Unverified Commit 41043319 authored by Christine Kim's avatar Christine Kim Committed by GitHub
Browse files

Dockerize FastAPI (#35) 



* wip docker

* added AWS stuff

* reduce service to q

* some changes

* some fixes and updates

* garbage

* Add forward slash

* Update Dockerfile

* moved things around

* Add kernels key

* Update accessing kernelset

* Bug fixes

* Add trycatch

* fix dockerfile typo

* add filter

* some test fixes

* update test kernel paths

* possible test fix

* working tests + inventory upgrades

* added highfive

---------

Co-authored-by: default avatarKelvin <krodriguez@usgs.gov>
Co-authored-by: default avataracpaquette <acpaquette@usgs.gov>
parent 57f802a5

CMakeLists.txt

+5 −9
Original line number Diff line number Diff line
@@ -46,9 +46,7 @@ option (SPICEQL_BUILD_LIB "Build the SpiceQL Library" ON) 
if(SPICEQL_BUILD_LIB)



  set(JSON_BuildTests OFF CACHE INTERNAL "")

  set(REDIS_PLUS_PLUS_BUILD_TEST OFF CACHE INTERNAL "")



  add_subdirectory("submodules/redis-plus-plus")

  add_subdirectory("submodules/gularkfilesystem")

  add_subdirectory("submodules/json")
@@ -56,7 +54,7 @@ if(SPICEQL_BUILD_LIB) 
  find_package(fmt REQUIRED)

  find_package(cereal REQUIRED)

  find_package(spdlog REQUIRED)

  find_package(hiredis REQUIRED)

  find_package(HighFive REQUIRED)



  set(SPICEQL_INSTALL_INCLUDE_DIR "include/SpiceQL")

  set(SPICEQL_SRC_FILES   ${CMAKE_CURRENT_SOURCE_DIR}/SpiceQL/src/spiceql.cpp
@@ -67,7 +65,7 @@ if(SPICEQL_BUILD_LIB) 
                          ${CMAKE_CURRENT_SOURCE_DIR}/SpiceQL/src/memoized_functions.cpp

                          ${CMAKE_CURRENT_SOURCE_DIR}/SpiceQL/src/config.cpp

                          ${CMAKE_CURRENT_SOURCE_DIR}/SpiceQL/src/inventory.cpp

                          ${CMAKE_CURRENT_SOURCE_DIR}/SpiceQL/src/database.cpp)

                          ${CMAKE_CURRENT_SOURCE_DIR}/SpiceQL/src/inventoryimpl.cpp)





  set(SPICEQL_HEADER_FILES ${SPICEQL_BUILD_INCLUDE_DIR}/spiceql.h
@@ -78,7 +76,7 @@ if(SPICEQL_BUILD_LIB) 
                           ${SPICEQL_BUILD_INCLUDE_DIR}/query.h

                           ${SPICEQL_BUILD_INCLUDE_DIR}/config.h

                           ${SPICEQL_BUILD_INCLUDE_DIR}/inventory.h

                           ${SPICEQL_BUILD_INCLUDE_DIR}/database.h)

                           ${SPICEQL_BUILD_INCLUDE_DIR}/inventoryimpl.h)



  set(SPICEQL_PRIVATE_HEADER_FILES ${SPICEQL_BUILD_INCLUDE_DIR}/memo.h)
@@ -121,14 +119,12 @@ if(SPICEQL_BUILD_LIB) 
  target_compile_definitions(SpiceQL PRIVATE SPDLOG_ACTIVE_LEVEL=SPDLOG_LEVEL_TRACE 

                                     PUBLIC -D_SOURCE_PREFIX="${CMAKE_CURRENT_SOURCE_DIR}")

  

  message(STATUS "redis++ inc: "  ${HIREDIS_INCLUDE_DIRS})

target_include_directories(SpiceQL

                            PUBLIC

                            $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/SpiceQL/include>

                            $<INSTALL_INTERFACE:include>

                            PRIVATE

                            ${CMAKE_CURRENT_SOURCE_DIR}/submodules/BTree/include/

                            ${CMAKE_CURRENT_SOURCE_DIR}/submodules/redis-plus-plus/src/

                            cereal

                            )
@@ -137,9 +133,9 @@ if(SPICEQL_BUILD_LIB) 
                        fmt::fmt-header-only

                        nlohmann_json::nlohmann_json

                        PRIVATE

                        redis++ 

                        cspice

                        spdlog::spdlog_header_only

                        HighFive

                        )

   

  install(TARGETS SpiceQL LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR})

Dockerfile

0 → 100644
+54 −0
Original line number Diff line number Diff line 
FROM condaforge/miniforge3



SHELL ["/bin/bash", "-c"]



# Clone SpiceQL repo instead of copying?

#git clone git@github.com:DOI-USGS/SpiceQL.git /repo



# RUN git clone https://github.com/chkim-usgs/SpiceQL.git /repo --recursive --branch docker

# RUN echo $(ls /repo)

# RUN chmod -R 755 /repo



RUN apt-get update && apt-get install build-essential -y



ARG DEBIAN_FRONTEND=noninteractive

RUN apt-get update

RUN apt-get install nginx curl -y 

COPY fastapi/config/nginx.conf /etc/nginx/nginx.conf



# CMD ["/bin/bash"]

# RUN /bin/bash -c "source activate spiceql"



 RUN mkdir /repo    

 COPY . /repo

 RUN echo $(ls /repo)

 RUN chmod -R 755 /repo



# Set repo root env

ENV SPICEQL_REPO_ROOT /repo



RUN mamba env create -f ${SPICEQL_REPO_ROOT}/environment.yml -n spiceql && \

    source /opt/conda/etc/profile.d/conda.sh && \

    conda init && \

    conda activate spiceql && \

    # conda install -c conda-forge spiceql && \

    echo "source activate spiceql" > ~/.bashrc && \ 

    conda activate spiceql && \ 

    cd $SPICEQL_REPO_ROOT && mkdir -p build && cd build && \ 

    cmake .. -DCMAKE_BUILD_TYPE=Release DCMAKE_INSTALL_PREFIX=$CONDA_PREFIX -DSPICEQL_BUILD_TESTS=OFF -DSPICEQL_BUILD_DOCS=OFF -GNinja && \ 

    ninja install 



RUN cd ${SPICEQL_REPO_ROOT}/fastapi

ENV PATH /opt/conda/envs/spiceql/bin:$PATH





WORKDIR ${SPICEQL_REPO_ROOT}/fastapi



EXPOSE 8080



COPY Entrypoint.sh /

RUN chmod +x /Entrypoint.sh



RUN mkdir /mnt/isisdata/



ENTRYPOINT ["/bin/bash", "/Entrypoint.sh"]

SpiceQL/db/apollo16.json

+3 −1
Original line number Diff line number Diff line
@@ -40,7 +40,9 @@ 
      "iak": {

        "kernels": "apollo16MetricAddendum[0-9]{3}.ti"

      },

      "deps" : ["/apollo16"]

      "pck" : { 

        "deps" : ["/base/pck"]

      }

    },

    "panoramic": {

      "ik": {

SpiceQL/db/smart1.json

+1 −2
Original line number Diff line number Diff line
@@ -15,8 +15,7 @@ 
            "kernels": ["naif[0-9]{4}.tls$"]

        },

        "pck": {

            "kernels": ["PCK[0-9]{5}.TPC$"],

            "deps" : ["/base/pck"]

            "kernels": ["pck0000[0-9].tpc", "PCK[0-9]{5}.TPC$"]

        },

        "sclk": {

            "kernels": ["SMART1_[0-9]{6}_STEP.TSC$"]

SpiceQL/db/voyager1.json

+3 −3
Original line number Diff line number Diff line
@@ -21,7 +21,8 @@ 
            "kernels": ["naif0009.tls$"]

        },

        "pck": {

            "kernels": ["pck00010_msgr_v23_europa2020.tpc$"]

            "kernels": ["pck00010_msgr_v23_europa2020.tpc$"],

            "deps" : ["/base/pck"]

        },

        "sclk": {

            "kernels": ["vg1[0-9]{5}.tsc$"]
@@ -30,7 +31,6 @@ 
            "reconstructed": {

                "kernels": ["vg1_sat.bsp$", "vg1_jup.bsp$", "vg1_[a-z]{3}_version[0-9]{1}_type[0-9]{1}_iss_sedr.bc$","vgr1_jup230.bsp$", "vgr1_sat336.bsp$"]

            }

        },

        "deps" : ["/base/pck"]

        }

    }

}
 
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