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annotate PostgreSQL/Plugins/PostgreSQLIndex.cpp @ 106:b559af8fe6e0

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Remove "ASSERT" in SQL for compatibility with older releases of PostgreSQL
author Sebastien Jodogne <s.jodogne@gmail.com>
date Tue, 22 Jan 2019 15:35:52 +0100
parents e61587582cef
children cc3dc759c989
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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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27
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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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44 namespace OrthancDatabases
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45 {
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46 IDatabase* PostgreSQLIndex::OpenInternal()
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47 {
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48 uint32_t expectedVersion = 6;
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49 if (context_)
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50 {
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51 expectedVersion = OrthancPluginGetExpectedDatabaseVersion(context_);
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52 }
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53 else
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54 {
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55 // This case only occurs during unit testing
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56 expectedVersion = 6;
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57 }
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58
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59 // Check the expected version of the database
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60 if (expectedVersion != 6)
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61 {
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62 LOG(ERROR) << "This database plugin is incompatible with your version of Orthanc "
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63 << "expecting the DB schema version " << expectedVersion
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64 << ", but this plugin is only compatible with version 6";
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65 throw Orthanc::OrthancException(Orthanc::ErrorCode_Plugin);
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66 }
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67
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68 std::auto_ptr<PostgreSQLDatabase> db(new PostgreSQLDatabase(parameters_));
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70 db->Open();
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72 if (parameters_.HasLock())
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73 {
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74 db->AdvisoryLock(42 /* some arbitrary constant */);
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75 }
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77 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 property = 0;
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179 if (!LookupGlobalIntegerProperty(property, *db, t,
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180 Orthanc::GlobalProperty_HasCreateInstance) ||
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181 property != 2)
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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 if (property == 1)
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186 {
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187 // Drop older, experimental versions of this extension
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188 db->Execute("DROP FUNCTION CreateInstance("
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189 "IN patient TEXT, IN study TEXT, IN series TEXT, in instance TEXT)");
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190 }
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191
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192 std::string query;
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193 Orthanc::EmbeddedResources::GetFileResource
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194 (query, Orthanc::EmbeddedResources::POSTGRESQL_CREATE_INSTANCE);
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195 db->Execute(query);
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196
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197 SetGlobalIntegerProperty(*db, t, Orthanc::GlobalProperty_HasCreateInstance, 2);
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198 }
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199
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200
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201 if (!LookupGlobalIntegerProperty(property, *db, t,
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202 Orthanc::GlobalProperty_GetTotalSizeIsFast) ||
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203 property != 1)
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204 {
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205 LOG(INFO) << "Installing the FastTotalSize extension";
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206
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207 std::string query;
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208 Orthanc::EmbeddedResources::GetFileResource
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209 (query, Orthanc::EmbeddedResources::POSTGRESQL_FAST_TOTAL_SIZE);
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210 db->Execute(query);
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211
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212 SetGlobalIntegerProperty(*db, t, Orthanc::GlobalProperty_GetTotalSizeIsFast, 1);
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213 }
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214
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215
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216 // Installing this extension requires the "GlobalIntegers" table
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217 // created by the "FastTotalSize" extension
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218 property = 0;
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219 if (!LookupGlobalIntegerProperty(property, *db, t,
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220 Orthanc::GlobalProperty_HasFastCountResources) ||
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221 property != 1)
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222 {
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223 LOG(INFO) << "Installing the FastCountResources extension";
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224
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225 std::string query;
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226 Orthanc::EmbeddedResources::GetFileResource
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227 (query, Orthanc::EmbeddedResources::POSTGRESQL_FAST_COUNT_RESOURCES);
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228 db->Execute(query);
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229
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230 SetGlobalIntegerProperty(*db, t, Orthanc::GlobalProperty_HasFastCountResources, 1);
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231 }
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232
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233
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234 // Installing this extension requires the "GlobalIntegers" table
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235 // created by the "GetLastChangeIndex" extension
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236 property = 0;
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237 if (!LookupGlobalIntegerProperty(property, *db, t,
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238 Orthanc::GlobalProperty_GetLastChangeIndex) ||
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239 property != 1)
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240 {
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241 LOG(INFO) << "Installing the GetLastChangeIndex extension";
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242
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243 std::string query;
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244 Orthanc::EmbeddedResources::GetFileResource
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245 (query, Orthanc::EmbeddedResources::POSTGRESQL_GET_LAST_CHANGE_INDEX);
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246 db->Execute(query);
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247
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248 SetGlobalIntegerProperty(*db, t, Orthanc::GlobalProperty_GetLastChangeIndex, 1);
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249 }
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250
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251 t.Commit();
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252 }
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253
0
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254 return db.release();
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255 }
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256
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257
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258 PostgreSQLIndex::PostgreSQLIndex(const PostgreSQLParameters& parameters) :
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259 IndexBackend(new Factory(*this)),
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260 context_(NULL),
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261 parameters_(parameters),
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262 clearAll_(false)
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263 {
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264 }
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265
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266
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267 int64_t PostgreSQLIndex::CreateResource(const char* publicId,
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268 OrthancPluginResourceType type)
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269 {
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270 DatabaseManager::CachedStatement statement(
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271 STATEMENT_FROM_HERE, GetManager(),
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272 "INSERT INTO Resources VALUES(${}, ${type}, ${id}, NULL) RETURNING internalId");
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273
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274 statement.SetParameterType("id", ValueType_Utf8String);
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275 statement.SetParameterType("type", ValueType_Integer64);
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276
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277 Dictionary args;
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278 args.SetUtf8Value("id", publicId);
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279 args.SetIntegerValue("type", static_cast<int>(type));
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280
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281 statement.Execute(args);
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282
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283 return ReadInteger64(statement, 0);
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284 }
71
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285
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286
72
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287 uint64_t PostgreSQLIndex::GetTotalCompressedSize()
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288 {
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289 // Fast version if extension "./FastTotalSize.sql" is installed
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290 uint64_t result;
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291
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292 {
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293 DatabaseManager::CachedStatement statement(
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294 STATEMENT_FROM_HERE, GetManager(),
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295 "SELECT value FROM GlobalIntegers WHERE key = 0");
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296
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297 statement.SetReadOnly(true);
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298 statement.Execute();
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299
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300 result = static_cast<uint64_t>(ReadInteger64(statement, 0));
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301 }
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302
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303 assert(result == IndexBackend::GetTotalCompressedSize());
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304 return result;
72
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305 }
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306
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307
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308 uint64_t PostgreSQLIndex::GetTotalUncompressedSize()
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309 {
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310 // Fast version if extension "./FastTotalSize.sql" is installed
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311 uint64_t result;
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312
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313 {
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314 DatabaseManager::CachedStatement statement(
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315 STATEMENT_FROM_HERE, GetManager(),
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316 "SELECT value FROM GlobalIntegers WHERE key = 1");
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317
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318 statement.SetReadOnly(true);
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319 statement.Execute();
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320
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321 result = static_cast<uint64_t>(ReadInteger64(statement, 0));
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322 }
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323
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324 assert(result == IndexBackend::GetTotalUncompressedSize());
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325 return result;
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326 }
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327
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328
78
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329 #if ORTHANC_PLUGINS_HAS_DATABASE_CONSTRAINT == 1
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330 void PostgreSQLIndex::CreateInstance(OrthancPluginCreateInstanceResult& result,
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331 const char* hashPatient,
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332 const char* hashStudy,
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333 const char* hashSeries,
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334 const char* hashInstance)
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335 {
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336 DatabaseManager::CachedStatement statement(
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337 STATEMENT_FROM_HERE, GetManager(),
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338 "SELECT * FROM CreateInstance(${patient}, ${study}, ${series}, ${instance})");
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339
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340 statement.SetParameterType("patient", ValueType_Utf8String);
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341 statement.SetParameterType("study", ValueType_Utf8String);
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342 statement.SetParameterType("series", ValueType_Utf8String);
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343 statement.SetParameterType("instance", ValueType_Utf8String);
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344
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345 Dictionary args;
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346 args.SetUtf8Value("patient", hashPatient);
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347 args.SetUtf8Value("study", hashStudy);
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348 args.SetUtf8Value("series", hashSeries);
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349 args.SetUtf8Value("instance", hashInstance);
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350
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351 statement.Execute(args);
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352
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353 if (statement.IsDone() ||
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354 statement.GetResultFieldsCount() != 8)
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355 {
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356 throw Orthanc::OrthancException(Orthanc::ErrorCode_Database);
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357 }
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358
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diff changeset
359 for (size_t i = 0; i < 8; i++)
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360 {
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361 statement.SetResultFieldType(i, ValueType_Integer64);
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362 }
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diff changeset
363
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diff changeset
364 result.isNewInstance = (ReadInteger64(statement, 3) == 1);
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diff changeset
365 result.instanceId = ReadInteger64(statement, 7);
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diff changeset
366
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diff changeset
367 if (result.isNewInstance)
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diff changeset
368 {
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diff changeset
369 result.isNewPatient = (ReadInteger64(statement, 0) == 1);
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diff changeset
370 result.isNewStudy = (ReadInteger64(statement, 1) == 1);
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371 result.isNewSeries = (ReadInteger64(statement, 2) == 1);
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diff changeset
372 result.patientId = ReadInteger64(statement, 4);
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diff changeset
373 result.studyId = ReadInteger64(statement, 5);
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374 result.seriesId = ReadInteger64(statement, 6);
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375 }
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376 }
73
aa81c1c80c75 fix compatibility with older sdk
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diff changeset
377 #endif
79
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378
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379
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diff changeset
380 uint64_t PostgreSQLIndex::GetResourceCount(OrthancPluginResourceType resourceType)
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381 {
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382 // Optimized version thanks to the "FastCountResources.sql" extension
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diff changeset
383
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diff changeset
384 assert(OrthancPluginResourceType_Patient == 0 &&
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diff changeset
385 OrthancPluginResourceType_Study == 1 &&
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386 OrthancPluginResourceType_Series == 2 &&
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diff changeset
387 OrthancPluginResourceType_Instance == 3);
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388
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389 uint64_t result;
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390
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diff changeset
391 {
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diff changeset
392 DatabaseManager::CachedStatement statement(
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diff changeset
393 STATEMENT_FROM_HERE, GetManager(),
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diff changeset
394 "SELECT value FROM GlobalIntegers WHERE key = ${key}");
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diff changeset
395
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diff changeset
396 statement.SetParameterType("key", ValueType_Integer64);
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397
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diff changeset
398 Dictionary args;
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diff changeset
399
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diff changeset
400 // For an explanation of the "+ 2" below, check out "FastCountResources.sql"
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diff changeset
401 args.SetIntegerValue("key", static_cast<int>(resourceType + 2));
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diff changeset
402
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diff changeset
403 statement.SetReadOnly(true);
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diff changeset
404 statement.Execute(args);
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diff changeset
405
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diff changeset
406 result = static_cast<uint64_t>(ReadInteger64(statement, 0));
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diff changeset
407 }
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diff changeset
408
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diff changeset
409 assert(result == IndexBackend::GetResourceCount(resourceType));
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diff changeset
410 return result;
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diff changeset
411 }
85
1012fe77241c new extension implemented for PostgreSQL and SQLite: GetLastChangeIndex
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diff changeset
412
1012fe77241c new extension implemented for PostgreSQL and SQLite: GetLastChangeIndex
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diff changeset
413
1012fe77241c new extension implemented for PostgreSQL and SQLite: GetLastChangeIndex
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diff changeset
414 int64_t PostgreSQLIndex::GetLastChangeIndex()
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diff changeset
415 {
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diff changeset
416 DatabaseManager::CachedStatement statement(
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diff changeset
417 STATEMENT_FROM_HERE, GetManager(),
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diff changeset
418 "SELECT value FROM GlobalIntegers WHERE key = 6");
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diff changeset
419
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diff changeset
420 statement.SetReadOnly(true);
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diff changeset
421 statement.Execute();
1012fe77241c new extension implemented for PostgreSQL and SQLite: GetLastChangeIndex
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422
1012fe77241c new extension implemented for PostgreSQL and SQLite: GetLastChangeIndex
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parents: 79
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423 return ReadInteger64(statement, 0);
1012fe77241c new extension implemented for PostgreSQL and SQLite: GetLastChangeIndex
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424 }
90
e61587582cef moved extension TagMostRecentPatient into stored procedure CreateInstance
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 88
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425
e61587582cef moved extension TagMostRecentPatient into stored procedure CreateInstance
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 88
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426
e61587582cef moved extension TagMostRecentPatient into stored procedure CreateInstance
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 88
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427 void PostgreSQLIndex::TagMostRecentPatient(int64_t patient)
e61587582cef moved extension TagMostRecentPatient into stored procedure CreateInstance
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 88
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428 {
e61587582cef moved extension TagMostRecentPatient into stored procedure CreateInstance
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 88
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429 // This behavior is implemented in "CreateInstance()", and no
e61587582cef moved extension TagMostRecentPatient into stored procedure CreateInstance
Sebastien Jodogne <s.jodogne@gmail.com>
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430 // backward compatibility is necessary
e61587582cef moved extension TagMostRecentPatient into stored procedure CreateInstance
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 88
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431 throw Orthanc::OrthancException(Orthanc::ErrorCode_Database);
e61587582cef moved extension TagMostRecentPatient into stored procedure CreateInstance
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parents: 88
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432 }
0
7cea966b6829 initial commit
Sebastien Jodogne <s.jodogne@gmail.com>
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433 }