Implement inplaceUpdate

compress_pipeline.cwl

@@ -42,54 +42,45 @@ steps:
       - issue_list
   - id: fix_ai_2013
     run: steps/fix_antenna_information_2013.cwl
-    when: $(inputs.list.includes("FIX_ANTENNA_TABLE"))
     in:
       - id: msin
         source: msin
-      - id: list
+      - id: apply
         source: identify_issues/issue_list
+        valueFrom: $(self.includes("FIX_ANTENNA_TABLE"))
     out:
       - id: msout
   - id: fix_weight_issue
     run: steps/fix_weightissue_flagging.cwl
-    when: $(inputs.list.includes("FIX_WEIGHT_SPECTRUM")) 
     in:
       - id: msin
         source:
           - fix_ai_2013/msout
-          - msin
-        pickValue: first_non_null
-      - id: list
+      - id: apply
         source: identify_issues/issue_list
+        valueFrom: $(self.includes("FIX_WEIGHT_SPECTRUM"))
     out:
       - id: msout
   - id: fix_ai_2015
     run: steps/fix_antenna_information_2015.cwl
-    when: $(inputs.list.includes("FIX_BROKEN_TILES"))
     in:
       - id: msin
         source:
           - fix_weight_issue/msout
-          - fix_ai_2013/msout
-          - msin
-        pickValue: first_non_null
-      - id: list
+      - id: apply
         source: identify_issues/issue_list
+        valueFrom: $(self.includes("FIX_BROKEN_TILES"))
     out:
       - id: msout
   - id: fix_baselines
     run: steps/fix_long_baselines.cwl
-    when: $(inputs.list.includes("FIX_STATION_ADDER"))
     in:
       - id: msin
         source:
           - fix_ai_2015/msout
-          - fix_weight_issue/msout
-          - fix_ai_2013/msout
-          - msin
-        pickValue: first_non_null
-      - id: list
+      - id: apply
         source: identify_issues/issue_list
+        valueFrom: $(self.includes("FIX_STATION_ADDER"))
     out:
       - id: msout
   - id: extract_sip_meta
@@ -108,13 +99,8 @@ steps:
       - id: msin
         source:
           - fix_baselines/msout
-          - fix_ai_2015/msout
-          - fix_weight_issue/msout
-          - fix_ai_2013/msout
-          - msin
-        pickValue: first_non_null
       - id: msout_name
-        source: msin
+        source: fix_baselines/msout
         valueFrom: '$("COMPRESSED_" + self.basename)'
       - id: writefullresflag
         default: true
@@ -148,11 +134,6 @@ steps:
       - id: input
         source:
           - fix_baselines/msout
-          - fix_ai_2015/msout
-          - fix_weight_issue/msout
-          - fix_ai_2013/msout
-          - msin
-        pickValue: first_non_null
     out:
       - id: output
       - id: flags_output

steps/fix_antenna_information_2013.cwl

 id: fix_antenna_information_2013
 label: Fix Antenna Information 2013
-cwlVersion: v1.0
+cwlVersion: v1.2
 class: CommandLineTool
-baseCommand: fixinfo
-
+baseCommand:
+  - bash
+  - script.sh
 inputs:
   - id: msin
     type: Directory
-
+  - id: apply
+    type: boolean
 outputs:
   - id: msout
     type: Directory
     outputBinding:
       glob: $(inputs.msin.basename)
 
-arguments:
-  - $(inputs.msin.basename)
-  - /opt/fixinfo
-
 requirements:
   - class: InitialWorkDirRequirement
     listing:
       - entry: $(inputs.msin)
         writable: true
         entryname: $(inputs.msin.basename)
+      - entryname: script.sh
+        entry: |
+          #!/bin/bash
+
+          execute=$(inputs.apply)
+          if [ $execute = 'true' ] ; then
+            echo "Appling fix antenna information 2013"
+            fixinfo $(inputs.msin.basename) /opt/fixinfo
+          fi
+          echo "Skipping apply fix antenna information 2013"
 
+  - class: InplaceUpdateRequirement
+    inplaceUpdate: true
 hints:
   - class: DockerRequirement
     dockerPull: "astronsdc/lofar-legacy:latest"

steps/fix_antenna_information_2015.cwl

 id: fix_antenna_information_2015
 label: Fix Antenna Information_2015
-cwlVersion: v1.0
+cwlVersion: v1.2
 class: CommandLineTool
-baseCommand: fixbeaminfo
+baseCommand:
+  - bash
+  - script.sh
 
 inputs:
   - id: msin
@@ -14,9 +16,6 @@ outputs:
     outputBinding:
       glob: $(inputs.msin.basename)
 
-arguments:
-  - $(inputs.msin.basename)
-  - /opt/fixbeaminfo
 
 requirements:
   - class: InitialWorkDirRequirement
@@ -24,7 +23,19 @@ requirements:
       - entry: $(inputs.msin)
         writable: true
         entryname: $(inputs.msin.basename)
+      - entryname: script.sh
+        entry: |
+          #!/bin/bash
 
+          execute=$(inputs.apply)
+          if [ $execute = 'true' ] ; then
+            echo "Appling fix antenna information 2015"
+            fixbeaminfo $(inputs.msin.basename) /opt/fixbeaminfo
+          fi
+          echo "Skipping apply fix antenna information 2015"
+
+  - class: InplaceUpdateRequirement
+    inplaceUpdate: true
 hints:
   - class: DockerRequirement
     dockerPull: "astronsdc/lofar-legacy:latest"

steps/fix_long_baselines.cwl

 id: fix_long_baseline
 label: Fix weighted sum for long baseline pipeline
-cwlVersion: v1.0
+cwlVersion: v1.2
 class: CommandLineTool
 baseCommand:
-  - fix_weightedsum_uvw
+  - bash
+  - script.sh
 
-arguments:
-  - -f
-  -  $(inputs.msin.basename)
 requirements:
   - class: InitialWorkDirRequirement
     listing:
       - entry: $(inputs.msin)
         writable: true
         entryname: $(inputs.msin.basename)
+      - entryname: script.sh
+        entry: |
+          #!/bin/bash
+
+          execute=$(inputs.apply)
+          if [ $execute = 'true' ] ; then
+            echo "Appling fix weighted sum UVW"
+            fix_weightedsum_uvw -f $(inputs.msin.basename) -n $(inputs.new_station)
+          fi
+          echo "Skipping apply fix weighted sum UVW"
+
+  - class: InplaceUpdateRequirement
+    inplaceUpdate: true
 inputs:
   - id: msin
     type: Directory
   - id: new_station
     doc: new station name (default ST001)
     type: string?
-    inputBinding:
-      prefix: -n
+    default: ST001
 outputs:
   - id: msout
     type: Directory

steps/fix_weightissue_flagging.cwl

 id: fix_weight_issue_flagging
 label: Fix Weight Issue Flagging
-cwlVersion: v1.0
+cwlVersion: v1.2
 class: CommandLineTool
-baseCommand: fix_weightspectrum
-arguments:
-  - $(inputs.msin.basename)
+baseCommand:
+  - bash
+  - script.sh
 requirements:
   - class: InitialWorkDirRequirement
     listing:
       - entry: $(inputs.msin)
         writable: true
         entryname: $(inputs.msin.basename)
+      - entryname: script.sh
+        entry: |
+          #!/bin/bash
+
+          execute=$(inputs.apply)
+          if [ $execute = 'true' ] ; then
+            echo "Appling fix weight issue flagging"
+            fix_weightspectrum $(inputs.msin.basename)
+          fi
+          echo "Skipping apply fix weight issue flagging"
+  - class: InplaceUpdateRequirement
+    inplaceUpdate: true
 inputs:
   - id: msin
     type: Directory

steps/identify_issues.cwl

@@ -4,7 +4,7 @@ class: CommandLineTool
 cwlVersion: v1.0
 hints:
   DockerRequirement:
-    dockerPull: astronsdc/lofar-legacy:latest
+    dockerPull: astronsdc/lofar-legacy
 
 inputs:
   - id: msin
@@ -19,6 +19,11 @@ outputs:
       glob: output.txt
       loadContents: true
       outputEval: $(JSON.parse(self[0].contents))
+
+  - id: msout
+    type: Directory
+    outputBinding:
+      glob: $(inputs.msin.basename)
 stdout: output.txt
 
 baseCommand:
@@ -27,3 +32,8 @@ baseCommand:
 
 requirements:
   - class: InlineJavascriptRequirement
+  - class: InitialWorkDirRequirement
+    listing:
+      - entry: $(inputs.msin)
+        writable: true
+        entryname: $(inputs.msin.basename)