Merge branch 'add_h5parmcollector' into 'master'

Add H5ParmCollector

See merge request eosc/prefactor3-cwl!1

.gitlab-ci.yml

@@ -64,6 +64,12 @@ NDPPP:
   script:
     - cwltool --no-container --preserve-environment LD_LIBRARY_PATH --preserve-environment PATH steps/DPPP.cwl test_jobs/NDPPP.json
 
+h5parm_collector:
+  stage: test_steps
+  allow_failure: true
+  script:
+    - cwltool --no-container --preserve-environment LD_LIBRARY_PATH --preserve-environment PATH --preserve-environment PYTHONPATH steps/H5ParmCollector.cwl test_jobs/h5parm_collector.json
+
 aoflagger:
   stage: test_steps
   allow_failure: true
@@ -82,6 +88,12 @@ interpolate_visibilities:
   script:
     - cwltool --no-container --preserve-environment LD_LIBRARY_PATH --preserve-environment PATH --preserve-environment PYTHONPATH steps/interpolate_visibilities.cwl test_jobs/interpolate_visibilities.json
 
+h5parm_collector:
+  stage: test_steps
+  allow_failure: true
+  script:
+    - cwltool --no-container --preserve-environment LD_LIBRARY_PATH --preserve-environment PATH --preserve-environment PYTHONPATH steps/H5ParmCollector.cwl test_jobs/h5parm_collector.json
+ 
 blsmooth:
   stage: test_steps
   allow_failure: true

Docker/Dockerfile

@@ -93,9 +93,13 @@ ARG LSMTool_TAG=master
 RUN apt-get update && apt-get install -y nodejs python3-pip git wsclean
 RUN python3 -m pip install cwltool cwl-runner -e "git://github.com/darafferty/LSMTool.git@${LSMTool_TAG}#egg=LSMTool"
 
+RUN python3 -m pip install git+https://github.com/revoltek/losoto.git
+
 ADD L570745_uv_first10.MS.tar.xz /data
 ADD skymodels.tar.gz /data/skymodels
+ADD example.h5 /data
 ADD ./test_data/* /data/
+
 ADD .entrypoint /home/lofaruser/.entrypoint
 RUN chown lofaruser:lofaruser /home/lofaruser/.entrypoint && \ 
     chmod +rx /home/lofaruser/.entrypoint

steps/H5ParmCollector.cwl

+#!/usr/bin/env cwl-runner
+
+class: CommandLineTool
+cwlVersion: v1.0
+id: h5parm_collector
+
+hints:
+  DockerRequirement:
+    dockerPull: tammojan/lofar-pipeline
+
+baseCommand:
+  - H5parm_collector.py
+inputs:
+  - id: h5parmFiles
+    type: File[]
+    doc: List of h5parm files
+    inputBinding:
+      position: 0
+  - id: insolset
+    type: string?
+    default: sol000
+    doc: Input solset name
+    inputBinding:
+      prefix: --insolset
+  - id: outh5parmname
+    type: string
+    doc: Output h5parm name
+    default: output.h5
+
+outputs:
+  - id: outh5parm
+    doc: Output h5parm
+    type: File
+    outputBinding:
+      glob: $(inputs.outh5parmname)
+label: H5parm_collector

test_jobs/h5parm_collector.json

+{
+   "h5parmFiles": [
+   {
+            "class": "File",
+            "path": "/data/example.h5"
+   }
+   ]
+}