galaxy.util package¶
Submodules¶
galaxy.util.aliaspickler module¶
galaxy.util.bunch module¶
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class
galaxy.util.bunch.Bunch(**kwds)[source]¶ Bases:
objecthttp://aspn.activestate.com/ASPN/Cookbook/Python/Recipe/52308
Often we want to just collect a bunch of stuff together, naming each item of the bunch; a dictionary’s OK for that, but a small do-nothing class is even handier, and prettier to use.
galaxy.util.checkers module¶
galaxy.util.compression_utils module¶
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galaxy.util.compression_utils.get_fileobj(filename, mode='r', compressed_formats=None)[source]¶ Returns a fileobj. If the file is compressed, return an appropriate file reader. In text mode, always use ‘utf-8’ encoding.
Parameters: - filename – path to file that should be opened
- mode – mode to pass to opener
- compressed_formats – list of allowed compressed file formats among ‘bz2’, ‘gzip’ and ‘zip’. If left to None, all 3 formats are allowed
galaxy.util.dictifiable module¶
galaxy.util.expressions module¶
Expression evaluation support.
For the moment this depends on python’s eval. In the future it should be replaced with a “safe” parser.
galaxy.util.filelock module¶
Code obtained from https://github.com/dmfrey/FileLock.
See full license at:
https://github.com/dmfrey/FileLock/blob/master/LICENSE.txt
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class
galaxy.util.filelock.FileLock(file_name, timeout=10, delay=0.05)[source]¶ Bases:
objectA file locking mechanism that has context-manager support so you can use it in a with statement. This should be relatively cross compatible as it doesn’t rely on msvcrt or fcntl for the locking.
galaxy.util.hash_util module¶
Utility functions for bi-directional Python version compatibility. Python 2.5 introduced hashlib which replaced sha in Python 2.4 and previous versions.
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galaxy.util.hash_util.md5()¶ Returns a md5 hash object; optionally initialized with a string
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galaxy.util.hash_util.sha1()¶ Returns a sha1 hash object; optionally initialized with a string
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galaxy.util.hash_util.sha()¶ Returns a sha1 hash object; optionally initialized with a string
galaxy.util.heartbeat module¶
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class
galaxy.util.heartbeat.Heartbeat(config, name='Heartbeat Thread', period=20, fname='heartbeat.log')[source]¶ Bases:
threading.ThreadThread that periodically dumps the state of all threads to a file
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get_interesting_stack_frame(stack_frames)[source]¶ Scans a given backtrace stack frames, returns a single quadraple of [filename, line, function-name, text] of the single, deepest, most interesting frame.
Interesting being:
inside the galaxy source code ("/lib/galaxy"), prefreably not an egg.
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run()[source]¶ Method representing the thread’s activity.
You may override this method in a subclass. The standard run() method invokes the callable object passed to the object’s constructor as the target argument, if any, with sequential and keyword arguments taken from the args and kwargs arguments, respectively.
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galaxy.util.heartbeat.get_current_thread_object_dict()[source]¶ Get a dictionary of all ‘Thread’ objects created via the threading module keyed by thread_id. Note that not all interpreter threads have a thread objects, only the main thread and any created via the ‘threading’ module. Threads created via the low level ‘thread’ module will not be in the returned dictionary.
- HACK: This mucks with the internals of the threading module since that
- module does not expose any way to match ‘Thread’ objects with intepreter thread identifiers (though it should).
galaxy.util.image_util module¶
Provides utilities for working with image files.
galaxy.util.inflection module¶
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class
galaxy.util.inflection.Base[source]¶ Bases:
objectLocale inflectors must inherit from this base class inorder to provide the basic Inflector functionality
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camelize(word)[source]¶ Returns given word as CamelCased Converts a word like “send_email” to “SendEmail”. It will remove non alphanumeric character from the word, so “who’s online” will be converted to “WhoSOnline”
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classify(table_name)[source]¶ Converts a table name to its class name according to rails naming conventions. Example: Converts “people” to “Person”
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cond_plural(number_of_records, word)[source]¶ Returns the plural form of a word if first parameter is greater than 1
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foreignKey(class_name, separate_class_name_and_id_with_underscore=1)[source]¶ Returns class_name in underscored form, with “_id” tacked on at the end. This is for use in dealing with the database.
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humanize(word, uppercase='')[source]¶ Returns a human-readable string from word Returns a human-readable string from word, by replacing underscores with a space, and by upper-casing the initial character by default. If you need to uppercase all the words you just have to pass ‘all’ as a second parameter.
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ordinalize(number)[source]¶ Converts number to its ordinal English form. This method converts 13 to 13th, 2 to 2nd …
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string_replace(word, find, replace)[source]¶ This function returns a copy of word, translating all occurrences of each character in find to the corresponding character in replace
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tableize(class_name)[source]¶ Converts a class name to its table name according to rails naming conventions. Example. Converts “Person” to “people”
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titleize(word, uppercase='')[source]¶ Converts an underscored or CamelCase word into a English sentence. The titleize function converts text like “WelcomePage”, “welcome_page” or “welcome page” to this “Welcome Page”. If second parameter is set to ‘first’ it will only capitalize the first character of the title.
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unaccent(text)[source]¶ Transforms a string to its unaccented version. This might be useful for generating “friendly” URLs
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underscore(word)[source]¶ Converts a word “into_it_s_underscored_version” Convert any “CamelCased” or “ordinary Word” into an “underscored_word”. This can be really useful for creating friendly URLs.
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class
galaxy.util.inflection.English[source]¶ Bases:
galaxy.util.inflection.BaseInflector for pluralize and singularize English nouns.
This is the default Inflector for the Inflector obj
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class
galaxy.util.inflection.Inflector(Inflector=<class 'galaxy.util.inflection.English'>)[source]¶ Bases:
objectInflector for pluralizing and singularizing nouns.
It provides methods for helping on creating programs based on naming conventions like on Ruby on Rails.
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camelize(word)[source]¶ Returns given word as CamelCased Converts a word like “send_email” to “SendEmail”. It will remove non alphanumeric character from the word, so “who’s online” will be converted to “WhoSOnline”
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classify(table_name)[source]¶ Converts a table name to its class name according to rails naming conventions. Example: Converts “people” to “Person”
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cond_plural(number_of_records, word)[source]¶ Returns the plural form of a word if first parameter is greater than 1
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foreignKey(class_name, separate_class_name_and_id_with_underscore=1)[source]¶ Returns class_name in underscored form, with “_id” tacked on at the end. This is for use in dealing with the database.
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humanize(word, uppercase='')[source]¶ Returns a human-readable string from word Returns a human-readable string from word, by replacing underscores with a space, and by upper-casing the initial character by default. If you need to uppercase all the words you just have to pass ‘all’ as a second parameter.
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ordinalize(number)[source]¶ Converts number to its ordinal form. This method converts 13 to 13th, 2 to 2nd …
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tableize(class_name)[source]¶ Converts a class name to its table name according to rails naming conventions. Example. Converts “Person” to “people”
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titleize(word, uppercase='')[source]¶ Converts an underscored or CamelCase word into a sentence. The titleize function converts text like “WelcomePage”, “welcome_page” or “welcome page” to this “Welcome Page”. If the “uppercase” parameter is set to ‘first’ it will only capitalize the first character of the title.
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unaccent(text)[source]¶ Transforms a string to its unaccented version. This might be useful for generating “friendly” URLs
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underscore(word)[source]¶ Converts a word “into_it_s_underscored_version” Convert any “CamelCased” or “ordinary Word” into an “underscored_word”. This can be really useful for creating friendly URLs.
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galaxy.util.json module¶
galaxy.util.lazy_process module¶
galaxy.util.object_wrapper module¶
Classes for wrapping Objects and Sanitizing string output.
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class
galaxy.util.object_wrapper.CallableSafeStringWrapper(value, safe_string_wrapper_function=<function wrap_with_safe_string>)[source]¶
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class
galaxy.util.object_wrapper.SafeStringWrapper(value, safe_string_wrapper_function=<function wrap_with_safe_string>)[source]¶ Bases:
objectClass that wraps and sanitizes any provided value’s attributes that will attempt to be cast into a string.
Attempts to mimic behavior of original class, including operands.
To ensure proper handling of e.g. subclass checks, the wrap_with_safe_string() method should be used.
This wrapping occurs in a recursive/parasitic fashion, as all called attributes of the originally wrapped object will also be wrapped and sanitized, unless the attribute is of a type found in __DONT_SANITIZE_TYPES__ + __DONT_WRAP_TYPES__, where e.g. ~(strings will still be sanitized, but not wrapped), and e.g. integers will have neither.
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galaxy.util.object_wrapper.sanitize_lists_to_string(values, valid_characters=set(['!', ' ', ')', '(', '+', '*', '-', ', ', '/', '.', '1', '0', '3', '2', '5', '4', '7', '6', '9', '8', ':', '=', '?', 'A', '@', 'C', 'B', 'E', 'D', 'G', 'F', 'I', 'H', 'K', 'J', 'M', 'L', 'O', 'N', 'Q', 'P', 'S', 'R', 'U', 'T', 'W', 'V', 'Y', 'X', 'Z', '_', '^', 'a', 'c', 'b', 'e', 'd', 'g', 'f', 'i', 'h', 'k', 'j', 'm', 'l', 'o', 'n', 'q', 'p', 's', 'r', 'u', 't', 'w', 'v', 'y', 'x', 'z']), character_map={'\t': '__tc__', '\n': '__cn__', '\r': '__cr__', '"': '__dq__', '#': '__pd__', "'": '__sq__', '<': '__lt__', '>': '__gt__', '[': '__ob__', ']': '__cb__', '{': '__oc__', '}': '__cc__'}, invalid_character='X')[source]¶
galaxy.util.odict module¶
Ordered dictionary implementation.
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class
galaxy.util.odict.odict(dict=None)[source]¶ Bases:
UserDict.UserDicthttp://aspn.activestate.com/ASPN/Cookbook/Python/Recipe/107747
This dictionary class extends UserDict to record the order in which items are added. Calling keys(), values(), items(), etc. will return results in this order.
galaxy.util.oset module¶
Ordered set implementation from https://code.activestate.com/recipes/576694/
galaxy.util.plugin_config module¶
galaxy.util.properties module¶
Module used to blend ini, environment, and explicit dictionary properties to determine application configuration. Some hard coded defaults for Galaxy but this should be reusable by tool shed and pulsar as well.
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galaxy.util.properties.find_config_file(names, exts=None, dirs=None, include_samples=False)[source]¶ Locate a config file in multiple directories, with multiple extensions.
>>> from shutil import rmtree >>> from tempfile import mkdtemp >>> def touch(d, f): ... open(os.path.join(d, f), 'w').close() >>> def _find_config_file(*args, **kwargs): ... return find_config_file(*args, **kwargs).replace(d, '') >>> d = mkdtemp() >>> d1 = os.path.join(d, 'd1') >>> d2 = os.path.join(d, 'd2') >>> os.makedirs(d1) >>> os.makedirs(d2) >>> touch(d1, 'foo.ini') >>> touch(d1, 'foo.bar') >>> touch(d1, 'baz.ini.sample') >>> touch(d2, 'foo.yaml') >>> touch(d2, 'baz.yml') >>> _find_config_file('foo', dirs=(d1, d2)) '/d1/foo.ini' >>> _find_config_file('baz', dirs=(d1, d2)) '/d2/baz.yml' >>> _find_config_file('baz', dirs=(d1, d2), include_samples=True) '/d2/baz.yml' >>> _find_config_file('baz', dirs=(d1,), include_samples=True) '/d1/baz.ini.sample' >>> _find_config_file('foo', dirs=(d2, d1)) '/d2/foo.yaml' >>> find_config_file('quux', dirs=(d,)) >>> _find_config_file('foo', exts=('bar', 'ini'), dirs=(d1,)) '/d1/foo.bar' >>> rmtree(d)
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galaxy.util.properties.load_app_properties(kwds={}, ini_file=None, ini_section=None, config_file=None, config_section=None, config_prefix='GALAXY_CONFIG_')[source]¶
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class
galaxy.util.properties.NicerConfigParser(filename, *args, **kw)[source]¶ Bases:
ConfigParser.ConfigParser
galaxy.util.simplegraph module¶
Fencepost-simple graph structure implementation.
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class
galaxy.util.simplegraph.SimpleGraph(nodes=None, edges=None)[source]¶ Bases:
objectEach node is unique (by id) and stores its own index in the node list/odict. Each edge is represented as two indeces into the node list/odict. Both nodes and edges allow storing extra information if needed.
- Allows:
- multiple edges between two nodes self referential edges (an edge from a node to itself)
These graphs are not specifically directed but since source and targets on the edges are listed - it could easily be used that way.
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add_edge(source_id, target_id, **data)[source]¶ Adds a new node only if it doesn’t already exist. :param source_id: the id of the source node :type source_id: (hashable) :param target_id: the id of the target node :type target_id: (hashable) :param data: any extra data that needs to be saved for the edge :type data: (variadic dictionary) :returns: the new node
..note: that, although this will create new nodes if necessary, there’s no way to pass data to them - so if you need to assoc. more data with the nodes, use add_node first.
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add_node(node_id, **data)[source]¶ Adds a new node only if it doesn’t already exist. :param node_id: some unique identifier :type node_id: (hashable) :param data: any extra data that needs to be saved :type data: (variadic dictionary) :returns: the new node
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as_dict()[source]¶ Returns a dictionary of the form:
{ 'nodes': <a list of node dictionaries>, 'edges': <a list of node dictionaries> }
galaxy.util.sleeper module¶
galaxy.util.specs module¶
galaxy.util.sqlite module¶
galaxy.util.tool_version module¶
galaxy.util.topsort module¶
Topological sort.
- From Tim Peters, see:
- http://mail.python.org/pipermail/python-list/1999-July/006660.html
topsort takes a list of pairs, where each pair (x, y) is taken to mean that x <= y wrt some abstract partial ordering. The return value is a list, representing a total ordering that respects all the input constraints. E.g.,
topsort( [(1,2), (3,3)] )
Valid topological sorts would be any of (but nothing other than)
[3, 1, 2] [1, 3, 2] [1, 2, 3]
… however this variant ensures that ‘key’ order (first element of tuple) is preserved so the following will be result returned:
[1, 3, 2]
because those are the permutations of the input elements that respect the “1 precedes 2” and “3 precedes 3” input constraints. Note that a constraint of the form (x, x) is really just a trick to make sure x appears somewhere in the output list.
If there’s a cycle in the constraints, say
topsort( [(1,2), (2,1)] )
then CycleError is raised, and the exception object supports many methods to help analyze and break the cycles. This requires a good deal more code than topsort itself!
galaxy.util.xml_macros module¶
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galaxy.util.xml_macros.load_with_references(path)[source]¶ Load XML documentation from file system and preprocesses XML macros.
Return the XML representation of the expanded tree and paths to referenced files that were imported (macros).
Module contents¶
Utility functions used systemwide.
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class
galaxy.util.Params(params, sanitize=True)[source]¶ Bases:
objectStores 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')]
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NEVER_SANITIZE= ['file_data', 'url_paste', 'URL', 'filesystem_paths']¶
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galaxy.util.build_url(base_url, port=80, scheme='http', pathspec=None, params=None, doseq=False)[source]¶
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galaxy.util.compare_urls(url1, url2, compare_scheme=True, compare_hostname=True, compare_path=True)[source]¶
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galaxy.util.config_directories_from_setting(directories_setting, galaxy_root='/home/docs/checkouts/readthedocs.org/user_builds/galaxy-lib/checkouts/latest/galaxy/util/../../..')[source]¶ Parse the
directories_settinginto a list of relative or absolute filesystem paths that will be searched to discover plugins.Parameters: - galaxy_root (string) – the root path of this galaxy installation
- directories_setting (string (default: None)) – 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.
Return type: list of strings
Returns: list of filesystem paths
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galaxy.util.directory_hash_id(id)[source]¶ >>> 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']
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galaxy.util.docstring_trim(docstring)[source]¶ Trimming python doc strings. Taken from: http://www.python.org/dev/peps/pep-0257/
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galaxy.util.download_to_file(url, dest_file_path, timeout=30, chunk_size=1048576)[source]¶ Download a URL to a file in chunks.
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galaxy.util.file_iter(fname, sep=None)[source]¶ 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
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galaxy.util.file_reader(fp, chunk_size=65536)[source]¶ This generator yields the open fileobject in chunks (default 64k). Closes the file at the end
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galaxy.util.find_instance_nested(item, instances, match_key=None)[source]¶ 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.
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galaxy.util.in_directory(file, directory, local_path_module=<module 'posixpath' from '/home/docs/checkouts/readthedocs.org/user_builds/galaxy-lib/envs/latest/lib/python2.7/posixpath.pyc'>)[source]¶ 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
directoryis a “trusted” path - supplied by Galaxy or by the admin andfileis 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
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galaxy.util.is_binary(value)[source]¶ 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’xcex94’ ) False >>> is_binary( b’x00’ ) True
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galaxy.util.is_uuid(value)[source]¶ This method returns True if value is a UUID, otherwise False. >>> is_uuid( “123e4567-e89b-12d3-a456-426655440000” ) True >>> is_uuid( “0x3242340298902834” ) False
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galaxy.util.listify(item, do_strip=False)[source]¶ 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.
Parameters: - item (object) – object to make a list from
- do_strip (bool) – strip whitespaces from around split items, if set to
True
Return type: list
Returns: The input as a list
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galaxy.util.mask_password_from_url(url)[source]¶ 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'
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galaxy.util.merge_sorted_iterables(operator, *iterables)[source]¶ >>> 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]
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galaxy.util.mkstemp_ln(src, prefix='mkstemp_ln_')[source]¶ 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.
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galaxy.util.nice_size(size)[source]¶ 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'
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galaxy.util.parse_non_hex_float(s)[source]¶ Parse string s into a float but throw a ValueError if the string is in the otherwise acceptable format d+ed+ (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
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galaxy.util.parse_resource_parameters(resource_param_file)[source]¶ Code shared between jobs and workflows for reading resource parameter configuration files.
TODO: Allow YAML in addition to XML.
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galaxy.util.pretty_print_time_interval(time=False, precise=False, utc=False)[source]¶ 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
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galaxy.util.read_build_sites(filename, check_builds=True)[source]¶ read db names to ucsc mappings from file, this file should probably be merged with the one above
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galaxy.util.ready_name_for_url(raw_name)[source]¶ 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'
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galaxy.util.remove_protocol_from_url(url)[source]¶ Supplied URL may be null, if not ensure http:// or https:// etc… is stripped off.
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galaxy.util.restore_text(text, character_map={'\t': '__tc__', '\n': '__cn__', '\r': '__cr__', '"': '__dq__', '#': '__pd__', "'": '__sq__', '<': '__lt__', '>': '__gt__', '@': '__at__', '[': '__ob__', ']': '__cb__', '{': '__oc__', '}': '__cc__'})[source]¶ Restores sanitized text
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galaxy.util.roundify(amount, sfs=2)[source]¶ Take a number in string form and truncate to ‘sfs’ significant figures.
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galaxy.util.safe_str_cmp(a, b)[source]¶ safely compare two strings in a timing-attack-resistant manner
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galaxy.util.sanitize_for_filename(text, default=None)[source]¶ 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.
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galaxy.util.sanitize_lists_to_string(values, valid_characters=set(['!', ' ', ')', '(', '+', '*', '-', ', ', '/', '.', '1', '0', '3', '2', '5', '4', '7', '6', '9', '8', ':', '=', '?', 'A', 'C', 'B', 'E', 'D', 'G', 'F', 'I', 'H', 'K', 'J', 'M', 'L', 'O', 'N', 'Q', 'P', 'S', 'R', 'U', 'T', 'W', 'V', 'Y', 'X', 'Z', '_', '^', 'a', 'c', 'b', 'e', 'd', 'g', 'f', 'i', 'h', 'k', 'j', 'm', 'l', 'o', 'n', 'q', 'p', 's', 'r', 'u', 't', 'w', 'v', 'y', 'x', 'z']), character_map={'\t': '__tc__', '\n': '__cn__', '\r': '__cr__', '"': '__dq__', '#': '__pd__', "'": '__sq__', '<': '__lt__', '>': '__gt__', '@': '__at__', '[': '__ob__', ']': '__cb__', '{': '__oc__', '}': '__cc__'}, invalid_character='X')[source]¶
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galaxy.util.sanitize_param(value, valid_characters=set(['!', ' ', ')', '(', '+', '*', '-', ', ', '/', '.', '1', '0', '3', '2', '5', '4', '7', '6', '9', '8', ':', '=', '?', 'A', 'C', 'B', 'E', 'D', 'G', 'F', 'I', 'H', 'K', 'J', 'M', 'L', 'O', 'N', 'Q', 'P', 'S', 'R', 'U', 'T', 'W', 'V', 'Y', 'X', 'Z', '_', '^', 'a', 'c', 'b', 'e', 'd', 'g', 'f', 'i', 'h', 'k', 'j', 'm', 'l', 'o', 'n', 'q', 'p', 's', 'r', 'u', 't', 'w', 'v', 'y', 'x', 'z']), character_map={'\t': '__tc__', '\n': '__cn__', '\r': '__cr__', '"': '__dq__', '#': '__pd__', "'": '__sq__', '<': '__lt__', '>': '__gt__', '@': '__at__', '[': '__ob__', ']': '__cb__', '{': '__oc__', '}': '__cc__'}, invalid_character='X')[source]¶ Clean incoming parameters (strings or lists)
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galaxy.util.sanitize_text(text, valid_characters=set(['!', ' ', ')', '(', '+', '*', '-', ', ', '/', '.', '1', '0', '3', '2', '5', '4', '7', '6', '9', '8', ':', '=', '?', 'A', 'C', 'B', 'E', 'D', 'G', 'F', 'I', 'H', 'K', 'J', 'M', 'L', 'O', 'N', 'Q', 'P', 'S', 'R', 'U', 'T', 'W', 'V', 'Y', 'X', 'Z', '_', '^', 'a', 'c', 'b', 'e', 'd', 'g', 'f', 'i', 'h', 'k', 'j', 'm', 'l', 'o', 'n', 'q', 'p', 's', 'r', 'u', 't', 'w', 'v', 'y', 'x', 'z']), character_map={'\t': '__tc__', '\n': '__cn__', '\r': '__cr__', '"': '__dq__', '#': '__pd__', "'": '__sq__', '<': '__lt__', '>': '__gt__', '@': '__at__', '[': '__ob__', ']': '__cb__', '{': '__oc__', '}': '__cc__'}, invalid_character='X')[source]¶ Restricts the characters that are allowed in text; accepts both strings and lists of strings; non-string entities will be cast to strings.
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galaxy.util.send_mail(frm, to, subject, body, config, html=None)[source]¶ Sends an email.
Parameters: - frm (str) – from address
- to (str) – to address
- subject (str) – Subject line
- body (str) – Body text (should be plain text)
- config (object) – Galaxy configuration object
- html (str) – Alternative HTML representation of the body content. If provided will convert the message to a MIMEMultipart. (Default ‘None’)
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galaxy.util.shrink_stream_by_size(value, size, join_by='..', left_larger=True, beginning_on_size_error=False, end_on_size_error=False)[source]¶ 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.
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galaxy.util.shrink_string_by_size(value, size, join_by='..', left_larger=True, beginning_on_size_error=False, end_on_size_error=False)[source]¶
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galaxy.util.size_to_bytes(size)[source]¶ Returns a number of bytes if given a reasonably formatted string with the size
>>> size_to_bytes('1024') 1024 >>> size_to_bytes('10 bytes') 10 >>> size_to_bytes('4k') 4096 >>> size_to_bytes('2.2 TB') 2418925581107
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galaxy.util.smart_str(s, encoding='utf-8', strings_only=False, errors='strict')[source]¶ 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'
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galaxy.util.string_as_bool_or_none(string)[source]¶ - 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.
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galaxy.util.strip_control_characters_nested(item)[source]¶ Recursively strips control characters from lists, dicts, tuples.
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galaxy.util.synchronized(func)[source]¶ This wrapper will serialize access to ‘func’ to a single thread. Use it as a decorator.
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galaxy.util.umask_fix_perms(path, umask, unmasked_perms, gid=None)[source]¶ umask-friendly permissions fixing
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galaxy.util.unicodify(value, encoding='utf-8', error='replace')[source]¶ 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�t�n str��g' >>> s = u'lâtín strìñg'; assert unicodify(s.encode('latin-1'), error='ignore') == u'ltn strg'
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galaxy.util.unique_id(KEY_SIZE=128)[source]¶ Generates an unique id
>>> ids = [ unique_id() for i in range(1000) ] >>> len(set(ids)) 1000