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# 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 WriterBase
class SingularityWriter(WriterBase):
name = "singularity"
def __init__(self, recipe=None): # pylint: disable=useless-super-delegation
"""a SingularityWriter will take a Recipe as input, and write
to a Singularity recipe file.
Parameters
==========
recipe: the Recipe object to write to file.
"""
super(SingularityWriter, self).__init__(recipe)
def validate(self):
"""validate that all (required) fields are included for the Docker
recipe. We minimimally just need a FROM image, and must ensure
it's in a valid format. If anything is missing, we exit with error.
"""
if self.recipe is None:
bot.exit("Please provide a Recipe() to the writer first.")
def convert(self, runscript="/bin/bash", force=False):
"""docker2singularity will return a Singularity build recipe based on
a the loaded recipe object. It doesn't take any arguments as the
recipe object contains the sections, and the calling function
determines saving / output logic.
"""
self.validate()
# Write single recipe that includes all layer
recipe = []
# Number of layers
num_layers = len(self.recipe)
count = 0
# Write each layer to new file
for stage, parser in self.recipe.items():
# Set the first and active stage
self.stage = stage
# From header is required
if parser.fromHeader is None:
bot.exit("Singularity recipe requires a from header.")
recipe += ["\n\n\nBootstrap: docker"]
recipe += ["From: %s" % parser.fromHeader]
recipe += ["Stage: %s\n\n\n" % stage]
# TODO: stopped here - bug with files being found
# Add global files, and then layer files
recipe += self._create_section("files")
for layer, files in parser.layer_files.items():
recipe += create_keyval_section(files, "files", layer)
# Sections with key value pairs
recipe += self._create_section("labels")
recipe += self._create_section("install", "post")
recipe += self._create_section("environ", "environment")
# If we are at the last layer, write the runscript
if count == num_layers - 1:
runscript = self._create_runscript(runscript, force)
# If a working directory was used, add it as a cd
if parser.workdir is not None:
runscript = ["cd " + parser.workdir] + [runscript]
# Finish the recipe, also add as startscript
recipe += finish_section(runscript, "runscript")
recipe += finish_section(runscript, "startscript")
if parser.test is not None:
recipe += finish_section(parser.test, "test")
count += 1
# Clean up extra white spaces
recipe = "\n".join(recipe).replace("\n\n", "\n").strip("\n")
return recipe.rstrip()
def _create_runscript(self, default="/bin/bash", force=False):
"""create_entrypoint is intended to create a singularity runscript
based on a Docker entrypoint or command. We first use the Docker
ENTRYPOINT, if defined. If not, we use the CMD. If neither is found,
we use function default.
Parameters
==========
default: set a default entrypoint, if the container does not have
an entrypoint or cmd.
force: If true, use default and ignore Dockerfile settings
"""
entrypoint = default
# Only look at Docker if not enforcing default
if not force:
if self.recipe[self.stage].entrypoint is not None:
# The provided entrypoint can be a string or a list
if isinstance(self.recipe[self.stage].entrypoint, list):
entrypoint = " ".join(self.recipe[self.stage].entrypoint)
else:
entrypoint = "".join(self.recipe[self.stage].entrypoint)
if self.recipe[self.stage].cmd is not None:
if isinstance(self.recipe[self.stage].cmd, list):
entrypoint = (
entrypoint + " " + " ".join(self.recipe[self.stage].cmd)
)
else:
entrypoint = entrypoint + " " + "".join(self.recipe[self.stage].cmd)
# Entrypoint should use exec
if not entrypoint.startswith("exec"):
entrypoint = "exec %s" % entrypoint
# Should take input arguments into account
if not re.search('"?[$]@"?', entrypoint):
entrypoint = '%s "$@"' % entrypoint
return entrypoint
def _create_section(self, attribute, name=None, stage=None):
"""create a section based on key, value recipe pairs,
This is used for files or label
Parameters
==========
attribute: the name of the data section, either labels or files
name: the name to write to the recipe file (e.g., %name).
if not defined, the attribute name is used.
"""
# Default section name is the same as attribute
if name is None:
name = attribute
# Put a space between sections
section = ["\n"]
# Only continue if we have the section and it's not empty
try:
section = getattr(self.recipe[self.stage], attribute)
except AttributeError:
bot.debug("Recipe does not have section for %s" % attribute)
return section
# if the section is empty, don't print it
if not section:
return section
# Files
if attribute in ["files", "labels"]:
return create_keyval_section(section, name, stage)
# An environment section needs exports
if attribute in ["environ"]:
return create_env_section(section, name)
# Post, Setup
return finish_section(section, name)
def finish_section(section, name):
"""finish_section will add the header to a section, to finish the recipe
take a custom command or list and return a section.
Parameters
==========
section: the section content, without a header
name: the name of the section for the header
"""
if not isinstance(section, list):
section = [section]
# Convert USER lines to change user
lines = []
for line in section:
if re.search("^USER", line):
username = line.replace("USER", "", 1).rstrip()
line = "su - %s" % username + " # " + line
lines.append(line)
header = ["%" + name]
return header + lines
def create_keyval_section(pairs, name, layer):
"""create a section based on key, value recipe pairs,
This is used for files or label
Parameters
==========
section: the list of values to return as a parsed list of lines
name: the name of the section to write (e.g., files)
layer: if a layer name is provided, name section
"""
if layer:
section = ["%" + name + " from %s" % layer]
else:
section = ["%" + name]
for pair in pairs:
section.append(" ".join(pair).strip().strip("\\"))
return section
def create_env_section(pairs, name):
"""environment key value pairs need to be joined by an equal, and
exported at the end.
Parameters
==========
section: the list of values to return as a parsed list of lines
name: the name of the section to write (e.g., files)
"""
section = ["%" + name]
for pair in pairs:
section.append("export %s" % pair)
return section
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