def load(self,template,vars):
dp=os.path.dirname(template)
if dp != '':
self.domain=dp
filename=os.path.basename(template)
try:
d=Domain(self.domain, quoting=None, errors=4) # fixme: what do we really want for quoting?
t=Domain(self.domain, errors=4).get_template(filename, quoting="str") # fixme: why create two Domains?
except Exception as e:
print "(domain is %s)" % self.domain
raise e
evars=evoque_dict() # special dict that returns missing keys as "${key}"
evars.update(vars)
yaml_txt=t.evoque(evars)
# fix eval errors:
# fixed_yaml=re.sub('\[EvalError\(([a-z_]+)\)]', "${\g<1>}", yaml_txt) # ooh, magic! great.
# fixed_yaml=re.sub('\[NameError: name ' ([a-z_]+)\)]', "${\g<1>}", yaml_txt) # ooh, magic! great.
# fixed_yaml=re.sub('<built-in function ([a-z_]+)>', "${\g<1>}", fixed_yaml) # christ, more magic
# warn("syml.load: fixed_yaml is %s" % fixed_yaml)
d=yaml.load(yaml_txt)
# "fix" config; ie, resolve referenced values
d=self._fix_hash(d,d)
return d
def load(self):
# get globals if necessary
if (self.globals == {}) and self.globals_file:
f = open(self.globals_file, "r")
self.globals = yaml.load(f)
f.close
# read config template (with globals)
if not self.config_file:
raise Exception("no config_file")
if not self.domain:
try:
self.domain = self.globals["domain"]
except:
self.domain = os.getcwd()
print "warning: looking for globals.yml in local directory!"
try:
t = Domain(self.domain).get_template(self.config_file)
except Exception as e:
print "(domain is %s)" % self.domain
raise e
conf_yaml = t.evoque(self.globals)
conf = yaml.load(conf_yaml)
# "fix" config; ie, resolve referenced values
conf = self._fix_hash(conf, conf)
conf.update({"globals": self.globals})
self.config = conf
def as_python(self):
template_filename=self.rnaseq.globals['step_template']
try: domain=self.rnaseq.globals['domain']
except: domain=os.getcwd()
t=Domain(domain).get_template(template_filename)
# step.template needs: name, input, output, pipeline_var_name
# fixme: we killed input_str(), etc, (not cmd_str(), tho)
vars={'input':self.flatten_attr('inputs'),
'output':self.flatten_attr('outputs'),
'name':self.name,
'pipeline_var_name':self.pipeline_var_name,
}
template=t.evoque(vars)
return template
