def compute_evaluation_order(self, aliases):
# Build the dependencies graph
dp = {}
for alias,(atype,(base,exp)) in aliases.items():
edges = []
for e in exp:
edges += self.get_name_dependencies()
dp[alias] = edges
# Topological Sort to find the order to compute aliases
# Just a slow implementation, O(n^3)...
unordered = copy.copy(list(aliases.keys()))
ordered = []
while unordered:
added = []
for i in xrange(len(unordered)):
ok = True
u = unordered[i]
for j in xrange(len(unordered)):
if i!=j:
for v in dp[unordered[j]]:
if u==v:
ok = False
break
if not ok: break
if ok: added.append(i)
if not added:
debug.warning('Looping dependencies detected!')
break
for i in reversed(added):
ordered.append(unordered[i])
del unordered[i]
return ordered
def open(self):
retry = True
while retry:
config = {'host': self.host,
'port': self.port,
'user': self.user}
# unfortunately keywords are not standard across libraries
if self.protocol == 'mysql':
config['db'] = self.db_name
if self.password is not None:
config['passwd'] = self.password
elif self.protocol == 'postgresql':
config['database'] = self.db_name
if self.password is not None:
config['password'] = self.password
try:
self.conn = self.get_db_lib().connect(**config)
break
except self.get_db_lib().Error, e:
debug.warning(str(e))
if (e[0] == 1045 or self.get_db_lib().OperationalError
and self.password is None):
passwd_dlg = QPasswordEntry()
if passwd_dlg.exec_():
self.password = passwd_dlg.get_password()
else:
retry = False
else:
raise ModuleError(self, str(e))
def download(self, url):
"""download(url:string) -> (result: int, downloaded_file: File,
local_filename:string)
Tries to download a file from url. It returns a tuple with:
result: 0 -> success
1 -> couldn't download the file, but found a cached version
2 -> failed (in this case downloaded_file will contain the
error message)
downloaded_file: The downloaded file or the error message in case it
failed
local_filename: the path to the local_filename
"""
self._parse_url(url)
opener = urllib2.build_opener()
local_filename = self._local_filename(url)
request = urllib2.Request(url)
try:
f1 = opener.open(url)
except urllib2.URLError, e:
if self._file_is_in_local_cache(local_filename):
debug.warning(('A network error occurred. HTTPFile will use'
' cached version of file'))
result = core.modules.basic_modules.File()
result.name = local_filename
return (1, result, local_filename)
else:
return (2, (str(e)), local_filename)
def linux_ubuntu_install(package_name):
qt = has_qt()
hide_splash_if_necessary()
if qt:
cmd = core.system.vistrails_root_directory()
cmd += '/gui/bundles/linux_ubuntu_install.py'
else:
cmd = 'apt-get install -y'
if type(package_name) == str:
cmd += ' ' + package_name
elif type(package_name) == list:
for package in package_name:
if type(package) != str:
raise TypeError("Expected string or list of strings")
cmd += ' ' + package
if qt:
sucmd = guess_graphical_sudo() + " '" + cmd + "'"
else:
debug.warning("VisTrails wants to install package(s) '%s'" %
package_name)
sucmd = "sudo " + cmd
result = os.system(sucmd)
return (result == 0) # 0 indicates success
def download(self, url):
"""download(url:string) -> (result: int, downloaded_file: File,
local_filename:string)
Tries to download a file from url. It returns a tuple with:
result: 0 -> success
1 -> couldn't download the file, but found a cached version
2 -> failed (in this case downloaded_file will contain the
error message)
downloaded_file: The downloaded file or the error message in case it
failed
local_filename: the path to the local_filename
"""
self._parse_url(url)
opener = urllib2.build_opener()
local_filename = self._local_filename(url)
request = urllib2.Request(url)
try:
f1 = opener.open(url)
except urllib2.URLError, e:
if self._file_is_in_local_cache(local_filename):
debug.warning(("A network error occurred. HTTPFile will use" " cached version of file"))
result = core.modules.basic_modules.File()
result.name = local_filename
return (1, result, local_filename)
else:
return (2, (str(e)), local_filename)
def addParameterChangesFromAliasesAction(self, pipeline, controller, vistrail, parent_version, aliases):
param_changes = []
newid = parent_version
print "addParameterChangesFromAliasesAction()"
print "Aliases: %s " % str( aliases )
print "Pipeline Aliases: %s " % str( pipeline.aliases )
aliasList = aliases.iteritems()
for k,value in aliasList:
alias = pipeline.aliases.get(k,None) # alias = (type, oId, parentType, parentId, mId)
if alias:
module = pipeline.modules[alias[4]]
function = module.function_idx[alias[3]]
old_param = function.parameter_idx[alias[1]]
#print alias, module, function, old_param
if old_param.strValue != value:
new_param = VistrailController.update_parameter(controller,
old_param,
value)
if new_param is not None:
op = ('change', old_param, new_param,
function.vtType, function.real_id)
param_changes.append(op)
print "Added parameter change for alias=%s, value=%s" % ( k, value )
else:
debug.warning("CDAT Package: Change parameter %s in widget %s was not generated"%(k, self.name))
else:
debug.warning( "CDAT Package: Alias %s does not exist in pipeline" % (k) )
if len(param_changes) > 0:
action = core.db.action.create_action(param_changes)
vistrail.add_action(action, parent_version, controller.current_session)
controller.set_changed(True)
controller.recompute_terse_graph()
controller.invalidate_version_tree()
newid = action.id
return newid
def linux_ubuntu_install(package_name):
qt = has_qt()
hide_splash_if_necessary()
if qt:
cmd = core.system.vistrails_root_directory()
cmd += '/gui/bundles/linux_ubuntu_install.py'
else:
cmd = 'apt-get install -y'
if type(package_name) == str:
cmd += ' ' + package_name
elif type(package_name) == list:
for package in package_name:
if type(package) != str:
raise TypeError("Expected string or list of strings")
cmd += ' ' + package
if qt:
sucmd = guess_graphical_sudo() + " '" + cmd + "'"
else:
debug.warning("VisTrails wants to install package(s) '%s'" %
package_name)
sucmd = "sudo " + cmd
result = os.system(sucmd)
return (result == 0) # 0 indicates success
def package_requirements():
import core.requirements
if not core.requirements.python_module_exists('vtk'):
raise core.requirements.MissingRequirement('vtk')
if not core.requirements.python_module_exists('PyQt4'):
from core import debug
debug.warning('PyQt4 is not available. There will be no interaction '
'between VTK and the spreadsheet.')
def package_requirements():
import core.requirements
if not core.requirements.python_module_exists('vtk'):
raise core.requirements.MissingRequirement('vtk')
if not core.requirements.python_module_exists('PyQt4'):
from core import debug
debug.warning('PyQt4 is not available. There will be no interaction '
'between VTK and the spreadsheet.')
import vtk
def _delete_files(dirname):
"""delete_files(dirname: str) -> None
Deletes all files inside dirname
"""
try:
for root, dirs, files in os.walk(dirname):
for fname in files:
os.unlink(os.path.join(root, fname))
except OSError, e:
debug.warning("Error when removing thumbnails: %s" % str(e))
def _delete_files(dirname):
"""delete_files(dirname: str) -> None
Deletes all files inside dirname
"""
try:
for root, dirs, files in os.walk(dirname):
for fname in files:
os.unlink(os.path.join(root,fname))
except OSError, e:
debug.warning("Error when removing thumbnails: %s"%str(e))
def package_requirements():
import core.requirements
if not core.requirements.python_module_exists('visit'):
raise core.requirements.MissingRequirement('visit')
if not core.requirements.python_module_exists('visit.pyqt_gui'):
raise core.requirements.MissingRequirement('visit.pyqt_gui')
# Figure out how to check on pvvariable
if not core.requirements.python_module_exists('PyQt4'):
from core import debug
debug.warning('PyQt4 is not available. There will be no interaction '
'between VisIt and the spreadsheet.')
import visit.pyqt_gui
import visit
def package_requirements():
import core.requirements
if not core.requirements.python_module_exists('visit'):
raise core.requirements.MissingRequirement('visit')
if not core.requirements.python_module_exists('visit.pyqt_gui'):
raise core.requirements.MissingRequirement('visit.pyqt_gui')
# Figure out how to check on pvvariable
if not core.requirements.python_module_exists('PyQt4'):
from core import debug
debug.warning('PyQt4 is not available. There will be no interaction '
'between VisIt and the spreadsheet.')
import visit.pyqt_gui
import visit
def _is_outdated(self, remoteHeader, localFile):
"""Checks whether local file is outdated."""
local_time = datetime.datetime.utcfromtimestamp(os.path.getmtime(localFile))
try:
remote_time = datetime.datetime.strptime(remoteHeader, "%a, %d %b %Y %H:%M:%S %Z")
except ValueError:
try:
remote_time = datetime.datetime.strptime(remoteHeader, "%a, %d %B %Y %H:%M:%S %Z")
except ValueError:
# unable to parse last-modified header, download file again
debug.warning("Unable to parse Last-Modified header" ", downloading file")
return True
return remote_time > local_time
def remove_lru(self, n=1):
elements = self.elements.values()
elements.sort(key=lambda obj: obj.time)
num = min(n, len(elements))
debug.debug("Will remove %s elements from cache..." % num)
debug.debug("Cache has %s elements and %s bytes" %
(len(elements), self.size()))
for i in range(num):
try:
del self.elements[elements[i].name]
os.unlink(elements[i].abs_name)
except os.error, e:
debug.warning("Could not remove file %s:" (
elements[i].abs_name, str(e)))
def remove_lru(self,n=1):
elements = self.elements.values()
elements.sort(key=lambda obj: obj.time)
num = min(n,len(elements))
debug.debug("Will remove %s elements from cache..."%num)
debug.debug("Cache has %s elements and %s bytes"%(len(elements),
self.size()))
for i in range(num):
try:
del self.elements[elements[i].name]
os.unlink(elements[i].abs_name)
except os.error, e:
debug.warning("Could not remove file %s:"(elements[i].abs_name,
str(e)))
def get_latest_vistrails_version():
"""get_latest_vistrails_version() -> string - Returns latest vistrails
release version as queried from vistrails.org"""
version = ''
version_url = \
"http://www.vistrails.org/download/download.php?id=release_version.txt"
try:
request = urllib2.Request(version_url)
get_latest_version = urllib2.urlopen(request)
version = get_latest_version.read().strip()
except urllib2.HTTPError, err:
debug.warning("Unable to check for updates: %s" % str(err))
return version
def get_latest_vistrails_version():
"""get_latest_vistrails_version() -> string - Returns latest vistrails
release version as queried from vistrails.org"""
version = ''
version_url = \
"http://www.vistrails.org/download/download.php?id=release_version.txt"
try:
request = urllib2.Request(version_url)
get_latest_version = urllib2.urlopen(request)
version = get_latest_version.read().strip()
except urllib2.HTTPError, err:
debug.warning("Unable to check for updates: %s" % str(err))
return version
def data_sync(self):
""" downloads/uploads/uses the local file depending on availability """
self.checksum_lookup()
# local file not on repository, so upload
if not self.on_server and os.path.isfile(self.in_file.name):
cookiejar = gui.repository.QRepositoryDialog.cookiejar
if cookiejar:
register_openers(cookiejar=cookiejar)
params = {
'dataset_file': open(self.in_file.name, 'rb'),
'name': self.in_file.name.split('/')[-1],
'origin': 'vistrails',
'checksum': self.checksum
}
upload_url = "%s/datasets/upload/" % self.base_url
datagen, headers = multipart_encode(params)
request = urllib2.Request(upload_url, datagen, headers)
try:
result = urllib2.urlopen(request)
if result.code != 200:
show_warning("Upload Failure",
"Data failed to upload to repository")
# make temporarily uncachable
self.is_cacheable = self.invalidate_cache
else:
debug.warning("Push to repository was successful")
# make sure module caches
self.is_cacheable = self.validate_cache
except Exception, e:
show_warning("Upload Failure",
"Data failed to upload to repository")
# make temporarily uncachable
self.is_cacheable = self.invalidate_cache
debug.warning('RepoSync uploaded %s to the repository' % \
self.in_file.name)
else:
show_warning("Please login", ("You must be logged into the web"
" repository in order to upload "
"data. No data was synced"))
# make temporarily uncachable
self.is_cacheable = self.invalidate_cache
# use local data
self.setResult("file", self.in_file)
def move_cache_directory(self, sourcedir, destdir):
"""change_cache_directory(sourcedir: str, dest_dir: str) -> None"
Moves files from sourcedir to destdir
"""
if os.path.exists(destdir):
for entry in self.elements.itervalues():
try:
srcname = entry.abs_name
dstname = os.path.join(destdir,entry.name)
shutil.move(srcname,dstname)
entry.abs_name = dstname
except shutil.Error, e:
debug.warning("Could not move thumbnail from %s to %s: %s" \
% (sourcedir, destdir, str(e)))
def move_cache_directory(self, sourcedir, destdir):
"""change_cache_directory(sourcedir: str, dest_dir: str) -> None"
Moves files from sourcedir to destdir
"""
if os.path.exists(destdir):
for entry in self.elements.itervalues():
try:
srcname = entry.abs_name
dstname = os.path.join(destdir, entry.name)
shutil.move(srcname, dstname)
entry.abs_name = dstname
except shutil.Error, e:
debug.warning("Could not move thumbnail from %s to %s: %s" \
% (sourcedir, destdir, str(e)))
def load_persistent_configuration(self):
(dom, element) = ( None, None )
for iAttempt in range(10):
try:
(dom, element) = self.find_own_dom_element()
break
except: time.sleep( 0.5 )
if element <> None:
configuration = enter_named_element(element, 'configuration')
if configuration and self.configuration:
if self.configuration: self.configuration.set_from_dom_node(configuration)
else: debug.warning("Error, missing configuration in package")
if dom <> None: dom.unlink()
else:
debug.warning("Error reading dom for package")
def data_sync(self):
""" downloads/uploads/uses the local file depending on availability """
self.checksum_lookup()
# local file not on repository, so upload
if not self.on_server and os.path.isfile(self.in_file.name):
cookiejar = gui.repository.QRepositoryDialog.cookiejar
if cookiejar:
register_openers(cookiejar=cookiejar)
params = {
"dataset_file": open(self.in_file.name, "rb"),
"name": self.in_file.name.split("/")[-1],
"origin": "vistrails",
"checksum": self.checksum,
}
upload_url = "%s/datasets/upload/" % self.base_url
datagen, headers = multipart_encode(params)
request = urllib2.Request(upload_url, datagen, headers)
try:
result = urllib2.urlopen(request)
if result.code != 200:
show_warning("Upload Failure", "Data failed to upload to repository")
# make temporarily uncachable
self.is_cacheable = self.invalidate_cache
else:
debug.warning("Push to repository was successful")
# make sure module caches
self.is_cacheable = self.validate_cache
except Exception, e:
show_warning("Upload Failure", "Data failed to upload to repository")
# make temporarily uncachable
self.is_cacheable = self.invalidate_cache
debug.warning("RepoSync uploaded %s to the repository" % self.in_file.name)
else:
show_warning(
"Please login",
("You must be logged into the web" " repository in order to upload " "data. No data was synced"),
)
# make temporarily uncachable
self.is_cacheable = self.invalidate_cache
# use local data
self.setResult("file", self.in_file)
def _is_outdated(self, remoteHeader, localFile):
"""Checks whether local file is outdated."""
local_time = \
datetime.datetime.utcfromtimestamp(os.path.getmtime(localFile))
try:
remote_time = datetime.datetime.strptime(
remoteHeader, "%a, %d %b %Y %H:%M:%S %Z")
except ValueError:
try:
remote_time = datetime.datetime.strptime(
remoteHeader, "%a, %d %B %Y %H:%M:%S %Z")
except ValueError:
# unable to parse last-modified header, download file again
debug.warning("Unable to parse Last-Modified header"
", downloading file")
return True
return remote_time > local_time
def create_user_packages_dir(userpackagesname=None):
debug.warning('Will try to create userpackages directory')
if userpackagesname is None:
userpackagesname = os.path.join(
self.temp_configuration.dotVistrails, 'userpackages')
if not os.path.isdir(userpackagesname):
try:
os.mkdir(userpackagesname)
self.configuration.userPackageDirectory = userpackagesname
self.temp_configuration.userPackageDirectory = \
userpackagesname
except:
msg = ("""Failed to create userpackages directory: '%s'.
This could be an indication of a permissions problem.
Make sure directory '%s' in writable.""" %
(userpackagesname, self.configuration.dotVistrails))
debug.critical(msg)
sys.exit(1)
create_user_packages_init(userpackagesname)
def guess_graphical_sudo():
"""Tries to guess what to call to run a shell with elevated
privileges."""
if core.system.executable_is_in_path("kdesu"):
return "kdesu -c"
elif core.system.executable_is_in_path("gksu"):
return "gksu"
elif core.system.executable_is_in_path("sudo") and core.system.executable_is_in_path("zenity"):
# This is a reasonably convoluted hack to only prompt for the password
# if user has not recently entered it
return (
'((echo "" | sudo -v -S -p "") || '
+ '(zenity --entry --title "sudo password prompt" --text "Please enter your password '
'to give the system install authorization." --hide-text="" | sudo -v -S -p "")); sudo -S -p ""'
)
else:
debug.warning("Could not find a graphical su-like command.")
debug.warning("Will use regular su")
return "su -c"
def addParameterChangesFromAliasesAction(self, pipeline, controller,
vistrail, parent_version,
aliases):
param_changes = []
newid = parent_version
print "addParameterChangesFromAliasesAction()"
print "Aliases: %s " % str(aliases)
print "Pipeline Aliases: %s " % str(pipeline.aliases)
aliasList = aliases.iteritems()
for k, value in aliasList:
alias = pipeline.aliases.get(
k, None) # alias = (type, oId, parentType, parentId, mId)
if alias:
module = pipeline.modules[alias[4]]
function = module.function_idx[alias[3]]
old_param = function.parameter_idx[alias[1]]
#print alias, module, function, old_param
if old_param.strValue != value:
new_param = VistrailController.update_parameter(
controller, old_param, value)
if new_param is not None:
op = ('change', old_param, new_param, function.vtType,
function.real_id)
param_changes.append(op)
print "Added parameter change for alias=%s, value=%s" % (
k, value)
else:
debug.warning(
"CDAT Package: Change parameter %s in widget %s was not generated"
% (k, self.name))
else:
debug.warning(
"CDAT Package: Alias %s does not exist in pipeline" % (k))
if len(param_changes) > 0:
action = core.db.action.create_action(param_changes)
vistrail.add_action(action, parent_version,
controller.current_session)
controller.set_changed(True)
controller.recompute_terse_graph()
controller.invalidate_version_tree()
newid = action.id
return newid
def create_startup_package_node(self):
(dom, element) = self.find_own_dom_element()
doc = dom.documentElement
disabledpackages = enter_named_element(doc, 'disabledpackages')
packages = enter_named_element(doc, 'packages')
oldpackage = self.find_disabledpackage_element(doc)
if oldpackage is not None:
# Must remove element from oldpackages,
# _and_ the element that was just created in find_own_dom_element()
disabledpackages.removeChild(oldpackage)
packages.removeChild(element)
packages.appendChild(oldpackage)
configuration = enter_named_element(oldpackage, 'configuration')
if configuration:
if self.configuration: self.configuration.set_from_dom_node(configuration)
else: debug.warning("Error, missing configuration in package")
get_vistrails_application().vistrailsStartup.write_startup_dom(dom)
dom.unlink()
def create_user_packages_dir(userpackagesname=None):
debug.warning('Will try to create userpackages directory')
if userpackagesname is None:
userpackagesname = os.path.join(self.temp_configuration.dotVistrails,
'userpackages')
if not os.path.isdir(userpackagesname):
try:
os.mkdir(userpackagesname)
self.configuration.userPackageDirectory = userpackagesname
self.temp_configuration.userPackageDirectory = \
userpackagesname
except:
msg = ("""Failed to create userpackages directory: '%s'.
This could be an indication of a permissions problem.
Make sure directory '%s' in writable.""" %
(userpackagesname,
self.configuration.dotVistrails))
debug.critical(msg)
sys.exit(1)
create_user_packages_init(userpackagesname)
def guess_graphical_sudo():
"""Tries to guess what to call to run a shell with elevated
privileges."""
if core.system.executable_is_in_path('kdesu'):
return 'kdesu -c'
elif core.system.executable_is_in_path('gksu'):
return 'gksu'
elif (core.system.executable_is_in_path('sudo')
and core.system.executable_is_in_path('zenity')):
# This is a reasonably convoluted hack to only prompt for the password
# if user has not recently entered it
return (
'((echo "" | sudo -v -S -p "") || ' +
'(zenity --entry --title "sudo password prompt" --text "Please enter your password '
'to give the system install authorization." --hide-text="" | sudo -v -S -p "")); sudo -S -p ""'
)
else:
debug.warning("Could not find a graphical su-like command.")
debug.warning("Will use regular su")
return 'su -c'
def initialize(*args, **keywords):
# import core.packagemanager
global webServicesDict
global package_cache
#Create a directory for the SUDSWebServices package
location = os.path.join(core.system.default_dot_vistrails(),
"SUDSWebServices")
if not os.path.isdir(location):
try:
debug.log("Creating SUDS cache directory...")
os.mkdir(location)
except:
debug.critical(
"""Could not create SUDS cache directory. Make sure
'%s' does not exist and parent directory is writable""" % location)
sys.exit(1)
# the number of days to cache wsdl files
days = 1
if configuration.check("cache_days"):
days = configuration.cache_days
suds.client.ObjectCache.protocol = 0 # windows needs this
package_cache = suds.client.ObjectCache(location, days=days)
#reg = core.modules.module_registry.get_module_registry()
#reg.add_module(SUDSWebService, abstract=True)
wsdlList = []
if configuration.check('wsdlList'):
wsdlList = configuration.wsdlList.split(";")
else:
configuration.wsdlList = ''
for wsdl in wsdlList:
if not wsdl.startswith('http://'):
wsdl = 'http://' + wsdl
if wsdl in webServicesDict:
debug.warning('Duplicate WSDL entry: '+wsdl)
continue
s = Service(wsdl)
if s.service:
webServicesDict[wsdl] = s
def linux_fedora_install(package_name):
qt = has_qt()
hide_splash_if_necessary()
if qt:
cmd = core.system.vistrails_root_directory()
cmd += '/gui/bundles/linux_fedora_install.py'
else:
cmd = 'yum -y install'
if type(package_name) == str:
cmd += ' ' + package_name
elif type(package_name) == list:
for package in package_name:
if type(package) != str:
raise TypeError("Expected string or list of strings")
cmd += ' ' + package
if qt:
sucmd = guess_graphical_sudo() + " " + cmd
else:
debug.warning(("VisTrails wants to install package(s) '%s' through "
"_sudo_. Make sure you are a sudoer.") % package_name)
sucmd = "sudo " + cmd
debug.warning("EXECUTING: sucmd")
result = os.system(sucmd)
debug.warning("RETURN VALUE: %s" % result)
return (result == 0)
def linux_fedora_install(package_name):
qt = has_qt()
hide_splash_if_necessary()
if qt:
cmd = core.system.vistrails_root_directory()
cmd += '/gui/bundles/linux_fedora_install.py'
else:
cmd = 'yum -y install'
if type(package_name) == str:
cmd += ' ' + package_name
elif type(package_name) == list:
for package in package_name:
if type(package) != str:
raise TypeError("Expected string or list of strings")
cmd += ' ' + package
if qt:
sucmd = guess_graphical_sudo() + " " + cmd
else:
debug.warning(("VisTrails wants to install package(s) '%s' through "
"_sudo_. Make sure you are a sudoer.") % package_name)
sucmd = "sudo " + cmd
debug.warning("EXECUTING: sucmd")
result = os.system(sucmd)
debug.warning("RETURN VALUE: %s" % result)
return (result == 0)
def initialize(*args, **keywords):
# import core.packagemanager
global webServicesDict
global package_cache
#Create a directory for the SUDSWebServices package
location = os.path.join(core.system.default_dot_vistrails(),
"SUDSWebServices")
if not os.path.isdir(location):
try:
debug.log("Creating SUDS cache directory...")
os.mkdir(location)
except:
debug.critical("""Could not create SUDS cache directory. Make sure
'%s' does not exist and parent directory is writable""" % location)
sys.exit(1)
# the number of days to cache wsdl files
days = 1
if configuration.check("cache_days"):
days = configuration.cache_days
suds.client.ObjectCache.protocol = 0 # windows needs this
package_cache = suds.client.ObjectCache(location, days=days)
#reg = core.modules.module_registry.get_module_registry()
#reg.add_module(SUDSWebService, abstract=True)
wsdlList = []
if configuration.check('wsdlList'):
wsdlList = configuration.wsdlList.split(";")
else:
configuration.wsdlList = ''
for wsdl in wsdlList:
if not wsdl.startswith('http://'):
wsdl = 'http://' + wsdl
if wsdl in webServicesDict:
debug.warning('Duplicate WSDL entry: ' + wsdl)
continue
s = Service(wsdl)
if s.service:
webServicesDict[wsdl] = s
def update_from_console(self):
config = self.find_connection_info(self._host, self._port, self._db)
if config is None:
# the problem here is if VisTrails is being run through command
# line from LaTex, stdout is being redirected to a log file, so
# the user does not see the prompt in raw_input. getpass uses the
# controlling terminal so it works fine. Just to make sure he sees
# the first message prompt we will the controlling terminal
try:
f = open('/dev/tty', 'w')
f.write("\nConnect to db with username [%s]: " % self._user)
f.close()
user = raw_input()
except:
debug.warning("Couldn't write to terminal. Will try stdout")
user = raw_input("Connecting to db with username[%s]: " %
self._user)
try:
if user != '':
self._user = user
passwd = getpass.getpass("password:")
self._passwd = passwd
config = {
'host': self._host,
'port': int(self._port),
'user': self._user,
'passwd': self._passwd,
'db': self._db
}
test_db_connection(config)
config['succeeded'] = True
config['name'] = '%s@%s' % (self._user, self._host)
config['id'] = -1
except VistrailsDBException, e:
debug.critical('VisTrails DB Exception', str(e))
config['succeeded'] = False
except Exception, e2:
debug.critical('VisTrails Exception', str(e2))
config['succeeded'] = False
class FileSink(NotCacheable, Module):
"""FileSink takes a file and writes it to a user-specified
location in the file system. The file is stored at location
specified by the outputPath. The overwrite flag allows users to
specify whether an existing path should be overwritten."""
def compute(self):
input_file = self.getInputFromPort("file")
output_path = self.getInputFromPort("outputPath")
full_path = output_path.name
try:
core.system.link_or_copy(input_file.name, full_path)
except OSError, e:
if self.hasInputFromPort("overwrite") and \
self.getInputFromPort("overwrite"):
try:
os.unlink(full_path)
core.system.link_or_copy(input_file.name, full_path)
except OSError:
msg = "(override true) Could not create file '%s'" % \
full_path
raise ModuleError(self, msg)
else:
msg = "Could not create file '%s': %s" % (full_path, e)
raise ModuleError(self, msg)
if (self.hasInputFromPort("publishFile") and
self.getInputFromPort("publishFile") or
not self.hasInputFromPort("publishFile")):
if self.moduleInfo.has_key('extra_info'):
if self.moduleInfo['extra_info'].has_key('pathDumpCells'):
folder = self.moduleInfo['extra_info']['pathDumpCells']
base_fname = os.path.basename(full_path)
(base_fname, file_extension) = os.path.splitext(base_fname)
base_fname = os.path.join(folder, base_fname)
# make a unique filename
filename = base_fname + file_extension
counter = 2
while os.path.exists(filename):
filename = base_fname + "_%d%s" % (counter,
file_extension)
counter += 1
try:
core.system.link_or_copy(input_file.name, filename)
except OSError:
msg = "Could not publish file '%s' \n on '%s': %s" % \
(full_path, filename, e)
# I am not sure whether we should raise an error
# I will just print a warning for now (Emanuele)
debug.warning("%s" % msg)
def update_from_console(self):
config = self.find_connection_info(self._host, self._port, self._db)
if config is None:
# the problem here is if VisTrails is being run through command
# line from LaTex, stdout is being redirected to a log file, so
# the user does not see the prompt in raw_input. getpass uses the
# controlling terminal so it works fine. Just to make sure he sees
# the first message prompt we will the controlling terminal
try:
f= open('/dev/tty', 'w')
f.write("\nConnect to db with username [%s]: "%self._user)
f.close()
user = raw_input()
except:
debug.warning("Couldn't write to terminal. Will try stdout")
user = raw_input("Connecting to db with username[%s]: "%self._user)
try:
if user != '':
self._user = user
passwd = getpass.getpass("password:")
self._passwd = passwd
config = {'host': self._host,
'port': int(self._port),
'user': self._user,
'passwd': self._passwd,
'db': self._db
}
test_db_connection(config)
config['succeeded'] = True
config['name'] = '%s@%s'%(self._user,self._host)
config['id'] = -1
except VistrailsDBException, e:
debug.critical('VisTrails DB Exception', str(e))
config['succeeded'] = False
except Exception, e2:
debug.critical('VisTrails Exception', str(e2))
config['succeeded'] = False
def __init__(self, category=None, detail=None):
"""detail can range from -2 to +1, with larger numbers returning more
information. Beware of +1, it can take several minutes for
system_profiler to generate the data."""
command = ['system_profiler', '-xml']
if category is not None:
command.append(str(category))
if detail is not None:
command.extend(['-detailLevel', '%d' % detail])
p = subprocess.Popen(command,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE)
stdout, stderr = p.communicate()
stderr = stderr.strip()
if stderr:
lines = stderr.splitlines()
if len(lines) > 1 or len(lines[0]) > 44:
line = "%s..." % lines[0][:41]
else:
line = lines[0]
debug.warning("Error output from system_profiler: %s" % line,
stderr)
self.document = ElementTree.XML(stdout)
def create_module(value, signature):
"""
Creates a module for value, in order to do the type checking.
"""
if type(value)==bool:
v_module = Boolean()
return v_module
elif type(value)==str:
v_module = String()
return v_module
elif type(value)==int:
if type(signature)==list:
signature = signature[0]
if signature[0]==Float().__class__:
v_module = Float()
else:
v_module = Integer()
return v_module
elif type(value)==float:
v_module = Float()
return v_module
elif type(value)==list:
v_module = List()
return v_module
elif type(value)==file:
v_module = File()
return v_module
elif type(value)==tuple:
v_modules = ()
for element in xrange(len(value)):
v_modules += (create_module(value[element], signature[element]),)
return v_modules
else:
debug.warning("Could not identify the type of the list element.")
debug.warning("Type checking is not going to be done inside Fold module.")
return None
def run_and_get_results(w_list,
parameters='',
workflow_info=None,
update_vistrail=True,
extra_info=None,
reason='Console Mode Execution'):
"""run_and_get_results(w_list: list of (locator, version), parameters: str,
workflow_info:str, update_vistrail: boolean,
extra_info:dict)
Run all workflows in w_list, and returns an interpreter result object.
version can be a tag name or a version id.
"""
elements = parameters.split("$&$")
aliases = {}
result = []
for locator, workflow in w_list:
(v, abstractions, thumbnails, mashups) = load_vistrail(locator)
controller = VistrailController(auto_save=update_vistrail)
controller.set_vistrail(v, locator, abstractions, thumbnails, mashups)
if type(workflow) == type("str"):
version = v.get_version_number(workflow)
elif type(workflow) in [type(1), long]:
version = workflow
elif workflow is None:
version = controller.get_latest_version_in_graph()
else:
msg = "Invalid version tag or number: %s" % workflow
raise VistrailsInternalError(msg)
controller.change_selected_version(version)
for e in elements:
pos = e.find("=")
if pos != -1:
key = e[:pos].strip()
value = e[pos + 1:].strip()
if controller.current_pipeline.has_alias(key):
aliases[key] = value
if workflow_info is not None and controller.current_pipeline is not None:
if is_running_gui():
from gui.pipeline_view import QPipelineView
pipeline_view = QPipelineView()
pipeline_view.scene().setupScene(controller.current_pipeline)
base_fname = "%s_%s_pipeline.pdf" % (locator.short_name,
version)
filename = os.path.join(workflow_info, base_fname)
pipeline_view.scene().saveToPDF(filename)
del pipeline_view
else:
debug.critical("Cannot save pipeline figure when not "
"running in gui mode")
base_fname = "%s_%s_pipeline.xml" % (locator.short_name, version)
filename = os.path.join(workflow_info, base_fname)
core.db.io.save_workflow(controller.current_pipeline, filename)
if not update_vistrail:
conf = get_vistrails_configuration()
if conf.has('thumbs'):
conf.thumbs.autoSave = False
(results, _) = \
controller.execute_current_workflow(custom_aliases=aliases,
extra_info=extra_info,
reason=reason)
new_version = controller.current_version
if new_version != version:
debug.warning("Version '%s' (%s) was upgraded. The actual "
"version executed was %s" % \
(workflow, version, new_version))
run = results[0]
run.workflow_info = (locator.name, new_version)
run.pipeline = controller.current_pipeline
if update_vistrail:
controller.write_vistrail(locator)
result.append(run)
return result
## - Redistributions in binary form must reproduce the above copyright
## notice, this list of conditions and the following disclaimer in the
## documentation and/or other materials provided with the distribution.
## - Neither the name of the University of Utah nor the names of its
## contributors may be used to endorse or promote products derived from
## this software without specific prior written permission.
##
## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
##
###############################################################################
# *** MOVED *** to gui.modules.query_configuration
import traceback
from core import debug
debug.warning("The use of core.modules.query_configuration is deprecated. "
"Please use gui.modules.query_configuration.",
''.join(traceback.format_stack()))
from gui.modules.query_configuration import *
## notice, this list of conditions and the following disclaimer in the
## documentation and/or other materials provided with the distribution.
## - Neither the name of the University of Utah nor the names of its
## contributors may be used to endorse or promote products derived from
## this software without specific prior written permission.
##
## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
##
###############################################################################
# *** MOVED *** to gui.modules.port_configure
import traceback
from core import debug
debug.warning(
"The use of core.modules.port_configure is deprecated. "
"Please use gui.modules.port_configure.",
''.join(traceback.format_stack()))
from gui.modules.port_configure import *
# the reference in the package list
package.remove_own_dom_element()
failed.append(package)
else:
if package.identifier not in self._package_versions:
self._package_versions[package.identifier] = {}
self._dependency_graph.add_vertex(package.identifier)
elif package.version in \
self._package_versions[package.identifier]:
raise VistrailsInternalError("Duplicate package version: "
"'%s' (version %s) in %s" % \
(package.identifier,
package.version,
package_codepath))
else:
debug.warning('Duplicate package identifier: %s' % \
package.identifier)
self._package_versions[package.identifier][package.version] = \
package
for pkg in failed:
del self._package_list[pkg.codepath]
failed = []
# determine dependencies
for package in self._package_list.itervalues():
try:
self.add_dependencies(package)
except Package.MissingDependency, e:
debug.critical("Will disable package %s" % package.name)
debug.critical(str(e))
# print "DEPENDENCIES FAILED TO LOAD, let's disable this"
def _vanilla_import(module_name):
return __import__(module_name, globals(), locals(), [])
def unknown_py_import(module_name, package_name):
return _vanilla_import(module_name)
def py_import(module_name, dependency_dictionary):
"""Tries to import a python module. If unsuccessful, tries to install
the appropriate bundle and then reimport. py_import tries to be smart
about which system it runs on."""
try:
result = _vanilla_import(module_name)
return result
except ImportError, e:
pass
debug.warning("Import failed. Will try to install bundle.")
success = core.bundles.installbundle.install(dependency_dictionary)
if not success:
debug.critical("Package installation failed.")
debug.critical("Package might not be available in the provided repositories.")
raise e
try:
result = _vanilla_import(module_name)
return result
except ImportError, e:
debug.critical("Package installation successful, but import still failed.")
debug.critical("This means py_import was called with bad arguments.")
debug.critical("Please report this bug to the package developer.")
## documentation and/or other materials provided with the distribution.
## - Neither the name of the University of Utah nor the names of its
## contributors may be used to endorse or promote products derived from
## this software without specific prior written permission.
##
## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
##
###############################################################################
# *** MOVED *** to gui.modules.query_configuration
import traceback
from core import debug
debug.warning(
"The use of core.modules.query_configuration is deprecated. " "Please use gui.modules.query_configuration.",
"".join(traceback.format_stack()),
)
from gui.modules.query_configuration import *
def load(self, loadworkflow=True):
config = ConfigParser.ConfigParser()
if config.read(self.config_file):
if config.has_section('global'):
if config.has_option('global', 'cellnum'):
self.cellnum = config.getint('global', 'cellnum')
if config.has_option('global', 'filenum'):
self.filenum = config.getint('global', 'filenum')
if config.has_option('global', 'varnum'):
self.varnum = config.getint('global', 'varnum')
print " ------ Loaded plot %s, varnum = %d ------ " % ( self.name, self.varnum )
if config.has_option('global', 'workflow_tag'):
self.workflow_tag = config.get('global', 'workflow_tag')
# else:
# debug.warning("CDAT Package: file %s does not contain a required option 'workflow_tag'. Widget will not be loaded."%self.config_file)
# self.loaded = False
# return
if config.has_option('global', 'filetypes'):
types = config.get('global', 'filetypes')
tlist = [t.strip() for t in types.split(";")]
for t in tlist:
kv = t.split(":")
self.filetypes[kv[0].strip()] = [v.strip()
for v in kv[1].split(",")]
if config.has_option('global', 'qt_filter'):
self.qt_filter = config.get('global', 'qt_filter')
if config.has_option('global', 'dependencies'):
deps = config.get('global', 'dependencies')
self.dependencies = [d.strip() for d in deps.split(",")]
if config.has_option('global', 'serialized_config_alias'):
self.serializedConfigAlias = config.get('global', 'serialized_config_alias')
for y in range(self.filenum):
self.files.append( 'Filename' + str(y+1) )
for v in range(self.varnum):
self.vars.append( 'VariableName' + str(v+1) )
self.axes.append( 'Axes' + str(v+1) )
for x in range(self.cellnum):
section_name = 'cell' + str(x+1)
if config.has_section(section_name):
cellType = config.get(section_name, 'celltype')
if config.has_option(section_name, 'address_alias'):
self.cells.append( Cell( cellType, None, None,
config.get(section_name, 'address_alias') ) )
else:
self.cells.append(Cell( cellType,"Row"+str(x+1), "Column"+str(x+1) ) )
else:
for y in range(self.filenum):
option_name = 'filename_alias' + str(y+1)
if config.has_option('global', option_name):
self.files.append(config.get('global', option_name))
for v in range(self.varnum):
option_name = 'varname_alias' + str(v+1)
if config.has_option('global', option_name):
self.vars.append(config.get('global', option_name))
axes_name = 'axes_alias' + str(v+1)
if config.has_option('global', axes_name):
self.axes.append(config.get('global', axes_name))
for x in range(self.cellnum):
section_name = 'cell' + str(x+1)
if (config.has_section(section_name) and
config.has_option(section_name, 'celltype') and
config.has_option(section_name, 'row_alias') and
config.has_option(section_name, 'col_alias')):
self.cells.append(Cell(config.get(section_name, 'celltype'),
config.get(section_name, 'row_alias'),
config.get(section_name, 'col_alias')))
if loadworkflow:
#load workflow in vistrail
#only if dependencies are enabled
manager = get_package_manager()
self.unsatisfied_deps = []
for dep in self.dependencies:
if not manager.has_package(dep):
self.unsatisfied_deps.append(dep)
if len(self.unsatisfied_deps) == 0:
try:
(self.plot_vistrail, abstractions , thumbnails, mashups) = load_vistrail(self.locator)
controller = VistrailController()
controller.set_vistrail(self.plot_vistrail, self.locator,
abstractions, thumbnails,
mashups)
self.workflow_version = self.plot_vistrail.get_version_number(self.workflow_tag) if self.workflow_tag else controller.get_latest_version_in_graph()
print " Loaded %s version: %s" % ( self.name, str( self.workflow_version ) )
controller.change_selected_version(self.workflow_version)
self.workflow = controller.current_pipeline
self.loaded = True
except Exception, err:
debug.warning( "Error loading workflow %s: %s" % ( self.name, err ) )
self.loaded = False
else:
debug.warning("UV-CDAT: %s widget could not be loaded \
because it depends on packages that are not loaded:"%self.name)
debug.warning(" %s"%", ".join(self.unsatisfied_deps))
self.loaded = False
else:
debug.warning("UV-CDAT: file %s does not contain a 'global'\
section. Widget will not be loaded."%self.config_file)
self.loaded = False
## - Redistributions in binary form must reproduce the above copyright
## notice, this list of conditions and the following disclaimer in the
## documentation and/or other materials provided with the distribution.
## - Neither the name of the University of Utah nor the names of its
## contributors may be used to endorse or promote products derived from
## this software without specific prior written permission.
##
## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
##
###############################################################################
# *** MOVED *** to gui.modules.tuple_configuration
import traceback
from core import debug
debug.warning("The use of core.modules.tuple_configuration is deprecated. "
"Please use gui.modules.tuple_configuration.",
''.join(traceback.format_stack()))
from gui.modules.tuple_configuration import *
# file on repository mirrors local file, so use local file
if self.up_to_date and os.path.isfile(self.in_file.name):
self.setResult("file", self.in_file)
else:
# local file not present or out of date, download or used cached
self.url = "%s/datasets/download/%s" % (self.base_url, self.checksum)
local_filename = package_directory + "/" + urllib.quote_plus(self.url)
if not self._file_is_in_local_cache(local_filename):
# file not in cache, download.
try:
urllib.urlretrieve(self.url, local_filename)
except IOError, e:
raise ModuleError(self, ("Invalid URL: %s" % e))
out_file = core.modules.basic_modules.File()
out_file.name = local_filename
debug.warning("RepoSync is using repository data")
self.setResult("file", out_file)
def compute(self):
# if server, grab local file using checksum id
if self.is_server:
self.checkInputPort("checksum")
self.checksum = self.getInputFromPort("checksum")
# get file path
path_url = "%s/datasets/path/%s/" % (self.base_url, self.checksum)
try:
dataset_path_request = urllib2.urlopen(url=path_url)
dataset_path = dataset_path_request.read()
except urllib2.HTTPError:
pass
def execDotVistrails(tried_once=False):
""" execDotVistrails() -> None
Actually execute the Vistrail initialization
"""
# if it is file, then must move old-style .vistrails to
# directory.
if os.path.isfile(self.temp_configuration.dotVistrails):
debug.warning(
"Old-style initialization hooks. Will try to set things correctly."
)
(fd, name) = tempfile.mkstemp()
os.close(fd)
shutil.copyfile(self.temp_configuration.dotVistrails, name)
try:
os.unlink(self.temp_configuration.dotVistrails)
except:
debug.critical("""Failed to remove old initialization file.
This could be an indication of a permissions problem.
Make sure file '%s' is writable.""" %
self.temp_configuration.dotVistrails)
sys.exit(1)
self.create_default_directory()
try:
destiny = os.path.join(
self.temp_configuration.dotVistrails, 'startup.py')
shutil.copyfile(name, destiny)
except:
debug.critical("""Failed to copy old initialization file to
newly-created initialization directory. This must have been
a race condition. Please remove '%s' and
restart VisTrails.""" %
self.temp_configuration.dotVistrails)
sys.exit(1)
debug.critical("Successful move!")
try:
os.unlink(name)
except:
debug.warning("Failed to erase temporary file.")
if os.path.isdir(self.temp_configuration.dotVistrails):
if self.temp_configuration.check('userPackageDirectory'):
userpackages = self.temp_configuration.userPackageDirectory
else:
userpackages = os.path.join(
self.temp_configuration.dotVistrails, 'userpackages')
startup = os.path.join(self.temp_configuration.dotVistrails,
'startup.py')
if self.temp_configuration.check('abstractionsDirectory'):
abstractions = self.temp_configuration.abstractionsDirectory
else:
abstractions = os.path.join(
self.temp_configuration.dotVistrails, 'subworkflows')
if (self.temp_configuration.has('thumbs')
and self.temp_configuration.thumbs.check(
'cacheDirectory')):
thumbnails = self.temp_configuration.thumbs.cacheDirectory
else:
thumbnails = os.path.join(
self.temp_configuration.dotVistrails, 'thumbs')
if not os.path.isdir(userpackages):
create_user_packages_dir(userpackages)
if not os.path.isfile(os.path.join(userpackages,
'__init__.py')):
create_user_packages_init(userpackages)
if not os.path.isdir(abstractions):
create_abstractions_dir(abstractions)
if not os.path.isdir(thumbnails):
create_thumbnails_dir(thumbnails)
try:
dotVistrails = file(startup)
g = {}
localsDir = {
'configuration': self.temp_configuration,
'addStartupHook': addStartupHook,
'addPackage': addPackage
}
old_path = copy.copy(sys.path)
sys.path.append(self.temp_configuration.dotVistrails)
exec dotVistrails in localsDir
sys.path = old_path
del localsDir['addPackage']
del localsDir['addStartupHook']
return localsDir
except IOError:
if tried_once:
debug.critical("""Still cannot find default file.
Something has gone wrong. Please make sure ~/.vistrails
exists, is writable, and ~/.vistrails/startup.py does
not exist.""")
sys.exit(1)
debug.critical('%s not found' % startup)
debug.critical('Will try to install default '
'startup file')
install_default_startup()
install_default_startupxml_if_needed()
return execDotVistrails(True)
elif not os.path.lexists(self.temp_configuration.dotVistrails):
debug.log('%s not found' %
self.temp_configuration.dotVistrails)
self.create_default_directory()
create_user_packages_dir()
create_abstractions_dir()
create_thumbnails_dir()
install_default_startup()
install_default_startupxml_if_needed()
return execDotVistrails(True)
def convertWarning(self, before, after, _from, to):
text = ["Value truncated when saving to database",
"%s truncated to %s\nwhile converting '%s' to '%s'"]
debug.warning(text[0], text[1] % (before, after, _from, to))
def unknown_py_import(module_name, package_name):
return _vanilla_import(module_name)
def py_import(module_name, dependency_dictionary):
"""Tries to import a python module. If unsuccessful, tries to install
the appropriate bundle and then reimport. py_import tries to be smart
about which system it runs on."""
try:
result = _vanilla_import(module_name)
return result
except ImportError, e:
pass
debug.warning("Import of python module '%s' failed. "
"Will try to install bundle." % module_name)
success = core.bundles.installbundle.install(dependency_dictionary)
if not success:
raise PyImportException(module_name, traceback.format_exc())
try:
result = _vanilla_import(module_name)
return result
except ImportError, e:
raise PyImportBug(module_name, traceback.format_exc())
##############################################################################
def execDotVistrails(tried_once=False):
""" execDotVistrails() -> None
Actually execute the Vistrail initialization
"""
# if it is file, then must move old-style .vistrails to
# directory.
if os.path.isfile(self.temp_configuration.dotVistrails):
debug.warning("Old-style initialization hooks. Will try to set things correctly.")
(fd, name) = tempfile.mkstemp()
os.close(fd)
shutil.copyfile(self.temp_configuration.dotVistrails, name)
try:
os.unlink(self.temp_configuration.dotVistrails)
except:
debug.critical("""Failed to remove old initialization file.
This could be an indication of a permissions problem.
Make sure file '%s' is writable."""
% self.temp_configuration.dotVistrails)
sys.exit(1)
self.create_default_directory()
try:
destiny = os.path.join(self.temp_configuration.dotVistrails,
'startup.py')
shutil.copyfile(name, destiny)
except:
debug.critical("""Failed to copy old initialization file to
newly-created initialization directory. This must have been
a race condition. Please remove '%s' and
restart VisTrails."""
% self.temp_configuration.dotVistrails)
sys.exit(1)
debug.critical("Successful move!")
try:
os.unlink(name)
except:
debug.warning("Failed to erase temporary file.")
if os.path.isdir(self.temp_configuration.dotVistrails):
if self.temp_configuration.check('userPackageDirectory'):
userpackages = self.temp_configuration.userPackageDirectory
else:
userpackages = os.path.join(self.temp_configuration.dotVistrails,
'userpackages')
startup = os.path.join(self.temp_configuration.dotVistrails,
'startup.py')
if self.temp_configuration.check('abstractionsDirectory'):
abstractions = self.temp_configuration.abstractionsDirectory
else:
abstractions = os.path.join(self.temp_configuration.dotVistrails,
'subworkflows')
if (self.temp_configuration.has('thumbs') and
self.temp_configuration.thumbs.check('cacheDirectory')):
thumbnails = self.temp_configuration.thumbs.cacheDirectory
else:
thumbnails = os.path.join(self.temp_configuration.dotVistrails,
'thumbs')
if not os.path.isdir(userpackages):
create_user_packages_dir(userpackages)
if not os.path.isfile(os.path.join(userpackages,
'__init__.py')):
create_user_packages_init(userpackages)
if not os.path.isdir(abstractions):
create_abstractions_dir(abstractions)
if not os.path.isdir(thumbnails):
create_thumbnails_dir(thumbnails)
try:
dotVistrails = file(startup)
g = {}
localsDir = {'configuration': self.temp_configuration,
'addStartupHook': addStartupHook,
'addPackage': addPackage}
old_path = copy.copy(sys.path)
sys.path.append(self.temp_configuration.dotVistrails)
exec dotVistrails in localsDir
sys.path = old_path
del localsDir['addPackage']
del localsDir['addStartupHook']
return localsDir
except IOError:
if tried_once:
debug.critical("""Still cannot find default file.
Something has gone wrong. Please make sure ~/.vistrails
exists, is writable, and ~/.vistrails/startup.py does
not exist.""")
sys.exit(1)
debug.critical('%s not found' % startup)
debug.critical('Will try to install default '
'startup file')
install_default_startup()
install_default_startupxml_if_needed()
return execDotVistrails(True)
elif not os.path.lexists(self.temp_configuration.dotVistrails):
debug.log('%s not found' % self.temp_configuration.dotVistrails)
self.create_default_directory()
create_user_packages_dir()
create_abstractions_dir()
create_thumbnails_dir()
install_default_startup()
install_default_startupxml_if_needed()
return execDotVistrails(True)
# the reference in the package list
package.remove_own_dom_element()
failed.append(package)
else:
if package.identifier not in self._package_versions:
self._package_versions[package.identifier] = {}
self._dependency_graph.add_vertex(package.identifier)
elif package.version in \
self._package_versions[package.identifier]:
raise VistrailsInternalError("Duplicate package version: "
"'%s' (version %s) in %s" % \
(package.identifier,
package.version,
package.codepath))
else:
debug.warning('Duplicate package identifier: %s' % \
package.identifier)
self._package_versions[package.identifier][package.version] = \
package
for pkg in failed:
del self._package_list[pkg.codepath]
failed = []
# determine dependencies
for package in self._package_list.itervalues():
try:
self.add_dependencies(package)
except Package.MissingDependency, e:
if report_missing_dependencies:
debug.critical(
"Dependencies of package %s are missing "
def run_and_get_results(w_list, parameters='', workflow_info=None,
update_vistrail=True, extra_info=None,
reason='Console Mode Execution'):
"""run_and_get_results(w_list: list of (locator, version), parameters: str,
workflow_info:str, update_vistrail: boolean,
extra_info:dict)
Run all workflows in w_list, and returns an interpreter result object.
version can be a tag name or a version id.
"""
elements = parameters.split("$&$")
aliases = {}
result = []
for locator, workflow in w_list:
(v, abstractions , thumbnails, mashups) = load_vistrail(locator)
controller = VistrailController(auto_save=update_vistrail)
controller.set_vistrail(v, locator, abstractions, thumbnails, mashups)
if type(workflow) == type("str"):
version = v.get_version_number(workflow)
elif type(workflow) in [ type(1), long]:
version = workflow
elif workflow is None:
version = controller.get_latest_version_in_graph()
else:
msg = "Invalid version tag or number: %s" % workflow
raise VistrailsInternalError(msg)
controller.change_selected_version(version)
for e in elements:
pos = e.find("=")
if pos != -1:
key = e[:pos].strip()
value = e[pos+1:].strip()
if controller.current_pipeline.has_alias(key):
aliases[key] = value
if workflow_info is not None and controller.current_pipeline is not None:
if is_running_gui():
from gui.pipeline_view import QPipelineView
pipeline_view = QPipelineView()
pipeline_view.scene().setupScene(controller.current_pipeline)
base_fname = "%s_%s_pipeline.pdf" % (locator.short_name, version)
filename = os.path.join(workflow_info, base_fname)
pipeline_view.scene().saveToPDF(filename)
del pipeline_view
else:
debug.critical("Cannot save pipeline figure when not "
"running in gui mode")
base_fname = "%s_%s_pipeline.xml" % (locator.short_name, version)
filename = os.path.join(workflow_info, base_fname)
core.db.io.save_workflow(controller.current_pipeline, filename)
if not update_vistrail:
conf = get_vistrails_configuration()
if conf.has('thumbs'):
conf.thumbs.autoSave = False
(results, _) = \
controller.execute_current_workflow(custom_aliases=aliases,
extra_info=extra_info,
reason=reason)
new_version = controller.current_version
if new_version != version:
debug.warning("Version '%s' (%s) was upgraded. The actual "
"version executed was %s" % \
(workflow, version, new_version))
run = results[0]
run.workflow_info = (locator.name, new_version)
run.pipeline = controller.current_pipeline
if update_vistrail:
controller.write_vistrail(locator)
result.append(run)
return result
## - Redistributions in binary form must reproduce the above copyright
## notice, this list of conditions and the following disclaimer in the
## documentation and/or other materials provided with the distribution.
## - Neither the name of the University of Utah nor the names of its
## contributors may be used to endorse or promote products derived from
## this software without specific prior written permission.
##
## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
##
###############################################################################
# *** MOVED *** to gui.modules.paramexplore
import traceback
from core import debug
debug.warning("The use of core.modules.paramexplore is deprecated. "
"Please use gui.modules.paramexplore.",
''.join(traceback.format_stack()))
from gui.modules.paramexplore import *
## - Redistributions in binary form must reproduce the above copyright
## notice, this list of conditions and the following disclaimer in the
## documentation and/or other materials provided with the distribution.
## - Neither the name of the University of Utah nor the names of its
## contributors may be used to endorse or promote products derived from
## this software without specific prior written permission.
##
## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
##
###############################################################################
# *** MOVED *** to gui.modules.source_configure
import traceback
from core import debug
debug.warning("The use of core.modules.source_configure is deprecated. "
"Please use gui.modules.source_configure.",
''.join(traceback.format_stack()))
from gui.modules.source_configure import *
