From 38083a7675d1df3592a7c7fd56b1b95555366309 Mon Sep 17 00:00:00 2001
From: frederick <frederick.allars@diamond.ac.uk>
Date: Wed, 19 Aug 2026 14:15:35 +0100
Subject: [PATCH] adding papermill step to the simple ePSIC notebook

---
 e02/templates/Notebook_simple.yaml | 57 ++++++++++++++++++++++++++++++
 1 file changed, 57 insertions(+)

diff --git a/e02/templates/Notebook_simple.yaml b/e02/templates/Notebook_simple.yaml
index 2991758..d3acb3e 100644
--- a/e02/templates/Notebook_simple.yaml
+++ b/e02/templates/Notebook_simple.yaml
@@ -54,11 +54,68 @@ spec:
           mkdir -p $OUTPUT
           echo "something!"
           echo '{{ .Files.Get "notebooks/Ptycho_calibration.ipynb" | b64enc }}' | base64 -d > $OUTPUT/Ptycho_calibration.ipynb
+
+    - name: process-notebook
+      inputs:
+        parameters:
+          - name: sample
+            value: "{{`{{workflow.parameters.sample}}`}}"
+          - name: timestamp
+            value: "{{`{{workflow.parameters.timestamp}}`}}"
+          - name: thresh_lower
+            value: "{{`{{workflow.parameters.thresh_lower}}`}}"
+          - name: thresh_upper
+            value: "{{`{{workflow.parameters.thresh_upper}}`}}"
+      script:
+        image: gitlab.diamond.ac.uk:5050/scisoft/ptychography/dimtools/mib2x
+        volumeMounts:
+          - name: session
+            mountPath: "{{`{{ workflow.parameters.visitdir }}`}}"
+          - name: tmp
+            mountPath: /tmp
+          - name: software
+            mountPath: /dls_sw/e02/medipix_mask
+        command: [bash]
+        source: |
+          ERROR_TXT="raise error"
+          ERROR_STR="An error occured within the notebook. Please open the output file to check"
+          OUTPUT="{{`{{workflow.parameters.visitdir}}`}}"/processing/workflows/
+          echo $OUTPUT
+          python -m papermill "{{`{{workflow.parameters.visitdir}}`}}"/processing/workflows/Ptycho_calibration.ipynb $OUTPUT/Calibrate-notebook.ipynb \
+            -p visit "{{`{{ workflow.parameters.visitdir }}`}}" \
+            -p sample "{{`{{ workflow.parameters.sample }}`}}" \
+            -p timestamp "{{`{{workflow.parameters.timestamp}}`}}" \
+            -p maskpath /software/29042024_12bitmask2.h5 \
+            -p lower "{{`{{workflow.parameters.thresh_lower}}`}}" \
+            -p upper "{{`{{workflow.parameters.thresh_upper}}`}}" \
+            > $OUTPUT/papermill.log 2>&1
+
+          python  -m jupyter nbconvert $OUTPUT/Calibrate-notebook.ipynb \
+            --to html 
+      outputs:
+        artifacts:
+          - name: phase-output
+            path: "{{`{{workflow.parameters.visitdir}}`}}/processing/workflows/Calibrate-notebook.html"
+            archive:
+              none: {}
+      podSpecPatch: |
+        containers:
+        - name: main
+          resources:
+            requests:
+              cpu: 1
+              memory: 50Gi
+            limits:
+              cpu: 1
+              memory: 50Gi
     - name: start
       dag:
         tasks:
         - name: setup
           template: mount-files
+        - name: run
+          template: process-notebook
+          dependencies: [setup]