diff --git a/lofar-cwl/.gitignore b/lofar-cwl/.gitignore deleted file mode 100644 index 8fe27bc44a909a7d26e8fb891cadc4b53d078a78..0000000000000000000000000000000000000000 --- a/lofar-cwl/.gitignore +++ /dev/null @@ -1,135 +0,0 @@ -test_data/*.MS -Docker/scripts -Docker/DP3 -Docker/Dysco -Docker/STMAN -Docker/idg -*.sif -# Byte-compiled / optimized / DLL files -__pycache__/ -*.py[cod] -*$py.class - -# C extensions -*.so - -# Distribution / packaging -.Python -build/ -develop-eggs/ -dist/ -downloads/ -eggs/ -.eggs/ -lib/ -lib64/ -parts/ -sdist/ -var/ -wheels/ -pip-wheel-metadata/ -share/python-wheels/ -*.egg-info/ -.installed.cfg -*.egg -MANIFEST - -# PyInstaller -# Usually these files are written by a python script from a template -# before PyInstaller builds the exe, so as to inject date/other infos into it. -*.manifest -*.spec - -# Installer logs -pip-log.txt -pip-delete-this-directory.txt - -# Unit test / coverage reports -htmlcov/ -.tox/ -.nox/ -.coverage -.coverage.* -.cache -nosetests.xml -coverage.xml -*.cover -*.py,cover -.hypothesis/ -.pytest_cache/ - -# Translations -*.mo -*.pot - -# Django stuff: -*.log -local_settings.py -db.sqlite3 -db.sqlite3-journal - -# Flask stuff: -instance/ -.webassets-cache - -# Scrapy stuff: -.scrapy - -# Sphinx documentation -docs/_build/ - -# PyBuilder -target/ - -# Jupyter Notebook -.ipynb_checkpoints - -# IPython -profile_default/ -ipython_config.py - -# pyenv -.python-version - -# pipenv -# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control. -# However, in case of collaboration, if having platform-specific dependencies or dependencies -# having no cross-platform support, pipenv may install dependencies that don't work, or not -# install all needed dependencies. -#Pipfile.lock - -# celery beat schedule file -celerybeat-schedule - -# SageMath parsed files -*.sage.py - -# Environments -.env -.venv -env/ -venv/ -ENV/ -env.bak/ -venv.bak/ - -# Spyder project settings -.spyderproject -.spyproject - -# Rope project settings -.ropeproject - -# mkdocs documentation -/site - -# mypy -.mypy_cache/ -.dmypy.json -dmypy.json - -# Pyre type checker -.pyre/ - -# Not idea -.idea diff --git a/lofar-cwl/.gitlab-ci.yml b/lofar-cwl/.gitlab-ci.yml deleted file mode 100644 index 3e7d60a3e3dfbf95be3a8cc490177244ea885f18..0000000000000000000000000000000000000000 --- a/lofar-cwl/.gitlab-ci.yml +++ /dev/null @@ -1,168 +0,0 @@ -image: lofareosc/lofar-pipeline-ci:latest - -variables: - TEST_DATASET_NAME: "L570745_uv_first10.MS.tar.xz" - PIP_CACHE_DIR: "$CI_PROJECT_DIR/.cache/pip" - -stages: - - build_docker - - push_docker - - validate_cwl_scripts - - test_steps - - integration_test - -before_script: - - mkdir workdir - - mkdir logs - -after_script: - - echo "All done" - -build_docker: - image: docker:latest - stage: build_docker - only: - - tags - script: - - apk add git subversion git-lfs bash - - cd Docker - - bash build_docker.sh - -push_docker_tags: - image: docker:latest - allow_failure: true - stage: push_docker - only: - - tags - script: - - docker login -u $CI_REGISTRY_USER -p $CI_REGISTRY_PASSWORD $CI_REGISTRY - - docker tag lofareosc/prefactor-ci:latest $CI_REGISTRY/prefactor-ci:$CI_COMMIT_REF_NAME - - docker push $CI_REGISTRY/prefactor-ci:$CI_COMMIT_REF_NAME - -validate_scripts: - stage: validate_cwl_scripts - script: - - for file in `find . -name 'steps/*.cwl'`; do cwltool --validate $file; done - -average_step_generator: - stage: test_steps - allow_failure: true - script: - - cwl-runner steps/DP3.AveragerStepGenerator.cwl test_jobs/averager_step_generator.json - - ! cwl-runner steps/DP3.AveragerStepGenerator.cwl test_jobs/averager_step_generator_error.json - -aoflagger_step_generator: - stage: test_steps - allow_failure: true - script: - - cwl-runner steps/DP3.AOFlaggerStepGenerator.cwl test_jobs/aoflagger_step_generator.json - -preflagger_step_generator: - stage: test_steps - allow_failure: true - script: - - cwl-runner steps/DP3.PreflaggerStepGenerator.cwl test_jobs/preflagger_step_generator.json - -losoto_abs: - stage: test_steps - allow_failure: true - script: - - cwl-runner --no-container steps/LoSoTo.Abs.cwl test_jobs/losoto_abs.json - -losoto_duplicate: - stage: test_steps - allow_failure: true - script: - - cwl-runner --no-container steps/LoSoTo.Duplicate.cwl test_jobs/losoto_duplicate.json - -losoto_plot: - stage: test_steps - allow_failure: true - script: - - cwl-runner --no-container steps/LoSoTo.Plot.cwl test_jobs/losoto_plot.json - -losoto_norm: - stage: test_steps - allow_failure: true - script: - - cwl-runner --no-container steps/LoSoTo.Norm.cwl test_jobs/losoto_norm.json - -losoto_replicateonaxis: - stage: test_steps - allow_failure: true - script: - - cwl-runner --no-container steps/LoSoTo.Replicateonaxis.cwl test_jobs/losoto_replicateonaxis.json - -losoto_reset: - stage: test_steps - allow_failure: true - script: - - cwl-runner --no-container steps/LoSoTo.Reset.cwl test_jobs/losoto_reset.json - -losoto_residual: - stage: test_steps - allow_failure: true - script: - - cwl-runner --no-container steps/LoSoTo.Residual.cwl test_jobs/losoto_residual.json - -parset_selector: - stage: test_steps - allow_failure: true - script: - - cwl-runner steps/DP3.Selector.cwl test_jobs/selector.json - -file_selector: - stage: test_steps - allow_failure: true - script: - - cwl-runner steps/FileSelector.cwl test_jobs/file_selector.json - -NDPPP: - stage: test_steps - allow_failure: true - script: - - cwltool --no-container --preserve-environment LD_LIBRARY_PATH --preserve-environment PATH steps/DPPP.cwl test_jobs/NDPPP.json - -DP3.Execute: - stage: test_steps - allow_failure: true - script: - - cwltool --no-container --preserve-environment LD_LIBRARY_PATH --preserve-environment PATH steps/DP3.Execute.cwl test_jobs/dp3_execute.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 - script: - - cwltool --no-container --preserve-environment LD_LIBRARY_PATH --preserve-environment PATH steps/AOFlagger.cwl test_jobs/aoflagger.json - -interpolate_visibilities: - stage: test_steps - allow_failure: true - 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 - -ddecal: - stage: test_steps - allow_failure: true - script: - - cwltool --no-container --preserve-environment LD_LIBRARY_PATH --preserve-environment PATH --preserve-environment PYTHONPATH steps/ddecal.cwl test_jobs/ddecal.json - -predict: - stage: test_steps - allow_failure: true - script: - - cwltool --no-container --preserve-environment LD_LIBRARY_PATH --preserve-environment PATH --preserve-environment PYTHONPATH steps/predict.cwl test_jobs/predict.json - - diff --git a/lofar-cwl/Docker/.entrypoint b/lofar-cwl/Docker/.entrypoint deleted file mode 100644 index cc2b666b7d5c93c2a7e7ea6715c17acd498f338d..0000000000000000000000000000000000000000 --- a/lofar-cwl/Docker/.entrypoint +++ /dev/null @@ -1,5 +0,0 @@ -#!/bin/bash -set -e - -exec "$@" - diff --git a/lofar-cwl/Docker/Dockerfile b/lofar-cwl/Docker/Dockerfile deleted file mode 100644 index ca101ba31e9139fd9ddf4cc3d4d6392b56b3e936..0000000000000000000000000000000000000000 --- a/lofar-cwl/Docker/Dockerfile +++ /dev/null @@ -1,148 +0,0 @@ -FROM kernsuite/base:5 as builder -SHELL ["/bin/bash", "-c"] - -RUN export DEBIAN_FRONTEND=noninteractive && \ - apt-get update && \ - apt-get install -y \ - casacore-data \ - casacore-dev \ - libboost-python-dev \ - libcfitsio-dev \ - python-dev \ - python3-numpy \ - cmake \ - build-essential \ - libhdf5-serial-dev \ - libarmadillo-dev \ - libboost-filesystem-dev \ - libboost-system-dev \ - libboost-date-time-dev \ - libboost-signals-dev \ - libboost-program-options-dev \ - libboost-test-dev \ - libxml2-dev \ - libpng-dev \ - pkg-config \ - aoflagger-dev \ - libgtkmm-3.0-dev \ - git \ - wget \ - libfftw3-dev \ - libgsl-dev - -RUN mkdir -p /src/ -WORKDIR /src/ - - -# Build the IDG version from source - - -ADD ./idg /src/idg/src -RUN mkdir idg/build && cd idg/build && cmake -DCMAKE_INSTALL_PREFIX=/usr/local/ ../src && make install -j2 - -ADD ./DP3 /src/dp3/src -RUN cd /src/dp3/ && \ - mkdir build && \ - cd build && \ - cmake ../src -DCMAKE_INSTALL_PREFIX=/usr/local/ -DPORTABLE=True &&\ - make -j2 && \ - make install -j2 - -ADD ./STMAN /src/STMAN/src -RUN cd /src/STMAN/ && \ - mkdir build && \ - cd build && \ - cmake ../src -DCMAKE_INSTALL_PREFIX=/usr/local/ -DPORTABLE=True && \ - make -j2 && \ - make install -j2 - -ADD ./Dysco /src/Dysco/src -RUN cd /src/Dysco/ && \ - mkdir build && \ - cd build && \ - cmake ../src -DCMAKE_INSTALL_PREFIX=/usr/local/ -DPORTABLE=True && \ - make -j2 && \ - make install -j2 - -#---------------------------------------------- -FROM kernsuite/base:5 as runner - -COPY --from=builder /usr/local/ /usr/local - -SHELL ["/bin/bash", "-c"] - -RUN export DEBIAN_FRONTEND=noninteractive && \ - apt-get update && \ - apt-get install -y \ - aoflagger \ - casacore-data \ - libarmadillo8 \ - libboost-date-time1.65.1 \ - libboost-filesystem1.65.1 \ - libboost-python1.65.1 \ - libboost-program-options1.65.1 \ - libboost-system1.65.1 \ - libboost-signals1.65.1 \ - libboost-test1.65.1 \ - libboost-python1.65-dev \ - libstationresponse2 \ - libcasa-* \ - libcfitsio5 \ - libgtkmm-3.0 \ - libfftw3-3 \ - libhdf5-cpp-100 \ - libpng16-16 \ - libxml2 \ - python3.7 \ - python3-casacore \ - python3-numpy \ - python3-scipy && \ - rm -rf /var/lib/apt/lists/* - - -RUN mkdir /home/lofaruser/ && \ - groupadd -r lofaruser && \ - useradd --no-log-init -r -g lofaruser lofaruser && \ - chown lofaruser:lofaruser /home/lofaruser - -ARG TOIL_VERSION=3.20.0 -LABEL toil.version=${TOIL_VERSION} - -ARG LSMTool_TAG=master -LABEL LSMTool.version.tag=${LSMTool_TAG} - -ARG LoSoTo_TAG=master -LABEL LoSoTo.version.tag=${LoSoTo_TAG} - -ARG STMAN_TAG=master -LABEL STMAN.version.tag=${STMAN_TAG} - -ARG Dysco_TAG=master -LABEL Dysco.version.tag=${Dysco_TAG} - - -RUN apt update && apt install -y nodejs python3-pip git wsclean -RUN python3 -m pip install cwltool cwl-runner -e "git://github.com/darafferty/LSMTool.git@${LSMTool_TAG}#egg=LSMTool" \ - "toil[cwl]"==${TOIL_VERSION} \ - matplotlib - -RUN python3 -m pip install -e "git+https://github.com/revoltek/losoto.git@${LoSoTo_TAG}#egg=LoSoTo" - -ADD losoto.patch /home/lofaruser/losoto.patch -RUN patch /src/losoto/losoto/operations/__init__.py /home/lofaruser/losoto.patch -ADD .entrypoint /home/lofaruser/.entrypoint -RUN chown lofaruser:lofaruser /home/lofaruser/.entrypoint && \ - chmod +rx /home/lofaruser/.entrypoint - -WORKDIR /home/lofaruser - - -RUN chmod +rx /usr/local/bin/* -ENTRYPOINT ["/home/lofaruser/.entrypoint"] -USER lofaruser - -ARG DP3_TAG=master -ARG IDG_TAG=master - -LABEL IDG.version.tag=${IDG_TAG} -LABEL DP3.version.tag=${DP3_TAG} diff --git a/lofar-cwl/Docker/Dockerfile_ci b/lofar-cwl/Docker/Dockerfile_ci deleted file mode 100644 index 63baad2426e2610d5975d353f07d15476114eb0f..0000000000000000000000000000000000000000 --- a/lofar-cwl/Docker/Dockerfile_ci +++ /dev/null @@ -1,8 +0,0 @@ -FROM lofareosc/lofar-pipeline:latest -SHELL ["/bin/bash", "-c"] - -ADD L570745_uv_first10.MS.tar.xz /data -ADD skymodels.tar.gz /data/skymodels -ADD test_data/A-Team_lowres.sourcedb /data/A-Team_lowres.sourcedb -ADD test_data/example.h5 /data/example.h5 -ADD test_data/L570745_SB001_uv_MODEL.MS /data/L570745_SB001_uv_MODEL.MS diff --git a/lofar-cwl/Docker/L570745_uv_first10.MS.tar.xz.REMOVED.git-id b/lofar-cwl/Docker/L570745_uv_first10.MS.tar.xz.REMOVED.git-id deleted file mode 100644 index 2266c40d2de8785cb1e771f88823e6fb2f02be07..0000000000000000000000000000000000000000 --- a/lofar-cwl/Docker/L570745_uv_first10.MS.tar.xz.REMOVED.git-id +++ /dev/null @@ -1 +0,0 @@ -fac322047acad1a9cf1425d64a08d7bc3548f462 \ No newline at end of file diff --git a/lofar-cwl/Docker/build_docker.sh b/lofar-cwl/Docker/build_docker.sh deleted file mode 100755 index b908b90fc708c4726fb1010c202c5945eafda4e2..0000000000000000000000000000000000000000 --- a/lofar-cwl/Docker/build_docker.sh +++ /dev/null @@ -1,52 +0,0 @@ -#! /bin/bash -set -e - -git_clone_or_pull () { - REPO=$1 - BRANCH=$2 - DIR=$3 - if [ -d $DIR ] - then - git -C "${DIR}" pull - else - git clone --depth 1 -b "${BRANCH}" "${REPO}" "${DIR}" - fi -} - -# SOFTWARE VERSIONS -DP3_TAG=v4.1 -IDG_TAG=0.6 -LSMTool_TAG=v1.4.2 -LoSoTo_TAG=f0398b -TOIL_VERSION=3.20.0 -STMAN_TAG=master -Dysco_TAG=v1.2 -Prefactor_TAG=master - -# FETCHES THE IDG -git_clone_or_pull https://gitlab.com/astron-idg/idg/ ${IDG_TAG} idg - -# FETCHES DP3 -git_clone_or_pull https://github.com/lofar-astron/DP3 ${DP3_TAG} DP3 - -# FETCHES STMAN -git_clone_or_pull https://github.com/lofar-astron/LofarStMan ${STMAN_TAG} STMAN - -# FETCHES Dysco -git_clone_or_pull https://github.com/aroffringa/dysco.git ${Dysco_TAG} Dysco - - -SCRIPT_PATH=$(realpath ${BASH_SOURCE[0]}) - -DOCKER_PATH=$(dirname ${SCRIPT_PATH}) - -docker build ${DOCKER_PATH} --build-arg=IDG_TAG=${IDG_TAG}\ - --build-arg=DP3_TAG=${DP3_TAG}\ - --build-arg=LSMTool_TAG=${LSMTool_TAG}\ - --build-arg=LoSoTo_TAG=${LoSoTo_TAG}\ - --build-arg=STMAN_TAG=${STMAN_TAG}\ - --build-arg=Dysco_TAG=${Dysco_TAG}\ - --build-arg=TOIL_VERSION=${TOIL_VERSION}\ - -t lofareosc/lofar-pipeline - -docker build ${DOCKER_PATH} -f ${DOCKER_PATH}/Dockerfile_ci -t lofareosc/lofar-pipeline-ci diff --git a/lofar-cwl/Docker/losoto.patch b/lofar-cwl/Docker/losoto.patch deleted file mode 100644 index fbdfb47754296d2b358e162afe777cd1e41fea75..0000000000000000000000000000000000000000 --- a/lofar-cwl/Docker/losoto.patch +++ /dev/null @@ -1,13 +0,0 @@ ---- /src/losoto/losoto/operations/__init__.py 2019-11-07 12:43:46.220577945 +0000 -+++ /src/losoto/losoto/operations/__init__.py 2019-11-07 12:43:34.401765786 +0000 -@@ -2,8 +2,7 @@ - - __all__ = [ os.path.basename(f)[:-3] for f in glob.glob(os.path.dirname(__file__)+"/*.py") if f[0] != '_'] - --for x in __all__: -- __import__(x, locals(), globals()) -+from . import * - - class Timer(object): - """ - diff --git a/lofar-cwl/Docker/skymodels.tar.gz.REMOVED.git-id b/lofar-cwl/Docker/skymodels.tar.gz.REMOVED.git-id deleted file mode 100644 index e2362e5aa6bd4e3fe266bd71966dee96de2449ae..0000000000000000000000000000000000000000 --- a/lofar-cwl/Docker/skymodels.tar.gz.REMOVED.git-id +++ /dev/null @@ -1 +0,0 @@ -2377705b2f6824c2a1bd59ddabfe5647a981f83e \ No newline at end of file diff --git a/lofar-cwl/Docker/test_data/A-Team_lowres.sourcedb b/lofar-cwl/Docker/test_data/A-Team_lowres.sourcedb deleted file mode 100644 index b4e89906093cc01438b6a7b81f3ea9bfb06ba520..0000000000000000000000000000000000000000 Binary files a/lofar-cwl/Docker/test_data/A-Team_lowres.sourcedb and /dev/null differ diff --git a/lofar-cwl/Docker/test_data/L570745_SB001_uv_MODEL.MS/ANTENNA/table.dat b/lofar-cwl/Docker/test_data/L570745_SB001_uv_MODEL.MS/ANTENNA/table.dat deleted file mode 100644 index 3670600f2692d3b4b77cc07eddbdb44261d3c214..0000000000000000000000000000000000000000 Binary files a/lofar-cwl/Docker/test_data/L570745_SB001_uv_MODEL.MS/ANTENNA/table.dat and /dev/null differ diff --git a/lofar-cwl/Docker/test_data/L570745_SB001_uv_MODEL.MS/ANTENNA/table.f0 b/lofar-cwl/Docker/test_data/L570745_SB001_uv_MODEL.MS/ANTENNA/table.f0 deleted file mode 100644 index 811482a52b56513bf3d8dc5c6083549f8092b2c0..0000000000000000000000000000000000000000 Binary files a/lofar-cwl/Docker/test_data/L570745_SB001_uv_MODEL.MS/ANTENNA/table.f0 and /dev/null differ diff --git a/lofar-cwl/Docker/test_data/L570745_SB001_uv_MODEL.MS/ANTENNA/table.info b/lofar-cwl/Docker/test_data/L570745_SB001_uv_MODEL.MS/ANTENNA/table.info deleted file mode 100644 index a1a976ed49439abda34d2c64cfd0360cfcdef651..0000000000000000000000000000000000000000 --- a/lofar-cwl/Docker/test_data/L570745_SB001_uv_MODEL.MS/ANTENNA/table.info +++ /dev/null @@ -1,3 +0,0 @@ -Type = -SubType = - diff --git a/lofar-cwl/Docker/test_data/L570745_SB001_uv_MODEL.MS/ANTENNA/table.lock b/lofar-cwl/Docker/test_data/L570745_SB001_uv_MODEL.MS/ANTENNA/table.lock deleted file mode 100644 index 0472b61a97b3474a8587d7db73c4914e1104166e..0000000000000000000000000000000000000000 Binary files a/lofar-cwl/Docker/test_data/L570745_SB001_uv_MODEL.MS/ANTENNA/table.lock and /dev/null differ diff --git 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d7d657412e746495a916cd47adf4b13ca2373497..0000000000000000000000000000000000000000 Binary files a/lofar-cwl/Docker/test_data/L570745_SB001_uv_MODEL.MS/table.f6 and /dev/null differ diff --git a/lofar-cwl/Docker/test_data/L570745_SB001_uv_MODEL.MS/table.f6_TSM0.REMOVED.git-id b/lofar-cwl/Docker/test_data/L570745_SB001_uv_MODEL.MS/table.f6_TSM0.REMOVED.git-id deleted file mode 100644 index 3ea3217072e12722bffbde57d4ba11baf5bf27d2..0000000000000000000000000000000000000000 --- a/lofar-cwl/Docker/test_data/L570745_SB001_uv_MODEL.MS/table.f6_TSM0.REMOVED.git-id +++ /dev/null @@ -1 +0,0 @@ -10891d14e7571d21ec73dd29362401082041c711 \ No newline at end of file diff --git a/lofar-cwl/Docker/test_data/L570745_SB001_uv_MODEL.MS/table.f7 b/lofar-cwl/Docker/test_data/L570745_SB001_uv_MODEL.MS/table.f7 deleted file mode 100644 index 92e945567782b8c27f4076795be9b77022ce2fc7..0000000000000000000000000000000000000000 Binary files a/lofar-cwl/Docker/test_data/L570745_SB001_uv_MODEL.MS/table.f7 and /dev/null differ diff --git a/lofar-cwl/Docker/test_data/L570745_SB001_uv_MODEL.MS/table.f7_TSM0.REMOVED.git-id b/lofar-cwl/Docker/test_data/L570745_SB001_uv_MODEL.MS/table.f7_TSM0.REMOVED.git-id deleted file mode 100644 index 38eb0c84b1e63548143a97f65b3a3f4176db1ea0..0000000000000000000000000000000000000000 --- a/lofar-cwl/Docker/test_data/L570745_SB001_uv_MODEL.MS/table.f7_TSM0.REMOVED.git-id +++ /dev/null @@ -1 +0,0 @@ -2dedb806a06539078faf5e62c82a98b21dc512b8 \ No newline at end of file diff --git a/lofar-cwl/Docker/test_data/L570745_SB001_uv_MODEL.MS/table.info b/lofar-cwl/Docker/test_data/L570745_SB001_uv_MODEL.MS/table.info deleted file mode 100644 index 105af65c13868a224843eb0cb3596828614e8fd0..0000000000000000000000000000000000000000 --- a/lofar-cwl/Docker/test_data/L570745_SB001_uv_MODEL.MS/table.info +++ /dev/null @@ -1,5 +0,0 @@ -Type = Measurement Set -SubType = - -This is a MeasurementSet Table holding measurements from a Telescope -This is a LOFAR MeasurementSet Table diff --git a/lofar-cwl/Docker/test_data/L570745_SB001_uv_MODEL.MS/table.lock b/lofar-cwl/Docker/test_data/L570745_SB001_uv_MODEL.MS/table.lock deleted file mode 100644 index c0c07ecaa3d0c0ff6d59a423b8d0e752b7070563..0000000000000000000000000000000000000000 Binary files a/lofar-cwl/Docker/test_data/L570745_SB001_uv_MODEL.MS/table.lock and /dev/null differ diff --git a/lofar-cwl/Docker/test_data/example.h5.REMOVED.git-id b/lofar-cwl/Docker/test_data/example.h5.REMOVED.git-id deleted file mode 100644 index ee55446f16fed96380113889ea423eb37e2bdbd0..0000000000000000000000000000000000000000 --- a/lofar-cwl/Docker/test_data/example.h5.REMOVED.git-id +++ /dev/null @@ -1 +0,0 @@ -554933b577a0dcf1b2aa3fa91c7de5b2477fd724 \ No newline at end of file diff --git a/lofar-cwl/LICENSE b/lofar-cwl/LICENSE deleted file mode 100644 index de57bbed812e2f1476351df4cee637ef6f5fe6c6..0000000000000000000000000000000000000000 --- a/lofar-cwl/LICENSE +++ /dev/null @@ -1,201 +0,0 @@ - Apache License - Version 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We also recommend that a - file or class name and description of purpose be included on the - same "printed page" as the copyright notice for easier - identification within third-party archives. - - Copyright 2019 EOSC - - Licensed under the Apache License, Version 2.0 (the "License"); - you may not use this file except in compliance with the License. - You may obtain a copy of the License at - - http://www.apache.org/licenses/LICENSE-2.0 - - Unless required by applicable law or agreed to in writing, software - distributed under the License is distributed on an "AS IS" BASIS, - WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - See the License for the specific language governing permissions and - limitations under the License. diff --git a/lofar-cwl/README.md b/lofar-cwl/README.md deleted file mode 100644 index 167c5f8f4bbd7e9a31258c58a60064183d42b64b..0000000000000000000000000000000000000000 --- a/lofar-cwl/README.md +++ /dev/null @@ -1,3 +0,0 @@ -# LOFAR-CWL - -Repository of LOFAR standard CWL steps \ No newline at end of file diff --git a/lofar-cwl/steps/AOFlagger.cwl b/lofar-cwl/steps/AOFlagger.cwl deleted file mode 100644 index e3421e14bc87cb1c9615f4e21f6a981a2849ebc8..0000000000000000000000000000000000000000 --- a/lofar-cwl/steps/AOFlagger.cwl +++ /dev/null @@ -1,121 +0,0 @@ -#!/usr/bin/env cwl-runner - -class: CommandLineTool -cwlVersion: v1.0 -id: aoflagger - -requirements: - - class: InlineJavascriptRequirement - - class: InitialWorkDirRequirement - listing: - - entry: $(inputs.msin) - writable: true - -hints: - DockerRequirement: - dockerPull: lofareosc/prefactor-ci:master - -baseCommand: - - aoflagger -inputs: - - id: msin - type: Directory[] - doc: Input measurement set - inputBinding: - position: 0 - - id: verbose - type: boolean? - - doc: will produce verbose output - inputBinding: - valueFrom: -v - - id: n_threads - type: int? - doc: | - overrides the number of threads specified in the strategy - (default: one thread for each CPU core) - inputBinding: - prefix: -j - - - id: strategy - type: File? - doc: | - specifies a customized strategy - inputBinding: - prefix: -strategy - -#### READ MODES - - id: direct_read - type: boolean? - doc: | - Will perform the slowest IO but will always work. - inputBinding: - prefix: -direct-read - - id: indirect_read - type: boolean? - doc: | - Will reorder the measurement set before starting, which is normally - faster but requires free disk space to reorder the data to. - inputBinding: - prefix: -indirect-read - - id: memory_read - type: boolean? - doc: | - Will read the entire measurement set in memory. This is the fastest, - but requires much memory. - inputBinding: - prefix: -memory-read - - id: auto_read - type: boolean? - doc: | - Will select either memory or direct mode based on available memory (default). - inputBinding: - prefix: -auto-read -############## - - id: skip_flagged - type: boolean? - doc: | - Will skip an ms if it has already been processed by AOFlagger according - to its HISTORY table. - inputBinding: - prefix: -skip-flagged - - id: uvw - type: File? - doc: Reads uvw values (some exotic strategies require these) - inputBinding: - prefix: -uvw - - id: column - type: string? - doc: Specify column to flag - inputBinding: - prefix: -column - - id: bands - type: int[]? - doc: Comma separated list of (zero-indexed) band ids to process - inputBinding: - prefix: -bands - itemSeparator: ',' - - id: fields - type: int[]? - doc: Comma separated list of (zero-indexed) field ids to process - inputBinding: - prefix: -fields - itemSeparator: ',' - - id: combine-spws - type: boolean? - doc: Join all SPWs together in frequency direction before flagging - inputBinding: - prefix: -combine-spws - - id: bandpass - type: File? - doc: Set bandpass correction file for any 'Apply passband' action - inputBinding: - prefix: bandpass - -outputs: - - id: output_ms - doc: Output image - type: Directory[] - outputBinding: - outputEval: $(inputs.msin) -label: AOFlagger diff --git a/lofar-cwl/steps/DP3.AOFlaggerStepGenerator.cwl b/lofar-cwl/steps/DP3.AOFlaggerStepGenerator.cwl deleted file mode 100755 index 2a70f602771d7e5e669ba46ee395550807bb379d..0000000000000000000000000000000000000000 --- a/lofar-cwl/steps/DP3.AOFlaggerStepGenerator.cwl +++ /dev/null @@ -1,132 +0,0 @@ -#!/usr/bin/env cwl-runner - -class: Workflow -cwlVersion: v1.0 -id: aoflagger_step_generator - -inputs: - - id: steps - type: Any[]? - default: [] - - id: step_name - type: string - doc: unique name for the step - default: aoflag - - id: count.save - type: boolean - default: false - doc: >- - If true, the flag percentages per frequency are saved to a table with - extension .flagfreq and percentages per station to a table with extension - .flagstat. The basename of the table is the MS name (without extension) - followed by the stepname and extension. - - id: count.path - type: string - default: "" - doc: >- - The directory where to create the flag percentages table. If empty, the - path of the input MS is used. - - id: strategy - type: File? - doc: >- - The name of the strategy file to use. If no name is given, the default - strategy is used which is fine for HBA. For LBA data the strategy - LBAdefault should be used. - - id: memoryperc - type: int - default: 0 - doc: >- - If >0, percentage of the machines memory to use. If memorymax nor - memoryperc is given, all memory will be used (minus 2 GB (at most 50%) for - other purposes). Accepts only integer values (LOFAR v2.16). Limiting the - available memory too much affects flagging accuracy; in general try to use - at least 10 GB of memory. - - id: memorymax - type: double - default: 0 - doc: >- - Maximum amount of memory (in GB) to use. ⇐0 means no maximum. As stated - above, this affects flagging accuracy. - - id: timewindow - type: int - default: 0 - doc: >- - Number of time slots to be flagged jointly. The larger the time window, - the better the flagging performs. 0 means that it will be deduced from the - memory to use. Note that the time window can be extended with an overlap - on the left and right side to minimize possible boundary effects. - - id: overlapperc - type: double - default: 0 - doc: >- - If >0, percentage of time window to be added to the left and right side - for overlap purposes (to minimize boundary effects). If overlapmax is not - given, it defaults to 1%. - - id: overlapmax - type: int - default: 0 - doc: Maximum overlap value (0 is no maximum). - - id: autocorr - type: boolean - default: true - doc: Flag autocorrelations? - - id: pulsar - type: boolean - default: false - doc: Use flagging strategy optimized for pulsar observations? - - id: pedantic - type: boolean - default: false - doc: Be more pedantic when flagging? - - id: keepstatistics - type: boolean - default: true - doc: Write the quality statistics? -outputs: - - id: augmented_steps - outputSource: - - DP3_GenericStep/augmented_steps - type: Any[] - -steps: - - id: DP3_GenericStep - in: - - id: step_type - default: 'aoflagger' - - id: step_id - source: step_name - - id: steps - source: steps - - id: parameters - valueFrom: $(inputs) - - id: count.save - source: count.save - - id: count.path - source: count.save - - id: strategy - source: strategy - - id: memoryperc - source: memoryperc - - id: memorymax - source: memorymax - - id: timewindow - source: timewindow - - id: overlapperc - source: overlapperc - - id: overlapmax - source: overlapmax - - id: autocorr - source: autocorr - - id: pulsar - source: pulsar - - id: pedantic - source: pedantic - - id: keepstatistics - source: keepstatistics - out: - - augmented_steps - run: ../steps/DP3.GenericStep.cwl -requirements: - - class: StepInputExpressionRequirement - - class: InlineJavascriptRequirement - - class: MultipleInputFeatureRequirement diff --git a/lofar-cwl/steps/DP3.AveragerStepGenerator.cwl b/lofar-cwl/steps/DP3.AveragerStepGenerator.cwl deleted file mode 100755 index d5424919111a6c38f65053bfec5f2e299a98c076..0000000000000000000000000000000000000000 --- a/lofar-cwl/steps/DP3.AveragerStepGenerator.cwl +++ /dev/null @@ -1,85 +0,0 @@ -#!/usr/bin/env cwl-runner - -class: Workflow -cwlVersion: v1.0 -id: average_step_generator - -inputs: - - id: steps - type: Any[]? - default: [] - - id: step_name - type: string - doc: unique name for the step - default: average - - id: timestep - type: int - doc: >- - Number of time slots to average. It is truncated if exceeding the actual - number of times. - default: 1 - - id: freqstep - type: int - doc: >- - Number of channels to average. It is truncated if exceeding the actual - number of channels. - default: 1 - - id: minpoints - type: int - doc: >- - If number of averaged unflagged input points < minpoints, the averaged - point is flagged. - default: 0 - - id: minperc - type: float - doc: 'Like minpoints, but expressed as a percentage of timestep*freqstep.' - default: 0 - - id: timeresolution - type: float - doc: >- - Target time resolution, in seconds. If this is given, and bigger than - zero, it overrides <step>.timestep - default: 0 - - id: freqresolution - type: float - doc: >- - Target frequency resolution, in Hz (or append "MHz" or "kHz" to specify it - in those units). If this is given, and bigger than zero, it overrides - <step>.freqstep - default: 0 -outputs: - - id: augmented_steps - outputSource: - - DP3_GenericStep/augmented_steps - type: Any[] - -steps: - - id: DP3_GenericStep - in: - - id: step_type - default: 'averager' - - id: step_id - source: step_name - - id: steps - source: steps - - id: parameters - valueFrom: $(inputs) - - id: timestep - source: timestep - - id: freqstep - source: freqstep - - id: minpoints - source: minpoints - - id: minperc - source: minperc - - id: timeresolution - source: timeresolution - - id: freqresolution - source: freqresolution - out: - - augmented_steps - run: ../steps/DP3.GenericStep.cwl -requirements: - - class: StepInputExpressionRequirement - - class: InlineJavascriptRequirement - - class: MultipleInputFeatureRequirement diff --git a/lofar-cwl/steps/DP3.DemixerStepGenerator.cwl b/lofar-cwl/steps/DP3.DemixerStepGenerator.cwl deleted file mode 100755 index c88bdd1721d9a544f872ef89f814c361eb56dee5..0000000000000000000000000000000000000000 --- a/lofar-cwl/steps/DP3.DemixerStepGenerator.cwl +++ /dev/null @@ -1,190 +0,0 @@ -#!/usr/bin/env cwl-runner - -class: Workflow -cwlVersion: v1.0 -$namespaces: - sbg: 'https://www.sevenbridges.com/' -id: demix_step_generator - -inputs: - - id: steps - type: Any[]? - default: [] - - id: step_name - type: string - doc: unique name for the step - default: demix - - id: baseline - default: "" - type: string - doc: Baselines to demix. See Description of baseline selection parameters. - - id: blrange - default: [] - type: double[] - doc: Baselines to demix. See Description of baseline selection parameters. - - id: corrtype - default: cross - type: string - doc: >- - Baselines to demix. Correlation type to match? Must be auto, cross, or an - empty string. - - id: timestep - default: 1 - type: int - doc: >- - Number of time slots to average when subtracting. It is truncated if - exceeding the actual number of times. Note that the data itself will also - be averaged by this amount. - - id: freqstep - default: 1 - type: int - doc: >- - Number of channels to average when subtracting. It is truncated if - exceeding the actual number of channels. Note that the data itself will - also be averaged by this amount. - - id: demixtimestep - default: 0 - type: int - doc: >- - Number of time slots to average when demixing. It is truncated if - exceeding the actual number of times. It defaults to the averaging used - for the subtract. - - id: demixfreqstep - default: 0 - type: int - doc: >- - Number of channels to average when demixing. It is truncated if exceeding - the actual number of channels. It defaults to the averaging used for the - subtract. - - id: ntimechunk - default: null - type: int - doc: >- - Number of demix time slots (after averaging) that are processed jointly in - as much a parallel way as possible. If subtract uses different time - averaging, it has to fit integrally. - - id: skymodel - default: sky - type: [File, Directory, string] - doc: The name of the SourceDB to use (i.e., the output of makesourcedb). - - id: instrumentmodel - default: instrument - type: string - doc: >- - The name of the ParmDB to use. The ParmDB does not need to exist. If it - does not exist it will be created. - - id: subtractsources - default: null - type: string[]? - doc: >- - Names of the sources to subtract. If none are given, demixing comes down - to averaging. The sources must exist as patches in the SourceDB. - - id: modelsources - default: [] - type: string[] - doc: >- - Names of sources with models to take into account when solving. the - sources must exist as patches in the SourceDB. Note that the target should - NOT be part of this parameter. If a model of the target has to be used, it - has to be given in parameter targetsource. - - id: targetsource - default: '' - type: string - doc: >- - It can be used to specify the name of the source model of the target. If - given, the target source model (its patch in the SourceDB) is taken into - account when solving; in this case parameter othersources cannot be given. - It cannot be given if ignoretarget=true. If not given, the target is - projected away or ignored (depending on parameter ignoretarget). - - id: ignoretarget - default: false - type: boolean - doc: false = project the target source away; true = ignore the target - - id: othersources - default: [] - type: string[] - doc: >- - Names of sources of which the direction is taken into account when - demixing by projecting the directions away. The direction needs to be - specified if the source is unknown (which is usually the case). It can be - done using parameters <step>.<sourcename>.phasecenter. - - id: propagatesolutions - default: true - type: boolean - doc: >- - If set to true, solutions of a time slot are used as initial values for - the next time slot. If set to false, the diagonal elements of the Jones - matrix are initialized to one and the off-diagonal elements to zero. - - id: defaultgain - default: 1 - type: double - doc: >- - The default and initial gain for the directional gains that are computed - internally. - - id: maxiter - default: 50 - type: int - doc: Maximum number of iterations used in the LM solve -outputs: -- id: augmented_steps - outputSource: - - DP3_GenericStep/augmented_steps - type: Any[] - -steps: - - id: DP3_GenericStep - in: - - id: steps - source: steps - - id: output_files - default: ["instrumentmodel"] - - - id: parameters - valueFrom: $(inputs) - - id: step_id - source: step_name - - id: step_type - default: 'demixer' - - id: baseline - source: baseline - - id: blrange - source: blrange - - id: corrtype - source: corrtype - - id: timestep - source: timestep - - id: freqstep - source: freqstep - - id: demixtimestep - source: demixtimestep - - id: demixfreqstep - source: demixfreqstep - - id: ntimechunk - source: ntimechunk - - id: skymodel - source: skymodel - - id: instrumentmodel - source: instrumentmodel - - id: subtractsources - source: subtractsources - - id: modelsources - source: modelsources - - id: targetsource - source: targetsource - - id: ignoretarget - source: ignoretarget - - id: othersources - source: othersources - - id: propagatesolutions - source: propagatesolutions - - id: defaultgain - source: defaultgain - - id: maxiter - source: maxiter - out: - - augmented_steps - run: ../steps/DP3.GenericStep.cwl -requirements: - - class: StepInputExpressionRequirement - - class: InlineJavascriptRequirement - - class: MultipleInputFeatureRequirement diff --git a/lofar-cwl/steps/DP3.EmptyParsetGenerator.cwl b/lofar-cwl/steps/DP3.EmptyParsetGenerator.cwl deleted file mode 100755 index f3e2c175ced26ad327e9d56e473bbaf0039996a5..0000000000000000000000000000000000000000 --- a/lofar-cwl/steps/DP3.EmptyParsetGenerator.cwl +++ /dev/null @@ -1,25 +0,0 @@ -#!/usr/bin/env cwl-runner - -cwlVersion: v1.0 -class: CommandLineTool -id: empty_parset_generator -baseCommand: [echo, 'steps=[]'] - -requirements: - InlineJavascriptRequirement: {} - -inputs: [] - -stdout: output_parset -outputs: - - id: output_parset - doc: Empty parset file - streamable: True - type: File - outputBinding: - glob: output_parset - - id: output_secondary_files - doc: files needed to execute the step - type: File[] - outputBinding: - outputEval: $([]) diff --git a/lofar-cwl/steps/DP3.Execute.cwl b/lofar-cwl/steps/DP3.Execute.cwl deleted file mode 100644 index bf15ea45d9ac61ab6d23521605ea0955324e7e45..0000000000000000000000000000000000000000 --- a/lofar-cwl/steps/DP3.Execute.cwl +++ /dev/null @@ -1,79 +0,0 @@ -class: Workflow -cwlVersion: v1.0 -id: dp3_execute -label: DP3.Execute -$namespaces: - sbg: 'https://www.sevenbridges.com/' -inputs: - - id: msout_name - type: string - 'sbg:x': -425.39886474609375 - 'sbg:y': 127 - - id: msin - type: Directory - 'sbg:x': -254.39886474609375 - 'sbg:y': 242 - - id: steps - type: 'Any[]?' - 'sbg:x': -518.3988647460938 - 'sbg:y': -88 -outputs: - - id: secondary_output_files - outputSource: - - dppp/secondary_output_files - type: Any - 'sbg:x': 213.60113525390625 - 'sbg:y': -184 - - id: secondary_output_directories - outputSource: - - dppp/secondary_output_directories - type: Any - 'sbg:x': 248.60113525390625 - 'sbg:y': -47 - - id: msout - outputSource: - - dppp/msout - type: Directory - 'sbg:x': 224.60113525390625 - 'sbg:y': 130 -steps: - - id: generic_step - in: - - id: steps - source: - - steps - out: - - id: parset - - id: input_files - - id: input_directories - - id: output_file_names - - id: output_directory_names - run: ./DP3.ParsetGenerator.cwl - 'sbg:x': -294 - 'sbg:y': -84 - - id: dppp - in: - - id: parset - source: generic_step/parset - - id: msin - source: msin - - id: msout_name - source: msout_name - - id: secondary_files - source: - - generic_step/input_files - - id: secondary_directories - source: - - generic_step/input_directories - - id: output_file_names - source: generic_step/output_file_names - - id: output_directory_names - source: generic_step/output_directory_names - out: - - id: msout - - id: secondary_output_files - - id: secondary_output_directories - run: ./DPPP.cwl - 'sbg:x': 26 - 'sbg:y': -46 -requirements: [] diff --git a/lofar-cwl/steps/DP3.GenericStep.cwl b/lofar-cwl/steps/DP3.GenericStep.cwl deleted file mode 100755 index 38829da42ed0deaac51bcf92c7c105e9139d4108..0000000000000000000000000000000000000000 --- a/lofar-cwl/steps/DP3.GenericStep.cwl +++ /dev/null @@ -1,63 +0,0 @@ -#!/usr/bin/env cwl-runner - -cwlVersion: v1.0 -class: ExpressionTool -id: generic_step - -requirements: - - class: InlineJavascriptRequirement - -inputs: - - id: steps - type: Any[] - - - id: parameters - type: Any? - -outputs: - - id: augmented_steps - type: Any[] -expression: |- - ${ - var step_type = inputs.parameters.step_type; - var step_id = inputs.parameters.step_id; - - var output_file_type = inputs.parameters.output_files; - var output_files = {} - - for(var index in output_file_type){ - var file_type = output_file_type[index] - if(file_type != undefined && file_type != null){ - output_files[file_type] = inputs.parameters[file_type] - } - } - - var input_secondary_files = inputs.parameters.input_secondary_files; - - delete inputs.parameters.step_type; - delete inputs.parameters.step_id; - delete inputs.parameters.steps; - delete inputs.parameters.parameters; - delete inputs.parameters.steps; - - - var new_step = {'step_type': step_type, - 'step_id': step_id, - 'parameters': inputs.parameters, - 'output_files': output_files}; - - - var in_parameters = inputs.steps; - - // Checks if the step_id is duplicate if so raised an exception - var step_ids = [] - for(var step in in_parameters){ - step = in_parameters[step] - step_ids.push(step.step_id) - } - if(step_ids.indexOf(step_id) >= 0) throw 'step_id has to be unique' - - var out_parameters = in_parameters == null ? [new_step] : in_parameters.concat(new_step) - - return {'augmented_steps': out_parameters}; - } diff --git a/lofar-cwl/steps/DP3.ParsetGenerator.cwl b/lofar-cwl/steps/DP3.ParsetGenerator.cwl deleted file mode 100644 index f5837e9a3528135180143bee7fb406ef736b1efb..0000000000000000000000000000000000000000 --- a/lofar-cwl/steps/DP3.ParsetGenerator.cwl +++ /dev/null @@ -1,148 +0,0 @@ -#!/usr/bin/env cwl-runner - -cwlVersion: v1.0 -class: CommandLineTool -id: generic_step - -requirements: - - class: InlineJavascriptRequirement - -baseCommand: - - python3 - -arguments: - - prefix: -c - valueFrom: | - import sys - - true = True - false = False - null = None - steps_list = $(inputs.steps) - steps_id_list = list(map(lambda item: item['step_id'], steps_list)) - - for step in steps_list: - try: - step_id = step.get('step_id') - step_type = step.get('step_type') - parameters = step.get('parameters') - - - line = '.'.join([step_id, 'type']) - line += '=%s' % step_type - print(line) - - for parameter_name, parameter in parameters.items(): - if isinstance(parameter, dict): - if parameter['class'] in ['File', 'Directory']: - parameter = parameter['basename'] - else: - raise NotImplemented() - if parameter is None: - continue - line = '.'.join([step_id, parameter_name]) - line = '%s=%s' % (line, parameter) - - print(line) - except KeyError as e: - print('invalid input for step ', step, ':', e) - sys.exit(1) - last_step_line = 'steps=[%s]' % ', '.join(steps_id_list) - print(last_step_line) -inputs: - - id: steps - type: Any[]? - -outputs: - - id: parset - doc: Parset output file - type: File - outputBinding: - glob: parset - - id: input_files - doc: additional input files - type: File[] - outputBinding: - outputEval: |- - ${ - var outfiles = [] - for(var step in inputs.steps){ - step = inputs.steps[step] - for(var parameter in step['parameters']){ - parameter = step['parameters'][parameter] - - if (parameter != null && parameter.class =='File'){ - outfiles.push(parameter) - } - } - } - return outfiles - } - - id: input_directories - doc: additional input directory - type: Directory[] - outputBinding: - outputEval: | - ${ - var outdirs = [] - for(var step in inputs.steps){ - step = inputs.steps[step] - for(var parameter in step['parameters']){ - parameter = step['parameters'][parameter] - if (parameter != null && parameter.class=='Directory'){ - outdirs.push(parameter) - } - } - } - return outdirs - } - - - id: output_file_names - doc: expected output files - type: Any - outputBinding: - outputEval: | - ${ - var out_names = {} - for(var step_idx in inputs.steps){ - var step = inputs.steps[step_idx] - var step_id = step['step_id'] - var step_dirs = {} - if(!step.hasOwnProperty("output_files")) continue; - - var step_files = {} - - for(var index in step['output_files']){ - var file_id = index - var file_name = step['output_files'][file_id] - step_files[file_id] = file_name - } - - out_names[step_id] = step_files - } - return out_names - } - - id: output_directory_names - doc: expected output directories - type: Any - outputBinding: - outputEval: |- - ${ - var out_names = {} - for(var step_idx in inputs.steps){ - var step = inputs.steps[step_idx] - var step_id = step['step_id'] - var step_dirs = {} - if(!step.hasOwnProperty("output_directories")) continue; - - for(var index in step['output_directories']){ - var file_id = index - var file_name = step['output_directories'][file_id] - step_dirs[file_id] = file_name - } - out_names[step_id] = step_dirs - } - return out_names - } -stdout: - parset diff --git a/lofar-cwl/steps/DP3.PreflaggerStepGenerator.cwl b/lofar-cwl/steps/DP3.PreflaggerStepGenerator.cwl deleted file mode 100755 index 03f6c11d6f16db4d72a38666e4a294a2f568fb28..0000000000000000000000000000000000000000 --- a/lofar-cwl/steps/DP3.PreflaggerStepGenerator.cwl +++ /dev/null @@ -1,246 +0,0 @@ -#!/usr/bin/env cwl-runner - -class: Workflow -cwlVersion: v1.0 -id: preflag_step_generator - -inputs: - - id: steps - type: Any[]? - default: [] - - id: step_name - type: string - doc: unique name for the step - default: preflag - - id: count.save - default: false - type: boolean - doc: >- - If true, the flag percentages per frequency are saved to a table with - extension .flagfreq and percentages per station to a table with extension - .flagstat. The basename of the table is the MS name (without extension) - followed by the stepname and extension. - - id: count.path - type: string? - doc: >- - The directory where to create the flag percentages table. If empty, the - path of the input MS is used. - - id: mode - default: set - type: string - doc: >- - Case-insensitive string telling what to do with the flags of the data - matching (or not matching) the selection criteria given in the other - parameters. - - id: expr - default: '' - type: string? - doc: >- - Expression of preflagger keyword sets (see above). Operators AND, OR, and - NOT are possible (or their equivalents &&,&, ||, |, and !). Parentheses - can be used to change precedence order. For example:: c1 and (c2 or c3) - - default: - id: timeofday - type: string? - doc: >- - Ranges of UTC time-of-day given as st..end or val+-delta. Each value must - be given as 12:34:56.789, 12h34m56.789, or as a value followed by a unit - like h, min, or s. - - id: abstime - default: [] - type: string[] - doc: >- - Ranges of absolute UTC date/time given as st..end or val+-delta. Each - value (except delta) must be given as a date/time in casacore MVTime - format, for instance 12-Mar-2010/11:31:00.000. A delta value must be given - as a time (for instance 1:30:0 or 20s). - - id: reltime - default: [] - type: string[] - doc: >- - Ranges of times (using .. or +-) since the start of the observation. A - time can be given like 1:30:0 or 20s. - - id: timeslot - default: [] - type: string[] - doc: >- - Time slot sequence numbers. First time slot is 0. st..end means end - inclusive. - - id: lst - default: [] - type: string[] - doc: >- - Ranges of Local Apparent Sidereal Times like 1:30:0 +- 20min. The LST of a - time slot is calculated for the array position, thus not per antenna. - - id: azimuth - default: [] - type: float[] - doc: >- - Ranges of azimuth angles given as st..end or val+-delta. Each value has to - be given as a casacore direction like 12:34:56.789 or 12h34m56.789, - 12.34.56.789 or 12d34m56.789, or a value followed by a unit like rad or - deg. - - id: elevation - type: string? - doc: >- - Ranges of elevation angles (similar to azimuth). For example:: - 0deg..10deg - - id: baseline - default: [] - type: string[] - doc: See Description of baseline selection parameters. - - id: corrtype - default: '' - type: string - doc: Correlation type to match? Must be auto, cross, or an empty string. - - id: blmin - default: -1 - type: float - doc: If blmin > 0, baselines with length < blmin meter will match. - - id: blmax - default: -1 - type: float - doc: If blmax > 0, baselines with length > blmax meter will match. - - id: uvmmin - default: -1 - type: float - doc: >- - If uvmmin > 0, baselines with UV-distance < uvmmin meter will match. Note - that the UV-distance is the projected baseline length. - - id: uvmmax - default: -1 - type: float - doc: If uvmmax > 0, baselines with UV-distance > uvmmax meter will match. - - id: freqrange - default: '' - type: string - doc: >- - Channels in the given frequency ranges will match. Each value in the - vector is a range which can be given as start..end or start+-delta. A - value can be followed by a unit like KHz. If only one value in a range has - a unit, the unit is also applied to the other value. If a range has no - unit, it defaults to MHz. For example: freqrange=[1.2 .. 1.4 MHz, - 1.8MHz+-50KHz] flags channels between 1.2MHz and 1.4MHz and between - 1.75MHz and 1.85MHz. The example shows that blanks can be used at will. - - id: chan - default: '' - type: string - doc: >- - The given channels will match (start counting at 0). Channels exceeding - the number of channels are ignored. Similar to msin, it is possible to - specify the channels as an expression of nchan. Furthermore, .. can be - used to specify ranges. For example: chan=[0..nchan/32-1, - 31*nchan/32..nchan-1] to flag the first and last 2 or 8 channels - (depending on 64 or 256 channels in the observation). - - id: amplmin - default: -1e+30 - type: float - doc: >- - Correlation data with amplitude < amplmin will match. It can be given per - correlation. For example, amplmin=[100,,,100] matches data points with XX - or YY amplitude < 100. The non-specified amplitudes get the default value. - - id: amplmax - default: 1e+30 - type: float - doc: Correlation data with amplitude > amplmax will match. - - id: phasemin - default: -1e+30 - type: float - doc: Correlation data with phase < phasemin (in radians) will match. - - id: phasemax - default: 1e+30 - type: float - doc: Correlation data with phase > phasemax (in radians) will match. - - id: realmin - default: -1e+30 - type: float - doc: Correlation data with real complex part < realmin will match. - - id: realmax - default: 1e+30 - type: float - doc: Correlation data with real complex part > realmax will match. - - id: imagmin - default: -1e+30 - type: float - doc: Correlation data with imaginary complex part < imagmin will match. - - id: imagmax - default: 1e+30 - type: float - doc: Correlation data with imaginary complex part > imagmax will match. -outputs: -- id: augmented_steps - outputSource: - - DP3_GenericStep/augmented_steps - type: Any[] - -steps: - - id: DP3_GenericStep - in: - - id: step_type - default: 'preflagger' - - id: step_id - source: step_name - - id: steps - source: steps - - id: parameters - valueFrom: $(inputs) - - id: count.save - source: count.save - - id: count.path - source: count.path - - id: mode - source: mode - - id: expr - source: expr - - id: abstime - source: abstime - - id: reltime - source: reltime - - id: timeslot - source: timeslot - - id: lst - source: lst - - id: azimuth - source: azimuth - - id: elevation - source: elevation - - id: baseline - source: baseline - - id: corrtype - source: corrtype - - id: blmin - source: blmin - - id: blmax - source: blmax - - id: uvmmin - source: uvmmin - - id: uvmmax - source: uvmmax - - id: freqrange - source: freqrange - - id: chan - source: chan - - id: amplmin - source: amplmin - - id: amplmax - source: amplmax - - id: phasemin - source: phasemin - - id: phasemax - source: phasemax - - id: realmin - source: realmin - - id: realmax - source: realmax - - id: imagmin - source: imagmin - - id: imagmax - source: imagmax - out: - - augmented_steps - run: ../steps/DP3.GenericStep.cwl - -requirements: - - class: StepInputExpressionRequirement - - class: InlineJavascriptRequirement - - class: MultipleInputFeatureRequirement diff --git a/lofar-cwl/steps/DP3.Selector.cwl b/lofar-cwl/steps/DP3.Selector.cwl deleted file mode 100755 index b50754a85ab040136df19917a0e01a5464e8c7c9..0000000000000000000000000000000000000000 --- a/lofar-cwl/steps/DP3.Selector.cwl +++ /dev/null @@ -1,24 +0,0 @@ -class: ExpressionTool -cwlVersion: v1.0 -id: selector -inputs: - - id: select_a - type: boolean - doc: 'if true selects a_steps if false selects b_steps' - - id: a_steps - type: Any[] - default: [] - - id: b_steps - type: Any[] - default: [] -outputs: - - id: selected_steps - type: Any -expression: | - $( - {'selected_steps': inputs.select_a ? inputs.a_steps : inputs.b_steps} - ) -label: Selector - -requirements: - - class: InlineJavascriptRequirement diff --git a/lofar-cwl/steps/DPPP.cwl b/lofar-cwl/steps/DPPP.cwl deleted file mode 100755 index 70d824f02518f594ecf5d9b8975041b1febee5bc..0000000000000000000000000000000000000000 --- a/lofar-cwl/steps/DPPP.cwl +++ /dev/null @@ -1,89 +0,0 @@ -class: CommandLineTool -cwlVersion: v1.0 -$namespaces: - sbg: 'https://www.sevenbridges.com/' -id: dppp -baseCommand: - - DPPP -inputs: - - id: parset - type: File? - inputBinding: - position: -1 - - id: msin - type: Directory? - inputBinding: - position: 0 - prefix: msin= - separate: false - doc: Input Measurement Set - - default: out.MS - id: msout_name - type: string - inputBinding: - position: 0 - prefix: msout= - separate: false - doc: Output Measurement Set - - id: secondary_files - type: 'File[]?' - doc: Secondary files needed for the step - - id: secondary_directories - type: 'Directory[]?' - doc: Secondary directories needed for the step - - id: output_file_names - type: Any - doc: Expected output file names - - id: output_directory_names - type: Any - doc: Expected output file names -outputs: - - id: msout - doc: Output Measurement Set - type: Directory - outputBinding: - glob: '$(inputs.msout_name=="."?inputs.msin:inputs.msout_name)' - - id: secondary_output_files - doc: Secondary output files - type: Any - outputBinding: - outputEval: |- - ${ - var output={} - for(var step_name in inputs.output_file_names){ - var file_per_idx = inputs.output_file_names[step_name]; - for(var file_idx in file_per_idx){ - var file_name = file_per_idx[file_idx]; - - output[file_idx] = {'class':'File', 'path': file_name}; - } - } - return output - } - - id: secondary_output_directories - doc: Secondary output directories - type: Any - outputBinding: - outputEval: |- - ${ - var output={} - for(var step_name in inputs.output_directory_names){ - var file_per_idx = inputs.output_directory_names[step_name]; - for(var file_idx in file_per_idx){ - var file_name = file_per_idx[file_idx]; - - output[file_idx] = {'class':'Directory', 'path': file_name}; - } - } - return output - } - - id: logfile - type: File? - outputBinding: - glob: DPPP.log -hints: - - class: DockerRequirement - dockerPull: lofareosc/prefactor -stdout: DPPP.log -requirements: - - class: InlineJavascriptRequirement diff --git a/lofar-cwl/steps/DirSelector.cwl b/lofar-cwl/steps/DirSelector.cwl deleted file mode 100644 index d5bd04038a703c3ecfbc5f07aa917892b87bd85d..0000000000000000000000000000000000000000 --- a/lofar-cwl/steps/DirSelector.cwl +++ /dev/null @@ -1,39 +0,0 @@ -class: ExpressionTool -cwlVersion: v1.0 -id: dirselector -inputs: - - id: inputs - type: Any - doc: input files - - id: step_name - type: string - doc: >- - id of the step that generates the output file or directory - (e.g. 'demixstepgenerator') - - id: key_name - type: string - doc: >- - key of the parset that contains the name of the outputfile - (e.g. 'instrumentmodel') -outputs: - - id: output - type: [Directory, 'Directory[]'] - -expression: | - ${ - var step_name = inputs.step_name - var key_name = inputs.key_name - - if(inputs.inputs.hasOwnProperty(step_name)){ - var inputs_per_step = inputs.inputs[step_name] - if(inputs_per_step.hasOwnProperty(key_name)){ - return {'output': inputs_per_step[key_name]} - } - } - return {'output': []} - - } -label: DirSelector - -requirements: - - class: InlineJavascriptRequirement diff --git a/lofar-cwl/steps/FileSelector.cwl b/lofar-cwl/steps/FileSelector.cwl deleted file mode 100644 index f935adca0125043812f663d913ef039819f6a52e..0000000000000000000000000000000000000000 --- a/lofar-cwl/steps/FileSelector.cwl +++ /dev/null @@ -1,31 +0,0 @@ -class: ExpressionTool -cwlVersion: v1.0 -id: fileselector -inputs: - - id: inputs - type: Any - doc: input files - - id: step_name - type: string - doc: >- - id of the step that generates the output file or directory - (e.g. 'demixstepgenerator') - - id: key_name - type: string - doc: >- - key of the parset that contains the name of the outputfile - (e.g. 'instrumentmodel') -outputs: - - id: output - type: File - -expression: | - ${ - var step_name = inputs.step_name - var key_name = inputs.key_name - return {'output': inputs.inputs[step_name][key_name]} - } -label: FileSelector - -requirements: - - class: InlineJavascriptRequirement diff --git a/lofar-cwl/steps/H5ParmCollector.cwl b/lofar-cwl/steps/H5ParmCollector.cwl deleted file mode 100755 index e2e33e20acab94f1e092866d37a2086185e93530..0000000000000000000000000000000000000000 --- a/lofar-cwl/steps/H5ParmCollector.cwl +++ /dev/null @@ -1,70 +0,0 @@ -class: CommandLineTool -cwlVersion: v1.0 -$namespaces: - sbg: 'https://www.sevenbridges.com/' - lofar: https://git.astron.nl/eosc/ontologies/raw/master/schema/lofar.owl -$schema: - - https://git.astron.nl/eosc/ontologies/raw/master/schema/lofar.owl - -id: h5parm_collector - -baseCommand: - - H5parm_collector.py -inputs: - - id: h5parmFiles - type: 'File[]' - format: lofar:#H5Parm - inputBinding: - position: 0 - doc: List of h5parm files - - default: sol000 - id: insolset - type: string? - inputBinding: - position: 0 - prefix: '--insolset' - doc: Input solset name - - default: output.h5 - id: outh5parmname - type: string - doc: Output h5parm name - - id: squeeze - type: boolean - default: false - inputBinding: - position: 0 - prefix: '-q' - doc: removes all axes with the length of 1 - - default: true - id: verbose - type: boolean - inputBinding: - position: 0 - prefix: '-v' - doc: verbose output - - default: true - id: clobber - type: boolean - inputBinding: - position: 0 - prefix: '-c' - doc: overwrite output -outputs: - - id: outh5parm - doc: Output h5parm - type: File - format: lofar:#H5Parm - outputBinding: - glob: $(inputs.outh5parmname) - - id: log - type: File - outputBinding: - glob: $(inputs.outh5parmname)-parm_collector_output.log -label: H5parm_collector -hints: - - class: DockerRequirement - dockerPull: 'lofareosc/prefactor-ci:master' -stdout: $(inputs.outh5parmname)-parm_collector_output.log -requirements: - - class: InlineJavascriptRequirement - diff --git a/lofar-cwl/steps/LoSoTo.Abs.cwl b/lofar-cwl/steps/LoSoTo.Abs.cwl deleted file mode 100755 index 43f5c28c5a5fd18157707d9ba273bd85c6620532..0000000000000000000000000000000000000000 --- a/lofar-cwl/steps/LoSoTo.Abs.cwl +++ /dev/null @@ -1,52 +0,0 @@ -#!/usr/bin/env cwl-runner - -class: CommandLineTool -cwlVersion: v1.0 -id: losoto_abs - -$namespaces: - lofar: https://git.astron.nl/eosc/ontologies/raw/master/schema/lofar.owl -doc: | - Take absolute value. Needed before smooth if amplitudes are negative! - WEIGHT: no need to be weight compliant - -requirements: - InitialWorkDirRequirement: - listing: - - entryname: 'parset.config' - entry: | - [abs] - soltab = $(inputs.soltab) - operation = ABS - - entryname: $(inputs.input_h5parm.basename) - entry: $(inputs.input_h5parm) - writable: true - -baseCommand: "losoto" - -arguments: - - $(inputs.input_h5parm.basename) - - parset.config - -hints: - DockerRequirement: - dockerPull: lofareosc/prefactor-ci:master - -inputs: - - id: input_h5parm - type: File - format: lofar:#H5Parm - - id: soltab - type: string - doc: "Solution table" - -outputs: - - id: output_h5parm - type: File - format: lofar:#H5Parm - outputBinding: - glob: $(inputs.input_h5parm.basename) - - -$schema: - - https://git.astron.nl/eosc/ontologies/raw/master/schema/lofar.owl diff --git a/lofar-cwl/steps/LoSoTo.Duplicate.cwl b/lofar-cwl/steps/LoSoTo.Duplicate.cwl deleted file mode 100644 index 9111602fa6ebde8aaca0b425afeef3c3d1e39d75..0000000000000000000000000000000000000000 --- a/lofar-cwl/steps/LoSoTo.Duplicate.cwl +++ /dev/null @@ -1,56 +0,0 @@ -#!/usr/bin/env cwl-runner - -class: CommandLineTool -cwlVersion: v1.0 -id: losoto_duplicate - -doc: | - Duplicate a table - -requirements: - InlineJavascriptRequirement: {} - InitialWorkDirRequirement: - listing: - - entryname: 'parset.config' - entry: | - [duplicate] - soltab = $(inputs.soltab) - operation = DUPLICATE - $(inputs.soltabOut !== null? 'soltabOut=' + inputs.soltabOut: '') - - - entryname: $(inputs.input_h5parm.basename) - entry: $(inputs.input_h5parm) - writable: true - -baseCommand: "losoto" - -arguments: - - $(inputs.input_h5parm.basename) - - parset.config - -hints: - DockerRequirement: - dockerPull: lofareosc/prefactor-ci:master - -inputs: - - id: input_h5parm - type: File - format: lofar:#H5Parm - - id: soltab - type: string - doc: "Solution table" - - id: soltabOut - type: string? - doc: Output table name. By default choose next available from table type. -outputs: - - id: output_h5parm - type: File - format: lofar:#H5Parm - outputBinding: - glob: $(inputs.input_h5parm.basename) - - -$namespaces: - lofar: https://git.astron.nl/eosc/ontologies/raw/master/schema/lofar.owl -$schema: - - https://git.astron.nl/eosc/ontologies/raw/master/schema/lofar.owl diff --git a/lofar-cwl/steps/LoSoTo.Norm.cwl b/lofar-cwl/steps/LoSoTo.Norm.cwl deleted file mode 100644 index f60ee4c469c938e01c52b5d226e275bba4fe2a1f..0000000000000000000000000000000000000000 --- a/lofar-cwl/steps/LoSoTo.Norm.cwl +++ /dev/null @@ -1,61 +0,0 @@ -#!/usr/bin/env cwl-runner - -class: CommandLineTool -cwlVersion: v1.0 -id: losoto_abs - -doc: | - Normalize the solutions to a given value WEIGHT: Weights compliant - -requirements: - InlineJavascriptRequirement: {} - InitialWorkDirRequirement: - listing: - - entryname: 'parset.config' - entry: | - [norm] - soltab = $(inputs.soltab) - operation = NORM - axesToNorm = $(inputs.axesToNorm) - $(inputs.normVal !== null? 'normVal=' + inputs.normVal: '') - - - entryname: $(inputs.input_h5parm.basename) - entry: $(inputs.input_h5parm) - writable: true - -baseCommand: "losoto" - -arguments: - - $(inputs.input_h5parm.basename) - - parset.config - -hints: - DockerRequirement: - dockerPull: lofareosc/prefactor-ci:master - -inputs: - - id: input_h5parm - type: File - format: lofar:#H5Parm - - id: soltab - type: string - doc: "Solution table" - - id: axesToNorm - type: string[] - doc: Axes along which compute the normalization - - id: normVal - type: float? - doc: Number to normalize to vals = vals * (normVal/valsMean), by default 1. - -outputs: - - id: output_h5parm - type: File - format: lofar:#H5Parm - outputBinding: - glob: $(inputs.input_h5parm.basename) - - -$namespaces: - lofar: https://git.astron.nl/eosc/ontologies/raw/master/schema/lofar.owl -$schema: - - https://git.astron.nl/eosc/ontologies/raw/master/schema/lofar.owl diff --git a/lofar-cwl/steps/LoSoTo.Plot.cwl b/lofar-cwl/steps/LoSoTo.Plot.cwl deleted file mode 100644 index e5d5cfb054bbda082cf00a311d9df0904ea22f1f..0000000000000000000000000000000000000000 --- a/lofar-cwl/steps/LoSoTo.Plot.cwl +++ /dev/null @@ -1,148 +0,0 @@ -#!/usr/bin/env cwl-runner - -class: CommandLineTool -cwlVersion: v1.0 -id: losoto_plot - -doc: | - This operation for LoSoTo implements basic plotting WEIGHT: - flag-only compliant, no need for weight - -requirements: - InlineJavascriptRequirement: - expressionLib: - - | - function get_config() { - var par = ['soltab = ' + inputs.soltab] - if (inputs.ncpu !== null) par.push('ncpu='+inputs.ncpu); - par.push('[plot]') - par.push('operation = PLOT') - for(var field_name in inputs){ - if(field_name === 'input_h5parm' || - field_name === 'soltab' || - field_name === 'ncpu') continue; - if(inputs[field_name] === null || - inputs[field_name] === 'null') continue; - par.push(field_name+'='+inputs[field_name]) - } - return par - } - InitialWorkDirRequirement: - listing: - - entryname: 'parset.config' - entry: $(get_config().join('\n')) - - entryname: $(inputs.input_h5parm.basename) - entry: $(inputs.input_h5parm) - writable: true - - -baseCommand: "losoto" - -arguments: - - $(inputs.input_h5parm.basename) - - parset.config - -hints: - DockerRequirement: - dockerPull: lofareosc/prefactor-ci:master - -inputs: - - id: input_h5parm - type: File - format: lofar:#H5Parm - - id: soltab - type: string[] - doc: "Tabs to plot" - - - id: axesInPlot - type: string[]? - default: [] - doc: | - 1- or 2-element array which says the coordinates to plot (2 for 3D plots). - - id: axisInTable - type: string? - doc: | - the axis to plot on a page - e.g. ant to get all antenna’s on one file. - - id: axisInCol - type: string? - doc: | - The axis to plot in different colours - e.g. pol to get correlations with - different colors. - - id: axisDiff - type: string? - doc: | - This must be a len=2 axis and the plot will have the differential value - - e.g. ‘pol’ to plot XX-YY. - - id: NColFig - type: int? - doc: | - Number of columns in a multi-table image. By default is automatically - chosen. - - id: figSize - type: int[] - default: [0,0] - doc: | - Size of the image [x,y], if one of the values is 0, then it is - automatically chosen. By default automatic set. - - id: markerSize - type: int? - default: 2 - doc: | - Size of the markers in the 2D plot. By default 2. - - id: minmax - type: float[]? - doc: | - Min max value for the independent variable (0 means automatic). - - id: log - type: string? - doc: | - Use Log=’XYZ’ to set which axes to put in Log. - - id: plotFlag - type: boolean? - default: false - doc: Whether to plot also flags as red points in 2D plots. - - id: doUnwrap - type: boolean? - default: false - doc: Unwrap phases. - - id: refAnt - type: string? - default: '' - doc: | - Reference antenna for phases. By default None. - - id: soltabsToAdd - type: string? - doc: | - Tables to “add” (e.g. ‘sol000/tec000’), it works only for tec and clock - to be added to phases. - - id: makeAntPlot - default: false - type: boolean? - doc: | - Make a plot containing antenna coordinates in x,y and in color the value - to plot, axesInPlot must be [ant]. - - id: makeMovie - default: false - type: boolean? - doc: | - Make a movie summing up all the produced plots. - - id: prefix - type: string? - default: 'losoto.plot.' - doc: | - Prefix to add before the self-generated filename. - - id: ncpu - type: int? - doc: Number of cpus, by default all available. - -outputs: - - id: output_plots - type: File[] - outputBinding: - glob: "$(inputs.prefix)*.png" - - -$namespaces: - lofar: https://git.astron.nl/eosc/ontologies/raw/master/schema/lofar.owl -$schema: - - https://git.astron.nl/eosc/ontologies/raw/master/schema/lofar.owl diff --git a/lofar-cwl/steps/LoSoTo.Replicateonaxis.cwl b/lofar-cwl/steps/LoSoTo.Replicateonaxis.cwl deleted file mode 100644 index c676467d19611e57252c17bdfd83b99d8a5fc821..0000000000000000000000000000000000000000 --- a/lofar-cwl/steps/LoSoTo.Replicateonaxis.cwl +++ /dev/null @@ -1,77 +0,0 @@ -#!/usr/bin/env cwl-runner - -class: CommandLineTool -cwlVersion: v1.0 -id: losoto_replicate_on_axis - -doc: | - Replace the values along a certain axis taking them from one specific axis - cell - -requirements: - InlineJavascriptRequirement: {} - InitialWorkDirRequirement: - listing: - - entryname: "replicate_axis.py" - entry: | - import sys - from losoto.h5parm import openSoltab - from losoto.operations import replicateonaxis - - soltab_address = "$(inputs.soltab)" - soltab = openSoltab(sys.argv[1], address=soltab_address) - - axisReplicate = "$(inputs.axisReplicate)" - fromCell = "$(inputs.fromCell !== null ? inputs.fromCell : 0)" - updateWeights = "$(inputs.updateWeights? inputs.updateWeights : 'True')" - - replicateonaxis.run(soltab, axisReplicate=axisReplicate, - fromCell=fromCell, - updateWeights=updateWeights) - - - entryname: $(inputs.input_h5parm.basename) - entry: $(inputs.input_h5parm) - writable: true - -baseCommand: "python3" - -arguments: - - replicate_axis.py - - $(inputs.input_h5parm.basename) - - -hints: - DockerRequirement: - dockerPull: lofareosc/prefactor-ci:master - -inputs: - - id: input_h5parm - type: File - format: lofar:#H5Parm - - id: soltab - type: string - doc: "Solution table" - - id: axisReplicate - type: string - doc: Axis along which replicate the values. - - id: fromCell - type: string? - doc: A cell value in axisReplicate from which to copy the data values. - - id: updateWeights - type: boolean? - doc: | - If False then weights are untouched, if True they are replicated - like data. Default: True. - -outputs: - - id: output_h5parm - type: File - format: lofar:#H5Parm - outputBinding: - glob: $(inputs.input_h5parm.basename) - - -$namespaces: - lofar: https://git.astron.nl/eosc/ontologies/raw/master/schema/lofar.owl -$schema: - - https://git.astron.nl/eosc/ontologies/raw/master/schema/lofar.owl diff --git a/lofar-cwl/steps/LoSoTo.Reset.cwl b/lofar-cwl/steps/LoSoTo.Reset.cwl deleted file mode 100644 index 99594d12046ee2d48622dda0e08de72e25c8efcd..0000000000000000000000000000000000000000 --- a/lofar-cwl/steps/LoSoTo.Reset.cwl +++ /dev/null @@ -1,57 +0,0 @@ -#!/usr/bin/env cwl-runner - -class: CommandLineTool -cwlVersion: v1.0 -id: losoto_reset - -doc: Subtract/divide two tables or a clock/tec/tec3rd/rm from a phase. - -requirements: - InlineJavascriptRequirement: {} - InitialWorkDirRequirement: - listing: - - entryname: 'parset.config' - entry: | - [reset] - soltab = $(inputs.soltab) - operation = RESET - $(inputs.dataVal !== null? 'dataVal=' + inputs.dataVal: '') - - - entryname: $(inputs.input_h5parm.basename) - entry: $(inputs.input_h5parm) - writable: true - -baseCommand: "losoto" - -arguments: - - $(inputs.input_h5parm.basename) - - parset.config - -hints: - DockerRequirement: - dockerPull: lofareosc/prefactor-ci:master - -inputs: - - id: input_h5parm - type: File - format: lofar:#H5Parm - - id: soltab - type: string - doc: "Solution table" - - id: dataVal - type: float? - doc: | - If given set values to this number, otherwise uses 1 for amplitude and 0 - for all other soltab types. -outputs: - - id: output_h5parm - type: File - format: lofar:#H5Parm - outputBinding: - glob: $(inputs.input_h5parm.basename) - - -$namespaces: - lofar: https://git.astron.nl/eosc/ontologies/raw/master/schema/lofar.owl -$schema: - - https://git.astron.nl/eosc/ontologies/raw/master/schema/lofar.owl diff --git a/lofar-cwl/steps/LoSoTo.Residual.cwl b/lofar-cwl/steps/LoSoTo.Residual.cwl deleted file mode 100644 index 4bc566cd7d878f8532d69cd74aad7a6d4a72bf8b..0000000000000000000000000000000000000000 --- a/lofar-cwl/steps/LoSoTo.Residual.cwl +++ /dev/null @@ -1,59 +0,0 @@ -#!/usr/bin/env cwl-runner - -class: CommandLineTool -cwlVersion: v1.0 -id: losoto_residual - -doc: Subtract/divide two tables or a clock/tec/tec3rd/rm from a phase. - -requirements: - InitialWorkDirRequirement: - listing: - - entryname: 'parset.config' - entry: | - [residuals] - soltab = $(inputs.soltab) - operation=RESIDUALS - soltabsToSub=$(inputs.soltabsToSub) - ratio=$(inputs.ratio) - - - entryname: $(inputs.input_h5parm.basename) - entry: $(inputs.input_h5parm) - writable: true - -baseCommand: "losoto" - -arguments: - - $(inputs.input_h5parm.basename) - - parset.config - -hints: - DockerRequirement: - dockerPull: lofareosc/prefactor-ci:master - -inputs: - - id: input_h5parm - type: File - format: lofar:#H5Parm - - id: soltab - type: string - doc: "Solution table" - - id: soltabsToSub - type: string[] - doc: List of soltabs to subtract - - id: ratio - type: boolean? - default: false - doc: Return the ratio instead of subtracting. - -outputs: - - id: output_h5parm - type: File - format: lofar#H5Parm - outputBinding: - glob: $(inputs.input_h5parm.basename) - -$namespaces: - lofar: https://git.astron.nl/eosc/ontologies/raw/master/schema/lofar.owl -$schema: - - https://git.astron.nl/eosc/ontologies/raw/master/schema/lofar.owl diff --git a/lofar-cwl/steps/check_ateam_separation.cwl b/lofar-cwl/steps/check_ateam_separation.cwl deleted file mode 100755 index 977d9f86e63f3b003833aee677d330f1f188253d..0000000000000000000000000000000000000000 --- a/lofar-cwl/steps/check_ateam_separation.cwl +++ /dev/null @@ -1,44 +0,0 @@ -class: CommandLineTool -cwlVersion: v1.0 -$namespaces: - sbg: 'https://www.sevenbridges.com/' -id: check_ateam_separation -baseCommand: - - python3 - - /usr/local/bin/check_Ateam_separation.py -inputs: - - id: ms - type: - - Directory - - type: array - items: Directory - inputBinding: - position: 0 - doc: Input measurement set - - default: Ateam_separation.png - id: output_image_name - type: string? - inputBinding: - position: 2 - prefix: '--outputimage' - - id: min_separation - type: int - inputBinding: - position: 1 - prefix: '--min_separation' -outputs: - - id: output_imag - doc: Output image - type: File? - outputBinding: - glob: $(inputs.output_image_name) - - id: logfile - type: File? - outputBinding: - glob: Ateam_separation.log -label: check_Ateam_separation -hints: - - class: DockerRequirement - dockerPull: lofareosc/prefactor - - class: InlineJavascriptRequirement -stdout: Ateam_separation.log diff --git a/lofar-cwl/steps/ddecal.cwl b/lofar-cwl/steps/ddecal.cwl deleted file mode 100644 index c534d5362f563941d9503b980ae0dd6a4b766acf..0000000000000000000000000000000000000000 --- a/lofar-cwl/steps/ddecal.cwl +++ /dev/null @@ -1,111 +0,0 @@ -#!/usr/bin/env cwl-runner - -class: CommandLineTool -cwlVersion: v1.0 -id: ddecal -baseCommand: [DPPP] - -requirements: - InlineJavascriptRequirement: {} - -hints: - DockerRequirement: - dockerPull: lofareosc/prefactor-ci:master - -arguments: - - steps=[ddecal] - - ddecal.mode=rotation+diagonal - - ddecal.uvlambdamin=300 - - ddecal.maxiter=50 - - ddecal.nchan=1 - - ddecal.solint=1 - - ddecal.propagateconvergedonly=True - - ddecal.flagdivergedonly=True - - ddecal.tolerance=1.e-3 - - ddecal.usemodelcolumn=True - - -inputs: - - id: msin - type: Directory? - doc: Input Measurement Set - inputBinding: - prefix: msin= - separate: false - - - id: msin_datacolumn - type: string - default: DATA - doc: Input data Column - inputBinding: - prefix: msin.datacolumn= - separate: false - - - id: msin_modelcolum - type: string - default: MODEL_DATA - doc: Model data Column - inputBinding: - prefix: msin.modelcolumn= - separate: false - - - id: output_name_h5parm - type: string - default: instrument.h5 - inputBinding: - prefix: ddecal.h5parm= - separate: false - - id: msout_name - type: string - doc: Output Measurement Set - default: out.MS - inputBinding: - prefix: msout= - separate: false - -#-------------------- - - id: propagate_solutions - type: boolean - default: true - inputBinding: - prefix: propagatesolutions=True - - id: flagunconverged - type: boolean - default: false - doc: | - Flag unconverged solutions (i.e., those from solves that did not converge - within maxiter iterations). - inputBinding: - prefix: flagdivergedonly=True - - id: flagdivergedonly - default: false - type: boolean - doc: | - Flag only the unconverged solutions for which divergence was detected. - At the moment, this option is effective only for rotation+diagonal - solves, where divergence is detected when the amplitudes of any station - are found to be more than a factor of 5 from the mean amplitude over all - stations. - If divergence for any one station is detected, all stations are flagged - for that solution interval. Only effective when flagunconverged=true - and mode=rotation+diagonal. - inputBinding: - prefix: flagdivergedonly=True -outputs: - - id: msout - doc: Output Measurement Set - type: Directory - outputBinding: - glob: $(inputs.msout_name=="."?inputs.msin:inputs.msout_name) - - - id: h5parm - doc: Filename of output H5Parm (to be read by e.g. losoto) - type: File - format: lofar:#H5Parm - outputBinding: - glob: $(inputs.output_name_h5parm) - -$namespaces: - lofar: https://git.astron.nl/eosc/ontologies/raw/master/schema/lofar.owl -$schema: - - https://git.astron.nl/eosc/ontologies/raw/master/schema/lofar.owl diff --git a/lofar-cwl/steps/interpolate_visibilities.cwl b/lofar-cwl/steps/interpolate_visibilities.cwl deleted file mode 100644 index 90772b4f072cdecd9f03fd5f1d6258b66b995d11..0000000000000000000000000000000000000000 --- a/lofar-cwl/steps/interpolate_visibilities.cwl +++ /dev/null @@ -1,52 +0,0 @@ -class: CommandLineTool -cwlVersion: v1.0 -$namespaces: - sbg: 'https://www.sevenbridges.com/' -id: interpolate_visibilities - -baseCommand: - - DPPP -arguments: - - msout.datacolumn=INTERP_DATA - - msout=. - - msin.datacolumn=DATA - - steps=[interpolate] -inputs: - - id: msin - type: Directory - inputBinding: - prefix: 'msin=' - separate: false - - id: storage_manager - type: string - default: Dysco - inputBinding: - separate: false - prefix: 'msout.storagemanager=' - - id: storage_manager_databitrate - type: int - default: 0 - inputBinding: - prefix: 'msout.storagemanager.databitrate=' - separate: false - - id: window_size - type: int - inputBinding: - prefix: 'interpolate.windowsize=' - separate: false - -outputs: - - id: msout - type: Directory - outputBinding: - glob: $(inputs.msin.basename) -label: interpolate_visibilities -hints: - - class: DockerRequirement - dockerPull: lofareosc/prefactor-ci:master - -requirements: - - class: InitialWorkDirRequirement - listing: - - entry: $(inputs.msin) - writable: true diff --git a/lofar-cwl/steps/makesourcedb.cwl b/lofar-cwl/steps/makesourcedb.cwl deleted file mode 100755 index eb5c2e7c7b8f09c0a2c97ea4512bb241cff17fb5..0000000000000000000000000000000000000000 --- a/lofar-cwl/steps/makesourcedb.cwl +++ /dev/null @@ -1,56 +0,0 @@ -class: CommandLineTool -cwlVersion: v1.0 -$namespaces: - sbg: 'https://www.sevenbridges.com/' -id: make_sourcedb -baseCommand: - - makesourcedb -inputs: - - id: sky_model - type: - - File - - string - inputBinding: - position: 0 - prefix: in= - separate: false - - default: Ateam.sourcedb - id: output_file_name - type: string? - inputBinding: - position: 1 - prefix: out= - separate: false - valueFrom: Ateam.sourcedb - - default: blob - id: outtype - type: string? - inputBinding: - position: 2 - prefix: outtype= - separate: false - - default: < - id: format - type: string? - inputBinding: - position: 3 - prefix: format= - separate: false -outputs: - - id: sourcedb - type: - - Directory - - File - outputBinding: - glob: $(inputs.output_file_name) - - id: log - type: File? - outputBinding: - glob: make_sourcedb_ateam.log -label: make_sourcedb_ateam -hints: - - class: DockerRequirement - dockerPull: 'lofareosc/prefactor:latest' -stdout: make_sourcedb_ateam.log -requirements: - - class: InlineJavascriptRequirement diff --git a/lofar-cwl/steps/ms_concat.cwl b/lofar-cwl/steps/ms_concat.cwl deleted file mode 100644 index d9038e8df9506c24c6093b7ed9c4b27fb2a88196..0000000000000000000000000000000000000000 --- a/lofar-cwl/steps/ms_concat.cwl +++ /dev/null @@ -1,59 +0,0 @@ -class: CommandLineTool -cwlVersion: v1.0 -$namespaces: - sbg: 'https://www.sevenbridges.com/' -id: ms_concat - - -baseCommand: - - concat_MS.py -inputs: - - id: min_length - type: int? - default: 50 - inputBinding: - position: 0 - prefix: '--min_length' - doc: Minimum amount of subbands to concatenate in frequency. - - id: overhead - type: float? - inputBinding: - position: 0 - prefix: '--overhead' - doc: | - Only use this fraction of the available memory for deriving the amount - of data to be concatenated. - - id: msin - type: 'Directory[]' - inputBinding: - position: 1 - shellQuote: false - - default: out.MS - id: msout - type: string - inputBinding: - position: 2 -outputs: - - id: concat_meta_ms - type: Directory[] - outputBinding: - glob: > - $(inputs.msout)_[0-9*] - - id: concat_additional_ms - type: Directory[] - outputBinding: - glob: $(inputs.msout)_*_CONCAT - - id: ms_outs - type: Directory[] - outputBinding: - outputEval: $(inputs.msin) -label: ms_concat -requirements: - - class: ShellCommandRequirement - - class: DockerRequirement - dockerPull: lofareosc/prefactor-ci:master - - class: InlineJavascriptRequirement - - class: InitialWorkDirRequirement - listing: - - entry: $(inputs.msin) - writable: true diff --git a/lofar-cwl/steps/msinfo.cwl b/lofar-cwl/steps/msinfo.cwl deleted file mode 100644 index 0c7e2f5b779360baef059c0fe61f753a428d8707..0000000000000000000000000000000000000000 --- a/lofar-cwl/steps/msinfo.cwl +++ /dev/null @@ -1,40 +0,0 @@ -#!/usr/bin/env cwl-runner - -class: CommandLineTool -cwlVersion: v1.1 -id: msinfo - -requirements: - - class: InlineJavascriptRequirement - - class: InitialWorkDirRequirement - listing: - - entryname: msinfo.py - entry: | - import sys - print(sys.argv) - - class: SchemaDefRequirement - types: - - $import: RadioDatatypes.yaml -hints: - DockerRequirement: - dockerPull: lofareosc/prefactor-ci:master - -baseCommand: - - python3 - - msinfo.py - -inputs: - data: - type: RadioDatatypes.yaml#MeasurementSet - inputBinding: - position: 0 - -stdout: std.output - -outputs: - info: - type: File - outputBinding: - glob: std.output -label: msinfo - diff --git a/lofar-cwl/steps/predict.cwl b/lofar-cwl/steps/predict.cwl deleted file mode 100644 index eeb14aef083ee2e7ec43056e68fd018c47023e50..0000000000000000000000000000000000000000 --- a/lofar-cwl/steps/predict.cwl +++ /dev/null @@ -1,71 +0,0 @@ -class: CommandLineTool -cwlVersion: v1.0 -$namespaces: - sbg: 'https://www.sevenbridges.com/' -id: predict -baseCommand: - - DPPP -inputs: - - id: msin - type: Directory - inputBinding: - position: 0 - prefix: msin= - separate: false - doc: Input Measurement Set - - default: DATA - id: msin_datacolumn - type: string - inputBinding: - position: 0 - prefix: msin.datacolumn= - separate: false - doc: Input data Column - - default: MODEL_DATA - id: msout_datacolumn - type: string - inputBinding: - position: 0 - prefix: msout.datacolumn= - separate: false - - id: sources_db - type: File - inputBinding: - position: 0 - prefix: predict.sourcedb= - separate: false - - default: null - id: sources - type: 'string[]' - inputBinding: - position: 0 - prefix: predict.sources= - separate: false - itemSeparator: ',' - valueFrom: '[$(self)]' - - default: false - id: usebeammodel - type: boolean - inputBinding: - position: 0 - prefix: predict.usebeammodel=True -outputs: - - id: msout - doc: Output Measurement Set - type: Directory - outputBinding: - glob: $(inputs.msin.basename) -arguments: - - 'steps=[predict]' - - predict.beammode=array_factor - - predict.usechannelfreq=False - - msout=. -requirements: - - class: InitialWorkDirRequirement - listing: - - entry: $(inputs.msin) - writable: true - - class: InlineJavascriptRequirement -hints: - - class: DockerRequirement - dockerPull: lofareosc/prefactor-ci:master diff --git a/lofar-cwl/steps/wsclean.cwl b/lofar-cwl/steps/wsclean.cwl deleted file mode 100644 index 2bb63f2066cf8237103211ced00a92b2c5c33170..0000000000000000000000000000000000000000 --- a/lofar-cwl/steps/wsclean.cwl +++ /dev/null @@ -1,42 +0,0 @@ -class: CommandLineTool -cwlVersion: v1.0 -id: wsclean -baseCommand: - - wsclean -inputs: - - id: image_size - type: int[] - default: [1000, 1000] - inputBinding: - position: 1 - prefix: -size - - id: image_scale - type: float - default: 0.01 - inputBinding: - position: 1 - prefix: -scale - valueFrom: $(self)deg - - id: image_name - default: image - type: string - inputBinding: - position: 1 - prefix: -name - - id: msin - type: Directory - inputBinding: - position: 2 -outputs: - dirty_image: - type: File - outputBinding: - glob: $(inputs.image_name)-dirty.fits - image: - type: File - outputBinding: - glob: $(inputs.image_name)-image.fits -label: WSClean -requirements: - - class: DockerRequirement - dockerPull: lofareosc/prefactor-ci:master diff --git a/lofar-cwl/test_data/A-Team_lowres.sourcedb b/lofar-cwl/test_data/A-Team_lowres.sourcedb deleted file mode 100644 index b4e89906093cc01438b6a7b81f3ea9bfb06ba520..0000000000000000000000000000000000000000 Binary files a/lofar-cwl/test_data/A-Team_lowres.sourcedb and /dev/null differ diff --git a/lofar-cwl/test_data/L570745_uv_first10.MS.tar.xz b/lofar-cwl/test_data/L570745_uv_first10.MS.tar.xz deleted file mode 100644 index 13ab4c559979bdb321d6bdf57d92f03bb84ca2f2..0000000000000000000000000000000000000000 --- a/lofar-cwl/test_data/L570745_uv_first10.MS.tar.xz +++ /dev/null @@ -1,3 +0,0 @@ -version https://git-lfs.github.com/spec/v1 -oid sha256:d6acef40bcf795c5ae94232654414fece4a20eb75494577ea630fc663673b3c1 -size 387119976 diff --git a/lofar-cwl/test_data/example.h5.REMOVED.git-id b/lofar-cwl/test_data/example.h5.REMOVED.git-id deleted file mode 100644 index ee55446f16fed96380113889ea423eb37e2bdbd0..0000000000000000000000000000000000000000 --- a/lofar-cwl/test_data/example.h5.REMOVED.git-id +++ /dev/null @@ -1 +0,0 @@ -554933b577a0dcf1b2aa3fa91c7de5b2477fd724 \ No newline at end of file diff --git a/lofar-cwl/test_data/skymodels/3C196-pandey.skymodel b/lofar-cwl/test_data/skymodels/3C196-pandey.skymodel deleted file mode 100644 index 47424b9f86b2b6e06d789f5a54d15a787dffca7c..0000000000000000000000000000000000000000 --- a/lofar-cwl/test_data/skymodels/3C196-pandey.skymodel +++ /dev/null @@ -1,11 +0,0 @@ -# (Name, Type, Patch, Ra, Dec, I, Q, U, V, ReferenceFrequency='150e6', SpectralIndex='[-0.76, -0.00]', MajorAxis, MinorAxis, Orientation) = format - -, , 3c196_4c, 08:13:36.0, 48.13.0 -3C196A1, GAUSSIAN, 3c196_4c, 08:13:35.925, +48.13.00.061, 33.5514, 0.0, 0.0, 0.0, 150e6, [-0.572, -0.042], 1.476, 1.091, 135.27 -3C196A2, GAUSSIAN, 3c196_4c, 08:13:35.772, +48.13.02.507, 12.3129, 0.0, 0.0, 0.0, 150e6, [-0.973, -0.319], 2.738, 1.754, 93.30 -3C196B1, GAUSSIAN, 3c196_4c, 08:13:36.182, +48.13.04.725, 14.6030, 0.0, 0.0, 0.0, 150e6, [-0.557, -0.270], 1.034, 0.248, 124.03 -3C196B2, GAUSSIAN, 3c196_4c, 08:13:36.389, +48.13.02.735, 22.6653, 0.0, 0.0, 0.0, 150e6, [-0.840, -0.288], 1.456, 2.159, 324.58 -# Pandey: 31July2014 converted for the normal bbs updated on April 17th from pandey_March26_2014. DO NOT DELETE THIS LINE -# Tag:fitted version 2: 17-Apr-2014: pandey@astron.nl using L192832_1CH12S -# Modified to include a patch name on 24.11.2015 by A. Horneffer - diff --git a/lofar-cwl/test_data/skymodels/3c147-SH.skymodel b/lofar-cwl/test_data/skymodels/3c147-SH.skymodel deleted file mode 100644 index d8e7cd7cab357223c68320e5662228f2e331af40..0000000000000000000000000000000000000000 --- a/lofar-cwl/test_data/skymodels/3c147-SH.skymodel +++ /dev/null @@ -1,8 +0,0 @@ -# (Name, Type, Patch, Ra, Dec, I, Q, U, V, ReferenceFrequency='74e6', SpectralIndex='[]', MajorAxis, MinorAxis, Orientation) = format - -# The above line defines the field order and is required. - -# Scaife and Heald Calibrator model. -, , 3c147, 05:42:36.1, 49.51.07 -3c147_1, POINT, 3c147, 05:42:36.1, 49.51.07, 66.738, 0.0, 0.0, 0.0, 150.e6, [-0.022, -1.012, 0.549] - diff --git a/lofar-cwl/test_data/skymodels/3c286-SH.skymodel b/lofar-cwl/test_data/skymodels/3c286-SH.skymodel deleted file mode 100644 index 817c01a72a7e141579d04a7c87d794abca143091..0000000000000000000000000000000000000000 --- a/lofar-cwl/test_data/skymodels/3c286-SH.skymodel +++ /dev/null @@ -1,8 +0,0 @@ -# (Name, Type, Patch, Ra, Dec, I, Q, U, V, ReferenceFrequency='74e6', SpectralIndex='[]', MajorAxis, MinorAxis, Orientation) = format - -# The above line defines the field order and is required. - -# Scaife and Heald Calibrator model. -, , 3c286, 13:31:08.3, 30.30.33 -3c286_1, POINT, 3c286, 13:31:08.3, 30.30.33, 27.477, 0.0, 0.0, 0.0, 150.e6, [-0.158, 0.032, -0.180] - diff --git a/lofar-cwl/test_data/skymodels/3c287-SH.skymodel b/lofar-cwl/test_data/skymodels/3c287-SH.skymodel deleted file mode 100644 index 692009b074139d50389774f206b435eed5bb8307..0000000000000000000000000000000000000000 --- a/lofar-cwl/test_data/skymodels/3c287-SH.skymodel +++ /dev/null @@ -1,8 +0,0 @@ -# (Name, Type, Patch, Ra, Dec, I, Q, U, V, ReferenceFrequency='74e6', SpectralIndex='[]', MajorAxis, MinorAxis, Orientation) = format - -# The above line defines the field order and is required. - -# Scaife and Heald Calibrator model. -, , 3c287, 13:30:37.7, 25.09.11 -3c287_1, POINT, 3c287, 13:30:37.7, 25.09.11, 16.367, 0.0, 0.0, 0.0, 150.e6, [-0.364] - diff --git a/lofar-cwl/test_data/skymodels/3c295-twocomp.skymodel b/lofar-cwl/test_data/skymodels/3c295-twocomp.skymodel deleted file mode 100644 index 957cadd564d9a2e8ea1010d5e2a35c5d8d33cb4b..0000000000000000000000000000000000000000 --- a/lofar-cwl/test_data/skymodels/3c295-twocomp.skymodel +++ /dev/null @@ -1,5 +0,0 @@ -# (Name, Type, Patch, Ra, Dec, I, Q, U, V, ReferenceFrequency='150.e6', SpectralIndex='[]', MajorAxis, MinorAxis, Orientation) = format - - , , 3c295_2c, 14:11:20.64, +52.12.09.30 -3c295A, POINT, 3c295_2c, 14:11:20.49, +52.12.10.70, 48.8815, 0.0, 0.0, 0.0, 150.e6, [-0.582, -0.298, 0.583, -0.363] -3c295B, POINT, 3c295_2c, 14:11:20.79, +52.12.07.90, 48.8815, 0.0, 0.0, 0.0, 150.e6, [-0.582, -0.298, 0.583, -0.363] diff --git a/lofar-cwl/test_data/skymodels/3c380-SH.skymodel b/lofar-cwl/test_data/skymodels/3c380-SH.skymodel deleted file mode 100644 index 5a911080bbac0d42bf8a66afc670085a910cdd57..0000000000000000000000000000000000000000 --- a/lofar-cwl/test_data/skymodels/3c380-SH.skymodel +++ /dev/null @@ -1,8 +0,0 @@ -# (Name, Type, Patch, Ra, Dec, I, Q, U, V, ReferenceFrequency='74e6', SpectralIndex='[]', MajorAxis, MinorAxis, Orientation) = format - -# The above line defines the field order and is required. - -# Scaife and Heald Calibrator model. -, , 3c380, 18:29:31.8, 48.44.46 -3c380_1, POINT, 3c380, 18:29:31.8, 48.44.46, 77.352, 0.0, 0.0, 0.0, 150.e6, [-0.767] - diff --git a/lofar-cwl/test_data/skymodels/3c48-SH.skymodel b/lofar-cwl/test_data/skymodels/3c48-SH.skymodel deleted file mode 100644 index e2c3f50da26c04a646fedde67ce861ead3e68133..0000000000000000000000000000000000000000 --- a/lofar-cwl/test_data/skymodels/3c48-SH.skymodel +++ /dev/null @@ -1,7 +0,0 @@ -# (Name, Type, Patch, Ra, Dec, I, Q, U, V, ReferenceFrequency='74e6', SpectralIndex='[]', MajorAxis, MinorAxis, Orientation) = format - -# The above line defines the field order and is required. - -# Scaife and Heald Calibrator models. -, , 3c48, 01:37:41.3, 33.09.35 -3c48_1, POINT, 3c48, 01:37:41.3, 33.09.35, 64.768, 0.0, 0.0, 0.0, 150.e6, [-0.387, -0.420, 0.181] diff --git a/lofar-cwl/test_data/skymodels/A-Team_4_Highres.skymodel.REMOVED.git-id b/lofar-cwl/test_data/skymodels/A-Team_4_Highres.skymodel.REMOVED.git-id deleted file mode 100644 index 3a77caad0a210449d18cd8cf9e7f9ff5094f0bd9..0000000000000000000000000000000000000000 --- a/lofar-cwl/test_data/skymodels/A-Team_4_Highres.skymodel.REMOVED.git-id +++ /dev/null @@ -1 +0,0 @@ -92830adec7ead19c19340071ea59a3131bd82212 \ No newline at end of file diff --git a/lofar-cwl/test_data/skymodels/A-Team_lowres.skymodel b/lofar-cwl/test_data/skymodels/A-Team_lowres.skymodel deleted file mode 100644 index cbb1296b7520bbbfede15403b33011cdfbad5e80..0000000000000000000000000000000000000000 --- a/lofar-cwl/test_data/skymodels/A-Team_lowres.skymodel +++ /dev/null @@ -1,78 +0,0 @@ -# (Name, Type, Patch, Ra, Dec, I, Q, U, V, ReferenceFrequency='74e6', SpectralIndex='[]', MajorAxis, MinorAxis, Orientation) = format - -# The above line defines the field order and is required. - -# models for the A-Team members - -, , CygA, 19:59:26, +40.44.00 -CygA_4_2, POINT, CygA, 19:59:30.433, +40.43.56.221, 4.827e+03, 0.0, 0.0, 0.0, 7.38000e+07, [-0.8], 7.63889e-03, 6.94444e-03, 1.00637e+02 -CygA_4_1, GAUSSIAN, CygA, 19:59:28.476, +40.44.01.804, 4.165e+03, 0.0, 0.0, 0.0, 7.38000e+07, [-0.8], 1.20516e-02, 5.34011e-03, 1.03230e+02 -CygA_4_3, POINT, CygA, 19:59:22.168, +40.44.28.591, 3.896e+03, 0.0, 0.0, 0.0, 7.38000e+07, [-0.8], 7.63889e-03, 6.94444e-03, 9.21061e+01 -CygA_4_4, POINT, CygA, 19:59:24.413, +40.44.18.617, 2.798e+03, 0.0, 0.0, 0.0, 7.38000e+07, [-0.8], 7.63889e-03, 6.94444e-03, 6.74922e+01 -CygA_4_5, POINT, CygA, 19:59:25.555, +40.43.52.813, 1.560e+02, 0.0, 0.0, 0.0, 7.38000e+07, [-0.8], 7.63889e-03, 6.94444e-03, 0.00000e+00 - -, , CasA, 23:23:28, +58.48.42 -CasA_4_3, GAUSSIAN, CasA,23:23:21.044, +58.49.42.000, 4.193e+03, 0.0, 0.0, 0.0, 7.37817e+07, [-0.8], 4.32664e-02, 1.79281e-02, 2.73207e+01 -CasA_4_2, GAUSSIAN, CasA,23:23:33.918, +58.50.13.374, 4.131e+03, 0.0, 0.0, 0.0, 7.37817e+07, [-0.8], 4.25963e-02, 1.87784e-02, 1.12516e+02 -CasA_4_8, GAUSSIAN, CasA,23:23:34.032, +58.47.29.883, 2.536e+03, 0.0, 0.0, 0.0, 7.37817e+07, [-0.8], 2.77739e-02, 1.42664e-02, 6.26062e+01 -CasA_4_5, GAUSSIAN, CasA,23:23:15.292, +58.50.00.221, 2.316e+03, 0.0, 0.0, 0.0, 7.37817e+07, [-0.8], 3.15448e-02, 9.02869e-03, 4.11857e+01 -CasA_4_1, GAUSSIAN, CasA,23:23:39.632, +58.48.32.671, 2.245e+03, 0.0, 0.0, 0.0, 7.37817e+07, [-0.8], 2.25927e-02, 1.70874e-02, 8.48056e+01 -CasA_4_7, GAUSSIAN, CasA,23:23:24.110, +58.47.43.607, 2.201e+03, 0.0, 0.0, 0.0, 7.37817e+07, [-0.8], 4.64283e-02, 1.49372e-02, 2.12611e+01 -CasA_4_4, GAUSSIAN, CasA,23:23:14.939, +58.48.09.511, 2.099e+03, 0.0, 0.0, 0.0, 7.37817e+07, [-0.8], 3.09146e-02, 1.42990e-02, 1.61549e+02 -CasA_4_9, GAUSSIAN, CasA,23:23:10.817, +58.48.46.409, 9.790e+02, 0.0, 0.0, 0.0, 7.37817e+07, [-0.8], 9.62058e-03, 7.79284e-03, 1.77482e+02 -CasA_4_6, GAUSSIAN, CasA,23:23:26.327, +58.51.14.147, 2.444e+02, 0.0, 0.0, 0.0, 7.37817e+07, [-0.8], 8.75852e-03, 6.94444e-03, 8.12790e+01 - -, , TauA, 05:34:32, +21.59.55 -TauA_4_1, GAUSSIAN, TauA, 05:34:32.269, +21.59.47.597, 1.911e+02, 0.0, 0.0, 0.0, 7.38000e+07, [-0.8], 3.94949e-02, 1.31559e-02, 1.65623e+02 -TauA_4_11, GAUSSIAN, TauA, 05:34:28.639, +22.00.53.809, 1.344e+02, 0.0, 0.0, 0.0, 7.38000e+07, [-0.8], 2.82500e-02, 1.22959e-02, 2.49193e+01 -TauA_4_3, GAUSSIAN, TauA, 05:34:25.671, +22.01.26.361, 1.247e+02, 0.0, 0.0, 0.0, 7.38000e+07, [-0.8], 2.76133e-02, 1.13962e-02, 5.60626e+01 -TauA_4_9, GAUSSIAN, TauA, 05:34:23.420, +22.00.12.563, 1.096e+02, 0.0, 0.0, 0.0, 7.38000e+07, [-0.8], 2.82128e-02, 1.71142e-02, 3.38306e+01 -TauA_4_15, GAUSSIAN, TauA, 05:34:22.884, +22.01.56.603, 9.243e+01, 0.0, 0.0, 0.0, 7.38000e+07, [-0.8], 1.99931e-02, 1.65627e-02, 1.76338e+02 -TauA_4_20, GAUSSIAN, TauA, 05:34:29.086, +21.59.21.722, 8.792e+01, 0.0, 0.0, 0.0, 7.38000e+07, [-0.8], 3.23261e-02, 9.03648e-03, 1.09196e+02 -TauA_4_10, GAUSSIAN, TauA, 05:34:37.530, +21.59.06.719, 8.641e+01, 0.0, 0.0, 0.0, 7.38000e+07, [-0.8], 2.13390e-02, 1.33726e-02, 1.27644e+02 -TauA_4_2, POINT, TauA, 05:34:30.550, +21.59.58.106, 8.276e+01, 0.0, 0.0, 0.0, 7.38000e+07, [-0.8], 7.63889e-03, 6.94444e-03, 0.00000e+00 -TauA_4_5, GAUSSIAN, TauA, 05:34:40.748, +21.59.31.921, 7.008e+01, 0.0, 0.0, 0.0, 7.38000e+07, [-0.8], 2.59971e-02, 1.25206e-02, 1.51745e+02 -TauA_4_14, GAUSSIAN, TauA, 05:34:30.570, +21.58.33.304, 6.187e+01, 0.0, 0.0, 0.0, 7.38000e+07, [-0.8], 1.87859e-02, 1.14519e-02, 8.42720e+01 -TauA_4_7, GAUSSIAN, TauA, 05:34:36.888, +22.01.01.174, 5.537e+01, 0.0, 0.0, 0.0, 7.38000e+07, [-0.8], 1.93364e-02, 1.21462e-02, 1.39794e+02 -TauA_4_8, GAUSSIAN, TauA, 05:34:35.324, +22.00.10.883, 5.525e+01, 0.0, 0.0, 0.0, 7.38000e+07, [-0.8], 1.81832e-02, 1.35652e-02, 1.06533e+02 -TauA_4_4, GAUSSIAN, TauA, 05:34:23.931, +21.58.55.252, 5.076e+01, 0.0, 0.0, 0.0, 7.38000e+07, [-0.8], 1.77800e-02, 1.52796e-02, 7.50003e+01 -TauA_4_13, GAUSSIAN, TauA, 05:34:36.235, +21.58.03.089, 4.862e+01, 0.0, 0.0, 0.0, 7.38000e+07, [-0.8], 3.59649e-02, 9.18833e-03, 8.58303e+01 -TauA_4_6, GAUSSIAN, TauA, 05:34:27.470, +21.58.50.002, 4.223e+01, 0.0, 0.0, 0.0, 7.38000e+07, [-0.8], 2.54141e-02, 7.87103e-03, 5.52923e+01 -TauA_4_21, GAUSSIAN, TauA, 05:34:34.585, +22.00.45.580, 4.175e+01, 0.0, 0.0, 0.0, 7.38000e+07, [-0.8], 3.19587e-02, 6.70123e-03, 1.72839e+02 -TauA_4_19, GAUSSIAN, TauA, 05:34:19.534, +22.01.07.470, 3.906e+01, 0.0, 0.0, 0.0, 7.38000e+07, [-0.8], 2.20399e-02, 1.14898e-02, 1.76500e+02 -TauA_4_17, GAUSSIAN, TauA, 05:34:29.426, +21.59.51.003, 2.848e+01, 0.0, 0.0, 0.0, 7.38000e+07, [-0.8], 1.10631e-02, 5.13228e-03, 1.27622e+02 -TauA_4_23, GAUSSIAN, TauA, 05:34:26.246, +22.02.05.085, 2.699e+01, 0.0, 0.0, 0.0, 7.38000e+07, [-0.8], 1.28687e-02, 1.05568e-02, 1.44302e+02 -TauA_4_16, GAUSSIAN, TauA, 05:34:32.269, +22.01.21.318, 2.557e+01, 0.0, 0.0, 0.0, 7.38000e+07, [-0.8], 1.16784e-02, 7.66067e-03, 1.43877e+02 -TauA_4_12, GAUSSIAN, TauA, 05:34:22.991, +22.00.33.000, 2.127e+01, 0.0, 0.0, 0.0, 7.38000e+07, [-0.8], 1.49607e-02, 8.16407e-03, 1.16642e+02 -TauA_4_18, GAUSSIAN, TauA, 05:34:26.292, +22.02.39.501, 1.727e+01, 0.0, 0.0, 0.0, 7.38000e+07, [-0.8], 2.19757e-02, 6.32082e-03, 1.08185e+02 -TauA_4_22, GAUSSIAN, TauA, 05:34:37.023, +21.58.27.987, 1.357e+01, 0.0, 0.0, 0.0, 7.38000e+07, [-0.8], 8.54110e-03, 5.01393e-03, 7.39302e+01 -TauA_4_24, GAUSSIAN, TauA, 05:34:31.108, +22.00.32.726, 1.106e+01, 0.0, 0.0, 0.0, 7.38000e+07, [-0.8], 2.59017e-02, 6.94444e-03, 5.84987e+01 -TauA_4_26, GAUSSIAN, TauA, 05:32:23.875, +21.50.58.488, 1.780e+00, 0.0, 0.0, 0.0, 7.38000e+07, [-0.8], 1.05524e-02, 3.94647e-03, 6.84955e+01 -TauA_4_25, POINT, TauA, 05:34:30.647, +21.59.16.928, 9.776e-01, 0.0, 0.0, 0.0, 7.38000e+07, [-0.8], 7.63889e-03, 6.94444e-03, 2.05933e+01 - -, , VirA, 12:30:35, +12.19.45 -VirA_4_17, GAUSSIAN, VirA, 12:30:34.383, +12.20.04.012, 3.219e+02, 0.0, 0.0, 0.0, 7.38000e+07, [-0.8], 8.42972e-02, 6.11535e-02, 6.50364e+01 -VirA_4_2, GAUSSIAN, VirA, 12:30:47.034, +12.23.43.975, 2.591e+02, 0.0, 0.0, 0.0, 7.38000e+07, [-0.8], 8.54400e-03, 4.07169e-03, 1.06884e+02 -VirA_4_1, POINT, VirA, 12:30:48.961, +12.23.33.770, 1.516e+02, 0.0, 0.0, 0.0, 7.38000e+07, [-0.8], 7.63889e-03, 6.94444e-03, 1.70815e+02 -VirA_4_19, GAUSSIAN, VirA, 12:30:41.047, +12.17.36.983, 1.094e+02, 0.0, 0.0, 0.0, 7.38000e+07, [-0.8], 4.63137e-02, 2.79725e-02, 8.64763e+01 -VirA_4_20, GAUSSIAN, VirA, 12:30:49.250, +12.24.02.102, 1.069e+02, 0.0, 0.0, 0.0, 7.38000e+07, [-0.8], 9.92793e-02, 2.33402e-02, 1.08930e+01 -VirA_4_7, GAUSSIAN, VirA, 12:31:00.320, +12.26.38.867, 8.851e+01, 0.0, 0.0, 0.0, 7.38000e+07, [-0.8], 3.83541e-02, 3.47954e-02, 1.53069e+02 -VirA_4_6, GAUSSIAN, VirA, 12:30:55.490, +12.23.49.301, 7.499e+01, 0.0, 0.0, 0.0, 7.38000e+07, [-0.8], 6.64979e-02, 1.79950e-02, 1.72468e+01 -VirA_4_4, GAUSSIAN, VirA, 12:30:59.933, +12.22.42.187, 7.388e+01, 0.0, 0.0, 0.0, 7.38000e+07, [-0.8], 1.52817e-01, 1.69367e-02, 3.28830e+01 -VirA_4_21, GAUSSIAN, VirA, 12:30:42.588, +12.22.06.778, 6.153e+01, 0.0, 0.0, 0.0, 7.38000e+07, [-0.8], 3.81610e-02, 1.87921e-02, 2.03833e+01 -VirA_4_9, GAUSSIAN, VirA, 12:30:50.661, +12.23.49.618, 5.456e+01, 0.0, 0.0, 0.0, 7.38000e+07, [-0.8], 7.36474e-02, 8.25082e-03, 8.58262e+01 -VirA_4_3, POINT, VirA, 12:30:48.239, +12.23.18.068, 5.398e+01, 0.0, 0.0, 0.0, 7.38000e+07, [-0.8], 7.63889e-03, 6.94444e-03, 1.11922e+02 -VirA_4_14, GAUSSIAN, VirA, 12:30:39.222, +12.23.13.204, 5.142e+01, 0.0, 0.0, 0.0, 7.38000e+07, [-0.8], 2.40448e-02, 1.75673e-02, 1.70476e+02 -VirA_4_5, POINT, VirA, 12:30:45.851, +12.23.49.562, 4.189e+01, 0.0, 0.0, 0.0, 7.38000e+07, [-0.8], 7.63889e-03, 6.94444e-03, 8.15603e+01 -VirA_4_8, GAUSSIAN, VirA, 12:30:52.150, +12.18.29.472, 3.936e+01, 0.0, 0.0, 0.0, 7.38000e+07, [-0.8], 3.38379e-02, 2.30198e-02, 1.60497e+02 -VirA_4_15, GAUSSIAN, VirA, 12:31:01.387, +12.24.37.942, 3.313e+01, 0.0, 0.0, 0.0, 7.38000e+07, [-0.8], 2.14509e-02, 1.18403e-02, 7.44971e+01 -VirA_4_12, GAUSSIAN, VirA, 12:31:03.637, +12.23.31.633, 2.835e+01, 0.0, 0.0, 0.0, 7.38000e+07, [-0.8], 3.23407e-02, 9.02810e-03, 3.03022e+00 -VirA_4_11, GAUSSIAN, VirA, 12:30:59.512, +12.22.44.364, 2.701e+01, 0.0, 0.0, 0.0, 7.38000e+07, [-0.8], 2.66163e-02, 1.08450e-02, 1.34667e+02 -VirA_4_13, GAUSSIAN, VirA, 12:31:00.272, +12.23.41.572, 2.676e+01, 0.0, 0.0, 0.0, 7.38000e+07, [-0.8], 1.52105e-02, 1.11420e-02, 1.04009e+02 -VirA_4_10, POINT, VirA, 12:30:48.452, +12.23.32.663, 2.217e+01, 0.0, 0.0, 0.0, 7.38000e+07, [-0.8], 7.63889e-03, 6.94444e-03, 0.00000e+00 -VirA_4_16, GAUSSIAN, VirA, 12:30:43.137, +12.23.59.978, 1.788e+01, 0.0, 0.0, 0.0, 7.38000e+07, [-0.8], 1.68245e-02, 9.05564e-03, 9.84731e+01 -VirA_4_24, GAUSSIAN, VirA, 12:30:36.867, +12.18.49.897, 1.130e+01, 0.0, 0.0, 0.0, 7.38000e+07, [-0.8], 2.28602e-02, 1.66793e-02, 1.45577e+02 -VirA_4_18, POINT, VirA, 12:30:47.114, +12.23.26.692, 8.179e+00, 0.0, 0.0, 0.0, 7.38000e+07, [-0.8], 7.63889e-03, 6.94444e-03, 0.00000e+00 -VirA_4_23, GAUSSIAN, VirA, 12:30:44.464, +12.19.17.889, 4.819e+00, 0.0, 0.0, 0.0, 7.38000e+07, [-0.8], 1.37460e-02, 1.36631e-02, 1.48507e+02 -VirA_4_22, GAUSSIAN, VirA, 12:30:44.127, +12.23.08.175, 4.207e+00, 0.0, 0.0, 0.0, 7.38000e+07, [-0.8], 8.85467e-03, 5.44859e-03, 1.33216e+02 - diff --git a/lofar-cwl/test_data/skymodels/Ateam_LBA_CC.skymodel.REMOVED.git-id b/lofar-cwl/test_data/skymodels/Ateam_LBA_CC.skymodel.REMOVED.git-id deleted file mode 100644 index c143443c567168c864095201d920d70a5351f4bc..0000000000000000000000000000000000000000 --- a/lofar-cwl/test_data/skymodels/Ateam_LBA_CC.skymodel.REMOVED.git-id +++ /dev/null @@ -1 +0,0 @@ -ce968f5b4fb7491d2a63c642cc51d01da2bce829 \ No newline at end of file diff --git a/lofar-cwl/test_data/skymodels/Calibrators_SH_lowres.skymodel b/lofar-cwl/test_data/skymodels/Calibrators_SH_lowres.skymodel deleted file mode 100644 index cbb1296b7520bbbfede15403b33011cdfbad5e80..0000000000000000000000000000000000000000 --- a/lofar-cwl/test_data/skymodels/Calibrators_SH_lowres.skymodel +++ /dev/null @@ -1,78 +0,0 @@ -# (Name, Type, Patch, Ra, Dec, I, Q, U, V, ReferenceFrequency='74e6', SpectralIndex='[]', MajorAxis, MinorAxis, Orientation) = format - -# The above line defines the field order and is required. - -# models for the A-Team members - -, , CygA, 19:59:26, +40.44.00 -CygA_4_2, POINT, CygA, 19:59:30.433, +40.43.56.221, 4.827e+03, 0.0, 0.0, 0.0, 7.38000e+07, [-0.8], 7.63889e-03, 6.94444e-03, 1.00637e+02 -CygA_4_1, GAUSSIAN, CygA, 19:59:28.476, +40.44.01.804, 4.165e+03, 0.0, 0.0, 0.0, 7.38000e+07, [-0.8], 1.20516e-02, 5.34011e-03, 1.03230e+02 -CygA_4_3, POINT, CygA, 19:59:22.168, +40.44.28.591, 3.896e+03, 0.0, 0.0, 0.0, 7.38000e+07, [-0.8], 7.63889e-03, 6.94444e-03, 9.21061e+01 -CygA_4_4, POINT, CygA, 19:59:24.413, +40.44.18.617, 2.798e+03, 0.0, 0.0, 0.0, 7.38000e+07, [-0.8], 7.63889e-03, 6.94444e-03, 6.74922e+01 -CygA_4_5, POINT, CygA, 19:59:25.555, +40.43.52.813, 1.560e+02, 0.0, 0.0, 0.0, 7.38000e+07, [-0.8], 7.63889e-03, 6.94444e-03, 0.00000e+00 - -, , CasA, 23:23:28, +58.48.42 -CasA_4_3, GAUSSIAN, CasA,23:23:21.044, +58.49.42.000, 4.193e+03, 0.0, 0.0, 0.0, 7.37817e+07, [-0.8], 4.32664e-02, 1.79281e-02, 2.73207e+01 -CasA_4_2, GAUSSIAN, CasA,23:23:33.918, +58.50.13.374, 4.131e+03, 0.0, 0.0, 0.0, 7.37817e+07, [-0.8], 4.25963e-02, 1.87784e-02, 1.12516e+02 -CasA_4_8, GAUSSIAN, CasA,23:23:34.032, +58.47.29.883, 2.536e+03, 0.0, 0.0, 0.0, 7.37817e+07, [-0.8], 2.77739e-02, 1.42664e-02, 6.26062e+01 -CasA_4_5, GAUSSIAN, CasA,23:23:15.292, +58.50.00.221, 2.316e+03, 0.0, 0.0, 0.0, 7.37817e+07, [-0.8], 3.15448e-02, 9.02869e-03, 4.11857e+01 -CasA_4_1, GAUSSIAN, CasA,23:23:39.632, +58.48.32.671, 2.245e+03, 0.0, 0.0, 0.0, 7.37817e+07, [-0.8], 2.25927e-02, 1.70874e-02, 8.48056e+01 -CasA_4_7, GAUSSIAN, CasA,23:23:24.110, +58.47.43.607, 2.201e+03, 0.0, 0.0, 0.0, 7.37817e+07, [-0.8], 4.64283e-02, 1.49372e-02, 2.12611e+01 -CasA_4_4, GAUSSIAN, CasA,23:23:14.939, +58.48.09.511, 2.099e+03, 0.0, 0.0, 0.0, 7.37817e+07, [-0.8], 3.09146e-02, 1.42990e-02, 1.61549e+02 -CasA_4_9, GAUSSIAN, CasA,23:23:10.817, +58.48.46.409, 9.790e+02, 0.0, 0.0, 0.0, 7.37817e+07, [-0.8], 9.62058e-03, 7.79284e-03, 1.77482e+02 -CasA_4_6, GAUSSIAN, CasA,23:23:26.327, +58.51.14.147, 2.444e+02, 0.0, 0.0, 0.0, 7.37817e+07, [-0.8], 8.75852e-03, 6.94444e-03, 8.12790e+01 - -, , TauA, 05:34:32, +21.59.55 -TauA_4_1, GAUSSIAN, TauA, 05:34:32.269, +21.59.47.597, 1.911e+02, 0.0, 0.0, 0.0, 7.38000e+07, [-0.8], 3.94949e-02, 1.31559e-02, 1.65623e+02 -TauA_4_11, GAUSSIAN, TauA, 05:34:28.639, +22.00.53.809, 1.344e+02, 0.0, 0.0, 0.0, 7.38000e+07, [-0.8], 2.82500e-02, 1.22959e-02, 2.49193e+01 -TauA_4_3, GAUSSIAN, TauA, 05:34:25.671, +22.01.26.361, 1.247e+02, 0.0, 0.0, 0.0, 7.38000e+07, [-0.8], 2.76133e-02, 1.13962e-02, 5.60626e+01 -TauA_4_9, GAUSSIAN, TauA, 05:34:23.420, +22.00.12.563, 1.096e+02, 0.0, 0.0, 0.0, 7.38000e+07, [-0.8], 2.82128e-02, 1.71142e-02, 3.38306e+01 -TauA_4_15, GAUSSIAN, TauA, 05:34:22.884, +22.01.56.603, 9.243e+01, 0.0, 0.0, 0.0, 7.38000e+07, [-0.8], 1.99931e-02, 1.65627e-02, 1.76338e+02 -TauA_4_20, GAUSSIAN, TauA, 05:34:29.086, +21.59.21.722, 8.792e+01, 0.0, 0.0, 0.0, 7.38000e+07, [-0.8], 3.23261e-02, 9.03648e-03, 1.09196e+02 -TauA_4_10, GAUSSIAN, TauA, 05:34:37.530, +21.59.06.719, 8.641e+01, 0.0, 0.0, 0.0, 7.38000e+07, [-0.8], 2.13390e-02, 1.33726e-02, 1.27644e+02 -TauA_4_2, POINT, TauA, 05:34:30.550, +21.59.58.106, 8.276e+01, 0.0, 0.0, 0.0, 7.38000e+07, [-0.8], 7.63889e-03, 6.94444e-03, 0.00000e+00 -TauA_4_5, GAUSSIAN, TauA, 05:34:40.748, +21.59.31.921, 7.008e+01, 0.0, 0.0, 0.0, 7.38000e+07, [-0.8], 2.59971e-02, 1.25206e-02, 1.51745e+02 -TauA_4_14, GAUSSIAN, TauA, 05:34:30.570, +21.58.33.304, 6.187e+01, 0.0, 0.0, 0.0, 7.38000e+07, [-0.8], 1.87859e-02, 1.14519e-02, 8.42720e+01 -TauA_4_7, GAUSSIAN, TauA, 05:34:36.888, +22.01.01.174, 5.537e+01, 0.0, 0.0, 0.0, 7.38000e+07, [-0.8], 1.93364e-02, 1.21462e-02, 1.39794e+02 -TauA_4_8, GAUSSIAN, TauA, 05:34:35.324, +22.00.10.883, 5.525e+01, 0.0, 0.0, 0.0, 7.38000e+07, [-0.8], 1.81832e-02, 1.35652e-02, 1.06533e+02 -TauA_4_4, GAUSSIAN, TauA, 05:34:23.931, +21.58.55.252, 5.076e+01, 0.0, 0.0, 0.0, 7.38000e+07, [-0.8], 1.77800e-02, 1.52796e-02, 7.50003e+01 -TauA_4_13, GAUSSIAN, TauA, 05:34:36.235, +21.58.03.089, 4.862e+01, 0.0, 0.0, 0.0, 7.38000e+07, [-0.8], 3.59649e-02, 9.18833e-03, 8.58303e+01 -TauA_4_6, GAUSSIAN, TauA, 05:34:27.470, +21.58.50.002, 4.223e+01, 0.0, 0.0, 0.0, 7.38000e+07, [-0.8], 2.54141e-02, 7.87103e-03, 5.52923e+01 -TauA_4_21, GAUSSIAN, TauA, 05:34:34.585, +22.00.45.580, 4.175e+01, 0.0, 0.0, 0.0, 7.38000e+07, [-0.8], 3.19587e-02, 6.70123e-03, 1.72839e+02 -TauA_4_19, GAUSSIAN, TauA, 05:34:19.534, +22.01.07.470, 3.906e+01, 0.0, 0.0, 0.0, 7.38000e+07, [-0.8], 2.20399e-02, 1.14898e-02, 1.76500e+02 -TauA_4_17, GAUSSIAN, TauA, 05:34:29.426, +21.59.51.003, 2.848e+01, 0.0, 0.0, 0.0, 7.38000e+07, [-0.8], 1.10631e-02, 5.13228e-03, 1.27622e+02 -TauA_4_23, GAUSSIAN, TauA, 05:34:26.246, +22.02.05.085, 2.699e+01, 0.0, 0.0, 0.0, 7.38000e+07, [-0.8], 1.28687e-02, 1.05568e-02, 1.44302e+02 -TauA_4_16, GAUSSIAN, TauA, 05:34:32.269, +22.01.21.318, 2.557e+01, 0.0, 0.0, 0.0, 7.38000e+07, [-0.8], 1.16784e-02, 7.66067e-03, 1.43877e+02 -TauA_4_12, GAUSSIAN, TauA, 05:34:22.991, +22.00.33.000, 2.127e+01, 0.0, 0.0, 0.0, 7.38000e+07, [-0.8], 1.49607e-02, 8.16407e-03, 1.16642e+02 -TauA_4_18, GAUSSIAN, TauA, 05:34:26.292, +22.02.39.501, 1.727e+01, 0.0, 0.0, 0.0, 7.38000e+07, [-0.8], 2.19757e-02, 6.32082e-03, 1.08185e+02 -TauA_4_22, GAUSSIAN, TauA, 05:34:37.023, +21.58.27.987, 1.357e+01, 0.0, 0.0, 0.0, 7.38000e+07, [-0.8], 8.54110e-03, 5.01393e-03, 7.39302e+01 -TauA_4_24, GAUSSIAN, TauA, 05:34:31.108, +22.00.32.726, 1.106e+01, 0.0, 0.0, 0.0, 7.38000e+07, [-0.8], 2.59017e-02, 6.94444e-03, 5.84987e+01 -TauA_4_26, GAUSSIAN, TauA, 05:32:23.875, +21.50.58.488, 1.780e+00, 0.0, 0.0, 0.0, 7.38000e+07, [-0.8], 1.05524e-02, 3.94647e-03, 6.84955e+01 -TauA_4_25, POINT, TauA, 05:34:30.647, +21.59.16.928, 9.776e-01, 0.0, 0.0, 0.0, 7.38000e+07, [-0.8], 7.63889e-03, 6.94444e-03, 2.05933e+01 - -, , VirA, 12:30:35, +12.19.45 -VirA_4_17, GAUSSIAN, VirA, 12:30:34.383, +12.20.04.012, 3.219e+02, 0.0, 0.0, 0.0, 7.38000e+07, [-0.8], 8.42972e-02, 6.11535e-02, 6.50364e+01 -VirA_4_2, GAUSSIAN, VirA, 12:30:47.034, +12.23.43.975, 2.591e+02, 0.0, 0.0, 0.0, 7.38000e+07, [-0.8], 8.54400e-03, 4.07169e-03, 1.06884e+02 -VirA_4_1, POINT, VirA, 12:30:48.961, +12.23.33.770, 1.516e+02, 0.0, 0.0, 0.0, 7.38000e+07, [-0.8], 7.63889e-03, 6.94444e-03, 1.70815e+02 -VirA_4_19, GAUSSIAN, VirA, 12:30:41.047, +12.17.36.983, 1.094e+02, 0.0, 0.0, 0.0, 7.38000e+07, [-0.8], 4.63137e-02, 2.79725e-02, 8.64763e+01 -VirA_4_20, GAUSSIAN, VirA, 12:30:49.250, +12.24.02.102, 1.069e+02, 0.0, 0.0, 0.0, 7.38000e+07, [-0.8], 9.92793e-02, 2.33402e-02, 1.08930e+01 -VirA_4_7, GAUSSIAN, VirA, 12:31:00.320, +12.26.38.867, 8.851e+01, 0.0, 0.0, 0.0, 7.38000e+07, [-0.8], 3.83541e-02, 3.47954e-02, 1.53069e+02 -VirA_4_6, GAUSSIAN, VirA, 12:30:55.490, +12.23.49.301, 7.499e+01, 0.0, 0.0, 0.0, 7.38000e+07, [-0.8], 6.64979e-02, 1.79950e-02, 1.72468e+01 -VirA_4_4, GAUSSIAN, VirA, 12:30:59.933, +12.22.42.187, 7.388e+01, 0.0, 0.0, 0.0, 7.38000e+07, [-0.8], 1.52817e-01, 1.69367e-02, 3.28830e+01 -VirA_4_21, GAUSSIAN, VirA, 12:30:42.588, +12.22.06.778, 6.153e+01, 0.0, 0.0, 0.0, 7.38000e+07, [-0.8], 3.81610e-02, 1.87921e-02, 2.03833e+01 -VirA_4_9, GAUSSIAN, VirA, 12:30:50.661, +12.23.49.618, 5.456e+01, 0.0, 0.0, 0.0, 7.38000e+07, [-0.8], 7.36474e-02, 8.25082e-03, 8.58262e+01 -VirA_4_3, POINT, VirA, 12:30:48.239, +12.23.18.068, 5.398e+01, 0.0, 0.0, 0.0, 7.38000e+07, [-0.8], 7.63889e-03, 6.94444e-03, 1.11922e+02 -VirA_4_14, GAUSSIAN, VirA, 12:30:39.222, +12.23.13.204, 5.142e+01, 0.0, 0.0, 0.0, 7.38000e+07, [-0.8], 2.40448e-02, 1.75673e-02, 1.70476e+02 -VirA_4_5, POINT, VirA, 12:30:45.851, +12.23.49.562, 4.189e+01, 0.0, 0.0, 0.0, 7.38000e+07, [-0.8], 7.63889e-03, 6.94444e-03, 8.15603e+01 -VirA_4_8, GAUSSIAN, VirA, 12:30:52.150, +12.18.29.472, 3.936e+01, 0.0, 0.0, 0.0, 7.38000e+07, [-0.8], 3.38379e-02, 2.30198e-02, 1.60497e+02 -VirA_4_15, GAUSSIAN, VirA, 12:31:01.387, +12.24.37.942, 3.313e+01, 0.0, 0.0, 0.0, 7.38000e+07, [-0.8], 2.14509e-02, 1.18403e-02, 7.44971e+01 -VirA_4_12, GAUSSIAN, VirA, 12:31:03.637, +12.23.31.633, 2.835e+01, 0.0, 0.0, 0.0, 7.38000e+07, [-0.8], 3.23407e-02, 9.02810e-03, 3.03022e+00 -VirA_4_11, GAUSSIAN, VirA, 12:30:59.512, +12.22.44.364, 2.701e+01, 0.0, 0.0, 0.0, 7.38000e+07, [-0.8], 2.66163e-02, 1.08450e-02, 1.34667e+02 -VirA_4_13, GAUSSIAN, VirA, 12:31:00.272, +12.23.41.572, 2.676e+01, 0.0, 0.0, 0.0, 7.38000e+07, [-0.8], 1.52105e-02, 1.11420e-02, 1.04009e+02 -VirA_4_10, POINT, VirA, 12:30:48.452, +12.23.32.663, 2.217e+01, 0.0, 0.0, 0.0, 7.38000e+07, [-0.8], 7.63889e-03, 6.94444e-03, 0.00000e+00 -VirA_4_16, GAUSSIAN, VirA, 12:30:43.137, +12.23.59.978, 1.788e+01, 0.0, 0.0, 0.0, 7.38000e+07, [-0.8], 1.68245e-02, 9.05564e-03, 9.84731e+01 -VirA_4_24, GAUSSIAN, VirA, 12:30:36.867, +12.18.49.897, 1.130e+01, 0.0, 0.0, 0.0, 7.38000e+07, [-0.8], 2.28602e-02, 1.66793e-02, 1.45577e+02 -VirA_4_18, POINT, VirA, 12:30:47.114, +12.23.26.692, 8.179e+00, 0.0, 0.0, 0.0, 7.38000e+07, [-0.8], 7.63889e-03, 6.94444e-03, 0.00000e+00 -VirA_4_23, GAUSSIAN, VirA, 12:30:44.464, +12.19.17.889, 4.819e+00, 0.0, 0.0, 0.0, 7.38000e+07, [-0.8], 1.37460e-02, 1.36631e-02, 1.48507e+02 -VirA_4_22, GAUSSIAN, VirA, 12:30:44.127, +12.23.08.175, 4.207e+00, 0.0, 0.0, 0.0, 7.38000e+07, [-0.8], 8.85467e-03, 5.44859e-03, 1.33216e+02 - diff --git a/lofar-cwl/test_jobs/NDPPP.json b/lofar-cwl/test_jobs/NDPPP.json deleted file mode 100644 index d010d681ec66a6e25ae050193c8a40ac871d40d6..0000000000000000000000000000000000000000 --- a/lofar-cwl/test_jobs/NDPPP.json +++ /dev/null @@ -1,21 +0,0 @@ -{ - "parset": { - "class": "File", - "path": "ndppp_step.parset" - }, - "msin": { - "class": "Directory", - "path": "/data/L570745_SB000_uv_first10.MS" - }, - "output_file_names": { - "gaincal": { - "name": "test.h5" - }, - }, - "output_directory_names": { - "count": { - "count_flagfreq": "L570745_SB000_uv_first10_count.flagfreq", - "count_flagstat": "L570745_SB000_uv_first10_count.flagstat" - } - } -} diff --git a/lofar-cwl/test_jobs/aoflagger.json b/lofar-cwl/test_jobs/aoflagger.json deleted file mode 100644 index 138c5022e2e071f4f84a79fdadbdd063b51bfe3f..0000000000000000000000000000000000000000 --- a/lofar-cwl/test_jobs/aoflagger.json +++ /dev/null @@ -1,12 +0,0 @@ -{ - "msin": [ - { - "class": "Directory", - "path": "/data/L570745_SB000_uv_first10.MS" - }, - { - "class": "Directory", - "path": "/data/L570745_SB001_uv_first10.MS" - } - ] -} diff --git a/lofar-cwl/test_jobs/aoflagger_step_generator.json b/lofar-cwl/test_jobs/aoflagger_step_generator.json deleted file mode 100644 index 4c6b5085d4492d2a008d0c0cdd0bbd4139c97132..0000000000000000000000000000000000000000 --- a/lofar-cwl/test_jobs/aoflagger_step_generator.json +++ /dev/null @@ -1,8 +0,0 @@ -{ - "input_parset": [{ - "step_type": "name", - "step_id": "id", - "parameters": [] -}], - "strategy": {"class":"File", "path":"/dev/null"} -} diff --git a/lofar-cwl/test_jobs/averager_step_generator.json b/lofar-cwl/test_jobs/averager_step_generator.json deleted file mode 100644 index 4bfe8ddc068c92271e8bb29fad6219214d24a199..0000000000000000000000000000000000000000 --- a/lofar-cwl/test_jobs/averager_step_generator.json +++ /dev/null @@ -1,7 +0,0 @@ -{ - "input_parset": [{ - "step_type": "name", - "step_id": "id", - "parameters": [] -}] -} diff --git a/lofar-cwl/test_jobs/averager_step_generator_error.json b/lofar-cwl/test_jobs/averager_step_generator_error.json deleted file mode 100644 index c0a124a2a47027e9261e360d5557c31a5de16b4e..0000000000000000000000000000000000000000 --- a/lofar-cwl/test_jobs/averager_step_generator_error.json +++ /dev/null @@ -1,9 +0,0 @@ -{ - "input_parset": [{ - "step_type": "name", - "step_id": "id", - "parameters": [] -}], - "step_id": "id", - "strategy": {"class":"File", "path":"/dev/null"} -} diff --git a/lofar-cwl/test_jobs/ddecal.json b/lofar-cwl/test_jobs/ddecal.json deleted file mode 100644 index 13a89c1f35db2da2d1be6966d5f213619360e514..0000000000000000000000000000000000000000 --- a/lofar-cwl/test_jobs/ddecal.json +++ /dev/null @@ -1,8 +0,0 @@ -{ - "msin": { - "class": "Directory", - "path": "/data/L570745_SB001_uv_MODEL.MS" - }, - "msin_datacolumn": "DATA", - "usemodelcolumn": true -} diff --git a/lofar-cwl/test_jobs/demo_prefactor.json b/lofar-cwl/test_jobs/demo_prefactor.json deleted file mode 100644 index ef2e0db960d13f382cdd2272969ce975e4c7d77f..0000000000000000000000000000000000000000 --- a/lofar-cwl/test_jobs/demo_prefactor.json +++ /dev/null @@ -1,17 +0,0 @@ -{ - "msin": [ - { - "class": "Directory", - "path": "/data/L570745_SB003_uv_first10.MS" - }, - { - "class": "Directory", - "path": "/data/L570745_SB005_uv_first10.MS" - }, - { - "class": "Directory", - "path": "/data/L570745_SB008_uv_first10.MS" - } - ] -} - diff --git a/lofar-cwl/test_jobs/dp3_execute.json b/lofar-cwl/test_jobs/dp3_execute.json deleted file mode 100644 index f21dff5b5c3fc6f6c7bd58edc1d6aee45ce5446b..0000000000000000000000000000000000000000 --- a/lofar-cwl/test_jobs/dp3_execute.json +++ /dev/null @@ -1,19 +0,0 @@ -{ - "msin": {"class": "Directory", "path":"/data/L570745_SB003_uv_first10.MS"}, - "steps": [ - { - "step_type": "averager", - "step_id": "average", - "parameters": { - "timestep": 1, - "freqstep": 1, - "minpoints": 0, - "minperc": 0, - "timeresolution": 0, - "freqresolution": 0 - }, - "output_files": {} - } - ], - "msout_name": "TEST" -} diff --git a/lofar-cwl/test_jobs/file_selector.json b/lofar-cwl/test_jobs/file_selector.json deleted file mode 100644 index 77e4a30217226c2250882fd1ca55810695577c13..0000000000000000000000000000000000000000 --- a/lofar-cwl/test_jobs/file_selector.json +++ /dev/null @@ -1,12 +0,0 @@ -{ - "inputs": { - "average": { - "parmdb": { - "class": "File", - "location": "ndppp_step.parset" - } - } - }, - "step_name": "average", - "key_name": "parmdb" -} diff --git a/lofar-cwl/test_jobs/find_skymodel_cal.json b/lofar-cwl/test_jobs/find_skymodel_cal.json deleted file mode 100644 index 1a0067244b08ded29eccd45b1ec5b3394f72b164..0000000000000000000000000000000000000000 --- a/lofar-cwl/test_jobs/find_skymodel_cal.json +++ /dev/null @@ -1,10 +0,0 @@ -{ - "msin": { - "class": "Directory", - "path": "/data/L570745_SB000_uv_first10.MS" - }, - "skymodels": { - "class": "Directory", - "path": "/data/skymodels" - } -} diff --git a/lofar-cwl/test_jobs/flag_average.json b/lofar-cwl/test_jobs/flag_average.json deleted file mode 100644 index 36154f55330703582bc2a83c16cf666d27560148..0000000000000000000000000000000000000000 --- a/lofar-cwl/test_jobs/flag_average.json +++ /dev/null @@ -1,6 +0,0 @@ -{ - "msin": { - "class": "Directory", - "path": "/data/L570745_SB001_uv_first10.MS" - } -} diff --git a/lofar-cwl/test_jobs/h5parm_collector.json b/lofar-cwl/test_jobs/h5parm_collector.json deleted file mode 100644 index 42c60bb8d15f9f8e49673c916c7d19cec07ae35a..0000000000000000000000000000000000000000 --- a/lofar-cwl/test_jobs/h5parm_collector.json +++ /dev/null @@ -1,9 +0,0 @@ -{ - "h5parmFiles": [ - { - "class": "File", - "path": "/data/example.h5", - "format": "lofar:#H5Parm" - } - ] -} diff --git a/lofar-cwl/test_jobs/integration_test_prefactor_calibrator.json b/lofar-cwl/test_jobs/integration_test_prefactor_calibrator.json deleted file mode 100644 index 672f979893679218fb67c1cc97ecb8721962aa7c..0000000000000000000000000000000000000000 --- a/lofar-cwl/test_jobs/integration_test_prefactor_calibrator.json +++ /dev/null @@ -1,14 +0,0 @@ -{ - "msin" : [ - {"class": "Directory", "path": "/data/L570745_SB000_uv_first10.MS"}, - {"class": "Directory", "path": "/data/L570745_SB001_uv_first10.MS"}, - {"class": "Directory", "path": "/data/L570745_SB002_uv_first10.MS"} - ], - "raw_data": false, - "demix": false, - "skymodels": { - "class": "Directory", - "path": "/data/skymodels" - }, - "A-Team_sky_model": "/data/skymodels/Ateam_LBA_CC.skymodel" -} diff --git a/lofar-cwl/test_jobs/interpolate_visibilities.json b/lofar-cwl/test_jobs/interpolate_visibilities.json deleted file mode 100644 index a9ce3dea491423d5a858e8a500f78b3df24a63d3..0000000000000000000000000000000000000000 --- a/lofar-cwl/test_jobs/interpolate_visibilities.json +++ /dev/null @@ -1,4 +0,0 @@ -{ - "msin": { "class":"Directory", "path":"/data/L570745_SB000_uv_first10.MS"}, - "window_size": 5 -} diff --git a/lofar-cwl/test_jobs/losoto_abs.json b/lofar-cwl/test_jobs/losoto_abs.json deleted file mode 100644 index a283362c08eefe03c690a9a3ad3791dbf4ed74bc..0000000000000000000000000000000000000000 --- a/lofar-cwl/test_jobs/losoto_abs.json +++ /dev/null @@ -1,8 +0,0 @@ -{ - "input_h5parm": { - "class": "File", - "path": "/data/example.h5", - "format": "lofar:#H5Parm" - }, - "soltab": "sol000/amplitude000" -} diff --git a/lofar-cwl/test_jobs/losoto_duplicate.json b/lofar-cwl/test_jobs/losoto_duplicate.json deleted file mode 100644 index a283362c08eefe03c690a9a3ad3791dbf4ed74bc..0000000000000000000000000000000000000000 --- a/lofar-cwl/test_jobs/losoto_duplicate.json +++ /dev/null @@ -1,8 +0,0 @@ -{ - "input_h5parm": { - "class": "File", - "path": "/data/example.h5", - "format": "lofar:#H5Parm" - }, - "soltab": "sol000/amplitude000" -} diff --git a/lofar-cwl/test_jobs/losoto_norm.json b/lofar-cwl/test_jobs/losoto_norm.json deleted file mode 100644 index d6d689949f55ce2c769956e474508c78c7c28f32..0000000000000000000000000000000000000000 --- a/lofar-cwl/test_jobs/losoto_norm.json +++ /dev/null @@ -1,9 +0,0 @@ -{ - "input_h5parm": { - "class": "File", - "path": "/data/example.h5", - "format": "lofar:#H5Parm" - }, - "soltab": "sol000/amplitude000", - "axesToNorm": ["time"] -} diff --git a/lofar-cwl/test_jobs/losoto_plot.json b/lofar-cwl/test_jobs/losoto_plot.json deleted file mode 100644 index 1316e959d7b7af2e331e320f412a16357d69643d..0000000000000000000000000000000000000000 --- a/lofar-cwl/test_jobs/losoto_plot.json +++ /dev/null @@ -1,6 +0,0 @@ -{ - "input_h5parm": {"class": "File", "path": "/data/example.h5", "format": "lofar:#H5Parm"}, - "soltab": ["sol000/phase000"], - "axesInPlot": ["time"], - "ncpu": 1 -} diff --git a/lofar-cwl/test_jobs/losoto_replicateonaxis.json b/lofar-cwl/test_jobs/losoto_replicateonaxis.json deleted file mode 100644 index 0abfc35d9280bdc84605590f00479a9b5d36d7c6..0000000000000000000000000000000000000000 --- a/lofar-cwl/test_jobs/losoto_replicateonaxis.json +++ /dev/null @@ -1,10 +0,0 @@ -{ - "input_h5parm": { - "class": "File", - "path": "/data/example.h5", - "format": "lofar:#H5Parm" - }, - "soltab": "sol000/amplitude000", - "axisReplicate": "time", - "updateWeight": true -} diff --git a/lofar-cwl/test_jobs/losoto_reset.json b/lofar-cwl/test_jobs/losoto_reset.json deleted file mode 100644 index 2d773afb6baa7bb4d83c8fe0d85becf472b54f69..0000000000000000000000000000000000000000 --- a/lofar-cwl/test_jobs/losoto_reset.json +++ /dev/null @@ -1,8 +0,0 @@ -{ - "input_h5parm": { - "class": "File", - "path": "/data/example.h5", - "format": "lofar:#H5Parm" - }, - "soltab": "sol000/amplitude000" -} diff --git a/lofar-cwl/test_jobs/losoto_residual.json b/lofar-cwl/test_jobs/losoto_residual.json deleted file mode 100644 index 4a56f1c6e77dcb29aac66414ba1cb19253597bd6..0000000000000000000000000000000000000000 --- a/lofar-cwl/test_jobs/losoto_residual.json +++ /dev/null @@ -1,9 +0,0 @@ -{ - "input_h5parm": { - "class": "File", - "path": "/data/example.h5", - "format": "lofar:#H5Parm" - }, - "soltab": "sol000/amplitude000", - "soltabsToSub": ["amplitude000"] -} diff --git a/lofar-cwl/test_jobs/ms_concat.json b/lofar-cwl/test_jobs/ms_concat.json deleted file mode 100644 index 935a917a5ee9ed30ebbb7782305899cecf88bd70..0000000000000000000000000000000000000000 --- a/lofar-cwl/test_jobs/ms_concat.json +++ /dev/null @@ -1,14 +0,0 @@ -{ - "min_length": 1, - "msin": [ - { - "class": "Directory", - "path": "../test_data/L570745_SB000_uv_first10.MS" - }, - { - "class": "Directory", - "path": "../test_data/L570745_SB001_uv_first10.MS" - } - ] -} - diff --git a/lofar-cwl/test_jobs/ndppp_step.parset b/lofar-cwl/test_jobs/ndppp_step.parset deleted file mode 100644 index 450d95c45cfad84ae9af23bd3d51de49035a55ea..0000000000000000000000000000000000000000 --- a/lofar-cwl/test_jobs/ndppp_step.parset +++ /dev/null @@ -1,7 +0,0 @@ -count.save=True -count.path="." -gaincal.parmdb=test.h5 -gaincal.usemodelcolumn=True -gaincal.caltype=diagonal -msin.modelcolumn=DATA -steps=[count, gaincal] diff --git a/lofar-cwl/test_jobs/parset_generator.json b/lofar-cwl/test_jobs/parset_generator.json deleted file mode 100644 index 5b3c748396c5cc9928b04ce0d57ae41842137835..0000000000000000000000000000000000000000 --- a/lofar-cwl/test_jobs/parset_generator.json +++ /dev/null @@ -1,7 +0,0 @@ -{ - "parameters_input": [{ - "step_type": "name", - "step_id": "id", - "parameters": {"timestep": 1} -}] -} diff --git a/lofar-cwl/test_jobs/parset_generator_file_input.json b/lofar-cwl/test_jobs/parset_generator_file_input.json deleted file mode 100644 index c29a5a08f0230adfe440117df3bac1a4ca0023fd..0000000000000000000000000000000000000000 --- a/lofar-cwl/test_jobs/parset_generator_file_input.json +++ /dev/null @@ -1,22 +0,0 @@ -{ - "parameters_input": [{ - "step_type": "averager", - "step_id": "average", - "output_files": { - "parmdb": "fily" - }, - "output_directories": { - "parmdb": "diry" - }, - "parameters": { - "timestep": 1, - "freqstep": 1, - "strategy": { - "class": "File", - "location": "file:///etc/hostname", - "size": 0, - "nameext": "" - } - } -}] -} diff --git a/lofar-cwl/test_jobs/predict.json b/lofar-cwl/test_jobs/predict.json deleted file mode 100644 index 2a493f8755d1350243a7d0f04783dbddc2dda7ea..0000000000000000000000000000000000000000 --- a/lofar-cwl/test_jobs/predict.json +++ /dev/null @@ -1,10 +0,0 @@ -{ - "msin": { - "class": "Directory", - "path": "/data/L570745_SB001_uv_first10.MS" - }, - "sources_db": { - "class": "File", - "path": "/data/A-Team_lowres.sourcedb" - } -} diff --git a/lofar-cwl/test_jobs/preflagger_step_generator.json b/lofar-cwl/test_jobs/preflagger_step_generator.json deleted file mode 100644 index 4c6b5085d4492d2a008d0c0cdd0bbd4139c97132..0000000000000000000000000000000000000000 --- a/lofar-cwl/test_jobs/preflagger_step_generator.json +++ /dev/null @@ -1,8 +0,0 @@ -{ - "input_parset": [{ - "step_type": "name", - "step_id": "id", - "parameters": [] -}], - "strategy": {"class":"File", "path":"/dev/null"} -} diff --git a/lofar-cwl/test_jobs/selector.json b/lofar-cwl/test_jobs/selector.json deleted file mode 100644 index 3025390d76a1ae4ba3d6aab8482129ece27319cb..0000000000000000000000000000000000000000 --- a/lofar-cwl/test_jobs/selector.json +++ /dev/null @@ -1,4 +0,0 @@ -{ - "select_a": true, - "a_arguments": [{"name": "a"}] -}