GuilloteauQ/study-docker-repro-longevity
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Fixed analysis and aggregate rules to get all ECG/analysis outputs for all possible dates. Written a function to get all available outputs for this purpose. Defined variables for arrays used multiple times. Simplified aggregate rule, but needs fix, because cannot have a list of shell commands apparently. Modified plotting rules according to those changes.

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antux18 2024-08-21 21:15:09 +02:00
parent e3d01ae34e
commit 2d5b043f8f
3 changed files with 131 additions and 71 deletions
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7
workflow.sh Executable file
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@ -0,0 +1,7 @@
#!/bin/bash
DATE=$(date +%Y%m%d)
rm -f blacklists/$DATE.csv
rm -rf outputs
snakemake --cores 4

183
workflow/Snakefile
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@ -12,22 +12,29 @@ BLACKLIST_FOLDER = config["folder_blacklists"]
EXTENSION = "json" EXTENSION = "json"
SYSTEM = config["system"] SYSTEM = config["system"]
PREFIX = config["prefix"] PREFIX = config["prefix"]
ECG_OUTPUTS = ["pkgs", "build_status", "artifact_hash"]
ANALYSIS_DIR = config["analysis_dir"] ANALYSIS_DIR = config["analysis_dir"]
ANALYSIS_CATS = ["sources_stats", "pkgs_changes", "build_status", "artifact"]
ANALYSIS_TYPES = ["moment", "long_term"]
ARTIFACTS = get_artifacts_to_build(ARTIFACTS_FOLDER_NICKEL, BLACKLIST_FOLDER) ARTIFACTS = get_artifacts_to_build(ARTIFACTS_FOLDER_NICKEL, BLACKLIST_FOLDER)
rule all: rule all:
input: input:
expand(f"{PREFIX}/{{folder}}/{{artifact}}/{{date}}.csv",\ expand(f"{ANALYSIS_DIR}/{{cat}}/aggregated/{{date}}.csv",
folder=["pkgs", "build_status", "artifact_hash"],\ cat = ANALYSIS_CATS,
artifact=ARTIFACTS,\ date = DATE
date=DATE
),
expand(f"{PREFIX}/{{folder}}/{{artifact}}/{{date}}.txt",\
folder=["logs"],\
artifact=ARTIFACTS,\
date=DATE
), ),
# expand(f"{PREFIX}/{{folder}}/{{artifact}}/{{date}}.csv",
# folder=["pkgs", "build_status", "artifact_hash"],
# artifact=ARTIFACTS,
# date=DATE
# ),
# expand(f"{PREFIX}/logs/{{artifact}}/{{date}}.txt",
# artifact=ARTIFACTS,
# date=DATE
# ),
f"{BLACKLIST_FOLDER}/{DATE}.csv" f"{BLACKLIST_FOLDER}/{DATE}.csv"
rule check_all: rule check_all:
@ -71,8 +78,8 @@ rule run_ecg:
rule update_blacklist: rule update_blacklist:
input: input:
build_status=expand(f"{PREFIX}/build_status/{{artifact}}/{{{{date}}}}.csv",\ build_status=expand(f"{PREFIX}/build_status/{{artifact}}/{{{{date}}}}.csv",
artifact=ARTIFACTS artifact=ARTIFACTS
) )
output: output:
f"{BLACKLIST_FOLDER}/{{date}}.csv" f"{BLACKLIST_FOLDER}/{{date}}.csv"
@ -82,91 +89,127 @@ rule update_blacklist:
rule analysis: rule analysis:
input: input:
expand(f"{PREFIX}/{{folder}}/{{artifact}}/{{{{date}}}}.csv",\ expand(f"{PREFIX}/{{output_dir}}/{{artifact}}/{{date}}.csv",
folder = ["pkgs", "build_status", "artifact_hash"],\ output_dir = ECG_OUTPUTS,
artifact = ARTIFACTS artifact = ARTIFACTS,
) date = get_analysis_dates("{PREFIX}/{wildcards.output_dir}")
output:
expand(f"{ANALYSIS_DIR}/{{folder}}/{{date}}.csv",\
folder = ["sources_stats", "pkgs_changes", "build_status", "artifact_hash"],\
date = DATE
) )
rule softenv_analysis: rule softenv_analysis:
wildcard_constraints:
date="\d+"
input: input:
expand(f"{PREFIX}/pkgs/{{artifact}}/{{{{date}}}}.csv",\ sources_stats = expand(f"{PREFIX}/pkgs/{{artifact}}/{{date}}.csv",
artifact = ARTIFACTS artifact = ARTIFACTS,
date = DATE
),
pkgs_changes = expand(f"{PREFIX}/pkgs/{{artifact}}/{{date}}.csv",
artifact = ARTIFACTS,
date = get_analysis_dates("{PREFIX}/pkgs")
) )
output: output:
sources_stats = f"{ANALYSIS_DIR}/sources_stats/{DATE}.csv",\ sources_stats = f"{ANALYSIS_DIR}/sources_stats/{{date}}.csv",
pkgs_changes = f"{ANALYSIS_DIR}/pkgs_changes/{DATE}.csv" pkgs_changes = f"{ANALYSIS_DIR}/pkgs_changes/{{date}}.csv"
shell: shell:
f"python3 analysis/softenv_analysis.py -t sources-stats -i {{input}} -o {{output.sources_stats}}" f"""
f"python3 analysis/softenv_analysis.py -t pkgs-changes -i {{input}} -o {{output.pkgs_changes}}" python3 analysis/softenv_analysis.py -t sources-stats -i {{input.sources_stats}} -o {{output.sources_stats}}
python3 analysis/softenv_analysis.py -t pkgs-changes -i {{input.pkgs_changes}} -o {{output.pkgs_changes}}
"""
rule buildstatus_analysis: rule buildstatus_analysis:
wildcard_constraints:
date="\d+"
input: input:
expand(f"{PREFIX}/build_status/{{artifact}}/{{{{date}}}}.csv",\ expand(f"{PREFIX}/build_status/{{artifact}}/{{date}}.csv",
artifact = ARTIFACTS artifact = ARTIFACTS,
date = DATE
) )
output: output:
f"{ANALYSIS_DIR}/build_status/{DATE}.csv" f"{ANALYSIS_DIR}/build_status/{{date}}.csv",
shell: shell:
f"python3 analysis/buildstatus_analysis.py -i {{input}} -o {{output}}" f"""
python3 analysis/buildstatus_analysis.py -i {{input}} -o {{output}}
"""
rule artifact_analysis: rule artifact_analysis:
wildcard_constraints:
date="\d+"
input: input:
expand(f"{PREFIX}/artifact_hash/{{artifact}}/{{{{date}}}}.csv",\ expand(f"{PREFIX}/artifact_hash/{{artifact}}/{{date}}.csv",
artifact = ARTIFACTS artifact = ARTIFACTS,
date = get_analysis_dates("{PREFIX}/artifact_hash")
) )
output: output:
f"{ANALYSIS_DIR}/artifact/{DATE}.csv" f"{ANALYSIS_DIR}/artifact/{{date}}.csv",
shell: shell:
f"python3 analysis/artifact_analysis.py -i {{input}} -o {{output}}" f"""
python3 analysis/artifact_analysis.py -i {{input}} -o {{output}}
"""
rule analysis_aggregate: rule analysis_aggregate:
input: input:
sources_stats = expand(f"{ANALYSIS_DIR}/sources_stats/{{{{date}}}}.csv"), expand(f"{ANALYSIS_DIR}/{{input_cat}}/{{date}}.csv",
pkgs_changes = expand(f"{ANALYSIS_DIR}/pkgs_changes/{{{{date}}}}.csv"), input_cat = ANALYSIS_CATS,
build_status = expand(f"{ANALYSIS_DIR}/build_status/{{{{date}}}}.csv"), date = get_analysis_dates("{ANALYSIS_DIR}/{wildcards.cat}")
artifact = expand(f"{ANALYSIS_DIR}/artifact/{{{{date}}}}.csv") )
# sources_stats = expand(f"{ANALYSIS_DIR}/sources_stats/{{date}}.csv", date = glob_wildcards(f"{ANALYSIS_DIR}/sources_stats/{{date}}.csv").date),
# pkgs_changes = expand(f"{ANALYSIS_DIR}/pkgs_changes/{{date}}.csv", date = glob_wildcards(f"{ANALYSIS_DIR}/pkgs_changes/{{date}}.csv").date),
# build_status = expand(f"{ANALYSIS_DIR}/build_status/{{date}}.csv", date = glob_wildcards(f"{ANALYSIS_DIR}/build_status/{{date}}.csv").date),
# artifact = expand(f"{ANALYSIS_DIR}/artifact/{{date}}.csv", date = glob_wildcards(f"{ANALYSIS_DIR}/artifact/{{date}}.csv").date)
output: output:
expand(f"{ANALYSIS_DIR}/{{output_cat}}/aggregated/{{{{date}}}}.csv",
output_cat = ANALYSIS_CATS
)
shell:
expand(f"cat {ANALYSIS_DIR}/{{cat}}/{{{{date}}}}.csv > {ANALYSIS_DIR}/{{cat}}/aggregated/{{{{date}}}}.csv",
cat = ANALYSIS_CATS
)
PLOT_HEADERS = {
"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_plot:
input:
expand(f"{ANALYSIS_DIR}/{{folder}}/aggregated/{{date}}.csv",
folder = ["sources_stats", "pkgs_changes", "build_status", "artifact"],
date = DATE
)
rule line_plot:
input:
sources_stats = f"{ANALYSIS_DIR}/sources_stats/aggregated/{DATE}.csv", sources_stats = f"{ANALYSIS_DIR}/sources_stats/aggregated/{DATE}.csv",
pkgs_changes = f"{ANALYSIS_DIR}/pkgs_changes/aggregated/{DATE}.csv", pkgs_changes = f"{ANALYSIS_DIR}/pkgs_changes/aggregated/{DATE}.csv",
build_status = f"{ANALYSIS_DIR}/build_status/aggregated/{DATE}.csv", build_status = f"{ANALYSIS_DIR}/build_status/aggregated/{DATE}.csv",
artifact = f"{ANALYSIS_DIR}/artifact/aggregated/{DATE}.csv" artifact = f"{ANALYSIS_DIR}/artifact/aggregated/{DATE}.csv"
output:
sources_stats = f"{ANALYSIS_DIR}/sources_stats/plot/line/{DATE}.csv",
pkgs_changes = f"{ANALYSIS_DIR}/pkgs_changes/plot/line/{DATE}.csv",
build_status = f"{ANALYSIS_DIR}/build_status/plot/line/{DATE}.csv",
artifact = f"{ANALYSIS_DIR}/artifact/plot/line/{DATE}.csv"
shell: shell:
f"cat {{input.sources_stats}} > {{output.sources_stats}}" f"""
f"cat {{input.pkgs_changes}} > {{output.pkgs_changes}}" Rscript plot.r line {{input.sources_stats}} {{output.sources_stats}} {{{{PLOT_HEADERS["sources_stats"]}}}}
f"cat {{input.build_status}} > {{output.build_status}}" Rscript plot.r line {{input.pkgs_changes}} {{output.pkgs_changes}} {{{{PLOT_HEADERS["pkgs_changes"]}}}}
f"cat {{input.artifact}} > {{output.artifact}}" Rscript plot.r line {{input.build_status}} {{output.build_status}} {{{{PLOT_HEADERS["build_status"]}}}}
Rscript plot.r line {{input.artifact}} {{output.artifact}} {{{{PLOT_HEADERS["artifact"]}}}}
"""
# PLOT_HEADERS = { rule bar_plot:
# "sources_stats": ["dpkg", "rpm", "pacman", "pip", "conda", "git", "misc"], input:
# "pkgs_changes": ["dpkg", "rpm", "pacman", "pip", "conda", "git", "misc"], sources_stats = f"{ANALYSIS_DIR}/sources_stats/aggregated/{DATE}.csv",
# "build_status": ["success", "package_install_failed", "baseimage_unavailable", "artifact_unavailable", "dockerfile_not_found", "script_crash", "job_time_exceeded", "unknown_error"], build_status = f"{ANALYSIS_DIR}/build_status/aggregated/{DATE}.csv",
# "artifact": ["available", "unavailable", "changed"] artifact = f"{ANALYSIS_DIR}/artifact/aggregated/{DATE}.csv"
# } output:
sources_stats = f"{ANALYSIS_DIR}/sources_stats/plot/bar/{DATE}.csv",
# rule plot_all: build_status = f"{ANALYSIS_DIR}/build_status/plot/bar/{DATE}.csv",
# input: artifact = f"{ANALYSIS_DIR}/artifact/plot/bar/{DATE}.csv"
# expand(f"{ANALYSIS_DIR}/{{folder}}/aggregated/{{date}}.csv",\ shell:
# folder = ["sources_stats", "pkgs_changes", "build_status", "artifact"],\ f"""
# date = DATE Rscript plot.r bar {{input.sources_stats}} {{output.sources_stats}} {{{{PLOT_HEADERS["sources_stats"]}}}}
# ) Rscript plot.r bar {{input.build_status}} {{output.build_status}} {{{{PLOT_HEADERS["build_status"]}}}}
Rscript plot.r bar {{input.artifact}} {{output.artifact}} {{{{PLOT_HEADERS["artifact"]}}}}
# rule line_plot: """
# input:
# expand(f"{ANALYSIS_DIR}/{{folder}}/{{artifact}}/{{date}}.csv",\
# folder = ["sources_stats", "pkgs_changes", "build_status", "artifact"],\
# artifact = ARTIFACTS,\
# date = DATE
# ),
# output:
# expand(f"{ANALYSIS_DIR}/{{folder}}/line.pdf",\
# folder = ["sources_stats", "pkgs_changes", "build_status", "artifact"],\
# artifact = ARTIFACTS,\
# date = DATE
# ),
# shell:
# f"Rscript plot.r line {{{{PLOT_HEADERS[wildcards.folder]}}}}"

12
workflow/utils.smk
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@ -1,8 +1,18 @@
import csv import csv
import os import os
def get_analysis_dates(directory):
outputs = []
if os.path.exists(directory):
for file in os.listdir(directory):
if not os.path.isdir(os.path.join(directory, file)):
outputs.append(os.path.splitext(file)[0])
if outputs == []:
outputs.append(datetime.datetime.now().strftime("%Y%m%d"))
return outputs
def find_last_blacklist(blacklist_dir_path): def find_last_blacklist(blacklist_dir_path):
last_blacklist = "0" last_blacklist = "0.csv"
for blacklist in os.listdir(blacklist_dir_path): for blacklist in os.listdir(blacklist_dir_path):
if not os.path.isdir(blacklist): if not os.path.isdir(blacklist):
# We want the latest one, so the one that has the most recent date # We want the latest one, so the one that has the most recent date