Started CWL implementation

reanahub · Apr 5, 2024 · ea3a267 · ea3a267
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diff --git a/cwl/clt/generate.cwl b/cwl/clt/generate.cwl
@@ -0,0 +1,19 @@
+cwlVersion: v1.2
+class: CommandLineTool
+requirements:
+  DockerRequirement:
+    dockerPull: docker.io/reanahub/reana-demo-bsm-search:1.0.0
+inputs:
+  nevents: int
+  outputfile: File
+  type: string
+baseCommand: [bash, -c]
+arguments:
+  - valueFrom: |
+      source /usr/local/bin/thisroot.sh
+      python /code/generantuple.py $(inputs.type) $(inputs.nevents) $(inputs.outputfile)
+outputs:
+  outputfile:
+    outputBinding:
+      glob: $(inputs.outputfile)
+    type: File
diff --git a/cwl/clt/hepdata.cwl b/cwl/clt/hepdata.cwl
@@ -0,0 +1,21 @@
+cwlVersion: v1.2
+class: CommandLineTool
+requirements:
+  DockerRequirement:
+    dockerPull: docker.io/reanahub/reana-demo-bsm-search:1.0.0
+inputs:
+  combined_model: File
+  hepdata_data1_yaml: string
+  hepdata_submission_yaml: string
+  hepdata_submission_zip: string
+baseCommand: [bash, -c]
+arguments:
+  - valueFrom: |
+      source /usr/local/bin/thisroot.sh
+      python /code/hepdata_export.py $(inputs.combined_model) $(inputs.hepdata_submission_yaml) $(inputs.hepdata_data1_yaml)
+      zip $(inputs.hepdata_submission_zip) $(inputs.hepdata_submission_yaml) $(inputs.hepdata_data1_yaml)
+outputs:
+  hepdata_submission_zip:
+    outputBinding:
+      glob: $(inputs.hepdata_submission_zip)
+    type: File
diff --git a/cwl/clt/histogram.cwl b/cwl/clt/histogram.cwl
@@ -0,0 +1,24 @@
+cwlVersion: v1.2
+class: CommandLineTool
+requirements:
+  DockerRequirement:
+    dockerPull: docker.io/reanahub/reana-demo-bsm-search:1.0.0
+inputs:
+  inputfile: File
+  outputfile: File
+  region: string
+  variations:
+    inputBinding:
+      itemSeparator: ','
+    type: string[]
+  weight: float
+baseCommand: [bash, -c]
+arguments:
+  - valueFrom: |
+      source /usr/local/bin/thisroot.sh
+      python /code/histogram.py $(inputs.inputfile) $(inputs.outputfile) $(inputs.name) $(inputs.weight) $(inputs.variations)
+outputs:
+  outputfile:
+    outputBinding:
+      glob: $(inputs.outputfile)
+    type: File
diff --git a/cwl/clt/histogram_shape.cwl b/cwl/clt/histogram_shape.cwl
@@ -0,0 +1,24 @@
+cwlVersion: v1.2
+class: CommandLineTool
+requirements:
+  DockerRequirement:
+    dockerPull: docker.io/reanahub/reana-demo-bsm-search:1.0.0
+inputs:
+  inputfile: File
+  outputfile: File
+  region: string
+  shapevar: string
+  variations:
+    inputBinding:
+      itemSeparator: ','
+    type: string[]
+baseCommand: [bash, -c]
+arguments:
+  - valueFrom: |
+      source /usr/local/bin/thisroot.sh
+      python /code/histogram.py $(inputs.inputfile) $(inputs.outputfile) $(inputs.name)_$(inputs.shapevar) $(inputs.weight) $(inputs.variations) '{{name}}'
+outputs:
+  outputfile:
+    outputBinding:
+      glob: $(inputs.outputfile)
+    type: File
diff --git a/cwl/clt/makews.cwl b/cwl/clt/makews.cwl
@@ -0,0 +1,19 @@
+cwlVersion: v1.2
+class: CommandLineTool
+requirements:
+  DockerRequirement:
+    dockerPull: docker.io/reanahub/reana-demo-bsm-search:1.0.0
+inputs:
+  data_bkg_hists: File
+  workspace_prefix: string
+  xml_dir: string
+baseCommand: [bash, -c]
+arguments:
+  - valueFrom: |
+      source /usr/local/bin/thisroot.sh
+      python /code/makews.py $(inputs.data_bkg_hists) $(inputs.workspace_prefix) $(inputs.xml_dir)
+outputs:
+  workspace:
+    outputBinding:
+      glob: $(inputs.workspace_prefix)*combined*model.root
+    type: File
diff --git a/cwl/clt/merge_root.cwl b/cwl/clt/merge_root.cwl
@@ -0,0 +1,18 @@
+cwlVersion: v1.2
+class: CommandLineTool
+requirements:
+  DockerRequirement:
+    dockerPull: docker.io/reanahub/reana-env-root6:6.18.04
+inputs:
+  mergedfile: string
+  inputs: File[]
+baseCommand: [bash, -c]
+arguments:
+  - valueFrom: |
+      source /usr/local/bin/thisroot.sh
+      hadd $(inputs.mergedfile) $(inputs.inputs)
+outputs:
+  mergedfile:
+    outputBinding:
+      glob: $(inputs.mergedfile)
+    type: File[]
diff --git a/cwl/clt/merge_root_allpars.cwl b/cwl/clt/merge_root_allpars.cwl
@@ -0,0 +1,20 @@
+cwlVersion: v1.2
+class: CommandLineTool
+requirements:
+  DockerRequirement:
+    dockerPull: docker.io/reanahub/reana-env-root6:6.18.04
+inputs:
+  background: string
+  data: string
+  mergedfile: string
+  signal: File[]
+baseCommand: [bash, -c]
+arguments:
+  - valueFrom: |
+      source /usr/local/bin/thisroot.sh
+      hadd $(inputs.mergedfile) $(inputs.signal) $(inputs.data) $(inputs.background)
+outputs:
+  mergedfile:
+    outputBinding:
+      glob: $(inputs.mergedfile)
+    type: File
diff --git a/cwl/clt/plot.cwl b/cwl/clt/plot.cwl
@@ -0,0 +1,28 @@
+cwlVersion: v1.2
+class: CommandLineTool
+requirements:
+  DockerRequirement:
+    dockerPull: docker.io/reanahub/reana-demo-bsm-search:1.0.0
+inputs:
+  combined_model: File
+  fit_results: string
+  nominal_vals: string
+  postfit_plot: string
+  prefit_plot: string
+baseCommand: [bash, select.sh]
+arguments:
+  - valueFrom: |
+      source /usr/local/bin/thisroot.sh
+      hfquickplot write-vardef $(inputs.combined_model) combined $(inputs.nominal_vals)
+      hfquickplot plot-channel 4(inputs.combined_model) combined channel1 x $(inputs.nominal_vals) -c qcd,mc2,mc1,signal -o $(inputs.prefit_plot)
+      hfquickplot fit $(inputs.combined_model) combined $(inputs.fit_results)
+      hfquickplot plot-channel $(inputs.combined_model) combined channel1 x $(inputs.fit_results) -c qcd,mc2,mc1,signal -o $(inputs.postfit_plot)
+outputs:
+  postfit:
+    outputBinding:
+      glob: $(inputs.postfit_plot)
+    type: File
+  prefit:
+    outputBinding:
+      glob: $(inputs.prefit_plot)
+    type: File
diff --git a/cwl/clt/select.cwl b/cwl/clt/select.cwl
@@ -0,0 +1,20 @@
+cwlVersion: v1.2
+class: CommandLineTool
+requirements:
+  DockerRequirement:
+    dockerPull: docker.io/reanahub/reana-demo-bsm-search:1.0.0   
+inputs:
+  inputfile: File
+  outputfile: File
+  region: string
+  variations: string
+baseCommand: [bash, select.sh]
+arguments:
+  - valueFrom: |
+      source /usr/local/bin/thisroot.sh
+      python /code/select.py $(inputs.inputfile) $(inputs.outputfile) $(inputs.region) nominal
+outputs:
+  outputfile:
+    outputBinding:
+      glob: $(inputs.outputfile)
+    type: File
diff --git a/cwl/clt/select_mc.cwl b/cwl/clt/select_mc.cwl
@@ -0,0 +1,23 @@
+cwlVersion: v1.2
+class: CommandLineTool
+requirements:
+  DockerRequirement:
+    dockerPull: docker.io/reanahub/reana-demo-bsm-search:1.0.0
+inputs:
+  inputfile: File
+  outputfile: File
+  region: string
+  variations:
+    inputBinding:
+      itemSeparator: ","
+    type: string[]
+baseCommand: [bash, -c]
+arguments:
+  - valueFrom: |
+      source /usr/local/bin/thisroot.sh
+      python /code/select.py $(inputs.inputfile) $(inputs.outputfile) $(inputs.region) $(inputs.variations)
+outputs:
+  outputfile:
+    outputBinding:
+      glob: $(inputs.outputfile)
+    type: File
diff --git a/cwl/databkgmc.cwl b/cwl/databkgmc.cwl
@@ -0,0 +1,77 @@
+cwlVersion: v1.2
+class: Workflow
+inputs: {}
+outputs:
+  postfit:
+    outputSource: plot/postfit.pdf
+    type: File
+  prefit:
+    outputSource: plot/prefit.pdf
+    type: File
+steps:
+  all_bkg_mc:
+    run: wflow_all_mc.cwl
+    in:
+      mcname:
+        default: ['mc1', 'mc2']
+      mcweight:
+        default: [0.01875, 0.0125]
+      nevents: 
+        default: 40000
+    out: [mergedfile]
+  data:
+    run: workflow_data.cwl
+    in:
+      nevents:
+        default: 20000
+    out: [mergedfile]
+  signal:
+    run: workflow_sig.cwl
+    in:
+      nevents:
+        default: 40000
+      mcweight:
+        default: 0.0025
+    out: [mergedfile]
+  merge:
+    run: clt/merge_root_allpars.cwl
+    in:
+      backgorund: all_bkg_mc/mergedfile
+      data: data/mergedfile
+      mergedfile:
+        valueFrom: 'merged.root'
+      signal: signal/mergedfile
+    out: [mergedfile]
+  makews:
+    run: clt/makews.cwl
+    in:
+      data_bkg_hists: merge/mergedfile
+      workspace_prefix:
+        default: 'results/workspace'
+      xml_dir:
+        default: 'xmldir'
+    out: [workspace]
+  plot:
+    run: clt/plot.cwl
+    in:
+      combined_model: makews/workspace
+      nominal_vals:
+        default: 'nominal_vals.yml'
+      fit_results:
+        default: 'fit_results.yml'
+      prefit_plot:
+        default: 'prefit.pdf'
+      postfit_plot:
+        default: 'postfit.pdf'
+    out: [postfit, prefit]
+  hepdata:
+    run: clt/hepdata.cwl
+    in:
+      combined_model: makews/workspace
+      hepdata_submission_zip:
+        default: 'submission.zip'
+      hepdata_submission_yaml:
+        default: 'submission.yaml'
+      hepdata_data1_yaml:
+        default: 'data1.yaml'
+    out: [hepdata_submission_zip]
diff --git a/cwl/wflow_all_mc.cwl b/cwl/wflow_all_mc.cwl
@@ -0,0 +1,34 @@
+cwlVersion: v1.2
+class: Workflow
+inputs:
+  nevents: int
+  mcname: string[]
+  mcweight: float[]
+outputs:
+  mergedfile:
+    outputSource: merge/mergedfile
+    type: File[]
+steps:
+  run_mc:
+    run: workflow_mc.cwl
+    in:
+      nevents: nevents
+      mcname: mcname
+      mcweight: mcweights
+      shapevars:
+        default:
+          - - shape_conv_up
+          - - shape_conv_dn
+      weightvariations:
+        default:
+          - 'nominal'
+          - 'weight_var1_up'
+          - 'weight_var1_dn'
+    out: [mergeallvars]
+  merge:
+    run: clt/merge_root.cwl
+    in:
+      inputs: run_mc/mergeallvars
+      mergedfile:
+        default: 'merged.root'
+    out: [mergedfile]