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How to use run_abort method in autotest
Best Python code snippet using autotest_python
configure_run.py
Source:configure_run.py 
1#!/usr/bin/python2from __future__ import print_function3__docformat__ = "restructuredtext en"4import subprocess5import logging6import time7import re8import os9from htsworkflow.pipelines.retrieve_config import \10 CONFIG_SYSTEM, CONFIG_USER, \11 FlowCellNotFound, getCombinedOptions, saveConfigFile, WebError40412from htsworkflow.pipelines.genome_mapper import DuplicateGenome, getAvailableGenomes, constructMapperDict13from htsworkflow.pipelines.run_status import GARunStatus14from pyinotify import WatchManager, ThreadedNotifier15from pyinotify import EventsCodes, ProcessEvent16LOGGER = logging.getLogger(__name__)17class ConfigInfo:18 def __init__(self):19 #run_path = firecrest analysis directory to run analysis from20 self.run_path = None21 self.bustard_path = None22 self.config_filepath = None23 self.status = None24 #top level directory where all analyses are placed25 self.base_analysis_dir = None26 #analysis_dir, top level analysis dir...27 # base_analysis_dir + '/070924_USI-EAS44_0022_FC12150'28 self.analysis_dir = None29 def createStatusObject(self):30 """31 Creates a status object which can be queried for32 status of running the pipeline33 returns True if object created34 returns False if object cannot be created35 """36 if self.config_filepath is None:37 return False38 self.status = GARunStatus(self.config_filepath)39 return True40####################################41# inotify event processor42s_firecrest_finished = re.compile('Firecrest[0-9\._\-A-Za-z]+/finished.txt')43s_bustard_finished = re.compile('Bustard[0-9\._\-A-Za-z]+/finished.txt')44s_gerald_finished = re.compile('GERALD[0-9\._\-A-Za-z]+/finished.txt')45s_gerald_all = re.compile('Firecrest[0-9\._\-A-Za-z]+/Bustard[0-9\._\-A-Za-z]+/GERALD[0-9\._\-A-Za-z]+/')46s_bustard_all = re.compile('Firecrest[0-9\._\-A-Za-z]+/Bustard[0-9\._\-A-Za-z]+/')47s_firecrest_all = re.compile('Firecrest[0-9\._\-A-Za-z]+/')48class RunEvent(ProcessEvent):49 def __init__(self, conf_info):50 self.run_status_dict = {'firecrest': False,51 'bustard': False,52 'gerald': False}53 self._ci = conf_info54 ProcessEvent.__init__(self)55 def process_IN_CREATE(self, event):56 fullpath = os.path.join(event.path, event.name)57 if s_finished.search(fullpath):58 LOGGER.info("File Found: %s" % (fullpath))59 if s_firecrest_finished.search(fullpath):60 self.run_status_dict['firecrest'] = True61 self._ci.status.updateFirecrest(event.name)62 elif s_bustard_finished.search(fullpath):63 self.run_status_dict['bustard'] = True64 self._ci.status.updateBustard(event.name)65 elif s_gerald_finished.search(fullpath):66 self.run_status_dict['gerald'] = True67 self._ci.status.updateGerald(event.name)68 #WARNING: The following order is important!!69 # Firecrest regex will catch all gerald, bustard, and firecrest70 # Bustard regex will catch all gerald and bustard71 # Gerald regex will catch all gerald72 # So, order needs to be Gerald, Bustard, Firecrest, or this73 # won't work properly.74 elif s_gerald_all.search(fullpath):75 self._ci.status.updateGerald(event.name)76 elif s_bustard_all.search(fullpath):77 self._ci.status.updateBustard(event.name)78 elif s_firecrest_all.search(fullpath):79 self._ci.status.updateFirecrest(event.name)80 #print "Create: %s" % (os.path.join(event.path, event.name))81 def process_IN_DELETE(self, event):82 #print "Remove %s" % (os.path.join(event.path, event.name))83 pass84#FLAGS85# Config Step Error86RUN_ABORT = 'abort'87# Run Step Error88RUN_FAILED = 'failed'89#####################################90# Configure Step (goat_pipeline.py)91#Info92s_start = re.compile('Starting Genome Analyzer Pipeline')93s_gerald = re.compile("[\S\s]+--GERALD[\S\s]+--make[\S\s]+")94s_generating = re.compile('^Generating journals, Makefiles')95s_seq_folder = re.compile('^Sequence folder: ')96s_seq_folder_sub = re.compile('want to make ')97s_stderr_taskcomplete = re.compile('^Task complete, exiting')98#Errors99s_invalid_cmdline = re.compile('Usage:[\S\s]*goat_pipeline.py')100s_species_dir_err = re.compile('Error: Lane [1-8]:')101s_goat_traceb = re.compile("^Traceback \(most recent call last\):")102s_missing_cycles = re.compile('^Error: Tile s_[1-8]_[0-9]+: Different number of cycles: [0-9]+ instead of [0-9]+')103SUPPRESS_MISSING_CYCLES = False104##Ignore - Example of out above each ignore regex.105#NOTE: Commenting out an ignore will cause it to be106# logged as DEBUG with the logging module.107#CF_STDERR_IGNORE_LIST = []108s_skip = re.compile('s_[0-8]_[0-9]+')109##########################################110# Pipeline Run Step (make -j8 recursive)111##Info112s_finished = re.compile('finished')113##Errors114s_make_error = re.compile('^make[\S\s]+Error')115s_no_gnuplot = re.compile('gnuplot: command not found')116s_no_convert = re.compile('^Can\'t exec "convert"')117s_no_ghostscript = re.compile('gs: command not found')118##Ignore - Example of out above each ignore regex.119#NOTE: Commenting out an ignore will cause it to be120# logged as DEBUG with the logging module.121#122PL_STDERR_IGNORE_LIST = []123# Info: PF 11802124PL_STDERR_IGNORE_LIST.append( re.compile('^Info: PF') )125# About to analyse intensity file s_4_0101_sig2.txt126PL_STDERR_IGNORE_LIST.append( re.compile('^About to analyse intensity file') )127# Will send output to standard output128PL_STDERR_IGNORE_LIST.append( re.compile('^Will send output to standard output') )129# Found 31877 clusters130PL_STDERR_IGNORE_LIST.append( re.compile('^Found [0-9]+ clusters') )131# Will use quality criterion ((CHASTITY>=0.6)132PL_STDERR_IGNORE_LIST.append( re.compile('^Will use quality criterion') )133# Quality criterion translated to (($F[5]>=0.6))134PL_STDERR_IGNORE_LIST.append( re.compile('^Quality criterion translated to') )135# opened /woldlab/trog/data1/king/070924_USI-EAS44_0022_FC12150/Data/C1-36_Firecrest1.9.1_14-11-2007_king.4/Bustard1.9.1_14-11-2007_king/s_4_0101_qhg.txt136# AND137# opened s_4_0103_qhg.txt138PL_STDERR_IGNORE_LIST.append( re.compile('^opened[\S\s]+qhg.txt') )139# 81129 sequences out of 157651 passed filter criteria140PL_STDERR_IGNORE_LIST.append( re.compile('^[0-9]+ sequences out of [0-9]+ passed filter criteria') )141def pl_stderr_ignore(line):142 """143 Searches lines for lines to ignore (i.e. not to log)144 returns True if line should be ignored145 returns False if line should NOT be ignored146 """147 for s in PL_STDERR_IGNORE_LIST:148 if s.search(line):149 return True150 return False151def config_stdout_handler(line, conf_info):152 """153 Processes each line of output from GOAT154 and stores useful information using the logging module155 Loads useful information into conf_info as well, for future156 use outside the function.157 returns True if found condition that signifies success.158 """159 # Skip irrelevant line (without logging)160 if s_skip.search(line):161 pass162 # Detect invalid command-line arguments163 elif s_invalid_cmdline.search(line):164 LOGGER.error("Invalid commandline options!")165 # Detect starting of configuration166 elif s_start.search(line):167 LOGGER.info('START: Configuring pipeline')168 # Detect it made it past invalid arguments169 elif s_gerald.search(line):170 LOGGER.info('Running make now')171 # Detect that make files have been generated (based on output)172 elif s_generating.search(line):173 LOGGER.info('Make files generted')174 return True175 # Capture run directory176 elif s_seq_folder.search(line):177 mo = s_seq_folder_sub.search(line)178 #Output changed when using --tiles=<tiles>179 # at least in pipeline v0.3.0b2180 if mo:181 firecrest_bustard_gerald_makefile = line[mo.end():]182 firecrest_bustard_gerald, junk = \183 os.path.split(firecrest_bustard_gerald_makefile)184 firecrest_bustard, junk = os.path.split(firecrest_bustard_gerald)185 firecrest, junk = os.path.split(firecrest_bustard)186 conf_info.bustard_path = firecrest_bustard187 conf_info.run_path = firecrest188 #Standard output handling189 else:190 print('Sequence line:', line)191 mo = s_seq_folder.search(line)192 conf_info.bustard_path = line[mo.end():]193 conf_info.run_path, temp = os.path.split(conf_info.bustard_path)194 # Log all other output for debugging purposes195 else:196 LOGGER.warning('CONF:?: %s' % (line))197 return False198def config_stderr_handler(line, conf_info):199 """200 Processes each line of output from GOAT201 and stores useful information using the logging module202 Loads useful information into conf_info as well, for future203 use outside the function.204 returns RUN_ABORT upon detecting failure;205 True on success message;206 False if neutral message207 (i.e. doesn't signify failure or success)208 """209 global SUPPRESS_MISSING_CYCLES210 # Detect invalid species directory error211 if s_species_dir_err.search(line):212 LOGGER.error(line)213 return RUN_ABORT214 # Detect goat_pipeline.py traceback215 elif s_goat_traceb.search(line):216 LOGGER.error("Goat config script died, traceback in debug output")217 return RUN_ABORT218 # Detect indication of successful configuration (from stderr; odd, but ok)219 elif s_stderr_taskcomplete.search(line):220 LOGGER.info('Configure step successful (from: stderr)')221 return True222 # Detect missing cycles223 elif s_missing_cycles.search(line):224 # Only display error once225 if not SUPPRESS_MISSING_CYCLES:226 LOGGER.error("Missing cycles detected; Not all cycles copied?")227 LOGGER.debug("CONF:STDERR:MISSING_CYCLES: %s" % (line))228 SUPPRESS_MISSING_CYCLES = True229 return RUN_ABORT230 # Log all other output as debug output231 else:232 LOGGER.debug('CONF:STDERR:?: %s' % (line))233 # Neutral (not failure; nor success)234 return False235#def pipeline_stdout_handler(line, conf_info):236# """237# Processes each line of output from running the pipeline238# and stores useful information using the logging module239#240# Loads useful information into conf_info as well, for future241# use outside the function.242#243# returns True if found condition that signifies success.244# """245#246# #f.write(line + '\n')247#248# return True249def pipeline_stderr_handler(line, conf_info):250 """251 Processes each line of stderr from pipelien run252 and stores useful information using the logging module253 ##FIXME: Future feature (doesn't actually do this yet)254 #Loads useful information into conf_info as well, for future255 #use outside the function.256 returns RUN_FAILED upon detecting failure;257 #True on success message; (no clear success state)258 False if neutral message259 (i.e. doesn't signify failure or success)260 """261 if pl_stderr_ignore(line):262 pass263 elif s_make_error.search(line):264 LOGGER.error("make error detected; run failed")265 return RUN_FAILED266 elif s_no_gnuplot.search(line):267 LOGGER.error("gnuplot not found")268 return RUN_FAILED269 elif s_no_convert.search(line):270 LOGGER.error("imagemagick's convert command not found")271 return RUN_FAILED272 elif s_no_ghostscript.search(line):273 LOGGER.error("ghostscript not found")274 return RUN_FAILED275 else:276 LOGGER.debug('PIPE:STDERR:?: %s' % (line))277 return False278def retrieve_config(conf_info, flowcell, cfg_filepath, genome_dir):279 """280 Gets the config file from server...281 requires config file in:282 /etc/ga_frontend/ga_frontend.conf283 or284 ~/.ga_frontend.conf285 with:286 [config_file_server]287 base_host_url: http://host:port288 return True if successful, False is failure289 """290 options = getCombinedOptions()291 if options.url is None:292 LOGGER.error("%s or %s missing base_host_url option" % \293 (CONFIG_USER, CONFIG_SYSTEM))294 return False295 try:296 saveConfigFile(flowcell, options.url, cfg_filepath)297 conf_info.config_filepath = cfg_filepath298 except FlowCellNotFound as e:299 LOGGER.error(e)300 return False301 except WebError404 as e:302 LOGGER.error(e)303 return False304 except IOError as e:305 LOGGER.error(e)306 return False307 except Exception as e:308 LOGGER.error(e)309 return False310 f = open(cfg_filepath, 'r')311 data = f.read()312 f.close()313 genome_dict = getAvailableGenomes(genome_dir)314 mapper_dict = constructMapperDict(genome_dict)315 LOGGER.debug(data)316 f = open(cfg_filepath, 'w')317 f.write(data % (mapper_dict))318 f.close()319 return True320def configure(conf_info):321 """322 Attempts to configure the GA pipeline using goat.323 Uses logging module to store information about status.324 returns True if configuration successful, otherwise False.325 """326 #ERROR Test:327 #pipe = subprocess.Popen(['goat_pipeline.py',328 # '--GERALD=config32bk.txt',329 # '--make .',],330 # #'.'],331 # stdout=subprocess.PIPE,332 # stderr=subprocess.PIPE)333 #ERROR Test (2), causes goat_pipeline.py traceback334 #pipe = subprocess.Popen(['goat_pipeline.py',335 # '--GERALD=%s' % (conf_info.config_filepath),336 # '--tiles=s_4_100,s_4_101,s_4_102,s_4_103,s_4_104',337 # '--make',338 # '.'],339 # stdout=subprocess.PIPE,340 # stderr=subprocess.PIPE)341 ##########################342 # Run configuration step343 # Not a test; actual configure attempt.344 #pipe = subprocess.Popen(['goat_pipeline.py',345 # '--GERALD=%s' % (conf_info.config_filepath),346 # '--make',347 # '.'],348 # stdout=subprocess.PIPE,349 # stderr=subprocess.PIPE)350 stdout_filepath = os.path.join(conf_info.analysis_dir,351 "pipeline_configure_stdout.txt")352 stderr_filepath = os.path.join(conf_info.analysis_dir,353 "pipeline_configure_stderr.txt")354 fout = open(stdout_filepath, 'w')355 ferr = open(stderr_filepath, 'w')356 pipe = subprocess.Popen(['goat_pipeline.py',357 '--GERALD=%s' % (conf_info.config_filepath),358 '--make',359 conf_info.analysis_dir],360 stdout=fout,361 stderr=ferr)362 print("Configuring pipeline: %s" % (time.ctime()))363 error_code = pipe.wait()364 # Clean up365 fout.close()366 ferr.close()367 ##################368 # Process stdout369 fout = open(stdout_filepath, 'r')370 stdout_line = fout.readline()371 complete = False372 while stdout_line != '':373 # Handle stdout374 if config_stdout_handler(stdout_line, conf_info):375 complete = True376 stdout_line = fout.readline()377 fout.close()378 #error_code = pipe.wait()379 if error_code:380 LOGGER.error('Recieved error_code: %s' % (error_code))381 else:382 LOGGER.info('We are go for launch!')383 #Process stderr384 ferr = open(stderr_filepath, 'r')385 stderr_line = ferr.readline()386 abort = 'NO!'387 stderr_success = False388 while stderr_line != '':389 stderr_status = config_stderr_handler(stderr_line, conf_info)390 if stderr_status == RUN_ABORT:391 abort = RUN_ABORT392 elif stderr_status is True:393 stderr_success = True394 stderr_line = ferr.readline()395 ferr.close()396 #Success requirements:397 # 1) The stdout completed without error398 # 2) The program exited with status 0399 # 3) No errors found in stdout400 print('#Expect: True, False, True, True')401 print(complete, bool(error_code), abort != RUN_ABORT, stderr_success is True)402 status = complete is True and \403 bool(error_code) is False and \404 abort != RUN_ABORT and \405 stderr_success is True406 # If everything was successful, but for some reason407 # we didn't retrieve the path info, log it.408 if status is True:409 if conf_info.bustard_path is None or conf_info.run_path is None:410 LOGGER.error("Failed to retrieve run_path")411 return False412 return status413def run_pipeline(conf_info):414 """415 Run the pipeline and monitor status.416 """417 # Fail if the run_path doesn't actually exist418 if not os.path.exists(conf_info.run_path):419 LOGGER.error('Run path does not exist: %s' \420 % (conf_info.run_path))421 return False422 # Change cwd to run_path423 stdout_filepath = os.path.join(conf_info.analysis_dir, 'pipeline_run_stdout.txt')424 stderr_filepath = os.path.join(conf_info.analysis_dir, 'pipeline_run_stderr.txt')425 # Create status object426 conf_info.createStatusObject()427 # Monitor file creation428 wm = WatchManager()429 mask = EventsCodes.IN_DELETE | EventsCodes.IN_CREATE430 event = RunEvent(conf_info)431 notifier = ThreadedNotifier(wm, event)432 notifier.start()433 wdd = wm.add_watch(conf_info.run_path, mask, rec=True)434 # Log pipeline starting435 LOGGER.info('STARTING PIPELINE @ %s' % (time.ctime()))436 # Start the pipeline (and hide!)437 #pipe = subprocess.Popen(['make',438 # '-j8',439 # 'recursive'],440 # stdout=subprocess.PIPE,441 # stderr=subprocess.PIPE)442 fout = open(stdout_filepath, 'w')443 ferr = open(stderr_filepath, 'w')444 pipe = subprocess.Popen(['make',445 '--directory=%s' % (conf_info.run_path),446 '-j8',447 'recursive'],448 stdout=fout,449 stderr=ferr)450 #shell=True)451 # Wait for run to finish452 retcode = pipe.wait()453 # Clean up454 notifier.stop()455 fout.close()456 ferr.close()457 # Process stderr458 ferr = open(stderr_filepath, 'r')459 run_failed_stderr = False460 for line in ferr:461 err_status = pipeline_stderr_handler(line, conf_info)462 if err_status == RUN_FAILED:463 run_failed_stderr = True464 ferr.close()465 # Finished file check!466 print('RUN SUCCESS CHECK:')467 for key, value in event.run_status_dict.items():468 print(' %s: %s' % (key, value))469 dstatus = event.run_status_dict470 # Success or failure check471 status = (retcode == 0) and \472 run_failed_stderr is False and \473 dstatus['firecrest'] is True and \474 dstatus['bustard'] is True and \475 dstatus['gerald'] is True...
deploy.py
Source:deploy.py
...25 """26 Aborts deploy if lock file is found27 """28 29 def run_abort():30 abort("Another deploy in progress")31 echo_subtask("Checking `deploy.lock` file presence")32 with settings(hide('warnings'), warn_only=True):33 if run('test -f %s' % '/'.join([fetch('deploy_to'), 'deploy.lock'])).succeeded:34 if fetch('ask_unlock_if_locked', default_value=False):35 if not confirm('Deploy lockfile exists. Continue?'): 36 run_abort()37 else:38 run_abort()39def lock():40 """41 Locks deploy42 Parallel deploys are not allowed43 """44 ensure('build_to')45 echo_subtask("Creating `deploy.lock` file")46 create_entity(47 '/'.join([fetch('deploy_to'), 'deploy.lock'])48 , entity_type='file', 49 protected=False50 )51def create_build_path():52 """...
cli.py
Source:cli.py
...75 systemd_template = "\n".join(systemd_template.split("\n")[1:-1])76 out.write(systemd_template)77 out.close()78 click.secho(f"Wrote systemd service file to {out.name}", fg="green", bold=True)79 run_abort("systemctl daemon-reload")80 service = os.path.basename(out.name)81 run_abort(f"systemctl start {service}")82 click.secho(f"Started {service}", fg="green", bold=True)83 # run_abort(f"systemctl unmask {service}")84 run_abort(f"systemctl enable {service}")85 click.secho(f"Enabled {service}", fg="green", bold=True)86def run_abort(cmd):87 try:88 subprocess.run(cmd.split(), check=True)89 except subprocess.CalledProcessError as ex:...
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