add scripts to configure R & Python duckdb

scripts/configure-duckdb.R

@@ -0,0 +1,3 @@
+con <- DBI::dbConnect(duckdb::duckdb())
+DBI::dbExecute(con, 'LOAD httpfs')
+DBI::dbExecute(con, glue::glue('SET s3_endpoint=\"{Sys.getenv("AWS_S3_ENDPOINT")}\"'))

scripts/configure-duckdb.py

@@ -0,0 +1,6 @@
+import os
+
+import duckdb
+
+duckdb.sql("LOAD httpfs")
+duckdb.sql(f"SET s3_endpoint=\"{os.getenv('AWS_S3_ENDPOINT')}\"")

scripts/install-duckdb-extensions.R

@@ -1,8 +1,5 @@
-library(glue)
-library(duckdb)
+con <- DBI::dbConnect(duckdb::duckdb())
 
-con <- dbConnect(duckdb())
-
-dbExecute(con, glue('SET extension_directory=\"{Sys.getenv("HOME")}\"'))
-dbExecute(con, 'INSTALL httpfs')
-dbExecute(con, 'INSTALL aws')
+DBI::dbExecute(con, glue::glue('SET extension_directory=\"{Sys.getenv("HOME")}\"'))
+DBI::dbExecute(con, 'INSTALL httpfs')
+DBI::dbExecute(con, 'INSTALL aws')

scripts/onyxia-init.sh

@@ -166,6 +166,7 @@ if [[ "$DARK_MODE" == "true" ]]; then
     fi
 fi
 
+# Configure duckdb CLI
 if [[ -n $AWS_S3_ENDPOINT ]] && command -v duckdb ; then
 cat <<EOF > ${HOME}/.duckdbrc
 -- Duck head prompt
@@ -176,6 +177,16 @@ SET s3_endpoint='$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