Bug 199146
| Summary: | new port: science/orthanc: DICOM (medical imaging) service for hospitals | ||||||||||||
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| Product: | Ports & Packages | Reporter: | mp39590 | ||||||||||
| Component: | Individual Port(s) | Assignee: | Dmitry Marakasov <amdmi3> | ||||||||||
| Status: | Closed FIXED | ||||||||||||
| Severity: | Affects Only Me | CC: | amdmi3, s.jodogne | ||||||||||
| Priority: | --- | ||||||||||||
| Version: | Latest | ||||||||||||
| Hardware: | Any | ||||||||||||
| OS: | Any | ||||||||||||
| Attachments: |
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Created attachment 155157 [details]
patch for new users/groups
Created attachment 155158 [details]
poudriere build logs
- patch-Core_MultiThreading_ThreadedCommandProcessor.cpp seem to be incorrect. That should be while (!(remainingCommands_ == 0)) or while (remainingCommands_ != 0), see currenct source
- What does patch-OrthancServer_Internals_StoreScp.cpp do? Haven't checked, but judging from the code there should be no warning here
- You can't hardcode /usr/local (patch-Resources_CMake_Compiler.cmake, patch-Resources_CMake_DcmtkConfiguration.cmake, probably more cmake files), as it may be changed. Use ${REINPLACE_CMD} -e 's|/usr/local|${LOCALBASE}|' to fix that.
- You should use /var instead of ${PREFIX}/var
- You should use single post-install target, no need for post-stage:
- What does glog IGNORE mean? If it's glog problem, it should be fixed/marked broken in glog itself. For me glog builds fine on 8.4 and 9.3.
It's nice that most patches were merged upstream.
jk(In reply to Dmitry Marakasov from comment #3) > - patch-Core_MultiThreading_ThreadedCommandProcessor.cpp seem to be > incorrect. That should be while (!(remainingCommands_ == 0)) or while > (remainingCommands_ != 0), see currenct source Originally my patch was fixing a warning, and it didn't change the logic of the loop, looking at the change in repo, it seem that the logic really has been changed[1]. I've sync'ed the chunk with upstream, but would like to ask Sébastien's opinion on it - is everything safe with the linked change? > - What does patch-OrthancServer_Internals_StoreScp.cpp do? Haven't checked, > but judging from the code there should be no warning here If you do == operation and use double parenthesis clang gives a warning, double parenthesis are for the case when you do assignment (=) inside an expression. > - You can't hardcode /usr/local (patch-Resources_CMake_Compiler.cmake, > patch-Resources_CMake_DcmtkConfiguration.cmake, probably more cmake files), > as it may be changed. Use ${REINPLACE_CMD} -e 's|/usr/local|${LOCALBASE}|' > to fix that. I've worked around this with passing proper CFLAGS and LDFLAGS, another /usr/local usage was in dcmtk dictionary detection - worked around with CMAKE_ARGS var addition. Offending chunks are removed. > - You should use /var instead of ${PREFIX}/var Fixed. %%PREFIX%%/var/lib/orthanc/db-v5 -> /var/db/orthanc/db-v5. Original intention was to be close to debian port, but seem hier(7) don't have /var/lib entry, so /var/db is used. > - You should use single post-install target, no need for post-stage: Fixed. > - What does glog IGNORE mean? If it's glog problem, it should be > fixed/marked broken in glog itself. For me glog builds fine on 8.4 and 9.3. At the time of submission of the shar I wasn't able to build glog on anything <10.1, also, no packages of glog were presented in pkg.freebsd.org for aforementioned releases, it looks like it has been fixed now. IGNORE removed. > It's nice that most patches were merged upstream. Few problem arose though: 1. GCC [not clang => 8.4, 9.3] compilation of Orthanc uses -pedantic, it doesn't like enum's with commas after last element, and those are presented in boost-lib, workarounded this with removing of -pedantic. 2. It looks like because of debugging features which are enabled on -current Orthanc, when being stopped (service orthanc stop), exits with SIGBUS signal, after investigation it looks like it's a fault of dcmtk lib, I've submitted bug 200544 about it, but I don't think it's a show-stopper. [1] - https://code.google.com/p/orthanc/source/detail?r=7f0aa3c0f659b1e0c531bfc7284ad7766a202bb7 Created attachment 157294 [details]
shell archive v2
(In reply to mp39590 from comment #4) > If you do == operation and use double parenthesis clang gives a warning, double parenthesis are for the case when you do assignment (=) inside an expression. Ok, I misunderstood the patch, I though it did the opposite. > Fixed. %%PREFIX%%/var/lib/orthanc/db-v5 -> /var/db/orthanc/db-v5. Original intention was to be close to debian port, but seem hier(7) don't have /var/lib entry, so /var/db is used. You could actually use /var/lib, but /var/db is preferred on FreeBSD. > At the time of submission of the shar I wasn't able to build glog on anything <10.1, also, no packages of glog were presented in pkg.freebsd.org for aforementioned releases, it looks like it has been fixed now. IGNORE removed. IGNORE was illegal regardless. Ports should not handle other ports' problems. > 1. GCC [not clang => 8.4, 9.3] compilation of Orthanc uses -pedantic, it doesn't like enum's with commas after last element, and those are presented in boost-lib, workarounded this with removing of -pedantic. This could probably be fixed in orthanc cmake: include_directories() supports SYSTEM argument which should be used for boost and other dependencies' includes. This should make warnings in these headers ignored. A commit references this bug: Author: amdmi3 Date: Thu Jun 4 14:07:38 UTC 2015 New revision: 388534 URL: https://svnweb.freebsd.org/changeset/ports/388534 Log: - Add science/orthanc Orthanc aims at providing a simple, yet powerful standalone DICOM server. It is designed to improve the DICOM flows in hospitals and to support research about the automated analysis of medical images. Orthanc can turn any computer running Windows, Linux, FreeBSD or OS X into a DICOM store (in other words, a mini-PACS system). Its architecture is lightweight and standalone, meaning that no complex database administration is required, nor the installation of third-party dependencies. What makes Orthanc unique is the fact that it provides a RESTful API. Thanks to this major feature, it is possible to drive Orthanc from any computer language. The DICOM tags of the stored medical images can be downloaded in the JSON file format. Furthermore, standard PNG images can be generated on-the-fly from the DICOM instances by Orthanc. Orthanc lets its users focus on the content of the DICOM files, hiding the complexity of the DICOM format and of the DICOM protocol. WWW: http://www.orthanc-server.com/ PR: 199146 Submitted by: mp39590@gmail.com Changes: head/GIDs head/UIDs head/science/Makefile head/science/orthanc/ head/science/orthanc/Makefile head/science/orthanc/distinfo head/science/orthanc/files/ head/science/orthanc/files/orthanc.in head/science/orthanc/files/patch-CMakeLists.txt head/science/orthanc/files/patch-Core_Compression_HierarchicalZipWriter.cpp head/science/orthanc/files/patch-Core_ImageFormats_ImageProcessing.cpp head/science/orthanc/files/patch-Core_MultiThreading_Mutex.cpp head/science/orthanc/files/patch-Core_MultiThreading_ThreadedCommandProcessor.cpp head/science/orthanc/files/patch-Core_Toolbox.cpp head/science/orthanc/files/patch-OrthancServer_Internals_StoreScp.cpp head/science/orthanc/files/patch-Plugins_Engine_PluginsManager.cpp head/science/orthanc/files/patch-Plugins_Engine_SharedLibrary.cpp head/science/orthanc/files/patch-Resources_CMake_AutoGeneratedCode.cmake head/science/orthanc/files/patch-Resources_CMake_BoostConfiguration.cmake head/science/orthanc/files/patch-Resources_CMake_Compiler.cmake head/science/orthanc/files/patch-Resources_CMake_SQLiteConfiguration.cmake head/science/orthanc/files/patch-Resources_Configuration.json head/science/orthanc/pkg-descr head/science/orthanc/pkg-plist |
Created attachment 155156 [details] shell archive Orthanc is a service which allows hospitals easily save, exchange and analyze results of patient's tomography stored in DICOM imaging format. RESTful API provides ways to access this data with simple web browser and other tools which can talk http protocol (curl, for example). This service drastically lower costs for hospitals in terms of paper work.