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get artifacts via /tmp for all steps #317

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Merged
daurer merged 1 commit into from
Aug 10, 2026
Merged

get artifacts via /tmp for all steps #317

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19 changes: 13 additions & 6 deletions i14/templates/xrf-tomo-template.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -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 }}`}}"
Expand All @@ -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: |
Expand Down Expand Up @@ -390,6 +392,8 @@ spec:

echo "Executing: ${cmd[*]}"
exec "${cmd[@]}"

cp -r $OUTPUT/httomo_output /tmp

volumeMounts:
- name: session
Expand All @@ -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:
Expand Down Expand Up @@ -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 }}`}}"
Expand All @@ -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: |
Expand Down