def __init__(self, content, sequence = None, output = None):
actions = [DSCFileLoader(content, sequence, output), DSCEntryFormatter()]
for a in actions:
a(self)
for name in list(self.keys()):
if name == 'DSC':
continue
else:
# double check if any computational routines are
# out of index
self[name]['meta']['exec'] = [tuple(x.split()) if isinstance(x, str) else x
for x in self[name]['meta']['exec']]
if ('exec_alias' in self[name]['meta'] and 'rule' not in self[name]['meta'] \
and len(self[name]['meta']['exec_alias']) != len(self[name]['meta']['exec'])) or \
('exec_alias' in self[name]['meta'] and 'rule' in self[name]['meta'] \
and len(self[name]['meta']['exec_alias']) != len(self[name]['meta']['rule'])):
raise FormatError('Alias does not match the length of exec, in block ``{}``!'.\
format(name))
if 'params' in self[name]:
max_exec = max(self[name]['params'].keys())
if max_exec > len(self[name]['meta']['exec']):
raise FormatError('Index for exec out of range: ``exec[{}]``.'.format(max_exec))
#
rlibs = try_get_value(self['DSC'], ('R_libs'))
if rlibs:
rlibs_md5 = textMD5(repr(rlibs) + str(datetime.date.today()))
if not os.path.exists('.sos/.dsc/RLib.{}.info'.format(rlibs_md5)):
install_r_libs(rlibs)
os.makedirs('.sos/.dsc', exist_ok = True)
os.system('echo "{}" > {}'.format(repr(rlibs),
'.sos/.dsc/RLib.{}.info'.format(rlibs_md5)))
def sos_hash_output(values, db_name):
if isinstance(values, str):
values = [values]
res = []
for value in values:
base, ext = value.rsplit('.', 1)
md5 = '{}.{}'.format(textMD5(base), ext)
res.append('{}/{}'.format(db_name, md5))
return res
def sos_hash_output(values, db_name = '', prefix = None, suffix = None):
if not isinstance(values, list):
md5 = textMD5(values)
if isinstance(prefix, str):
md5 = '{}:{}'.format(prefix, md5)
if isinstance(suffix, str):
md5 = '{}:{}'.format(md5, suffix)
res = os.path.join(db_name, md5)
return res
else:
res = []
for value in values:
md5 = textMD5(value)
if isinstance(prefix, str):
md5 = '{}:{}'.format(prefix, md5)
if isinstance(suffix, str):
md5 = '{}:{}'.format(md5, suffix)
res.append(os.path.join(db_name, md5))
return res
def RemoveObsoleteOutput(self):
# Remove file signature when files are deleted
runtime_dir = os.path.expanduser('~/.sos/.runtime') \
if os.path.isabs(os.path.expanduser(self.name)) \
else '.sos/.runtime'
for k, x in self.maps.items():
x = os.path.join(self.name, x)
if not os.path.isfile(x):
try:
os.remove('{}/{}.file_info'.\
format(runtime_dir, textMD5(os.path.abspath(os.path.expanduser(x)))))
except:
sys.stderr.write('Obsolete file {} has already been purged!\n'.format(x))
def __reset_block(self, data, exe, exe_name, exec_path):
'''Intermediate data to be appended to self.data'''
data.command = ' '.join([self.__search_exec(exe[0], exec_path)] + list(exe[1:]))
plugin = Plugin(os.path.splitext(exe[0])[1].lstrip('.'), textMD5(data.command)[:10])
# re.sub(r'^([0-9])(.*?)', r'\2', textMD5(data.command)))
if (data.plugin.name is not None and (not plugin.name) != (not data.plugin.name)):
raise StepError("A mixture of plugin codes and other executables are not allowed " \
"in the same block ``{}``.".format(data.name))
else:
data.plugin = plugin
# if data.plugin.name:
# executable(data.plugin.name)
data.plugin.reset()
data.parameters = []
# FIXME: currently only one output ext is set
data.output_ext = []
data.output_vars = []
data.exe = ' '.join([x for x in exe if not x.startswith('$')]) if exe_name is None else exe_name