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switch to usual logger
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@andrewprzh
andrewprzh committed Feb 12, 2024
1 parent 8bfaef1 commit 38f5194
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Showing 2 changed files with 51 additions and 91 deletions.
4 changes: 2 additions & 2 deletions .github/workflows/SIRVs.Set4.R10.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -7,9 +7,9 @@ on:

env:
RUN_NAME: SIRVs.Set4.R10
LAUNCHER: ${{github.workspace}}/tests/teamcity/run_pipeline.py
LAUNCHER: ${{github.workspace}}/tests/github/run_pipeline.py
CFG_DIR: /abga/work/andreyp/ci_isoquant/data
BIN_PATH: /abga/work/andreyp/ci_isoquant/bin
BIN_PATH: /abga/work/andreyp/ci_isoquant/bin/

jobs:
launch-runner:
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138 changes: 49 additions & 89 deletions tests/teamcity/run_pipeline.py → tests/github/run_pipeline.py
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Original file line number Diff line number Diff line change
Expand Up @@ -15,6 +15,7 @@
import glob
from traceback import print_exc
import subprocess
import logging


_quote = {"'": "|'", "|": "||", "\n": "|n", "\r": "|r", '[': '|[', ']': '|]'}
Expand All @@ -25,58 +26,22 @@
RT_TRANSCRIPTS = "transcripts"


def escape_value(value):
return "".join(_quote.get(x, x) for x in value)
log = logging.getLogger('GitHubRunner')


class TeamCityLog:

text = ""

def _tc_out(self, token, **attributes):
message = "##teamcity[%s" % token

for k in sorted(attributes.keys()):
value = attributes[k]
if value is None:
continue

message += (" %s='%s'" % (k, escape_value(value)))

message += "]\n"
sys.stdout.write(message)
sys.stdout.flush()

def start_block(self, name, desc):
sys.stdout.flush()
self._tc_out("blockOpened", name = name, description = desc)

def end_block(self, name):
sys.stdout.flush()
self._tc_out("blockClosed", name = name)

def log(self, s):
self.text += s + "\n"
self._tc_out("message", text = s)

def warn(self, s):
msg = "WARNING: " + s + "\n"
self.text += msg
self._tc_out("message", text = s, status = 'WARNING')

def err(self, s, context = ""):
msg = "ERROR: " + s + "\n"
self.text += msg
self._tc_out("message", text = s, status = 'ERROR', errorDetails = context)

def print_log(self):
print(self.text)
def set_logger(args, logger_instance):
if "debug" not in args.__dict__ or not args.debug:
output_level = logging.INFO
else:
output_level = logging.DEBUG
logger_instance.setLevel(output_level)

def get_log(self):
return self.text
ch = logging.StreamHandler(sys.stdout)
ch.setLevel(logging.INFO)

def record_metric(self, name, value):
self._tc_out("buildStatisticValue", key=name, value=value)
formatter = logging.Formatter('%(asctime)s - %(levelname)s - %(message)s')
ch.setFormatter(formatter)
logger_instance.addHandler(ch)


def load_tsv_config(config_file):
Expand Down Expand Up @@ -109,7 +74,7 @@ def parse_args():
return args


def run_isoquant(args, config_dict, log):
def run_isoquant(args, config_dict):
source_dir = os.path.dirname(os.path.realpath(__file__))
isoquant_dir = os.path.join(source_dir, "../../")
config_file = args.config_file
Expand All @@ -134,7 +99,7 @@ def run_isoquant(args, config_dict, log):
genome = fix_path(config_file, config_dict["genome"])
config_dict["label"] = run_name

log.start_block('isoquant', 'Running IsoQuant')
log.info('== Running IsoQuant ==')
isoquant_command_list = ["python3", os.path.join(isoquant_dir, "isoquant.py"), "-o", output_folder,
"-r", genome, "-d", config_dict["datatype"], "-p", run_name]
if genedb:
Expand All @@ -149,40 +114,39 @@ def run_isoquant(args, config_dict, log):
isoquant_command_list.append(reads)

if "isoquant_options" in config_dict:
log.log("Appending additional options: %s" % config_dict["isoquant_options"])
log.info("Appending additional options: %s" % config_dict["isoquant_options"])
opts = config_dict["isoquant_options"].replace('"', '').split()
for o in opts:
isoquant_command_list.append(o)

log.log("IsoQuant command line: " + " ".join(isoquant_command_list))
log.info("IsoQuant command line: " + " ".join(isoquant_command_list))
result = subprocess.run(isoquant_command_list)
if result.returncode != 0:
log.err("IsoQuant exited with non-zero status: %d" % result.returncode)
log.error("IsoQuant exited with non-zero status: %d" % result.returncode)
return -11

log.end_block('isoquant')
return 0


def check_value(etalon_value, output_value, name, log):
def check_value(etalon_value, output_value, name):
lower_bound = etalon_value * 0.99
upper_bound = etalon_value * 1.01
exit_code = 0
if output_value < lower_bound:
log.err("Value of %s = %2.2f is lower than the expected value %2.2f" % (name, output_value, lower_bound))
log.error("Value of %s = %2.2f is lower than the expected value %2.2f" % (name, output_value, lower_bound))
exit_code = -41
else:
log.log("Value of %s = %2.2f >= %2.2f as expected" % (name, output_value, lower_bound))
log.info("Value of %s = %2.2f >= %2.2f as expected" % (name, output_value, lower_bound))
if output_value > upper_bound:
log.err("Value of %s = %2.2f is higher than the expected value %2.2f" % (name, output_value, upper_bound))
log.error("Value of %s = %2.2f is higher than the expected value %2.2f" % (name, output_value, upper_bound))
exit_code = -42
else:
log.log("Value of %s = %2.2f <= %2.2f as expected" % (name, output_value, upper_bound))
log.info("Value of %s = %2.2f <= %2.2f as expected" % (name, output_value, upper_bound))
return exit_code


def run_assignment_quality(args, config_dict, log):
log.start_block('quality', 'Running quality assessment')
def run_assignment_quality(args, config_dict):
log.info('== Running quality assessment ==')
config_file = args.config_file
source_dir = os.path.dirname(os.path.realpath(__file__))
isoquant_dir = os.path.join(source_dir, "../../")
Expand All @@ -197,7 +161,7 @@ def run_assignment_quality(args, config_dict, log):
if "bam" not in config_dict:
bam = glob.glob(os.path.join(output_folder, "%s/aux/%s*.bam" % (label, label)))
if not bam:
log.err("BAM file was not found")
log.error("BAM file was not found")
return -21
bam = bam[0]
else:
Expand All @@ -209,38 +173,36 @@ def run_assignment_quality(args, config_dict, log):
"--mapping", bam, "--fasta", reads]

if "qa_options" in config_dict:
log.log("Appending additional options: %s" % config_dict["qa_options"])
log.info("Appending additional options: %s" % config_dict["qa_options"])
opts = config_dict["qa_options"].replace('"', '').split()
for o in opts:
qa_command_list.append(o)

log.log("QA command line: " + " ".join(qa_command_list))
log.info("QA command line: " + " ".join(qa_command_list))
result = subprocess.run(qa_command_list)
if result.returncode != 0:
log.err("QA exited with non-zero status: %d" % result.returncode)
log.error("QA exited with non-zero status: %d" % result.returncode)
return -13
log.end_block('quality')

if "etalon" not in config_dict:
return 0

log.start_block('assessment', 'Checking quality metrics')
log.info('== Checking quality metrics ==')
etalon_qaulity_dict = load_tsv_config(fix_path(config_file, config_dict["etalon"]))
quality_report_dict = load_tsv_config(quality_report)
exit_code = 0
new_etalon_outf = open(os.path.join(output_folder, "new_assignment_etalon.tsv"), "w")
for k, v in etalon_qaulity_dict.items():
if k not in quality_report_dict:
log.err("Metric %s was not found in the report" % k)
log.error("Metric %s was not found in the report" % k)
exit_code = -22
continue
new_etalon_outf.write("%s\t%.2f\n" % (k, float(quality_report_dict[k])))
err_code = check_value(float(v), float(quality_report_dict[k]), k, log)
err_code = check_value(float(v), float(quality_report_dict[k]), k)
if err_code != 0:
exit_code = err_code

new_etalon_outf.close()
log.end_block('assessment')
return exit_code


Expand All @@ -254,8 +216,8 @@ def parse_gffcomapre(stats_file):
return -1, -1


def run_transcript_quality(args, config_dict, log):
log.start_block('quality', 'Running quality assessment')
def run_transcript_quality(args, config_dict):
log.info('== Running quality assessment ==')
config_file = args.config_file
source_dir = os.path.dirname(os.path.realpath(__file__))
isoquant_dir = os.path.join(source_dir, "../../")
Expand All @@ -265,25 +227,24 @@ def run_transcript_quality(args, config_dict, log):
output_folder = os.path.join(args.output if args.output else config_dict["output"], name)
out_gtf = os.path.join(output_folder, "%s/%s.transcript_models.gtf" % (label, label))
if not out_gtf:
log.err("Output GTF file was not found")
log.error("Output GTF file was not found")
return -31

quality_output = os.path.join(output_folder, "gffcompare")
genedb_prefix = fix_path(config_file, config_dict["reduced_db"])
qa_command_list = ["python3", os.path.join(isoquant_dir, "misc/reduced_db_gffcompare.py"),
"-o", quality_output, "--genedb", genedb_prefix, "--gtf", out_gtf, "--tool", "isoquant"]

log.log("QA command line: " + " ".join(qa_command_list))
log.info("QA command line: " + " ".join(qa_command_list))
result = subprocess.run(qa_command_list)
if result.returncode != 0:
log.err("Transcript evaluation exited with non-zero status: %d" % result.returncode)
log.error("Transcript evaluation exited with non-zero status: %d" % result.returncode)
return -13
log.end_block('quality')

if "etalon" not in config_dict:
return 0

log.start_block('assessment', 'Checking quality metrics')
log.info('== Checking quality metrics ==')
etalon_qaulity_dict = load_tsv_config(fix_path(config_file, config_dict["etalon"]))
exit_code = 0
new_etalon_outf = open(os.path.join(quality_output, "new_gtf_etalon.tsv"), "w")
Expand All @@ -293,56 +254,55 @@ def run_transcript_quality(args, config_dict, log):
if metric_name in etalon_qaulity_dict:
new_etalon_outf.write("%s\t%.2f\n" % (metric_name, recall))
etalon_recall = float(etalon_qaulity_dict[metric_name])
err_code = check_value(etalon_recall, recall , metric_name, log)
err_code = check_value(etalon_recall, recall , metric_name)
if err_code != 0:
exit_code = err_code
metric_name = gtf_type + "_precision"
if metric_name in etalon_qaulity_dict:
new_etalon_outf.write("%s\t%.2f\n" % (metric_name, precision))
etalon_precision = float(etalon_qaulity_dict[metric_name])
err_code = check_value(etalon_precision, precision, metric_name, log)
err_code = check_value(etalon_precision, precision, metric_name)
if err_code != 0:
exit_code = err_code
new_etalon_outf.close()
log.end_block('assessment')
return exit_code


def main():
log = TeamCityLog()
args = parse_args()
set_logger(args, log)
if not args.config_file:
log.err("Provide configuration file")
log.error("Provide configuration file")
exit(-2)

config_file = args.config_file
if not os.path.exists(config_file):
log.err("Provide correct path to configuration file")
log.error("Provide correct path to configuration file")
exit(-3)

log.log("Loading config from %s" % config_file)
log.info("Loading config from %s" % config_file)
config_dict = load_tsv_config(config_file)
required = ["output", "name"]
if "resume" not in config_dict:
required += ["genome", "datatype"]
for k in required:
if k not in config_dict:
log.err(k + " is not set in the config")
log.error(k + " is not set in the config")
return -10

err_code = run_isoquant(args, config_dict, log)
err_code = run_isoquant(args, config_dict)
if err_code != 0:
return err_code

run_type = config_dict["run_type"]
if run_type == RT_VOID:
err_code = 0
elif run_type == RT_ASSIGNMENT:
err_code = run_assignment_quality(args, config_dict, log)
err_code = run_assignment_quality(args, config_dict)
elif run_type == RT_TRANSCRIPTS:
err_code = run_transcript_quality(args, config_dict, log)
err_code = run_transcript_quality(args, config_dict)
else:
log.err("Test type %s is not supported" % run_type)
log.error("Test type %s is not supported" % run_type)
err_code = -50

return err_code
Expand Down

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