can't preconfigure aws endpoint in python & r

InseeFrLab · Jan 6, 2024 · d9d81a9 · d9d81a9
1 parent 1c070bf
commit d9d81a9
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Showing 6 changed files with 3 additions and 21 deletions.
diff --git a/python-minimal/Dockerfile b/python-minimal/Dockerfile
@@ -24,7 +24,7 @@ RUN wget -q "https://github.com/conda-forge/miniforge/releases/latest/download/M
     # Install essential Python packages
     mamba env update -n base -f conda-env.yml && \
     # Install duckdb extensions
-    mamba run -n base python opt/install-duckdb-extensions.py && \
+    mamba run -n base python /opt/install-duckdb-extensions.py && \
     # Activate custom Conda env by default in shell
     echo ". ${MAMBA_DIR}/etc/profile.d/conda.sh && conda activate" >> ${HOME}/.bashrc && \
     # Fix permissions

diff --git a/r-minimal/Dockerfile b/r-minimal/Dockerfile
@@ -47,7 +47,7 @@ RUN /rocker_scripts/setup_R.sh && \
         targets \
         vaultr && \
     # Install duckdb extensions
-    Rscript opt/install-duckdb-extensions.R && \
+    Rscript /opt/install-duckdb-extensions.R && \
     # Fix permissions
     chown -R ${USERNAME}:${GROUPNAME} ${HOME} ${R_HOME} && \
     # Clean

diff --git a/scripts/configure-duckdb.R b/scripts/configure-duckdb.R
diff --git a/scripts/configure-duckdb.py b/scripts/configure-duckdb.py
diff --git a/scripts/install-duckdb-extensions.R b/scripts/install-duckdb-extensions.R
@@ -3,3 +3,4 @@ con <- DBI::dbConnect(duckdb::duckdb())
 DBI::dbExecute(con, glue::glue('SET extension_directory=\"{Sys.getenv("HOME")}\"'))
 DBI::dbExecute(con, 'INSTALL httpfs')
 DBI::dbExecute(con, 'INSTALL aws')
+DBI::dbDisconnect(con, shutdown=TRUE)
diff --git a/scripts/onyxia-init.sh b/scripts/onyxia-init.sh
@@ -177,16 +177,6 @@ SET s3_endpoint='$AWS_S3_ENDPOINT';
 EOF
 fi
 
-# Configure duckdb Python API
-if [[ -n $AWS_S3_ENDPOINT ]] && command -v python ; then
-    mamba run -n base python opt/configure-dubkdb.py
-fi
-
-# Configure duckdb R API
-if [[ -n $AWS_S3_ENDPOINT ]] && command -v R ; then
-    Rscript opt/configure-duckdb.R
-fi
-
 if [[ -e "$HOME/work" ]]; then
   if [[ $(id -u) = 0 ]]; then
     echo "cd $HOME/work" >> /etc/profile