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# SPDX-License-Identifier: Apache-2.0
"""CWL Expression parsing."""
import asyncio
import copy
import inspect
import json
from collections.abc import Awaitable, MutableMapping
from typing import Any, Optional, Union, cast
from schema_salad.utils import json_dumps
from cwl_utils.errors import JavascriptException, SubstitutionError, WorkflowException
from cwl_utils.loghandler import _logger
from cwl_utils.sandboxjs import JSEngine, default_timeout, get_js_engine, param_re
from cwl_utils.types import CWLObjectType, CWLOutputType
from cwl_utils.utils import bytes2str_in_dicts
def _convert_dumper(string: str) -> str:
return f"{json.dumps(string)} + "
def scanner(scan: str) -> Optional[tuple[int, int]]:
"""Find JS relevant punctuation in a string."""
DEFAULT = 0
DOLLAR = 1
PAREN = 2
BRACE = 3
SINGLE_QUOTE = 4
DOUBLE_QUOTE = 5
BACKSLASH = 6
i = 0
stack = [DEFAULT]
start = 0
while i < len(scan):
state = stack[-1]
c = scan[i]
if state == DEFAULT:
if c == "$":
stack.append(DOLLAR)
elif c == "\\":
stack.append(BACKSLASH)
elif state == BACKSLASH:
stack.pop()
if stack[-1] == DEFAULT:
return i - 1, i + 1
elif state == DOLLAR:
if c == "(":
start = i - 1
stack.append(PAREN)
elif c == "{":
start = i - 1
stack.append(BRACE)
else:
stack.pop()
i -= 1
elif state == PAREN:
if c == "(":
stack.append(PAREN)
elif c == ")":
stack.pop()
if stack[-1] == DOLLAR:
return start, i + 1
elif c == "'":
stack.append(SINGLE_QUOTE)
elif c == '"':
stack.append(DOUBLE_QUOTE)
elif state == BRACE:
if c == "{":
stack.append(BRACE)
elif c == "}":
stack.pop()
if stack[-1] == DOLLAR:
return start, i + 1
elif c == "'":
stack.append(SINGLE_QUOTE)
elif c == '"':
stack.append(DOUBLE_QUOTE)
elif state == SINGLE_QUOTE:
if c == "'":
stack.pop()
elif c == "\\":
stack.append(BACKSLASH)
elif state == DOUBLE_QUOTE:
if c == '"':
stack.pop()
elif c == "\\":
stack.append(BACKSLASH)
i += 1
if len(stack) > 1 and not (len(stack) == 2 and stack[1] in (BACKSLASH, DOLLAR)):
raise SubstitutionError(
"Substitution error, unfinished block starting at position {}: '{}' stack was {}".format(
start, scan[start:], stack
)
)
return None
def evaluator(
js_engine: JSEngine,
ex: str,
obj: CWLObjectType,
jslib: str,
fullJS: bool,
**kwargs: Any,
) -> Optional[CWLOutputType]:
js_engine = js_engine or get_js_engine()
expression_parse_exception = None
if (match := param_re.match(ex)) is not None:
first_symbol = match.group(1)
first_symbol_end = match.end(1)
if first_symbol_end + 1 == len(ex) and first_symbol == "null":
return None
try:
if first_symbol not in obj:
raise WorkflowException("%s is not defined" % first_symbol)
if inspect.iscoroutinefunction(js_engine.regex_eval):
return asyncio.get_event_loop().run_until_complete(
cast(
Awaitable[CWLOutputType],
js_engine.regex_eval(
first_symbol,
ex[first_symbol_end:-1],
cast(CWLOutputType, obj[first_symbol]),
**kwargs,
),
)
)
else:
return cast(
CWLOutputType,
js_engine.regex_eval(
first_symbol,
ex[first_symbol_end:-1],
cast(CWLOutputType, obj[first_symbol]),
**kwargs,
),
)
except WorkflowException as werr:
expression_parse_exception = werr
if fullJS:
if inspect.iscoroutinefunction(js_engine.eval):
return asyncio.get_event_loop().run_until_complete(
cast(Awaitable[CWLOutputType], js_engine.eval(ex, jslib, **kwargs))
)
else:
return cast(CWLOutputType, js_engine.eval(ex, jslib, **kwargs))
else:
if expression_parse_exception is not None:
raise JavascriptException(
"Syntax error in parameter reference '%s': %s. This could be "
"due to using Javascript code without specifying "
"InlineJavascriptRequirement." % (ex[1:-1], expression_parse_exception)
)
else:
raise JavascriptException(
"Syntax error in parameter reference '%s'. This could be due "
"to using Javascript code without specifying "
"InlineJavascriptRequirement." % ex
)
def interpolate(
scan: str,
rootvars: CWLObjectType,
jslib: str = "",
fullJS: bool = False,
strip_whitespace: bool = True,
escaping_behavior: int = 2,
convert_to_expression: bool = False,
js_engine: Optional[JSEngine] = None,
**kwargs: Any,
) -> Optional[CWLOutputType]:
"""
Interpolate and evaluate.
Note: only call with convert_to_expression=True on CWL Expressions in $()
form that need interpolation.
"""
if strip_whitespace:
scan = scan.strip()
parts = []
if convert_to_expression:
dump = _convert_dumper
parts.append("${return ")
else:
def dump(string: str) -> str:
return string
w = scanner(scan)
while w:
if convert_to_expression:
parts.append(f'"{scan[0: w[0]]}" + ') # noqa: B907
else:
parts.append(scan[0 : w[0]])
if scan[w[0]] == "$":
if not convert_to_expression:
js_engine = js_engine or get_js_engine()
e = evaluator(
js_engine, scan[w[0] + 1 : w[1]], rootvars, jslib, fullJS, **kwargs
)
if w[0] == 0 and w[1] == len(scan) and len(parts) <= 1:
return e
leaf = json_dumps(e, sort_keys=True)
if leaf[0] == '"':
leaf = json.loads(leaf)
parts.append(leaf)
else:
parts.append(
"function(){var item ="
+ scan[w[0] : w[1]][2:-1]
+ '; if (typeof(item) === "string"){ return item; } '
"else { return JSON.stringify(item); }}() + "
)
elif scan[w[0]] == "\\":
if escaping_behavior == 1:
# Old behavior. Just skip the next character.
e = scan[w[1] - 1]
parts.append(dump(e))
elif escaping_behavior == 2:
# Backslash quoting requires a three character lookahead.
e = scan[w[0] : w[1] + 1]
if e in ("\\$(", "\\${"):
# Suppress start of a parameter reference, drop the
# backslash.
parts.append(dump(e[1:]))
w = (w[0], w[1] + 1)
elif e[1] == "\\":
# Double backslash, becomes a single backslash
parts.append(dump("\\"))
else:
# Some other text, add it as-is (including the
# backslash) and resume scanning.
parts.append(dump(e[:2]))
else:
raise Exception("Unknown escaping behavior %s" % escaping_behavior)
scan = scan[w[1] :]
w = scanner(scan)
if convert_to_expression:
parts.append(f'"{scan}"') # noqa: B907
parts.append(";}")
else:
parts.append(scan)
return "".join(parts)
def jshead(engine_config: list[str], rootvars: CWLObjectType) -> str:
"""Make sure all the byte strings are converted to str in `rootvars` dict."""
return "\n".join(
engine_config
+ [f"var {k} = {json_dumps(v, indent=4)};" for k, v in rootvars.items()]
)
def needs_parsing(snippet: Any) -> bool:
return isinstance(snippet, str) and ("$(" in snippet or "${" in snippet)
def do_eval(
ex: Optional[CWLOutputType],
jobinput: CWLObjectType,
requirements: list[CWLObjectType],
outdir: Optional[str],
tmpdir: Optional[str],
resources: dict[str, Union[float, int]],
context: Optional[CWLOutputType] = None,
timeout: float = default_timeout,
strip_whitespace: bool = True,
cwlVersion: str = "",
**kwargs: Any,
) -> Optional[CWLOutputType]:
"""
Evaluate the given CWL expression, in context.
:param timeout: The maximum number of seconds to wait while executing.
"""
runtime = cast(MutableMapping[str, Union[int, str, None]], copy.deepcopy(resources))
runtime["tmpdir"] = tmpdir if tmpdir else None
runtime["outdir"] = outdir if outdir else None
rootvars = cast(
CWLObjectType,
bytes2str_in_dicts({"inputs": jobinput, "self": context, "runtime": runtime}),
)
if isinstance(ex, str) and needs_parsing(ex):
fullJS = False
jslib = ""
for r in reversed(requirements):
if r["class"] == "InlineJavascriptRequirement":
fullJS = True
jslib = jshead(cast(list[str], r.get("expressionLib", [])), rootvars)
break
try:
return interpolate(
ex,
rootvars,
timeout=timeout,
fullJS=fullJS,
jslib=jslib,
strip_whitespace=strip_whitespace,
escaping_behavior=(
1
if cwlVersion
in (
"v1.0",
"v1.1.0-dev1",
"v1.1",
"v1.2.0-dev1",
"v1.2.0-dev2",
"v1.2.0-dev3",
)
else 2
),
**kwargs,
)
except Exception as e:
_logger.exception(e)
raise WorkflowException("Expression evaluation error:\n%s" % str(e)) from e
else:
return ex
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