Mercurial > hg > orthanc-databases

annotate PostgreSQL/Plugins/PostgreSQLIndex.cpp @ 88:eb08ec14fb04 db-changes

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new extension implemented: TagMostRecentPatient
author Sebastien Jodogne <s.jodogne@gmail.com>
date Tue, 15 Jan 2019 21:10:50 +0100
parents 1012fe77241c
children e61587582cef
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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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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 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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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 if (clearAll_)
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78 {
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79 db->ClearAll();
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80 }
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82 {
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83 PostgreSQLTransaction t(*db);
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84
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85 if (!db->DoesTableExist("Resources"))
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86 {
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87 std::string query;
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88
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89 Orthanc::EmbeddedResources::GetFileResource
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90 (query, Orthanc::EmbeddedResources::POSTGRESQL_PREPARE_INDEX);
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91 db->Execute(query);
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92
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93 SetGlobalIntegerProperty(*db, t, Orthanc::GlobalProperty_DatabaseSchemaVersion, expectedVersion);
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94 SetGlobalIntegerProperty(*db, t, Orthanc::GlobalProperty_DatabasePatchLevel, 1);
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95 SetGlobalIntegerProperty(*db, t, Orthanc::GlobalProperty_HasTrigramIndex, 0);
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96 }
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97
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98 if (!db->DoesTableExist("Resources"))
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99 {
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100 LOG(ERROR) << "Corrupted PostgreSQL database";
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101 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError);
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102 }
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103
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104 int version = 0;
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105 if (!LookupGlobalIntegerProperty(version, *db, t, Orthanc::GlobalProperty_DatabaseSchemaVersion) ||
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106 version != 6)
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107 {
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108 LOG(ERROR) << "PostgreSQL plugin is incompatible with database schema version: " << version;
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109 throw Orthanc::OrthancException(Orthanc::ErrorCode_Database);
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110 }
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111
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112 int revision;
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113 if (!LookupGlobalIntegerProperty(revision, *db, t, Orthanc::GlobalProperty_DatabasePatchLevel))
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114 {
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115 revision = 1;
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116 SetGlobalIntegerProperty(*db, t, Orthanc::GlobalProperty_DatabasePatchLevel, revision);
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117 }
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118
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119 if (revision != 1)
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120 {
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121 LOG(ERROR) << "PostgreSQL plugin is incompatible with database schema revision: " << revision;
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122 throw Orthanc::OrthancException(Orthanc::ErrorCode_Database);
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123 }
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124
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125 t.Commit();
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126 }
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127
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128 {
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129 PostgreSQLTransaction t(*db);
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130
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131 int hasTrigram = 0;
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132 if (!LookupGlobalIntegerProperty(hasTrigram, *db, t,
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133 Orthanc::GlobalProperty_HasTrigramIndex) ||
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134 hasTrigram != 1)
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135 {
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136 /**
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137 * Apply fix for performance issue (speed up wildcard search
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138 * by using GIN trigrams). This implements the patch suggested
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139 * in issue #47, BUT we also keep the original
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140 * "DicomIdentifiersIndexValues", as it leads to better
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141 * performance for "strict" searches (i.e. searches involving
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142 * no wildcard).
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143 * https://www.postgresql.org/docs/current/static/pgtrgm.html
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144 * https://bitbucket.org/sjodogne/orthanc/issues/47/index-improvements-for-pg-plugin
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145 **/
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146 try
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147 {
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148 // We've observed 9 minutes on DB with 100000 studies
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149 LOG(WARNING) << "Trying to enable trigram matching on the PostgreSQL database "
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150 << "to speed up wildcard searches. This may take several minutes";
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151
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152 db->Execute(
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153 "CREATE EXTENSION IF NOT EXISTS pg_trgm; "
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154 "CREATE INDEX DicomIdentifiersIndexValues2 ON DicomIdentifiers USING gin(value gin_trgm_ops);");
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155
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156 SetGlobalIntegerProperty(*db, t, Orthanc::GlobalProperty_HasTrigramIndex, 1);
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157 LOG(WARNING) << "Trigram index has been created";
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158
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159 t.Commit();
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160 }
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161 catch (Orthanc::OrthancException&)
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162 {
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163 LOG(WARNING) << "Performance warning: Your PostgreSQL server does "
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164 << "not support trigram matching";
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165 LOG(WARNING) << "-> Consider installing the \"pg_trgm\" extension on the "
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166 << "PostgreSQL server, e.g. on Debian: sudo apt install postgresql-contrib";
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167 }
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168 }
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169 else
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170 {
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171 t.Commit();
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172 }
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173 }
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174
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175 {
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176 PostgreSQLTransaction t(*db);
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177
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178 int hasCreateInstance = 0;
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179 if (!LookupGlobalIntegerProperty(hasCreateInstance, *db, t,
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180 Orthanc::GlobalProperty_HasCreateInstance) ||
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181 hasCreateInstance != 1)
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182 {
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183 LOG(INFO) << "Installing the CreateInstance extension";
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184
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185 std::string query;
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186 Orthanc::EmbeddedResources::GetFileResource
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187 (query, Orthanc::EmbeddedResources::POSTGRESQL_CREATE_INSTANCE);
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188 db->Execute(query);
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189
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190 SetGlobalIntegerProperty(*db, t, Orthanc::GlobalProperty_HasCreateInstance, 1);
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191 }
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192
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193 t.Commit();
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194 }
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195
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196 {
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197 PostgreSQLTransaction t(*db);
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198
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199 int hasFastTotalSize = 0;
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200 if (!LookupGlobalIntegerProperty(hasFastTotalSize, *db, t,
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201 Orthanc::GlobalProperty_GetTotalSizeIsFast) ||
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202 hasFastTotalSize != 1)
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203 {
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204 LOG(INFO) << "Installing the FastTotalSize extension";
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205
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206 std::string query;
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207 Orthanc::EmbeddedResources::GetFileResource
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208 (query, Orthanc::EmbeddedResources::POSTGRESQL_FAST_TOTAL_SIZE);
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209 db->Execute(query);
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210
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211 SetGlobalIntegerProperty(*db, t, Orthanc::GlobalProperty_GetTotalSizeIsFast, 1);
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212 }
72
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213
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214 t.Commit();
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215 }
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216
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217 {
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218 PostgreSQLTransaction t(*db);
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219
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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 int 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
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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
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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 t.Commit();
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238 }
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239
85
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240 {
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241 PostgreSQLTransaction t(*db);
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242
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243 // Installing this extension requires the "GlobalIntegers" table
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244 // created by the "GetLastChangeIndex" extension
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245 int property = 0;
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246 if (!LookupGlobalIntegerProperty(property, *db, t,
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247 Orthanc::GlobalProperty_GetLastChangeIndex) ||
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248 property != 1)
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249 {
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250 LOG(INFO) << "Installing the GetLastChangeIndex extension";
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251
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252 std::string query;
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253 Orthanc::EmbeddedResources::GetFileResource
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254 (query, Orthanc::EmbeddedResources::POSTGRESQL_GET_LAST_CHANGE_INDEX);
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255 db->Execute(query);
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256
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257 SetGlobalIntegerProperty(*db, t, Orthanc::GlobalProperty_GetLastChangeIndex, 1);
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258 }
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259
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260 t.Commit();
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261 }
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262
0
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263 return db.release();
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264 }
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265
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266
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267 PostgreSQLIndex::PostgreSQLIndex(const PostgreSQLParameters& parameters) :
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268 IndexBackend(new Factory(*this)),
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269 context_(NULL),
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270 parameters_(parameters),
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271 clearAll_(false)
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272 {
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273 }
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274
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275
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276 int64_t PostgreSQLIndex::CreateResource(const char* publicId,
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277 OrthancPluginResourceType type)
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278 {
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279 DatabaseManager::CachedStatement statement(
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280 STATEMENT_FROM_HERE, GetManager(),
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281 "INSERT INTO Resources VALUES(${}, ${type}, ${id}, NULL) RETURNING internalId");
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282
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283 statement.SetParameterType("id", ValueType_Utf8String);
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284 statement.SetParameterType("type", ValueType_Integer64);
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285
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286 Dictionary args;
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287 args.SetUtf8Value("id", publicId);
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288 args.SetIntegerValue("type", static_cast<int>(type));
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289
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290 statement.Execute(args);
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291
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292 return ReadInteger64(statement, 0);
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293 }
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294
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295
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296 uint64_t PostgreSQLIndex::GetTotalCompressedSize()
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297 {
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298 // Fast version if extension "./FastTotalSize.sql" is installed
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299 uint64_t result;
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300
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301 {
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302 DatabaseManager::CachedStatement statement(
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303 STATEMENT_FROM_HERE, GetManager(),
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304 "SELECT value FROM GlobalIntegers WHERE key = 0");
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305
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306 statement.SetReadOnly(true);
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307 statement.Execute();
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308
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309 result = static_cast<uint64_t>(ReadInteger64(statement, 0));
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310 }
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311
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312 assert(result == IndexBackend::GetTotalCompressedSize());
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313 return result;
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314 }
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315
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316
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317 uint64_t PostgreSQLIndex::GetTotalUncompressedSize()
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318 {
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319 // Fast version if extension "./FastTotalSize.sql" is installed
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320 uint64_t result;
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321
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322 {
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323 DatabaseManager::CachedStatement statement(
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324 STATEMENT_FROM_HERE, GetManager(),
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325 "SELECT value FROM GlobalIntegers WHERE key = 1");
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326
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327 statement.SetReadOnly(true);
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328 statement.Execute();
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329
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330 result = static_cast<uint64_t>(ReadInteger64(statement, 0));
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331 }
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332
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333 assert(result == IndexBackend::GetTotalUncompressedSize());
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334 return result;
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335 }
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336
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337
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338 #if ORTHANC_PLUGINS_HAS_DATABASE_CONSTRAINT == 1
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339 void PostgreSQLIndex::CreateInstance(OrthancPluginCreateInstanceResult& result,
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340 const char* hashPatient,
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341 const char* hashStudy,
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342 const char* hashSeries,
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343 const char* hashInstance)
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344 {
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345 DatabaseManager::CachedStatement statement(
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346 STATEMENT_FROM_HERE, GetManager(),
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347 "SELECT * FROM CreateInstance(${patient}, ${study}, ${series}, ${instance})");
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348
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349 statement.SetParameterType("patient", ValueType_Utf8String);
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350 statement.SetParameterType("study", ValueType_Utf8String);
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351 statement.SetParameterType("series", ValueType_Utf8String);
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352 statement.SetParameterType("instance", ValueType_Utf8String);
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353
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354 Dictionary args;
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355 args.SetUtf8Value("patient", hashPatient);
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356 args.SetUtf8Value("study", hashStudy);
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357 args.SetUtf8Value("series", hashSeries);
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358 args.SetUtf8Value("instance", hashInstance);
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359
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360 statement.Execute(args);
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361
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362 if (statement.IsDone() ||
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363 statement.GetResultFieldsCount() != 8)
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364 {
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365 throw Orthanc::OrthancException(Orthanc::ErrorCode_Database);
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366 }
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367
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368 for (size_t i = 0; i < 8; i++)
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369 {
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370 statement.SetResultFieldType(i, ValueType_Integer64);
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371 }
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372
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373 result.isNewInstance = (ReadInteger64(statement, 3) == 1);
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374 result.instanceId = ReadInteger64(statement, 7);
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375
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376 if (result.isNewInstance)
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377 {
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378 result.isNewPatient = (ReadInteger64(statement, 0) == 1);
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379 result.isNewStudy = (ReadInteger64(statement, 1) == 1);
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380 result.isNewSeries = (ReadInteger64(statement, 2) == 1);
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381 result.patientId = ReadInteger64(statement, 4);
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382 result.studyId = ReadInteger64(statement, 5);
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383 result.seriesId = ReadInteger64(statement, 6);
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384
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385 // TODO - Move this to the stored procedure
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386 TagMostRecentPatient(result.patientId);
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387 }
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388 }
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389 #endif
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390
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391
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392 uint64_t PostgreSQLIndex::GetResourceCount(OrthancPluginResourceType resourceType)
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393 {
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394 // Optimized version thanks to the "FastCountResources.sql" extension
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395
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396 assert(OrthancPluginResourceType_Patient == 0 &&
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397 OrthancPluginResourceType_Study == 1 &&
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398 OrthancPluginResourceType_Series == 2 &&
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399 OrthancPluginResourceType_Instance == 3);
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400
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401 uint64_t result;
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402
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403 {
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404 DatabaseManager::CachedStatement statement(
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405 STATEMENT_FROM_HERE, GetManager(),
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406 "SELECT value FROM GlobalIntegers WHERE key = ${key}");
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407
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408 statement.SetParameterType("key", ValueType_Integer64);
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409
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410 Dictionary args;
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411
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412 // For an explanation of the "+ 2" below, check out "FastCountResources.sql"
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413 args.SetIntegerValue("key", static_cast<int>(resourceType + 2));
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414
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415 statement.SetReadOnly(true);
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416 statement.Execute(args);
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417
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418 result = static_cast<uint64_t>(ReadInteger64(statement, 0));
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419 }
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420
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421 assert(result == IndexBackend::GetResourceCount(resourceType));
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422 return result;
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423 }
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424
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425
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426 int64_t PostgreSQLIndex::GetLastChangeIndex()
1012fe77241c new extension implemented for PostgreSQL and SQLite: GetLastChangeIndex
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427 {
1012fe77241c new extension implemented for PostgreSQL and SQLite: GetLastChangeIndex
Sebastien Jodogne <s.jodogne@gmail.com>
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428 DatabaseManager::CachedStatement statement(
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429 STATEMENT_FROM_HERE, GetManager(),
1012fe77241c new extension implemented for PostgreSQL and SQLite: GetLastChangeIndex
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430 "SELECT value FROM GlobalIntegers WHERE key = 6");
1012fe77241c new extension implemented for PostgreSQL and SQLite: GetLastChangeIndex
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parents: 79
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431
1012fe77241c new extension implemented for PostgreSQL and SQLite: GetLastChangeIndex
Sebastien Jodogne <s.jodogne@gmail.com>
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432 statement.SetReadOnly(true);
1012fe77241c new extension implemented for PostgreSQL and SQLite: GetLastChangeIndex
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433 statement.Execute();
1012fe77241c new extension implemented for PostgreSQL and SQLite: GetLastChangeIndex
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parents: 79
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434
1012fe77241c new extension implemented for PostgreSQL and SQLite: GetLastChangeIndex
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435 return ReadInteger64(statement, 0);
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parents: 79
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436 }
0
7cea966b6829 initial commit
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437 }