Remove old files

README.md

@@ -14,13 +14,10 @@ This is a CWL workflow used to compress Lofar imaging data.
 ## Docker images
 
 - astronsdc/lofar-legacy
-- imaging-compress-pipeline-identify-issues `# build by this repo`
 
 ## Running the workflow
 
 ```bash
-# Build the docker images
-./build_images.sh
 # Run the workflow
 cwltool compress_pipeline.cwl [--flag_autocorrelation] --msin MEASUREMENT_SET 
 ```

build_images.sh

-#!/usr/bin/bash
-docker build -t imaging-compress-pipeline-identify-issues -f docker/Dockerfile.identify_issues scripts/
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conditonal_fix.cwl

-class: Workflow
-cwlVersion: v1.2
-
-inputs:
-  msin: Directory
-outputs: []
-
-steps:
-  identify_issues:
-    run: steps/identify_issues.cwl
-    in:
-      msin: msin
-    out:
-      - issue_list
-  fix_a:
-    run: steps/dummy_fix_a.cwl
-    when: $( inputs.list.includes("FIX_ANTENNA_TABLE") )
-    in:
-      list: identify_issues/issue_list
-    out: []
-  fix_b:
-    run: steps/dummy_fix_b.cwl
-    when: $( inputs.list.includes("FIX_WEIGHT_SPECTRUM") )
-    in:
-      list: identify_issues/issue_list
-    out: []
-  fix_c:
-    run: steps/dummy_fix_a.cwl
-    when: $( inputs.list.includes("FIX_BROKEN_TILES") )
-    in:
-      list: identify_issues/issue_list
-    out: []
-  fix_d:
-    run: steps/dummy_fix_b.cwl
-    when: $( inputs.list.includes("FIX_STATION_ADDER") )
-    in:
-      list: identify_issues/issue_list
-    out: []
-
-requirements:
-  InlineJavascriptRequirement: {}

scripts/fix_common_ms_issues.py

-import json
-from argparse import ArgumentParser
-from datetime import datetime
-from datetime import timezone as tz
-
-from astropy.time import Time
-from casacore.tables import table as MSTable
-
-_DAY_IN_SECONDS = 24 * 60 * 60
-
-_TIME_RANGES= {
-    'FIX_ANTENNA_TABLE': (
-        datetime(year=2013, month=2, day=13),
-        datetime(year=2014, month=2, day=10)),
-    'FIX_WEIGHT_SPECTRUM': (
-        datetime(year=2014, month=3, day=19),
-        datetime(year=2014, month=10, day=31)),
-    'FIX_BROKEN_TILES': (
-        datetime(year=2015, month=1, day=26),
-        datetime(year=2015, month=2, day=25)),
-    'FIX_STATION_ADDER': (
-        datetime(year=1999, month=1, day=26),
-        datetime(year=2015, month=7, day=28)),
-}
-
-def parse_args():
-    parser = ArgumentParser(description='Fix common LOFAR observing issues')
-    parser.add_argument('msin', help='Measurement Set input')
-    return parser.parse_args()
-
-def date_to_fix_string(obs_date):
-    fixes = []
-    for fix_string, (start_date, end_date) in _TIME_RANGES.items():
-        if obs_date > start_date and obs_date < end_date:
-            fixes.append(fix_string)
-    return json.dumps(fixes)    # dump proper json for CWL
-
-def check_observing_date(msin):
-    observation_table = MSTable(f'{msin}/OBSERVATION', ack=False)
-    start_mjd, end_mjd = observation_table.getcell('TIME_RANGE', 0)
-    start_datetime, end_datetime = map(mjd_to_local, (start_mjd, end_mjd))
-    return start_datetime, end_datetime
-
-def mjd_to_local(mjd):
-    return Time(mjd / _DAY_IN_SECONDS, format='mjd').to_datetime()
-
-
-def main():
-    args = parse_args()
-    start_datetime_obs, _ = check_observing_date(args.msin)
-    print(date_to_fix_string(start_datetime_obs))
-
-
-if __name__ == '__main__':
-    main()

scripts/requirements.txt

-astropy
-python-casacore
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steps/dummy_fix_a.cwl

-id: dummy_fix_a
-label: Dummy Fix A
-cwlVersion: v1.0
-class: CommandLineTool
-baseCommand: echo
-arguments:
-    - "A"
-inputs: []
-outputs: []

steps/dummy_fix_b.cwl

-id: dummy_fix_b
-label: Dummy Fix B
-cwlVersion: v1.0
-class: CommandLineTool
-baseCommand: echo
-arguments:
-    - "B"
-inputs: []
-outputs: []

steps/noop.cwl

-class: ExpressionTool
-id: noop
-cwlVersion: v1.2
-inputs:
-  - id: msin
-    type: Directory
-outputs:
-  - id: msout
-    type: Directory
-expression: |
-  $({msout: inputs.msin})
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