diff --git a/Docker/Dockerfile-vlbi b/Docker/Dockerfile-vlbi index 7ba7f1bb28b8613028004ab8627af356236f0d28..e3e948aaf9a6103e7e5813df09ae323a531efbdf 100644 --- a/Docker/Dockerfile-vlbi +++ b/Docker/Dockerfile-vlbi @@ -3,5 +3,12 @@ FROM lofareosc/prefactor3-cwl RUN python3 -m pip install -Iv pyvo==0.9.3 RUN apt-get update && \ apt-get install -y git -RUN git clone https://github.com/lonbar/VLBI-cwl.git /root/VLBI-cwl -ENV PYTHONPATH=/root/VLBI-cwl/scripts/:$PYTHONPATH + +RUN groupadd -r lofaruser && \ + useradd -r -l -m -g lofaruser lofaruser + +WORKDIR /home/lofaruser + +USER lofaruser +RUN git clone https://github.com/lonbar/VLBI-cwl.git /home/lofaruser/VLBI-cwl +ENV PYTHONPATH=/home/lofaruser/VLBI-cwl/scripts/:$PYTHONPATH diff --git a/scripts/compareStationListVLBI.py b/scripts/compareStationListVLBI.py index b29ee0df57fe68904fd44b1a9c73ad13ff54fde4..d0fc8739d173ec7854a823c3741ba10f6ffc9ac0 100644 --- a/scripts/compareStationListVLBI.py +++ b/scripts/compareStationListVLBI.py @@ -28,7 +28,8 @@ def plugin_main(args, **kwargs): filter = kwargs['filter'] #data = DataMap.load(mapfile_in) #mslist = [data[i].file for i in xrange(len(data))] - mslist = args['mss'] + mslist = args #['mss'] + print(mslist) if len(mslist) == 0: raise ValueError("Did not find any existing directory in input MS list!") diff --git a/steps/check_station_mismatch.cwl b/steps/check_station_mismatch.cwl index 474c8555c7adfb866f858c5d806d04493e687957..fc90ed773df23578eab89abdc2169fe05d0cad8a 100644 --- a/steps/check_station_mismatch.cwl +++ b/steps/check_station_mismatch.cwl @@ -33,7 +33,9 @@ requirements: entry: | import sys import json - from compareStationListVLBI import main as compareStationList + import os + print(os.environ) + from compareStationListVLBI import plugin_main as compareStationList mss = sys.argv[1:] inputs = json.loads(r"""$(inputs)""") @@ -42,7 +44,7 @@ requirements: filter = inputs['filter_baselines'] print(mss) - output = compareStationList(mss = mss, + output = compareStationList(mss, h5parmdb = h5parmdb, solset_name = solset_name, filter = filter) @@ -69,7 +71,7 @@ outputs: hints: DockerRequirement: - dockerPull: vlbi-cwl + dockerPull: vlbi-cwl:latest stdout: compareStationMismatch.log stderr: compareStationMismatch_err.log diff --git a/test.json b/test.json index f9d2002de32b784478329b2a0c2c29b933ca3549..6aa2493d09e3e50dc9a09023dedc47e81dfbe376 100644 --- a/test.json +++ b/test.json @@ -1,14 +1,6 @@ { - "msin": { - "class": "Directory", - "path": [ - "/home/tjlv53/test_data/L693719_SB000_uv.MS" - ] - }, - "solset": [ - { - "class": "File", - "path": "/home/tjlv54/test_data/P205+55/Pre-Facet-Calibrator/results/cal_values/cal_solutions.h5" - } - ] + "msin": [ + {"class": "Directory", "path": "/home/tjlv53/software/VLBI-cwl/test_data/L693719_SB000_uv.MS"} + ], + "solset": {"class": "File", "path": "/home/tjlv53/software/VLBI-cwl/test_data/P205+55:Pre-Facet-Calibrator/results/cal_values/cal_solutions.h5"} }