File size: 8,206 Bytes
5631464 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 | """Run subprocess jobs."""
import os
import shlex
import subprocess
from contextlib import suppress
from pathlib import Path
from haddock.core.defaults import cns_exec as global_cns_exec
from haddock.core.exceptions import (
CNSRunningError,
JobRunningError,
KnownCNSError,
)
from haddock.core.typing import Any, FilePath, Optional, ParamDict
from haddock.gear.known_cns_errors import KNOWN_ERRORS as KNOWN_CNS_ERRORS
from haddock.libs.libio import gzip_files
class BaseJob:
"""Base class for a subprocess job."""
def __init__(
self, input_: Path, output: Path, executable: Path, *args: Any
) -> None:
self.input = input_
self.output = output
self.executable = executable
self.args = args
self.cmd: str
def run(self) -> bytes:
"""Execute job in subprocess."""
self.make_cmd()
with open(self.output, "w") as outf:
p = subprocess.Popen(
shlex.split(self.cmd),
stdout=outf,
close_fds=True,
)
out, error = p.communicate()
p.kill()
if error:
raise JobRunningError(error)
return out
def make_cmd(self) -> None:
"""Execute subprocess job."""
raise NotImplementedError()
class Job(BaseJob):
"""
Instantiate a standard job.
Runs with the following scheme:
$ cmd ARGS INPUT
"""
def make_cmd(self) -> None:
"""Execute subprocess job."""
self.cmd = " ".join(
[
os.fspath(self.executable),
"".join(map(str, self.args)), # empty string if no args
os.fspath(self.input),
]
)
return
class JobInputFirst(BaseJob):
"""
Instantiate a subprocess job with inverted args and input.
Runs with the following scheme, INPUT comes first:
$ cmd INPUT ARGS
"""
def make_cmd(self) -> None:
"""Execute job in subprocess."""
self.cmd = " ".join(
[
os.fspath(self.executable),
os.fspath(self.input),
"".join(map(str, self.args)), # empty string if no args
]
)
return
class CNSJob:
"""A CNS job script."""
def __init__(
self,
input_file: FilePath,
output_file: Optional[FilePath] = None,
error_file: Optional[FilePath] = None,
envvars: Optional[ParamDict] = None,
cns_exec: Optional[FilePath] = None,
) -> None:
"""
CNS subprocess.
To execute the job, call the `.run()` method.
Parameters
----------
input_file : str or pathlib.Path
The path to the .inp CNS file.
output_file : str or pathlib.Path
The path to the .out CNS file, where the standard output
will be saved.
envvars : dict
A dictionary containing the environment variables needed for
the CNSJob. These will be passed to subprocess.Popen.env
argument.
"""
self.input_file = input_file
self.output_file = output_file
self.error_file = error_file
self.envvars = envvars
self.cns_exec = cns_exec
def __repr__(self) -> str:
_input_file = self.input_file
if isinstance(self.input_file, str):
_input_file = "IO Stream"
return (
f"CNSJob({_input_file}, {self.output_file}, "
f"envvars={self.envvars}, cns_exec={self.cns_exec})"
)
def __str__(self) -> str:
return repr(self)
@property
def envvars(self) -> ParamDict:
"""CNS environment vars."""
return self._envvars
@envvars.setter
def envvars(self, envvars: Optional[ParamDict]) -> None:
"""CNS environment vars."""
self._envvars = envvars or {}
if not isinstance(self._envvars, dict):
raise ValueError("`envvars` must be a dictionary.")
for k, v in self._envvars.items():
if isinstance(v, Path):
self._envvars[k] = str(v)
@property
def cns_exec(self) -> FilePath:
"""CNS executable path."""
return self._cns_exec
@cns_exec.setter
def cns_exec(self, cns_exec_path: Optional[FilePath]) -> None:
if not cns_exec_path:
cns_exec_path = global_cns_exec # global cns_exec
if not os.access(cns_exec_path, mode=os.X_OK):
raise ValueError(
f"{str(cns_exec_path)!r} binary file not found, or is not executable."
)
self._cns_exec = cns_exec_path
def run(
self,
compress_inp: bool = False,
compress_out: bool = True,
compress_seed: bool = False,
compress_err: bool = True,
) -> bytes:
"""
Run this CNS job script.
Parameters
----------
compress_inp : bool
Compress the ``*.inp`` file to '.gz' after the run. Defaults to
``False``.
compress_out : bool
Compress the ``*.out`` file to '.gz' after the run. Defaults to
``True``.
compress_seed : bool
Compress the ``*.seed`` file to '.gz' after the run. Defaults to
``False``.
"""
if isinstance(self.input_file, str):
p = subprocess.Popen(
self.cns_exec,
stdin=subprocess.PIPE,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
close_fds=True,
env=self.envvars,
)
out, error = p.communicate(input=self.input_file.encode())
p.kill()
elif isinstance(self.input_file, Path) and self.output_file is not None:
with open(self.input_file) as inp:
p = subprocess.Popen(
self.cns_exec,
stdin=inp,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
close_fds=True,
env=self.envvars,
)
out, error = p.communicate()
p.kill()
# Write out file
with open(self.output_file, "wb+") as outf:
outf.write(out)
if compress_inp:
gzip_files(self.input_file, remove_original=True)
if compress_out:
gzip_files(self.output_file, remove_original=True)
if compress_seed:
with suppress(FileNotFoundError):
gzip_files(
Path(Path(self.output_file).stem).with_suffix(".seed"),
remove_original=True,
)
# If undetected error or detect an error in the STDOUT
if error or self.contains_cns_stdout_error(out):
# Write .err file (only if an error file was provided, otherwise
# the diagnostic raise below would be masked by a TypeError)
if self.error_file is not None:
with open(self.error_file, "wb+") as errf:
errf.write(out)
# Compress it
if compress_err:
gzip_files(self.error_file, remove_original=True)
if error:
raise CNSRunningError(error)
# Return STDOUT
return out
@staticmethod
def contains_cns_stdout_error(out: bytes) -> bool:
# Decode end of STDOUT
# Search in last 24000 characters (300 lines * 80 characters)
sout = out[-24000:].split(bytes(os.linesep, "utf-8"))
# Reverse loop on lines (read backward)
for bytes_line in reversed(sout):
line = bytes_line.decode("utf-8")
# This checks for an unknown CNS error
# triggered when CNS is about to crash due to internal error
if "^^^^^" in line:
return True
# Check if a known error is found
elif any([error in line for error in KNOWN_CNS_ERRORS.keys()]):
return True
return False
|