Updates to cttso stacks

Update script to collect pieriandx access token in safe-path chmod of lambda codes to executables
umccr · May 27, 2024 · 67e9528 · 67e9528
1 parent 7ad155d
commit 67e9528
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Showing 8 changed files with 16 additions and 1 deletion.
diff --git a/deploy/cttso-ica-to-pieriandx-cdk/assets/cttso-ica-to-pieriandx-wrapper.sh b/deploy/cttso-ica-to-pieriandx-cdk/assets/cttso-ica-to-pieriandx-wrapper.sh
@@ -31,7 +31,19 @@ get_pieriandx_access_token() {
   : '
   Collect the PierianDx access token
   '
-  local access_token_temp_file="$(mktemp access_token.XXX.json)"
+  local access_token_tmpdir
+  local access_token_temp_file
+
+  access_token_tmpdir="$(
+    mktemp \
+      --directory \
+      "${CONTAINER_MOUNT_POINT}/${sample_name}.access_token.XXX"
+  )"
+  access_token_temp_file="$( \
+    mktemp \
+      --tmpdir="${access_token_tmpdir}" \
+      "${sample_name}.access_token.XXX"
+  )"
 
   # Run the lambda command to collect the access token
   aws lambda invoke --function-name "${PIERIANDX_ACCESS_TOKEN_LAMBDA_FUNCTION_NAME}" "${access_token_temp_file}" 1>/dev/null

diff --git a/deploy/cttso-ica-to-pieriandx-cdk/lambdas/cttso_ica_to_pieriandx/cttso_ica_to_pieriandx.py b/deploy/cttso-ica-to-pieriandx-cdk/lambdas/cttso_ica_to_pieriandx/cttso_ica_to_pieriandx.py
diff --git a/...k/lambdas/get_metadata_from_portal_and_defaults_and_launch_validation_workflow/Dockerfile b/...k/lambdas/get_metadata_from_portal_and_defaults_and_launch_validation_workflow/Dockerfile
@@ -20,6 +20,7 @@ COPY ${APP_ROOT}/${THIS_DIR_NAME}/lambda_code.py ./
 COPY ${APP_ROOT}/layers/ ./layers/
 
 RUN ( \
+      chmod +rx ./lambda_code.py && \
       cd layers && \
       python setup.py install \
     )

diff --git a/...mbdas/get_metadata_from_portal_and_defaults_and_launch_validation_workflow/lambda_code.py b/...mbdas/get_metadata_from_portal_and_defaults_and_launch_validation_workflow/lambda_code.py
diff --git a/...x-cdk/lambdas/get_metadata_from_portal_and_redcap_and_launch_clinical_workflow/Dockerfile b/...x-cdk/lambdas/get_metadata_from_portal_and_redcap_and_launch_clinical_workflow/Dockerfile
@@ -20,6 +20,7 @@ COPY ${APP_ROOT}/${THIS_DIR_NAME}/lambda_code.py ./
 COPY ${APP_ROOT}/layers/ ./layers/
 
 RUN ( \
+      chmod +rx ./lambda_code.py && \
       cd layers && \
       python setup.py install \
     )

diff --git a/...k/lambdas/get_metadata_from_portal_and_redcap_and_launch_clinical_workflow/lambda_code.py b/...k/lambdas/get_metadata_from_portal_and_redcap_and_launch_clinical_workflow/lambda_code.py
diff --git a/...to-pieriandx-cdk/lambdas/launch_available_payloads_and_update_cttso_lims_sheet/Dockerfile b/...to-pieriandx-cdk/lambdas/launch_available_payloads_and_update_cttso_lims_sheet/Dockerfile
@@ -20,6 +20,7 @@ COPY ${APP_ROOT}/${THIS_DIR_NAME}/lambda_code.py ./
 COPY ${APP_ROOT}/layers/ ./layers/
 
 RUN ( \
+      chmod +rx ./lambda_code.py && \
       cd layers && \
       python setup.py install \
     )

diff --git a/...ieriandx-cdk/lambdas/launch_available_payloads_and_update_cttso_lims_sheet/lambda_code.py b/...ieriandx-cdk/lambdas/launch_available_payloads_and_update_cttso_lims_sheet/lambda_code.py