Develop to Master merge #100
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Fixed Database issue with GitHub Actions
Adds database interface
`POSTGRES_HOST_AUTH_METHOD: trust` allows all connections to be established without needing the password. Removing this before I forget about it.
Refactors codebase + fixes double processing
Feat crosswalk
…anc-TMI into feat-crosswalk
Feat crosswalk
| <project version="4"> | ||
| <component name="ProjectModuleManager"> | ||
| <modules> | ||
| <module fileurl="file://$PROJECT_DIR$/.idea/Orthanc-TMI.iml" filepath="$PROJECT_DIR$/.idea/Orthanc-TMI.iml" /> | ||
| <module fileurl="file://$PROJECT_DIR$/.idea/Orthanc_TMI.iml" filepath="$PROJECT_DIR$/.idea/Orthanc_TMI.iml" /> | ||
| </modules> | ||
| </component> |
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Not sure how any .idea/ files got in. I thought the directory was ignored in .gitignore.
We should delete this file and any others in there.
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| ADD ./setup-environment.sh ./setup-environment.sh | ||
| RUN dos2unix ./setup-environment.sh |
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surely there is a better solution
| "DataAnon": { | ||
| "HardlinksUseHashBins" : true, | ||
| "Hardlinks": { | ||
| "/by-study-date/": "0008,0020", | ||
| "/by-pid/": "0010,0020", | ||
| "/by-dob/": "0010,0030" | ||
| }, | ||
| "DateTruncation": { | ||
| "default": "YYYYMM01", | ||
| "0010,0030": "YYY0MM01" | ||
| }, | ||
| "Filter": { | ||
| "blacklist": [ | ||
| "0010" | ||
| ], | ||
| "whitelist": [ | ||
| "0010,0030" | ||
| ] | ||
| } | ||
| }, |
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This would have been nice to move into its own config file. Then we could have detected it's presence and created a default file if missing.
| static void Emplace(const void* instance_data, std::string md5, size_t size); | ||
| static void Emplace(const void* instance_data, std::string uuid); | ||
| static void Emplace(const void* instance_data, const DicomFile& file); | ||
| static bool Emplace(std::string md5); |
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These in particular really need better names.. I think. I think?
| #pragma once | ||
| /* | ||
| #include <mutex> | ||
| #include <atomic> | ||
| #include <queue> | ||
| #include <condition_variable> | ||
| #include <functional> | ||
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| class JobQueue { | ||
| private: | ||
| std::atomic_bool keep_running; | ||
| std::atomic_bool has_work; | ||
| std::condition_variable cv; | ||
| std::mutex queue_lock; | ||
| std::queue<std::function<void()>> jqueue; | ||
| // this class is the only thing that can instantiate itself now | ||
| JobQueue(){} | ||
| public: | ||
| static JobQueue& GetInstance(); | ||
| void AddJob(std::function<void()> job); | ||
| void Process(); | ||
| void Stop(); | ||
| }; | ||
| /**/ |
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These two files should be deleted before merging to master
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actually 3 (.h .cpp, and the unit test .cpp)
| db_init_job = std::thread([](){ | ||
| std::this_thread::sleep_for(std::chrono::seconds(2)); | ||
| if(!DBInterface::Initialize()){ | ||
| std::cerr << "DB Initialize job failed. Terminating.." << std::endl; | ||
| std::abort(); // abnormal termination | ||
| } |
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This should be documented. It's there because Orthanc's tables haven't yet initialized (potentially) yet and so we can't initialize ours yet. But we need it to initialize from our plugin initialize function, so we spawn a thread with a delay. A comment should explain this
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| CREATE TABLE IF NOT EXISTS crosswalk ( | |||
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In an ideal world, we break this file up into smaller portions and load those files instead of copy pasting the code in this file as string in numerous locations.
| //#define UNIT_TEST | ||
| #include <core.h> | ||
| #include <functional> | ||
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| extern fs::path GetProjRoot(); | ||
| extern void TestWithDicomFiles(std::function<void(const fs::path&)> test); | ||
| namespace uuid { | ||
| extern std::string generate_uuid_v4(); |
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I don't think this function is used. It should be removed if that's the case.
Merge develop to master