From 6cd9d77a8a40bbe33a55ef0e55bcb55a9b4544cf Mon Sep 17 00:00:00 2001
From: Matthijs van der Wild <matthijs.van-der-wild@durham.ac.uk>
Date: Wed, 26 Jan 2022 12:35:12 +0000
Subject: [PATCH] Debugging first step.
---
Docker/Dockerfile-vlbi | 11 +++++++++--
scripts/compareStationListVLBI.py | 3 ++-
steps/check_station_mismatch.cwl | 8 +++++---
test.json | 16 ++++------------
4 files changed, 20 insertions(+), 18 deletions(-)
diff --git a/Docker/Dockerfile-vlbi b/Docker/Dockerfile-vlbi
index 7ba7f1bb..e3e948aa 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 b29ee0df..d0fc8739 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 474c8555..fc90ed77 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 f9d2002d..6aa2493d 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"}
}
--
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