diff --git a/i14/templates/xrf-tomo-template.yaml b/i14/templates/xrf-tomo-template.yaml index 45a63eb..4ebab84 100644 --- a/i14/templates/xrf-tomo-template.yaml +++ b/i14/templates/xrf-tomo-template.yaml @@ -304,6 +304,8 @@ spec: --prepare-only \ python -m jupyter nbconvert --to html --execute --output "alignment_${ELEMENT}" --output-dir $OUTPUT/_assets --embed-images "$OUTPUT/alignment_${ELEMENT}-${TRANSITION}.ipynb" + cp -r $OUTPUT/_assets/* /tmp/ + volumeMounts: - name: session mountPath: "{{`{{ workflow.parameters.prefix }}`}}/{{`{{ workflow.parameters.visitdir }}`}}" @@ -312,7 +314,7 @@ spec: outputs: artifacts: - name: alignment - path: "{{`{{ workflow.parameters.prefix }}`}}/{{`{{ workflow.parameters.visitdir }}`}}/processing/workflows/{{`{{ workflow.parameters.outputFolder }}`}}/_assets/alignment_{{`{{= sprig.mustFromJson(inputs.parameters.edge).edgeElement }}`}}.html" + path: "/tmp/alignment_{{`{{= sprig.mustFromJson(inputs.parameters.edge).edgeElement }}`}}.html" archive: none: {} podSpecPatch: | @@ -390,6 +392,8 @@ spec: echo "Executing: ${cmd[*]}" exec "${cmd[@]}" + + cp -r $OUTPUT/httomo_output /tmp volumeMounts: - name: session @@ -399,7 +403,7 @@ spec: outputs: artifacts: - name: images32bit_tif - path: "{{`{{ workflow.parameters.prefix }}`}}/{{`{{ workflow.parameters.visitdir }}`}}/processing/workflows/{{`{{ workflow.parameters.outputFolder }}`}}/httomo_output/{{`{{= sprig.mustFromJson(inputs.parameters.edge).edgeElement }}`}}-{{`{{= sprig.mustFromJson(inputs.parameters.edge).edgeTransition }}`}}/images32bit_tif" + path: "/tmp/httomo_output/{{`{{= sprig.mustFromJson(inputs.parameters.edge).edgeElement }}`}}-{{`{{= sprig.mustFromJson(inputs.parameters.edge).edgeTransition }}`}}/images32bit_tif" podSpecPatch: | containers: @@ -456,6 +460,9 @@ spec: --prepare-only \ python -m jupyter nbconvert --to html --execute --output plotting --output-dir $OUTPUT/_assets --embed-images "$OUTPUT/plotting.ipynb" + + cp -r $OUTPUT/_assets/* /tmp/ + volumeMounts: - name: session mountPath: "{{`{{ workflow.parameters.prefix }}`}}/{{`{{ workflow.parameters.visitdir }}`}}" @@ -464,19 +471,19 @@ spec: outputs: artifacts: - name: plotting - path: "{{`{{ workflow.parameters.prefix }}`}}/{{`{{ workflow.parameters.visitdir }}`}}/processing/workflows/{{`{{ workflow.parameters.outputFolder }}`}}/_assets/plotting.html" + path: "/tmp/plotting.html" archive: none: {} - name: overview_transverse - path: "{{`{{ workflow.parameters.prefix }}`}}/{{`{{ workflow.parameters.visitdir }}`}}/processing/workflows/{{`{{ workflow.parameters.outputFolder }}`}}/_assets/recons_transverse.png" + path: "/tmp/recons_transverse.png" archive: none: {} - name: overview_sagittal - path: "{{`{{ workflow.parameters.prefix }}`}}/{{`{{ workflow.parameters.visitdir }}`}}/processing/workflows/{{`{{ workflow.parameters.outputFolder }}`}}/_assets/recons_sagittal.png" + path: "/tmp/recons_sagittal.png" archive: none: {} - name: overview_coronal - path: "{{`{{ workflow.parameters.prefix }}`}}/{{`{{ workflow.parameters.visitdir }}`}}/processing/workflows/{{`{{ workflow.parameters.outputFolder }}`}}/_assets/recons_coronal.png" + path: "/tmp/recons_coronal.png" archive: none: {} podSpecPatch: |