update, small fixes

Former-commit-id: 648aff69

lofar-cwl/steps/check_ateam_separation.cwl

@@ -39,6 +39,6 @@ outputs:
 label: check_Ateam_separation
 hints:
   - class: DockerRequirement
-    dockerPull: lofareosc/prefactor
+    dockerPull: lofareosc/prefactor:HBAcalibrator
   - class: InlineJavascriptRequirement
 stdout: Ateam_separation.log

lofar-cwl/steps/makesourcedb.cwl

@@ -51,7 +51,7 @@ outputs:
 label: make_sourcedb_ateam
 hints:
   - class: DockerRequirement
-    dockerPull: 'lofareosc/prefactor:latest'
+    dockerPull: 'lofareosc/prefactor:HBAcalibrator'
 stdout: make_sourcedb_ateam.log
 requirements:
   - class: InlineJavascriptRequirement

steps/blsmooth.cwl

@@ -82,7 +82,7 @@ outputs:
       glob: $(inputs.msin.basename)
 hints:
  - class: DockerRequirement
-   dockerPull: lofareosc/prefactor-ci:master
+   dockerPull: lofareosc/prefactor:HBAcalibrator-ci:master
 requirements:
  - class: InitialWorkDirRequirement
    listing:

steps/check_ateam_separation.cwl

@@ -39,6 +39,6 @@ outputs:
 label: check_Ateam_separation
 hints:
   - class: DockerRequirement
-    dockerPull: lofareosc/prefactor
+    dockerPull: lofareosc/prefactor:HBAcalibrator
   - class: InlineJavascriptRequirement
 stdout: Ateam_separation.log

steps/find_skymodel_cal.cwl

@@ -5,25 +5,44 @@ $namespaces:
 id: find_skymodel_cal_py
 baseCommand:
   - python3
-  - /usr/local/bin/find_skymodel_cal.py
 inputs:
-  - id: ms
-    type:
-      - Directory
-      - type: array
-        items: Directory
-    inputBinding:
-      position: 0
-    doc: Input measurement set
-  - id: DirSkymodelCal
-    type:
-      - Directory
-      - string
-    default: '/data/skymodels'
-    doc: Directory containing the sky models
-    inputBinding:
-      position: 1
-      prefix: '--DirSky'
+    - id: msin
+      type: Directory[]
+      doc: MS containing the calibrator
+      inputBinding:
+        position: 0
+    - id: skymodels
+      type: Directory?
+      doc: Directory containing the sky models
+    - id: skymodels_extension
+      type: string?
+      doc: path extension of the sky models
+
+label: find_skymodel_cal.py
+arguments:
+  - '-c'
+  - |
+    import sys
+
+    from unittest.mock import MagicMock
+    sys.modules['lofarpipe.support.data_map'] = MagicMock()
+
+
+    from find_skymodel_cal import main as find_skymodel
+    import json
+    mss = sys.argv[1:]
+    skymodels = "$(inputs.skymodels.path)"
+
+    extension = "$(inputs.skymodels_extension)"
+    output = {}
+    if extension != 'null':
+        output = find_skymodel(mss, skymodels, extension)
+    else:
+        output = find_skymodel(mss, skymodels)
+
+    cwl_output = {'class': 'File', 'path': output['SkymodelCal']}
+    with open('./out.json', 'w') as fp:
+        json.dump(cwl_output, fp)
 outputs:
   - id: output_models
     type: File
@@ -31,10 +50,10 @@ outputs:
         loadContents: true
         glob: 'out.json'
         outputEval: $(JSON.parse(self[0].contents))
-label: find_skymodel_cal.py
+
 requirements:
   - class: InlineJavascriptRequirement
 
 hints:
   DockerRequirement:
-    dockerPull: lofareosc/prefactor
+    dockerPull: lofareosc/prefactor-ci:master
\ No newline at end of file

workflows/prefactor_calibrator/prep.cwl

@@ -218,11 +218,9 @@ steps:
     'sbg:y': 300
   - id: find_skymodel_cal
     in:
-      - id: ms
+      - id: msin
         source: msin
-      - id: max_seperation_arcmin
-        source: max_separation_arcmin
-      - id: DirSkymodelCal
+      - id: skymodels
         source: calibrator_path_skymodel
     out:
       - id: output_models