# HG changeset patch
# User Sebastien Jodogne <s.jodogne@gmail.com>
# Date 1444751310 -7200
# Node ID 2ad22b2970a2f0f1ca352fddf96faab635177d8a
# Parent 275780da54aeaa5f779c243e95bb7b190275b455
SearchableStudies
diff -r 275780da54ae -r 2ad22b2970a2 CMakeLists.txt
--- a/CMakeLists.txt Tue Oct 13 16:57:55 2015 +0200
+++ b/CMakeLists.txt Tue Oct 13 17:48:30 2015 +0200
@@ -240,6 +240,7 @@
PREPARE_DATABASE ${CMAKE_CURRENT_SOURCE_DIR}/OrthancServer/PrepareDatabase.sql
UPGRADE_DATABASE_3_TO_4 ${CMAKE_CURRENT_SOURCE_DIR}/OrthancServer/Upgrade3To4.sql
UPGRADE_DATABASE_4_TO_5 ${CMAKE_CURRENT_SOURCE_DIR}/OrthancServer/Upgrade4To5.sql
+ UPGRADE_DATABASE_5_TO_6 ${CMAKE_CURRENT_SOURCE_DIR}/OrthancServer/Upgrade5To6.sql
CONFIGURATION_SAMPLE ${CMAKE_CURRENT_SOURCE_DIR}/Resources/Configuration.json
DICOM_CONFORMANCE_STATEMENT ${CMAKE_CURRENT_SOURCE_DIR}/Resources/DicomConformanceStatement.txt
LUA_TOOLBOX ${CMAKE_CURRENT_SOURCE_DIR}/Resources/Toolbox.lua
diff -r 275780da54ae -r 2ad22b2970a2 OrthancServer/DatabaseWrapper.cpp
--- a/OrthancServer/DatabaseWrapper.cpp Tue Oct 13 16:57:55 2015 +0200
+++ b/OrthancServer/DatabaseWrapper.cpp Tue Oct 13 17:48:30 2015 +0200
@@ -359,11 +359,13 @@
if (version_ == 5)
{
LOG(WARNING) << "Upgrading database version from 5 to 6";
- // No change in the DB schema, the step from version 5 to 6 only
- // consists in reconstructing the main DICOM tags information.
db_.BeginTransaction();
+ ExecuteUpgradeScript(db_, EmbeddedResources::UPGRADE_DATABASE_5_TO_6);
+ // Reconstruct the main DICOM tags information.
+ Toolbox::ReconstructMainDicomTags(*this, storageArea, ResourceType_Patient);
Toolbox::ReconstructMainDicomTags(*this, storageArea, ResourceType_Study);
Toolbox::ReconstructMainDicomTags(*this, storageArea, ResourceType_Series);
+ Toolbox::ReconstructMainDicomTags(*this, storageArea, ResourceType_Instance);
db_.CommitTransaction();
version_ = 6;
}
@@ -484,5 +486,4 @@
target[key] = s.ColumnString(1);
}
}
-
}
diff -r 275780da54ae -r 2ad22b2970a2 OrthancServer/DatabaseWrapper.h
--- a/OrthancServer/DatabaseWrapper.h Tue Oct 13 16:57:55 2015 +0200
+++ b/OrthancServer/DatabaseWrapper.h Tue Oct 13 17:48:30 2015 +0200
@@ -329,6 +329,11 @@
virtual void Upgrade(unsigned int targetVersion,
IStorageArea& storageArea);
+ virtual void StoreStudyModule(int64_t id,
+ const DicomMap& module)
+ {
+ base_.StoreStudyModule(id, module);
+ }
/**
diff -r 275780da54ae -r 2ad22b2970a2 OrthancServer/DatabaseWrapperBase.cpp
--- a/OrthancServer/DatabaseWrapperBase.cpp Tue Oct 13 16:57:55 2015 +0200
+++ b/OrthancServer/DatabaseWrapperBase.cpp Tue Oct 13 17:48:30 2015 +0200
@@ -33,6 +33,8 @@
#include "PrecompiledHeadersServer.h"
#include "DatabaseWrapperBase.h"
+#include "../Core/DicomFormat/DicomArray.h"
+
#include <stdio.h>
namespace Orthanc
@@ -309,6 +311,13 @@
s.BindInt64(0, id);
s.Run();
}
+
+ // New in DB v6 (Orthanc >= 0.9.5)
+ {
+ SQLite::Statement s(db_, SQLITE_FROM_HERE, "DELETE FROM SearchableStudies WHERE id=?");
+ s.BindInt64(0, id);
+ s.Run();
+ }
}
@@ -712,4 +721,27 @@
target.push_back(s.ColumnInt64(0));
}
}
+
+
+ void DatabaseWrapperBase::StoreStudyModule(int64_t id,
+ const DicomMap& module)
+ {
+ DicomArray a(module);
+
+ for (size_t i = 0; i < a.GetSize(); i++)
+ {
+ const DicomTag& tag = a.GetElement(i).GetTag();
+ const DicomValue& value = a.GetElement(i).GetValue();
+
+ if (!value.IsNull())
+ {
+ SQLite::Statement s(db_, SQLITE_FROM_HERE, "INSERT INTO SearchableStudies VALUES(?, ?, ?, ?)");
+ s.BindInt64(0, id);
+ s.BindInt(1, tag.GetGroup());
+ s.BindInt(2, tag.GetElement());
+ s.BindString(3, value.AsString());
+ s.Run();
+ }
+ }
+ }
}
diff -r 275780da54ae -r 2ad22b2970a2 OrthancServer/DatabaseWrapperBase.h
--- a/OrthancServer/DatabaseWrapperBase.h Tue Oct 13 16:57:55 2015 +0200
+++ b/OrthancServer/DatabaseWrapperBase.h Tue Oct 13 17:48:30 2015 +0200
@@ -42,6 +42,7 @@
#include "ServerEnumerations.h"
#include <list>
+#include <boost/noncopyable.hpp>
namespace Orthanc
@@ -51,7 +52,7 @@
* database plugin whose code is in
* "../Plugins/Samples/DatabasePlugin".
**/
- class DatabaseWrapperBase
+ class DatabaseWrapperBase : public boost::noncopyable
{
private:
SQLite::Connection& db_;
@@ -192,6 +193,9 @@
void LookupIdentifier(std::list<int64_t>& target,
const std::string& value);
+
+ void StoreStudyModule(int64_t id,
+ const DicomMap& module);
};
}
diff -r 275780da54ae -r 2ad22b2970a2 OrthancServer/IDatabaseWrapper.h
--- a/OrthancServer/IDatabaseWrapper.h Tue Oct 13 16:57:55 2015 +0200
+++ b/OrthancServer/IDatabaseWrapper.h Tue Oct 13 17:48:30 2015 +0200
@@ -193,5 +193,8 @@
virtual void Upgrade(unsigned int targetVersion,
IStorageArea& storageArea) = 0;
+
+ virtual void StoreStudyModule(int64_t id,
+ const DicomMap& module) = 0;
};
}
diff -r 275780da54ae -r 2ad22b2970a2 OrthancServer/PrepareDatabase.sql
--- a/OrthancServer/PrepareDatabase.sql Tue Oct 13 16:57:55 2015 +0200
+++ b/OrthancServer/PrepareDatabase.sql Tue Oct 13 17:48:30 2015 +0200
@@ -27,6 +27,15 @@
PRIMARY KEY(id, tagGroup, tagElement)
);
+-- The following table was added in Orthanc 0.9.5 (database v6)
+CREATE TABLE SearchableStudies(
+ id INTEGER REFERENCES Resources(internalId) ON DELETE CASCADE,
+ tagGroup INTEGER,
+ tagElement INTEGER,
+ value TEXT, -- assumed to be in upper case
+ PRIMARY KEY(id, tagGroup, tagElement)
+ );
+
CREATE TABLE Metadata(
id INTEGER REFERENCES Resources(internalId) ON DELETE CASCADE,
type INTEGER,
@@ -86,6 +95,10 @@
CREATE INDEX DicomIdentifiersIndex2 ON DicomIdentifiers(tagGroup, tagElement);
CREATE INDEX DicomIdentifiersIndexValues ON DicomIdentifiers(value COLLATE BINARY);
+-- The 2 following indexes were added in Orthanc 0.9.5 (database v6)
+CREATE INDEX SearchableStudiesIndex1 ON SearchableStudies(id);
+CREATE INDEX SearchableStudiesIndexValues ON SearchableStudies(value COLLATE BINARY);
+
CREATE INDEX ChangesIndex ON Changes(internalId);
CREATE TRIGGER AttachedFileDeleted
diff -r 275780da54ae -r 2ad22b2970a2 OrthancServer/ServerIndex.cpp
--- a/OrthancServer/ServerIndex.cpp Tue Oct 13 16:57:55 2015 +0200
+++ b/OrthancServer/ServerIndex.cpp Tue Oct 13 17:48:30 2015 +0200
@@ -687,7 +687,14 @@
{
study = CreateResource(hasher.HashStudy(), ResourceType_Study);
Toolbox::SetMainDicomTags(db_, study, ResourceType_Study, dicomSummary, true);
- Toolbox::SetMainDicomTags(db_, study, ResourceType_Patient, dicomSummary, false); // New in version 0.9.5 (db v6)
+
+ // New in version 0.9.5 (db v6)
+ Toolbox::SetMainDicomTags(db_, study, ResourceType_Patient, dicomSummary, false);
+
+ DicomMap module;
+ Toolbox::ExtractModule(module, dicomSummary, DicomModule_Patient, true /* normalize */);
+ Toolbox::ExtractModule(module, dicomSummary, DicomModule_Study, true /* normalize */);
+ db_.StoreStudyModule(study, module);
}
// Create the patient if needed
diff -r 275780da54ae -r 2ad22b2970a2 OrthancServer/ServerToolbox.cpp
--- a/OrthancServer/ServerToolbox.cpp Tue Oct 13 16:57:55 2015 +0200
+++ b/OrthancServer/ServerToolbox.cpp Tue Oct 13 17:48:30 2015 +0200
@@ -307,11 +307,19 @@
break;
case ResourceType_Study:
+ {
Toolbox::SetMainDicomTags(database, resource, ResourceType_Study, dicomSummary, true);
// Duplicate the patient tags at the study level (new in Orthanc 0.9.5 - db v6)
Toolbox::SetMainDicomTags(database, resource, ResourceType_Patient, dicomSummary, false);
+
+ DicomMap module;
+ Toolbox::ExtractModule(module, dicomSummary, DicomModule_Patient, true /* normalize */);
+ Toolbox::ExtractModule(module, dicomSummary, DicomModule_Study, true /* normalize */);
+ database.StoreStudyModule(resource, module);
+
break;
+ }
case ResourceType_Series:
Toolbox::SetMainDicomTags(database, resource, ResourceType_Series, dicomSummary, true);
@@ -326,5 +334,34 @@
}
}
}
+
+
+ void ExtractModule(DicomMap& result, // WARNING: Will not be cleared!
+ const DicomMap& summary,
+ DicomModule module,
+ bool normalize)
+ {
+ typedef std::set<DicomTag> ModuleTags;
+ ModuleTags moduleTags;
+ DicomTag::AddTagsForModule(moduleTags, module);
+
+ for (ModuleTags::const_iterator tag = moduleTags.begin(); tag != moduleTags.end(); ++tag)
+ {
+ const DicomValue* value = summary.TestAndGetValue(*tag);
+ if (value != NULL &&
+ !value->IsNull())
+ {
+ std::string t = value->AsString();
+
+ if (normalize)
+ {
+ t = StripSpaces(ConvertToAscii(t));
+ ToUpperCase(t);
+ }
+
+ result.SetValue(*tag, t);
+ }
+ }
+ }
}
}
diff -r 275780da54ae -r 2ad22b2970a2 OrthancServer/ServerToolbox.h
--- a/OrthancServer/ServerToolbox.h Tue Oct 13 16:57:55 2015 +0200
+++ b/OrthancServer/ServerToolbox.h Tue Oct 13 17:48:30 2015 +0200
@@ -60,5 +60,10 @@
void ReconstructMainDicomTags(IDatabaseWrapper& database,
IStorageArea& storageArea,
ResourceType level);
+
+ void ExtractModule(DicomMap& result, // WARNING: Will not be cleared!
+ const DicomMap& summary,
+ DicomModule module,
+ bool normalize);
}
}
diff -r 275780da54ae -r 2ad22b2970a2 OrthancServer/Upgrade5To6.sql
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/OrthancServer/Upgrade5To6.sql Tue Oct 13 17:48:30 2015 +0200
@@ -0,0 +1,21 @@
+-- This SQLite script updates the version of the Orthanc database from 5 to 6.
+
+
+-- Add a new table to enable full-text indexed search over studies
+
+CREATE TABLE SearchableStudies(
+ id INTEGER REFERENCES Resources(internalId) ON DELETE CASCADE,
+ tagGroup INTEGER,
+ tagElement INTEGER,
+ value TEXT, -- assumed to be in upper case
+ PRIMARY KEY(id, tagGroup, tagElement)
+ );
+
+CREATE INDEX SearchableStudiesIndex1 ON SearchableStudies(id);
+CREATE INDEX SearchableStudiesIndexValues ON SearchableStudies(value COLLATE BINARY);
+
+
+-- Change the database version
+-- The "1" corresponds to the "GlobalProperty_DatabaseSchemaVersion" enumeration
+
+UPDATE GlobalProperties SET value="6" WHERE property=1;
diff -r 275780da54ae -r 2ad22b2970a2 Plugins/Engine/OrthancPluginDatabase.cpp
--- a/Plugins/Engine/OrthancPluginDatabase.cpp Tue Oct 13 16:57:55 2015 +0200
+++ b/Plugins/Engine/OrthancPluginDatabase.cpp Tue Oct 13 17:48:30 2015 +0200
@@ -869,6 +869,14 @@
}
+ void OrthancPluginDatabase::StoreStudyModule(int64_t id,
+ const DicomMap& module)
+ {
+ // TODO
+ throw OrthancException(ErrorCode_NotImplemented);
+ }
+
+
void OrthancPluginDatabase::AnswerReceived(const _OrthancPluginDatabaseAnswer& answer)
{
if (answer.type == _OrthancPluginDatabaseAnswerType_None)
diff -r 275780da54ae -r 2ad22b2970a2 Plugins/Engine/OrthancPluginDatabase.h
--- a/Plugins/Engine/OrthancPluginDatabase.h Tue Oct 13 16:57:55 2015 +0200
+++ b/Plugins/Engine/OrthancPluginDatabase.h Tue Oct 13 17:48:30 2015 +0200
@@ -254,6 +254,9 @@
virtual void Upgrade(unsigned int targetVersion,
IStorageArea& storageArea);
+ virtual void StoreStudyModule(int64_t id,
+ const DicomMap& module);
+
void AnswerReceived(const _OrthancPluginDatabaseAnswer& answer);
};
}