Mercurial > repos > shellac > guppy_basecaller
view env/lib/python3.7/site-packages/boltons/tableutils.py @ 0:26e78fe6e8c4 draft
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
author | shellac |
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date | Sat, 02 May 2020 07:14:21 -0400 |
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# -*- coding: utf-8 -*- """If there is one recurring theme in ``boltons``, it is that Python has excellent datastructures that constitute a good foundation for most quick manipulations, as well as building applications. However, Python usage has grown much faster than builtin data structure power. Python has a growing need for more advanced general-purpose data structures which behave intuitively. The :class:`Table` class is one example. When handed one- or two-dimensional data, it can provide useful, if basic, text and HTML renditions of small to medium sized data. It also heuristically handles recursive data of various formats (lists, dicts, namedtuples, objects). For more advanced :class:`Table`-style manipulation check out the `pandas`_ DataFrame. .. _pandas: http://pandas.pydata.org/ """ from __future__ import print_function try: from html import escape as html_escape except ImportError: from cgi import escape as html_escape import types from itertools import islice try: from collections.abc import Sequence, Mapping, MutableSequence except ImportError: from collections import Sequence, Mapping, MutableSequence try: string_types, integer_types = (str, unicode), (int, long) from cgi import escape as html_escape except NameError: # Python 3 compat unicode = str string_types, integer_types = (str, bytes), (int,) from html import escape as html_escape try: from typeutils import make_sentinel _MISSING = make_sentinel(var_name='_MISSING') except ImportError: _MISSING = object() """ Some idle feature thoughts: * shift around column order without rearranging data * gotta make it so you can add additional items, not just initialize with * maybe a shortcut would be to allow adding of Tables to other Tables * what's the perf of preallocating lists and overwriting items versus starting from empty? * is it possible to effectively tell the difference between when a Table is from_data()'d with a single row (list) or with a list of lists? * CSS: white-space pre-line or pre-wrap maybe? * Would be nice to support different backends (currently uses lists exclusively). Sometimes large datasets come in list-of-dicts and list-of-tuples format and it's desirable to cut down processing overhead. TODO: make iterable on rows? """ __all__ = ['Table'] def to_text(obj, maxlen=None): try: text = unicode(obj) except Exception: try: text = unicode(repr(obj)) except Exception: text = unicode(object.__repr__(obj)) if maxlen and len(text) > maxlen: text = text[:maxlen - 3] + '...' # TODO: inverse of ljust/rjust/center return text def escape_html(obj, maxlen=None): text = to_text(obj, maxlen=maxlen) return html_escape(text, quote=True) _DNR = set((type(None), bool, complex, float, type(NotImplemented), slice, types.FunctionType, types.MethodType, types.BuiltinFunctionType, types.GeneratorType) + string_types + integer_types) class UnsupportedData(TypeError): pass class InputType(object): def __init__(self, *a, **kw): pass def get_entry_seq(self, data_seq, headers): return [self.get_entry(entry, headers) for entry in data_seq] class DictInputType(InputType): def check_type(self, obj): return isinstance(obj, Mapping) def guess_headers(self, obj): return sorted(obj.keys()) def get_entry(self, obj, headers): return [obj.get(h) for h in headers] def get_entry_seq(self, obj, headers): return [[ci.get(h) for h in headers] for ci in obj] class ObjectInputType(InputType): def check_type(self, obj): return type(obj) not in _DNR and hasattr(obj, '__class__') def guess_headers(self, obj): headers = [] for attr in dir(obj): # an object's __dict__ could technically have non-string keys try: val = getattr(obj, attr) except Exception: # seen on greenlet: `run` shows in dir() but raises # AttributeError. Also properties misbehave. continue if callable(val): continue headers.append(attr) return headers def get_entry(self, obj, headers): values = [] for h in headers: try: values.append(getattr(obj, h)) except Exception: values.append(None) return values # might be better to hardcode list support since it's so close to the # core or might be better to make this the copy-style from_* importer # and have the non-copy style be hardcoded in __init__ class ListInputType(InputType): def check_type(self, obj): return isinstance(obj, MutableSequence) def guess_headers(self, obj): return None def get_entry(self, obj, headers): return obj def get_entry_seq(self, obj_seq, headers): return obj_seq class TupleInputType(InputType): def check_type(self, obj): return isinstance(obj, tuple) def guess_headers(self, obj): return None def get_entry(self, obj, headers): return list(obj) def get_entry_seq(self, obj_seq, headers): return [list(t) for t in obj_seq] class NamedTupleInputType(InputType): def check_type(self, obj): return hasattr(obj, '_fields') and isinstance(obj, tuple) def guess_headers(self, obj): return list(obj._fields) def get_entry(self, obj, headers): return [getattr(obj, h, None) for h in headers] def get_entry_seq(self, obj_seq, headers): return [[getattr(obj, h, None) for h in headers] for obj in obj_seq] class Table(object): """ This Table class is meant to be simple, low-overhead, and extensible. Its most common use would be for translation between in-memory data structures and serialization formats, such as HTML and console-ready text. As such, it stores data in list-of-lists format, and *does not* copy lists passed in. It also reserves the right to modify those lists in a "filling" process, whereby short lists are extended to the width of the table (usually determined by number of headers). This greatly reduces overhead and processing/validation that would have to occur otherwise. General description of headers behavior: Headers describe the columns, but are not part of the data, however, if the *headers* argument is omitted, Table tries to infer header names from the data. It is possible to have a table with no headers, just pass in ``headers=None``. Supported inputs: * :class:`list` of :class:`list` objects * :class:`dict` (list/single) * :class:`object` (list/single) * :class:`collections.namedtuple` (list/single) * TODO: DB API cursor? * TODO: json Supported outputs: * HTML * Pretty text (also usable as GF Markdown) * TODO: CSV * TODO: json * TODO: json lines To minimize resident size, the Table data is stored as a list of lists. """ # order definitely matters here _input_types = [DictInputType(), ListInputType(), NamedTupleInputType(), TupleInputType(), ObjectInputType()] _html_tr, _html_tr_close = '<tr>', '</tr>' _html_th, _html_th_close = '<th>', '</th>' _html_td, _html_td_close = '<td>', '</td>' _html_thead, _html_thead_close = '<thead>', '</thead>' _html_tbody, _html_tbody_close = '<tbody>', '</tbody>' # _html_tfoot, _html_tfoot_close = '<tfoot>', '</tfoot>' _html_table_tag, _html_table_tag_close = '<table>', '</table>' def __init__(self, data=None, headers=_MISSING, metadata=None): if headers is _MISSING: headers = [] if data: headers, data = list(data[0]), islice(data, 1, None) self.headers = headers or [] self.metadata = metadata or {} self._data = [] self._width = 0 self.extend(data) def extend(self, data): """ Append the given data to the end of the Table. """ if not data: return self._data.extend(data) self._set_width() self._fill() def _set_width(self, reset=False): if reset: self._width = 0 if self._width: return if self.headers: self._width = len(self.headers) return self._width = max([len(d) for d in self._data]) def _fill(self): width, filler = self._width, [None] if not width: return for d in self._data: rem = width - len(d) if rem > 0: d.extend(filler * rem) return @classmethod def from_dict(cls, data, headers=_MISSING, max_depth=1, metadata=None): """Create a Table from a :class:`dict`. Operates the same as :meth:`from_data`, but forces interpretation of the data as a Mapping. """ return cls.from_data(data=data, headers=headers, max_depth=max_depth, _data_type=DictInputType(), metadata=metadata) @classmethod def from_list(cls, data, headers=_MISSING, max_depth=1, metadata=None): """Create a Table from a :class:`list`. Operates the same as :meth:`from_data`, but forces the interpretation of the data as a Sequence. """ return cls.from_data(data=data, headers=headers, max_depth=max_depth, _data_type=ListInputType(), metadata=metadata) @classmethod def from_object(cls, data, headers=_MISSING, max_depth=1, metadata=None): """Create a Table from an :class:`object`. Operates the same as :meth:`from_data`, but forces the interpretation of the data as an object. May be useful for some :class:`dict` and :class:`list` subtypes. """ return cls.from_data(data=data, headers=headers, max_depth=max_depth, _data_type=ObjectInputType(), metadata=metadata) @classmethod def from_data(cls, data, headers=_MISSING, max_depth=1, **kwargs): """Create a Table from any supported data, heuristically selecting how to represent the data in Table format. Args: data (object): Any object or iterable with data to be imported to the Table. headers (iterable): An iterable of headers to be matched to the data. If not explicitly passed, headers will be guessed for certain datatypes. max_depth (int): The level to which nested Tables should be created (default: 1). _data_type (InputType subclass): For advanced use cases, do not guess the type of the input data, use this data type instead. """ # TODO: seen/cycle detection/reuse ? # maxdepth follows the same behavior as find command # i.e., it doesn't work if max_depth=0 is passed in metadata = kwargs.pop('metadata', None) _data_type = kwargs.pop('_data_type', None) if max_depth < 1: # return data instead? return cls(headers=headers, metadata=metadata) is_seq = isinstance(data, Sequence) if is_seq: if not data: return cls(headers=headers, metadata=metadata) to_check = data[0] if not _data_type: for it in cls._input_types: if it.check_type(to_check): _data_type = it break else: # not particularly happy about this rewind-y approach is_seq = False to_check = data else: if type(data) in _DNR: # hmm, got scalar data. # raise an exception or make an exception, nahmsayn? return cls([[data]], headers=headers, metadata=metadata) to_check = data if not _data_type: for it in cls._input_types: if it.check_type(to_check): _data_type = it break else: raise UnsupportedData('unsupported data type %r' % type(data)) if headers is _MISSING: headers = _data_type.guess_headers(to_check) if is_seq: entries = _data_type.get_entry_seq(data, headers) else: entries = [_data_type.get_entry(data, headers)] if max_depth > 1: new_max_depth = max_depth - 1 for i, entry in enumerate(entries): for j, cell in enumerate(entry): if type(cell) in _DNR: # optimization to avoid function overhead continue try: entries[i][j] = cls.from_data(cell, max_depth=new_max_depth) except UnsupportedData: continue return cls(entries, headers=headers, metadata=metadata) def __len__(self): return len(self._data) def __getitem__(self, idx): return self._data[idx] def __repr__(self): cn = self.__class__.__name__ if self.headers: return '%s(headers=%r, data=%r)' % (cn, self.headers, self._data) else: return '%s(%r)' % (cn, self._data) def to_html(self, orientation=None, wrapped=True, with_headers=True, with_newlines=True, with_metadata=False, max_depth=1): """Render this Table to HTML. Configure the structure of Table HTML by subclassing and overriding ``_html_*`` class attributes. Args: orientation (str): one of 'auto', 'horizontal', or 'vertical' (or the first letter of any of those). Default 'auto'. wrapped (bool): whether or not to include the wrapping '<table></table>' tags. Default ``True``, set to ``False`` if appending multiple Table outputs or an otherwise customized HTML wrapping tag is needed. with_newlines (bool): Set to ``True`` if output should include added newlines to make the HTML more readable. Default ``False``. with_metadata (bool/str): Set to ``True`` if output should be preceded with a Table of preset metadata, if it exists. Set to special value ``'bottom'`` if the metadata Table HTML should come *after* the main HTML output. max_depth (int): Indicate how deeply to nest HTML tables before simply reverting to :func:`repr`-ing the nested data. Returns: A text string of the HTML of the rendered table. """ lines = [] headers = [] if with_metadata and self.metadata: metadata_table = Table.from_data(self.metadata, max_depth=max_depth) metadata_html = metadata_table.to_html(with_headers=True, with_newlines=with_newlines, with_metadata=False, max_depth=max_depth) if with_metadata != 'bottom': lines.append(metadata_html) lines.append('<br />') if with_headers and self.headers: headers.extend(self.headers) headers.extend([None] * (self._width - len(self.headers))) if wrapped: lines.append(self._html_table_tag) orientation = orientation or 'auto' ol = orientation[0].lower() if ol == 'a': ol = 'h' if len(self) > 1 else 'v' if ol == 'h': self._add_horizontal_html_lines(lines, headers=headers, max_depth=max_depth) elif ol == 'v': self._add_vertical_html_lines(lines, headers=headers, max_depth=max_depth) else: raise ValueError("expected one of 'auto', 'vertical', or" " 'horizontal', not %r" % orientation) if with_metadata and self.metadata and with_metadata == 'bottom': lines.append('<br />') lines.append(metadata_html) if wrapped: lines.append(self._html_table_tag_close) sep = '\n' if with_newlines else '' return sep.join(lines) def get_cell_html(self, value): """Called on each value in an HTML table. By default it simply escapes the HTML. Override this method to add additional conditions and behaviors, but take care to ensure the final output is HTML escaped. """ return escape_html(value) def _add_horizontal_html_lines(self, lines, headers, max_depth): esc = self.get_cell_html new_depth = max_depth - 1 if max_depth > 1 else max_depth if max_depth > 1: new_depth = max_depth - 1 if headers: _thth = self._html_th_close + self._html_th lines.append(self._html_thead) lines.append(self._html_tr + self._html_th + _thth.join([esc(h) for h in headers]) + self._html_th_close + self._html_tr_close) lines.append(self._html_thead_close) trtd, _tdtd, _td_tr = (self._html_tr + self._html_td, self._html_td_close + self._html_td, self._html_td_close + self._html_tr_close) lines.append(self._html_tbody) for row in self._data: if max_depth > 1: _fill_parts = [] for cell in row: if isinstance(cell, Table): _fill_parts.append(cell.to_html(max_depth=new_depth)) else: _fill_parts.append(esc(cell)) else: _fill_parts = [esc(c) for c in row] lines.append(''.join([trtd, _tdtd.join(_fill_parts), _td_tr])) lines.append(self._html_tbody_close) def _add_vertical_html_lines(self, lines, headers, max_depth): esc = self.get_cell_html new_depth = max_depth - 1 if max_depth > 1 else max_depth tr, th, _th = self._html_tr, self._html_th, self._html_th_close td, _tdtd = self._html_td, self._html_td_close + self._html_td _td_tr = self._html_td_close + self._html_tr_close for i in range(self._width): line_parts = [tr] if headers: line_parts.extend([th, esc(headers[i]), _th]) if max_depth > 1: new_depth = max_depth - 1 _fill_parts = [] for row in self._data: cell = row[i] if isinstance(cell, Table): _fill_parts.append(cell.to_html(max_depth=new_depth)) else: _fill_parts.append(esc(row[i])) else: _fill_parts = [esc(row[i]) for row in self._data] line_parts.extend([td, _tdtd.join(_fill_parts), _td_tr]) lines.append(''.join(line_parts)) def to_text(self, with_headers=True, maxlen=None): """Get the Table's textual representation. Only works well for Tables with non-recursive data. Args: with_headers (bool): Whether to include a header row at the top. maxlen (int): Max length of data in each cell. """ lines = [] widths = [] headers = list(self.headers) text_data = [[to_text(cell, maxlen=maxlen) for cell in row] for row in self._data] for idx in range(self._width): cur_widths = [len(cur) for cur in text_data] if with_headers: cur_widths.append(len(to_text(headers[idx], maxlen=maxlen))) widths.append(max(cur_widths)) if with_headers: lines.append(' | '.join([h.center(widths[i]) for i, h in enumerate(headers)])) lines.append('-|-'.join(['-' * w for w in widths])) for row in text_data: lines.append(' | '.join([cell.center(widths[j]) for j, cell in enumerate(row)])) return '\n'.join(lines)