def write_ConvertToHDF5Action_interpolate(yaml, start, end):
log.info('Writing ConvertToHDF5Action.dat for INTERPOLATE GRIDS action')
with open('./ConvertToHDF5Action.dat', 'w') as f:
f.write('<begin_file>\n')
f.write('\n')
f.write('! Written by GetMeteoPy\n')
f.write('{0:30}{1}'.format('ACTION', ': ' + 'INTERPOLATE GRIDS' + '\n'))
f.write('{0:30}{1}'.format('TYPE_OF_INTERPOLATION', ': ' + str(yaml['typeOfInterpolation']) + '\n'))
f.write('\n')
f.write('{0:30}{1}'.format('START', ': ' + datetime.strftime(start, '%Y %m %d %H %M %S') + '\n'))
f.write('{0:30}{1}'.format('END', ': ' + datetime.strftime(end, '%Y %m %d %H %M %S') + '\n'))
f.write('\n')
f.write('{0:30}{1}'.format('OUTPUTFILENAME', ': ' +
yaml['outputPrefix']+'_'+datetime.strftime(start, '%Y-%m-%d')+'_'+datetime.strftime(end, '%Y-%m-%d')+'.hdf5' + '\n'))
f.write('{0:30}{1}'.format('NEW_GRID_FILENAME', ': ' + yaml['bathymetry'] + '\n'))
f.write('\n')
for meteoModel in yaml['meteoModels'].keys():
f.write('{0:30}{1}'.format('FATHER_FILENAME', ': ' + meteoModel + '.hdf5' + '\n'))
f.write('{0:30}{1}'.format('FATHER_GRID_FILENAME', ': ' + yaml['meteoModels'][meteoModel]['meteoDatFile'] + '\n'))
f.write('\n')
if 'propertiesToInterpolate' in yaml.keys():
f.write('<<BeginFields>>\n')
for p in yaml['propertiesToInterpolate']:
f.write(p+'\n')
f.write('<<EndFields>>\n')
f.write('\n')
if ('mohidKeywords' in yaml.keys()) and ('INTERPOLATE GRIDS' in yaml['mohidKeywords'].keys()):
f.write('! Additional keywords\n')
for keyword in yaml['mohidKeywords']['INTERPOLATE GRIDS'].keys():
try: f.write('{0:30}{1}'.format(keyword, ': ' + yaml['mohidKeywords']['INTERPOLATE GRIDS'][keyword] + '\n'))
except TypeError: f.write('{0:30}{1}'.format(keyword, ': ' + str(yaml['mohidKeywords']['INTERPOLATE GRIDS'][keyword]) + '\n'))
f.write('\n')
f.write('<end_file>\n')
copy2('./ConvertToHDF5Action.dat', './ConvertToHDF5Action-INTERPOLATE_GRIDS.dat')
def patch_styles(yaml):
'''
Following the release of 1.0 any user with a config generated by version
0.8 will crash without this method to restructure the style parts of the
config file.
'''
if 'console_style' in yaml.keys():
yaml['console_style'] = {
'fontsize': {
'default': 11,
'user': 11
},
'background_color': {
'default': 'Gray',
'user': '******'
},
'font_color': {
'default': 'Black',
'user': '******'
}
}
if 'edit_area_style' in yaml.keys():
yaml['edit_area_style'] = {'fontsize': {'default': 14, 'user': 14}}
return yaml
def load_qc_input(path):
data = {}
yaml = load_yaml(path)
assert len(yaml.keys()) == 1
patient = list(yaml.keys())[0]
for patient, patient_data in yaml.items():
for sample, sample_data in patient_data.items():
for library, library_data in sample_data.items():
data[(sample, library)] = {
data_label: data
for data_label, data in library_data.items()
}
return data, patient
def write_ConvertToHDF5Action_glue(yaml, meteoModel, start, end, files_to_glue):
log.info('Writing ConvertToHDF5Action.dat for GLUES HDF5 FILES action')
with open('./ConvertToHDF5Action.dat', 'w') as f:
f.write('<begin_file>\n')
f.write('\n')
f.write('! Written by GetMeteoPy\n')
f.write('{0:30}{1}'.format('ACTION', ': ' + 'GLUES HDF5 FILES' + '\n'))
f.write('{0:30}{1}'.format('OUTPUTFILENAME', ': ' + meteoModel + '.hdf5' + '\n'))
f.write('\n')
f.write('{0:30}{1}'.format('START', ': ' + datetime.strftime(start, '%Y %m %d %H %M %S') + '\n'))
f.write('{0:30}{1}'.format('END', ': ' + datetime.strftime(end, '%Y %m %d %H %M %S') + '\n'))
f.write('\n')
f.write('<<begin_list>>\n')
for hdf5_file in files_to_glue:
f.write(hdf5_file+'\n')
f.write('<<end_list>>\n')
f.write('\n')
if ('mohidKeywords' in yaml.keys()) and ('GLUES HDF5 FILES' in yaml['mohidKeywords'].keys()):
f.write('! Additional keywords\n')
for keyword in yaml['mohidKeywords']['GLUES HDF5 FILES'].keys():
try: f.write('{0:30}{1}'.format(keyword, ': ' + yaml['mohidKeywords']['GLUES HDF5 FILES'][keyword] + '\n'))
except TypeError: f.write('{0:30}{1}'.format(keyword, ': ' + str(yaml['GLUES HDF5 FILES']['mohidKeywords'][keyword]) + '\n'))
f.write('\n')
f.write('<end_file>\n')
copy2('./ConvertToHDF5Action.dat', './ConvertToHDF5Action-GLUES_HDF5_FILES.dat')
def generate_table(data):
global qty_images
images = []
default = ""
# Iterate over per input (depth 1)
for yaml in data['devices']:
# Iterate over vendors
for vendor in yaml.keys():
# Iterate over board (depth 2)
for board in yaml[vendor]:
# Iterate over per board
for key in board.keys():
# Check if there is an image for the board
if 'images' in key:
# Iterate over image (depth 3)
for image in board[key]:
images.append("{} ({})".format(
image.get('name', default),
image.get('architecture', default)))
if 'images' not in board.keys():
print("[i] Possible issue with: " +
board.get('board', default) + " (no images)")
table = "| [Image Name](images.html) (Architecture) |\n"
table += "|---------------------------|\n"
# iterate over all the devices
for device in sorted(set(images)):
table += "| {} |\n".format(device)
qty_images = len(set(images))
return table
def patch_styles(yaml):
'''
Following the release of 1.0 any user with a config generated by version
0.8 will crash without this method to restructure the style parts of the
config file.
'''
if 'console_style' in yaml.keys():
yaml['console_style'] = {'fontsize': {'default': 11, 'user': 11},
'background_color': {'default': 'Gray',
'user': '******'},
'font_color': {'default': 'Black',
'user': '******'}}
if 'edit_area_style' in yaml.keys():
yaml['edit_area_style'] = {'fontsize': {'default': 14, 'user': 14}}
return yaml
def languages_lang_file():
"""
Returns the list of languages present in the language file
with their respective type and group
"""
yaml = read_langs_file()
return list(yaml.keys())
def extract_node_include_info(reduced, root_node_address, sub_node_address,
yaml, defs, structs, y_sub):
node = reduced[sub_node_address]
node_compat = get_compat(reduced[root_node_address])
label_override = None
if node_compat not in yaml.keys():
return {}, {}
if y_sub is None:
y_node = yaml[node_compat]
else:
y_node = y_sub
if yaml[node_compat].get('use-property-label', False):
for yp in y_node['properties']:
if yp.get('label') is not None:
if node['props'].get('label') is not None:
label_override = convert_string_to_label(
node['props']['label']).upper()
break
# check to see if we need to process the properties
for yp in y_node['properties']:
for k, v in yp.items():
if 'properties' in v:
for c in reduced:
if root_node_address + '/' in c:
extract_node_include_info(
reduced, root_node_address, c, yaml, defs, structs,
v)
if 'generation' in v:
prefix = []
if v.get('use-name-prefix') is not None:
prefix = [convert_string_to_label(k.upper())]
for c in node['props'].keys():
if c.endswith("-names"):
pass
if re.match(k + '$', c):
if 'pinctrl-' in c:
names = node['props'].get('pinctrl-names', [])
else:
names = node['props'].get(c[:-1] + '-names', [])
if not names:
names = node['props'].get(c + '-names', [])
if not isinstance(names, list):
names = [names]
extract_property(
node_compat, yaml, sub_node_address, c, v, names,
prefix, defs, label_override)
return
def extract_node_include_info(reduced, root_node_address, sub_node_address,
yaml, defs, structs, y_sub):
node = reduced[sub_node_address]
node_compat = get_compat(reduced[root_node_address])
label_override = None
if node_compat not in yaml.keys():
return {}, {}
if y_sub is None:
y_node = yaml[node_compat]
else:
y_node = y_sub
if yaml[node_compat].get('use-property-label', False):
for yp in y_node['properties']:
if yp.get('label') is not None:
if node['props'].get('label') is not None:
label_override = convert_string_to_label(
node['props']['label']).upper()
break
# check to see if we need to process the properties
for yp in y_node['properties']:
for k, v in yp.items():
if 'properties' in v:
for c in reduced:
if root_node_address + '/' in c:
extract_node_include_info(
reduced, root_node_address, c, yaml, defs, structs,
v)
if 'generation' in v:
prefix = []
if v.get('use-name-prefix') is not None:
prefix = [convert_string_to_label(k.upper())]
for c in node['props'].keys():
if c.endswith("-names"):
pass
if re.match(k + '$', c):
if 'pinctrl-' in c:
names = node['props'].get('pinctrl-names', [])
else:
names = node['props'].get(c[:-1] + '-names', [])
if not names:
names = node['props'].get(c + '-names', [])
if not isinstance(names, list):
names = [names]
extract_property(
node_compat, yaml, sub_node_address, c, v, names,
prefix, defs, label_override)
return
def inject_yaml_data(sql, yaml):
dict_keys = yaml.keys()
for key in dict_keys:
if isinstance(yaml[key], str):
sql = sql.replace("{{" + key + "}}", str(yaml[key]))
return sql
def fix_old_default_project_yaml(yaml):
'''
Method to ensure compatability between old config files and verisons
of nammu > 0.8
'''
if 'projects' in yaml.keys():
if isinstance(yaml['projects']['default'], basestring):
yaml['projects']['default'] = [yaml['projects']['default']]
return yaml
def fix_old_default_project_yaml(yaml):
'''
Method to ensure compatability between old config files and verisons
of nammu > 0.8
'''
if 'projects' in yaml.keys():
if isinstance(yaml['projects']['default'], basestring):
yaml['projects']['default'] = [yaml['projects']['default']]
return yaml
def get_number_bits(yaml):
"""Extract the numebr of bits in yaml circuit."""
bits = 0
if "steps" in yaml.keys():
for step in yaml["steps"]:
if "gates" in step:
for gate in step["gates"]:
if "bit" in gate:
bits = max(bits, gate["bit"] + 1)
return bits
def extract_node_include_info(reduced, root_node_address, sub_node_address,
yaml, y_sub):
filter_list = ['interrupt-names', 'reg-names', 'phandle', 'linux,phandle']
node = reduced[sub_node_address]
node_compat = get_compat(root_node_address)
if node_compat not in yaml.keys():
return {}, {}
if y_sub is None:
y_node = yaml[node_compat]
else:
y_node = y_sub
# check to see if we need to process the properties
for k, v in y_node['properties'].items():
if 'properties' in v:
for c in reduced:
if root_node_address + '/' in c:
extract_node_include_info(reduced, root_node_address, c,
yaml, v)
if 'generation' in v:
match = False
for c in node['props'].keys():
# if prop is in filter list - ignore it
if c in filter_list:
continue
if re.match(k + '$', c):
if 'pinctrl-' in c:
names = deepcopy(node['props'].get(
'pinctrl-names', []))
else:
if not c.endswith("-names"):
names = deepcopy(node['props'].get(
c[:-1] + '-names', []))
if not names:
names = deepcopy(node['props'].get(
c + '-names', []))
if not isinstance(names, list):
names = [names]
extract_property(node_compat, yaml, sub_node_address, c, v,
names)
match = True
# Handle the case that we have a boolean property, but its not
# in the dts
if not match:
if v['type'] == "boolean":
extract_property(node_compat, yaml, sub_node_address, k, v,
None)
def extract_node_include_info(reduced, root_node_address, sub_node_address,
yaml, y_sub):
node = reduced[sub_node_address]
node_compat = get_compat(root_node_address)
label_override = None
if node_compat not in yaml.keys():
return {}, {}
if y_sub is None:
y_node = yaml[node_compat]
else:
y_node = y_sub
if yaml[node_compat].get('use-property-label', False):
try:
label = y_node['properties']['label']
label_override = convert_string_to_label(node['props']['label'])
except KeyError:
pass
# check to see if we need to process the properties
for k, v in y_node['properties'].items():
if 'properties' in v:
for c in reduced:
if root_node_address + '/' in c:
extract_node_include_info(
reduced, root_node_address, c, yaml, v)
if 'generation' in v:
for c in node['props'].keys():
if c.endswith("-names"):
pass
if re.match(k + '$', c):
if 'pinctrl-' in c:
names = deepcopy(node['props'].get(
'pinctrl-names', []))
else:
if not c.endswith("-names"):
names = deepcopy(node['props'].get(
c[:-1] + '-names', []))
if not names:
names = deepcopy(node['props'].get(
c + '-names', []))
else:
names = []
if not isinstance(names, list):
names = [names]
extract_property(
node_compat, yaml, sub_node_address, c, v, names,
label_override)
def patch_server_settings(yaml):
'''
Following the change in server address we need to update user's config
files without overwriting their other settings.
'''
old_url = 'http://oracc.museum.upenn.edu'
new_url = 'http://build-oracc.museum.upenn.edu'
if 'servers' in yaml.keys() and 'upenn' in yaml['servers'].keys():
if yaml['servers']['upenn']['url'] == old_url:
yaml['servers']['upenn']['url'] = new_url
return yaml
def parse_source_file(source, yaml):
for key in yaml.keys():
if key == 'download':
source = DownloadSourceFile(source)
source.parse(yaml[key])
return source
elif key == 'source':
source = VCSSourceFile(source)
source.parse(yaml[key])
return source
else:
pbs.log.error('invalid type of source file:', key)
def patch_server_settings(yaml):
'''
Following the change in server address we need to update user's config
files without overwriting their other settings.
'''
old_url = 'http://oracc.museum.upenn.edu'
new_url = 'http://build-oracc.museum.upenn.edu'
if 'servers' in yaml.keys() and 'upenn' in yaml['servers'].keys():
if yaml['servers']['upenn']['url'] == old_url:
yaml['servers']['upenn']['url'] = new_url
return yaml
def get_scales_from_fitopt_file(self):
if self.sys_file_in is None:
return {}
self.logger.debug(f"Loading sys scaling from {self.sys_file_in}")
yaml = read_yaml(self.sys_file_in)
if 'FLAG_USE_SAME_EVENTS' in yaml.keys():
yaml.pop('FLAG_USE_SAME_EVENTS')
raw = {
k: float(v.split(maxsplit=1)[0])
for _, d in yaml.items() for k, v in d.items()
}
return raw
def inject_yaml_data(str_data, yaml):
dict_keys = yaml.keys()
# print('before ', str_data)
for key in dict_keys:
if isinstance(yaml[key], dict):
str_data = recurse_replace_yaml(str_data, yaml[key])
elif not (isinstance(yaml[key], list)
or isinstance(yaml[key], dict)):
str_data = str_data.replace("{{" + key + "}}", str(yaml[key]))
# print('after ', str_data)
return str_data
def generate_table(data):
global qty_devices, qty_images, qty_image_kali, qty_image_community, qty_image_eol, qty_image_unknown
images = []
default = ""
table = "| [Device Name](https://www.kali.org/docs/arm/) | [Build-Script](https://gitlab.com/kalilinux/build-scripts/kali-arm/) | [Official Image](https://www.kali.org/get-kali/#kali-arm) | Community Image | EOL/Retired Image |\n"
table += "|---------------|--------------|----------------|-----------------|---------------|\n"
# Iterate over per input (depth 1)
for yaml in data['devices']:
# Iterate over vendors
for vendor in yaml.keys():
# Iterate over board (depth 2)
for board in yaml[vendor]:
qty_devices += 1
# Iterate over per board
for key in board.keys():
# Check if there is an image for the board
if 'images' in key:
# Iterate over image (depth 3)
for image in board[key]:
if image['name'] not in images:
images.append(image['name']) # ALT: images.append(image['image'])
qty_images += 1
build_script = image.get('build-script', default)
if build_script:
build_script = "[{0}](https://gitlab.com/kalilinux/build-scripts/kali-arm/-/blob/master/{0})".format(build_script)
name = image.get('name', default)
slug = image.get('slug', default)
if name and slug:
name = "[{}](https://www.kali.org/docs/arm/{}/)".format(name, slug)
support = image.get('support', default)
if support == "kali":
status = "x | | "
qty_image_kali += 1
elif support == "community":
status = " | x | "
qty_image_community += 1
elif support == "eol":
status = " | | x"
qty_image_eol += 1
else:
status = " | | "
qty_image_unknown += 1
table += "| {} | {} | {} |\n".format(name,
build_script,
status)
#else:
# print('DUP {} / {}'.format(image['name'], image['image']))
if 'images' not in board.keys():
print("[i] Possible issue with: " + board.get('board', default) + " (no images)")
return table
def _yaml_check_map(yaml, required_fields, optional_fields, check_valid=True):
if not isinstance(yaml, dict):
raise SpecParseError('{} must be a map. Use "key: value" syntax.'.format(yaml))
for key in required_fields:
if key not in yaml:
raise SpecParseError('Required field "{}" not found in {}.'.format(key, yaml))
if check_valid:
valid_fields = required_fields + optional_fields
for key in yaml.keys():
if key not in valid_fields:
raise SpecParseError('Unknown field "{}" in {}. Valid fields: {}'.format(
key, yaml, valid_fields))
def check_unsupported(yaml, required, path=''):
try:
passed = True
if not yaml:
raise FailedInitialization(
"YAML file is corrupt or truncated, nothing left to parse")
if isinstance(yaml, list):
for index, element in enumerate(yaml):
for yk in element.keys():
listpath = f"{path}.{yk}[{index}]"
yamlValue = dict(element).get(yk, None)
for rk in required:
supportedSubkeys = rk.get(yk, None)
if supportedSubkeys:
break
if not supportedSubkeys:
_LOGGER.info(f"'{listpath}' option is unsupported")
return
subkeyList = supportedSubkeys.get('keys', None)
if subkeyList:
passed = check_unsupported(yamlValue, subkeyList,
listpath) and passed
elif isinstance(yaml, dict) or isinstance(yaml, Configuration):
for yk in yaml.keys():
currentpath = path + yk if path == '' else path + '.' + yk
yamlValue = dict(yaml).get(yk, None)
for rk in required:
supportedSubkeys = rk.get(yk, None)
if supportedSubkeys:
break
if not supportedSubkeys:
_LOGGER.info(f"'{currentpath}' option is unsupported")
return
subkeyList = supportedSubkeys.get('keys', None)
if subkeyList:
passed = check_unsupported(yamlValue, subkeyList,
currentpath) and passed
else:
raise FailedInitialization('Unexpected YAML checking error')
except FailedInitialization:
raise
except Exception as e:
raise FailedInitialization(f"Unexpected exception: {e}")
return passed
def get_number_qubits(yaml):
"""Extract the number of qubits in yaml circuit."""
qubits = 0
if "steps" in yaml.keys():
for step in yaml["steps"]:
if "gates" in step:
for gate in step["gates"]:
if "controls" in gate:
for ctrl_info in gate["controls"]:
qubits = max(qubits, ctrl_info["target"] + 1)
if "targets" in gate:
for target in gate["targets"]:
qubits = max(qubits, target + 1)
if "gates" in gate:
for gate in gate["gates"]:
for target in gate["targets"]:
qubits = max(qubits, target + 1)
return qubits
def generate_table(data):
global qty_devices, qty_images
default = ""
table = "| Vendor | [Board](devices.html) | [Images](images.html) |\n"
table += "|--------|-----------------------|-----------------------|\n"
# Iterate over per input (depth 1)
for yaml in data['devices']:
# Iterate over vendors
for vendor in yaml.keys():
# Iterate over board (depth 2)
for board in yaml[vendor]:
qty_devices += 1
qty_images += len(board.get('images', default))
table += "| {} | {} | {} |\n".format(
vendor, board.get('name', default),
len(board.get('images', default)))
return table
def generate_table(data):
global qty_devices, qty_images, qty_images_released
images = []
images_released = []
default = ""
table = "| Image Name | Filename | Architecture | Preferred | Support | [Documentation](https://www.kali.org/docs/arm/) | [Kernel](kernel-stats.html) | Kernel Version | Notes |\n"
table += "|------------|----------|--------------|-----------|---------|-------------------------------------------------|-----------------------|----------------|-------|\n"
# Iterate over per input (depth 1)
for yaml in data['devices']:
# Iterate over vendors
for vendor in yaml.keys():
# Iterate over board (depth 2)
for board in yaml[vendor]:
qty_devices += 1
# Iterate over per board
for key in board.keys():
# Check if there is an image for the board
if 'images' in key:
# Iterate over image (depth 3)
for image in board[key]:
#qty_images += 1
images.append("{}".format(image.get('name', default)))
support = image.get('support', default)
if support == "kali":
#qty_images_released += 1
images_released.append("{}".format(image.get('name', default)))
slug = image.get('slug', default)
if slug:
slug = "[{0}](https://www.kali.org/docs/arm/{0}/)".format(slug)
table += "| {} | {} | {} | {} | {} | {} | {} | {} |\n".format(image.get('name', default),
image.get('image', default),
image.get('architecture', default),
image.get('preferred-image', default),
image.get('support', default),
slug,
image.get('kernel', default),
image.get('kernel-version', default),
image.get('image-notes', default))
if 'images' not in board.keys():
print("[i] Possible issue with: " + board.get('board', default) + " (no images)")
qty_images = len(set(images))
qty_images_released = len(set(images_released))
return table
def extract_node_include_info(reduced, node_address, yaml, defs, structs):
node = reduced[node_address]
node_compat = get_compat(node)
if not node_compat in yaml.keys():
return {}, {}
y_node = yaml[node_compat]
# check to see if we need to process the properties
for yp in y_node['properties']:
for k, v in yp.items():
if 'generation' in v:
if v['generation'] == 'define':
label = v.get('define_string')
storage = defs
else:
label = v.get('structures_string')
storage = structs
prefix = []
if v.get('use-name-prefix') != None:
prefix = [convert_string_to_label(k.upper())]
for c in node['props'].keys():
if c.endswith("-names"):
pass
if re.match(k + '$', c):
if 'pinctrl-' in c:
names = node['props'].get('pinctrl-names', [])
else:
names = node['props'].get(c[:-1] + '-names', [])
if not names:
names = node['props'].get(c + '-names', [])
if not isinstance(names, list):
names = [names]
extract_property(yaml, node_address, c, v, names,
prefix, defs)
return
def extract_node_include_info(reduced, node_address, yaml, defs, structs):
node = reduced[node_address]
node_compat = get_compat(node)
if not node_compat in yaml.keys():
return {}, {}
y_node = yaml[node_compat]
# check to see if we need to process the properties
for yp in y_node['properties']:
for k,v in yp.items():
if 'generation' in v:
if v['generation'] == 'define':
label = v.get('define_string')
storage = defs
else:
label = v.get('structures_string')
storage = structs
prefix = []
if v.get('use-name-prefix') != None:
prefix = [convert_string_to_label(k.upper())]
for c in node['props'].keys():
if c.endswith("-names"):
pass
if re.match(k + '$', c):
if 'pinctrl-' in c:
names = node['props'].get('pinctrl-names', [])
else:
names = node['props'].get(c[:-1] + '-names', [])
if not names:
names = node['props'].get(c + '-names', [])
if not isinstance(names, list):
names = [names]
extract_property(yaml, node_address, c, v, names, prefix, defs)
return
def generate_table(data):
global qty_devices
default = ""
table = "| Vendor | Board | CPU | CPU Cores | GPU | RAM | RAM Size (MB) | Ethernet | Ethernet Speed (MB) | Wi-Fi | Bluetooth | USB2 | USB3 | Storage | Notes |\n"
table += "|--------|-------|-----|-----------|-----|-----|---------------|----------|---------------------|-------|-----------|------|------|---------|---------------------|\n"
# Iterate over per input (depth 1)
for yaml in data['devices']:
# Iterate over vendors
for vendor in yaml.keys():
# Iterate over board (depth 2)
for board in yaml[vendor]:
qty_devices += 1
ram_size = ""
storage = ""
i = 0
for f in natural_sort(board.get('ram-size', default)):
if i > 0:
ram_size += ", "
ram_size += f
i += 1
i = 0
for f in natural_sort(board.get('storage', default)):
if i > 0:
storage += ", "
storage += f
i += 1
table += "| {} | {} | {} | {} | {} | {} | {} | {} | {} | {} | {} | {} | {} | {} | {} |\n".format(vendor,
board.get('name', default),
board.get('cpu', default),
board.get('cpu-cores', default),
board.get('gpu', default),
board.get('ram', default),
ram_size,
board.get('ethernet', default),
board.get('ethernet-speed', default),
board.get('wifi', default),
board.get('bluetooth', default),
board.get('usb2', default),
board.get('usb3', default),
storage,
board.get('notes', default))
return table
def normalize_yaml(yaml):
"""Normalize the YAML from project and role lookups.
These are returned as a list of tuples.
"""
if isinstance(yaml, list):
# Normalize the roles YAML data
normalized_yaml = [(x['name'], x['src'], x.get('version', 'HEAD'))
for x in yaml]
else:
# Extract the project names from the roles YAML and create a list of
# tuples.
projects = [x[:-9] for x in yaml.keys() if x.endswith('git_repo')]
normalized_yaml = []
for project in projects:
repo_url = yaml['{0}_git_repo'.format(project)]
commit_sha = yaml['{0}_git_install_branch'.format(project)]
normalized_yaml.append((project, repo_url, commit_sha))
return normalized_yaml
def generate_manifest(data):
global release, qty_devices, qty_images, qty_release_images
default = ""
devices = {}
# Iterate over per input (depth 1)
for yaml in data['devices']:
# Iterate over vendors
for vendor in yaml.keys():
# Ready to have a unique name in the entry
img_seen = set()
# Iterate over board (depth 2)
for board in yaml[vendor]:
qty_devices += 1
# Iterate over per board
for key in board.keys():
# Check if there is an image for the board
if 'images' in key:
# Iterate over image (depth 3)
for image in board[key]:
qty_images += 1
# Check that it's not EOL or community supported
if image.get('support') == "kali":
name = image.get('name', default)
# If we haven't seen this image before for this vendor
if name not in img_seen:
img_seen.add(name)
qty_release_images += 1
filename = "kali-linux-{}-{}".format(
release, image.get('image', default))
preferred = image.get(
'preferred-image', default)
slug = image.get('slug', default)
jsonarray(devices, vendor, name, filename,
preferred, slug)
return json.dumps(devices, indent=2)
def generate_table(data):
global qty_kernels, qty_versions
images = []
default = "unknown"
# Iterate over per input (depth 1)
for yaml in data['devices']:
# Iterate over vendors
for vendor in yaml.keys():
# Iterate over board (depth 2)
for board in yaml[vendor]:
# Iterate over per board
for key in board.keys():
# Check if there is an image for the board
if 'images' in key:
# Iterate over image (depth 3)
for image in board[key]:
if image['name'] not in images:
images.append(
image['name']
) # ALT: images.append(image['image'])
qty_kernels += 1
qty_versions[(image.get('kernel',
default))] += 1
#else:
# print('DUP {} / {}'.format(image['name'], image['image']))
if 'images' not in board.keys():
print("[i] Possible issue with: " +
board.get('board', default) + " (no images)")
table = "| Kernel | Qty |\n"
table += "|--------|-----|\n"
# iterate over all the devices
for v in qty_versions:
table += "| {} | {} |\n".format(v.capitalize(), str(qty_versions[v]))
return table
def __init__(self, yaml):
sim = dict()
ins = dict()
logic = dict()
python = dict()
gen = dict()
func = dict()
py2cnf = dict()
#aima = dict()
eqntott = {"and": "&",
"or": "|",
"not": "!",
"False": "ZERO",
"True": "ONE"}
#aimaC = {"and": "&",
# "or": "|",
# "not": "~",
# "False": "0",
# "True": "1"}
for modname in yaml.keys():
if "primitive" in yaml.get(modname):
prim = yaml.get(modname)["primitive"]
inputs = yaml.get(modname)["inputs"].keys()
evalStr = "lambda "
for i in range(0, len(inputs)-1):
evalStr += inputs[i] + ","
evalStr += inputs[len(inputs)-1] + ": "
simStr = evalStr + prim
logicStr = evalStr + self.__primToLogic__(inputs, prim, eqntott)
pyStr = evalStr + self.__primToLogic__(inputs, prim)
#aimaStr = evalStr + self.__primToLogic__(inputs, prim, aimaC)
genStr = self.__getGenerator__(yaml, modname, eqntott)
d = {}
exec genStr.strip() in d
#setattr(self.__class__, modname, d[modname])
gen[modname] = d[modname]
funcStr = self.__getFunction__(yaml, modname, eqntott)
f = {}
exec funcStr.strip() in f
func[modname] = f[modname]
sim[modname] = eval(simStr)
logic[modname] = eval(logicStr)
python[modname] = eval(pyStr)
py2cnf[modname] = Gate2CNF.Gate2CNF(prim)
#aima[modname] = eval(aimaStr)
ins[modname] = inputs
self.__sim = sim
self.__inputs = ins
self.__logic = logic
self.__python = python
self.__gen = gen
self.__func = func
self.__py2cnf = py2cnf
st.header("Hybrid Genome Browser")
# Create a second instance of our component whose `name` arg will vary
# based on a text_input widget.
#
# We use the special "key" argument to assign a fixed identity to this
# component instance. By default, when a component's arguments change,
# it is considered a new instance and will be re-mounted on the frontend
# and lose its current state. In this case, we want to vary the component's
# "name" argument without having it get recreated.
# name_input = st.text_input("Enter a file name", value="../../bt142/ont2_ngmlr.bam")
try:
yaml = load_samples("hgb/config.yaml")
ref = st.sidebar.selectbox("Which references to use?",
list(yaml.keys()), 1)
name_input = st.sidebar.multiselect("Which files to load?",
yaml[ref]["samples"],
list(yaml[ref]["default"]))
refs = reference_hash(yaml[ref]["samples"][0])
default_range = yaml[ref]["range"][0]
except:
name_input = st.sidebar.text_input("Which file to explore?")
refs = reference_hash(name_input)
if len(refs) > 0:
default_range = "{}:1-10001".format(next(iter(refs)))
else:
default_range = ""
#range_candidate = st.sidebar
def extract_node_include_info(reduced, root_node_address, sub_node_address,
yaml, y_sub):
filter_list = ['interrupt-names', 'reg-names', 'phandle', 'linux,phandle']
node = reduced[sub_node_address]
node_compat = get_compat(root_node_address)
if node_compat not in yaml.keys():
return {}, {}
if y_sub is None:
y_node = yaml[node_compat]
else:
y_node = y_sub
# check to see if we need to process the properties
for k, v in y_node['properties'].items():
if 'properties' in v:
for c in reduced:
if root_node_address + '/' in c:
extract_node_include_info(reduced, root_node_address, c,
yaml, v)
if 'generation' in v:
match = False
# Handle any per node extraction first. For example we
# extract a few different defines for a flash partition so its
# easier to handle the partition node in one step
if 'partition@' in sub_node_address:
flash.extract_partition(sub_node_address)
continue
# Handle each property individually, this ends up handling common
# patterns for things like reg, interrupts, etc that we don't need
# any special case handling at a node level
for c in node['props'].keys():
# if prop is in filter list - ignore it
if c in filter_list:
continue
if re.match(k + '$', c):
if 'pinctrl-' in c:
names = deepcopy(node['props'].get(
'pinctrl-names', []))
else:
if not c.endswith("-names"):
names = deepcopy(node['props'].get(
c[:-1] + '-names', []))
if not names:
names = deepcopy(node['props'].get(
c + '-names', []))
if not isinstance(names, list):
names = [names]
extract_property(node_compat, yaml, sub_node_address, c, v,
names)
match = True
# Handle the case that we have a boolean property, but its not
# in the dts
if not match:
if v['type'] == "boolean":
extract_property(node_compat, yaml, sub_node_address, k, v,
None)
def check_required_keys(yaml, required, path='') -> bool:
passed = True
for keywords in required:
for rk, rv in keywords.items():
currentpath = path + rk if path == '' else path + '.' + rk
requiredKey = rv.get('required')
requiredSubkeys = rv.get('keys')
keyType = rv.get('type', None)
typeStr = '' if not keyType else f" (type is '{keyType.__name__}')"
if not yaml:
raise FailedInitialization(f"YAML file is corrupt or truncated, expecting to find '{rk}' and found nothing")
if isinstance(yaml, list):
for index, element in enumerate(yaml):
path = f"{currentpath}[{index}]"
yamlKeys = element.keys()
if requiredKey:
if rk not in yamlKeys:
_LOGGER.error(f"'{currentpath}' is required for operation {typeStr}")
passed = False
continue
yamlValue = dict(element).get(rk, None)
if yamlValue is None:
return passed
if rk in yamlKeys and keyType and not isinstance(yamlValue, keyType):
_LOGGER.error(f"'{currentpath}' should be type '{keyType.__name__}'")
passed = False
if isinstance(requiredSubkeys, list):
if len(requiredSubkeys):
passed = check_required_keys(yamlValue, requiredSubkeys, path) and passed
else:
raise FailedInitialization(Exception('Unexpected YAML checking error'))
elif isinstance(yaml, dict) or isinstance(yaml, Configuration):
yamlKeys = yaml.keys()
if requiredKey:
if rk not in yamlKeys:
_LOGGER.error(f"'{currentpath}' is required for operation {typeStr}")
passed = False
continue
yamlValue = dict(yaml).get(rk, None)
if yamlValue is None:
return passed
if rk in yamlKeys and keyType and not isinstance(yamlValue, keyType):
_LOGGER.error(f"'{currentpath}' should be type '{keyType.__name__}'")
passed = False
if isinstance(requiredSubkeys, list):
if len(requiredSubkeys):
passed = check_required_keys(yamlValue, requiredSubkeys, currentpath) and passed
else:
raise FailedInitialization('Unexpected YAML checking error')
else:
raise FailedInitialization('Unexpected YAML checking error')
return passed
def generate_manifest(data):
global release, qty_devices, qty_images, qty_release_images
default = ""
devices = {}
# Iterate over per input (depth 1)
for yaml in data['devices']:
# Iterate over vendors
for vendor in yaml.keys():
# @g0tmi1k: Feels like there is a cleaner way todo this
if not vendor == "raspberrypi":
continue
# Ready to have a unique name in the entry
img_seen = set()
# Iterate over board (depth 2)
for board in yaml[vendor]:
qty_devices += 1
# Iterate over per board
for key in board.keys():
# Check if there is an image for the board
if 'images' in key:
# Iterate over image (depth 3)
for image in board[key]:
qty_images += 1
# Check that it's not EOL or community supported
if image.get('support') == "kali":
name = image.get('name', default)
# If we haven't seen this image before for this vendor
if name not in img_seen:
img_seen.add(name)
qty_release_images += 1
filename = "kali-linux-{}-{}".format(
release, image.get('image', default))
# Check to make sure files got created
for ext in file_ext:
check_file = '{}/{}.{}'.format(
imagedir, filename, ext)
if not os.path.isfile(check_file):
bail(
"Missing: '{}'".format(
check_file),
"Please create the image before running"
)
with open('{}/{}.xz.sha256sum'.format(
imagedir, filename)) as f:
image_download_sha256 = f.read().split(
)[0]
with open('{}/{}.sha256sum'.format(
imagedir, filename)) as f:
extract_sha256 = f.read().split()[0]
url = "https://kali.download/arm-images/kali-{}/{}.xz".format(
release, filename)
# @g0tmi1k: not happy about external OS, rather keep it in python (import lzma)
try:
unxz = subprocess.check_output(
"unxz --verbose --list {}/{}.xz | grep 'Uncompressed'"
.format(imagedir, filename),
shell=True)
extract_size = re.findall(
r'\((.*?) B\)', str(unxz))[0]
extract_size = extract_size.replace(
',', '')
extract_size = int(extract_size)
except subprocess.CalledProcessError as e:
#print("command '{}' return with error (code {})".format(e.cmd, e.returncode))
extract_size = 0
#image_download_size = os.stat('{}/{}.xz'.format(imagedir, filename)).st_size
image_download_size = os.path.getsize(
'{}/{}.xz'.format(imagedir, filename))
jsonarray(devices, 'os_list', name, url,
extract_size, extract_sha256,
image_download_size,
image_download_sha256)
return json.dumps(devices, indent=2)