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Merge pull request #142 from nmfs-opensci/eeholmes-patch-1
switch user at start of script
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,44 +1,59 @@ | ||
| #!/bin/bash | ||
| # Required User: NB_USER | ||
|
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| echo "Running install-conda-packages.sh" | ||
|
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| echo " Checking for ${REPO_DIR}/childimage/..." | ||
| if [ -d "${REPO_DIR}/childimage/" ]; then | ||
| cd "${REPO_DIR}/childimage/" || exit 1 | ||
|
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||
| 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 | ||
|
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||
| if test -f "conda-lock.yml"; then | ||
| echo " Using conda-lock.yml" | ||
| ${NB_PYTHON_PREFIX}/bin/conda-lock install --name ${CONDA_ENV} | ||
| ${NB_PYTHON_PREFIX}/bin/pip install --no-deps jupyter-remote-desktop-proxy | ||
| INSTALLATION_HAPPENED=true | ||
| elif test -f "environment.yml"; then | ||
| echo " Using environment.yml" | ||
| ${CONDA_DIR}/condabin/mamba env update --name ${CONDA_ENV} -f environment.yml | ||
| ${NB_PYTHON_PREFIX}/bin/pip install --no-deps jupyter-remote-desktop-proxy | ||
| INSTALLATION_HAPPENED=true | ||
| fi | ||
|
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||
| # Only run cleanup if installation occurred | ||
| if [ "$INSTALLATION_HAPPENED" = true ]; then | ||
| ${CONDA_DIR}/condabin/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 | ||
| # Check if a filename argument is provided | ||
| if [ -z "$1" ]; then | ||
| echo "Error: install-conda-packages.sh requires a file name (either conda-lock.yml or environment.yml)." >&2 | ||
| echo "Usage: RUN /pyrocket_scripts/install-conda-packages.sh <filename.yml>" >&2 | ||
| exit 1 | ||
| fi | ||
|
|
||
| # Check if running as root and switch to NB_USER if needed | ||
| 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 $1" # Pass along the filename argument | ||
| fi | ||
|
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||
| # Main script execution as NB_USER | ||
| echo "Running install-conda-packages.sh as ${NB_USER}" | ||
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| # Set the file variable to the provided argument | ||
| ENV_FILE="$1" | ||
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| # Verify the file exists and is readable | ||
| if [ ! -f "$ENV_FILE" ]; then | ||
| echo " Error: File '$ENV_FILE' not found. Please provide a valid file path." >&2 | ||
| echo " Usage: RUN /pyrocket_scripts/install-conda-packages.sh <filename.yml>" >&2 | ||
| exit 1 | ||
| fi | ||
|
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||
| echo " Found file: $ENV_FILE" | ||
|
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||
| # Determine file type based on content | ||
| if grep -q "lock_set" "$ENV_FILE"; then | ||
| echo " Detected conda-lock.yml file." | ||
| ${NB_PYTHON_PREFIX}/bin/conda-lock install --name ${CONDA_ENV} -f "$ENV_FILE" | ||
| INSTALLATION_HAPPENED=true | ||
| elif grep -q "name:" "$ENV_FILE"; then | ||
| echo " Detected environment.yml file." | ||
| ${CONDA_DIR}/condabin/mamba env update --name ${CONDA_ENV} -f "$ENV_FILE" | ||
| INSTALLATION_HAPPENED=true | ||
| else | ||
| echo " Directory ${REPO_DIR}/childimage/ does not exist. Skipping script." | ||
| # If neither condition matches, output a helpful error message | ||
| echo "Error: Unrecognized file format in '${env_file}'." | ||
| echo " - For an environment.yml file, ensure it includes a 'name:' entry. Any name is acceptable." | ||
| echo " - For a conda-lock.yml file, ensure it includes a 'lock_set:' entry." | ||
| exit 1 | ||
| fi | ||
|
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||
| # Run cleanup if installation occurred | ||
| if [ "$INSTALLATION_HAPPENED" = true ]; then | ||
| ${CONDA_DIR}/condabin/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 | ||
|
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||
| echo " Success! install-conda-packages.sh" |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,25 +1,40 @@ | ||
| #!/bin/bash | ||
| # Required User: NB_USER | ||
|
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||
| echo "Running install-pip-packages.sh" | ||
|
|
||
| echo " Checking for ${REPO_DIR}/childimage/..." | ||
| if [ -d "${REPO_DIR}/childimage/" ]; then | ||
| cd "${REPO_DIR}/childimage/" || exit 1 | ||
|
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||
| 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 | ||
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| 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." | ||
| # Check if a filename argument is provided | ||
| if [ -z "$1" ]; then | ||
| echo "Error: install-pip-packages.sh requires an input file of package names (typically called requirements.txt)." >&2 | ||
| echo "Usage: RUN /pyrocket_scripts/install-pip-packages.sh <filename>" >&2 | ||
| exit 1 | ||
| fi | ||
|
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| # Check if running as root and switch to NB_USER if needed | ||
| 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 $1" # Pass along the filename argument | ||
| fi | ||
|
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| # Main script execution as NB_USER | ||
| echo "Running install-pip-packages.sh as ${NB_USER}" | ||
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| # Set variable for the provided file | ||
| requirements_file="$1" | ||
| echo " Using packages file: ${requirements_file}" | ||
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| # Check if the specified file exists | ||
| if [ ! -f "${requirements_file}" ]; then | ||
| echo " Error: File '${requirements_file}' not found. Ensure the file exists and try again." | ||
| exit 1 | ||
| fi | ||
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| echo " Installing pip packages from ${requirements_file} as ${NB_USER}..." | ||
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| # Install pip packages and handle errors | ||
| if ! ${NB_PYTHON_PREFIX}/bin/pip install --no-cache -r "${requirements_file}"; then | ||
| echo " Error: Installation of packages from '${requirements_file}' failed. Please check the package names and try again." | ||
| exit 1 | ||
| fi | ||
|
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||
| echo " Success! install-pip-packages.sh" | ||
|
|
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,38 @@ | ||
| #!/bin/bash | ||
| # Required User: NB_USER | ||
|
|
||
| # Check if a filename argument is provided | ||
| if [ -z "$1" ]; then | ||
| echo "Error: install-r-packages.sh requires an input file (an R script and typically called install.R)." >&2 | ||
| echo "Usage: RUN /pyrocket_scripts/install-r-packages.sh <filename>" >&2 | ||
| exit 1 | ||
| fi | ||
|
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||
| # Check if running as root and switch to NB_USER if needed | ||
| 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 $1" # Pass along the filename argument | ||
| fi | ||
|
|
||
| # Main script execution as NB_USER | ||
| echo "Running install-r-packages.sh as ${NB_USER}" | ||
|
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||
| # Set the file variable to the provided argument | ||
| INSTALL_FILE="$1" | ||
|
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||
| # Verify the file exists and is readable | ||
| if [ ! -f "$INSTALL_FILE" ]; then | ||
| echo " Error: File '$INSTALL_FILE' not found. Please provide a valid R script file." >&2 | ||
| echo " Usage: RUN /pyrocket_scripts/install-r-packages.sh <filename>" >&2 | ||
| exit 1 | ||
| fi | ||
|
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| echo " Found file: $INSTALL_FILE" | ||
|
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| # Install R packages using the provided R script | ||
| if ! Rscript "$INSTALL_FILE"; then | ||
| echo " Error: Installation of packages from '$INSTALL_FILE' failed. Please check the script for errors." >&2 | ||
| exit 1 | ||
| fi | ||
|
|
||
| echo " Success! install-r-packages.sh" |
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