From 976f1160e3bfc336af0c9aa610a78a26ad9b0a7f Mon Sep 17 00:00:00 2001
From: Klaas Kliffen <kliffen@astron.nl>
Date: Fri, 8 Oct 2021 09:53:17 +0200
Subject: [PATCH] Remove old files
---
README.md | 3 --
build_images.sh | 2 --
conditonal_fix.cwl | 41 ------------------------
scripts/fix_common_ms_issues.py | 55 ---------------------------------
scripts/requirements.txt | 2 --
steps/dummy_fix_a.cwl | 9 ------
steps/dummy_fix_b.cwl | 9 ------
steps/noop.cwl | 11 -------
8 files changed, 132 deletions(-)
delete mode 100755 build_images.sh
delete mode 100644 conditonal_fix.cwl
delete mode 100644 scripts/fix_common_ms_issues.py
delete mode 100644 scripts/requirements.txt
delete mode 100644 steps/dummy_fix_a.cwl
delete mode 100644 steps/dummy_fix_b.cwl
delete mode 100644 steps/noop.cwl
diff --git a/README.md b/README.md
index 76a8eb7..ed89219 100644
--- a/README.md
+++ b/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
```
diff --git a/build_images.sh b/build_images.sh
deleted file mode 100755
index 2fb91c0..0000000
--- a/build_images.sh
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/usr/bin/bash
-docker build -t imaging-compress-pipeline-identify-issues -f docker/Dockerfile.identify_issues scripts/
\ No newline at end of file
diff --git a/conditonal_fix.cwl b/conditonal_fix.cwl
deleted file mode 100644
index 8e59079..0000000
--- a/conditonal_fix.cwl
+++ /dev/null
@@ -1,41 +0,0 @@
-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: {}
diff --git a/scripts/fix_common_ms_issues.py b/scripts/fix_common_ms_issues.py
deleted file mode 100644
index 8108ea4..0000000
--- a/scripts/fix_common_ms_issues.py
+++ /dev/null
@@ -1,55 +0,0 @@
-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()
diff --git a/scripts/requirements.txt b/scripts/requirements.txt
deleted file mode 100644
index 6ac4892..0000000
--- a/scripts/requirements.txt
+++ /dev/null
@@ -1,2 +0,0 @@
-astropy
-python-casacore
\ No newline at end of file
diff --git a/steps/dummy_fix_a.cwl b/steps/dummy_fix_a.cwl
deleted file mode 100644
index 178d083..0000000
--- a/steps/dummy_fix_a.cwl
+++ /dev/null
@@ -1,9 +0,0 @@
-id: dummy_fix_a
-label: Dummy Fix A
-cwlVersion: v1.0
-class: CommandLineTool
-baseCommand: echo
-arguments:
- - "A"
-inputs: []
-outputs: []
diff --git a/steps/dummy_fix_b.cwl b/steps/dummy_fix_b.cwl
deleted file mode 100644
index 56ea3bc..0000000
--- a/steps/dummy_fix_b.cwl
+++ /dev/null
@@ -1,9 +0,0 @@
-id: dummy_fix_b
-label: Dummy Fix B
-cwlVersion: v1.0
-class: CommandLineTool
-baseCommand: echo
-arguments:
- - "B"
-inputs: []
-outputs: []
diff --git a/steps/noop.cwl b/steps/noop.cwl
deleted file mode 100644
index 0ecca93..0000000
--- a/steps/noop.cwl
+++ /dev/null
@@ -1,11 +0,0 @@
-class: ExpressionTool
-id: noop
-cwlVersion: v1.2
-inputs:
- - id: msin
- type: Directory
-outputs:
- - id: msout
- type: Directory
-expression: |
- $({msout: inputs.msin})
\ No newline at end of file
--
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