def get_workflow_name_and_version_from_config(config_file, dont_raise=False):
filesnpaths.is_file_json_formatted(config_file)
config = json.load(open(config_file))
workflow_name = config.get('workflow_name')
# Notice that if there is no config_version then we return "0".
# This is in order to accomodate early config files that had no such parameter.
version = config.get('config_version', "0")
if (not dont_raise) and (not workflow_name):
raise ConfigError('Config files must contain a workflow_name.')
return (workflow_name, version)
def __init__(self):
if 'args' not in self.__dict__:
raise ConfigError(
"You need to initialize `WorkflowSuperClass` from within a class that\
has a member `self.args`.")
A = lambda x: self.args.__dict__[x
] if x in self.args.__dict__ else None
# FIXME: it is redundant to have both config and config_file
# Alon and Meren will discuss how to do this right.
# but for now this is how it is so things would work.
# basically, when this class is called from a snakefile
# then a config (dictionary) will be provided.
# When this class is called from anvi-run-snakemake-workflow
# for sanity checks and things like that, then a config file
# will be provided.
self.config = A('config')
self.config_file = A('config_file')
self.default_config_output_path = A('get_default_config')
self.save_workflow_graph = A('save_workflow_graph')
self.list_dependencies = A('list_dependencies')
self.dry_run_only = A('dry_run')
self.additional_params = A('additional_params')
if self.additional_params:
run.warning(
"OK, SO THIS IS SERIOUS, AND WHEN THINGS ARE SERIOUS THEN WE USE CAPS. \
WE SEE THAT YOU ARE USING --additional-params AND THAT'S GREAT, BUT WE \
WANT TO REMIND YOU THAT ANYTHING THAT FOLLOWS --additional-params WILL \
BE CONSIDERED AS A snakemake PARAM THAT IS TRANSFERRED TO snakemake DIRECTLY. \
So make sure that these don't include anything that you didn't mean to \
include as an additional param: %s." %
', '.join(str(i) for i in self.additional_params))
if self.save_workflow_graph:
self.dry_run_only = True
# if this class is being inherited from a snakefile that was 'included' from
# within another snakefile.
self.slave_mode = A('slave_mode')
if self.config_file:
filesnpaths.is_file_json_formatted(self.config_file)
self.config = json.load(open(self.config_file))
self.rules = []
self.rule_acceptable_params_dict = {}
self.dirs_dict = {}
self.general_params = []
self.default_config = {}
self.rules_dependencies = {}
self.forbidden_params = {}
def __init__(self):
if 'args' not in self.__dict__:
raise ConfigError("You need to initialize `WorkflowSuperClass` from within a class that\
has a member `self.args`.")
A = lambda x: self.args.__dict__[x] if x in self.args.__dict__ else None
# FIXME: it is redundant to have both config and config_file
# Alon and Meren will discuss how to do this right.
# but for now this is how it is so things would work.
# basically, when this class is called from a snakefile
# then a config (dictionary) will be provided.
# When this class is called from anvi-run-snakemake-workflow
# for sanity checks and things like that, then a config file
# will be provided.
self.config = A('config')
self.config_file = A('config_file')
self.default_config_output_path = A('get_default_config')
self.save_workflow_graph = A('save_workflow_graph')
self.list_dependencies = A('list_dependencies')
self.dry_run_only = A('dry_run')
self.additional_params = A('additional_params')
if self.additional_params:
run.warning("OK, SO THIS IS SERIOUS, AND WHEN THINGS ARE SERIOUS THEN WE USE CAPS. \
WE SEE THAT YOU ARE USING --additional-params AND THAT'S GREAT, BUT WE \
WANT TO REMIND YOU THAT ANYTHING THAT FOLLOWS --additional-params WILL \
BE CONSIDERED AS A snakemake PARAM THAT IS TRANSFERRED TO snakemake DIRECTLY. \
So make sure that these don't include anything that you didn't mean to \
include as an additional param: %s." % ', '.join(str(i) for i in self.additional_params))
if self.save_workflow_graph:
self.dry_run_only = True
# if this class is being inherited from a snakefile that was 'included' from
# within another snakefile.
self.slave_mode = A('slave_mode')
if self.config_file:
filesnpaths.is_file_json_formatted(self.config_file)
self.config = json.load(open(self.config_file))
self.rules = []
self.rule_acceptable_params_dict = {}
self.dirs_dict = {}
self.general_params = []
self.default_config = {}
self.rules_dependencies = {}
self.forbidden_params = {}
def __init__(self):
if 'args' not in self.__dict__:
raise ConfigError("You need to initialize `WorkflowSuperClass` from within a class that "
"has a member `self.args`.")
A = lambda x: self.args.__dict__[x] if x in self.args.__dict__ else None
# FIXME: it is redundant to have both config and config_file
# Alon and Meren will discuss how to do this right.
# but for now this is how it is so things would work.
# basically, when this class is called from a snakefile
# then a config (dictionary) will be provided.
# When this class is called from anvi-run-snakemake-workflow
# for sanity checks and things like that, then a config file
# will be provided.
self.config = A('config')
self.config_file = A('config_file')
self.default_config_output_path = A('get_default_config')
self.save_workflow_graph = A('save_workflow_graph')
self.list_dependencies = A('list_dependencies')
self.dry_run_only = A('dry_run')
self.additional_params = A('additional_params')
self.skip_version_check = A('skip_version_check')
if self.additional_params:
run.warning("OK, SO THIS IS SERIOUS, AND WHEN THINGS ARE SERIOUS THEN WE USE CAPS. "
"WE SEE THAT YOU ARE USING --additional-params AND THAT'S GREAT, BUT WE "
"WANT TO REMIND YOU THAT ANYTHING THAT FOLLOWS --additional-params WILL "
"BE CONSIDERED AS A snakemake PARAM THAT IS TRANSFERRED TO snakemake DIRECTLY. "
"So make sure that these don't include anything that you didn't mean to "
"include as an additional param: %s." % ', '.join(str(i) for i in self.additional_params))
if self.save_workflow_graph:
self.dry_run_only = True
# if this class is being inherited from a snakefile that was 'included' from
# within another snakefile.
self.this_workflow_is_inherited_by_another = A('this_workflow_is_inherited_by_another')
if self.config_file:
filesnpaths.is_file_json_formatted(self.config_file)
self.config = json.load(open(self.config_file))
if self.config and ('config_version' not in self.config or 'workflow_name' not in self.config):
raise ConfigError(f"You config file '{self.config_file}' is probably too old as it is missing some key varaibles "
f"in it. Please make sure your config includes entries for both `config_version` and "
f"`workflow_name`.")
# If a config exists, check that its current
if self.config and not self.skip_version_check:
if self.config['config_version'] != workflow_config_version:
raise ConfigError(f"Anvi'o couldn't get things moving because the version of your config file is out "
f"of date (your version: {self.config['config_version']}; up-to-date version: "
f"{workflow_config_version}). Not a problem though, simply run `anvi-migrate {self.config_file} "
f"--migrate-dbs-safely` and it will be updated. Then re-run the command producing "
f"this error message.")
self.rules = []
self.rule_acceptable_params_dict = {}
self.dirs_dict = {}
self.general_params = []
self.default_config = {}
self.rules_dependencies = {}
self.forbidden_params = {}
