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task.py
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task.py
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"""
Local task runner
"""
import logging
import math
import os
import json
import traceback
import glob
import threading
import shutil
import regex
from typing import Tuple, List, Dict, Optional, Callable, Set, Any, Union, TYPE_CHECKING
from contextlib import ExitStack, suppress
from collections import Counter
from .. import Error, Type, Env, Value, StdLib, Tree, Expr, _util
from .._util import (
write_atomic,
write_values_json,
provision_run_dir,
TerminationSignalFlag,
chmod_R_plus,
path_really_within,
LoggingFileHandler,
compose_coroutines,
pathsize,
link_force,
symlink_force,
rmtree_atomic,
)
from .._util import StructuredLogMessage as _
from . import config, _statusbar
from .download import able as downloadable, run_cached as download
from .cache import CallCache, new as new_call_cache
from .error import OutputError, Interrupted, Terminated, RunFailed, error_json
if TYPE_CHECKING: # otherwise-delayed heavy imports
from .task_container import TaskContainer
def run_local_task( # type: ignore[return]
cfg: config.Loader,
task: Tree.Task,
inputs: Env.Bindings[Value.Base],
run_id: Optional[str] = None,
run_dir: Optional[str] = None,
logger_prefix: Optional[List[str]] = None,
_run_id_stack: Optional[List[str]] = None,
_cache: Optional[CallCache] = None,
_plugins: Optional[List[Callable[..., Any]]] = None,
) -> Tuple[str, Env.Bindings[Value.Base]]:
"""
Run a task locally.
Inputs shall have been typechecked already. File inputs are presumed to be local POSIX file
paths that can be mounted into a container.
:param run_id: unique ID for the run, defaults to workflow name
:param run_dir: directory under which to create a timestamp-named subdirectory for this run
(defaults to current working directory).
If the final path component is ".", then operate in run_dir directly.
"""
from .task_container import new as new_task_container # delay heavy import
_run_id_stack = _run_id_stack or []
run_id = run_id or task.name
logger_prefix = (logger_prefix or ["wdl"]) + ["t:" + run_id]
logger = logging.getLogger(".".join(logger_prefix))
with ExitStack() as cleanup:
terminating = cleanup.enter_context(TerminationSignalFlag(logger))
if terminating():
raise Terminated(quiet=True)
# provision run directory and log file
run_dir = provision_run_dir(task.name, run_dir, last_link=not _run_id_stack)
logfile = os.path.join(run_dir, "task.log")
cleanup.enter_context(
LoggingFileHandler(
logger,
logfile,
)
)
if cfg.has_option("logging", "json") and cfg["logging"].get_bool("json"):
cleanup.enter_context(
LoggingFileHandler(
logger,
logfile + ".json",
json=True,
)
)
logger.notice(
_(
"task setup",
name=task.name,
source=task.pos.uri,
line=task.pos.line,
column=task.pos.column,
dir=run_dir,
thread=threading.get_ident(),
)
)
write_values_json(inputs, os.path.join(run_dir, "inputs.json"))
if not _run_id_stack:
cache = _cache or cleanup.enter_context(new_call_cache(cfg, logger))
cache.flock(logfile, exclusive=True) # no containing workflow; flock task.log
else:
cache = _cache
assert cache
cleanup.enter_context(_statusbar.task_slotted())
maybe_container = None
try:
cache_key = f"{task.name}/{task.digest}/{Value.digest_env(inputs)}"
cached = cache.get(cache_key, inputs, task.effective_outputs)
if cached is not None:
for decl in task.outputs:
v = cached[decl.name]
vj = json.dumps(v.json)
logger.info(
_(
"cached output",
name=decl.name,
value=(v.json if len(vj) < 4096 else "(((large)))"),
)
)
# create out/ and outputs.json
_outputs = link_outputs(
cache,
cached,
run_dir,
hardlinks=cfg["file_io"].get_bool("output_hardlinks"),
use_relative_output_paths=cfg["file_io"].get_bool("use_relative_output_paths"),
)
write_values_json(
cached, os.path.join(run_dir, "outputs.json"), namespace=task.name
)
logger.notice("done (cached)")
# returning `cached`, not the rewritten `_outputs`, to retain opportunity to find
# cached downstream inputs
return (run_dir, cached)
# start plugin coroutines and process inputs through them
with compose_coroutines(
[
(
lambda kwargs, cor=cor: cor( # type: ignore
cfg, logger, _run_id_stack + [run_id], run_dir, task, **kwargs
)
)
for cor in (
[cor2 for _, cor2 in sorted(config.load_plugins(cfg, "task"))]
+ (_plugins or [])
)
],
{"inputs": inputs},
) as plugins:
recv = next(plugins)
inputs = recv["inputs"]
# download input files, if needed
posix_inputs = _download_input_files(
cfg,
logger,
logger_prefix,
run_dir,
_add_downloadable_defaults(cfg, task.available_inputs, inputs),
cache,
)
# create TaskContainer according to configuration
container = new_task_container(cfg, logger, run_id, run_dir)
maybe_container = container
# evaluate input/postinput declarations, including mapping from host to
# in-container file paths
container_env = _eval_task_inputs(logger, task, posix_inputs, container)
# evaluate runtime fields
stdlib = InputStdLib(task.effective_wdl_version, logger, container)
_eval_task_runtime(
cfg, logger, run_id, task, posix_inputs, container, container_env, stdlib
)
# interpolate command
# pylint: disable=E1101
placeholder_re = regex.compile(
cfg["task_runtime"]["placeholder_regex"], flags=regex.POSIX
)
setattr(
stdlib,
"_placeholder_regex",
placeholder_re,
) # hack to pass regex to WDL.Expr.Placeholder._eval
command = _util.strip_leading_whitespace(
task.command.eval(container_env, stdlib).value
)[1]
delattr(stdlib, "_placeholder_regex")
logger.debug(_("command", command=command.strip()))
# process command & container through plugins
recv = plugins.send({"command": command, "container": container})
command, container = (recv[k] for k in ("command", "container"))
# start container & run command (and retry if needed)
_try_task(cfg, task, logger, container, command, terminating)
# evaluate output declarations
outputs = _eval_task_outputs(logger, run_id, task, container_env, container)
# create output_links
outputs = link_outputs(
cache,
outputs,
run_dir,
hardlinks=cfg["file_io"].get_bool("output_hardlinks"),
use_relative_output_paths=cfg["file_io"].get_bool("use_relative_output_paths"),
)
# process outputs through plugins
recv = plugins.send({"outputs": outputs})
outputs = recv["outputs"]
# clean up, if so configured, and make sure output files will be accessible to
# downstream tasks
_delete_work(cfg, logger, container, True)
chmod_R_plus(run_dir, file_bits=0o660, dir_bits=0o770)
_warn_output_basename_collisions(logger, outputs)
# write outputs.json
write_values_json(
outputs, os.path.join(run_dir, "outputs.json"), namespace=task.name
)
logger.notice("done")
if not run_id.startswith("download-"):
cache.put(cache_key, outputs, run_dir=run_dir)
return (run_dir, outputs)
except Exception as exn:
tbtxt = traceback.format_exc()
logger.debug(tbtxt)
wrapper = RunFailed(task, run_id, run_dir)
logmsg = _(
str(wrapper),
dir=run_dir,
**error_json(
exn, traceback=tbtxt if not isinstance(exn, Error.RuntimeError) else None
),
)
if isinstance(exn, Terminated) and getattr(exn, "quiet", False):
logger.debug(logmsg)
else:
logger.error(logmsg)
try:
write_atomic(
json.dumps(
error_json(
wrapper,
cause=exn,
traceback=tbtxt if not isinstance(exn, Error.RuntimeError) else None,
),
indent=2,
),
os.path.join(run_dir, "error.json"),
)
except Exception as exn2:
logger.debug(traceback.format_exc())
logger.critical(_("failed to write error.json", dir=run_dir, message=str(exn2)))
try:
if maybe_container:
_delete_work(cfg, logger, maybe_container, False)
except Exception as exn2:
logger.debug(traceback.format_exc())
logger.error(_("delete_work also failed", exception=str(exn2)))
raise wrapper from exn
def _download_input_files(
cfg: config.Loader,
logger: logging.Logger,
logger_prefix: List[str],
run_dir: str,
inputs: Env.Bindings[Value.Base],
cache: CallCache,
) -> Env.Bindings[Value.Base]:
"""
Find all File & Directory input values that are downloadable URIs (including any nested within
compound values). Download them to some location under run_dir and return a copy of the inputs
with the URI values replaced by the downloaded paths.
"""
downloads = 0
download_bytes = 0
cached_hits = 0
def rewriter(v: Union[Value.Directory, Value.File]) -> str:
nonlocal downloads, download_bytes, cached_hits
directory = isinstance(v, Value.Directory)
uri = v.value
if downloadable(cfg, uri, directory=directory):
logger.info(_(f"download input {'directory' if directory else 'file'}", uri=uri))
cached, filename = download(
cfg,
logger,
cache,
uri,
directory=directory,
run_dir=os.path.join(run_dir, "download", str(downloads), "."),
logger_prefix=logger_prefix + [f"download{downloads}"],
)
if cached:
cached_hits += 1
else:
sz = pathsize(filename)
logger.info(_("downloaded input", uri=uri, path=filename, bytes=sz))
downloads += 1
download_bytes += sz
return filename
return uri
ans = Value.rewrite_env_paths(inputs, rewriter)
if downloads or cached_hits:
logger.notice(
_(
"processed input URIs",
downloaded=downloads,
downloaded_bytes=download_bytes,
cached=cached_hits,
)
)
return ans
def _add_downloadable_defaults(
cfg: config.Loader, available_inputs: Env.Bindings[Tree.Decl], inputs: Env.Bindings[Value.Base]
) -> Env.Bindings[Value.Base]:
"""
Look for available File/Directory inputs that default to a string constant appearing to be a
downloadable URI. For each one, add a binding for that default to the user-supplied inputs (if
not already overridden in them).
This is to trigger download of the default URIs even though we otherwise don't evaluate input
declarations until after processing downloads.
"""
ans = inputs
for b in available_inputs:
if (
isinstance(b.value.type, (Type.File, Type.Directory))
and b.name not in ans
and isinstance(b.value.expr, Expr.String)
):
directory = isinstance(b.value.type, Type.Directory)
maybe_uri = b.value.expr.literal
if maybe_uri and downloadable(cfg, maybe_uri.value, directory=directory):
v = (
Value.Directory(maybe_uri.value, b.value.expr)
if directory
else Value.File(maybe_uri.value, b.value.expr)
)
ans = ans.bind(b.name, v)
return ans
def _eval_task_inputs(
logger: logging.Logger,
task: Tree.Task,
posix_inputs: Env.Bindings[Value.Base],
container: "TaskContainer",
) -> Env.Bindings[Value.Base]:
# Preprocess inputs: if None value is supplied for an input declared with a default but without
# the ? type quantifier, remove the binding entirely so that the default will be used. In
# contrast, if the input declaration has an -explicitly- optional type, then we'll allow the
# supplied None to override any default.
input_decls = task.available_inputs
posix_inputs = posix_inputs.filter(
lambda b: not (
isinstance(b.value, Value.Null)
and b.name in input_decls
and input_decls[b.name].expr
and not input_decls[b.name].type.optional
)
)
# Map all the provided input File & Directory paths to in-container paths
container.add_paths(_fspaths(posix_inputs))
_warn_input_basename_collisions(logger, container)
# copy posix_inputs with all File & Directory values mapped to their in-container paths
def map_paths(fn: Union[Value.File, Value.Directory]) -> str:
p = fn.value.rstrip("/")
if isinstance(fn, Value.Directory):
p += "/"
return container.input_path_map[p]
container_inputs = Value.rewrite_env_paths(posix_inputs, map_paths)
# initialize value environment with the inputs
container_env: Env.Bindings[Value.Base] = Env.Bindings()
for b in container_inputs:
assert isinstance(b, Env.Binding)
v = b.value
assert isinstance(v, Value.Base)
container_env = container_env.bind(b.name, v)
vj = json.dumps(v.json)
logger.info(_("input", name=b.name, value=(v.json if len(vj) < 4096 else "(((large)))")))
# collect remaining declarations requiring evaluation.
decls_to_eval = []
for decl in (task.inputs or []) + (task.postinputs or []):
if not container_env.has_binding(decl.name):
decls_to_eval.append(decl)
# topsort them according to internal dependencies. prior static validation
# should have ensured they're acyclic.
decls_by_id, decls_adj = Tree._decl_dependency_matrix(decls_to_eval)
decls_to_eval = [decls_by_id[did] for did in _util.topsort(decls_adj)]
assert len(decls_by_id) == len(decls_to_eval)
# evaluate each declaration in that order
# note: the write_* functions call container.add_paths as a side-effect
stdlib = InputStdLib(task.effective_wdl_version, logger, container)
for decl in decls_to_eval:
assert isinstance(decl, Tree.Decl)
v = Value.Null()
if decl.expr:
try:
v = decl.expr.eval(container_env, stdlib=stdlib).coerce(decl.type)
except Error.RuntimeError as exn:
setattr(exn, "job_id", decl.workflow_node_id)
raise exn
except Exception as exn:
exn2 = Error.EvalError(decl, str(exn))
setattr(exn2, "job_id", decl.workflow_node_id)
raise exn2 from exn
else:
assert decl.type.optional
vj = json.dumps(v.json)
logger.info(_("eval", name=decl.name, value=(v.json if len(vj) < 4096 else "(((large)))")))
container_env = container_env.bind(decl.name, v)
return container_env
def _fspaths(env: Env.Bindings[Value.Base]) -> Set[str]:
"""
Get the unique paths of all File & Directory values in the environment. Directory paths will
have a trailing '/'.
"""
ans = set()
def collector(v: Value.Base) -> None:
if isinstance(v, Value.File):
assert not v.value.endswith("/")
ans.add(v.value)
elif isinstance(v, Value.Directory):
ans.add(v.value.rstrip("/") + "/")
for ch in v.children:
collector(ch)
for b in env:
collector(b.value)
return ans
def _warn_input_basename_collisions(logger: logging.Logger, container: "TaskContainer") -> None:
basenames = Counter(
[os.path.basename((p[:-1] if p.endswith("/") else p)) for p in container.input_path_map_rev]
)
collisions = [nm for nm, n in basenames.items() if n > 1]
if collisions:
logger.warning(
_(
"mounting input files with colliding basenames in separate container directories",
basenames=collisions,
)
)
def _eval_task_runtime(
cfg: config.Loader,
logger: logging.Logger,
run_id: str,
task: Tree.Task,
inputs: Env.Bindings[Value.Base],
container: "TaskContainer",
env: Env.Bindings[Value.Base],
stdlib: StdLib.Base,
) -> None:
# evaluate runtime{} expressions (merged with any configured defaults)
runtime_defaults = cfg.get_dict("task_runtime", "defaults")
if run_id.startswith("download-"):
runtime_defaults.update(cfg.get_dict("task_runtime", "download_defaults"))
runtime_values = {}
for key, v in runtime_defaults.items():
runtime_values[key] = Value.from_json(Type.Any(), v)
for key, expr in task.runtime.items(): # evaluate expressions in source code
runtime_values[key] = expr.eval(env, stdlib)
for b in inputs.enter_namespace("runtime"):
runtime_values[b.name] = b.value # input overrides
logger.debug(_("runtime values", **dict((key, str(v)) for key, v in runtime_values.items())))
# have container implementation validate & postprocess into container.runtime_values
container.process_runtime(logger, runtime_values)
if container.runtime_values:
logger.info(_("effective runtime", **container.runtime_values))
# add any configured overrides for in-container environment variables
container.runtime_values.setdefault("env", {})
env_vars_override = {}
env_vars_skipped = []
for ev_name, ev_value in cfg["task_runtime"].get_dict("env").items():
if ev_value is None:
try:
env_vars_override[ev_name] = os.environ[ev_name]
except KeyError:
env_vars_skipped.append(ev_name)
else:
env_vars_override[ev_name] = str(ev_value)
if env_vars_skipped:
logger.warning(
_("skipping pass-through of undefined environment variable(s)", names=env_vars_skipped)
)
if cfg.get_bool("file_io", "mount_tmpdir") or task.name in cfg.get_list(
"file_io", "mount_tmpdir_for"
):
env_vars_override["TMPDIR"] = os.path.join(
container.container_dir, "work", "_miniwdl_tmpdir"
)
if env_vars_override:
# usually don't dump values into log, as they may often be auth tokens
logger.notice(
_(
"overriding environment variables (portability warning)",
names=list(env_vars_override.keys()),
)
)
logger.debug(
_("overriding environment variables (portability warning)", **env_vars_override)
)
container.runtime_values["env"].update(env_vars_override)
# process decls with "env" decorator (EXPERIMENTAL)
env_decls: Dict[str, Value.Base] = {}
for decl in (task.inputs or []) + task.postinputs:
if decl.decor.get("env", False) is True:
if not env_decls:
logger.warning(
"task env declarations are an experimental feature, subject to change"
)
v = env[decl.name]
if isinstance(v, (Value.String, Value.File, Value.Directory)):
v = v.value
else:
v = json.dumps(v.json)
env_decls[decl.name] = v
container.runtime_values["env"].update(env_decls)
unused_keys = list(
key
for key in runtime_values
if key not in ("memory", "docker", "container") and key not in container.runtime_values
)
if unused_keys:
logger.warning(_("ignored runtime settings", keys=unused_keys))
def _try_task(
cfg: config.Loader,
task: Tree.Task,
logger: logging.Logger,
container: "TaskContainer",
command: str,
terminating: Callable[[], bool],
) -> None:
"""
Run the task command in the container, retrying up to runtime.preemptible occurrences of
Interrupted errors, plus up to runtime.maxRetries occurrences of any error.
"""
from docker.errors import BuildError as DockerBuildError # delay heavy import
max_retries = container.runtime_values.get("maxRetries", 0)
max_interruptions = container.runtime_values.get("preemptible", 0)
retries = 0
interruptions = 0
while True:
if terminating():
raise Terminated()
# copy input files, if needed
if cfg.get_bool("file_io", "copy_input_files") or task.name in cfg.get_list(
"file_io", "copy_input_files_for"
):
container.copy_input_files(logger)
host_tmpdir = (
os.path.join(container.host_work_dir(), "_miniwdl_tmpdir")
if cfg.get_bool("file_io", "mount_tmpdir")
or task.name in cfg.get_list("file_io", "mount_tmpdir_for")
else None
)
try:
# start container & run command
if host_tmpdir:
logger.debug(_("creating task temp directory", TMPDIR=host_tmpdir))
os.mkdir(host_tmpdir, mode=0o770)
try:
return container.run(logger, command)
finally:
if host_tmpdir:
logger.info(_("deleting task temp directory", TMPDIR=host_tmpdir))
rmtree_atomic(host_tmpdir)
if (
"preemptible" in container.runtime_values
and cfg.has_option("task_runtime", "_mock_interruptions")
and interruptions < cfg["task_runtime"].get_int("_mock_interruptions")
):
raise Interrupted("mock interruption") from None
except Exception as exn:
if isinstance(exn, Interrupted) and interruptions < max_interruptions:
logger.error(
_(
"interrupted task will be retried",
error=exn.__class__.__name__,
message=str(exn),
prev_interruptions=interruptions,
max_interruptions=max_interruptions,
)
)
interruptions += 1
elif (
not isinstance(exn, (Terminated, DockerBuildError))
and retries < max_retries
and not terminating()
):
logger.error(
_(
"failed task will be retried",
error=exn.__class__.__name__,
message=str(exn),
prev_retries=retries,
max_retries=max_retries,
)
)
retries += 1
else:
raise
_delete_work(cfg, logger, container, False)
container.reset(logger)
def _eval_task_outputs(
logger: logging.Logger,
run_id: str,
task: Tree.Task,
env: Env.Bindings[Value.Base],
container: "TaskContainer",
) -> Env.Bindings[Value.Base]:
stdout_file = os.path.join(container.host_dir, "stdout.txt")
with suppress(FileNotFoundError):
if os.path.getsize(stdout_file) > 0 and not run_id.startswith("download-"):
# If the task produced nonempty stdout that isn't used in the WDL outputs, generate a
# courtesy log message directing user where to find it
stdout_used = False
expr_stack = [outp.expr for outp in task.outputs]
while expr_stack:
expr = expr_stack.pop()
assert isinstance(expr, Expr.Base)
if isinstance(expr, Expr.Apply) and expr.function_name == "stdout":
stdout_used = True
else:
expr_stack.extend(expr.children) # type: ignore[arg-type]
if not stdout_used:
logger.info(
_(
"command stdout unused; consider output `File cmd_out = stdout()`"
" or redirect command to stderr log >&2",
stdout_file=stdout_file,
)
)
# Helpers to rewrite File/Directory from in-container paths to host paths
# First pass -- convert nonexistent output paths to None/Null
def rewriter1(v: Union[Value.File, Value.Directory], output_name: str) -> Optional[str]:
container_path = v.value
if isinstance(v, Value.Directory) and not container_path.endswith("/"):
container_path += "/"
if container.host_path(container_path) is None:
logger.warning(
_(
"output path not found in container (error unless declared type is optional)",
output=output_name,
path=container_path,
)
)
return None
return v.value
# Second pass -- convert in-container paths to host paths
def rewriter2(v: Union[Value.File, Value.Directory], output_name: str) -> Optional[str]:
container_path = v.value
if isinstance(v, Value.Directory) and not container_path.endswith("/"):
container_path += "/"
host_path = container.host_path(container_path)
assert host_path is not None
if isinstance(v, Value.Directory):
if host_path.endswith("/"):
host_path = host_path[:-1]
_check_directory(host_path, output_name)
logger.debug(_("output dir", container=container_path, host=host_path))
else:
logger.debug(_("output file", container=container_path, host=host_path))
return host_path
stdlib = OutputStdLib(task.effective_wdl_version, logger, container)
outputs: Env.Bindings[Value.Base] = Env.Bindings()
for decl in task.outputs:
assert decl.expr
try:
v = decl.expr.eval(env, stdlib=stdlib).coerce(decl.type)
except Error.RuntimeError as exn:
setattr(exn, "job_id", decl.workflow_node_id)
raise exn
except Exception as exn:
exn2 = Error.EvalError(decl, str(exn))
setattr(exn2, "job_id", decl.workflow_node_id)
raise exn2 from exn
_warn_struct_extra(logger, decl.name, v)
vj = json.dumps(v.json)
logger.info(
_("output", name=decl.name, value=(v.json if len(vj) < 4096 else "(((large)))"))
)
# Now, a delicate sequence for postprocessing File outputs (including Files nested within
# compound values)
# First convert nonexistent paths to None/Null, and bind this in the environment for
# evaluating subsequent output expressions.
v = Value.rewrite_paths(v, lambda w: rewriter1(w, decl.name))
env = env.bind(decl.name, v)
# check if any nonexistent paths were provided for (non-optional) File/Directory types
# Value.Null.coerce has a special behavior for us to raise FileNotFoundError for a
# non-optional File/Directory type.
try:
v = v.coerce(decl.type)
except FileNotFoundError:
err = OutputError("File/Directory path not found in task output " + decl.name)
setattr(err, "job_id", decl.workflow_node_id)
raise err
# Rewrite in-container paths to host paths
v = Value.rewrite_paths(v, lambda w: rewriter2(w, decl.name))
outputs = outputs.bind(decl.name, v)
return outputs
def _check_directory(host_path: str, output_name: str) -> None:
"""
traverse output directory to check that all symlinks are relative & resolve inside the dir
"""
def raiser(exc: OSError):
raise exc
for root, subdirs, files in os.walk(host_path, onerror=raiser, followlinks=False):
for fn in files:
fn = os.path.join(root, fn)
if os.path.islink(fn) and (
not os.path.exists(fn)
or os.path.isabs(os.readlink(fn))
or not path_really_within(fn, host_path)
):
raise OutputError(f"Directory in output {output_name} contains unusable symlink")
def _warn_struct_extra(
logger: logging.Logger, decl_name: str, v: Value.Base, warned_keys: Optional[Set[str]] = None
) -> None:
"""
Log notices about extraneous keys found in struct initialization from JSON/Map/Object
"""
if warned_keys is None:
warned_keys = set()
if isinstance(v, Value.Struct) and v.extra:
extra_keys = set(k for k in v.extra if not k.startswith("#"))
if extra_keys - warned_keys:
logger.notice(
_(
"extraneous keys in struct initializer",
decl=decl_name,
struct=str(v.type),
extra_keys=list(extra_keys),
)
)
warned_keys.update(extra_keys)
for ch in v.children:
_warn_struct_extra(logger, decl_name, ch, warned_keys)
def link_outputs(
cache: CallCache,
outputs: Env.Bindings[Value.Base],
run_dir: str,
hardlinks: bool = False,
use_relative_output_paths: bool = False,
) -> Env.Bindings[Value.Base]:
"""
Following a successful run, the output files may be scattered throughout a complex directory
tree used for execution. To help navigating this, generate a subdirectory of the run directory
containing nicely organized symlinks to the output files, and rewrite File values in the
outputs env to use these symlinks.
"""
def link1(target: str, link: str, directory: bool) -> None:
if hardlinks:
# TODO: what if target is an input from a different filesystem?
if directory:
shutil.copytree(target, link, symlinks=True, copy_function=link_force)
else:
link_force(target, link)
else:
symlink_force(target, link)
def map_paths(v: Value.Base, dn: str) -> Value.Base:
if isinstance(v, (Value.File, Value.Directory)):
target = (
v.value
if os.path.exists(v.value)
else cache.get_download(v.value, isinstance(v, Value.Directory))
)
if target:
target = os.path.realpath(target)
assert os.path.exists(target)
if not hardlinks and path_really_within(target, os.path.dirname(run_dir)):
# make symlink relative
target = os.path.relpath(target, start=os.path.realpath(dn))
link = os.path.join(dn, os.path.basename(v.value.rstrip("/")))
os.makedirs(dn, exist_ok=False)
link1(target, link, isinstance(v, Value.Directory))
# Drop a dotfile alongside Directory outputs, to inform a program crawling the out/
# directory without reference to the output types or JSON for whatever reason. It
# might otherwise have trouble distinguishing Directory outputs among the
# structured subdirectories we create for compound types.
if isinstance(v, Value.Directory):
with open(os.path.join(dn, ".WDL_Directory"), "w") as dotfile:
pass
v.value = link
# recurse into compound values
elif isinstance(v, Value.Array) and v.value:
d = int(math.ceil(math.log10(len(v.value)))) # how many digits needed
for i in range(len(v.value)):
v.value[i] = map_paths(v.value[i], os.path.join(dn, str(i).rjust(d, "0")))
elif isinstance(v, Value.Map):
# create a subdirectory for each key, as long as the key names seem to make reasonable
# path components; otherwise, treat the dict as a list of its values
keys_ok = (
sum(
1
for b in v.value
if regex.fullmatch("[-_a-zA-Z0-9][-_a-zA-Z0-9.]*", str(b[0]).strip("'\""))
is None
)
== 0
)
d = int(math.ceil(math.log10(len(v.value))))
for i, b in enumerate(v.value):
v.value[i] = (
b[0],
map_paths(
b[1],
os.path.join(
dn, str(b[0]).strip("'\"") if keys_ok else str(i).rjust(d, "0")
),
),
)
elif isinstance(v, Value.Pair):
v.value = (
map_paths(v.value[0], os.path.join(dn, "left")),
map_paths(v.value[1], os.path.join(dn, "right")),
)
elif isinstance(v, Value.Struct):
for key in v.value:
v.value[key] = map_paths(v.value[key], os.path.join(dn, key))
return v
os.makedirs(os.path.join(run_dir, "out"), exist_ok=False)
if use_relative_output_paths:
return link_outputs_relative(link1, cache, outputs, run_dir, hardlinks=hardlinks)
return outputs.map(
lambda binding: Env.Binding(
binding.name,
map_paths(
Value.rewrite_paths(binding.value, lambda v: v.value), # nop to deep copy
os.path.join(run_dir, "out", binding.name),
),
)
)
def link_outputs_relative(
link1: Callable[[str, str, bool], None],
cache: CallCache,
outputs: Env.Bindings[Value.Base],
run_dir: str,
hardlinks: bool = False,
) -> Env.Bindings[Value.Base]:
"""
link_outputs with [file_io] use_relative_output_paths = true. We organize the links to reflect
the generated files' paths relative to their task working directory.
"""
link_destinations: Dict[str, str] = dict()
def map_path_relative(v: Union[Value.File, Value.Directory]) -> str:
target = (
v.value
if os.path.exists(v.value)
else cache.get_download(v.value, isinstance(v, Value.Directory))
)
if target:
real_target = os.path.realpath(target)
rel_link = None
if path_really_within(target, os.path.join(run_dir, "work")):
# target was generated by current task; use its path relative to the task work dir
if not os.path.basename(run_dir).startswith("download-"): # except download tasks
rel_link = os.path.relpath(
real_target, os.path.realpath(os.path.join(run_dir, "work"))
)
else:
# target is an out/ link generated by a call in the current workflow OR a cached
# run; use the link's path relative to that out/ dir, which by induction should
# equal its path relative to the original work/ dir.
# we need heuristic to find the out/ dir in a task/workflow run directory, since the
# user's cwd or the task-generated relative path might coincidentally have
# something named 'out'.
p = None
for p in reversed([m.span()[0] for m in regex.finditer("/out(?=/)", target)]):
if p and (
os.path.isfile(os.path.join(target[:p], "task.log"))
or os.path.isfile(os.path.join(target[:p], "workflow.log"))
):
break
p = None
if p and p + 5 < len(target):
rel_link = os.path.relpath(target, target[: p + 5])
# if neither of the above cases applies, then fall back to just the target basename
rel_link = rel_link or os.path.basename(target)
abs_link = os.path.join(os.path.join(run_dir, "out"), rel_link)
if link_destinations.get(abs_link, real_target) != real_target:
raise FileExistsError(
"Output filename collision; to allow this, set"
" [file_io] use_relative_output_paths = false. Affected path: " + abs_link
)
os.makedirs(os.path.dirname(abs_link), exist_ok=True)
link1(real_target, abs_link, isinstance(v, Value.Directory))
link_destinations[abs_link] = real_target
return abs_link
return v.value
return Value.rewrite_env_paths(outputs, map_path_relative)
def _warn_output_basename_collisions(
logger: logging.Logger, outputs: Env.Bindings[Value.Base]
) -> None:
targets_by_basename: Dict[str, Set[str]] = {}
def walker(v: Union[Value.File, Value.Directory]) -> str:
target = v.value
if os.path.exists(target):
target = os.path.realpath(target)
basename = os.path.basename(target)
targets_by_basename.setdefault(basename, set()).add(target)
return v.value
Value.rewrite_env_paths(outputs, walker)
collisions = [bn for bn, targets in targets_by_basename.items() if len(targets) > 1]
if collisions:
logger.warning(
_(
"multiple output files share the same basename; while miniwdl supports this,"
" consider modifying WDL to ensure distinct output basenames",
basenames=collisions,
)
)
def _delete_work(
cfg: config.Loader,
logger: logging.Logger,
container: "Optional[TaskContainer]",
success: bool,
) -> None:
opt = cfg["file_io"]["delete_work"].strip().lower()
if container and (
opt == "always" or (success and opt == "success") or (not success and opt == "failure")
):
if success and not cfg["file_io"].get_bool("output_hardlinks"):