Add psrfits file to quality

steps/format_quality.cwl

@@ -7,6 +7,8 @@ requirements:
 - class: InlineJavascriptRequirement
 
 inputs:
+- id: summary_psrfits_file
+  type: File?
 - id: summary_file
   type: File?
 - id: plots
@@ -31,6 +33,9 @@ expression: |
       if(inputs.summary_file){
         plots.push(inputs.summary_file);
       }
+      if(inputs.summary_psrfits_file){
+        plots.push(inputs.summary_psrfits_file)
+      }
 
       var summary = {}
       for (var s_idx in inputs.summaries) {

steps/join_contents.cwl

+#!/usr/bin/env cwl-runner
+
 cwlVersion: v1.2
 class: CommandLineTool
+
+requirements:
+- class: InlineJavascriptRequirement
+- class: InitialWorkDirRequirement
+  listing:
+  - entryname: summary.json
+    entry: $(inputs.metadata)
+  - entryname: script.py
+    entry: |
+      #!/usr/bin/env python3
+      import os
+      import sys
+      import json
+      SIZE_FACTORS = ["B", "kB", "MB", "GB", "TB", "PB", "EB"]
+      def size_to_string(size: int):
+          for factor_index, label in enumerate(SIZE_FACTORS):
+              factor = 1024 ** factor_index
+              next_factor = 1024 * factor
+              if size < next_factor:
+                  return "{:.2f} {}".format(size / factor, label).strip()
+          else:
+              return None
+
+      files_in = sys.argv[1:]
+      file_out_path = sys.argv[1].split('/')[-1]
+      sasid = file_out_path.split('-')[0].lstrip('L')
+      with open('summary.json', 'r') as fin:
+          summaries = json.load(fin)
+
+      total_input = 0
+      total_output = 0
+      for summary in summaries:
+          total_input += summary['input_size']
+          total_output += summary['output_size']
+
+      with open(file_out_path, 'w') as fout:
+          fout.write('#'*97+'\n')
+          fout.write('There are %s tarballs processed for the SASId %s\n' % (len(summaries), sasid))
+          fout.write('The total size of all input tarballs: %s \n' % (size_to_string(total_input), ))
+          fout.write('The total size of all output tarballs: %s \n' % (size_to_string(total_output), ))
+          fout.write('The size ratio (output/input) is: %.2f \n' % (total_output/total_input, ))
+          fout.write('#'*97+'\n')
+          for file in files_in:
+              with open(file, 'r') as fin:
+                  fout.write(fin.read())
+
 inputs:
-  - id: metadata
-    type: Any[]
-  - id: summary_files
-    type: File[]
-    inputBinding:
-      position: 1
+- id: metadata
+  type: Any[]
+- id: summary_files
+  type: File[]?
+  inputBinding:
+    position: 1
+
 outputs:
-  - id: summary_file
-    type: File
-    outputBinding:
-      glob: "$(inputs.summary_files[0].basename)"
+- id: summary_file
+  type: File
+  outputBinding:
+    glob: $(inputs.summary_files[0].basename)
+
 baseCommand:
 - python3
 - script.py
 
 hints:
-  - class: DockerRequirement
-    dockerPull: git.astron.nl:5000/ldv/bf_double_tgz:latest
-requirements:
-  - class: InlineJavascriptRequirement
-  - class: InitialWorkDirRequirement
-    listing:
-    - entryname: summary.json
-      entry: $(inputs.metadata)
-    - entryname: script.py
-      entry: |
-        #!/usr/bin/env python3
-        import os
-        import sys
-        import json
-        SIZE_FACTORS = ["B", "kB", "MB", "GB", "TB", "PB", "EB"]
-        def size_to_string(size: int):
-            for factor_index, label in enumerate(SIZE_FACTORS):
-                factor = 1024 ** factor_index
-                next_factor = 1024 * factor
-                if size < next_factor:
-                    return "{:.2f} {}".format(size / factor, label).strip()
-            else:
-                return None
-
-        files_in = sys.argv[1:]
-        file_out_path = sys.argv[1].split('/')[-1]
-        sasid = file_out_path.split('-')[0].lstrip('L')
-        with open('summary.json', 'r') as fin:
-            summaries = json.load(fin)
-
-        total_input = 0
-        total_output = 0
-        for summary in summaries:
-            total_input += summary['input_size']
-            total_output += summary['output_size']
-
-        with open(file_out_path, 'w') as fout:
-            fout.write('#'*97+'\n')
-            fout.write('There are %s tarballs processed for the SASId %s\n' % (len(summaries), sasid))
-            fout.write('The total size of all input tarballs: %s \n' % (size_to_string(total_input), ))
-            fout.write('The total size of all output tarballs: %s \n' % (size_to_string(total_output), ))
-            fout.write('The size ratio (output/input) is: %.2f \n' % (total_output/total_input, ))
-            fout.write('#'*97+'\n')
-            for file in files_in:
-                with open(file, 'r') as fin:
-                    fout.write(fin.read())
+- class: DockerRequirement
+  dockerPull: git.astron.nl:5000/ldv/bf_double_tgz:latest

workflow/download_and_run_psrfits_requantisation.cwl

@@ -23,7 +23,7 @@ outputs:
   type: File[]
   outputSource: requantise/summary_file
 - id: summary_psrfits_file
-  type: File[]
+  type: File[]?
   outputSource: requantise/summary_psrfits_file
 - id: ingest
   type: Any
@@ -63,8 +63,19 @@ steps:
   run: ../steps/join_contents.cwl
   out:
   - id: summary_file
+- id: join_contents_psrfits
+  in:
+  - id: summary_files
+    source: requantise/summary_psrfits_file
+  - id: metadata
+    source: requantise/summary
+  run: ../steps/join_contents.cwl
+  out:
+  - id: summary_file
 - id: format_quality
   in:
+  - id: summary_psrfits_file
+    source: join_contents_psrfits/summary_file
   - id: summary_file
     source: join_contents/summary_file
   - id: plots