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# SPDX-License-Identifier: Apache-2.0
"""Miscellaneous utility functions."""
import os
import pathlib
import subprocess # nosec
import sys
import urllib.error
import urllib.parse
import urllib.request
from collections.abc import MutableMapping, MutableSequence
from copy import deepcopy
from io import StringIO
from typing import Any, Dict, List, Optional, Union
from urllib.parse import urlparse
from ruamel.yaml.main import YAML
from ruamel.yaml.parser import ParserError
from ruamel.yaml.scanner import ScannerError
from cwl_utils.errors import MissingKeyField
from cwl_utils.loghandler import _logger
# Type hinting
from cwl_utils.parser import InputRecordSchemaTypes
# Load as 1.2 files
from cwl_utils.parser.cwl_v1_2 import InputArraySchema as InputArraySchemaV1_2
from cwl_utils.parser.cwl_v1_2 import InputEnumSchema as InputEnumSchemaV1_2
fast_yaml = YAML(typ="safe")
_USERNS: Optional[bool] = None
def _is_github_symbolic_link(base_url: urllib.parse.ParseResult, contents: str) -> bool:
"""
Test if link is a GitHub style symbolic link.
Look for remote path with contents that is a single line with no new
line with an extension.
https://github.com/rabix/sbpack/blob/b8404a0859ffcbe1edae6d8f934e51847b003320/sbpack/lib.py
"""
if base_url.scheme in ["file://", ""]:
return False
idx = contents.find("\n")
if idx > -1:
return False
if "." not in contents:
return False
return True
def bytes2str_in_dicts(
inp: Union[MutableMapping[str, Any], MutableSequence[Any], Any],
) -> Union[str, MutableSequence[Any], MutableMapping[str, Any]]:
"""
Convert any present byte string to unicode string, inplace.
input is a dict of nested dicts and lists
"""
# if input is dict, recursively call for each value
if isinstance(inp, MutableMapping):
for k in inp:
inp[k] = bytes2str_in_dicts(inp[k])
return inp
# if list, iterate through list and fn call
# for all its elements
if isinstance(inp, MutableSequence):
for idx, value in enumerate(inp):
inp[idx] = bytes2str_in_dicts(value)
return inp
# if value is bytes, return decoded string,
elif isinstance(inp, bytes):
return inp.decode("utf-8")
# simply return elements itself
return inp
def load_linked_file(
base_url: urllib.parse.ParseResult, link: str, is_import: bool = False
) -> tuple[Any, urllib.parse.ParseResult]:
"""From https://github.com/rabix/sbpack/blob/b8404a0859ffcbe1edae6d8f934e51847b003320/sbpack/lib.py ."""
new_url = resolved_path(base_url, link)
if new_url.scheme in ["file://", ""]:
contents = pathlib.Path(new_url.path).open().read()
else:
try:
contents = (
urllib.request.urlopen(new_url.geturl()).read().decode("utf-8") # nosec
)
except urllib.error.HTTPError as e:
_logger.error("Could not find linked file: %s", new_url.geturl())
raise SystemExit(e) from e
if _is_github_symbolic_link(new_url, contents):
# This is an exception for symbolic links on github
sys.stderr.write(
f"{new_url.geturl()}: found file-like string in contents.\n"
f"Treating as github symbolic link to {contents}\n"
)
return load_linked_file(new_url, contents, is_import=is_import)
if is_import:
try:
_node = fast_yaml.load(contents)
except ParserError as e:
e.context = f"\n===\nMalformed file: {new_url.geturl()}\n===\n" + e.context
raise SystemExit(e) from e
except ScannerError as e:
e.problem = f"\n===\nMalformed file: {new_url.geturl()}\n===\n" + e.problem
raise SystemExit(e) from e
else:
_node = contents
return _node, new_url
def normalize_to_map(
obj: Union[list[Any], dict[str, Any]], key_field: str
) -> dict[str, Any]:
"""From https://github.com/rabix/sbpack/blob/b8404a0859ffcbe1edae6d8f934e51847b003320/sbpack/lib.py ."""
if isinstance(obj, dict):
return deepcopy(obj)
elif isinstance(obj, list):
map_obj = {}
for v in obj:
if not isinstance(v, dict):
raise RuntimeError("Expecting a dict here")
k = v.get(key_field)
if k is None:
raise MissingKeyField(key_field)
v.pop(key_field, None)
map_obj[k] = v
return map_obj
else:
raise RuntimeError("Expecting a dictionary or a list here")
def normalize_to_list(
obj: Union[list[Any], dict[str, Any]], key_field: str, value_field: Optional[str]
) -> list[Any]:
"""From https://github.com/rabix/sbpack/blob/b8404a0859ffcbe1edae6d8f934e51847b003320/sbpack/lib.py ."""
if isinstance(obj, list):
return deepcopy(obj)
elif isinstance(obj, dict):
map_list = []
for k, v in obj.items():
if not isinstance(v, dict):
if value_field is None:
raise RuntimeError(f"Expecting a dict here, got {v}")
v = {value_field: v}
v.update({key_field: k})
map_list += [v]
return map_list
else:
raise RuntimeError("Expecting a dictionary or a list here")
def resolved_path(
base_url: urllib.parse.ParseResult, link: str
) -> urllib.parse.ParseResult:
"""
Derive a resolved path.
This function will
1. Resolve the path, which means dot and double dot components are resolved
2. Use the OS appropriate path resolution for local paths, and network
appropriate resolution for network paths
From https://github.com/rabix/sbpack/blob/b8404a0859ffcbe1edae6d8f934e51847b003320/sbpack/lib.py
:param base_url: "this document"
:param link: "string in this document"
:returns: new URL that allows us to retrieve the linked document
"""
link_url = urllib.parse.urlparse(link)
# The link will always Posix
if link_url.scheme == "file://":
# Absolute local path
return link_url
elif link_url.scheme == "":
# Relative path, can be local or remote
if base_url.scheme in ["file://", ""]:
# Local relative path
if link == "":
return base_url
else:
return urllib.parse.urlparse(
urllib.parse.urljoin(base_url.geturl(), link_url.geturl())
)
else:
# Remote relative path
return urllib.parse.urlparse(
urllib.parse.urljoin(base_url.geturl(), link_url.path)
)
# We need urljoin because we need to resolve relative links in a
# platform independent manner
# Absolute remote path
return link_url
def singularity_supports_userns() -> bool:
"""Confirm if the version of Singularity install supports the --userns flag."""
global _USERNS # pylint: disable=global-statement
if _USERNS is None:
try:
hello_image = os.path.join(os.path.dirname(__file__), "hello.simg")
result = subprocess.Popen( # nosec
["singularity", "exec", "--userns", hello_image, "true"],
stderr=subprocess.PIPE,
stdout=subprocess.DEVNULL,
universal_newlines=True,
).communicate(timeout=60)[1]
_USERNS = (
"No valid /bin/sh" in result
or "/bin/sh doesn't exist in container" in result
or "executable file not found in" in result
)
except subprocess.TimeoutExpired:
_USERNS = False
return _USERNS
def yaml_dumps(obj: Any) -> str:
"""
Shortcut.
Don't use if you have a file descriptor (like sys.stdout) available.
"""
yaml = YAML()
stream = StringIO()
yaml.dump(obj, stream)
return stream.getvalue()
def to_pascal_case(name: str) -> str:
"""
Convert a string to PascalCase.
fastq-list-row to FastqListRow
fastq_list_row to FastqListRow
:param name:
:return:
"""
return "".join(
map(lambda word: word.capitalize(), name.replace("_", "-").split("-"))
)
def sanitise_schema_field(
schema_field_item: Union[Dict[str, Any], str],
) -> Union[Dict[str, Any], str]:
"""
Schemas need to be resolved before converted to JSON properties.
Convert
{
'type': 'Directory?'
}
To
{
'type': ['null', 'Directory']
}
Convert
{
'type': 'string[]'
}
To
InputArraySchema(
type_=array,
items=string
)
Convert
{
'type': 'File[]?'
}
To
{
'type': [
'null', InputArraySchema(
type_=array,
items=File
)
]
}
Convert
{
'type': 'Enum',
'symbols': ['A', 'B', 'C']
}
To
{
'type': InputEnumSchema(
type_=enum,
symbols=['A', 'B', 'C']
)
}
Convert
{
'type': 'array',
'items': {
'$import': '../../../schemas/fastq-list-row/1.0.0/fastq-list-row__1.0.0.yaml#fastq-list-row'
}
}
To
{
'type': InputArraySchema(
type_=array,
items={
'$import': '../../../schemas/fastq-list-row/1.0.0/fastq-list-row__1.0.0.yaml#fastq-list-row'
}
)
}
:param schema_field_item:
:return:
"""
# We might be just a string, in which case, just return
# This happens in the case that type is a list of primitive types
if isinstance(schema_field_item, str):
return schema_field_item
# Copy schema field
schema_field_item = deepcopy(schema_field_item)
required = True
if isinstance(schema_field_item, InputRecordSchemaTypes):
return schema_field_item
if isinstance(schema_field_item.get("type"), List):
if "null" in schema_field_item.get("type", []):
required = False
schema_field_item["type"] = list(
filter(
lambda type_item: type_item != "null", schema_field_item.get("type", [])
)
)
if len(schema_field_item["type"]) == 1:
schema_field_item["type"] = schema_field_item["type"][0]
else:
# Recursively get items
schema_field_item["type"] = list(
map(
lambda field_subtypes: sanitise_schema_field(field_subtypes),
schema_field_item.get("type", []),
)
)
if isinstance(schema_field_item.get("type"), str):
if schema_field_item.get("type", "").endswith("?"):
required = False
schema_field_item["type"] = schema_field_item.get("type", "").replace(
"?", ""
)
if schema_field_item.get("type", "").endswith("[]"):
# Strip list
schema_field_item["type"] = schema_field_item.get("type", "").replace(
"[]", ""
)
# Convert to array
schema_field_item["type"] = InputArraySchemaV1_2(
type_="array", items=schema_field_item.get("type", "")
)
if isinstance(schema_field_item.get("type"), Dict):
# Likely an enum
if schema_field_item.get("type", {}).get("type", "") == "enum":
schema_field_item["type"] = InputEnumSchemaV1_2(
type_="enum",
symbols=schema_field_item.get("type", {}).get("symbols", ""),
)
elif schema_field_item.get("type", {}).get("type", "") == "array":
schema_field_item["type"] = InputArraySchemaV1_2(
type_="array", items=schema_field_item.get("type", {}).get("items", "")
)
elif "$import" in schema_field_item.get("type", {}).keys():
# Leave import as is
pass
else:
raise ValueError(f"Unknown type: {schema_field_item.get('type')}")
if not required:
if isinstance(schema_field_item.get("type"), List):
schema_field_item["type"] = ["null"] + schema_field_item.get("type", [])
else:
schema_field_item["type"] = ["null", schema_field_item.get("type", "")]
return schema_field_item
def is_uri(uri: str) -> bool:
"""
Given a URI return True if it is a URI.
:param uri:
:return:
"""
if not urlparse(uri).scheme == "":
return True
else:
return False
def is_local_uri(uri: str) -> bool:
"""Given a uri, first check if it is a uri, then check if it is a local uri."""
if is_uri(uri) and urlparse(uri).scheme == "file":
return True
return False
def get_value_from_uri(uri: str) -> str:
"""
Given a URI, return the value after #.
file://path/to/imported/record#my_workflow_name/record_name
Returns
record_name
:param uri:
:return:
"""
url_obj = urlparse(uri)
return url_obj.fragment.rsplit("/")[-1]
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