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Source code for galaxy.util
# -*- coding: utf-8 -*-
"""
Utility functions used systemwide.
"""
from __future__ import absolute_import
import binascii
import collections
import errno
import importlib
import json
import os
import random
import re
import shutil
import smtplib
import stat
import string
import sys
import tempfile
import threading
import time
import unicodedata
import xml.dom.minidom
from datetime import datetime
from hashlib import md5
from os.path import relpath
from xml.etree import ElementInclude, ElementTree
from xml.etree.ElementTree import ParseError
try:
import grp
except ImportError:
# For Pulsar on Windows (which does not use the function that uses grp)
grp = None
from boltons.iterutils import (
default_enter,
remap,
)
from six import binary_type, iteritems, PY2, string_types, text_type
from six.moves import email_mime_multipart, email_mime_text, xrange, zip
from six.moves.urllib import (
parse as urlparse,
request as urlrequest
)
from six.moves.urllib.request import urlopen
try:
import docutils.core as docutils_core
import docutils.writers.html4css1 as docutils_html4css1
except ImportError:
docutils_core = None
docutils_html4css1 = None
from .inflection import English, Inflector
from .logging import get_logger
from .path import safe_contains, safe_makedirs, safe_relpath # noqa: F401
inflector = Inflector(English)
log = get_logger(__name__)
_lock = threading.RLock()
CHUNK_SIZE = 65536 # 64k
DATABASE_MAX_STRING_SIZE = 32768
DATABASE_MAX_STRING_SIZE_PRETTY = '32K'
gzip_magic = b'\x1f\x8b'
bz2_magic = b'BZh'
DEFAULT_ENCODING = os.environ.get('GALAXY_DEFAULT_ENCODING', 'utf-8')
NULL_CHAR = b'\x00'
BINARY_CHARS = [NULL_CHAR]
FILENAME_VALID_CHARS = '.,^_-()[]0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ'
defaultdict = collections.defaultdict
[docs]def remove_protocol_from_url(url):
""" Supplied URL may be null, if not ensure http:// or https://
etc... is stripped off.
"""
if url is None:
return url
# We have a URL
if url.find('://') > 0:
new_url = url.split('://')[1]
else:
new_url = url
return new_url.rstrip('/')
[docs]def is_binary(value):
"""
File is binary if it contains a null-byte by default (e.g. behavior of grep, etc.).
This may fail for utf-16 files, but so would ASCII encoding.
>>> is_binary( string.printable )
False
>>> is_binary( b'\\xce\\x94' )
False
>>> is_binary( b'\\x00' )
True
"""
value = smart_str(value)
for binary_char in BINARY_CHARS:
if binary_char in value:
return True
return False
[docs]def is_uuid(value):
"""
This method returns True if value is a UUID, otherwise False.
>>> is_uuid( "123e4567-e89b-12d3-a456-426655440000" )
True
>>> is_uuid( "0x3242340298902834" )
False
"""
uuid_re = re.compile("[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}")
if re.match(uuid_re, str(value)):
return True
else:
return False
[docs]def directory_hash_id(id):
"""
>>> directory_hash_id( 100 )
['000']
>>> directory_hash_id( "90000" )
['090']
>>> directory_hash_id("777777777")
['000', '777', '777']
>>> directory_hash_id("135ee48a-4f51-470c-ae2f-ce8bd78799e6")
['1', '3', '5']
"""
s = str(id)
l = len(s)
# Shortcut -- ids 0-999 go under ../000/
if l < 4:
return ["000"]
if not is_uuid(s):
# Pad with zeros until a multiple of three
padded = ((3 - len(s) % 3) * "0") + s
# Drop the last three digits -- 1000 files per directory
padded = padded[:-3]
# Break into chunks of three
return [padded[i * 3:(i + 1) * 3] for i in range(len(padded) // 3)]
else:
# assume it is a UUID
return list(iter(s[0:3]))
[docs]def get_charset_from_http_headers(headers, default=None):
rval = headers.get('content-type', None)
if rval and 'charset=' in rval:
rval = rval.split('charset=')[-1].split(';')[0].strip()
if rval:
return rval
return default
[docs]def synchronized(func):
"""This wrapper will serialize access to 'func' to a single thread. Use it as a decorator."""
def caller(*params, **kparams):
_lock.acquire(True) # Wait
try:
return func(*params, **kparams)
finally:
_lock.release()
return caller
[docs]def file_iter(fname, sep=None):
"""
This generator iterates over a file and yields its lines
splitted via the C{sep} parameter. Skips empty lines and lines starting with
the C{#} character.
>>> lines = [ line for line in file_iter(__file__) ]
>>> len(lines) != 0
True
"""
for line in open(fname):
if line and line[0] != '#':
yield line.split(sep)
[docs]def file_reader(fp, chunk_size=CHUNK_SIZE):
"""This generator yields the open fileobject in chunks (default 64k). Closes the file at the end"""
while 1:
data = fp.read(chunk_size)
if not data:
break
yield data
fp.close()
[docs]def unique_id(KEY_SIZE=128):
"""
Generates an unique id
>>> ids = [ unique_id() for i in range(1000) ]
>>> len(set(ids))
1000
"""
random_bits = text_type(random.getrandbits(KEY_SIZE)).encode("UTF-8")
return md5(random_bits).hexdigest()
[docs]def parse_xml(fname):
"""Returns a parsed xml tree"""
# handle deprecation warning for XMLParsing a file with DOCTYPE
class DoctypeSafeCallbackTarget(ElementTree.TreeBuilder):
def doctype(*args):
pass
tree = ElementTree.ElementTree()
try:
root = tree.parse(fname, parser=ElementTree.XMLParser(target=DoctypeSafeCallbackTarget()))
for elem in root.iter('*'):
if elem.text is not None:
elem.text = elem.text.strip()
if elem.tail is not None:
elem.tail = elem.tail.strip()
except ParseError:
log.exception("Error parsing file %s", fname)
raise
ElementInclude.include(root)
return tree
[docs]def parse_xml_string(xml_string):
tree = ElementTree.fromstring(xml_string)
for elem in tree.iter('*'):
if elem.text is not None:
elem.text = elem.text.strip()
if elem.tail is not None:
elem.tail = elem.tail.strip()
return tree
[docs]def xml_to_string(elem, pretty=False):
"""
Returns a string from an xml tree.
"""
try:
if elem is not None:
if PY2:
xml_str = ElementTree.tostring(elem, encoding='utf-8')
else:
xml_str = ElementTree.tostring(elem, encoding='unicode')
else:
xml_str = ''
except TypeError as e:
# we assume this is a comment
if hasattr(elem, 'text'):
return "<!-- %s -->\n" % elem.text
else:
raise e
if xml_str and pretty:
pretty_string = xml.dom.minidom.parseString(xml_str).toprettyxml(indent=' ')
return "\n".join([line for line in pretty_string.split('\n') if not re.match(r'^[\s\\nb\']*$', line)])
return xml_str
[docs]def xml_element_compare(elem1, elem2):
if not isinstance(elem1, dict):
elem1 = xml_element_to_dict(elem1)
if not isinstance(elem2, dict):
elem2 = xml_element_to_dict(elem2)
return elem1 == elem2
[docs]def xml_element_list_compare(elem_list1, elem_list2):
return [xml_element_to_dict(elem) for elem in elem_list1] == [xml_element_to_dict(elem) for elem in elem_list2]
[docs]def xml_element_to_dict(elem):
rval = {}
if elem.attrib:
rval[elem.tag] = {}
else:
rval[elem.tag] = None
sub_elems = list(elem)
if sub_elems:
sub_elem_dict = dict()
for sub_sub_elem_dict in map(xml_element_to_dict, sub_elems):
for key, value in iteritems(sub_sub_elem_dict):
if key not in sub_elem_dict:
sub_elem_dict[key] = []
sub_elem_dict[key].append(value)
for key, value in iteritems(sub_elem_dict):
if len(value) == 1:
rval[elem.tag][key] = value[0]
else:
rval[elem.tag][key] = value
if elem.attrib:
for key, value in iteritems(elem.attrib):
rval[elem.tag]["@%s" % key] = value
if elem.text:
text = elem.text.strip()
if text and sub_elems or elem.attrib:
rval[elem.tag]['#text'] = text
else:
rval[elem.tag] = text
return rval
[docs]def pretty_print_xml(elem, level=0):
pad = ' '
i = "\n" + level * pad
if len(elem):
if not elem.text or not elem.text.strip():
elem.text = i + pad + pad
if not elem.tail or not elem.tail.strip():
elem.tail = i
for e in elem:
pretty_print_xml(e, level + 1)
if not elem.tail or not elem.tail.strip():
elem.tail = i
else:
if level and (not elem.tail or not elem.tail.strip()):
elem.tail = i + pad
return elem
[docs]def get_file_size(value, default=None):
try:
# try built-in
return os.path.getsize(value)
except Exception:
try:
# try built-in one name attribute
return os.path.getsize(value.name)
except Exception:
try:
# try tell() of end of object
offset = value.tell()
value.seek(0, 2)
rval = value.tell()
value.seek(offset)
return rval
except Exception:
# return default value
return default
[docs]def shrink_stream_by_size(value, size, join_by=b"..", left_larger=True, beginning_on_size_error=False, end_on_size_error=False):
"""
Shrinks bytes read from `value` to `size`.
`value` needs to implement tell/seek, so files need to be opened in binary mode.
Returns unicode text with invalid characters replaced.
"""
rval = b''
join_by = smart_str(join_by)
if get_file_size(value) > size:
start = value.tell()
len_join_by = len(join_by)
min_size = len_join_by + 2
if size < min_size:
if beginning_on_size_error:
rval = value.read(size)
value.seek(start)
return rval
elif end_on_size_error:
value.seek(-size, 2)
rval = value.read(size)
value.seek(start)
return rval
raise ValueError('With the provided join_by value (%s), the minimum size value is %i.' % (join_by, min_size))
left_index = right_index = int((size - len_join_by) / 2)
if left_index + right_index + len_join_by < size:
if left_larger:
left_index += 1
else:
right_index += 1
rval = value.read(left_index) + join_by
value.seek(-right_index, 2)
rval += value.read(right_index)
else:
while True:
data = value.read(CHUNK_SIZE)
if not data:
break
rval += data
return unicodify(rval)
[docs]def shrink_string_by_size(value, size, join_by="..", left_larger=True, beginning_on_size_error=False, end_on_size_error=False):
if len(value) > size:
len_join_by = len(join_by)
min_size = len_join_by + 2
if size < min_size:
if beginning_on_size_error:
return value[:size]
elif end_on_size_error:
return value[-size:]
raise ValueError('With the provided join_by value (%s), the minimum size value is %i.' % (join_by, min_size))
left_index = right_index = int((size - len_join_by) / 2)
if left_index + right_index + len_join_by < size:
if left_larger:
left_index += 1
else:
right_index += 1
value = "%s%s%s" % (value[:left_index], join_by, value[-right_index:])
return value
[docs]def pretty_print_time_interval(time=False, precise=False, utc=False):
"""
Get a datetime object or a int() Epoch timestamp and return a
pretty string like 'an hour ago', 'Yesterday', '3 months ago',
'just now', etc
credit: http://stackoverflow.com/questions/1551382/user-friendly-time-format-in-python
"""
if utc:
now = datetime.utcnow()
else:
now = datetime.now()
if type(time) is int:
diff = now - datetime.fromtimestamp(time)
elif isinstance(time, datetime):
diff = now - time
elif isinstance(time, string_types):
try:
time = datetime.strptime(time, "%Y-%m-%dT%H:%M:%S.%f")
except ValueError:
# MySQL may not support microseconds precision
time = datetime.strptime(time, "%Y-%m-%dT%H:%M:%S")
diff = now - time
else:
diff = now - now
second_diff = diff.seconds
day_diff = diff.days
if day_diff < 0:
return ''
if precise:
if day_diff == 0:
if second_diff < 10:
return "just now"
if second_diff < 60:
return str(second_diff) + " seconds ago"
if second_diff < 120:
return "a minute ago"
if second_diff < 3600:
return str(second_diff / 60) + " minutes ago"
if second_diff < 7200:
return "an hour ago"
if second_diff < 86400:
return str(second_diff / 3600) + " hours ago"
if day_diff == 1:
return "yesterday"
if day_diff < 7:
return str(day_diff) + " days ago"
if day_diff < 31:
return str(day_diff / 7) + " weeks ago"
if day_diff < 365:
return str(day_diff / 30) + " months ago"
return str(day_diff / 365) + " years ago"
else:
if day_diff == 0:
return "today"
if day_diff == 1:
return "yesterday"
if day_diff < 7:
return "less than a week"
if day_diff < 31:
return "less than a month"
if day_diff < 365:
return "less than a year"
return "a few years ago"
[docs]def pretty_print_json(json_data, is_json_string=False):
if is_json_string:
json_data = json.loads(json_data)
return json.dumps(json_data, sort_keys=True, indent=4)
# characters that are valid
valid_chars = set(string.ascii_letters + string.digits + " -=_.()/+*^,:?!")
# characters that are allowed but need to be escaped
mapped_chars = {'>': '__gt__',
'<': '__lt__',
"'": '__sq__',
'"': '__dq__',
'[': '__ob__',
']': '__cb__',
'{': '__oc__',
'}': '__cc__',
'@': '__at__',
'\n': '__cn__',
'\r': '__cr__',
'\t': '__tc__',
'#': '__pd__'}
[docs]def restore_text(text, character_map=mapped_chars):
"""Restores sanitized text"""
if not text:
return text
for key, value in character_map.items():
text = text.replace(value, key)
return text
[docs]def sanitize_text(text, valid_characters=valid_chars, character_map=mapped_chars, invalid_character='X'):
"""
Restricts the characters that are allowed in text; accepts both strings
and lists of strings; non-string entities will be cast to strings.
"""
if isinstance(text, list):
return [sanitize_text(x, valid_characters=valid_characters, character_map=character_map, invalid_character=invalid_character) for x in text]
if not isinstance(text, string_types):
text = smart_str(text)
return _sanitize_text_helper(text, valid_characters=valid_characters, character_map=character_map)
def _sanitize_text_helper(text, valid_characters=valid_chars, character_map=mapped_chars, invalid_character='X'):
"""Restricts the characters that are allowed in a string"""
out = []
for c in text:
if c in valid_characters:
out.append(c)
elif c in character_map:
out.append(character_map[c])
else:
out.append(invalid_character) # makes debugging easier
return ''.join(out)
[docs]def sanitize_lists_to_string(values, valid_characters=valid_chars, character_map=mapped_chars, invalid_character='X'):
if isinstance(values, list):
rval = []
for value in values:
rval.append(sanitize_lists_to_string(value,
valid_characters=valid_characters,
character_map=character_map,
invalid_character=invalid_character))
values = ",".join(rval)
else:
values = sanitize_text(values, valid_characters=valid_characters, character_map=character_map, invalid_character=invalid_character)
return values
[docs]def sanitize_param(value, valid_characters=valid_chars, character_map=mapped_chars, invalid_character='X'):
"""Clean incoming parameters (strings or lists)"""
if isinstance(value, string_types):
return sanitize_text(value, valid_characters=valid_characters, character_map=character_map, invalid_character=invalid_character)
elif isinstance(value, list):
return [sanitize_text(x, valid_characters=valid_characters, character_map=character_map, invalid_character=invalid_character) for x in value]
else:
raise Exception('Unknown parameter type (%s)' % (type(value)))
valid_filename_chars = set(string.ascii_letters + string.digits + '_.')
invalid_filenames = ['', '.', '..']
[docs]def sanitize_for_filename(text, default=None):
"""
Restricts the characters that are allowed in a filename portion; Returns default value or a unique id string if result is not a valid name.
Method is overly aggressive to minimize possible complications, but a maximum length is not considered.
"""
out = []
for c in text:
if c in valid_filename_chars:
out.append(c)
else:
out.append('_')
out = ''.join(out)
if out in invalid_filenames:
if default is None:
return sanitize_for_filename(str(unique_id()))
return default
return out
[docs]def find_instance_nested(item, instances, match_key=None):
"""
Recursively find instances from lists, dicts, tuples.
`instances` should be a tuple of valid instances
If match_key is given the key must match for an instance to be added to the list of found instances.
"""
matches = []
def visit(path, key, value):
if isinstance(value, instances):
if match_key is None or match_key == key:
matches.append(value)
return key, value
def enter(path, key, value):
if isinstance(value, instances):
return None, False
return default_enter(path, key, value)
remap(item, visit, reraise_visit=False, enter=enter)
return matches
[docs]def mask_password_from_url(url):
"""
Masks out passwords from connection urls like the database connection in galaxy.ini
>>> mask_password_from_url( 'sqlite+postgresql://user:password@localhost/' )
'sqlite+postgresql://user:********@localhost/'
>>> mask_password_from_url( 'amqp://user:amqp@localhost' )
'amqp://user:********@localhost'
>>> mask_password_from_url( 'amqp://localhost')
'amqp://localhost'
"""
split = urlparse.urlsplit(url)
if split.password:
if url.count(split.password) == 1:
url = url.replace(split.password, "********")
else:
# This can manipulate the input other than just masking password,
# so the previous string replace method is preferred when the
# password doesn't appear twice in the url
split = split._replace(netloc=split.netloc.replace("%s:%s" % (split.username, split.password), '%s:********' % split.username))
url = urlparse.urlunsplit(split)
return url
[docs]def ready_name_for_url(raw_name):
u""" General method to convert a string (i.e. object name) to a URL-ready
slug.
>>> ready_name_for_url( "My Cool Object" )
'My-Cool-Object'
>>> ready_name_for_url( "!My Cool Object!" )
'My-Cool-Object'
>>> ready_name_for_url( "Hello₩◎ґʟⅾ" )
'Hello'
"""
# Replace whitespace with '-'
slug_base = re.sub("\s+", "-", raw_name)
# Remove all non-alphanumeric characters.
slug_base = re.sub("[^a-zA-Z0-9\-]", "", slug_base)
# Remove trailing '-'.
if slug_base.endswith('-'):
slug_base = slug_base[:-1]
return slug_base
[docs]def which(file):
# http://stackoverflow.com/questions/5226958/which-equivalent-function-in-python
for path in os.environ["PATH"].split(":"):
if os.path.exists(path + "/" + file):
return path + "/" + file
return None
[docs]def in_directory(file, directory, local_path_module=os.path):
"""
Return true, if the common prefix of both is equal to directory
e.g. /a/b/c/d.rst and directory is /a/b, the common prefix is /a/b.
This function isn't used exclusively for security checks, but if it is
used for such checks it is assumed that ``directory`` is a "trusted" path -
supplied by Galaxy or by the admin and ``file`` is something generated by
a tool, configuration, external web server, or user supplied input.
local_path_module is used by Pulsar to check Windows paths while running on
a POSIX-like system.
>>> base_dir = tempfile.mkdtemp()
>>> safe_dir = os.path.join(base_dir, "user")
>>> os.mkdir(safe_dir)
>>> good_file = os.path.join(safe_dir, "1")
>>> with open(good_file, "w") as f: _ = f.write("hello")
>>> in_directory(good_file, safe_dir)
True
>>> in_directory("/other/file/is/here.txt", safe_dir)
False
>>> unsafe_link = os.path.join(safe_dir, "2")
>>> os.symlink("/other/file/bad.fasta", unsafe_link)
>>> in_directory(unsafe_link, safe_dir)
False
"""
if local_path_module != os.path:
_safe_contains = importlib.import_module('galaxy.util.path.%s' % local_path_module.__name__).safe_contains
else:
directory = os.path.realpath(directory)
_safe_contains = safe_contains
return _safe_contains(directory, file)
[docs]def merge_sorted_iterables(operator, *iterables):
"""
>>> operator = lambda x: x
>>> list( merge_sorted_iterables( operator, [1,2,3], [4,5] ) )
[1, 2, 3, 4, 5]
>>> list( merge_sorted_iterables( operator, [4, 5], [1,2,3] ) )
[1, 2, 3, 4, 5]
>>> list( merge_sorted_iterables( operator, [1, 4, 5], [2], [3] ) )
[1, 2, 3, 4, 5]
"""
first_iterable = iterables[0]
if len(iterables) == 1:
for el in first_iterable:
yield el
else:
for el in __merge_two_sorted_iterables(
operator,
iter(first_iterable),
merge_sorted_iterables(operator, *iterables[1:])
):
yield el
def __merge_two_sorted_iterables(operator, iterable1, iterable2):
unset = object()
continue_merge = True
next_1 = unset
next_2 = unset
while continue_merge:
try:
if next_1 is unset:
next_1 = next(iterable1)
if next_2 is unset:
next_2 = next(iterable2)
if operator(next_2) < operator(next_1):
yield next_2
next_2 = unset
else:
yield next_1
next_1 = unset
except StopIteration:
continue_merge = False
if next_1 is not unset:
yield next_1
if next_2 is not unset:
yield next_2
for el in iterable1:
yield el
for el in iterable2:
yield el
[docs]class Params(object):
"""
Stores and 'sanitizes' parameters. Alphanumeric characters and the
non-alphanumeric ones that are deemed safe are let to pass through (see L{valid_chars}).
Some non-safe characters are escaped to safe forms for example C{>} becomes C{__lt__}
(see L{mapped_chars}). All other characters are replaced with C{X}.
Operates on string or list values only (HTTP parameters).
>>> values = { 'status':'on', 'symbols':[ 'alpha', '<>', '$rm&#!' ] }
>>> par = Params(values)
>>> par.status
'on'
>>> par.value == None # missing attributes return None
True
>>> par.get('price', 0)
0
>>> par.symbols # replaces unknown symbols with X
['alpha', '__lt____gt__', 'XrmX__pd__!']
>>> sorted(par.flatten()) # flattening to a list
[('status', 'on'), ('symbols', 'XrmX__pd__!'), ('symbols', '__lt____gt__'), ('symbols', 'alpha')]
"""
# is NEVER_SANITIZE required now that sanitizing for tool parameters can be controlled on a per parameter basis and occurs via InputValueWrappers?
NEVER_SANITIZE = ['file_data', 'url_paste', 'URL', 'filesystem_paths']
[docs] def __init__(self, params, sanitize=True):
if sanitize:
for key, value in params.items():
# sanitize check both ungrouped and grouped parameters by
# name. Anything relying on NEVER_SANITIZE should be
# changed to not require this and NEVER_SANITIZE should be
# removed.
if (value is not None and
key not in self.NEVER_SANITIZE and
True not in [key.endswith("|%s" % nonsanitize_parameter) for
nonsanitize_parameter in self.NEVER_SANITIZE]):
self.__dict__[key] = sanitize_param(value)
else:
self.__dict__[key] = value
else:
self.__dict__.update(params)
[docs] def flatten(self):
"""
Creates a tuple list from a dict with a tuple/value pair for every value that is a list
"""
flat = []
for key, value in self.__dict__.items():
if isinstance(value, list):
for v in value:
flat.append((key, v))
else:
flat.append((key, value))
return flat
def __getattr__(self, name):
"""This is here to ensure that we get None for non existing parameters"""
return None
def __str__(self):
return '%s' % self.__dict__
def __len__(self):
return len(self.__dict__)
def __iter__(self):
return iter(self.__dict__)
[docs]def rst_to_html(s, error=False):
"""Convert a blob of reStructuredText to HTML"""
log = get_logger("docutils")
if docutils_core is None:
raise Exception("Attempted to use rst_to_html but docutils unavailable.")
class FakeStream(object):
def write(self, str):
if len(str) > 0 and not str.isspace():
if error:
raise Exception(str)
log.warning(str)
settings_overrides = {
"embed_stylesheet": False,
"template": os.path.join(os.path.dirname(__file__), "docutils_template.txt"),
"warning_stream": FakeStream(),
"doctitle_xform": False, # without option, very different rendering depending on
# number of sections in help content.
}
return unicodify(docutils_core.publish_string(
s, writer=docutils_html4css1.Writer(),
settings_overrides=settings_overrides))
[docs]def xml_text(root, name=None):
"""Returns the text inside an element"""
if name is not None:
# Try attribute first
val = root.get(name)
if val:
return val
# Then try as element
elem = root.find(name)
else:
elem = root
if elem is not None and elem.text:
text = ''.join(elem.text.splitlines())
return text.strip()
# No luck, return empty string
return ''
[docs]def parse_resource_parameters(resource_param_file):
"""Code shared between jobs and workflows for reading resource parameter configuration files.
TODO: Allow YAML in addition to XML.
"""
resource_parameters = {}
if os.path.exists(resource_param_file):
resource_definitions = parse_xml(resource_param_file)
resource_definitions_root = resource_definitions.getroot()
for parameter_elem in resource_definitions_root.findall("param"):
name = parameter_elem.get("name")
resource_parameters[name] = parameter_elem
return resource_parameters
# asbool implementation pulled from PasteDeploy
truthy = frozenset(['true', 'yes', 'on', 'y', 't', '1'])
falsy = frozenset(['false', 'no', 'off', 'n', 'f', '0'])
[docs]def asbool(obj):
if isinstance(obj, string_types):
obj = obj.strip().lower()
if obj in truthy:
return True
elif obj in falsy:
return False
else:
raise ValueError("String is not true/false: %r" % obj)
return bool(obj)
[docs]def string_as_bool(string):
if str(string).lower() in ('true', 'yes', 'on', '1'):
return True
else:
return False
[docs]def string_as_bool_or_none(string):
"""
Returns True, None or False based on the argument:
True if passed True, 'True', 'Yes', or 'On'
None if passed None or 'None'
False otherwise
Note: string comparison is case-insensitive so lowecase versions of those
function equivalently.
"""
string = str(string).lower()
if string in ('true', 'yes', 'on'):
return True
elif string == 'none':
return None
else:
return False
[docs]def listify(item, do_strip=False):
"""
Make a single item a single item list.
If *item* is a string, it is split on comma (``,``) characters to produce the list. Optionally, if *do_strip* is
true, any extra whitespace around the split items is stripped.
If *item* is a list it is returned unchanged. If *item* is a tuple, it is converted to a list and returned. If
*item* evaluates to False, an empty list is returned.
:type item: object
:param item: object to make a list from
:type do_strip: bool
:param do_strip: strip whitespaces from around split items, if set to ``True``
:rtype: list
:returns: The input as a list
"""
if not item:
return []
elif isinstance(item, list) or isinstance(item, tuple):
return list(item)
elif isinstance(item, string_types) and item.count(','):
if do_strip:
return [token.strip() for token in item.split(',')]
else:
return item.split(',')
else:
return [item]
[docs]def commaify(amount):
orig = amount
new = re.sub("^(-?\d+)(\d{3})", '\g<1>,\g<2>', amount)
if orig == new:
return new
else:
return commaify(new)
[docs]def roundify(amount, sfs=2):
"""
Take a number in string form and truncate to 'sfs' significant figures.
"""
if len(amount) <= sfs:
return amount
else:
return amount[0:sfs] + '0' * (len(amount) - sfs)
[docs]def unicodify(value, encoding=DEFAULT_ENCODING, error='replace'):
u"""
Returns a Unicode string or None.
>>> assert unicodify(None) is None
>>> assert unicodify('simple string') == u'simple string'
>>> assert unicodify(3) == u'3'
>>> assert unicodify(bytearray([115, 116, 114, 196, 169, 195, 177, 103])) == u'strĩñg'
>>> assert unicodify(Exception('message')) == u'message'
>>> assert unicodify('cómplǐcḁtëd strĩñg') == u'cómplǐcḁtëd strĩñg'
>>> s = u'cómplǐcḁtëd strĩñg'; assert unicodify(s) == s
>>> s = u'lâtín strìñg'; assert unicodify(s.encode('latin-1'), 'latin-1') == s
>>> s = u'lâtín strìñg'; assert unicodify(s.encode('latin-1')) == u'l\ufffdt\ufffdn str\ufffd\ufffdg'
>>> s = u'lâtín strìñg'; assert unicodify(s.encode('latin-1'), error='ignore') == u'ltn strg'
"""
if value is None or isinstance(value, text_type):
return value
try:
if isinstance(value, bytearray):
value = bytes(value)
elif not isinstance(value, string_types) and not isinstance(value, binary_type):
# In Python 2, value is not an instance of basestring
# In Python 3, value is not an instance of bytes or str
value = str(value)
# Now in Python 2, value is an instance of basestring, but may be not unicode
# Now in Python 3, value is an instance of bytes or str
if not isinstance(value, text_type):
value = text_type(value, encoding, error)
except Exception:
msg = "Value '%s' could not be coerced to Unicode" % value
log.exception(msg)
raise Exception(msg)
return value
[docs]def smart_str(s, encoding=DEFAULT_ENCODING, strings_only=False, errors='strict'):
u"""
Returns a bytestring version of 's', encoded as specified in 'encoding'.
If strings_only is True, don't convert (some) non-string-like objects.
Adapted from an older, simpler version of django.utils.encoding.smart_str.
>>> assert smart_str(None) == b'None'
>>> assert smart_str(None, strings_only=True) is None
>>> assert smart_str(3) == b'3'
>>> assert smart_str(3, strings_only=True) == 3
>>> s = b'a bytes string'; assert smart_str(s) == s
>>> s = bytearray(b'a bytes string'); assert smart_str(s) == s
>>> assert smart_str(u'a simple unicode string') == b'a simple unicode string'
>>> assert smart_str(u'à strange ünicode ڃtring') == b'\\xc3\\xa0 strange \\xc3\\xbcnicode \\xda\\x83tring'
>>> assert smart_str(b'\\xc3\\xa0n \\xc3\\xabncoded utf-8 string', encoding='latin-1') == b'\\xe0n \\xebncoded utf-8 string'
>>> assert smart_str(bytearray(b'\\xc3\\xa0n \\xc3\\xabncoded utf-8 string'), encoding='latin-1') == b'\\xe0n \\xebncoded utf-8 string'
"""
if strings_only and isinstance(s, (type(None), int)):
return s
if not isinstance(s, string_types) and not isinstance(s, (binary_type, bytearray)):
# In Python 2, s is not an instance of basestring or bytearray
# In Python 3, s is not an instance of str, bytes or bytearray
s = str(s)
# Now in Python 2, value is an instance of basestring or bytearray
# Now in Python 3, value is an instance of str, bytes or bytearray
if not isinstance(s, (binary_type, bytearray)):
return s.encode(encoding, errors)
elif s and encoding != DEFAULT_ENCODING:
return s.decode(DEFAULT_ENCODING, errors).encode(encoding, errors)
else:
return s
[docs]def strip_control_characters(s):
"""Strip unicode control characters from a string."""
return "".join(c for c in unicodify(s) if unicodedata.category(c)[0] != "C")
[docs]def strip_control_characters_nested(item):
"""Recursively strips control characters from lists, dicts, tuples."""
def visit(path, key, value):
if isinstance(key, string_types):
key = strip_control_characters(key)
if isinstance(value, string_types):
value = strip_control_characters(value)
return key, value
return remap(item, visit)
[docs]class ParamsWithSpecs(collections.defaultdict):
"""
"""
[docs] def __init__(self, specs=None, params=None):
self.specs = specs or dict()
self.params = params or dict()
for name, value in self.params.items():
if name not in self.specs:
self._param_unknown_error(name)
if 'map' in self.specs[name]:
try:
self.params[name] = self.specs[name]['map'](value)
except Exception:
self._param_map_error(name, value)
if 'valid' in self.specs[name]:
if not self.specs[name]['valid'](value):
self._param_vaildation_error(name, value)
self.update(self.params)
def __missing__(self, name):
return self.specs[name]['default']
def __getattr__(self, name):
return self[name]
def _param_unknown_error(self, name):
raise NotImplementedError()
def _param_map_error(self, name, value):
raise NotImplementedError()
def _param_vaildation_error(self, name, value):
raise NotImplementedError()
[docs]def compare_urls(url1, url2, compare_scheme=True, compare_hostname=True, compare_path=True):
url1 = urlparse.urlparse(url1)
url2 = urlparse.urlparse(url2)
if compare_scheme and url1.scheme and url2.scheme and url1.scheme != url2.scheme:
return False
if compare_hostname and url1.hostname and url2.hostname and url1.hostname != url2.hostname:
return False
if compare_path and url1.path and url2.path and url1.path != url2.path:
return False
return True
[docs]def read_dbnames(filename):
""" Read build names from file """
class DBNames(list):
default_value = "?"
default_name = "unspecified (?)"
db_names = DBNames()
try:
ucsc_builds = {}
man_builds = [] # assume these are integers
name_to_db_base = {}
if filename is None:
# Should only be happening with the galaxy.tools.parameters.basic:GenomeBuildParameter docstring unit test
filename = os.path.join('tool-data', 'shared', 'ucsc', 'builds.txt.sample')
for line in open(filename):
try:
if line[0:1] == "#":
continue
fields = line.replace("\r", "").replace("\n", "").split("\t")
# Special case of unspecified build is at top of list
if fields[0] == "?":
db_names.insert(0, (fields[0], fields[1]))
continue
try: # manual build (i.e. microbes)
int(fields[0])
man_builds.append((fields[1], fields[0]))
except Exception: # UCSC build
db_base = fields[0].rstrip('0123456789')
if db_base not in ucsc_builds:
ucsc_builds[db_base] = []
name_to_db_base[fields[1]] = db_base
# we want to sort within a species numerically by revision number
build_rev = re.compile(r'\d+$')
try:
build_rev = int(build_rev.findall(fields[0])[0])
except Exception:
build_rev = 0
ucsc_builds[db_base].append((build_rev, fields[0], fields[1]))
except Exception:
continue
sort_names = sorted(name_to_db_base.keys())
for name in sort_names:
db_base = name_to_db_base[name]
ucsc_builds[db_base].sort()
ucsc_builds[db_base].reverse()
ucsc_builds[db_base] = [(build, name) for _, build, name in ucsc_builds[db_base]]
db_names = DBNames(db_names + ucsc_builds[db_base])
if len(db_names) > 1 and len(man_builds) > 0:
db_names.append((db_names.default_value, '----- Additional Species Are Below -----'))
man_builds.sort()
man_builds = [(build, name) for name, build in man_builds]
db_names = DBNames(db_names + man_builds)
except Exception as e:
log.error("ERROR: Unable to read builds file: %s", e)
if len(db_names) < 1:
db_names = DBNames([(db_names.default_value, db_names.default_name)])
return db_names
[docs]def read_build_sites(filename, check_builds=True):
""" read db names to ucsc mappings from file, this file should probably be merged with the one above """
build_sites = []
try:
for line in open(filename):
try:
if line[0:1] == "#":
continue
fields = line.replace("\r", "").replace("\n", "").split("\t")
site_name = fields[0]
site = fields[1]
if check_builds:
site_builds = fields[2].split(",")
site_dict = {'name': site_name, 'url': site, 'builds': site_builds}
else:
site_dict = {'name': site_name, 'url': site}
build_sites.append(site_dict)
except Exception:
continue
except Exception:
log.error("ERROR: Unable to read builds for site file %s", filename)
return build_sites
[docs]def relativize_symlinks(path, start=None, followlinks=False):
for root, dirs, files in os.walk(path, followlinks=followlinks):
rel_start = None
for file_name in files:
symlink_file_name = os.path.join(root, file_name)
if os.path.islink(symlink_file_name):
symlink_target = os.readlink(symlink_file_name)
if rel_start is None:
if start is None:
rel_start = root
else:
rel_start = start
rel_path = relpath(symlink_target, rel_start)
os.remove(symlink_file_name)
os.symlink(rel_path, symlink_file_name)
[docs]def stringify_dictionary_keys(in_dict):
# returns a new dictionary
# changes unicode keys into strings, only works on top level (does not recurse)
# unicode keys are not valid for expansion into keyword arguments on method calls
out_dict = {}
for key, value in iteritems(in_dict):
out_dict[str(key)] = value
return out_dict
[docs]def mkstemp_ln(src, prefix='mkstemp_ln_'):
"""
From tempfile._mkstemp_inner, generate a hard link in the same dir with a
random name. Created so we can persist the underlying file of a
NamedTemporaryFile upon its closure.
"""
dir = os.path.dirname(src)
names = tempfile._get_candidate_names()
for seq in xrange(tempfile.TMP_MAX):
name = next(names)
file = os.path.join(dir, prefix + name)
try:
os.link(src, file)
return (os.path.abspath(file))
except OSError as e:
if e.errno == errno.EEXIST:
continue # try again
raise
raise IOError(errno.EEXIST, "No usable temporary file name found")
[docs]def umask_fix_perms(path, umask, unmasked_perms, gid=None):
"""
umask-friendly permissions fixing
"""
perms = unmasked_perms & ~umask
try:
st = os.stat(path)
except OSError as e:
log.exception('Unable to set permissions or group on %s', path)
return
# fix modes
if stat.S_IMODE(st.st_mode) != perms:
try:
os.chmod(path, perms)
except Exception as e:
log.warning('Unable to honor umask (%s) for %s, tried to set: %s but mode remains %s, error was: %s' % (oct(umask),
path,
oct(perms),
oct(stat.S_IMODE(st.st_mode)),
e))
# fix group
if gid is not None and st.st_gid != gid:
try:
os.chown(path, -1, gid)
except Exception as e:
try:
desired_group = grp.getgrgid(gid)
current_group = grp.getgrgid(st.st_gid)
except Exception:
desired_group = gid
current_group = st.st_gid
log.warning('Unable to honor primary group (%s) for %s, group remains %s, error was: %s' % (desired_group,
path,
current_group,
e))
[docs]def docstring_trim(docstring):
"""Trimming python doc strings. Taken from: http://www.python.org/dev/peps/pep-0257/"""
if not docstring:
return ''
# Convert tabs to spaces (following the normal Python rules)
# and split into a list of lines:
lines = docstring.expandtabs().splitlines()
# Determine minimum indentation (first line doesn't count):
indent = sys.maxsize
for line in lines[1:]:
stripped = line.lstrip()
if stripped:
indent = min(indent, len(line) - len(stripped))
# Remove indentation (first line is special):
trimmed = [lines[0].strip()]
if indent < sys.maxsize:
for line in lines[1:]:
trimmed.append(line[indent:].rstrip())
# Strip off trailing and leading blank lines:
while trimmed and not trimmed[-1]:
trimmed.pop()
while trimmed and not trimmed[0]:
trimmed.pop(0)
# Return a single string:
return '\n'.join(trimmed)
[docs]def nice_size(size):
"""
Returns a readably formatted string with the size
>>> nice_size(100)
'100 bytes'
>>> nice_size(10000)
'9.8 KB'
>>> nice_size(1000000)
'976.6 KB'
>>> nice_size(100000000)
'95.4 MB'
"""
words = ['bytes', 'KB', 'MB', 'GB', 'TB', 'PB', 'EB']
prefix = ''
try:
size = float(size)
if size < 0:
size = abs(size)
prefix = '-'
except Exception:
return '??? bytes'
for ind, word in enumerate(words):
step = 1024 ** (ind + 1)
if step > size:
size = size / float(1024 ** ind)
if word == 'bytes': # No decimals for bytes
return "%s%d bytes" % (prefix, size)
return "%s%.1f %s" % (prefix, size, word)
return '??? bytes'
[docs]def size_to_bytes(size):
"""
Returns a number of bytes if given a reasonably formatted string with the size
"""
# Assume input in bytes if we can convert directly to an int
try:
return int(size)
except ValueError:
pass
# Otherwise it must have non-numeric characters
size_re = re.compile('([\d\.]+)\s*([tgmk]b?|b|bytes?)$')
size_match = re.match(size_re, size.lower())
assert size_match is not None
size = float(size_match.group(1))
multiple = size_match.group(2)
if multiple.startswith('t'):
return int(size * 1024 ** 4)
elif multiple.startswith('g'):
return int(size * 1024 ** 3)
elif multiple.startswith('m'):
return int(size * 1024 ** 2)
elif multiple.startswith('k'):
return int(size * 1024)
elif multiple.startswith('b'):
return int(size)
[docs]def send_mail(frm, to, subject, body, config, html=None):
"""
Sends an email.
:type frm: str
:param frm: from address
:type to: str
:param to: to address
:type subject: str
:param subject: Subject line
:type body: str
:param body: Body text (should be plain text)
:type config: object
:param config: Galaxy configuration object
:type html: str
:param html: Alternative HTML representation of the body content. If
provided will convert the message to a MIMEMultipart. (Default 'None')
"""
to = listify(to)
if html:
msg = email_mime_multipart.MIMEMultipart('alternative')
else:
msg = email_mime_text.MIMEText(body.encode('ascii', 'replace'))
msg['To'] = ', '.join(to)
msg['From'] = frm
msg['Subject'] = subject
if config.smtp_server is None:
log.error("Mail is not configured for this Galaxy instance.")
log.info(msg)
return
if html:
mp_text = email_mime_text.MIMEText(body.encode('ascii', 'replace'), 'plain')
mp_html = email_mime_text.MIMEText(html.encode('ascii', 'replace'), 'html')
msg.attach(mp_text)
msg.attach(mp_html)
smtp_ssl = asbool(getattr(config, 'smtp_ssl', False))
if smtp_ssl:
s = smtplib.SMTP_SSL()
else:
s = smtplib.SMTP()
s.connect(config.smtp_server)
if not smtp_ssl:
try:
s.starttls()
log.debug('Initiated SSL/TLS connection to SMTP server: %s' % config.smtp_server)
except RuntimeError as e:
log.warning('SSL/TLS support is not available to your Python interpreter: %s' % e)
except smtplib.SMTPHeloError as e:
log.error("The server didn't reply properly to the HELO greeting: %s" % e)
s.close()
raise
except smtplib.SMTPException as e:
log.warning('The server does not support the STARTTLS extension: %s' % e)
if config.smtp_username and config.smtp_password:
try:
s.login(config.smtp_username, config.smtp_password)
except smtplib.SMTPHeloError as e:
log.error("The server didn't reply properly to the HELO greeting: %s" % e)
s.close()
raise
except smtplib.SMTPAuthenticationError as e:
log.error("The server didn't accept the username/password combination: %s" % e)
s.close()
raise
except smtplib.SMTPException as e:
log.error("No suitable authentication method was found: %s" % e)
s.close()
raise
s.sendmail(frm, to, msg.as_string())
s.quit()
[docs]def force_symlink(source, link_name):
try:
os.symlink(source, link_name)
except OSError as e:
if e.errno == errno.EEXIST:
os.remove(link_name)
os.symlink(source, link_name)
else:
raise e
[docs]def move_merge(source, target):
# when using shutil and moving a directory, if the target exists,
# then the directory is placed inside of it
# if the target doesn't exist, then the target is made into the directory
# this makes it so that the target is always the target, and if it exists,
# the source contents are moved into the target
if os.path.isdir(source) and os.path.exists(target) and os.path.isdir(target):
for name in os.listdir(source):
move_merge(os.path.join(source, name), os.path.join(target, name))
else:
return shutil.move(source, target)
[docs]def safe_str_cmp(a, b):
"""safely compare two strings in a timing-attack-resistant manner
"""
if len(a) != len(b):
return False
rv = 0
for x, y in zip(a, b):
rv |= ord(x) ^ ord(y)
return rv == 0
galaxy_root_path = os.path.join(__path__[0], "..", "..", "..")
[docs]def config_directories_from_setting(directories_setting, galaxy_root=galaxy_root_path):
"""
Parse the ``directories_setting`` into a list of relative or absolute
filesystem paths that will be searched to discover plugins.
:type galaxy_root: string
:param galaxy_root: the root path of this galaxy installation
:type directories_setting: string (default: None)
:param directories_setting: the filesystem path (or paths)
to search for plugins. Can be CSV string of paths. Will be treated as
absolute if a path starts with '/', relative otherwise.
:rtype: list of strings
:returns: list of filesystem paths
"""
directories = []
if not directories_setting:
return directories
for directory in listify(directories_setting):
directory = directory.strip()
if not directory.startswith('/'):
directory = os.path.join(galaxy_root, directory)
if not os.path.exists(directory):
log.warning('directory not found: %s', directory)
continue
directories.append(directory)
return directories
[docs]def parse_int(value, min_val=None, max_val=None, default=None, allow_none=False):
try:
value = int(value)
if min_val is not None and value < min_val:
return min_val
if max_val is not None and value > max_val:
return max_val
return value
except ValueError:
if allow_none:
if default is None or value == "None":
return None
if default:
return default
else:
raise
[docs]def parse_non_hex_float(s):
"""
Parse string `s` into a float but throw a `ValueError` if the string is in
the otherwise acceptable format `\d+e\d+` (e.g. 40000000000000e5.)
This can be passed into `json.loads` to prevent a hex string in the above
format from being incorrectly parsed as a float in scientific notation.
>>> parse_non_hex_float( '123.4' )
123.4
>>> parse_non_hex_float( '2.45e+3' )
2450.0
>>> parse_non_hex_float( '2.45e-3' )
0.00245
>>> parse_non_hex_float( '40000000000000e5' )
Traceback (most recent call last):
...
ValueError: could not convert string to float: 40000000000000e5
"""
f = float(s)
# successfully parsed as float if here - check for format in original string
if 'e' in s and not ('+' in s or '-' in s):
raise ValueError('could not convert string to float: ' + s)
return f
[docs]def build_url(base_url, port=80, scheme='http', pathspec=None, params=None, doseq=False):
if params is None:
params = dict()
if pathspec is None:
pathspec = []
parsed_url = urlparse.urlparse(base_url)
if scheme != 'http':
parsed_url.scheme = scheme
assert parsed_url.scheme in ('http', 'https', 'ftp'), 'Invalid URL scheme: %s' % scheme
if port != 80:
url = '%s://%s:%d/%s' % (parsed_url.scheme, parsed_url.netloc.rstrip('/'), int(port), parsed_url.path)
else:
url = '%s://%s/%s' % (parsed_url.scheme, parsed_url.netloc.rstrip('/'), parsed_url.path.lstrip('/'))
if len(pathspec) > 0:
url = '%s/%s' % (url.rstrip('/'), '/'.join(pathspec))
if parsed_url.query:
for query_parameter in parsed_url.query.split('&'):
key, value = query_parameter.split('=')
params[key] = value
if params:
url += '?%s' % urlparse.urlencode(params, doseq=doseq)
return url
[docs]def url_get(base_url, password_mgr=None, pathspec=None, params=None):
"""Make contact with the uri provided and return any contents."""
# Uses system proxy settings if they exist.
proxy = urlrequest.ProxyHandler()
if password_mgr is not None:
auth = urlrequest.HTTPDigestAuthHandler(password_mgr)
urlopener = urlrequest.build_opener(proxy, auth)
else:
urlopener = urlrequest.build_opener(proxy)
urlrequest.install_opener(urlopener)
full_url = build_url(base_url, pathspec=pathspec, params=params)
response = urlopener.open(full_url)
content = response.read()
response.close()
return content
[docs]def download_to_file(url, dest_file_path, timeout=30, chunk_size=2 ** 20):
"""Download a URL to a file in chunks."""
src = urlopen(url, timeout=timeout)
with open(dest_file_path, 'wb') as f:
while True:
chunk = src.read(chunk_size)
if not chunk:
break
f.write(chunk)
[docs]class ExecutionTimer(object):
def __str__(self):
return "(%0.3f ms)" % (self.elapsed * 1000)
@property
def elapsed(self):
return (time.time() - self.begin)
if __name__ == '__main__':
import doctest
doctest.testmod(sys.modules[__name__], verbose=False)