diff --git a/.gitignore b/.gitignore index 6ada2877b3453550a6cec11b68ffad30847f84bf..b0502826fa48314208d9ccc2a7342bd20769c0c3 100644 --- a/.gitignore +++ b/.gitignore @@ -1,5 +1,6 @@ test_data/*.MS Docker/scripts +Docker/prefactor *.sif # Byte-compiled / optimized / DLL files __pycache__/ diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index c6be0c29784542c0548ddb274c98bc2a0de64517..0efe8139e9797ac32568180278f4bb0a6d522268 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -1,4 +1,4 @@ -image: lofareosc/prefactor-ci:master +image: lofareosc/prefactor-ci:latest variables: TEST_DATASET_NAME: "L570745_uv_first10.MS.tar.xz" @@ -56,6 +56,11 @@ blsmooth: script: - cwltool --no-container --preserve-environment LD_LIBRARY_PATH --preserve-environment PATH --preserve-environment PYTHONPATH steps/blsmooth.cwl test_jobs/blsmooth.json +pol_align: + stage: integration_test + script: + - cwltool --no-container subworkflow/pol_align.cwl test_jobs/pol_align.json + prefactor_calibrator: stage: integration_test script: diff --git a/Docker/Dockerfile b/Docker/Dockerfile index 7b8b78a8b7f7c7fff4f642458082b1559993bbfb..b2d0d68f506300c9c3891a932d91d146288a4974 100644 --- a/Docker/Dockerfile +++ b/Docker/Dockerfile @@ -1,10 +1,10 @@ FROM lofareosc/lofar-pipeline:latest - +USER root COPY prefactor/scripts/* /opt/lofar/scripts/ COPY prefactor/skymodels/* /data/skymodels/ COPY prefactor/rfistrategies/* /data/rfistrategies/ COPY prefactor/solutions/ /data/solutions/* - +RUN apt update && apt install vim RUN ln -sf /opt/lofar/scripts/* /usr/local/bin/ RUN chmod +rx /usr/local/bin/* diff --git a/subworkflow/pol_align.cwl b/subworkflow/pol_align.cwl new file mode 100644 index 0000000000000000000000000000000000000000..91666c3f84f2a439e81d3306ac2784d3e44b5732 --- /dev/null +++ b/subworkflow/pol_align.cwl @@ -0,0 +1,71 @@ +class: Workflow +cwlVersion: v1.0 +id: pol_align +label: PolAlign +$namespaces: + sbg: 'https://www.sevenbridges.com/' + lofar: 'https://git.astron.nl/eosc/ontologies/raw/master/schema/lofar.owl' +inputs: + - id: refAnt + type: string? + 'sbg:x': -451.3746643066406 + 'sbg:y': -493.92510986328125 + - id: input_h5parm + type: File + 'sbg:x': -743.1871948242188 + 'sbg:y': -316.5615234375 +outputs: + - id: output_h5parm + outputSource: + - losoto_residual/output_h5parm + type: File + 'sbg:x': 152.59103393554688 + 'sbg:y': -289.2899169921875 +steps: + - id: losoto_duplicate + in: + - id: input_h5parm + source: input_h5parm + - id: soltab + default: sol000/phase000 + - id: soltabOut + default: phaseOrig + out: + - id: output_h5parm + run: ../lofar-cwl/steps/LoSoTo.Duplicate.cwl + 'sbg:x': -423.6229248046875 + 'sbg:y': -287.8958435058594 + - id: losoto_polalign + in: + - id: input_h5parm + source: losoto_duplicate/output_h5parm + - id: soltab + default: sol000/phase000 + - id: soltabout + default: polalign + - id: average + default: true + - id: replace + default: true + - id: refAnt + source: refAnt + out: + - id: output_h5parm + run: ../lofar-cwl/steps/LoSoTo.Polalign.cwl + 'sbg:x': -203.663818359375 + 'sbg:y': -292.61700439453125 + - id: losoto_residual + in: + - id: input_h5parm + source: losoto_polalign/output_h5parm + - id: soltab + default: sol000/phase000 + - id: soltabsToSub + default: + - polalign + out: + - id: output_h5parm + run: ../lofar-cwl/steps/LoSoTo.Residual.cwl + 'sbg:x': -0.012040258385241032 + 'sbg:y': -287.7294006347656 +requirements: [] diff --git a/test_jobs/pol_align.json b/test_jobs/pol_align.json new file mode 100644 index 0000000000000000000000000000000000000000..0cdbed898de539d8a086933afbb8b98b601a80d8 --- /dev/null +++ b/test_jobs/pol_align.json @@ -0,0 +1,7 @@ +{ + "input_h5parm": { + "class": "File", + "format": "lofar:#H5Parm", + "path": "/data/example.h5" + } +}