diff --git a/i14/templates/xrf-tomo-template.yaml b/i14/templates/xrf-tomo-template.yaml index 5dc4d73..abfe763 100644 --- a/i14/templates/xrf-tomo-template.yaml +++ b/i14/templates/xrf-tomo-template.yaml @@ -66,7 +66,7 @@ spec: image: debian:stable-slim volumeMounts: - name: session - mountPath: "{{`{{ workflow.parameters.prefix }}`}}/{{`{{ workflow.parameters.visitdir }}`}}" + mountPath: "{{`{{ workflow.parameters.prefix }}`}}{{`{{ workflow.parameters.visitdir }}`}}" command: [bash] source: | OUTPUT="{{`{{ workflow.parameters.visitdir }}`}}"/processing/workflows/"{{`{{ workflow.parameters.outputFolder }}`}}" @@ -92,7 +92,7 @@ spec: volumes: - name: session hostPath: - path: "{{`{{ workflow.parameters.prefix }}`}}/{{`{{ workflow.parameters.visitdir }}`}}" + path: "{{`{{ workflow.parameters.prefix }}`}}{{`{{ workflow.parameters.visitdir }}`}}" type: Directory - name: xrf-tomo-stack-projections @@ -104,7 +104,7 @@ spec: image: ghcr.io/diamondlightsource/nxstacker:latest volumeMounts: - name: session - mountPath: "{{`{{ workflow.parameters.prefix }}`}}/{{`{{ workflow.parameters.visitdir }}`}}" + mountPath: "{{`{{ workflow.parameters.prefix }}`}}{{`{{ workflow.parameters.visitdir }}`}}" - name: tmp mountPath: /tmp env: @@ -141,7 +141,7 @@ spec: volumes: - name: session hostPath: - path: "{{`{{ workflow.parameters.prefix }}`}}/{{`{{ workflow.parameters.visitdir }}`}}" + path: "{{`{{ workflow.parameters.prefix }}`}}{{`{{ workflow.parameters.visitdir }}`}}" type: Directory - name: xrf-tomo-copy-stacked-projections @@ -153,7 +153,7 @@ spec: image: debian:stable-slim volumeMounts: - name: session - mountPath: "{{`{{ workflow.parameters.prefix }}`}}/{{`{{ workflow.parameters.visitdir }}`}}" + mountPath: "{{`{{ workflow.parameters.prefix }}`}}{{`{{ workflow.parameters.visitdir }}`}}" - name: tmp mountPath: /tmp env: @@ -186,7 +186,7 @@ spec: volumes: - name: session hostPath: - path: "{{`{{ workflow.parameters.prefix }}`}}/{{`{{ workflow.parameters.visitdir }}`}}" + path: "{{`{{ workflow.parameters.prefix }}`}}{{`{{ workflow.parameters.visitdir }}`}}" type: Directory - name: xrf-tomo-generate-shifts @@ -223,14 +223,14 @@ spec: volumeMounts: - name: session - mountPath: "{{`{{ workflow.parameters.prefix }}`}}/{{`{{ workflow.parameters.visitdir }}`}}" + mountPath: "{{`{{ workflow.parameters.prefix }}`}}{{`{{ workflow.parameters.visitdir }}`}}" - name: tmp mountPath: /tmp outputs: parameters: - name: initcor valueFrom: - path: "{{`{{ workflow.parameters.prefix }}`}}/{{`{{ workflow.parameters.visitdir }}`}}/processing/workflows/{{`{{ workflow.parameters.outputFolder }}`}}/{{`{{ workflow.parameters.elementToAlign }}`}}-{{`{{ workflow.parameters.transitionToAlign }}`}}_cor.txt" + path: "{{`{{ workflow.parameters.prefix }}`}}{{`{{ workflow.parameters.visitdir }}`}}/processing/workflows/{{`{{ workflow.parameters.outputFolder }}`}}/{{`{{ workflow.parameters.elementToAlign }}`}}-{{`{{ workflow.parameters.transitionToAlign }}`}}_cor.txt" artifacts: - name: align_initial path: "/tmp/align_initial.html" @@ -268,7 +268,7 @@ spec: volumes: - name: session hostPath: - path: "{{`{{ workflow.parameters.prefix }}`}}/{{`{{ workflow.parameters.visitdir }}`}}" + path: "{{`{{ workflow.parameters.prefix }}`}}{{`{{ workflow.parameters.visitdir }}`}}" type: Directory - name: xrf-tomo-align-and-normalise @@ -308,7 +308,7 @@ spec: volumeMounts: - name: session - mountPath: "{{`{{ workflow.parameters.prefix }}`}}/{{`{{ workflow.parameters.visitdir }}`}}" + mountPath: "{{`{{ workflow.parameters.prefix }}`}}{{`{{ workflow.parameters.visitdir }}`}}" - name: tmp mountPath: /tmp outputs: @@ -345,7 +345,7 @@ spec: volumes: - name: session hostPath: - path: "{{`{{ workflow.parameters.prefix }}`}}/{{`{{ workflow.parameters.visitdir }}`}}" + path: "{{`{{ workflow.parameters.prefix }}`}}{{`{{ workflow.parameters.visitdir }}`}}" type: Directory - name: xrf-tomo-reconstruct @@ -376,11 +376,6 @@ spec: OUTPUT=$VISIT/processing/workflows/"{{`{{ workflow.parameters.outputFolder }}`}}" ELEMENT="{{`{{= sprig.mustFromJson(inputs.parameters.edge).edgeElement }}`}}" TRANSITION="{{`{{= sprig.mustFromJson(inputs.parameters.edge).edgeTransition }}`}}" - mkdir -p $OUTPUT/httomo_output - mkdir -p $OUTPUT/httomo_output/${ELEMENT}-${TRANSITION} - mkdir -p /tmp/httomo_output - - ln -s $OUTPUT/httomo_output/${ELEMENT}-${TRANSITION} /tmp/httomo_output/${ELEMENT}-${TRANSITION} COR_ESTIMATE="{{`{{ inputs.parameters.initcor }}`}}" [[ $COR_ESTIMATE != "nil" ]] && sed -i 's//'"${COR_ESTIMATE}"'/' $OUTPUT/httomo.yaml @@ -399,13 +394,13 @@ spec: volumeMounts: - name: session - mountPath: "{{`{{ workflow.parameters.prefix }}`}}/{{`{{ workflow.parameters.visitdir }}`}}" + mountPath: "{{`{{ workflow.parameters.prefix }}`}}{{`{{ workflow.parameters.visitdir }}`}}" - name: tmp mountPath: /tmp outputs: artifacts: - name: images32bit_tif - path: "/tmp/httomo_output/{{`{{= sprig.mustFromJson(inputs.parameters.edge).edgeElement }}`}}-{{`{{= sprig.mustFromJson(inputs.parameters.edge).edgeTransition }}`}}/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" podSpecPatch: | containers: @@ -434,7 +429,7 @@ spec: volumes: - name: session hostPath: - path: "{{`{{ workflow.parameters.prefix }}`}}/{{`{{ workflow.parameters.visitdir }}`}}" + path: "{{`{{ workflow.parameters.prefix }}`}}{{`{{ workflow.parameters.visitdir }}`}}" type: Directory - name: xrf-tomo-plotting @@ -467,7 +462,7 @@ spec: volumeMounts: - name: session - mountPath: "{{`{{ workflow.parameters.prefix }}`}}/{{`{{ workflow.parameters.visitdir }}`}}" + mountPath: "{{`{{ workflow.parameters.prefix }}`}}{{`{{ workflow.parameters.visitdir }}`}}" - name: tmp mountPath: /tmp outputs: @@ -516,7 +511,7 @@ spec: volumes: - name: session hostPath: - path: "{{`{{ workflow.parameters.prefix }}`}}/{{`{{ workflow.parameters.visitdir }}`}}" + path: "{{`{{ workflow.parameters.prefix }}`}}{{`{{ workflow.parameters.visitdir }}`}}" type: Directory - name: xrf-tomo-alignment-pipeline