Squashed 'external/deimos/' content from commit 5f97c45466

git-subtree-dir: external/deimos
git-subtree-split: 5f97c4546617aca666bd6f217f81af78607830c4

.clang-format

+---
+Language:        Cpp
+AccessModifierOffset: -2
+AlignAfterOpenBracket: AlwaysBreak
+AlignConsecutiveAssignments: true
+AlignConsecutiveDeclarations: false
+AlignEscapedNewlines: Right
+AlignOperands:   true
+AlignTrailingComments: true
+AllowAllParametersOfDeclarationOnNextLine: true
+AllowShortBlocksOnASingleLine: false
+AllowShortCaseLabelsOnASingleLine: false
+AllowShortFunctionsOnASingleLine: Inline
+AllowShortIfStatementsOnASingleLine: true
+AllowShortLoopsOnASingleLine: false
+AlwaysBreakAfterDefinitionReturnType: None
+AlwaysBreakAfterReturnType: None
+AlwaysBreakBeforeMultilineStrings: false
+AlwaysBreakTemplateDeclarations: Yes
+BinPackArguments: true
+BinPackParameters: false
+BraceWrapping:   
+  AfterClass:      false
+  AfterControlStatement: false
+  AfterEnum:       false
+  AfterFunction:   true
+  AfterNamespace:  false
+  AfterObjCDeclaration: false
+  AfterStruct:     false
+  AfterUnion:      false
+  AfterExternBlock: false
+  BeforeCatch:     true
+  BeforeElse:      true
+  IndentBraces:    false
+  SplitEmptyFunction: true
+  SplitEmptyRecord: true
+  SplitEmptyNamespace: true
+BreakBeforeBinaryOperators: NonAssignment
+BreakBeforeBraces: Stroustrup
+BreakBeforeInheritanceComma: false
+BreakInheritanceList: AfterColon
+BreakBeforeTernaryOperators: false
+BreakConstructorInitializersBeforeComma: false
+BreakConstructorInitializers: AfterColon
+BreakAfterJavaFieldAnnotations: false
+BreakStringLiterals: false
+ColumnLimit:     80
+CommentPragmas:  '^ *@'
+CompactNamespaces: false
+ConstructorInitializerAllOnOneLineOrOnePerLine: true
+ConstructorInitializerIndentWidth: 4
+ContinuationIndentWidth: 4
+Cpp11BracedListStyle: true
+DerivePointerAlignment: false
+DisableFormat:   false
+ExperimentalAutoDetectBinPacking: false
+FixNamespaceComments: true
+ForEachMacros:   
+  - foreach
+  - Q_FOREACH
+  - BOOST_FOREACH
+IncludeBlocks:   Preserve
+IncludeCategories: 
+  - Regex:           '^"(llvm|llvm-c|clang|clang-c)/'
+    Priority:        2
+  - Regex:           '^(<|"(gtest|gmock|isl|json)/)'
+    Priority:        3
+  - Regex:           '.*'
+    Priority:        1
+IncludeIsMainRegex: '(Test)?$'
+IndentCaseLabels: true
+IndentPPDirectives: None
+IndentWidth:     4
+IndentWrappedFunctionNames: false
+JavaScriptQuotes: Leave
+JavaScriptWrapImports: true
+KeepEmptyLinesAtTheStartOfBlocks: true
+MacroBlockBegin: ''
+MacroBlockEnd:   ''
+MaxEmptyLinesToKeep: 2
+NamespaceIndentation: None
+ObjCBinPackProtocolList: Auto
+ObjCBlockIndentWidth: 2
+ObjCSpaceAfterProperty: true
+ObjCSpaceBeforeProtocolList: false
+PenaltyBreakAssignment: 2
+PenaltyBreakBeforeFirstCallParameter: 19
+PenaltyBreakComment: 300
+PenaltyBreakFirstLessLess: 120
+PenaltyBreakString: 1000
+PenaltyBreakTemplateDeclaration: 10
+PenaltyExcessCharacter: 1000000
+PenaltyReturnTypeOnItsOwnLine: 200
+PointerAlignment: Left
+ReflowComments:  true
+SortIncludes:    true
+SortUsingDeclarations: true
+SpaceAfterCStyleCast: false
+SpaceAfterTemplateKeyword: false
+SpaceBeforeAssignmentOperators: true
+SpaceBeforeCpp11BracedList: false
+SpaceBeforeCtorInitializerColon: true
+SpaceBeforeInheritanceColon: true
+SpaceBeforeParens: ControlStatements
+SpaceBeforeRangeBasedForLoopColon: true
+SpaceInEmptyParentheses: false
+SpacesBeforeTrailingComments: 2
+SpacesInAngles:  false
+SpacesInContainerLiterals: true
+SpacesInCStyleCastParentheses: false
+SpacesInParentheses: false
+SpacesInSquareBrackets: false
+Standard:        Cpp11
+TabWidth:        8
+UseTab:          Never
+...
+

.clang-tidy

+---
+Checks:          clang-diagnostic-*,
+                 clang-analyzer-*,
+                 clang-diagnostic-*,
+                 clang-analyzer-*,
+                 -clang-analyzer-security.insecureAPI.rand,
+                 mpi-*,
+                 readability-braces-around-statements,
+                 readability-redundant-string-init,
+                 readability-container-size-empty,
+                 readability-implicit-bool-conversion,
+                 readability-identifier-naming,
+                 modernize-redundant-void-arg
+WarningsAsErrors: '*'
+HeaderFilterRegex: ''
+AnalyzeTemporaryDtors: false
+FormatStyle:     none
+User:            Deimos
+CheckOptions:    
+  - key:             google-readability-braces-around-statements.ShortStatementLines
+    value:           '1'
+  - key:             google-readability-function-size.StatementThreshold
+    value:           '800'
+  - key:             google-readability-namespace-comments.ShortNamespaceLines
+    value:           '10'
+  - key:             google-readability-namespace-comments.SpacesBeforeComments
+    value:           '2'
+  - key:             modernize-loop-convert.MaxCopySize
+    value:           '16'
+  - key:             modernize-loop-convert.MinConfidence
+    value:           reasonable
+  - key:             modernize-loop-convert.NamingStyle
+    value:           CamelCase
+  - key:             modernize-pass-by-value.IncludeStyle
+    value:           llvm
+  - key:             modernize-replace-auto-ptr.IncludeStyle
+    value:           llvm
+  - key:             modernize-use-nullptr.NullMacros
+    value:           'NULL'
+  - key:             readability-braces-around-statements.ShortStatementLines
+    value:           '0'
+  - key:             readability-implicit-bool-conversion.AllowIntegerConditions
+    value:           '0'
+  - key:             readability-implicit-bool-conversion.AllowPointerConditions
+    value:           '0'
+  - key:             cppcoreguidelines-special-member-functions.AllowSoleDefaultDtor
+    value:           '1'
+#
+# Identifier Naming
+#
+# TODO: Add TypeDefCase, TypeAliasCase, EnumCase, EnumConstantCase, ClassCase,
+#       and UnionCase
+  - key:             readability-identifier-naming.NamespaceCase
+    value:           lower_case
+  - key:             readability-identifier-naming.MemberCase
+    value:           lower_case
+  - key:             readability-identifier-naming.PrivateMemberCase
+    value:           lower_case
+  - key:             readability-identifier-naming.PrivateMemberPrefix
+    value:           m_
+  - key:             readability-identifier-naming.ProtectedMemberCase
+    value:           lower_case
+  - key:             readability-identifier-naming.ProtectedMemberPrefix
+    value:           m_
+  - key:             readability-identifier-naming.FunctionCase
+    value:           lower_case
+  - key:             readability-identifier-naming.ParameterCase
+    value:           lower_case
+  - key:             readability-identifier-naming.VariableCase
+    value:           lower_case
+  - key:             readability-identifier-naming.TemplateParameterCase
+    value:           CamelCase
+  - key:             readability-identifier-naming.MacroDefinitionCase
+    value:           UPPER_CASE
+  - key:             readability-identifier-naming.MacroDefinitionPrefix
+    value:           DEIMOS_
+...
+

.gitignore

+*.swp
+todo.txt
+.DS_Store

.gitlab-ci.yml

+image: ciaranorourke/fiphoboserver:debian 
+
+.snippets:
+    - &start_phobos
+        /home/superfiphoboserver/tools/build_phobos.sh -r
+    - &configure
+        mkdir build
+        && pushd build
+        && (
+            set -x;
+            cmake
+            -DCMAKE_VERBOSE_MAKEFILE=ON
+            -DCMAKE_EXPORT_COMPILE_COMMANDS=ON
+            -DCMAKE_C_COMPILER=${CC}
+            -DCMAKE_CXX_COMPILER=${CXX}
+            -DDEIMOS_BUILD_TESTS="${DEIMOS_BUILD_TESTS}"
+            -DCMAKE_PREFIX_PATH="${DEPS_DIR}"
+            -DCUSTOM_DOCU_PATH="${DEIMOS_DOC_DIR}"
+            -DDEIMOS_BUILD_DOCUMENTATION="${DEIMOS_BUILD_DOCUMENTATION}"
+            -DDEIMOS_DISABLE_AUTHORISATION="${DEIMOS_DISABLE_AUTHORISATION}"
+            ..
+        )
+        && popd
+    - &build
+        make -C build
+    - &unit_test
+        make -C build test ARGS=-V
+    - &integration_test
+        cd test/integration_tests
+        && python3 -m unittest client
+
+.cmake_variables:
+    default_cmake_variables: &default_cmake_variables
+        CC: gcc
+        CXX: g++
+        DEPS_DIR: /home/superfiphoboserver/build/install
+        DEIMOS_DOC_DIR: ""
+        DEIMOS_BUILD_TESTS: "ON"
+        DEIMOS_DISABLE_AUTHORISATION: "OFF"
+
+.default_job: &default_job
+    tags:
+        - docker
+    variables:
+        <<: *default_cmake_variables
+    before_script:
+        - apt-get update
+        - apt-get install -y
+            cmake
+            clang clang-tidy
+            libspdlog-dev
+    script:
+        - *start_phobos
+        - *configure
+        - *build
+        - *unit_test
+        - *integration_test
+
+stages:
+    - static analysis
+    - build
+    - test
+
+Format:
+    <<: *default_job
+    stage: static analysis
+    variables:
+        CC: clang
+        CXX: clang++
+    before_script:
+        - apt-get update
+        - apt-get install -y
+            git
+            clang-format
+        - pip3 install yapf
+    script:
+        - ./tools/run_format.sh
+            && git status
+            && git diff-index --quiet HEAD
+            || { echo "This commit contains unformatted files! Run tools/run_format.sh on the project to format them correctly."; false; }
+
+Lint:
+    <<: *default_job
+    stage: static analysis
+    variables:
+        <<: *default_cmake_variables
+        CC: clang
+        CXX: clang++
+    script:
+        - *configure
+        - *build
+        - ./tools/run_lint.sh build
+
+Documentation:
+    <<: *default_job
+    stage: build 
+    variables:
+        <<: *default_cmake_variables
+        DEIMOS_BUILD_DOCUMENTATION: "ON"
+        DEIMOS_DOC_DIR: /home/superfiphoboserver/external/doxygen-xml-parser/src
+        CC: clang
+        CXX: clang++
+    before_script:
+        - apt-get update
+        - apt-get install -y
+            cmake
+            doxygen
+            graphviz
+            clang
+    script:
+        - *configure
+        - make -C build/doc
+            && git status
+            && git diff-index --quiet HEAD
+            || { echo "This commit contains changes to the documentation! Run doxygen-XML-parser on the project update the documentation."; false; }
+
+
+Default:
+    <<: *default_job
+    stage: test
+
+Authorisation Disabled:
+    <<: *default_job
+    variables:
+        <<: *default_cmake_variables
+        DEIMOS_DISABLE_AUTHORISATION: "ON"
+    stage: test

CMakeLists.txt

+cmake_minimum_required(VERSION 3.0)
+
+project(deimos)
+
+set(CUSTOM_OUTPUT_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
+
+find_package(proxygen REQUIRED)
+
+#
+# Provide options to build or skip building the 
+# programs/libraries in the given subdirectories
+#
+option(
+    DEIMOS_BUILD_TESTS
+    "build Deimos tests. Depends on Catch2."
+    OFF
+)
+option(
+    DEIMOS_BUILD_DOCUMENTATION
+    "build Deimos Documentation. Depends on Doxygen."
+    OFF
+)
+option(
+    DEIMOS_DISABLE_AUTHORISATION
+    "build Deimos with AWS authorisation disabled. Default is enabled"
+    OFF
+)
+
+add_subdirectory(src)
+
+target_include_directories(
+    server SYSTEM PUBLIC
+    $<BUILD_INTERFACE:${CMAKE_CURRENT_LIST_DIR}/include>
+)
+
+if(DEIMOS_BUILD_DOCUMENTATION)
+    add_subdirectory(doc)
+endif(DEIMOS_BUILD_DOCUMENTATION)
+
+# Build tests
+if(DEIMOS_BUILD_TESTS)
+    add_subdirectory(test/unit_tests)
+    enable_testing()
+endif(DEIMOS_BUILD_TESTS)

README.md

+# Deimos
+
+## Dependencies Installation Instructions
+
+Deimos has many dependencies that require much patience to build. It may be simpler to invoke a prebuilt Docker image using a Dockerfile such as;
+
+```
+FROM ciaranorourke/deimos:debian 
+
+RUN apt-get -y update && apt-get -y upgrade
+RUN apt-get -y install doxygen graphviz
+RUN apt-get -y install \
+        [personal installation preferences]
+CMD /home/superdeimos/tools/build_phobos.sh -r && [favourite shell]
+```
+
+Alternatively, see [SuperDeimos](https://git.ichec.ie/oilgas/ltfs/superdeimos) for instructions on how to create your own build environment. 
+
+It is recommended to run this Docker image by mounting your local branch of the Deimos project with `docker run -it -v /path/to/deimos:/destination [name]:[tag]`
+
+To use the Phobos raid1 layout which is compatible with FIFOs, the following environment variables must be set;
+
+```
+export PHOBOS_STORE_layout=raid1
+export PHOBOS_LAYOUT_RAID1_repl_count={1,2,3,...}
+```
+
+## Build Instructions
+
+To configure and build Deimos, a C++14 compatible compiler is required, and CMake >= 3.0.
+
+```
+# Make a directory to hold the temporary build files
+mkdir -p build
+
+# Change directory to the build directory
+cd build
+
+# Configure the Deimos build using CMake
+cmake \
+    -DCMAKE_PREFIX_PATH=/path/to/proxygen \
+    [more options below] \
+    /path/to/deimos/project
+
+# Build the Deimos project
+make
+```
+
+### Build instructions using the superbuild
+
+When using the Docker image from [SuperDeimos](https://git.ichec.ie/oilgas/ltfs/superdeimos), some specific values make life a bit easier:
+* docker image should be run with `/home/superdeimos/external/deimos` as `destination` for the mount option (example: `docker run -it -v ./deimos:/home/superdeimos/external/deimos phobos:debian`).
+* the `CMAKE_PREFIX_PATH` need to be set to `/home/superdeimos/build/install`
+* An example script to build this project can be found inside the container under `/home/superdeimos/tools/build_deimos.sh`.
+
+### Useful Options
+
+#### Setting Compile/Link Flags
+Option | Effect
+------ | ------
+`-DCMAKE_CXX_COMPILER=...` | Set the C++ compiler.
+`-DCMAKE_CXX_FLAGS=...`    | Set the flags to pass to the C++ compiler. Overrides the default flags.
+
+#### Enabling/Disabling Sections of Deimos
+Option | Effect
+------ | ------
+`-DDEIMOS_BUILD_TESTS=...`     | Set to `ON` to build Deimos tests and enable the `make test` target, or `OFF` to skip (Default `OFF`).
+`-DDEIMOS_DISABLE_AUTHORISATION=...`     | Set to `ON` to disable AWS V4 authorisation (= letting everything through), or `OFF` to authorise requests (Default `OFF`). 
+`-DDEIMOS_BUILD_DOCUMENTATION=...`     | Set to `ON` to build Deimos Doxygen documentation, or `OFF` to skip (Default `OFF`). 
+`-DCUSTOM_DOCU_PATH=...`  | Set to the path to the `src` folder in [DoxygenXMLParser](https://git.ichec.ie/sophie.wenzel-teuber/doxygen-xml-parser) to create the Markdown output from the Doxygen XML, that can also be found [here](doc/Markdown/deimos) or don't set to skip (Default `not set`).
+
+## Testing
+
+Units test can be run with `make -C build tests`, given `DEIMOS_BUILD_TESTS` was set to `ON` during the build process.
+Integration tests can be run from the `test/integration_tests/` directory with `python -m unittest client`.
+
+## Documentation
+The Doxygen documentation can be found [here](doc/Markdown/deimos).
+
+## Usage
+
+The `deimos` executable requires exactly one subcommand.
+
+#### Subcommands
+Subcommand | Effect
+---------- | ------
+`start [hostname]` | Start the server daemon, listening to `hostname`.
+`stop`             | Stop the server daemon.
+
+The `start` subcommand supports a number of optional flags and options.
+
+#### Flags/Options
+Flag/Option | Effect
+----------- | ------
+`--http INT`             | Set the port to listen on with HTTP protocol (Default `11000`).
+`--http2 INT`            | Set the port to listen on with HTTP2 protocol (Default `11002`).
+`-t,--threads INT`       | Set the number of threads to listen on, <= 0 will use number of available cores (Default `0`).
+`-w,--write-config TEXT` | Write the configuration to `TEXT`. 
+`-l,--logfile`           | Set the filename to write logs to (Default `/tmp/deimos_log.txt"). 
+
+Options can also be given to the `start` subcommand using `--config [config_filename]`. Note that if `hostname` is specified in the configuration file then the `--config` options must be suppied before the `start` subcommand;
+```
+deimos --config [config_filename] start
+```
+
+### Authentication
+The server uses the [Amazon S3 Authentication](https://docs.aws.amazon.com/AmazonS3/latest/API/sig-v4-authenticating-requests.html) to ensure the requests that are reaching it are from legitimate users.
+
+Since we do not have a proper database for users yet, they are currently stored along with their keys in [users.txt](test/users.txt). This file is copied into the `/tmp` folder by CMake and then read from there for authentication.
+
+Since the authentication is checked for every request, you need to use one of the users and keys from that file for testing the server!
+
+One possible way most SDKs use automatically is the file `~/.aws/credentials`. The tests for the server are done with a file like this:
+
+```
+[default] 
+aws_access_key_id = OPEN_KEY 
+aws_secret_access_key = SECRET_KEY
+```

doc/CMakeLists.txt

+find_package(Doxygen REQUIRED)
+
+# Write a Doxyfile including the main doc/Doxyfile.
+# This sets the @INCLUDE_PATH variable to the project root.
+configure_file(
+    ${CMAKE_CURRENT_SOURCE_DIR}/Doxyfile.in
+    ${CMAKE_CURRENT_BINARY_DIR}/Doxyfile
+    @ONLY
+)
+
+set(INCLUDE_DOXYFILE "@INCLUDE = ${CMAKE_CURRENT_BINARY_DIR}/Doxyfile")
+
+# Custom command to run doxygen on build/doc/Doxyfile in the build/doc dir.
+# Running doxygen is tied to the html/index.html file.
+# TODO: The main dependency is currently doc/Doxyfile, but there should be
+#       a depencency on *every* file being documented!
+add_custom_command(
+    OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/xml/index.xml
+    COMMAND ${DOXYGEN_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/Doxyfile"
+    MAIN_DEPENDENCY ${CMAKE_CURRENT_SOURCE_DIR}/Doxyfile.in
+    WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+    COMMENT "Building the documentation..."
+)
+
+if(CUSTOM_DOCU_PATH)
+    add_custom_command(
+        OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/docu.json
+        COMMAND python3
+        ARGS "${CUSTOM_DOCU_PATH}/xml_to_json_parser/xml_to_json_parser.py" "${CMAKE_CURRENT_BINARY_DIR}/xml" docu.json
+        MAIN_DEPENDENCY ${CMAKE_CURRENT_BINARY_DIR}/xml/index.xml
+        WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+        COMMENT "Parsing the documentation XML..."
+    )
+    add_custom_command(
+        OUTPUT ${CMAKE_CURRENT_SOURCE_DIR}/Markdown/index.md
+        COMMAND python3
+        ARGS "${CUSTOM_DOCU_PATH}/json_to_Markdown_converter/json_to_Markdown_converter.py" docu.json "${CMAKE_CURRENT_SOURCE_DIR}/Markdown"
+        MAIN_DEPENDENCY ${CMAKE_CURRENT_BINARY_DIR}/docu.json
+        WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+        COMMENT "Creating the Markdown documentation..."
+    )
+    # Target to wire up building the documentation to the ALL target.
+    add_custom_target(
+        doc ALL
+        DEPENDS
+            ${CMAKE_CURRENT_SOURCE_DIR}/Markdown/index.md
+    )
+else(CUSTOM_DOCU_PATH)
+    # Target to wire up building the documentation to the ALL target.
+    add_custom_target(
+        doc ALL
+        DEPENDS
+            ${CMAKE_CURRENT_BINARY_DIR}/xml/index.xml
+    )
+
+endif(CUSTOM_DOCU_PATH)
+
+

doc/Doxyfile.in

+# Doxyfile 1.8.13
+
+#
+# This is a template file used for configuration in doc/CMakeLists.txt.
+#
+
+PROJECT_NAME           = Deimos
+
+# Extraction options
+EXTRACT_PRIVATE        = YES
+EXTRACT_PACKAGE        = YES
+EXTRACT_STATIC         = YES
+EXTRACT_LOCAL_METHODS  = YES
+EXTRACT_ANON_NSPACES   = YES
+EXCLUDE_SYMBOLS        = detail
+
+# Generate case sensitive filenames
+CASE_SENSE_NAMES       = YES
+
+# Warning options
+# Warn on everything possible, and fail on warning
+QUIET                  = YES
+WARNINGS               = YES
+WARN_IF_UNDOCUMENTED   = NO
+WARN_IF_DOC_ERROR      = YES
+WARN_NO_PARAMDOC       = YES
+WARN_AS_ERROR          = YES
+
+# Input directories
+INPUT                  = @CMAKE_SOURCE_DIR@/src
+
+EXCLUDE			= @CMAKE_SOURCE_DIR@/src/main.cc
+EXCLUDE_PATTERNS	= */phobos_cpp_wrapper/*
+
+RECURSIVE              = YES
+
+# HTML output options
+GENERATE_HTML          = YES
+HTML_OUTPUT            = html
+HTML_FILE_EXTENSION    = .html
+GENERATE_TREEVIEW      = YES
+
+# Latex font size
+FORMULA_FONTSIZE       = 10
+
+# Macro options
+ENABLE_PREPROCESSING   = YES
+MACRO_EXPANSION        = YES
+PREDEFINED             = __cplusplus
+SEARCH_INCLUDES        = YES
+
+GENERATE_XML           = YES

doc/Markdown/deimos/DeimosException.md

+# <a name='deimos-DeimosException' /> public deimos::DeimosException
+
+exception class for all user defined exceptions in Deimos 
+
+
+
+
+## Inheritance:
+Is inherited by [deimos::IOException][deimos-IOException], [deimos::storage::PhobosException][deimos-storage-PhobosException].
+
+## Protected Attributes
+| Name | Description | 
+| ---- | ---- |
+| [m_message](#deimos-DeimosException-m_message) | the internal message  |
+
+
+## Public Functions
+| Name | Description | 
+| ---- | ---- |
+| [DeimosException](#deimos-DeimosException-DeimosException) | default constructor  |
+| [DeimosException](#deimos-DeimosException-DeimosException-1) | constructor for a message with information on the exception  |
+| [what](#deimos-DeimosException-what) | get information on this exception  |
+| [get_inner_error](#deimos-DeimosException-get_inner_error) | return the inner error value that caused this exception  |
+
+
+
+## Protected Attributes
+### <a name='deimos-DeimosException-m_message' /> protected deimos::DeimosException::m_message 
+
+the internal message 
+
+
+
+
+
+
+
+
+[Go to Top](#deimos-DeimosException)
+