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Fixed further issues in the dpc template
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i14/templates/dpc-template.yaml

Lines changed: 17 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -9,7 +9,7 @@ metadata:
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workflows.diamond.ac.uk/parameter-schema: |
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{{- .Files.Get "schema/dpcSchema.json" | nindent 6 }}
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workflows.diamond.ac.uk/ui-schema: |
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{{- .Files.Get "schema/dpcUISchema.json" | nindent 6 }}
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{{- .Files.Get "schema/dpcUiSchema.json" | nindent 6 }}
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spec:
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entrypoint: dpc
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arguments:
@@ -19,13 +19,24 @@ spec:
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configMapKeyRef:
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name: sessionspaces
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key: data_directory
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volumeClaimTemplates:
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- metadata:
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name: tmp
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spec:
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accessModes:
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- ReadWriteOnce
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resources:
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requests:
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storage: 1Gi
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storageClassName: netapp
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templates:
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- name: dpc-mount-files
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script:
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image: gitlab.diamond.ac.uk:5050/i14/i14_utility/dpc:v0.1
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command: [bash]
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source: |
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echo '{{ .Files.Get "notebooks/dpc_autoprocess3.ipynb" | b64enc }}' | base64 -d > /tmp/notebook.ipynb
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ls /tmp
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volumeMounts:
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- name: tmp
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mountPath: /tmp
@@ -35,19 +46,20 @@ spec:
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- name: outputFolder
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value: /tmp/output
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- name: singleFirst
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value: 1
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value: 280793
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script:
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image: gitlab.diamond.ac.uk:5050/i14/i14_utility/dpc:v0.1
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command: [bash]
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source: |
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python -m papermill /tmp/notebook.ipynb /tmp/notebook-parametrized.ipynb \
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-p visitDir '{{`{{workflow.parameters.visitdir}}`}}' \
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-p outputFolder '{{`{{inputs.parameters.outputFolder}}`}}' \
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-p singleFirst '{{`{{inputs.parameters.singleFirst}}`}}'
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-p inpath '{{`{{workflow.parameters.visitdir}}`}}'/nexus/i14-'{{`{{inputs.parameters.singleFirst}}`}}'.nxs \
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-p outpath '{{`{{inputs.parameters.outputFolder}}`}}'
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python -m jupyter nbconvert --execute --allow-errors --to html --output notebook --output-dir /tmp /tmp/notebook-parametrized.ipynb
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volumeMounts:
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- name: session
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mountPath: "{{`{{workflow.parameters.visitdir}}`}}"
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- name: tmp
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mountPath: /tmp
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outputs:
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artifacts:
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- name: dpc

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