Merge pull request #139 from nmfs-opensci/eeholmes-patch-1

Update install-r-package.sh
nmfs-opensci · Nov 4, 2024 · 24af2c9 · 24af2c9
2 parents b6145bd + 760199a
commit 24af2c9
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Showing 9 changed files with 202 additions and 78 deletions.
diff --git a/appendix b/appendix
@@ -1,5 +1,8 @@
 USER root
 
+# Clean up extra files in ${REPO_DIR}
+RUN rm -rf ${REPO_DIR}/book ${REPO_DIR}/docs
+
 # repo2docker does not set this. This is the default env in repo2docker type images
 ENV CONDA_ENV=notebook
 # Tell applications where to open desktop apps - this allows notebooks to pop open GUIs
@@ -38,9 +41,6 @@ RUN mandb
 RUN cp ${REPO_DIR}/custom_jupyter_server_config.json ${NB_PYTHON_PREFIX}/etc/jupyter/jupyter_server_config.d/
 RUN cp ${REPO_DIR}/custom_jupyter_server_config.json ${NB_PYTHON_PREFIX}/etc/jupyter/jupyter_notebook_config.d/
 
-# Clean up extra files in ${REPO_DIR}
-RUN rm -rf ${REPO_DIR}/book ${REPO_DIR}/docs
-
 # Copy scripts into /pyrocket_scripts directory in the image
 RUN mkdir -p /pyrocket_scripts && cp -r ${REPO_DIR}/scripts /pyrocket_scripts
 
@@ -51,6 +51,9 @@ RUN chown -R root:root /pyrocket_scripts && \
 # Convert NB_USER to ENV (from ARG) so that it passes to the child dockerfile
 ENV NB_USER=${NB_USER}
 
+# Copy the child repo files into childimage so they are available to scripts
+ONBUILD COPY --chown=${NB_USER}:${NB_USER} . ${REPO_DIR}/childimage
+
 # Revert to default user and home as pwd
 USER ${NB_USER}
 WORKDIR ${HOME}
diff --git a/scripts/copy-files.sh b/scripts/copy-files.sh
diff --git a/scripts/install-apt-packages.sh b/scripts/install-apt-packages.sh
@@ -1,13 +1,30 @@
 #!/bin/bash
-/scripts/copy-files.sh
-
-echo "Checking for apt.txt..."
-cd "${REPO_DIR}/childimage/" || exit 1
-if test -f "apt.txt"; then
-    package_list=$(grep -v '^\s*#' apt.txt | grep -v '^\s*$' | sed 's/\r//g; s/#.*//; s/^[[:space:]]*//; s/[[:space:]]*$//' | awk '{$1=$1};1')
-    apt-get update --fix-missing > /dev/null
-    apt-get install --yes --no-install-recommends $package_list
-    apt-get autoremove --purge
-    apt-get clean
-    rm -rf /var/lib/apt/lists/*
+# Required User: root
+
+echo "Running install-apt-packages.sh"
+echo "  Checking for ${REPO_DIR}/childimage/..."
+if [ -d "${REPO_DIR}/childimage/" ]; then
+    cd "${REPO_DIR}/childimage/" || exit 1
+
+    echo "  Checking for apt.txt in ${REPO_DIR}/childimage/..."
+    if test -f "apt.txt"; then
+        # Check if the script is run as root
+        if [[ $(id -u) -ne 0 ]]; then
+            echo "  Error: This script must be run as root." >&2  # Output error message to standard error
+            exit 1  # Exit with a non-zero status to indicate failure
+        fi
+
+        echo "  Running install-apt-packages.sh as root. Proceeding with installation..."
+
+        package_list=$(grep -v '^\s*#' apt.txt | grep -v '^\s*$' | sed 's/\r//g; s/#.*//; s/^[[:space:]]*//; s/[[:space:]]*$//' | awk '{$1=$1};1')
+        apt-get update --fix-missing > /dev/null
+        apt-get install --yes --no-install-recommends $package_list
+        apt-get autoremove --purge
+        apt-get clean
+        rm -rf /var/lib/apt/lists/*
+    else
+        echo "  No apt.txt found. Skipping package installation."
+    fi
+else
+    echo "  Directory ${REPO_DIR}/childimage/ does not exist. Skipping script."
 fi
diff --git a/scripts/install-conda-packages.sh b/scripts/install-conda-packages.sh
@@ -1,20 +1,44 @@
 #!/bin/bash
-/scripts/copy-files.sh
+# Required User: NB_USER
 
-echo "Checking for conda-lock.yml or environment.yml..."
-cd "${REPO_DIR}/childimage/" || exit 1
-if test -f "conda-lock.yml"; then
-    echo "Using conda-lock.yml"
-    conda-lock install --name ${CONDA_ENV}
-    pip install --no-deps jupyter-remote-desktop-proxy
-elif test -f "environment.yml"; then
-    echo "Using environment.yml"
-    mamba env update --name ${CONDA_ENV} -f environment.yml
-    pip install --no-deps jupyter-remote-desktop-proxy
-fi
-mamba clean -yaf
-find ${CONDA_DIR} -follow -type f -name '*.a' -delete
-find ${CONDA_DIR} -follow -type f -name '*.js.map' -delete
-if ls ${NB_PYTHON_PREFIX}/lib/python*/site-packages/bokeh/server/static > /dev/null 2>&1; then
-    find ${NB_PYTHON_PREFIX}/lib/python*/site-packages/bokeh/server/static -follow -type f -name '*.js' ! -name '*.min.js' -delete
+echo "Running install-conda-packages.sh"
+
+echo "  Checking for ${REPO_DIR}/childimage/..."
+if [ -d "${REPO_DIR}/childimage/" ]; then
+    cd "${REPO_DIR}/childimage/" || exit 1
+
+    echo "  Checking for conda-lock.yml or environment.yml in ${REPO_DIR}/childimage/..."
+    if test -f "conda-lock.yml" || test -f "environment.yml"; then
+        # Switch to NB_USER only if the relevant files exist
+        if [[ $(id -u) -eq 0 ]]; then
+            echo "  Switching to ${NB_USER} to run install-conda-packages.sh"
+            exec su "${NB_USER}" -c "/bin/bash $0"  # Switches to NB_USER and reruns the script
+        fi
+
+        if test -f "conda-lock.yml"; then
+            echo "  Using conda-lock.yml"
+            conda-lock install --name ${CONDA_ENV}
+            pip install --no-deps jupyter-remote-desktop-proxy
+            INSTALLATION_HAPPENED=true
+        elif test -f "environment.yml"; then
+            echo "  Using environment.yml"
+            mamba env update --name ${CONDA_ENV} -f environment.yml
+            pip install --no-deps jupyter-remote-desktop-proxy
+            INSTALLATION_HAPPENED=true
+        fi
+
+        # Only run cleanup if installation occurred
+        if [ "$INSTALLATION_HAPPENED" = true ]; then
+            mamba clean -yaf
+            find ${CONDA_DIR} -follow -type f -name '*.a' -delete
+            find ${CONDA_DIR} -follow -type f -name '*.js.map' -delete
+            if ls ${NB_PYTHON_PREFIX}/lib/python*/site-packages/bokeh/server/static > /dev/null 2>&1; then
+                find ${NB_PYTHON_PREFIX}/lib/python*/site-packages/bokeh/server/static -follow -type f -name '*.js' ! -name '*.min.js' -delete
+            fi
+        fi
+    else
+        echo "  No conda-lock.yml or environment.yml found. Skipping installation."
+    fi
+else
+    echo "  Directory ${REPO_DIR}/childimage/ does not exist. Skipping script."
 fi
diff --git a/scripts/install-pip-packages.sh b/scripts/install-pip-packages.sh
@@ -1,8 +1,25 @@
 #!/bin/bash
-/scripts/copy-files.sh
+# Required User: NB_USER
 
-echo "Checking for pip requirements.txt..."
-cd "${REPO_DIR}/childimage/" || exit 1
-if test -f "requirements.txt"; then
-    ${NB_PYTHON_PREFIX}/bin/pip install --no-cache -r requirements.txt
+echo "Running install-pip-packages.sh"
+
+echo "  Checking for ${REPO_DIR}/childimage/..."
+if [ -d "${REPO_DIR}/childimage/" ]; then
+    cd "${REPO_DIR}/childimage/" || exit 1
+
+    echo "  Checking for requirements.txt in ${REPO_DIR}/childimage/..."
+    if test -f "requirements.txt"; then
+        # Switch to NB_USER only if requirements.txt exists
+        if [[ $(id -u) -eq 0 ]]; then
+            echo "Switching to ${NB_USER} to run install-pip-packages.sh"
+            exec su "${NB_USER}" -c "/bin/bash $0"  # Switches to NB_USER and reruns the script
+        fi
+
+        echo "  Installing pip packages from requirements.txt as ${NB_USER}..."
+        ${NB_PYTHON_PREFIX}/bin/pip install --no-cache -r requirements.txt
+    else
+        echo "  No requirements.txt found. Skipping pip installation."
+    fi
+else
+    echo "  Directory ${REPO_DIR}/childimage/ does not exist. Skipping script."
 fi
diff --git a/scripts/install-r-package.sh b/scripts/install-r-package.sh
@@ -1,9 +1,25 @@
 #!/bin/bash
-/scripts/copy-files.sh
+# Required User: NB_USER
 
-echo "Checking for install.R..."
-cd "${REPO_DIR}/childimage/" || exit 1
-if test -f "install.R"; then
-    echo "Using install.R"
-    Rscript install.R
+echo "Running install-r-packages.sh"
+
+echo "  Checking for ${REPO_DIR}/childimage/..."
+if [ -d "${REPO_DIR}/childimage/" ]; then
+    cd "${REPO_DIR}/childimage/" || exit 1
+
+    echo "  Checking for install.R in ${REPO_DIR}/childimage/..."
+    if test -f "install.R"; then
+        # Switch to NB_USER only if install.R exists
+        if [[ $(id -u) -eq 0 ]]; then
+            echo "Switching to ${NB_USER} to run install-r-packages.sh"
+            exec su "${NB_USER}" -c "/bin/bash $0"  # Switches to NB_USER and reruns the script
+        fi
+
+        echo "  Using install.R to install R packages as ${NB_USER}..."
+        Rscript install.R
+    else
+        echo "  No install.R found. Skipping R package installation."
+    fi
+else
+    echo "  Directory ${REPO_DIR}/childimage/ does not exist. Skipping script."
 fi
diff --git a/scripts/run-postbuild.sh b/scripts/run-postbuild.sh
@@ -1,14 +1,30 @@
 #!/bin/bash
-/scripts/copy-files.sh
-
-echo "Checking for postBuild..."
-cd "${REPO_DIR}/childimage/" || exit 1
-if test -f "postBuild"; then
-    chmod +x postBuild
-    ./postBuild
-    rm -rf /tmp/*
-    rm -rf ${HOME}/.cache ${HOME}/.npm ${HOME}/.yarn
-    rm -rf ${NB_PYTHON_PREFIX}/share/jupyter/lab/staging
-    find ${CONDA_DIR} -follow -type f -name '*.a' -delete
-    find ${CONDA_DIR} -follow -type f -name '*.js.map' -delete
+
+echo "Running run-postbuild.sh"
+
+echo "  Checking for ${REPO_DIR}/childimage/..."
+if [ -d "${REPO_DIR}/childimage/" ]; then
+    cd "${REPO_DIR}/childimage/" || exit 1
+
+    echo "  Checking for postBuild..."
+    if test -f "postBuild"; then
+        # Check the user and output which user the script is running as
+        if [[ $(id -u) -eq 0 ]]; then
+            echo "  Running run-postbuild.sh as root."
+        else
+            echo "  Running run-postbuild.sh as ${NB_USER}."
+        fi
+
+        chmod +x postBuild
+        ./postBuild
+        rm -rf /tmp/*
+        rm -rf ${HOME}/.cache ${HOME}/.npm ${HOME}/.yarn
+        rm -rf ${NB_PYTHON_PREFIX}/share/jupyter/lab/staging
+        find ${CONDA_DIR} -follow -type f -name '*.a' -delete
+        find ${CONDA_DIR} -follow -type f -name '*.js.map' -delete
+    else
+        echo "  No postBuild file found. Skipping execution."
+    fi
+else
+    echo "  Directory ${REPO_DIR}/childimage/ does not exist. Skipping script."
 fi
diff --git a/scripts/setup-desktop.sh b/scripts/setup-desktop.sh
@@ -1,12 +1,36 @@
 #!/bin/bash
-# Ensure files are copied before proceeding
-/scripts/copy-files.sh
-
-echo "Checking for Desktop directory..."
-cd "${REPO_DIR}/childimage/" || exit 1
-if test -d Desktop; then
-    mkdir -p "${REPO_DIR}/Desktop"
-    cp -r Desktop/* "${REPO_DIR}/Desktop/" 2>/dev/null
-    chmod +x "${REPO_DIR}/desktop.sh"
-    "${REPO_DIR}/desktop.sh"
+# Required User: root
+
+echo "Running setup-desktop.sh"
+
+echo "  Checking for ${REPO_DIR}/childimage/..."
+if [ -d "${REPO_DIR}/childimage/" ]; then
+    cd "${REPO_DIR}/childimage/" || exit 1
+
+    echo "  Checking for Desktop directory..."
+    if test -d "${REPO_DIR}/childimage/Desktop"; then
+        # Check if the script is run as root
+        if [[ $(id -u) -ne 0 ]]; then
+            echo "  Error: This script must be run as root." >&2  # Output error message to standard error
+            exit 1  # Exit with a non-zero status to indicate failure
+        fi
+
+        echo "  Running setup-desktop.sh as root. Proceeding with installation..."
+
+        mkdir -p "${REPO_DIR}/Desktop"
+        cp -r ${REPO_DIR}/childimage/Desktop/* "${REPO_DIR}/Desktop/" 2>/dev/null
+
+        # Check if desktop.sh exists before executing
+        if test -f "${REPO_DIR}/desktop.sh"; then
+            echo "  Running ${REPO_DIR}/desktop.sh."
+            chmod +x "${REPO_DIR}/desktop.sh"
+            "${REPO_DIR}/desktop.sh"
+        else
+            echo "  Warning: desktop.sh not found. Skipping execution."
+        fi
+    else
+        echo "  No Desktop directory found in ${REPO_DIR}/childimage/. Skipping setup."
+    fi
+else
+    echo "  Directory ${REPO_DIR}/childimage/ does not exist. Skipping script."
 fi
diff --git a/scripts/setup-start.sh b/scripts/setup-start.sh
@@ -1,8 +1,24 @@
 #!/bin/bash
-/scripts/copy-files.sh
+# Required User: NB_USER
 
-echo "Checking for start..."
-cd "${REPO_DIR}/childimage/" || exit 1
-if test -f "start"; then
-    chmod +x start
+echo "Running setup-start.sh"
+
+echo "  Checking for ${REPO_DIR}/childimage/..."
+if [ -d "${REPO_DIR}/childimage/" ]; then
+    cd "${REPO_DIR}/childimage/" || exit 1
+
+    echo "  Checking for start in ${REPO_DIR}/childimage/..."
+    if test -f "start"; then
+        echo "  start found in ${REPO_DIR}/childimage/."
+        # Switch to NB_USER only if the start file exists
+        if [[ $(id -u) -eq 0 ]]; then
+            echo "  Switching to ${NB_USER} to run setup-start.sh"
+            exec su "${NB_USER}" -c "/bin/bash $0"  # Switches to NB_USER and reruns the script
+        fi
+        chmod +x start
+    else
+        echo "  No start file found in ${REPO_DIR}/childimage/. Skipping."
+    fi
+else
+    echo "  Directory ${REPO_DIR}/childimage/ does not exist. Skipping."
 fi