bugfix missing frequencies

lofar-cwl/steps/applybeam.cwl

@@ -2,7 +2,7 @@ class: CommandLineTool
 cwlVersion: v1.0
 $namespaces:
   sbg: 'https://www.sevenbridges.com/'
-id: applycal
+id: applybeam
 baseCommand:
   - DPPP
 inputs:

lofar-cwl/steps/check_ateam_separation.cwl

-class: CommandLineTool
-cwlVersion: v1.0
-id: check_ateam_separation
-baseCommand:
-  - python3
-  - /usr/local/bin/check_Ateam_separation.py
-inputs:
-  - id: ms
-    type:
-      - Directory
-      - type: array
-        items: Directory
-    inputBinding:
-      position: 0
-    doc: Input measurement set
-  - default: Ateam_separation.png
-    id: output_image_name
-    type: string?
-    inputBinding:
-      position: 2
-      prefix: '--outputimage'
-  - id: min_separation
-    type: int
-    inputBinding:
-      position: 1
-      prefix: '--min_separation'
-outputs:
-  - id: output_imag
-    doc: Output image
-    type: File?
-    outputBinding:
-      glob: $(inputs.output_image_name)
-  - id: logfile
-    type: File?
-    outputBinding:
-      glob: Ateam_separation.log
-label: check_Ateam_separation
-hints:
-  - class: DockerRequirement
-    dockerPull: lofareosc/prefactor:HBAcalibrator
-  - class: InlineJavascriptRequirement
-stdout: Ateam_separation.log

lofar-cwl/steps/dpppconcat.cwl

@@ -8,13 +8,16 @@ baseCommand:
 inputs:
   - id: msin
     type: 'Directory[]'
+    doc: Input Measurement Set
+  - id: msin_fname
+    doc: Input Measurement Set string (including dummy.ms)
+    type: 'string[]'
     inputBinding:
       position: 0
       prefix: msin=
       separate: false
       itemSeparator: ','
-      valueFrom: $(concatenate_path(self))
-    doc: Input Measurement Set
+      valueFrom: "[$(self.join(','))]"
   - id: msout_name
     type: string
     inputBinding:
@@ -87,7 +90,7 @@ inputs:
   - id: missingdata
     type: boolean
     inputBinding:
-      prefix: msout.missingdata=True
+      prefix: msin.missingdata=True
       separate: false
       shellQuote: false
       position: 0
@@ -127,7 +130,7 @@ outputs:
       glob: concat*.log
 arguments:
   - 'steps=[filter,avg,count]'
-  - msout.orderms=False
+  - msin.orderms=False
   - avg.type=average
 requirements:
   - class: ShellCommandRequirement
@@ -137,5 +140,9 @@ requirements:
 hints:
   - class: DockerRequirement
     dockerPull: 'lofareosc/prefactor:HBAcalibrator'
+  - class: InitialWorkDirRequirement
+    listing:
+      - entry: $(inputs.msin)
+        writable: false
 stdout: concat.log
 stderr: concat_err.log

steps/check_ateam_separation.cwl

 class: CommandLineTool
 cwlVersion: v1.0
-$namespaces:
-  sbg: 'https://www.sevenbridges.com/'
 id: check_ateam_separation
 baseCommand:
   - python3
-  - /usr/local/bin/check_Ateam_separation.py
+  - -m
+  - check_Ateam_separation
 inputs:
   - id: ms
     type:

steps/filter_ms_group.cwl

@@ -22,8 +22,14 @@ outputs:
     type: Directory[]
     outputBinding:
       loadContents: true
-      glob: selected_ms.json
+      glob: 'selected_ms.json'
       outputEval: '$(JSON.parse(self[0].contents))'
+  - id: selected_ms
+    type: string[]
+    outputBinding:
+        loadContents: true
+        glob: 'out.json'
+        outputEval: $(JSON.parse(self[0].contents).selected_ms)
 label: filter_ms_group
 
 requirements:
@@ -47,8 +53,14 @@ requirements:
         
         with open(json_file, 'r') as f_stream:
             selected_ms = json.load(f_stream)[group_id]
-        print(selected_ms, ms_by_name)
-        selected_ms = [ms_by_name[os.path.basename(ms_name)] for ms_name in selected_ms]
+            
+        selected_ms = [os.path.basename(ms_name) for ms_name in selected_ms]
+        cwl_output  = {'selected_ms': selected_ms}
+
+        with open('./out.json', 'w') as fp:
+            json.dump(cwl_output, fp)
+            
+        selected_ms = [ms_by_name[ms_name] for ms_name in selected_ms if ms_name != 'dummy.ms']
             
         
         with open(output_file, 'w') as f_stream:
@@ -56,3 +68,11 @@ requirements:
               
         
 
+hints:
+  - class: InitialWorkDirRequirement
+    listing:
+      - entry: $(inputs.measurement_sets)
+        writable: true
+    
+stdout: filter_ms_by_group.log
+stderr: filter_ms_by_group_err.log
\ No newline at end of file

subworkflow/concat.cwl

@@ -58,6 +58,7 @@ steps:
           - msin
     out:
       - id: output
+      - id: selected_ms
     run: ../steps/filter_ms_group.cwl
     label: filter_ms_group
     'sbg:x': -500
@@ -66,7 +67,9 @@ steps:
     in:
       - id: msin
         source:
-          - filter_ms_group/output
+          - msin
+      - id: msin_fname
+        source: filter_ms_group/selected_ms
       - id: msout_name
         source: group_id
       - id: msin_datacolumn

workflows/prefactor_calibrator/prep.cwl

@@ -311,7 +311,7 @@ steps:
     out:
       - id: output_imag
       - id: logfile
-    run: ../../lofar-cwl/steps/check_ateam_separation.cwl
+    run: ../../steps/check_ateam_separation.cwl
     label: check_Ateam_separation
     'sbg:x': 254.234375
     'sbg:y': 1440

workflows/prefactor_target/prep.cwl

@@ -225,7 +225,7 @@ steps:
     out:
       - id: output_imag
       - id: logfile
-    run: ../../lofar-cwl/steps/check_ateam_separation.cwl
+    run: ../../steps/check_ateam_separation.cwl
     label: check_Ateam_separation
     'sbg:x': -500
     'sbg:y': -300