def __init__(
self, input_to_select, remove_file_extension=None, type_hint=File, **kwargs
):
"""
:param input_to_select: The name of the input to select
:param remove_file_extension: Call basename() and remove the file extension
:param type_hint: Janis can't determine the type of the input to select until translation time,
so providing a hint type might suppress false warnings. This is similar to using .as_type(dt)
"""
if not isinstance(input_to_select, str):
raise Exception(
f"Expected input_to_select to be string, not {type(input_to_select)}: {str(input_to_select)}"
)
# maybe worth validating the input_to_select identifier
self.input_to_select = input_to_select
self.type_hint = get_instantiated_type(type_hint) or File()
if "use_basename" in kwargs:
use_basename = kwargs["use_basename"]
if remove_file_extension is None:
remove_file_extension = use_basename
Logger.warn(
f"The 'use_basename' key is deprecated, please use 'remove_file_extension' instead: "
f'InputSelector("{self.input_to_select}", remove_file_extension={str(use_basename)})'
)
self.remove_file_extension = remove_file_extension
def stop_engine(self):
if self._logger:
self._logger.terminate()
self.should_stop = True
if self._timer_thread:
self._timer_thread.set()
if self._logfp:
self._logfp.flush()
os.fsync(self._logfp.fileno())
self._logfp.close()
if not self.process_id:
Logger.warn("Could not find a cromwell process to end, SKIPPING")
return
Logger.info("Stopping cromwell")
if self.process_id:
try:
process = os.getpgid(int(self.process_id))
os.killpg(process, signal.SIGTERM)
Logger.info("Stopped cromwell")
except Exception as e:
# can't do
Logger.warn("Couldn't stop Cromwell process: " + str(e))
pass
else:
Logger.warn(
"Couldn't stop Cromwell process as Janis wasn't managing it")
self.is_started = False
def get_workflow_metadatadb(execpath, wid, readonly=False):
connection = None
sqlpath = WorkflowDbManager.get_sql_path_base(execpath)
if not wid:
Logger.debug("Opening database connection to get wid from: " +
sqlpath)
try:
connection = sqlite3.connect(f"file:{sqlpath}?mode=ro",
uri=True)
except:
Logger.critical("Error when opening DB connection to: " +
sqlpath)
raise
wid = RunDbProvider(db=connection).get_latest()
if not wid:
raise Exception("Couldn't get WID in task directory")
retval = WorkflowMetadataDbProvider(sqlpath, wid, readonly=readonly)
if connection:
connection.close()
return retval
def __new__(cls, *args, **kwargs):
multiplier = None
src, *otherargs = args
if len(otherargs) == 1:
f = otherargs[0].lower()
multiplier_heirarchy = [
("ki" in f, 1024),
("k" in f, 1000),
("mi" in f, 1.024),
("gi" in f, 0.001024),
("g" in f, 0.001),
]
if not any(m[0] for m in multiplier_heirarchy):
Logger.warn(
f"Couldn't determine prefix {f} for FileSizeOperator, defaulting to MB"
)
else:
multiplier = [m[1] for m in multiplier_heirarchy if m[0] is True][0]
instance = super(FileSizeOperator, cls).__new__(cls)
instance.__init__(args[0])
if multiplier is not None and multiplier != 1:
return instance * multiplier
return instance
def __init__(
self,
wf,
identifier: str,
datatype: DataType,
source: ConnectionSource,
doc: OutputDocumentation = None,
output_folder: Union[str, InputSelector,
List[Union[str, InputSelector]]] = None,
output_name: Union[str, InputSelector] = None,
skip_typecheck=False,
):
super().__init__(wf, NodeType.OUTPUT, identifier)
self.datatype = datatype
# if source[0].node_type != NodeType.STEP:
# raise Exception(
# f"Unsupported connection type: {"Output"} → {source[0].node_type}"
# )
stype = source[0].outputs()[source[1]].outtype
snode = source[0]
if isinstance(snode, StepNode) and snode.scatter:
stype = Array(stype)
if not skip_typecheck and not datatype.can_receive_from(stype):
Logger.critical(
f"Mismatch of types when joining to output node '{source[0].id()}.{source[1]}' to '{identifier}' "
f"({stype.id()} -/→ {datatype.id()})")
self.source = verify_or_try_get_source(source)
self.doc = (doc if isinstance(doc, OutputDocumentation) else
OutputDocumentation(doc=doc))
self.output_folder = output_folder
self.output_name = output_name
def second_formatter(secs):
if secs is None:
return "N/A"
if not secs:
return "0s"
try:
remainder = int(secs)
except:
Logger.critical(f"second_formatter received non-int type: '{secs}'")
return str(secs)
intervals = []
ranges = [60, 3600, 86400]
extensions = ["s", "m", "h", "d"]
under_first_interval = False
for r in ranges[::-1]:
if under_first_interval or remainder >= r:
under_first_interval = True
val = remainder // r
remainder -= val * r
intervals.append(val)
intervals.append(remainder)
maxintervals = len(intervals) - 1
outp = str(intervals[0]) + extensions[maxintervals]
for i in range(1, len(intervals)):
ivl = intervals[i]
outp += ":" + str(ivl).zfill(2) + extensions[maxintervals - i]
return outp
def do_docs(args):
try:
import webbrowser
webbrowser.open(DOCS_URL)
except Exception as e:
Logger.critical(f"Failed to open {DOCS_URL} ({e})")
def rm_dir(self, directory):
Logger.info(f"Removing local directory '{directory}'")
try:
return shutil.rmtree(directory)
except Exception as e:
Logger.critical(f"Error removing directory '{directory}': {e}")
return False
def __init__(self, format: str, **kwargs):
self._format: str = format
keywords, balance = get_keywords_between_braces(self._format)
if balance > 0:
Logger.warn(
"There was an imbalance of braces in the string _format, this might cause issues with concatenation"
)
skwargs = set(kwargs.keys())
if not keywords == skwargs:
# what's the differences
if not keywords.issubset(skwargs):
raise IncorrectArgsException(
"The _format required additional arguments to be provided by "
"**kwargs, requires the keys:" +
", ".join(keywords - skwargs))
else:
raise TooManyArgsException(
"The **kwargs contained unrecognised keys: " +
", ".join(skwargs - keywords))
self.kwargs = kwargs
def translate_tool(
self,
tool,
to_console=True,
to_disk=False,
export_path=None,
with_docker=True,
with_resource_overrides=False,
max_cores=None,
max_mem=None,
):
tool_out = self.stringify_translated_tool(
self.translate_tool_internal(
tool,
with_docker=with_docker,
with_resource_overrides=with_resource_overrides,
))
if to_console:
print(tool_out)
if to_disk:
d = ExportPathKeywords.resolve(export_path,
workflow_spec=self.name,
workflow_name=tool.id())
if not os.path.exists(d):
os.makedirs(d)
fn_tool = self.tool_filename(tool)
with open(os.path.join(d, fn_tool), "w+") as wf:
Logger.log(f"Writing {fn_tool} to disk")
wf.write(tool_out)
Logger.log(f"Wrote {fn_tool} to disk")
return tool_out
def __init__(
self,
wf,
identifier: str,
datatype: DataType,
source: ConnectionSource,
doc: str = None,
output_tag: Union[str, InputSelector] = None,
output_prefix: Union[
str, InputSelector, List[Union[str, InputSelector]]
] = None,
):
super().__init__(wf, NodeTypes.OUTPUT, identifier)
self.datatype = datatype
if source[0].node_type != NodeTypes.STEP:
raise Exception(
f"Unsupported connection type: {NodeTypes.OUTPUT} → {source[0].node_type}"
)
stype = source[0].outputs()[source[1]].output_type
snode = source[0]
if isinstance(snode, StepNode) and snode.scatter:
stype = Array(stype)
if not datatype.can_receive_from(stype):
Logger.critical(
f"Mismatch of types when joining to output node '{source[0].id()}.{source[1]}' to '{identifier}' "
f"({stype.id()} -/→ {datatype.id()})"
)
self.source = verify_or_try_get_source(source)
self.doc = doc
self.output_tag = output_tag
self.output_prefix = output_prefix
def __init__(self, **connections):
super().__init__(metadata_class=WorkflowMetadata)
self.connections = connections
Logger.log(f"Creating workflow with identifier: '{self.id()}'")
if not Validators.validate_identifier(self.id()):
raise Exception(
f"The identifier '{self.id()}' was invalid because {Validators.reason_for_failure(self.id())}"
)
# The following variables allow us to quickly check data about the graph
self.nodes: Dict[str, Node] = {}
self.input_nodes: Dict[str, InputNode] = {}
self.step_nodes: Dict[str, StepNode] = {}
self.output_nodes: Dict[str, OutputNode] = {}
# Flags for different requirements that a workflow might need
self.has_scatter = False
self.has_subworkflow = False
self.has_multiple_inputs = False
# Now that we've initialised everything, we can "construct" the workflows for that subclass this class
# else, for the WorkflowBuilder it will do nothing and they'll add workflows later
self.constructor()
def get_recipe_for_keys(self, keys: List[str]):
self.load_recipes()
if not keys:
return {}
rec = {}
for key in keys:
found_key = False
if key in self._files_by_key:
found_key = True
rec.update(
self.get_cascaded_dict_from_yamls(
self._files_by_key[key]))
if key in self.recipes:
found_key = True
rec.update(self.recipes[key] or {})
if not found_key:
Logger.critical(f"Couldn't find '{key}' in known recipes")
return rec
def map_to_wdl(t: NativeType):
import wdlgen as wdl
if t == NativeTypes.kBool:
return wdl.PrimitiveType.kBoolean
elif t == NativeTypes.kInt:
return wdl.PrimitiveType.kInt
elif (t == NativeTypes.kLong or t == NativeTypes.kFloat
or t == NativeTypes.kDouble):
return wdl.PrimitiveType.kFloat
elif t == NativeTypes.kStr:
return wdl.PrimitiveType.kString
elif t == NativeTypes.kFile:
return wdl.PrimitiveType.kFile
elif t == NativeTypes.kStdout:
return wdl.PrimitiveType.kFile
elif t == NativeTypes.kStderr:
return wdl.PrimitiveType.kFile
elif t == NativeTypes.kDirectory:
Logger.log(
"Using data_type 'Directory' for wdl, this requires cromwell>=37 and language=development"
)
return wdl.PrimitiveType.kDirectory
elif t == NativeTypes.kArray:
return wdl.ArrayType.kArray
raise Exception(
f"Unhandled primitive type {t}, expected one of {', '.join(NativeTypes.all)}"
)
def get_value_for_key(d, key, default):
val = d.get(key)
if not val:
return default.get(key) if default else None
Logger.log(f"Got value '{val}' for key '{key}'")
return val
def resolve(path, workflow_spec, workflow_name):
if not path:
Logger.critical("Output path was invalid, changed to working directory")
path = "."
if ExportPathKeywords.workflow_spec in path and workflow_spec is None:
raise Exception(
f"path ('{path}') contained parameter {ExportPathKeywords.workflow_spec} "
"but caller of .resolve did not pass language"
)
if ExportPathKeywords.workflow_name in path and workflow_name is None:
raise Exception(
f"path ('{path}') contained parameter {ExportPathKeywords.workflow_name} "
"but caller of .resolve did not pass tool name"
)
path = p.expanduser(path)
if (len(path) == 1 and path == ".") or path[:2] == "./":
path = getcwd() + (path[1:] if len(path) > 1 else "")
elif path[0] != "/":
path = p.join(getcwd(), path)
return path.replace(
ExportPathKeywords.workflow_spec,
workflow_spec.lower() if workflow_spec else "",
).replace(
ExportPathKeywords.workflow_name,
workflow_name.lower() if workflow_name else "",
)
def poll_metadata(self):
if self._timer_thread.is_set() or self.should_stop:
return
for engine_id_to_poll in self.progress_callbacks:
try:
meta = self.metadata(engine_id_to_poll)
if meta:
for callback in self.progress_callbacks[engine_id_to_poll]:
callback(meta)
except Exception as e:
Logger.critical(
f"Received a critical error ({repr(e)}) when getting metadata for "
f"Cromwell task {engine_id_to_poll}, hence terminating task with status=SUSPENDED"
)
meta = RunModel(
id_=None,
submission_id=None,
status=TaskStatus.SUSPENDED,
engine_id=engine_id_to_poll,
name=None,
execution_dir=None,
)
for callback in self.progress_callbacks[engine_id_to_poll]:
callback(meta)
# call timer again
time = self.get_poll_interval()
threading.Timer(time, self.poll_metadata).start()
def do_rm(args):
wids = args.wid
for wid in wids:
try:
ConfigManager.manager().remove_task(wid, keep_output=args.keep)
except Exception as e:
Logger.critical(f"Can't remove {wid}: " + str(e))
def rm_dir(self, directory):
import urllib.request
Logger.info(f"Issuing HTTP.DELETE request for directory '{directory}'")
req = urllib.request.Request(directory)
req.get_method = lambda: "DELETE"
return urllib.request.urlopen(req)
def do_version(_):
from tabulate import tabulate
import importlib_metadata
from janis_assistant.__meta__ import __version__ as jr_version
from janis_core.__meta__ import __version__ as jc_version
import janis_core.toolbox.entrypoints as EP
fields = [["janis-core", jc_version], ["janis-assistant", jr_version]]
# eps = pkg_resources.iter_entry_points(group=EP.EXTENSIONS)
eps = importlib_metadata.entry_points().get(EP.EXTENSIONS, [])
skip_eps = {"assistant"}
for entrypoint in eps:
if entrypoint.name in skip_eps:
continue
try:
version = entrypoint.load().__version__
if version:
fields.append(["janis-" + entrypoint.name, version])
skip_eps.add(entrypoint.name)
except Exception as e:
Logger.log_ex(e)
print(tabulate(fields))
def add_tool(tool: Tool) -> bool:
v: Optional[str] = tool.version()
if not v:
t = f"The tool {tool.id()} did not have a version and will not be registered"
Logger.critical(t)
return False
return JanisShed._toolshed.register(tool.id().lower(), v.lower(), tool)
def do_rm(args):
wids = args.wid
for wid in wids:
try:
ConfigManager.get_from_path_or_submission_lazy(
wid, readonly=True).remove_task(wid, keep_output=args.keep)
except Exception as e:
Logger.critical(f"Can't remove {wid}: " + str(e))
def get_file_size(self, path) -> Optional[int]:
try:
stat = os.stat(path)
if not stat:
return None
return stat.st_size
except Exception as e:
Logger.warn(f"Couldn't get file size of path '{path}': {repr(e)}")
return None
def add_tool(tool: Tool) -> bool:
v: Optional[str] = tool.version()
if not v:
t = f"The tool {tool.id()} did not have a version and will not be registered"
Logger.critical(t)
return False
Logger.log("Adding tool: " + tool.id())
JanisShed._byclassname.register(tool.__class__.__name__, tool)
return JanisShed._toolshed.register(tool.id().lower(), v.lower(), tool)
def cwl_type(self, has_default=False):
inner_types = [a.cwl_type(has_default=has_default) for a in self.subtypes]
try:
inner_types = list(set(inner_types))
except Exception as e:
Logger.debug(f"Error creating set from ({inner_types}): {e}")
if len(inner_types) == 1:
return inner_types[0]
return inner_types
def get_cascaded_dict_from_yamls(files):
d = {}
for f in files:
try:
with open(f) as rl:
adr = ruamel.yaml.load(rl, Loader=ruamel.yaml.Loader)
d.update(adr)
except Exception as e:
Logger.critical(f"Couldn't parse file '{f}': {e}")
return d
def convert_generic_class(t,
ignore_fields=None,
get_string_repr_func=None,
workflow_id: str = None):
options = []
get_string_repr_func2 = lambda obj: (get_string_repr_func or
JanisTranslator.get_string_repr)(
obj, workflow_id=workflow_id)
try:
has_init_dict = not isinstance(
t, (Tool, WorkflowBase, PythonTool, StepNode)) and hasattr(
t, "init_dictionary")
except KeyError:
has_init_dict = False
if has_init_dict:
options.extend(f"{k}={get_string_repr_func2(v)}"
for k, v in t.init_dictionary().items())
else:
ignore_fields = set((ignore_fields if ignore_fields else []) +
["self", "args", "kwargs"])
params = inspect.signature(type(t).__init__).parameters
param_map = {}
if not isinstance(t, (StepNode, WorkflowBase)) and hasattr(
t, "init_key_map"):
param_map = t.init_key_map
# fields = fields_to_check if fields_to_check \
# else [f for f in dict(params).keys() if f not in ignore_fields]
for fkey in params:
if fkey in ignore_fields:
continue
opts = params[fkey]
t_key = param_map.get(fkey, fkey)
if t_key is None:
continue
if hasattr(t, t_key):
v = t.__getattribute__(t_key)
else:
Logger.warn(
f"Object '{t.__class__.__name__}' didn't have attribute {t_key}, setting to None and it might get skipped"
)
v = None
if (v is None and opts.default is None) or v == opts.default:
continue
options.append(fkey + "=" + get_string_repr_func2(v))
return f"{t.__class__.__name__}({', '.join(options)})"
def check_types(self):
from janis_core.workflow.workflow import InputNode, StepNode
stoolin: TOutput = self.start.outputs()[
self.stag
] if self.stag is not None else first_value(self.start.outputs())
ftoolin: TInput = self.finish.inputs()[
self.ftag
] if self.ftag is not None else first_value(self.finish.inputs())
stype = stoolin.outtype
ftype = ftoolin.intype
start_is_scattered = (
isinstance(self.start, StepNode) and self.start.scatter is not None
)
if start_is_scattered:
Logger.log(
f"This edge merges the inputs from '{full_dot(self.start, self.stag)}' for "
f"'{full_dot(self.finish, self.ftag)}'"
)
stype = Array(stype)
if self.scatter:
if not isinstance(stype, Array):
raise Exception(
f"Scatter was required for '{self.start.id()}.{self.stag} → '{self.finish.id()}.{self.ftag}' but "
f"the input type was {type(stype).__name__} and not an array"
)
stype = stype.subtype()
source_has_default = (
isinstance(self.start, InputNode) and self.start.default is not None
)
# Scatters are handled automatically by the StepTagInput Array unwrapping
# Merges are handled automatically by the `start_is_scattered` Array wrap
self.compatible_types = ftype.can_receive_from(stype, source_has_default)
if not self.compatible_types:
if isinstance(ftype, Array) and ftype.subtype().can_receive_from(stype):
self.compatible_types = True
if not self.compatible_types:
s = full_dot(self.start, self.stag)
f = full_dot(self.finish, self.ftag)
message = (
f"Mismatch of types when joining '{s}' to '{f}': "
f"{stoolin.outtype.id()} -/→ {ftoolin.intype.id()}"
)
if isinstance(stype, Array) and ftype.can_receive_from(stype.subtype()):
message += " (did you forget to SCATTER?)"
Logger.critical(message)
def terminate(self):
self.should_terminate = True
if self.logfp:
try:
self.logfp.flush()
os.fsync(self.logfp.fileno())
except Exception as e:
# This isn't a proper error, there's nothing we could do
# and doesn't prohibit the rest of the shutdown of Janis.
Logger.critical("Couldn't flush engine stderr to disk: " +
str(e))
def __init__(self, d: dict, default: dict):
d = d if d else {}
self.id = JanisConfiguration.get_value_for_key(
d, self.Keys.Id, default)
Logger.log("Got template ID: " + str(self.id))
# remove this id from the dictionary: https://stackoverflow.com/a/15411146/
d.pop(self.Keys.Id.value, None)
self.template = from_template(self.id, d)
