CreateInstance("
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193 "IN patient TEXT, IN study TEXT, IN series TEXT, in instance TEXT)");
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194 }
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195
136
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196 std::string query;
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197 Orthanc::EmbeddedResources::GetFileResource
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198 (query, Orthanc::EmbeddedResources::POSTGRESQL_CREATE_INSTANCE);
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199 db->Execute(query);
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200
136
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201 SetGlobalIntegerProperty(*db, t, Orthanc::GlobalProperty_HasCreateInstance, 2);
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202 }
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203
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204
136
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205 if (!LookupGlobalIntegerProperty(property, *db, t,
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206 Orthanc::GlobalProperty_GetTotalSizeIsFast) ||
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207 property != 1)
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208 {
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209 LOG(INFO) << "Installing the FastTotalSize extension";
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210
136
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211 std::string query;
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212 Orthanc::EmbeddedResources::GetFileResource
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213 (query, Orthanc::EmbeddedResources::POSTGRESQL_FAST_TOTAL_SIZE);
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214 db->Execute(query);
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215
136
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216 SetGlobalIntegerProperty(*db, t, Orthanc::GlobalProperty_GetTotalSizeIsFast, 1);
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217 }
72
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218
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219
136
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220 // Installing this extension requires the "GlobalIntegers" table
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221 // created by the "FastTotalSize" extension
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222 property = 0;
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223 if (!LookupGlobalIntegerProperty(property, *db, t,
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224 Orthanc::GlobalProperty_HasFastCountResources) ||
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225 property != 1)
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226 {
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227 LOG(INFO) << "Installing the FastCountResources extension";
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228
136
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229 std::string query;
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230 Orthanc::EmbeddedResources::GetFileResource
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231 (query, Orthanc::EmbeddedResources::POSTGRESQL_FAST_COUNT_RESOURCES);
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232 db->Execute(query);
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233
136
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234 SetGlobalIntegerProperty(*db, t, Orthanc::GlobalProperty_HasFastCountResources, 1);
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235 }
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236
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237
136
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238 // Installing this extension requires the "GlobalIntegers" table
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239 // created by the "GetLastChangeIndex" extension
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240 property = 0;
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241 if (!LookupGlobalIntegerProperty(property, *db, t,
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242 Orthanc::GlobalProperty_GetLastChangeIndex) ||
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243 property != 1)
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244 {
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245 LOG(INFO) << "Installing the GetLastChangeIndex extension";
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246
136
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247 std::string query;
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248 Orthanc::EmbeddedResources::GetFileResource
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249 (query, Orthanc::EmbeddedResources::POSTGRESQL_GET_LAST_CHANGE_INDEX);
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250 db->Execute(query);
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251
136
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252 SetGlobalIntegerProperty(*db, t, Orthanc::GlobalProperty_GetLastChangeIndex, 1);
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253 }
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254
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255 t.Commit();
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256 }
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257 }
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258
0
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259 return db.release();
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260 }
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261
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262
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263 PostgreSQLIndex::PostgreSQLIndex(const PostgreSQLParameters& parameters) :
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264 IndexBackend(new Factory(*this)),
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265 context_(NULL),
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266 parameters_(parameters),
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267 clearAll_(false)
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268 {
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269 }
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270
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271
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272 int64_t PostgreSQLIndex::CreateResource(const char* publicId,
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273 OrthancPluginResourceType type)
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274 {
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275 DatabaseManager::CachedStatement statement(
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276 STATEMENT_FROM_HERE, GetManager(),
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277 "INSERT INTO Resources VALUES(${}, ${type}, ${id}, NULL) RETURNING internalId");
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278
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279 statement.SetParameterType("id", ValueType_Utf8String);
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280 statement.SetParameterType("type", ValueType_Integer64);
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281
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282 Dictionary args;
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283 args.SetUtf8Value("id", publicId);
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284 args.SetIntegerValue("type", static_cast<int>(type));
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285
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286 statement.Execute(args);
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287
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288 return ReadInteger64(statement, 0);
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289 }
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290
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291
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292 uint64_t PostgreSQLIndex::GetTotalCompressedSize()
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293 {
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294 // Fast version if extension "./FastTotalSize.sql" is installed
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295 uint64_t result;
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296
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297 {
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298 DatabaseManager::CachedStatement statement(
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299 STATEMENT_FROM_HERE, GetManager(),
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300 "SELECT value FROM GlobalIntegers WHERE key = 0");
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301
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302 statement.SetReadOnly(true);
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303 statement.Execute();
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304
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305 result = static_cast<uint64_t>(ReadInteger64(statement, 0));
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306 }
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307
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308 assert(result == IndexBackend::GetTotalCompressedSize());
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309 return result;
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310 }
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311
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312
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313 uint64_t PostgreSQLIndex::GetTotalUncompressedSize()
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314 {
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315 // Fast version if extension "./FastTotalSize.sql" is installed
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316 uint64_t result;
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317
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318 {
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319 DatabaseManager::CachedStatement statement(
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320 STATEMENT_FROM_HERE, GetManager(),
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321 "SELECT value FROM GlobalIntegers WHERE key = 1");
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322
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323 statement.SetReadOnly(true);
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324 statement.Execute();
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325
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326 result = static_cast<uint64_t>(ReadInteger64(statement, 0));
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327 }
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328
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329 assert(result == IndexBackend::GetTotalUncompressedSize());
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330 return result;
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331 }
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332
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333
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334 #if ORTHANC_PLUGINS_HAS_DATABASE_CONSTRAINT == 1
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335 void PostgreSQLIndex::CreateInstance(OrthancPluginCreateInstanceResult& result,
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336 const char* hashPatient,
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337 const char* hashStudy,
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338 const char* hashSeries,
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339 const char* hashInstance)
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340 {
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341 DatabaseManager::CachedStatement statement(
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342 STATEMENT_FROM_HERE, GetManager(),
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343 "SELECT * FROM CreateInstance(${patient}, ${study}, ${series}, ${instance})");
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344
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345 statement.SetParameterType("patient", ValueType_Utf8String);
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346 statement.SetParameterType("study", ValueType_Utf8String);
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347 statement.SetParameterType("series", ValueType_Utf8String);
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348 statement.SetParameterType("instance", ValueType_Utf8String);
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349
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350 Dictionary args;
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351 args.SetUtf8Value("patient", hashPatient);
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352 args.SetUtf8Value("study", hashStudy);
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353 args.SetUtf8Value("series", hashSeries);
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354 args.SetUtf8Value("instance", hashInstance);
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355
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356 statement.Execute(args);
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357
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358 if (statement.IsDone() ||
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359 statement.GetResultFieldsCount() != 8)
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360 {
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361 throw Orthanc::OrthancException(Orthanc::ErrorCode_Database);
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362 }
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363
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364 for (size_t i = 0; i < 8; i++)
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365 {
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366 statement.SetResultFieldType(i, ValueType_Integer64);
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367 }
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368
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369 result.isNewInstance = (ReadInteger64(statement, 3) == 1);
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370 result.instanceId = ReadInteger64(statement, 7);
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371
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372 if (result.isNewInstance)
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373 {
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374 result.isNewPatient = (ReadInteger64(statement, 0) == 1);
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375 result.isNewStudy = (ReadInteger64(statement, 1) == 1);
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376 result.isNewSeries = (ReadInteger64(statement, 2) == 1);
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377 result.patientId = ReadInteger64(statement, 4);
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378 result.studyId = ReadInteger64(statement, 5);
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379 result.seriesId = ReadInteger64(statement, 6);
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380 }
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381 }
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382 #endif
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383
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384
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385 uint64_t PostgreSQLIndex::GetResourceCount(OrthancPluginResourceType resourceType)
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386 {
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387 // Optimized version thanks to the "FastCountResources.sql" extension
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388
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389 assert(OrthancPluginResourceType_Patient == 0 &&
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390 OrthancPluginResourceType_Study == 1 &&
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391 OrthancPluginResourceType_Series == 2 &&
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392 OrthancPluginResourceType_Instance == 3);
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393
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394 uint64_t result;
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395
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396 {
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397 DatabaseManager::CachedStatement statement(
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398 STATEMENT_FROM_HERE, GetManager(),
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399 "SELECT value FROM GlobalIntegers WHERE key = ${key}");
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400
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401 statement.SetParameterType("key", ValueType_Integer64);
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402
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403 Dictionary args;
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404
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405 // For an explanation of the "+ 2" below, check out "FastCountResources.sql"
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406 args.SetIntegerValue("key", static_cast<int>(resourceType + 2));
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407
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408 statement.SetReadOnly(true);
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409 statement.Execute(args);
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410
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411 result = static_cast<uint64_t>(ReadInteger64(statement, 0));
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412 }
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413
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414 assert(result == IndexBackend::GetResourceCount(resourceType));
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415 return result;
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416 }
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417
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418
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419 int64_t PostgreSQLIndex::GetLastChangeIndex()
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420 {
1012fe77241c new extension implemented for PostgreSQL and SQLite: GetLastChangeIndex
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421 DatabaseManager::CachedStatement statement(
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422 STATEMENT_FROM_HERE, GetManager(),
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423 "SELECT value FROM GlobalIntegers WHERE key = 6");
1012fe77241c new extension implemented for PostgreSQL and SQLite: GetLastChangeIndex
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424
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425 statement.SetReadOnly(true);
1012fe77241c new extension implemented for PostgreSQL and SQLite: GetLastChangeIndex
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426 statement.Execute();
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 return ReadInteger64(statement, 0);
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429 }
90
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430
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431
e61587582cef moved extension TagMostRecentPatient into stored procedure CreateInstance
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432 void PostgreSQLIndex::TagMostRecentPatient(int64_t patient)
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433 {
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434 // This behavior is implemented in "CreateInstance()", and no
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Sebastien Jodogne <s.jodogne@gmail.com>
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435 // backward compatibility is necessary
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436 throw Orthanc::OrthancException(Orthanc::ErrorCode_Database);
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437 }
0
7cea966b6829 initial commit
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438 }