def main(argv=sys.argv):
if len(argv) != 4:
print "\n Usage: %s [option] out_dir"%argv[0]
print "\n [option]"
print " -f pdb_file"
print " -l file. pdb file in each line"
print " out_dir: where to save extracted protein(s), ligand(s), and water(s)"
print "\n a file named 'names_pro_lig.log' will be generated"
print ""
sys.exit(1)
outf_log = open("names_pro_lig.log","a")
if argv[1] == "-f":
tools.process(argv[2], argv[3], outf_log)
elif argv[1] == "-l":
inf = open(argv[2],"r")
for line in inf:
if line.startswith('#'):
continue
tools.process(line.strip(), argv[3], outf_log)
inf.close()
else:
print "Error: invalid option ",argv[1]
outf_log.close()
def checkCachedClones(self, stable=True, integration=True):
"""Clone the official repository in a local cache"""
cacheStable = self.getCachedRemote(False)
cacheIntegration = self.getCachedRemote(True)
if not os.path.isdir(cacheStable) and stable:
logging.info('Cloning stable repository into cache...')
# For faster clone, we will copy the integration clone if it exists.
if os.path.isdir(cacheIntegration):
shutil.copytree(cacheIntegration, cacheStable)
repo = git.Git(cacheStable, C.get('git'))
repo.setRemote('origin', C.get('remotes.stable'))
# The repository is not updated at this stage, it has to be done manually.
else:
logging.info('This is going to take a while...')
process('%s clone --mirror %s %s' % (C.get('git'), C.get('remotes.stable'), cacheStable))
if not os.path.isdir(cacheIntegration) and integration:
logging.info('Cloning integration repository into cache...')
# For faster clone, we will copy the integration clone if it exists.
if os.path.isdir(cacheStable):
shutil.copytree(cacheStable, cacheIntegration)
repo = git.Git(cacheIntegration, C.get('git'))
repo.setRemote('origin', C.get('remotes.integration'))
# The repository is not updated at this stage, it has to be done manually.
else:
logging.info('Have a break, this operation is slow...')
process('%s clone --mirror %s %s' % (C.get('git'), C.get('remotes.integration'), cacheIntegration))
def run(cls, script, path, arguments=None, cmdkwargs={}):
"""Executes a script at in a certain directory"""
# Converts arguments to a string.
arguments = '' if arguments == None else arguments
if type(arguments) == list:
arguments = ' '.join(arguments)
arguments = ' ' + arguments
cli = cls.find(script)
if cli.endswith('.php'):
dest = os.path.join(path, 'mdkscriptrun.php')
logging.debug('Copying %s to %s' % (cli, dest))
shutil.copyfile(cli, dest)
cmd = '%s %s %s' % (C.get('php'), dest, arguments)
result = process(cmd, cwd=path, **cmdkwargs)
os.remove(dest)
elif cli.endswith('.sh'):
dest = os.path.join(path, 'mdkscriptrun.sh')
logging.debug('Copying %s to %s' % (cli, dest))
shutil.copyfile(cli, dest)
os.chmod(dest, stat.S_IRUSR | stat.S_IXUSR)
cmd = '%s %s' % (dest, arguments)
result = process(cmd, cwd=path, **cmdkwargs)
os.remove(dest)
else:
raise UnsupportedScript('Script not supported')
return result[0]
def checkCachedClones(self, stable = True, integration = True):
"""Clone the official repository in a local cache"""
cacheStable = os.path.join(self.cache, 'moodle.git')
cacheIntegration = os.path.join(self.cache, 'integration.git')
if not os.path.isdir(cacheStable) and stable:
debug('Cloning stable repository into cache...')
result = process('%s clone %s %s' % (C.get('git'), C.get('remotes.stable'), cacheStable))
result = process('%s fetch -a' % C.get('git'), cacheStable)
if not os.path.isdir(cacheIntegration) and integration:
debug('Cloning integration repository into cache...')
result = process('%s clone %s %s' % (C.get('git'), C.get('remotes.integration'), cacheIntegration))
result = process('%s fetch -a' % C.get('git'), cacheIntegration)
def checkCachedClones(self, stable=True, integration=True):
"""Clone the official repository in a local cache"""
cacheStable = self.getCachedRemote(False)
cacheIntegration = self.getCachedRemote(True)
if not os.path.isdir(cacheStable) and stable:
logging.info('Cloning stable repository into cache...')
logging.info('That\'s going to take a while...')
process('%s clone --mirror %s %s' % (C.get('git'), C.get('remotes.stable'), cacheStable))
if not os.path.isdir(cacheIntegration) and integration:
logging.info('Cloning integration repository into cache...')
logging.info('Have a break, this operation is slow...')
process('%s clone --mirror %s %s' % (C.get('git'), C.get('remotes.integration'), cacheIntegration))
def resolveIssueNumber(view, folders):
"""Try to find an issue number"""
issue = None
# Read from the content of the file.
if view:
for region in view.sel():
if region.empty():
region = view.word(region)
word = view.substr(region)
issue = extractIssueNumberFromText(word)
if issue != None:
break
# Read from the folders.
if not issue:
for folder in folders:
result = process('git symbolic-ref -q HEAD', cwd=folder)
if result[0] == 0 and result[1] != '':
issue = extractIssueNumberFromText(result[1])
if issue != None:
break
return issue
def execute(self):
executable = C.get('lessc')
if not executable:
raise Exception('Could not find executable path')
cmd = [executable]
sourcePath = os.path.relpath(self._source, self._cwd)
sourceDir = os.path.dirname(sourcePath)
if self._debug:
cmd.append('--source-map-rootpath=' + sourceDir)
cmd.append('--source-map-map-inline')
self.setCompress(False)
if self._compress:
cmd.append('--compress')
"""Append the source and destination"""
cmd.append(sourcePath)
cmd.append(os.path.relpath(self._dest, self._cwd))
(code, out, err) = process(cmd, self._cwd)
if code != 0 or len(out) != 0:
raise CssCompileFailed('Error during compile')
def initBehat(self, switchcompletely=False):
"""Initialise the Behat environment"""
if self.branch_compare(25, '<'):
raise Exception('Behat is only available from Moodle 2.5')
# Force switch completely for PHP < 5.4
(none, phpVersion, none) = process('%s -r "echo version_compare(phpversion(), \'5.4\');"' % (C.get('php')))
if int(phpVersion) <= 0:
switchcompletely = True
# Set Behat data root
behat_dataroot = self.get('dataroot') + '_behat'
self.updateConfig('behat_dataroot', behat_dataroot)
# Set Behat DB prefix
behat_prefix = 'zbehat_'
self.updateConfig('behat_prefix', behat_prefix)
# Switch completely?
if switchcompletely:
self.updateConfig('behat_switchcompletely', switchcompletely)
self.updateConfig('behat_wwwroot', self.get('wwwroot'))
else:
self.removeConfig('behat_switchcompletely')
self.removeConfig('behat_wwwroot')
# Force a cache purge
self.purge()
# Run the init script.
self.cli('admin/tool/behat/cli/init.php', stdout=None, stderr=None)
# Force a cache purge
self.purge()
def initBehat(self, switchcompletely=False):
"""Initialise the Behat environment"""
if self.branch_compare(25, "<"):
raise Exception("Behat is only available from Moodle 2.5")
# Force switch completely for PHP < 5.4
(none, phpVersion, none) = process("%s -r \"echo version_compare(phpversion(), '5.4');\"" % (C.get("php")))
if int(phpVersion) <= 0:
switchcompletely = True
# Set Behat data root
behat_dataroot = self.get("dataroot") + "_behat"
self.updateConfig("behat_dataroot", behat_dataroot)
# Set Behat DB prefix
behat_prefix = "zbehat_"
self.updateConfig("behat_prefix", behat_prefix)
# Switch completely?
if switchcompletely:
self.updateConfig("behat_switchcompletely", switchcompletely)
self.updateConfig("behat_wwwroot", self.get("wwwroot"))
else:
self.removeConfig("behat_switchcompletely")
self.removeConfig("behat_wwwroot")
# Force a cache purge
self.purge()
# Run the init script.
self.cli("admin/tool/behat/cli/init.php", stdout=None, stderr=None)
# Force a cache purge
self.purge()
def cli(self, cli, args='', **kwargs):
"""Executes a command line tool script"""
cli = os.path.join(self.get('path'), cli.lstrip('/'))
if not os.path.isfile(cli):
raise Exception('Could not find script to call')
if type(args) == 'list':
args = ' '.join(args)
cmd = '%s %s %s' % (C.get('php'), cli, args)
return process(cmd, cwd=self.get('path'), **kwargs)
def cli(self, cli, args='', **kwargs):
"""Executes a command line tool script"""
cli = os.path.join(self.get('path'), cli.lstrip('/'))
if not os.path.isfile(cli):
raise Exception('Could not find script to call')
if type(args) == 'list':
args = ' '.join(args)
cmd = '%s %s %s' % (C.get('php'), cli, args)
return process(cmd, cwd=self.get('path'), **kwargs)
def cli(self, cli, args="", **kwargs):
"""Executes a command line tool script"""
cli = os.path.join(self.get("path"), cli.lstrip("/"))
if not os.path.isfile(cli):
raise Exception("Could not find script to call")
if type(args) == "list":
args = " ".join(args)
cmd = "%s %s %s" % (C.get("php"), cli, args)
return process(cmd, cwd=self.get("path"), **kwargs)
def run(cls, script, path, cmdkwargs={}):
"""Executes a script at in a certain directory"""
cli = cls.find(script)
if cli.endswith('.php'):
dest = os.path.join(path, 'mdkscriptrun.php')
shutil.copyfile(cli, dest)
cmd = '%s %s' % (C.get('php'), dest)
result = process(cmd, cwd=path, **cmdkwargs)
os.remove(dest)
else:
raise UnsupportedScript('Script not supported')
return result[0]
def main(argv=sys.argv):
if len(argv) != 4:
print "\n Usage: %s [option] out_dir" % argv[0]
print "\n [option]"
print " -f pdb_file"
print " -l file. pdb file in each line"
print " out_dir: where to save extracted protein(s), ligand(s), and water(s)"
print "\n a file named 'names_pro_lig.log' will be generated"
print ""
sys.exit(1)
outf_log = open("names_pro_lig.log", "a")
if argv[1] == "-f":
tools.process(argv[2], argv[3], outf_log)
elif argv[1] == "-l":
inf = open(argv[2], "r")
for line in inf:
if line.startswith('#'):
continue
tools.process(line.strip(), argv[3], outf_log)
inf.close()
else:
print "Error: invalid option ", argv[1]
outf_log.close()
def initBehat(self, switchcompletely=False):
"""Initialise the Behat environment"""
if self.branch_compare(25, '<'):
raise Exception('Behat is only available from Moodle 2.5')
# Force switch completely for PHP < 5.4
(none, phpVersion, none) = process('%s -r "echo version_compare(phpversion(), \'5.4\');"' % (C.get('php')))
if int(phpVersion) <= 0:
switchcompletely = True
# Set Behat data root
behat_dataroot = self.get('dataroot') + '_behat'
self.updateConfig('behat_dataroot', behat_dataroot)
# Set Behat DB prefix
behat_prefix = 'zbehat_'
self.updateConfig('behat_prefix', behat_prefix)
# Switch completely?
if self.branch_compare(27, '<'):
if switchcompletely:
self.updateConfig('behat_switchcompletely', switchcompletely)
self.updateConfig('behat_wwwroot', self.get('wwwroot'))
else:
self.removeConfig('behat_switchcompletely')
self.removeConfig('behat_wwwroot')
else:
# Defining wwwroot.
wwwroot = '%s://%s/' % (C.get('scheme'), C.get('behat.host'))
if C.get('path') != '' and C.get('path') != None:
wwwroot = wwwroot + C.get('path') + '/'
wwwroot = wwwroot + self.identifier
self.updateConfig('behat_wwwroot', wwwroot)
# Force a cache purge
self.purge()
# Run the init script.
result = self.cli('admin/tool/behat/cli/init.php', stdout=None, stderr=None)
if result[0] != 0:
raise Exception('Error while initialising Behat. Please try manually.')
# Force a cache purge
self.purge()
def execute(self):
executable = C.get('recess')
if not executable:
raise Exception('Could not find executable path')
cmd = [executable, self._source, '--compile']
if self._compress:
cmd.append('--compress')
(code, out, err) = process(cmd, self._cwd)
if code != 0 or len(out) == 0:
raise CssCompileFailed('Error during compile')
# Saving to destination
with open(self._dest, 'w') as f:
f.write(out)
def create(self, name=None, version='master', integration=False, useCacheAsRemote=False):
"""Creates a new instance of Moodle.
The parameter useCacheAsRemote has been deprecated.
"""
if name == None:
name = self.generateInstanceName(version, integration=integration)
installDir = os.path.join(self.path, name)
wwwDir = os.path.join(installDir, self.wwwDir)
dataDir = os.path.join(installDir, self.dataDir)
linkDir = os.path.join(self.www, name)
if self.isMoodle(name):
raise CreateException('The Moodle instance %s already exists' % name)
elif os.path.isdir(installDir):
raise CreateException('Installation path exists: %s' % installDir)
self.checkCachedClones(not integration, integration)
self.updateCachedClones(stable=not integration, integration=integration, verbose=False)
mkdir(installDir, 0755)
mkdir(wwwDir, 0755)
mkdir(dataDir, 0777)
repository = self.getCachedRemote(integration)
# Clone the instances
logging.info('Cloning repository...')
process('%s clone %s %s' % (C.get('git'), repository, wwwDir))
# Symbolic link
if os.path.islink(linkDir):
os.remove(linkDir)
if os.path.isfile(linkDir) or os.path.isdir(linkDir): # No elif!
logging.warning('Could not create symbolic link. Please manually create: ln -s %s %s' % (wwwDir, linkDir))
else:
os.symlink(wwwDir, linkDir)
# Symlink to dataDir in wwwDir
if type(C.get('symlinkToData')) == str:
linkDataDir = os.path.join(wwwDir, C.get('symlinkToData'))
if not os.path.isfile(linkDataDir) and not os.path.isdir(linkDataDir) and not os.path.islink(linkDataDir):
os.symlink(dataDir, linkDataDir)
logging.info('Checking out branch...')
repo = git.Git(wwwDir, C.get('git'))
# Removing the default remote origin coming from the clone
repo.delRemote('origin')
# Setting up the correct remote names
repo.setRemote(C.get('myRemote'), C.get('remotes.mine'))
repo.setRemote(C.get('upstreamRemote'), repository)
# Creating, fetch, pulling branches
repo.fetch(C.get('upstreamRemote'))
branch = stableBranch(version)
track = '%s/%s' % (C.get('upstreamRemote'), branch)
if not repo.hasBranch(branch) and not repo.createBranch(branch, track):
logging.error('Could not create branch %s tracking %s' % (branch, track))
else:
repo.checkout(branch)
repo.pull(remote=C.get('upstreamRemote'))
# Fixing up remote URLs if need be, this is done after pulling the cache one because we
# do not want to contact the real origin server from here, it is slow and pointless.
if not C.get('useCacheAsUpstreamRemote'):
realupstream = C.get('remotes.integration') if integration else C.get('remotes.stable')
if realupstream:
repo.setRemote(C.get('upstreamRemote'), realupstream)
M = self.get(name)
return M
def create(self, name = None, version = 'master', integration = False, useCacheAsRemote = False):
"""Creates a new instance of Moodle"""
if name == None:
if integration:
name = C.get('wording.prefixIntegration') + prefixVersion
else:
name = C.get('wording.prefixStable') + prefixVersion
installDir = os.path.join(self.path, name)
wwwDir = os.path.join(installDir, self.wwwDir)
dataDir = os.path.join(installDir, self.dataDir)
linkDir = os.path.join(self.www, name)
if self.isMoodle(name):
raise Exception('The Moodle instance %s already exists' % name)
elif os.path.isdir(installDir):
raise Exception('Installation path exists: %s' % installDir)
self.checkCachedClones(not integration, integration)
os.mkdir(installDir, 0755)
os.mkdir(wwwDir, 0755)
os.mkdir(dataDir, 0777)
if integration:
repository = os.path.join(self.cache, 'integration.git')
upstreamRepository = C.get('remotes.integration')
else:
repository = os.path.join(self.cache, 'moodle.git')
upstreamRepository = C.get('remotes.stable')
# Clone the instances
debug('Cloning repository...')
if useCacheAsRemote:
result = process('%s clone %s %s' % (C.get('git'), repository, wwwDir))
upstreamRepository = repository
else:
copy_tree(repository, wwwDir)
# Symbolic link
if os.path.islink(linkDir):
os.remove(linkDir)
if os.path.isfile(linkDir) or os.path.isdir(linkDir): # No elif!
debug('Could not create symbolic link')
debug('Please manually create: ln -s %s %s' (wwwDir, linkDir))
else:
os.symlink(wwwDir, linkDir)
# Symlink to dataDir in wwwDir
if type(C.get('symlinkToData')) == str:
linkDataDir = os.path.join(wwwDir, C.get('symlinkToData'))
if not os.path.isfile(linkDataDir) and not os.path.isdir(linkDataDir) and not os.path.islink(linkDataDir):
os.symlink(dataDir, linkDataDir)
debug('Checking out branch...')
repo = git.Git(wwwDir, C.get('git'))
# Setting up the correct remote names
repo.setRemote(C.get('myRemote'), C.get('remotes.mine'))
repo.setRemote(C.get('upstreamRemote'), upstreamRepository)
# Creating, fetch, pulling branches
result = repo.fetch(C.get('upstreamRemote'))
if version == 'master':
repo.checkout('master')
else:
track = '%s/MOODLE_%s_STABLE' % (C.get('upstreamRemote'), version)
branch = 'MOODLE_%s_STABLE' % version
if not repo.hasBranch(branch) and not repo.createBranch(branch, track):
debug('Could not create branch %s tracking %s' % (branch, track))
else:
repo.checkout(branch)
repo.pull(remote = C.get('upstreamRemote'))
M = self.get(name)
return M
def create(self, name=None, version='master', integration=False, useCacheAsRemote=False):
"""Creates a new instance of Moodle.
The parameter useCacheAsRemote has been deprecated.
"""
if name == None:
name = self.generateInstanceName(version, integration=integration)
installDir = os.path.join(self.path, name)
wwwDir = os.path.join(installDir, self.wwwDir)
dataDir = os.path.join(installDir, self.dataDir)
linkDir = os.path.join(self.www, name)
if self.isMoodle(name):
raise CreateException('The Moodle instance %s already exists' % name)
elif os.path.isdir(installDir):
raise CreateException('Installation path exists: %s' % installDir)
self.checkCachedClones(not integration, integration)
self.updateCachedClones(stable=not integration, integration=integration, verbose=False)
os.mkdir(installDir, 0755)
os.mkdir(wwwDir, 0755)
os.mkdir(dataDir, 0777)
if integration:
repository = os.path.join(self.cache, 'integration.git')
else:
repository = os.path.join(self.cache, 'moodle.git')
# Clone the instances
logging.info('Cloning repository...')
process('%s clone %s %s' % (C.get('git'), repository, wwwDir))
# Symbolic link
if os.path.islink(linkDir):
os.remove(linkDir)
if os.path.isfile(linkDir) or os.path.isdir(linkDir): # No elif!
logging.warning('Could not create symbolic link. Please manually create: ln -s %s %s' (wwwDir, linkDir))
else:
os.symlink(wwwDir, linkDir)
# Symlink to dataDir in wwwDir
if type(C.get('symlinkToData')) == str:
linkDataDir = os.path.join(wwwDir, C.get('symlinkToData'))
if not os.path.isfile(linkDataDir) and not os.path.isdir(linkDataDir) and not os.path.islink(linkDataDir):
os.symlink(dataDir, linkDataDir)
logging.info('Checking out branch...')
repo = git.Git(wwwDir, C.get('git'))
# Setting up the correct remote names
repo.setRemote(C.get('myRemote'), C.get('remotes.mine'))
repo.setRemote(C.get('upstreamRemote'), repository)
# Creating, fetch, pulling branches
repo.fetch(C.get('upstreamRemote'))
branch = stableBranch(version)
track = '%s/%s' % (C.get('upstreamRemote'), branch)
if not repo.hasBranch(branch) and not repo.createBranch(branch, track):
logging.error('Could not create branch %s tracking %s' % (branch, track))
else:
repo.checkout(branch)
repo.pull(remote=C.get('upstreamRemote'))
M = self.get(name)
return M
def initBehat(self, switchcompletely=False):
"""Initialise the Behat environment"""
if self.branch_compare(25, '<'):
raise Exception('Behat is only available from Moodle 2.5')
# Force switch completely for PHP < 5.4
(none, phpVersion, none) = process(
'%s -r "echo version_compare(phpversion(), \'5.4\');"' %
(C.get('php')))
if int(phpVersion) <= 0:
switchcompletely = True
# Set Behat data root
behat_dataroot = self.get('dataroot') + '_behat'
self.updateConfig('behat_dataroot', behat_dataroot)
# Set Behat DB prefix
behat_prefix = 'zbehat_'
self.updateConfig('behat_prefix', behat_prefix)
# Switch completely?
if switchcompletely:
self.updateConfig('behat_switchcompletely', switchcompletely)
self.updateConfig('behat_wwwroot', self.get('wwwroot'))
else:
self.removeConfig('behat_switchcompletely')
self.removeConfig('behat_wwwroot')
# Drop the tables
def drop():
result = (None, None, None)
try:
debug('Dropping database')
result = self.cli('/admin/tool/behat/cli/util.php',
args='--drop',
stdout=None,
stderr=None)
except:
pass
return result
# Enabling Behat (or updating the definitions)
def enable():
result = (None, None, None)
try:
debug('Enabling Behat')
result = self.cli('/admin/tool/behat/cli/util.php',
args='--enable')
except:
pass
return result
# Install the tables
def install():
result = (None, None, None)
try:
debug('Installing Behat tables')
result = self.cli('/admin/tool/behat/cli/util.php',
args='--install',
stdout=None,
stderr=None)
except:
pass
return result
# Force a cache purge
self.purge()
# Not really proud of this logic, but it works for now. Ideally there shouldn't be any duplicated call to enable().
result = enable()
if result[0] == 251:
raise Exception(
'Error: Behat requires PHP 5.4 or the flag --switch-completely to be set'
)
elif result[0] == 254:
# Installation required
installResult = install()
if installResult[0] != 0:
raise Exception(
'Unknown error while installing Behat. \nError code: %s\nStdout: %s\nStderr: %s'
% (result))
result = enable()
elif result[0] > 0:
# Need to drop the tables
drop()
installResult = install()
if installResult[0] != 0:
raise Exception(
'Unknown error while installing Behat. \nError code: %s\nStdout: %s\nStderr: %s'
% (result))
result = enable()
# Could not enable Behat
if result[0] != 0:
raise Exception(
'Unknown error while enabling Behat. \nError code: %s\nStdout: %s\nStderr: %s'
% (result))
target_dqn = dqn.DQN(session, height, width, num_actions, "target", None)
session.run(tf.global_variables_initializer())
target_dqn.tranfer_variables_from(main_dqn)
steps_epoch = []
reward_epoch = []
steps_to_train = training_hz
steps_to_transfer = transfer_hz
time_last_save = time.time()
for epoch in range(num_epoch):
print "\nEpoch: ", epoch
state, _, crashed = agent.start_game()
state = process(state, height, width)
step = 0
total_reward = 0
while step < len_epoch and not crashed:
# keep track how many pretraining steps we still have to execute
pretraining_steps = max(pretraining_steps - 1, 0)
explore = rnd.rand() <= explore_prob or pretraining_steps > 0
action = rnd.randint(num_actions) if explore else main_dqn.get_action(
state)
state_next, reward, crashed = agent.do_action(action)
print "action: {}\t crashed: {}\t random action: {} (prob: {})" \
.format(game_agent.GameAgent.actions[action], crashed, explore, round(explore_prob,2))
state_next = process(state_next, height, width)
vertexBunch.append(tools.Vertex(13, 2))
vertexBunch.append(tools.Vertex(14, 5))
vertexBunch.append(tools.Vertex(15, 9))
linkBunch.append(tools.Link(1, 3, 2))
linkBunch.append(tools.Link(1, 4, 2))
linkBunch.append(tools.Link(2, 4, 1))
linkBunch.append(tools.Link(2, 6, 2))
linkBunch.append(tools.Link(3, 5, 4))
linkBunch.append(tools.Link(3, 7, 3))
linkBunch.append(tools.Link(3, 9, 3))
linkBunch.append(tools.Link(4, 6, 4))
linkBunch.append(tools.Link(5, 12, 4))
linkBunch.append(tools.Link(5, 14, 4))
linkBunch.append(tools.Link(6, 5, 1))
linkBunch.append(tools.Link(6, 8, 1))
linkBunch.append(tools.Link(6, 11, 2))
linkBunch.append(tools.Link(6, 15, 2))
linkBunch.append(tools.Link(8, 10, 3))
linkBunch.append(tools.Link(8, 13, 4))
linkBunch.append(tools.Link(9, 11, 2))
linkBunch.append(tools.Link(9, 12, 2))
linkBunch.append(tools.Link(10, 12, 2))
linkBunch.append(tools.Link(11, 13, 3))
linkBunch.append(tools.Link(12, 13, 3))
linkBunch.append(tools.Link(14, 15, 3))
familyBunch = tools.createFamilies(vertexBunch, linkBunch)
tasks, transmissions, coreAmount, totalTime = tools.process(familyBunch)
tools.draw(tasks, transmissions, coreAmount, totalTime)
def initBehat(self, switchcompletely=False):
"""Initialise the Behat environment"""
if self.branch_compare(25, '<'):
raise Exception('Behat is only available from Moodle 2.5')
# Force switch completely for PHP < 5.4
(none, phpVersion, none) = process('%s -r "echo version_compare(phpversion(), \'5.4\');"' % (C.get('php')))
if int(phpVersion) <= 0:
switchcompletely = True
# Set Behat data root
behat_dataroot = self.get('dataroot') + '_behat'
self.updateConfig('behat_dataroot', behat_dataroot)
# Set Behat DB prefix
behat_prefix = 'zbehat_'
self.updateConfig('behat_prefix', behat_prefix)
# Switch completely?
if switchcompletely:
self.updateConfig('behat_switchcompletely', switchcompletely)
self.updateConfig('behat_wwwroot', self.get('wwwroot'))
else:
self.removeConfig('behat_switchcompletely')
self.removeConfig('behat_wwwroot')
# Drop the tables
def drop():
result = (None, None, None)
try:
debug('Dropping database')
result = self.cli('/admin/tool/behat/cli/util.php', args='--drop', stdout=None, stderr=None)
except:
pass
return result
# Enabling Behat (or updating the definitions)
def enable():
result = (None, None, None)
try:
debug('Enabling Behat')
result = self.cli('/admin/tool/behat/cli/util.php', args='--enable')
except:
pass
return result
# Install the tables
def install():
result = (None, None, None)
try:
debug('Installing Behat tables')
result = self.cli('/admin/tool/behat/cli/util.php', args='--install', stdout=None, stderr=None)
except:
pass
return result
# Force a cache purge
self.purge()
# Not really proud of this logic, but it works for now. Ideally there shouldn't be any duplicated call to enable().
result = enable()
if result[0] == 251:
raise Exception('Error: Behat requires PHP 5.4 or the flag --switch-completely to be set')
elif result[0] == 254:
# Installation required
installResult = install()
if installResult[0] != 0:
raise Exception('Unknown error while installing Behat. \nError code: %s\nStdout: %s\nStderr: %s' % (result))
result = enable()
elif result[0] > 0:
# Need to drop the tables
drop()
installResult = install()
if installResult[0] != 0:
raise Exception('Unknown error while installing Behat. \nError code: %s\nStdout: %s\nStderr: %s' % (result))
result = enable()
# Could not enable Behat
if result[0] != 0:
raise Exception('Unknown error while enabling Behat. \nError code: %s\nStdout: %s\nStderr: %s' % (result))
