diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index ab043a38a1a847a41884325cdce999a4cc6a6c66..b7b08443fc0584fa9729cccecd49cf401c58d402 100644 --- a/.gitlab-ci.yml +++ b/.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 diff --git a/Docker/Dockerfile b/Docker/Dockerfile index cf33dffa7fb9cad29a1d3224c18d1833e2df0634..516becf3e383588a2430943e4cdacb09cfa065c2 100644 --- a/Docker/Dockerfile +++ b/Docker/Dockerfile @@ -93,8 +93,11 @@ 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 .entrypoint /home/lofaruser/.entrypoint RUN chown lofaruser:lofaruser /home/lofaruser/.entrypoint && \ chmod +rx /home/lofaruser/.entrypoint diff --git a/steps/H5ParmCollector.cwl b/steps/H5ParmCollector.cwl new file mode 100755 index 0000000000000000000000000000000000000000..46442b33e0c212f67179fa7371fa684d733e94c8 --- /dev/null +++ b/steps/H5ParmCollector.cwl @@ -0,0 +1,36 @@ +#!/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 diff --git a/test_data/example.h5 b/test_data/example.h5 new file mode 100644 index 0000000000000000000000000000000000000000..554933b577a0dcf1b2aa3fa91c7de5b2477fd724 Binary files /dev/null and b/test_data/example.h5 differ diff --git a/test_jobs/h5parm_collector.json b/test_jobs/h5parm_collector.json new file mode 100644 index 0000000000000000000000000000000000000000..958493f2d5d8a497720e0cd2a5dfa048be960d09 --- /dev/null +++ b/test_jobs/h5parm_collector.json @@ -0,0 +1,8 @@ +{ + "h5parmFiles": [ + { + "class": "File", + "path": "/data/example.h5" + } + ] +}