update documentation

Author: rchau88

.Rbuildignore

@@ -1,8 +1,33 @@
-**/.git
-**/.gitignore
+# ignore file extensions
+*.DS_Store
 *.Rmd
 *.html
 *.md
 *.Rhistory
+*.gitignore
+*.Rbuildignore
+*.Rproj
+
+# ignore folders
+**.git
+**.github
+**.Rproj.user
 *docs
-docker.compose.yml
+*vignettes
+*man
+*docker
+*inst
+*data
+*pkgdown
+
+# ignore specific files
+change_log.txt
+MIRA-INSTALL.sh
+install_docker.sh
+docker-compose.yml
+docker-compose-*.yml
+_pkgdown.yml
+MIRA-INSTALL.sh
+MIRA.code-workspace
+NAMESPACE
+

.dockerignore

@@ -14,10 +14,11 @@ scripts/__pycache__/muscle.cpython-37.pyc
 *.Rhistory
 *.Rbuildignore
 *.Rproj
-vignettes/*.html
+*.Rproj.user
 
 # ignore folders
 **/.Rproj.user
 
-
-.Rproj.user
+# ignore specific files
+change_log.txt
+docker-compose-dev.yml

.gitignore

@@ -1,117 +1,82 @@
-
-# Create a build argument
-ARG BUILD_STAGE
-ARG BUILD_STAGE=${BUILD_STAGE:-prod}
-
-############# Build Stage: Dependencies ##################
-
-# Start from a base image
-FROM --platform=linux/amd64 ubuntu:focal as base
-
-# Define a system argument
-ARG DEBIAN_FRONTEND=noninteractive
-
-# Install system libraries of general use
-RUN apt-get update --allow-releaseinfo-change && apt-get install --no-install-recommends -y \
-    build-essential \ 
-    iptables \
-    libdevmapper1.02.1 \
-    python3.7\
-    python3-pip \
-    python3-setuptools \
-    python3-dev \
-    dpkg \
-    sudo \
-    wget \
-    curl \
-    dos2unix
-
-############# Build Stage: Development ##################
-
-# Build from the base image for dev
-FROM base as dev
-
-# Create working directory variable
-ENV WORKDIR=/data
-
-# Create a stage enviroment
-ENV STAGE=dev
-
-############# Build Stage: Production ##################
-
-# Build from the base image for prod
-FROM base as prod
-
-# Create working directory variable
-ENV WORKDIR=/data
-
-# Create a stage enviroment
-ENV STAGE=prod
-
-# Copy all scripts to docker images
-COPY . /MIRA
-
-############# Build Stage: Final ##################
-
-# Build the final image 
-FROM ${BUILD_STAGE} as final
-
-# Set up volume directory in docker
-VOLUME ${WORKDIR}
-
-# Set up working directory in docker
-WORKDIR ${WORKDIR}
-
-# Allow permission to read and write files to current working directory
-RUN chmod -R a+rwx ${WORKDIR}
-
-############# Install Docker ##################
-
-# Copy all files to docker images
-COPY docker /MIRA/docker
-
-# Copy all files to docker images
-COPY install_docker.sh /MIRA/install_docker.sh
-
-# Convert bash script from Windows style line endings to Unix-like control characters
-RUN dos2unix /MIRA/install_docker.sh
-
-# Allow permission to excute the bash script
-RUN chmod a+x /MIRA/install_docker.sh
-
-# Execute bash script to install the package
-RUN bash /MIRA/install_docker.sh
-
-############# Install python packages ##################
-
-# Copy python requirements file to docker images
-COPY requirements.txt /MIRA/requirements.txt
-
-# Install python requirements
-RUN pip3 install --no-cache-dir -r /MIRA/requirements.txt
-
-############# Launch MIRA dashboard ##################
-
-# Copy all files to docker images
-COPY dashboard-kickoff /MIRA/dashboard-kickoff
-
-# Convert bash script from Windows style line endings to Unix-like control characters
-RUN dos2unix /MIRA/dashboard-kickoff
-
-# Allow permission to excute the bash scripts
-RUN chmod a+x /MIRA/dashboard-kickoff
-
-# Allow permission to read and write files to MIRA directory
-RUN chmod -R a+rwx /MIRA
-
-# Make the app available at port 8050
-EXPOSE 8050
-
-# Clean up
-RUN apt-get autoremove -y && apt-get clean -y && rm -rf /var/lib/apt/lists/*
-
-# Export bash script to path
-ENV PATH "$PATH:/MIRA"
-
-# Execute the pipeline 
-ENTRYPOINT ["bash", "dashboard-kickoff"]
+# Create an argument to pull a particular version of dias image
+ARG spyne_image
+ARG spyne_image=${spyne_image:-cdcgov/spyne:latest}
+
+############# spyne image as base ##################
+FROM ${spyne_image} as spyne
+RUN echo "Getting spyne image"
+
+# local apt mirror support
+# start every stage with updated apt sources
+ARG APT_MIRROR_NAME=
+RUN if [ -n "$APT_MIRROR_NAME" ]; then sed -i.bak -E '/security/! s^https?://.+?/(debian|ubuntu)^http://'"$APT_MIRROR_NAME"'/\1^' /etc/apt/sources.list && grep '^deb' /etc/apt/sources.list; fi
+
+# Install and update system libraries of general use
+RUN apt-get update --allow-releaseinfo-change --fix-missing \
+  && apt-get install --no-install-recommends -y \
+  build-essential \ 
+  iptables \
+  python3.7 \
+  python3-pip \
+  python3-setuptools \
+  dos2unix
+
+# Create a working directory variable
+ENV WORKDIR=/data
+
+# Set up volume directory 
+VOLUME ${WORKDIR}
+
+# Set up working directory 
+WORKDIR ${WORKDIR}
+
+# Create a program variable
+ENV MIRA_PROGRAM_DIR=/MIRA
+
+# Set up volume directory 
+VOLUME ${MIRA_PROGRAM_DIR}
+
+# Copy all scripts to docker images
+COPY . ${MIRA_PROGRAM_DIR}
+
+############# Install python packages ##################
+
+# Copy python requirements file to docker images
+COPY requirements.txt ${MIRA_PROGRAM_DIR}/requirements.txt
+
+# Install python requirements
+RUN pip3 install --no-cache-dir -r ${MIRA_PROGRAM_DIR}/requirements.txt
+
+############# Launch MIRA dashboard ##################
+
+# Copy all files to docker images
+COPY dashboard-kickoff ${MIRA_PROGRAM_DIR}/dashboard-kickoff
+
+# Convert bash script from Windows style line endings to Unix-like control characters
+RUN dos2unix ${MIRA_PROGRAM_DIR}/dashboard-kickoff
+
+# Allow permission to excute the bash scripts
+RUN chmod a+x ${MIRA_PROGRAM_DIR}/dashboard-kickoff
+
+# Allow permission to read and write files to MIRA directory
+RUN chmod -R a+rwx ${MIRA_PROGRAM_DIR}
+
+# Make the app available at port 8050
+EXPOSE 8050
+
+# Clean up and remove unwanted files
+RUN apt-get autoremove -y \
+  && apt-get clean -y \
+  && rm -rf /var/lib/{apt,dpkg,cache,log}/
+
+# Export dais-ribosome script to path
+ENV PATH "$PATH:/dais-ribosome"
+
+# Export irma script to path
+ENV PATH "$PATH:/flu-amd"
+
+# Export spyne script to path
+ENV PATH "$PATH:/spyne"
+
+# Execute the pipeline 
+ENTRYPOINT ["/bin/bash", "-c", "/MIRA/dashboard-kickoff"]