def init(self):
self.clear()
ExpandableWorkflow.activate()
self.find_config()
self.load_config()
self.config_expander = ConfigExpander(self)
ExpandableWorkflow.default_params(mem=self.mem())
def unload(cls):
log.debug("Unloading ConfigMgr")
ExpandableWorkflow.clear()
if cls.__instance:
cls.__instance.cache.close()
cls.__instance = None
from ymp.stage import Stage, StageStack
StageStack.stacks = {}
Stage.active = None
def __init__(self, root, conffiles):
log.debug("Inizializing ConfigMgr")
self._root = root
self._conffiles = conffiles
self._config = ymp.yaml.load(self._conffiles)
# lazy filled by accessors
self._snakefiles = None
prj_cfg = self._config.get(self.KEY_PROJECTS) or {}
self._datasets = {
project: DatasetConfig(self, project, cfg)
for project, cfg in prj_cfg.items()
}
ref_cfg = self._config.get(self.KEY_REFERENCES) or {}
self._references = load_references(self, ref_cfg)
self._workflow = ExpandableWorkflow.register_expanders(
SnakemakeExpander(),
RecursiveExpander(),
ConfigExpander(self),
CondaPathExpander(self),
OverrideExpander(self),
DefaultExpander(params=([], {
'mem': self.mem(),
'walltime': self.limits.default_walltime
})),
InheritanceExpander(),
StageExpander()
)
def __init__(self, root, conffiles):
log.debug("Inizializing ConfigMgr")
self.root = root
self.conffiles = conffiles
if os.path.dirname(conffiles[-1]) == root:
self.cachedir = os.path.join(self.root, ".ymp")
else:
self.cachedir = os.path.join(XDG_CACHE_HOME, "ymp")
self._config = ymp.yaml.load(conffiles, root)
self.cache = cache = Cache(self.cachedir)
# lazy filled by accessors
self._snakefiles = None
self.projects = cache.get_cache(
"projects",
itemloadfunc=Project,
itemdata=self._config.get(self.KEY_PROJECTS) or {},
dependfiles=conffiles)
self.references = cache.get_cache(
"references",
itemloadfunc=Reference,
itemdata=self._config.get(self.KEY_REFERENCES) or {},
dependfiles=conffiles)
self.pipelines = cache.get_cache(
"pipelines",
itemloadfunc=Pipeline,
itemdata=self._config.get(self.KEY_PIPELINES) or {},
dependfiles=conffiles)
ExpandableWorkflow.register_expanders(
SnakemakeExpander(),
RecursiveExpander(),
CondaPathExpander(self),
StageExpander(),
ConfigExpander(self),
ResourceLimitsExpander(self._config.get(self.KEY_LIMITS)),
OverrideExpander(self),
InheritanceExpander(),
)
def load_workflow(self, file_path: str) -> ExpandableWorkflow:
"""Load the Snakefile"""
workflow = ExpandableWorkflow(snakefile=file_path)
workflow.include(file_path)
return workflow
def reload(self):
log.debug("Reloading ConfigMgr")
ExpandableWorkflow.clear()
self.__init__(*self.find_config())