def _delete_previous_repo_versions(self):
base_name = self.name + '-' + \
self.version + '-' + \
self.deploy_type + '-'
dirs = os.listdir(self.base_deploy_dir)
remove_dirs = []
for dirname in dirs:
if base_name in dirname:
if self.deploy_name not in dirname:
remove_dir = os.path.join(self.base_deploy_dir, dirname)
remove_dirs.append(remove_dir)
for remove_dir in remove_dirs:
removed_dir = util.remove_directory(remove_dir, True)
def _delete_previous_repo_versions(self):
base_name = self.name + '-' + \
self.version + '-' + \
self.deploy_type + '-'
dirs = os.listdir(self.base_deploy_dir)
remove_dirs = []
for dirname in dirs:
if base_name in dirname:
if self.deploy_name not in dirname:
remove_dir = os.path.join(self.base_deploy_dir, dirname)
remove_dirs.append(remove_dir)
for remove_dir in remove_dirs:
removed_dir = util.remove_directory(remove_dir, True)
def deploy_apps(deploy_config, force_remove=False, remove_repos=False):
env = environment.BashEnvironment()
# launch status thread
threads = []
log.info('Starting status thread.')
t = deploy.StatusThread()
t.start()
threads.append(t)
# launch worker threads
try:
num_threads = int(deploy_config.get('global', 'max-deploy-threads'))
except:
log.debug('Missing max-deploy-threads section. Setting to 1.')
num_threads = 1
log.info('Starting %s deploy threads.' % num_threads)
for i in range(num_threads):
t = deploy.WorkerThread()
t.start()
threads.append(t)
# create final deploy directory location if it doesn't exist
deploy_dir = deploy_config.get('global', 'final-deploy-directory')
deploy_dir = os.path.expanduser(deploy_dir)
deploy_dir = os.path.abspath(deploy_dir)
if os.path.exists(deploy_dir):
log.debug('Final deploy directory already exists: %s' % deploy_dir)
else:
log.debug('Creating final deploy directory: %s' % deploy_dir)
os.makedirs(deploy_dir)
# identify data and application sections in the config file
all_sect = deploy_config.sections()
req_sect = ['dependencies', 'global']
data_sect = [x for x in all_sect if 'data-' in x]
app_sect = list(set(all_sect) - (set(req_sect) | set(data_sect)))
log.debug('All config sections: %s' % all_sect)
log.debug('Required config sections: %s' % req_sect)
log.debug('Data config sections: %s' % data_sect)
log.debug('Application config sections: %s' % app_sect)
log.info('Running deploy for data and apps without dependencies.')
# locate the python and r executables that we should use for the deploy
# process (if required)
custom_py_exe = get_executable_path(log, deploy_config, app_sect, 'python',
'python')
custom_r_exe = get_executable_path(log, deploy_config, app_sect, 'r', 'R')
# create application objects for all apps to deploy
all_apps_to_deploy = []
remaining_apps_to_deploy = []
for app_name in app_sect:
a = application.Application(app_name, env, deploy_config,
custom_py_exe, custom_r_exe, remove_repos)
remaining_apps_to_deploy.append(a)
all_apps_to_deploy.append(a)
# create and schedule all data objects
for data_name in data_sect:
d = data.Data(data_name, env, deploy_config)
deploy.WORK_Q.put(d)
# immediately schedule all applications that do not contain dependencies
for app in list(remaining_apps_to_deploy):
if not app.deps:
log.debug('Putting %s in the queue to deploy.' % app.name)
deploy.WORK_Q.put(app)
remaining_apps_to_deploy.remove(app)
remaining_names = [app.name for app in remaining_apps_to_deploy]
log.info('Launched initial deploy, remaining apps: %s' % remaining_names)
# schedule applications with dependencies once all of an applications
# dependencies have completed successfully
log.info('Deploying remaining apps.')
while remaining_apps_to_deploy:
for app in list(remaining_apps_to_deploy):
all_deps_complete = True
all_deps_successful = True
for dep in app.deps:
if not is_app_complete(dep, all_apps_to_deploy):
log.debug('%s dependencies remaining:%s' %
(app.name, app.deps))
all_deps_complete = False
if not is_app_successful(dep, all_apps_to_deploy):
log.debug('%s dependencies not yet successful:%s' %
(app.name, app.deps))
all_deps_successful = False
if dep not in app_sect:
log.error('Application will never complete, dependency' + \
'does not exist: %s' % dep)
app.success = False
app.complete = True
deploy.FAILED_Q.put(app)
remaining_apps_to_deploy.remove(app)
if not app.complete:
if all_deps_complete and all_deps_successful:
log.debug('Putting %s in the queue to deploy.' % app.name)
deploy.WORK_Q.put(app)
remaining_apps_to_deploy.remove(app)
if all_deps_complete and (not all_deps_successful):
app.success = False
app.complete = True
log.error('Dependencies failed for %s.' % app.name)
deploy.FAILED_Q.put(app)
remaining_apps_to_deploy.remove(app)
remaining_names = [app.name for app in remaining_apps_to_deploy]
log.debug('Applications waiting on dependencies: %s' % remaining_names)
log.debug('Control thread sleeping: %s seconds' % SLEEP_SECS)
time.sleep(SLEEP_SECS)
# wait for everything to complete
deploy.WORK_Q.join()
deploy.DONE = True
for t in threads:
t.join()
summary = '\n\n'
summary += 'DEPLOYMENT SUMMARY\n\n'
# print out successful deployments
first = True
summary += 'Packages deployed successfully:\n'
while not deploy.COMPLETE_Q.empty():
item = deploy.COMPLETE_Q.get(False)
if item:
if not first:
summary += ', %s' % item.name
else:
summary += '%s' % item.name
first = False
summary += '\n'
# print out skipped deployments
first = True
summary += '\nPackages skipped (assumed successful):\n'
while not deploy.SKIPPED_Q.empty():
item = deploy.SKIPPED_Q.get(False)
if item:
if not first:
summary += ', %s' % item.name
else:
summary += '%s' % item.name
first = False
summary += '\n'
# print out failed applications at the end and perform cleanup
failed_items = False
first = True
failed_list = []
summary += '\nPackages failed to deploy:\n'
while not deploy.FAILED_Q.empty():
item = deploy.FAILED_Q.get(False)
if item:
failed_dir = util.remove_directory(item.deploy_dir, force_remove)
if failed_dir:
failed_list.append(failed_dir)
if not first:
summary += ', %s' % item.name
else:
summary += '%s' % item.name
first = False
failed_items = True
summary += '\n\n'
if failed_list:
summary += 'Directories of failed applications must be removed ' + \
'manually or --force-remove-failed-dirs must be specified:'
summary += '\n'
for failed_dir in failed_list:
summary += failed_dir
summary += '\n'
summary += '\n'
# build and write out activate.sh
log.debug('Writing new environment variables to activate.sh')
log.debug('Print environment: %s' % env.get_print_env())
try:
append_bashrc = deploy_config.get('global',
'append-environment-to-bashrc')
if append_bashrc == 'yes':
append_bashrc = True
else:
append_bashrc = False
except:
log.debug(
'Did not find append-environment-to-bashrc option, skipping.')
append_bashrc = False
try:
append_bashprofile = deploy_config.get(
'global', 'append-environment-to-bashprofile')
if append_bashprofile == 'yes':
append_bashprofile = True
else:
append_bashprofile = False
except:
log.debug(
'Did not find append-environment-to-bashprofile option, skipping.')
append_bashprofile = False
generate_activate_file(env.get_print_env(), deploy_dir, append_bashrc,
append_bashprofile)
# run any custom finalization code, in QIIME's case, this is where
# the QIIME config file is generated and written
rc = custom.custom_finalize(custom_py_exe, deploy_dir, all_apps_to_deploy,
log)
sys.stdout.write(summary)
if failed_items:
rc = 1
return rc
def deploy_apps(deploy_config, force_remove=False, remove_repos=False):
env = environment.BashEnvironment()
# launch status thread
threads = []
log.info('Starting status thread.')
t = deploy.StatusThread()
t.start()
threads.append(t)
# launch worker threads
try:
num_threads = int(deploy_config.get('global', 'max-deploy-threads'))
except:
log.debug('Missing max-deploy-threads section. Setting to 1.')
num_threads = 1
log.info('Starting %s deploy threads.' % num_threads)
for i in range(num_threads):
t = deploy.WorkerThread()
t.start()
threads.append(t)
# create final deploy directory location if it doesn't exist
deploy_dir = deploy_config.get('global', 'final-deploy-directory')
deploy_dir = os.path.expanduser(deploy_dir)
deploy_dir = os.path.abspath(deploy_dir)
if os.path.exists(deploy_dir):
log.debug('Final deploy directory already exists: %s' % deploy_dir)
else:
log.debug('Creating final deploy directory: %s' % deploy_dir)
os.makedirs(deploy_dir)
# identify data and application sections in the config file
all_sect = deploy_config.sections()
req_sect = ['dependencies', 'global']
data_sect = [x for x in all_sect if 'data-' in x]
app_sect = list(set(all_sect) - (set(req_sect) | set(data_sect)))
log.debug('All config sections: %s' % all_sect)
log.debug('Required config sections: %s' % req_sect)
log.debug('Data config sections: %s' % data_sect)
log.debug('Application config sections: %s' % app_sect)
log.info('Running deploy for data and apps without dependencies.')
# locate the python exe that we should use for the deploy process (if
# required)
log.info('Searching for python...')
custom_py_exe = None
try:
custom_py_exe = deploy_config.get('global', 'python-exe')
if custom_py_exe == 'None':
custom_py_exe = None
else:
custom_py_exe = os.path.expanduser(custom_py_exe)
log.info('python-exe specified, using: %s' % custom_py_exe)
except:
log.info('python-exe is not specified.')
custom_py_exe = None
if not custom_py_exe:
if 'python' in app_sect:
log.info('Looks like python is being deployed, using that version')
base_dir = deploy_config.get('global', 'final-deploy-directory')
python_version = deploy_config.get('python', 'version')
try:
release_location = deploy_config.get('python', 'release-location')
deploy_type = 'release'
except:
log.debug('%s has no release-location' % 'python')
deploy_type = 'repository'
python_dir = 'python-' + python_version + '-' + deploy_type
custom_py_exe = os.path.join(base_dir, python_dir)
custom_py_exe = os.path.join(custom_py_exe, 'bin/python')
log.info('Setting python: %s' % custom_py_exe)
else:
log.info('Could not find a python, setting \'python\'')
custom_py_exe = 'python'
# create application objects for all apps to deploy
all_apps_to_deploy = []
remaining_apps_to_deploy = []
for app_name in app_sect:
a = application.Application(app_name,
env,
deploy_config,
custom_py_exe,
remove_repos)
remaining_apps_to_deploy.append(a)
all_apps_to_deploy.append(a)
# create and schedule all data objects
for data_name in data_sect:
d = data.Data(data_name, env, deploy_config)
deploy.WORK_Q.put(d)
# immediately schedule all applications that do not contain dependencies
for app in list(remaining_apps_to_deploy):
if not app.deps:
log.debug('Putting %s in the queue to deploy.' % app.name)
deploy.WORK_Q.put(app)
remaining_apps_to_deploy.remove(app)
remaining_names = [app.name for app in remaining_apps_to_deploy]
log.info('Launched initial deploy, remaining apps: %s' % remaining_names)
# schedule applications with dependencies once all of an applications
# dependencies have completed successfully
log.info('Deploying remaining apps.')
while remaining_apps_to_deploy:
for app in list(remaining_apps_to_deploy):
all_deps_complete = True
all_deps_successful = True
for dep in app.deps:
if not is_app_complete(dep, all_apps_to_deploy):
log.debug('%s dependencies remaining:%s' % (app.name, app.deps))
all_deps_complete = False
if not is_app_successful(dep, all_apps_to_deploy):
log.debug('%s dependencies not yet successful:%s' % (app.name, app.deps))
all_deps_successful = False
if dep not in app_sect:
log.error('Application will never complete, dependency' + \
'does not exist: %s' % dep)
app.success = False
app.complete = True
deploy.FAILED_Q.put(app)
remaining_apps_to_deploy.remove(app)
if not app.complete:
if all_deps_complete and all_deps_successful:
log.debug('Putting %s in the queue to deploy.' % app.name)
deploy.WORK_Q.put(app)
remaining_apps_to_deploy.remove(app)
if all_deps_complete and (not all_deps_successful):
app.success = False
app.complete = True
log.error('Dependencies failed for %s.' % app.name)
deploy.FAILED_Q.put(app)
remaining_apps_to_deploy.remove(app)
remaining_names = [app.name for app in remaining_apps_to_deploy]
log.debug('Applications waiting on dependencies: %s' % remaining_names)
log.debug('Control thread sleeping: %s seconds' % SLEEP_SECS)
time.sleep(SLEEP_SECS)
# wait for everything to complete
deploy.WORK_Q.join()
deploy.DONE = True
for t in threads:
t.join()
summary = '\n\n'
summary += 'DEPLOYMENT SUMMARY\n\n'
# print out successful deployments
first = True
summary += 'Packages deployed successfully:\n'
while not deploy.COMPLETE_Q.empty():
item = deploy.COMPLETE_Q.get(False)
if item:
if not first:
summary += ', %s' % item.name
else:
summary += '%s' % item.name
first = False
summary += '\n'
# print out skipped deployments
first = True
summary += '\nPackages skipped (assumed successful):\n'
while not deploy.SKIPPED_Q.empty():
item = deploy.SKIPPED_Q.get(False)
if item:
if not first:
summary += ', %s' % item.name
else:
summary += '%s' % item.name
first = False
summary += '\n'
# print out failed applications at the end and perform cleanup
failed_items = False
first = True
failed_list = []
summary += '\nPackages failed to deploy:\n'
while not deploy.FAILED_Q.empty():
item = deploy.FAILED_Q.get(False)
if item:
failed_dir = util.remove_directory(item.deploy_dir, force_remove)
if failed_dir:
failed_list.append(failed_dir)
if not first:
summary += ', %s' % item.name
else:
summary += '%s' % item.name
first = False
failed_items = True
summary += '\n\n'
if failed_list:
summary += 'Directories of failed applications must be removed ' + \
'manually or --force-remove-failed-dirs must be specified:'
summary += '\n'
for failed_dir in failed_list:
summary += failed_dir
summary += '\n'
summary += '\n'
# build and write out activate.sh
log.debug('Writing new environment variables to activate.sh')
log.debug('Print environment: %s' % env.get_print_env())
try:
append_bashrc = deploy_config.get('global', 'append-environment-to-bashrc')
if append_bashrc == 'yes':
append_bashrc = True
else:
append_bashrc = False
except:
log.debug('Did not find append-environment-to-bashrc option, skipping.')
append_bashrc = False
try:
append_bashprofile = deploy_config.get('global', 'append-environment-to-bashprofile')
if append_bashprofile == 'yes':
append_bashprofile = True
else:
append_bashprofile = False
except:
log.debug('Did not find append-environment-to-bashprofile option, skipping.')
append_bashprofile = False
generate_activate_file(env.get_print_env(),
deploy_dir,
append_bashrc,
append_bashprofile)
# run any custom finalization code, in QIIME's case, this is where
# the QIIME config file is generated and written
rc = custom.custom_finalize(custom_py_exe, deploy_dir, all_apps_to_deploy, log)
sys.stdout.write(summary)
if failed_items:
rc = 1
return rc