import warnings
import time
_t0 = time.time()
import sys
import os as _os
# ensure that any `import omfit.xxx` refers to this installation of OMFIT
sys.path.insert(0, _os.path.dirname(_os.path.abspath(__file__)))
from omfit_classes.startup_framework import *
# import utilities
from utils import _available_to_user_math, _available_to_user_util, _available_to_user_plot, _available_to_user_fusion
# ---------------------
# classes under the `class` folder and starting with OMFIT
# ---------------------
_loaded_omfit_class_files = []
import omfit_classes.omfit_base
from omfit_classes.omfit_base import *
from omfit_classes.omfit_base import _moduleAttrs, itemTagsValues
from omfit_classes import unix_os as os
from omfit_classes.omfit_clusters import OMFITclusters
# override sys.exit to prevent external packages from quitting the session
_exit = sys.exit
sys.exit = lambda *args, **kw: None
import omfit_classes.omfit_python
from omfit_classes.omfit_python import *
_k = 0
for _file in sorted(glob.glob(OMFITsrc + '/omfit_classes/omfit_*.py')):
_python_module = os.path.splitext(os.path.split(_file)[1])[0]
try:
exec("import omfit_classes." + _python_module, globals(), locals())
try:
getattr(omfit_classes, _python_module).__all__
except AttributeError:
raise OMFITexception(
'Exception in omfit/%s: OMFIT does not allow modules under omfit/classes'
'not to have an __all__ attribute which explicitly specifies what symbols '
'will be exported when from <module> import * is used on the module' % _python_module
)
# all classes must be available in omfit_base and omfit_python since that's where the OMFITtree is defined
if _python_module != 'omfit_base':
for item in getattr(omfit_classes, _python_module).__all__:
setattr(omfit_classes.omfit_base, item, getattr(getattr(omfit_classes, _python_module), item))
if _python_module != 'omfit_python':
for item in getattr(omfit_classes, _python_module).__all__:
setattr(omfit_classes.omfit_python, item, getattr(getattr(omfit_classes, _python_module), item))
exec("from omfit_classes import " + _python_module, globals(), locals())
exec("from omfit_classes." + _python_module + ' import *', globals(), locals())
_k += 1
_loaded_omfit_class_files.append(('%2d)%s' % (_k, _python_module.replace('omfit_', ''))).ljust(20))
except Exception:
printe('Offending module: ' + _python_module)
raise
sys.exit = _exit
for item in omfit_classes.omfit_python.__all__:
setattr(omfit_classes.omfit_base, item, getattr(omfit_python, item))
# backward compatibility with old classes location in `classes` folder instead of `omfit_classes`
for item in list(sys.modules.keys()):
if item.startswith('omfit_classes.'):
# allow `import classes.omfit_classname` # how Python environment with local OMFIT installation can use OMFIT classes
sys.modules[re.sub('^omfit_classes\.', 'classes.', item)] = sys.modules[item]
print('Loaded OMFIT classes:')
while len(_loaded_omfit_class_files):
print(''.join(_loaded_omfit_class_files[:4]))
_loaded_omfit_class_files = _loaded_omfit_class_files[4:]
[docs]def reload_python(moduleName, quiet=False):
"""
This function extends the Python builtin `reload` function to easily reload OMFIT classes
>>> reload_python(omfit_classes.omfit_onetwo)
:param moduleName: module or module name
:param quiet: bool
Suppress print statements listing reloaded objects
"""
from matplotlib.cbook.deprecation import MatplotlibDeprecationWarning
warnings.filterwarnings('ignore', category=MatplotlibDeprecationWarning)
if not isinstance(moduleName, str):
moduleName = moduleName.__name__
if not (moduleName.startswith('omfit_') or moduleName.startswith('omfit_classes.omfit_')):
printe('reload_python is meant for class containing modules (in omfit_classes) that start with `omfit_`')
printe('Try instead:\n\nreload({0})\nfrom {0} import *'.format(moduleName))
return
if moduleName in ['omfit_tree', 'omfit_gui']:
printe('Can not reload omfit_tree or omfit_gui')
return
tmp = {}
exec("import %s" % moduleName, tmp)
from importlib import reload
reload(eval(moduleName))
exec("from " + moduleName + " import *", tmp)
# Keep track of reloaded objects to avoid storing them in the persistent OMFITconsoleDict namespace
OMFITreloadedDict.update(tmp)
# Find objects in the OMFIT tree that should be reloaded
OMtr = traverse(OMFIT, string='OMFIT', onlyDict=True, skipDynaLoad=True)
OMtr_cls = {}
for loc in OMtr:
if hasattr(eval(loc), '__class__') and eval(loc).__class__.__name__ in list(tmp.keys()):
OMtr_cls.setdefault(eval(loc).__class__.__name__, []).append(loc)
# Select only the items that should be reloaded
items = list(tmp.keys())
if hasattr(eval(moduleName), '__all__'):
items = eval(moduleName).__all__
if '__builtins__' in items:
items.remove('__builtins__')
# Loop through items to reload
updated = {}
for item in items:
# Loop through python modules
for mod in list(sys.modules.keys()):
if hasattr(sys.modules[mod], '__dict__') and item in sys.modules[mod].__dict__:
sys.modules[mod].__dict__[item] = tmp[item]
updated.setdefault(mod, []).append(item)
# Loop through OMFIT objects
if item in OMtr_cls:
for loc in OMtr_cls[item]:
if not quiet:
print(loc)
eval(loc).__class__ = tmp[item]
# Update OMFIT data types
omfit_classes.omfit_base._updateTypes()
if not quiet:
printi('*' * 20)
printi('Updated python modules')
printi('*' * 20)
pprinti(updated)
printi('')
printi('*' * 20)
printi('Updated OMFIT tree entries')
printi('*' * 20)
pprinti(OMtr_cls)
return
omfit_classes.omfit_python.reload_python = reload_python
# ---------------------
# OMFIT main tree
# ---------------------
_availableModulesCache = {}
[docs]class OMFITmaintree(OMFITproject):
_save_method = '_save_with_info'
def __init__(self, filename=''):
OMFITproject.__init__(self, filename)
self._OMFITparent = None
self._OMFITkeyName = ''
self.prj_options = {}
[docs] def start(self, filename=''):
self.clear()
self.filename = filename
self.reset()
self.onlyRunningCopy()
OMFIT['MainSettings'].sort()
[docs] def projectName(self):
if not len(self.filename):
return ''
if re.findall('OMFITsave.txt', self.filename):
return os.path.split(self.filename.split(os.sep + 'OMFITsave.txt')[0])[1]
else:
return os.path.splitext(os.path.split(self.filename)[1])[0]
[docs] def onlyRunningCopy(self, deletePID=False):
"""
:param delete: whether to remove PID from list of running OMFIT processes (this should be done only at exit)
:return: return True/False wether this is the only running copy of OMFIT on this computer
"""
filename = os.sep.join([OMFITsessionsDir, str(os.getpid())])
# OMFITsessionsDir should always exist! -- if not return False
if not os.path.exists(OMFITsessionsDir):
printe('Something is wrong! OMFITsessionsDir (%s) has been deleted!' % OMFITsessionsDir)
return False
else:
try:
# this is in a try/except because
# in some extreme circumstances there can be
# errors if the system cannot allocate memory
if not os.path.exists(filename):
open(filename, 'w').close()
pids = []
for file in glob.glob(os.sep.join([OMFITsessionsDir, '*'])):
pid = os.path.split(file)[1]
if is_running(pid):
pids.append(pid)
elif deletePID:
try:
os.remove(file)
except OSError:
pass
if deletePID and os.path.exists(filename):
os.remove(filename)
return len(pids) == 1
except OSError:
return False
[docs] def reset(self):
# always use saving as .zip as the default
self.zip = True
# clear
self.clear()
OMFITconsoleDict.clear()
OMFITscriptsDict.clear()
# remove all files under current temporary directory
try:
shutil.rmtree(OMFITcwd)
except Exception:
pass
if not os.path.exists(OMFITcwd):
os.makedirs(OMFITcwd)
os.chdir(OMFITcwd)
# fill special locations
super().__setitem__('scratch', OMFITmainscratch())
super().__setitem__('commandBox', OMFITconsoleDict)
super().__setitem__('scriptsRun', OMFITscriptsDict)
super().__setitem__('shotBookmarks', OMFITshotBookmarks)
# create main settings
self.addMainSettings(restore='user')
OMFIT['MainSettings']['EXPERIMENT']['runid'] = 'sim1'
self['MainSettings']['SETUP']['version'] = repo_active_branch_commit
self['MainSettings']['SETUP']['python_environment'] = SortedDict(python_environment())
# initialize main scratch
self['scratch'].initialize()
# set the localhost
SERVER.setLocalhost()
[docs] def newProvenanceID(self):
self['MainSettings']['EXPERIMENT']['provenanceID'] = omfit_hash(utils_base.now("%Y-%m-%d_%H_%M_%S_%f"))
[docs] def newProjectID(self):
self['MainSettings']['EXPERIMENT']['projectID'] = 'projectID__'
self['MainSettings']['EXPERIMENT']['projectID'] += repo_active_branch_commit + '__'
self['MainSettings']['EXPERIMENT']['projectID'] += utils_base.now("%Y-%m-%d_%H_%M_%S_%f")
self['MainSettings']['EXPERIMENT']['projectID'] = self['MainSettings']['EXPERIMENT']['projectID'].replace(' ', '')
[docs] def addMainSettings(self, updateUserSettings=False, restore=''):
# read the user namelist file
self.userMainSettings = OMFITsettingsDir + os.sep + 'MainSettings.txt'
self.userMainSettingsNamelistDump = OMFITsettingsDir + os.sep + 'MainSettingsNamelistDump.txt'
self.userMainSettingsNamelist = OMFITsettingsDir + os.sep + 'MainSettingsNamelist.txt'
if not os.path.exists(os.path.split(self.userMainSettings)[0]):
os.makedirs(os.path.split(self.userMainSettings)[0])
if not os.path.exists(self.userMainSettings):
open(self.userMainSettings, 'w').close()
updateUserSettings = True
if not os.path.exists(self.userMainSettingsNamelist):
open(self.userMainSettingsNamelist, 'w').close()
updateUserSettings = True
# keep project options
for k in list(OMFIT.prj_options_choices.keys()):
if k not in self.prj_options:
if k == 'persistent_projectID':
self.prj_options[k] = False
else:
self.prj_options[k] = ''
# force restore of skel main settings if necessary
self.apply_bindings()
if 'MainSettings' not in self or restore != '':
# skeleton settings
skelMainSettings = OMFITsrc + os.sep + 'omfit_classes' + os.sep + 'skeleton' + os.sep + 'skeletonMainSettings.txt'
self.tmpSkel = OMFITtree(skelMainSettings, quiet=True)
if platform.system() == 'Darwin':
skelMainSettings = (
OMFITsrc + os.sep + 'omfit_classes' + os.sep + 'skeleton' + os.sep + 'skeletonMainSettingsNamelistOSX.txt'
)
else:
skelMainSettings = (
OMFITsrc + os.sep + 'omfit_classes' + os.sep + 'skeleton' + os.sep + 'skeletonMainSettingsNamelistUNIX.txt'
)
self.tmpSkel['MainSettings'].recursiveUpdate(namelist.NamelistFile(skelMainSettings), overwrite=True)
# institution settings
if os.path.exists(os.environ.get('OMFIT_INSTITUTION_FILE', '/does not exist')):
tmp = namelist.NamelistFile(os.environ['OMFIT_INSTITUTION_FILE'])
else:
filename = os.sep.join([OMFITsrc, '..', 'institution'])
if os.path.exists(filename):
tmp = namelist.NamelistFile(filename)
else:
institution_files = glob.glob(os.sep.join([OMFITsrc, '..', 'institutions', '']) + '*')
institution_files.append(None)
for filename in institution_files:
tmp = namelist.NamelistFile(filename)
if 'SETUP' in tmp and 'stats_file' in tmp['SETUP'] and os.path.exists(tmp['SETUP']['stats_file']):
break
self.tmpSkel['MainSettings'].recursiveUpdate(tmp, overwrite=True)
# user settings
self.tmpUser = OMFITtree(self.userMainSettings, quiet=True)
if 'MainSettings' not in self:
self['MainSettings'] = OMFITmainSettings()
self['MainSettings'].filename = OMFITcwd + os.sep + os.path.split(self.userMainSettingsNamelist)[1]
if not len(self.tmpUser):
restore = 'skel'
updateUserSettings = True
# The main settings are built starting from the skeleton, the user local preference in ~/.OMFIT/ and the edits that the users have made
if restore == '':
self['MainSettings'].recursiveUpdate(self.tmpSkel['MainSettings'])
def f_traverse(me):
for kid in list(me.keys()):
if isinstance(me[kid], dict):
f_traverse(me[kid])
if re.match(hide_ptrn, kid):
del me[kid]
f_traverse(self['MainSettings'])
self.add_bindings_to_main_settings()
elif restore.startswith('diff_'):
restore = restore[5:]
tmp = OMFITmainSettings()
if restore == 'skel':
tmp.recursiveUpdate(self.tmpSkel['MainSettings'])
elif restore == 'user' and 'MainSettings' in self.tmpUser:
tmp.recursiveUpdate(self.tmpSkel['MainSettings'])
tmp.recursiveUpdate(self.tmpUser['MainSettings'], overwrite=True)
elif restore == 'S3':
tmp.recursiveUpdate(self.tmpSkel['MainSettings'])
tmp.recursiveUpdate(self.tmpUser['MainSettings'], overwrite=True)
tmp1 = OMFITobject_fromS3(tmp['SETUP']['email'] + "_" + 'MainSettings.txt', s3bucket='omfit')
tmp2 = OMFITobject_fromS3(tmp['SETUP']['email'] + "_" + 'MainSettingsNamelist.txt', s3bucket='omfit')
shutil.copy2(tmp2.filename, os.path.split(tmp1.filename)[0] + os.sep + os.path.split(tmp2.filename)[1])
tmp0 = OMFITtree(tmp1.filename, quiet=True)
tmp.recursiveUpdate(tmp0['MainSettings'], overwrite=True)
printi('Loaded MainSettings from the cloud')
diffTreeGUI(OMFIT['MainSettings'], tmp)
else:
self['MainSettings'].clear()
if restore == 'skel':
self['MainSettings'].recursiveUpdate(self.tmpSkel['MainSettings'])
elif restore == 'user' and 'MainSettings' in self.tmpUser:
self['MainSettings'].recursiveUpdate(self.tmpSkel['MainSettings'])
self['MainSettings'].recursiveUpdate(self.tmpUser['MainSettings'], overwrite=True)
elif restore == 'S3':
self['MainSettings'].recursiveUpdate(self.tmpSkel['MainSettings'])
self['MainSettings'].recursiveUpdate(self.tmpUser['MainSettings'], overwrite=True)
tmp1 = OMFITobject_fromS3(self['MainSettings']['SETUP']['email'] + "_" + 'MainSettings.txt', s3bucket='omfit')
tmp2 = OMFITobject_fromS3(self['MainSettings']['SETUP']['email'] + "_" + 'MainSettingsNamelist.txt', s3bucket='omfit')
shutil.copy2(tmp2.filename, os.path.split(tmp1.filename)[0] + os.sep + os.path.split(tmp2.filename)[1])
tmp = OMFITtree(tmp1.filename, quiet=True)
self['MainSettings'].recursiveUpdate(tmp['MainSettings'], overwrite=True)
printi('Restored MainSettings from the cloud')
self.apply_bindings()
# generate unique projectID if that's not already there
if 'projectID' not in self['MainSettings']['EXPERIMENT']:
self.newProjectID()
# generate unique provenanceID if that's not already there
if 'provenanceID' not in self['MainSettings']['EXPERIMENT']:
self.newProvenanceID()
# make sure auto-save is not more often than 15 minutes
try:
self['MainSettings']['SETUP']['autosave_minutes'] = int(self['MainSettings']['SETUP']['autosave_minutes'])
if self['MainSettings']['SETUP']['autosave_minutes'] < 15:
raise OMFITexception('Auto-save time must be >= than 15 minutes')
except Exception as _excp:
printe('Error in setting Auto-save time\n' + repr(_excp))
self['MainSettings']['SETUP']['autosave_minutes'] = 15
# if default_tunnel is None, then set it based on what servers the user has access
if self['MainSettings']['SERVER']['default_tunnel'] is None:
favorite_tunnels = ['cybele', 'portal', 'cmodws', 'shenma', 'itm_gateway', 'iter_login', 'cfetr']
default_tunnel = 'cybele'
if os.path.exists(os.environ['HOME'] + '/.ssh/known_hosts'):
with open(os.environ['HOME'] + '/.ssh/known_hosts', 'r') as f:
lines = [_f for _f in f.read().strip().split('\n') if _f]
known_tunnels = []
for line in lines:
try:
for server in line.split()[0].split(','):
try:
SERVER[server]
if SERVER(server) in favorite_tunnels:
known_tunnels.append(SERVER(server))
except Exception:
pass
except IndexError:
pass
for tunnel in favorite_tunnels:
if tunnel in known_tunnels:
default_tunnel = tunnel
break
self['MainSettings']['SERVER']['default_tunnel'] = default_tunnel
if updateUserSettings:
# find differences of current MainSettings with respect to skeleton
tmpU = OMFITtree()
tmpU['MainSettings'] = copy.deepcopy(OMFIT['MainSettings'])
ptrn = self.tmpSkel.pretty_diff(tmpU)
# do not store projectID, provenanceID, or runid
for k in ['projectID', 'provenanceID', 'runid']:
if k in list(ptrn['MainSettings']['EXPERIMENT'].keys()):
del ptrn['MainSettings']['EXPERIMENT'][k]
# keep only differences
tmpU = prune_mask(tmpU, ptrn)
# remove entries that are deprecated
_clearDeprecatedMainSettings(tmpU['MainSettings'])
# remove entries that are not in the skeleton
for item in list(tmpU['MainSettings'].keys()):
if item in list(tmpU['MainSettings'].keys()) and item not in self.tmpSkel['MainSettings']:
del tmpU['MainSettings'][item]
if item in list(tmpU['MainSettings'].keys()) and item != 'SERVER':
for subitem in list(tmpU['MainSettings'][item].keys()):
if (
subitem in list(tmpU['MainSettings'][item].keys())
and subitem not in self.tmpSkel['MainSettings'][item]
and subitem != 'KeyBindings'
):
del tmpU['MainSettings'][item][subitem]
elif subitem == 'KeyBindings':
for desc, event in list(tmpU['MainSettings'][item][subitem].items()):
if (
desc in global_event_bindings.default_desc_event
and global_event_bindings.default_desc_event[desc] == event
):
del tmpU['MainSettings'][item][subitem][desc]
# save only differences (if there are any)
if len(tmpU):
tmpU._save(filename=self.userMainSettings, only="['MainSettings']", onlyOMFITsave=True)
global OMFITexpressionsReturnNone
tmpExp = OMFITexpressionsReturnNone
OMFITexpressionsReturnNone = True
try:
tmpU['MainSettings'].saveas(self.userMainSettingsNamelist)
finally:
OMFITexpressionsReturnNone = tmpExp
self.tmpUser = tmpU
printi(self.userMainSettings + ' has been updated')
if updateUserSettings == 'S3':
OMFITascii(OMFITsettingsDir + os.sep + 'MainSettings.txt').deploy(
self['MainSettings']['SETUP']['email'] + "_" + 'MainSettings.txt', s3bucket='omfit'
)
OMFITascii(OMFITsettingsDir + os.sep + 'MainSettingsNamelist.txt').deploy(
self['MainSettings']['SETUP']['email'] + "_" + 'MainSettingsNamelist.txt', s3bucket='omfit'
)
printi('Saved user MainSettings in the cloud')
# save a version of MainSettings in plain text
if updateUserSettings or not os.path.exists(self.userMainSettingsNamelistDump):
self['MainSettings'].deploy(self.userMainSettingsNamelistDump)
def __setitem__(self, key, value):
# TODO: handle 'MainSettings' the same way
if key in ['scratch', 'commandBox', 'scriptsRun', 'shotBookmarks']:
raise RuntimeError(f"OMFIT['{key}'] is write-protected")
else:
super().__setitem__(key, value)
def __delitem__(self, key):
if key in ['scratch', 'commandBox', 'scriptsRun', 'shotBookmarks', 'MainSettings']:
raise RuntimeError(f"OMFIT['{key}'] is delete-protected")
else:
super().__delitem__(key)
[docs] def add_bindings_to_main_settings(self):
"""
Take the descriptions and events from global_events_bindings and insert
them in self['MainSettings']['SETUP']['KeyBindings'][desc] = <event>
"""
printd('Calling add_bindings_to_main_settings', level=2, topic='keybindings')
if 'KeyBindings' not in self['MainSettings']['SETUP']:
self['MainSettings']['SETUP']['KeyBindings'] = namelist.NamelistName()
for di, d in enumerate(global_event_bindings.descs):
self['MainSettings']['SETUP']['KeyBindings'][d.replace(' ', '_')] = global_event_bindings.events[di]
[docs] def apply_bindings(self):
"""
Take the descriptions and events from
self['MainSettings']['SETUP']['KeyBindings']
and use them to update the global_event_bindings
"""
if ('MainSettings' not in self) or ('SETUP' not in self['MainSettings']) or ('KeyBindings' not in self['MainSettings']['SETUP']):
printd("No key bindings in MainSettings['SETUP']['KeyBindings'] -> unable to update", topic='keybindings')
return
for d, e in list(self['MainSettings']['SETUP']['KeyBindings'].items()):
try:
global_event_bindings.set(d.replace('_', ' '), e)
except ValueError:
del self['MainSettings']['SETUP']['KeyBindings'][d]
self.add_bindings_to_main_settings()
[docs] def save(self, quiet=None, skip_save_errors=False):
"""
Writes the content of the OMFIT tree to the filesystem
using the same filename and zip options of the last saveas
:param quiet: whether to print save progress to screen
:param skip_save_errors: skip errors when saving objects
"""
if quiet is None:
quiet = bool(eval(os.environ.get('OMFIT_PROGRESS_BAR_QUIET', '0')))
self.filename = self._save_with_info(self.filename, zip=self.zip, quiet=quiet, skip_save_errors=skip_save_errors)
return self.filename
def _save_with_info(self, filename, zip=False, quiet=False, updateExistingDir=False, skip_save_errors=False):
"""
Wrapper function around the OMFITtree._save method which
handles the prj_options dictionary that is only part of the main OMFIT tree
"""
# this method should have the same signature of the ._save() method
if filename:
# by default the first time the projects directory is created,
# assign permissions so that it is readeable but not writeable
# by other users. Users can always override these default permissions
# once the directory is created.
projpath = os.path.split(os.path.split(filename)[0])[0]
if not os.path.exists(projpath):
# create projects directory
os.makedirs(projpath)
# by default, remove group and others write permission
for perm in [stat.S_IWGRP, stat.S_IWOTH]:
st_mode = os.lstat(projpath).st_mode
os.chmod(projpath, st_mode & ~perm)
# by default, add group and others read and browse permission
for perm in [stat.S_IRGRP, stat.S_IROTH, stat.S_IXGRP, stat.S_IXOTH]:
st_mode = os.lstat(projpath).st_mode
os.chmod(projpath, st_mode | perm)
# update list of shots/times from mainSettings and modules settings
modules = self.moduleDict()
for k in ['device', 'shot', 'time']:
self.prj_options[k] = []
for k in ['device', 'shot', 'shots', 'time', 'times']:
self.prj_options[k.rstrip('s')].extend(tolist(evalExpr(self['MainSettings']['EXPERIMENT'][k])))
try:
for module in list(modules.keys()):
mod = eval('OMFIT' + module)
self.prj_options.setdefault(k.rstrip('s'), []).extend(
tolist(evalExpr(mod['SETTINGS'].get('EXPERIMENT', {}).get(k, None)))
)
self.prj_options[k.rstrip('s')] = list([_f for _f in self.prj_options[k.rstrip('s')] if _f])
except Exception as _excp:
printe('Error accessing `%s` of module `OMFIT%s` : %s' % (k, module, repr(_excp)))
for k in ['device', 'shot', 'time']:
self.prj_options[k] = np.unique(list([_f for _f in self.prj_options[k.rstrip('s')] if _f])).tolist()
# if the GUI is open update the GUI elements info
if OMFITaux['GUI']:
commands = []
commandNames = []
for k in range(len(OMFITaux['GUI'].command)):
tmp = OMFITaux['GUI'].command[k].get(1.0, tk.END).strip()
if len(tmp):
commands.append(OMFITaux['GUI'].command[k].get(1.0, tk.END))
commandNames.append(OMFITaux['GUI'].commandNames[k])
if not len(commands):
commands.append('')
commandNames.append('1')
OMFIT.prj_options['commands'] = commands
OMFIT.prj_options['commandNames'] = commandNames
OMFIT.prj_options['namespace'] = OMFITaux['GUI'].commandBoxNamespace
OMFIT.prj_options['notes'] = OMFITaux['GUI'].notes.get(1.0, tk.END).strip()
OMFIT.prj_options['console'] = OMFITaux['console'].get()
OMFIT.prj_options.setdefault('color', '')
if OMFIT.prj_options['color'] not in list(OMFIT.prj_options_choices['color'].keys()):
OMFIT.prj_options['color'] = ''
if OMFIT.prj_options['type'] not in OMFIT.prj_options_choices['type']:
OMFIT.prj_options['type'] = ''
try:
OMFITaux['hardLinks'] = True
self['__GUISAVE__'] = self.prj_options
cb = OMFITtree()
for k, v in enumerate(self['__GUISAVE__']['commands']):
if not v.strip():
continue
try:
cb['%d.py' % (k + 1)] = OMFITascii(filename='%d.py' % (k + 1), fromString=v.rstrip())
except Exception as _excp:
printe(_excp)
if list(cb.keys()):
self['__COMMANDBOX__'] = cb
orig_version = self['MainSettings']['SETUP']['version']
orig_environ = self['MainSettings']['SETUP']['python_environment']
self['MainSettings']['SETUP']['version'] = repo_active_branch_commit
self['MainSettings']['SETUP']['python_environment'] = SortedDict(python_environment())
return self._save(
filename,
zip=zip,
quiet=quiet,
skipStorage=False,
updateExistingDir=updateExistingDir,
skip_save_errors=skip_save_errors,
)
except Exception:
self['MainSettings']['SETUP']['version'] = orig_version
self['MainSettings']['SETUP']['python_environment'] = orig_environ
raise
finally:
if '__GUISAVE__' in self:
del self['__GUISAVE__']
if '__COMMANDBOX__' in self:
del self['__COMMANDBOX__']
OMFITaux['hardLinks'] = False
else:
raise IOError('Last saved directory was not defined')
[docs] def saveas(self, filename, zip=None, quiet=None, skip_save_errors=False):
"""
Writes the content of the OMFIT tree to the filesystem
and permanently changes the name of the project
:param filename: project filename to save to
:param zip: whether the save should occur as a zip file
:param quiet: whether to print save progress to screen
:param skip_save_errors: skip errors when saving objects
"""
if quiet is None:
quiet = bool(eval(os.environ.get('OMFIT_PROGRESS_BAR_QUIET', '0')))
oldZip = self.zip
oldFilename = self.filename
oldPrj_options = self.prj_options
if zip is not None:
self.zip = zip
self.filename = filename
try:
return self.save(quiet=quiet, skip_save_errors=skip_save_errors)
except Exception:
self.zip = oldZip
self.filename = oldFilename
self.prj_options = oldPrj_options
raise
[docs] def loadModule(
self,
filename,
location=None,
withSubmodules=True,
availableModulesList=None,
checkLicense=True,
developerMode=None,
depth=0,
quiet=False,
startup_lib=None,
**kw,
):
r"""
Load a module in OMFIT
:param filename: * full path to the module to be loaded
* if just the module name is provided, this will be loaded from the public modules
* remote/branch:module format will load a module from a specific git remote and branch
* module:remote/branch format will load a module from a specific git remote and branch
:param location: string with the location where to place the module in the OMFIT tree
:param withSubmodules: load submodules or not
:param availableModulesList: list of available modules generated by ``OMFIT.availableModules()``
If this list is not passed, then the availableModulesList is generated internally
:param checkLicense: Check license files at load
:param developerMode: Load module with developer mode option (ie. scripts loaded as modifyOriginal)
if None then default behavior is set by ``OMFIT['MainSettings']['SETUP']['developer_mode_by_default']``
Note: public OMFIT installation cannot be loaded in developer mode
:param depth: parameter used internally by for keeping track of the recursion depth
:param quiet: load modules silently or not
:param startup_lib: Used internally for executing OMFITlib_startup scripts
:param \**kw: additional keywords passed to OMFITmodule() class
:return: instance of the loaded module
"""
if os.sep not in filename or ':' in filename:
# if there is a semicolumn in the filename, then a specific remote/branch is been requested
if ':' in filename:
work_repo = repo.clone()
remote, branch = [x for x in filename.split(':') if '/' in x][0].split('/')
filename = [x for x in filename.split(':') if '/' not in x][0]
work_repo.switch_branch(branch, remote)
filename = os.sep.join([work_repo.git_dir, 'modules', filename, 'OMFITsave.txt'])
else:
# if it's just a module name, load it from the first of the OMFITmodule directories
filename = os.sep.join([OMFITmodule.directories()[0], filename, 'OMFITsave.txt'])
filename = os.path.abspath(filename)
# get list of available modules
if availableModulesList is None:
availableModulesList = self.availableModules(quiet=True, same_path_as=filename)
# handle developerMode switch
OMFITsrc = os.path.split(os.path.split(os.path.split(filename)[0])[0])[0] + os.sep + 'omfit'
if os.path.exists(os.sep.join([OMFITsrc, '..', 'public'])):
developerMode = False
if developerMode is None:
developerMode = OMFIT['MainSettings']['SETUP']['developer_mode_by_default']
# load the module
moduleName = OMFITmodule.info(filename).get('ID', 'unknown_module')
if location is None:
location = "self['" + moduleName + "']"
# handle printing
kw.pop('quiet', None)
quiet_module = True
if not quiet:
quiet_module = {
'newline': False,
'clean': False,
'quiet': bool(eval(os.environ.get('OMFIT_PROGRESS_BAR_QUIET', '0'))),
'style': ' [{sfill}{svoid}] {perc:3.2f}% ' + '*' * (depth + 1) + ' ' + moduleName + '{mess}',
}
# load module
tmp = OMFITmodule(filename, developerMode=developerMode, quiet=quiet_module, **kw)
# remove the module filename as there is no point of keeping it once it's loaded from the repo
# OMFITtree (and derived classes) filenames are used for saving them external to the project
tmp.filename = ''
# if loading as a submodule, then place at the top
loc = parseLocation(location)
if isinstance(eval(buildLocation(loc[:-1])), OMFITmodule):
eval(buildLocation(loc[:-1])).insert(0, loc[-1], tmp)
else:
eval(buildLocation(loc[:-1]))[loc[-1]] = tmp
# add extra commit info to MODULE
if filename in availableModulesList:
for k in _moduleAttrs:
if k in availableModulesList[filename]:
tmp['SETTINGS']['MODULE'][k] = availableModulesList[filename][k]
# fill in missing infos (e.g. when starting a new module)
if not tmp['SETTINGS']['MODULE']['commit']:
tmp['SETTINGS']['MODULE']['commit'] = repo.get_hash('HEAD')
if tmp['SETTINGS']['MODULE']['contact'] is None:
tmp['SETTINGS']['MODULE']['contact'] = []
if not len(tmp['SETTINGS']['MODULE']['contact']) and OMFIT['MainSettings']['SETUP']['email']:
tmp['SETTINGS']['MODULE']['contact'].append(OMFIT['MainSettings']['SETUP']['email'])
# Check license
if checkLicense and 'license' in eval(location):
license = eval(location)['license']
email_dict = {}
with open(license.filename, 'r') as f:
for k in f.readlines():
k = str(k)
if 'OMFIT_license_email_notify' in k:
notify = [x.strip() for x in re.sub(r'OMFIT_license_email_notify\:(.*)', r'\1', k).strip().split(',')]
email_dict = {
'email_address': notify,
'email_prompt': 'Please describe planned research using ' + moduleName,
'fromm': self['MainSettings']['SETUP']['email'],
}
break
try:
OMFITlicenses[moduleName] = License(moduleName, license.filename, email_dict=email_dict, rootGUI=OMFITaux['rootGUI'])
if OMFITaux['rootGUI']:
OMFITlicenses[moduleName].check()
except LicenseException:
exec('del ' + location, globals(), locals())
raise
except tk.TclError: # If there is no DISPLAY, allow access
pass
except IndexError: # If gui element fails to load, allow access
pass
# load the submodules (will set DEPENDENCIES, SETTINGS['EXPERIMENT'], and honor LIB['OMFITlib_startup'] scripts)
if withSubmodules:
# find the submodules (one level deep)
moduleDict = eval(location).moduleDict(level=0)
# save the dependencies
depsDict = {}
for subMod in moduleDict:
depsDict[subMod] = eval(location + subMod)['SETTINGS']['DEPENDENCIES']
# load the submodules
if startup_lib is None:
startup_lib = []
for subMod in moduleDict:
found = False
for avMod in availableModulesList:
if moduleDict[subMod]['ID'] == availableModulesList[avMod]['ID']:
OMFIT.loadModule(
availableModulesList[avMod]['path'],
location + subMod,
withSubmodules=True,
availableModulesList=availableModulesList,
checkLicense=checkLicense,
developerMode=developerMode,
depth=depth + 1,
quiet=quiet,
startup_lib=startup_lib,
**kw,
)
found = True
break
if not found:
raise IOError(
'Module %s is a submodule of %s, and it could not found in %s'
% (moduleDict[subMod]['ID'], moduleName, os.path.split(os.path.split(filename)[0])[0])
)
# restore the dependencies
for subMod in moduleDict:
for avMod in availableModulesList:
if moduleDict[subMod]['ID'] == availableModulesList[avMod]['ID']:
eval(location + subMod)['SETTINGS']['DEPENDENCIES'].update(depsDict[subMod])
break
# freeze the root['SETTINGS']['EXPERIMENT'] entries if this is a top-level import that is not a submodule
if depth == 0 and 'SETTINGS' in eval(location) and 'EXPERIMENT' in eval(location)['SETTINGS']:
freeze = True
for tmpName in reversed(traverseLocation(location)[:-1]):
if eval(tmpName).__class__ is OMFITmodule and tmpName != 'OMFIT':
freeze = False
if freeze:
for item in list(OMFITaux['moduleSkeletonCache']['SETTINGS']['EXPERIMENT'].keys()):
eval(location)['SETTINGS']['EXPERIMENT'][item] = evalExpr(eval(location)['SETTINGS']['EXPERIMENT'][item])
# execute startup script (the OMFITmodulePath variable is setup to point to the OMFITsave.txt file of the module that is being loaded)
if 'LIB' in eval(location) and 'OMFITlib_startup' in eval(location)['LIB']:
startup_lib.append((moduleName, location, eval(location)['LIB']['OMFITlib_startup']))
if depth == 0:
for k, (mname, loc, st_lib) in enumerate(startup_lib):
if not quiet:
if k == 0:
printi("Running OMFITlib_startup:", end='')
printi(f' {mname}', end='')
try:
with quiet_environment():
st_lib.runNoGUI()
except Exception as _excp:
printe("Error in %s['LIB']['OMFITlib_startup'] : " % (loc) + repr(_excp))
if not quiet:
printi('')
# store settings at load time
# NOTE: this is done both here and in OMFITmodule.__init__ because this one will get execution of OMFITlib_startup and the other instead is needed when reloading a module
eval(location)._save_settings_at_import()
# return the module
return eval(location)
[docs] def load(self, filename, persistent_projectID=False):
"""
loads an OMFITproject in OMFIT
:param filename: filename of the project to load (if `-1` then the most recent project is loaded)
:param persistent_projectID: whether the projectID should remain the same
"""
try:
# open the last project
if filename == '-1':
projects = OMFIT.recentProjects()
if len(projects):
filename = list(projects.keys())[0]
persistent_projectID = projects[filename].get('persistent_projectID', False)
# keep aside user 'SETUP','SERVER'
tmp = {}
for item in ['SETUP', 'SERVER']:
if item in self['MainSettings']:
tmp[item] = copy.deepcopy(self['MainSettings'][item])
self.filename = os.path.abspath(filename)
oldDir = os.getcwd()
TMPnoCopyToCWD = OMFITaux['noCopyToCWD']
OMFITaux['noCopyToCWD'] = False
try:
self._load(filename)
finally:
os.chdir(oldDir)
OMFITaux['noCopyToCWD'] = TMPnoCopyToCWD
if zipfile.is_zipfile(self.filename):
self.zip = True
projectName = os.path.split(self.filename)[1]
else:
self.zip = False
projectName = os.path.split(os.path.split(self.filename)[0])[1]
# for older projects we calculate provenanceID based on institution and projectName
# very old projects do not even have institution info
if 'provenanceID' not in self['MainSettings']['EXPERIMENT']:
self['MainSettings']['EXPERIMENT']['provenanceID'] = omfit_hash(
self['MainSettings']['SETUP'].get('institution', 'old_project') + '_' + projectName
)
# SETUP is overwritten (but not version nor python_environment)
project_version = self['MainSettings']['SETUP'].get('version', '?')
project_environ = self['MainSettings']['SETUP'].get('python_environment', {})
self['MainSettings']['SETUP'] = tmp['SETUP']
self['MainSettings']['SETUP']['version'] = project_version
self['MainSettings']['SETUP']['python_environment'] = project_environ
# SERVER is updated
self['MainSettings'].setdefault('SERVER', NamelistName()).update(tmp.get('SERVER', {}))
# load project options
self.prj_options.clear()
tmp = OMFITproject.info(self.filename)
for k in OMFIT.prj_options_choices:
self.prj_options[k] = tmp.get(k, '')
for whereSave in ['__GUISAVE__', '__COMMANDBOX__']:
if whereSave in OMFIT:
del OMFIT[whereSave]
if self.prj_options['color'] not in list(self.prj_options_choices['color'].keys()):
self.prj_options['color'] = ''
if self.prj_options['type'] not in self.prj_options_choices['type']:
self.prj_options['type'] = ''
if 'namespace' not in self.prj_options or not self.prj_options['namespace']:
self.prj_options['namespace'] = 'OMFIT'
# update projectID
self.prj_options['persistent_projectID'] = persistent_projectID
if not persistent_projectID:
self.newProjectID()
# keep MainSettings in check
self.updateMainSettings()
self['MainSettings'].sort()
# set the localhost
SERVER.setLocalhost()
# remote projects are loaded in OMFITtmpDir
# reset the filename to force users to decide how/where to save it
if OMFITtmpDir in self.filename:
self.filename = ''
except Exception:
self.start()
raise
[docs] def updateCWD(self):
global OMFITcwd
self._save(filename=OMFITcwd + os.sep + 'OMFITsave.txt', skipStorage=False)
[docs] def updateMainSettings(self):
self.addMainSettings()
self.keyOrder.remove('scratch')
self.keyOrder.append('scratch')
self.keyOrder.remove('commandBox')
self.keyOrder.append('commandBox')
self.keyOrder.remove('scriptsRun')
self.keyOrder.append('scriptsRun')
self.keyOrder.remove('shotBookmarks')
self.keyOrder.append('shotBookmarks')
self.keyOrder.remove('MainSettings')
self.keyOrder.append('MainSettings')
[docs] def saveMainSettingsSkeleton(self):
"""
This utility function updates the MainSettingsSkeleton for the current OMFIT installation
"""
self['MainSettings'].sort()
tmp = copy.deepcopy(self['MainSettings'])
self.addMainSettings(restore='skel')
keys = self['MainSettings'].keys()
for k in keys:
if k.startswith('__comment'):
del self['MainSettings'][k]
self['MainSettings'].sort()
try:
self['MainSettings'].filename = self['MainSettings']['SETUP']['workDir'] + '../' + 'skeletonMainSettingsNamelist.txt'
self['MainSettings']['SETUP']['version'] = '?'
self['MainSettings']['SETUP']['python_environment'] = {}
del self['MainSettings']['EXPERIMENT']['projectID']
del self['MainSettings']['EXPERIMENT']['provenanceID']
self['MainSettings']['SETUP']['browser'] = None
self['MainSettings']['SETUP']['Extensions'].clear()
# Avoid changes made by institution file
self['MainSettings']['SETUP']['stats_file'] = OMFITexpression("os.path.abspath(OMFITsettingsDir+'/OMFITstats.txt')")
self['MainSettings']['SETUP']['institution'] = 'PERSONAL'
if 'institutionProjectsDir' in self['MainSettings']['SETUP']:
del self['MainSettings']['SETUP']['institutionProjectsDir']
self['MainSettings']['EXPERIMENT']['device'] = None
for k in tmp['SERVER']:
if k not in self['MainSettings']['SERVER']:
self['MainSettings']['SERVER'][k] = tmp['SERVER'][k]
if isinstance(tmp['SERVER'][k], namelist.NamelistName):
self['MainSettings']['SERVER'][k].update(tmp['SERVER'][k])
self['MainSettings']['SERVER']['localhost'] = namelist.NamelistName()
self['MainSettings']['SERVER']['localhost']['workDir'] = OMFITexpression("OMFITcwd+os.sep+'remote_runs'+os.sep")
self['MainSettings']['SERVER']['localhost']['server'] = 'localhost'
self['MainSettings']['SERVER']['localhost']['tunnel'] = ''
self['MainSettings']['SERVER']['localhost']['idl'] = ''
self['MainSettings']['SERVER']['localhost']['matlab'] = ''
self['MainSettings']['SERVER']['default_tunnel'] = None
finally:
self['MainSettings'].sort()
self._save(
filename=OMFITsrc + os.sep + 'omfit_classes' + os.sep + 'skeleton' + os.sep + 'skeletonMainSettings.txt',
only="['MainSettings']",
updateExistingDir=True,
)
self['MainSettings'] = tmp
[docs] def availableModules(self=None, quiet=None, directories=None, same_path_as=None, force=False):
"""
Index available OMFIT modules in directories
:param quiet: verbosity
:param directories: list of directories to index. If `None` this is taken from OMFIT['MainSettings']['SETUP']['modulesDir']
:param same_path_as: sample OMFITsave.txt path to set directory to index
:param force: force rebuild of .modulesInfoCache file
:return: This method returns a dictionary with the available OMFIT modules.
Each element in the dictionary is a dictionary itself with the details of the available modules.
"""
if quiet is None:
quiet = bool(eval(os.environ.get('OMFIT_PROGRESS_BAR_QUIET', '0')))
if directories is None:
directories = OMFITmodule.directories()
else:
directories = tolist(directories)
if same_path_as is None:
pass
elif 'OMFITsave.txt' in same_path_as and os.path.exists(same_path_as):
directories = [os.path.split(os.path.split(same_path_as)[0])[0]]
else:
raise IOError('%s file is not a valid OMFITsave.txt file' % same_path_as)
updatePersistentCache = []
moduleDict = {}
for directory in directories: # the user inputs the directory where the modules are
if not quiet:
tmp = 'Modules directory: ' + directory
printi('=' * len(tmp))
printi(tmp)
printi('=' * len(tmp))
print('', end='')
if not force and os.path.exists(directory + os.sep + '.modulesInfoCache'):
try:
with open(directory + os.sep + '.modulesInfoCache', 'rb') as f:
_availableModulesCache[directory] = pickle.load(f)
except Exception:
_availableModulesCache[directory] = {}
printw('-- Failed to load persistent git modules cache --')
else:
_availableModulesCache[directory] = {}
# modules in directory
modules_list_in_dir = sorted(
[os.path.abspath(x) for x in glob.glob(os.sep.join([directory, '*', 'OMFITsave.txt']))], key=lambda x: x.lower()
)
# try handling git repository of modules twice
# first as if git root directory parent directory of modules directory
# second as if git root directory is modules directory
cases_errors = []
cases = []
if os.path.split(directory)[1] == 'modules':
cases.append([os.path.split(directory)[0], 'modules'])
cases.append([directory, ''])
for repo_dir, modules_subpath in cases:
try:
# try to access as a git repository
repo = OMFITgit(repo_dir)
commit = repo("log -1 --pretty='%H'")
branch = repo('rev-parse --abbrev-ref HEAD')
remote = repo.get_branches().get(branch, {'remote': ''})['remote']
changed_modules = []
# if same remote/branch and commit
if (
np.all([k in _availableModulesCache[directory] for k in ['branch', 'remote', commit]])
and _availableModulesCache[directory]['remote'] == remote
and _availableModulesCache[directory]['branch'] == branch
):
changes = list([_f for _f in repo("ls-files -m --others --exclude-standard " + directory).split('\n') if _f])
for mod_path in modules_list_in_dir:
if (
mod_path not in _availableModulesCache[directory][commit]
or len(_availableModulesCache[directory][commit][mod_path]['modified'])
or len(_availableModulesCache[directory][commit][mod_path]['untracked'])
):
changes.append(os.sep.join(mod_path.split(os.sep)[[-2, -3][len(modules_subpath) > 0] :]))
if len(changes):
if not quiet:
printi('-- some modules changes are not part of git --')
for mod in tolist(np.unique([x.split(os.sep)[[0, 1][len(modules_subpath) > 0]] for x in changes])):
mod_path = directory + os.sep + mod
if not os.path.exists(mod_path):
raise Exception(mod_path + ' does not exist')
tmp = repo.get_module_params(quiet=quiet, path=modules_subpath, key='path', modules=[mod_path])
_availableModulesCache[directory][commit].update(tmp)
changed_modules.append(os.path.abspath(mod_path + os.sep + 'OMFITsave.txt'))
elif not quiet:
printi('-- modules cache is valid --')
else:
# if same remote/branch then try to update since recorded commit (faster: only need to loop over modules that changed)
if (
np.all([k in _availableModulesCache[directory] for k in ['branch', 'remote']])
and len(_availableModulesCache[directory]) == 3
and _availableModulesCache[directory]['remote'] == remote
and _availableModulesCache[directory]['branch'] == branch
):
printi('-- updating modules cache since last commit --')
try:
old_commit = [
item for item in list(_availableModulesCache[directory].keys()) if item not in ['branch', 'remote']
][0]
changes = np.unique(
[
modules_subpath + '/' + re.sub('^' + modules_subpath + '/', '', x).split(os.sep)[0]
for x in repo('diff --name-only %s %s -- %s' % (old_commit, commit, modules_subpath)).split()
]
).tolist()
changed_modules = [os.sep.join([repo_dir, x, 'OMFITsave.txt']) for x in changes]
_availableModulesCache[directory][commit] = _availableModulesCache[directory][old_commit]
del _availableModulesCache[directory][old_commit]
_availableModulesCache[directory][commit].update(
repo.get_module_params(quiet=quiet, path=modules_subpath, key='path', modules=changed_modules)
)
except Exception as _excp:
printw('Failed to update available modules cache: ' + repr(_excp))
del _availableModulesCache[directory]
else:
printi('-- rebuilding modules cache from scratch --')
if directory in _availableModulesCache:
del _availableModulesCache[directory]
# if directory is not in _availableModulesCache then must build everything from scratch
if directory not in _availableModulesCache:
_availableModulesCache[directory] = {}
_availableModulesCache[directory]['branch'] = branch
_availableModulesCache[directory]['remote'] = remote
_availableModulesCache[directory][commit] = repo.get_module_params(
quiet=quiet, path=modules_subpath, key='path'
)
updatePersistentCache.append(directory)
# delete modules from cache if these are not found on hard drive
for mod_path in list(_availableModulesCache[directory][commit].keys()):
if not os.path.exists(_availableModulesCache[directory][commit][mod_path]['path']):
del _availableModulesCache[directory][commit][mod_path]
# update list of modules
moduleDict.update(_availableModulesCache[directory][commit])
# do not try 2nd case if 1st one worked
break
except Exception as _excp:
cases_errors.append(_excp)
if len(cases_errors) == len(cases):
_availableModulesCache[directory].clear()
# if the path is not a valid git repository or the data was modified then get modules by hand
for mod_path in modules_list_in_dir:
if mod_path in moduleDict:
continue
mod = os.path.split(mod_path)[0]
mod_name = os.path.split(mod)[1]
if not quiet:
printi(mod_name.ljust(20) + ' (untracked)')
moduleDict[mod_path] = {}
moduleDict[mod_path]['path'] = mod_path
moduleDict[mod_path]['untracked'] = mod_path # just for compatibility with data returned by `get_module_params`
moduleDict[mod_path]['modified'] = mod_path # just for compatibility with data returned by `get_module_params`
moduleDict[mod_path]['edited_by'] = os.environ['USER']
moduleDict[mod_path]['date'] = convertDateFormat(time.time())
moduleDict[mod_path]['commit'] = ''
moduleDict[mod_path]['description'] = ''
info = OMFITmodule.info(moduleDict[mod_path]['path'])
info.pop('date', None)
info.pop('edited_by', None)
info.pop('commit', None)
moduleDict[mod_path].update(info)
# save modules info cache
if directory in updatePersistentCache or not os.path.exists(directory + os.sep + '.modulesInfoCache'):
try:
with open(directory + os.sep + '.modulesInfoCache', 'wb') as f:
pickle.dump(_availableModulesCache[directory], f, pickle.OMFIT_PROTOCOL)
printi('-- Updated persistent git modules cache --')
except IOError:
pass
return moduleDict
[docs] def quit(self, deepClean=False):
"""
Cleanup current OMFIT session directory `OMFITsessionDir` and PID from `OMFITsessionsDir`
Also close all SSH related tunnels and connections
:param deepClean: if deepClean is True, then the `OMFITtmpDir` and `OMFITsessionsDir` get deleted
"""
if OMFITcwd is None:
return
onlyRunningCopy = OMFIT.onlyRunningCopy(deletePID=True)
if onlyRunningCopy:
OMFIT.reset_connections() # reset_connections() will also close_mds_connections()
else:
omfit_classes.omfit_mds.close_mds_connections()
try:
if os.path.exists(OMFITsessionDir):
shutil.rmtree(OMFITsessionDir)
except Exception:
printw('Some files and directories could not be deleted!')
if deepClean:
if os.path.exists(OMFITsessionsDir):
try:
shutil.rmtree(OMFITsessionsDir)
os.makedirs(OMFITsessionsDir)
except OSError:
printw('Some files and directories under %s could not be deleted!' % OMFITsessionsDir)
if os.path.exists(OMFITtmpDir):
try:
shutil.rmtree(OMFITtmpDir)
except Exception:
printw('Some files and directories under %s could not be deleted!' % OMFITtmpDir)
return onlyRunningCopy
[docs] def reset_connections(self, server=None, mds_cache=True):
"""
Reset connections, stored passwords, and MDSplus cache
:param server: only reset SSH connections to this server
"""
import utils_widgets
serverPicker = ''
if server is None:
printi('Reset OMFIT stored passwords')
utils_widgets.stored_passwords.clear()
printi('Reset OMFIT server cache')
SERVER_cache.clear()
if mds_cache:
printi('Purge OMFIT MDSplus cache')
OMFITmdsCache().purge()
else:
printi('OMFIT MDSplus cache not purged; use OMFITmdsCache().purge() to purge it')
printi('Reset OMFIT SSH connections')
printi('Reset OMFIT MDSplus connections')
omfit_classes.omfit_mds.close_mds_connections()
printi('Reset OMFIT SQL connections')
for k in ['MDSserverReachable', 'RDBserverReachable', 'batch_js', 'sshTunnel', 'sysinfo']:
OMFITaux[k] = copy.deepcopy(OMFITaux.defaults[k])
else:
if server:
serverPicker = parse_server(SERVER[server]['server'])[2]
printi('Reset OMFIT SSH connections to %s' % serverPicker)
sshServices = ['OMFITssh', 'OMFITsshTunnel', 'OMFITsshControlmaster', 'OMFITsshGit']
# Have to create tmpdir since OMFIT tmp directory may have been cleaned up already
import tempfile, shutil
tmpdir = tempfile.mkdtemp()
s = subprocess.Popen("ps xw", stdout=subprocess.PIPE, shell=True, cwd=tmpdir)
std_out, std_err = s.communicate()
shutil.rmtree(tmpdir)
for item in b2s(std_out).split('\n'):
service = [s for s in sshServices if re.search(s, item)]
if len(service) and re.search(serverPicker, item):
pid = int([_f for _f in item.split(' ') if _f][0])
try:
printi('kill %s' % (item))
os.kill(int(pid), signal.SIGKILL)
except OSError as e:
printw('Failed! %s' % repr(e))
[docs] def recentProjects(self, only_read=False):
"""
This routine keeps track of the recent projects
and is also in charge of deleting auto-saves if they do not appear in the project list.
:param read_only: only read projects file (don't do any maintenance on it)
"""
# do not log projects that are in OMFITtmpDir
if OMFITtmpDir in OMFIT.filename:
return
filename_old = OMFITsettingsDir + os.sep + 'OMFITrecentProjects.txt'
filename = OMFITsettingsDir + os.sep + 'OMFITprojects.txt'
autoSaveLinkDir = os.path.abspath(OMFIT['MainSettings']['SETUP']['projectsDir'].rstrip('/\\')) + os.sep + 'auto-save' + os.sep
if not os.path.exists(filename) and os.path.exists(filename_old):
shutil.copyfile(filename_old, filename)
# read the projects
projects = SortedDict()
if os.path.exists(filename):
with open(filename, 'r') as f:
lines = f.readlines()
for k, line in enumerate(lines):
line = line.strip()
tmp = line.split('{')
if len(tmp) == 1:
path = tmp[0].strip()
opts = {}
else:
path = tmp[0].strip()
opts = eval('{' + '{'.join(tmp[1:]))
if os.path.exists(path):
projects[path] = opts
# add extra info (eg. file size)
for item in list(projects.keys()):
if 'size' not in projects[item] and os.path.exists(item) and item.endswith('.zip') and zipfile.is_zipfile(item):
projects[item]['size'] = os.stat(item).st_size
if only_read:
return projects
# this switch will be set to True if the recent projects file needs to be updated
doWrite = False
# delete `Self-Destruct` projects that have not been accessed in more than 30 days
for item in list(projects.keys()):
if projects[item].get('type', '') == 'Self-Destruct' and os.stat(item).st_atime < (time.time() - 30 * 86400):
if os.path.isdir(item):
shutil.rmtree(item)
else:
os.remove(item)
del projects[item]
doWrite = True
# add projects which for some reason were not already there at the bottom of the list
if os.path.exists(os.path.abspath(evalExpr(OMFIT['MainSettings']['SETUP']['projectsDir']))):
for item in glob.glob(os.path.abspath(evalExpr(OMFIT['MainSettings']['SETUP']['projectsDir'])) + os.sep + '*'):
if os.path.isdir(item):
if os.path.exists(item + os.sep + 'OMFITsave.txt'):
item = item + os.sep + 'OMFITsave.txt'
else:
continue
if item not in projects:
projects[item] = {}
doWrite = True
# try to read prj_options for the projects which do not have them
for item in list(projects.keys()):
if 'device' not in projects[item]:
try:
tmp = OMFITproject.info(item)
except Exception as _excp:
printe('%s looks like an invalid OMFIT project' % (item))
del projects[item]
continue
tmp.setdefault('notes', '')
for opt in OMFIT.prj_options_choices:
if opt in tmp:
projects[item][opt] = tmp[opt]
doWrite = True
# if the current project has been saved put it at the top of the list
if (
OMFIT.filename is not None
and len(OMFIT.filename)
and autoSaveLinkDir not in OMFIT.filename
and OMFITautosaveDir not in OMFIT.filename
):
item = os.path.abspath(OMFIT.filename)
if item in list(projects.keys()):
del projects[item]
projects.insert(0, item, copy.deepcopy(OMFIT.prj_options))
if item.endswith('.zip') and zipfile.is_zipfile(item):
projects[item]['size'] = os.stat(item).st_size
elif item.endswith('OMFITsave.txt'):
projects[item]['size'] = size_of_dir(os.path.split(item)[0])
doWrite = True
# do not store console output, commands, and namespace in OMFITprojects.txt
for item in list(projects.keys()):
for opt in ['console', 'commands', 'namespace']:
if opt in projects[item]:
del projects[item][opt]
doWrite = True
# only store modules locations
for item in list(projects.keys()):
if isinstance(projects[item]['modules'], dict):
projects[item]['modules'] = list(projects[item]['modules'].keys())
# write OMFITprojects.txt~ then move to OMFITprojects.txt if successful
# this is to have as much of an atomic operation as possible
if doWrite:
with open(filename_old + '~', 'w') as f_old, open(filename + '~', 'w') as f:
for item in list(projects.keys()):
f.write('%s %s\n' % (item, projects[item]))
f_old.write('%s\n' % (item))
shutil.move(filename + '~', filename)
shutil.move(filename_old + '~', filename_old)
# delete auto-saves that are older than one week
# process one old auto-save at the time ones that were accessed first (deleting large auto-saves can take some time)
for dir in [OMFITautosaveDir, autoSaveLinkDir]:
# sort auto-saves by time
files = glob.glob(dir + os.sep + '*')
# delete broken links (otherwise getatime will fail)
remove = []
for path in files:
if os.path.islink(path) and not os.path.exists(path):
os.remove(path)
remove.append(path)
files = list(set(files).difference(set(remove)))
# sort files
files.sort(key=lambda x: os.path.getatime(x))
for path in files:
# delete auto-saves that have not been accessed in more than one week
if not os.path.islink(path) and os.path.isdir(path) and os.stat(path).st_atime < (time.time() - 7 * 86400):
shutil.rmtree(path)
break # delete one old auto-save at the time
# delete broken links
if os.path.islink(path) and not os.path.exists(path):
os.remove(path)
return projects
[docs] def showExecDiag(self):
"""
display execution diagram
"""
def printMe(tmp, depth):
for child in tmp:
filename = re.sub('__console__.py', '', os.path.split(child['filename'])[1])
printi('* ' * (depth + 1) + " %s %3.3fs [%s]" % (filename, child['time'], sizeof_fmt(child['memory'])))
printMe(child['child'], depth + 1)
printi('\nExecution diagram:\n------------------')
from omfit_classes.omfit_python import ExecDiagPtr
printMe(ExecDiagPtr, 0)
[docs]class OMFITmainscratch(OMFITtmp):
def __init__(self):
self.required = list(map(lambda x: os.path.splitext(os.path.basename(x))[0], glob.glob(OMFITsrc + '/framework_guis/*.py')))
[docs] def initialize(self):
for item in self.required:
self.load_framework_gui(item)
[docs] def load_framework_gui(self, item):
dev_acceptable = os.access(OMFITsrc + os.sep + 'framework_guis' + os.sep + item + '.py', os.W_OK) and not os.path.exists(
os.sep.join([OMFITsrc, '..', 'public'])
)
self[f'__{item}__'] = OMFITpythonGUI(
OMFITsrc + os.sep + 'framework_guis' + os.sep + item + '.py',
modifyOriginal=OMFIT['MainSettings']['SETUP']['developer_mode_by_default'] & dev_acceptable,
)
def __delitem__(self, key):
if key in self.required:
self.load_framework_gui(key)
else:
super().__delitem__(key)
# --------------------------------
# Setup the global variable OMFIT
# --------------------------------
OMFIT.__class__ = OMFITmaintree # root of the OMFIT tree
OMFIT.modifyOriginal = False
OMFIT.readOnly = False
OMFIT._OMFITkeyName = 'OMFIT'
OMFIT.prj_options = {}
OMFIT.prj_options_choices = {
'notes': '',
'commands': '',
'commandNames': [],
'namespace': '',
'console': '',
'shot': '',
'time': '',
'device': '',
'modules': '',
'type': ['Self-Destruct', 'Test', 'Working', 'Done', 'VIP'],
'persistent_projectID': False,
'color': OrderedDict(
(
('red', 'red2'),
('orange', 'dark orange'),
('yellow', 'orange'),
('green', 'forest green'),
('blue', 'mediumblue'),
('purple', 'medium orchid'),
('gray', 'gray25'),
)
),
}
atexit.register(OMFIT.quit) # Register final automatic cleanup
# ------------------------------------
# location from root requires knowing what `OMFIT` is
# ------------------------------------
[docs]def locationFromRoot(location):
"""
:param location: tree location
:return: tree location from the closest root
"""
tmp = location
location = parseBuildLocation(location)
for k in 1 + np.array(list(range(len(location) - 1))):
loc = eval('OMFIT' + parseBuildLocation(location[:k]))
if loc.__class__ is OMFITmodule:
tmp = "root" + parseBuildLocation(location[k:])
return tmp
[docs]def rootLocation(location, *args, **kw):
"""
:param location: tree location
:return: tree location of the root
"""
if len(args) >= 1:
OMFIT = args[0]
if len(args) >= 2:
kw['rootName'] = args[1]
rootName = kw.setdefault('rootName', 'OMFIT')
location = parseBuildLocation(location)
root = 'OMFIT'
for k in 1 + np.array(list(range(len(location) - 1))):
loc = eval('OMFIT' + parseBuildLocation(location[:k]))
if loc.__class__ is OMFITmodule:
root = 'OMFIT' + parseBuildLocation(location[:k])
root = rootName + root[5:]
return root
# ---------------------
# Import OMFIT APIs
# and make it available to users Python scripts and expressions
# ---------------------
from omfit_classes import OMFITx
setattr(omfit_classes.omfit_python, 'OMFITx', OMFITx)
setattr(omfit_classes.omfit_base, 'OMFITx', OMFITx)
# ---------------------
# graphics
# ---------------------
from omfit_plot import *
# ---------------------
# update classes
# ---------------------
omfit_classes.omfit_base._updateTypes()
# ---------------------
# S3
# ---------------------
[docs]def OMFITobject_fromS3(filename, s3bucket):
"""
Recovers OMFITobject from S3 and reloads it with the right class and original keyword parameters
:return: object loaded from S3
"""
s3connection = boto3.resource('s3', **boto_credentials())
obj = s3connection.Object(s3bucket, filename)
cls = eval(eval(obj.metadata.get('__class__', "'OMFITobject'")))
orig_filename = eval(obj.metadata.get('__filename__', filename))
tmp = cls(filename, s3bucket=s3bucket, **{k: eval(obj.metadata[k]) for k in obj.metadata if k not in ['__class__', '__filename__']})
if os.path.split(tmp.filename)[1] != orig_filename:
shutil.move(tmp.filename, os.path.split(tmp.filename)[0] + os.sep + os.path.split(orig_filename)[1])
tmp.filename = os.path.split(tmp.filename)[0] + os.sep + os.path.split(orig_filename)[1]
tmp.originalFilename = tmp.filename
tmp.link = tmp.filename
return tmp
# ---------------------
# backwards compatibility
# ---------------------
isNone = is_none
[docs]class OMFITfileASCII(OMFITascii):
"""
Use of this class is deprecated: use OMFITascii instead
"""
[docs]class OMFIT_Ufile(OMFITuFile):
"""
Use of this class is deprecated: use OMFITuFile instead
"""
[docs]class OMFITdict(SortedDict):
"""
Use of this class is deprecated: use SortedDict instead
"""
expr_value = evalExpr
[docs]class chebyfit(omfit_classes.utils_fit.fitCH):
"""
Use of this class is deprecated: use fitCH instead
"""
[docs]class OMFITdependenceException(RuntimeError):
"""
Use of this class is deprecated: use RuntimeError instead
"""
# ------------------
# this version time (follows last version time in startup.py)
# ------------------
_filename = OMFITsettingsDir + os.sep + 'OMFITlastRun.txt'
if float(thisVersionTime) > float(latestVersionTime):
with open(_filename, 'w') as _f:
_f.write(str(thisVersionTime))
# --------------------------------------
# load main settings and override / fix
# older versions of users main settings
# NOTE: after this point on OMFIT['MainSettings'] is available and can be accessed
# --------------------------------------
def _clearDeprecatedMainSettings(MainSettings):
# keep track if there has been a change
updated = False
keep = {}
# clear if last version is before given time or if `tmpDir` is found within one month after given time
# (this is done to manage transition between versions of OMFIT that are already running)
if latestVersionTime < 1427916944 or (
'SETUP' in MainSettings and 'tmpDir' in MainSettings['SETUP'] and thisVersionTime < (1427916944 + 60 * 60 * 24 * 30)
):
keep['SETUP'] = {}
keep['SETUP']['email'] = ''
keep['SETUP']['modulesDir'] = ''
keep['SETUP']['editor'] = ''
keep['SETUP']['browser'] = ''
keep['SETUP']['error_report'] = ''
for k in ['Extensions', 'KeyBindings', 'GUIappearance']:
if k in MainSettings['SETUP']:
keep['SETUP'][k] = copy.deepcopy(MainSettings['SETUP'][k])
keep['EXPERIMENT'] = {}
keep['EXPERIMENT']['device'] = ''
keep['EXPERIMENT']['shot'] = ''
keep['EXPERIMENT']['time'] = ''
keep['SERVER'] = {}
keep['SERVER']['ALCF_username'] = ''
keep['SERVER']['GA_username'] = ''
keep['SERVER']['PPPL_username'] = ''
keep['SERVER']['NERSC_username'] = ''
keep['SERVER']['UCSD_username'] = ''
keep['SERVER']['ITM_username'] = ''
keep['SERVER']['MIT_username'] = ''
keep['SERVER']['default'] = ''
keep['SERVER']['idl'] = ''
keep['SERVER']['matlab'] = ''
tmp = prune_mask(MainSettings, keep)
MainSettings.clear()
MainSettings.update(tmp)
updated = True
if 'SERVER' in MainSettings:
# delete deprecated servers and localhost (localhost entry will be re-created)
for server in (
['thea', 'harvest', 'venus', 'venus_tmp', 'venus_scratch', 'hopper', 'zeus', 'lohan', 'philos', 'edison']
+ list(['lohan%d' % x for x in range(20)])
+ ['localhost']
):
if server in list(MainSettings['SERVER'].keys()):
del MainSettings['SERVER'][server]
if server != 'localhost':
updated = '1. deprecated_server:' + server
# delete references to the deprecated servers
for item in list(MainSettings['SERVER'].keys()):
if (
'localhost' not in [item, server]
and isinstance(MainSettings['SERVER'][item], str)
and MainSettings['SERVER'][item] == server
):
del MainSettings['SERVER'][item]
updated = '2. deprecated_server: (%s,%s)' % (server, item)
# delete servers if any of their entries is set to None
for server in list(MainSettings['SERVER'].keys()):
if isinstance(MainSettings['SERVER'][server], namelist.NamelistName):
for item in list(MainSettings['SERVER'][server].keys()):
if MainSettings['SERVER'][server][item] == None:
del MainSettings['SERVER'][server]
updated = 'none_server'
break
# freeze usernames
username_keys = [item for item in MainSettings['SERVER'] if item.endswith('_username')]
for username_key in username_keys:
# if OMFIT is running at a recognized institution set username to match os.environ['USER'] if OMFITexpression or empty string
if (
(isinstance(MainSettings['SERVER'][username_key], OMFITexpression) or not MainSettings['SERVER'][username_key])
and ('institution' in MainSettings['SETUP'])
and username_key == (MainSettings['SETUP']['institution'] + '_username')
):
MainSettings['SERVER'][username_key] = os.environ['USER']
updated = 'freeze_username_institution'
# for all other servers set username to empty string if username is an OMFITexpression
elif isinstance(MainSettings['SERVER'][username_key], OMFITexpression):
MainSettings['SERVER'][username_key] = ''
updated = 'freeze_username_expression'
# NFRI renamed themselves to KFE
if (
'KFE_username' in MainSettings['SERVER']
and not MainSettings['SERVER']['KFE_username']
and 'NFRI_username' in MainSettings['SERVER']
and MainSettings['SERVER']['NFRI_username']
):
MainSettings['SERVER']['KFE_username'] = MainSettings['SERVER']['NFRI_username']
# prevent users to change workDir in bad ways
if 'SETUP' in MainSettings and 'workDir' in MainSettings['SETUP'] and OMFITcwd not in str(MainSettings['SETUP']['workDir']):
MainSettings['SETUP']['workDir'] = OMFITexpression("OMFITcwd+os.sep+'runs'+os.sep")
updated = 'workdir'
if (
'SETUP' in MainSettings
and 'GUIappearance' in MainSettings['SETUP']
and 'persistent_projectID' in MainSettings['SETUP']['GUIappearance']
):
del MainSettings['SETUP']['GUIappearance']['persistent_projectID']
updated = 'persistent_project_id'
if 'EXPERIMENT' in MainSettings and 'runid' in MainSettings['EXPERIMENT'] and MainSettings['EXPERIMENT']['runid'] == None:
MainSettings['EXPERIMENT']['runid'] = 'sim1'
updated = 'experiment'
return updated
OMFIT.reset()
_updated = _clearDeprecatedMainSettings(OMFIT['MainSettings'])
if _updated:
OMFIT.addMainSettings(updateUserSettings=True)
# set OMFIT repos directory where the users projects are stored
# rationale: home directory have quotas, scratch directories get automatically cleaned
omfit_classes.utils_base.OMFITreposDir = (
os.path.split(os.path.abspath(evalExpr(OMFIT['MainSettings']['SETUP']['projectsDir'])))[0] + os.sep + '.repos'
)
# ------------------------------------
# Initialize OMFIT tree
# ------------------------------------
if not np.any([('sphinx' in k and not 'sphinxcontrib' in k) for k in sys.modules]):
OMFIT.start()
print('Time to load omfit_tree: %g seconds' % (time.time() - _t0))
# ------------------------------------
# Set new modules skeleton
# ------------------------------------
if os.path.exists(OMFITsessionDir + os.sep + 'NEW_MODULE_skeleton'):
shutil.rmtree(OMFITsessionDir + os.sep + 'NEW_MODULE_skeleton', ignore_errors=True)
shutil.copytree(
OMFITsrc + os.sep + 'omfit_classes' + os.sep + 'skeleton' + os.sep + 'NEW_MODULE', OMFITsessionDir + os.sep + 'NEW_MODULE_skeleton'
)
OMFITaux['moduleSkeletonCache'] = OMFITtree(
OMFITsessionDir + os.sep + 'NEW_MODULE_skeleton' + os.sep + 'OMFITsave.txt', quiet=True, modifyOriginal=True, readOnly=True
)
