study-docker-repro-longevity/workflow/Snakefile

configfile: "config/config.yaml"

include: "utils.smk"

import os
import datetime
DATE = datetime.datetime.now().strftime("%Y%m%d")

ARTIFACTS_FOLDER_NICKEL = config["folder_artifacts_nickel"]
ARTIFACTS_FOLDER_JSON   = config["folder_artifacts_json"]
BLACKLIST_FOLDER = config["folder_blacklists"]
EXTENSION = "json"
SYSTEM = config["system"]

ARTIFACTS = get_artifacts_to_build(ARTIFACTS_FOLDER_NICKEL, BLACKLIST_FOLDER)

PREFIX = config["prefix"]
ECG_OUTPUTS = ["pkgs", "build_status", "artifact_hash"]
SHELLS_ECG = {
  "local": f"./{{input.ecg_wrapper}} {{input.ecg}} {ARTIFACTS_FOLDER_JSON}/{{wildcards.artifact}}.{EXTENSION} {{output.pkg}} {{output.build_status}} {{output.artifact_hash}} {{output.log}}",
  "g5k": f"python3 {{input.execo_wrapper}} --path {os.getcwd()} --script {{input.oar_wrapper}} --site {config['site']} --cluster {config['cluster']} --max-duration {config['max_duration']} --checkpoint {config['checkpoint']} {'--besteffort' if config['besteffort'] else ''} --sleep_time {config['sleep_time']} --build_status_file {{output.build_status}} --artifact {{wildcards.artifact}} -- '"
}

ANALYSIS_DIR = config["analysis_dir"]
ANALYSIS_CATS = ["sources_stats", "pkgs_changes", "build_status", "artifact"]
ANALYSIS_SCRIPTS_DIR = "analysis"
ANALYSIS_WRAPPER = "workflow/scripts/analysis_wrapper.sh"
AGGREGATE_WRAPPER = "workflow/scripts/aggregate_wrapper.sh"
ARTIFACT_ANALYSIS_DIRS = " ".join(expand(f"{PREFIX}/artifact_hash/{{artifact}}",
  artifact = ARTIFACTS
))
SOFTENV_ANALYSIS_DIRS = " ".join(expand(f"{PREFIX}/pkgs/{{artifact}}",
  artifact = ARTIFACTS
))

PLOT_DIR = config["plot_dir"]
PLOT_HEADERS = {
  #"softenv": "dpkg rpm pacman pip conda git misc",
  "sources_stats": "dpkg rpm pacman pip conda git misc",
  "pkgs_changes": "dpkg rpm pacman pip conda git misc",
  "build_status": "success package_install_failed baseimage_unavailable artifact_unavailable dockerfile_not_found script_crash job_time_exceeded unknown_error",
  "artifact": "available unavailable changed"
}

rule all:
  input:
    expand(f"{ANALYSIS_DIR}/{{analysis_cat}}/plot/line/{{date}}.pdf",
      analysis_cat = ANALYSIS_CATS,
      date = DATE
    ),
    expand(f"{ANALYSIS_DIR}/{{analysis_cat}}/plot/bar/{{date}}.pdf",
      analysis_cat = ["sources_stats", "build_status", "artifact"],
      date = DATE
    ),
    f"{BLACKLIST_FOLDER}/{DATE}.csv"

# Artifacts configuration files:

rule check_all:
  input:
    expand(f"{ARTIFACTS_FOLDER_JSON}/{{artifact}}.json", artifact=ARTIFACTS)

rule check_artifact:
  input:
    "flake.nix",
    "flake.lock",
    contract="workflow/nickel/artifact_contract.ncl",
    artifact=f"{ARTIFACTS_FOLDER_NICKEL}/{{artifact}}.ncl"
  output:
    f"{ARTIFACTS_FOLDER_JSON}/{{artifact}}.json"
  shell:
    """
    nickel export --format json --output {output} <<< 'let {{Artifact, ..}} = import "{input.contract}" in ((import "{input.artifact}") | Artifact)'
    """

# ECG:

rule run_ecg:
  input:
    "flake.nix",
    "flake.lock",
    ecg="ecg.py",
    ecg_wrapper="workflow/scripts/ecg_wrapper.sh",
    execo_wrapper="workflow/scripts/submission_g5k.py",
    oar_wrapper="workflow/scripts/ecg_oar_wrapper.oar.bash",
    artifact=f"{ARTIFACTS_FOLDER_JSON}/{{artifact}}.{EXTENSION}"
  output:
    log           = f"{PREFIX}/logs/{{artifact}}/{{date}}.txt",
    pkg           = f"{PREFIX}/pkgs/{{artifact}}/{{date}}.csv",
    build_status  = f"{PREFIX}/build_status/{{artifact}}/{{date}}.csv",
    artifact_hash = f"{PREFIX}/artifact_hash/{{artifact}}/{{date}}.csv",
  shell:
    (SHELLS_ECG["g5k"] if SYSTEM == "g5k" else "") + SHELLS_ECG["local"] + ("'" if SYSTEM == "g5k" else "")

rule update_blacklist:
  input:
    build_status=expand(f"{PREFIX}/build_status/{{artifact}}/{{{{date}}}}.csv",
      artifact=ARTIFACTS
    )
  output:
    f"{BLACKLIST_FOLDER}/{{date}}.csv"
  shell:
    # We need to ignore lines where build is successful:
    f"cat {{input}} | grep -v ',success' > {{output}} || true"

# Analysis:

rule softenv_analysis:
  wildcard_constraints:
    date="\d+"
  input:
    expand(f"{PREFIX}/pkgs/{{artifact}}/{{{{date}}}}.csv",
      artifact = ARTIFACTS
    )
  output:
    sources_stats = f"{ANALYSIS_DIR}/sources_stats/{{date}}.csv",
    pkgs_changes = f"{ANALYSIS_DIR}/pkgs_changes/{{date}}.csv"
  shell:
    f"""
    {ANALYSIS_WRAPPER} files {ANALYSIS_SCRIPTS_DIR}/softenv_analysis.py -t sources-stats {{output.sources_stats}} {{input}}
    {ANALYSIS_WRAPPER} dirs {ANALYSIS_SCRIPTS_DIR}/softenv_analysis.py -t pkgs-changes {{output.pkgs_changes}} {SOFTENV_ANALYSIS_DIRS}
    """

rule buildstatus_analysis:
  wildcard_constraints:
    date="\d+"
  input:
    expand(f"{PREFIX}/build_status/{{artifact}}/{{{{date}}}}.csv",
      artifact = ARTIFACTS
    ),
  output:
    f"{ANALYSIS_DIR}/build_status/{{date}}.csv"
  shell:
    f"""
    {ANALYSIS_WRAPPER} files {ANALYSIS_SCRIPTS_DIR}/buildstatus_analysis.py {{output}} {{input}}
    """

rule artifact_analysis:
  wildcard_constraints:
    date="\d+"
  input:
    expand(f"{PREFIX}/artifact_hash/{{artifact}}/{{{{date}}}}.csv",
      artifact = ARTIFACTS
    )
  output:
    f"{ANALYSIS_DIR}/artifact/{{date}}.csv"
  shell:
    f"""
    {ANALYSIS_WRAPPER} dirs {ANALYSIS_SCRIPTS_DIR}/artifact_analysis.py {{output}} {ARTIFACT_ANALYSIS_DIRS}
    """

# Analysis aggregate:

rule analysis_aggregate:
  input:
    expand(f"{ANALYSIS_DIR}/{{cat}}/aggregated/{{date}}.csv",
      cat = ANALYSIS_CATS,
      date = DATE
    )

rule aggregate_by_type:
  input:
    data=f"{ANALYSIS_DIR}/{{type}}/{{date}}.csv",
    script="workflow/scripts/aggregate_wrapper.sh"
  output:
    f"{ANALYSIS_DIR}/{{type}}/aggregated/{{date}}.csv"
  shell:
    f"{input.script} {ANALYSIS_DIR}/{{type}} {{output}}"

# Plot:

rule plot:
  input:
    script = "plot/plot.r",
    data = f"{ANALYSIS_DIR}/{{type}}/aggregated/{{date}}.csv",
  output:
    f"{ANALYSIS_DIR}/{{type}}/{{plot}}/{{date}}.pdf"
  params:
    header = lambda w: PLOT_HEADERS[w.type]
  shell:
    "Rscript {input.script} {wildcards.plot} {input.data} {output} {params.header} timestamp"