/usr/lib/python3/dist-packages/snakemake/gui.py is in snakemake 4.3.1-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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__copyright__ = "Copyright 2015, Johannes Köster"
__email__ = "koester@jimmy.harvard.edu"
__license__ = "MIT"
import json
import os
import threading
from flask import Flask, render_template, request
from snakemake.version import __version__
LOCK = threading.Lock()
app = Flask("snakemake", template_folder=os.path.dirname(__file__))
#app.debug=True
app.extensions = {
"dag": None,
"run_snakemake": None,
"progress": "",
"log": [],
"status": {"running": False},
"args": None,
"targets": [],
"rule_info": [],
"resources": []
}
def register(run_snakemake, args):
app.extensions["run_snakemake"] = run_snakemake
app.extensions["args"] = dict(targets=args.target,
cluster=args.cluster,
workdir=args.directory,
touch=args.touch,
forcetargets=args.force,
forceall=args.forceall,
forcerun=args.forcerun,
prioritytargets=args.prioritize,
stats=args.stats,
keepgoing=args.keep_going,
jobname=args.jobname,
immediate_submit=args.immediate_submit,
ignore_ambiguity=args.allow_ambiguity,
lock=not args.nolock,
force_incomplete=args.rerun_incomplete,
ignore_incomplete=args.ignore_incomplete,
jobscript=args.jobscript,
notemp=args.notemp,
latency_wait=args.latency_wait)
target_rules = []
def log_handler(msg):
if msg["level"] == "rule_info":
target_rules.append(msg["name"])
run_snakemake(list_target_rules=True, log_handler=log_handler)
for target in args.target:
target_rules.remove(target)
app.extensions["targets"] = args.target + target_rules
resources = []
def log_handler(msg):
if msg["level"] == "info":
resources.append(msg["msg"])
run_snakemake(list_resources=True, log_handler=log_handler)
app.extensions["resources"] = resources
app.extensions["snakefilepath"] = os.path.abspath(args.snakefile)
def run_snakemake(**kwargs):
args = dict(app.extensions["args"])
args.update(kwargs)
app.extensions["run_snakemake"](**args)
@app.route("/")
def index():
args = app.extensions["args"]
return render_template("gui.html",
targets=app.extensions["targets"],
cores_label="Nodes" if args["cluster"] else "Cores",
resources=app.extensions["resources"],
snakefilepath=app.extensions["snakefilepath"],
version=__version__,
node_width=15,
node_padding=10)
@app.route("/dag")
def dag():
if app.extensions["dag"] is None:
def record(msg):
if msg["level"] == "d3dag":
app.extensions["dag"] = msg
elif msg["level"] in ("error", "info"):
app.extensions["log"].append(msg)
run_snakemake(printd3dag=True, log_handler=record)
return json.dumps(app.extensions["dag"])
@app.route("/log/<int:id>")
def log(id):
log = app.extensions["log"][id:]
return json.dumps(log)
@app.route("/progress")
def progress():
return json.dumps(app.extensions["progress"])
def _run(dryrun=False):
def log_handler(msg):
level = msg["level"]
if level == "progress":
app.extensions["progress"] = msg
elif level in ("info", "error", "job_info", "job_finished"):
app.extensions["log"].append(msg)
with LOCK:
app.extensions["status"]["running"] = True
run_snakemake(log_handler=log_handler, dryrun=dryrun)
with LOCK:
app.extensions["status"]["running"] = False
return ""
@app.route("/run")
def run():
_run()
@app.route("/dryrun")
def dryrun():
_run(dryrun=True)
@app.route("/status")
def status():
with LOCK:
return json.dumps(app.extensions["status"])
@app.route("/targets")
def targets():
return json.dumps(app.extensions["targets"])
@app.route("/get_args")
def get_args():
return json.dumps(app.extensions["args"])
@app.route("/set_args", methods=["POST"])
def set_args():
app.extensions["args"].update({
name: value
for name, value in request.form.items() if not name.endswith("[]")
})
targets = request.form.getlist("targets[]")
if targets != app.extensions["args"]["targets"]:
app.extensions["dag"] = None
app.extensions["args"]["targets"] = targets
return ""
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