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Source code for galaxy.datatypes.dataproviders.base

"""
Base class(es) for all DataProviders.
"""
# there's a blurry line between functionality here and functionality in datatypes module
# attempting to keep parsing to a minimum here and focus on chopping/pagination/reformat(/filtering-maybe?)
#   and using as much pre-computed info/metadata from the datatypes module as possible
# also, this shouldn't be a replacement/re-implementation of the tool layer
#   (which provides traceability/versioning/reproducibility)

import logging
from collections import deque

import six

from . import exceptions

log = logging.getLogger(__name__)

_TODO = """
hooks into datatypes (define providers inside datatype modules) as factories
capture tell() when provider is done
    def stop( self ): self.endpoint = source.tell(); raise StopIteration()
implement __len__ sensibly where it can be (would be good to have where we're giving some progress - '100 of 300')
    seems like sniffed files would have this info
unit tests
add datum entry/exit point methods: possibly decode, encode
    or create a class that pipes source through - how would decode work then?

icorporate existing visualization/dataproviders
some of the sources (esp. in datasets) don't need to be re-created
YAGNI: InterleavingMultiSourceDataProvider, CombiningMultiSourceDataProvider

datasets API entry point:
    kwargs should be parsed from strings 2 layers up (in the DatasetsAPI) - that's the 'proper' place for that.
    but how would it know how/what to parse if it doesn't have access to the classes used in the provider?
        Building a giant list by sweeping all possible dprov classes doesn't make sense
    For now - I'm burying them in the class __init__s - but I don't like that
"""


# ----------------------------------------------------------------------------- base classes
[docs]class HasSettings(type): """ Metaclass for data providers that allows defining and inheriting a dictionary named 'settings'. Useful for allowing class level access to expected variable types passed to class `__init__` functions so they can be parsed from a query string. """ # yeah - this is all too acrobatic def __new__(cls, name, base_classes, attributes): settings = {} # get settings defined in base classes for base_class in base_classes: base_settings = getattr(base_class, 'settings', None) if base_settings: settings.update(base_settings) # get settings defined in this class new_settings = attributes.pop('settings', None) if new_settings: settings.update(new_settings) attributes['settings'] = settings return type.__new__(cls, name, base_classes, attributes)
# ----------------------------------------------------------------------------- base classes
[docs]@six.add_metaclass(HasSettings) class DataProvider(six.Iterator): """ Base class for all data providers. Data providers: (a) have a source (which must be another file-like object) (b) implement both the iterator and context manager interfaces (c) do not allow write methods (but otherwise implement the other file object interface methods) """ # a definition of expected types for keyword arguments sent to __init__ # useful for controlling how query string dictionaries can be parsed into correct types for __init__ # empty in this base class settings = {}
[docs] def __init__(self, source, **kwargs): """ :param source: the source that this iterator will loop over. (Should implement the iterable interface and ideally have the context manager interface as well) """ self.source = self.validate_source(source)
[docs] def validate_source(self, source): """ Is this a valid source for this provider? :raises InvalidDataProviderSource: if the source is considered invalid. Meant to be overridden in subclasses. """ if not source or not hasattr(source, '__iter__'): # that's by no means a thorough check raise exceptions.InvalidDataProviderSource(source) return source
# TODO: (this might cause problems later...) # TODO: some providers (such as chunk's seek and read) rely on this... remove def __getattr__(self, name): if name == 'source': # if we're inside this fn, source hasn't been set - provide some safety just for this attr return None # otherwise, try to get the attr from the source - allows us to get things like provider.encoding, etc. if hasattr(self.source, name): return getattr(self.source, name) # raise the proper error return self.__getattribute__(name) # write methods should not be allowed
[docs] def truncate(self, size): raise NotImplementedError('Write methods are purposely disabled')
[docs] def write(self, string): raise NotImplementedError('Write methods are purposely disabled')
[docs] def writelines(self, sequence): raise NotImplementedError('Write methods are purposely disabled')
# TODO: route read methods through next? # def readline( self ): # return self.next()
[docs] def readlines(self): return [line for line in self]
# iterator interface def __iter__(self): # it's generators all the way up, Timmy with self: for datum in self.source: yield datum def __next__(self): return next(self.source) # context manager interface def __enter__(self): # make the source's context manager interface optional if hasattr(self.source, '__enter__'): self.source.__enter__() return self def __exit__(self, *args): # make the source's context manager interface optional, call on source if there if hasattr(self.source, '__exit__'): self.source.__exit__(*args) # alternately, call close() elif hasattr(self.source, 'close'): self.source.close() def __str__(self): """ String representation for easier debugging. Will call `__str__` on its source so this will display piped dataproviders. """ # we need to protect against recursion (in __getattr__) if self.source hasn't been set source_str = str(self.source) if hasattr(self, 'source') else '' return '%s(%s)' % (self.__class__.__name__, str(source_str))
[docs]class FilteredDataProvider(DataProvider): """ Passes each datum through a filter function and yields it if that function returns a non-`None` value. Also maintains counters: - `num_data_read`: how many data have been consumed from the source. - `num_valid_data_read`: how many data have been returned from `filter`. - `num_data_returned`: how many data has this provider yielded. """ # not useful here - we don't want functions over the query string # settings.update({ 'filter_fn': 'function' })
[docs] def __init__(self, source, filter_fn=None, **kwargs): """ :param filter_fn: a lambda or function that will be passed a datum and return either the (optionally modified) datum or None. """ super(FilteredDataProvider, self).__init__(source, **kwargs) self.filter_fn = filter_fn if hasattr(filter_fn, '__call__') else None # count how many data we got from the source self.num_data_read = 0 # how many valid data have we gotten from the source # IOW, data that's passed the filter and been either provided OR have been skipped due to offset self.num_valid_data_read = 0 # how many lines have been provided/output self.num_data_returned = 0
def __iter__(self): parent_gen = super(FilteredDataProvider, self).__iter__() for datum in parent_gen: self.num_data_read += 1 datum = self.filter(datum) if datum is not None: self.num_valid_data_read += 1 self.num_data_returned += 1 yield datum # TODO: may want to squash this into DataProvider
[docs] def filter(self, datum): """ When given a datum from the provider's source, return None if the datum 'does not pass' the filter or is invalid. Return the datum if it's valid. :param datum: the datum to check for validity. :returns: the datum, a modified datum, or None Meant to be overridden. """ if self.filter_fn: return self.filter_fn(datum) # also can be overriden entirely return datum
[docs]class LimitedOffsetDataProvider(FilteredDataProvider): """ A provider that uses the counters from FilteredDataProvider to limit the number of data and/or skip `offset` number of data before providing. Useful for grabbing sections from a source (e.g. pagination). """ # define the expected types of these __init__ arguments so they can be parsed out from query strings settings = { 'limit' : 'int', 'offset': 'int' } # TODO: may want to squash this into DataProvider
[docs] def __init__(self, source, offset=0, limit=None, **kwargs): """ :param offset: the number of data to skip before providing. :param limit: the final number of data to provide. """ super(LimitedOffsetDataProvider, self).__init__(source, **kwargs) # how many valid data to skip before we start outputing data - must be positive # (diff to support neg. indeces - must be pos.) self.offset = max(offset, 0) # how many valid data to return - must be positive (None indicates no limit) self.limit = limit if self.limit is not None: self.limit = max(self.limit, 0)
def __iter__(self): """ Iterate over the source until `num_valid_data_read` is greater than `offset`, begin providing datat, and stop when `num_data_returned` is greater than `offset`. """ if self.limit is not None and self.limit <= 0: return parent_gen = super(LimitedOffsetDataProvider, self).__iter__() for datum in parent_gen: self.num_data_returned -= 1 # print 'self.num_data_returned:', self.num_data_returned # print 'self.num_valid_data_read:', self.num_valid_data_read if self.num_valid_data_read > self.offset: self.num_data_returned += 1 yield datum if self.limit is not None and self.num_data_returned >= self.limit: break
# TODO: skipping lines is inefficient - somehow cache file position/line_num pair and allow provider # to seek to a pos/line and then begin providing lines # the important catch here is that we need to have accurate pos/line pairs # in order to preserve the functionality of limit and offset # if file_seek and len( file_seek ) == 2: # seek_pos, new_line_num = file_seek # self.seek_and_set_curr_line( seek_pos, new_line_num ) # def seek_and_set_curr_line( self, file_seek, new_curr_line_num ): # self.seek( file_seek, os.SEEK_SET ) # self.curr_line_num = new_curr_line_num
[docs]class MultiSourceDataProvider(DataProvider): """ A provider that iterates over a list of given sources and provides data from one after another. An iterator over iterators. """
[docs] def __init__(self, source_list, **kwargs): """ :param source_list: an iterator of iterables """ self.source_list = deque(source_list)
def __iter__(self): """ Iterate over the source_list, then iterate over the data in each source. Skip a given source in `source_list` if it is `None` or invalid. """ for source in self.source_list: # just skip falsy sources if not source: continue try: self.source = self.validate_source(source) except exceptions.InvalidDataProviderSource: continue parent_gen = super(MultiSourceDataProvider, self).__iter__() for datum in parent_gen: yield datum