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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380
|
# Copyright (C) 2017-2022 Vanessa Sochat.
# This Source Code Form is subject to the terms of the
# Mozilla Public License, v. 2.0. If a copy of the MPL was not distributed
# with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
import re
from spython.logger import bot
from .base import ParserBase
class SingularityParser(ParserBase):
name = "singularity"
def __init__(self, filename="Singularity", load=True):
"""a SingularityParser parses a Singularity file into expected fields of
labels, environment, and install/runtime commands. The base class
ParserBase will instantiate an empty Recipe() object to populate,
and call parse() here on the recipe.
Parameters
==========
filename: the recipe file (Singularity) to parse
load: load and parse the recipe (defaults to True)
"""
super(SingularityParser, self).__init__(filename, load)
def parse(self):
"""parse is the base function for parsing the recipe, and extracting
elements into the correct data structures. Everything is parsed into
lists or dictionaries that can be assembled again on demand.
Singularity: we parse files/labels first, then install.
cd first in a line is parsed as WORKDIR
"""
self.load_recipe()
return self.recipe
# Setup for each Parser
def _setup(self, lines):
"""setup required adding content from the host to the rootfs,
so we try to capture with with ADD.
"""
bot.warning("SETUP is error prone, please check output.")
for line in lines:
# For all lines, replace rootfs with actual root /
line = re.sub("[$]{?SINGULARITY_ROOTFS}?", "", "$SINGULARITY_ROOTFS")
# If we have nothing left, don't continue
if line in ["", None]:
continue
# If the line starts with copy or move, assume is file from host
if re.search("(^cp|^mv)", line):
line = re.sub("(^cp|^mv)", "", line)
self.files.append(line)
# If it's a general command, add to install routine
else:
self.install.append(line)
# From Parser
def _from(self, line):
"""get the FROM container image name from a FROM line!
Parameters
==========
line: the line from the recipe file to parse for FROM
"""
self.recipe[self.active_layer].fromHeader = line
bot.debug("FROM %s" % self.recipe[self.active_layer].fromHeader)
# Run and Test Parser
def _test(self, lines):
"""A healthcheck is generally a test command
Parameters
==========
line: the line from the recipe file to parse for FROM
"""
self._write_script("/tests.sh", lines)
self.recipe[self.active_layer].test = "/bin/bash /tests.sh"
# Env Parser
def _env(self, lines):
"""env will parse a list of environment lines and simply remove any
blank lines, and exports. Dockerfiles don't usually
have exports.
Parameters
==========
lines: A list of environment pair lines.
"""
environ = [re.sub("^export", "", x).strip() for x in lines if "=" in x]
self.recipe[self.active_layer].environ += environ
# Files for container
def _files(self, lines, layer=None):
"""parse_files will simply add the list of files to the correct object
Parameters
==========
lines: pairs of files, one pair per line
"""
if not layer:
self.recipe[self.active_layer].files += lines
else:
if layer not in self.recipe[self.active_layer].layer_files:
self.recipe[self.active_layer].layer_files[layer] = []
self.recipe[self.active_layer].layer_files[layer] += lines
# Comments and Help
def _comments(self, lines):
"""comments is a wrapper for comment, intended to be given a list
of comments.
Parameters
==========
lines: the list of lines to parse
"""
for line in lines:
comment = self._comment(line)
if comment not in self.recipe[self.active_layer].comments:
self.recipe[self.active_layer].comments.append(comment)
def _comment(self, line):
"""Simply add the line to the install as a comment. Add an extra # to be
extra careful.
Parameters
==========
line: the line from the recipe file to parse to INSTALL
"""
return "# %s" % line.strip().strip("#")
# Runscript Command
def _run(self, lines):
"""_parse the runscript to be the Docker CMD. If we have one line,
call it directly. If not, write the entrypoint into a script.
Parameters
==========
lines: the line from the recipe file to parse for CMD
"""
lines = [x for x in lines if x not in ["", None]]
# Default runscript is first index
runscript = lines[0]
# Multiple line runscript needs multiple lines written to script
if len(lines) > 1:
bot.warning("More than one line detected for runscript!")
bot.warning("These will be echoed into a single script to call.")
self._write_script("/entrypoint.sh", lines)
runscript = "/bin/bash /entrypoint.sh"
self.recipe[self.active_layer].cmd = runscript
# Labels
def _labels(self, lines):
"""_labels simply adds the labels to the list to save.
Parameters
==========
lines: the lines from the recipe with key,value pairs
"""
self.recipe[self.active_layer].labels += lines
def _post(self, lines):
"""the main core of commands, to be added to the install section
Parameters
==========
lines: the lines from the recipe with install commands
"""
self.recipe[self.active_layer].install += lines
# Main Parsing Functions
def _get_mapping(self, section):
"""mapping will take the section name from a Singularity recipe
and return a map function to add it to the appropriate place.
Any lines that don't cleanly map are assumed to be comments.
Parameters
==========
section: the name of the Singularity recipe section
Returns
=======
function: to map a line to its command group (e.g., install)
"""
# Ensure section is lowercase
section = section.lower()
mapping = {
"environment": self._env,
"comments": self._comments,
"runscript": self._run,
"labels": self._labels,
"setup": self._setup,
"files": self._files,
"from": self._from,
"post": self._post,
"test": self._test,
"help": self._comments,
}
if section in mapping:
return mapping[section]
return self._comments
# Loading Functions
def _load_from(self, line):
"""load the From section of the recipe for the Dockerfile."""
# Remove any comments
line = line.split("#", 1)[0]
line = re.sub("from:", "", line.lower()).strip()
self.recipe[self.active_layer].fromHeader = line
def _check_bootstrap(self, line):
"""checks that the bootstrap is Docker, otherwise we exit on fail."""
if not re.search("docker", line, re.IGNORECASE):
raise NotImplementedError("Only docker is supported.")
def _load_section(self, lines, section, layer=None):
"""read in a section to a list, and stop when we hit the next section"""
members = []
while True:
if not lines:
break
next_line = lines[0]
# We have a start of another bootstrap
if re.search("bootstrap:", next_line, re.IGNORECASE):
break
# The end of a section
if next_line.strip().startswith("%"):
break
# Still in current section!
else:
new_member = lines.pop(0).strip()
if new_member not in ["", None]:
members.append(new_member)
# Add the list to the config
if members and section is not None:
# Get the correct parsing function
parser = self._get_mapping(section)
# Parse it, if appropriate
if not parser:
bot.warning("%s is an unrecognized section, skipping." % section)
else:
if section == "files":
parser(members, layer)
else:
parser(members)
def load_recipe(self):
"""load_recipe will return a loaded in singularity recipe. The idea
is that these sections can then be parsed into a Dockerfile,
or printed back into their original form.
Returns
=======
config: a parsed recipe Singularity recipe
"""
# Comments between sections, add to top of file
lines = self.lines[:]
fromHeader = None
stage = None
section = None
comments = []
while lines:
# Clean up white trailing/leading space
line = lines.pop(0)
stripped = line.strip()
# Bootstrap Line
if re.search("bootstrap", line, re.IGNORECASE):
self._check_bootstrap(stripped)
# From Line
elif re.search("from:", stripped, re.IGNORECASE):
fromHeader = stripped
if stage is None:
self._load_from(fromHeader)
# Identify stage
elif re.search("stage:", stripped, re.IGNORECASE):
stage = re.sub("stage:", "", stripped.lower()).strip()
self._multistage("as %s" % stage)
self._load_from(fromHeader)
# Comment
elif stripped.startswith("#") and stripped not in comments:
comments.append(stripped)
# Section
elif stripped.startswith("%"):
section, layer = self._get_section(stripped)
bot.debug("Found section %s" % section)
# If we have a section, and are adding it
elif section is not None:
lines = [line] + lines
self._load_section(lines=lines, section=section, layer=layer)
self._comments(comments)
def _get_section(self, line):
"""parse a line for a section, and return the name of the section
Parameters
==========
line: the line to parse
"""
# Remove any comments
line = line.split("#", 1)[0].strip()
# Is there a section name?
parts = [word.strip() for word in line.split(" ") if word]
section = re.sub(r"[%]|(\s+)", "", parts[0]).lower()
# Is there a named layer?
layer = None
if len(parts) == 3 and parts[1].lower() == "from":
layer = parts[2]
return section, layer
def _write_script(self, path, lines, chmod=True):
"""write a script with some lines content to path in the image. This
is done by way of adding echo statements to the install section.
Parameters
==========
path: the path to the file to write
lines: the lines to echo to the file
chmod: If true, change permission to make u+x
"""
for line in lines:
self.recipe[self.active_layer].install.append(
'echo "%s" >> %s' % (line, path)
)
if chmod:
self.recipe[self.active_layer].install.append("chmod u+x %s" % path)
|