Merge branch 'add_fixing_issues_scripts' into 'master'

Add fixing issues scripts

See merge request !1

.gitignore

+# Virtual env
+.venv
+
+# Measurement Sets
+*.MS
\ No newline at end of file

LICENSE

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README.md

+# Lofar imaging compression pipeline
+
+This is a CWL workflow used to compress Lofar imaging data.
+
+## Workflow steps
+
+![Pipeline Overview](pipeline.png)
+
+- identify known issues and apply them if necessary. It uses in place updates to prevent copying the measurement set
+    - in place update does not work well with CWL conditional steps, so a small bash script is used which either calls the fixing script or does nothing depending if the specific issue for the step was found
+- Compress the measurement set with Dysco
+- Produces inspection plots and collects metrics to quantify the amount of missing/flagged data
+
+
+## Requirements
+
+- CWL v1.2 compatible runner (e.g. cwltool/toil)
+- Docker
+
+## Docker images
+
+- astronsdc/lofar-legacy
+- astronsdc/lofar-ms-software
+
+## Running the workflow
+In the repositories there are two workflows.
+One is capable to process the data as described in section [workflow steps](#workflow-steps) and can be executed as following
+```bash
+# Run the workflow
+cwltool compress_pipeline.cwl [--flag_autocorrelation] --msin MEASUREMENT_SET
+```
+
+Another workflow, that is meant to be executed by the LDV infrastructure, takes as an input instead of a measurement set a SURL link of the data. Such a workflow can be execute with the command
+```bash
+# Run the workflow
+cwltool download_and_compress_pipeline.cwl [--flag_autocorrelation] --surls [list of surl to process] 
+```
+
+## License
+
+See `LICENSE`

compress_pipeline.cwl

 class: Workflow
-cwlVersion: v1.1
+cwlVersion: v1.2
 id: compress_pipeline_cwl
 label: compress_pipeline.cwl
 inputs:
@@ -33,6 +33,57 @@ outputs:
     outputSource:
       - inspect_flagging_dataloss/flags_output
 steps:
+  - id: identify_issues
+    run: steps/identify_issues.cwl
+    in:
+      - id: msin
+        source: msin
+    out:
+      - issue_list
+      - msout
+  - id: fix_ai_2013
+    run: steps/fix_antenna_information_2013.cwl
+    in:
+      - id: msin
+        source: identify_issues/msout
+      - id: apply
+        source: identify_issues/issue_list
+        valueFrom: $(self.includes("FIX_ANTENNA_TABLE"))
+    out:
+      - id: msout
+  - id: fix_weight_issue
+    run: steps/fix_weightissue_flagging.cwl
+    in:
+      - id: msin
+        source:
+          - fix_ai_2013/msout
+      - id: apply
+        source: identify_issues/issue_list
+        valueFrom: $(self.includes("FIX_WEIGHT_SPECTRUM"))
+    out:
+      - id: msout
+  - id: fix_ai_2015
+    run: steps/fix_antenna_information_2015.cwl
+    in:
+      - id: msin
+        source:
+          - fix_weight_issue/msout
+      - id: apply
+        source: identify_issues/issue_list
+        valueFrom: $(self.includes("FIX_BROKEN_TILES"))
+    out:
+      - id: msout
+  - id: fix_baselines
+    run: steps/fix_long_baselines.cwl
+    in:
+      - id: msin
+        source:
+          - fix_ai_2015/msout
+      - id: apply
+        source: identify_issues/issue_list
+        valueFrom: $(self.includes("FIX_STATION_ADDER"))
+    out:
+      - id: msout
   - id: extract_sip_meta
     in:
       - id: msin
@@ -47,9 +98,10 @@ steps:
       - id: parset
         source: define_parset/output
       - id: msin
-        source: msin
+        source:
+          - fix_baselines/msout
       - id: msout_name
-        source: msin
+        source: fix_baselines/msout
         valueFrom: '$("COMPRESSED_" + self.basename)'
       - id: writefullresflag
         default: true
@@ -81,7 +133,8 @@ steps:
   - id: inspect_flagging_dataloss
     in:
       - id: input
-        source: msin
+        source:
+          - fix_baselines/msout
     out:
       - id: output
       - id: flags_output
@@ -105,3 +158,4 @@ steps:
 requirements:
   - class: StepInputExpressionRequirement
   - class: InlineJavascriptRequirement
+  - class: MultipleInputFeatureRequirement

docker/Dockerfile.identify_issues

+FROM python:3.9-slim
+
+WORKDIR /scripts
+COPY requirements.txt /scripts/
+RUN pip install -r requirements.txt
+COPY fix_common_ms_issues.py /scripts/
\ No newline at end of file

steps/fix_antenna_information_2013.cwl

+id: fix_antenna_information_2013
+label: Fix Antenna Information 2013
+cwlVersion: v1.2
+class: CommandLineTool
+baseCommand:
+  - bash
+  - script.sh
+inputs:
+  - id: msin
+    type: Directory
+  - id: apply
+    type: boolean
+outputs:
+  - id: msout
+    type: Directory
+    outputBinding:
+      glob: $(inputs.msin.basename)
+
+requirements:
+  - class: InitialWorkDirRequirement
+    listing:
+      - entry: $(inputs.msin)
+        writable: true
+        entryname: $(inputs.msin.basename)
+      - entryname: script.sh
+        entry: |
+          #!/bin/bash
+
+          execute=$(inputs.apply)
+          if [ $execute = 'true' ] ; then
+            echo "Appling fix antenna information 2013"
+            fixinfo $(inputs.msin.basename) /opt/fixinfo
+          fi
+          echo "Skipping apply fix antenna information 2013"
+
+  - class: InplaceUpdateRequirement
+    inplaceUpdate: true
+hints:
+  - class: DockerRequirement
+    dockerPull: "astronsdc/lofar-legacy:latest"

steps/fix_antenna_information_2015.cwl

+id: fix_antenna_information_2015
+label: Fix Antenna Information_2015
+cwlVersion: v1.2
+class: CommandLineTool
+baseCommand:
+  - bash
+  - script.sh
+
+inputs:
+  - id: msin
+    type: Directory
+  - id: apply
+    type: boolean
+
+outputs:
+  - id: msout
+    type: Directory
+    outputBinding:
+      glob: $(inputs.msin.basename)
+
+
+requirements:
+  - class: InitialWorkDirRequirement
+    listing:
+      - entry: $(inputs.msin)
+        writable: true
+        entryname: $(inputs.msin.basename)
+      - entryname: script.sh
+        entry: |
+          #!/bin/bash
+
+          execute=$(inputs.apply)
+          if [ $execute = 'true' ] ; then
+            echo "Appling fix antenna information 2015"
+            fixbeaminfo $(inputs.msin.basename) /opt/fixbeaminfo
+          fi
+          echo "Skipping apply fix antenna information 2015"
+
+  - class: InplaceUpdateRequirement
+    inplaceUpdate: true
+hints:
+  - class: DockerRequirement
+    dockerPull: "astronsdc/lofar-legacy:latest"

steps/fix_long_baselines.cwl

+id: fix_long_baseline
+label: Fix weighted sum for long baseline pipeline
+cwlVersion: v1.2
+class: CommandLineTool
+baseCommand:
+  - bash
+  - script.sh
+
+requirements:
+  - class: InitialWorkDirRequirement
+    listing:
+      - entry: $(inputs.msin)
+        writable: true
+        entryname: $(inputs.msin.basename)
+      - entryname: script.sh
+        entry: |
+          #!/bin/bash
+
+          execute=$(inputs.apply)
+          if [ $execute = 'true' ] ; then
+            echo "Appling fix weighted sum UVW"
+            fix_weightedsum_uvw -f $(inputs.msin.basename) -n $(inputs.new_station)
+          fi
+          echo "Skipping apply fix weighted sum UVW"
+
+  - class: InplaceUpdateRequirement
+    inplaceUpdate: true
+inputs:
+  - id: msin
+    type: Directory
+  - id: new_station
+    doc: new station name (default ST001)
+    type: string?
+    default: ST001
+  - id: apply
+    type: boolean
+outputs:
+  - id: msout
+    type: Directory
+    outputBinding:
+      glob: $(inputs.msin.basename)
+
+hints:
+  - class: DockerRequirement
+    dockerPull: "astronsdc/lofar-legacy:latest"

steps/fix_weightissue_flagging.cwl

+id: fix_weight_issue_flagging
+label: Fix Weight Issue Flagging
+cwlVersion: v1.2
+class: CommandLineTool
+baseCommand:
+  - bash
+  - script.sh
+requirements:
+  - class: InitialWorkDirRequirement
+    listing:
+      - entry: $(inputs.msin)
+        writable: true
+        entryname: $(inputs.msin.basename)
+      - entryname: script.sh
+        entry: |
+          #!/bin/bash
+
+          execute=$(inputs.apply)
+          if [ $execute = 'true' ] ; then
+            echo "Appling fix weight issue flagging"
+            fix_weightspectrum $(inputs.msin.basename)
+          fi
+          echo "Skipping apply fix weight issue flagging"
+  - class: InplaceUpdateRequirement
+    inplaceUpdate: true
+inputs:
+  - id: msin
+    type: Directory
+  - id: apply
+    type: boolean
+outputs:
+  - id: msout
+    type: Directory
+    outputBinding:
+      glob: $(inputs.msin.basename)
+hints:
+  - class: DockerRequirement
+    dockerPull: "astronsdc/lofar-legacy:latest"

steps/identify_issues.cwl

+id: identify_issues
+label: Identify Known issues
+class: CommandLineTool
+cwlVersion: v1.0
+hints:
+  DockerRequirement:
+    dockerPull: astronsdc/lofar-legacy:latest
+
+inputs:
+  - id: msin
+    type: Directory
+    inputBinding:
+      position: 1
+
+outputs:
+  - id: issue_list
+    type: string[]
+    outputBinding:
+      glob: output.txt
+      loadContents: true
+      outputEval: $(JSON.parse(self[0].contents))
+
+  - id: msout
+    type: Directory
+    outputBinding:
+      glob: $(inputs.msin.basename)
+stdout: output.txt
+
+baseCommand:
+  - python3
+  - /usr/local/bin/fix_common_ms_issues
+
+requirements:
+  - class: InlineJavascriptRequirement
+  - class: InitialWorkDirRequirement
+    listing:
+      - entry: $(inputs.msin)
+        writable: true
+        entryname: $(inputs.msin.basename)

steps/plot_uvw_coverage.cwl

@@ -18,6 +18,9 @@ outputs:
     type: File
     outputBinding:
       glob: $(inputs.output_name)
+hints:
+  - class: DockerRequirement
+    dockerPull: astronsdc/lofar-ms-software
 requirements:
   - class: InlineJavascriptRequirement
   - class: InitialWorkDirRequirement