Mercurial > hg > orthanc-databases

annotate PostgreSQL/Plugins/PostgreSQLIndex.cpp @ 199:8cae98f73d53

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refactoring
author Sebastien Jodogne <s.jodogne@gmail.com>
date Thu, 18 Mar 2021 14:52:06 +0100
parents 3236894320d6
children 42990b2dd51b
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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) 2017-2021 Osimis S.A., Belgium
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6 *
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7 * This program is free software: you can redistribute it and/or
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8 * modify it under the terms of the GNU Affero General Public License
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9 * as published by the Free Software Foundation, either version 3 of
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10 * the License, or (at your option) any later version.
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11 *
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12 * This program is distributed in the hope that it will be useful, but
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13 * WITHOUT ANY WARRANTY; without even the implied warranty of
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14 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
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15 * Affero General Public License for more details.
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16 *
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17 * You should have received a copy of the GNU Affero General Public License
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18 * along with this program. If not, see <http://www.gnu.org/licenses/>.
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19 **/
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21
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22 #include "PostgreSQLIndex.h"
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24 #include "../../Framework/Plugins/GlobalProperties.h"
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25 #include "../../Framework/PostgreSQL/PostgreSQLDatabase.h"
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26 #include "../../Framework/PostgreSQL/PostgreSQLTransaction.h"
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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 <Compatibility.h> // For std::unique_ptr<>
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32 #include <Logging.h>
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33 #include <OrthancException.h>
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36 namespace Orthanc
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37 {
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38 // Some aliases for internal properties
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39 static const GlobalProperty GlobalProperty_HasTrigramIndex = GlobalProperty_DatabaseInternal0;
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40 static const GlobalProperty GlobalProperty_HasCreateInstance = GlobalProperty_DatabaseInternal1;
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41 static const GlobalProperty GlobalProperty_HasFastCountResources = GlobalProperty_DatabaseInternal2;
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42 static const GlobalProperty GlobalProperty_GetLastChangeIndex = GlobalProperty_DatabaseInternal3;
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43 }
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44
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46 namespace OrthancDatabases
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47 {
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48 IDatabase* PostgreSQLIndex::OpenInternal()
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49 {
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50 uint32_t expectedVersion = 6;
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51
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52 if (GetContext()) // "GetContext()" can possibly be NULL in the unit tests
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53 {
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54 expectedVersion = OrthancPluginGetExpectedDatabaseVersion(GetContext());
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55 }
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56
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57 // Check the expected version of the database
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58 if (expectedVersion != 6)
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59 {
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60 LOG(ERROR) << "This database plugin is incompatible with your version of Orthanc "
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61 << "expecting the DB schema version " << expectedVersion
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62 << ", but this plugin is only compatible with version 6";
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63 throw Orthanc::OrthancException(Orthanc::ErrorCode_Plugin);
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64 }
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65
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66 std::unique_ptr<PostgreSQLDatabase> db(new PostgreSQLDatabase(parameters_));
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67
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68 db->Open();
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69
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70 if (parameters_.HasLock())
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71 {
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72 db->AdvisoryLock(POSTGRESQL_LOCK_INDEX);
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73 }
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75 {
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76 PostgreSQLDatabase::TransientAdvisoryLock lock(*db, POSTGRESQL_LOCK_DATABASE_SETUP);
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78 if (clearAll_)
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79 {
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80 db->ClearAll();
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81 }
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82
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83 {
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84 PostgreSQLTransaction t(*db);
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85
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86 if (!db->DoesTableExist("Resources"))
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87 {
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88 std::string query;
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89
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90 Orthanc::EmbeddedResources::GetFileResource
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91 (query, Orthanc::EmbeddedResources::POSTGRESQL_PREPARE_INDEX);
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92 db->Execute(query);
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93
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94 SetGlobalIntegerProperty(*db, t, Orthanc::GlobalProperty_DatabaseSchemaVersion, expectedVersion);
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95 SetGlobalIntegerProperty(*db, t, Orthanc::GlobalProperty_DatabasePatchLevel, 1);
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96 SetGlobalIntegerProperty(*db, t, Orthanc::GlobalProperty_HasTrigramIndex, 0);
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97 }
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98
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99 if (!db->DoesTableExist("Resources"))
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100 {
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101 LOG(ERROR) << "Corrupted PostgreSQL database";
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102 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError);
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103 }
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104
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105 int version = 0;
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106 if (!LookupGlobalIntegerProperty(version, *db, t, Orthanc::GlobalProperty_DatabaseSchemaVersion) ||
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107 version != 6)
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108 {
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109 LOG(ERROR) << "PostgreSQL plugin is incompatible with database schema version: " << version;
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110 throw Orthanc::OrthancException(Orthanc::ErrorCode_Database);
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111 }
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112
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113 int revision;
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114 if (!LookupGlobalIntegerProperty(revision, *db, t, Orthanc::GlobalProperty_DatabasePatchLevel))
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115 {
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116 revision = 1;
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117 SetGlobalIntegerProperty(*db, t, Orthanc::GlobalProperty_DatabasePatchLevel, revision);
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118 }
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119
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120 if (revision != 1)
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121 {
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122 LOG(ERROR) << "PostgreSQL plugin is incompatible with database schema revision: " << revision;
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123 throw Orthanc::OrthancException(Orthanc::ErrorCode_Database);
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124 }
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125
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126 t.Commit();
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127 }
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128
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129 {
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130 PostgreSQLTransaction t(*db);
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131
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132 int hasTrigram = 0;
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133 if (!LookupGlobalIntegerProperty(hasTrigram, *db, t,
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134 Orthanc::GlobalProperty_HasTrigramIndex) ||
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135 hasTrigram != 1)
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136 {
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137 /**
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138 * Apply fix for performance issue (speed up wildcard search
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139 * by using GIN trigrams). This implements the patch suggested
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140 * in issue #47, BUT we also keep the original
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141 * "DicomIdentifiersIndexValues", as it leads to better
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142 * performance for "strict" searches (i.e. searches involving
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143 * no wildcard).
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144 * https://www.postgresql.org/docs/current/static/pgtrgm.html
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145 * https://bitbucket.org/sjodogne/orthanc/issues/47/index-improvements-for-pg-plugin
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146 **/
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147 try
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148 {
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149 // We've observed 9 minutes on DB with 100000 studies
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150 LOG(WARNING) << "Trying to enable trigram matching on the PostgreSQL database "
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151 << "to speed up wildcard searches. This may take several minutes";
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152
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153 db->Execute(
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154 "CREATE EXTENSION IF NOT EXISTS pg_trgm; "
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155 "CREATE INDEX DicomIdentifiersIndexValues2 ON DicomIdentifiers USING gin(value gin_trgm_ops);");
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156
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157 SetGlobalIntegerProperty(*db, t, Orthanc::GlobalProperty_HasTrigramIndex, 1);
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158 LOG(WARNING) << "Trigram index has been created";
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159
136
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160 t.Commit();
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161 }
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162 catch (Orthanc::OrthancException&)
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163 {
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164 LOG(WARNING) << "Performance warning: Your PostgreSQL server does "
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165 << "not support trigram matching";
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166 LOG(WARNING) << "-> Consider installing the \"pg_trgm\" extension on the "
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167 << "PostgreSQL server, e.g. on Debian: sudo apt install postgresql-contrib";
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168 }
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169 }
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170 else
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171 {
136
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172 t.Commit();
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173 }
136
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174 }
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175
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176 {
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177 PostgreSQLTransaction t(*db);
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178
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179 int property = 0;
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180 if (!LookupGlobalIntegerProperty(property, *db, t,
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181 Orthanc::GlobalProperty_HasCreateInstance) ||
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182 property != 2)
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183 {
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184 LOG(INFO) << "Installing the CreateInstance extension";
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185
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186 if (property == 1)
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187 {
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188 // Drop older, experimental versions of this extension
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189 db->Execute("DROP FUNCTION CreateInstance("
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190 "IN patient TEXT, IN study TEXT, IN series TEXT, in instance TEXT)");
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191 }
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192
136
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193 std::string query;
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194 Orthanc::EmbeddedResources::GetFileResource
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195 (query, Orthanc::EmbeddedResources::POSTGRESQL_CREATE_INSTANCE);
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196 db->Execute(query);
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197
136
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198 SetGlobalIntegerProperty(*db, t, Orthanc::GlobalProperty_HasCreateInstance, 2);
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199 }
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200
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201
136
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202 if (!LookupGlobalIntegerProperty(property, *db, t,
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203 Orthanc::GlobalProperty_GetTotalSizeIsFast) ||
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204 property != 1)
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205 {
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206 LOG(INFO) << "Installing the FastTotalSize extension";
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207
136
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208 std::string query;
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209 Orthanc::EmbeddedResources::GetFileResource
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210 (query, Orthanc::EmbeddedResources::POSTGRESQL_FAST_TOTAL_SIZE);
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211 db->Execute(query);
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212
136
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213 SetGlobalIntegerProperty(*db, t, Orthanc::GlobalProperty_GetTotalSizeIsFast, 1);
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214 }
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215
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216
136
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217 // Installing this extension requires the "GlobalIntegers" table
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218 // created by the "FastTotalSize" extension
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219 property = 0;
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220 if (!LookupGlobalIntegerProperty(property, *db, t,
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221 Orthanc::GlobalProperty_HasFastCountResources) ||
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222 property != 1)
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223 {
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224 LOG(INFO) << "Installing the FastCountResources extension";
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225
136
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226 std::string query;
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227 Orthanc::EmbeddedResources::GetFileResource
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228 (query, Orthanc::EmbeddedResources::POSTGRESQL_FAST_COUNT_RESOURCES);
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229 db->Execute(query);
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230
136
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231 SetGlobalIntegerProperty(*db, t, Orthanc::GlobalProperty_HasFastCountResources, 1);
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232 }
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233
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234
136
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235 // Installing this extension requires the "GlobalIntegers" table
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236 // created by the "GetLastChangeIndex" extension
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237 property = 0;
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238 if (!LookupGlobalIntegerProperty(property, *db, t,
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239 Orthanc::GlobalProperty_GetLastChangeIndex) ||
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240 property != 1)
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241 {
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242 LOG(INFO) << "Installing the GetLastChangeIndex extension";
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243
136
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244 std::string query;
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245 Orthanc::EmbeddedResources::GetFileResource
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246 (query, Orthanc::EmbeddedResources::POSTGRESQL_GET_LAST_CHANGE_INDEX);
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247 db->Execute(query);
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248
136
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249 SetGlobalIntegerProperty(*db, t, Orthanc::GlobalProperty_GetLastChangeIndex, 1);
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250 }
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251
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252 t.Commit();
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253 }
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254 }
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255
0
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256 return db.release();
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257 }
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258
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259
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260 PostgreSQLIndex::PostgreSQLIndex(const PostgreSQLParameters& parameters) :
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261 IndexBackend(new Factory(*this)),
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262 parameters_(parameters),
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263 clearAll_(false)
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264 {
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265 }
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266
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267
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268 int64_t PostgreSQLIndex::CreateResource(const char* publicId,
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269 OrthancPluginResourceType type)
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270 {
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271 DatabaseManager::CachedStatement statement(
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272 STATEMENT_FROM_HERE, GetManager(),
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273 "INSERT INTO Resources VALUES(${}, ${type}, ${id}, NULL) RETURNING internalId");
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274
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275 statement.SetParameterType("id", ValueType_Utf8String);
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276 statement.SetParameterType("type", ValueType_Integer64);
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277
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278 Dictionary args;
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279 args.SetUtf8Value("id", publicId);
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280 args.SetIntegerValue("type", static_cast<int>(type));
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281
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282 statement.Execute(args);
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283
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284 return ReadInteger64(statement, 0);
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285 }
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286
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287
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288 uint64_t PostgreSQLIndex::GetTotalCompressedSize()
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289 {
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290 // Fast version if extension "./FastTotalSize.sql" is installed
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291 uint64_t result;
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292
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293 {
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294 DatabaseManager::CachedStatement statement(
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295 STATEMENT_FROM_HERE, GetManager(),
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296 "SELECT value FROM GlobalIntegers WHERE key = 0");
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297
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298 statement.SetReadOnly(true);
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299 statement.Execute();
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300
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301 result = static_cast<uint64_t>(ReadInteger64(statement, 0));
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302 }
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303
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304 assert(result == IndexBackend::GetTotalCompressedSize());
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305 return result;
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306 }
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307
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308
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309 uint64_t PostgreSQLIndex::GetTotalUncompressedSize()
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310 {
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311 // Fast version if extension "./FastTotalSize.sql" is installed
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312 uint64_t result;
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313
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314 {
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315 DatabaseManager::CachedStatement statement(
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316 STATEMENT_FROM_HERE, GetManager(),
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317 "SELECT value FROM GlobalIntegers WHERE key = 1");
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318
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319 statement.SetReadOnly(true);
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320 statement.Execute();
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321
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322 result = static_cast<uint64_t>(ReadInteger64(statement, 0));
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323 }
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324
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325 assert(result == IndexBackend::GetTotalUncompressedSize());
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326 return result;
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327 }
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328
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329
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330 #if ORTHANC_PLUGINS_HAS_DATABASE_CONSTRAINT == 1
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331 void PostgreSQLIndex::CreateInstance(OrthancPluginCreateInstanceResult& result,
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332 const char* hashPatient,
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333 const char* hashStudy,
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334 const char* hashSeries,
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335 const char* hashInstance)
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336 {
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337 DatabaseManager::CachedStatement statement(
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338 STATEMENT_FROM_HERE, GetManager(),
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339 "SELECT * FROM CreateInstance(${patient}, ${study}, ${series}, ${instance})");
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340
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341 statement.SetParameterType("patient", ValueType_Utf8String);
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342 statement.SetParameterType("study", ValueType_Utf8String);
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343 statement.SetParameterType("series", ValueType_Utf8String);
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344 statement.SetParameterType("instance", ValueType_Utf8String);
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345
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346 Dictionary args;
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347 args.SetUtf8Value("patient", hashPatient);
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348 args.SetUtf8Value("study", hashStudy);
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349 args.SetUtf8Value("series", hashSeries);
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350 args.SetUtf8Value("instance", hashInstance);
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351
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352 statement.Execute(args);
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353
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354 if (statement.IsDone() ||
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355 statement.GetResultFieldsCount() != 8)
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356 {
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357 throw Orthanc::OrthancException(Orthanc::ErrorCode_Database);
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358 }
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359
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360 for (size_t i = 0; i < 8; i++)
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361 {
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362 statement.SetResultFieldType(i, ValueType_Integer64);
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363 }
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364
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365 result.isNewInstance = (ReadInteger64(statement, 3) == 1);
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366 result.instanceId = ReadInteger64(statement, 7);
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367
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368 if (result.isNewInstance)
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369 {
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370 result.isNewPatient = (ReadInteger64(statement, 0) == 1);
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371 result.isNewStudy = (ReadInteger64(statement, 1) == 1);
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372 result.isNewSeries = (ReadInteger64(statement, 2) == 1);
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373 result.patientId = ReadInteger64(statement, 4);
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374 result.studyId = ReadInteger64(statement, 5);
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375 result.seriesId = ReadInteger64(statement, 6);
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376 }
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377 }
73
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378 #endif
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379
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380
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381 uint64_t PostgreSQLIndex::GetResourceCount(OrthancPluginResourceType resourceType)
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382 {
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383 // Optimized version thanks to the "FastCountResources.sql" extension
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384
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385 assert(OrthancPluginResourceType_Patient == 0 &&
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386 OrthancPluginResourceType_Study == 1 &&
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387 OrthancPluginResourceType_Series == 2 &&
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388 OrthancPluginResourceType_Instance == 3);
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389
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390 uint64_t result;
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391
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392 {
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393 DatabaseManager::CachedStatement statement(
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394 STATEMENT_FROM_HERE, GetManager(),
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395 "SELECT value FROM GlobalIntegers WHERE key = ${key}");
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396
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397 statement.SetParameterType("key", ValueType_Integer64);
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398
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399 Dictionary args;
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400
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401 // For an explanation of the "+ 2" below, check out "FastCountResources.sql"
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402 args.SetIntegerValue("key", static_cast<int>(resourceType + 2));
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403
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404 statement.SetReadOnly(true);
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405 statement.Execute(args);
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406
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407 result = static_cast<uint64_t>(ReadInteger64(statement, 0));
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408 }
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409
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410 assert(result == IndexBackend::GetResourceCount(resourceType));
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411 return result;
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412 }
85
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413
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414
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415 int64_t PostgreSQLIndex::GetLastChangeIndex()
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416 {
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417 DatabaseManager::CachedStatement statement(
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418 STATEMENT_FROM_HERE, GetManager(),
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419 "SELECT value FROM GlobalIntegers WHERE key = 6");
1012fe77241c new extension implemented for PostgreSQL and SQLite: GetLastChangeIndex
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420
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421 statement.SetReadOnly(true);
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422 statement.Execute();
1012fe77241c new extension implemented for PostgreSQL and SQLite: GetLastChangeIndex
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 79
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423
1012fe77241c new extension implemented for PostgreSQL and SQLite: GetLastChangeIndex
Sebastien Jodogne <s.jodogne@gmail.com>
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424 return ReadInteger64(statement, 0);
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425 }
90
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Sebastien Jodogne <s.jodogne@gmail.com>
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426
e61587582cef moved extension TagMostRecentPatient into stored procedure CreateInstance
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427
e61587582cef moved extension TagMostRecentPatient into stored procedure CreateInstance
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428 void PostgreSQLIndex::TagMostRecentPatient(int64_t patient)
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Sebastien Jodogne <s.jodogne@gmail.com>
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429 {
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Sebastien Jodogne <s.jodogne@gmail.com>
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430 // This behavior is implemented in "CreateInstance()", and no
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Sebastien Jodogne <s.jodogne@gmail.com>
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431 // backward compatibility is necessary
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Sebastien Jodogne <s.jodogne@gmail.com>
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432 throw Orthanc::OrthancException(Orthanc::ErrorCode_Database);
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433 }
0
7cea966b6829 initial commit
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434 }