ATO-648 - workflowToJSON.sh - porting the code from the TPC gitlab to the O2DPG tools

[miranov25]

Parser - workflowToJSON.sh

First of the series script to be ported from the TPC gitlab to the DPG script:

• duPython.py duQuery.sh monalisaQuery.py monalisaQuery.sh workflowToJSON.sh

Described in detail in the
https://indico.cern.ch/event/1423563/contributions/5987247/attachments/2868815/5022209/ATO-648%20-synchronization%20AliEn%20%E2%86%92%20GSI%20and%20ALICE%20monalisa%20queries.pdf

Overview of the Shell Script

• • Purpose: Convert workflow configuration logs into structured JSON format for enhanced data analysis and readability.
• • Components:
  • Initialization: Sets up the environment for script execution.
  • • Parsing: Transforms verbose workflow logs into a JSON format.
  • • Comparison: Compares JSON files to identify differences.
  • • Usage: Interactive Analysis: Facilitates easier data manipulation and analysis.
  • • Integration: Can be integrated into larger data processing pipelines.

[github-actions]

REQUEST FOR PRODUCTION RELEASES:
To request your PR to be included in production software, please add the corresponding labels called "async-" to your PR. Add the labels directly (if you have the permissions) or add a comment of the form (note that labels are separated by a ",")

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The following labels are available
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[miranov25]

Initialization:

Apptainer> source /scratch/alice/miranov/alicesw2/O2DPG/UTILS/Parsers/workflowToJSON.sh
0001:       Function Overview: init648
0002:
0003:       This function initializes the script environment and provides access to a series of utility commands designed to assist in handling and transforming workflow logs.
0004:
0005:       Available Commands:
0006:       - \[init648]: Initializes the necessary environment settings for script execution. Use this before running other related functions to ensure all configurations are correctly set.
0007:       - \[description]: Provides a comprehensive explanation of the workflow processing, detailing each step and its purpose within the system.
0008:       - \[makeParse]: Executes the log parsing process, transforming verbose workflow logs into a structured JSON format, facilitating easier data manipulation and analysis.
0009:       - \[makeDiffExample]: Demonstrates how to compare two JSON files derived from workflow logs, highlighting differences.
0010:
0011:       Usage:
0012:       To learn more about each command, type the command followed by 'help'. This will display detailed information about the command's function and usage examples.
0013:
0014:       Example:
0015:         $ init648 help   # Displays help information for the init648 command.
0016:
0017:       Note: Tests were conducted in the directory:
0018:

[miranov25]

Make Parse of the worklow log file

• help
• documenatation slide
• usage

help

Apptainer> makeParse
0001: makeParse: Parse the workflow log and create an output.json file.
0002: Usage:
0003:     makeParse <workflowconfig.log>
0004:
0005: Example usage:
0006:     #makeParse workflowconfig.log  > ~/output.json            # To parse a specific log file.
0007:     makeParse /lustre/alice/tpcdata/Run3/SCDprodTests/fullRec/PbPb_Streamers_Tune_ClusterErrors-merge-streamer/avgCharge_fullTPC_sampling_TimeBins16-Average0_rejectEdgeCl-Seed0-Track0-margin0/LHC23zzh.b5p/544116.38kHz/0110/workflowconfig.log  > workflow.json
0008:     cat workflow.json | jq '.[] | select(.command | test("^o2-dpl"))'   # Filter DPL workflows.
0009:     jq '.[] | select(.command | test("^o2-gpu"))' workflow.json  # Filter GPU related commands.
0010:

usage

Apptainer> makeParse workflowconfig.log  

[
  {
    "command": "o2-ctf-reader-workflow",
    "switches": {
      "session": "default_337_5438",
      "severity": "info",
      "shm-segment-id": "1664",
      "shm-segment-size": "",
      "resources-monitoring": "50",
      "resources-monitoring-dump-interval": "50",
      "early-forward-policy": "noraw",
      "fairmq-rate-logging": "0",
      "shm-mlock-segment-on-creation": "1",
      "timeframes-rate-limit": "35",
      "timeframes-rate-limit-ipcid": "1730516608",
      "ans-version": "compat",
      "delay": "1",
      "loop": "",
      "ctf-input": "list.list",
      "copy-cmd": "file://?dst\"",
      "onlyDet": "ITS,TPC,TOF,FV0,FT0,FDD,MID,MFT,MCH,TRD,EMC,PHS,CPV,HMP,ZDC,CTP",
      "emcal-decoded-subspec": "1",
      "timeframes-shm-limit": "33333333333",
      "pipeline": "",
      "remote-regex": "\"^alien:///alice/data/.+\"",
      "allow-missing-detectors": "",
      "its-digits": true,
      "mft-digits": true,
      "configKeyValues": "|"
    },
    "configKeyValues": {
      "keyval.input_dir": "/workdir",
      "keyval.output_dir": "/dev/null"
    }
  },
  {
    "command": "o2-tfidinfo-writer-workflow",
    "switches": {
      "session": "default_337_5438",
      "severity": "info",
...

[miranov25]

makeDiffExample - Comparing JSON Files

Description

This function provides examples of parsing workflow logs into JSON format and then comparing these JSON files using diff.

---

Steps

1. Parse Logs into JSON

   makeParse /path/to/workflowconfig.log > workflow0.json
   makeParse /path/to/other_workflowconfig.log > workflow1.json

2. Compare JSON Files

   diff <(jq --sort-keys . workflow1.json) <(jq --sort-keys . workflow0.json)

3. Side-by-Side Comparison with Color

   diff --side-by-side --left-column --color=always \
     <(jq --sort-keys . workflow1.json) <(jq --sort-keys . workflow0.json) | less -R

4. Compare Only Specific Workflow Commands

   diff --side-by-side --left-column --color=always \
     <(jq '.[] | select(.command | test("^o2-gpu"))' workflow1.json | jq --sort-keys .) \
     <(jq '.[] | select(.command | test("^o2-gpu"))' workflow0.json | jq --sort-keys .) | less -R

---

Highlighted Example

• Functionality: Compare workflow0.json and workflow1.json for differences.
• Specific Command Filtering: Focuses on commands containing "^o2-gpu" for targeted comparison.
• Enhanced Readability: Side-by-side display with syntax highlighting for easier analysis.

[miranov25]

Hello @sawenzel, @shahor02 , @davidrohr and @chiarazampolli

I want to merge script above and later to add another script to recursively print the tree sizes.

• https://mattermost.web.cern.ch/alice/pl/6ht3yriwe3rrdmz8d7p6s4f1fr
  Should I update this pull request or add the new?

Regards
Marian

[shahor02]

Merging since it is a standalone script not affecting productions. Please open another one for your size checker.