Mercurial > hg > orthanc

annotate OrthancServer/Sources/ServerToolbox.cpp @ 5294:e0e2aee4453e

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Modality worklists plugin: allow searching on private tags (exact match only)
author Alain Mazy <am@osimis.io>
date Wed, 10 May 2023 12:52:35 +0200
parents 28f0e38e4082
children 48b8dae6dc77
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
213
4ce7fdcc8879 access to tags, simplified-tags and file of an instance
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1 /**
4ce7fdcc8879 access to tags, simplified-tags and file of an instance
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
2 * Orthanc - A Lightweight, RESTful DICOM Store
1900
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1870
diff changeset
3 * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics
1288
6e7e5ed91c2d upgrade to year 2015
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 831
diff changeset
4 * Department, University Hospital of Liege, Belgium
5185
0ea402b4d901 upgrade to year 2023
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 5184
diff changeset
5 * Copyright (C) 2017-2023 Osimis S.A., Belgium
0ea402b4d901 upgrade to year 2023
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 5184
diff changeset
6 * Copyright (C) 2021-2023 Sebastien Jodogne, ICTEAM UCLouvain, Belgium
213
4ce7fdcc8879 access to tags, simplified-tags and file of an instance
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
7 *
4ce7fdcc8879 access to tags, simplified-tags and file of an instance
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
8 * This program is free software: you can redistribute it and/or
4ce7fdcc8879 access to tags, simplified-tags and file of an instance
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
9 * modify it under the terms of the GNU General Public License as
4ce7fdcc8879 access to tags, simplified-tags and file of an instance
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
10 * published by the Free Software Foundation, either version 3 of the
4ce7fdcc8879 access to tags, simplified-tags and file of an instance
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
11 * License, or (at your option) any later version.
4ce7fdcc8879 access to tags, simplified-tags and file of an instance
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
12 *
4ce7fdcc8879 access to tags, simplified-tags and file of an instance
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
13 * This program is distributed in the hope that it will be useful, but
4ce7fdcc8879 access to tags, simplified-tags and file of an instance
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
14 * WITHOUT ANY WARRANTY; without even the implied warranty of
4ce7fdcc8879 access to tags, simplified-tags and file of an instance
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
15 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
4ce7fdcc8879 access to tags, simplified-tags and file of an instance
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
16 * General Public License for more details.
4ce7fdcc8879 access to tags, simplified-tags and file of an instance
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
17 *
4ce7fdcc8879 access to tags, simplified-tags and file of an instance
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
18 * You should have received a copy of the GNU General Public License
4ce7fdcc8879 access to tags, simplified-tags and file of an instance
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
19 * along with this program. If not, see <http://www.gnu.org/licenses/>.
4ce7fdcc8879 access to tags, simplified-tags and file of an instance
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
20 **/
4ce7fdcc8879 access to tags, simplified-tags and file of an instance
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
21
4ce7fdcc8879 access to tags, simplified-tags and file of an instance
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
22
831
84513f2ee1f3 pch for unit tests and server
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 824
diff changeset
23 #include "PrecompiledHeadersServer.h"
213
4ce7fdcc8879 access to tags, simplified-tags and file of an instance
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
24 #include "ServerToolbox.h"
4ce7fdcc8879 access to tags, simplified-tags and file of an instance
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
25
4045
05b8fd21089c fix path
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 4044
diff changeset
26 #include "../../OrthancFramework/Sources/DicomParsing/ParsedDicomFile.h"
05b8fd21089c fix path
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 4044
diff changeset
27 #include "../../OrthancFramework/Sources/FileStorage/StorageAccessor.h"
4792
434843934307 Added a StorageCache in the StorageAccessor
Alain Mazy <am@osimis.io>
parents: 4640
diff changeset
28 #include "../../OrthancFramework/Sources/FileStorage/StorageCache.h"
4045
05b8fd21089c fix path
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 4044
diff changeset
29 #include "../../OrthancFramework/Sources/Logging.h"
05b8fd21089c fix path
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 4044
diff changeset
30 #include "../../OrthancFramework/Sources/OrthancException.h"
3093
2e1808b6146a reorganization of folders
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 3089
diff changeset
31 #include "Database/IDatabaseWrapper.h"
3099
9c71abbff70f removing build dependency on plugins
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 3094
diff changeset
32 #include "Database/ResourcesContent.h"
4140
0ddc5297a8ab centralization of default parameters for JSON/DicomMap conversions from DCMTK
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 4139
diff changeset
33 #include "OrthancConfiguration.h"
3083
683d572424b6 IDatabaseWrapper::SetResourcesContent
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 3061
diff changeset
34 #include "ServerContext.h"
213
4ce7fdcc8879 access to tags, simplified-tags and file of an instance
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
35
234
7c1faef915a4 cleaning room
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 226
diff changeset
36 #include <cassert>
7c1faef915a4 cleaning room
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 226
diff changeset
37
213
4ce7fdcc8879 access to tags, simplified-tags and file of an instance
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
38 namespace Orthanc
4ce7fdcc8879 access to tags, simplified-tags and file of an instance
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
39 {
3083
683d572424b6 IDatabaseWrapper::SetResourcesContent
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 3061
diff changeset
40 static const DicomTag PATIENT_IDENTIFIERS[] =
683d572424b6 IDatabaseWrapper::SetResourcesContent
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 3061
diff changeset
41 {
683d572424b6 IDatabaseWrapper::SetResourcesContent
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 3061
diff changeset
42 DICOM_TAG_PATIENT_ID,
683d572424b6 IDatabaseWrapper::SetResourcesContent
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 3061
diff changeset
43 DICOM_TAG_PATIENT_NAME,
683d572424b6 IDatabaseWrapper::SetResourcesContent
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 3061
diff changeset
44 DICOM_TAG_PATIENT_BIRTH_DATE
683d572424b6 IDatabaseWrapper::SetResourcesContent
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 3061
diff changeset
45 };
683d572424b6 IDatabaseWrapper::SetResourcesContent
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 3061
diff changeset
46
683d572424b6 IDatabaseWrapper::SetResourcesContent
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 3061
diff changeset
47 static const DicomTag STUDY_IDENTIFIERS[] =
683d572424b6 IDatabaseWrapper::SetResourcesContent
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 3061
diff changeset
48 {
683d572424b6 IDatabaseWrapper::SetResourcesContent
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 3061
diff changeset
49 DICOM_TAG_PATIENT_ID,
683d572424b6 IDatabaseWrapper::SetResourcesContent
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 3061
diff changeset
50 DICOM_TAG_PATIENT_NAME,
683d572424b6 IDatabaseWrapper::SetResourcesContent
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 3061
diff changeset
51 DICOM_TAG_PATIENT_BIRTH_DATE,
683d572424b6 IDatabaseWrapper::SetResourcesContent
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 3061
diff changeset
52 DICOM_TAG_STUDY_INSTANCE_UID,
683d572424b6 IDatabaseWrapper::SetResourcesContent
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 3061
diff changeset
53 DICOM_TAG_ACCESSION_NUMBER,
683d572424b6 IDatabaseWrapper::SetResourcesContent
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 3061
diff changeset
54 DICOM_TAG_STUDY_DESCRIPTION,
683d572424b6 IDatabaseWrapper::SetResourcesContent
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 3061
diff changeset
55 DICOM_TAG_STUDY_DATE
683d572424b6 IDatabaseWrapper::SetResourcesContent
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 3061
diff changeset
56 };
683d572424b6 IDatabaseWrapper::SetResourcesContent
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 3061
diff changeset
57
683d572424b6 IDatabaseWrapper::SetResourcesContent
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 3061
diff changeset
58 static const DicomTag SERIES_IDENTIFIERS[] =
683d572424b6 IDatabaseWrapper::SetResourcesContent
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 3061
diff changeset
59 {
683d572424b6 IDatabaseWrapper::SetResourcesContent
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 3061
diff changeset
60 DICOM_TAG_SERIES_INSTANCE_UID
683d572424b6 IDatabaseWrapper::SetResourcesContent
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 3061
diff changeset
61 };
683d572424b6 IDatabaseWrapper::SetResourcesContent
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 3061
diff changeset
62
683d572424b6 IDatabaseWrapper::SetResourcesContent
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 3061
diff changeset
63 static const DicomTag INSTANCE_IDENTIFIERS[] =
683d572424b6 IDatabaseWrapper::SetResourcesContent
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 3061
diff changeset
64 {
683d572424b6 IDatabaseWrapper::SetResourcesContent
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 3061
diff changeset
65 DICOM_TAG_SOP_INSTANCE_UID
683d572424b6 IDatabaseWrapper::SetResourcesContent
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 3061
diff changeset
66 };
683d572424b6 IDatabaseWrapper::SetResourcesContent
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 3061
diff changeset
67
683d572424b6 IDatabaseWrapper::SetResourcesContent
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 3061
diff changeset
68
2120
4b02ec79728a refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1900
diff changeset
69 namespace ServerToolbox
213
4ce7fdcc8879 access to tags, simplified-tags and file of an instance
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
70 {
1668
de1413733c97 reconstructing main dicom tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1486
diff changeset
71 bool FindOneChildInstance(int64_t& result,
4591
ff8170d17d90 moving all accesses to databases from IDatabaseWrapper to ITransaction
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 4498
diff changeset
72 IDatabaseWrapper::ITransaction& transaction,
1668
de1413733c97 reconstructing main dicom tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1486
diff changeset
73 int64_t resource,
de1413733c97 reconstructing main dicom tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1486
diff changeset
74 ResourceType type)
de1413733c97 reconstructing main dicom tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1486
diff changeset
75 {
de1413733c97 reconstructing main dicom tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1486
diff changeset
76 for (;;)
de1413733c97 reconstructing main dicom tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1486
diff changeset
77 {
de1413733c97 reconstructing main dicom tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1486
diff changeset
78 if (type == ResourceType_Instance)
de1413733c97 reconstructing main dicom tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1486
diff changeset
79 {
de1413733c97 reconstructing main dicom tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1486
diff changeset
80 result = resource;
de1413733c97 reconstructing main dicom tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1486
diff changeset
81 return true;
de1413733c97 reconstructing main dicom tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1486
diff changeset
82 }
de1413733c97 reconstructing main dicom tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1486
diff changeset
83
de1413733c97 reconstructing main dicom tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1486
diff changeset
84 std::list<int64_t> children;
4591
ff8170d17d90 moving all accesses to databases from IDatabaseWrapper to ITransaction
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 4498
diff changeset
85 transaction.GetChildrenInternalId(children, resource);
1668
de1413733c97 reconstructing main dicom tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1486
diff changeset
86 if (children.empty())
de1413733c97 reconstructing main dicom tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1486
diff changeset
87 {
de1413733c97 reconstructing main dicom tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1486
diff changeset
88 return false;
de1413733c97 reconstructing main dicom tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1486
diff changeset
89 }
de1413733c97 reconstructing main dicom tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1486
diff changeset
90
de1413733c97 reconstructing main dicom tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1486
diff changeset
91 resource = children.front();
de1413733c97 reconstructing main dicom tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1486
diff changeset
92 type = GetChildResourceType(type);
de1413733c97 reconstructing main dicom tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1486
diff changeset
93 }
de1413733c97 reconstructing main dicom tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1486
diff changeset
94 }
de1413733c97 reconstructing main dicom tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1486
diff changeset
95
de1413733c97 reconstructing main dicom tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1486
diff changeset
96
4591
ff8170d17d90 moving all accesses to databases from IDatabaseWrapper to ITransaction
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 4498
diff changeset
97 void ReconstructMainDicomTags(IDatabaseWrapper::ITransaction& transaction,
1668
de1413733c97 reconstructing main dicom tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1486
diff changeset
98 IStorageArea& storageArea,
de1413733c97 reconstructing main dicom tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1486
diff changeset
99 ResourceType level)
de1413733c97 reconstructing main dicom tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1486
diff changeset
100 {
de1413733c97 reconstructing main dicom tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1486
diff changeset
101 // WARNING: The database should be locked with a transaction!
de1413733c97 reconstructing main dicom tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1486
diff changeset
102
2129
0c09d1af22f3 "/tools/invalidate-tags" to invalidate the JSON summary of all the DICOM files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2123
diff changeset
103 // TODO: This function might consume much memory if level ==
0c09d1af22f3 "/tools/invalidate-tags" to invalidate the JSON summary of all the DICOM files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2123
diff changeset
104 // ResourceType_Instance. To improve this, first download the
0c09d1af22f3 "/tools/invalidate-tags" to invalidate the JSON summary of all the DICOM files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2123
diff changeset
105 // list of studies, then remove the instances for each single
0c09d1af22f3 "/tools/invalidate-tags" to invalidate the JSON summary of all the DICOM files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2123
diff changeset
106 // study (check out OrthancRestApi::InvalidateTags for an
0c09d1af22f3 "/tools/invalidate-tags" to invalidate the JSON summary of all the DICOM files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2123
diff changeset
107 // example). Take this improvement into consideration for the
0c09d1af22f3 "/tools/invalidate-tags" to invalidate the JSON summary of all the DICOM files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2123
diff changeset
108 // next upgrade of the database schema.
0c09d1af22f3 "/tools/invalidate-tags" to invalidate the JSON summary of all the DICOM files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2123
diff changeset
109
4934
94a7b681b340 added configuration for extra main dicom tags + save signature in metadata + show warning if inconsistent main dicom tags
Alain Mazy <am@osimis.io>
parents: 4932
diff changeset
110 const char* plural = Orthanc::GetResourceTypeText(level, true, true);
1669
a412ad57f0f9 refactoring of sample plugins, OrthancPluginReconstructMainDicomTags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1668
diff changeset
111
a412ad57f0f9 refactoring of sample plugins, OrthancPluginReconstructMainDicomTags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1668
diff changeset
112 LOG(WARNING) << "Upgrade: Reconstructing the main DICOM tags of all the " << plural << "...";
a412ad57f0f9 refactoring of sample plugins, OrthancPluginReconstructMainDicomTags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1668
diff changeset
113
1668
de1413733c97 reconstructing main dicom tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1486
diff changeset
114 std::list<std::string> resources;
4591
ff8170d17d90 moving all accesses to databases from IDatabaseWrapper to ITransaction
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 4498
diff changeset
115 transaction.GetAllPublicIds(resources, level);
1668
de1413733c97 reconstructing main dicom tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1486
diff changeset
116
de1413733c97 reconstructing main dicom tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1486
diff changeset
117 for (std::list<std::string>::const_iterator
1847
559956d5ceb2 cppcheck
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1747
diff changeset
118 it = resources.begin(); it != resources.end(); ++it)
1668
de1413733c97 reconstructing main dicom tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1486
diff changeset
119 {
de1413733c97 reconstructing main dicom tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1486
diff changeset
120 // Locate the resource and one of its child instances
de1413733c97 reconstructing main dicom tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1486
diff changeset
121 int64_t resource, instance;
de1413733c97 reconstructing main dicom tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1486
diff changeset
122 ResourceType tmp;
de1413733c97 reconstructing main dicom tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1486
diff changeset
123
4591
ff8170d17d90 moving all accesses to databases from IDatabaseWrapper to ITransaction
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 4498
diff changeset
124 if (!transaction.LookupResource(resource, tmp, *it) ||
1668
de1413733c97 reconstructing main dicom tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1486
diff changeset
125 tmp != level ||
4591
ff8170d17d90 moving all accesses to databases from IDatabaseWrapper to ITransaction
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 4498
diff changeset
126 !FindOneChildInstance(instance, transaction, resource, level))
1668
de1413733c97 reconstructing main dicom tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1486
diff changeset
127 {
2955
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2951
diff changeset
128 throw OrthancException(ErrorCode_InternalError,
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2951
diff changeset
129 "Cannot find an instance for " +
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2951
diff changeset
130 std::string(EnumerationToString(level)) +
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2951
diff changeset
131 " with identifier " + *it);
1668
de1413733c97 reconstructing main dicom tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1486
diff changeset
132 }
de1413733c97 reconstructing main dicom tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1486
diff changeset
133
de1413733c97 reconstructing main dicom tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1486
diff changeset
134 // Get the DICOM file attached to some instances in the resource
de1413733c97 reconstructing main dicom tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1486
diff changeset
135 FileInfo attachment;
4627
f7d5372b59b3 handling revisions of attachments
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 4623
diff changeset
136 int64_t revision;
f7d5372b59b3 handling revisions of attachments
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 4623
diff changeset
137 if (!transaction.LookupAttachment(attachment, revision, instance, FileContentType_Dicom))
1668
de1413733c97 reconstructing main dicom tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1486
diff changeset
138 {
2955
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2951
diff changeset
139 throw OrthancException(ErrorCode_InternalError,
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2951
diff changeset
140 "Cannot retrieve the DICOM file associated with instance " +
4591
ff8170d17d90 moving all accesses to databases from IDatabaseWrapper to ITransaction
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 4498
diff changeset
141 transaction.GetPublicId(instance));
1668
de1413733c97 reconstructing main dicom tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1486
diff changeset
142 }
de1413733c97 reconstructing main dicom tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1486
diff changeset
143
1870
a6c431193c79 Improved logging information if upgrade fails
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1860
diff changeset
144 try
a6c431193c79 Improved logging information if upgrade fails
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1860
diff changeset
145 {
a6c431193c79 Improved logging information if upgrade fails
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1860
diff changeset
146 // Read and parse the content of the DICOM file
5184
dd085f7e7e71 cleaning new constructors of StorageAccessor
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 5048
diff changeset
147 StorageAccessor accessor(storageArea); // no cache
1673
0bbcfd9695e5 UpgradeDatabase in the sample plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1669
diff changeset
148
1870
a6c431193c79 Improved logging information if upgrade fails
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1860
diff changeset
149 std::string content;
a6c431193c79 Improved logging information if upgrade fails
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1860
diff changeset
150 accessor.Read(content, attachment);
a6c431193c79 Improved logging information if upgrade fails
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1860
diff changeset
151
a6c431193c79 Improved logging information if upgrade fails
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1860
diff changeset
152 ParsedDicomFile dicom(content);
1668
de1413733c97 reconstructing main dicom tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1486
diff changeset
153
1870
a6c431193c79 Improved logging information if upgrade fails
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1860
diff changeset
154 // Update the tags of this resource
a6c431193c79 Improved logging information if upgrade fails
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1860
diff changeset
155 DicomMap dicomSummary;
4140
0ddc5297a8ab centralization of default parameters for JSON/DicomMap conversions from DCMTK
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 4139
diff changeset
156 OrthancConfiguration::DefaultExtractDicomSummary(dicomSummary, dicom);
1668
de1413733c97 reconstructing main dicom tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1486
diff changeset
157
4591
ff8170d17d90 moving all accesses to databases from IDatabaseWrapper to ITransaction
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 4498
diff changeset
158 transaction.ClearMainDicomTags(resource);
3083
683d572424b6 IDatabaseWrapper::SetResourcesContent
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 3061
diff changeset
159
4623
95ffe3b6ef7c handling of revisions for metadata
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 4591
diff changeset
160 ResourcesContent tags(false /* prevent the setting of metadata */);
4934
94a7b681b340 added configuration for extra main dicom tags + save signature in metadata + show warning if inconsistent main dicom tags
Alain Mazy <am@osimis.io>
parents: 4932
diff changeset
161 tags.AddResource(resource, level, dicomSummary);
4591
ff8170d17d90 moving all accesses to databases from IDatabaseWrapper to ITransaction
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 4498
diff changeset
162 transaction.SetResourcesContent(tags);
4934
94a7b681b340 added configuration for extra main dicom tags + save signature in metadata + show warning if inconsistent main dicom tags
Alain Mazy <am@osimis.io>
parents: 4932
diff changeset
163
94a7b681b340 added configuration for extra main dicom tags + save signature in metadata + show warning if inconsistent main dicom tags
Alain Mazy <am@osimis.io>
parents: 4932
diff changeset
164 transaction.DeleteMetadata(resource, MetadataType_MainDicomTagsSignature);
94a7b681b340 added configuration for extra main dicom tags + save signature in metadata + show warning if inconsistent main dicom tags
Alain Mazy <am@osimis.io>
parents: 4932
diff changeset
165 transaction.SetMetadata(resource, MetadataType_MainDicomTagsSignature, DicomMap::GetMainDicomTagsSignature(level), 0);
1870
a6c431193c79 Improved logging information if upgrade fails
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1860
diff changeset
166 }
a6c431193c79 Improved logging information if upgrade fails
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1860
diff changeset
167 catch (OrthancException&)
a6c431193c79 Improved logging information if upgrade fails
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1860
diff changeset
168 {
a6c431193c79 Improved logging information if upgrade fails
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1860
diff changeset
169 LOG(ERROR) << "Cannot decode the DICOM file with UUID " << attachment.GetUuid()
4591
ff8170d17d90 moving all accesses to databases from IDatabaseWrapper to ITransaction
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 4498
diff changeset
170 << " associated with instance " << transaction.GetPublicId(instance);
1870
a6c431193c79 Improved logging information if upgrade fails
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1860
diff changeset
171 throw;
a6c431193c79 Improved logging information if upgrade fails
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1860
diff changeset
172 }
213
4ce7fdcc8879 access to tags, simplified-tags and file of an instance
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
173 }
4ce7fdcc8879 access to tags, simplified-tags and file of an instance
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
174 }
2121
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
175
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
176
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
177 void LoadIdentifiers(const DicomTag*& tags,
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
178 size_t& size,
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
179 ResourceType level)
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
180 {
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
181 switch (level)
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
182 {
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
183 case ResourceType_Patient:
3083
683d572424b6 IDatabaseWrapper::SetResourcesContent
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 3061
diff changeset
184 tags = PATIENT_IDENTIFIERS;
683d572424b6 IDatabaseWrapper::SetResourcesContent
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 3061
diff changeset
185 size = sizeof(PATIENT_IDENTIFIERS) / sizeof(DicomTag);
2121
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
186 break;
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
187
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
188 case ResourceType_Study:
3083
683d572424b6 IDatabaseWrapper::SetResourcesContent
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 3061
diff changeset
189 tags = STUDY_IDENTIFIERS;
683d572424b6 IDatabaseWrapper::SetResourcesContent
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 3061
diff changeset
190 size = sizeof(STUDY_IDENTIFIERS) / sizeof(DicomTag);
2121
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
191 break;
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
192
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
193 case ResourceType_Series:
3083
683d572424b6 IDatabaseWrapper::SetResourcesContent
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 3061
diff changeset
194 tags = SERIES_IDENTIFIERS;
683d572424b6 IDatabaseWrapper::SetResourcesContent
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 3061
diff changeset
195 size = sizeof(SERIES_IDENTIFIERS) / sizeof(DicomTag);
2121
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
196 break;
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
197
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
198 case ResourceType_Instance:
3083
683d572424b6 IDatabaseWrapper::SetResourcesContent
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 3061
diff changeset
199 tags = INSTANCE_IDENTIFIERS;
683d572424b6 IDatabaseWrapper::SetResourcesContent
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 3061
diff changeset
200 size = sizeof(INSTANCE_IDENTIFIERS) / sizeof(DicomTag);
2121
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
201 break;
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
202
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
203 default:
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
204 throw OrthancException(ErrorCode_ParameterOutOfRange);
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
205 }
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
206 }
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
207
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
208
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
209 std::string NormalizeIdentifier(const std::string& value)
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
210 {
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
211 std::string t;
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
212 t.reserve(value.size());
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
213
5284
56cd3444a2d8 NormalizeIdentifier: suggestion for future implementations
Alain Mazy <am@osimis.io>
parents: 5277
diff changeset
214 #if 0
56cd3444a2d8 NormalizeIdentifier: suggestion for future implementations
Alain Mazy <am@osimis.io>
parents: 5277
diff changeset
215 // This version solves some indexing issue (https://discourse.orthanc-server.org/t/postgress-index-effectively-disabled-when-searching-for-greek-names/3371)
56cd3444a2d8 NormalizeIdentifier: suggestion for future implementations
Alain Mazy <am@osimis.io>
parents: 5277
diff changeset
216 // and seems functional: I could run the integration tests with both SQLite and PG + the DicomWeb tests with PG.
56cd3444a2d8 NormalizeIdentifier: suggestion for future implementations
Alain Mazy <am@osimis.io>
parents: 5277
diff changeset
217 // However, it can not go into production because NormalizeIdentifier is used both at ingest time and at search time;
56cd3444a2d8 NormalizeIdentifier: suggestion for future implementations
Alain Mazy <am@osimis.io>
parents: 5277
diff changeset
218 // therefore, if we change it while we have an already populated DB, the searches won't work anymore and, on very large
56cd3444a2d8 NormalizeIdentifier: suggestion for future implementations
Alain Mazy <am@osimis.io>
parents: 5277
diff changeset
219 // systems, running the Housekeeper to rebuild the indexes might take months ...
56cd3444a2d8 NormalizeIdentifier: suggestion for future implementations
Alain Mazy <am@osimis.io>
parents: 5277
diff changeset
220 // We keep it here because it might be handy once we refactor the DicomIdentifier searches in the future.
2121
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
221 for (size_t i = 0; i < value.size(); i++)
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
222 {
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
223 if (value[i] == '%' ||
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
224 value[i] == '_')
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
225 {
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
226 t.push_back(' '); // These characters might break wildcard queries in SQL
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
227 }
5284
56cd3444a2d8 NormalizeIdentifier: suggestion for future implementations
Alain Mazy <am@osimis.io>
parents: 5277
diff changeset
228 else if (//isascii(value[i]) &&
2121
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
229 !iscntrl(value[i]) &&
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
230 (!isspace(value[i]) || value[i] == ' '))
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
231 {
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
232 t.push_back(value[i]);
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
233 }
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
234 }
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
235
5284
56cd3444a2d8 NormalizeIdentifier: suggestion for future implementations
Alain Mazy <am@osimis.io>
parents: 5277
diff changeset
236 //Toolbox::ToUpperCase(t);
56cd3444a2d8 NormalizeIdentifier: suggestion for future implementations
Alain Mazy <am@osimis.io>
parents: 5277
diff changeset
237 t = Toolbox::ToUpperCaseWithAccents(t);
56cd3444a2d8 NormalizeIdentifier: suggestion for future implementations
Alain Mazy <am@osimis.io>
parents: 5277
diff changeset
238 #else
56cd3444a2d8 NormalizeIdentifier: suggestion for future implementations
Alain Mazy <am@osimis.io>
parents: 5277
diff changeset
239 for (size_t i = 0; i < value.size(); i++)
56cd3444a2d8 NormalizeIdentifier: suggestion for future implementations
Alain Mazy <am@osimis.io>
parents: 5277
diff changeset
240 {
56cd3444a2d8 NormalizeIdentifier: suggestion for future implementations
Alain Mazy <am@osimis.io>
parents: 5277
diff changeset
241 if (value[i] == '%' ||
56cd3444a2d8 NormalizeIdentifier: suggestion for future implementations
Alain Mazy <am@osimis.io>
parents: 5277
diff changeset
242 value[i] == '_')
56cd3444a2d8 NormalizeIdentifier: suggestion for future implementations
Alain Mazy <am@osimis.io>
parents: 5277
diff changeset
243 {
56cd3444a2d8 NormalizeIdentifier: suggestion for future implementations
Alain Mazy <am@osimis.io>
parents: 5277
diff changeset
244 t.push_back(' '); // These characters might break wildcard queries in SQL
56cd3444a2d8 NormalizeIdentifier: suggestion for future implementations
Alain Mazy <am@osimis.io>
parents: 5277
diff changeset
245 }
5285
bb07c12e3472 re-enabled the old NormalizeIdentifier code
Alain Mazy <am@osimis.io>
parents: 5284
diff changeset
246 else if (isascii(value[i]) &&
bb07c12e3472 re-enabled the old NormalizeIdentifier code
Alain Mazy <am@osimis.io>
parents: 5284
diff changeset
247 !iscntrl(value[i]) &&
5284
56cd3444a2d8 NormalizeIdentifier: suggestion for future implementations
Alain Mazy <am@osimis.io>
parents: 5277
diff changeset
248 (!isspace(value[i]) || value[i] == ' '))
56cd3444a2d8 NormalizeIdentifier: suggestion for future implementations
Alain Mazy <am@osimis.io>
parents: 5277
diff changeset
249 {
56cd3444a2d8 NormalizeIdentifier: suggestion for future implementations
Alain Mazy <am@osimis.io>
parents: 5277
diff changeset
250 t.push_back(value[i]);
56cd3444a2d8 NormalizeIdentifier: suggestion for future implementations
Alain Mazy <am@osimis.io>
parents: 5277
diff changeset
251 }
56cd3444a2d8 NormalizeIdentifier: suggestion for future implementations
Alain Mazy <am@osimis.io>
parents: 5277
diff changeset
252 }
56cd3444a2d8 NormalizeIdentifier: suggestion for future implementations
Alain Mazy <am@osimis.io>
parents: 5277
diff changeset
253
5286
Alain Mazy <am@osimis.io>
parents: 5285
diff changeset
254 Toolbox::ToUpperCase(t);
5284
56cd3444a2d8 NormalizeIdentifier: suggestion for future implementations
Alain Mazy <am@osimis.io>
parents: 5277
diff changeset
255 #endif
2121
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
256
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
257 return Toolbox::StripSpaces(t);
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
258 }
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
259
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
260
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
261 bool IsIdentifier(const DicomTag& tag,
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
262 ResourceType level)
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
263 {
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
264 const DicomTag* tags;
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
265 size_t size;
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
266
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
267 LoadIdentifiers(tags, size, level);
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
268
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
269 for (size_t i = 0; i < size; i++)
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
270 {
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
271 if (tag == tags[i])
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
272 {
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
273 return true;
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
274 }
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
275 }
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
276
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
277 return false;
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
278 }
2209
e3fd5bc429a2 URI to reconstruct the main DICOM tags, the JSON summary and the metadata
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2129
diff changeset
279
e3fd5bc429a2 URI to reconstruct the main DICOM tags, the JSON summary and the metadata
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2129
diff changeset
280
e3fd5bc429a2 URI to reconstruct the main DICOM tags, the JSON summary and the metadata
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2129
diff changeset
281 void ReconstructResource(ServerContext& context,
4988
8fba26292a9f Housekeeper plugin: finalizing + integration tests ok
Alain Mazy <am@osimis.io>
parents: 4934
diff changeset
282 const std::string& resource,
8fba26292a9f Housekeeper plugin: finalizing + integration tests ok
Alain Mazy <am@osimis.io>
parents: 4934
diff changeset
283 bool reconstructFiles)
2209
e3fd5bc429a2 URI to reconstruct the main DICOM tags, the JSON summary and the metadata
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2129
diff changeset
284 {
e3fd5bc429a2 URI to reconstruct the main DICOM tags, the JSON summary and the metadata
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2129
diff changeset
285 LOG(WARNING) << "Reconstructing resource " << resource;
e3fd5bc429a2 URI to reconstruct the main DICOM tags, the JSON summary and the metadata
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2129
diff changeset
286
e3fd5bc429a2 URI to reconstruct the main DICOM tags, the JSON summary and the metadata
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2129
diff changeset
287 std::list<std::string> instances;
e3fd5bc429a2 URI to reconstruct the main DICOM tags, the JSON summary and the metadata
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2129
diff changeset
288 context.GetIndex().GetChildInstances(instances, resource);
e3fd5bc429a2 URI to reconstruct the main DICOM tags, the JSON summary and the metadata
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2129
diff changeset
289
e3fd5bc429a2 URI to reconstruct the main DICOM tags, the JSON summary and the metadata
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2129
diff changeset
290 for (std::list<std::string>::const_iterator
e3fd5bc429a2 URI to reconstruct the main DICOM tags, the JSON summary and the metadata
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2129
diff changeset
291 it = instances.begin(); it != instances.end(); ++it)
e3fd5bc429a2 URI to reconstruct the main DICOM tags, the JSON summary and the metadata
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2129
diff changeset
292 {
e3fd5bc429a2 URI to reconstruct the main DICOM tags, the JSON summary and the metadata
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2129
diff changeset
293 ServerContext::DicomCacheLocker locker(context, *it);
e3fd5bc429a2 URI to reconstruct the main DICOM tags, the JSON summary and the metadata
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2129
diff changeset
294
4498
7b99e8bb8246 IStorageArea::HasReadRange()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 4437
diff changeset
295 // Delay the reconstruction of DICOM-as-JSON to its next access through "ServerContext"
4640
66109d24d26e "ETag" headers for metadata and attachments now allow strong comparison (MD5 is included)
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 4627
diff changeset
296 context.GetIndex().DeleteAttachment(*it, FileContentType_DicomAsJson, false /* no revision */,
66109d24d26e "ETag" headers for metadata and attachments now allow strong comparison (MD5 is included)
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 4627
diff changeset
297 -1 /* dummy revision */, "" /* dummy MD5 */);
4498
7b99e8bb8246 IStorageArea::HasReadRange()
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 4437
diff changeset
298
2209
e3fd5bc429a2 URI to reconstruct the main DICOM tags, the JSON summary and the metadata
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2129
diff changeset
299 context.GetIndex().ReconstructInstance(locker.GetDicom());
4988
8fba26292a9f Housekeeper plugin: finalizing + integration tests ok
Alain Mazy <am@osimis.io>
parents: 4934
diff changeset
300
8fba26292a9f Housekeeper plugin: finalizing + integration tests ok
Alain Mazy <am@osimis.io>
parents: 4934
diff changeset
301 if (reconstructFiles)
8fba26292a9f Housekeeper plugin: finalizing + integration tests ok
Alain Mazy <am@osimis.io>
parents: 4934
diff changeset
302 {
8fba26292a9f Housekeeper plugin: finalizing + integration tests ok
Alain Mazy <am@osimis.io>
parents: 4934
diff changeset
303 std::string resultPublicId; // ignored
8fba26292a9f Housekeeper plugin: finalizing + integration tests ok
Alain Mazy <am@osimis.io>
parents: 4934
diff changeset
304 std::unique_ptr<DicomInstanceToStore> dicomInstancetoStore(DicomInstanceToStore::CreateFromParsedDicomFile(locker.GetDicom()));
8fba26292a9f Housekeeper plugin: finalizing + integration tests ok
Alain Mazy <am@osimis.io>
parents: 4934
diff changeset
305
5224
feba2b0e91bc Fix a crash in /tools/reconstruct triggered by the Housekeeper plugin when only changing the StorageCompression.
Alain Mazy <am@osimis.io>
parents: 5185
diff changeset
306 // TODO: TranscodeAndStore and specifically ServerIndex::Store have been "poluted" by the isReconstruct parameter
feba2b0e91bc Fix a crash in /tools/reconstruct triggered by the Housekeeper plugin when only changing the StorageCompression.
Alain Mazy <am@osimis.io>
parents: 5185
diff changeset
307 // we should very likely refactor it
4988
8fba26292a9f Housekeeper plugin: finalizing + integration tests ok
Alain Mazy <am@osimis.io>
parents: 4934
diff changeset
308 context.TranscodeAndStore(resultPublicId, dicomInstancetoStore.get(), StoreInstanceMode_OverwriteDuplicate, true);
8fba26292a9f Housekeeper plugin: finalizing + integration tests ok
Alain Mazy <am@osimis.io>
parents: 4934
diff changeset
309 }
2209
e3fd5bc429a2 URI to reconstruct the main DICOM tags, the JSON summary and the metadata
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2129
diff changeset
310 }
e3fd5bc429a2 URI to reconstruct the main DICOM tags, the JSON summary and the metadata
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2129
diff changeset
311 }
5244
72dfa0ac84eb lookup for labels in orthanc explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 5224
diff changeset
312
72dfa0ac84eb lookup for labels in orthanc explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 5224
diff changeset
313
72dfa0ac84eb lookup for labels in orthanc explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 5224
diff changeset
314 bool IsValidLabel(const std::string& label)
72dfa0ac84eb lookup for labels in orthanc explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 5224
diff changeset
315 {
72dfa0ac84eb lookup for labels in orthanc explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 5224
diff changeset
316 if (label.empty())
72dfa0ac84eb lookup for labels in orthanc explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 5224
diff changeset
317 {
72dfa0ac84eb lookup for labels in orthanc explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 5224
diff changeset
318 return false;
72dfa0ac84eb lookup for labels in orthanc explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 5224
diff changeset
319 }
5247
eb2684260c19 support labels for mysql
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 5244
diff changeset
320
eb2684260c19 support labels for mysql
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 5244
diff changeset
321 if (label.size() > 64)
eb2684260c19 support labels for mysql
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 5244
diff changeset
322 {
eb2684260c19 support labels for mysql
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 5244
diff changeset
323 // This limitation is for MySQL, which cannot use a TEXT
eb2684260c19 support labels for mysql
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 5244
diff changeset
324 // column of undefined length as a primary key
eb2684260c19 support labels for mysql
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 5244
diff changeset
325 return false;
eb2684260c19 support labels for mysql
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 5244
diff changeset
326 }
5244
72dfa0ac84eb lookup for labels in orthanc explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 5224
diff changeset
327
72dfa0ac84eb lookup for labels in orthanc explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 5224
diff changeset
328 for (size_t i = 0; i < label.size(); i++)
72dfa0ac84eb lookup for labels in orthanc explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 5224
diff changeset
329 {
5250
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 5247
diff changeset
330 if (!(label[i] == '_' ||
5244
72dfa0ac84eb lookup for labels in orthanc explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 5224
diff changeset
331 label[i] == '-' ||
72dfa0ac84eb lookup for labels in orthanc explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 5224
diff changeset
332 (label[i] >= 'a' && label[i] <= 'z') ||
72dfa0ac84eb lookup for labels in orthanc explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 5224
diff changeset
333 (label[i] >= 'A' && label[i] <= 'Z') ||
72dfa0ac84eb lookup for labels in orthanc explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 5224
diff changeset
334 (label[i] >= '0' && label[i] <= '9')))
72dfa0ac84eb lookup for labels in orthanc explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 5224
diff changeset
335 {
72dfa0ac84eb lookup for labels in orthanc explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 5224
diff changeset
336 return false;
72dfa0ac84eb lookup for labels in orthanc explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 5224
diff changeset
337 }
72dfa0ac84eb lookup for labels in orthanc explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 5224
diff changeset
338 }
72dfa0ac84eb lookup for labels in orthanc explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 5224
diff changeset
339
72dfa0ac84eb lookup for labels in orthanc explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 5224
diff changeset
340 return true;
72dfa0ac84eb lookup for labels in orthanc explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 5224
diff changeset
341 }
72dfa0ac84eb lookup for labels in orthanc explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 5224
diff changeset
342
72dfa0ac84eb lookup for labels in orthanc explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 5224
diff changeset
343
72dfa0ac84eb lookup for labels in orthanc explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 5224
diff changeset
344 void CheckValidLabel(const std::string& label)
72dfa0ac84eb lookup for labels in orthanc explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 5224
diff changeset
345 {
72dfa0ac84eb lookup for labels in orthanc explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 5224
diff changeset
346 if (!IsValidLabel(label))
72dfa0ac84eb lookup for labels in orthanc explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 5224
diff changeset
347 {
72dfa0ac84eb lookup for labels in orthanc explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 5224
diff changeset
348 throw OrthancException(ErrorCode_ParameterOutOfRange,
72dfa0ac84eb lookup for labels in orthanc explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 5224
diff changeset
349 "A label must be a non-empty, alphanumeric string, "
5250
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 5247
diff changeset
350 "possibly with '_' or '-' characters, "
5247
eb2684260c19 support labels for mysql
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 5244
diff changeset
351 "with maximum 64 characters, but got: " + label);
5244
72dfa0ac84eb lookup for labels in orthanc explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 5224
diff changeset
352 }
72dfa0ac84eb lookup for labels in orthanc explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 5224
diff changeset
353 }
213
4ce7fdcc8879 access to tags, simplified-tags and file of an instance
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
354 }
4ce7fdcc8879 access to tags, simplified-tags and file of an instance
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
355 }